One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/18/peak-motifs.2026-03-18.171158_2026-03-18.171158_kZmdaJ/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/2026/03/18/peak-motifs.2026-03-18.171158_2026-03-18.171158_kZmdaJ/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |
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; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; wvAAGCTAsg
; Alignment reference
a 4 4 15 15 0 0 0 15 2 2
c 2 5 0 0 0 14 0 0 4 2
g 2 4 0 0 15 0 1 0 6 8
t 7 2 0 0 0 1 14 0 3 3
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| oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |
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; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wvAAGCTAsg
; cor=; Ncor=
a 4 4 15 15 0 0 0 15 2 2
c 2 5 0 0 0 14 0 0 4 2
g 2 4 0 0 15 0 1 0 6 8
t 7 2 0 0 0 1 14 0 3 3
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2) |
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; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; cGCSGCsGCsg
; Alignment reference
a 1 1 0 0 0 0 0 0 0 4 2
c 12 2 15 13 1 16 12 1 18 7 3
g 4 14 2 5 17 1 5 16 0 6 12
t 1 1 1 0 0 1 1 1 0 1 1
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| oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2) |
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; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; cGCSGCsGCsg
; cor=; Ncor=
a 1 1 0 0 0 0 0 0 0 4 2
c 12 2 15 13 1 16 12 1 18 7 3
g 4 14 2 5 17 1 5 16 0 6 12
t 1 1 1 0 0 1 1 1 0 1 1
|
| oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |
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; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.834902; CgCCGCCGCCg
; cor=; Ncor=
a 2 3 0 0 1 0 2 1 0 2 3
c 13 1 12 15 1 14 13 1 14 12 2
g 0 10 3 0 11 0 0 12 0 0 8
t 0 1 0 0 2 1 0 1 1 1 2
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |
 |
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; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; yrGTGTAAha
; Alignment reference
a 1 2 0 0 0 0 7 7 3 4
c 2 1 0 0 0 0 0 0 2 1
g 1 3 7 0 6 0 0 0 0 1
t 3 1 0 7 1 7 0 0 2 1
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| oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |
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; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; yrGTGTAAha
; cor=; Ncor=
a 1 2 0 0 0 0 7 7 3 4
c 2 1 0 0 0 0 0 0 2 1
g 1 3 7 0 6 0 0 0 0 1
t 3 1 0 7 1 7 0 0 2 1
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |
 |
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; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; drAAGATAGma
; Alignment reference
a 6 7 14 14 1 14 0 14 1 7 10
c 0 1 1 0 0 0 0 1 0 4 3
g 5 4 0 1 12 0 0 0 14 1 1
t 4 3 0 0 2 1 15 0 0 3 1
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| oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |
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; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; drAAGATAGma
; cor=; Ncor=
a 6 7 14 14 1 14 0 14 1 7 10
c 0 1 1 0 0 0 0 1 0 4 3
g 5 4 0 1 12 0 0 0 14 1 1
t 4 3 0 0 2 1 15 0 0 3 1
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4) |
 |
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; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; awTCCAGGAww
; Alignment reference
a 11 6 0 1 0 16 0 0 15 7 5
c 2 1 0 14 16 0 0 0 1 2 3
g 4 4 0 1 0 0 18 18 2 3 3
t 1 7 18 2 2 2 0 0 0 6 7
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| oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4) |
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; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; awTCCAGGAww
; cor=; Ncor=
a 11 6 0 1 0 16 0 0 15 7 5
c 2 1 0 14 16 0 0 0 1 2 3
g 4 4 0 1 0 0 18 18 2 3 3
t 1 7 18 2 2 2 0 0 0 6 7
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |
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; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; CgCCGCCGCCgC
; Alignment reference
a 2 3 0 0 1 0 2 1 0 2 3 0
c 13 1 12 15 1 14 13 1 14 12 2 11
g 0 10 3 0 11 0 0 12 0 0 8 2
t 0 1 0 0 2 1 0 1 1 1 2 2
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| oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |
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; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; CgCCGCCGCCgC
; cor=; Ncor=
a 2 3 0 0 1 0 2 1 0 2 3 0
c 13 1 12 15 1 14 13 1 14 12 2 11
g 0 10 3 0 11 0 0 12 0 0 8 2
t 0 1 0 0 2 1 0 1 1 1 2 2
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| oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2) |
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; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.834902; cGCSGCsGCsg-
; cor=; Ncor=
a 1 1 0 0 0 0 0 0 0 4 2 0
c 12 2 15 13 1 16 12 1 18 7 3 0
g 4 14 2 5 17 1 5 16 0 6 12 0
t 1 1 1 0 0 1 1 1 0 1 1 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |
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; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; maCACAGGCwc
; Alignment reference
a 4 6 0 12 1 10 0 2 0 4 1
c 7 2 12 0 11 0 0 0 12 1 7
g 1 2 0 0 0 0 12 10 0 2 2
t 0 2 0 0 0 2 0 0 0 5 2
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| oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |
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; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; maCACAGGCwc
; cor=; Ncor=
a 4 6 0 12 1 10 0 2 0 4 1
c 7 2 12 0 11 0 0 0 12 1 7
g 1 2 0 0 0 0 12 10 0 2 2
t 0 2 0 0 0 2 0 0 0 5 2
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