One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.211454_2026-02-26.211454_TYLWqA/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/2026/02/26/peak-motifs.2026-02-26.211454_2026-02-26.211454_TYLWqA/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=5; ncol=16; -----ahaCCCAGCwm ; Alignment reference a 0 0 0 0 0 222 154 279 16 27 9 490 12 13 178 164 c 0 0 0 0 0 111 159 72 533 513 550 40 12 530 122 183 g 0 0 0 0 0 127 119 99 11 16 5 29 540 15 83 90 t 0 0 0 0 0 118 146 128 18 22 14 19 14 20 195 141

oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----ahaCCCAGCwm ; cor=; Ncor= a 0 0 0 0 0 222 154 279 16 27 9 490 12 13 178 164 c 0 0 0 0 0 111 159 72 533 513 550 40 12 530 122 183 g 0 0 0 0 0 127 119 99 11 16 5 29 540 15 83 90 t 0 0 0 0 0 118 146 128 18 22 14 19 14 20 195 141

oligos_6nt_mkv3_m7_shift5 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m7; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=5; score=0.774394; -----kyaCCCAGGmw ; cor=; Ncor= a 0 0 0 0 0 158 157 414 21 38 14 587 14 22 211 175 c 0 0 0 0 0 109 167 49 574 566 599 11 14 25 181 119 g 0 0 0 0 0 168 128 110 31 10 11 28 602 572 110 155 t 0 0 0 0 0 212 195 74 21 33 23 21 17 28 145 198

dyads_m6_shift6 (dyads_m6)
; oligos_6nt_mkv3_m3 versus dyads_m6; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=6; score=0.661445; ------csCCCACCyc ; cor=; Ncor= a 0 0 0 0 0 0 81 122 9 21 8 416 6 3 95 91 c 0 0 0 0 0 0 224 171 476 469 516 26 510 488 177 220 g 0 0 0 0 0 0 105 143 39 34 9 79 18 41 129 119 t 0 0 0 0 0 0 129 103 15 15 6 18 5 7 138 109

dyads_m2_shift0 (dyads_m2)
; oligos_6nt_mkv3_m3 versus dyads_m2; m=4/4; ncol2=19; w=-5; offset=-5; strand=D; shift=0; score=0.405818; ssccCcCcCCCmGCCC ; cor=; Ncor= a 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 c 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 g 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 t 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; rwAAAGGAAww ; Alignment reference a 113 132 354 331 329 2 3 351 349 133 123 c 76 52 1 10 10 14 3 3 5 44 75 g 94 92 5 3 2 348 352 3 5 64 81 t 90 97 13 29 32 9 15 16 14 132 94

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; rwAAAGGAAww ; cor=; Ncor= a 113 132 354 331 329 2 3 351 349 133 123 c 76 52 1 10 10 14 3 3 5 44 75 g 94 92 5 3 2 348 352 3 5 64 81 t 90 97 13 29 32 9 15 16 14 132 94

oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m6; m=2/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.864203; -rrAAGGAArr ; cor=; Ncor= a 0 158 190 417 405 0 0 414 420 165 132 c 0 69 47 0 16 16 0 1 1 57 75 g 0 107 118 2 0 404 417 0 0 115 114 t 0 87 66 2 0 1 4 6 0 84 100

dyads_m7_shift0 (dyads_m7)
; oligos_7nt_mkv4_m2 versus dyads_m7; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.737351; wrAAAGGAAGG ; cor=; Ncor= a 82 78 199 231 233 7 23 228 234 23 17 c 43 55 16 9 10 15 4 9 8 11 16 g 59 84 28 11 6 218 226 5 11 202 211 t 71 38 12 4 6 15 2 13 2 19 11

oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m9; m=4/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.659738; -wmAAGCAAww ; cor=; Ncor= a 0 104 108 285 278 0 0 274 288 93 91 c 0 41 75 0 13 1 288 0 2 46 62 g 0 48 60 2 1 291 0 18 0 55 46 t 0 99 49 5 0 0 4 0 2 98 93

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift0 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=11; shift=0; ncol=11; whACAGAGTww ; Alignment reference a 194 167 598 7 594 17 586 33 79 226 226 c 112 174 9 605 6 25 8 16 71 111 99 g 96 135 13 10 7 554 11 576 53 126 149 t 239 165 21 19 34 45 36 16 438 178 167

dyads_m10_shift0 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; whACAGAGTww ; cor=; Ncor= a 194 167 598 7 594 17 586 33 79 226 226 c 112 174 9 605 6 25 8 16 71 111 99 g 96 135 13 10 7 554 11 576 53 126 149 t 239 165 21 19 34 45 36 16 438 178 167

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; dyads_m10 versus oligos_6nt_mkv3_m2; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.939926; wmACAGAGcwr ; cor=; Ncor= a 154 148 514 6 513 10 493 25 79 199 180 c 110 162 9 497 2 9 15 7 306 94 97 g 98 121 15 9 6 503 14 508 54 104 146 t 183 114 7 33 24 23 23 5 106 148 122

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; wwtTAAAAATAAAwAwww ; Alignment reference a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 305 121 184 141 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 12 27 35 46 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 23 31 55 33 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227 35 196 101 155

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/4; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwtTAAAAATAAAwAwww ; cor=; Ncor= a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 305 121 184 141 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 12 27 35 46 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 23 31 55 33 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227 35 196 101 155

dyads_m1_shift1 (dyads_m1)
; dyads_m4 versus dyads_m1; m=2/4; ncol2=16; w=0; offset=1; strand=D; shift=1; score=0.798853; -wwtTAAAATAAATAww- ; cor=; Ncor= a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 223 112 125 0 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 18 41 33 0 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 18 43 37 0 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215 27 90 91 0

oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; dyads_m4 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.553762; --wwTAAAATAAww---- ; cor=; Ncor= a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 0 0 0 0 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 0 0 0 0 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 0 0 0 0 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234 0 0 0 0

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; dyads_m4 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.479161; ----wwAAACAAAwa--- ; cor=; Ncor= a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 232 0 0 0 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 77 0 0 0 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 53 0 0 0 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154 102 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m6_shift0 (oligos_7nt_mkv4_m6)
; oligos_7nt_mkv4_m6; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAACCCTAww ; Alignment reference a 72 96 253 250 21 32 28 9 272 72 98 c 50 40 14 7 229 235 244 8 3 49 66 g 61 45 4 12 6 2 2 3 5 56 40 t 103 105 15 17 30 17 12 266 6 109 82

oligos_7nt_mkv4_m6_shift0 (oligos_7nt_mkv4_m6)
; oligos_7nt_mkv4_m6 versus oligos_7nt_mkv4_m6; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAACCCTAww ; cor=; Ncor= a 72 96 253 250 21 32 28 9 272 72 98 c 50 40 14 7 229 235 244 8 3 49 66 g 61 45 4 12 6 2 2 3 5 56 40 t 103 105 15 17 30 17 12 266 6 109 82

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=11; shift=0; ncol=11; kyaCCCAGGmw ; Alignment reference a 158 157 414 21 38 14 587 14 22 211 175 c 109 167 49 574 566 599 11 14 25 181 119 g 168 128 110 31 10 11 28 602 572 110 155 t 212 195 74 21 33 23 21 17 28 145 198

oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; kyaCCCAGGmw ; cor=; Ncor= a 158 157 414 21 38 14 587 14 22 211 175 c 109 167 49 574 566 599 11 14 25 181 119 g 168 128 110 31 10 11 28 602 572 110 155 t 212 195 74 21 33 23 21 17 28 145 198

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m3; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.774394; ahaCCCAGCwm ; cor=; Ncor= a 222 154 279 16 27 9 490 12 13 178 164 c 111 159 72 533 513 550 40 12 530 122 183 g 127 119 99 11 16 5 29 540 15 83 90 t 118 146 128 18 22 14 19 14 20 195 141

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; mvaCCCCATCyc ; Alignment reference a 104 90 190 10 7 14 8 246 2 7 66 54 c 95 77 37 263 258 246 273 15 20 265 77 118 g 38 80 31 8 6 17 5 23 19 9 41 62 t 56 46 35 12 22 16 7 9 252 12 109 59

