One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.121311_2025-11-07.121311_NLkiRA/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/2025/11/07/peak-motifs.2025-11-07.121311_2025-11-07.121311_NLkiRA/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; swTaAAAAATyh ; Alignment reference a 153 165 75 426 613 610 617 616 591 33 139 204 c 181 84 33 9 9 11 6 8 16 11 193 166 g 178 116 35 104 3 4 8 6 17 27 123 101 t 129 276 498 102 16 16 10 11 17 570 186 170

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; swTaAAAAATyh ; cor=; Ncor= a 153 165 75 426 613 610 617 616 591 33 139 204 c 181 84 33 9 9 11 6 8 16 11 193 166 g 178 116 35 104 3 4 8 6 17 27 123 101 t 129 276 498 102 16 16 10 11 17 570 186 170

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.860023; wwGAAAAAATav ; cor=; Ncor= a 219 221 75 521 576 590 594 564 491 45 253 165 c 98 102 33 59 21 5 3 3 11 9 137 197 g 85 107 452 14 9 8 4 9 9 15 108 184 t 212 184 54 20 8 11 13 38 103 545 116 68

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m3 versus positions_6nt_m1; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.855633; rdCAAAAAATkm ; cor=; Ncor= a 288 233 73 666 711 673 665 713 756 32 144 319 c 154 60 620 6 18 90 3 31 1 25 141 259 g 209 235 35 101 49 11 92 33 15 22 266 109 t 131 254 54 9 4 8 22 5 10 703 231 95

dyads_m2_shift0 (dyads_m2)
; positions_6nt_m3 versus dyads_m2; m=4/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.752042; rmwGAAAAATGm ; cor=; Ncor= a 227 239 251 28 572 654 635 655 640 9 47 294 c 51 193 116 93 89 3 25 4 2 4 50 174 g 254 97 133 511 3 6 3 7 25 7 459 135 t 139 142 171 39 7 8 8 5 4 651 115 68

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; tsTTGCCAGCrgc ; Alignment reference a 113 56 89 16 86 3 0 572 4 18 229 39 125 c 122 291 3 9 5 562 578 4 7 465 38 33 209 g 121 195 85 4 474 4 2 0 478 6 185 372 121 t 224 38 403 551 15 11 0 4 91 91 128 136 125

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; tsTTGCCAGCrgc ; cor=; Ncor= a 113 56 89 16 86 3 0 572 4 18 229 39 125 c 122 291 3 9 5 562 578 4 7 465 38 33 209 g 121 195 85 4 474 4 2 0 478 6 185 372 121 t 224 38 403 551 15 11 0 4 91 91 128 136 125

dyads_m5_shift0 (dyads_m5)
; dyads_m4 versus dyads_m5; m=2/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.761221; gyTTgCCAGWmwy ; cor=; Ncor= a 62 56 15 9 15 2 1 322 2 235 133 160 20 c 41 144 31 10 83 327 335 1 0 9 114 18 133 g 192 30 11 0 219 2 0 4 330 3 33 22 25 t 41 106 279 317 19 5 0 9 4 89 56 136 158

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; kmAGCGCCTkg ; Alignment reference a 255 607 1546 47 88 99 223 9 21 303 335 c 393 498 13 183 1431 6 1276 1570 187 365 389 g 524 180 3 1285 3 1500 15 20 105 535 548 t 440 327 50 97 90 7 98 13 1299 409 340

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; kmAGCGCCTkg ; cor=; Ncor= a 255 607 1546 47 88 99 223 9 21 303 335 c 393 498 13 183 1431 6 1276 1570 187 365 389 g 524 180 3 1285 3 1500 15 20 105 535 548 t 440 327 50 97 90 7 98 13 1299 409 340

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=10; shift=0; ncol=10; AsAGATAArw ; Alignment reference a 194 58 273 0 273 0 273 260 110 82 c 20 71 0 0 0 0 0 0 22 37 g 26 112 0 273 0 0 0 0 111 44 t 33 32 0 0 0 273 0 13 30 110

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; AsAGATAArw ; cor=; Ncor= a 194 58 273 0 273 0 273 260 110 82 c 20 71 0 0 0 0 0 0 22 37 g 26 112 0 273 0 0 0 0 111 44 t 33 32 0 0 0 273 0 13 30 110

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwGAAAAAATav ; Alignment reference a 219 221 75 521 576 590 594 564 491 45 253 165 c 98 102 33 59 21 5 3 3 11 9 137 197 g 85 107 452 14 9 8 4 9 9 15 108 184 t 212 184 54 20 8 11 13 38 103 545 116 68

