One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/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.2026-02-26.200629_2026-02-26.200629_uoww0v/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 6 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; wwAATGTATww ; Alignment reference a 169 187 449 472 33 77 18 515 19 244 186 c 69 62 34 21 15 16 7 5 28 48 100 g 95 79 8 23 4 430 4 11 16 97 53 t 212 217 54 29 493 22 516 14 482 156 206

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAATGTATww ; cor=; Ncor= a 169 187 449 472 33 77 18 515 19 244 186 c 69 62 34 21 15 16 7 5 28 48 100 g 95 79 8 23 4 430 4 11 16 97 53 t 212 217 54 29 493 22 516 14 482 156 206

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m5; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.994275; wwAATGTATww ; cor=; Ncor= a 190 202 473 490 16 69 10 539 67 251 186 c 76 68 27 20 15 10 5 3 36 48 100 g 95 96 6 22 3 464 2 9 46 99 65 t 199 194 54 28 526 17 543 9 411 162 209

dyads_m6_shift0 (dyads_m6)
; oligos_7nt_mkv4_m2 versus dyads_m6; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.852198; waAATGTAww- ; cor=; Ncor= a 105 127 283 294 3 4 0 292 81 115 0 c 43 41 2 3 25 1 0 3 52 32 0 g 51 71 4 2 1 293 1 0 52 64 0 t 100 60 10 0 270 1 298 4 114 88 0

oligos_6nt_mkv3_m9_rc_shift0 (oligos_6nt_mkv3_m9_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m9_rc; m=4/5; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.847287; waTATGTATww ; cor=; Ncor= a 210 349 66 688 31 139 31 696 64 354 227 c 102 80 33 20 3 27 16 12 20 74 105 g 108 155 8 42 25 560 16 37 24 124 94 t 356 192 669 26 717 50 713 31 668 224 350

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_7nt_mkv4_m2 versus positions_6nt_m1; m=5/5; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.680202; -awATGTAAwt ; cor=; Ncor= a 0 102 79 252 0 2 3 247 241 106 63 c 0 47 62 1 19 0 0 4 4 44 40 g 0 46 33 4 0 253 1 4 3 37 53 t 0 62 83 0 238 2 253 2 9 70 101

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---wwGAGTGCAkw ; Alignment reference a 0 0 0 99 128 10 329 15 29 16 25 356 70 106 c 0 0 0 65 33 13 8 10 11 11 341 13 81 82 g 0 0 0 92 97 357 17 354 10 341 7 7 137 54 t 0 0 0 137 135 13 39 14 343 25 20 17 105 151

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---wwGAGTGCAkw ; cor=; Ncor= a 0 0 0 99 128 10 329 15 29 16 25 356 70 106 c 0 0 0 65 33 13 8 10 11 11 341 13 81 82 g 0 0 0 92 97 357 17 354 10 341 7 7 137 54 t 0 0 0 137 135 13 39 14 343 25 20 17 105 151

oligos_8nt_mkv5_m2_shift2 (oligos_8nt_mkv5_m2)
; oligos_7nt_mkv4_m3 versus oligos_8nt_mkv5_m2; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.847356; --ctGGAGTGCAgt ; cor=; Ncor= a 0 0 49 62 14 5 220 13 9 9 11 240 56 57 c 0 0 120 30 8 13 11 16 13 10 231 3 47 42 g 0 0 47 60 227 237 9 217 10 213 11 11 110 61 t 0 0 41 105 8 2 17 11 225 25 4 3 44 97

oligos_8nt_mkv5_m3_rc_shift0 (oligos_8nt_mkv5_m3_rc)
; oligos_7nt_mkv4_m3 versus oligos_8nt_mkv5_m3_rc; m=3/3; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.488439; kgCTGGAGTGmr-- ; cor=; Ncor= a 49 63 4 30 10 15 265 12 24 5 93 131 0 0 c 42 56 299 5 3 35 25 12 4 16 96 34 0 0 g 138 138 5 11 291 256 13 281 13 283 66 105 0 0 t 85 57 6 268 10 8 11 9 273 10 59 44 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift5 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift5 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=11; shift=5; ncol=16; -----wwATACATAtw ; Alignment reference a 0 0 0 0 0 350 224 668 31 713 50 717 26 669 192 356 c 0 0 0 0 0 94 124 24 37 16 560 25 42 8 155 108 g 0 0 0 0 0 105 74 20 12 16 27 3 20 33 80 102 t 0 0 0 0 0 227 354 64 696 31 139 31 688 66 349 210

oligos_6nt_mkv3_m9_shift5 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----wwATACATAtw ; cor=; Ncor= a 0 0 0 0 0 350 224 668 31 713 50 717 26 669 192 356 c 0 0 0 0 0 94 124 24 37 16 560 25 42 8 155 108 g 0 0 0 0 0 105 74 20 12 16 27 3 20 33 80 102 t 0 0 0 0 0 227 354 64 696 31 139 31 688 66 349 210

oligos_7nt_mkv4_m2_rc_shift5 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m9 versus oligos_7nt_mkv4_m2_rc; m=2/6; ncol2=11; w=0; offset=0; strand=R; shift=5; score=0.847287; -----wwATACATTww ; cor=; Ncor= a 0 0 0 0 0 206 156 482 14 516 22 493 29 54 217 212 c 0 0 0 0 0 53 97 16 11 4 430 4 23 8 79 95 g 0 0 0 0 0 100 48 28 5 7 16 15 21 34 62 69 t 0 0 0 0 0 186 244 19 515 18 77 33 472 449 187 169

oligos_6nt_mkv3_m5_rc_shift5 (oligos_6nt_mkv3_m5_rc)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m5_rc; m=3/6; ncol2=11; w=0; offset=0; strand=R; shift=5; score= 0.84; -----wwATACATTww ; cor=; Ncor= a 0 0 0 0 0 209 162 411 9 543 17 526 28 54 194 199 c 0 0 0 0 0 65 99 46 9 2 464 3 22 6 96 95 g 0 0 0 0 0 100 48 36 3 5 10 15 20 27 68 76 t 0 0 0 0 0 186 251 67 539 10 69 16 490 473 202 190

dyads_m6_rc_shift6 (dyads_m6_rc)
; oligos_6nt_mkv3_m9 versus dyads_m6_rc; m=4/6; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.694553; ------wwTACATTtw ; cor=; Ncor= a 0 0 0 0 0 0 88 114 4 298 1 270 0 10 60 100 c 0 0 0 0 0 0 64 52 0 1 293 1 2 4 71 51 g 0 0 0 0 0 0 32 52 3 0 1 25 3 2 41 43 t 0 0 0 0 0 0 115 81 292 0 4 3 294 283 127 105

positions_6nt_m1_rc_shift5 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m9 versus positions_6nt_m1_rc; m=5/6; ncol2=10; w=0; offset=0; strand=R; shift=5; score=0.686302; -----awTTACATwt- ; cor=; Ncor= a 0 0 0 0 0 101 70 9 2 253 2 238 0 83 62 0 c 0 0 0 0 0 53 37 3 4 1 253 0 4 33 46 0 g 0 0 0 0 0 40 44 4 4 0 0 19 1 62 47 0 t 0 0 0 0 0 63 106 241 247 3 2 0 252 79 102 0

dyads_m10_shift0 (dyads_m10)
; oligos_6nt_mkv3_m9 versus dyads_m10; m=6/6; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.486235; wwATAAAATAAATAAw ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 228 115 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 13 28 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 20 42 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30 46 122

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m10_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m10_shift2 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=10; shift=2; ncol=12; --aaAAAGAAaw ; Alignment reference a 0 0 208 224 504 506 499 0 505 503 198 182 c 0 0 88 90 0 1 8 0 0 5 96 87 g 0 0 98 90 3 0 0 506 0 0 109 99 t 0 0 114 104 1 1 1 2 3 0 105 140

oligos_6nt_mkv3_m10_shift2 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --aaAAAGAAaw ; cor=; Ncor= a 0 0 208 224 504 506 499 0 505 503 198 182 c 0 0 88 90 0 1 8 0 0 5 96 87 g 0 0 98 90 3 0 0 506 0 0 109 99 t 0 0 114 104 1 1 1 2 3 0 105 140

dyads_m7_shift2 (dyads_m7)
; oligos_6nt_mkv3_m10 versus dyads_m7; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.76385; --rrAGAGAArd ; cor=; Ncor= a 0 0 161 120 406 1 426 0 437 414 171 134 c 0 0 77 100 29 1 17 0 2 25 61 72 g 0 0 111 127 4 441 0 442 2 4 117 126 t 0 0 95 97 5 1 1 2 3 1 95 112

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.604028; -wwgAAATAAAw ; cor=; Ncor= a 0 218 254 124 543 542 540 4 554 512 492 217 c 0 105 37 35 14 12 9 6 4 25 16 80 g 0 112 98 334 15 9 11 5 5 24 29 100 t 0 147 193 89 10 19 22 567 19 21 45 185

dyads_m2_shift0 (dyads_m2)
; oligos_6nt_mkv3_m10 versus dyads_m2; m=4/4; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.602942; waAGAAATAAaw ; cor=; Ncor= a 258 242 558 87 582 601 584 17 580 537 270 241 c 73 125 10 22 16 7 14 21 15 32 93 107 g 127 131 24 461 16 13 17 31 18 27 112 90 t 175 135 41 63 19 12 18 564 20 37 158 195

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m3_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv5_m3_shift2 (oligos_8nt_mkv5_m3)
; oligos_8nt_mkv5_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --ykCACTCCAGcm ; Alignment reference a 0 0 44 59 10 273 9 11 8 10 268 6 57 85 c 0 0 105 66 283 13 281 13 256 291 11 5 138 138 g 0 0 34 96 16 4 12 25 35 3 5 299 56 42 t 0 0 131 93 5 24 12 265 15 10 30 4 63 49

oligos_8nt_mkv5_m3_shift2 (oligos_8nt_mkv5_m3)
; oligos_8nt_mkv5_m3 versus oligos_8nt_mkv5_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ykCACTCCAGcm ; cor=; Ncor= a 0 0 44 59 10 273 9 11 8 10 268 6 57 85 c 0 0 105 66 283 13 281 13 256 291 11 5 138 138 g 0 0 34 96 16 4 12 25 35 3 5 299 56 42 t 0 0 131 93 5 24 12 265 15 10 30 4 63 49

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_8nt_mkv5_m3 versus oligos_7nt_mkv4_m1; m=2/5; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.597366; -dsCCACTGCAsy- ; cor=; Ncor= a 0 106 77 14 12 355 9 22 7 11 280 96 69 0 c 0 77 129 312 386 17 370 29 12 369 47 122 119 0 g 0 117 131 17 2 9 9 13 366 11 31 108 83 0 t 0 102 65 59 2 21 14 338 17 11 44 76 131 0

oligos_8nt_mkv5_m2_rc_shift0 (oligos_8nt_mkv5_m2_rc)
; oligos_8nt_mkv5_m3 versus oligos_8nt_mkv5_m2_rc; m=3/5; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.593804; acTGCACTCCag-- ; cor=; Ncor= a 97 44 3 4 25 225 11 17 2 8 105 41 0 0 c 61 110 11 11 213 10 217 9 237 227 60 47 0 0 g 42 47 3 231 10 13 16 11 13 8 30 120 0 0 t 57 56 240 11 9 9 13 220 5 14 62 49 0 0

oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)
; oligos_8nt_mkv5_m3 versus oligos_6nt_mkv3_m7; m=4/5; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.583538; --syCACTGCas-- ; cor=; Ncor= a 0 0 90 81 7 398 11 27 7 3 159 101 0 0 c 0 0 150 156 435 16 431 40 8 446 110 134 0 0 g 0 0 141 99 10 27 8 40 437 3 98 141 0 0 t 0 0 74 119 3 14 5 348 3 3 88 79 0 0

oligos_7nt_mkv4_m3_rc_shift0 (oligos_7nt_mkv4_m3_rc)
; oligos_8nt_mkv5_m3 versus oligos_7nt_mkv4_m3_rc; m=5/5; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.488439; wmTGCACTCww--- ; cor=; Ncor= a 151 105 17 20 25 343 14 39 13 135 137 0 0 0 c 54 137 7 7 341 10 354 17 357 97 92 0 0 0 g 82 81 13 341 11 11 10 8 13 33 65 0 0 0 t 106 70 356 25 16 29 15 329 10 128 99 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv5_m2_shift2 (oligos_8nt_mkv5_m2)
; oligos_8nt_mkv5_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --ctGGAGTGCAgt ; Alignment reference a 0 0 49 62 14 5 220 13 9 9 11 240 56 57 c 0 0 120 30 8 13 11 16 13 10 231 3 47 42 g 0 0 47 60 227 237 9 217 10 213 11 11 110 61 t 0 0 41 105 8 2 17 11 225 25 4 3 44 97

oligos_8nt_mkv5_m2_shift2 (oligos_8nt_mkv5_m2)
; oligos_8nt_mkv5_m2 versus oligos_8nt_mkv5_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ctGGAGTGCAgt ; cor=; Ncor= a 0 0 49 62 14 5 220 13 9 9 11 240 56 57 c 0 0 120 30 8 13 11 16 13 10 231 3 47 42 g 0 0 47 60 227 237 9 217 10 213 11 11 110 61 t 0 0 41 105 8 2 17 11 225 25 4 3 44 97

