One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.083405_2026-04-21.083405_7S6poV/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.2026-04-21.083405_2026-04-21.083405_7S6poV/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5) |
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; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; vbwCTTTCksy
; Alignment reference
a 2 0 4 0 0 0 0 0 0 0 0
c 2 2 0 6 0 0 0 6 0 4 2
g 2 2 0 0 0 0 0 0 2 2 0
t 0 2 2 0 6 6 6 0 4 0 4
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| oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5) |
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; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; vbwCTTTCksy
; cor=; Ncor=
a 2 0 4 0 0 0 0 0 0 0 0
c 2 2 0 6 0 0 0 6 0 4 2
g 2 2 0 0 0 0 0 0 2 2 0
t 0 2 2 0 6 6 6 0 4 0 4
|
| oligos_7nt_mkv1_m3_rc_shift3 (oligos_7nt_mkv1_m3_rc) |
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; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m3_rc; m=2/2; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.507563; ---CyTTCTCT
; cor=; Ncor=
a 0 0 0 0 0 0 0 0 0 0 0
c 0 0 0 4 2 0 0 4 0 4 0
g 0 0 0 0 0 0 0 0 0 0 0
t 0 0 0 0 2 4 4 0 4 0 4
|
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=13; shift=0; ncol=13; CCGGAAGGCACTC
; Alignment reference
a 0 0 0 0 2 2 0 0 0 2 0 0 0
c 2 2 0 0 0 0 0 0 2 0 2 0 2
g 0 0 2 2 0 0 2 2 0 0 0 0 0
t 0 0 0 0 0 0 0 0 0 0 0 2 0
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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=13; w=0; offset=0; strand=D; shift=0; score= 1; CCGGAAGGCACTC
; cor=; Ncor=
a 0 0 0 0 2 2 0 0 0 2 0 0 0
c 2 2 0 0 0 0 0 0 2 0 2 0 2
g 0 0 2 2 0 0 2 2 0 0 0 0 0
t 0 0 0 0 0 0 0 0 0 0 0 2 0
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift0 ; 2 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=10; shift=0; ncol=10; CCCGCTACCG
; Alignment reference
a 0 0 0 0 0 0 2 0 0 0
c 2 2 2 0 2 0 0 2 2 0
g 0 0 0 2 0 0 0 0 0 2
t 0 0 0 0 0 2 0 0 0 0
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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=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; CCCGCTACCG
; cor=; Ncor=
a 0 0 0 0 0 0 2 0 0 0
c 2 2 2 0 2 0 0 2 2 0
g 0 0 0 2 0 0 0 0 0 2
t 0 0 0 0 0 2 0 0 0 0
|
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=14; shift=0; ncol=14; GAGGAGTGAGATTA
; Alignment reference
a 0 3 0 0 3 0 0 0 3 0 3 0 0 3
c 0 0 0 0 0 0 0 0 0 0 0 0 0 0
g 3 0 3 3 0 3 0 3 0 3 0 0 0 0
t 0 0 0 0 0 0 3 0 0 0 0 3 3 0
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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=14; w=0; offset=0; strand=D; shift=0; score= 1; GAGGAGTGAGATTA
; cor=; Ncor=
a 0 3 0 0 3 0 0 0 3 0 3 0 0 3
c 0 0 0 0 0 0 0 0 0 0 0 0 0 0
g 3 0 3 3 0 3 0 3 0 3 0 0 0 0
t 0 0 0 0 0 0 3 0 0 0 0 3 3 0
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift2 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |
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; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --yyGAACCGAks
; Alignment reference
a 0 0 0 0 0 6 6 0 0 0 6 0 0
c 0 0 3 3 0 0 0 6 6 0 0 0 3
g 0 0 0 0 6 0 0 0 0 6 0 3 3
t 0 0 3 3 0 0 0 0 0 0 0 3 0
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| oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |
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; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --yyGAACCGAks
; cor=; Ncor=
a 0 0 0 0 0 6 6 0 0 0 6 0 0
c 0 0 3 3 0 0 0 6 6 0 0 0 3
g 0 0 0 0 6 0 0 0 0 6 0 3 3
t 0 0 3 3 0 0 0 0 0 0 0 3 0
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| oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |
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; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/2; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.435194; CGCCGAACCGATC
; cor=; Ncor=
a 0 0 0 0 0 3 3 0 0 0 3 0 0
c 3 0 3 3 0 0 0 3 3 0 0 0 3
g 0 3 0 0 3 0 0 0 0 3 0 0 0
t 0 0 0 0 0 0 0 0 0 0 0 3 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 3 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; msGAGAGAArG
; Alignment reference
a 2 0 0 4 0 4 0 4 4 2 0
c 2 2 0 0 0 0 0 0 0 0 0
g 0 2 4 0 4 0 4 0 0 2 4
t 0 0 0 0 0 0 0 0 0 0 0
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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=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; msGAGAGAArG
; cor=; Ncor=
a 2 0 0 4 0 4 0 4 4 2 0
c 2 2 0 0 0 0 0 0 0 0 0
g 0 2 4 0 4 0 4 0 0 2 4
t 0 0 0 0 0 0 0 0 0 0 0
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| oligos_6nt_mkv1_m5_rc_shift3 (oligos_6nt_mkv1_m5_rc) |
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; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m5_rc; m=2/2; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.507563; ---rsmGAAAG
; cor=; Ncor=
a 0 0 0 4 0 4 0 6 6 6 0
c 0 0 0 0 2 2 0 0 0 0 0
g 0 0 0 2 4 0 6 0 0 0 6
t 0 0 0 0 0 0 0 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) |
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; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=22; shift=0; ncol=22; CGCCGAACCGATCCGGGACGGC
; Alignment reference
a 0 0 0 0 0 3 3 0 0 0 3 0 0 0 0 0 0 3 0 0 0 0
c 3 0 3 3 0 0 0 3 3 0 0 0 3 3 0 0 0 0 3 0 0 3
g 0 3 0 0 3 0 0 0 0 3 0 0 0 0 3 3 3 0 0 3 3 0
t 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0
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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=1/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; CGCCGAACCGATCCGGGACGGC
; cor=; Ncor=
a 0 0 0 0 0 3 3 0 0 0 3 0 0 0 0 0 0 3 0 0 0 0
c 3 0 3 3 0 0 0 3 3 0 0 0 3 3 0 0 0 0 3 0 0 3
g 0 3 0 0 3 0 0 0 0 3 0 0 0 0 3 3 3 0 0 3 3 0
t 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0
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| oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |
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; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=2/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.435194; --yyGAACCGAks---------
; cor=; Ncor=
a 0 0 0 0 0 6 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0
c 0 0 3 3 0 0 0 6 6 0 0 0 3 0 0 0 0 0 0 0 0 0
g 0 0 0 0 6 0 0 0 0 6 0 3 3 0 0 0 0 0 0 0 0 0
t 0 0 3 3 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0
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