One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.091929_2025-06-19.091929_ZGCM7J/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.2025-06-19.091929_2025-06-19.091929_ZGCM7J/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
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) |
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; oligos_6-8nt_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; bscCCCATGCAbs
; Alignment reference
a 12 19 9 2 2 2 95 3 3 3 86 23 17
c 32 26 67 90 89 91 3 3 6 92 7 26 35
g 30 41 12 1 3 3 1 1 87 3 7 25 32
t 26 14 12 7 6 4 1 93 4 2 0 26 16
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| 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=13; w=0; offset=0; strand=D; shift=0; score= 1; bscCCCATGCAbs
; cor=; Ncor=
a 12 19 9 2 2 2 95 3 3 3 86 23 17
c 32 26 67 90 89 91 3 3 6 92 7 26 35
g 30 41 12 1 3 3 1 1 87 3 7 25 32
t 26 14 12 7 6 4 1 93 4 2 0 26 16
|
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) |
 |
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; oligos_6-8nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; ycgGCACGCCCsg
; Alignment reference
a 26 26 13 2 0 116 3 1 3 2 10 22 31
c 39 52 27 7 117 7 116 2 119 111 91 43 31
g 31 25 71 113 7 3 3 122 4 10 21 34 36
t 32 25 17 6 4 2 6 3 2 5 6 29 30
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| 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=13; w=0; offset=0; strand=D; shift=0; score= 1; ycgGCACGCCCsg
; cor=; Ncor=
a 26 26 13 2 0 116 3 1 3 2 10 22 31
c 39 52 27 7 117 7 116 2 119 111 91 43 31
g 31 25 71 113 7 3 3 122 4 10 21 34 36
t 32 25 17 6 4 2 6 3 2 5 6 29 30
|
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; ssCCCCGCCCcs
; Alignment reference
a 58 58 11 14 14 13 15 6 7 7 61 48
c 110 114 282 280 281 275 42 292 286 291 121 118
g 91 94 14 15 11 9 244 11 10 14 58 95
t 56 49 8 6 9 18 14 6 12 3 75 54
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| 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; ssCCCCGCCCcs
; cor=; Ncor=
a 58 58 11 14 14 13 15 6 7 7 61 48
c 110 114 282 280 281 275 42 292 286 291 121 118
g 91 94 14 15 11 9 244 11 10 14 58 95
t 56 49 8 6 9 18 14 6 12 3 75 54
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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) |
 |
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; oligos_6-8nt_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; yvTACCGTAss
; Alignment reference
a 28 43 5 137 0 9 3 7 133 29 35
c 52 40 8 3 147 124 7 8 7 51 43
g 36 42 5 11 5 15 142 7 12 41 45
t 41 32 139 6 5 9 5 135 5 36 34
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| 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=11; w=0; offset=0; strand=D; shift=0; score= 1; yvTACCGTAss
; cor=; Ncor=
a 28 43 5 137 0 9 3 7 133 29 35
c 52 40 8 3 147 124 7 8 7 51 43
g 36 42 5 11 5 15 142 7 12 41 45
t 41 32 139 6 5 9 5 135 5 36 34
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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; ssCCCATCGCvs
; Alignment reference
a 22 20 3 9 7 123 3 1 6 5 37 29
c 46 45 130 132 137 4 6 137 5 140 43 54
g 50 55 9 4 3 12 19 6 135 2 44 40
t 30 28 6 3 1 9 120 4 2 1 24 25
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| 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; ssCCCATCGCvs
; cor=; Ncor=
a 22 20 3 9 7 123 3 1 6 5 37 29
c 46 45 130 132 137 4 6 137 5 140 43 54
g 50 55 9 4 3 12 19 6 135 2 44 40
t 30 28 6 3 1 9 120 4 2 1 24 25
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