One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.184326_2026-01-25.184326_ptOhrJ/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/2026/01/25/peak-motifs.2026-01-25.184326_2026-01-25.184326_ptOhrJ/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)
; oligos_6-8nt_m9; m=0 (reference); ncol1=14; shift=2; ncol=16; --awAAACAACAAAma ; Alignment reference a 0 0 150 129 275 318 329 26 327 321 38 323 323 275 130 125 c 0 0 58 64 53 18 16 286 15 14 282 14 19 37 93 66 g 0 0 84 70 25 14 9 20 12 17 13 19 16 19 65 88 t 0 0 79 108 18 21 17 39 17 19 38 15 13 40 83 92

oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)
; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --awAAACAACAAAma ; cor=; Ncor= a 0 0 150 129 275 318 329 26 327 321 38 323 323 275 130 125 c 0 0 58 64 53 18 16 286 15 14 282 14 19 37 93 66 g 0 0 84 70 25 14 9 20 12 17 13 19 16 19 65 88 t 0 0 79 108 18 21 17 39 17 19 38 15 13 40 83 92

dyads_m6_shift0 (dyads_m6)
; oligos_6-8nt_m9 versus dyads_m6; m=2/4; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.668618; rcmACAACAACAAcaa ; cor=; Ncor= a 171 88 158 351 12 354 327 44 332 373 15 360 334 57 175 190 c 67 199 165 22 373 26 33 337 39 13 372 26 26 278 84 70 g 118 71 57 31 16 22 30 16 28 20 12 16 36 35 96 103 t 61 59 37 13 16 15 27 20 18 11 18 15 21 47 62 54

oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; oligos_6-8nt_m9 versus oligos_6-8nt_m7; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.585238; --rwAAACAAAha--- ; cor=; Ncor= a 0 0 249 233 703 665 716 5 682 645 688 215 280 0 0 0 c 0 0 144 158 9 31 24 640 27 42 25 199 146 0 0 0 g 0 0 198 142 18 24 9 33 21 32 26 144 176 0 0 0 t 0 0 173 231 34 44 15 86 34 45 25 206 162 0 0 0

positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; oligos_6-8nt_m9 versus positions_6-8nt_m6; m=4/4; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.557465; -arTAAACAAAaa--- ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 172 0 0 0 c 0 90 78 38 17 16 9 345 12 17 15 81 72 0 0 0 g 0 86 113 17 5 5 11 8 7 6 12 66 84 0 0 0 t 0 99 85 301 11 11 8 30 8 8 14 102 89 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=19; shift=0; ncol=19; awATAAATAAAAATAataw ; Alignment reference a 81 64 133 29 151 151 159 26 147 140 141 148 152 30 147 125 40 70 75 c 25 27 16 12 8 11 5 23 10 14 16 14 9 13 8 20 13 37 24 g 34 32 16 15 8 6 8 7 18 9 6 3 11 5 13 12 19 33 35 t 46 63 21 130 19 18 14 130 11 23 23 21 14 138 18 29 114 46 52

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/5; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; awATAAATAAAAATAataw ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 148 152 30 147 125 40 70 75 c 25 27 16 12 8 11 5 23 10 14 16 14 9 13 8 20 13 37 24 g 34 32 16 15 8 6 8 7 18 9 6 3 11 5 13 12 19 33 35 t 46 63 21 130 19 18 14 130 11 23 23 21 14 138 18 29 114 46 52

oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; dyads_m5 versus oligos_6-8nt_m8; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.558093; wwATAAATAwww------- ; cor=; Ncor= a 232 183 433 17 573 471 548 10 575 267 221 205 0 0 0 0 0 0 0 c 94 108 38 12 15 47 23 22 16 105 105 119 0 0 0 0 0 0 0 g 123 109 76 24 10 28 29 17 16 81 117 93 0 0 0 0 0 0 0 t 176 225 78 572 27 79 25 576 18 172 182 208 0 0 0 0 0 0 0

positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; dyads_m5 versus positions_6-8nt_m6; m=3/5; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.508417; -arTAAACAAAaa------ ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 172 0 0 0 0 0 0 c 0 90 78 38 17 16 9 345 12 17 15 81 72 0 0 0 0 0 0 g 0 86 113 17 5 5 11 8 7 6 12 66 84 0 0 0 0 0 0 t 0 99 85 301 11 11 8 30 8 8 14 102 89 0 0 0 0 0 0

oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; dyads_m5 versus oligos_6-8nt_m7; m=4/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.432677; --rwAAACAAAha------ ; cor=; Ncor= a 0 0 249 233 703 665 716 5 682 645 688 215 280 0 0 0 0 0 0 c 0 0 144 158 9 31 24 640 27 42 25 199 146 0 0 0 0 0 0 g 0 0 198 142 18 24 9 33 21 32 26 144 176 0 0 0 0 0 0 t 0 0 173 231 34 44 15 86 34 45 25 206 162 0 0 0 0 0 0

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; dyads_m5 versus oligos_6-8nt_m3; m=5/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.416086; atrTAcATAta-------- ; cor=; Ncor= a 179 107 171 6 437 24 355 0 430 104 190 0 0 0 0 0 0 0 0 c 58 94 66 7 9 288 25 6 11 102 75 0 0 0 0 0 0 0 0 g 102 86 116 4 1 32 34 21 3 78 96 0 0 0 0 0 0 0 0 t 110 162 96 432 2 105 35 422 5 165 88 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m4_shift2 (oligos_6-8nt_m4)
; oligos_6-8nt_m4; m=0 (reference); ncol1=13; shift=2; ncol=15; --rgaGAGcGAGAgr ; Alignment reference a 0 0 187 100 341 11 483 23 129 13 478 36 377 93 195 c 0 0 113 94 71 7 9 11 347 7 14 29 64 87 123 g 0 0 141 280 74 497 21 479 30 496 28 423 54 268 145 t 0 0 85 52 40 11 13 13 20 10 6 38 31 78 63

oligos_6-8nt_m4_shift2 (oligos_6-8nt_m4)
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --rgaGAGcGAGAgr ; cor=; Ncor= a 0 0 187 100 341 11 483 23 129 13 478 36 377 93 195 c 0 0 113 94 71 7 9 11 347 7 14 29 64 87 123 g 0 0 141 280 74 497 21 479 30 496 28 423 54 268 145 t 0 0 85 52 40 11 13 13 20 10 6 38 31 78 63

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_6-8nt_m4 versus dyads_m2_rc; m=2/2; ncol2=17; w=-2; offset=-2; strand=R; shift=0; score=0.674334; rggGAGAGrGAGAGr ; cor=; Ncor= a 111 42 62 15 213 18 198 19 72 14 219 12 198 15 67 c 47 44 19 25 19 8 23 10 31 14 13 8 24 16 32 g 66 138 144 206 4 220 17 212 137 220 8 225 16 215 144 t 28 28 27 6 16 6 14 11 12 4 12 7 14 6 9

