One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.084811_2026-04-21.084811_BWoAyt/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/2026/04/21/peak-motifs.2026-04-21.084811_2026-04-21.084811_BWoAyt/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 3 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; vSAAGGAGhW
; Alignment reference
a 1 0 4 4 0 0 4 0 2 3
c 2 1 0 0 0 0 0 0 1 0
g 1 3 0 0 4 4 0 4 0 0
t 0 0 0 0 0 0 0 0 1 1
|
| oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |
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; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; vSAAGGAGhW
; cor=; Ncor=
a 1 0 4 4 0 0 4 0 2 3
c 2 1 0 0 0 0 0 0 1 0
g 1 3 0 0 4 4 0 4 0 0
t 0 0 0 0 0 0 0 0 1 1
|
| oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |
 |
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; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.574683; -CAAGGAGCA
; cor=; Ncor=
a 0 0 1 1 0 0 1 0 0 1
c 0 1 0 0 0 0 0 0 1 0
g 0 0 0 0 1 1 0 1 0 0
t 0 0 0 0 0 0 0 0 0 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5) |
 |
|
|
; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; GCCGCGTACTG
; Alignment reference
a 0 0 0 0 0 0 0 1 0 0 0
c 0 1 1 0 1 0 0 0 1 0 0
g 1 0 0 1 0 1 0 0 0 0 1
t 0 0 0 0 0 0 1 0 0 1 0
|
| oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5) |
|
|
|
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; GCCGCGTACTG
; cor=; Ncor=
a 0 0 0 0 0 0 0 1 0 0 0
c 0 1 1 0 1 0 0 0 1 0 0
g 1 0 0 1 0 1 0 0 0 0 1
t 0 0 0 0 0 0 1 0 0 1 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4) |
 |
|
|
; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; rsCCCGATCyT
; Alignment reference
a 1 0 0 0 0 0 2 0 0 0 0
c 0 1 2 2 2 0 0 0 2 1 0
g 1 1 0 0 0 2 0 0 0 0 0
t 0 0 0 0 0 0 0 2 0 1 2
|
| oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4) |
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; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; rsCCCGATCyT
; cor=; Ncor=
a 1 0 0 0 0 0 2 0 0 0 0
c 0 1 2 2 2 0 0 0 2 1 0
g 1 1 0 0 0 2 0 0 0 0 0
t 0 0 0 0 0 0 0 2 0 1 2
|
| oligos_6nt_mkv1_m4_rc_shift0 (oligos_6nt_mkv1_m4_rc) |
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; oligos_7nt_mkv1_m4 versus oligos_6nt_mkv1_m4_rc; m=2/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.798464; vSSCCGAKhn-
; cor=; Ncor=
a 1 0 0 0 0 0 4 0 1 1 0
c 2 3 3 4 4 0 0 0 2 1 0
g 1 1 1 0 0 4 0 1 0 1 0
t 0 0 0 0 0 0 0 3 1 1 0
|
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) |
 |
|
|
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; wbCAGCAsrw
; Alignment reference
a 1 0 0 3 0 0 3 0 1 1
c 0 1 3 0 0 3 0 1 0 0
g 0 1 0 0 3 0 0 2 2 0
t 2 1 0 0 0 0 0 0 0 2
|
| 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; wbCAGCAsrw
; cor=; Ncor=
a 1 0 0 3 0 0 3 0 1 1
c 0 1 3 0 0 3 0 1 0 0
g 0 1 0 0 3 0 0 2 2 0
t 2 1 0 0 0 0 0 0 0 2
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2) |
 |
|
|
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -hmGAGAGGAms
; Alignment reference
a 0 2 2 0 7 0 7 0 0 7 4 1
c 0 2 4 0 0 0 0 0 0 0 2 2
g 0 1 0 7 0 7 0 7 7 0 1 4
t 0 2 1 0 0 0 0 0 0 0 0 0
|
| oligos_6nt_mkv1_m2_shift1 (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=1; score= 1; -hmGAGAGGAms
; cor=; Ncor=
a 0 2 2 0 7 0 7 0 0 7 4 1
c 0 2 4 0 0 0 0 0 0 0 2 2
g 0 1 0 7 0 7 0 7 7 0 1 4
t 0 2 1 0 0 0 0 0 0 0 0 0
|
| oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |
 |
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; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=2/2; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.818946; hnMGAGAGGAAs
; cor=; Ncor=
a 2 1 1 0 4 0 4 0 0 4 4 0
c 1 1 3 0 0 0 0 0 0 0 0 2
g 0 1 0 4 0 4 0 4 4 0 0 2
t 1 1 0 0 0 0 0 0 0 0 0 0
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5) |