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; mvaCCCCATCyc ; cor=; Ncor= a 104 90 190 10 7 14 8 246 2 7 66 54 c 95 77 37 263 258 246 273 15 20 265 77 118 g 38 80 31 8 6 17 5 23 19 9 41 62 t 56 46 35 12 22 16 7 9 252 12 109 59

One-to-n matrix alignment; reference matrix: dyads_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift1 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=16; shift=1; ncol=17; -wwtTAAAATAAATAww ; Alignment reference a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 223 112 125 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 18 41 33 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 18 43 37 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215 27 90 91

dyads_m1_shift1 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -wwtTAAAATAAATAww ; cor=; Ncor= a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 223 112 125 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 18 41 33 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 18 43 37 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215 27 90 91

dyads_m4_shift0 (dyads_m4)
; dyads_m1 versus dyads_m4; m=2/4; ncol2=18; w=-1; offset=-1; strand=D; shift=0; score=0.798853; wwtTAAAAATAAAwAww ; cor=; Ncor= a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 305 121 184 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 12 27 35 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 23 31 55 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227 35 196 101

oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; dyads_m1 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.696891; --wwTAAAATAAww--- ; cor=; Ncor= a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 0 0 0 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 0 0 0 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 0 0 0 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234 0 0 0

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; dyads_m1 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.514001; ----wwAAACAAAwa-- ; cor=; Ncor= a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 232 0 0 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 77 0 0 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 53 0 0 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154 102 0 0

One-to-n matrix alignment; reference matrix: dyads_m6_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift1 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=10; shift=1; ncol=11; -csCCCACCyc ; Alignment reference a 0 81 122 9 21 8 416 6 3 95 91 c 0 224 171 476 469 516 26 510 488 177 220 g 0 105 143 39 34 9 79 18 41 129 119 t 0 129 103 15 15 6 18 5 7 138 109

dyads_m6_shift1 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -csCCCACCyc ; cor=; Ncor= a 0 81 122 9 21 8 416 6 3 95 91 c 0 224 171 476 469 516 26 510 488 177 220 g 0 105 143 39 34 9 79 18 41 129 119 t 0 129 103 15 15 6 18 5 7 138 109

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; dyads_m6 versus oligos_6nt_mkv3_m3; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.661445; ahaCCCAGCwm ; cor=; Ncor= a 222 154 279 16 27 9 490 12 13 178 164 c 111 159 72 533 513 550 40 12 530 122 183 g 127 119 99 11 16 5 29 540 15 83 90 t 118 146 128 18 22 14 19 14 20 195 141

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwTAAAATAAww ; Alignment reference a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234

oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwTAAAATAAww ; cor=; Ncor= a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234

dyads_m1_shift1 (dyads_m1)
; oligos_6nt_mkv3_m4 versus dyads_m1; m=2/4; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.696891; -wwtTAAAATAAAT ; cor=; Ncor= a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215

dyads_m4_shift0 (dyads_m4)
; oligos_6nt_mkv3_m4 versus dyads_m4; m=3/4; ncol2=18; w=-2; offset=-2; strand=D; shift=0; score=0.553762; wwtTAAAAATAAAw ; cor=; Ncor= a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.549807; ----wwAAACAAAw ; cor=; Ncor= a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154

One-to-n matrix alignment; reference matrix: dyads_m2_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift2 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=19; shift=2; ncol=21; --ssccCcCcCCCmGCCCyss ; Alignment reference a 0 0 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 34 47 58 c 0 0 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 135 138 141 g 0 0 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 59 119 90 t 0 0 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22 103 27 42

dyads_m2_shift2 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --ssccCcCcCCCmGCCCyss ; cor=; Ncor= a 0 0 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 34 47 58 c 0 0 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 135 138 141 g 0 0 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 59 119 90 t 0 0 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22 103 27 42

dyads_m9_shift2 (dyads_m9)
; dyads_m2 versus dyads_m9; m=2/4; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.827478; --csCCCCCCCCCsCCCsCss ; cor=; Ncor= a 0 0 58 49 29 24 30 25 32 16 34 21 31 44 26 29 9 47 23 78 56 c 0 0 201 185 274 304 291 285 279 312 285 308 278 131 319 293 322 117 294 169 180 g 0 0 85 121 70 47 60 55 66 54 61 52 57 193 43 60 44 198 71 113 108 t 0 0 58 47 29 27 21 37 25 20 22 21 36 34 14 20 27 40 14 42 58

dyads_m5_shift0 (dyads_m5)
; dyads_m2 versus dyads_m5; m=3/4; ncol2=20; w=-2; offset=-2; strand=D; shift=0; score=0.615749; smgsCCCvsgCCcCCCCCss- ; cor=; Ncor= a 20 46 17 12 14 13 6 63 8 7 6 7 13 8 13 9 11 12 29 23 0 c 75 69 39 48 137 126 136 49 45 37 145 141 109 131 125 137 131 130 73 83 0 g 57 40 106 106 19 31 25 48 116 119 21 22 40 31 26 20 21 20 50 51 0 t 24 21 14 10 6 6 9 16 7 13 4 6 14 6 12 10 13 14 24 19 0

oligos_6nt_mkv3_m3_shift7 (oligos_6nt_mkv3_m3)
; dyads_m2 versus oligos_6nt_mkv3_m3; m=4/4; ncol2=11; w=0; offset=5; strand=D; shift=7; score=0.405818; -------ahaCCCAGCwm--- ; cor=; Ncor= a 0 0 0 0 0 0 0 222 154 279 16 27 9 490 12 13 178 164 0 0 0 c 0 0 0 0 0 0 0 111 159 72 533 513 550 40 12 530 122 183 0 0 0 g 0 0 0 0 0 0 0 127 119 99 11 16 5 29 540 15 83 90 0 0 0 t 0 0 0 0 0 0 0 118 146 128 18 22 14 19 14 20 195 141 0 0 0

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=13; shift=0; ncol=13; syCCCssyCTCcs ; Alignment reference a 167 131 17 28 14 131 153 132 7 27 9 150 147 c 232 206 621 548 626 247 191 230 640 64 659 210 200 g 176 170 40 47 31 190 235 138 29 65 17 167 188 t 117 185 14 69 21 124 113 192 16 536 7 165 157

dyads_m8_shift0 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; syCCCssyCTCcs ; cor=; Ncor= a 167 131 17 28 14 131 153 132 7 27 9 150 147 c 232 206 621 548 626 247 191 230 640 64 659 210 200 g 176 170 40 47 31 190 235 138 29 65 17 167 188 t 117 185 14 69 21 124 113 192 16 536 7 165 157

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwAAACAAAwa ; Alignment reference a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 232 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 77 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 53 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154 102

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wwAAACAAAwa ; cor=; Ncor= a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 232 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 77 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 53 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154 102

oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m4; m=2/4; ncol2=12; w=-2; offset=-2; strand=D; shift=2; score=0.549807; --wwTAAAATAAww- ; cor=; Ncor= a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 0 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 0 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 0 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234 0

dyads_m1_shift1 (dyads_m1)
; oligos_6nt_mkv3_m5 versus dyads_m1; m=3/4; ncol2=16; w=-3; offset=-3; strand=D; shift=1; score=0.514001; -wwtTAAAATAAATA ; cor=; Ncor= a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 223 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 18 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 18 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215 27

dyads_m4_shift0 (dyads_m4)
; oligos_6nt_mkv3_m5 versus dyads_m4; m=4/4; ncol2=18; w=-4; offset=-4; strand=D; shift=0; score=0.479161; wwtTAAAAATAAAwA ; cor=; Ncor= a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 305 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 12 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 23 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227 35

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 3 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; wwGAATGGAww ; Alignment reference a 106 112 12 304 302 9 23 5 305 115 113 c 34 56 3 9 12 2 6 7 15 57 45 g 70 59 302 6 12 7 302 285 3 68 45 t 127 110 20 18 11 319 6 40 14 97 134