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=16; shift=0; ncol=16; rcmACAACAACAAcaa ; Alignment reference a 171 88 158 351 12 354 327 44 332 373 15 360 334 57 175 190 c 67 199 165 22 373 26 33 337 39 13 372 26 26 278 84 70 g 118 71 57 31 16 22 30 16 28 20 12 16 36 35 96 103 t 61 59 37 13 16 15 27 20 18 11 18 15 21 47 62 54

dyads_m6_shift0 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/2; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; rcmACAACAACAAcaa ; cor=; Ncor= a 171 88 158 351 12 354 327 44 332 373 15 360 334 57 175 190 c 67 199 165 22 373 26 33 337 39 13 372 26 26 278 84 70 g 118 71 57 31 16 22 30 16 28 20 12 16 36 35 96 103 t 61 59 37 13 16 15 27 20 18 11 18 15 21 47 62 54

oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)
; dyads_m6 versus oligos_6-8nt_m9; m=2/2; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.668618; --awAAACAACAAAma ; cor=; Ncor= a 0 0 150 129 275 318 329 26 327 321 38 323 323 275 130 125 c 0 0 58 64 53 18 16 286 15 14 282 14 19 37 93 66 g 0 0 84 70 25 14 9 20 12 17 13 19 16 19 65 88 t 0 0 79 108 18 21 17 39 17 19 38 15 13 40 83 92

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; gcrGCAGCAGCAGCrgc ; Alignment reference a 77 65 115 36 27 310 24 17 298 20 15 326 28 33 122 93 76 c 93 186 36 37 336 15 12 348 22 20 356 13 20 328 26 82 193 g 166 62 207 305 24 42 345 17 55 342 11 33 331 12 201 172 62 t 56 79 34 14 5 25 11 10 17 10 10 20 13 19 43 45 61

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; gcrGCAGCAGCAGCrgc ; cor=; Ncor= a 77 65 115 36 27 310 24 17 298 20 15 326 28 33 122 93 76 c 93 186 36 37 336 15 12 348 22 20 356 13 20 328 26 82 193 g 166 62 207 305 24 42 345 17 55 342 11 33 331 12 201 172 62 t 56 79 34 14 5 25 11 10 17 10 10 20 13 19 43 45 61

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m1_shift4 (oligos_6-8nt_m1)
; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----crCACrCACAca ; Alignment reference a 0 0 0 0 106 234 30 545 10 170 11 553 14 501 79 244 c 0 0 0 0 301 103 505 10 571 25 574 19 582 25 320 109 g 0 0 0 0 90 183 40 26 11 384 12 19 4 41 96 139 t 0 0 0 0 106 83 28 22 11 24 6 12 3 36 108 111

oligos_6-8nt_m1_shift4 (oligos_6-8nt_m1)
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----crCACrCACAca ; cor=; Ncor= a 0 0 0 0 106 234 30 545 10 170 11 553 14 501 79 244 c 0 0 0 0 301 103 505 10 571 25 574 19 582 25 320 109 g 0 0 0 0 90 183 40 26 11 384 12 19 4 41 96 139 t 0 0 0 0 106 83 28 22 11 24 6 12 3 36 108 111

oligos_6-8nt_m5_shift4 (oligos_6-8nt_m5)
; oligos_6-8nt_m1 versus oligos_6-8nt_m5; m=2/4; ncol2=15; w=0; offset=0; strand=D; shift=4; score=0.735221; ----crCACrCACwCA ; cor=; Ncor= a 0 0 0 0 47 111 17 239 7 83 5 264 5 112 3 223 c 0 0 0 0 161 46 225 10 265 14 269 7 276 12 263 19 g 0 0 0 0 25 85 21 17 9 172 6 7 3 32 11 25 t 0 0 0 0 54 45 24 21 6 18 7 9 3 131 10 20

dyads_m1_shift0 (dyads_m1)
; oligos_6-8nt_m1 versus dyads_m1; m=3/4; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.663322; caCaCACACACACAcr ; cor=; Ncor= a 155 363 107 519 60 658 35 674 43 654 34 680 34 630 99 384 c 420 130 557 67 685 30 710 31 678 34 679 17 678 31 440 116 g 99 187 52 137 20 71 22 55 37 71 35 60 35 88 124 199 t 122 116 80 73 31 37 29 36 38 37 48 39 49 47 133 97

oligos_6-8nt_m2_shift4 (oligos_6-8nt_m2)
; oligos_6-8nt_m1 versus oligos_6-8nt_m2; m=4/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.634019; ----cmcaCGCACAGT ; cor=; Ncor= a 0 0 0 0 31 50 21 110 9 21 4 155 1 139 6 14 c 0 0 0 0 64 46 94 20 136 7 150 8 163 12 31 10 g 0 0 0 0 38 36 34 20 16 134 6 3 3 13 125 10 t 0 0 0 0 37 38 21 20 9 8 10 4 3 6 8 136

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; crCACrCACwCACac ; Alignment reference a 47 111 17 239 7 83 5 264 5 112 3 223 10 126 35 c 161 46 225 10 265 14 269 7 276 12 263 19 250 49 148 g 25 85 21 17 9 172 6 7 3 32 11 25 15 68 49 t 54 45 24 21 6 18 7 9 3 131 10 20 12 44 55

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; crCACrCACwCACac ; cor=; Ncor= a 47 111 17 239 7 83 5 264 5 112 3 223 10 126 35 c 161 46 225 10 265 14 269 7 276 12 263 19 250 49 148 g 25 85 21 17 9 172 6 7 3 32 11 25 15 68 49 t 54 45 24 21 6 18 7 9 3 131 10 20 12 44 55

dyads_m1_shift0 (dyads_m1)
; oligos_6-8nt_m5 versus dyads_m1; m=2/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.835407; caCaCACACACACAc ; cor=; Ncor= a 155 363 107 519 60 658 35 674 43 654 34 680 34 630 99 c 420 130 557 67 685 30 710 31 678 34 679 17 678 31 440 g 99 187 52 137 20 71 22 55 37 71 35 60 35 88 124 t 122 116 80 73 31 37 29 36 38 37 48 39 49 47 133

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m5 versus oligos_6-8nt_m1; m=3/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.735221; crCACrCACAca--- ; cor=; Ncor= a 106 234 30 545 10 170 11 553 14 501 79 244 0 0 0 c 301 103 505 10 571 25 574 19 582 25 320 109 0 0 0 g 90 183 40 26 11 384 12 19 4 41 96 139 0 0 0 t 106 83 28 22 11 24 6 12 3 36 108 111 0 0 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=13; shift=0; ncol=13; rrAAGmrrAAGda ; Alignment reference a 102 75 285 290 1 88 100 82 283 294 0 86 112 c 65 64 1 7 3 81 59 61 1 3 2 61 72 g 77 93 4 0 292 68 76 91 6 2 295 76 57 t 55 67 9 2 3 62 64 65 9 0 2 76 58

dyads_m10_shift0 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rrAAGmrrAAGda ; cor=; Ncor= a 102 75 285 290 1 88 100 82 283 294 0 86 112 c 65 64 1 7 3 81 59 61 1 3 2 61 72 g 77 93 4 0 292 68 76 91 6 2 295 76 57 t 55 67 9 2 3 62 64 65 9 0 2 76 58

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; gsCGCCGCCGcy ; Alignment reference a 132 86 24 27 23 16 19 30 18 39 140 126 c 108 202 523 8 531 544 12 527 548 36 223 218 g 230 173 18 553 20 8 564 22 7 509 128 108 t 137 146 42 19 33 39 12 28 34 23 116 155