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwGAAAAAATav ; cor=; Ncor= a 219 221 75 521 576 590 594 564 491 45 253 165 c 98 102 33 59 21 5 3 3 11 9 137 197 g 85 107 452 14 9 8 4 9 9 15 108 184 t 212 184 54 20 8 11 13 38 103 545 116 68

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.860023; swTaAAAAATyh ; cor=; Ncor= a 153 165 75 426 613 610 617 616 591 33 139 204 c 181 84 33 9 9 11 6 8 16 11 193 166 g 178 116 35 104 3 4 8 6 17 27 123 101 t 129 276 498 102 16 16 10 11 17 570 186 170

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m4 versus positions_6nt_m1; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.846334; rdCAAAAAATkm ; cor=; Ncor= a 288 233 73 666 711 673 665 713 756 32 144 319 c 154 60 620 6 18 90 3 31 1 25 141 259 g 209 235 35 101 49 11 92 33 15 22 266 109 t 131 254 54 9 4 8 22 5 10 703 231 95

dyads_m2_shift0 (dyads_m2)
; positions_6nt_m4 versus dyads_m2; m=4/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.698651; rmwGAAAAATGm ; cor=; Ncor= a 227 239 251 28 572 654 635 655 640 9 47 294 c 51 193 116 93 89 3 25 4 2 4 50 174 g 254 97 133 511 3 6 3 7 25 7 459 135 t 139 142 171 39 7 8 8 5 4 651 115 68

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; wbACAAAATGkw ; Alignment reference a 242 80 363 15 455 465 451 370 15 10 59 130 c 36 141 3 448 6 1 1 9 9 15 64 55 g 32 130 94 1 6 2 2 88 115 430 203 51 t 160 119 10 6 3 2 16 3 331 15 144 234

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wbACAAAATGkw ; cor=; Ncor= a 242 80 363 15 455 465 451 370 15 10 59 130 c 36 141 3 448 6 1 1 9 9 15 64 55 g 32 130 94 1 6 2 2 88 115 430 203 51 t 160 119 10 6 3 2 16 3 331 15 144 234

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; dyads_m3 versus oligos_6nt_mkv3_m1; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.736489; ahACAAAArk-- ; cor=; Ncor= a 258 104 407 0 407 407 407 407 167 64 0 0 c 61 132 0 407 0 0 0 0 29 62 0 0 g 29 53 0 0 0 0 0 0 148 162 0 0 t 59 118 0 0 0 0 0 0 63 119 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 5 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=10; shift=0; ncol=10; ahACAAAArk ; Alignment reference a 258 104 407 0 407 407 407 407 167 64 c 61 132 0 407 0 0 0 0 29 62 g 29 53 0 0 0 0 0 0 148 162 t 59 118 0 0 0 0 0 0 63 119

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ahACAAAArk ; cor=; Ncor= a 258 104 407 0 407 407 407 407 167 64 c 61 132 0 407 0 0 0 0 29 62 g 29 53 0 0 0 0 0 0 148 162 t 59 118 0 0 0 0 0 0 63 119

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m1 versus dyads_m3; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.736489; wbACAAAATG ; cor=; Ncor= a 242 80 363 15 455 465 451 370 15 10 c 36 141 3 448 6 1 1 9 9 15 g 32 130 94 1 6 2 2 88 115 430 t 160 119 10 6 3 2 16 3 331 15

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.547156; -rrCAAAAAA ; cor=; Ncor= a 0 188 166 26 583 600 511 546 538 488 c 0 153 113 547 2 5 86 14 66 12 g 0 176 224 15 9 7 8 52 3 21 t 0 98 112 27 21 3 10 3 8 94

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_6nt_mkv3_m1 versus positions_6nt_m1; m=4/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.513161; -rdCAAAAAA ; cor=; Ncor= a 0 288 233 73 666 711 673 665 713 756 c 0 154 60 620 6 18 90 3 31 1 g 0 209 235 35 101 49 11 92 33 15 t 0 131 254 54 9 4 8 22 5 10

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -rrCAAAAAAGca ; Alignment reference a 0 188 166 26 583 600 511 546 538 488 42 102 275 c 0 153 113 547 2 5 86 14 66 12 25 292 108 g 0 176 224 15 9 7 8 52 3 21 515 130 115 t 0 98 112 27 21 3 10 3 8 94 33 91 117