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwGAATGGAww ; cor=; Ncor= a 106 112 12 304 302 9 23 5 305 115 113 c 34 56 3 9 12 2 6 7 15 57 45 g 70 59 302 6 12 7 302 285 3 68 45 t 127 110 20 18 11 319 6 40 14 97 134

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; oligos_7nt_mkv4_m4 versus positions_6nt_m1_rc; m=2/2; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.478795; ---aaTGGAAT ; cor=; Ncor= a 0 0 0 126 118 1 2 2 316 308 18 c 0 0 0 71 62 13 11 0 0 8 3 g 0 0 0 46 70 9 307 317 1 3 0 t 0 0 0 77 70 297 0 1 3 1 299

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; rwGAGTTGAww ; Alignment reference a 86 121 7 300 6 36 27 27 302 145 91 c 72 30 0 3 3 7 7 3 7 46 71 g 95 46 295 4 307 11 12 279 5 45 56 t 72 128 23 18 9 271 279 16 11 89 107

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; rwGAGTTGAww ; cor=; Ncor= a 86 121 7 300 6 36 27 27 302 145 91 c 72 30 0 3 3 7 7 3 7 46 71 g 95 46 295 4 307 11 12 279 5 45 56 t 72 128 23 18 9 271 279 16 11 89 107

oligos_8nt_mkv5_m1_shift0 (oligos_8nt_mkv5_m1)
; oligos_7nt_mkv4_m5 versus oligos_8nt_mkv5_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.873769; vdGAGTTGAAt ; cor=; Ncor= a 91 124 15 343 29 18 18 15 332 332 87 c 94 22 10 2 22 19 5 30 4 8 87 g 95 92 321 4 284 11 9 290 14 4 70 t 74 116 8 5 19 306 322 19 4 10 110

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; hkATTCCAtt ; Alignment reference a 88 70 299 1 3 1 0 297 70 77 c 82 67 0 3 1 317 307 9 70 46 g 41 102 3 8 0 0 11 13 62 71 t 109 81 18 308 316 2 2 1 118 126

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; hkATTCCAtt ; cor=; Ncor= a 88 70 299 1 3 1 0 297 70 77 c 82 67 0 3 1 317 307 9 70 46 g 41 102 3 8 0 0 11 13 62 71 t 109 81 18 308 316 2 2 1 118 126

oligos_7nt_mkv4_m4_rc_shift2 (oligos_7nt_mkv4_m4_rc)
; positions_6nt_m1 versus oligos_7nt_mkv4_m4_rc; m=2/2; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.478795; --wwTCCATT ; cor=; Ncor= a 0 0 134 97 14 40 6 319 11 18 c 0 0 45 68 3 285 302 7 12 6 g 0 0 45 57 15 7 6 2 12 9 t 0 0 113 115 305 5 23 9 302 304

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=10; shift=4; ncol=14; ----mgCCTCCCvv ; Alignment reference a 0 0 0 0 177 108 18 5 24 6 11 6 181 169 c 0 0 0 0 217 157 615 615 26 616 605 611 178 185 g 0 0 0 0 143 236 18 26 71 21 33 36 181 200 t 0 0 0 0 122 158 8 13 538 16 10 6 119 105

oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----mgCCTCCCvv ; cor=; Ncor= a 0 0 0 0 177 108 18 5 24 6 11 6 181 169 c 0 0 0 0 217 157 615 615 26 616 605 611 178 185 g 0 0 0 0 143 236 18 26 71 21 33 36 181 200 t 0 0 0 0 122 158 8 13 538 16 10 6 119 105

oligos_6nt_mkv3_m8_shift4 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m8; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.795134; ----ykCCTTCCkb ; cor=; Ncor= a 0 0 0 0 105 87 9 6 4 6 3 1 76 93 c 0 0 0 0 132 98 407 413 9 46 436 423 111 116 g 0 0 0 0 76 128 25 26 21 21 6 23 115 116 t 0 0 0 0 138 138 10 6 417 378 6 4 149 126

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m1 versus dyads_m3; m=3/3; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.570289; ymTtCTCCTCCCTc ; cor=; Ncor= a 67 99 22 24 28 17 5 10 18 5 7 17 41 58 c 92 89 30 55 223 31 281 277 9 223 279 271 27 113 g 66 50 37 29 17 21 8 7 9 50 7 8 23 68 t 85 72 221 202 42 241 16 16 274 32 17 14 219 71

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m6_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=1; ncol=11; -rrAAGGAArr ; Alignment reference a 0 158 190 417 405 0 0 414 420 165 132 c 0 69 47 0 16 16 0 1 1 57 75 g 0 107 118 2 0 404 417 0 0 115 114 t 0 87 66 2 0 1 4 6 0 84 100

oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -rrAAGGAArr ; cor=; Ncor= a 0 158 190 417 405 0 0 414 420 165 132 c 0 69 47 0 16 16 0 1 1 57 75 g 0 107 118 2 0 404 417 0 0 115 114 t 0 87 66 2 0 1 4 6 0 84 100

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m6 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.864203; rwAAAGGAAww ; cor=; Ncor= a 113 132 354 331 329 2 3 351 349 133 123 c 76 52 1 10 10 14 3 3 5 44 75 g 94 92 5 3 2 348 352 3 5 64 81 t 90 97 13 29 32 9 15 16 14 132 94

oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m9; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.761639; -wmAAGCAAww ; cor=; Ncor= a 0 104 108 285 278 0 0 274 288 93 91 c 0 41 75 0 13 1 288 0 2 46 62 g 0 48 60 2 1 291 0 18 0 55 46 t 0 99 49 5 0 0 4 0 2 98 93

dyads_m7_shift0 (dyads_m7)
; oligos_6nt_mkv3_m6 versus dyads_m7; m=4/4; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.680155; wrAAAGGAAGG ; cor=; Ncor= a 82 78 199 231 233 7 23 228 234 23 17 c 43 55 16 9 10 15 4 9 8 11 16 g 59 84 28 11 6 218 226 5 11 202 211 t 71 38 12 4 6 15 2 13 2 19 11

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift0 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=13; shift=0; ncol=13; wrAAAGGAAGGaw ; Alignment reference a 82 78 199 231 233 7 23 228 234 23 17 87 93 c 43 55 16 9 10 15 4 9 8 11 16 49 32 g 59 84 28 11 6 218 226 5 11 202 211 58 53 t 71 38 12 4 6 15 2 13 2 19 11 61 77

dyads_m7_shift0 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wrAAAGGAAGGaw ; cor=; Ncor= a 82 78 199 231 233 7 23 228 234 23 17 87 93 c 43 55 16 9 10 15 4 9 8 11 16 49 32 g 59 84 28 11 6 218 226 5 11 202 211 58 53 t 71 38 12 4 6 15 2 13 2 19 11 61 77

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; dyads_m7 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.737351; rwAAAGGAAww-- ; cor=; Ncor= a 113 132 354 331 329 2 3 351 349 133 123 0 0 c 76 52 1 10 10 14 3 3 5 44 75 0 0 g 94 92 5 3 2 348 352 3 5 64 81 0 0 t 90 97 13 29 32 9 15 16 14 132 94 0 0

oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; dyads_m7 versus oligos_6nt_mkv3_m6; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.680155; -rrAAGGAArr-- ; cor=; Ncor= a 0 158 190 417 405 0 0 414 420 165 132 0 0 c 0 69 47 0 16 16 0 1 1 57 75 0 0 g 0 107 118 2 0 404 417 0 0 115 114 0 0 t 0 87 66 2 0 1 4 6 0 84 100 0 0

oligos_6nt_mkv3_m8_rc_shift3 (oligos_6nt_mkv3_m8_rc)
; dyads_m7 versus oligos_6nt_mkv3_m8_rc; m=4/4; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.66523; ---vmGGAAGGmr ; cor=; Ncor= a 0 0 0 126 149 4 6 378 417 6 10 138 138 c 0 0 0 116 115 23 6 21 21 26 25 128 76 g 0 0 0 116 111 423 436 46 9 413 407 98 132 t 0 0 0 93 76 1 3 6 4 6 9 87 105

