One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/06/02/peak-motifs.2026-06-02.215618_2026-06-02.215618_Ihs9Yt/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/2026/06/02/peak-motifs.2026-06-02.215618_2026-06-02.215618_Ihs9Yt/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --rrAAGGGAArr ; Alignment reference a 0 0 231 296 558 527 102 38 99 566 568 251 190 c 0 0 93 95 13 29 23 8 21 19 11 93 121 g 0 0 202 158 20 19 463 552 480 21 23 165 186 t 0 0 84 61 19 35 22 12 10 4 8 101 113

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --rrAAGGGAArr ; cor=; Ncor= a 0 0 231 296 558 527 102 38 99 566 568 251 190 c 0 0 93 95 13 29 23 8 21 19 11 93 121 g 0 0 202 158 20 19 463 552 480 21 23 165 186 t 0 0 84 61 19 35 22 12 10 4 8 101 113

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.722739; -rrAAAAGGAAAa ; cor=; Ncor= a 0 96 105 257 264 259 242 14 16 258 260 220 107 c 0 63 37 5 7 5 4 6 0 4 6 14 53 g 0 71 97 19 4 10 28 260 268 15 10 26 68 t 0 54 45 3 9 10 10 4 0 7 8 24 56

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=3/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.672985; mrrAAAAGGAAar ; cor=; Ncor= a 132 165 144 415 435 425 384 17 34 397 381 275 170 c 166 85 58 14 11 12 16 11 3 18 26 53 92 g 74 131 206 30 8 15 43 423 420 36 36 85 117 t 93 84 57 6 11 13 22 14 8 14 22 52 86

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -rrAAAAGGAAAar ; Alignment reference a 0 96 105 257 264 259 242 14 16 258 260 220 107 76 c 0 63 37 5 7 5 4 6 0 4 6 14 53 46 g 0 71 97 19 4 10 28 260 268 15 10 26 68 100 t 0 54 45 3 9 10 10 4 0 7 8 24 56 62

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -rrAAAAGGAAAar ; cor=; Ncor= a 0 96 105 257 264 259 242 14 16 258 260 220 107 76 c 0 63 37 5 7 5 4 6 0 4 6 14 53 46 g 0 71 97 19 4 10 28 260 268 15 10 26 68 100 t 0 54 45 3 9 10 10 4 0 7 8 24 56 62

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=2/3; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.921583; mrrAAAAGGAAarr ; cor=; Ncor= a 132 165 144 415 435 425 384 17 34 397 381 275 170 135 c 166 85 58 14 11 12 16 11 3 18 26 53 92 83 g 74 131 206 30 8 15 43 423 420 36 36 85 117 144 t 93 84 57 6 11 13 22 14 8 14 22 52 86 103

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.722739; --rrAAGGGAArr- ; cor=; Ncor= a 0 0 231 296 558 527 102 38 99 566 568 251 190 0 c 0 0 93 95 13 29 23 8 21 19 11 93 121 0 g 0 0 202 158 20 19 463 552 480 21 23 165 186 0 t 0 0 84 61 19 35 22 12 10 4 8 101 113 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; mrAAAAATAww ; Alignment reference a 248 197 524 539 561 560 549 0 602 195 205 c 162 144 34 40 13 23 24 33 21 109 127 g 133 161 43 24 23 19 38 32 9 151 125 t 95 136 37 35 41 36 27 573 6 183 181

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; mrAAAAATAww ; cor=; Ncor= a 248 197 524 539 561 560 549 0 602 195 205 c 162 144 34 40 13 23 24 33 21 109 127 g 133 161 43 24 23 19 38 32 9 151 125 t 95 136 37 35 41 36 27 573 6 183 181

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; gsaCGCACGCacs ; Alignment reference a 63 50 145 11 18 5 253 6 11 15 191 53 66 c 68 96 47 251 8 233 12 261 6 225 40 117 83 g 102 76 63 8 264 15 18 6 261 12 46 66 102 t 57 68 35 20 0 37 7 17 12 38 13 54 39

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; gsaCGCACGCacs ; cor=; Ncor= a 63 50 145 11 18 5 253 6 11 15 191 53 66 c 68 96 47 251 8 233 12 261 6 225 40 117 83 g 102 76 63 8 264 15 18 6 261 12 46 66 102 t 57 68 35 20 0 37 7 17 12 38 13 54 39