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_8nt_mkv5_m2 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.847356; ---wwGAGTGCAkw ; cor=; Ncor= a 0 0 0 99 128 10 329 15 29 16 25 356 70 106 c 0 0 0 65 33 13 8 10 11 11 341 13 81 82 g 0 0 0 92 97 357 17 354 10 341 7 7 137 54 t 0 0 0 137 135 13 39 14 343 25 20 17 105 151

oligos_8nt_mkv5_m3_rc_shift0 (oligos_8nt_mkv5_m3_rc)
; oligos_8nt_mkv5_m2 versus oligos_8nt_mkv5_m3_rc; m=3/3; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.593804; kgCTGGAGTGmr-- ; cor=; Ncor= a 49 63 4 30 10 15 265 12 24 5 93 131 0 0 c 42 56 299 5 3 35 25 12 4 16 96 34 0 0 g 138 138 5 11 291 256 13 281 13 283 66 105 0 0 t 85 57 6 268 10 8 11 9 273 10 59 44 0 0

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift0 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; rrAGAGAArd ; Alignment reference a 161 120 406 1 426 0 437 414 171 134 c 77 100 29 1 17 0 2 25 61 72 g 111 127 4 441 0 442 2 4 117 126 t 95 97 5 1 1 2 3 1 95 112

dyads_m7_shift0 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; rrAGAGAArd ; cor=; Ncor= a 161 120 406 1 426 0 437 414 171 134 c 77 100 29 1 17 0 2 25 61 72 g 111 127 4 441 0 442 2 4 117 126 t 95 97 5 1 1 2 3 1 95 112

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; dyads_m7 versus oligos_6nt_mkv3_m10; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.76385; aaAAAGAAaw ; cor=; Ncor= a 208 224 504 506 499 0 505 503 198 182 c 88 90 0 1 8 0 0 5 96 87 g 98 90 3 0 0 506 0 0 109 99 t 114 104 1 1 1 2 3 0 105 140

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; whATTCAAww ; Alignment reference a 85 75 270 0 1 0 264 271 75 105 c 44 70 0 3 1 273 0 3 61 45 g 63 51 5 0 0 0 10 0 64 47 t 83 79 0 272 273 2 1 1 75 78

oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; whATTCAAww ; cor=; Ncor= a 85 75 270 0 1 0 264 271 75 105 c 44 70 0 3 1 273 0 3 61 45 g 63 51 5 0 0 0 10 0 64 47 t 83 79 0 272 273 2 1 1 75 78

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

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=22; shift=0; ncol=22; yycCctCCTCcsCCTCCCmaky ; Alignment reference a 10 24 6 4 11 25 3 9 4 6 23 5 15 10 7 4 2 6 33 69 29 14 c 68 30 78 98 80 8 110 102 10 97 72 63 92 89 21 105 110 98 54 21 28 43 g 9 16 15 5 4 25 2 4 9 6 17 35 2 11 6 4 1 5 17 10 31 24 t 31 48 19 11 23 60 3 3 95 9 6 15 9 8 84 5 5 9 14 18 30 37

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; yycCctCCTCcsCCTCCCmaky ; cor=; Ncor= a 10 24 6 4 11 25 3 9 4 6 23 5 15 10 7 4 2 6 33 69 29 14 c 68 30 78 98 80 8 110 102 10 97 72 63 92 89 21 105 110 98 54 21 28 43 g 9 16 15 5 4 25 2 4 9 6 17 35 2 11 6 4 1 5 17 10 31 24 t 31 48 19 11 23 60 3 3 95 9 6 15 9 8 84 5 5 9 14 18 30 37

oligos_6nt_mkv3_m6_shift10 (oligos_6nt_mkv3_m6)
; dyads_m4 versus oligos_6nt_mkv3_m6; m=2/2; ncol2=10; w=0; offset=10; strand=D; shift=10; score=0.415303; ----------msCCTCCCmv-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 156 91 7 4 20 7 8 4 165 152 0 0 c 0 0 0 0 0 0 0 0 0 0 175 150 533 531 9 519 510 522 145 144 0 0 g 0 0 0 0 0 0 0 0 0 0 110 216 14 21 48 22 37 33 141 166 0 0 t 0 0 0 0 0 0 0 0 0 0 125 109 12 10 489 18 11 7 115 104 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m6_shift10 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m6_shift10 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=10; ncol=20; ----------msCCTCCCmv ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 156 91 7 4 20 7 8 4 165 152 c 0 0 0 0 0 0 0 0 0 0 175 150 533 531 9 519 510 522 145 144 g 0 0 0 0 0 0 0 0 0 0 110 216 14 21 48 22 37 33 141 166 t 0 0 0 0 0 0 0 0 0 0 125 109 12 10 489 18 11 7 115 104

oligos_6nt_mkv3_m6_shift10 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=10; score= 1; ----------msCCTCCCmv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 156 91 7 4 20 7 8 4 165 152 c 0 0 0 0 0 0 0 0 0 0 175 150 533 531 9 519 510 522 145 144 g 0 0 0 0 0 0 0 0 0 0 110 216 14 21 48 22 37 33 141 166 t 0 0 0 0 0 0 0 0 0 0 125 109 12 10 489 18 11 7 115 104

dyads_m9_shift10 (dyads_m9)
; oligos_6nt_mkv3_m6 versus dyads_m9; m=2/3; ncol2=16; w=0; offset=0; strand=D; shift=10; score=0.464715; ----------mvCCcCCCAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 42 41 19 13 28 6 14 11 117 6 c 0 0 0 0 0 0 0 0 0 0 55 43 111 122 95 142 125 133 21 19 g 0 0 0 0 0 0 0 0 0 0 27 45 22 9 17 2 12 16 12 128 t 0 0 0 0 0 0 0 0 0 0 37 32 9 17 21 11 10 1 11 8

dyads_m4_shift0 (dyads_m4)
; oligos_6nt_mkv3_m6 versus dyads_m4; m=3/3; ncol2=22; w=-10; offset=-10; strand=D; shift=0; score=0.415303; yycCctCCTCcsCCTCCCma ; cor=; Ncor= a 10 24 6 4 11 25 3 9 4 6 23 5 15 10 7 4 2 6 33 69 c 68 30 78 98 80 8 110 102 10 97 72 63 92 89 21 105 110 98 54 21 g 9 16 15 5 4 25 2 4 9 6 17 35 2 11 6 4 1 5 17 10 t 31 48 19 11 23 60 3 3 95 9 6 15 9 8 84 5 5 9 14 18

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift0 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=17; shift=0; ncol=17; wwATAAAATAAATAAww ; Alignment reference a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 228 115 115 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 13 28 37 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 20 42 42 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30 46 122 113

dyads_m10_shift0 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAAATAAATAAww ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 228 115 115 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 13 28 37 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 20 42 42 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30 46 122 113

dyads_m1_shift0 (dyads_m1)
; dyads_m10 versus dyads_m1; m=2/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.714943; wwATAAAATAAtww--- ; cor=; Ncor= a 150 149 306 30 370 371 381 385 12 359 354 88 169 164 0 0 0 c 51 83 34 23 14 11 8 11 7 9 20 34 50 67 0 0 0 g 79 47 16 11 16 13 6 15 8 19 15 42 58 54 0 0 0 t 152 153 76 368 32 37 37 21 405 45 43 268 155 147 0 0 0

dyads_m2_shift5 (dyads_m2)
; dyads_m10 versus dyads_m2; m=3/5; ncol2=12; w=0; offset=5; strand=D; shift=5; score=0.575208; -----waAGAAATAAaw ; cor=; Ncor= a 0 0 0 0 0 258 242 558 87 582 601 584 17 580 537 270 241 c 0 0 0 0 0 73 125 10 22 16 7 14 21 15 32 93 107 g 0 0 0 0 0 127 131 24 461 16 13 17 31 18 27 112 90 t 0 0 0 0 0 175 135 41 63 19 12 18 564 20 37 158 195

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; dyads_m10 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.561263; --wwgAAATAAAww--- ; cor=; Ncor= a 0 0 218 254 124 543 542 540 4 554 512 492 217 224 0 0 0 c 0 0 105 37 35 14 12 9 6 4 25 16 80 92 0 0 0 g 0 0 112 98 334 15 9 11 5 5 24 29 100 87 0 0 0 t 0 0 147 193 89 10 19 22 567 19 21 45 185 179 0 0 0

oligos_6nt_mkv3_m9_shift5 (oligos_6nt_mkv3_m9)
; dyads_m10 versus oligos_6nt_mkv3_m9; m=5/5; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.486235; -----wwATACATAtw- ; cor=; Ncor= a 0 0 0 0 0 350 224 668 31 713 50 717 26 669 192 356 0 c 0 0 0 0 0 94 124 24 37 16 560 25 42 8 155 108 0 g 0 0 0 0 0 105 74 20 12 16 27 3 20 33 80 102 0 t 0 0 0 0 0 227 354 64 696 31 139 31 688 66 349 210 0

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=16; shift=0; ncol=16; mvCCcCCCAGCCCass ; Alignment reference a 42 41 19 13 28 6 14 11 117 6 6 10 6 80 37 32 c 55 43 111 122 95 142 125 133 21 19 146 133 140 34 42 47 g 27 45 22 9 17 2 12 16 12 128 7 6 10 25 59 48 t 37 32 9 17 21 11 10 1 11 8 2 12 5 22 23 34

dyads_m9_shift0 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/2; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; mvCCcCCCAGCCCass ; cor=; Ncor= a 42 41 19 13 28 6 14 11 117 6 6 10 6 80 37 32 c 55 43 111 122 95 142 125 133 21 19 146 133 140 34 42 47 g 27 45 22 9 17 2 12 16 12 128 7 6 10 25 59 48 t 37 32 9 17 21 11 10 1 11 8 2 12 5 22 23 34

oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)
; dyads_m9 versus oligos_6nt_mkv3_m6; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.464715; msCCTCCCmv------ ; cor=; Ncor= a 156 91 7 4 20 7 8 4 165 152 0 0 0 0 0 0 c 175 150 533 531 9 519 510 522 145 144 0 0 0 0 0 0 g 110 216 14 21 48 22 37 33 141 166 0 0 0 0 0 0 t 125 109 12 10 489 18 11 7 115 104 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; tyacCCAGGCwg ; Alignment reference a 108 101 258 35 15 13 401 5 17 31 131 86 c 90 118 51 306 416 411 18 11 20 404 76 108 g 95 97 105 82 19 25 29 434 405 8 95 162 t 165 142 44 35 8 9 10 8 16 15 156 102

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; tyacCCAGGCwg ; cor=; Ncor= a 108 101 258 35 15 13 401 5 17 31 131 86 c 90 118 51 306 416 411 18 11 20 404 76 108 g 95 97 105 82 19 25 29 434 405 8 95 162 t 165 142 44 35 8 9 10 8 16 15 156 102