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv5_m2_shift0 (oligos_8nt_mkv5_m2)
; oligos_8nt_mkv5_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; wsCAAATATChw ; Alignment reference a 116 82 33 334 326 323 17 295 10 14 123 105 c 66 99 272 5 6 6 14 20 5 296 100 79 g 43 93 32 7 8 8 9 15 5 18 13 56 t 124 75 12 3 9 12 309 19 329 21 113 109

oligos_8nt_mkv5_m2_shift0 (oligos_8nt_mkv5_m2)
; oligos_8nt_mkv5_m2 versus oligos_8nt_mkv5_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wsCAAATATChw ; cor=; Ncor= a 116 82 33 334 326 323 17 295 10 14 123 105 c 66 99 272 5 6 6 14 20 5 296 100 79 g 43 93 32 7 8 8 9 15 5 18 13 56 t 124 75 12 3 9 12 309 19 329 21 113 109

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv5_m1_shift0 (oligos_8nt_mkv5_m1)
; oligos_8nt_mkv5_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; vdGAGTTGAAtr ; Alignment reference a 91 124 15 343 29 18 18 15 332 332 87 106 c 94 22 10 2 22 19 5 30 4 8 87 69 g 95 92 321 4 284 11 9 290 14 4 70 108 t 74 116 8 5 19 306 322 19 4 10 110 71

oligos_8nt_mkv5_m1_shift0 (oligos_8nt_mkv5_m1)
; oligos_8nt_mkv5_m1 versus oligos_8nt_mkv5_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; vdGAGTTGAAtr ; cor=; Ncor= a 91 124 15 343 29 18 18 15 332 332 87 106 c 94 22 10 2 22 19 5 30 4 8 87 69 g 95 92 321 4 284 11 9 290 14 4 70 108 t 74 116 8 5 19 306 322 19 4 10 110 71

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_8nt_mkv5_m1 versus oligos_7nt_mkv4_m5; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.873769; rwGAGTTGAww- ; cor=; Ncor= a 86 121 7 300 6 36 27 27 302 145 91 0 c 72 30 0 3 3 7 7 3 7 46 71 0 g 95 46 295 4 307 11 12 279 5 45 56 0 t 72 128 23 18 9 271 279 16 11 89 107 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m8_shift4 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ykCCTTCCkb ; Alignment reference a 0 0 0 0 105 87 9 6 4 6 3 1 76 93 c 0 0 0 0 132 98 407 413 9 46 436 423 111 116 g 0 0 0 0 76 128 25 26 21 21 6 23 115 116 t 0 0 0 0 138 138 10 6 417 378 6 4 149 126

oligos_6nt_mkv3_m8_shift4 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----ykCCTTCCkb ; cor=; Ncor= a 0 0 0 0 105 87 9 6 4 6 3 1 76 93 c 0 0 0 0 132 98 407 413 9 46 436 423 111 116 g 0 0 0 0 76 128 25 26 21 21 6 23 115 116 t 0 0 0 0 138 138 10 6 417 378 6 4 149 126

oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m1; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.795134; ----mgCCTCCCvv ; cor=; Ncor= a 0 0 0 0 177 108 18 5 24 6 11 6 181 169 c 0 0 0 0 217 157 615 615 26 616 605 611 178 185 g 0 0 0 0 143 236 18 26 71 21 33 36 181 200 t 0 0 0 0 122 158 8 13 538 16 10 6 119 105

dyads_m7_rc_shift4 (dyads_m7_rc)
; oligos_6nt_mkv3_m8 versus dyads_m7_rc; m=3/4; ncol2=13; w=0; offset=0; strand=R; shift=4; score=0.66523; ----wtCCTTCCTT ; cor=; Ncor= a 0 0 0 0 77 61 11 19 2 13 2 15 6 4 c 0 0 0 0 53 58 211 202 11 5 226 218 6 11 g 0 0 0 0 32 49 16 11 8 9 4 15 10 9 t 0 0 0 0 93 87 17 23 234 228 23 7 233 231

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m8 versus dyads_m3; m=4/4; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.516571; ymTtCTCCTCCCTc ; cor=; Ncor= a 67 99 22 24 28 17 5 10 18 5 7 17 41 58 c 92 89 30 55 223 31 281 277 9 223 279 271 27 113 g 66 50 37 29 17 21 8 7 9 50 7 8 23 68 t 85 72 221 202 42 241 16 16 274 32 17 14 219 71

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=1; ncol=11; -wmAAGCAAww ; Alignment reference a 0 104 108 285 278 0 0 274 288 93 91 c 0 41 75 0 13 1 288 0 2 46 62 g 0 48 60 2 1 291 0 18 0 55 46 t 0 99 49 5 0 0 4 0 2 98 93

oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wmAAGCAAww ; cor=; Ncor= a 0 104 108 285 278 0 0 274 288 93 91 c 0 41 75 0 13 1 288 0 2 46 62 g 0 48 60 2 1 291 0 18 0 55 46 t 0 99 49 5 0 0 4 0 2 98 93

oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m6; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.761639; -rrAAGGAArr ; cor=; Ncor= a 0 158 190 417 405 0 0 414 420 165 132 c 0 69 47 0 16 16 0 1 1 57 75 g 0 107 118 2 0 404 417 0 0 115 114 t 0 87 66 2 0 1 4 6 0 84 100

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m9 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.659738; rwAAAGGAAww ; cor=; Ncor= a 113 132 354 331 329 2 3 351 349 133 123 c 76 52 1 10 10 14 3 3 5 44 75 g 94 92 5 3 2 348 352 3 5 64 81 t 90 97 13 29 32 9 15 16 14 132 94

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=20; shift=0; ncol=20; smgsCCCvsgCCcCCCCCss ; Alignment reference a 20 46 17 12 14 13 6 63 8 7 6 7 13 8 13 9 11 12 29 23 c 75 69 39 48 137 126 136 49 45 37 145 141 109 131 125 137 131 130 73 83 g 57 40 106 106 19 31 25 48 116 119 21 22 40 31 26 20 21 20 50 51 t 24 21 14 10 6 6 9 16 7 13 4 6 14 6 12 10 13 14 24 19

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; smgsCCCvsgCCcCCCCCss ; cor=; Ncor= a 20 46 17 12 14 13 6 63 8 7 6 7 13 8 13 9 11 12 29 23 c 75 69 39 48 137 126 136 49 45 37 145 141 109 131 125 137 131 130 73 83 g 57 40 106 106 19 31 25 48 116 119 21 22 40 31 26 20 21 20 50 51 t 24 21 14 10 6 6 9 16 7 13 4 6 14 6 12 10 13 14 24 19

dyads_m9_shift1 (dyads_m9)
; dyads_m5 versus dyads_m9; m=2/3; ncol2=19; w=0; offset=1; strand=D; shift=1; score=0.708928; -csCCCCCCCCCsCCCsCss ; cor=; Ncor= a 0 58 49 29 24 30 25 32 16 34 21 31 44 26 29 9 47 23 78 56 c 0 201 185 274 304 291 285 279 312 285 308 278 131 319 293 322 117 294 169 180 g 0 85 121 70 47 60 55 66 54 61 52 57 193 43 60 44 198 71 113 108 t 0 58 47 29 27 21 37 25 20 22 21 36 34 14 20 27 40 14 42 58

dyads_m2_shift2 (dyads_m2)
; dyads_m5 versus dyads_m2; m=3/3; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.615749; --ssccCcCcCCCmGCCCys ; cor=; Ncor= a 0 0 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 34 47 c 0 0 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 135 138 g 0 0 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 59 119 t 0 0 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22 103 27

