czty commited on Jul 9

Commit

c43c227

verified ·

1 Parent(s): d354448

Add files using upload-large-folder tool

Browse files

This view is limited to 50 files because it contains too many changes. See raw diff

Files changed (50) hide show

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000000.fa +369 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000001.fa +289 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000004.fa +226 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000005.fa +184 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000006.fa +103 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000008.fa +91 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000010.fa +118 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000012.fa +49 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000013.fa +78 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000014.fa +101 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000017.fa +81 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000019.fa +28 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000021.fa +73 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000023.fa +57 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000025.fa +29 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000026.fa +56 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000031.fa +64 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000032.fa +43 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000035.fa +22 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000036.fa +56 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000039.fa +189 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000040.fa +63 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000043.fa +22 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000044.fa +50 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000045.fa +56 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000047.fa +98 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000048.fa +43 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000049.fa +63 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000050.fa +64 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000052.fa +43 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000053.fa +36 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000060.fa +49 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000067.fa +48 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000068.fa +19 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000072.fa +54 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000075.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000076.fa +144 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000077.fa +48 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000078.fa +49 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000084.fa +54 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000089.fa +55 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000090.fa +49 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000091.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000095.fa +54 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000104.fa +126 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000105.fa +25 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000106.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000110.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000112.fa +49 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000115.fa +37 -0

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000000.fa ADDED Viewed

	@@ -0,0 +1,369 @@

+>0_60
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT---------------------
+----------------
+>0_1289
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSERARRE
+ALQVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYI---------------------
+----------------
+>0_1892
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS---------------------
+----------------
+>0_2007
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYI---------------------
+----------------
+>0_2050
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYI---------------------
+----------------
+>0_2217
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN---------------------
+----------------
+>1_10
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN---------------------
+----------------
+>1_36
+MTHANAPLTPTGRLRMVHRHLNDGIPQSHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPEGGGWRTHGRDSEAGRASKRG-
+-SGQRVGYTYLHSAIDGYTRLAYTEALEDERTVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALQVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT---------------------
+----------------
+>1_125
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT---------------------
+----------------
+>1_297
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRG-
+-AGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARRE
+ALQVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT---------------------
+----------------
+>1_336
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHHCPAQLDIAILAEIEALRRDQKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDCENARAAKRG-
+-PGRRVGYTYLHSAVDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIT-VDRVITD
+NGANYRAAEFTMKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYN---------------------
+----------------
+>1_1079
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAEHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYN---------------------
+----------------
+>1_1117
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS---------------------
+----------------
+>1_1192
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYN---------------------
+----------------
+>1_1768
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYI---------------------
+----------------
+>1_1771
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT---------------------
+----------------
+>1_1918
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYI---------------------
+----------------
+>1_1921
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHYLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS---------------------
+----------------
+>1_2024
+MIHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYS---------------------
+----------------
+>2_37
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGIT-LDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+AMQVWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYT---------------------
+----------------
+>2_137
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------MTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>2_217
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT---------------------
+----------------
+>2_538
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGIT-LDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+AMQVWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYS---------------------
+----------------
+>2_674
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGIT-LDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+AMQVWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYT---------------------
+----------------
+>2_761
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLPSASRPGGSPRGAGAHGAPGREEDRKDPRGGGWRAHGRDSEAGRASKRG-
+-PGARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>2_1469
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRG-
+-PGARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>2_1475
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKVGRIPDGGGWRIHGRNSDQARTAGRAK
+SAGAKRGYTYLHSAVDGFSRLSYTEPLTDEKGPTAAAFLARAKAWFAAHGISHIHRVITD
+NGACYRSADF-ARIVGNRTRHQKTRPYTPRHNGKVERYQRILAEELLYAREFESEEARDT
+AIGIWNIHYNYHRPHSGAGGHPPASRLRAGVTNVWPSYS---------------------
+----------------
+>2_1706
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT---------------------
+----------------
+>2_1737
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGCRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>2_2285
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGCRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>2_2288
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------MAYTESLENEKATTAVAFLNRAREWFASHGITRIERVITD
+NGACYRSAAFTAALD--GADHRRTRPYTPKHNGKVERYNRILAEEFLYARTWTSEEQREK
+ALETWNLHYNYHRPHGVHDGKPPASATPSRVNNVLASYS---------------------
+----------------
+>2_2418
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRG-
+-PGARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>2_2499
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT---------------------
+----------------
+>2_2555
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRG-
+-PGARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYN---------------------
+----------------
+>2_2573
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIR-IDRAVTD
+NGNNYRAAEFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLHARPYSSETARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMTSYT---------------------
+----------------
+>2_2578
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGCRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYI---------------------
+----------------
+>4_265
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS---------------------
+----------------
+>4_495
+---------------MAQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYSSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYN---------------------
+----------------
+>4_770
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYT---------------------
+----------------
+>4_845
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN---------------------
+----------------
+>4_1128
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYI---------------------
+----------------
+>4_1492
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS---------------------
+----------------
+>4_1516
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALQVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT---------------------
+----------------
+>4_1937
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARRE
+ALTVWVNHYNYHRPHTSCGDAPPTSLAPARVYNVMPSYS---------------------
+----------------
+>4_2042
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT---------------------
+----------------
+>4_2046
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYNYLFGLLMVTRSPECALLGHGP
+DQRGWLLDTYLRGLRP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000001.fa ADDED Viewed

	@@ -0,0 +1,289 @@

+>0_166
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_564
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_577
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GSEVNPDTAPALEFS-------------A
+>0_578
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGRV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSGKL--------------PTV----AEHLDAARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVTNT
+GDEVDPDTELTLGLS-------------A
+>0_598
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVTDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSNQDPDTPS
+TTGASAEVMPTL----------------A
+>0_687
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_1025
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GSEVNPDTAPALEFS-------------A
+>0_1155
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKL--------------PAV----AEHLGDARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTPVEDT
+GSEVGTDTDTALELS-------------A
+>0_1346
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPL-DAGPYRFVAADALVLKVREHGRV
+VKVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLV
+EAAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMID
+SLATHL--------------PAA----AEHLEGARDEVLTFTKFPKEVWKKIWSNNPNER
+LNKEIRRRTDVVGIFPSRVEVIRLLGAVLAEQHDEWTESRRYMSLELLTAT-DTMLAEAA
+AKAAAEQA--ALQVSDTMTDDPGHAALAA
+>0_1351
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_1451
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVAGAWPGSGWSPLMPTPGSR
+TPSPRTCP----VRCGNAAAPT--------------------------------------
+------------------------------------------------------------
+-----TRRT---------------------------------------------------
+-----------------------------
+>0_1452
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------MGITPKSMWPAVKAMLHSGYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTD---EGPRAVATRALGAT-RACC----
+-----------------------------
+>0_1969
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKL--------------PAV----AEHLGDARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTPVEDT
+GSEVGTDTDTALELS-------------A
+>0_2003
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFSATGL------------------------
+------------------------------------------------------------
+-----------WAR----------------------------------------------
+------------------------------------------------------------
+---------------PARS-------------------------------C-SSPPTP--
+-----------------------------
+>0_2004
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------MFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRL--------------PAV----AAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_2165
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTETGAAWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_2168
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGQASQSRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRL--------------PAV----AAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_2170
+------------------------------------------------------------
+---------------------------------------------MVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRL--------------PAV----AAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_2171
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPN-----------------------GCSS---
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------AAN-------------------------GPS----------
+------------------------------------------------------------
+---------------PH-------------------------------------------
+-----------------------------
+>0_2205
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRL--------------PAV----AAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>0_2210
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GSEVNPDTAPALEFS-------------A
+>1_1087
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQT------------------------------------------------RHHGPV
+-----------------EIAGLR-------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------DE-------------------------
+-----------------------------
+>1_1088
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------MSKDLDAQVEAFRTRPL-DAGPYRFVAADALVLKVREHGRV
+VKVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLV
+EAAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMID
+SLATHL--------------PAA----AEHLEGARDEVLTFTKFPKEVWKKIWSNNPNER
+LNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTESRRYMSLELLTAT-DTMLAEAA
+AKAAAEQA--ALQVSDTMTDDPGHAALAA
+>2_673
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKL--------------PAV----AEHLDAARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLHRC-RLTPVSNT
+GDEVDTDT--ALELS-------------A
+>2_703
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GNEVNPDTAPALEFS-------------A
+>2_876
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEALPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLLYGGRAPGRCPGGHPGLHDLPEGRVDAGLVEQSGRAAQPRD---------PPP-
+-----HRRG---GHLPQPGS-HRQAGRCGAGRADR-------------------------
+-----------------------------
+>2_2445
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GNEVNPDTAPALEFS-------------A
+>2_2612
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGPV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGLRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSEKL--------------PTV----AEHLDAARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVTNT
+GDEVDPDTELTLGLS-------------A
+>4_1295
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAPVEAFRTRPL-DAGPYRFVAADALVLKVREHGRV
+VKVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLV
+EAAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMID
+SLATHL--------------PAA----AEHLEGARDEVLTFTKFPKEVWKKIWSNNPNER
+LNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTESRRYMSLELLTAT-DTMLAEAA
+AKAAAEQA--ALQVSDTMTDDPGHAALAA
+>4_1936
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPL-DAGPYRFVAADALVLKVREHGRV
+VKVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLV
+EAAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMID
+SLATHL--------------PAA----AEHLEGARDEVLTFTKFPKEVWKKIWSNNPNER
+LNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTESRRYMSLELLTAT-DTMLAEAA
+AKAAAEQA--ALQVSDTMTDDPGHAALAA
+>4_2137
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKL--------------PAV----AEHLGDARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTPVEDT
+GSEVGTDTDTALELS-------------A
+>4_2154
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKL--------------PAV----AEHLGDARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTPVEDT
+GSEVGTDTDTALELS-------------A

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000004.fa ADDED Viewed

	@@ -0,0 +1,226 @@

+>0_355
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>0_1345
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>0_2008
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTP--------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------LTQTS-------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
+>0_2051
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>0_2216
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_339
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_973
+M-----------------------------------------------------------
+----------------------------------GRTQWPLT----------DVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_976
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVCK----
+--RP--------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
+>1_1086
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_1696
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_1769
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_1964
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_218
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------MVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_219
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEAPKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYA----------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
+>2_625
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEAPKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_875
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------MVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_879
+MTD-----TA-----------DAQNPLAGVLSADQVDALVNAAEDLGEGRHGVEELLSRM
+TQAVLERALETEMSEHLGYEAGDPAGAGTGNSRNGKT--TKSVQTLQGPGQITVPRDRNG
+SFEPVIVPKRSRRLGRVEDMILSLYARGMTTRDIGSHLEEIYGSKVSAATISRVTDVVAD
+EVAQWQSRPLETVYPIVYIDAIWLKIRDGGVVTNKACHVAVGVDLEGRKQVLGLWLGVSE
+GAKFWANVLTEIRNRGTKDILILCCDGLSGLPAAVNSIYPETVVQTCVVHLLRSAMKYAS
+YADRKTMAKDMRPIYTAATVEAAQLALEAF-AEIWQTKAPGAVLAWRTAWEDFIPFLAFT
+PEIRKVIYTTNQIESINYQLRKITKTRGSFPSDEAAIKLVYLGIRNIETRRGGEL-----
+--------------GTGTQGWHQALNAFAVQFPNRL-P-L
+>2_1476
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEAPKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_2052
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYGKGSEDASKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>3_1790
+MSESTTEMTGPMIDPVTGEIIDQKDLAEQ---------LLAQAKEQGVRLVGPGGLLNQL
+TKNVLETALEAELTEHLGHDHGQTPIA--ANMRNGTR--SKTVLTEIGPVEIEVPRDRDG
+SFEPVIVPKRKRRLDGTDQIVLSLSARGLTTGEIAVHFEEVYGAKVSKDTISRITEKVAG
+ELAEWSSRPLDPL-----------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
+>4_111
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>4_1493
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>4_1495
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>4_1821
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>4_1914
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000005.fa ADDED Viewed

	@@ -0,0 +1,184 @@

+>1_1728
+MDGPGVLAVPQARLRIGRLAEHDPVGLAEAAMELGISRRRVYVLLERYRRG--SGLVTRSDGGKGGGRLTEPQIIRELVC
+QRLTRQKRSIASLHREITRACAVQGLPAPARNTV--AARIARMNPVEVGRRREGAESVRPLQSAGDEVPVVVQIDHTVMD
+LIVVD-----------------------DRDRQ---PIGRPYLTVAIDVCSRCLVGMVVTLEPPSAVSVGLCLAHAAGDK
+RRLGIDAAWPMSGKPKALYVDNAREFKSEALTRGCDQHGISLDYRPLGRPHYGGIVERVIGTAMRQILPSNPVERGAYDA
+EKMAALTIAELERWLVLAVATY-HDTVHSTLGQTPAGRWVESVAATSTPMTTANPTAFLVDFLPVRKLTRTGFVLDHVHY
+FANALKPWIARREAIRRDPRDISRIWVLDPEALSNPAVSVWEHRQALARLRERGATEVDESGLFRMIEQMRTISETAQKT
+TKPPVVPTDLDVVARFGEIEQ
+>2_1257
+MSHANAALTPRHRLIVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTG--EPMQDRSSRPHHSPNKTNQQTARRCVR
+LR-LRLREGPVQLASRLG-------IAPSTVHRILTDVHLNRLSHV----DRATGEPV--RRYEHDHPGSMLHVDVKKLG
+NIPDGGGWRYVGRRQGDKNRAATPDK--PKNKHYDPLMGMAYVHTVIDDHSR--VAYTEIHDDETARTATAVLIRAVEWF
+NARGVTV--------ERVLSDNGGAYRSHLWRDTCAELGIRHKRTRPYRPQTNGKIERFHRTLADGW---AYARCYTSEA
+ERRGELD---------DWLHYYNHHRPHTACGNLPPFSRL-------------------INVS-----------------
+----------------------------------------GQYS------------------------------------
+---------------------
+>2_2224
+MSHANAALTPRTRLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTSPAVVKQIVA
+AR-WRQRLGPAQIASELG-------IPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDAYTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYARFYSSET
+ERRAALP---------GWLHFYNHHRVHSAIGATPA-TRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_212
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTSPAVVKQIVA
+AR-RRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_213
+M----------------------------------------------------------------------------VVQ
+LR-TVEKWGPARIAGHLSTVGGSINISPATVWRILNRNGISRLRDL----DMPTGESKRPRRYEHAAPGDMIHVDVKKVG
+RIPEGGGWAVHGRG---TEEALASRRVASR------RPGYVYIHAAVDDHSR--LAYAEVHPDERAGTAAAFWLRAVLFY
+REHGITT-------FSRCLTDNGPAYRSKVFNDALAGTGTAHKYTRPHTPRTNGKVERFNRTMKEEW---LYVRAYASDG
+ERTAALA---------AFLNTYNHDRPHSSLGNKPPASRVPITSYRVQPQPKV------LDVPQI----------EGL--
+----------------------------------------GHEP-----------------TLFDLL-------------
+---------------------
+>3_298
+MSHANAALTPRARLRLAKLIVEEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTSPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_301
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPAQIASELG-------IPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+ARLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYARFYGSES
+ERRSALP---------GWLHFYNHHRHHSAIGAPPI-SRID------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_431
+-------------------------------------------------------MVDRSSRPATMPTRTSPAVVKQIVA
+AR-RRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHS------------------------------------
+---------------------
+>3_610
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_614
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHI------------------------------------
+---------------------
+>3_624
+MSHADAALTPRHRLKVARLVVDDGWPISEAAARFQVSWPTVKRWVDRYLSG--EPMSDRSSRPKSSPNRTPRVVAKRCVS
+LR-MRLREGPVQLAARLG-------IAPSTVHRILTTARMNRLSYV----DRATGEPI--RRYEHPHPGSLVHVDVKKLG
+NIPDGGGWRYVGRLQGGRNRAATPDK--PRNQYGGPKLGYAFVHTVIDDHSR--VAYTEVHDDETAITAVAVLHRAVEWF
+ADLGVTI--------ERVLSDNGGAYRSHLWRDTCEALSITPKRTRPYRPQTNGKVERFHRTMADGW---AYARCYTSEA
+ERRGALS---------GWLHQYNQHRPHTACSNQPPFSRL-------------------INVP-----------------
+----------------------------------------EQYT------------------------------------
+---------------------
+>3_628
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPAQIASELG-------IPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+ARLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYARFYGSES
+ERRSALP---------GWLHFYNHHRHHSAIGAPPI-SRID------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_635
+MSHPNAALTPRHGLLVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTG--QPMQDRSSRPHHSPNKTSAKTTRRCIQ
+LR-LRLREGPVQLACRLG-------IAPSTVHRILTDAHLNRLSHV----DRATGEPV--RRYEHDHPGAMLHVDVKKLG
+NIPDGGGWRYVGRRQGEKNRAATPGK--PRNKYRDPLMGKAYVHTVIDDHSR--VAYAEIHDDETAITATAVLVRAVEWF
+NARGVTV--------ERVLSDNGGAYKSHLWRDTCVELGIKHKRTRPYRPQTNGKIERFHRTLADGW---AYARCYTSED
+ERPGELE---------GWLHYYNHHRPHTACGDQPPFSRL-------------------TNVP-----------------
+----------------------------------------GQYT------------------------------------
+---------------------
+>3_661
+MDA-------SERWRILRLHVEDAIPLATLARSTGVTERTLQRWLARYRTGGYAALAD-DARADHGVRRTAPELVRLVEG
+LALTKPRPSIATIHRQVGVHCAERGLPSPSYSAV--RSIVNGLDPGMVTLYRDKHELL--LRRRADRPNAIWQADHTMLD
+LLIVG-----------------------PNGK-----PARPWLTVILDDYSRAICGYMVFLGAPSAANTALALRQAIWHK
+P----EPDWPVCGIPDVLYTDHGSDFTSHRLGDTAAVLHLRIIHSQVARPQGRGKIERFFGTINTELLPTLPGHFAAGSS
+APTPALDLGGVDSAISTFIRSY-NARTHRELRTSPLHAWIADGWLPRLPESLEQLDGFLLTVPTTRVVQRDGIHFEGLRY
+TAATLAPFVGSTVSVRYDPRDVTEIRVFHRDVFLCTAISTEHQTETISLKQIQAARNAHRRALRGQIERIAIVNPKLDDT
+TTPAAVETDRPRLKTYEEDRS
+>3_733
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_1335
+MTHLNAALTPRHRLKVARLVVEDGHPISEVAARFQVSWPTVKRWVDRYLAG--ESMNDRSSRPKSSPKKTNKAVTKRCVS
+LR-MRLREGPIQLAARLG-------IAPSTVHRILTAARLNRLSYV----DRATGEPV--RRYEHPHPGSLVHVDVKKIG
+NIPDGGGWRYVGRRQGQKNRAATPDK--PKNKWHSPKLGYAFVHTVIDDHSR--VAYTEVHDDETAITAVAVLHRAVEWF
+AERGVTI--------ERVLSDNGGAYRSYLWRDTCEALSIRPKFTRPYRPQTNGKVERFHRTMGDGW---AYARCYTSEQ
+ERRDALP---------DWLHHYNQHRPHSACGNQPPFSRL-------------------INVP-----------------
+----------------------------------------GQYN------------------------------------
+---------------------
+>3_1757
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_1781
+MSHANAALTPRHRLKVAQLVVDDGWPISEVAARFQVSWPTVKRWADRHRAG--ESMQDRSSRPHHSPNKTSPTVTRRCIQ
+LR-LRLREGPVQLACRLG-------IAPSTVHRILTDAHLNRLSHV----DRATGEPV--RRYEHDHPGAMLHVDVKKLG
+NIPDGGGWRYVGRRQGEKNRAATPGK--LRSKYSDPLMGKAYVHTVIDDHSR--VAYAEIHDDETAVTASAVLVRAVEWF
+NRRGVTV--------ERVLSDNGGAYRSHLWRDTCHELGIKHKRTRPYRPQTNGKIERFHRTLADGW---AYARCYTSEA
+ERRGELD---------GWLHYYNQHRPHTACGNQPPFSRL-------------------TNVP-----------------
+----------------------------------------DQYI------------------------------------
+---------------------
+>3_1793
+MSHKNAALTPRHRLKVARLVVEDGWPISEIAARFQVSWPTVKRWVDRYLAG--ESMEDRSSRPRVSPNKTPKTVTKRCVS
+LR-MRLREGPVQLAARLG-------IAPSTVHRILTTARLNRLSYV----DRATGEPI--RRYEHPHPGSLVHVDVKKLG
+NIPDGGGWRYVGRLQGERNRAATPGK--PKNKWHNPKLGYAFVHTVIDDHSR--VAYTEVHDDETAITAVAVLHRAVEWF
+ANRGVTI--------ERVLSDNGGAYRSHLWRDTCD--------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------
+>3_1796
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTSPAVVKQIVA
+AR-RRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHI------------------------------------
+---------------------
+>3_1847
+MSHANAALTPRARLRLAKLIVDEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTPPAVVKQIVA
+AR-RRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+ARLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWLHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>3_2111
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHI------------------------------------
+---------------------
+>3_2154
+--------------------------------------------------------------------------------
+-------------------------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHS------------------------------------
+---------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000006.fa ADDED Viewed

	@@ -0,0 +1,103 @@

+>0_149
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>0_993
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>0_1244
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>0_1336
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETGDSQNVRTE
+>0_2016
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>1_972
+------------------------------------------------------------
+-MVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>1_1065
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>1_1073
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>1_1075
+MSERIACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINRFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>1_1971
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMEIGDSQNVRTE
+>2_1189
+----MACRLVGLSRSAYRRPLKGDTVADPDRALRQWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>4_563
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>4_565
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVVDW
+AGTRTGLWADPVS-----------------------------------------------
+-------------------------------
+>4_1201
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>4_1290
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTH-------------
+>4_1826
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLGHV---------------------
+>4_2145
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000008.fa ADDED Viewed

	@@ -0,0 +1,91 @@

+>0_685
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>0_1350
+MEGS---------------------------------------------------LEGSH
+GDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>0_1449
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>0_2164
+M-----------------------------------------------------------
+--------------------------LWK-------------------------------
+----------------------------------VRSKAP--------------------
+-----------------TVTASVSKMVVATGEGY--TTIRDSTPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>0_2166
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEV--------
+-----------------------V
+>1_80
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>1_327
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>1_974
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>1_1350
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>1_2226
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>4_581
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>4_971
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>4_1111
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>4_1300
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>4_2104
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000010.fa ADDED Viewed