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rrCAAAAAAGca ; cor=; Ncor= a 0 188 166 26 583 600 511 546 538 488 42 102 275 c 0 153 113 547 2 5 86 14 66 12 25 292 108 g 0 176 224 15 9 7 8 52 3 21 515 130 115 t 0 98 112 27 21 3 10 3 8 94 33 91 117

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.811216; -rdCAAAAAATkm ; cor=; Ncor= a 0 288 233 73 666 711 673 665 713 756 32 144 319 c 0 154 60 620 6 18 90 3 31 1 25 141 259 g 0 209 235 35 101 49 11 92 33 15 22 266 109 t 0 131 254 54 9 4 8 22 5 10 703 231 95

dyads_m2_shift0 (dyads_m2)
; positions_6nt_m2 versus dyads_m2; m=3/4; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.649511; rmwGAAAAATGma ; cor=; Ncor= a 227 239 251 28 572 654 635 655 640 9 47 294 287 c 51 193 116 93 89 3 25 4 2 4 50 174 84 g 254 97 133 511 3 6 3 7 25 7 459 135 143 t 139 142 171 39 7 8 8 5 4 651 115 68 157

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; positions_6nt_m2 versus oligos_6nt_mkv3_m1; m=4/4; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.547156; ahACAAAArk--- ; cor=; Ncor= a 258 104 407 0 407 407 407 407 167 64 0 0 0 c 61 132 0 407 0 0 0 0 29 62 0 0 0 g 29 53 0 0 0 0 0 0 148 162 0 0 0 t 59 118 0 0 0 0 0 0 63 119 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift1 ; 3 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=11; shift=1; ncol=12; -ssGGTTCGAhy ; Alignment reference a 0 233 235 38 97 54 93 67 58 1327 459 283 c 0 519 577 87 90 2 6 1295 2 91 391 501 g 0 618 514 1417 1264 86 181 87 1482 115 169 56 t 0 177 221 5 96 1405 1267 98 5 14 528 707

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -ssGGTTCGAhy ; cor=; Ncor= a 0 233 235 38 97 54 93 67 58 1327 459 283 c 0 519 577 87 90 2 6 1295 2 91 391 501 g 0 618 514 1417 1264 86 181 87 1482 115 169 56 t 0 177 221 5 96 1405 1267 98 5 14 528 707

oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.59763; msGGATTCGmw- ; cor=; Ncor= a 409 270 8 29 1131 98 17 254 90 573 385 0 c 514 385 6 7 95 33 3 997 4 374 212 0 g 261 501 1374 1273 82 99 30 97 1211 283 311 0 t 217 245 13 92 93 1171 1351 53 96 171 493 0

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 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; wwtTGATstasATCAaww ; Alignment reference a 83 82 23 5 8 218 10 45 40 132 58 180 9 3 228 163 74 81 c 40 41 23 6 1 12 33 67 47 22 71 18 2 229 3 32 43 37 g 37 44 33 3 229 2 19 72 22 47 67 33 12 1 5 23 42 40 t 81 74 162 227 3 9 179 57 132 40 45 10 218 8 5 23 82 83

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/1; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwtTGATstasATCAaww ; cor=; Ncor= a 83 82 23 5 8 218 10 45 40 132 58 180 9 3 228 163 74 81 c 40 41 23 6 1 12 33 67 47 22 71 18 2 229 3 32 43 37 g 37 44 33 3 229 2 19 72 22 47 67 33 12 1 5 23 42 40 t 81 74 162 227 3 9 179 57 132 40 45 10 218 8 5 23 82 83

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 3 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=12; shift=0; ncol=12; gwTAGCTCAgyk ; Alignment reference a 108 238 2 435 3 3 0 0 450 87 101 94 c 105 4 5 0 3 504 1 537 85 85 149 43 g 215 88 0 98 531 3 4 0 0 360 130 171 t 109 207 530 4 0 27 532 0 2 5 157 229

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gwTAGCTCAgyk ; cor=; Ncor= a 108 238 2 435 3 3 0 0 450 87 101 94 c 105 4 5 0 3 504 1 537 85 85 149 43 g 215 88 0 98 531 3 4 0 0 360 130 171 t 109 207 530 4 0 27 532 0 2 5 157 229

oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m5_rc; m=2/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.797988; rdTAGCTCmv-- ; cor=; Ncor= a 188 174 0 525 2 0 1 0 298 132 0 0 c 55 4 0 0 4 441 0 525 211 171 0 0 g 192 143 0 0 519 84 0 0 7 210 0 0 t 90 204 525 0 0 0 524 0 9 12 0 0