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; mrrAAAAGGAAarr ; Alignment reference a 132 165 144 415 435 425 384 17 34 397 381 275 170 135 c 166 85 58 14 11 12 16 11 3 18 26 53 92 83 g 74 131 206 30 8 15 43 423 420 36 36 85 117 144 t 93 84 57 6 11 13 22 14 8 14 22 52 86 103

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; mrrAAAAGGAAarr ; cor=; Ncor= a 132 165 144 415 435 425 384 17 34 397 381 275 170 135 c 166 85 58 14 11 12 16 11 3 18 26 53 92 83 g 74 131 206 30 8 15 43 423 420 36 36 85 117 144 t 93 84 57 6 11 13 22 14 8 14 22 52 86 103

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/3; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.921583; -rrAAAAGGAAAar ; cor=; Ncor= a 0 96 105 257 264 259 242 14 16 258 260 220 107 76 c 0 63 37 5 7 5 4 6 0 4 6 14 53 46 g 0 71 97 19 4 10 28 260 268 15 10 26 68 100 t 0 54 45 3 9 10 10 4 0 7 8 24 56 62

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.672985; --rrAAGGGAArr- ; cor=; Ncor= a 0 0 231 296 558 527 102 38 99 566 568 251 190 0 c 0 0 93 95 13 29 23 8 21 19 11 93 121 0 g 0 0 202 158 20 19 463 552 480 21 23 165 186 0 t 0 0 84 61 19 35 22 12 10 4 8 101 113 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; wbCAATCAwr ; Alignment reference a 36 22 0 116 116 0 0 116 34 36 c 28 30 116 0 0 0 116 0 22 24 g 16 33 0 0 0 0 0 0 20 31 t 36 31 0 0 0 116 0 0 40 25

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wbCAATCAwr ; cor=; Ncor= a 36 22 0 116 116 0 0 116 34 36 c 28 30 116 0 0 0 116 0 22 24 g 16 33 0 0 0 0 0 0 20 31 t 36 31 0 0 0 116 0 0 40 25

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; wrCATGCATGyw ; Alignment reference a 117 112 36 405 8 8 4 419 7 37 74 150 c 76 101 322 7 9 7 421 4 21 45 153 97 g 97 153 45 21 4 421 7 9 7 322 101 76 t 150 74 37 7 419 4 8 8 405 36 112 117

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wrCATGCATGyw ; cor=; Ncor= a 117 112 36 405 8 8 4 419 7 37 74 150 c 76 101 322 7 9 7 421 4 21 45 153 97 g 97 153 45 21 4 421 7 9 7 322 101 76 t 150 74 37 7 419 4 8 8 405 36 112 117

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wgTACAGTAmt ; Alignment reference a 80 63 16 231 7 239 12 10 243 69 67 c 54 62 14 17 237 3 9 9 5 69 60 g 51 91 10 15 19 3 239 10 9 68 54 t 88 57 233 10 10 28 13 244 16 67 92

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wgTACAGTAmt ; cor=; Ncor= a 80 63 16 231 7 239 12 10 243 69 67 c 54 62 14 17 237 3 9 9 5 69 60 g 51 91 10 15 19 3 239 10 9 68 54 t 88 57 233 10 10 28 13 244 16 67 92

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; ymyGTACGTACrt ; Alignment reference a 44 83 28 10 8 192 6 14 1 171 11 70 42 c 53 51 88 18 11 3 179 4 10 9 148 33 39 g 39 33 23 162 8 4 7 177 3 12 27 57 47 t 64 33 61 10 173 1 8 5 186 8 14 40 72

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ymyGTACGTACrt ; cor=; Ncor= a 44 83 28 10 8 192 6 14 1 171 11 70 42 c 53 51 88 18 11 3 179 4 10 9 148 33 39 g 39 33 23 162 8 4 7 177 3 12 27 57 47 t 64 33 61 10 173 1 8 5 186 8 14 40 72

