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_m1/peak-motifs_oligos_6nt_mkv3_m1.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_m1/peak-motifs_oligos_6nt_mkv3_m1_vs_db_Homer
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1) |
 |
|
|
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -ccgCCTCCCmm
; Alignment reference
a 0 62 100 37 6 5 11 12 8 4 131 107
c 0 190 142 66 402 397 7 386 380 375 117 133
g 0 76 90 261 2 8 32 11 15 21 83 101
t 0 89 85 53 7 7 367 8 14 17 86 76
|
| homer_317_Znf263_shift0 (homer_317_Znf263) |
 |
|
|
; oligos_6nt_mkv3_m1 versus homer_317_Znf263; m=1/2; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score= 0.5594; crsTsCTCCc--
; cor=; Ncor=
a 15.2 33.3 0.5 0.1 0.1 0.1 0.1 0.1 0.1 13.8 0 0
c 41.3 24 33.4 0.1 51.2 99.7 0.1 99.7 99.7 65.8 0 0
g 24.2 30.9 66 0.1 48.6 0.1 0.1 0.1 0.1 0.2 0 0
t 19.3 11.8 0.1 99.7 0.1 0.1 99.7 0.1 0.1 20.3 0 0
|
| homer_63_Egr2_rc_shift3 (homer_63_Egr2_rc) |
 |
|
|
; oligos_6nt_mkv3_m1 versus homer_63_Egr2_rc; m=2/2; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.45297; ---cmCrCCCAC
; cor=; Ncor=
a 0 0 0 20.4 32.9 1.4 25.3 0.1 0.1 0.1 86.1 0.1
c 0 0 0 35.7 51.3 95.3 0.1 99.7 99.7 94.3 13.7 99.7
g 0 0 0 19.2 6.6 0.1 58.7 0.1 0.1 0.1 0.1 0.1
t 0 0 0 24.8 9.2 3.2 15.9 0.1 0.1 5.5 0.1 0.1
|