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=10; shift=0; ncol=10; kcTCCAGAyt ; Alignment reference a 129 125 0 40 0 480 0 566 26 70 c 108 227 15 526 566 0 0 0 268 112 g 183 93 0 0 0 0 566 0 85 101 t 146 121 551 0 0 86 0 0 187 283

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; kcTCCAGAyt ; cor=; Ncor= a 129 125 0 40 0 480 0 566 26 70 c 108 227 15 526 566 0 0 0 268 112 g 183 93 0 0 0 0 566 0 85 101 t 146 121 551 0 0 86 0 0 187 283

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=2; ncol=12; --bkGAGCTAhy ; Alignment reference a 0 0 12 9 0 524 0 0 0 525 204 90 c 0 0 210 7 0 0 84 519 0 0 143 192 g 0 0 171 211 525 0 441 4 0 0 4 55 t 0 0 132 298 0 1 0 2 525 0 174 188

oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --bkGAGCTAhy ; cor=; Ncor= a 0 0 12 9 0 524 0 0 0 525 204 90 c 0 0 210 7 0 0 84 519 0 0 143 192 g 0 0 171 211 525 0 441 4 0 0 4 55 t 0 0 132 298 0 1 0 2 525 0 174 188

oligos_7nt_mkv4_m3_rc_shift0 (oligos_7nt_mkv4_m3_rc)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m3_rc; m=2/2; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.797988; mrcTGAGCTAwc ; cor=; Ncor= a 229 157 5 2 0 532 27 0 4 530 207 109 c 171 130 360 0 0 4 3 531 98 0 88 215 g 43 149 85 85 537 1 504 3 0 5 4 105 t 94 101 87 450 0 0 3 3 435 2 238 108

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; rmwGAAAAATGma ; Alignment reference a 227 239 251 28 572 654 635 655 640 9 47 294 287 c 51 193 116 93 89 3 25 4 2 4 50 174 84 g 254 97 133 511 3 6 3 7 25 7 459 135 143 t 139 142 171 39 7 8 8 5 4 651 115 68 157

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rmwGAAAAATGma ; cor=; Ncor= a 227 239 251 28 572 654 635 655 640 9 47 294 287 c 51 193 116 93 89 3 25 4 2 4 50 174 84 g 254 97 133 511 3 6 3 7 25 7 459 135 143 t 139 142 171 39 7 8 8 5 4 651 115 68 157

positions_6nt_m3_shift0 (positions_6nt_m3)
; dyads_m2 versus positions_6nt_m3; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.752042; swTaAAAAATyh- ; cor=; Ncor= a 153 165 75 426 613 610 617 616 591 33 139 204 0 c 181 84 33 9 9 11 6 8 16 11 193 166 0 g 178 116 35 104 3 4 8 6 17 27 123 101 0 t 129 276 498 102 16 16 10 11 17 570 186 170 0

positions_6nt_m1_shift0 (positions_6nt_m1)
; dyads_m2 versus positions_6nt_m1; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.724732; rdCAAAAAATkm- ; cor=; Ncor= a 288 233 73 666 711 673 665 713 756 32 144 319 0 c 154 60 620 6 18 90 3 31 1 25 141 259 0 g 209 235 35 101 49 11 92 33 15 22 266 109 0 t 131 254 54 9 4 8 22 5 10 703 231 95 0

positions_6nt_m4_shift0 (positions_6nt_m4)
; dyads_m2 versus positions_6nt_m4; m=4/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.698651; wwGAAAAAATav- ; cor=; Ncor= a 219 221 75 521 576 590 594 564 491 45 253 165 0 c 98 102 33 59 21 5 3 3 11 9 137 197 0 g 85 107 452 14 9 8 4 9 9 15 108 184 0 t 212 184 54 20 8 11 13 38 103 545 116 68 0

positions_6nt_m2_shift1 (positions_6nt_m2)
; dyads_m2 versus positions_6nt_m2; m=5/5; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.649511; -rrCAAAAAAGca ; cor=; Ncor= a 0 188 166 26 583 600 511 546 538 488 42 102 275 c 0 153 113 547 2 5 86 14 66 12 25 292 108 g 0 176 224 15 9 7 8 52 3 21 515 130 115 t 0 98 112 27 21 3 10 3 8 94 33 91 117