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gsCGCCGCCGcy ; cor=; Ncor= a 132 86 24 27 23 16 19 30 18 39 140 126 c 108 202 523 8 531 544 12 527 548 36 223 218 g 230 173 18 553 20 8 564 22 7 509 128 108 t 137 146 42 19 33 39 12 28 34 23 116 155

dyads_m7_shift1 (dyads_m7)
; dyads_m4 versus dyads_m7; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.704246; -ycGCCACCGvc ; cor=; Ncor= a 0 160 177 33 17 8 702 23 39 75 225 169 c 0 262 261 38 752 754 23 715 700 62 205 264 g 0 189 197 709 31 37 53 33 31 628 204 201 t 0 205 181 36 16 17 38 45 46 51 182 182

positions_6-8nt_m4_shift0 (positions_6-8nt_m4)
; dyads_m4 versus positions_6-8nt_m4; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.584933; ggCGGCGChs-- ; cor=; Ncor= a 54 38 0 0 0 0 0 0 62 43 0 0 c 52 41 235 0 0 235 0 235 68 67 0 0 g 86 104 0 235 235 0 235 0 42 82 0 0 t 43 52 0 0 0 0 0 0 63 43 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m6; m=0 (reference); ncol1=11; shift=0; ncol=11; kvTGGACAtms ; Alignment reference a 71 102 10 5 5 342 2 339 40 96 87 c 85 94 9 9 1 5 318 8 50 129 94 g 113 93 14 347 303 6 27 12 40 85 94 t 93 73 329 1 53 9 15 3 232 52 87

oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m6 versus oligos_6-8nt_m6; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; kvTGGACAtms ; cor=; Ncor= a 71 102 10 5 5 342 2 339 40 96 87 c 85 94 9 9 1 5 318 8 50 129 94 g 113 93 14 347 303 6 27 12 40 85 94 t 93 73 329 1 53 9 15 3 232 52 87

One-to-n matrix alignment; reference matrix: dyads_m7_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift1 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=11; shift=1; ncol=12; -ycGCCACCGvc ; Alignment reference a 0 160 177 33 17 8 702 23 39 75 225 169 c 0 262 261 38 752 754 23 715 700 62 205 264 g 0 189 197 709 31 37 53 33 31 628 204 201 t 0 205 181 36 16 17 38 45 46 51 182 182

dyads_m7_shift1 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -ycGCCACCGvc ; cor=; Ncor= a 0 160 177 33 17 8 702 23 39 75 225 169 c 0 262 261 38 752 754 23 715 700 62 205 264 g 0 189 197 709 31 37 53 33 31 628 204 201 t 0 205 181 36 16 17 38 45 46 51 182 182

dyads_m4_shift0 (dyads_m4)
; dyads_m7 versus dyads_m4; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.704246; gsCGCCGCCGcy ; cor=; Ncor= a 132 86 24 27 23 16 19 30 18 39 140 126 c 108 202 523 8 531 544 12 527 548 36 223 218 g 230 173 18 553 20 8 564 22 7 509 128 108 t 137 146 42 19 33 39 12 28 34 23 116 155

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=10; shift=0; ncol=10; agCAGCTGct ; Alignment reference a 162 95 0 430 0 0 0 1 88 98 c 84 104 429 0 0 430 0 0 143 86 g 86 143 0 0 430 0 0 429 104 84 t 98 88 1 0 0 0 430 0 95 162

dyads_m8_shift0 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; agCAGCTGct ; cor=; Ncor= a 162 95 0 430 0 0 0 1 88 98 c 84 104 429 0 0 430 0 0 143 86 g 86 143 0 0 430 0 0 429 104 84 t 98 88 1 0 0 0 430 0 95 162

One-to-n matrix alignment; reference matrix: positions_6-8nt_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)
; positions_6-8nt_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; ggCGGCGChs ; Alignment reference a 54 38 0 0 0 0 0 0 62 43 c 52 41 235 0 0 235 0 235 68 67 g 86 104 0 235 235 0 235 0 42 82 t 43 52 0 0 0 0 0 0 63 43

positions_6-8nt_m4_shift0 (positions_6-8nt_m4)
; positions_6-8nt_m4 versus positions_6-8nt_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ggCGGCGChs ; cor=; Ncor= a 54 38 0 0 0 0 0 0 62 43 c 52 41 235 0 0 235 0 235 68 67 g 86 104 0 235 235 0 235 0 42 82 t 43 52 0 0 0 0 0 0 63 43

dyads_m4_shift0 (dyads_m4)
; positions_6-8nt_m4 versus dyads_m4; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.584933; gsCGCCGCCG ; cor=; Ncor= a 132 86 24 27 23 16 19 30 18 39 c 108 202 523 8 531 544 12 527 548 36 g 230 173 18 553 20 8 564 22 7 509 t 137 146 42 19 33 39 12 28 34 23

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; caCaCACACACACAcr ; Alignment reference a 155 363 107 519 60 658 35 674 43 654 34 680 34 630 99 384 c 420 130 557 67 685 30 710 31 678 34 679 17 678 31 440 116 g 99 187 52 137 20 71 22 55 37 71 35 60 35 88 124 199 t 122 116 80 73 31 37 29 36 38 37 48 39 49 47 133 97

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; caCaCACACACACAcr ; cor=; Ncor= a 155 363 107 519 60 658 35 674 43 654 34 680 34 630 99 384 c 420 130 557 67 685 30 710 31 678 34 679 17 678 31 440 116 g 99 187 52 137 20 71 22 55 37 71 35 60 35 88 124 199 t 122 116 80 73 31 37 29 36 38 37 48 39 49 47 133 97

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; dyads_m1 versus oligos_6-8nt_m5; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.835407; crCACrCACwCACac- ; cor=; Ncor= a 47 111 17 239 7 83 5 264 5 112 3 223 10 126 35 0 c 161 46 225 10 265 14 269 7 276 12 263 19 250 49 148 0 g 25 85 21 17 9 172 6 7 3 32 11 25 15 68 49 0 t 54 45 24 21 6 18 7 9 3 131 10 20 12 44 55 0

oligos_6-8nt_m1_shift4 (oligos_6-8nt_m1)
; dyads_m1 versus oligos_6-8nt_m1; m=3/3; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.663322; ----crCACrCACAca ; cor=; Ncor= a 0 0 0 0 106 234 30 545 10 170 11 553 14 501 79 244 c 0 0 0 0 301 103 505 10 571 25 574 19 582 25 320 109 g 0 0 0 0 90 183 40 26 11 384 12 19 4 41 96 139 t 0 0 0 0 106 83 28 22 11 24 6 12 3 36 108 111

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; tcyCTCTCyCTCTCccy ; Alignment reference a 41 24 9 6 14 7 12 4 12 11 14 6 16 6 27 28 28 c 61 138 144 215 16 225 8 220 137 212 17 220 4 206 144 138 66 g 58 45 32 16 24 8 13 14 31 10 23 8 19 25 19 44 47 t 92 45 67 15 198 12 219 14 72 19 198 18 213 15 62 42 111

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; tcyCTCTCyCTCTCccy ; cor=; Ncor= a 41 24 9 6 14 7 12 4 12 11 14 6 16 6 27 28 28 c 61 138 144 215 16 225 8 220 137 212 17 220 4 206 144 138 66 g 58 45 32 16 24 8 13 14 31 10 23 8 19 25 19 44 47 t 92 45 67 15 198 12 219 14 72 19 198 18 213 15 62 42 111

oligos_6-8nt_m4_rc_shift2 (oligos_6-8nt_m4_rc)
; dyads_m2 versus oligos_6-8nt_m4_rc; m=2/3; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.674334; --ycTCTCgCTCtcy-- ; cor=; Ncor= a 0 0 63 78 31 38 6 10 20 13 13 11 40 52 85 0 0 c 0 0 145 268 54 423 28 496 30 479 21 497 74 280 141 0 0 g 0 0 123 87 64 29 14 7 347 11 9 7 71 94 113 0 0 t 0 0 195 93 377 36 478 13 129 23 483 11 341 100 187 0 0

dyads_m9_shift3 (dyads_m9)
; dyads_m2 versus dyads_m9; m=3/3; ncol2=20; w=0; offset=3; strand=D; shift=3; score=0.441764; ---ysCTCCyyctcsyb ; cor=; Ncor= a 0 0 0 77 55 15 21 4 13 96 72 59 97 63 50 84 71 c 0 0 0 140 130 379 12 368 327 126 146 204 87 179 158 142 122 g 0 0 0 89 128 7 19 21 26 67 85 79 68 93 107 74 105 t 0 0 0 105 98 10 359 18 45 122 108 69 159 76 96 111 113