One-to-n matrix alignment; reference matrix: dyads_m9_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift1 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=19; shift=1; ncol=20; -csCCCCCCCCCsCCCsCss ; Alignment reference a 0 58 49 29 24 30 25 32 16 34 21 31 44 26 29 9 47 23 78 56 c 0 201 185 274 304 291 285 279 312 285 308 278 131 319 293 322 117 294 169 180 g 0 85 121 70 47 60 55 66 54 61 52 57 193 43 60 44 198 71 113 108 t 0 58 47 29 27 21 37 25 20 22 21 36 34 14 20 27 40 14 42 58

dyads_m9_shift1 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -csCCCCCCCCCsCCCsCss ; cor=; Ncor= a 0 58 49 29 24 30 25 32 16 34 21 31 44 26 29 9 47 23 78 56 c 0 201 185 274 304 291 285 279 312 285 308 278 131 319 293 322 117 294 169 180 g 0 85 121 70 47 60 55 66 54 61 52 57 193 43 60 44 198 71 113 108 t 0 58 47 29 27 21 37 25 20 22 21 36 34 14 20 27 40 14 42 58

dyads_m2_shift1 (dyads_m2)
; dyads_m9 versus dyads_m2; m=2/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score=0.827478; -ssccCcCcCCCmGCCCyss ; cor=; Ncor= a 0 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 34 47 58 c 0 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 135 138 141 g 0 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 59 119 90 t 0 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22 103 27 42

dyads_m5_shift0 (dyads_m5)
; dyads_m9 versus dyads_m5; m=3/3; ncol2=20; w=-1; offset=-1; strand=D; shift=0; score=0.708928; smgsCCCvsgCCcCCCCCss ; cor=; Ncor= a 20 46 17 12 14 13 6 63 8 7 6 7 13 8 13 9 11 12 29 23 c 75 69 39 48 137 126 136 49 45 37 145 141 109 131 125 137 131 130 73 83 g 57 40 106 106 19 31 25 48 116 119 21 22 40 31 26 20 21 20 50 51 t 24 21 14 10 6 6 9 16 7 13 4 6 14 6 12 10 13 14 24 19

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 3 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=11; shift=0; ncol=11; wmACAGAGcwr ; Alignment reference a 154 148 514 6 513 10 493 25 79 199 180 c 110 162 9 497 2 9 15 7 306 94 97 g 98 121 15 9 6 503 14 508 54 104 146 t 183 114 7 33 24 23 23 5 106 148 122

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wmACAGAGcwr ; cor=; Ncor= a 154 148 514 6 513 10 493 25 79 199 180 c 110 162 9 497 2 9 15 7 306 94 97 g 98 121 15 9 6 503 14 508 54 104 146 t 183 114 7 33 24 23 23 5 106 148 122

dyads_m10_shift0 (dyads_m10)
; oligos_6nt_mkv3_m2 versus dyads_m10; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.939926; whACAGAGTww ; cor=; Ncor= a 194 167 598 7 594 17 586 33 79 226 226 c 112 174 9 605 6 25 8 16 71 111 99 g 96 135 13 10 7 554 11 576 53 126 149 t 239 165 21 19 34 45 36 16 438 178 167

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ymTtCTCCTCCCTch ; Alignment reference a 67 99 22 24 28 17 5 10 18 5 7 17 41 58 94 c 92 89 30 55 223 31 281 277 9 223 279 271 27 113 81 g 66 50 37 29 17 21 8 7 9 50 7 8 23 68 55 t 85 72 221 202 42 241 16 16 274 32 17 14 219 71 80

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ymTtCTCCTCCCTch ; cor=; Ncor= a 67 99 22 24 28 17 5 10 18 5 7 17 41 58 94 c 92 89 30 55 223 31 281 277 9 223 279 271 27 113 81 g 66 50 37 29 17 21 8 7 9 50 7 8 23 68 55 t 85 72 221 202 42 241 16 16 274 32 17 14 219 71 80

oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; dyads_m3 versus oligos_6nt_mkv3_m1; m=2/3; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.570289; ----mgCCTCCCvv- ; cor=; Ncor= a 0 0 0 0 177 108 18 5 24 6 11 6 181 169 0 c 0 0 0 0 217 157 615 615 26 616 605 611 178 185 0 g 0 0 0 0 143 236 18 26 71 21 33 36 181 200 0 t 0 0 0 0 122 158 8 13 538 16 10 6 119 105 0

oligos_6nt_mkv3_m8_shift4 (oligos_6nt_mkv3_m8)
; dyads_m3 versus oligos_6nt_mkv3_m8; m=3/3; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.516571; ----ykCCTTCCkb- ; cor=; Ncor= a 0 0 0 0 105 87 9 6 4 6 3 1 76 93 0 c 0 0 0 0 132 98 407 413 9 46 436 423 111 116 0 g 0 0 0 0 76 128 25 26 21 21 6 23 115 116 0 t 0 0 0 0 138 138 10 6 417 378 6 4 149 126 0

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; ywGGCCTCAma ; Alignment reference a 120 185 43 36 24 15 34 20 476 157 196 c 171 104 17 9 483 538 19 517 48 144 118 g 119 113 481 491 14 5 25 19 19 142 118 t 161 169 30 35 50 13 493 15 28 128 139

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; ywGGCCTCAma ; cor=; Ncor= a 120 185 43 36 24 15 34 20 476 157 196 c 171 104 17 9 483 538 19 517 48 144 118 g 119 113 481 491 14 5 25 19 19 142 118 t 161 169 30 35 50 13 493 15 28 128 139

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=11; shift=0; ncol=11; wwgTAAGTAtw ; Alignment reference a 83 89 60 0 232 192 6 1 240 60 91 c 40 43 30 2 2 21 4 1 1 44 45 g 37 38 111 3 2 7 227 1 5 51 33 t 87 77 46 242 11 27 10 244 1 92 78

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwgTAAGTAtw ; cor=; Ncor= a 83 89 60 0 232 192 6 1 240 60 91 c 40 43 30 2 2 21 4 1 1 44 45 g 37 38 111 3 2 7 227 1 5 51 33 t 87 77 46 242 11 27 10 244 1 92 78

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=5; ncol=16; -----ahaCCCAGCwm ; Alignment reference a 0 0 0 0 0 222 154 279 16 27 9 490 12 13 178 164 c 0 0 0 0 0 111 159 72 533 513 550 40 12 530 122 183 g 0 0 0 0 0 127 119 99 11 16 5 29 540 15 83 90 t 0 0 0 0 0 118 146 128 18 22 14 19 14 20 195 141
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----ahaCCCAGCwm ; cor=; Ncor= a 0 0 0 0 0 222 154 279 16 27 9 490 12 13 178 164 c 0 0 0 0 0 111 159 72 533 513 550 40 12 530 122 183 g 0 0 0 0 0 127 119 99 11 16 5 29 540 15 83 90 t 0 0 0 0 0 118 146 128 18 22 14 19 14 20 195 141
oligos_6nt_mkv3_m7_shift5 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m7; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=5; score=0.774394; -----kyaCCCAGGmw ; cor=; Ncor= a 0 0 0 0 0 158 157 414 21 38 14 587 14 22 211 175 c 0 0 0 0 0 109 167 49 574 566 599 11 14 25 181 119 g 0 0 0 0 0 168 128 110 31 10 11 28 602 572 110 155 t 0 0 0 0 0 212 195 74 21 33 23 21 17 28 145 198
dyads_m6_shift6 (dyads_m6)				; oligos_6nt_mkv3_m3 versus dyads_m6; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=6; score=0.661445; ------csCCCACCyc ; cor=; Ncor= a 0 0 0 0 0 0 81 122 9 21 8 416 6 3 95 91 c 0 0 0 0 0 0 224 171 476 469 516 26 510 488 177 220 g 0 0 0 0 0 0 105 143 39 34 9 79 18 41 129 119 t 0 0 0 0 0 0 129 103 15 15 6 18 5 7 138 109
dyads_m2_shift0 (dyads_m2)				; oligos_6nt_mkv3_m3 versus dyads_m2; m=4/4; ncol2=19; w=-5; offset=-5; strand=D; shift=0; score=0.405818; ssccCcCcCCCmGCCC ; cor=; Ncor= a 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 c 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 g 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 t 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; rwAAAGGAAww ; Alignment reference a 113 132 354 331 329 2 3 351 349 133 123 c 76 52 1 10 10 14 3 3 5 44 75 g 94 92 5 3 2 348 352 3 5 64 81 t 90 97 13 29 32 9 15 16 14 132 94
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; rwAAAGGAAww ; cor=; Ncor= a 113 132 354 331 329 2 3 351 349 133 123 c 76 52 1 10 10 14 3 3 5 44 75 g 94 92 5 3 2 348 352 3 5 64 81 t 90 97 13 29 32 9 15 16 14 132 94
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m6; m=2/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.864203; -rrAAGGAArr ; cor=; Ncor= a 0 158 190 417 405 0 0 414 420 165 132 c 0 69 47 0 16 16 0 1 1 57 75 g 0 107 118 2 0 404 417 0 0 115 114 t 0 87 66 2 0 1 4 6 0 84 100
dyads_m7_shift0 (dyads_m7)				; oligos_7nt_mkv4_m2 versus dyads_m7; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.737351; wrAAAGGAAGG ; cor=; Ncor= a 82 78 199 231 233 7 23 228 234 23 17 c 43 55 16 9 10 15 4 9 8 11 16 g 59 84 28 11 6 218 226 5 11 202 211 t 71 38 12 4 6 15 2 13 2 19 11
oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m9; m=4/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.659738; -wmAAGCAAww ; cor=; Ncor= a 0 104 108 285 278 0 0 274 288 93 91 c 0 41 75 0 13 1 288 0 2 46 62 g 0 48 60 2 1 291 0 18 0 55 46 t 0 99 49 5 0 0 4 0 2 98 93