	@@ -0,0 +1,118 @@

+>0_432
+MLHPTF---ATPDLTTFCRLDELGL----VAVGQLIEPDRATIECRVVEDDPWCRKCGVE
+GVPRDTVTRRLAHEPFGHRPTTLLVRVRRYRCG--HCRR-TWRQDMTRAAAPRAKISRGG
+LEWALRGIVIDHLTVTRVAAGLGVSWSAANAAVLAEGKRRLIDDPARFDGVTTIGVDEHV
+WRHTR--------LGDKYVTVIIDLTPARNKTGPARLLDMVEGRSKAVFKQWLAARPADW
+AKRIEVVAMDGFAGFKTAAAEELPDAVPVMDPFHVVRLAGDALDVCRRRVQQDTTGHRGL
+KGDPLYKARRTLHTGASLLTDRQRARLDAVF-ASEEHIEVEATWGIYQRIVAAYREPDKK
+KAKAMMQEVIATISSGVPAALVEVRKLGRTMKQRAGDILAFFDRPGTSNGPTEAINGRLE
+HLRGSALGFRNLTHYIARSLLEAGGFRPALHPRS-
+>0_815
+M-----------------------------------------------------------
+---------------------------RRYRCS--GCGY-VWRQDTTASAEPRAKLSRRA
+LRWALEGIVVQHLTVARVAEGLGVAWDTANDAVLAEGKRVLIDEEHRFEGVKVVGVDEHV
+WRHTR--------RGDRYVTVIIDLTPVRDGTGPARLLNMVEGRSKQAFKTWLADRPQDW
+RDGVEVVAMDGFTGFKTAAVEELPDVVTVLDPFHVTRLAGEALDECRRRVQQAICGHRGR
+KGDPLYAARRTLSTGVDLLNDKQKDRLDTLF-ADDAHVEVEVTWSVYQRMIAAYRHENRR
+HGRELMARLIDSISTGVPKALVEITKLGRTLKKRAADVLAYFDRPSTSNGPTEAINGRLE
+HLRGSALGFRNLTNYIARSLLETGGFRPRLHPGFG
+>0_1344
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------MSLLTDRQEEHLSVLF-AHEKHAAVEAAWEIYQAMVAAYREFDRA
+KAKAKMEKVIAALSKKVPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLE
+HLRGSALGFRNLTNYIARSLLESGGFRPLLHPQMR
+>1_1085
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------MSLLTDRQKEHLSVLF-AHEKHAAVEAAWEIYQAMVAAYREFDRA
+KAKAKMEKVIAALSKKVPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLE
+HLRGSALGFRNLTNYIARSLLESGGFRPLLHPQTR
+>2_99
+ML----------------------------------------------------------
+----------------------ILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRA
+ISWAIGQLRREHGTIAGLARQLGTSWKTLWRAIRPE-LEHLADDESRFEGVTSLGVDEHI
+WHHVDRRR-----RGPRELTGMVDLSRDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAF
+RRGVQVAALDPFAGYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGR
+KGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLA
+DGRAIAERLADSLHTS---PIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIE
+LHRRLARGFRNRDNYRLRMLLAAGGLTP-------
+>2_490
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------MVDLSRDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAF
+RRGVQVAALDPFAGYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGR
+KGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLA
+DGRAIAERLADSLHTS---PIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIE
+LHRRLARGFRNRDNYRLRMLLAAGGLTP-------
+>2_491
+ML----------------------------------------------------------
+----------------------ILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRA
+ISWAIGQLRREHGTIAGLARQLGTSWKTLWRAIRPE-LEHLADDESRFEGVTSLGVDEHI
+WHHVDRRR-----RGPKS------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------
+>2_1070
+ML----------------------------------------------------------
+----------------------ILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRA
+ISWAIGQLRREHGTIAGLARQLGTSWKTLWRAIRPE-LEHLADDESRFEGVTSLGVDEHI
+WHHVDRRR-----RGPKS------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------
+>2_1071
+MT-------------------RSG------------------------------------
+----------------------VACRSRRW---------------------------TRS
+C-----------------------------------------------------------
+------------------------------------------------------------
+-------------GYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGR
+KGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLA
+DGRAIAERLADSLHTS---PIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIE
+LHRRLARGFRNRDNYRLRMLLAAGGLTP-------
+>3_613
+MPEPTLYCRARGDYCTCCDL-LVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVI
+ARGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRA
+CRWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPL-LQAADEDPSRFEGVAILGVDEHV
+WHHVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAF
+RARIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGR
+KSDPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHA
+AGRAVAEKILATFTSC---PIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIE
+LHRRIARGFRNRDNYRLRMLLIGGGLDMTHHTQR-
+>3_621
+MPEPTLYCRARGDYCTCCDL-LVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVI
+ARGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRA
+CRWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPL-LQAADEDPSRFEGVAILGVDEHV
+WHHVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAF
+RARIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGR
+KSDPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHA
+AGRAVAEKILATFTSC---PIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIE
+LHRRIARGFRNRDNYRLRMLLIGGGLDMTHHTQR-
+>3_820
+MPEPTLYCRARGDYCTCCDL-LVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVI
+ARGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRA
+CRWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPL-LQAADEDPSRFEGVAILGVDEHV
+WHHVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAF
+RARIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGR
+KSDPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHA
+AGRAVAEKILATFTSC---PIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIE
+LHRRIARGFRNRDNYRLRMLLIGGGLDMTHHTQR-
+>4_1294
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------MSLLTDRQKEHLSVLF-AHEKHAAVEAAWEIYQAMVAAYREFDRA
+KAKAKMEKVIAALSKKVPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLE
+HLRGSALGFRNLTNYIARSLLESGGFRPLLHPQMR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000012.fa ADDED Viewed

	@@ -0,0 +1,49 @@

+>0_148
+MK-------------------------------------GA---AQLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>0_151
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVL--------GPAVG---
+------------------------------------------------------------
+---------
+>0_1030
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>0_2002
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>1_282
+MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL
+AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC
+SADQVCRYL
+>1_322
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>1_329
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>1_758
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>2_702
+------------------------------------------------------------
+-----MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>2_704
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPM---
+---------------------------------------------------------KWC
+SG-------
+>3_2171
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>4_979
+------------------------------------------------------------
+-----MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000013.fa ADDED Viewed

	@@ -0,0 +1,78 @@

+>1_325
+-----MKELAAVGIPVAVTCRVLKLSRQPYYRWLADPVTDAELAEAYRANALFDAHQDDP
+EFGYRFLVDEAKEAGEVMCERSAWRICRDNGWWSVFGKKRGKNGKKPGPPVHDDL-----
+----VERDFTAGGSNQLWLTDVTEHRTAEGKLYMCAIKDVFSGRIVGYSIDSRMKARLAV
+QALQNAVARRG---DVAGCIVHSDRGSQFRSRKFVHALNRHGLVGSMGKVGAAGDNAAME
+SFFALLQKNVLDRRSWTTRDELRIAIVTWTERTYHRRRRQARLGRLTPIEYETMMKPAVT
+LPA
+>1_1715
+-MYPLVSELAADQIPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAYRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCGFGAKRGKYGTRPGPPVHDDH-----
+----VRRDFSAEAPNRLWLTDITEHPTSEGKLYLCAIKDLYAGRIVGYSMAGRMQASLAV
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTTHGLIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPA
+DAA
+>2_688
+MMYPHVKELATDGIPVVVSVRMLKLARQPYCRWLENPLTRTDLDQAYRANALHAAHQNEK
+ALAHR-------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+SAS
+>2_2226
+-MYPLVSELAADGVPVAVSLRVLKLARQPYYRWREKPVAVSEVEQAHRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDR-----
+----VRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAV
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDELRAGIITWIERSYHRRRRQVRLGRLTPVEYELIMDHTPA
+DPA
+>2_2440
+------------------------------------------------------------
+--------------------------------------------------MHDDR-----
+----VRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAG
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPA
+DPA
+>2_2441
+-MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGGQARQ------------------
+----------------------------ERALYL--------------------------
+-ALP--------------CMMTASAGTSL-------------------------------
+-------------------PKLRTGCG---------------------------------
+---
+>2_2557
+-MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDR-----
+----VRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAG
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPA
+DPA
+>2_2577
+------------------------------------------MEQAHRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDR-----
+----VRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAV
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDDLRAGIITWIERAYHRRRRQVRLGRLTPVEYELIMDHTPA
+DPA
+>3_1844
+-MHPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDEAYRANALFDAHKDDP
+EFGYRFLADEAREAGESMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAVTD
+EKGRIRHQFNADAVNELWIGDITEHRTGEDRLYLCAFKDVYSNRIVGYSIDSRMKSSLAV
+TALNNAVARRG---EVAGCVVHTDRGSQCRSRKFVHALNRHGMVGSMGRVGATGDNAAMA
+SFFALLQKNVLERRSWATREDLRIAIVTWIERTYHRRRRQVALGRLTPIEYEAIMTTPAS
+QAA
+>4_864
+-MYPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDETYRANALFDAHKDDP
+EFGYRFLADEAREAGELMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAATD
+EKGRIWHQFNADAVNELWIGDITEHRTGEGRLYLCAFKDVYSNRIVGYSIDSRMKSSLAV
+TALNNAVARRG---EVAGCVVHTDRGSQFRSRKFVHALNRHGMVGSMGRVGAAGDNAAME
+SFFSLLQKNVLDRRSWATREDLRIAIVTSIERTYHRRRRQAALGRLTPIEYEAIMTTPAS
+QAA
+>4_1490
+MTYPLVAELADAGILVTVSCRVLKLARQPYYRWRNAPVRDADMLRAYRINALHDAHHDDP
+TFGYRYLADEARRAGWRMSRRTAWKLCSQAGILSSAQRRRRGKGKKTGPPVFDDH-----
+----VQRVFRADAPNRLWLTDITEHRTSEGKLYCCAIKDVFSNRIVGYSISDRMTAKLAV
+DAVRNAVARRG---EVAGCILHADRGSQFRSRAMARELRRHDMVGSMGRVGAAGDNAAME
+SFWSLLQTNVLNQQRWTTRQELRLVIVVWIERKYHRQRAQDILGGLTPIEFEAKLAEPHT
+LAA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000014.fa ADDED Viewed

	@@ -0,0 +1,101 @@

+>0_152
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>0_1029
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>0_1999
+MNEAVP--HFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLA
+AAEARHTAQDAG-RFPGLT-ATAGPVDMEALIAGKRALVENVRSDKYVDLVADYGWELRH
+GNAVFTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAME
+LDEVPESLLVIGGGYVALEQAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGI
+RVIRRSTVSSITQD-TDGGIAAQADIAGGRETLRASKVLVATGRRPVTDGLNLAGVSVKT
+GDKGEVVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLP
+RVTFTSPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRI
+VGITAVAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSC
+CAA
+>1_283
+MPT-----KYDLAIIGSGGGAFAAAIRATTLGKSVVMIERGTLGGTCVNTGCVPSKALIA
+AADARHSAADAADRFPGIA-TTAGPVDMPALIAGKQALVESLRGEKYADVADSYGWAVRR
+GDAAFAGTPDAPVLQVAGDDGSTETIEAGHFLVATGSRPWAPPIDGLDETGYLTSTTAME
+LTELPESLLVLGGGYVALEQAQLFARLGSQVTVLVRSRLASKEEPEVSRTLEEVFADEGI
+RVVRRALPTRVSRDAATGQAVVTADVAGGREEFRADQVLVALGRRPVTDGLGLDRVGVET
+GDLGEVVVSDRMQSSHPRIWAAGDVTGHPEFVYVAAHHGTLVAENAFADADRAVDYARLP
+RVTFTGPAIGAVGMTEKDVVAAGIRCDCRVLPLHHVPRALVNRDTRGFVKIVVDADTGKI
+LGITAVAKDAGELAAAGVHVL--GKTVAEVADAWAPYLTMAEGIRIAAKAFTTDPSLLSC
+CA-
+>1_321
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>1_330
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>1_757
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>2_705
+MTATANSRSYDLAMIGSGGAAFAAAIRATSLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>3_2168
+MNEAVP--HFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLA
+AAEARHTAQDAG-RFPGLT-ATAGPVDMEALIAGERALVENVRSDKYVDLVADYGWELRH
+GNAVFTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMD
+LDEVPESLLVIGGGYVALEHAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGI
+RVIRRSTVSSITQD-TDGGIAAQADIAGGRETLRASKVLIATGRRPVTDGLNLAGVSVKT
+GDKGEVVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLP
+RVTFTSPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRI
+VGITAVAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSC
+CAA
+>4_978
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDGHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000017.fa ADDED Viewed

	@@ -0,0 +1,81 @@

+>0_519
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVTLADEAVALGGETAADS
+YLVIGKILDAAERAGADAVHPGYGFLSENADFARAVTDAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT
+GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV
+SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGEAVSG
+AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS
+ALTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGKRGAPVA-AAVSTDALTAPMQGT
+VVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATIADAE
+>0_1855
+MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT
+YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP
+DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG
+HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV
+TEEVFGVDLVREQFRIAAGELLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG
+EYDSLLAKLIVWGEDRAQAIARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES
+PYLGAE-VPAGGRTSVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPADAAGAG---KPDDDGAVASPVTGT
+LASWKVEDGAEVAEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAISRLGA--
+>1_253
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVTLADEAVALGGETAADS
+YLVIGKILGAAERAGADAVHPGYGFLSENADFARAVADAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT
+GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV
+SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSG
+AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS
+ALTPAEPAP---ARRAT---------------------------------------------------------------
+-------------------------------------------------------------P
+>1_1562
+MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT
+YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP
+DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG
+HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDKQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV
+TEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG
+EYDSLLAKLIVWGEDRAQAVARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES
+PYLSAE-VPAGGRTAVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPAGAAGAG---KPDDDGAVASPVTGT
+LASWKVEDGAEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA--
+>2_2354
+MSIADAPQASVIPPRDPKAERRFSRVLIANRGEIAVRVVRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGETAADS
+YLLVEKILDAAERSGADAVHPGYGFLSENADFARAVEAAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT
+GTEEVVAFADEHGLPVAIKAAYGGGGRGIKVARSREEIPELYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+GVVVMSTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILKEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV
+TEEVTGIDLVREQFRLARGEALGY-EDPVVRGHSFEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDTGVVEGETVSG
+AFDSMVAKLIVTGADRRQALQRAARALGEAEIAGMPSVLPFHRAVVTDPAFAPEIAGAAEPFTVHTRWIETEFANHIEPS
+EHAPADPTSREPRRTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGRRGAPVA-AAVSTDALTAPMQGT
+VVKVAAENGQTVAEGDLIVVVEAMKMEQPLTAHRAGVVSGLEVEPGQTVSAGTVIATIADAD
+>3_861
+MSTPSTT-----------ASRPVTRVLIANRGEIAVRVARACRDHGIASIAVYSDPDAQAMHVAVADEAYALPGSTSAET
+YLDIAAVLDVARRSGADAVHPGYGFLSENADFAQAVIDAGLTWIGPSPQAIRDLGDKITARAIAQRAGAPLVPGSDGPVP
+DAAAARAFAQEHGLPIAIKAAFGGGGRGIKVVRELSEVEDAFESAVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG
+AVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRQRIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV
+TEEVFGVDLVREQFRIAAGEPLSIPEDPAPRGHAIEFRLNAEDPAHGFLPVPGPVEAFEAPTGPGVRMDSGVRTGSVVPG
+EYDSLLAKLIVVGEDRSQAIARARDALAELRIEGVPTVVPFHRAVLEEEAFT-----SAEALGVYTTWIESEFAAPLAAS
+PHLGAS-VPGGGRTTVTVEVDGRAVRLGLPA---DLHAALLGGGGARTGA--SAPAE--------QSVDEGAVTSPVTGT
+LASWKVEDGAQVAEGDTIAVVEAMKMETPVRAPRAGRVERAAGDAPAAVTRGQVLASVRA--
+>3_2235
+MTNASAPQASA--DIAEAPGRPFSRVLIANRGEIAVRVIRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGETAADS
+YLVIQKVLDAAERSGADAVHPGYGFLSENAEFARAVEAAGLVWIGPPADAIDALGDKVSARRIATKVGAPLAPGTTSPVN
+GTDEVVAFADEFGLPVAVKAAYGGGGRGIKVARTREEIPELYESAVREAVAAFGRGECFVERFLDRPRHVETQCLADAHG
+NVVVVSTRDCSLQRRNQKLVEEAPAPFLTDEQNTRLVESSKALLKEAGYVGAGTCEFLVGQDGTLSFLEVNTRLQVEHPV
+SEEVTGIDLVREQFRIARGEALGY-GDPEARGHSFEFRLNGEDPGRNFLPAPGTLTRFRMPSGPGVRVDAGVTEGETVSG
+AFDSMVGKLIVTGADRRQALQRAARALAEAEIAGMPSVLPFHRAVVADPAFAPELAGSEEPFAVHTRWIETEFAHQIEPT
+ALTPAAAPDRPERHTVTVEVNGKRVDVTLPTWGEAMHQ--LQGAAARAGAGRRRPRGARRAGAAPAAPGTDSLTAPMQGT
+VVKVAAQNGDRVAEGDLIVVMEAMKMEQPLTAHRAGVVSGLEVAAGDALTAGAVIAVIADAE
+>4_522
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGESAADS
+YLVVGKILDAAERAGADAVHPGYGFLSENADFARAVADAGLVWIGPPAAAIDRLGDKVSARQLATKVGAPLAPGTTSPVT
+GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV
+SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSG
+AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS
+ALTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGKRGAPVA-AAVSTDALTAPMQGT
+VVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATIADAE
+>4_1776
+MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT
+YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP
+DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG
+HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV
+TEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG
+EYDSLLAKLIVWGEDRAQAVARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES
+PYLSAE-VPAGGRTAVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPAGAAGAG---KPDDDGAVASPVTGT
+LASWKVEDGAEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA--

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000019.fa ADDED Viewed

	@@ -0,0 +1,28 @@

+>1_326
+MPAPYPQEFRDDVVRVARSREEGVTLAQIAKDFGTHEMTLSKWMRQADVEDGAKPGTTKA
+ESAENRELKKRIRLLEQENEVLRRAAAYLSQANLPGKGSTRS
+>1_1716
+MPAPYPKEFRDDVVRVAQNREPGTHLKDIAKDFGISESCLTNWIRQADIEAGNIPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>2_2225
+MPAPYPQEFRDEVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>2_2442
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>2_2558
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>2_2575
+MPAPYPQEFRDDVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>3_1843
+MSKPYPKEFRDDVVRIARNREPGVELSQIAKDFGIHFTTLYAWMKKADIEDGDRPGTTEA
+QYAELREAKRRIRTLEQEVEVLRRAAAYLSQAHLPGK-----
+>4_865
+MSKPYPKEFRDDVVRVARNRGPGVELSQIAKDSGIHVTTLYAWMKKADIEDGDRPGTTEA
+QSAELREAKRRIRTLEQEVEVLRRAAAYLSQAHPPGK-----
+>4_1489
+MPGPCPREFREDVVAVARSRESGVTIKQIATDFGVSEATLQNWLRQADVEDGNRPGQTAA
+DAAEARELKKRIRLLEQENEVLRRAAAYLSQANLRLGGSPK-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000021.fa ADDED Viewed

	@@ -0,0 +1,73 @@

+>0_546
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------MHAGWSLG
+AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASARGAADQSPA
+PS-ETSAPPAPAAQALP--RRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITERGLDP
+AAAVLGASTLLGAQFVGRLAGDRTLAVLGRRGALTAGLGAVVVGLGLAL-APLPGPVAVP
+AAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA
+VGLAPALTVFLGLAAVGTVLAARLPA---AP---
+>0_547
+MSEAPPHLPTADDGVAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP
+AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG
+AGHGAGTAAAWLLWVFAGLVLASGVLDAVVDTAQNAQGLQV-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------
+>1_279
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------MHAGWSLG
+AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASARGAADQSPA
+PS-ETSTPPAPAAQALP--RRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITERGLDP
+AAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLAL-APLPEPVAVP
+AAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA
+VGLAPALTVFLGLAAVGAVLAARLPA---AP---
+>1_280
+MSEAPPHLPTADDGVAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP
+AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG
+AGHGAGTAAAWPLWVFAGLVVASGVLDAVVDTAQNAQGLQV-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------
+>2_2322
+MPSASPSSPAARRARAHPVARRDVVRARWAATLAFLTNGGMLGALIPHYPQAKAAFGLDA
+DAFGLLVVALAAGAAAAGSLPAPVLRRWGSRRVMLAGTVVMAVVVVAAGLVVDLSAPAQG
+R------PWAGAVWLFAALLGVAGILDAVVDTAQNAQGLTVQTRLARPVLTSMHAGWSLG
+AGLGAGLGALAVGAGMPAGLHLGLNGAACVAVLVAAGRRFLPD------------DARPA
+P-----DADAPEGTAAPAPGPSP-------------------------------------
+-----------------------------RRPAR----------------PPPPRP-APP
+---------------------------PGWPC----------------------------
+-----------------------------SP---
+>2_2323
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------MAGFGVEEFGNAWTALFLQSERGLDV
+AAAGLGASTLLLAQFVGRLVGDRVLHRLGRRRTLAGSLAVVVAALVLVLTAP-----AAP
+AVFAGLALAGLGCAVVVPTAYALGDEVPGLPPRTGLAVVSWLMRVAGIGLSPLVGLLATG
+LPLPAALAVFPALAVLGLVGTGVVGRRRRRP---
+>3_2201
+MTSAPADTPR--------IDRRAATRSRWAATAAFFTNGALAAAMIPHYPQAKAAFGLDP
+AGFGLLVTVMTLGAACAGPAGAPILRRAGSRATVLWGSLAIAVVLTGAGLALDLGARSDA
+AG-----PWLGA---YAAAVFASGLCDAVVDTAQNAQGLRAQHALGRPVLTSMHAGWSLG
+AAVGAALGAAAVGAGVPAGLHLGLNGAACVLLLALTLPRFLPDTP----------DHAPA
+PALLTADDPGPESEATPASHRHPWLLLAPIVVISMAGFSVEEFGNSWTSLFLQAERGLDP
+ATAGLGASTLLGAQFLGRLTGDRVLAALGRTRALTGGLAVVLAGLTVTLLVP-----TPA
+AMFTGLALAGLGSAVVVPTAFALADEVPGLPAQTGLAVVSWLMRLAGLGLSPLVGLLAGV
+LPLTAALGAFVVLAALGTVLALTLRAPRLAPDFR
+>4_548
+MSEAPPHLPTADDGFAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP
+AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG
+AGHGAGTAAAWPLWVFAGLVLASGVLDAVVDTAQNAQGLQVQTRLARPVLTTMHAGWSLG
+AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPTDSASARDASDQSPA
+PS-ETSTPPAPAAQALP--RRAAVAALLPAVVIAMAGFGVEEFGNAWATLFLITERGLDP
+AAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLAL-APLPGPVAVP
+AAFVGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA
+VGLAPALTVFLGLAAVGAVLAARLPA---AP---

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000023.fa ADDED Viewed

	@@ -0,0 +1,57 @@

+>0_2177
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKVDLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVA----QAVE--KLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINIL
+AQFRLVKAALPHLKP---GSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSY
+VVGATIPVTGGMPTP---------
+>1_1890
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVA----QAVE--KLGGLDVLVNNAGKQVAQDSIEDIDDEQLEATFDVNIL
+AQFRLVKAALPHLKP---GSTIINTTSVVTYMAPPQLVDYASTKAAINTFTKALGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQKSEDLPEFGQSTPLGRAGQPTELAPAYVFLASPESSY
+VVGATIPVTGGMPTP---------
+>2_495
+MANDDANTTTTDQLTLQDPVKRYPVISPPEQSLPGTGLDAEMTPKADLGEHSYRGTGRLT
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDARNVLAVLEKEGRTAVGIAGD
+LRDRQFCQDVVA----QAVE--AMGGLDVLVNNGGKQVAQKEFEAIDDEQLEATFDVNIL
+AQFRLVRAALPHLKP---GASIINTTSVVSYMPPETLIDYASTKAAINNFTKGLGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQPTEELPDFGQSTPLGRAGQPTELAPAFVFLASAESSY
+VVGATIAVTGGMPTP---------
+>3_423
+MTDVSTSTDTAVG-------------------------DSDTRPAAART-DAPAATVLLA
+GRAALVTGGTLGIGSGIAASLRDAGARVAVTGLTEQECAAAR------EAGFPAYVL--D
+VRDRAACAEVVG----AVVE--EFGGLDVLASNAGI-YPQARIADMTDEDIDLIFDVNVK
+GTIHAVQAALPALVASGRGRVVITSSITGNHTGYPAWSHYGATKAAQLGFVRSAAIELAR
+QGVTVNAVLPGNIITPGLEEMGQ--EYLDSMARSVPAGHLGEPADIGATVAFLASDGARY
+ITGQGIVVDGGQILPETPEALEGL
+>3_437
+MANDDTNTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVLTYLPEEEKDAQHVKEVIEAEGRKAVTVSGD
+LRDKQFCKDLVE----RAVQ--ELGGLDILVNNGGKQVAQEEFEQIDDEQLEATFDINIL
+AQFRLVRAALPHLKP---GSTIINTTSVVAYMAPEQLVDYSSTKAAINTFTKALGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSY
+VVGATIPVTGGMPTP---------
+>3_633
+M-----------------------------------------------------------
+-----------GI------------------HYARDSTAAEAVVERVNEAGASGVLIRAD
+LAEGAAGAAHLATRWRDEVRRHDARGTDVLVSNAGINGAQ-SLSELDEGTVARVVNVNLV
+APLMLVHHLSDHIND---HGRVIGISSGFARIAAPTHVAYTASKAGLEAAFRAIAAELAE
+RDITVNTVRPGVIDTDINADWINEPGARDAVAAAAALRRVGQPDDVADIVAFLASHSSRW
+MTGQSLDATGGTQL----------
+>3_1824
+MSTHD----------LPDPLTQFPRFAPERQTQEEPGLSARMDPEPDCGEDTYVGIGRLK
+GRRALVTGGDSGIGRAVALAYAREGADVVFTHLPEEAEDAARTTELLDAEGVRHVAREVD
+LRDEAATRALVR----DAVK--FLGGLDLIANVAGEQRYVDDLAELDPRQVRDTFEINVF
+ALIWIVQEALPHLPA---GAAIVNTASTQATTPLPGLVDYAGTKGAIVSITKALAQQLTP
+RGIRVNAVVPGAIWTPIQVSLGRAPEQVDVLGQDAPLGRPGQPAEMAPAYVFLASTEASY
+VSGEVLGATGGTLY----------
+>4_2110
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAAGIPGD
+LRDKTFCADLVA----QAVE--KLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINIL
+AQFRLVKAALPHLKP---GSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSY
+VVGATIPVTGGMPTP---------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000025.fa ADDED Viewed