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m4 versus dyads_m3; m=2/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.909977; wyaCCCAGGCwg ; cor=; Ncor= a 75 66 179 12 8 8 262 3 3 15 157 53 c 47 78 22 235 265 264 8 6 11 267 32 65 g 56 45 68 41 17 13 20 280 268 5 19 112 t 119 108 28 9 7 12 7 8 15 10 89 67

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwgAAATAAAww ; Alignment reference a 0 0 218 254 124 543 542 540 4 554 512 492 217 224 c 0 0 105 37 35 14 12 9 6 4 25 16 80 92 g 0 0 112 98 334 15 9 11 5 5 24 29 100 87 t 0 0 147 193 89 10 19 22 567 19 21 45 185 179

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwgAAATAAAww ; cor=; Ncor= a 0 0 218 254 124 543 542 540 4 554 512 492 217 224 c 0 0 105 37 35 14 12 9 6 4 25 16 80 92 g 0 0 112 98 334 15 9 11 5 5 24 29 100 87 t 0 0 147 193 89 10 19 22 567 19 21 45 185 179

dyads_m2_shift1 (dyads_m2)
; oligos_6nt_mkv3_m1 versus dyads_m2; m=2/7; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.791679; -waAGAAATAAaw- ; cor=; Ncor= a 0 258 242 558 87 582 601 584 17 580 537 270 241 0 c 0 73 125 10 22 16 7 14 21 15 32 93 107 0 g 0 127 131 24 461 16 13 17 31 18 27 112 90 0 t 0 175 135 41 63 19 12 18 564 20 37 158 195 0

oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3; m=3/7; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.668036; ---waaAACAAAaa ; cor=; Ncor= a 0 0 0 184 185 217 431 430 0 421 423 428 163 169 c 0 0 0 60 71 72 0 2 430 1 0 5 94 82 g 0 0 0 79 75 71 0 1 0 7 2 0 76 87 t 0 0 0 110 102 73 2 0 3 4 8 0 100 95

dyads_m1_shift0 (dyads_m1)
; oligos_6nt_mkv3_m1 versus dyads_m1; m=4/7; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.666432; wwATAAAATAAtww ; cor=; Ncor= a 150 149 306 30 370 371 381 385 12 359 354 88 169 164 c 51 83 34 23 14 11 8 11 7 9 20 34 50 67 g 79 47 16 11 16 13 6 15 8 19 15 42 58 54 t 152 153 76 368 32 37 37 21 405 45 43 268 155 147

oligos_6nt_mkv3_m10_shift3 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m10; m=5/7; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.604028; ---aaAAAGAAaw- ; cor=; Ncor= a 0 0 0 208 224 504 506 499 0 505 503 198 182 0 c 0 0 0 88 90 0 1 8 0 0 5 96 87 0 g 0 0 0 98 90 3 0 0 506 0 0 109 99 0 t 0 0 0 114 104 1 1 1 2 3 0 105 140 0

dyads_m8_shift4 (dyads_m8)
; oligos_6nt_mkv3_m1 versus dyads_m8; m=6/7; ncol2=10; w=0; offset=2; strand=D; shift=4; score=0.59988; ----aaAACAAAaa ; cor=; Ncor= a 0 0 0 0 184 203 428 428 0 420 421 426 163 166 c 0 0 0 0 71 77 0 1 430 0 0 5 89 82 g 0 0 0 0 73 76 3 1 0 7 2 0 81 82 t 0 0 0 0 103 75 0 1 1 4 8 0 98 101

dyads_m10_shift0 (dyads_m10)
; oligos_6nt_mkv3_m1 versus dyads_m10; m=7/7; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.561263; wwATAAAATAAATA ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAATGTATww ; Alignment reference a 190 202 473 490 16 69 10 539 67 251 186 c 76 68 27 20 15 10 5 3 36 48 100 g 95 96 6 22 3 464 2 9 46 99 65 t 199 194 54 28 526 17 543 9 411 162 209

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAATGTATww ; cor=; Ncor= a 190 202 473 490 16 69 10 539 67 251 186 c 76 68 27 20 15 10 5 3 36 48 100 g 95 96 6 22 3 464 2 9 46 99 65 t 199 194 54 28 526 17 543 9 411 162 209

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m2; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.994275; wwAATGTATww ; cor=; Ncor= a 169 187 449 472 33 77 18 515 19 244 186 c 69 62 34 21 15 16 7 5 28 48 100 g 95 79 8 23 4 430 4 11 16 97 53 t 212 217 54 29 493 22 516 14 482 156 206

dyads_m6_shift0 (dyads_m6)
; oligos_6nt_mkv3_m5 versus dyads_m6; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.878775; waAATGTAww- ; cor=; Ncor= a 105 127 283 294 3 4 0 292 81 115 0 c 43 41 2 3 25 1 0 3 52 32 0 g 51 71 4 2 1 293 1 0 52 64 0 t 100 60 10 0 270 1 298 4 114 88 0

oligos_6nt_mkv3_m9_rc_shift0 (oligos_6nt_mkv3_m9_rc)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m9_rc; m=4/5; ncol2=11; w=0; offset=0; strand=R; shift=0; score= 0.84; waTATGTATww ; cor=; Ncor= a 210 349 66 688 31 139 31 696 64 354 227 c 102 80 33 20 3 27 16 12 20 74 105 g 108 155 8 42 25 560 16 37 24 124 94 t 356 192 669 26 717 50 713 31 668 224 350

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_6nt_mkv3_m5 versus positions_6nt_m1; m=5/5; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.724183; -awATGTAAwt ; cor=; Ncor= a 0 102 79 252 0 2 3 247 241 106 63 c 0 47 62 1 19 0 0 4 4 44 40 g 0 46 33 4 0 253 1 4 3 37 53 t 0 62 83 0 238 2 253 2 9 70 101

One-to-n matrix alignment; reference matrix: dyads_m6_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift4 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=10; shift=4; ncol=14; ----waAATGTAww ; Alignment reference a 0 0 0 0 105 127 283 294 3 4 0 292 81 115 c 0 0 0 0 43 41 2 3 25 1 0 3 52 32 g 0 0 0 0 51 71 4 2 1 293 1 0 52 64 t 0 0 0 0 100 60 10 0 270 1 298 4 114 88

dyads_m6_shift4 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----waAATGTAww ; cor=; Ncor= a 0 0 0 0 105 127 283 294 3 4 0 292 81 115 c 0 0 0 0 43 41 2 3 25 1 0 3 52 32 g 0 0 0 0 51 71 4 2 1 293 1 0 52 64 t 0 0 0 0 100 60 10 0 270 1 298 4 114 88

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; dyads_m6 versus oligos_6nt_mkv3_m5; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.878775; ----wwAATGTATw ; cor=; Ncor= a 0 0 0 0 190 202 473 490 16 69 10 539 67 251 c 0 0 0 0 76 68 27 20 15 10 5 3 36 48 g 0 0 0 0 95 96 6 22 3 464 2 9 46 99 t 0 0 0 0 199 194 54 28 526 17 543 9 411 162

oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)
; dyads_m6 versus oligos_7nt_mkv4_m2; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.852198; ----wwAATGTATw ; cor=; Ncor= a 0 0 0 0 169 187 449 472 33 77 18 515 19 244 c 0 0 0 0 69 62 34 21 15 16 7 5 28 48 g 0 0 0 0 95 79 8 23 4 430 4 11 16 97 t 0 0 0 0 212 217 54 29 493 22 516 14 482 156

positions_6nt_m1_shift5 (positions_6nt_m1)
; dyads_m6 versus positions_6nt_m1; m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.70136; -----awATGTAAw ; cor=; Ncor= a 0 0 0 0 0 102 79 252 0 2 3 247 241 106 c 0 0 0 0 0 47 62 1 19 0 0 4 4 44 g 0 0 0 0 0 46 33 4 0 253 1 4 3 37 t 0 0 0 0 0 62 83 0 238 2 253 2 9 70

oligos_6nt_mkv3_m9_rc_shift4 (oligos_6nt_mkv3_m9_rc)
; dyads_m6 versus oligos_6nt_mkv3_m9_rc; m=5/6; ncol2=11; w=0; offset=0; strand=R; shift=4; score=0.694553; ----waTATGTATw ; cor=; Ncor= a 0 0 0 0 210 349 66 688 31 139 31 696 64 354 c 0 0 0 0 102 80 33 20 3 27 16 12 20 74 g 0 0 0 0 108 155 8 42 25 560 16 37 24 124 t 0 0 0 0 356 192 669 26 717 50 713 31 668 224

oligos_8nt_mkv5_m1_rc_shift0 (oligos_8nt_mkv5_m1_rc)
; dyads_m6 versus oligos_8nt_mkv5_m1_rc; m=6/6; ncol2=12; w=-4; offset=-4; strand=R; shift=0; score=0.426213; wwGTAAAATGww-- ; cor=; Ncor= a 102 103 41 21 304 302 312 301 10 11 108 115 0 0 c 57 38 15 12 7 7 5 3 2 14 64 62 0 0 g 67 51 242 21 10 10 7 10 13 292 58 68 0 0 t 104 138 32 276 9 11 6 16 305 13 100 85 0 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -awATGTAAwt ; Alignment reference a 0 102 79 252 0 2 3 247 241 106 63 c 0 47 62 1 19 0 0 4 4 44 40 g 0 46 33 4 0 253 1 4 3 37 53 t 0 62 83 0 238 2 253 2 9 70 101

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -awATGTAAwt ; cor=; Ncor= a 0 102 79 252 0 2 3 247 241 106 63 c 0 47 62 1 19 0 0 4 4 44 40 g 0 46 33 4 0 253 1 4 3 37 53 t 0 62 83 0 238 2 253 2 9 70 101

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; positions_6nt_m1 versus oligos_6nt_mkv3_m5; m=2/6; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.724183; wwAATGTATww ; cor=; Ncor= a 190 202 473 490 16 69 10 539 67 251 186 c 76 68 27 20 15 10 5 3 36 48 100 g 95 96 6 22 3 464 2 9 46 99 65 t 199 194 54 28 526 17 543 9 411 162 209

dyads_m6_shift0 (dyads_m6)
; positions_6nt_m1 versus dyads_m6; m=3/6; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.70136; waAATGTAww- ; cor=; Ncor= a 105 127 283 294 3 4 0 292 81 115 0 c 43 41 2 3 25 1 0 3 52 32 0 g 51 71 4 2 1 293 1 0 52 64 0 t 100 60 10 0 270 1 298 4 114 88 0

oligos_6nt_mkv3_m9_rc_shift0 (oligos_6nt_mkv3_m9_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m9_rc; m=4/6; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.686302; waTATGTATww ; cor=; Ncor= a 210 349 66 688 31 139 31 696 64 354 227 c 102 80 33 20 3 27 16 12 20 74 105 g 108 155 8 42 25 560 16 37 24 124 94 t 356 192 669 26 717 50 713 31 668 224 350

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; positions_6nt_m1 versus oligos_7nt_mkv4_m2; m=5/6; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.680202; wwAATGTATww ; cor=; Ncor= a 169 187 449 472 33 77 18 515 19 244 186 c 69 62 34 21 15 16 7 5 28 48 100 g 95 79 8 23 4 430 4 11 16 97 53 t 212 217 54 29 493 22 516 14 482 156 206

oligos_8nt_mkv5_m1_rc_shift3 (oligos_8nt_mkv5_m1_rc)
; positions_6nt_m1 versus oligos_8nt_mkv5_m1_rc; m=6/6; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.411042; ---wwGTAAAA ; cor=; Ncor= a 0 0 0 102 103 41 21 304 302 312 301 c 0 0 0 57 38 15 12 7 7 5 3 g 0 0 0 67 51 242 21 10 10 7 10 t 0 0 0 104 138 32 276 9 11 6 16