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift0 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; wwtTAAAAATAAAwAwww ; Alignment reference a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 305 121 184 141 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 12 27 35 46 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 23 31 55 33 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227 35 196 101 155
dyads_m4_shift0 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/4; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwtTAAAAATAAAwAwww ; cor=; Ncor= a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 305 121 184 141 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 12 27 35 46 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 23 31 55 33 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227 35 196 101 155
dyads_m1_shift1 (dyads_m1)				; dyads_m4 versus dyads_m1; m=2/4; ncol2=16; w=0; offset=1; strand=D; shift=1; score=0.798853; -wwtTAAAATAAATAww- ; cor=; Ncor= a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 223 112 125 0 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 18 41 33 0 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 18 43 37 0 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215 27 90 91 0
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; dyads_m4 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.553762; --wwTAAAATAAww---- ; cor=; Ncor= a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 0 0 0 0 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 0 0 0 0 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 0 0 0 0 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234 0 0 0 0
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; dyads_m4 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.479161; ----wwAAACAAAwa--- ; cor=; Ncor= a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 232 0 0 0 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 77 0 0 0 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 53 0 0 0 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154 102 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift1 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=16; shift=1; ncol=17; -wwtTAAAATAAATAww ; Alignment reference a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 223 112 125 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 18 41 33 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 18 43 37 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215 27 90 91
dyads_m1_shift1 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -wwtTAAAATAAATAww ; cor=; Ncor= a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 223 112 125 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 18 41 33 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 18 43 37 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215 27 90 91
dyads_m4_shift0 (dyads_m4)				; dyads_m1 versus dyads_m4; m=2/4; ncol2=18; w=-1; offset=-1; strand=D; shift=0; score=0.798853; wwtTAAAAATAAAwAww ; cor=; Ncor= a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 305 121 184 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 12 27 35 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 23 31 55 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227 35 196 101
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; dyads_m1 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.696891; --wwTAAAATAAww--- ; cor=; Ncor= a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 0 0 0 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 0 0 0 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 0 0 0 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234 0 0 0
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; dyads_m1 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.514001; ----wwAAACAAAwa-- ; cor=; Ncor= a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 232 0 0 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 77 0 0 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 53 0 0 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154 102 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwTAAAATAAww ; Alignment reference a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwTAAAATAAww ; cor=; Ncor= a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234
dyads_m1_shift1 (dyads_m1)				; oligos_6nt_mkv3_m4 versus dyads_m1; m=2/4; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.696891; -wwtTAAAATAAAT ; cor=; Ncor= a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215
dyads_m4_shift0 (dyads_m4)				; oligos_6nt_mkv3_m4 versus dyads_m4; m=3/4; ncol2=18; w=-2; offset=-2; strand=D; shift=0; score=0.553762; wwtTAAAAATAAAw ; cor=; Ncor= a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.549807; ----wwAAACAAAw ; cor=; Ncor= a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift2 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=19; shift=2; ncol=21; --ssccCcCcCCCmGCCCyss ; Alignment reference a 0 0 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 34 47 58 c 0 0 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 135 138 141 g 0 0 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 59 119 90 t 0 0 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22 103 27 42
dyads_m2_shift2 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --ssccCcCcCCCmGCCCyss ; cor=; Ncor= a 0 0 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 34 47 58 c 0 0 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 135 138 141 g 0 0 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 59 119 90 t 0 0 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22 103 27 42
dyads_m9_shift2 (dyads_m9)				; dyads_m2 versus dyads_m9; m=2/4; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.827478; --csCCCCCCCCCsCCCsCss ; cor=; Ncor= a 0 0 58 49 29 24 30 25 32 16 34 21 31 44 26 29 9 47 23 78 56 c 0 0 201 185 274 304 291 285 279 312 285 308 278 131 319 293 322 117 294 169 180 g 0 0 85 121 70 47 60 55 66 54 61 52 57 193 43 60 44 198 71 113 108 t 0 0 58 47 29 27 21 37 25 20 22 21 36 34 14 20 27 40 14 42 58
dyads_m5_shift0 (dyads_m5)				; dyads_m2 versus dyads_m5; m=3/4; ncol2=20; w=-2; offset=-2; strand=D; shift=0; score=0.615749; smgsCCCvsgCCcCCCCCss- ; cor=; Ncor= a 20 46 17 12 14 13 6 63 8 7 6 7 13 8 13 9 11 12 29 23 0 c 75 69 39 48 137 126 136 49 45 37 145 141 109 131 125 137 131 130 73 83 0 g 57 40 106 106 19 31 25 48 116 119 21 22 40 31 26 20 21 20 50 51 0 t 24 21 14 10 6 6 9 16 7 13 4 6 14 6 12 10 13 14 24 19 0
oligos_6nt_mkv3_m3_shift7 (oligos_6nt_mkv3_m3)				; dyads_m2 versus oligos_6nt_mkv3_m3; m=4/4; ncol2=11; w=0; offset=5; strand=D; shift=7; score=0.405818; -------ahaCCCAGCwm--- ; cor=; Ncor= a 0 0 0 0 0 0 0 222 154 279 16 27 9 490 12 13 178 164 0 0 0 c 0 0 0 0 0 0 0 111 159 72 533 513 550 40 12 530 122 183 0 0 0 g 0 0 0 0 0 0 0 127 119 99 11 16 5 29 540 15 83 90 0 0 0 t 0 0 0 0 0 0 0 118 146 128 18 22 14 19 14 20 195 141 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwAAACAAAwa ; Alignment reference a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 232 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 77 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 53 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154 102
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wwAAACAAAwa ; cor=; Ncor= a 0 0 0 0 214 181 382 422 454 0 429 432 446 156 232 c 0 0 0 0 65 73 3 10 1 417 4 9 4 108 77 g 0 0 0 0 65 54 10 4 3 1 14 0 0 46 53 t 0 0 0 0 120 156 69 28 6 46 17 23 14 154 102
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m4; m=2/4; ncol2=12; w=-2; offset=-2; strand=D; shift=2; score=0.549807; --wwTAAAATAAww- ; cor=; Ncor= a 0 0 298 290 127 648 662 684 676 20 638 637 299 280 0 c 0 0 111 90 34 18 13 15 13 31 24 27 117 115 0 g 0 0 105 124 49 26 14 9 9 18 30 28 98 99 0 t 0 0 214 224 518 36 39 20 30 659 36 36 214 234 0
dyads_m1_shift1 (dyads_m1)				; oligos_6nt_mkv3_m5 versus dyads_m1; m=3/4; ncol2=16; w=-3; offset=-3; strand=D; shift=1; score=0.514001; -wwtTAAAATAAATA ; cor=; Ncor= a 0 97 101 69 44 235 256 247 264 30 265 218 224 50 223 c 0 49 55 20 12 11 6 10 2 6 2 20 21 16 18 g 0 43 33 13 10 9 9 4 4 15 6 16 14 5 18 t 0 97 97 184 220 31 15 25 16 235 13 32 27 215 27
dyads_m4_shift0 (dyads_m4)				; oligos_6nt_mkv3_m5 versus dyads_m4; m=4/4; ncol2=18; w=-4; offset=-4; strand=D; shift=0; score=0.479161; wwtTAAAAATAAAwA ; cor=; Ncor= a 134 138 88 65 309 308 332 332 333 41 336 272 321 101 305 c 41 42 53 18 21 12 4 13 7 14 9 49 15 23 12 g 58 46 19 30 10 6 12 9 19 19 16 16 14 24 23 t 142 149 215 262 35 49 27 21 16 301 14 38 25 227 35