	@@ -0,0 +1,29 @@

+>0_95
+M-------------------NFALDGRNYEIDLSKEHAAELREFLKPYMKK---------
+--GRAVAP-------PSPK-----VEAAQIRKWAAENGYEVSSRGRLHRDVVEAYRNAKR
+K-
+>1_2059
+M-------------------NFALDGRNYEIDLSKEHAAELREFLKPYMKK---------
+--GRAVAP-------PSPK-----VEAAQIRKWAAENGYEVSSRGRLHRDVVEAYRNAKR
+K-
+>2_277
+M-------------------NFALDGRNYEIDLSKEHADELREFLKPYMKK---------
+--GRAVAP-------PSPK-----VEAAQIRKWAAENGYEVSSRGRLHRDVVEAYRNARR
+K-
+>3_600
+MATITTIADDFDNSTPAETTYFSVNGKEYAIDLNEEHRRELEDVLEEVAERLSKYTAVAR
+PLGKSSAPARKSSKSPSSR-SGASYDAGAVRSWAEENGYKVADRGRISADVLEAY-NASK
+KG
+>3_653
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGR----TPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGK
+KG
+>4_90
+M-------------------NFALDGRNYEIDLSKEHAAELREFLKPYMKK---------
+--GRAVAP-------PSPK-----VEAAQIRKWAAENGYEVSSRGRLHRDVVEAYRNAKR
+K-
+>4_1954
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGR----TPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGK
+KG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000026.fa ADDED Viewed

	@@ -0,0 +1,56 @@

+>0_126
+MS------------------------------TSPSGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY
+GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT
+TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH
+GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF
+VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT
+VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI--------
+---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED
+>1_2091
+MS------------------------------TSPSGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY
+GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT
+TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH
+GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF
+VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT
+VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI--------
+---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED
+>2_241
+MS------------------------------TSPSGSRVAE---PGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY
+GSAGGIQAAGPGVILSFLIAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT
+AYMAFWFPEVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQAGLANLVDH
+GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF
+VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT
+VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI--------
+---PDSRQA-----LIIGLVWVAVLTLAWFVTGVRKAAAVHDRTGTLPVASGEEAAASHR
+>3_176
+MN------------------------------ASPSGAHAVDHPRDDAAHAAQSQLHRGLSQRHIMFIALGTAIGTGLFY
+GSAGGIQTAGPGVILSFLIAGFAVYLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAVT
+KYMAFWFPGVPAWAWVAATILVIGLVNLTHVGNFGEAEFWLTLIKIGAIVAMIFGGLILMFTGASFTDGTPAGLHNLVDH
+GGFLPHGFGGVLIALTIVTFSFGGIETLGVAAGEAKDPETALPKAINTVPVRILLFYVLTMVVIMSLVPWSAVDGKTSPF
+VQIFEGLGVPFAPHILNFVVLTAAISAINACIYASGRLLYAMAHDGQAPRAFTRTTANGVPWLTVAVMLGVMVLGAILIT
+VNP-DAFGLIAGVASFAVVLTWTMIFLSHRAMRARVKEAGAPPSVYPMPFGIVGTVLGLAFVATVVITMATI--------
+---PESRQA-----LLIGLAWVVALTAAWFVTGVRKTAALHDRTGQLPVVHRHH------
+>3_177
+MQ------------------------------STPA-----------PEAPAQAQLQRGLNPRHITFIALGTAVGTGLFY
+GSAAGIQAAGPGVVLAFMLAGAAVYLVMRALGEMAVREPISGSFVAYASRYLGPFAGFLTGWTYVFELAVVIVADTTAVT
+VYMAFWYPDVPAWVWVAATMVVLGLINVTHVGSFGEAEFWFSLIKVLAIVGMIFGGVILMFSGASFQDGVTPGPHNLVEH
+GGFLPHGLMGVLTALTIVTFSFGGTETLGIAAGEAEDPASALPRAVNTVPVRILFFYIGSMLVIMSLVPWTTVDGETSPF
+VQIFETLGVPFAPHLLNFVVLTAAVSAINACIFTNARLLHHMAHDGHAPRVFTAVTRGGVPWVTVVAMLGVMAAGAVFMS
+VKE-DTFGIVAGVATFAVVFTWALILASHLGMRRALARHGQAPGAFPMPGGRVGAWLGLAFVAVVAGTMAFDQGGAVLGA
+LGGPDALQTALAQPFVIGVLWLAVLAAAWAVPAVRRSAHRHDRHGTPPPLTWDV------
+>3_2128
+MTPERRGPGTSPGGRYGVRVNEPPALPEPTGAAPPAPSPAGGATAAPSHGAADARLRRGLSMRHIQFIALGSAIGTGLFY
+GSATAIQLAGPAVILAYLVAGAAVFMVMRALGELAVRHPVPGSFGQYADRYLGPFAGFVTGWTFVFEMVVVAIADVTAFG
+VYMGFWFPDTPRWIWVTAVILFIAAVNTRHVKVFGELEFWLSIVKVSAILAMVIGGVALLVMGVSLDAATPAGVQNLVDH
+GGFAPHGAAGVLAALSVVVFAFGGVETIGITAGEAQDPGRAIPRAVNAVPARILLFYVMTMVVIMSLVPWDRITGEASPF
+VEIFSTLGVPAAPAILNLVVITAAISAINADTFSAGRMLFGMAQQGRAPAVFASVSRGGVPWMAAVVMGLALAVGAVLNA
+VIPEDVFVVVASIATFATVWVWLMILLAHIAMRREVARRGLPASAFPVPLWPAASWAAVAFVLLVVGLLGWF--------
+---SDTRVA-----MIVGLVWLVLLGAAY-----RLFLHGHGR--SRPDLEEGAA--SSP
+>4_134
+MS------------------------------TSPFGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY
+GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT
+TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH
+GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF
+VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT
+VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI--------
+---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000031.fa ADDED Viewed

	@@ -0,0 +1,64 @@

+>0_164
+---------------------MPGRLIGW-----PRKPTLLELLFG--------------
+---LAMWEHAVMQIISFFNHKGGVGKTTMLFNAAVEMGRLGKRILMVDFDAQANLTAISI
+DDDMLSMIYAPDEDGKTVAHAFAPLVGGSGDVFAPEAIEVREGKVWLAAGDLRLSEFDAI
+LPSAWTEALAGNERGFRVTSAPYRLICEIAEE---------IKADY--VFVDLGPNV--G
+ALNRAVLLGSDYMIIPMAADLFSIRALPSVGNSVDTWVRQWNTARSVAPRL----NFD--
+IQKGLPKVLGYVSQQFNIYRGEATLAFSHWIDEMPAQIQSGLLEPLAVHSDGKGATLADP
+AQSKGPGVGDLKNFHSLVPHAQTLRKAIFELRADDVVRGGQVTRARQSEEQFKELCANII
+ARAV
+>0_1359
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA---
+-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI
+LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G
+LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA
+TVAATP-ITLFAENHDGAKAYRQLARELIS-------RGG--------------------
+--AP
+>1_1098
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA---
+-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI
+LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G
+LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA
+TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG--------------------
+--AP
+>2_1459
+---------------------MQTSLEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLSSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRKVLMVDFDPQGALSA---
+-----GLGANPHDLETTVYN-----VLMERSVTA----------------------RDAI
+LPTPF-EGMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G
+LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDKVFETVIKRS----IKFADA
+TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG--------------------
+--AP
+>3_1370
+--------------------------------MTPKEPIPVMTVHGEPVLGPTGRPKHEF
+PEPTPLAGHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRKVLMVDFDPQGALSA---
+-----GLGADPYELDVTVYN-----VLMERKVTA----------------------RDAI
+LPTAF-ENMDVLPANIDLSAAEVQLVNEVAREQVLDRALRQVKDDYDVVLIDCQPSL--G
+LLTVNALTASDGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVDGFGDRVFETVIKRS----IKFADA
+TVAATP-ITVFAENHDGAKAYRQLARELIC-------RGG--------------------
+--AP
+>3_2178
+------------------------------------------------------------
+-----------MHTLMVYSEAGGVAKTTTAVSLAMSWAEQGRQVVLIDLDPRAAATK---
+-----WVDVEPTEPGLHIGA-----VIGNPDPTG-----------WV---------QDLA
+VPSGWHENLRVVPSDRSLSHQESDRADHAHLR--LRMALSDLQADL--VVIDC-PNRQGG
+PLTQNAFTASDGVIYAARPTSDGCDGVHGARQSVA----------AFKQSMALLGAPDRL
+VE-----VGIVVSDYRD----HITPKDQTVAVEELRETGLLLTPLVPARS-----IVPKA
+RLACDW-LGRYEKGEPVAAAYADLAGLIFE-------R--------------------I-
+--TA
+>4_1308
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA---
+-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI
+LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G
+LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA
+TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG--------------------
+--AP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000032.fa ADDED Viewed

	@@ -0,0 +1,43 @@

+>0_236
+MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG
+AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG
+YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR
+MIGAEEAERIGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGI
+AFERRVFHAAFATADQKEGMDAFTAKREAGWQHR------
+>1_84
+MST-----------GLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETD
+GVVITGSGQKAFAAGADIREL------QHKSVQEMTARGMQHAMTALRESSLISVAAVNG
+LALGGGFELALSCDIRLATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQ
+PISADRAHQLGLVSELHEAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGL
+EIELLAQAAIFGTQEREEGLNAFLERRTPSFIPRPRPRKD
+>1_88
+MTD-----------RIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVR
+AILLRGEG-KAFCAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRR
+YALGAGLEMALAADLIVAEPQAKLGLPFVLRGI---AAGTSLLPKRAPVQLVQRMLYLGE
+MITAEDAHRMGVVGHLAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDAL
+AVQVGATAASVLTEDFTEGKVAFTQKRDPEFGGR------
+>1_2199
+MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG
+AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG
+YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR
+MIGAEEAERIGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGI
+AFERRVFHSAFATADQKEGMDAFTAKREAGWQHR------
+>2_115
+MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG
+AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG
+YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR
+MIGAEEAERIGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGI
+AFERRVFHSAFATTDQKEGMDAFANKREAGWQHR------
+>3_84
+MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG
+AILLLGSA-KAFAAGADIKEM------KDKDAADMYAADWFRRWEDLARLRTPIVACVQG
+YALGGGCELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGR
+MVEAEEAERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGL
+VFERRVFHGVFSSEDQAEGMAAFAEKRSPVWKHR------
+>4_236
+MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIG
+AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG
+YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR
+MIGAEEAERIGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGI
+AFERRVFHSAFATADQKEGMDAFTAKREAGWRHR------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000035.fa ADDED Viewed

	@@ -0,0 +1,22 @@

+>0_602
+MPAAYPREFRQDVVAIARKGQIPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>1_356
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>2_373
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>2_377
+MPAAYHREFRQDVIAIARKGQMPIAQVAKDFGIAESRLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>2_394
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>3_2137
+MPAAYPREFRQDVVAIARNGQMPIAQVAKDLGITASCLRRWLAQDDVEAGIRPGLTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>4_579
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000036.fa ADDED Viewed

	@@ -0,0 +1,56 @@

+>0_606
+MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL---------------------------
+-----------------------AGPPLFHEHLEQA--------------------------------------------
+GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA
+GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR
+LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL
+TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG-
+------GSGVGLAISRALIQTHGGTLSATSTT--AGATFTIDLPTKQPPTSPP----------TGAPVYPP--
+>2_387
+MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL---------------------------
+-----------------------AGPPLFREHLEPA--------------------------------------------
+GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA
+GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR
+LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL
+TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG-
+------GSGVGLAISRALIQAHGGTLSATSTT--AGATFTIDLPTKQPPDQPTYRRTRSSTVNTGAP---PLA
+>2_1228
+M-------------RTRLSTLLALVLVLSLAVSGITAYAVLRITVNDRIEASLQRAVEQVALLSETGVDPETGEPPDSAA
+AFIRLAMLRVLPHDNEGILG---LAPDRAELAASDAVELRLEEDPELVAWALARVGDQEARAETVTTASATYRAVVVPVT
+GWGQDDAGALLLAVDVDAEVGRLDRTFLGFAGGALLTTVFALAVGVPLLRRVFAPLESLQEAVGEVTEHDLDRRVEVIGH
+-DDVAALGHSFNAMLER-----LEDSFASQRRLLDDAGHELRTPVTIVQGHLEVMDPDDPADV----RETTRLTLDELDR
+MSRLVDDLLVLAKAQHPDF-LRPAPVDV--AELTRGVL-----ARASGFDGHVWELDGV-AEATVSLDAQRITQAWLQLA
+AN---AVRYSEPGS-----------------VVRLGSAVEGDTLRLWVQDHGVGVRPEDRAQIFERFGRGAHGTRAD---
+------GSGLGLAIVSSIAAAHGGEVSLDSVPG-LGSVFRIELPLSTPSRPAG----------SLTPGKDP-A
+>2_1305
+MTRSKPTGRLSASGRARVVAWILGVSALGMVLMLVSIVLTLRWVERDAIETSLTQESDEVAVFAQNGRDPETGEPFATPE
+RFVGHYLERQRVEPTELMFGGTAATPVIAQIHGDAA------APVELLAPATRQ-AMEQPRSRGTLVDPTHGRISYANLT
+VTTPADTGHVVVAVFHERYEQRVMTQTLLLSALALAALAATAAAAWLVSSRILGHTVEFHRAVDASLKDRGLRRLPENGS
+-EEYAGLARRANDLVRR-----ADRRLEEERRFAEDVTFALRTPLTVIEGGL-----RNPGGDEQERRTSYRHIGAEATR
+VRGLLEDLVILSRLQQDDVVLERTPVDV--GVLVATAAQAWRERHPDAADEPRLDVEAPAEGLTAVTDRARLVQVLEELL
+DNARHAVRFAPGSDLPRDLTAVTPLERTLSVRVREEERDGEPWAVVEVADRGRGIPEEDREEVFERLANASNDPYP----
+------GNGLGLPVAALLSTALDGELTLEPGPGAAGTVARLAVPLTADQDGEDA-------------------
+>3_434
+M-------------------------------------------------------------------------------
+------------SPTPALRGRPAPGP-----------------DAALVARAARRIGLRTALACAALVLGGAG--VFFGY-
+-------------------------------------------LWWQIAHPGVDPRDA--DATVTVQLDLVDLATAAILA
+GAAAVLITGFASLWFSRSAVQPLADALRRQREFVSNASHELRTPLTVLSARTQVLQARVPAGDPL--EPLADELRRDTDV
+MAGVVEDMLSTAR-------LDSAPEGMCDAGEVAAAACA--DLSLVGAEERGVRLRADLPSLPVALPEAALRRMLAALL
+DN---ALGFAPPGT-----------------EVTVSGERVRGVVELRVADRGAGIQGVEPDHVFDRFARGRPAAVPGSGP
+GAVPRSSHGIGLALVRETAHRYRGEVRVESTGP-EGTVMLLTLPAAQEAR-----------------------
+>3_2146
+MT-----------SRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL---------------------------
+-----------------------AGPPLFHEHLEQA--------------------------------------------
+GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA
+GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGGQLAR
+LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLDNLL
+TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG-
+------GSGVGLAISRALIQTHGGTLSVTSTT--AGATFTIDLPTKQPPDQPTYRRTRLSTVNTGAP---PLE
+>4_575
+MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL---------------------------
+-----------------------AGPPLFHEHLEQA--------------------------------------------
+GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA
+GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR
+LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL
+TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG-
+------GSGVGLAISRALIQTHGGTLSATSTT--AGATFTIDLPTKQPPTSPP----------TGAPVYPP--