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=10; shift=0; ncol=10; vgGGTAGAgm ; Alignment reference a 182 108 7 1 0 655 0 477 121 277 c 192 119 1 0 0 0 1 83 113 239 g 190 265 641 654 2 0 566 6 318 33 t 91 163 6 0 653 0 88 89 103 106

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; vgGGTAGAgm ; cor=; Ncor= a 182 108 7 1 0 655 0 477 121 277 c 192 119 1 0 0 0 1 83 113 239 g 190 265 641 654 2 0 566 6 318 33 t 91 163 6 0 653 0 88 89 103 106

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -wkCGAATCCsk ; Alignment reference a 0 493 171 96 53 1351 1171 93 92 13 245 217 c 0 311 283 1211 97 30 99 82 1273 1374 501 261 g 0 212 374 4 997 3 33 95 7 6 385 514 t 0 385 573 90 254 17 98 1131 29 8 270 409

oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wkCGAATCCsk ; cor=; Ncor= a 0 493 171 96 53 1351 1171 93 92 13 245 217 c 0 311 283 1211 97 30 99 82 1273 1374 501 261 g 0 212 374 4 997 3 33 95 7 6 385 514 t 0 385 573 90 254 17 98 1131 29 8 270 409

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.59763; rdTCGAACCss- ; cor=; Ncor= a 707 528 14 5 98 1267 1405 96 5 221 177 0 c 56 169 115 1482 87 181 86 1264 1417 514 618 0 g 501 391 91 2 1295 6 2 90 87 577 519 0 t 283 459 1327 58 67 93 54 97 38 235 233 0

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; gyTTgCCAGWmwy ; Alignment reference a 62 56 15 9 15 2 1 322 2 235 133 160 20 c 41 144 31 10 83 327 335 1 0 9 114 18 133 g 192 30 11 0 219 2 0 4 330 3 33 22 25 t 41 106 279 317 19 5 0 9 4 89 56 136 158

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; gyTTgCCAGWmwy ; cor=; Ncor= a 62 56 15 9 15 2 1 322 2 235 133 160 20 c 41 144 31 10 83 327 335 1 0 9 114 18 133 g 192 30 11 0 219 2 0 4 330 3 33 22 25 t 41 106 279 317 19 5 0 9 4 89 56 136 158

dyads_m4_shift0 (dyads_m4)
; dyads_m5 versus dyads_m4; m=2/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.761221; tsTTGCCAGCrgc ; cor=; Ncor= a 113 56 89 16 86 3 0 572 4 18 229 39 125 c 122 291 3 9 5 562 578 4 7 465 38 33 209 g 121 195 85 4 474 4 2 0 478 6 185 372 121 t 224 38 403 551 15 11 0 4 91 91 128 136 125

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -rdCAAAAAATkm ; Alignment reference a 0 288 233 73 666 711 673 665 713 756 32 144 319 c 0 154 60 620 6 18 90 3 31 1 25 141 259 g 0 209 235 35 101 49 11 92 33 15 22 266 109 t 0 131 254 54 9 4 8 22 5 10 703 231 95

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rdCAAAAAATkm ; cor=; Ncor= a 0 288 233 73 666 711 673 665 713 756 32 144 319 c 0 154 60 620 6 18 90 3 31 1 25 141 259 g 0 209 235 35 101 49 11 92 33 15 22 266 109 t 0 131 254 54 9 4 8 22 5 10 703 231 95

positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m1 versus positions_6nt_m3; m=2/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.855633; -swTaAAAAATyh ; cor=; Ncor= a 0 153 165 75 426 613 610 617 616 591 33 139 204 c 0 181 84 33 9 9 11 6 8 16 11 193 166 g 0 178 116 35 104 3 4 8 6 17 27 123 101 t 0 129 276 498 102 16 16 10 11 17 570 186 170

positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_6nt_m1 versus positions_6nt_m4; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.846334; -wwGAAAAAATav ; cor=; Ncor= a 0 219 221 75 521 576 590 594 564 491 45 253 165 c 0 98 102 33 59 21 5 3 3 11 9 137 197 g 0 85 107 452 14 9 8 4 9 9 15 108 184 t 0 212 184 54 20 8 11 13 38 103 545 116 68