One-to-n matrix alignment; reference matrix: positions_6-8nt_m6_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; positions_6-8nt_m6; m=0 (reference); ncol1=12; shift=1; ncol=13; -arTAAACAAAaa ; Alignment reference a 0 142 141 61 384 385 389 34 390 386 376 168 172 c 0 90 78 38 17 16 9 345 12 17 15 81 72 g 0 86 113 17 5 5 11 8 7 6 12 66 84 t 0 99 85 301 11 11 8 30 8 8 14 102 89

positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; positions_6-8nt_m6 versus positions_6-8nt_m6; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -arTAAACAAAaa ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 172 c 0 90 78 38 17 16 9 345 12 17 15 81 72 g 0 86 113 17 5 5 11 8 7 6 12 66 84 t 0 99 85 301 11 11 8 30 8 8 14 102 89

oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; positions_6-8nt_m6 versus oligos_6-8nt_m7; m=2/5; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.887598; --rwAAACAAAha ; cor=; Ncor= a 0 0 249 233 703 665 716 5 682 645 688 215 280 c 0 0 144 158 9 31 24 640 27 42 25 199 146 g 0 0 198 142 18 24 9 33 21 32 26 144 176 t 0 0 173 231 34 44 15 86 34 45 25 206 162

oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; positions_6-8nt_m6 versus oligos_6-8nt_m8; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.596291; wwATAAATAwww- ; cor=; Ncor= a 232 183 433 17 573 471 548 10 575 267 221 205 0 c 94 108 38 12 15 47 23 22 16 105 105 119 0 g 123 109 76 24 10 28 29 17 16 81 117 93 0 t 176 225 78 572 27 79 25 576 18 172 182 208 0

oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)
; positions_6-8nt_m6 versus oligos_6-8nt_m9; m=4/5; ncol2=14; w=0; offset=1; strand=D; shift=2; score=0.557465; --awAAACAACAA ; cor=; Ncor= a 0 0 150 129 275 318 329 26 327 321 38 323 323 c 0 0 58 64 53 18 16 286 15 14 282 14 19 g 0 0 84 70 25 14 9 20 12 17 13 19 16 t 0 0 79 108 18 21 17 39 17 19 38 15 13

dyads_m5_shift0 (dyads_m5)
; positions_6-8nt_m6 versus dyads_m5; m=5/5; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.508417; awATAAATAAAAA ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 148 152 c 25 27 16 12 8 11 5 23 10 14 16 14 9 g 34 32 16 15 8 6 8 7 18 9 6 3 11 t 46 63 21 130 19 18 14 130 11 23 23 21 14

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m10; m=0 (reference); ncol1=11; shift=0; ncol=11; yaCAGATACas ; Alignment reference a 105 168 20 453 19 437 9 425 21 176 115 c 144 115 444 13 36 36 31 32 435 112 142 g 106 114 23 21 426 11 23 20 23 88 137 t 146 104 14 14 20 17 438 24 22 125 107

oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m10 versus oligos_6-8nt_m10; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; yaCAGATACas ; cor=; Ncor= a 105 168 20 453 19 437 9 425 21 176 115 c 144 115 444 13 36 36 31 32 435 112 142 g 106 114 23 21 426 11 23 20 23 88 137 t 146 104 14 14 20 17 438 24 22 125 107

One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; wyATTTTCww ; Alignment reference a 76 51 279 0 11 7 4 0 87 80 c 61 76 0 0 0 1 0 279 61 61 g 56 57 0 0 0 1 0 0 58 57 t 86 95 0 279 268 270 275 0 73 81

positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wyATTTTCww ; cor=; Ncor= a 76 51 279 0 11 7 4 0 87 80 c 61 76 0 0 0 1 0 279 61 61 g 56 57 0 0 0 1 0 0 58 57 t 86 95 0 279 268 270 275 0 73 81

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; oligos_6-8nt_m7; m=0 (reference); ncol1=11; shift=2; ncol=13; --rwAAACAAAha ; Alignment reference a 0 0 249 233 703 665 716 5 682 645 688 215 280 c 0 0 144 158 9 31 24 640 27 42 25 199 146 g 0 0 198 142 18 24 9 33 21 32 26 144 176 t 0 0 173 231 34 44 15 86 34 45 25 206 162

oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --rwAAACAAAha ; cor=; Ncor= a 0 0 249 233 703 665 716 5 682 645 688 215 280 c 0 0 144 158 9 31 24 640 27 42 25 199 146 g 0 0 198 142 18 24 9 33 21 32 26 144 176 t 0 0 173 231 34 44 15 86 34 45 25 206 162

positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; oligos_6-8nt_m7 versus positions_6-8nt_m6; m=2/4; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.887598; -arTAAACAAAaa ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 172 c 0 90 78 38 17 16 9 345 12 17 15 81 72 g 0 86 113 17 5 5 11 8 7 6 12 66 84 t 0 99 85 301 11 11 8 30 8 8 14 102 89

oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)
; oligos_6-8nt_m7 versus oligos_6-8nt_m9; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=2; score=0.585238; --awAAACAACAA ; cor=; Ncor= a 0 0 150 129 275 318 329 26 327 321 38 323 323 c 0 0 58 64 53 18 16 286 15 14 282 14 19 g 0 0 84 70 25 14 9 20 12 17 13 19 16 t 0 0 79 108 18 21 17 39 17 19 38 15 13

dyads_m5_shift0 (dyads_m5)
; oligos_6-8nt_m7 versus dyads_m5; m=4/4; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.432677; awATAAATAAAAA ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 148 152 c 25 27 16 12 8 11 5 23 10 14 16 14 9 g 34 32 16 15 8 6 8 7 18 9 6 3 11 t 46 63 21 130 19 18 14 130 11 23 23 21 14

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m8_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATAAATAwww ; Alignment reference a 232 183 433 17 573 471 548 10 575 267 221 205 c 94 108 38 12 15 47 23 22 16 105 105 119 g 123 109 76 24 10 28 29 17 16 81 117 93 t 176 225 78 572 27 79 25 576 18 172 182 208

oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8 versus oligos_6-8nt_m8; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAATAwww ; cor=; Ncor= a 232 183 433 17 573 471 548 10 575 267 221 205 c 94 108 38 12 15 47 23 22 16 105 105 119 g 123 109 76 24 10 28 29 17 16 81 117 93 t 176 225 78 572 27 79 25 576 18 172 182 208