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000039.fa ADDED Viewed

	@@ -0,0 +1,189 @@

+>0_851
+MN------------------------------------------------------------------------------
+------THH-----------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------PDR--------------------------------------------
+--------------------------------------------------------------------------------
+------------------LTDAAGVRVLLYGDVDLNVI---DGSATWLPSLAETLAR-----------------------
+TGASVDVQLKAV-ERRDL---LTAPLRALTGVRVLTAEPAAGQGGMTPSRAADVLAR-------RDEESRYDVVLVRGIH
+ACLELADRGA--------------------------FPGRLWS--------------YVTEYGYVED--------GFPAG
+RVEELGRIA-AASRLMLAQTPQARA-VLEAMVPAAA-----------GRTELLSPMVPDGLVPAERAEAPADGPVRLVYT
+GKFAHDWRTDL-MPDVLTA----------------------------------LHEAGVPATLTMVG-------------
+--------------------------------------------------------------------------------
+--------DKVHP---------------------ERDRPGWAAAMRSRLEAERPDFEWTGA--------LSREESMAR-T
+AAADVSLGWRA----------PA-------LDLSLEISTKVLESCAVG------VPPLLN-RTVAHEELLGADYPLFVDG
+VRDSARDVAA--RIAAARHDLPALSRRVVE-AAAPYRMAARARALTGVMDRLGLLDRRPARGGS---RTRVVLAGHDLKF
+AGELVDLLRDDPGVELRIDHWQGLHRHDEAASRRLVEWADVVVCEWAGPNAVWYARH---KRPGQRLVVRLHMFELRGGW
+LSALETEAVDRLVTVSDLYRDLVREHLPIEPTRVTVIPNAVSVADLDRPGLPGRRFRLGLVGVVPLRKRLDRAVDLLEIL
+RAHDERFTLHVRGRMPWEYPHEWRKPLQREGYLDLFARLGAGP-LREAVAFEPFGAD---MGSWL-TKIGWVLSPSTTES
+FHLAPAEGMVSGAVPLVWDRPGARGVFGDEFVLDDTDAAARRVLEAVADDARWDALSALARERVR-AYDERVVAGLW-RE
+ALGLD---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------
+>0_861
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------------------MNVAGARLRRWAGRA---RIVGERAAATAGDAGAS
+ALRAARGARG----------------------------LATLPERTWRAAD-VHV----PDASAALPLPAAAVLRRALTG
+ARV--PSLDAFSPLGPRPAAAPAVLLLPVDE-PAARGWSVEAAAELAARRCADLEMP-AGAPGLHTV--LMSDPASRRAL
+TAALRTAGGRLPGVLVVACPDPATAAGR-----ARVLAALGLVDAVLAPEGTRLDPPLARAAARAGRAVIGP--------
+--DRAA---------ETWERLAAAGRAARLDALTPAEAAG-PPAAPA------------PRVRVTAEPRRVVVAGHDLKF
+AGALMDRLRAD-GHEVRVDAWRGHARHDVERSRALAAWADVVHCEWSLGNLAWYSRHLDSPHRTTRLTSRLHLQEAGTAF
+PSRVRQDALDEWVFVAEHVRAQVLRDTRFPASRTSVVPNAVAVPPTLPDGDDDRRFVLGLVGVLPERKGLHRALDLLAAL
+RRVEPRYTLRIRGHHPEEVGWMAQRPAAAAYYRAQLRRIETDPVLAGAVTWDPHGPD---MPAWY-ARVGVALSVSDFES
+FHFTLPDGAAHGCLPAALAWAGADLLYPAAWLSPDVATMAEALRRATADARAWRSAVAQARRDVAHTYAEEDVVPALVRR
+ILGGA---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AA-
+>1_582
+MN------------------------------------------------------------------------------
+------THH-----------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------PDR--------------------------------------------
+--------------------------------------------------------------------------------
+------------------LTDAAGVRVLLYGDVDLNVI---DGSATWLPSLAETLAR-----------------------
+TGASVDVQLKAV-ERRDL---LTAPLRALTGVRVLPAEPAAGQGGMTPSRAADVLAR-------RDEESRYDVVLVRGIH
+ACLELADRGA--------------------------FPGRLWS--------------YVTEYGYVED--------GFPAG
+RVEELGRIA-AASRLMLAQTPQARA-VLEAMVPAAA-----------GRTELLSPMVPDGLAPAERAEAPADGPVRLVYT
+GKFAHDWRTDL-MPDVLTA----------------------------------LHEAGVPATLTMVG-------------
+--------------------------------------------------------------------------------
+--------DKVHP---------------------ERDRPGWAAAMRSRLEADRPDFEWTGA--------LSREESMAR-T
+AAADVSLGWRA----------PA-------LDLSLEISTKVLESCAVG------VPPLLN-RTVAHEELLGADYPLFVDG
+VRDSARDVAA--RIAAVRHDLPALSRRVVE-AAAPYRVAARARALTGVMDRLGLLDRRPARGGS---RTRVVLAGHDLKF
+AGELVDLLRDDPGVELRIDHWQGLHRHDEAASRRLVEWADVVVCEWAGPNAVWYARH---KRPGQRLVVRLHMFELRGGW
+LSALETDAVDRLVTVSDLYRDLVREHLPIDPARVSVIPNAVSVADLDRPGLPGRRFRLGLVGVVPLRKRLDRAVDLLEVL
+RAHDERFTLHVRGRMPWEYPHEWRKPLQREGYLDLFARLGAGP-LREAVAFEPFGAD---MGSWL-TKIGWVLSPSTTES
+FHLAPAEGMVSGAVPLVWDRPGARGVFGEEFVLDDTDAAARRVLEATADDARWDALSALARDRVR-SYDERVVAGLW-RE
+ALGLD---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------
+>1_592
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------------------MNVAGARLRRWAGRA---RVVGERAVVTAGDAGAS
+ALRAARGARG----------------------------TATLPERTWRAAD-VHV----PDAAAALPLPAAAALRRALTG
+VRD--PSLDAFSPLGPRPAAAPAVLLLPVDDGPAARGWSVEAAAELAARRCADLQMP-AGAPGLHTV--LVTDPASRGAL
+IAALRPAGARLPGVLVVACPDPATAAGR-----ARALAALGLVDAVLAPEGTRLDPALPSVAARAGRAVIGP--------
+--DRAA---------ETWERLAAAGRAARLDSLTPAEATG-PPAAPG------------PRVRVTAEPRRVVVAGHDLKF
+AGALMERLRAD-GHEVRVDAWLGHARHDAERSRALAAWADVVHCEWSLGNLAWYSRHLDSPHRTTRLTSRLHLQEAGTAF
+PSRVRQDALDEWVFVAEHVRAQVLRDTRFPAARTSVVPNAVAVPPTLPDGDDDRRFVLGLVGVLPERKGLHRALDLLAVL
+RRTEPRFTLRIRGHHPEEVGWMAQRPAAAAYYRAQLRRIETDPMLAGAVAWDPHGPD---MPAWY-ARVGVALSVSDFES
+FHFTLPDGAAHGCLPAALAWAGADLLYPAAWLSPDVATMADALRRATADARAWRSAVAQARRDVAHTYAEEDVVPALVCR
+ILGGT---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AT-
+>2_2002
+MGEAD---------------------------------------------------------------------------
+---------------------------------------------------------------TPAP-------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--TPEGPL------------------------------------------------------------------------
+--AGRSFRLVAVAERPDWEPGLIAQLRAAGAAVVSTTEVV------------------------RTSSAHVDVLLAVDVE
+SAAALRAAGW--------------------------DRFQVWT-------------------VVQTDPGTPLMPRGLSAA
+G---VGRAV-AESRRVVVFDEASRS-AVESTLWNAA-----------GKVVVMP---------------------RF---
+------------TAEEVEA-------------------------------------------------------------
+------------------------------------VSFGGNRVEGPH-EPGEAI----LVLHAGLLGSEGA---HVLRE
+YSDAVRARRHVRK---VLVVAP----------------GDLRVAVRSEEGQRHLA-RIPGASLIDGGAELSRAAAGRR-T
+VTVL--PRWST----------PQDSRAEDLLAWAAAVGAQVWAEPGA-------VPPQVSGRPVG--QLPGDN-------
+-LSAALDWAD--QHAGGTTFGAAPINRVAQ-AFAPH-----VPALST----------VPAHPNA---PLKVLFVGADYKF
+AGDLVEALILRPDAEVRVDQWKTNGDRPTPNSAELLAWADVVICEFASRNAVWASQH---IREHQRLIVHLHGYELRNPL
+IHDIVMDRVHTVVFASEFYRADAVVTTGWRVEQTAVIPNSVQSAELRRPKTADARFHLGLAGYVPELKRMDRALDLLEEL
+LRRDDRFVLHLRGRHPWNYPYVWRHPLRRDTYLANYERLRSNPRLRRAVVFDDFGPD---MGNWF-RNIGWMLSPSTRET
+FHLAPAEGMASGAVPVVWRREGSDGIFPPESLVTDAASAADRIHRTAGDRDAYNSAARSAIEFAT-RYEAGAVVDHWLRL
+ILHGERPGGPPSPEHLQRARPVATALAGRADWNRVGRLLRDGRVEQAAAVAQEESRPAWEQPEDVRRLAAHVNGYSALAQ
+RAHRLVPSAPCVPPLLPLAAGADSARSLTLTEGPAGTYVTRSGDIAVGRGDILDDVNAEFDRLVDQAFRIGAQNRATALT
+VIGDEMLALAGGAVAGWLGIPFVWDLTSQPAARDLLMRMRALPDAPTPQGRLALLAAASATRLIGAGPAERLPVPFETFI
+GMADLDRPRRVGVIGRSLGDLVGRSWGEPVNLSPGRWREQTVPRLDVALLDAQVLHPRNAWRASEGNTGPLGALITHVRR
+HATPLAIVDLGHEGLDSAGIAQARRVDAVVTAHPDDVQRLHDVRIVPSQVAVSTAPWGIRSGEEHVLRPGDRVRLAMRML
+GVAETH
+>3_1900
+MRQIDEMALWTSRDVGVRVRYAGAEELIRGVRSRADATHDASDGGTDLEAADVAGPGTPEPSDHVAEVPWRLRVLNTGRV
+RQIRRWIYHARRAPAHAAAARVKRLLRTPGRWSETLRRPLARTRAAAPAPERADAAVA-----TPAPAAEPTGERTLAAL
+RAALAERPSASALHALVAALYRD-GQLRAPAAALEEHPELVGQFTPAQAKLARNVREQARLLDHPPVVPARAVGTALRPE
+AGRILYCAHGVHPYQ-SNGYAIRTRGIVAGLRDAGHDVVVAARPGFPWDAKVTRAAR----KKQSYPELVDGIEHVYSFG
+PSLRNQALAAYLESAVDSYLQVIARNRPAHVHAASNHITALPALIAARLSGLPFTYEVRGFWEYGMEPGEEGLQERGE--
+LAGRLEDLVMVEADHVFVLTAEMRDELRGRGVDPDRMTVTPNGVDPEQFQPLPAVGELHRRLGL-DPDRAVIGYLGSLVS
+YEGLEDLLEACLQLAEERDDFQLVVAGDGPVLPRLKEIAAERDTSLPVHLLGRIDADLIPALMSEVDVVACPRTATRVTR
+LVSPLKPLEALAAGVPVVLSDLPVLRSL-AEECGGAVVFPAGDRHGLAEAIAGLLDDPERRLDLGRSGRAWALRERRWDV
+LGAHLGSGILAAVPSTGAE----GGSRPLSTVRLGVIADTFTTSGLAEQVQTVPLQRAGQGWRRQLAEERLDAVF---VE
+SAWSGNDGAWTRGVGHYSDEESADLRALLEDCRAAGVPTVFWNKEDPVHFNRFVENARLFDLVLTTDNRSIQGYQARVDR
+SRQTVGSMAFFAQPSLHHPVTDGPAVADRPVMYAGSYYGDRYRDRSEVLRGLLHVARPFGVTIYDRQADLPDSPYRF--P
+EELQPFVEGGLPYSEMVKAYRRYPLHVNVNSVTASETMFSRRVMEISCAGGVVASGPSAGVNHMFRGLVPTIGRREVAER
+AMSTLLSDPGLRNVQGWNLRRLVRRSHTLSDRLLVLLRRLGLAV-SPDPTPGTTVVLTGPADRADWDGLLAQT-RPVDRV
+VAD--EMSETVRE---RLSAAG-----------------IEVSAGSASLDPAHLAWEWDGA-RLDRV--VHED------L
+ANVLLDSGYSA-------------AVLD-----TTPVTDLATPLAVVG------GAPVPSGASLVLRWGGGD--------
+--DGVVTVRR--GLLESVEDLGAKQRPAAV-ALTPEALDRMER------------------------PLRVVVAGHDLKF
+AGELINRFRSD-GHEVRLDQWASHQDHDDELSRELVDWADVVLCEWGLGNAVWYSKH---KREGQRLYVRVHSQELFRDN
+WSRMNLPAVDRFIFVAPHIRDSARRYRGVAARPSEVIPNIV-LPGAGLKRDPDSRFVLGLVGIVPRGKRFDRALDLLAML
+RREDPRYSLRVKGKQPEDYPWMAAREEEMAYYGTIRERIAQDPALQGAVHLDGFSTDRAELDRWY-SSIGIGLSVSDFES
+FHFTSVDGAQNGAVPAVLAWPGADRIFPAEWLSPTLESMARRIL-GLREPEVFRAAADTARRETSARFDGGRSLDRWSEL
+VAG-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----E
+>4_812
+MIQLF-------------LRFSRRQQLVMGL----------------FILLAVVGSVLAFLVDHAILIVALFWMLCAAVF
+VMI---MYH---------------------------RRLNAKINRTARAARMGSSAVAGRGGTRPATGRRISTQESLDSL
+QAAFARRRTVAAGLPLARKLIQERGDLSGAREVLDQLRGKSG-LTDSEENFVRRVDSLNRLLEADYPLPARHRTCNYLPV
+RGRVLY-AVGMSPVSVTNGYTSRTKGVAAGLVAQGLDVVVAPLPGKPWDKKSVVPGRRVPVKQRRDVSEIDGVRHVHNPG
+LPAWEGDLDVFFQVAADAYVREAMIEKPEFILAASNYLSALPALIAARRLGVPFVYEMRGFWEVSAASVRPGWEQSDQYR
+LDRRYEDLVAREADRVVVITDEMREDLAARGIDADKVTVAPNCVDPEVFAPLGKDHALLRGLGFTDTEAPVVGFAGSVTD
+YEGLDLVTDALATLKAEGVRFNFLIIGGGAYLDTLKARIATRGLDPETRFVMNVPNADMPAYLSSIDVFPLARKSLPVTE
+LVSPLKPLEAMAVGGAVVLSDVSPHKVFCGPDGDTAVSFQKDDLASLVERLRETLAAPDAARAMGVRARRWVKENRRWPV
+TGERIAASLMALAEEFRAS--LDDAERPLTDYTVAFIGDEFTTDTFVPELTALRVRP--EDWRETFEDHRVDALF---IE
+SAWRGNDSAWTGIIGYYDDETHAPVVELIAHCRLHEIPVMFWNKEDPVHFNRFKRTAALCDYVFTTDARTIVDYNALPDN
+QITTVASAPFAAQPLLHNPLPSTRA-QDEAIAYGGTYYGDKYATRKQGLDFLFYESAPHGLAIYERVHNDPNSPYRL--P
+DRFRRYARGSLSYPEMCQAYKAHPIHLNGNSVVDSPSMFSRRVVEITASGSTVLSSAGRGVDETLAGTVPTVTTPDEAAA
+YLEGWKSSEQRRHAGLWEAFRHVYETHTCAHRLVYMMRVAGFRVRSPQAAP-IAV----ECAAADVPLFEAQTMRPALYL
+VTDTTEGVDAASP---VVLAAP-----------------PERAAKLQEAGIRNVVIHREGAPALDEH--LVED------F
+SLALHFGHWKAVGTRTVEW-SPGDAHVR-----IAALTADIDEGTVLV------DADVYAGSVLGERPALAD--------
+--DEVFAWQHVVEHVGKVTYTDSTAVPIDT-AVVHEEADPLPPVASG--------EAGPPVGETQTVPLNVLVAGHDLKF
+LPQIMAQLEAA-GHRVIVDQWDGHDIHDEERSLRLLAEADVIFCEWALGNVKWYSHH---KQDDQRLVVRLHAQELRTRY
+LKDADLSAVDTFVFVSPVGMRRAQLLFGVPVDRSVVIGNTFDFERFAAPRNAPDPHALGLVGSVPHSKRLDLALDVTELL
+ASHDPTYRLDVMGKEYHEYAWLMKRTAERSYFEAQYLRIESSAVLREAVRFGGHSYD---IAEWYRAKPGIILSTSDHEG
+THQAIAEGGAAGCVPVIFPWAGAEAVYDDRWVVEGVRDAADRIRRYSSDPALFLEESERAQAFMRERFSPEEIGAQILAV
+VEGRR---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000040.fa ADDED Viewed

	@@ -0,0 +1,63 @@

+>0_974
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVVAPAYTLTSGLGPTISTVG-T
+HVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQIT
+GSQAIADLAGNLWVNIPLTLVYLA---LAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG---AGFDPTPV
+QLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSALAVISWAGIGSEGL
+G----AGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFA
+TWVCAGFAGLFYVVTRLL---SENALWDTIT---------ALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPL
+IGGLVLLVMFCVTAMDSTDPDYGSGSSVFG-VGTVFILGMGVLAIGVVLMMWT----RLRHPAYFRGETLPQTDSTRPIP
+IIRPDDDGSAVVRDPNERTHS
+>1_697
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVVAPAYTLTSGLGPTISTVG-T
+HVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQIT
+GSQAIADLAGNLWVNIPLTVVYLA---LAGWISHRGMETTKHLQYILVAFQILALGAFAIAALTQSSRG---AGFDPTPV
+QLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSALAVISWAGIGSEGL
+G----AGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFA
+TWVCAGFAGLFYVVTRLL---SENALWDTIT---------ALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPL
+IGGLVLLVMFCVTAMDSTDPDYGSGSSVFG-VGTVFILGMGVLAIGVVLMMWT----RLRHPAYFRGETLPQTDSTRPIP
+IIRPDDDGTAVVRDPNERTHS
+>2_804
+MSS------VLDAAGTPATPHPSPAAPSARV--PSSSGGGRLGAGRIGVPALVCMIVAASAPLTAVAGGITSNFAVTGLL
+GVPLSFLVLGVVLLLFSVGYAAMSRHVHNAGAFFAYVARGMGKPAG-------VGAALVALVSYACMQVG-----IAGMF
+GFATSSFLEGTFGIAVPWWASALAAWVLVGVLGLYRVDFSAKVLMGVVALEFLVVCVYTVLGLRAAPEGVSAAGLLPGQL
+-------FTSG----VGAALVFSVAAFMGFESGAIYNEEVKDPKRTAGRATLISVVLIAVFYAFSA-----WAMVMTEGP
+GGVVAAAQAVGPDVVFAFLGAHAPLWFTDLANILFIVSLLAALLAFHNIVARYAFALGREHVLPAFLAHTSTRTGAPVGG
+SLVQSGAALVVLVVFALAGSRSDDPLFPVVTLFTWLTNMGAFGLVLLM--ALTSVSVIGYLRRH--RDEFGVFTRVVAPA
+LAAVGLLTLFVLTMVNFPVLLGADGTTPLSWLLPALVVTPG--ALGTAWALWL----RARRPATYAG-------------
+IAR---GGEL----------S
+>2_1837
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVVAPAYTLTSGLGPTISTVG-T
+HVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQIT
+GSQAIADLAGNLWVNIPLTLVYLA---LAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG---AGFDPTPV
+QLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVLVIIAVYILSALAVISWAGIGSEGL
+G----AGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFA
+TWVCAGFAGLFYVVTRLL---SENALWDTIT---------ALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPL
+IGGLVLLVMFCVTALDSTDPDYGSGSSVFG-VGTVFVLGMGVLAIGVVLMMWT----RLRHPAYFRGETLPQTDSTRPIP
+IIRPDDDGTAVVRDPNERTHS
+>3_2203
+MLSTHQ---------------------------------------------SVSVSTSSVAPVYSAVVTVPLVVGLVG-S
+GAPLAYLLALLPILGVWAGMSANDEREPDKGSVYSWAVTGH-PVLGWTAGWCLALTGIVATSGLAYVALD------AWLP
+GLGA--------GVKVLIGAGIIA---AATALASANVRITAAVQTAGVLVQVA-----ATAYLAWVLAR---VGLTPLPP
+---------AGTVQDWVHAVLLAVFAFWGFDAVYALSEESH--RGVPRRSAAVSLGLLAAIFLVFS------------AL
+G-------ASEDPAAVAALTHPVV-------MAGVVVSCVGAIGSTLIPTARGLSAMAERGHLSAVLA--------PLRA
+AEVVSALLAIAWLVVSLA---VPGVFEDSIE---------MLSVFVGGYFTISSATAAAH--ASGGARMLHAATAVVMGL
+ITAASLAWMF--------EPDYGA-TVVGG-VGGVGLLAVGFAVLGLILAVGAGHRGRAVHPT--SG-------------
+--------------------V
+>4_917
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVVAPAYTLTSGLGPTISTVG-T
+HVPAILLLGFIPMLLVALG-------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------
+>4_918
+--------------------------------------------------------------------------------
+--------------------------MPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQIT
+GSQAIADLAGNLWVNIPLTLVYLA---LAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG---AGFDPTPV
+QLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSALAVISWAGIGSEGL
+G----AGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFA
+TWVCAGFAGLFYVVTRLL---SENALWDTIT---------ALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPL
+IGGLVLLVMFCVTAMDSTDPDYGSGSSVFG-VGTVFILGMGVLAIGVVLMMWT----RLRHPAYFRGETLPQTDSTRPIP
+IIRPDDDGTAVVRDPNERTHS

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000043.fa ADDED Viewed

	@@ -0,0 +1,22 @@

+>0_1349
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>1_1091
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSDVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>2_396
+MPKEQTAGKPTTRRYSPEE-AAAVRMVRTMRAELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>3_311
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVQRVATQLGYGVESVRMWVK
+HADIDDGVTSGVSSAEAQRVRELEQEVRKLRRANEVLKRAASFFGAELDRHYRK
+>3_631
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>3_2164
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>4_1298
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000044.fa ADDED Viewed

	@@ -0,0 +1,50 @@

+>0_1353
+MAVSGSFPGHLWAAFHGRLHSVRDEELIPQLVELWETNYRVYGVRKLWKTARRAGIDIGR
+DQTGRLMRAAGIKGATRSKRVKTTRPDPTAARHPDLVKREFTAPAPNRLWVTDLAFVTTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLSESNSASLHQTQGASGPTLWSP
+TRSILDRAARPLRKF
+>1_1092
+MAPSSYYAAKTRAP---SARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DQAARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDPRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK------------------
+---------------
+>2_397
+MAPSSYYAAKTRAP---SARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DRAARLMRAAGIEGARRSKRVKTTRPDPASARYPDLVKREFTAPAPNRLWATDLTFVPTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIAMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNSLAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHTTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIQ------------------
+---------------
+>3_312
+MAPSSYYAAKTRTP---SARAARDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DQTARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTW
+AGVAYVCFIIDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYDKAELIRGPARPGPWRTTDDVELAT
+LGWVHWHNNQRLHGYLDDLPLTEFEERFYATQQGQYALVEIK------------------
+---------------
+>3_632
+MAPSSYYAAKTRAP---SARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DQTARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK------------------
+---------------
+>3_2165
+MAPSSYYAAKTRAP---SARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DQTARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK------------------
+---------------
+>4_1302
+MG----------------------------------------------------------
+---------------------------------------SFSWP----------------
+-------------------------------------------------LTHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK------------------
+---------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000045.fa ADDED Viewed

	@@ -0,0 +1,56 @@

+>0_1536
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQWAISGYTLVFGMVLVPAGRA
+GDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVMGVGAGLLNPQVTGFIQSEFSGTSRARAFGALGAVVGVSVA
+VGPLLSGGLIAWLGGDLGWRATFLVNVPIALGALVVARHWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFL---DRE
+LGPWRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMFVVIAMFMQNGLG-----
+---YPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRK-IVVLGIALALLAVVGSIGVAWANR-----EFGLSP--WWLLL
+TLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTGQRVGTAVGTAVIVGVFLGVASGADW----------------
+--DGAFMAAFT-----LVAGCMALALLVALADLRGPRTAAPRG------------------------
+>1_1258
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQWAISGYTLVFGMVLVPAGRA
+GDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVMGVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVA
+VGPLLSGGLIAWLGGDLGWRATFLVNVPIALGALIVARQWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFL---DRG
+LGPWRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMFVVIAMFMQNGLG-----
+---YPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRK-IVVLGIALALLAVVGSIGVAWANR-----EFGLSP--WWLLL
+TLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTGQRVGTAVGTAVIVGVFLGVASGADW----------------
+--DGAFMAAFT-----LVAGCMALALLVALADLRGPRTAAPRG------------------------
+>3_626
+M--------------------------LFASFMDLLDVTIVTVAAPHIAADLNASPAQLQWMLAAYTLALGSGLITGGRI
+GDDYGRRRVFLAALAAFAIASAACALAPTAGALIAVRAVQGLAGGFMVPQVFGIIRSSFEPAAMAKAFGAYGAVQGLASV
+AGPLIGGALADADLWGLGWRTIFWINIPIALVALVLGWRVLPDS--RAAARSRLDGVGALLAAVGVLLVLLPLVQGRDWG
+WPTWGWALLAAGVLVLAGFLRYENALARRGGEPVLDPDLLRVRPFVAGLAASVLFFGGLASFFLVVSIYLQAGTG-----
+---RSAWDTGLVILPYAIGSMLTSGAGVALAARAGRA-LLLTG-SLTLAA--SQALLWWLVR-----DGSTTPDYWPLAG
+AMFLGGLGLGLGAPILVNVVLAGVPGRRAGAAGGVLSTVNQIGGAVGVAVLGTVFFNAASSAGP----------------
+--ATAPAELFGDALAQVMPWQVATYLLAAVAMLALPKTAAPHQD-----------------------
+>3_696
+M----------AGDCIRQIPRWGFVLSLAATILMMAAASAPSLFYPQIAERLGLIPVATTLVFAVYTFTLLAALLYLGPL
+SDHVGRRPVVAAGSLALALSVAMFWFAGSLAALLVARALQGLAAGLLIPALSAMM-IDFESPSH-RNIAALWNTIGPMIG
+LG---AGALGAALLLDLTSEPTTAVFGSLVLAFLIVA----------------------------TVVWSTPEL------
+---------------------VPKTQIRRGD---LRPRFTVPPHL---RRMFTVGVPVIIAGWATNGLFLALGADLVGSE
+LGGSTHTQAGIVLFALAISGVTASS---VLQRRSART-ISLYA-TSALAF--GTAVSIGAL------ALGSYP---AYVA
+SVAIVGSGFGTAFLGVLRTLMPHTASSERAAVMAVIYTVAYLAFGVPTIVAGLLV-----------------------PV
+LTLSGTMTILG-------AIIIALSLVATVLRLRIPHPAAGPAEADDFPEPPTGSHRRSAPDREEQP
+>3_1216
+M----NPSAGTSGGVFTARQRRVLAVLLVPVFMSLLAVSSINVALPSLQRGLGASDAELQWSISGYTLAFGMVLVPAGRA
+GDLLGRARLFRIGVLGFGLGALLSGLAPSGLLLVLARVLMGVGAGLLNPQVSGFIQAEFEGQARARAFGALGSTVGVSVA
+AGPLLAGGLIAVLGGDLGWRATFLVNVPIALAAVLIARGWLPEESPAPAGRRDFDPVGVALLASALVAVMLPFL---DRG
+LGPWRFALLPLGAALAAGWAVWERGYRARGRAPMVDLSLFGLPGFRNGALMIGVYFTGSTSLFIVVAMFMQNGLG-----
+---YGALQAALVGLPSAVCSSVMATVAGRLVLRAGRR-LVVVGVSLVLAAVVGSIGVVAAHQ-----AFGLSP--WWLLA
+TLGLFGMGQGLTVSPNQTLSLAEVPRPQSGTAGGILQTGQRVGTSVGSAVIVGVYLGVAGTGGP----------------
+--DRGFMAALG-----LIAVSIAAALAVAVADQR--RRARQGGR-----------------------
+>3_1789
+M----------------PRPRLLLAVILLAQFVIPLSISGTAVALPAIASDLGSDPTPLQWVVNGFNVAFAVCTIVWGAC
+SDRIGYTRSFRIGIAIAIAGGIVSMFAPNIAVLDAGRIIAGIGSAAVLTSAAPILSHLFEGKARAQAFALFGTINGLGLA
+AGPALSGLLLSA----WGWQGIFAAHT-------------------------------IVLIVAFIGAARLPQL---GRG
+GTSLR---------------------------EILDFSALKAPKF---LAMTLVPIAGAI-GFVTFLTYLPSALGAIHGL
+TAGVTGALMLVMTIPVLIAPVAVH----RLMERSHLTPTAIVAVSFACLI-VGGIGVLLLLRPDLPVALGVTP-------
+-MILLGLGFGLPLGFVDAEALAAVPAERAGAASGVINLFRIGSEAVFVAAYGALLAAVITTTLPGTTGELIASGSPGEPW
+IYHSGLMAAAG-----TMIGLVAIAGVTFLALTRAANRSAVTARQ-----------------VEVAR
+>4_1463
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQWAISGYTLVFGMVLVPAGRA
+GDLFGRRRLFLVGLGVFALGALLSGLAPTGVLLVLARLVMGVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVA
+VGPLLSGGLIAWLGGDLGWRATFLVNVPIALGALIVARQWLPRTVPERARRPDLDPVGVVLLAGALVAVMLPFL---DRG
+LGPWRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMFVVIAMFMQNGLG-----
+---YPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRK-IVVLGIALALLAVVGSIGVAWANR-----EFGLSP--WWLLL
+TLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTGQRVGTAVGTAVIVGVFLGVASSADW----------------
+--DGAFMAAFA-----LVAGCMALALLVALADLRGPRTAAPRG------------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000047.fa ADDED Viewed