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=4/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.811216; -rrCAAAAAAGca ; cor=; Ncor= a 0 188 166 26 583 600 511 546 538 488 42 102 275 c 0 153 113 547 2 5 86 14 66 12 25 292 108 g 0 176 224 15 9 7 8 52 3 21 515 130 115 t 0 98 112 27 21 3 10 3 8 94 33 91 117

dyads_m2_shift1 (dyads_m2)
; positions_6nt_m1 versus dyads_m2; m=5/6; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.724732; -rmwGAAAAATGm ; cor=; Ncor= a 0 227 239 251 28 572 654 635 655 640 9 47 294 c 0 51 193 116 93 89 3 25 4 2 4 50 174 g 0 254 97 133 511 3 6 3 7 25 7 459 135 t 0 139 142 171 39 7 8 8 5 4 651 115 68

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; positions_6nt_m1 versus oligos_6nt_mkv3_m1; m=6/6; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.513161; ahACAAAArk--- ; cor=; Ncor= a 258 104 407 0 407 407 407 407 167 64 0 0 0 c 61 132 0 407 0 0 0 0 29 62 0 0 0 g 29 53 0 0 0 0 0 0 148 162 0 0 0 t 59 118 0 0 0 0 0 0 63 119 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; swTaAAAAATyh ; Alignment reference a 153 165 75 426 613 610 617 616 591 33 139 204 c 181 84 33 9 9 11 6 8 16 11 193 166 g 178 116 35 104 3 4 8 6 17 27 123 101 t 129 276 498 102 16 16 10 11 17 570 186 170
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; swTaAAAAATyh ; cor=; Ncor= a 153 165 75 426 613 610 617 616 591 33 139 204 c 181 84 33 9 9 11 6 8 16 11 193 166 g 178 116 35 104 3 4 8 6 17 27 123 101 t 129 276 498 102 16 16 10 11 17 570 186 170
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m3 versus positions_6nt_m4; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.860023; wwGAAAAAATav ; cor=; Ncor= a 219 221 75 521 576 590 594 564 491 45 253 165 c 98 102 33 59 21 5 3 3 11 9 137 197 g 85 107 452 14 9 8 4 9 9 15 108 184 t 212 184 54 20 8 11 13 38 103 545 116 68
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m3 versus positions_6nt_m1; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.855633; rdCAAAAAATkm ; cor=; Ncor= a 288 233 73 666 711 673 665 713 756 32 144 319 c 154 60 620 6 18 90 3 31 1 25 141 259 g 209 235 35 101 49 11 92 33 15 22 266 109 t 131 254 54 9 4 8 22 5 10 703 231 95
dyads_m2_shift0 (dyads_m2)				; positions_6nt_m3 versus dyads_m2; m=4/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.752042; rmwGAAAAATGm ; cor=; Ncor= a 227 239 251 28 572 654 635 655 640 9 47 294 c 51 193 116 93 89 3 25 4 2 4 50 174 g 254 97 133 511 3 6 3 7 25 7 459 135 t 139 142 171 39 7 8 8 5 4 651 115 68

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwGAAAAAATav ; Alignment reference a 219 221 75 521 576 590 594 564 491 45 253 165 c 98 102 33 59 21 5 3 3 11 9 137 197 g 85 107 452 14 9 8 4 9 9 15 108 184 t 212 184 54 20 8 11 13 38 103 545 116 68
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwGAAAAAATav ; cor=; Ncor= a 219 221 75 521 576 590 594 564 491 45 253 165 c 98 102 33 59 21 5 3 3 11 9 137 197 g 85 107 452 14 9 8 4 9 9 15 108 184 t 212 184 54 20 8 11 13 38 103 545 116 68
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m4 versus positions_6nt_m3; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.860023; swTaAAAAATyh ; cor=; Ncor= a 153 165 75 426 613 610 617 616 591 33 139 204 c 181 84 33 9 9 11 6 8 16 11 193 166 g 178 116 35 104 3 4 8 6 17 27 123 101 t 129 276 498 102 16 16 10 11 17 570 186 170
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m4 versus positions_6nt_m1; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.846334; rdCAAAAAATkm ; cor=; Ncor= a 288 233 73 666 711 673 665 713 756 32 144 319 c 154 60 620 6 18 90 3 31 1 25 141 259 g 209 235 35 101 49 11 92 33 15 22 266 109 t 131 254 54 9 4 8 22 5 10 703 231 95
dyads_m2_shift0 (dyads_m2)				; positions_6nt_m4 versus dyads_m2; m=4/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.698651; rmwGAAAAATGm ; cor=; Ncor= a 227 239 251 28 572 654 635 655 640 9 47 294 c 51 193 116 93 89 3 25 4 2 4 50 174 g 254 97 133 511 3 6 3 7 25 7 459 135 t 139 142 171 39 7 8 8 5 4 651 115 68