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m8 versus oligos_6-8nt_m3; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.780915; atrTAcATAta- ; cor=; Ncor= a 179 107 171 6 437 24 355 0 430 104 190 0 c 58 94 66 7 9 288 25 6 11 102 75 0 g 102 86 116 4 1 32 34 21 3 78 96 0 t 110 162 96 432 2 105 35 422 5 165 88 0

positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; oligos_6-8nt_m8 versus positions_6-8nt_m6; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.596291; -arTAAACAAAa ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 c 0 90 78 38 17 16 9 345 12 17 15 81 g 0 86 113 17 5 5 11 8 7 6 12 66 t 0 99 85 301 11 11 8 30 8 8 14 102

dyads_m5_shift0 (dyads_m5)
; oligos_6-8nt_m8 versus dyads_m5; m=4/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.558093; awATAAATAAAA ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 148 c 25 27 16 12 8 11 5 23 10 14 16 14 g 34 32 16 15 8 6 8 7 18 9 6 3 t 46 63 21 130 19 18 14 130 11 23 23 21

One-to-n matrix alignment; reference matrix: positions_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; positions_6-8nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; ktAGATTAth ; Alignment reference a 37 37 144 0 146 7 6 154 23 53 c 35 16 4 6 0 7 1 1 37 40 g 39 33 6 112 7 12 0 1 24 23 t 45 70 2 38 3 130 149 0 72 40

positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; positions_6-8nt_m3 versus positions_6-8nt_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ktAGATTAth ; cor=; Ncor= a 37 37 144 0 146 7 6 154 23 53 c 35 16 4 6 0 7 1 1 37 40 g 39 33 6 112 7 12 0 1 24 23 t 45 70 2 38 3 130 149 0 72 40

One-to-n matrix alignment; reference matrix: dyads_m9_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift3 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=20; shift=3; ncol=23; ---ysCTCCyyctcsybCTCCcy ; Alignment reference a 0 0 0 77 55 15 21 4 13 96 72 59 97 63 50 84 71 18 19 11 9 102 72 c 0 0 0 140 130 379 12 368 327 126 146 204 87 179 158 142 122 370 7 374 339 125 128 g 0 0 0 89 128 7 19 21 26 67 85 79 68 93 107 74 105 8 19 13 18 85 88 t 0 0 0 105 98 10 359 18 45 122 108 69 159 76 96 111 113 15 366 13 45 99 123

dyads_m9_shift3 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/2; ncol2=20; w=0; offset=0; strand=D; shift=3; score= 1; ---ysCTCCyyctcsybCTCCcy ; cor=; Ncor= a 0 0 0 77 55 15 21 4 13 96 72 59 97 63 50 84 71 18 19 11 9 102 72 c 0 0 0 140 130 379 12 368 327 126 146 204 87 179 158 142 122 370 7 374 339 125 128 g 0 0 0 89 128 7 19 21 26 67 85 79 68 93 107 74 105 8 19 13 18 85 88 t 0 0 0 105 98 10 359 18 45 122 108 69 159 76 96 111 113 15 366 13 45 99 123

dyads_m2_shift0 (dyads_m2)
; dyads_m9 versus dyads_m2; m=2/2; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.441764; tcyCTCTCyCTCTCccy------ ; cor=; Ncor= a 41 24 9 6 14 7 12 4 12 11 14 6 16 6 27 28 28 0 0 0 0 0 0 c 61 138 144 215 16 225 8 220 137 212 17 220 4 206 144 138 66 0 0 0 0 0 0 g 58 45 32 16 24 8 13 14 31 10 23 8 19 25 19 44 47 0 0 0 0 0 0 t 92 45 67 15 198 12 219 14 72 19 198 18 213 15 62 42 111 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m2_shift0 (positions_6-8nt_m2)
; positions_6-8nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; mmAACGCTsy ; Alignment reference a 38 27 104 108 0 0 1 0 23 21 c 28 38 0 0 108 1 107 0 32 35 g 19 23 0 0 0 107 0 0 27 25 t 23 20 4 0 0 0 0 108 26 27

positions_6-8nt_m2_shift0 (positions_6-8nt_m2)
; positions_6-8nt_m2 versus positions_6-8nt_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; mmAACGCTsy ; cor=; Ncor= a 38 27 104 108 0 0 1 0 23 21 c 28 38 0 0 108 1 107 0 32 35 g 19 23 0 0 0 107 0 0 27 25 t 23 20 4 0 0 0 0 108 26 27

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift0 ; 3 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=16; shift=0; ncol=16; cmcaCGCACAGTGGsv ; Alignment reference a 31 50 21 110 9 21 4 155 1 139 6 14 14 7 26 45 c 64 46 94 20 136 7 150 8 163 12 31 10 14 13 54 47 g 38 36 34 20 16 134 6 3 3 13 125 10 135 138 53 53 t 37 38 21 20 9 8 10 4 3 6 8 136 7 12 37 25

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/2; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cmcaCGCACAGTGGsv ; cor=; Ncor= a 31 50 21 110 9 21 4 155 1 139 6 14 14 7 26 45 c 64 46 94 20 136 7 150 8 163 12 31 10 14 13 54 47 g 38 36 34 20 16 134 6 3 3 13 125 10 135 138 53 53 t 37 38 21 20 9 8 10 4 3 6 8 136 7 12 37 25

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m2 versus oligos_6-8nt_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.634019; crCACrCACAca---- ; cor=; Ncor= a 106 234 30 545 10 170 11 553 14 501 79 244 0 0 0 0 c 301 103 505 10 571 25 574 19 582 25 320 109 0 0 0 0 g 90 183 40 26 11 384 12 19 4 41 96 139 0 0 0 0 t 106 83 28 22 11 24 6 12 3 36 108 111 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m5_shift0 (positions_6-8nt_m5)
; positions_6-8nt_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; sdAGGCTCyr ; Alignment reference a 16 24 78 0 3 3 0 1 14 28 c 24 12 2 0 1 68 0 79 21 18 g 21 23 0 80 72 9 0 0 16 26 t 19 21 0 0 4 0 80 0 29 8

positions_6-8nt_m5_shift0 (positions_6-8nt_m5)
; positions_6-8nt_m5 versus positions_6-8nt_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; sdAGGCTCyr ; cor=; Ncor= a 16 24 78 0 3 3 0 1 14 28 c 24 12 2 0 1 68 0 79 21 18 g 21 23 0 80 72 9 0 0 16 26 t 19 21 0 0 4 0 80 0 29 8

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; atrTAcATAta ; Alignment reference a 179 107 171 6 437 24 355 0 430 104 190 c 58 94 66 7 9 288 25 6 11 102 75 g 102 86 116 4 1 32 34 21 3 78 96 t 110 162 96 432 2 105 35 422 5 165 88

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; atrTAcATAta ; cor=; Ncor= a 179 107 171 6 437 24 355 0 430 104 190 c 58 94 66 7 9 288 25 6 11 102 75 g 102 86 116 4 1 32 34 21 3 78 96 t 110 162 96 432 2 105 35 422 5 165 88

oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m3 versus oligos_6-8nt_m8; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.780915; wwATAAATAww ; cor=; Ncor= a 232 183 433 17 573 471 548 10 575 267 221 c 94 108 38 12 15 47 23 22 16 105 105 g 123 109 76 24 10 28 29 17 16 81 117 t 176 225 78 572 27 79 25 576 18 172 182

dyads_m5_shift0 (dyads_m5)
; oligos_6-8nt_m3 versus dyads_m5; m=3/3; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.416086; awATAAATAAA ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 c 25 27 16 12 8 11 5 23 10 14 16 g 34 32 16 15 8 6 8 7 18 9 6 t 46 63 21 130 19 18 14 130 11 23 23