	@@ -0,0 +1,98 @@

+>0_1747
+M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI
+VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE
+EGGPSPEE-------AVARAQAWLRKRRYRVER----RLE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK
+YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFDRESETH---YGQPLDYTAVMDVREGSGGELQ
+RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF
+FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG
+SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVAL
+RAAMEKWWPIVAATETADDAAAGAAPQSTPTAPETPAGPA----------------------------------------
+--------------------------------------------------------------------DARS---GD---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>1_1455
+M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI
+VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE
+DGGPGPEE-------AVARAQAWLRKRRYRVEH----RPE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK
+YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFERQSETT---YGQPLDYTAVMDVREGTGGELQ
+RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF
+FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG
+SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLVISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVAL
+RSAMERWWPVAAPESEEEAVASAAAVGHTGTTPETLAGPR----------------------------------------
+--------------------------------------------------------------------TPRS---GD---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>2_381
+M------SRTEDQDPG-----RRPEVAL----PALGFWGTLRFAWTQLTSMRTALMLLLLLAVAAVPGSLFPQRPAGPGI
+VQDYIDDNPVLGEWLDR--FQMFDVYSSVWFSAIYLLLFISLIGCVAPRAVKHAQALRSAPPRTPRRLSRLPEYGRVVLE
+PGGPAPVE-------AVEQAARYLKRRGYRIEV----RQEDAGGASVGAARGYLREVGNIVFHLSLIGVLVFMATGSLLS
+YRGQKILVEGEGFANTLVAYDAFTPGSAFSEEMLTPFSMTLKRVEYVYDRQSPTH---YGQPLD----------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>2_1047
+MGDAPVSSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI
+VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE
+EGGPSPEE-------AVARAQAWLRKRRYRVEH----RPE-ASGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK
+YYGQKIIVEGEGFANNLVSYDSFTPGTYFSADDLQPFSLTLDSFDVVFDRESEAL---YGQPLDYTAVMQVQEGGGGEPR
+EEILKVNHPLSMDGVRVYLVGNGYAPVLTVRDGEGDIAFQGPVVTRVQDV-NFNSLVTLKVPD------ARPDQLGFVGQ
+FMPAAVEDESGVAVSVDPELYNPQLILDSYYGDLGLDGGVPQNVYVLDTETLTELNSRKNENGGIVLSQGQTYELPEGKG
+SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVAL
+RAAMEKWWPVAAATAPE-------------TTPETPCRPRRRPIRRLTVFNPTAPVNEQLALYSDLFMLIAAFVYAAAFV
+LFTIDMATSSATIRRLEEDLAAQRGPARLAPARETVGAGFGGSSLGGSSSVGSTGAGSSAGGPGVLPGEARAAGLGDEPG
+LVDEDMDYTGGGRRPIANVAVAVLAVGWALHAFAVIARGLAASRVPWGNLYEFMTTGALVITTVYLLFLFRKDLRFVGTF
+VTGLVVAMMCAATMGFPTPVGHLQPPLQSPWLVIHVSIAVLATALFTLTAAMSMLQLIQDRAEKRAAATGERPWAFLRLV
+PSAQALENWSYRINAVGFVMWTFTLIAGAIWAEASWGRYWNWDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVG
+FLCVVFNYTIVNTYFPGLHSYAGLPG
+>2_2582
+M------SRPSDYDDG-----TGAGGTLRAESPELGFAGWLRWFWRQLTSMRVALILLLLLAVAAIPGSLVPQRGADPNG
+VVQYQKDHPDLFPILDAFPIQAFDVYGSVWFSAIYLLLFISLIGCVLPRIAHHWKAWRGRPPKTPARLQRMAGFSEIRLS
+NPDATPAEREAFAARAVDEAAAILKKLRYRVEVQRASRRG-VDEVSVSAERGYLRETGNLLFHVSLLGVLVSVGLGGVFT
+FNGQKVLIEGETMVNQLIDYDTATSGRSFDSSSLEPFSLRLDTLDVTYNTPDDGNVQAIGLVKDYTANMTLISPEGDE-S
+EHVIRVNHPLRVHGSPIYLIANGYAPKITIRNAEGTVVYSEAMPFIPQDNLNMTSLGVVKVPDGIVDESGEPVQLGLRGF
+FYPTKADLDTGAYTSNYPDLENPVLTLDVFVGDLGINDGIPKSVYALDTSDMEQVTGRAVDLDSIELRPGEQTELPNGFG
+TIEFESVPRYASFDVMQNPAQEWILVFAVLALGGLMWSLFVPRRRMWVKALPSEDG-VVLQYAALARGDDPALERAVEEL
+RDRHRELL------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>3_983
+MGDAPVSSTSAPKDPAPRNRTRDD-VTL----PALGVGGTLRWAWTQLTSMRTALLLLLLLAVAAVPGSLVPQRRAGPEA
+VDQWIEDNPFWGPILDA--LQFFDVYTSVWFSAIYLLLFISLVGCVLPRALKHAKALRQPPARTPRNLGRLPESGVVVLE
+AGGPAPEE-------AVRQAQRWLKRKRYRVEL----RPE-AGGASVGAERGYLREIGNILFHFSLIGVLAFMAYGGMTK
+YTGQKIIVEGEGFANNLVAYDSFTPGMYFDAASLQPFQLTLKSFDATFERQSQTH---WGAPLDYTAVMEVRHGTGGDPE
+EQVLKVNHPLEIDGAKVYLVGNGYAPVVTVRDGNGDIAFQGPVVTRVTDQ-NFNSLAVIKAPD------ARPDQLGFVGQ
+FMPAAADVGQGVEVSVDPEPLNPKLILNSYSGDLGLDAGVPQNVYVLDTSTLTELNSRRSENGGITLSVGQTHVLPDGKG
+SISLDGVRRYVGLDIHYDAGKWGVGVFSVLALIGLAVSLFTRRRRVWVRARTGDDGRTRVEYALLARGEEFGLREEHVAL
+REAFEKMWPVSAPEADTGE-----------TTPATPA-PAAAP-------------------------------------
+--------------------------------------------------------------------TPRS---GD---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>4_1669
+M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI
+VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE
+EGGPSPEE-------AVARAQAWLRKRRYRVEH----RPE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK
+YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFDRESETH---YGQPLDYTAVMDVREGSGGELQ
+RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF
+FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG
+SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVAL
+RAAMEKWWPIVAATETADDAAAGAAPQSTSTTPETPAGPA----------------------------------------
+--------------------------------------------------------------------DARS---GD---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000048.fa ADDED Viewed

	@@ -0,0 +1,43 @@

+>0_1749
+MQ--------------T-PRPSRRTVLTGLSL-LGLAPVLAACS-GDDSLTRQAGNADGK
+NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP
+HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--EVLLNMTDYVP
+PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA-----------------
+--
+>1_1457
+MQ--------------T-PRPSRRTVLTGLSL-LGLAPVLAACS-GDDSLTRQAGNADGK
+NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP
+HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--EVLLNMTDYVP
+PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA-----------------
+--
+>2_382
+MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAG-VASLPLLAACS-AEDPLAAQAGKADGK
+NYIAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAP
+DLQALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGG--QVLLAMTDYVP
+PQAVPTTIVLDHQGRVSARILGIAE-RSTLRTLITTVLDEQA------------------
+--
+>2_1045
+MH--------------TPPRPSRRTLLTGLAL-ASLAPALAACSGGDDSLARQAGNADGK
+NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP
+HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDTRG--DVLLNMADYVP
+PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA-----------------
+--
+>2_2584
+MN--------------------RRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGK
+GYVSGDGSSLSIAPDQRTEPVEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAP
+DLVEAYDEFSPQGVKFVGVNTRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVP
+LNAVPTTLVLDAEGRVAHRVLGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEAT
+EQ
+>3_981
+MP--------------FPPRPSRRAALAGLSA-AALAPLLAACSGTDDSLAQQAGNAGGK
+NYIAGDGSVVEYAADQRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAP
+HLVKLHGEFEPKGVRFLGVNVRDTVTTAQAFERTFGIPYSSVDDTSG--SVLLAMSDYVP
+PQAVPSTLVLDRQGRVAARVLGAVE-EGTLRALLDTVVAEA-------------------
+--
+>4_1671
+MH--------------TPPRPSRRTLLTGLAL-ASLAPALAACSGGDDSLARQAGNADGK
+NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP
+HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--DVLLNMTDYVP
+PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA-----------------
+--

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000049.fa ADDED Viewed

	@@ -0,0 +1,63 @@

+>0_1944
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR
+SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP
+DYGWAFETLEDTN-DGEHPVLVTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV
+MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEIIRRAQQILRPYTLDVKEV
+AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERK
+EIAKNLIDFDKEWSTLMATPTSELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERS
+CDTNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH
+PDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN-
+>1_1665
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR
+SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP
+DYGWAFETLEDTN-DGEHPVLVTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV
+MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEIIRRAQQILRPYTLDVKEV
+AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERK
+EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERS
+CDTNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH
+PDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN-
+>2_818
+MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRSHRLEIGQADGIQAR
+SVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEP
+DYGWSFESLEDSA-EGEYPVLVTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGV
+MDALAVSDFPDIRTKCAIHS-STGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEIIRRAQQIIRPYTLEVKDV
+AWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERK
+EIAKNLIDFDKEWSTLMAKPTSELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERS
+CDTNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQDARFDVKVVYQQKQTEFAH
+PDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISRDGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS-
+>3_756
+MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTRIIERRGKRLEIGQADGIQAR
+SVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRTSLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATP
+DYGWEFVSLDDSDQDAERPVQVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV
+MDVLADSNFPDIRTKCAIHS-SSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEVIRRAQQIIRPYTLDVKDV
+AWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERK
+EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERS
+CDTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQDERFDLKVVYQQKQTEFAF
+PDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVSRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN-
+>4_165
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------FIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQ
+QIAENLIEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGVPIGKRFESAAVRRV
+ADTSPRQLGHLFEADGRWRLYAFAD-----EDRTAVGELADWLADSPDSPVRRFTPESADLNSVFDAKVVYQQPYQEVEL
+ADVPALFLPKMGPYQLTDKEVVFAA---DLADDIFEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV
+>4_166
+MR---------------------------------------------------------------------GAAD-----
+----------------------------P---------RRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGP-----
+---------------------------------------QGQERTVRAKYVVGCDGSRSRVRDCTGIEVVRDPSAHAWSV
+MDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGFLARFYVSLGSI--DDAPRPRS------------------------
+--------------------------------------------------------------------------------
+---------------------------------------------------------------GG---GIRACSSPATPA
+TPTPPR-------------------------------------------------PARA---------------------
+--------------------------------------------------------------------------------
+>4_1883
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR
+SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP
+DYGWAFETLEDTN-DGEHPVLVTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV
+MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEIIRRAQQILRPYTLDVKEV
+AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERK
+EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERS
+CDTNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH
+PDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000050.fa ADDED Viewed

	@@ -0,0 +1,64 @@

+>0_2028
+-MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVG
+ADGMGVLMTLSGLGFLLLGVPLGIVVDR-HLSPRLLAA---TGLAKAAVLGSLVAAWALD
+ALTFGHLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAA
+GVLVGSLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFG
+KDAAEGWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGA
+VGALTASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALW-G
+FMVLLGNITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALA-
+-GWQVLAVVSLAAVVPAARWV---------DAGRDDVD
+>1_1744
+-MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVG
+ADGMGVLMTLSGLGFLLLGVPLGIVVDR-HLSPRLLAA---TGLAKAAVLGSLVAAWALD
+ALTFGHLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAA
+GVLVGSLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFG
+KDAAEGWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGA
+VGALTASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALW-G
+FMVLLGNITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALA-
+-GWQVLAVVSLAAVVPAARHL------GPRTAER----
+>2_676
+-MSTDPRRQTPAPRVPDTGTRPPPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVG
+ADGMGVLMTLSGLGFLLLGVPIGIVVDR-HLSPRLLAA---TGLAKAAVLGSLVVAWALD
+ALTFGHLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAA
+GVLVGSLGAGPVLGIATSFLFAAAIVALRVRLRPSAAVDIPDDDGDPGVADVLSRWARFG
+KDAAEGWTVLRRAPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGVQITAGA
+VGALAASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALW-G
+FMVLLGNITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALA-
+-GWQVLAVVSLAAVVPATRHL------GPRTAER----
+>2_1283
+MVSSPLTDDTTAP---ENAAPAKRLGRARWLVASNALDAGGRSATDVAIDVLAVLALGVG
+AAQMGVLMTLSGLGFLLLGVPIGILVDR-HLSPRLLVA---TDLAKAALLGTLVLAWALD
+ALTFAHLAAVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAA
+GLLVAALGAGPVLGIAAAFLAAAALVALKVRMNPAPVTEDTRDEETPAAAVVLTRWSRFW
+SEAAHGWTTLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGA
+LGALTVSALAPRAIDTLGEKGCILAGSAGCAAAVALHLAAFFDRAHAGPLLLAGAALW-G
+FMVVLGNITSGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLA-
+-GWQAMALLSLAFAFAATR-----------LARRPQ--
+>3_645
+----------------MTRVSAWRSRDFRRLWGASTASALGGEIGELAMPVLALVWLGAS
+AEELSWVRVATFLPYLVLPLWLGVLVDRWRRRPLMITAETVSGITLLGIAGAALAGW---
+-LTVPALVAAAAVLGAMSVLHMLADFSFTPQVVSRAALPDANAKMTATYSAIGIGGSGVG
+GALVQWLTAPFAVAINGAGRLLSVVLLRRIQTHEPPA-EAPDTSAR--------------
+QQAREGFLALLRHRVVRALAAEATIWNLGNEVFMLALTVLIVDARDDGPLVLGLIFMAGG
+LGAFLGAGISARLTERFGYGRSLITAMLVGNTAPLIGVLFSSDTSVTSLVVLAAAFFASG
+FGTGIANSQAVTVRQVTVPEELRGRVNASYRMLSWGALAIGALLGGWLISAVG-GWLAAA
+LGTAAMAASTLPVALSPVRQMRDLDDGAPPAAE-----
+>3_2185
+-MSSPLTDDTTAP---ENAARAKRLGHARWLVASNALDAGGRSATDVAIDVLAVLALGVG
+AAQMGVLMTLSGLGFLLLGVPIGILVDR-HLSPRLLVA---TDLAKAALLGTLVLAWALD
+ALTFAHLAAVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAA
+GLLVAALGAGPVLGIAAAFLATAALVALKVRINPAPVTEDTQDEETPAAAVVLTRWSRFW
+SEAAHGWTTLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGA
+LGALTVSTLAPRAIDTLGEKGCILAGAAGCAAAVALHLAAFFDRAHAGPLLLAGAALW-G
+FMVVLGNITSGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLA-
+-GWQAMALLSLAFAIAATR-----------LARRPH--
+>4_1968
+-MSTDPRRQTPAPRTPDTGTPPPPEGRARWLVASNALDAGGRSASDVALDVLAVLLLGVG
+ADGMGVLMALSGLGFLLLGVPIGIVVDR-HLSPRLLAA---TGLAKAAVLGSLVVAWALD
+ALTFGHLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAA
+GVLVGSLGAGPVLGTATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFG
+KDAAEGWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGA
+VGALTASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALW-G
+FMVLLGNITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALA-
+-GWQVLAVVSLAAVVPAARWV---------DAGRDDVD

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000052.fa ADDED Viewed

	@@ -0,0 +1,43 @@

+>0_2099
+MS-SE-ETVPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA
+DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP
+PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE
+EQQAAVASLTPREHEVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV
+LIAHRAGLVQ-----------F
+>1_1823
+MS-SE-ETVPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA
+DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP
+PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE
+EQQAAVASLTPREHEVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV
+LIAHRAGLVQ-----------F
+>2_571
+MT--------TRVLLVDDQPLIRLGFAAILQSQ---DDIEVVGEAGDGAECLERAAALDP
+DVICMDVQMPRMDGIEATRALAEAG-TRAAVLILTTFDRDDFLFETLEAGASGFLLKSAE
+AEHLIDAVRVLGRGDALLDPQVTRRVLRRMASAAPEGVDGPAGVGQPRDDDGAAPGQAEA
+SDAVGKAGLTGREAEILTLMARGLSNGEIAGQLFVGESTVKTHVSNVLMKLGARDRVHAV
+IWAFEHGVAG------------
+>2_580
+MS-TDAENAPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA
+DVVLMDVRMPEMDGIEATRTLLQRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP
+PEELLAAIRTVHRGDAVIAPSTTRRLMAHMA---------------PRLRSDHARTAECE
+HEQAAVESLTPREREVLVLMAQGSANLEIAGELVLSEATVKTHVGRVLAKLGARDRVQAV
+LIAHRAGLVQ-----------F
+>2_2524
+M--------------VLPDAGVRGGVRVRTSRTGVVGDIRLVEGAVSG------------
+DLDSADLLLGGVNSLGETRQVARQGRDVPPFLLVAEATIVEELSGIDASGAAAVLAYPLD
+TVELAS----VAHGIAGSGPFLSPRL--------------------PQLSVEPLG-----
+------EGLSAREAEVVVALGEGLSDAEIAQALCVSVKTVHTHVLNLRRKLGARNRAHAV
+SLARSVGPLGDACSEPGLVAAL
+>3_503
+MSPDDAQPTPIRVALVDDQALIRSGLAMLIDSQ---PDLTVVAQASDGREAAASVAVAGA
+DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEHVMDAIEAGASGFLLKDAP
+PEELLAAIRTVHGGDAVIAPSTTRRLLAHMA---------------PRLRQDAARSAECA
+DEQAAVGSLTPREREVLVLMGQGAANPEIAAQLVLSEATVKTHVGRVLAKLSARDRVQAV
+LIAHRTGLVG-----------F
+>4_2044
+MS-SE-ETAPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA
+DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP
+PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE
+EQQAAVASLTPREREVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV
+LIAHRAGLVQ-----------F

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000053.fa ADDED Viewed

	@@ -0,0 +1,36 @@

+>0_2185
+MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE
+LEYFGEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL
+--------VFDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR
+GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R
+>0_2200
+MD------HKQ--ILHDGLRRQRAALLQKLEGLSERDARLPRTPTGTNLLGLVKHAAVVE
+LEYFGETFDRPAEVQLPWAAAGQSEEDNVDMFAAEGESLEDVLEFARRCFAHADATITAL
+--------GADAHGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLR
+APGNNLPVWGADRWAAHVDRLTAIAEGSGGPGRN
+>1_1898
+MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE
+LECFGEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL
+--------VLDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR
+GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R
+>3_401
+MD------HKQ--ILHDGLRRQRAALLHKLEGLSERDARLPRTPTGTNLLGLVKHAAVIE
+LEYFGGTFGRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFVHADATITAL
+--------GADAPGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQVGLR
+SPGNNLPPWDADRWAAHVDRLTAIAEGSGGVGWN
+>3_405
+MGFLTPQAHGELAVLTTYALQQLAQMRTTVHGLTDEQAHSVPSASALNLTGLLLHTGEVA
+VYWTAAAASAPGEPVLPED---VNEDHSLDELVADGRPLAQVLERFDRCVEVARQNLAAV
+ADLSAPVPVPDA----PWFPADLKTWEARWALLHVTAEVARHVGHADLIRESIDGTGSY-
+-------------------ELNDLADAAAQ---G
+>4_2118
+MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE
+LEYFDEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL
+--------VFDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR
+GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R
+>4_2132
+MD------HKQ--ILHDGLRRQRAALLQKLEGLSERNARLPRTPTGTNLLGLVKHAAVVE
+LEYFGETFGRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFAHADATIAAL
+--------DADAPGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLR
+APGNNLPPWDADRWAAHVDRLTAIAEGSGGPGRN

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000060.fa ADDED Viewed

	@@ -0,0 +1,49 @@

+>0_59
+MTPEWWMALAALVLLALLVVVVVVLAVRQVRLGVQHERTRLLVDALDARVGGVQRRLEEV
+PGIGTGRHEVALVLNPIKTHADRVRRELERLAEAEGLGEVLVLETQEDDPGT-AMARQAL
+DAGARLVIAAGGDGTVRTVA------EQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQ
+CLRIAVGGRQ------RRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKS
+LAGWLAYSEA-GMRHLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKL
+DDGLLDVMVLSPRHALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGD-
+---ATGVITALDARVQPDSLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>1_2023
+MTPEWWMALAALVLLALLVVVVVVLAARQVRLGVQHKRMRLRVDALDARVGGVQRRLEKV
+PGIGTGRHEVALVLNPIKTNAGQVRRELERLAEAEGLGEVLVLETQEDDPGT-AMARQAL
+GAGARLVIAAGGDGTVRTVA------EQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQ
+CLRIAVGGRQ------RRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKD
+LAGWLAYSEA-GIRHLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKL
+DDGLLDVMVLSPRHALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGD-
+---ATGVITALDARVRPDSLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>2_191
+------M-------------------------------TPGSPDD---------------
+DGAPAVRRRVLVLLNPHAGRRRSLARAQARLRTHPGLALDLVVPDPADHAAQLAAGRTAL
+ADGVDAVVVRGGDGMVAAGVGLVGDHAEATGRRVPLGIVPAGTGNDLARAAGLHRRDPGA
+ALEAVLRALEDPAAPVRRIDALRLTVTRAGAVVERRWAANSVNIGFDARVNARA-NALGA
+VPGPLRYLAALGLEARAFAAVEMGLGLDDGPVRRERVALVSVQNGPTIGGGIPLAPGARL
+DDGRAEATVVGPLPTAGLALLFPLVYVRAHRLLRPLCTERARRVRVAVPDGVPVYADGDE
+VLPASHGGAAVEVEAVPGAVALLG--------------------------
+>2_317
+------MALVALVLGAVLAVAVIVLAVRHRGLAERHERTRGQLDAVEHRLDAAQRRLGEL
+PGVDRPRQEIALVLNPVKARADEVRRTLEAMADREGLGSVLVLETEEDDPGT-QMAKDAL
+EAGVRLVIAAGGDGTVRTVA------EQLTGTDVALGVVPLGTGNLLARNLDLPINDIEE
+CLRIALTGRQ------RRIDTVDVRFTHEEGEVTRQTFTVIGGAGYDADIMADTKDELKD
+VAGWLAYSEA-GMRHLRGKRHDVSISLDGGASRRFKVRTVMVANCGMLTGGVELLPEAKL
+DDGLLDVLVLSPRHALDWARIAAKTVTRHGANIPVMHTEQAQRVKVEFADPMPSQLDGD-
+---ATGHIVALDARVQPDSLVVMLLDEKEASVHDDGRSEAAPVPEPAPHI
+>3_259
+------MALAALVLAALFAVAVVVLGLRLRRLDGAHERTRGQLDAVEARLGDLRRRAGRA
+PGVDLPGPQVALVLNPVKARADEVRRAMEALAEKEGLGEVLVLETTEEDPGT-AMTREAL
+TAGVRLVVAAGGDGTVRTVA------EQLAGTDVALGVMPLGTGNLLARNLDLPINDIEE
+CLRIALTGRQ------RRIDTVDVRLTHEDGARTRQTFTVIGGAGYDADIMGDTKDELKD
+MAGWLAYSEA-GMRHLRGRRHEVSITLDGGAVQRFKVRSVMVANCGMLTGGMELLPEAKL
+DDGLLDVLVLSPRHALDWVRIAAKTLTRHRASIPVMHTEQAQRVQVRFAEPMSSQLDGD-
+---ATGDITALDARIQPDSLVVMLGDEDDASVEDGGRSAEAPVPEPAPHI
+>4_54
+------MALAALVLLAVLAVVVVVLAVRQVRLGVQHQRTRLLVDALDARVGGVQRRLEEV
+PGIGTGRHEVALVLNPIKTHADRVRRELERLAAAEGLGEVLVLETQEDDPGT-AMARQAL
+DAGARLVIAAGGDGTVRTVA------EQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQ
+CLRIAVGGRQ------RRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKD
+LAGWLAYSEA-GIRHLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKL
+DDGLLDVMVLSPRHALDWARIAVKTVTRSRSSIPVMHTEQAQRVKVEFAEPMPSQLDGD-
+---ATGVITALDARVQPDSLVVMLVAEDDASVRDDGVSAAAPVPQPAPRI

