One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/Homer/Homer_motifs.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_vs_db_Homer
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift3 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5) |
 |
|
|
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=3; ncol=13; ---svCGaGCGss
; Alignment reference
a 0 0 0 55 62 14 11 160 7 9 11 52 54
c 0 0 0 66 69 208 13 26 5 216 11 78 73
g 0 0 0 81 70 8 219 45 233 13 216 72 77
t 0 0 0 45 46 17 4 16 2 9 9 45 43
|
| homer_326_ZNF519_shift0 (homer_326_ZNF519) |
 |
|
|
; oligos_6nt_mkv3_m5 versus homer_326_ZNF519; m=1/1; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.482002; GAGsCCGAGC---
; cor=; Ncor=
a 0.45 443.67 0.45 8.9 4.89 9.35 0.45 424.97 0.45 0.45 0 0 0
c 0.45 0.45 0.45 214.94 432.99 411.62 29.37 11.12 0.45 432.09 0 0 0
g 443.67 0.45 443.67 150.86 4.45 0.45 414.74 7.12 441.88 0.45 0 0 0
t 0.45 0.45 0.45 70.31 2.67 23.59 0.45 1.78 2.23 12.02 0 0 0
|