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; syCCCACCbs ; Alignment reference a 76 92 11 17 8 377 13 3 92 75 c 166 139 389 398 433 9 413 423 132 163 g 114 104 50 31 8 61 18 29 117 121 t 100 121 6 10 7 9 12 1 115 97

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; syCCCACCbs ; cor=; Ncor= a 76 92 11 17 8 377 13 3 92 75 c 166 139 389 398 433 9 413 423 132 163 g 114 104 50 31 8 61 18 29 117 121 t 100 121 6 10 7 9 12 1 115 97

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m1_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv5_m1_shift2 (oligos_8nt_mkv5_m1)
; oligos_8nt_mkv5_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwCATTTTACww ; Alignment reference a 0 0 85 100 13 305 16 6 11 9 276 32 138 104 c 0 0 68 58 292 13 10 7 10 10 21 242 51 67 g 0 0 62 64 14 2 3 5 7 7 12 15 38 57 t 0 0 115 108 11 10 301 312 302 304 21 41 103 102

oligos_8nt_mkv5_m1_shift2 (oligos_8nt_mkv5_m1)
; oligos_8nt_mkv5_m1 versus oligos_8nt_mkv5_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwCATTTTACww ; cor=; Ncor= a 0 0 85 100 13 305 16 6 11 9 276 32 138 104 c 0 0 68 58 292 13 10 7 10 10 21 242 51 67 g 0 0 62 64 14 2 3 5 7 7 12 15 38 57 t 0 0 115 108 11 10 301 312 302 304 21 41 103 102

dyads_m1_rc_shift0 (dyads_m1_rc)
; oligos_8nt_mkv5_m1 versus dyads_m1_rc; m=2/4; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.600109; wwaTTATTTTATww ; cor=; Ncor= a 147 155 268 43 45 405 21 37 37 32 368 76 153 152 c 54 58 42 15 19 8 15 6 13 16 11 16 47 79 g 67 50 34 20 9 7 11 8 11 14 23 34 83 51 t 164 169 88 354 359 12 385 381 371 370 30 306 149 150

dyads_m6_rc_shift0 (dyads_m6_rc)
; oligos_8nt_mkv5_m1 versus dyads_m6_rc; m=3/4; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.426213; wwTACATTtw---- ; cor=; Ncor= a 88 114 4 298 1 270 0 10 60 100 0 0 0 0 c 64 52 0 1 293 1 2 4 71 51 0 0 0 0 g 32 52 3 0 1 25 3 2 41 43 0 0 0 0 t 115 81 292 0 4 3 294 283 127 105 0 0 0 0

positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)
; oligos_8nt_mkv5_m1 versus positions_6nt_m1_rc; m=4/4; ncol2=10; w=0; offset=4; strand=R; shift=6; score=0.411042; ------awTTACAT ; cor=; Ncor= a 0 0 0 0 0 0 101 70 9 2 253 2 238 0 c 0 0 0 0 0 0 53 37 3 4 1 253 0 4 g 0 0 0 0 0 0 40 44 4 4 0 0 19 1 t 0 0 0 0 0 0 63 106 241 247 3 2 0 252

One-to-n matrix alignment; reference matrix: dyads_m2_shift5 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift5 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=12; shift=5; ncol=17; -----waAGAAATAAaw ; Alignment reference a 0 0 0 0 0 258 242 558 87 582 601 584 17 580 537 270 241 c 0 0 0 0 0 73 125 10 22 16 7 14 21 15 32 93 107 g 0 0 0 0 0 127 131 24 461 16 13 17 31 18 27 112 90 t 0 0 0 0 0 175 135 41 63 19 12 18 564 20 37 158 195

dyads_m2_shift5 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----waAGAAATAAaw ; cor=; Ncor= a 0 0 0 0 0 258 242 558 87 582 601 584 17 580 537 270 241 c 0 0 0 0 0 73 125 10 22 16 7 14 21 15 32 93 107 g 0 0 0 0 0 127 131 24 461 16 13 17 31 18 27 112 90 t 0 0 0 0 0 175 135 41 63 19 12 18 564 20 37 158 195

oligos_6nt_mkv3_m1_shift6 (oligos_6nt_mkv3_m1)
; dyads_m2 versus oligos_6nt_mkv3_m1; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=6; score=0.791679; ------wwgAAATAAAw ; cor=; Ncor= a 0 0 0 0 0 0 218 254 124 543 542 540 4 554 512 492 217 c 0 0 0 0 0 0 105 37 35 14 12 9 6 4 25 16 80 g 0 0 0 0 0 0 112 98 334 15 9 11 5 5 24 29 100 t 0 0 0 0 0 0 147 193 89 10 19 22 567 19 21 45 185

dyads_m1_shift4 (dyads_m1)
; dyads_m2 versus dyads_m1; m=3/5; ncol2=14; w=-1; offset=-1; strand=D; shift=4; score=0.604735; ----wwATAAAATAAtw ; cor=; Ncor= a 0 0 0 0 150 149 306 30 370 371 381 385 12 359 354 88 169 c 0 0 0 0 51 83 34 23 14 11 8 11 7 9 20 34 50 g 0 0 0 0 79 47 16 11 16 13 6 15 8 19 15 42 58 t 0 0 0 0 152 153 76 368 32 37 37 21 405 45 43 268 155

oligos_6nt_mkv3_m10_shift7 (oligos_6nt_mkv3_m10)
; dyads_m2 versus oligos_6nt_mkv3_m10; m=4/5; ncol2=10; w=0; offset=2; strand=D; shift=7; score=0.602942; -------aaAAAGAAaw ; cor=; Ncor= a 0 0 0 0 0 0 0 208 224 504 506 499 0 505 503 198 182 c 0 0 0 0 0 0 0 88 90 0 1 8 0 0 5 96 87 g 0 0 0 0 0 0 0 98 90 3 0 0 506 0 0 109 99 t 0 0 0 0 0 0 0 114 104 1 1 1 2 3 0 105 140

dyads_m10_shift0 (dyads_m10)
; dyads_m2 versus dyads_m10; m=5/5; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.575208; wwATAAAATAAATAAww ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 228 115 115 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 13 28 37 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 20 42 42 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30 46 122 113

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 4 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; dsCCACTGCAsy ; Alignment reference a 106 77 14 12 355 9 22 7 11 280 96 69 c 77 129 312 386 17 370 29 12 369 47 122 119 g 117 131 17 2 9 9 13 366 11 31 108 83 t 102 65 59 2 21 14 338 17 11 44 76 131

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; dsCCACTGCAsy ; cor=; Ncor= a 106 77 14 12 355 9 22 7 11 280 96 69 c 77 129 312 386 17 370 29 12 369 47 122 119 g 117 131 17 2 9 9 13 366 11 31 108 83 t 102 65 59 2 21 14 338 17 11 44 76 131

oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m7; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.787733; -syCACTGCas- ; cor=; Ncor= a 0 90 81 7 398 11 27 7 3 159 101 0 c 0 150 156 435 16 431 40 8 446 110 134 0 g 0 141 99 10 27 8 40 437 3 98 141 0 t 0 74 119 3 14 5 348 3 3 88 79 0

oligos_8nt_mkv5_m3_shift1 (oligos_8nt_mkv5_m3)
; oligos_7nt_mkv4_m1 versus oligos_8nt_mkv5_m3; m=3/3; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.597366; -ykCACTCCAGc ; cor=; Ncor= a 0 44 59 10 273 9 11 8 10 268 6 57 c 0 105 66 283 13 281 13 256 291 11 5 138 g 0 34 96 16 4 12 25 35 3 5 299 56 t 0 131 93 5 24 12 265 15 10 30 4 63

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; wwATAAAATAAtww ; Alignment reference a 150 149 306 30 370 371 381 385 12 359 354 88 169 164 c 51 83 34 23 14 11 8 11 7 9 20 34 50 67 g 79 47 16 11 16 13 6 15 8 19 15 42 58 54 t 152 153 76 368 32 37 37 21 405 45 43 268 155 147

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAAATAAtww ; cor=; Ncor= a 150 149 306 30 370 371 381 385 12 359 354 88 169 164 c 51 83 34 23 14 11 8 11 7 9 20 34 50 67 g 79 47 16 11 16 13 6 15 8 19 15 42 58 54 t 152 153 76 368 32 37 37 21 405 45 43 268 155 147

dyads_m10_shift0 (dyads_m10)
; dyads_m1 versus dyads_m10; m=2/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.714943; wwATAAAATAAATA ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; dyads_m1 versus oligos_6nt_mkv3_m1; m=3/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.666432; --wwgAAATAAAww ; cor=; Ncor= a 0 0 218 254 124 543 542 540 4 554 512 492 217 224 c 0 0 105 37 35 14 12 9 6 4 25 16 80 92 g 0 0 112 98 334 15 9 11 5 5 24 29 100 87 t 0 0 147 193 89 10 19 22 567 19 21 45 185 179

dyads_m2_shift1 (dyads_m2)
; dyads_m1 versus dyads_m2; m=4/5; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.604735; -waAGAAATAAaw- ; cor=; Ncor= a 0 258 242 558 87 582 601 584 17 580 537 270 241 0 c 0 73 125 10 22 16 7 14 21 15 32 93 107 0 g 0 127 131 24 461 16 13 17 31 18 27 112 90 0 t 0 175 135 41 63 19 12 18 564 20 37 158 195 0

oligos_8nt_mkv5_m1_rc_shift0 (oligos_8nt_mkv5_m1_rc)
; dyads_m1 versus oligos_8nt_mkv5_m1_rc; m=5/5; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.600109; wwGTAAAATGww-- ; cor=; Ncor= a 102 103 41 21 304 302 312 301 10 11 108 115 0 0 c 57 38 15 12 7 7 5 3 2 14 64 62 0 0 g 67 51 242 21 10 10 7 10 13 292 58 68 0 0 t 104 138 32 276 9 11 6 16 305 13 100 85 0 0

One-to-n matrix alignment; reference matrix: dyads_m8_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m8_shift2 (dyads_m8)
; dyads_m8; m=0 (reference); ncol1=10; shift=2; ncol=12; --aaAACAAAaa ; Alignment reference a 0 0 184 203 428 428 0 420 421 426 163 166 c 0 0 71 77 0 1 430 0 0 5 89 82 g 0 0 73 76 3 1 0 7 2 0 81 82 t 0 0 103 75 0 1 1 4 8 0 98 101

dyads_m8_shift2 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --aaAACAAAaa ; cor=; Ncor= a 0 0 184 203 428 428 0 420 421 426 163 166 c 0 0 71 77 0 1 430 0 0 5 89 82 g 0 0 73 76 3 1 0 7 2 0 81 82 t 0 0 103 75 0 1 1 4 8 0 98 101

oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)
; dyads_m8 versus oligos_6nt_mkv3_m3; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.908885; -waaAACAAAaa ; cor=; Ncor= a 0 184 185 217 431 430 0 421 423 428 163 169 c 0 60 71 72 0 2 430 1 0 5 94 82 g 0 79 75 71 0 1 0 7 2 0 76 87 t 0 110 102 73 2 0 3 4 8 0 100 95

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; dyads_m8 versus oligos_6nt_mkv3_m1; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.59988; wwgAAATAAAww ; cor=; Ncor= a 218 254 124 543 542 540 4 554 512 492 217 224 c 105 37 35 14 12 9 6 4 25 16 80 92 g 112 98 334 15 9 11 5 5 24 29 100 87 t 147 193 89 10 19 22 567 19 21 45 185 179

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; wmAAGCAAww ; Alignment reference a 106 95 291 284 1 0 266 290 85 90 c 40 83 2 10 0 295 1 4 58 54 g 51 56 1 0 294 0 27 1 56 61 t 98 61 1 1 0 0 1 0 96 90

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wmAAGCAAww ; cor=; Ncor= a 106 95 291 284 1 0 266 290 85 90 c 40 83 2 10 0 295 1 4 58 54 g 51 56 1 0 294 0 27 1 56 61 t 98 61 1 1 0 0 1 0 96 90