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=10; shift=4; ncol=14; ----mgCCTCCCvv ; Alignment reference a 0 0 0 0 177 108 18 5 24 6 11 6 181 169 c 0 0 0 0 217 157 615 615 26 616 605 611 178 185 g 0 0 0 0 143 236 18 26 71 21 33 36 181 200 t 0 0 0 0 122 158 8 13 538 16 10 6 119 105
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----mgCCTCCCvv ; cor=; Ncor= a 0 0 0 0 177 108 18 5 24 6 11 6 181 169 c 0 0 0 0 217 157 615 615 26 616 605 611 178 185 g 0 0 0 0 143 236 18 26 71 21 33 36 181 200 t 0 0 0 0 122 158 8 13 538 16 10 6 119 105
oligos_6nt_mkv3_m8_shift4 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m8; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.795134; ----ykCCTTCCkb ; cor=; Ncor= a 0 0 0 0 105 87 9 6 4 6 3 1 76 93 c 0 0 0 0 132 98 407 413 9 46 436 423 111 116 g 0 0 0 0 76 128 25 26 21 21 6 23 115 116 t 0 0 0 0 138 138 10 6 417 378 6 4 149 126
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m1 versus dyads_m3; m=3/3; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.570289; ymTtCTCCTCCCTc ; cor=; Ncor= a 67 99 22 24 28 17 5 10 18 5 7 17 41 58 c 92 89 30 55 223 31 281 277 9 223 279 271 27 113 g 66 50 37 29 17 21 8 7 9 50 7 8 23 68 t 85 72 221 202 42 241 16 16 274 32 17 14 219 71

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=1; ncol=11; -rrAAGGAArr ; Alignment reference a 0 158 190 417 405 0 0 414 420 165 132 c 0 69 47 0 16 16 0 1 1 57 75 g 0 107 118 2 0 404 417 0 0 115 114 t 0 87 66 2 0 1 4 6 0 84 100
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -rrAAGGAArr ; cor=; Ncor= a 0 158 190 417 405 0 0 414 420 165 132 c 0 69 47 0 16 16 0 1 1 57 75 g 0 107 118 2 0 404 417 0 0 115 114 t 0 87 66 2 0 1 4 6 0 84 100
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m6 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.864203; rwAAAGGAAww ; cor=; Ncor= a 113 132 354 331 329 2 3 351 349 133 123 c 76 52 1 10 10 14 3 3 5 44 75 g 94 92 5 3 2 348 352 3 5 64 81 t 90 97 13 29 32 9 15 16 14 132 94
oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m9; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.761639; -wmAAGCAAww ; cor=; Ncor= a 0 104 108 285 278 0 0 274 288 93 91 c 0 41 75 0 13 1 288 0 2 46 62 g 0 48 60 2 1 291 0 18 0 55 46 t 0 99 49 5 0 0 4 0 2 98 93
dyads_m7_shift0 (dyads_m7)				; oligos_6nt_mkv3_m6 versus dyads_m7; m=4/4; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.680155; wrAAAGGAAGG ; cor=; Ncor= a 82 78 199 231 233 7 23 228 234 23 17 c 43 55 16 9 10 15 4 9 8 11 16 g 59 84 28 11 6 218 226 5 11 202 211 t 71 38 12 4 6 15 2 13 2 19 11

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift0 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=13; shift=0; ncol=13; wrAAAGGAAGGaw ; Alignment reference a 82 78 199 231 233 7 23 228 234 23 17 87 93 c 43 55 16 9 10 15 4 9 8 11 16 49 32 g 59 84 28 11 6 218 226 5 11 202 211 58 53 t 71 38 12 4 6 15 2 13 2 19 11 61 77
dyads_m7_shift0 (dyads_m7)				; dyads_m7 versus dyads_m7; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wrAAAGGAAGGaw ; cor=; Ncor= a 82 78 199 231 233 7 23 228 234 23 17 87 93 c 43 55 16 9 10 15 4 9 8 11 16 49 32 g 59 84 28 11 6 218 226 5 11 202 211 58 53 t 71 38 12 4 6 15 2 13 2 19 11 61 77
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; dyads_m7 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.737351; rwAAAGGAAww-- ; cor=; Ncor= a 113 132 354 331 329 2 3 351 349 133 123 0 0 c 76 52 1 10 10 14 3 3 5 44 75 0 0 g 94 92 5 3 2 348 352 3 5 64 81 0 0 t 90 97 13 29 32 9 15 16 14 132 94 0 0
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)				; dyads_m7 versus oligos_6nt_mkv3_m6; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.680155; -rrAAGGAArr-- ; cor=; Ncor= a 0 158 190 417 405 0 0 414 420 165 132 0 0 c 0 69 47 0 16 16 0 1 1 57 75 0 0 g 0 107 118 2 0 404 417 0 0 115 114 0 0 t 0 87 66 2 0 1 4 6 0 84 100 0 0
oligos_6nt_mkv3_m8_rc_shift3 (oligos_6nt_mkv3_m8_rc)				; dyads_m7 versus oligos_6nt_mkv3_m8_rc; m=4/4; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.66523; ---vmGGAAGGmr ; cor=; Ncor= a 0 0 0 126 149 4 6 378 417 6 10 138 138 c 0 0 0 116 115 23 6 21 21 26 25 128 76 g 0 0 0 116 111 423 436 46 9 413 407 98 132 t 0 0 0 93 76 1 3 6 4 6 9 87 105

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m8_shift4 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ykCCTTCCkb ; Alignment reference a 0 0 0 0 105 87 9 6 4 6 3 1 76 93 c 0 0 0 0 132 98 407 413 9 46 436 423 111 116 g 0 0 0 0 76 128 25 26 21 21 6 23 115 116 t 0 0 0 0 138 138 10 6 417 378 6 4 149 126
oligos_6nt_mkv3_m8_shift4 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----ykCCTTCCkb ; cor=; Ncor= a 0 0 0 0 105 87 9 6 4 6 3 1 76 93 c 0 0 0 0 132 98 407 413 9 46 436 423 111 116 g 0 0 0 0 76 128 25 26 21 21 6 23 115 116 t 0 0 0 0 138 138 10 6 417 378 6 4 149 126
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m1; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.795134; ----mgCCTCCCvv ; cor=; Ncor= a 0 0 0 0 177 108 18 5 24 6 11 6 181 169 c 0 0 0 0 217 157 615 615 26 616 605 611 178 185 g 0 0 0 0 143 236 18 26 71 21 33 36 181 200 t 0 0 0 0 122 158 8 13 538 16 10 6 119 105
dyads_m7_rc_shift4 (dyads_m7_rc)				; oligos_6nt_mkv3_m8 versus dyads_m7_rc; m=3/4; ncol2=13; w=0; offset=0; strand=R; shift=4; score=0.66523; ----wtCCTTCCTT ; cor=; Ncor= a 0 0 0 0 77 61 11 19 2 13 2 15 6 4 c 0 0 0 0 53 58 211 202 11 5 226 218 6 11 g 0 0 0 0 32 49 16 11 8 9 4 15 10 9 t 0 0 0 0 93 87 17 23 234 228 23 7 233 231
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m8 versus dyads_m3; m=4/4; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.516571; ymTtCTCCTCCCTc ; cor=; Ncor= a 67 99 22 24 28 17 5 10 18 5 7 17 41 58 c 92 89 30 55 223 31 281 277 9 223 279 271 27 113 g 66 50 37 29 17 21 8 7 9 50 7 8 23 68 t 85 72 221 202 42 241 16 16 274 32 17 14 219 71

