updating info on mindel annotations

README.md

@@ -35,7 +35,14 @@ You can find these by clicking on the [files and versions](https://huggingface.c
 - **mindel_promoters** (csv): The promoters used by the Barkai lab to evaluate the
   overlap between perturbation and binding in the Mahendrawada 2025 set in
   [this preprint](https://www.biorxiv.org/content/10.1101/2025.10.12.681120v1.abstract).
-  See scripts/create_promoter_bed_from_mindel.R.
+  See scripts/create_promoter_bed_from_mindel.R. The column `in_mahendrawada_features` is
+  `TRUE` if the locus_tag is in the feature set used by Mahendrawada 2025, which is
+  only protein coding genes which are not labeled dubious. The column `promoter_exact_aligns`
+  provides a tally of how many times the promoter sequence aligns exactly from end to end
+  with no gaps in the genome. Most align only once, which is what we would expect for a
+  700+ bp sequence. However, there are 12 loci with up to 4 exact alignments. I didn't examine
+  these beyond confirming the multiple alignments -- I suspect that it is due to repeat regions.
+  It is noted because it is surprising that such long sequences had multiple perfect alignments.
 - **gal_tss_sgd-5-1_verified_orf** (bed): Genomic coordinates of Transcription Start Sites
   (TSS) for verified ORFs under Galactose culture conditions. These are derived from
   annotation version S288C-R64-5-1. See scripts/create_tss_files.R