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -waaAACAAAaa ; Alignment reference a 0 184 185 217 431 430 0 421 423 428 163 169 c 0 60 71 72 0 2 430 1 0 5 94 82 g 0 79 75 71 0 1 0 7 2 0 76 87 t 0 110 102 73 2 0 3 4 8 0 100 95

oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -waaAACAAAaa ; cor=; Ncor= a 0 184 185 217 431 430 0 421 423 428 163 169 c 0 60 71 72 0 2 430 1 0 5 94 82 g 0 79 75 71 0 1 0 7 2 0 76 87 t 0 110 102 73 2 0 3 4 8 0 100 95

dyads_m8_shift2 (dyads_m8)
; oligos_6nt_mkv3_m3 versus dyads_m8; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.908885; --aaAACAAAaa ; cor=; Ncor= a 0 0 184 203 428 428 0 420 421 426 163 166 c 0 0 71 77 0 1 430 0 0 5 89 82 g 0 0 73 76 3 1 0 7 2 0 81 82 t 0 0 103 75 0 1 1 4 8 0 98 101

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.668036; wwgAAATAAAww ; cor=; Ncor= a 218 254 124 543 542 540 4 554 512 492 217 224 c 105 37 35 14 12 9 6 4 25 16 80 92 g 112 98 334 15 9 11 5 5 24 29 100 87 t 147 193 89 10 19 22 567 19 21 45 185 179

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m7_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=10; shift=1; ncol=11; -syCACTGCas ; Alignment reference a 0 90 81 7 398 11 27 7 3 159 101 c 0 150 156 435 16 431 40 8 446 110 134 g 0 141 99 10 27 8 40 437 3 98 141 t 0 74 119 3 14 5 348 3 3 88 79

oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -syCACTGCas ; cor=; Ncor= a 0 90 81 7 398 11 27 7 3 159 101 c 0 150 156 435 16 431 40 8 446 110 134 g 0 141 99 10 27 8 40 437 3 98 141 t 0 74 119 3 14 5 348 3 3 88 79

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.787733; dsCCACTGCAs ; cor=; Ncor= a 106 77 14 12 355 9 22 7 11 280 96 c 77 129 312 386 17 370 29 12 369 47 122 g 117 131 17 2 9 9 13 366 11 31 108 t 102 65 59 2 21 14 338 17 11 44 76

oligos_8nt_mkv5_m3_shift1 (oligos_8nt_mkv5_m3)
; oligos_6nt_mkv3_m7 versus oligos_8nt_mkv5_m3; m=3/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.583538; -ykCACTCCAG ; cor=; Ncor= a 0 44 59 10 273 9 11 8 10 268 6 c 0 105 66 283 13 281 13 256 291 11 5 g 0 34 96 16 4 12 25 35 3 5 299 t 0 131 93 5 24 12 265 15 10 30 4

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

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; wyaCCCAGGCwgg ; Alignment reference a 75 66 179 12 8 8 262 3 3 15 157 53 56 c 47 78 22 235 265 264 8 6 11 267 32 65 54 g 56 45 68 41 17 13 20 280 268 5 19 112 132 t 119 108 28 9 7 12 7 8 15 10 89 67 55

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wyaCCCAGGCwgg ; cor=; Ncor= a 75 66 179 12 8 8 262 3 3 15 157 53 56 c 47 78 22 235 265 264 8 6 11 267 32 65 54 g 56 45 68 41 17 13 20 280 268 5 19 112 132 t 119 108 28 9 7 12 7 8 15 10 89 67 55

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; dyads_m3 versus oligos_6nt_mkv3_m4; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.909977; tyacCCAGGCwg- ; cor=; Ncor= a 108 101 258 35 15 13 401 5 17 31 131 86 0 c 90 118 51 306 416 411 18 11 20 404 76 108 0 g 95 97 105 82 19 25 29 434 405 8 95 162 0 t 165 142 44 35 8 9 10 8 16 15 156 102 0

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; wwAATGTATww ; Alignment reference a 169 187 449 472 33 77 18 515 19 244 186 c 69 62 34 21 15 16 7 5 28 48 100 g 95 79 8 23 4 430 4 11 16 97 53 t 212 217 54 29 493 22 516 14 482 156 206
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAATGTATww ; cor=; Ncor= a 169 187 449 472 33 77 18 515 19 244 186 c 69 62 34 21 15 16 7 5 28 48 100 g 95 79 8 23 4 430 4 11 16 97 53 t 212 217 54 29 493 22 516 14 482 156 206
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m5; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.994275; wwAATGTATww ; cor=; Ncor= a 190 202 473 490 16 69 10 539 67 251 186 c 76 68 27 20 15 10 5 3 36 48 100 g 95 96 6 22 3 464 2 9 46 99 65 t 199 194 54 28 526 17 543 9 411 162 209
dyads_m6_shift0 (dyads_m6)				; oligos_7nt_mkv4_m2 versus dyads_m6; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.852198; waAATGTAww- ; cor=; Ncor= a 105 127 283 294 3 4 0 292 81 115 0 c 43 41 2 3 25 1 0 3 52 32 0 g 51 71 4 2 1 293 1 0 52 64 0 t 100 60 10 0 270 1 298 4 114 88 0
oligos_6nt_mkv3_m9_rc_shift0 (oligos_6nt_mkv3_m9_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m9_rc; m=4/5; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.847287; waTATGTATww ; cor=; Ncor= a 210 349 66 688 31 139 31 696 64 354 227 c 102 80 33 20 3 27 16 12 20 74 105 g 108 155 8 42 25 560 16 37 24 124 94 t 356 192 669 26 717 50 713 31 668 224 350
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_7nt_mkv4_m2 versus positions_6nt_m1; m=5/5; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.680202; -awATGTAAwt ; cor=; Ncor= a 0 102 79 252 0 2 3 247 241 106 63 c 0 47 62 1 19 0 0 4 4 44 40 g 0 46 33 4 0 253 1 4 3 37 53 t 0 62 83 0 238 2 253 2 9 70 101

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---wwGAGTGCAkw ; Alignment reference a 0 0 0 99 128 10 329 15 29 16 25 356 70 106 c 0 0 0 65 33 13 8 10 11 11 341 13 81 82 g 0 0 0 92 97 357 17 354 10 341 7 7 137 54 t 0 0 0 137 135 13 39 14 343 25 20 17 105 151
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---wwGAGTGCAkw ; cor=; Ncor= a 0 0 0 99 128 10 329 15 29 16 25 356 70 106 c 0 0 0 65 33 13 8 10 11 11 341 13 81 82 g 0 0 0 92 97 357 17 354 10 341 7 7 137 54 t 0 0 0 137 135 13 39 14 343 25 20 17 105 151
oligos_8nt_mkv5_m2_shift2 (oligos_8nt_mkv5_m2)				; oligos_7nt_mkv4_m3 versus oligos_8nt_mkv5_m2; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.847356; --ctGGAGTGCAgt ; cor=; Ncor= a 0 0 49 62 14 5 220 13 9 9 11 240 56 57 c 0 0 120 30 8 13 11 16 13 10 231 3 47 42 g 0 0 47 60 227 237 9 217 10 213 11 11 110 61 t 0 0 41 105 8 2 17 11 225 25 4 3 44 97
oligos_8nt_mkv5_m3_rc_shift0 (oligos_8nt_mkv5_m3_rc)				; oligos_7nt_mkv4_m3 versus oligos_8nt_mkv5_m3_rc; m=3/3; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.488439; kgCTGGAGTGmr-- ; cor=; Ncor= a 49 63 4 30 10 15 265 12 24 5 93 131 0 0 c 42 56 299 5 3 35 25 12 4 16 96 34 0 0 g 138 138 5 11 291 256 13 281 13 283 66 105 0 0 t 85 57 6 268 10 8 11 9 273 10 59 44 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m9_shift5 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=11; shift=5; ncol=16; -----wwATACATAtw ; Alignment reference a 0 0 0 0 0 350 224 668 31 713 50 717 26 669 192 356 c 0 0 0 0 0 94 124 24 37 16 560 25 42 8 155 108 g 0 0 0 0 0 105 74 20 12 16 27 3 20 33 80 102 t 0 0 0 0 0 227 354 64 696 31 139 31 688 66 349 210
oligos_6nt_mkv3_m9_shift5 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----wwATACATAtw ; cor=; Ncor= a 0 0 0 0 0 350 224 668 31 713 50 717 26 669 192 356 c 0 0 0 0 0 94 124 24 37 16 560 25 42 8 155 108 g 0 0 0 0 0 105 74 20 12 16 27 3 20 33 80 102 t 0 0 0 0 0 227 354 64 696 31 139 31 688 66 349 210
oligos_7nt_mkv4_m2_rc_shift5 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m9 versus oligos_7nt_mkv4_m2_rc; m=2/6; ncol2=11; w=0; offset=0; strand=R; shift=5; score=0.847287; -----wwATACATTww ; cor=; Ncor= a 0 0 0 0 0 206 156 482 14 516 22 493 29 54 217 212 c 0 0 0 0 0 53 97 16 11 4 430 4 23 8 79 95 g 0 0 0 0 0 100 48 28 5 7 16 15 21 34 62 69 t 0 0 0 0 0 186 244 19 515 18 77 33 472 449 187 169
oligos_6nt_mkv3_m5_rc_shift5 (oligos_6nt_mkv3_m5_rc)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m5_rc; m=3/6; ncol2=11; w=0; offset=0; strand=R; shift=5; score= 0.84; -----wwATACATTww ; cor=; Ncor= a 0 0 0 0 0 209 162 411 9 543 17 526 28 54 194 199 c 0 0 0 0 0 65 99 46 9 2 464 3 22 6 96 95 g 0 0 0 0 0 100 48 36 3 5 10 15 20 27 68 76 t 0 0 0 0 0 186 251 67 539 10 69 16 490 473 202 190
dyads_m6_rc_shift6 (dyads_m6_rc)				; oligos_6nt_mkv3_m9 versus dyads_m6_rc; m=4/6; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.694553; ------wwTACATTtw ; cor=; Ncor= a 0 0 0 0 0 0 88 114 4 298 1 270 0 10 60 100 c 0 0 0 0 0 0 64 52 0 1 293 1 2 4 71 51 g 0 0 0 0 0 0 32 52 3 0 1 25 3 2 41 43 t 0 0 0 0 0 0 115 81 292 0 4 3 294 283 127 105
positions_6nt_m1_rc_shift5 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m9 versus positions_6nt_m1_rc; m=5/6; ncol2=10; w=0; offset=0; strand=R; shift=5; score=0.686302; -----awTTACATwt- ; cor=; Ncor= a 0 0 0 0 0 101 70 9 2 253 2 238 0 83 62 0 c 0 0 0 0 0 53 37 3 4 1 253 0 4 33 46 0 g 0 0 0 0 0 40 44 4 4 0 0 19 1 62 47 0 t 0 0 0 0 0 63 106 241 247 3 2 0 252 79 102 0
dyads_m10_shift0 (dyads_m10)				; oligos_6nt_mkv3_m9 versus dyads_m10; m=6/6; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.486235; wwATAAAATAAATAAw ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 228 115 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 13 28 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 20 42 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30 46 122

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m10_shift2 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=10; shift=2; ncol=12; --aaAAAGAAaw ; Alignment reference a 0 0 208 224 504 506 499 0 505 503 198 182 c 0 0 88 90 0 1 8 0 0 5 96 87 g 0 0 98 90 3 0 0 506 0 0 109 99 t 0 0 114 104 1 1 1 2 3 0 105 140
oligos_6nt_mkv3_m10_shift2 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --aaAAAGAAaw ; cor=; Ncor= a 0 0 208 224 504 506 499 0 505 503 198 182 c 0 0 88 90 0 1 8 0 0 5 96 87 g 0 0 98 90 3 0 0 506 0 0 109 99 t 0 0 114 104 1 1 1 2 3 0 105 140
dyads_m7_shift2 (dyads_m7)				; oligos_6nt_mkv3_m10 versus dyads_m7; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.76385; --rrAGAGAArd ; cor=; Ncor= a 0 0 161 120 406 1 426 0 437 414 171 134 c 0 0 77 100 29 1 17 0 2 25 61 72 g 0 0 111 127 4 441 0 442 2 4 117 126 t 0 0 95 97 5 1 1 2 3 1 95 112
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.604028; -wwgAAATAAAw ; cor=; Ncor= a 0 218 254 124 543 542 540 4 554 512 492 217 c 0 105 37 35 14 12 9 6 4 25 16 80 g 0 112 98 334 15 9 11 5 5 24 29 100 t 0 147 193 89 10 19 22 567 19 21 45 185
dyads_m2_shift0 (dyads_m2)				; oligos_6nt_mkv3_m10 versus dyads_m2; m=4/4; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.602942; waAGAAATAAaw ; cor=; Ncor= a 258 242 558 87 582 601 584 17 580 537 270 241 c 73 125 10 22 16 7 14 21 15 32 93 107 g 127 131 24 461 16 13 17 31 18 27 112 90 t 175 135 41 63 19 12 18 564 20 37 158 195

