One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/05/29/peak-motifs.2026-05-29.162601_2026-05-29.162601_GTDdF8/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/2026/05/29/peak-motifs.2026-05-29.162601_2026-05-29.162601_GTDdF8/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m3_shift0 (dyads_m3) |
 |
|
|
; dyads_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; yyCACTymmmtdCACym
; Alignment reference
a 2 4 0 18 0 3 4 8 11 9 3 6 0 19 0 2 5
c 6 5 18 0 19 3 9 8 6 9 4 0 19 0 19 8 9
g 0 3 0 1 0 0 1 0 1 1 0 7 0 0 0 0 1
t 11 7 1 0 0 13 5 3 1 0 12 6 0 0 0 9 4
|
| dyads_m3_shift0 (dyads_m3) |
|
|
|
; dyads_m3 versus dyads_m3; m=1/1; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; yyCACTymmmtdCACym
; cor=; Ncor=
a 2 4 0 18 0 3 4 8 11 9 3 6 0 19 0 2 5
c 6 5 18 0 19 3 9 8 6 9 4 0 19 0 19 8 9
g 0 3 0 1 0 0 1 0 1 1 0 7 0 0 0 0 1
t 11 7 1 0 0 13 5 3 1 0 12 6 0 0 0 9 4
|
One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m5_shift0 (dyads_m5) |
 |
|
|
; dyads_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; wtCCAawcwCAAcy
; Alignment reference
a 8 3 0 0 28 17 8 7 8 0 29 29 7 4
c 3 5 29 29 0 5 5 9 6 29 0 0 14 8
g 1 4 0 0 0 2 4 6 1 0 0 0 5 6
t 17 17 0 0 1 5 12 7 14 0 0 0 3 11
|
| dyads_m5_shift0 (dyads_m5) |
|
|
|
; dyads_m5 versus dyads_m5; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wtCCAawcwCAAcy
; cor=; Ncor=
a 8 3 0 0 28 17 8 7 8 0 29 29 7 4
c 3 5 29 29 0 5 5 9 6 29 0 0 14 8
g 1 4 0 0 0 2 4 6 1 0 0 0 5 6
t 17 17 0 0 1 5 12 7 14 0 0 0 3 11
|
One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m6_shift0 (dyads_m6) |
 |
|
|
; dyads_m6; m=0 (reference); ncol1=15; shift=0; ncol=15; wkAAGadddAGAAda
; Alignment reference
a 20 9 45 37 0 25 13 12 15 35 0 42 37 13 20
c 5 6 1 4 0 6 6 7 1 1 0 2 0 3 9
g 7 16 0 0 46 6 12 13 15 5 45 0 4 18 7
t 14 15 0 5 0 9 15 14 15 5 1 2 5 12 10
|
| dyads_m6_shift0 (dyads_m6) |
|
|
|
; dyads_m6 versus dyads_m6; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wkAAGadddAGAAda
; cor=; Ncor=
a 20 9 45 37 0 25 13 12 15 35 0 42 37 13 20
c 5 6 1 4 0 6 6 7 1 1 0 2 0 3 9
g 7 16 0 0 46 6 12 13 15 5 45 0 4 18 7
t 14 15 0 5 0 9 15 14 15 5 1 2 5 12 10
|
| dyads_m2_shift2 (dyads_m2) |
 |
|
|
; dyads_m6 versus dyads_m2; m=2/2; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.642266; --wwGATkrAGAwg-
; cor=; Ncor=
a 0 0 13 15 0 31 0 4 8 27 0 29 15 6 0
c 0 0 6 4 0 0 1 4 3 3 0 0 4 4 0
g 0 0 4 3 31 0 0 8 14 0 31 0 3 15 0
t 0 0 8 9 0 0 30 15 6 1 0 2 9 6 0
|
One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m10_shift0 (dyads_m10) |
 |
|
|
; dyads_m10; m=0 (reference); ncol1=27; shift=0; ncol=27; kkACGmsrwaawwgmthrgyctGTCcy
; Alignment reference
a 2 2 20 0 1 8 3 8 10 12 7 8 7 1 9 3 6 7 5 5 5 5 0 1 2 4 4
c 3 4 0 20 2 7 7 1 0 1 4 4 3 2 7 2 6 2 5 6 6 3 0 0 18 12 6
g 6 7 0 1 17 3 7 8 4 4 5 2 3 13 1 3 1 10 8 3 5 3 21 1 1 1 5
t 10 8 1 0 1 3 4 4 7 4 5 7 8 5 4 13 8 2 3 7 5 10 0 19 0 4 6
|
| dyads_m10_shift0 (dyads_m10) |
|
|
|