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)				; oligos_6-8nt_m9; m=0 (reference); ncol1=14; shift=2; ncol=16; --awAAACAACAAAma ; Alignment reference a 0 0 150 129 275 318 329 26 327 321 38 323 323 275 130 125 c 0 0 58 64 53 18 16 286 15 14 282 14 19 37 93 66 g 0 0 84 70 25 14 9 20 12 17 13 19 16 19 65 88 t 0 0 79 108 18 21 17 39 17 19 38 15 13 40 83 92
oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)				; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --awAAACAACAAAma ; cor=; Ncor= a 0 0 150 129 275 318 329 26 327 321 38 323 323 275 130 125 c 0 0 58 64 53 18 16 286 15 14 282 14 19 37 93 66 g 0 0 84 70 25 14 9 20 12 17 13 19 16 19 65 88 t 0 0 79 108 18 21 17 39 17 19 38 15 13 40 83 92
dyads_m6_shift0 (dyads_m6)				; oligos_6-8nt_m9 versus dyads_m6; m=2/4; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.668618; rcmACAACAACAAcaa ; cor=; Ncor= a 171 88 158 351 12 354 327 44 332 373 15 360 334 57 175 190 c 67 199 165 22 373 26 33 337 39 13 372 26 26 278 84 70 g 118 71 57 31 16 22 30 16 28 20 12 16 36 35 96 103 t 61 59 37 13 16 15 27 20 18 11 18 15 21 47 62 54
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; oligos_6-8nt_m9 versus oligos_6-8nt_m7; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.585238; --rwAAACAAAha--- ; cor=; Ncor= a 0 0 249 233 703 665 716 5 682 645 688 215 280 0 0 0 c 0 0 144 158 9 31 24 640 27 42 25 199 146 0 0 0 g 0 0 198 142 18 24 9 33 21 32 26 144 176 0 0 0 t 0 0 173 231 34 44 15 86 34 45 25 206 162 0 0 0
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; oligos_6-8nt_m9 versus positions_6-8nt_m6; m=4/4; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.557465; -arTAAACAAAaa--- ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 172 0 0 0 c 0 90 78 38 17 16 9 345 12 17 15 81 72 0 0 0 g 0 86 113 17 5 5 11 8 7 6 12 66 84 0 0 0 t 0 99 85 301 11 11 8 30 8 8 14 102 89 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=19; shift=0; ncol=19; awATAAATAAAAATAataw ; Alignment reference a 81 64 133 29 151 151 159 26 147 140 141 148 152 30 147 125 40 70 75 c 25 27 16 12 8 11 5 23 10 14 16 14 9 13 8 20 13 37 24 g 34 32 16 15 8 6 8 7 18 9 6 3 11 5 13 12 19 33 35 t 46 63 21 130 19 18 14 130 11 23 23 21 14 138 18 29 114 46 52
dyads_m5_shift0 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/5; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; awATAAATAAAAATAataw ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 148 152 30 147 125 40 70 75 c 25 27 16 12 8 11 5 23 10 14 16 14 9 13 8 20 13 37 24 g 34 32 16 15 8 6 8 7 18 9 6 3 11 5 13 12 19 33 35 t 46 63 21 130 19 18 14 130 11 23 23 21 14 138 18 29 114 46 52
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)				; dyads_m5 versus oligos_6-8nt_m8; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.558093; wwATAAATAwww------- ; cor=; Ncor= a 232 183 433 17 573 471 548 10 575 267 221 205 0 0 0 0 0 0 0 c 94 108 38 12 15 47 23 22 16 105 105 119 0 0 0 0 0 0 0 g 123 109 76 24 10 28 29 17 16 81 117 93 0 0 0 0 0 0 0 t 176 225 78 572 27 79 25 576 18 172 182 208 0 0 0 0 0 0 0
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; dyads_m5 versus positions_6-8nt_m6; m=3/5; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.508417; -arTAAACAAAaa------ ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 172 0 0 0 0 0 0 c 0 90 78 38 17 16 9 345 12 17 15 81 72 0 0 0 0 0 0 g 0 86 113 17 5 5 11 8 7 6 12 66 84 0 0 0 0 0 0 t 0 99 85 301 11 11 8 30 8 8 14 102 89 0 0 0 0 0 0
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; dyads_m5 versus oligos_6-8nt_m7; m=4/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.432677; --rwAAACAAAha------ ; cor=; Ncor= a 0 0 249 233 703 665 716 5 682 645 688 215 280 0 0 0 0 0 0 c 0 0 144 158 9 31 24 640 27 42 25 199 146 0 0 0 0 0 0 g 0 0 198 142 18 24 9 33 21 32 26 144 176 0 0 0 0 0 0 t 0 0 173 231 34 44 15 86 34 45 25 206 162 0 0 0 0 0 0
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)				; dyads_m5 versus oligos_6-8nt_m3; m=5/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.416086; atrTAcATAta-------- ; cor=; Ncor= a 179 107 171 6 437 24 355 0 430 104 190 0 0 0 0 0 0 0 0 c 58 94 66 7 9 288 25 6 11 102 75 0 0 0 0 0 0 0 0 g 102 86 116 4 1 32 34 21 3 78 96 0 0 0 0 0 0 0 0 t 110 162 96 432 2 105 35 422 5 165 88 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m1_shift4 (oligos_6-8nt_m1)				; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----crCACrCACAca ; Alignment reference a 0 0 0 0 106 234 30 545 10 170 11 553 14 501 79 244 c 0 0 0 0 301 103 505 10 571 25 574 19 582 25 320 109 g 0 0 0 0 90 183 40 26 11 384 12 19 4 41 96 139 t 0 0 0 0 106 83 28 22 11 24 6 12 3 36 108 111
oligos_6-8nt_m1_shift4 (oligos_6-8nt_m1)				; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----crCACrCACAca ; cor=; Ncor= a 0 0 0 0 106 234 30 545 10 170 11 553 14 501 79 244 c 0 0 0 0 301 103 505 10 571 25 574 19 582 25 320 109 g 0 0 0 0 90 183 40 26 11 384 12 19 4 41 96 139 t 0 0 0 0 106 83 28 22 11 24 6 12 3 36 108 111
oligos_6-8nt_m5_shift4 (oligos_6-8nt_m5)				; oligos_6-8nt_m1 versus oligos_6-8nt_m5; m=2/4; ncol2=15; w=0; offset=0; strand=D; shift=4; score=0.735221; ----crCACrCACwCA ; cor=; Ncor= a 0 0 0 0 47 111 17 239 7 83 5 264 5 112 3 223 c 0 0 0 0 161 46 225 10 265 14 269 7 276 12 263 19 g 0 0 0 0 25 85 21 17 9 172 6 7 3 32 11 25 t 0 0 0 0 54 45 24 21 6 18 7 9 3 131 10 20
dyads_m1_shift0 (dyads_m1)				; oligos_6-8nt_m1 versus dyads_m1; m=3/4; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.663322; caCaCACACACACAcr ; cor=; Ncor= a 155 363 107 519 60 658 35 674 43 654 34 680 34 630 99 384 c 420 130 557 67 685 30 710 31 678 34 679 17 678 31 440 116 g 99 187 52 137 20 71 22 55 37 71 35 60 35 88 124 199 t 122 116 80 73 31 37 29 36 38 37 48 39 49 47 133 97
oligos_6-8nt_m2_shift4 (oligos_6-8nt_m2)				; oligos_6-8nt_m1 versus oligos_6-8nt_m2; m=4/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.634019; ----cmcaCGCACAGT ; cor=; Ncor= a 0 0 0 0 31 50 21 110 9 21 4 155 1 139 6 14 c 0 0 0 0 64 46 94 20 136 7 150 8 163 12 31 10 g 0 0 0 0 38 36 34 20 16 134 6 3 3 13 125 10 t 0 0 0 0 37 38 21 20 9 8 10 4 3 6 8 136

