One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.092836_2025-06-19.092836_d6nk31/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.2025-06-19.092836_2025-06-19.092836_d6nk31/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 3 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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|
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; oligos_6-8nt_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; bsCCCATGCAvmsvc
; Alignment reference
a 13 13 3 5 2 74 3 2 1 70 28 24 15 22 10
c 26 28 70 71 77 3 1 6 78 5 24 22 25 23 37
g 22 24 3 3 3 1 1 74 1 6 22 18 24 23 19
t 21 17 6 3 0 4 77 0 2 1 8 18 18 14 16
|
| oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |
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; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; bsCCCATGCAvmsvc
; cor=; Ncor=
a 13 13 3 5 2 74 3 2 1 70 28 24 15 22 10
c 26 28 70 71 77 3 1 6 78 5 24 22 25 23 37
g 22 24 3 3 3 1 1 74 1 6 22 18 24 23 19
t 21 17 6 3 0 4 77 0 2 1 8 18 18 14 16
|
| oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |
 |
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; oligos_6-8nt_m3 versus oligos_6-8nt_m1; m=2/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.843563; ssCCCATGCAAks--
; cor=; Ncor=
a 8 8 1 4 2 43 0 2 0 42 32 11 10 0 0
c 12 19 42 40 39 0 0 5 42 2 4 9 14 0 0
g 15 12 1 1 3 0 1 38 0 1 8 12 13 0 0
t 10 6 1 0 1 2 44 0 3 0 1 13 8 0 0
|
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=12; shift=0; ncol=12; msAACCTGCCrs
; Alignment reference
a 15 11 40 42 1 3 1 0 1 3 15 7
c 15 17 4 2 44 44 2 3 43 40 11 16
g 6 12 1 3 2 0 2 44 3 2 14 13
t 11 7 2 0 0 0 42 0 0 2 7 11
|
| 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=12; w=0; offset=0; strand=D; shift=0; score= 1; msAACCTGCCrs
; cor=; Ncor=
a 15 11 40 42 1 3 1 0 1 3 15 7
c 15 17 4 2 44 44 2 3 43 40 11 16
g 6 12 1 3 2 0 2 44 3 2 14 13
t 11 7 2 0 0 0 42 0 0 2 7 11
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 3 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=13; shift=0; ncol=13; ssCCCATGCAAks
; Alignment reference
a 8 8 1 4 2 43 0 2 0 42 32 11 10
c 12 19 42 40 39 0 0 5 42 2 4 9 14
g 15 12 1 1 3 0 1 38 0 1 8 12 13
t 10 6 1 0 1 2 44 0 3 0 1 13 8
|
| oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |
|
|
|
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ssCCCATGCAAks
; cor=; Ncor=
a 8 8 1 4 2 43 0 2 0 42 32 11 10
c 12 19 42 40 39 0 0 5 42 2 4 9 14
g 15 12 1 1 3 0 1 38 0 1 8 12 13
t 10 6 1 0 1 2 44 0 3 0 1 13 8
|
| oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |
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; oligos_6-8nt_m1 versus oligos_6-8nt_m3; m=2/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.843563; bsCCCATGCAvms
; cor=; Ncor=
a 13 13 3 5 2 74 3 2 1 70 28 24 15
c 26 28 70 71 77 3 1 6 78 5 24 22 25
g 22 24 3 3 3 1 1 74 1 6 22 18 24
t 21 17 6 3 0 4 77 0 2 1 8 18 18
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