One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/24/peak-motifs.2026-03-24.175732_2026-03-24.175732_d4HBn3/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/2026/03/24/peak-motifs.2026-03-24.175732_2026-03-24.175732_d4HBn3/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |
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; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; atATACATAta
; Alignment reference
a 168 66 308 6 332 10 314 11 331 60 167
c 52 73 12 19 9 259 7 18 5 75 56
g 52 49 11 8 8 15 13 7 7 43 48
t 83 167 24 322 6 71 21 319 12 177 84
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| oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |
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; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; atATACATAta
; cor=; Ncor=
a 168 66 308 6 332 10 314 11 331 60 167
c 52 73 12 19 9 259 7 18 5 75 56
g 52 49 11 8 8 15 13 7 7 43 48
t 83 167 24 322 6 71 21 319 12 177 84
|
| oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |
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; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.891277; awATAcATATw
; cor=; Ncor=
a 148 72 251 15 249 25 256 19 248 2 119
c 29 60 2 4 7 184 2 7 1 23 34
g 38 31 7 3 8 10 4 1 9 3 39
t 56 108 11 249 7 52 9 244 13 243 79
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3) |
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; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; dmCAGCTGwh
; Alignment reference
a 39 38 0 130 0 2 1 5 35 40
c 19 34 128 1 0 134 1 1 32 37
g 38 32 1 1 134 0 0 130 32 19
t 40 32 7 4 2 0 134 0 37 40
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| oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3) |
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; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; dmCAGCTGwh
; cor=; Ncor=
a 39 38 0 130 0 2 1 5 35 40
c 19 34 128 1 0 134 1 1 32 37
g 38 32 1 1 134 0 0 130 32 19
t 40 32 7 4 2 0 134 0 37 40
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5) |
 |
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; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; hwTCATCAth
; Alignment reference
a 17 19 0 0 61 0 0 61 15 17
c 17 9 0 61 0 0 61 0 9 17
g 11 10 0 0 0 0 0 0 14 7
t 16 23 61 0 0 61 0 0 23 20
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| oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5) |
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; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; hwTCATCAth
; cor=; Ncor=
a 17 19 0 0 61 0 0 61 15 17
c 17 9 0 61 0 0 61 0 9 17
g 11 10 0 0 0 0 0 0 14 7
t 16 23 61 0 0 61 0 0 23 20
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |
 |
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; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; ymkCCGCCGay
; Alignment reference
a 48 57 43 8 9 17 14 7 6 82 38
c 70 61 28 195 204 9 182 198 4 41 71
g 39 48 90 2 0 170 8 5 199 43 50
t 62 53 58 14 6 23 15 9 10 53 60
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| oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |
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; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ymkCCGCCGay
; cor=; Ncor=
a 48 57 43 8 9 17 14 7 6 82 38
c 70 61 28 195 204 9 182 198 4 41 71
g 39 48 90 2 0 170 8 5 199 43 50
t 62 53 58 14 6 23 15 9 10 53 60
|
One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_7nt_m1_shift0 (positions_7nt_m1) |
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; positions_7nt_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; awAAGCAAAyr
; Alignment reference
a 53 33 109 111 0 0 96 97 109 21 42
c 17 13 0 1 0 101 4 3 3 39 12
g 20 24 1 1 116 1 8 8 2 24 34
t 27 47 7 4 1 15 9 9 3 33 29
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| positions_7nt_m1_shift0 (positions_7nt_m1) |
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; positions_7nt_m1 versus positions_7nt_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; awAAGCAAAyr
; cor=; Ncor=
a 53 33 109 111 0 0 96 97 109 21 42
c 17 13 0 1 0 101 4 3 3 39 12
g 20 24 1 1 116 1 8 8 2 24 34
t 27 47 7 4 1 15 9 9 3 33 29
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| positions_6nt_m1_shift2 (positions_6nt_m1) |
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; positions_7nt_m1 versus positions_6nt_m1; m=2/2; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.585892; --srGCAAACd
; cor=; Ncor=
a 0 0 16 25 0 0 72 71 72 0 27
c 0 0 19 12 0 72 0 0 0 72 9
g 0 0 22 19 72 0 0 0 0 0 18
t 0 0 15 16 0 0 0 1 0 0 18
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One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |
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; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; rrCTATCGATAGyy
; Alignment reference
a 27 23 7 4 64 1 0 5 70 8 63 12 16 15
c 13 16 51 6 2 0 67 2 3 0 1 4 19 19
g 19 19 4 1 0 3 2 67 0 2 6 51 16 13
t 15 16 12 63 8 70 5 0 1 64 4 7 23 27
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| oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |
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; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rrCTATCGATAGyy
; cor=; Ncor=
a 27 23 7 4 64 1 0 5 70 8 63 12 16 15
c 13 16 51 6 2 0 67 2 3 0 1 4 19 19
g 19 19 4 1 0 3 2 67 0 2 6 51 16 13
t 15 16 12 63 8 70 5 0 1 64 4 7 23 27
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| oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4) |
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; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.78708; -awTATCGATAwt-
; cor=; Ncor=
a 0 54 75 16 161 2 5 11 174 13 137 51 44 0
c 0 43 34 15 4 0 158 4 2 0 10 18 37 0
g 0 37 18 10 0 2 4 158 0 4 15 34 43 0
t 0 44 51 137 13 174 11 5 2 161 16 75 54 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |
 |