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000067.fa ADDED Viewed

	@@ -0,0 +1,48 @@

+>0_199
+M------------STAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQTLEKGLFD
+GLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAH
+EGRYFTVPGHAVT-EPSVQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELA
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSAVETFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPGAFEDV
+VEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR--
+>1_2143
+M------------STAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQTLEKGLFD
+GLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAH
+EGRYFTVPGHAVT-EPSVQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELA
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSTVETFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPGTFEDI
+VEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR--
+>2_174
+MAEHPAARPEQDATTSTSAATSTSPASRAGRELLFNAFDMNCVAHQSPGLWRHPEDRARDYNTLGYWTHLAQTLEKGLFD
+GLFIADVLGPYSVYGGTAEAAIRSGAQTPVNDPFLLVSAMAAVTGHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVRYDKETGVFADPAKVHDIGH
+EGRYFKVPGAAVT-EPSPQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELT
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSAVEAFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGYNLAYHITPGTFEDV
+VEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPEGHHGASFALRRR-G
+>3_120
+M------------STAENAGAGAPTRPDEHREILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTRLAQTLEKGLFD
+GLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAH
+EGTWFKVPGHAVT-EPSVQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELA
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSAVETFQKASGTDEGWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPGTFEDI
+VEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFAFRNRRG
+>3_122
+M------------STPTPTLGIA-------------------LTTQTPA------------DARGHWTRLSQALEETSLD
+WAVLTDPLGTAPQAG------------THRIDAVLAACWTATRTHRIGLVPEVTTTHTEPFHVSIGLATLDHVSHGRAGW
+LATVSAAPEVSALFGRRRHPAERTPGLQASRVDLELWEELQDAVAAVRDLWE-SWEPDAEIRDIATGRFIDRERVHHVDV
+EAERFSVRGPSITPRPPQGRLPVLVEA-AGPAGLEAARRTADVVLLPAAEVGRTDAARLPDRRRRGATPAVPVEPTRIVA
+DVTLEGDGARVADAVRHALQAGADGARLVPNPTADPFDALALAADVHDRLDDIRPPDTGTVPLRECLGLAPALSPWRHPE
+DPT--------------ARPTDEEATA-----------------------------------------------------
+--------------------------------------------------
+>4_199
+M------------STAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQTLEKGLFD
+GLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAH
+EGRYFTVPGHAVT-EPSVQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELA
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSAVETFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPGAFEDV
+VEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR--

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000068.fa ADDED Viewed

	@@ -0,0 +1,19 @@

+>0_208
+M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE
+DLFTP--DGNAG-----
+>1_2152
+M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE
+DLFTP--DGNAG-----
+>2_157
+M---ENSLPAERARLGWSQQRLADELGVSRQTVISLEKGRHDPSLALAFRLAETFGTRIE
+DLFSP--DPPA------
+>2_2156
+----------------MSIDRLAEAAAIHRRTIIQIEAGRTAPRVTTLYAIAEATGTPLR
+DLLAP--LDEALERGTR
+>3_307
+MARLARAFKVHKANSGMTYDQLAEATGLARQTLLNLAAGRTYGDLRTWLILAKVWGVTLD
+DLTAAAWRGHAGG----
+>4_208
+M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE
+DLFTP--DGNAG-----

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000072.fa ADDED Viewed

	@@ -0,0 +1,54 @@

+>0_241
+MTVQDPTAVAAPSPTEVFRVARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE
+RTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA
+EDLAKFAGVGEGLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDAADAATELAPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMARYGVTSFCAPPT
+VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVTL
+IDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS
+PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK
+IRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLHR----
+>1_2204
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE
+RTFAELSAASSRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA
+EDLAKFAGVGEDLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGGVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMERYGVTSFCAPPT
+VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTL
+LDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS
+PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK
+IRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLQR----
+>2_111
+MTVQDRTPADAASPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQDPARQDVPALIIAEDDGRSTE
+RTFAELSAASNRAANWLAEQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSADLEDRVSRADAAWAVAGA
+EDLAKFAGVGEGLRLVHVPGVFAEGEARRAPEVPGHTVLSYDDAAGASAELSPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMDRYGVTSFCAPPT
+VWRMLIKADLAQLKTPPTKTISAGEPLNAEVIDQVQKAWGATIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVVL
+IDPLTGQEA---AEGEICLRLDPRPVGLLKSYFGNQEKTDEVFRDGVFHTGDIASRDENGVLTYVGRADDVFKSSDYKVS
+PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETAQSILQFTLTQLPPYKRIRRIEFLELPKTISGK
+IRRVELRKAEVERSETGTAPSGYGTEFREEDLDLTR----
+>3_79
+--------MTTTSVTERLRAARDLLVECQEDYDRARAEFEWPRFEHFNFGFDWFDQLAARPDRADVPALIISDAGGGHLS
+RTYAELSAASNRAANWLRERGITPGDRVILMLDNQVELWELMLACIKLRVVMVPTTTQMTSADLADRVERAEARWVVASA
+ENLAKFDGVDSGLHLVHIPGVAAQGDARTAPVVAGHEVLSYDDAASASPELTPDSPTPADETLLLYFTSGTTSKPKLVEH
+THTSYPVGHLTTVYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDAAALMADMDEFGVTSLCAPPT
+VWRMLIKADLSLLKTPPVKTISAGEPLNAEVIDQVHRAWGTTIRDGFGMTETTLQIANTPGQKLVIGSMGRPLPGMDVVL
+IDPLTGEEA---AEGEICLRLDPRPVGLLKSYYGNEEKTAEVFRDGVFHSGDIASLDESGVLTYVGRADDVFKSSDYKIS
+PFELESVLVEHPAVMEAAIVPSPDEVRLAVPKAFVTLAPSYEPTAETARQILQHTLTQLPPYKRIRRIEFRELPKTISGK
+IRRVELRKAEAERAETGQAPEGYGIEHREEDLDLKR----
+>3_2414
+-----------MSVTARLRAARDLLVEHQQDYAGARAAFEWPRFETVNFGSDWFDAVAATPERADQDALVIVEEDGTVLR
+RSYARMSADTDRVAGWLQHLGVGRGDTVIVMLDNQVELWEAMLACMKIGAVVIPTTTQLVAADLQDRVDRAGARWAIANA
+GNLVKFADVVGDCTLIHVPGVYASEAEHALPEVPGHPVHSYGDAASFAGTWSLETPTSADDPLLLYFTSGTTSLPKLVEH
+TQASYTVGHLSTMYWVGLRPGDVHLNVASPGWGKHAWSSFFAPWLAEATIFVLNFRRFDAATLMRAMDEGGVTSFCAPPT
+VWRMLIKADLTQLQAPPRNAISAGEPLNAAVIDQVQRGWGVTVRDGFGQTESTLQIANTPGQRVVIGAMGRPLPGFDIEL
+RDPQTGDRVDGEGEGEICVGLDPRPVGLFQRYHGDPEKTAEAFRDGVYHTGDIARRDEHGIYTYVGRADDLFKSSDYKLS
+PFELESVLMTHPAVLEAAVVPAPDELRLSVPKAFVTLAAGHEPGEEAARAILQHVTDRVPAYKRIRRIEFRPLPKTVSGK
+VRRVELR-AEEEQRRAGVA--GLGVEHREEDLGIRRQRRA
+>4_241
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE
+RTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA
+EDLAKFAGVGEDLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMERYGVTSFCAPPT
+VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTL
+LDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS
+PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK
+IRRVELRKAEVERAQTGAAPDGCGTEFREEDLDLQR----

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000075.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>0_273
+MT----------GG-----------------DPAALMDALGAWFHPLTALLVALDAPI--
+PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA
+WWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS
+LAWSSSMVGLGWITGRATGLPWWASAMVGMVFGTLAGLMIAGIMAHRRRGRKG-------
+---
+>1_2239
+MT----------GG-----------------DPAALMDALGAWFHPLTALLVALDAPI--
+PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA
+WWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS
+LAWSGSMVGLGWLTGRATGLPWWASAVVGMVFGTLAGLMIAGIMAHRRRGRKG-------
+---
+>2_62
+MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPI--
+PPVPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGD-VGLYALFRHGLADRLD--RWA
+WWRRVHRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS
+LAWSGWMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVA-RRRARKG-------
+---
+>3_48
+MT-----------------------------DVTALLEGLGPWFHPLTFLLVALDAPV--
+PPTPSEVLVIGSGSLAAAGRLGLATSVLTAWLGCWAGD-VGLYALFRHRLTSVLD--RWG
+WGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGGRTASMAAAGVAGVRWRPFLWLSGTGS
+LAWSVYMVGLGWITGSATGLPWWASAVVGVVLGTLLGAAVAAVIAWRRRGKEGA------
+---
+>3_433
+MPVLTNIL-----------------------DAASILHSLGPWTLGGIGSMVFIESGVLF
+PFLPGDSLLVTAAALHVELGIALWAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVL
+KTERLAQA-EAFFERRGPLALVLG----RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGA
+VAWVCSMVAVGALLGQIPGITKSIDGIMILIIVISVAPIAIQALRARRKARRDAVMTEGQ
+PVA
+>4_272
+MT----------GG-----------------DPAALMDALGVWFHPLTALLVALDAPI--
+PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA
+WWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS
+LAWSGSMVGLGWITGRATGLPWWASAVVGMVFGTLAGLMIAGIMAHRRRGRKG-------
+---

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000076.fa ADDED Viewed

	@@ -0,0 +1,144 @@

+>0_278
+M-----SGPA-ESAAGTAT--PAADVVLGRFTEPTRAWFTGAFETPTPAQLGAWDAISSGRHALVIAPTGSGKTLSSFLW
+ALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAAHQGRPVPRVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSQARAA---LTGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDAPVQRIGLSATVEPAAEVARF
+LGGTQPVTVVRPASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDE----GAVTGGSIWPHVEERIVDLVAER
+RSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTP----------------------------DPTGFH
+GPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVDQVIQVESPPSVASGLQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLRIPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPF
+ATLPF------SAYESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGAD
+GTPGGAAAGDTAESAGTASAGSARSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPEAGRTRLGAAGLDPWAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAE--VGGSA
+LFAARFRE----NAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAGRVSS
+RAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLGTEELRELLDAEVIAEVEAQLQRLA
+PDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEAEE------------AADEAAVAGMLAELERAGRAFRLRQDGVER
+FAAVEDAARLRDALGTPIPHGVPTAFLDPVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTG
+AFRPEGTPGAASLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRPPATLEGVDGVAT
+VLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGEATGNDGWVALHPADAVDLTLRLPE------PA
+EETPADAAL--RAAVLEVLAGGGAWFFPQLVERVRAVQAAAGDGGTGTAGGTGGP-DPHRDPADLARGPAVLAALWGLVW
+DGRVGNDTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAAGAAA---GRGLGGRLAGVRGRGRYAGLTSSEGGARGTAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGFAGQYRLLTRMEDAGQVRR
+GHFVDGLGGAQFSTGAVVDRLRGFQRDE-EDA------------------------------------------------
+--------AVDTAPLALALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLAF
+TEESGELRAAAEALVWALRTGHTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRFRN
+>0_1898
+M-TTSVEGFS------------ALDPVIQHHIVNTLRW-----PDLRPLQKASVASLLAGHDALLLAPTAGGKTEAAFFP
+VLTRAEREQ----WTGTSVLYVAPLKALLNNVESRAMEYTSWLGRSA------------SVRHGDTTQAERRRQGTERPD
+VLMTTPESLESMLISPTVNVTDFFSELRTIIVDEVHAFAGDDRGWHLLSVLERLSAVVRRPIQRIGLSATVGNPEELLTW
+LQGGNAAAGL-PAS-------VIAPPVDRTGAAAPELRLDF-VGSEDNAATVI----SRLHGG------EKR--------
+---LVFAESRRTVELLGNALHE---------------------------------------------------RDVTTFL
+----------------------SHSSLSLSERRRSEQAFAEAQDCVIISTSTLELGIDVGDLDRVLQLGAPSTVASFLQR
+LGRTGRRPGAQRNMLFLELKPADLLRAAGLLLLHGEGYVEPIQPPPAPHHIVAQQILA------LTLQK--GQLQRGAAL
+AGLQALGMSDSTTYRTIEDGLL------EHGHL------DSDGGLLFVGPETQR----RYGGLYFRDLMAVF--------
+----------TVE-----AEFPVFHGRTEIGSVAPNWIATDPDDQPLLILAGRSWKVSFIDWKRHLVHVERSDRGLAPRW
+ASPPRALSWALSDAMRRVL--LGADP-------AGVVLTGRAQDA----LADHREAEGYTAAADHTVLASTADDLRWW--
+----TWGGAGANALLVAALEQVAPEL-----LGEKLRFDNFSLRLRGDVDAASLGRALRQATSNFGGDLAGVDPLVDDAA
+VRGLKFHEMLPLDLARATLAARL--ADHTGVARVLERPVQMLRTAE----------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------DGR---------------MWG---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------
+>1_2251
+M-----SGPA-ETAAGAPT--PAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAPTGSGKTLSSFLW
+ALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAAHQGRPVPRVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSQARAA---LAGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARF
+LGGTQPVTVVRPASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDE----GAVTGGSIWPHVEERIVDLVAER
+RSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTP----------------------------DPTGFH
+GPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVDQVIQVESPPSVASGLQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLRIPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPF
+ATLPF------SAYESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGAD
+GAPGGAAAGDTAESASTASAGSARSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAE--VGGSA
+LFAARFRE----NAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLSALKELAGRVSS
+RAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLGTEELRELLDAEVIAEVEAQLQRLA
+PDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEAEE------------AADEDAVAGMLAELERAGRAFRLRQDGVER
+FAAVEDAARLRDALGTPIPHGVPTAFLDPVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTG
+AFRPEGTPGATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRPPATLEGVDGVAT
+VLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGEATGNDGWVALHPADAVDLTLRLPE------PA
+EETPADAAL--RAAVLEVLAGGGAWFFPQLVERVRAVQAAGGDA--GGAGRAVGP-DPHRDPADLARGPAVLAALWGLVW
+DGRVGNDTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAAGAAA---GRGLGGRLAGVRGRGRYAGLTSPEGGARGSAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGFAGQYRLLTRMEDAGQVRR
+GHFVDGLGGAQFSTGAVVDRLRGFQRDE-EDA------------------------------------------------
+--------AVDTAPLALALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLAF
+TEDPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRFRN
+>2_58
+M-----SGPA-ETAAGAPT--PAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAPTGSGKTLSSFLW
+ALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAAGLGRPVPRVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSQARSA---LAGVRTVIVDEVHAVAGTKRGAHLAVSLERLDSLLETPVQRIGLSATVEPASEVARF
+LGGTQPVTVVRPASAKRWDLTVTVPVPDLTDLSSPSAAHDLGPGSSPGGPGAEGGPGGAVTGGSIWPHVEERIVDLVAER
+RSTLVFANSRRLAERLTGRLNEIWEARLEAAAAVEDPDAVPGFRTPGAG----------------AGAASSTPATPSSSY
+-PAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGRIRCVVATSSLELGIDMGAVDQVIQVESPPSVASGLQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIEALRIPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPF
+ATLPL------SAYESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGPD
+GAPGGAAAGDTAE-----SAGSARSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPAAGRERLAAAGLDAWAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELEEIVTAE--VGGSA
+LFAARFRE----NAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKDLAGRVAS
+RAVRLVEVTTPAPSPFSQSILFGYVAQFIYEGDSPLAERRAAALSLDPTLLAELLGTEELRELLDAGIIAEVEAQLQRLA
+PDRRARGVEGVADLLRLLGPLSAAEAARRVRPEAGADD-------DGGAAAADVAAVGEMLAGLERAGRAFRLRQDGVER
+FAAVEDAARLRDTLGTPIPHGVPAAFLEPVDDPLGDLVSRYARTHGPFTAAEVGAALGLGGAVVLPVLQRLATERRVSTG
+AFRPDGAPGATGLDAEWCDAEVLRRIRLRSLAALRAEVEPVDQSAYARFLADWQHLRPRVGRDGAWRPPATLEGVDGVAT
+VLDQLAGTPLPASAWESLVLPTRVRDYAPALLDELLATGEYVWSGVAEAAGNDGWVALHPADAVDLTLRLPERPDGTGPD
+AAAPRDAAL--RADVREVLAGGGAWFFPQLVERVRAAQSARL--------GTGGP-DGH--GADLARGPAVLEALWGLVW
+AGEVGNDTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAGAGTA---GRGLGGRLAGVRGRGRYAGLASPDGGARGTAG
+PAAGMAGLSAAEQARAAGRWSLLPAAERDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGFAGQYRLLTRMEDAGQVRR
+GHFVAGLGGAQFSTGAVVDRLRGFQDDDGADAPA----APRLDAFGLPLPAAP---------------------------
+--------AEQRTPAALALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIRGELALYMERGGKTLLCF
+TQGAAELKAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEAMLAAGFYSSPSGLRYRS
+>3_37
+MREDGGEGPAPEEAAPSPAAVPDADAVLARFSEPTRRWFTGAFAAPTAAQLGAWDAISSGRHALVVAPTGSGKTLSSFLW
+ALDSFVREPAEPDVSATRVLYVSPLKALGVDVERNLRAPLIGITQTARSLGAPVPEVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSKARSA---LSGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDSPVQRIGLSATVEPAAEVARF
+LGGVQPVTVVRPVSAKRWDLTVTVPLPDMTDLSTPPPSA-LDAGRDGAAAGVP----GEATGGSIWPHIEERIVDLVAPR
+RSTIVFANSRRLAERLTGRLNEIWEARQEAAAAVHDPDLVPGFRTPSTAGEVLTDWLGTATGQTPAGAPRPPGGSAATSF
+-PAQVAGQTGTGSGTVSDFARAHHGSVSKEQRALVEEALKTGRIRCVVATSSLELGIDMGAVDQVIQVESPPSVASALQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMAAGRIEALRIPQNPLDILAQQTVAAVALEDVDAEEWFDLVRRSAPF
+SALPH------SAYESVLDLLAGRYPSDEFAELRPRILWDRELGELSARPGAQRLAVTSGGTIPDRGLFGVFLATE-ASD
+GAPGGAALGDTAESASGASSGSKRSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPDAARDRLAAAGLDEWARENLLTYLADQRESTGRLPTEQALVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRVPLMDAEPPGAELFEFSAEELEEIVTAE--VGGSA
+LFAARFRE----NAARALLLPRRDPGRRTPLWQQRQRSAQLLDVARKYPSFPVILETVREVLQDVYDLPALKDLAGRIAS
+RAVQMVEVTTPAPSPFAQSILFGYVAQFIYEGDSPLAERRAAALSLDPALLAELLGTEELRELLDPEVIARVEAELQRTA
+PDRRVRGAEALADLLRIVGPLSVAEAAARTLPVEDAAPAPADEAAAGAPSAAHLAAVTAHLEGLERTGRAYRVRLNGEER
+FAAVEDAARLRDALGAPIPLGVPVAFHEPVEDPVGDLVSRYARTHGPFTAAEAGAALGLGGAVVLPVLQALASQRRVSQG
+AYRPDGTPGATGLEAEWIAAEVLQKVRRRSLAALRAEVEPVDQAAYARFLADWQHLRPRPGRPS----PATLEGVDGVAT
+VLDQLAGVPLPASAWESLVLPSRVRDYTPGLLDELLATGEYVWSGTADAPGNDGWVALHPADAVDLTLRRPE------PP
+AQDVAAERLTARDHLLTVLAGGGAWFFGPLVERVRADAARAAE---AEAGGEDGPRDPHAAAATLPRGPVILEALWDLVW
+AGRVGNDTFAPIRGLLSLGKTAHRTGRQTPRARTARTGGAALSAAGTGGRGLGGRLAGVRGRGRYAGLAAPGSGAGAGTL
+PGAGLVGLSAAEEARAAGRWSLLPDPEPDPTIRAHAAAEVLLDRYGVITRGSVVAEEVPGGFAGQYQLLTRMEDAGQVRR
+GHFVDRLGGAQFSTGAVVDRLRSFQRDEDGPSPAEEEPAPRLDAFGMPVDESPRTDWSGWVADGVGGWTPAPQGHGAGMG
+TVGGAAGAREEPLPPALALAATDPANPYGAALDWPDLPAGPDGVAPTGHRPGRKAGAVVVLVHGALALYMERGGRTLLAF
+TQDGPVLRAAAQALVWALRAARTDKLSLEKVNGGPLLGTPLAEALLAAGFYSSPSGIRYRS
+>4_284
+M-----SGPA-ETAAGAPT--PAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAPTGSGKTLSSFLW
+ALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAAHQGRPVPRVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSQARAA---LAGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARF
+LGGTQPVTVVRPASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDE----GAVTGGSIWPHVEERIVDLVAER
+RSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTP----------------------------DPTGFH
+GPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVDQVIQVESPPSVASGLQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLRIPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPF
+ATLPF------SAYESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGAD
+GAPGGAAAGDTAESASTASAGSARSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAE--VGGSA
+LFAARFRE----NAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAGRVSS
+RAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLGTEELRELLDAGVIAEVEAQLQRLA
+PDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEAEE------------AADEDAVAGMLAELERAGRAFRLRQDGVER
+FAAVEDAARLRDALGTPIPHGVPTAFLDPVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTG
+AFRPEGTPGATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRPPATLEGVDGVAT
+VLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGEATGNDGWVALHPADAVDLTLRLPE------PA
+EETPADAAL--RAAVLEVLAGGGAWFFPQLVERVRAVQAAAGDGGTGAAGGAVGP-DPHRDPADLARGPAVLAALWGLVW
+DGRVGNDTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAAGAAA---GRGLGGRLAGVRGRGRYAGLTAPEVGARGSAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGFAGQYRLLTRMEDAGQVRR
+GHFVDGLGGAQFSTGAVVDRLRGFQRDE-EDA------------------------------------------------
+--------AVDAAPLALALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLAF
+TEEPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRFRN