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)				; oligos_6-8nt_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; crCACrCACwCACac ; Alignment reference a 47 111 17 239 7 83 5 264 5 112 3 223 10 126 35 c 161 46 225 10 265 14 269 7 276 12 263 19 250 49 148 g 25 85 21 17 9 172 6 7 3 32 11 25 15 68 49 t 54 45 24 21 6 18 7 9 3 131 10 20 12 44 55
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)				; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; crCACrCACwCACac ; cor=; Ncor= a 47 111 17 239 7 83 5 264 5 112 3 223 10 126 35 c 161 46 225 10 265 14 269 7 276 12 263 19 250 49 148 g 25 85 21 17 9 172 6 7 3 32 11 25 15 68 49 t 54 45 24 21 6 18 7 9 3 131 10 20 12 44 55
dyads_m1_shift0 (dyads_m1)				; oligos_6-8nt_m5 versus dyads_m1; m=2/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.835407; caCaCACACACACAc ; cor=; Ncor= a 155 363 107 519 60 658 35 674 43 654 34 680 34 630 99 c 420 130 557 67 685 30 710 31 678 34 679 17 678 31 440 g 99 187 52 137 20 71 22 55 37 71 35 60 35 88 124 t 122 116 80 73 31 37 29 36 38 37 48 39 49 47 133
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)				; oligos_6-8nt_m5 versus oligos_6-8nt_m1; m=3/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.735221; crCACrCACAca--- ; cor=; Ncor= a 106 234 30 545 10 170 11 553 14 501 79 244 0 0 0 c 301 103 505 10 571 25 574 19 582 25 320 109 0 0 0 g 90 183 40 26 11 384 12 19 4 41 96 139 0 0 0 t 106 83 28 22 11 24 6 12 3 36 108 111 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift0 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; gsCGCCGCCGcy ; Alignment reference a 132 86 24 27 23 16 19 30 18 39 140 126 c 108 202 523 8 531 544 12 527 548 36 223 218 g 230 173 18 553 20 8 564 22 7 509 128 108 t 137 146 42 19 33 39 12 28 34 23 116 155
dyads_m4_shift0 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gsCGCCGCCGcy ; cor=; Ncor= a 132 86 24 27 23 16 19 30 18 39 140 126 c 108 202 523 8 531 544 12 527 548 36 223 218 g 230 173 18 553 20 8 564 22 7 509 128 108 t 137 146 42 19 33 39 12 28 34 23 116 155
dyads_m7_shift1 (dyads_m7)				; dyads_m4 versus dyads_m7; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.704246; -ycGCCACCGvc ; cor=; Ncor= a 0 160 177 33 17 8 702 23 39 75 225 169 c 0 262 261 38 752 754 23 715 700 62 205 264 g 0 189 197 709 31 37 53 33 31 628 204 201 t 0 205 181 36 16 17 38 45 46 51 182 182
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)				; dyads_m4 versus positions_6-8nt_m4; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.584933; ggCGGCGChs-- ; cor=; Ncor= a 54 38 0 0 0 0 0 0 62 43 0 0 c 52 41 235 0 0 235 0 235 68 67 0 0 g 86 104 0 235 235 0 235 0 42 82 0 0 t 43 52 0 0 0 0 0 0 63 43 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift0 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; caCaCACACACACAcr ; Alignment reference a 155 363 107 519 60 658 35 674 43 654 34 680 34 630 99 384 c 420 130 557 67 685 30 710 31 678 34 679 17 678 31 440 116 g 99 187 52 137 20 71 22 55 37 71 35 60 35 88 124 199 t 122 116 80 73 31 37 29 36 38 37 48 39 49 47 133 97
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; caCaCACACACACAcr ; cor=; Ncor= a 155 363 107 519 60 658 35 674 43 654 34 680 34 630 99 384 c 420 130 557 67 685 30 710 31 678 34 679 17 678 31 440 116 g 99 187 52 137 20 71 22 55 37 71 35 60 35 88 124 199 t 122 116 80 73 31 37 29 36 38 37 48 39 49 47 133 97
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)				; dyads_m1 versus oligos_6-8nt_m5; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.835407; crCACrCACwCACac- ; cor=; Ncor= a 47 111 17 239 7 83 5 264 5 112 3 223 10 126 35 0 c 161 46 225 10 265 14 269 7 276 12 263 19 250 49 148 0 g 25 85 21 17 9 172 6 7 3 32 11 25 15 68 49 0 t 54 45 24 21 6 18 7 9 3 131 10 20 12 44 55 0
oligos_6-8nt_m1_shift4 (oligos_6-8nt_m1)				; dyads_m1 versus oligos_6-8nt_m1; m=3/3; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.663322; ----crCACrCACAca ; cor=; Ncor= a 0 0 0 0 106 234 30 545 10 170 11 553 14 501 79 244 c 0 0 0 0 301 103 505 10 571 25 574 19 582 25 320 109 g 0 0 0 0 90 183 40 26 11 384 12 19 4 41 96 139 t 0 0 0 0 106 83 28 22 11 24 6 12 3 36 108 111

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift0 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; tcyCTCTCyCTCTCccy ; Alignment reference a 41 24 9 6 14 7 12 4 12 11 14 6 16 6 27 28 28 c 61 138 144 215 16 225 8 220 137 212 17 220 4 206 144 138 66 g 58 45 32 16 24 8 13 14 31 10 23 8 19 25 19 44 47 t 92 45 67 15 198 12 219 14 72 19 198 18 213 15 62 42 111
dyads_m2_shift0 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; tcyCTCTCyCTCTCccy ; cor=; Ncor= a 41 24 9 6 14 7 12 4 12 11 14 6 16 6 27 28 28 c 61 138 144 215 16 225 8 220 137 212 17 220 4 206 144 138 66 g 58 45 32 16 24 8 13 14 31 10 23 8 19 25 19 44 47 t 92 45 67 15 198 12 219 14 72 19 198 18 213 15 62 42 111
oligos_6-8nt_m4_rc_shift2 (oligos_6-8nt_m4_rc)				; dyads_m2 versus oligos_6-8nt_m4_rc; m=2/3; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.674334; --ycTCTCgCTCtcy-- ; cor=; Ncor= a 0 0 63 78 31 38 6 10 20 13 13 11 40 52 85 0 0 c 0 0 145 268 54 423 28 496 30 479 21 497 74 280 141 0 0 g 0 0 123 87 64 29 14 7 347 11 9 7 71 94 113 0 0 t 0 0 195 93 377 36 478 13 129 23 483 11 341 100 187 0 0
dyads_m9_shift3 (dyads_m9)				; dyads_m2 versus dyads_m9; m=3/3; ncol2=20; w=0; offset=3; strand=D; shift=3; score=0.441764; ---ysCTCCyyctcsyb ; cor=; Ncor= a 0 0 0 77 55 15 21 4 13 96 72 59 97 63 50 84 71 c 0 0 0 140 130 379 12 368 327 126 146 204 87 179 158 142 122 g 0 0 0 89 128 7 19 21 26 67 85 79 68 93 107 74 105 t 0 0 0 105 98 10 359 18 45 122 108 69 159 76 96 111 113