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=1; ncol=11; -wmAAGCAAww ; Alignment reference a 0 104 108 285 278 0 0 274 288 93 91 c 0 41 75 0 13 1 288 0 2 46 62 g 0 48 60 2 1 291 0 18 0 55 46 t 0 99 49 5 0 0 4 0 2 98 93
oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wmAAGCAAww ; cor=; Ncor= a 0 104 108 285 278 0 0 274 288 93 91 c 0 41 75 0 13 1 288 0 2 46 62 g 0 48 60 2 1 291 0 18 0 55 46 t 0 99 49 5 0 0 4 0 2 98 93
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m6; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.761639; -rrAAGGAArr ; cor=; Ncor= a 0 158 190 417 405 0 0 414 420 165 132 c 0 69 47 0 16 16 0 1 1 57 75 g 0 107 118 2 0 404 417 0 0 115 114 t 0 87 66 2 0 1 4 6 0 84 100
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m9 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.659738; rwAAAGGAAww ; cor=; Ncor= a 113 132 354 331 329 2 3 351 349 133 123 c 76 52 1 10 10 14 3 3 5 44 75 g 94 92 5 3 2 348 352 3 5 64 81 t 90 97 13 29 32 9 15 16 14 132 94

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=20; shift=0; ncol=20; smgsCCCvsgCCcCCCCCss ; Alignment reference a 20 46 17 12 14 13 6 63 8 7 6 7 13 8 13 9 11 12 29 23 c 75 69 39 48 137 126 136 49 45 37 145 141 109 131 125 137 131 130 73 83 g 57 40 106 106 19 31 25 48 116 119 21 22 40 31 26 20 21 20 50 51 t 24 21 14 10 6 6 9 16 7 13 4 6 14 6 12 10 13 14 24 19
dyads_m5_shift0 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; smgsCCCvsgCCcCCCCCss ; cor=; Ncor= a 20 46 17 12 14 13 6 63 8 7 6 7 13 8 13 9 11 12 29 23 c 75 69 39 48 137 126 136 49 45 37 145 141 109 131 125 137 131 130 73 83 g 57 40 106 106 19 31 25 48 116 119 21 22 40 31 26 20 21 20 50 51 t 24 21 14 10 6 6 9 16 7 13 4 6 14 6 12 10 13 14 24 19
dyads_m9_shift1 (dyads_m9)				; dyads_m5 versus dyads_m9; m=2/3; ncol2=19; w=0; offset=1; strand=D; shift=1; score=0.708928; -csCCCCCCCCCsCCCsCss ; cor=; Ncor= a 0 58 49 29 24 30 25 32 16 34 21 31 44 26 29 9 47 23 78 56 c 0 201 185 274 304 291 285 279 312 285 308 278 131 319 293 322 117 294 169 180 g 0 85 121 70 47 60 55 66 54 61 52 57 193 43 60 44 198 71 113 108 t 0 58 47 29 27 21 37 25 20 22 21 36 34 14 20 27 40 14 42 58
dyads_m2_shift2 (dyads_m2)				; dyads_m5 versus dyads_m2; m=3/3; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.615749; --ssccCcCcCCCmGCCCys ; cor=; Ncor= a 0 0 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 34 47 c 0 0 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 135 138 g 0 0 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 59 119 t 0 0 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22 103 27

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m9_shift1 (dyads_m9)				; dyads_m9; m=0 (reference); ncol1=19; shift=1; ncol=20; -csCCCCCCCCCsCCCsCss ; Alignment reference a 0 58 49 29 24 30 25 32 16 34 21 31 44 26 29 9 47 23 78 56 c 0 201 185 274 304 291 285 279 312 285 308 278 131 319 293 322 117 294 169 180 g 0 85 121 70 47 60 55 66 54 61 52 57 193 43 60 44 198 71 113 108 t 0 58 47 29 27 21 37 25 20 22 21 36 34 14 20 27 40 14 42 58
dyads_m9_shift1 (dyads_m9)				; dyads_m9 versus dyads_m9; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -csCCCCCCCCCsCCCsCss ; cor=; Ncor= a 0 58 49 29 24 30 25 32 16 34 21 31 44 26 29 9 47 23 78 56 c 0 201 185 274 304 291 285 279 312 285 308 278 131 319 293 322 117 294 169 180 g 0 85 121 70 47 60 55 66 54 61 52 57 193 43 60 44 198 71 113 108 t 0 58 47 29 27 21 37 25 20 22 21 36 34 14 20 27 40 14 42 58
dyads_m2_shift1 (dyads_m2)				; dyads_m9 versus dyads_m2; m=2/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score=0.827478; -ssccCcCcCCCmGCCCyss ; cor=; Ncor= a 0 48 48 28 27 22 32 24 32 15 16 14 150 20 15 19 17 34 47 58 c 0 151 147 209 222 235 215 236 222 260 268 281 100 68 279 247 255 135 138 141 g 0 86 85 58 54 41 60 45 50 35 31 26 53 225 19 42 37 59 119 90 t 0 46 51 36 28 33 24 26 27 21 16 10 28 18 18 23 22 103 27 42
dyads_m5_shift0 (dyads_m5)				; dyads_m9 versus dyads_m5; m=3/3; ncol2=20; w=-1; offset=-1; strand=D; shift=0; score=0.708928; smgsCCCvsgCCcCCCCCss ; cor=; Ncor= a 20 46 17 12 14 13 6 63 8 7 6 7 13 8 13 9 11 12 29 23 c 75 69 39 48 137 126 136 49 45 37 145 141 109 131 125 137 131 130 73 83 g 57 40 106 106 19 31 25 48 116 119 21 22 40 31 26 20 21 20 50 51 t 24 21 14 10 6 6 9 16 7 13 4 6 14 6 12 10 13 14 24 19

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift0 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ymTtCTCCTCCCTch ; Alignment reference a 67 99 22 24 28 17 5 10 18 5 7 17 41 58 94 c 92 89 30 55 223 31 281 277 9 223 279 271 27 113 81 g 66 50 37 29 17 21 8 7 9 50 7 8 23 68 55 t 85 72 221 202 42 241 16 16 274 32 17 14 219 71 80
dyads_m3_shift0 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ymTtCTCCTCCCTch ; cor=; Ncor= a 67 99 22 24 28 17 5 10 18 5 7 17 41 58 94 c 92 89 30 55 223 31 281 277 9 223 279 271 27 113 81 g 66 50 37 29 17 21 8 7 9 50 7 8 23 68 55 t 85 72 221 202 42 241 16 16 274 32 17 14 219 71 80
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; dyads_m3 versus oligos_6nt_mkv3_m1; m=2/3; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.570289; ----mgCCTCCCvv- ; cor=; Ncor= a 0 0 0 0 177 108 18 5 24 6 11 6 181 169 0 c 0 0 0 0 217 157 615 615 26 616 605 611 178 185 0 g 0 0 0 0 143 236 18 26 71 21 33 36 181 200 0 t 0 0 0 0 122 158 8 13 538 16 10 6 119 105 0
oligos_6nt_mkv3_m8_shift4 (oligos_6nt_mkv3_m8)				; dyads_m3 versus oligos_6nt_mkv3_m8; m=3/3; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.516571; ----ykCCTTCCkb- ; cor=; Ncor= a 0 0 0 0 105 87 9 6 4 6 3 1 76 93 0 c 0 0 0 0 132 98 407 413 9 46 436 423 111 116 0 g 0 0 0 0 76 128 25 26 21 21 6 23 115 116 0 t 0 0 0 0 138 138 10 6 417 378 6 4 149 126 0