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000077.fa ADDED Viewed

	@@ -0,0 +1,48 @@

+>0_286
+MLSE------------------------------------KSRPVIEATA--AAVAEHMPEITPL---------------
+--------------------------------------------------------------------------------
+-----FYAHMFEAHPELLDGVFSRANQRNGEQAQALAGSIVKFAVH----LLENPGTLPEAVLSRIAHKHTALGIVEEQY
+PIVYENLFWAIGEVL-------GDAVTPEVADAWTEVYWLMADALIKIEKGLYAQQANDRMWTDWKVVAKEPTGNAAVTF
+RFEPADDTPQSRGKAGGYVSVRLKVEDGLRQCRQYSLSEKAESATERVITVKLDEGGEVSPMLIQNVEVGDVIELSNPYG
+DITLED-EDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLLLHGDASWEAVALREQVTESLAALAHGDARLFLGVRP
+EQD---PEGVTTVEGVMHFDDVELP--RDGHYILCGPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA-
+>1_3
+MLSE------------------------------------KSRPVIEATA--AAVAEHMPEITPK---------------
+--------------------------------------------------------------------------------
+-----FYAHMFEAHPELLDGLFSRANQRNGEQAQALAGSIVRFAVH----LLENPGTLPEAVLARIAHKHTALGITEDQY
+QIVYENLFWAIADVL-------GDAVTPEVAEAWTEVYWLMADALIKLEKGLYAKQANDKMWLDWKVVSKEPTGNAAVTF
+RFEPADDTPQTPGEAGGFVSVRVKVADGLRQARQYSLSDHAASTTERVITVKLDEGGEVSPMLIQNVEVGDVIELSNPYG
+DITLED-EDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDASWEAVALREQVTESLAALPHGDARLFLGVRP
+EQD---PEGVTTVEGVMHFDDVELP--RDGHYILCGPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA-
+>2_50
+MLSE------------------------------------KSRPVIEATA--AVVAEHMPEITPK---------------
+--------------------------------------------------------------------------------
+-----FYAHMFEAHPELLDGVFSRANQRSGEQAQALAGSIVTFAVH----LLEHPDTLPEAVLARIAHKHTALGIVPEQY
+QIVYENLFWAIADVL-------GEAVTPEVAEAWTEVYWLMADALIKIEEGLYAQQANTKMWTDWKVVAKEPTGNAAVTF
+RFAPADETPQTPGRPGGYLSVRLKVEDGLRQCRQYSLSDHAESTDERVITVKLDEGGEVSPVLIQNVEVGDVIELSNPYG
+DITLRD--DAETPLVLATAGIGITPAAAILDTLASRGSQREVHFFHGDASWDSVALREQVAESLQALENGTGRLWLGVPP
+QEA---PAAFTTTEGLMEFDDVELP--ADASYLLCGPLAFMQATRSKLIDAGVPATSIRYEIFGPDLWLAA-
+>3_28
+MLSE------------------------------------KSRPVIEATA--AVVSANMPQITPA---------------
+--------------------------------------------------------------------------------
+-----FYGHMFEAHPELLDGTFSRANQLNGEQAQALAGSIVHFAAH----LLEHPDSLPEAVLARIAHKHTALGITEDQY
+QVVYENLFWAIAQVL-------GDAVTPEVAEAWTEVYWLMADALITLEKDLYAVQANDRMWTDWKVVAKEPTGNAAVTF
+RLEPADDTPQTPGRPGGYVSVRVTVADGLRQARQYSLSESASSTGQRVITVKLDEAGEVSPVLIQEVEVGDVVELSNPYG
+DITLQD---SDAPLVLMTAGIGITPAAAILDSLAASGSQREVRVLHGDASWDSVALRDQVLEDVASLPHAQADLWFGVAP
+ETA---PEGVSVHEGKVDTAAAALP--EGADYILCGPLAFMKSERSALIEAGVPAPRIRYEIFGPDLWIAAT
+>3_1198
+MPAHGWGARAGRTSFREHPVDVQECLWRGAHASSHDRSALHSRPSRGGSADPAPADRPPPPLTPAPGPAGIRDRPAGRIP
+AWWRDASGSLLWLVLLAVTALWVHGGGVQDLAAVGSGLTSLGRLTGLIASALLLAQVFLMARVPLVEQAWGQDRLTRVHR
+RVGFTSFTLMF-AHLALITAGYA------WDTPAGLWGTLVDFAVDYPGMLLAIAGTAALVMVVVTSFKAARARLRYESW
+HLIHLYGYLGAGLALPHQLWTGQEFLASPVATAFWWTLWAVTAGAVVVFRALLPLWCSAR--AGLRVQSVTAAGPHAVTV
+TVA-GRGAHRLHARGGQFFQWRFLDGPGWTRAHPYSLSAAPDGRTLQFTAAVVGDGTG----RLWDMRPGTRVLVEGPYG
+R--MHDGVRTGRKALLMGAGIGITPMKALLESLPADAG--EITVVHRVSDPDDPTLHADLLAAARTRGARYIRLEGRRRP
+GADSWLPASAGDVDDVTALRRI-CPDLAEHDVFVCGAPAWTDLVRQAARRGGVPAERIHDERFSF-------
+>4_293
+MLSE------------------------------------KSRPVIEATA--AVVAEHMPEITPL---------------
+--------------------------------------------------------------------------------
+-----FYAHMFEAHPELLDGVFSRANQRNGEQAQALAGSIVKFAVH----LLENPGTLPEAVLSRIAHKHTALGIVEEQY
+PIVYENLFWAIGEVL-------GDAVTPAVADAWTEVYWLMADALIKIEKGLYSQQANDRMWTDWRVVAKEPTGNAAVTF
+RFEPADDTPQSRGRAGGYVSVRLKVEDGLRQCRQYSLSEKAESTTERVITVKLDEGGEVSPMLIQNVEVGDVIELSNPYG
+DITLED-EDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDASWEAVALREQVTESLAALPHGDARLFLGVRP
+EQD---PEGVTTVEGVMHFDDVELP--RDGHYILCGPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000078.fa ADDED Viewed

	@@ -0,0 +1,49 @@

+>0_297
+MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ
+-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE
+YVAVPAGQLMAVPDGVGLVEA------AALPEVACTVHSTLVGRAGVQAGDRVLVHGATG
+GIGSFAVQFLTAVGARVLGTAGGPEKVALGRGLGAEHMFDHRAAESGAFAPWVKEVTDGH
+GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL
+RSRSVTDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV
+TDPADARRPSGDRA
+>1_21
+MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ
+-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE
+YVAVPTGQLMAVPDGVGLVEA------AALPEVACTVHSALVGRAGVQAGDRVLVHGATG
+GIGSFAVQFLAALGARVLGTAGGPEKVALGRRLGTEHMFDHRAAESGAFAPWVKEVTDGH
+GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL
+RSRSVVDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV
+TDPADARRPSGDRA
+>2_22
+MSETTRTPGTGRGTMRAVRFTGEGGAGSLAVGQEPIPTPGPGEVLVKVAAAGLNRADVMQ
+-REGKYPPPPGASDVPGLEVSGVVVALGEEAGLPGEGRFAPGDEVCAL----LAGGGYAE
+HVVVPAGQLMAVPPGVDLVTA------AALPEVACTVWSTMSERGGVRAGDVVLVHGGSG
+GIGTFAVQYLAAIGARVLATAGGPAKCERVRGLGAEDVFDHRSGEPGAFADWVLERTGGR
+GADVVLDVVGGPYLDANVRCLAEEGRIVVIA--VQGGPKADGFNLMRLVSKRGWLTGATL
+RARSVVDKARIVAGTERAVAPLVAAGRIDLAVGARFPLDDAAAAHRRFEAEDRVGRVLLV
+TDPADALWPQEDRT
+>3_18
+MD----TA----PDMLAVRFAGAGGTDVIRVGREPVPEPGPGEVLVRVAAAGLNRADVVQ
+-REGHYPVPPGASEVPGLEVSGTVVALGPQAGVAGEGRFAVGDRVCAL----LAGGGYAE
+HVAVPAGQLMSVPDGLDLVSA------AGLPEVACTVHSNLEGRAGVRPGEWALVHGATG
+GIGAFAVQYLSAVGVRVLATAGGPAKVARALELGADAAFDHRAAAPGAFADWVREITGGH
+GADVVLDVVGGPYLAPNVKALAMDGRIVVIA--AQDGPVPEDFHLMRLAARRGWVTGSLL
+RPRPPDEKAGIVAAAERAVWPLVAAGRIDPGVTARFPLREAAAAHAHFEGAARMGKVLLV
+TDDADALLPGG-AA
+>3_637
+MHPS--LP----RTMLAAIIPAPGGRPELR--QCPVPEPGPGEVLVRVMASSVNPTDVMT
+WRRGMFVTGQTVPFVGGYDMSGIVVKLG-----RGVTALDVGDAVTGMPRFPAPAAAFAQ
+YSAVPARHLARIPTGTEDLSAGAWGRWAGLPLAGLTAYQALVDTAHLQSGQTVLVHAASG
+GVGSLACQLAVNLGAQVTAVTSDRGR-TLVEVLGTRHVVDR------ATVDW--QRFAG-
+CFDVVLDTVGGDTTPRSLAMASPDGVVVALHPYAHDDLAQRDPRLRRMLVE---------
+-----PDHHALELLIEQA-----ARGRLTVQVGAGYPLSDLGDALLHVETNKTPGKTIIH
+I--------QGDNA
+>4_304
+MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ
+-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE
+YVAVPAGQLMAVPDGVGLVEA------AALPEVACTVHSALVGRAGVQAGDRVLVHGATG
+GIGSFAVQFLAALGARVLGTAGGPEKVALGRRLGAEHMFDHRAAESGAFAPWVKEVTDGH
+GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL
+RSRSVVDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV
+TDPADARRPSGDRA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000084.fa ADDED Viewed

	@@ -0,0 +1,54 @@

+>0_397
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERR---------GTTADTADTAGEQAAAPAAPTRLSR
+LDEVAAEQDARPAAAVKPAGGPAA------------SETAAAGRETDESVA--GVAGGAGVTVDQQDAPRTDATAET-SR
+PTA--APTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDEQTPAADVAAAPASPSPVTETPA--PAAPAAEAPQ
+HRSHLTP----APEHVHGTVPAEEVAAEHTPTKEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTQQNDADGAE
+RSAAGSLRIDGTPGVPGRVAEAGREPARTED-------------HRADAAQPAAVEPAAERPSLEAAAERPSLEATPATR
+RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAAAGTAA-TAGTAGTAAPTS
+STPTTVAPDT--------STSSAPTNEEPAEDDTEGAALPDLRADRDE-------------TRGSDAEGESKL-------
+AQAGAVAASAFETVRDKVAIPLRDNVAVPAK--DKAVKVVKDKLAQAQERRWGK--------------R
+>1_127
+MPQSTLYWIIAAIIVVLLILIIVSVIASRRRREAEAEAAETRLERR---------GV---SADTAGEQAAAPAAPTRLSR
+LDEVAAEKDARPAPAVRPAGGLAA------------FDTAAADRETDESGA--GVAGGAGVTVDQQDAPSTEATAQTHRR
+DAA--APATRGTLRPAPAVPSTVREADTVGLGAAGVAGGSGVTLDEQTPAADVPATPASPSPVTETPA--PAAPVAEAPQ
+QRSHLTP----APEHVHGTVPADEVAAEHTPTKEFATDGIPVPQGEHLETHTVATTAHGSVTVVATESDQAQQTGVDGTE
+RSAAGSLRIDGTPGVPGRVAEADREPARTDD-------------HGADVAQPAAVEPAAERPPLEAA---------PATR
+RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAA-------AGTAGTAAPTS
+STPTTVAPDT--------STSSAPTDEEPAEDDTEGAALPDLRADRDE-------------TRASDAEGESKL-------
+AQAGAVAASAFETVRDKVAVPLRDNVAVPAK--DKVVKVVKDKLSQAQERRWGK--------------R
+>2_2485
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------PTDAEPAADDTEGAALPVQDATRADAVRP-------GTARTDASAGDSKL-------
+AQAGAAAGTVLETVRDKVAIPLRDNVAIPAK--DKAVKVLKAKLAEAQERRRNK--------------R
+>2_2486
+MGESTLYWIIGAIIVVLLILIILSVVASRRRRAAEAEAAEAQLERR--RVTPTAAGVGASHEDALEETHDADARPHTVA-
+----STGGDVAPAAAAGAAAGTTRLSQLDDVA----PVAAAAADADAESLPADGVAAGSGVTVDQQ-----DASDQS-VR
+PAAPAAPAGADTRGPNASVKSAGAAAAAVGLGAAGVAGGRGVTVDQQDAAADVPSTPASPSPVAQTPAAPSSAGATTAQD
+DRADRTAQDAADAEPVKGTVPLSEDAHAVPPAADPPSGGDAVADDAHLEAHTVATTEHGSVVVVTAEQDEDDQATA----
+--------------------------------------------------------------------------ASRETE
+--TETDDSRG-----DDAGQDRDAERAVAEGVAGGTGVTVDQKAV--------AEAAATQGAPASAAGAASAAGAAARRR
+DRGRRLDPACGGARLLQDRRH--AGHARPRRLRGAGRGRG---GDR--PARPPRRRP-----------GDARLHHPRDAP
+GRRAG------------AGPGRRRRGLPQGRGRDPAAPPRGRRPGAKPRRRPTSTRPRPRPPRRTAPAR
+>3_2354
+MPQSTLYWIIGIIIVVLVIILIVSSLRAKRGREEEAAAAGRHADSAPAPLAATAARGGTVGASTVPATGDAPADRTDGR-
+----AAGATALPSFDVDEVDRRAAEQREQDVVERRRATGAEAGAAGHAAVP--GVTGGSGVSVDEAEGVAKDATGQD-VT
+PVA-------DAQRRNGSSAAPAATGAGLGLAAAGVAGGTGVTVDDAGTGADLPAPKGSPAGVVEVAE--TQAEAAQA--
+--------DAAPAEHT--VVP-------------------GVAGGDAVTVDTADVQSSSAPQGAQAAAGRSDLTDAE---
+---ARTYPVTGLPGVPSAVDPEQVAAARVQDAAELKAAEGQGAEHERGASQPADPESVPGTVPLTGE--EAVIEAPVHTH
+--EMPEPVLGTPAYIQDSTTGQDPTEDLPEGQVYGTTPLSGEDAIVEPADQLPAEAAETEDRAASDAGTASAETAVVPVE
+ETETAVVPVA--------ETR--SADAGPSEDSVALTGQGVETADRVEPAAPVAGTPARDEARTHD-EHRSRLEIVKDAV
+AETAGTVATTAGTAAEKAAPVVRSAARTVGKAAGSAASTLKDKLAQAQERRWGK--------------R
+>4_400
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERR---------GTTADTADTAGEQAAAPAAPTRLSR
+LDEVAAEQDARPAAAVKPAGGPAA------------SETAAAGRETDESVA--GVAGGAGVTVDQQDAPRTDATAET-SR
+PTA--APTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDEQTPAADVAAAPASPSPVTETPA--PAAPAAEAPQ
+HRSHLTP----APEHVHGTVPAEEVAAEHTPTKEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTRQNDADGAE
+RSAAGSLRIDGTPGVPGRVAEAGREPARTED-------------HRADAAQPAAVEPAAERPSLEAAAERPSLEATPATR
+RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAAAGTAA-TAGTAGTAAPTS
+STPTTVAPDT--------STSSAPTNEEPAEDDTEGAALPDLRADRDE-------------TRGSDAEGESKL-------
+AQAGAVAASAFETVRDKVAIPLRDNVAVPAK--DKAVKVVKDKLAQAQERRWGK--------------R

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000089.fa ADDED Viewed

	@@ -0,0 +1,55 @@

+>0_486
+M--------------------------------------------------IP-EAARTT
+PAPLT--LWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARQRAGAPALLSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPITVVRNGV
+DVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRLTLAGAGP
+LEGELRAQAEALGVAEAVDLPGFVEPWETM-----AEHDVLVQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVHET-TPAAIADAVVRAAADGPGEVRVGDVETMARA
+TAEATLEVLGRRVGKVGT-R--------
+>1_215
+M--------------------------------------------------IP-EDATTT
+PAPLT--LWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLCPAAVHTHLAYADLAAFTALGAGRALRRAGAPALLSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPLTVVRNGV
+DVPAVRAAAAGRRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRVTLAGSGP
+LEGQLRAQAEDLGVADAVHLPGFVEPWGTM-----AEHDVLVQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVRET-TPEAIADAVVRAAAEGPGEVRVGDVETMARA
+TAEATLEVLGRRVGKGGH-R--------
+>2_1193
+MTRRLLLFANSFPYGKQEPYLMRECHYLDAFDEVYIFSLSIRKHQRDHRRDLPLERVTVV
+PIPFKSPLFYAAVSPRALVSRAFVTELRQLLRDRRFTVARAVQALSQFSRAEHEASVIG-
+-----------RFLRD---NITPSPSDETVFYAYRFLYQPYLMSRLAAKFSSSRLIGRAH
+GI---DLFEERQSTDYLPGRA--INLGALDELHSVSRAGAEYLR----ARHPEFVEKIKV
+SYLGTEDHGVRPPRSSSQVLRLVSCSEVAPVKRLELLVEALREVSD-SIQVEWSHYGEGP
+DMDRVRAMASTLPGHVSATFHGWTRNDEILEAYRSGRHDVFINVSSSEGLPVSIMESSSC
+GLPTIATDVGGTGEIVSDGVNGRLISANPMPREIAAAVEEFARMAP--------EAFARR
+SAAA-RETWSTHFDSDRNYRQFVAKMLS
+>2_2388
+M--------------------------------------------------TP-EAATTT
+PAPLT--LWVVPVADLGGVARHVLDVAAHGLPGLRLVVLCPEGALAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTAFGPGRARRRAGAPALVSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGTGAPITVVRNGV
+DVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRLTLAGVGP
+LEGQLRAQAEALGVADAVDLPGFVEPWGAM-----AEHDVLVQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVHET-TPAAIADAVMRATVEGPGEVRVGDVETMARA
+TAEATLEVLGRRAGKTSG----------
+>3_2271
+M--------------------------------------------------IP-EAATTT
+PAPLT--LWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTALGPGRARRRAGAPALLSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPLTVVRNGV
+DVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKGLDRLIAALPALRERDPGTRLTLAGSGP
+LEGQLRAQAEDLGVADAVDLPGFVEPWETM-----AEHDVLVQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVHET-TPAAIADAVTRAAAEGPGEVRVDDVEGMAEA
+TARAERDVVETQDARRRKTR--------
+>4_485
+M--------------------------------------------------IP-EAARTA
+LAPLT--LWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARRRTSAPALLSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPITVVRNGV
+DVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRLTLAGSGP
+LEGQLRAQAEALGVAEAVDLPGFVEPWETM-----AEHDVLAQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVRET-TPAAIADAVVRAAADGPGEVLVGDVETMARA
+TAEATLEVLGRRVGKAGT-R--------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000090.fa ADDED Viewed

	@@ -0,0 +1,49 @@

+>0_498
+MTPRGSCWSSLPVGARFRLWNTLDPMHLLVTGGAGFIGSNFVHHVVRETGHDVVV-----
+-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAARKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGADGEKNNREVVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP
+AKAAVEATYRAQG---------------Q
+>1_229
+-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVA-----
+-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVRATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP
+AKAAVEATYRAQG---------------Q
+>2_1194
+-------------------------MRFVVTGAGGFLGSNVVRELLAETDHDVVAVSSQT
+DRELAAQLERAPYPALRRFPQVHPRTRL-LEAG----------FLRDGDIVINCAFPWNR
+GGRAMADGLEYLTR----LFQSAHAVALH--TFVNVSSQSVYSQARTEAA---DESSPVE
+CDTPYSTGKYAMELAAELVLPPKVLVNARMSSLIGPGYDVRIVNRFIARFLAD-----EP
+VSIQGGDQVFDFMDVRDAARALIAVALAGPPEGSAALNIGSGAPRTLRDIAQTVADVVRT
+HTGHDPRIAWEPSAGDDRTLGLDSGLLRREYGFAPRHTLEDSALS---------------
+---ILQAMTSAQSASVGETPTGSVEGGRR
+>2_2375
+-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVV-----
+-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAQSDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPQFTDIRAGLADTVRWYRENEAWWRP
+AKAAVEAKYRAAG---------------Q
+>3_2257
+-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVV-----
+-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGQGINVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNKEIVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPQFTDIRAGLADTVRWYRENEAWWRP
+AKDAVEATYRAQG---------------Q
+>4_498
+-------------------------MRILVTGGAGFIGSNFVHHLVRETDHDVVV-----
+-------LDKLTYAGNRDNLVGLPESRVRLEIGDICDAALVDRLVAESDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGHGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP
+AKAAVEATYRAQG---------------Q

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000091.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>0_524
+MH-PDDAPTPDLTWLDSAGSTQDELLARL----DREGHRHGAAVATADQRAGRGRHSRVW
+SAAPGAALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLA
+TDGRKLCGVLATVALS-----SDGK-GPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADA
+VPAPRDLAVELRDAVVAAVDRFAAGVAGQAAAVDGRHPAVAAVADRLSTLGRAVRAELPG
+GGVLEGTAVGLGPGGTLRVKRVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>1_258
+MH-PDDAPTPDLTWLDSAGSTQDELLARL----DREGHRHGAAVATADQRAGRGRHSRVW
+SAAPGAALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLA
+TDGRKLCGVLATVALS-----SDGK-GPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADA
+VPAPRDLAVELRDAVVAAVDRFAAGVAGQTAAVDGHHPAVAAVADRLSTLGRAVRAELPG
+GGVLEGTAVGLGPGGTLRMRHVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>2_2346
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------MGVNLDHRGAAPVATATDLAEQIGAEA
+VPAPRGLAAALRDAVVGAADRFAAAVAGEAEAVDGRHPAVAAVTQRLSTLGREVRAELPG
+GDVLEGTAVALGPGGALRVSHVTADRGRIETEVSAGDVAHLRGDVHRGA
+>2_2347
+MHAPHDPAAPGLVWLDSAGSTQDEVLARV----GREGPRHGLAVATADQRAGRGRHSRVW
+SAAPGAALALSVHLRPAAGGTPLAPVHLSWLSLVASAAVVEHLAGLGAAAHLKWPNDVLA
+PDGRKLCGVLATVAPA-----ADGG-GPGWSWAWG-------------------------
+------------------------------------------------------------
+-------------------------------------------------
+>3_2230
+MG--YTWGMGTLLWLDAADSTQDELLRRLAAADGAARPGHGDGVGTADQRAGRGRHGRAW
+QAPPGAALALSVHLRPTGPSGPLAPAHLSWLSLVASAAVARRLVGLGVPAHLKWPNDVLD
+AEGRKLCGVLATLAPAPVFPGADAGETPGVVVGMGVNVDLSSGRPVPTAAALTDHLPGAE
+VPAPRDLAQALLRDVAAAADRLARDLDGVVEPVDGTHPALAEVAAVLSTPGRRIRAELPG
+GEVLEGVATGLGAGGVLAVRVVTGERETITREISAGDVVHLRGDVRRGG
+>4_527
+MH-PDDAPTPDLTWLDSAGSTQDELLARL----DREGHRHGAAVATADQRAGRGRHSRVW
+SAAPGAALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVLTHVKWPNDVLA
+TDGRKLCGVLATVALS-----SDGK-GPGVVVGMGVNLDHRGAAPVDTASDLAEWIGADA
+VPAPRDLAVELRDAVVAAVDRFAAGVAGQTAAVDGRHPAVAAVADRLSTLGRAVRAELPG
+GGVLEGTAVGLGPGGTLRVKHVTPDRGTIETEVSAGDVAHLRGDVHRGA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000095.fa ADDED Viewed

	@@ -0,0 +1,54 @@

+>0_586
+MT------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------S
+T----------------DPTPAKAAS------------------------------------------------------
+------------------------------------------------------------APNRQRRAKIIVWVVLAALV
+LAGVV-AFFAARAPS--TPEAAPAQAGQAASSGTGQTAAS---EAAP-VVRPDSRVLSQAPNEKAVLVEFLDFECEGCKA
+AHPVVEELRAEYADTVTFVHRYFPLPGHPNSMTAAVAVEAAAQQGAYEAMYQKMFDTQEQWSHTGQDRSPVFRGYAEDLG
+LDMTAYDKAVADPATRARIEADVADGVALGVQGTPTFFLDGQVLTLN-TLEQFRAEVDAAASN--------
+>1_311
+MS--------------------------TP--------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------T
+R----------------NPTPSDPST------------------------------------------------------
+------------------------------------------------------------PGTTSRKAKTIVWVVLAAVV
+LAGLIVGVVAASGPR----DAAPQGSGQTASSGTGQSAPS---EATP-VMRPDSRVLSKAPNEQAVLVEFLDFECEGCKA
+AYPVVEELRAEYADTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFRGYAEDLG
+LDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLN-TLEQFRAEVDAAATT-------D
+>1_1721
+MT--------------------------SP--------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------DPTASTPSS------------------------------------------------------
+-----------------------------------------------------------PTPSRQRRAKIVVWVLLGLVV
+AAALI-GYLVARGTA----TAQQQDPNQSTAQSTGQSTGS----AGQ-LVRENSRVLSQAPNEKAVLVEFLDFECEACAA
+AYPFVEDLRAEYADTVTFVHRYFPLPGHPNSVTAAIAVEAAAQQGAYESMYQKMFETQTEWSHTTEDRSPVFRAYAEELG
+LDMAAYDAAVADPATRDRVELDVADGTALGVAGTPTFYLDGEPLTVN-SLEEFTAAVEAATQD--------
+>2_2293
+MS--------------------------TP--------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------T
+R----------------NPTPANSST------------------------------------------------------
+------------------------------------------------------------SGTTSRKAKTIVWVVLAAVV
+VAGVIAGVVAVGAARNATPDAAATQAGQSAAQGSGPTTAE---EAGELVVRPNSRVLSKAPNEQAVLVEFLDFECEGCGA
+AYPVVEELRAEYADTVTFVTRYFPLPGHRNAMPAAVAVEAAAQQGEYEAMYQRMFETQAQWGEATEDKSPVFRGYAEELG
+LDMAAYDKAVADPATRARVEADVADGIALGVQGTPTFFLDGEMLTLT-SLEQFRAEVDAAASN--------
+>3_1166
+MSWRTIRTEAGSAVLLVVVTAVALLWANSPLSEAYFGLWDVEIGFDVGGFGLHMNLHHWINDGLMMTFFLVVGLEVRQEF
+AHGTLRDASRARLALIAGVVGVALPAVFYILIVAAAGGEGLGGWGAVVGTDTAFLLGALALVGPKLSGQLRVFLLTLTVV
+DDFLAVSIIGIVYSDEIRLVPLLIAGACLVGLWLLGRSRQWSATPYVLIVIVLWFATVESGVHASLAGMVAGLLIPAYPT
+RRQQVVEARQLFRDFWQSPSAASARAVDRGLAQGISVNERMHEVLRMPTALVIVPIFALANAGVDLRGGVLVDSFQSSVT
+WGVIVGLVLGKLLGIGLATFVAVKLGAGRLPEGVGMGSVFGGAALSGIGFTVSLLVIGLAFGSTSDLGRQATVGVLVAMV
+LATALGWLIF-----------------RVAAKRWGEETADLPMVLTP-PVDPEVDHIRGPEDAQLTLVEYIDFECAYCAH
+ATGSWDDLRSRFGDDLRYVVR--QLPHHPHGPLAARASEAASNQGMFWPWLDFVFTRQDAL-----EREDLIR-YAEELG
+LDVAQFTADLDSAAVGARVERDLESADASGAHATPTFFVDGRRLLGSYDARTLTSALEASRRGTRTQEVRS
+>4_1948
+MS--------------------------TP--------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------T
+R----------------NPTPSDPST------------------------------------------------------
+------------------------------------------------------------PGTTSRKAKTIVWVVLAAVV
+LAGLIVGVVAASGPR----DAAPQGSGQTASSGTGQSAPS---EATP-VMRPDSRVLSKAPNEQAVLVEFLDFECEGCKA
+AYPVVEELRAEYADTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFRGYAEDLG
+LDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLN-TLEQFRAEVDAAATT-------D