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv5_m3_shift2 (oligos_8nt_mkv5_m3)				; oligos_8nt_mkv5_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --ykCACTCCAGcm ; Alignment reference a 0 0 44 59 10 273 9 11 8 10 268 6 57 85 c 0 0 105 66 283 13 281 13 256 291 11 5 138 138 g 0 0 34 96 16 4 12 25 35 3 5 299 56 42 t 0 0 131 93 5 24 12 265 15 10 30 4 63 49
oligos_8nt_mkv5_m3_shift2 (oligos_8nt_mkv5_m3)				; oligos_8nt_mkv5_m3 versus oligos_8nt_mkv5_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ykCACTCCAGcm ; cor=; Ncor= a 0 0 44 59 10 273 9 11 8 10 268 6 57 85 c 0 0 105 66 283 13 281 13 256 291 11 5 138 138 g 0 0 34 96 16 4 12 25 35 3 5 299 56 42 t 0 0 131 93 5 24 12 265 15 10 30 4 63 49
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_8nt_mkv5_m3 versus oligos_7nt_mkv4_m1; m=2/5; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.597366; -dsCCACTGCAsy- ; cor=; Ncor= a 0 106 77 14 12 355 9 22 7 11 280 96 69 0 c 0 77 129 312 386 17 370 29 12 369 47 122 119 0 g 0 117 131 17 2 9 9 13 366 11 31 108 83 0 t 0 102 65 59 2 21 14 338 17 11 44 76 131 0
oligos_8nt_mkv5_m2_rc_shift0 (oligos_8nt_mkv5_m2_rc)				; oligos_8nt_mkv5_m3 versus oligos_8nt_mkv5_m2_rc; m=3/5; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.593804; acTGCACTCCag-- ; cor=; Ncor= a 97 44 3 4 25 225 11 17 2 8 105 41 0 0 c 61 110 11 11 213 10 217 9 237 227 60 47 0 0 g 42 47 3 231 10 13 16 11 13 8 30 120 0 0 t 57 56 240 11 9 9 13 220 5 14 62 49 0 0
oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)				; oligos_8nt_mkv5_m3 versus oligos_6nt_mkv3_m7; m=4/5; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.583538; --syCACTGCas-- ; cor=; Ncor= a 0 0 90 81 7 398 11 27 7 3 159 101 0 0 c 0 0 150 156 435 16 431 40 8 446 110 134 0 0 g 0 0 141 99 10 27 8 40 437 3 98 141 0 0 t 0 0 74 119 3 14 5 348 3 3 88 79 0 0
oligos_7nt_mkv4_m3_rc_shift0 (oligos_7nt_mkv4_m3_rc)				; oligos_8nt_mkv5_m3 versus oligos_7nt_mkv4_m3_rc; m=5/5; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.488439; wmTGCACTCww--- ; cor=; Ncor= a 151 105 17 20 25 343 14 39 13 135 137 0 0 0 c 54 137 7 7 341 10 354 17 357 97 92 0 0 0 g 82 81 13 341 11 11 10 8 13 33 65 0 0 0 t 106 70 356 25 16 29 15 329 10 128 99 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv5_m2_shift2 (oligos_8nt_mkv5_m2)				; oligos_8nt_mkv5_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --ctGGAGTGCAgt ; Alignment reference a 0 0 49 62 14 5 220 13 9 9 11 240 56 57 c 0 0 120 30 8 13 11 16 13 10 231 3 47 42 g 0 0 47 60 227 237 9 217 10 213 11 11 110 61 t 0 0 41 105 8 2 17 11 225 25 4 3 44 97
oligos_8nt_mkv5_m2_shift2 (oligos_8nt_mkv5_m2)				; oligos_8nt_mkv5_m2 versus oligos_8nt_mkv5_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ctGGAGTGCAgt ; cor=; Ncor= a 0 0 49 62 14 5 220 13 9 9 11 240 56 57 c 0 0 120 30 8 13 11 16 13 10 231 3 47 42 g 0 0 47 60 227 237 9 217 10 213 11 11 110 61 t 0 0 41 105 8 2 17 11 225 25 4 3 44 97
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_8nt_mkv5_m2 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.847356; ---wwGAGTGCAkw ; cor=; Ncor= a 0 0 0 99 128 10 329 15 29 16 25 356 70 106 c 0 0 0 65 33 13 8 10 11 11 341 13 81 82 g 0 0 0 92 97 357 17 354 10 341 7 7 137 54 t 0 0 0 137 135 13 39 14 343 25 20 17 105 151
oligos_8nt_mkv5_m3_rc_shift0 (oligos_8nt_mkv5_m3_rc)				; oligos_8nt_mkv5_m2 versus oligos_8nt_mkv5_m3_rc; m=3/3; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.593804; kgCTGGAGTGmr-- ; cor=; Ncor= a 49 63 4 30 10 15 265 12 24 5 93 131 0 0 c 42 56 299 5 3 35 25 12 4 16 96 34 0 0 g 138 138 5 11 291 256 13 281 13 283 66 105 0 0 t 85 57 6 268 10 8 11 9 273 10 59 44 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m6_shift10 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=10; ncol=20; ----------msCCTCCCmv ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 156 91 7 4 20 7 8 4 165 152 c 0 0 0 0 0 0 0 0 0 0 175 150 533 531 9 519 510 522 145 144 g 0 0 0 0 0 0 0 0 0 0 110 216 14 21 48 22 37 33 141 166 t 0 0 0 0 0 0 0 0 0 0 125 109 12 10 489 18 11 7 115 104
oligos_6nt_mkv3_m6_shift10 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=10; score= 1; ----------msCCTCCCmv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 156 91 7 4 20 7 8 4 165 152 c 0 0 0 0 0 0 0 0 0 0 175 150 533 531 9 519 510 522 145 144 g 0 0 0 0 0 0 0 0 0 0 110 216 14 21 48 22 37 33 141 166 t 0 0 0 0 0 0 0 0 0 0 125 109 12 10 489 18 11 7 115 104
dyads_m9_shift10 (dyads_m9)				; oligos_6nt_mkv3_m6 versus dyads_m9; m=2/3; ncol2=16; w=0; offset=0; strand=D; shift=10; score=0.464715; ----------mvCCcCCCAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 42 41 19 13 28 6 14 11 117 6 c 0 0 0 0 0 0 0 0 0 0 55 43 111 122 95 142 125 133 21 19 g 0 0 0 0 0 0 0 0 0 0 27 45 22 9 17 2 12 16 12 128 t 0 0 0 0 0 0 0 0 0 0 37 32 9 17 21 11 10 1 11 8
dyads_m4_shift0 (dyads_m4)				; oligos_6nt_mkv3_m6 versus dyads_m4; m=3/3; ncol2=22; w=-10; offset=-10; strand=D; shift=0; score=0.415303; yycCctCCTCcsCCTCCCma ; cor=; Ncor= a 10 24 6 4 11 25 3 9 4 6 23 5 15 10 7 4 2 6 33 69 c 68 30 78 98 80 8 110 102 10 97 72 63 92 89 21 105 110 98 54 21 g 9 16 15 5 4 25 2 4 9 6 17 35 2 11 6 4 1 5 17 10 t 31 48 19 11 23 60 3 3 95 9 6 15 9 8 84 5 5 9 14 18