; dyads_m10 versus dyads_m10; m=1/1; ncol2=27; w=0; offset=0; strand=D; shift=0; score= 1; kkACGmsrwaawwgmthrgyctGTCcy
; cor=; Ncor=
a 2 2 20 0 1 8 3 8 10 12 7 8 7 1 9 3 6 7 5 5 5 5 0 1 2 4 4
c 3 4 0 20 2 7 7 1 0 1 4 4 3 2 7 2 6 2 5 6 6 3 0 0 18 12 6
g 6 7 0 1 17 3 7 8 4 4 5 2 3 13 1 3 1 10 8 3 5 3 21 1 1 1 5
t 10 8 1 0 1 3 4 4 7 4 5 7 8 5 4 13 8 2 3 7 5 10 0 19 0 4 6
|
One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m4_shift0 (dyads_m4) |
 |
|
|
; dyads_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; ryCGArmwwkwwwGGCrt
; Alignment reference
a 8 4 2 2 31 11 13 17 13 5 10 11 11 2 1 2 10 7
c 4 12 28 0 1 4 9 1 6 7 5 6 6 0 2 27 6 5
g 14 6 1 29 0 10 6 5 1 9 7 6 3 30 26 1 9 4
t 6 10 1 1 0 7 4 9 12 11 10 9 12 0 3 2 7 16
|
| dyads_m4_shift0 (dyads_m4) |
|
|
|
; dyads_m4 versus dyads_m4; m=1/1; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; ryCGArmwwkwwwGGCrt
; cor=; Ncor=
a 8 4 2 2 31 11 13 17 13 5 10 11 11 2 1 2 10 7
c 4 12 28 0 1 4 9 1 6 7 5 6 6 0 2 27 6 5
g 14 6 1 29 0 10 6 5 1 9 7 6 3 30 26 1 9 4
t 6 10 1 1 0 7 4 9 12 11 10 9 12 0 3 2 7 16
|
One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m9_shift0 (dyads_m9) |
 |
|
|
; dyads_m9; m=0 (reference); ncol1=11; shift=0; ncol=11; wtTAAaATAwa
; Alignment reference
a 16 9 0 37 37 19 37 0 37 12 23
c 4 6 0 0 0 7 0 0 0 2 1
g 4 4 0 0 0 4 0 0 0 3 4
t 13 18 37 0 0 7 0 37 0 20 9
|
| dyads_m9_shift0 (dyads_m9) |
|
|
|
; dyads_m9 versus dyads_m9; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wtTAAaATAwa
; cor=; Ncor=
a 16 9 0 37 37 19 37 0 37 12 23
c 4 6 0 0 0 7 0 0 0 2 1
g 4 4 0 0 0 4 0 0 0 3 4
t 13 18 37 0 0 7 0 37 0 20 9
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift8 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift8 (oligos_6-8nt_m1) |
 |
|
|
; oligos_6-8nt_m1; m=0 (reference); ncol1=10; shift=8; ncol=18; --------kwCATGCCkw
; Alignment reference
a 0 0 0 0 0 0 0 0 5 7 0 20 0 0 1 0 3 9
c 0 0 0 0 0 0 0 0 4 3 19 0 3 0 20 21 1 3
g 0 0 0 0 0 0 0 0 6 3 0 0 2 21 0 0 8 3
t 0 0 0 0 0 0 0 0 6 8 2 1 16 0 0 0 9 6
|
| oligos_6-8nt_m1_shift8 (oligos_6-8nt_m1) |
|
|
|
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=8; score= 1; --------kwCATGCCkw
; cor=; Ncor=
a 0 0 0 0 0 0 0 0 5 7 0 20 0 0 1 0 3 9
c 0 0 0 0 0 0 0 0 4 3 19 0 3 0 20 21 1 3
g 0 0 0 0 0 0 0 0 6 3 0 0 2 21 0 0 8 3
t 0 0 0 0 0 0 0 0 6 8 2 1 16 0 0 0 9 6
|
| dyads_m1_shift0 (dyads_m1) |
 |
|
|
; oligos_6-8nt_m1 versus dyads_m1; m=2/2; ncol2=18; w=-8; offset=-8; strand=D; shift=0; score=0.508921; mgGCaTGaawcwkGCCkw
; cor=; Ncor=
a 9 4 1 1 21 1 3 17 12 10 8 19 3 0 0 4 6 11
c 14 3 0 30 3 5 1 3 5 5 21 0 4 0 33 27 6 4
g 3 19 31 2 6 1 28 5 8 5 0 5 11 33 0 0 11 2
t 7 7 1 0 3 26 1 8 8 13 4 9 15 0 0 2 10 16
|
One-to-n matrix alignment; reference matrix: dyads_m2_shift2 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m2_shift2 (dyads_m2) |
|
|
|
; dyads_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwGATkrAGAwg
; Alignment reference
a 0 0 13 15 0 31 0 4 8 27 0 29 15 6
c 0 0 6 4 0 0 1 4 3 3 0 0 4 4
g 0 0 4 3 31 0 0 8 14 0 31 0 3 15