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; positions_6-8nt_m6; m=0 (reference); ncol1=12; shift=1; ncol=13; -arTAAACAAAaa ; Alignment reference a 0 142 141 61 384 385 389 34 390 386 376 168 172 c 0 90 78 38 17 16 9 345 12 17 15 81 72 g 0 86 113 17 5 5 11 8 7 6 12 66 84 t 0 99 85 301 11 11 8 30 8 8 14 102 89
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; positions_6-8nt_m6 versus positions_6-8nt_m6; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -arTAAACAAAaa ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 172 c 0 90 78 38 17 16 9 345 12 17 15 81 72 g 0 86 113 17 5 5 11 8 7 6 12 66 84 t 0 99 85 301 11 11 8 30 8 8 14 102 89
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; positions_6-8nt_m6 versus oligos_6-8nt_m7; m=2/5; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.887598; --rwAAACAAAha ; cor=; Ncor= a 0 0 249 233 703 665 716 5 682 645 688 215 280 c 0 0 144 158 9 31 24 640 27 42 25 199 146 g 0 0 198 142 18 24 9 33 21 32 26 144 176 t 0 0 173 231 34 44 15 86 34 45 25 206 162
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)				; positions_6-8nt_m6 versus oligos_6-8nt_m8; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.596291; wwATAAATAwww- ; cor=; Ncor= a 232 183 433 17 573 471 548 10 575 267 221 205 0 c 94 108 38 12 15 47 23 22 16 105 105 119 0 g 123 109 76 24 10 28 29 17 16 81 117 93 0 t 176 225 78 572 27 79 25 576 18 172 182 208 0
oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)				; positions_6-8nt_m6 versus oligos_6-8nt_m9; m=4/5; ncol2=14; w=0; offset=1; strand=D; shift=2; score=0.557465; --awAAACAACAA ; cor=; Ncor= a 0 0 150 129 275 318 329 26 327 321 38 323 323 c 0 0 58 64 53 18 16 286 15 14 282 14 19 g 0 0 84 70 25 14 9 20 12 17 13 19 16 t 0 0 79 108 18 21 17 39 17 19 38 15 13
dyads_m5_shift0 (dyads_m5)				; positions_6-8nt_m6 versus dyads_m5; m=5/5; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.508417; awATAAATAAAAA ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 148 152 c 25 27 16 12 8 11 5 23 10 14 16 14 9 g 34 32 16 15 8 6 8 7 18 9 6 3 11 t 46 63 21 130 19 18 14 130 11 23 23 21 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; oligos_6-8nt_m7; m=0 (reference); ncol1=11; shift=2; ncol=13; --rwAAACAAAha ; Alignment reference a 0 0 249 233 703 665 716 5 682 645 688 215 280 c 0 0 144 158 9 31 24 640 27 42 25 199 146 g 0 0 198 142 18 24 9 33 21 32 26 144 176 t 0 0 173 231 34 44 15 86 34 45 25 206 162
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --rwAAACAAAha ; cor=; Ncor= a 0 0 249 233 703 665 716 5 682 645 688 215 280 c 0 0 144 158 9 31 24 640 27 42 25 199 146 g 0 0 198 142 18 24 9 33 21 32 26 144 176 t 0 0 173 231 34 44 15 86 34 45 25 206 162
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; oligos_6-8nt_m7 versus positions_6-8nt_m6; m=2/4; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.887598; -arTAAACAAAaa ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 172 c 0 90 78 38 17 16 9 345 12 17 15 81 72 g 0 86 113 17 5 5 11 8 7 6 12 66 84 t 0 99 85 301 11 11 8 30 8 8 14 102 89
oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)				; oligos_6-8nt_m7 versus oligos_6-8nt_m9; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=2; score=0.585238; --awAAACAACAA ; cor=; Ncor= a 0 0 150 129 275 318 329 26 327 321 38 323 323 c 0 0 58 64 53 18 16 286 15 14 282 14 19 g 0 0 84 70 25 14 9 20 12 17 13 19 16 t 0 0 79 108 18 21 17 39 17 19 38 15 13
dyads_m5_shift0 (dyads_m5)				; oligos_6-8nt_m7 versus dyads_m5; m=4/4; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.432677; awATAAATAAAAA ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 148 152 c 25 27 16 12 8 11 5 23 10 14 16 14 9 g 34 32 16 15 8 6 8 7 18 9 6 3 11 t 46 63 21 130 19 18 14 130 11 23 23 21 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)				; oligos_6-8nt_m8; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATAAATAwww ; Alignment reference a 232 183 433 17 573 471 548 10 575 267 221 205 c 94 108 38 12 15 47 23 22 16 105 105 119 g 123 109 76 24 10 28 29 17 16 81 117 93 t 176 225 78 572 27 79 25 576 18 172 182 208
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)				; oligos_6-8nt_m8 versus oligos_6-8nt_m8; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAATAwww ; cor=; Ncor= a 232 183 433 17 573 471 548 10 575 267 221 205 c 94 108 38 12 15 47 23 22 16 105 105 119 g 123 109 76 24 10 28 29 17 16 81 117 93 t 176 225 78 572 27 79 25 576 18 172 182 208
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)				; oligos_6-8nt_m8 versus oligos_6-8nt_m3; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.780915; atrTAcATAta- ; cor=; Ncor= a 179 107 171 6 437 24 355 0 430 104 190 0 c 58 94 66 7 9 288 25 6 11 102 75 0 g 102 86 116 4 1 32 34 21 3 78 96 0 t 110 162 96 432 2 105 35 422 5 165 88 0
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; oligos_6-8nt_m8 versus positions_6-8nt_m6; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.596291; -arTAAACAAAa ; cor=; Ncor= a 0 142 141 61 384 385 389 34 390 386 376 168 c 0 90 78 38 17 16 9 345 12 17 15 81 g 0 86 113 17 5 5 11 8 7 6 12 66 t 0 99 85 301 11 11 8 30 8 8 14 102
dyads_m5_shift0 (dyads_m5)				; oligos_6-8nt_m8 versus dyads_m5; m=4/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.558093; awATAAATAAAA ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 148 c 25 27 16 12 8 11 5 23 10 14 16 14 g 34 32 16 15 8 6 8 7 18 9 6 3 t 46 63 21 130 19 18 14 130 11 23 23 21

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)				; oligos_6-8nt_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; atrTAcATAta ; Alignment reference a 179 107 171 6 437 24 355 0 430 104 190 c 58 94 66 7 9 288 25 6 11 102 75 g 102 86 116 4 1 32 34 21 3 78 96 t 110 162 96 432 2 105 35 422 5 165 88
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)				; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; atrTAcATAta ; cor=; Ncor= a 179 107 171 6 437 24 355 0 430 104 190 c 58 94 66 7 9 288 25 6 11 102 75 g 102 86 116 4 1 32 34 21 3 78 96 t 110 162 96 432 2 105 35 422 5 165 88
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)				; oligos_6-8nt_m3 versus oligos_6-8nt_m8; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.780915; wwATAAATAww ; cor=; Ncor= a 232 183 433 17 573 471 548 10 575 267 221 c 94 108 38 12 15 47 23 22 16 105 105 g 123 109 76 24 10 28 29 17 16 81 117 t 176 225 78 572 27 79 25 576 18 172 182
dyads_m5_shift0 (dyads_m5)				; oligos_6-8nt_m3 versus dyads_m5; m=3/3; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.416086; awATAAATAAA ; cor=; Ncor= a 81 64 133 29 151 151 159 26 147 140 141 c 25 27 16 12 8 11 5 23 10 14 16 g 34 32 16 15 8 6 8 7 18 9 6 t 46 63 21 130 19 18 14 130 11 23 23