 |
|
|
; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; bsACRTAGrn
; Alignment reference
a 0 0 4 0 1 0 4 0 2 1
c 1 2 0 4 0 0 0 0 0 1
g 1 2 0 0 3 0 0 4 2 1
t 2 0 0 0 0 4 0 0 0 1
|
| oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5) |
|
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; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; bsACRTAGrn
; cor=; Ncor=
a 0 0 4 0 1 0 4 0 2 1
c 1 2 0 4 0 0 0 0 0 1
g 1 2 0 0 3 0 0 4 2 1
t 2 0 0 0 0 4 0 0 0 1
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |
|
|
|
; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -CAAGGAGCAGCA
; Alignment reference
a 0 0 1 1 0 0 1 0 0 1 0 0 1
c 0 1 0 0 0 0 0 0 1 0 0 1 0
g 0 0 0 0 1 1 0 1 0 0 1 0 0
t 0 0 0 0 0 0 0 0 0 0 0 0 0
|
| oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |
|
|
|
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -CAAGGAGCAGCA
; cor=; Ncor=
a 0 0 1 1 0 0 1 0 0 1 0 0 1
c 0 1 0 0 0 0 0 0 1 0 0 1 0
g 0 0 0 0 1 1 0 1 0 0 1 0 0
t 0 0 0 0 0 0 0 0 0 0 0 0 0
|
| oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |
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; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=2/2; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.574683; vSAAGGAGhW---
; cor=; Ncor=
a 1 0 4 4 0 0 4 0 2 3 0 0 0
c 2 1 0 0 0 0 0 0 1 0 0 0 0
g 1 3 0 0 4 4 0 4 0 0 0 0 0
t 0 0 0 0 0 0 0 0 1 1 0 0 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |
 |
|
|
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; hbCAGmTCAvs
; Alignment reference
a 1 0 0 3 0 2 0 0 3 1 0
c 1 1 3 0 0 1 0 3 0 1 2
g 0 1 0 0 3 0 0 0 0 1 1
t 1 1 0 0 0 0 3 0 0 0 0
|
| oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |
|
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; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; hbCAGmTCAvs
; cor=; Ncor=
a 1 0 0 3 0 2 0 0 3 1 0
c 1 1 3 0 0 1 0 3 0 1 2
g 0 1 0 0 3 0 0 0 0 1 1
t 1 1 0 0 0 0 3 0 0 0 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |
|
|
|
; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; hnMGAGAGGAAsm
; Alignment reference
a 2 1 1 0 4 0 4 0 0 4 4 0 2
c 1 1 3 0 0 0 0 0 0 0 0 2 2
g 0 1 0 4 0 4 0 4 4 0 0 2 0
t 1 1 0 0 0 0 0 0 0 0 0 0 0
|
| oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |
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; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; hnMGAGAGGAAsm
; cor=; Ncor=
a 2 1 1 0 4 0 4 0 0 4 4 0 2
c 1 1 3 0 0 0 0 0 0 0 0 2 2
g 0 1 0 4 0 4 0 4 4 0 0 2 0
t 1 1 0 0 0 0 0 0 0 0 0 0 0
|
| oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2) |
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; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.818946; -hmGAGAGGAms-
; cor=; Ncor=
a 0 2 2 0 7 0 7 0 0 7 4 1 0
c 0 2 4 0 0 0 0 0 0 0 2 2 0
g 0 1 0 7 0 7 0 7 7 0 1 4 0
t 0 2 1 0 0 0 0 0 0 0 0 0 0
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m4_shift1 (oligos_6nt_mkv1_m4) |
 |
|
|
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=1; ncol=11; -ndMTCGGSSb
; Alignment reference
a 0 1 1 3 0 0 0 0 0 0 0
c 0 1 0 1 0 4 0 0 1 1 1
g 0 1 2 0 0 0 4 4 3 3 2
t 0 1 1 0 4 0 0 0 0 0 1
|
| oligos_6nt_mkv1_m4_shift1 (oligos_6nt_mkv1_m4) |
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; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ndMTCGGSSb
; cor=; Ncor=
a 0 1 1 3 0 0 0 0 0 0 0
c 0 1 0 1 0 4 0 0 1 1 1
g 0 1 2 0 0 0 4 4 3 3 2
t 0 1 1 0 4 0 0 0 0 0 1
|
| oligos_7nt_mkv1_m4_rc_shift0 (oligos_7nt_mkv1_m4_rc) |
 |
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; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m4_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.798464; ArGATCGGGsy
; cor=; Ncor=
a 2 1 0 2 0 0 0 0 0 0 0
c 0 0 0 0 0 2 0 0 0 1 1
g 0 1 2 0 0 0 2 2 2 1 0
t 0 0 0 0 2 0 0 0 0 0 1
|