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m10_shift0 (dyads_m10)				; dyads_m10; m=0 (reference); ncol1=17; shift=0; ncol=17; wwATAAAATAAATAAww ; Alignment reference a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 228 115 115 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 13 28 37 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 20 42 42 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30 46 122 113
dyads_m10_shift0 (dyads_m10)				; dyads_m10 versus dyads_m10; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAAATAAATAAww ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 228 115 115 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 13 28 37 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 20 42 42 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30 46 122 113
dyads_m1_shift0 (dyads_m1)				; dyads_m10 versus dyads_m1; m=2/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.714943; wwATAAAATAAtww--- ; cor=; Ncor= a 150 149 306 30 370 371 381 385 12 359 354 88 169 164 0 0 0 c 51 83 34 23 14 11 8 11 7 9 20 34 50 67 0 0 0 g 79 47 16 11 16 13 6 15 8 19 15 42 58 54 0 0 0 t 152 153 76 368 32 37 37 21 405 45 43 268 155 147 0 0 0
dyads_m2_shift5 (dyads_m2)				; dyads_m10 versus dyads_m2; m=3/5; ncol2=12; w=0; offset=5; strand=D; shift=5; score=0.575208; -----waAGAAATAAaw ; cor=; Ncor= a 0 0 0 0 0 258 242 558 87 582 601 584 17 580 537 270 241 c 0 0 0 0 0 73 125 10 22 16 7 14 21 15 32 93 107 g 0 0 0 0 0 127 131 24 461 16 13 17 31 18 27 112 90 t 0 0 0 0 0 175 135 41 63 19 12 18 564 20 37 158 195
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; dyads_m10 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.561263; --wwgAAATAAAww--- ; cor=; Ncor= a 0 0 218 254 124 543 542 540 4 554 512 492 217 224 0 0 0 c 0 0 105 37 35 14 12 9 6 4 25 16 80 92 0 0 0 g 0 0 112 98 334 15 9 11 5 5 24 29 100 87 0 0 0 t 0 0 147 193 89 10 19 22 567 19 21 45 185 179 0 0 0
oligos_6nt_mkv3_m9_shift5 (oligos_6nt_mkv3_m9)				; dyads_m10 versus oligos_6nt_mkv3_m9; m=5/5; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.486235; -----wwATACATAtw- ; cor=; Ncor= a 0 0 0 0 0 350 224 668 31 713 50 717 26 669 192 356 0 c 0 0 0 0 0 94 124 24 37 16 560 25 42 8 155 108 0 g 0 0 0 0 0 105 74 20 12 16 27 3 20 33 80 102 0 t 0 0 0 0 0 227 354 64 696 31 139 31 688 66 349 210 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwgAAATAAAww ; Alignment reference a 0 0 218 254 124 543 542 540 4 554 512 492 217 224 c 0 0 105 37 35 14 12 9 6 4 25 16 80 92 g 0 0 112 98 334 15 9 11 5 5 24 29 100 87 t 0 0 147 193 89 10 19 22 567 19 21 45 185 179
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwgAAATAAAww ; cor=; Ncor= a 0 0 218 254 124 543 542 540 4 554 512 492 217 224 c 0 0 105 37 35 14 12 9 6 4 25 16 80 92 g 0 0 112 98 334 15 9 11 5 5 24 29 100 87 t 0 0 147 193 89 10 19 22 567 19 21 45 185 179
dyads_m2_shift1 (dyads_m2)				; oligos_6nt_mkv3_m1 versus dyads_m2; m=2/7; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.791679; -waAGAAATAAaw- ; cor=; Ncor= a 0 258 242 558 87 582 601 584 17 580 537 270 241 0 c 0 73 125 10 22 16 7 14 21 15 32 93 107 0 g 0 127 131 24 461 16 13 17 31 18 27 112 90 0 t 0 175 135 41 63 19 12 18 564 20 37 158 195 0
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3; m=3/7; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.668036; ---waaAACAAAaa ; cor=; Ncor= a 0 0 0 184 185 217 431 430 0 421 423 428 163 169 c 0 0 0 60 71 72 0 2 430 1 0 5 94 82 g 0 0 0 79 75 71 0 1 0 7 2 0 76 87 t 0 0 0 110 102 73 2 0 3 4 8 0 100 95
dyads_m1_shift0 (dyads_m1)				; oligos_6nt_mkv3_m1 versus dyads_m1; m=4/7; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.666432; wwATAAAATAAtww ; cor=; Ncor= a 150 149 306 30 370 371 381 385 12 359 354 88 169 164 c 51 83 34 23 14 11 8 11 7 9 20 34 50 67 g 79 47 16 11 16 13 6 15 8 19 15 42 58 54 t 152 153 76 368 32 37 37 21 405 45 43 268 155 147
oligos_6nt_mkv3_m10_shift3 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m10; m=5/7; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.604028; ---aaAAAGAAaw- ; cor=; Ncor= a 0 0 0 208 224 504 506 499 0 505 503 198 182 0 c 0 0 0 88 90 0 1 8 0 0 5 96 87 0 g 0 0 0 98 90 3 0 0 506 0 0 109 99 0 t 0 0 0 114 104 1 1 1 2 3 0 105 140 0
dyads_m8_shift4 (dyads_m8)				; oligos_6nt_mkv3_m1 versus dyads_m8; m=6/7; ncol2=10; w=0; offset=2; strand=D; shift=4; score=0.59988; ----aaAACAAAaa ; cor=; Ncor= a 0 0 0 0 184 203 428 428 0 420 421 426 163 166 c 0 0 0 0 71 77 0 1 430 0 0 5 89 82 g 0 0 0 0 73 76 3 1 0 7 2 0 81 82 t 0 0 0 0 103 75 0 1 1 4 8 0 98 101
dyads_m10_shift0 (dyads_m10)				; oligos_6nt_mkv3_m1 versus dyads_m10; m=7/7; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.561263; wwATAAAATAAATA ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAATGTATww ; Alignment reference a 190 202 473 490 16 69 10 539 67 251 186 c 76 68 27 20 15 10 5 3 36 48 100 g 95 96 6 22 3 464 2 9 46 99 65 t 199 194 54 28 526 17 543 9 411 162 209
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAATGTATww ; cor=; Ncor= a 190 202 473 490 16 69 10 539 67 251 186 c 76 68 27 20 15 10 5 3 36 48 100 g 95 96 6 22 3 464 2 9 46 99 65 t 199 194 54 28 526 17 543 9 411 162 209
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m2; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.994275; wwAATGTATww ; cor=; Ncor= a 169 187 449 472 33 77 18 515 19 244 186 c 69 62 34 21 15 16 7 5 28 48 100 g 95 79 8 23 4 430 4 11 16 97 53 t 212 217 54 29 493 22 516 14 482 156 206
dyads_m6_shift0 (dyads_m6)				; oligos_6nt_mkv3_m5 versus dyads_m6; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.878775; waAATGTAww- ; cor=; Ncor= a 105 127 283 294 3 4 0 292 81 115 0 c 43 41 2 3 25 1 0 3 52 32 0 g 51 71 4 2 1 293 1 0 52 64 0 t 100 60 10 0 270 1 298 4 114 88 0
oligos_6nt_mkv3_m9_rc_shift0 (oligos_6nt_mkv3_m9_rc)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m9_rc; m=4/5; ncol2=11; w=0; offset=0; strand=R; shift=0; score= 0.84; waTATGTATww ; cor=; Ncor= a 210 349 66 688 31 139 31 696 64 354 227 c 102 80 33 20 3 27 16 12 20 74 105 g 108 155 8 42 25 560 16 37 24 124 94 t 356 192 669 26 717 50 713 31 668 224 350
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_6nt_mkv3_m5 versus positions_6nt_m1; m=5/5; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.724183; -awATGTAAwt ; cor=; Ncor= a 0 102 79 252 0 2 3 247 241 106 63 c 0 47 62 1 19 0 0 4 4 44 40 g 0 46 33 4 0 253 1 4 3 37 53 t 0 62 83 0 238 2 253 2 9 70 101

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m6_shift4 (dyads_m6)				; dyads_m6; m=0 (reference); ncol1=10; shift=4; ncol=14; ----waAATGTAww ; Alignment reference a 0 0 0 0 105 127 283 294 3 4 0 292 81 115 c 0 0 0 0 43 41 2 3 25 1 0 3 52 32 g 0 0 0 0 51 71 4 2 1 293 1 0 52 64 t 0 0 0 0 100 60 10 0 270 1 298 4 114 88
dyads_m6_shift4 (dyads_m6)				; dyads_m6 versus dyads_m6; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----waAATGTAww ; cor=; Ncor= a 0 0 0 0 105 127 283 294 3 4 0 292 81 115 c 0 0 0 0 43 41 2 3 25 1 0 3 52 32 g 0 0 0 0 51 71 4 2 1 293 1 0 52 64 t 0 0 0 0 100 60 10 0 270 1 298 4 114 88
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; dyads_m6 versus oligos_6nt_mkv3_m5; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.878775; ----wwAATGTATw ; cor=; Ncor= a 0 0 0 0 190 202 473 490 16 69 10 539 67 251 c 0 0 0 0 76 68 27 20 15 10 5 3 36 48 g 0 0 0 0 95 96 6 22 3 464 2 9 46 99 t 0 0 0 0 199 194 54 28 526 17 543 9 411 162
oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)				; dyads_m6 versus oligos_7nt_mkv4_m2; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.852198; ----wwAATGTATw ; cor=; Ncor= a 0 0 0 0 169 187 449 472 33 77 18 515 19 244 c 0 0 0 0 69 62 34 21 15 16 7 5 28 48 g 0 0 0 0 95 79 8 23 4 430 4 11 16 97 t 0 0 0 0 212 217 54 29 493 22 516 14 482 156
positions_6nt_m1_shift5 (positions_6nt_m1)				; dyads_m6 versus positions_6nt_m1; m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.70136; -----awATGTAAw ; cor=; Ncor= a 0 0 0 0 0 102 79 252 0 2 3 247 241 106 c 0 0 0 0 0 47 62 1 19 0 0 4 4 44 g 0 0 0 0 0 46 33 4 0 253 1 4 3 37 t 0 0 0 0 0 62 83 0 238 2 253 2 9 70
oligos_6nt_mkv3_m9_rc_shift4 (oligos_6nt_mkv3_m9_rc)				; dyads_m6 versus oligos_6nt_mkv3_m9_rc; m=5/6; ncol2=11; w=0; offset=0; strand=R; shift=4; score=0.694553; ----waTATGTATw ; cor=; Ncor= a 0 0 0 0 210 349 66 688 31 139 31 696 64 354 c 0 0 0 0 102 80 33 20 3 27 16 12 20 74 g 0 0 0 0 108 155 8 42 25 560 16 37 24 124 t 0 0 0 0 356 192 669 26 717 50 713 31 668 224
oligos_8nt_mkv5_m1_rc_shift0 (oligos_8nt_mkv5_m1_rc)				; dyads_m6 versus oligos_8nt_mkv5_m1_rc; m=6/6; ncol2=12; w=-4; offset=-4; strand=R; shift=0; score=0.426213; wwGTAAAATGww-- ; cor=; Ncor= a 102 103 41 21 304 302 312 301 10 11 108 115 0 0 c 57 38 15 12 7 7 5 3 2 14 64 62 0 0 g 67 51 242 21 10 10 7 10 13 292 58 68 0 0 t 104 138 32 276 9 11 6 16 305 13 100 85 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -awATGTAAwt ; Alignment reference a 0 102 79 252 0 2 3 247 241 106 63 c 0 47 62 1 19 0 0 4 4 44 40 g 0 46 33 4 0 253 1 4 3 37 53 t 0 62 83 0 238 2 253 2 9 70 101
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -awATGTAAwt ; cor=; Ncor= a 0 102 79 252 0 2 3 247 241 106 63 c 0 47 62 1 19 0 0 4 4 44 40 g 0 46 33 4 0 253 1 4 3 37 53 t 0 62 83 0 238 2 253 2 9 70 101
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)				; positions_6nt_m1 versus oligos_6nt_mkv3_m5; m=2/6; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.724183; wwAATGTATww ; cor=; Ncor= a 190 202 473 490 16 69 10 539 67 251 186 c 76 68 27 20 15 10 5 3 36 48 100 g 95 96 6 22 3 464 2 9 46 99 65 t 199 194 54 28 526 17 543 9 411 162 209
dyads_m6_shift0 (dyads_m6)				; positions_6nt_m1 versus dyads_m6; m=3/6; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.70136; waAATGTAww- ; cor=; Ncor= a 105 127 283 294 3 4 0 292 81 115 0 c 43 41 2 3 25 1 0 3 52 32 0 g 51 71 4 2 1 293 1 0 52 64 0 t 100 60 10 0 270 1 298 4 114 88 0
oligos_6nt_mkv3_m9_rc_shift0 (oligos_6nt_mkv3_m9_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m9_rc; m=4/6; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.686302; waTATGTATww ; cor=; Ncor= a 210 349 66 688 31 139 31 696 64 354 227 c 102 80 33 20 3 27 16 12 20 74 105 g 108 155 8 42 25 560 16 37 24 124 94 t 356 192 669 26 717 50 713 31 668 224 350
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; positions_6nt_m1 versus oligos_7nt_mkv4_m2; m=5/6; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.680202; wwAATGTATww ; cor=; Ncor= a 169 187 449 472 33 77 18 515 19 244 186 c 69 62 34 21 15 16 7 5 28 48 100 g 95 79 8 23 4 430 4 11 16 97 53 t 212 217 54 29 493 22 516 14 482 156 206
oligos_8nt_mkv5_m1_rc_shift3 (oligos_8nt_mkv5_m1_rc)				; positions_6nt_m1 versus oligos_8nt_mkv5_m1_rc; m=6/6; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.411042; ---wwGTAAAA ; cor=; Ncor= a 0 0 0 102 103 41 21 304 302 312 301 c 0 0 0 57 38 15 12 7 7 5 3 g 0 0 0 67 51 242 21 10 10 7 10 t 0 0 0 104 138 32 276 9 11 6 16

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv5_m1_shift2 (oligos_8nt_mkv5_m1)				; oligos_8nt_mkv5_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwCATTTTACww ; Alignment reference a 0 0 85 100 13 305 16 6 11 9 276 32 138 104 c 0 0 68 58 292 13 10 7 10 10 21 242 51 67 g 0 0 62 64 14 2 3 5 7 7 12 15 38 57 t 0 0 115 108 11 10 301 312 302 304 21 41 103 102
oligos_8nt_mkv5_m1_shift2 (oligos_8nt_mkv5_m1)				; oligos_8nt_mkv5_m1 versus oligos_8nt_mkv5_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwCATTTTACww ; cor=; Ncor= a 0 0 85 100 13 305 16 6 11 9 276 32 138 104 c 0 0 68 58 292 13 10 7 10 10 21 242 51 67 g 0 0 62 64 14 2 3 5 7 7 12 15 38 57 t 0 0 115 108 11 10 301 312 302 304 21 41 103 102
dyads_m1_rc_shift0 (dyads_m1_rc)				; oligos_8nt_mkv5_m1 versus dyads_m1_rc; m=2/4; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.600109; wwaTTATTTTATww ; cor=; Ncor= a 147 155 268 43 45 405 21 37 37 32 368 76 153 152 c 54 58 42 15 19 8 15 6 13 16 11 16 47 79 g 67 50 34 20 9 7 11 8 11 14 23 34 83 51 t 164 169 88 354 359 12 385 381 371 370 30 306 149 150
dyads_m6_rc_shift0 (dyads_m6_rc)				; oligos_8nt_mkv5_m1 versus dyads_m6_rc; m=3/4; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.426213; wwTACATTtw---- ; cor=; Ncor= a 88 114 4 298 1 270 0 10 60 100 0 0 0 0 c 64 52 0 1 293 1 2 4 71 51 0 0 0 0 g 32 52 3 0 1 25 3 2 41 43 0 0 0 0 t 115 81 292 0 4 3 294 283 127 105 0 0 0 0
positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)				; oligos_8nt_mkv5_m1 versus positions_6nt_m1_rc; m=4/4; ncol2=10; w=0; offset=4; strand=R; shift=6; score=0.411042; ------awTTACAT ; cor=; Ncor= a 0 0 0 0 0 0 101 70 9 2 253 2 238 0 c 0 0 0 0 0 0 53 37 3 4 1 253 0 4 g 0 0 0 0 0 0 40 44 4 4 0 0 19 1 t 0 0 0 0 0 0 63 106 241 247 3 2 0 252