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000104.fa ADDED Viewed

	@@ -0,0 +1,126 @@

+>0_705
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSAP-----ARGPELAVVTEHGP
+DAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALP
+RPVTPEPPAVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA--
+-RADALVRRR------------AQAALSPGAVARAVRSGATDRF-----------------------GLTSG-ADEAVA-
+------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW
+AVFQLLRHAVAADGAFVVEAGGVRRTWWSGGSGPRLLVSAPEDAA--LDPAWRAWRAAIGGDA--GTTPT-ARADLPWTR
+Y------------------------------------------------------DFTGPSPAPGDA-VVDLRGRTVVVP
+AEQQRF---------EDVTADGLADGTLVAWLTELADDVVDLGLLP--ADDGDGTLTPPGQVGARDAVDGLTVTLARSGD
+-ETGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV
+GTASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL
+AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ
+------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVENYAAG
+DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG
+GRAETLAAVVEVALRSGRP----VAVLDGTGEAAA-AARS---------GTPVLTPDAEGA--GEAAL------------
+---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRE-LATGRL
+LLHLPHRFFVPAGTNAEHRLIW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA-------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------
+>1_445
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGRRSVTYAEGVGSAP-----ARGPELAVVTEHGP
+DAGRIVPLGEGGLSVGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRATGRLWDGRSPLPVGRTALGLVRGPGSALP
+RPITPEPPVVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPMFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA--
+-RADAVVRRR------------ARVALSPGAVARAVRSGATDRF-----------------------GLTAG-ADEAVA-
+------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW
+AVFQLLRHAVAADGAFVVEAGGVRRIWWSGGSGPQLLVMAPEDAA--LDPAWRAWRAAIGDDA--GTTPT-ARTDLPWTR
+Y------------------------------------------------------DFTGPPPAPGDA-VVDLRGRTVVVP
+AEQQRF---------EDMAADGLADGTLVAWLTELADDVVDLGLLP--TDDGDGTLTPPGQVGARDAVDGLTVALARSRD
+-EAGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV
+GAASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL
+AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ
+------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVENYAAG
+DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG
+GRAETLAAVVEVAMRSGRP----VAVLDGTGEAAT-AARS---------GTPVLTPDSEGA--GEAVL------------
+---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPAAAGLRLAVFGGRE-LATGRL
+LLHLPHRFFVPAGTNAEHRLVW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA-------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------
+>2_2172
+MGWTVRILGGRTPETWRVSPLPRDPTLRDRAVRERAPGRSLRAVASGPGSVTYAPWGGAEP-----APGPELSVVTERGP
+DGGRLAPLTGGGVSVGRGRARLLLDDPAAPSRPTRLRLAAAGLHVEGAVEGAPRLWDGRRPHRIGRTTLGLVRGPQPPLP
+PPSLPAPPCVDLGSPPAGQSLAIPLLTAAAPLVIGVALVLVMRNPIFLLFGLLSVAVALTMLGLQRRARMRHAALLAE--
+-RAAAVTAHR------------ASAALSPGDVARAVRARTPDRF-----------------------GLTGA-AEGPAT-
+------LSWGLGMGALGLSRDD-----PDQAWVAAVTARREALTVPSPAARTVVLG-----PPR--------EAAGVCRW
+VVFQLLRHAVAAGACLVVESGGSRRCWWAGGTGGALLVTAPADAA--LEAAWTAWTAGIGG------APG-ERTGAQPAR
+I------------------------------------------------------DFTGADCAPGET-VVDLRGGMLTDP
+GQEQRI---------TGLEADGIAPATLPGWAAELADDVVDLGLLP--ADAGAGALFPPADVGTRDAVDALRVSLEAGSD
+GGPGALALDLAAD---GPHLLLAGTTGSGKSDLLLSLLLGVAAHHPPAEAAFLLLDFKGGASFGPLAALPHTMSLETNHV
+GAASL--RALNAIRAELHRREALFAEAG----VSDYPAFRRRH-----PEAALPRLVVAVDELRVLVDDHPDAAAVLQRL
+AATGRSLGFHLVLATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAATRLDPRRPGSAILSTAGREPVPFRASR
+------------------WAVDGGAPVWRR---LG-----------EAAETPAAAPW---------KAVVAQLVERYAAG
+RWPTP-PPVVTPALPERWVPDRTRRAGATA---------------LALLDDAAHGRHRPWRWAPGGGGRAAWIVE--PAG
+GRAEALAAVLEVGVRGGAP----VVVLDGTGEAAAIAAPE---------GVRLLRPDEEGA--GERAA------------
+---------------ACLRELAAAGGTAVLTGWTTWAGLRLGESYRTLEEDAQGWLGGREAAGLRVAAFGGRE-LATSRL
+LLHLPHRFFVPAGTSAEHRLVW-PRLVEV-EPLPGRAVHVSPDVPEPGLPC--QLASPGAHRSGAADAASTL--------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------
+>3_328
+MTRRL-----------------------------------VHR-----------------P-------------------
+--GRTVP-----------PARLLPED--------------------------------------------VITGPQ----
+----PVDPAMDQGSGP-NLLMIVPMVAAAASMLTMMAFRQSPFAAVGALAMVVTLTAMLILYGSQAGKARRRRTTLRETY
+TRYLDRQRRRLIAEDEQARAIAASAAPPPGALLDVVR--RPDRLWERRRTDEDFLQTRVGLGARPVRALRVA-VQDNATQ
+VQDEFMLKQAESLATRFRTTDDMPVSLPLDSLGNLAVVGPREFGLTA--ARSLVLGACVQQAPEDLVVALLVPPERRADW
+PWFDRLPHARVADAA--------------SPTGNRLLVAADADDLMRMLRADLARRAGIAAETLRASTRD-GRAATELSR
+LVIVVDSHGEPAAGLPLEGSHLPLVSRGITLITLVSDRLDEPSDVRLRLSATGGTDVTGAAEFQVDD-ARQDEGRPTVSH
+GRLDTFDAATALGVATDLQPLRLSADSLEHAEDDLSSTQTFLQMLGLSPELTLEELRRRWRPRGQDEF--LRVPIGEDDR
+GDAVHLDLKEAAQLGMGPHGLCVGATGSGKSELLRALVFALLASHAPERMSLLLVDFKGGATFAPFHGAPHVAGIITNLS
+DDLSLVERVYASLSGEILRRQEVLKAAGNLANITDYQVHRERELAQGRSVEALPHLIVIIDEFGELLTARPDFIDLFLSI
+GRIGRSIGVHLLLSSQRIESGRLRGLETYLSYRLGLRTLSESESRTVLDTADAFHLPP-LPGFGYLKVDTSVYTRFRSGY
+VSSPLEEEAAARAEQERVLTADDDVPPALPVPDYGLQLVLPTEGAEPQLSSGAGAAQVMEEPEDHRPTIMETLMD--RLR
+EVPSPVEPLWLPPLPEALTLDQAAGDVAVTDHGLRLPAGGDLEVPIGLIDDPEHQWQGLWMLDF-ASGSGHLIVQGGPRS
+GKSTLLQTIVTSLALTHSPQQVGVYCVDLLGSSLL-PLQG----LPHVGGVAIRTNREMVTRTLREVSAMLTLREKLFEA
+EGIDSMTTLRRRHADGSLPDLGSADVFLVLDGYG-----QVNEEFADLTPVLNGLISRGAAYGIHIITTVARQGEIRSTQ
+QTFFTHRVELRLSTPSDSAIDR-KAAEEVREDTPGRGLASTRLHGQVALPRVDGAADPGTAAEGLAETVQRIAESARGEA
+MAVRVLPPTTERPPLEQLEDPGRLPVGLLEDDLSVRSLDIDGRERHVVALGDAQTGRSSMLRQFARHFMDTHADTEMMFV
+VFDPRGELKGVIPDAYMAGYAGNATVAVPLARALVSELEKRQSTDPKDAGPMRQARIVVLVDDYDVLTVAGDSPLAPLLP
+YLPMARELKLHVFLTRRMKGASRGLYEKFLASLVSQDAVTLMFSGDRSEGVLFDGLRPKRLPPGRAVLIGASRRHETVQT
+FTGPPAPGRG
+>3_2047
+MTWRVRVLGLPVEQDWAVSELPLDVDGQDRVVAEHFAPLRVERARGGGTTLTYVAHPSGTPPVPAAGSGPELAVGTSAGP
+DAGRLVPLTAAGLTVGRGRSRMLLDDPQCPSRPVRLALGPSGVSVDDG--RTRRTWDGLDGLPIGDSILRLVRGRQRPLP
+PALTPPPAQIDLGAAPAEQSLLVSLAMAVGPVLIGLVLAVTTRSPLFLLFGIVSLLGVGVLLGVQRRTRRRHADLLRE--
+-RALDVVRRR------------VAAVSGPADVSAACRAKAEDRF-----------------------GLVSARPGDGPA-
+------LLWGRARGSVAFTRGD-----VADHWRSAACVDQPVLGVAAADRGTVLCG-----TGR--------PAQAAARW
+TLFQLLRHAVATGSSLVVRSPDGARVWWPAVPGAPTIALELEDTA-PLAGAWEVWTASLGAEM--SETRRHGCADEVLVR
+--------------------------------------------------------CTGTPPADLDADVVDLDARQATLP
+GQGLEL---------TDLTPLGISADTLQWWLAELADDVAHLGLGG--PPASAPPLRRPHDVGAHRAVRNLAVPLTSSSA
+GDAAPMVLDLAAD---GPHALIAGTTGSGKSDLLLSVLVGLAARHAPAEVSFVLLDFKGGASFGPLRRLPHTMSVETNHV
+GAASL--RALQAIGAELRRREALFAEAR----VADYPAFRAAH-----PDTALPRLVVAVDELRVLVDEHPDANAVLQRL
+AATGRSLGFHLLLATQRPGGAVSADVRSNLGTTIALRTATEQESWDLVGSAAASRIDPAAPGTALLARGTGAPVPFRASP
+------------------WSAGPVRPRWTP---WGV----------PVASAASGTDW---------PSVVEDLVQACRDR
+DLPIP-EPVVSPPLPGSFAPDRSRRRSADV---------------LALVDDAARARHVPWRWPLGAQGNGAWIVE--PAG
+GRALVLAAVLEAAGRTSPA----VLILDGSGECAA-ALPTVADALPDLADVTLLTPEAQPADVGEQVC------------
+---------------GAVADLAAVGGTLVITGWQSWAGVRVGETYRTLDEELHRLLGTQAARGLRVAAVGGRE-LVTARI
+APHLPHRFYVPAGTTPDHRLVWPPKLVEV-EQLPGRAVHVHPGGPTVGVPA--QLAFPAHSAAGAGTDSDDQ--------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------Q
+>4_669
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSAP-----ARGPELAVVTEHGP
+DAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALP
+RPVTPEPPAVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA--
+-RADAVVRRR------------AQAALSPGAVARAVRSGATDRF-----------------------GLTSG-ADEAVA-
+------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW
+AVFQLLRHAVAADGAFVVEAGGVRRTWWSGGSGPRLLVSAPEDAA--LDPAWRAWRAAIGGDA--GTTPT-ARADLPWTR
+H------------------------------------------------------DFTGPSPAPGDA-VVDLRGRTVVVP
+AEQQRF---------EDVTADGLADGTLVAWLTELADDVVDLGLLP--TDDGDGTLTPPGQVGARDAVDGLTVTLARSGD
+-ETGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV
+GTASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL
+AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ
+------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVEKYAAG
+DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG
+GRAETLAAVVEVALRSGRP----VAVLDGTGEAAA-AARS---------GTPVLTPDVEGA--GEAAL------------
+---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRE-LATGRL
+LLHLPHRFFVPAGTNAEHRLIW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA-------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000105.fa ADDED Viewed

	@@ -0,0 +1,25 @@

+>0_720
+------------------------------------------------------------
+----------------------------MLSGFCLALGTWSTVAAEAADAALARRWGAAA
+RLWTAHLGLGLVAVVVGWGAGLGLHAVLAG
+>0_721
+MSGAGYEVFALFQVALLACLAAGGVLGALARRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGG-------------------------------------------------
+------------------------------
+>1_460
+MSGAGYEVFALFQVALLACLAAGGALGALARGRLTDRLGPRGLLTANTTAALVLGATVGL
+AVPELVYASESWGDGQGL--MLVAAVSAVVSGFCLALGTWSTVAAEAADAALARRWGAAA
+RLWTAHLGLGLVAVVVGWGAGLGLHAVLAG
+>2_2133
+MSPALMGASPWEWVLGLAVLAAGGALGALLRLTLQEHLPRRGVLAANTLAAGVLGFSLAL
+ALPSLVYASGLAGDPLGVAGLLVASLTA---GFCLALGTWSTVAGQAADAVLAGRWGAAG
+RIWAAHLGLGLLAAAAGWGLGLGARLLVA-
+>3_2027
+MS-----AGTVLLTVLLAGLAA--AVGAGLRHLADHRWGGRGVLLANVTASALAG-----
+ALFAIGFGPGSA-DPEGPAGAALALGAA--GAFVLALGTWSTVAFQAAQEVLAGRTRRAV
+RVWLVHLASGTAAAVVGV---LAVGFLVR-
+>4_685
+MSGAGYEVFALLQVALLACLAAGGALGALVRRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGGGGDGQGL--VLVAAVSAVVSGFCLALGTWSTVAAEAADAVLARRWGTAA
+RLWAAHLGLGLVAVVVGWGAGLGLHAVLAG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000106.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>0_735
+MNASFPAGAAAATPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG
+WFRRFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM
+TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMG-GRVVASGSPRDVLT
+VENLDIAYGRGALHGPSTAVEDAADFLDDPAG--GRRH
+>1_474
+MNASFPAGAAATPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG
+WFRRFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM
+TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMG-GRVVASGPPRDVLT
+VENLDIAYGRGALHGPSTAVEDAADFLDDPAG--GRRH
+>2_2119
+MSRSAAVVPEAAPAPLAVAEHLELRHGDHLAVEASSFTLPAGCVVAVIGPNGSGKSTLLQ
+ALAGVLDPAAGRLEVRG---ESPSRHGRLTSFVMQSLQFPQGVPLTVRDVVTMGRYTTAG
+WFRRLGATDRAAVAAAMERVRVTDLADRHLDQLSGGQRQRVYVAQGLAQEHDVLMLDEPV
+TGLDIVSARTIDEIIHEQPERGVSVVYTTHDLDEAAAADHVVLMD-GRVVASGPPAQVLT
+AANLDAVYGRGALHAPLLV------HLDDPADCSPDRG
+>3_511
+MN---PAAPAPAIRLADVSAAYDRRRPVFTG---ADLVIDGPGLVRVHGRNGGGKSTLIE
+LVSGYLRPSDGQVRIGGLPAHDPRAHERRRVCRTEPALYPL-----------MDVHDHVV
+FASRWAGADPAEGLARAERYGLGPWMHAPAQTLSTGNRRRLWIVQCTVGAFDTVVLDEPF
+NGLDDESSAVLAAELAAW-ARTRCVVLICHLPPPGLAFDRVVRWPPGQAAADPAP-----
+-----------------------------PAD-PGVRP
+>3_2013
+MTRTVPTAPTPGAGVLAEARGLELRRAAHVAVAPSDLTLPAGVLVAVIGPNGSGKSTLLH
+ALAGTLEPAAGSLTVRG---ESPSRHARRTAFVMQTIPVPQGVPLTVRDVVRMGRYPRVG
+WFGRFGAADREAVDAAMERMSVTDLARRHLDELSGGQRQRVYVAQALAQEHDVLMLDEPL
+TGLDLVSARTIDRLLHEEPARGVSVVHTTHDLDEAAAADFVVLMS-GRVVAAGTPRQVLT
+EANLEAAYGHGVLHGPRLP------FLDDPVD--GVR-
+>4_699
+MNASFPAGAAAAPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG
+WFRRFRREDRDIVGAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM
+TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMS-GRVVASGPPRDVLT
+VENLDIAYGRGALHGPSTAVEDAAEFLDDPAG--GIRH

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000110.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>0_929
+MTEH------------S-AAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRS
+RTPMLAQWVSVLQPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQ
+DPVDLAFAVPPGREHVTWTALTPPRGGWTPVAEVADEELTEVATRGADAVWDALPENPGE
+ALVRKIRAQMWGPLLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFV
+LGRPAMAV--------------------
+>1_651
+MTEH------------SAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRS
+RTPMLAQWVSVLQPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQ
+DPVDLAFAVPPGREHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGE
+ALVRKVRAQMWGPLLGGEALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFV
+LGRPAMAV--------------------
+>2_1882
+MTEP------------S-AAPVLRFADERAVRDLEQFATRARRVSDTGMRLHVVPAAGPS
+RTPMLAQWVSVLQPAGLGDEVPVVLGLRTVPLATAEMAADLDAVVALGAVTERTARMRSR
+QPVDLDFSVPPGREQVTWTALTPPRSGWTPAAEVADEELADVAERGVAAVRETLPENPGE
+AMVRKVRAQMWGPLLGGDALGFPAGMAFGAHALGFLQPGGRARLSTAGPWTRLDTPGGFV
+LGRPAMAV--------------------
+>3_691
+MPAR------------------LILADAPPARDALTFAQRAAQAGAHGVRL---------
+------QAAAALTPRGPLDRTPTILVLRTL---RSDPELQCDVTVDTLTAT--------A
+DP--LTLALPETALAPAWTSVEPPQHGWRLIADVTSLTLMRSARAGIEAVAQALPDKPGD
+DVVRKIRGTVWGTPDTAL-ASLPQGVAFAAYVFGFLSRGNGATISTAGRWTRLTLPTGHV
+LLRGPVASGLTPIRRTRPRVSKSVTSIE
+>3_1830
+MPDQPSSRRDARDAARA-AVPVLRLTDERAVRDLDQFATRARRVADTGMRLHVVPEAGPR
+RTPMLAQWVSVLQPHGLGDGVPVVLGLRTVGLTSADAVEDLDAVVPLGAVTERTARMLGG
+TPVALDLPVPPGRERVTWTALTPPRAGWTVRAEVPDDELAEVAVKGAEAIRDALPQDPGE
+AMVRQVRAQMWGPRLGGE-IGFPAGMAFGAHALGFLRPGGRARLSTAGPWVRLDTPGGFV
+LGRSAVGV--------------------
+>4_875
+MTEH------------SAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRS
+RTPMLAQWVSVLQPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQ
+DPVDLAFAVPPGREHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGE
+ALVRKIRAQMWGPLLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDAPGGFV
+LGRPAMAV--------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000112.fa ADDED Viewed

	@@ -0,0 +1,49 @@

+>0_971
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV
+TAAFFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA
+AGEGLVRYDVEV-DGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAM
+QLAPGVAGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGT
+DTFTVDFHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAF
+RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR
+LGLTD
+>1_694
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV
+TAAFFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA
+AGEGLVRYDVEV-DGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAM
+QLAPGVAGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGT
+DTFTVDFHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAF
+RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR
+LGLTD
+>2_1840
+M-----------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------THLGDRPLVWDSAM
+QLAPGVEGAEIVHLVAAPTMENTYAEVVTEPAHGEVFAFRDSEHSELRAWYIPEEGFVGT
+---------------------------------------------------DTAAALAAF
+RGDEAAPAPEDEEE----------------------------------------------
+-----
+>2_1841
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGSFQAVDHENV
+TTAFFQTYDGYDPEDLTLTITPVAEDGTRLEGGQEVGFTALDVIDGGAVDVLETRRALGA
+AGEGLVRYDVVA-DGQMLNMGITLQADADLADDQGTAVHSVEA-----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------RR-
+-----
+>3_1727
+MFV--TRPSCAPRLAAAVLASGL-AAAALAAPASAEQAYDWTDDHGYPHGLFFGMDPESV
+DEATFQTFYGFDPADLTVTVSPSDAEGTPTGPAAAVPFTAVDVLDGGTIDVLETRRVLGE
+AGTGTVAYHVFSGDQKELDMALVVGPDADLADATGGALVAAPGPVRAVLGDMPLSWSADV
+VMAPGVRAMEVRYPVDPALFDDVHPMVMTEAAHGTVVTFRDREDLSVRTWYVPDAGFTGT
+DTFSLDLTSDHVAHLPTVTVHVGQELPAAAAGAPDAQDGVLGGMPLDVEDPAIAAMLQQM
+GALPPAP------EATVPETTVSAEQHTRPGKVQTGGEPIWWLASAAVLGAGALVAARRR
+PGMAG
+>4_914
+MSVIRTRRPSLRHLPVAVAAAGLVTTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV
+TTALFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA
+AGAGLVRYDVVA-DGQMLNMGITLQADTDLADDQGAAVHSVDGPQMAHLGDRPLIWDSAM
+QLAPGVAGAEIVHLVAAPTMESTYAEVVAEPAHGEVFAFRDSGHSELRAWYIPEEGFVGT
+DTFTVDFHSEHVAHVQTVTVHVGEEIPAAYDGFLDAEEGVLNGKPLDLTDPDTAAALAAF
+RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR
+LGLTD

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000115.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>0_989
+MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR
+AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE
+QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG
+GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------
+-----
+>1_713
+MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR
+AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE
+QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG
+GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------
+-----
+>2_176
+MS--EALSRIL--QVWPEIVVALGQTLTMLAVTIPLAVLLGTPLGIWLFTHAPGGLSPSP
+RLHRVVD-AAVSMLRSFPFLILLIAIIPVTRLIVGTTIGTAAVIVPLTVNAIPYFARFVE
+QNLAQLGPGPVEAARAMGATRGQIVRDVLLVDARPALVGSLTIMSVSFISYSAMAGLVGG
+GGIGDFAIRYGYYRYETPLMVVAILLMIGLVALLQFAGTRLSQRLDHRRPRTARRPRRRA
+LAPAG
+>2_1817
+MTWLETLTTNP--AITDALPEALVETLLMVAISGVATVLIGGLLGIVLHVTRPGGLNPMP
+ALYTVLSTVIVNITRSVPYAILMVALIPLTKWLVGTAIGPIAATVSLTIGTAPFFARLVE
+SALREIPSGTVDAAQVMGSTRGQVIRKVLLPEAMPGLIAATTTTLVTLVGYSAMAGLIGG
+GGLGRLAYNYGYQRFQTEVMVVTIVVIVILVQLIQWIGDLLIRRVDHR------------
+-----
+>3_1705
+MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWAFILGGILGLLVGLVLYTTRPGGIFANR
+AVYLVTN-FVVNLIRPIPFVILIAALQPLTIAVLGSGIGNTAVVFCMIWASTFGIARIVE
+QNLVSLDPGVIEAARAMGASRMRIVRTVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG
+GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------
+-----
+>4_933
+MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR
+AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE
+QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG
+GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------
+-----