t 0 0 8 9 0 0 30 15 6 1 0 2 9 6
|
| dyads_m2_shift2 (dyads_m2) |
|
|
|
; dyads_m2 versus dyads_m2; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwGATkrAGAwg
; cor=; Ncor=
a 0 0 13 15 0 31 0 4 8 27 0 29 15 6
c 0 0 6 4 0 0 1 4 3 3 0 0 4 4
g 0 0 4 3 31 0 0 8 14 0 31 0 3 15
t 0 0 8 9 0 0 30 15 6 1 0 2 9 6
|
| dyads_m6_shift0 (dyads_m6) |
|
|
|
; dyads_m2 versus dyads_m6; m=2/2; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.642266; wkAAGadddAGAAd
; cor=; Ncor=
a 20 9 45 37 0 25 13 12 15 35 0 42 37 13
c 5 6 1 4 0 6 6 7 1 1 0 2 0 3
g 7 16 0 0 46 6 12 13 15 5 45 0 4 18
t 14 15 0 5 0 9 15 14 15 5 1 2 5 12
|
One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m8_shift0 (dyads_m8) |
 |
|
|
; dyads_m8; m=0 (reference); ncol1=20; shift=0; ncol=20; wtTTAwwwwwwwwwwTAAaw
; Alignment reference
a 18 10 0 0 46 14 14 15 14 16 17 15 16 17 21 0 46 46 23 17
c 6 7 0 0 0 3 9 6 9 9 4 8 9 6 8 0 0 0 6 5
g 5 6 0 0 0 8 6 9 8 4 9 9 6 9 3 0 0 0 7 6
t 17 23 46 46 0 21 17 16 15 17 16 14 15 14 14 46 0 0 10 18
|
| dyads_m8_shift0 (dyads_m8) |
|
|
|
; dyads_m8 versus dyads_m8; m=1/1; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; wtTTAwwwwwwwwwwTAAaw
; cor=; Ncor=
a 18 10 0 0 46 14 14 15 14 16 17 15 16 17 21 0 46 46 23 17
c 6 7 0 0 0 3 9 6 9 9 4 8 9 6 8 0 0 0 6 5
g 5 6 0 0 0 8 6 9 8 4 9 9 6 9 3 0 0 0 7 6
t 17 23 46 46 0 21 17 16 15 17 16 14 15 14 14 46 0 0 10 18
|
One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m1_shift0 (dyads_m1) |
|
|
|
; dyads_m1; m=0 (reference); ncol1=18; shift=0; ncol=18; mgGCaTGaawcwkGCCkw
; Alignment reference
a 9 4 1 1 21 1 3 17 12 10 8 19 3 0 0 4 6 11
c 14 3 0 30 3 5 1 3 5 5 21 0 4 0 33 27 6 4
g 3 19 31 2 6 1 28 5 8 5 0 5 11 33 0 0 11 2
t 7 7 1 0 3 26 1 8 8 13 4 9 15 0 0 2 10 16
|
| dyads_m1_shift0 (dyads_m1) |
|
|
|
; dyads_m1 versus dyads_m1; m=1/2; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; mgGCaTGaawcwkGCCkw
; cor=; Ncor=
a 9 4 1 1 21 1 3 17 12 10 8 19 3 0 0 4 6 11
c 14 3 0 30 3 5 1 3 5 5 21 0 4 0 33 27 6 4
g 3 19 31 2 6 1 28 5 8 5 0 5 11 33 0 0 11 2
t 7 7 1 0 3 26 1 8 8 13 4 9 15 0 0 2 10 16
|
| oligos_6-8nt_m1_shift8 (oligos_6-8nt_m1) |
|
|
|
; dyads_m1 versus oligos_6-8nt_m1; m=2/2; ncol2=10; w=0; offset=8; strand=D; shift=8; score=0.508921; --------kwCATGCCkw
; cor=; Ncor=
a 0 0 0 0 0 0 0 0 5 7 0 20 0 0 1 0 3 9
c 0 0 0 0 0 0 0 0 4 3 19 0 3 0 20 21 1 3
g 0 0 0 0 0 0 0 0 6 3 0 0 2 21 0 0 8 3
t 0 0 0 0 0 0 0 0 6 8 2 1 16 0 0 0 9 6
|
One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m7_shift0 (dyads_m7) |
 |
|
|
; dyads_m7; m=0 (reference); ncol1=11; shift=0; ncol=11; tdACGAGGAdr
; Alignment reference
a 5 9 27 3 0 25 2 1 24 10 7
c 3 0 0 22 0 1 0 0 0 4 6
g 5 10 1 0 27 0 21 27 1 7 10
t 15 9 0 3 1 2 5 0 3 7 5
|
| dyads_m7_shift0 (dyads_m7) |
|
|
|
; dyads_m7 versus dyads_m7; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; tdACGAGGAdr
; cor=; Ncor=
a 5 9 27 3 0 25 2 1 24 10 7
c 3 0 0 22 0 1 0 0 0 4 6
g 5 10 1 0 27 0 21 27 1 7 10
t 15 9 0 3 1 2 5 0 3 7 5
|