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift5 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=12; shift=5; ncol=17; -----waAGAAATAAaw ; Alignment reference a 0 0 0 0 0 258 242 558 87 582 601 584 17 580 537 270 241 c 0 0 0 0 0 73 125 10 22 16 7 14 21 15 32 93 107 g 0 0 0 0 0 127 131 24 461 16 13 17 31 18 27 112 90 t 0 0 0 0 0 175 135 41 63 19 12 18 564 20 37 158 195
dyads_m2_shift5 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----waAGAAATAAaw ; cor=; Ncor= a 0 0 0 0 0 258 242 558 87 582 601 584 17 580 537 270 241 c 0 0 0 0 0 73 125 10 22 16 7 14 21 15 32 93 107 g 0 0 0 0 0 127 131 24 461 16 13 17 31 18 27 112 90 t 0 0 0 0 0 175 135 41 63 19 12 18 564 20 37 158 195
oligos_6nt_mkv3_m1_shift6 (oligos_6nt_mkv3_m1)				; dyads_m2 versus oligos_6nt_mkv3_m1; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=6; score=0.791679; ------wwgAAATAAAw ; cor=; Ncor= a 0 0 0 0 0 0 218 254 124 543 542 540 4 554 512 492 217 c 0 0 0 0 0 0 105 37 35 14 12 9 6 4 25 16 80 g 0 0 0 0 0 0 112 98 334 15 9 11 5 5 24 29 100 t 0 0 0 0 0 0 147 193 89 10 19 22 567 19 21 45 185
dyads_m1_shift4 (dyads_m1)				; dyads_m2 versus dyads_m1; m=3/5; ncol2=14; w=-1; offset=-1; strand=D; shift=4; score=0.604735; ----wwATAAAATAAtw ; cor=; Ncor= a 0 0 0 0 150 149 306 30 370 371 381 385 12 359 354 88 169 c 0 0 0 0 51 83 34 23 14 11 8 11 7 9 20 34 50 g 0 0 0 0 79 47 16 11 16 13 6 15 8 19 15 42 58 t 0 0 0 0 152 153 76 368 32 37 37 21 405 45 43 268 155
oligos_6nt_mkv3_m10_shift7 (oligos_6nt_mkv3_m10)				; dyads_m2 versus oligos_6nt_mkv3_m10; m=4/5; ncol2=10; w=0; offset=2; strand=D; shift=7; score=0.602942; -------aaAAAGAAaw ; cor=; Ncor= a 0 0 0 0 0 0 0 208 224 504 506 499 0 505 503 198 182 c 0 0 0 0 0 0 0 88 90 0 1 8 0 0 5 96 87 g 0 0 0 0 0 0 0 98 90 3 0 0 506 0 0 109 99 t 0 0 0 0 0 0 0 114 104 1 1 1 2 3 0 105 140
dyads_m10_shift0 (dyads_m10)				; dyads_m2 versus dyads_m10; m=5/5; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.575208; wwATAAAATAAATAAww ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 228 115 115 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 13 28 37 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 20 42 42 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30 46 122 113

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; dsCCACTGCAsy ; Alignment reference a 106 77 14 12 355 9 22 7 11 280 96 69 c 77 129 312 386 17 370 29 12 369 47 122 119 g 117 131 17 2 9 9 13 366 11 31 108 83 t 102 65 59 2 21 14 338 17 11 44 76 131
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; dsCCACTGCAsy ; cor=; Ncor= a 106 77 14 12 355 9 22 7 11 280 96 69 c 77 129 312 386 17 370 29 12 369 47 122 119 g 117 131 17 2 9 9 13 366 11 31 108 83 t 102 65 59 2 21 14 338 17 11 44 76 131
oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m7; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.787733; -syCACTGCas- ; cor=; Ncor= a 0 90 81 7 398 11 27 7 3 159 101 0 c 0 150 156 435 16 431 40 8 446 110 134 0 g 0 141 99 10 27 8 40 437 3 98 141 0 t 0 74 119 3 14 5 348 3 3 88 79 0
oligos_8nt_mkv5_m3_shift1 (oligos_8nt_mkv5_m3)				; oligos_7nt_mkv4_m1 versus oligos_8nt_mkv5_m3; m=3/3; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.597366; -ykCACTCCAGc ; cor=; Ncor= a 0 44 59 10 273 9 11 8 10 268 6 57 c 0 105 66 283 13 281 13 256 291 11 5 138 g 0 34 96 16 4 12 25 35 3 5 299 56 t 0 131 93 5 24 12 265 15 10 30 4 63

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift0 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; wwATAAAATAAtww ; Alignment reference a 150 149 306 30 370 371 381 385 12 359 354 88 169 164 c 51 83 34 23 14 11 8 11 7 9 20 34 50 67 g 79 47 16 11 16 13 6 15 8 19 15 42 58 54 t 152 153 76 368 32 37 37 21 405 45 43 268 155 147
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAAATAAtww ; cor=; Ncor= a 150 149 306 30 370 371 381 385 12 359 354 88 169 164 c 51 83 34 23 14 11 8 11 7 9 20 34 50 67 g 79 47 16 11 16 13 6 15 8 19 15 42 58 54 t 152 153 76 368 32 37 37 21 405 45 43 268 155 147
dyads_m10_shift0 (dyads_m10)				; dyads_m1 versus dyads_m10; m=2/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.714943; wwATAAAATAAATA ; cor=; Ncor= a 120 140 226 38 262 262 235 272 49 235 244 252 41 251 c 31 44 25 13 12 9 13 7 7 11 17 11 12 13 g 43 33 14 14 8 9 4 6 10 10 8 18 12 13 t 113 90 42 242 25 27 55 22 241 51 38 26 242 30
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; dyads_m1 versus oligos_6nt_mkv3_m1; m=3/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.666432; --wwgAAATAAAww ; cor=; Ncor= a 0 0 218 254 124 543 542 540 4 554 512 492 217 224 c 0 0 105 37 35 14 12 9 6 4 25 16 80 92 g 0 0 112 98 334 15 9 11 5 5 24 29 100 87 t 0 0 147 193 89 10 19 22 567 19 21 45 185 179
dyads_m2_shift1 (dyads_m2)				; dyads_m1 versus dyads_m2; m=4/5; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.604735; -waAGAAATAAaw- ; cor=; Ncor= a 0 258 242 558 87 582 601 584 17 580 537 270 241 0 c 0 73 125 10 22 16 7 14 21 15 32 93 107 0 g 0 127 131 24 461 16 13 17 31 18 27 112 90 0 t 0 175 135 41 63 19 12 18 564 20 37 158 195 0
oligos_8nt_mkv5_m1_rc_shift0 (oligos_8nt_mkv5_m1_rc)				; dyads_m1 versus oligos_8nt_mkv5_m1_rc; m=5/5; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.600109; wwGTAAAATGww-- ; cor=; Ncor= a 102 103 41 21 304 302 312 301 10 11 108 115 0 0 c 57 38 15 12 7 7 5 3 2 14 64 62 0 0 g 67 51 242 21 10 10 7 10 13 292 58 68 0 0 t 104 138 32 276 9 11 6 16 305 13 100 85 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m8_shift2 (dyads_m8)				; dyads_m8; m=0 (reference); ncol1=10; shift=2; ncol=12; --aaAACAAAaa ; Alignment reference a 0 0 184 203 428 428 0 420 421 426 163 166 c 0 0 71 77 0 1 430 0 0 5 89 82 g 0 0 73 76 3 1 0 7 2 0 81 82 t 0 0 103 75 0 1 1 4 8 0 98 101
dyads_m8_shift2 (dyads_m8)				; dyads_m8 versus dyads_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --aaAACAAAaa ; cor=; Ncor= a 0 0 184 203 428 428 0 420 421 426 163 166 c 0 0 71 77 0 1 430 0 0 5 89 82 g 0 0 73 76 3 1 0 7 2 0 81 82 t 0 0 103 75 0 1 1 4 8 0 98 101
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)				; dyads_m8 versus oligos_6nt_mkv3_m3; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.908885; -waaAACAAAaa ; cor=; Ncor= a 0 184 185 217 431 430 0 421 423 428 163 169 c 0 60 71 72 0 2 430 1 0 5 94 82 g 0 79 75 71 0 1 0 7 2 0 76 87 t 0 110 102 73 2 0 3 4 8 0 100 95
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; dyads_m8 versus oligos_6nt_mkv3_m1; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.59988; wwgAAATAAAww ; cor=; Ncor= a 218 254 124 543 542 540 4 554 512 492 217 224 c 105 37 35 14 12 9 6 4 25 16 80 92 g 112 98 334 15 9 11 5 5 24 29 100 87 t 147 193 89 10 19 22 567 19 21 45 185 179

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -waaAACAAAaa ; Alignment reference a 0 184 185 217 431 430 0 421 423 428 163 169 c 0 60 71 72 0 2 430 1 0 5 94 82 g 0 79 75 71 0 1 0 7 2 0 76 87 t 0 110 102 73 2 0 3 4 8 0 100 95
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -waaAACAAAaa ; cor=; Ncor= a 0 184 185 217 431 430 0 421 423 428 163 169 c 0 60 71 72 0 2 430 1 0 5 94 82 g 0 79 75 71 0 1 0 7 2 0 76 87 t 0 110 102 73 2 0 3 4 8 0 100 95
dyads_m8_shift2 (dyads_m8)				; oligos_6nt_mkv3_m3 versus dyads_m8; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.908885; --aaAACAAAaa ; cor=; Ncor= a 0 0 184 203 428 428 0 420 421 426 163 166 c 0 0 71 77 0 1 430 0 0 5 89 82 g 0 0 73 76 3 1 0 7 2 0 81 82 t 0 0 103 75 0 1 1 4 8 0 98 101
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.668036; wwgAAATAAAww ; cor=; Ncor= a 218 254 124 543 542 540 4 554 512 492 217 224 c 105 37 35 14 12 9 6 4 25 16 80 92 g 112 98 334 15 9 11 5 5 24 29 100 87 t 147 193 89 10 19 22 567 19 21 45 185 179

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=10; shift=1; ncol=11; -syCACTGCas ; Alignment reference a 0 90 81 7 398 11 27 7 3 159 101 c 0 150 156 435 16 431 40 8 446 110 134 g 0 141 99 10 27 8 40 437 3 98 141 t 0 74 119 3 14 5 348 3 3 88 79
oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -syCACTGCas ; cor=; Ncor= a 0 90 81 7 398 11 27 7 3 159 101 c 0 150 156 435 16 431 40 8 446 110 134 g 0 141 99 10 27 8 40 437 3 98 141 t 0 74 119 3 14 5 348 3 3 88 79
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.787733; dsCCACTGCAs ; cor=; Ncor= a 106 77 14 12 355 9 22 7 11 280 96 c 77 129 312 386 17 370 29 12 369 47 122 g 117 131 17 2 9 9 13 366 11 31 108 t 102 65 59 2 21 14 338 17 11 44 76
oligos_8nt_mkv5_m3_shift1 (oligos_8nt_mkv5_m3)				; oligos_6nt_mkv3_m7 versus oligos_8nt_mkv5_m3; m=3/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.583538; -ykCACTCCAG ; cor=; Ncor= a 0 44 59 10 273 9 11 8 10 268 6 c 0 105 66 283 13 281 13 256 291 11 5 g 0 34 96 16 4 12 25 35 3 5 299 t 0 131 93 5 24 12 265 15 10 30 4