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --rrAAGGGAArr ; Alignment reference a 0 0 231 296 558 527 102 38 99 566 568 251 190 c 0 0 93 95 13 29 23 8 21 19 11 93 121 g 0 0 202 158 20 19 463 552 480 21 23 165 186 t 0 0 84 61 19 35 22 12 10 4 8 101 113
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --rrAAGGGAArr ; cor=; Ncor= a 0 0 231 296 558 527 102 38 99 566 568 251 190 c 0 0 93 95 13 29 23 8 21 19 11 93 121 g 0 0 202 158 20 19 463 552 480 21 23 165 186 t 0 0 84 61 19 35 22 12 10 4 8 101 113
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.722739; -rrAAAAGGAAAa ; cor=; Ncor= a 0 96 105 257 264 259 242 14 16 258 260 220 107 c 0 63 37 5 7 5 4 6 0 4 6 14 53 g 0 71 97 19 4 10 28 260 268 15 10 26 68 t 0 54 45 3 9 10 10 4 0 7 8 24 56
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=3/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.672985; mrrAAAAGGAAar ; cor=; Ncor= a 132 165 144 415 435 425 384 17 34 397 381 275 170 c 166 85 58 14 11 12 16 11 3 18 26 53 92 g 74 131 206 30 8 15 43 423 420 36 36 85 117 t 93 84 57 6 11 13 22 14 8 14 22 52 86

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -rrAAAAGGAAAar ; Alignment reference a 0 96 105 257 264 259 242 14 16 258 260 220 107 76 c 0 63 37 5 7 5 4 6 0 4 6 14 53 46 g 0 71 97 19 4 10 28 260 268 15 10 26 68 100 t 0 54 45 3 9 10 10 4 0 7 8 24 56 62
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -rrAAAAGGAAAar ; cor=; Ncor= a 0 96 105 257 264 259 242 14 16 258 260 220 107 76 c 0 63 37 5 7 5 4 6 0 4 6 14 53 46 g 0 71 97 19 4 10 28 260 268 15 10 26 68 100 t 0 54 45 3 9 10 10 4 0 7 8 24 56 62
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=2/3; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.921583; mrrAAAAGGAAarr ; cor=; Ncor= a 132 165 144 415 435 425 384 17 34 397 381 275 170 135 c 166 85 58 14 11 12 16 11 3 18 26 53 92 83 g 74 131 206 30 8 15 43 423 420 36 36 85 117 144 t 93 84 57 6 11 13 22 14 8 14 22 52 86 103
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.722739; --rrAAGGGAArr- ; cor=; Ncor= a 0 0 231 296 558 527 102 38 99 566 568 251 190 0 c 0 0 93 95 13 29 23 8 21 19 11 93 121 0 g 0 0 202 158 20 19 463 552 480 21 23 165 186 0 t 0 0 84 61 19 35 22 12 10 4 8 101 113 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; mrrAAAAGGAAarr ; Alignment reference a 132 165 144 415 435 425 384 17 34 397 381 275 170 135 c 166 85 58 14 11 12 16 11 3 18 26 53 92 83 g 74 131 206 30 8 15 43 423 420 36 36 85 117 144 t 93 84 57 6 11 13 22 14 8 14 22 52 86 103
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; mrrAAAAGGAAarr ; cor=; Ncor= a 132 165 144 415 435 425 384 17 34 397 381 275 170 135 c 166 85 58 14 11 12 16 11 3 18 26 53 92 83 g 74 131 206 30 8 15 43 423 420 36 36 85 117 144 t 93 84 57 6 11 13 22 14 8 14 22 52 86 103
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/3; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.921583; -rrAAAAGGAAAar ; cor=; Ncor= a 0 96 105 257 264 259 242 14 16 258 260 220 107 76 c 0 63 37 5 7 5 4 6 0 4 6 14 53 46 g 0 71 97 19 4 10 28 260 268 15 10 26 68 100 t 0 54 45 3 9 10 10 4 0 7 8 24 56 62
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.672985; --rrAAGGGAArr- ; cor=; Ncor= a 0 0 231 296 558 527 102 38 99 566 568 251 190 0 c 0 0 93 95 13 29 23 8 21 19 11 93 121 0 g 0 0 202 158 20 19 463 552 480 21 23 165 186 0 t 0 0 84 61 19 35 22 12 10 4 8 101 113 0