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; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; yaCACACACac
; Alignment reference
a 67 158 11 316 16 322 18 326 12 186 77
c 153 58 329 17 322 17 323 13 308 63 135
g 46 81 8 17 9 16 9 14 22 46 66
t 98 67 16 14 17 9 14 11 22 69 86
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| oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |
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; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; yaCACACACac
; cor=; Ncor=
a 67 158 11 316 16 322 18 326 12 186 77
c 153 58 329 17 322 17 323 13 308 63 135
g 46 81 8 17 9 16 9 14 22 46 66
t 98 67 16 14 17 9 14 11 22 69 86
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One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m1_shift2 (positions_6nt_m1) |
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; positions_6nt_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --srGCAAACdw
; Alignment reference
a 0 0 16 25 0 0 72 71 72 0 27 24
c 0 0 19 12 0 72 0 0 0 72 9 12
g 0 0 22 19 72 0 0 0 0 0 18 17
t 0 0 15 16 0 0 0 1 0 0 18 19
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| positions_6nt_m1_shift2 (positions_6nt_m1) |
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; positions_6nt_m1 versus positions_6nt_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --srGCAAACdw
; cor=; Ncor=
a 0 0 16 25 0 0 72 71 72 0 27 24
c 0 0 19 12 0 72 0 0 0 72 9 12
g 0 0 22 19 72 0 0 0 0 0 18 17
t 0 0 15 16 0 0 0 1 0 0 18 19
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| positions_7nt_m1_shift0 (positions_7nt_m1) |
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; positions_6nt_m1 versus positions_7nt_m1; m=2/2; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.585892; awAAGCAAAyr-
; cor=; Ncor=
a 53 33 109 111 0 0 96 97 109 21 42 0
c 17 13 0 1 0 101 4 3 3 39 12 0
g 20 24 1 1 116 1 8 8 2 24 34 0
t 27 47 7 4 1 15 9 9 3 33 29 0
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One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |
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; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; awATAcATATwt
; Alignment reference
a 148 72 251 15 249 25 256 19 248 2 119 60
c 29 60 2 4 7 184 2 7 1 23 34 48
g 38 31 7 3 8 10 4 1 9 3 39 32
t 56 108 11 249 7 52 9 244 13 243 79 131
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| oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |
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; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; awATAcATATwt
; cor=; Ncor=
a 148 72 251 15 249 25 256 19 248 2 119 60
c 29 60 2 4 7 184 2 7 1 23 34 48
g 38 31 7 3 8 10 4 1 9 3 39 32
t 56 108 11 249 7 52 9 244 13 243 79 131
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| oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |
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; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.891277; atATACATAta-
; cor=; Ncor=
a 168 66 308 6 332 10 314 11 331 60 167 0
c 52 73 12 19 9 259 7 18 5 75 56 0
g 52 49 11 8 8 15 13 7 7 43 48 0
t 83 167 24 322 6 71 21 319 12 177 84 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5) |
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; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; arGAGGAGGArs
; Alignment reference
a 37 29 8 86 5 4 86 6 2 88 30 20
c 20 10 3 5 2 9 4 4 10 1 18 37
g 20 45 83 0 89 83 0 84 84 4 38 27
t 19 12 2 5 0 0 6 2 0 3 10 12
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| oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5) |
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; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; arGAGGAGGArs
; cor=; Ncor=
a 37 29 8 86 5 4 86 6 2 88 30 20
c 20 10 3 5 2 9 4 4 10 1 18 37
g 20 45 83 0 89 83 0 84 84 4 38 27
t 19 12 2 5 0 0 6 2 0 3 10 12
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3) |
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; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; tyTCTCTCTCtc
; Alignment reference
a 20 16 1 4 1 5 3 2 0 7 9 22
c 23 47 5 96 5 93 1 98 1 82 19 43
g 20 9 10 0 3 1 1 0 5 6 21 18
t 42 33 89 5 96 6 100 5 99 10 56 22
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| oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3) |
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; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; tyTCTCTCTCtc
; cor=; Ncor=
a 20 16 1 4 1 5 3 2 0 7 9 22
c 23 47 5 96 5 93 1 98 1 82 19 43
g 20 9 10 0 3 1 1 0 5 6 21 18
t 42 33 89 5 96 6 100 5 99 10 56 22
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4) |
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; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=1; ncol=13; -awTATCGATAwt
; Alignment reference
a 0 54 75 16 161 2 5 11 174 13 137 51 44
c 0 43 34 15 4 0 158 4 2 0 10 18 37
g 0 37 18 10 0 2 4 158 0 4 15 34 43
t 0 44 51 137 13 174 11 5 2 161 16 75 54
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| oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4) |
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; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -awTATCGATAwt
; cor=; Ncor=
a 0 54 75 16 161 2 5 11 174 13 137 51 44
c 0 43 34 15 4 0 158 4 2 0 10 18 37
g 0 37 18 10 0 2 4 158 0 4 15 34 43
t 0 44 51 137 13 174 11 5 2 161 16 75 54
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| oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |
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; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=2/2; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.78708; rrCTATCGATAGy
; cor=; Ncor=
a 27 23 7 4 64 1 0 5 70 8 63 12 16
c 13 16 51 6 2 0 67 2 3 0 1 4 19
g 19 19 4 1 0 3 2 67 0 2 6 51 16
t 15 16 12 63 8 70 5 0 1 64 4 7 23
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