One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/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/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |
 |
|
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; oligos_6-8nt_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; rsGAGGTwTArvw
; Alignment reference
a 1 0 0 3 0 0 0 1 0 3 1 1 1
c 0 1 0 0 0 0 0 0 0 0 0 1 0
g 2 2 3 0 3 3 0 0 0 0 2 1 0
t 0 0 0 0 0 0 3 2 3 0 0 0 2
|
| oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |
|
|
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; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rsGAGGTwTArvw
; cor=; Ncor=
a 1 0 0 3 0 0 0 1 0 3 1 1 1
c 0 1 0 0 0 0 0 0 0 0 0 1 0
g 2 2 3 0 3 3 0 0 0 0 2 1 0
t 0 0 0 0 0 0 3 2 3 0 0 0 2
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |
 |
|
|
; oligos_6-8nt_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; rrGGAAGTAAss
; Alignment reference
a 1 1 0 0 2 2 0 0 2 2 0 0
c 0 0 0 0 0 0 0 0 0 0 1 1
g 1 1 2 2 0 0 2 0 0 0 1 1
t 0 0 0 0 0 0 0 2 0 0 0 0
|
| oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |
|
|
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; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; rrGGAAGTAAss
; cor=; Ncor=
a 1 1 0 0 2 2 0 0 2 2 0 0
c 0 0 0 0 0 0 0 0 0 0 1 1
g 1 1 2 2 0 0 2 0 0 0 1 1
t 0 0 0 0 0 0 0 2 0 0 0 0
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |
 |
|
|
; oligos_6-8nt_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; ycCCTACCym
; Alignment reference
a 1 1 0 0 0 6 0 0 1 2
c 2 3 6 6 0 0 6 6 3 4
g 1 1 0 0 0 0 0 0 0 0
t 2 1 0 0 6 0 0 0 2 0
|
| oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |
|
|
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; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ycCCTACCym
; cor=; Ncor=
a 1 1 0 0 0 6 0 0 1 2
c 2 3 6 6 0 0 6 6 3 4
g 1 1 0 0 0 0 0 0 0 0
t 2 1 0 0 6 0 0 0 2 0
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |
 |
|
|
; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; swATTAGAGAsm
; Alignment reference
a 0 1 2 0 0 2 0 2 0 2 0 1
c 1 0 0 0 0 0 0 0 0 0 1 1
g 1 0 0 0 0 0 2 0 2 0 1 0
t 0 1 0 2 2 0 0 0 0 0 0 0
|
| oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |
|
|
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; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; swATTAGAGAsm
; cor=; Ncor=
a 0 1 2 0 0 2 0 2 0 2 0 1
c 1 0 0 0 0 0 0 0 0 0 1 1
g 1 0 0 0 0 0 2 0 2 0 1 0
t 0 1 0 2 2 0 0 0 0 0 0 0
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |
 |
|
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; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; krGCGGGGACgs
; Alignment reference
a 1 2 0 0 0 0 0 0 5 1 1 0
c 1 1 0 6 0 0 0 1 0 5 1 2
g 2 2 6 0 6 6 6 5 1 0 4 3
t 2 1 0 0 0 0 0 0 0 0 0 1
|
| oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |
|
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; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; krGCGGGGACgs
; cor=; Ncor=
a 1 2 0 0 0 0 0 0 5 1 1 0
c 1 1 0 6 0 0 0 1 0 5 1 2
g 2 2 6 0 6 6 6 5 1 0 4 3
t 2 1 0 0 0 0 0 0 0 0 0 1
|