One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.091816_2025-06-19.091816_x3rpdD/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.2025-06-19.091816_2025-06-19.091816_x3rpdD/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=13; shift=0; ncol=13; cssCCGCCGCCss
; Alignment reference
a 32 21 31 5 5 5 2 2 7 7 10 35 32
c 59 60 55 141 142 9 142 141 14 137 136 55 51
g 35 43 45 5 4 141 9 7 136 6 4 48 43
t 31 33 26 6 6 2 4 7 0 7 7 19 31
|
| oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |
|
|
|
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; cssCCGCCGCCss
; cor=; Ncor=
a 32 21 31 5 5 5 2 2 7 7 10 35 32
c 59 60 55 141 142 9 142 141 14 137 136 55 51
g 35 43 45 5 4 141 9 7 136 6 4 48 43
t 31 33 26 6 6 2 4 7 0 7 7 19 31
|
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=11; shift=0; ncol=11; ssCCAACCcss
; Alignment reference
a 24 29 3 1 113 122 0 0 13 15 25
c 38 42 116 113 1 1 120 119 76 45 33
g 32 34 3 8 9 0 1 4 20 45 42
t 31 20 3 3 2 2 4 2 16 20 25
|
| oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |
|
|
|
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCCAACCcss
; cor=; Ncor=
a 24 29 3 1 113 122 0 0 13 15 25
c 38 42 116 113 1 1 120 119 76 45 33
g 32 34 3 8 9 0 1 4 20 45 42
t 31 20 3 3 2 2 4 2 16 20 25
|
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=14; shift=0; ncol=14; cscCCCATTCCGcs
; Alignment reference
a 19 17 8 5 2 2 63 1 1 0 1 2 9 16
c 27 27 47 56 71 68 9 3 8 78 65 5 40 23
g 14 24 14 13 4 6 3 2 5 1 7 69 13 25
t 19 11 10 5 2 3 4 73 65 0 6 3 17 15
|
| oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |
|
|
|
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; cscCCCATTCCGcs
; cor=; Ncor=
a 19 17 8 5 2 2 63 1 1 0 1 2 9 16
c 27 27 47 56 71 68 9 3 8 78 65 5 40 23
g 14 24 14 13 4 6 3 2 5 1 7 69 13 25
t 19 11 10 5 2 3 4 73 65 0 6 3 17 15
|
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=12; shift=0; ncol=12; csCCACGCCCcc
; Alignment reference
a 26 17 1 1 123 9 9 3 6 4 36 30
c 62 67 141 152 14 124 4 138 142 146 65 56
g 38 40 11 2 9 13 136 13 4 2 31 31
t 29 31 2 0 9 9 6 1 3 3 23 38
|
| oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |
|
|
|
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; csCCACGCCCcc
; cor=; Ncor=
a 26 17 1 1 123 9 9 3 6 4 36 30
c 62 67 141 152 14 124 4 138 142 146 65 56
g 38 40 11 2 9 13 136 13 4 2 31 31
t 29 31 2 0 9 9 6 1 3 3 23 38
|
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=10; shift=0; ncol=10; skGCACGCvs
; Alignment reference
a 27 25 0 0 125 0 0 0 35 22
c 41 25 0 125 0 125 0 125 35 36
g 32 36 125 0 0 0 125 0 34 38
t 25 39 0 0 0 0 0 0 21 29
|
| oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |
|
|
|
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; skGCACGCvs
; cor=; Ncor=
a 27 25 0 0 125 0 0 0 35 22
c 41 25 0 125 0 125 0 125 35 36
g 32 36 125 0 0 0 125 0 34 38
t 25 39 0 0 0 0 0 0 21 29
|