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_m4/peak-motifs_oligos_6nt_mkv3_m4.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_m4/peak-motifs_oligos_6nt_mkv3_m4_vs_db_Homer
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4) |
 |
|
|
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ssGCGCCGCss
; Alignment reference
a 41 47 7 8 8 8 9 13 13 35 35
c 132 113 34 279 46 250 253 21 255 141 114
g 93 100 254 18 243 42 39 261 31 102 109
t 42 48 13 3 11 8 7 13 9 30 50
|
| homer_266_Sp1_shift1 (homer_266_Sp1) |
 |
|
|
; oligos_6nt_mkv3_m4 versus homer_266_Sp1; m=1/1; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.611456; -gGCCCCGCCC
; cor=; Ncor=
a 0 18.1 5 1.3 3.3 4.9 0.1 2.5 0.1 0.1 0.1
c 0 21.8 0.1 87 81.5 94.9 99.7 0.1 99.7 99.7 88.1
g 0 54.1 94.8 6.1 0.1 0.1 0.1 97.3 0.1 0.1 0.1
t 0 6 0.1 5.6 15.1 0.1 0.1 0.1 0.1 0.1 11.7
|