One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/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.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
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=10; shift=0; ncol=10; wrTAcATAya
; Alignment reference
a 179 218 6 668 62 480 0 663 136 218
c 172 150 4 24 473 77 2 22 198 166
g 161 193 16 0 67 95 19 3 151 155
t 186 137 672 6 96 46 677 10 213 159
|
| oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |
|
|
|
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wrTAcATAya
; cor=; Ncor=
a 179 218 6 668 62 480 0 663 136 218
c 172 150 4 24 473 77 2 22 198 166
g 161 193 16 0 67 95 19 3 151 155
t 186 137 672 6 96 46 677 10 213 159
|
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=13; shift=0; ncol=13; ccCCCtCCCCycc
; Alignment reference
a 180 140 33 14 25 49 17 11 25 84 127 130 152
c 412 461 868 940 902 227 895 916 900 709 379 428 426
g 222 218 54 20 27 77 39 46 37 105 148 238 246
t 175 170 34 15 35 636 38 16 27 91 335 193 165
|
| oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |
|
|
|
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ccCCCtCCCCycc
; cor=; Ncor=
a 180 140 33 14 25 49 17 11 25 84 127 130 152
c 412 461 868 940 902 227 895 916 900 709 379 428 426
g 222 218 54 20 27 77 39 46 37 105 148 238 246
t 175 170 34 15 35 636 38 16 27 91 335 193 165
|
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) |
 |
|
|
; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCCCATGCAss
; Alignment reference
a 119 90 15 33 18 556 32 8 12 546 135 138
c 180 187 544 521 568 24 16 15 599 26 167 198
g 199 230 39 45 27 19 18 591 12 29 198 180
t 130 121 30 29 15 29 562 14 5 27 128 112
|
| oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |
|
|
|
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCCCATGCAss
; cor=; Ncor=
a 119 90 15 33 18 556 32 8 12 546 135 138
c 180 187 544 521 568 24 16 15 599 26 167 198
g 199 230 39 45 27 19 18 591 12 29 198 180
t 130 121 30 29 15 29 562 14 5 27 128 112
|
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) |
 |
|
|
; oligos_6-8nt_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; yrTACAGTAtyw
; Alignment reference
a 74 95 8 311 15 253 14 4 303 46 77 86
c 87 75 10 5 292 25 13 14 16 49 85 72
g 82 90 12 15 13 25 294 5 10 46 78 81
t 92 75 305 4 15 32 14 312 6 194 95 96
|
| oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |
|
|
|
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; yrTACAGTAtyw
; cor=; Ncor=
a 74 95 8 311 15 253 14 4 303 46 77 86
c 87 75 10 5 292 25 13 14 16 49 85 72
g 82 90 12 15 13 25 294 5 10 46 78 81
t 92 75 305 4 15 32 14 312 6 194 95 96
|
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=11; shift=0; ncol=11; gcCAAAATGgm
; Alignment reference
a 161 157 46 553 573 579 583 8 32 160 162
c 159 189 521 27 12 21 23 24 35 157 171
g 188 151 51 39 33 23 24 20 556 182 153
t 137 148 27 26 27 22 15 593 22 146 159
|
| oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |
|
|
|
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; gcCAAAATGgm
; cor=; Ncor=
a 161 157 46 553 573 579 583 8 32 160 162
c 159 189 521 27 12 21 23 24 35 157 171
g 188 151 51 39 33 23 24 20 556 182 153
t 137 148 27 26 27 22 15 593 22 146 159
|