One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.092718_2025-06-19.092718_Z1kkIg/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.2025-06-19.092718_2025-06-19.092718_Z1kkIg/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
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=10; shift=0; ncol=10; gsCCACGGcy
; Alignment reference
a 5 5 0 0 45 0 0 0 8 10
c 11 15 45 45 0 45 0 0 19 12
g 18 16 0 0 0 0 45 45 10 10
t 11 9 0 0 0 0 0 0 8 13
|
| 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=10; w=0; offset=0; strand=D; shift=0; score= 1; gsCCACGGcy
; cor=; Ncor=
a 5 5 0 0 45 0 0 0 8 10
c 11 15 45 45 0 45 0 0 19 12
g 18 16 0 0 0 0 45 45 10 10
t 11 9 0 0 0 0 0 0 8 13
|
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=10; shift=0; ncol=10; ysCGTGCCmy
; Alignment reference
a 12 6 0 0 0 0 0 0 14 10
c 17 21 55 0 0 0 55 55 15 18
g 11 18 0 55 0 55 0 0 13 13
t 15 10 0 0 55 0 0 0 13 14
|
| 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=10; w=0; offset=0; strand=D; shift=0; score= 1; ysCGTGCCmy
; cor=; Ncor=
a 12 6 0 0 0 0 0 0 14 10
c 17 21 55 0 0 0 55 55 15 18
g 11 18 0 55 0 55 0 0 13 13
t 15 10 0 0 55 0 0 0 13 14
|
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; ccCCTCCCCCys
; Alignment reference
a 12 9 1 1 5 1 3 2 7 3 15 15
c 44 45 83 83 16 80 78 74 75 79 33 36
g 16 14 0 2 4 3 3 6 3 1 16 22
t 14 18 2 0 61 2 2 4 1 3 22 13
|
| 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; ccCCTCCCCCys
; cor=; Ncor=
a 12 9 1 1 5 1 3 2 7 3 15 15
c 44 45 83 83 16 80 78 74 75 79 33 36
g 16 14 0 2 4 3 3 6 3 1 16 22
t 14 18 2 0 61 2 2 4 1 3 22 13
|
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; ssCCCATGCAss
; Alignment reference
a 14 17 4 3 3 62 1 1 0 62 16 12
c 28 24 57 61 64 3 1 2 68 3 18 20
g 19 20 3 3 2 1 3 65 1 3 25 28
t 9 9 6 3 1 4 65 2 1 2 11 10
|
| 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; ssCCCATGCAss
; cor=; Ncor=
a 14 17 4 3 3 62 1 1 0 62 16 12
c 28 24 57 61 64 3 1 2 68 3 18 20
g 19 20 3 3 2 1 3 65 1 3 25 28
t 9 9 6 3 1 4 65 2 1 2 11 10
|
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=12; shift=0; ncol=12; csCCCATCCCcs
; Alignment reference
a 14 14 2 3 1 62 5 1 0 2 16 16
c 28 34 70 70 73 7 6 65 67 71 29 20
g 16 22 2 0 0 2 7 3 6 2 15 25
t 17 5 1 2 1 4 57 6 2 0 15 14
|
| 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=12; w=0; offset=0; strand=D; shift=0; score= 1; csCCCATCCCcs
; cor=; Ncor=
a 14 14 2 3 1 62 5 1 0 2 16 16
c 28 34 70 70 73 7 6 65 67 71 29 20
g 16 22 2 0 0 2 7 3 6 2 15 25
t 17 5 1 2 1 4 57 6 2 0 15 14
|