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=10; shift=0; ncol=10; ahACAAAArk ; Alignment reference a 258 104 407 0 407 407 407 407 167 64 c 61 132 0 407 0 0 0 0 29 62 g 29 53 0 0 0 0 0 0 148 162 t 59 118 0 0 0 0 0 0 63 119
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ahACAAAArk ; cor=; Ncor= a 258 104 407 0 407 407 407 407 167 64 c 61 132 0 407 0 0 0 0 29 62 g 29 53 0 0 0 0 0 0 148 162 t 59 118 0 0 0 0 0 0 63 119
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m1 versus dyads_m3; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.736489; wbACAAAATG ; cor=; Ncor= a 242 80 363 15 455 465 451 370 15 10 c 36 141 3 448 6 1 1 9 9 15 g 32 130 94 1 6 2 2 88 115 430 t 160 119 10 6 3 2 16 3 331 15
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.547156; -rrCAAAAAA ; cor=; Ncor= a 0 188 166 26 583 600 511 546 538 488 c 0 153 113 547 2 5 86 14 66 12 g 0 176 224 15 9 7 8 52 3 21 t 0 98 112 27 21 3 10 3 8 94
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_6nt_mkv3_m1 versus positions_6nt_m1; m=4/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.513161; -rdCAAAAAA ; cor=; Ncor= a 0 288 233 73 666 711 673 665 713 756 c 0 154 60 620 6 18 90 3 31 1 g 0 209 235 35 101 49 11 92 33 15 t 0 131 254 54 9 4 8 22 5 10

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -rrCAAAAAAGca ; Alignment reference a 0 188 166 26 583 600 511 546 538 488 42 102 275 c 0 153 113 547 2 5 86 14 66 12 25 292 108 g 0 176 224 15 9 7 8 52 3 21 515 130 115 t 0 98 112 27 21 3 10 3 8 94 33 91 117
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rrCAAAAAAGca ; cor=; Ncor= a 0 188 166 26 583 600 511 546 538 488 42 102 275 c 0 153 113 547 2 5 86 14 66 12 25 292 108 g 0 176 224 15 9 7 8 52 3 21 515 130 115 t 0 98 112 27 21 3 10 3 8 94 33 91 117
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.811216; -rdCAAAAAATkm ; cor=; Ncor= a 0 288 233 73 666 711 673 665 713 756 32 144 319 c 0 154 60 620 6 18 90 3 31 1 25 141 259 g 0 209 235 35 101 49 11 92 33 15 22 266 109 t 0 131 254 54 9 4 8 22 5 10 703 231 95
dyads_m2_shift0 (dyads_m2)				; positions_6nt_m2 versus dyads_m2; m=3/4; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.649511; rmwGAAAAATGma ; cor=; Ncor= a 227 239 251 28 572 654 635 655 640 9 47 294 287 c 51 193 116 93 89 3 25 4 2 4 50 174 84 g 254 97 133 511 3 6 3 7 25 7 459 135 143 t 139 142 171 39 7 8 8 5 4 651 115 68 157
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; positions_6nt_m2 versus oligos_6nt_mkv3_m1; m=4/4; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.547156; ahACAAAArk--- ; cor=; Ncor= a 258 104 407 0 407 407 407 407 167 64 0 0 0 c 61 132 0 407 0 0 0 0 29 62 0 0 0 g 29 53 0 0 0 0 0 0 148 162 0 0 0 t 59 118 0 0 0 0 0 0 63 119 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift0 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; rmwGAAAAATGma ; Alignment reference a 227 239 251 28 572 654 635 655 640 9 47 294 287 c 51 193 116 93 89 3 25 4 2 4 50 174 84 g 254 97 133 511 3 6 3 7 25 7 459 135 143 t 139 142 171 39 7 8 8 5 4 651 115 68 157
dyads_m2_shift0 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rmwGAAAAATGma ; cor=; Ncor= a 227 239 251 28 572 654 635 655 640 9 47 294 287 c 51 193 116 93 89 3 25 4 2 4 50 174 84 g 254 97 133 511 3 6 3 7 25 7 459 135 143 t 139 142 171 39 7 8 8 5 4 651 115 68 157
positions_6nt_m3_shift0 (positions_6nt_m3)				; dyads_m2 versus positions_6nt_m3; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.752042; swTaAAAAATyh- ; cor=; Ncor= a 153 165 75 426 613 610 617 616 591 33 139 204 0 c 181 84 33 9 9 11 6 8 16 11 193 166 0 g 178 116 35 104 3 4 8 6 17 27 123 101 0 t 129 276 498 102 16 16 10 11 17 570 186 170 0
positions_6nt_m1_shift0 (positions_6nt_m1)				; dyads_m2 versus positions_6nt_m1; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.724732; rdCAAAAAATkm- ; cor=; Ncor= a 288 233 73 666 711 673 665 713 756 32 144 319 0 c 154 60 620 6 18 90 3 31 1 25 141 259 0 g 209 235 35 101 49 11 92 33 15 22 266 109 0 t 131 254 54 9 4 8 22 5 10 703 231 95 0
positions_6nt_m4_shift0 (positions_6nt_m4)				; dyads_m2 versus positions_6nt_m4; m=4/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.698651; wwGAAAAAATav- ; cor=; Ncor= a 219 221 75 521 576 590 594 564 491 45 253 165 0 c 98 102 33 59 21 5 3 3 11 9 137 197 0 g 85 107 452 14 9 8 4 9 9 15 108 184 0 t 212 184 54 20 8 11 13 38 103 545 116 68 0
positions_6nt_m2_shift1 (positions_6nt_m2)				; dyads_m2 versus positions_6nt_m2; m=5/5; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.649511; -rrCAAAAAAGca ; cor=; Ncor= a 0 188 166 26 583 600 511 546 538 488 42 102 275 c 0 153 113 547 2 5 86 14 66 12 25 292 108 g 0 176 224 15 9 7 8 52 3 21 515 130 115 t 0 98 112 27 21 3 10 3 8 94 33 91 117

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -rdCAAAAAATkm ; Alignment reference a 0 288 233 73 666 711 673 665 713 756 32 144 319 c 0 154 60 620 6 18 90 3 31 1 25 141 259 g 0 209 235 35 101 49 11 92 33 15 22 266 109 t 0 131 254 54 9 4 8 22 5 10 703 231 95
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rdCAAAAAATkm ; cor=; Ncor= a 0 288 233 73 666 711 673 665 713 756 32 144 319 c 0 154 60 620 6 18 90 3 31 1 25 141 259 g 0 209 235 35 101 49 11 92 33 15 22 266 109 t 0 131 254 54 9 4 8 22 5 10 703 231 95
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m1 versus positions_6nt_m3; m=2/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.855633; -swTaAAAAATyh ; cor=; Ncor= a 0 153 165 75 426 613 610 617 616 591 33 139 204 c 0 181 84 33 9 9 11 6 8 16 11 193 166 g 0 178 116 35 104 3 4 8 6 17 27 123 101 t 0 129 276 498 102 16 16 10 11 17 570 186 170
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_6nt_m1 versus positions_6nt_m4; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.846334; -wwGAAAAAATav ; cor=; Ncor= a 0 219 221 75 521 576 590 594 564 491 45 253 165 c 0 98 102 33 59 21 5 3 3 11 9 137 197 g 0 85 107 452 14 9 8 4 9 9 15 108 184 t 0 212 184 54 20 8 11 13 38 103 545 116 68
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=4/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.811216; -rrCAAAAAAGca ; cor=; Ncor= a 0 188 166 26 583 600 511 546 538 488 42 102 275 c 0 153 113 547 2 5 86 14 66 12 25 292 108 g 0 176 224 15 9 7 8 52 3 21 515 130 115 t 0 98 112 27 21 3 10 3 8 94 33 91 117
dyads_m2_shift1 (dyads_m2)				; positions_6nt_m1 versus dyads_m2; m=5/6; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.724732; -rmwGAAAAATGm ; cor=; Ncor= a 0 227 239 251 28 572 654 635 655 640 9 47 294 c 0 51 193 116 93 89 3 25 4 2 4 50 174 g 0 254 97 133 511 3 6 3 7 25 7 459 135 t 0 139 142 171 39 7 8 8 5 4 651 115 68
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; positions_6nt_m1 versus oligos_6nt_mkv3_m1; m=6/6; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.513161; ahACAAAArk--- ; cor=; Ncor= a 258 104 407 0 407 407 407 407 167 64 0 0 0 c 61 132 0 407 0 0 0 0 29 62 0 0 0 g 29 53 0 0 0 0 0 0 148 162 0 0 0 t 59 118 0 0 0 0 0 0 63 119 0 0 0