One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.211242_2026-02-26.211242_nt22t5/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.2026-02-26.211242_2026-02-26.211242_nt22t5/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift0 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=15; shift=0; ncol=15; ssCGCcssGCCCGsc ; Alignment reference a 85 60 16 78 26 56 96 72 31 14 14 29 47 43 67 c 147 184 367 33 379 196 142 162 64 368 362 339 55 130 200 g 133 136 44 314 32 111 148 123 324 49 43 40 317 199 108 t 86 71 24 26 14 88 65 94 32 20 32 43 32 79 76

dyads_m10_shift0 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/1; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCcssGCCCGsc ; cor=; Ncor= a 85 60 16 78 26 56 96 72 31 14 14 29 47 43 67 c 147 184 367 33 379 196 142 162 64 368 362 339 55 130 200 g 133 136 44 314 32 111 148 123 324 49 43 40 317 199 108 t 86 71 24 26 14 88 65 94 32 20 32 43 32 79 76

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; wvAGCCAArr ; Alignment reference a 112 106 383 3 4 1 361 367 110 156 c 90 105 25 0 413 402 4 42 89 65 g 74 148 10 416 1 16 54 3 151 118 t 144 61 2 1 2 1 1 8 70 81

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; wvAGCCAArr ; cor=; Ncor= a 112 106 383 3 4 1 361 367 110 156 c 90 105 25 0 413 402 4 42 89 65 g 74 148 10 416 1 16 54 3 151 118 t 144 61 2 1 2 1 1 8 70 81

oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)
; positions_6nt_m1 versus oligos_6nt_mkv3_m10; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.579298; -wdGCCAAGG ; cor=; Ncor= a 0 217 196 80 16 11 504 534 17 37 c 0 94 104 59 595 609 57 40 6 6 g 0 144 180 461 9 6 43 24 607 584 t 0 186 161 41 21 15 37 43 11 14

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift4 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----awAAACAAAwa ; Alignment reference a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----awAAACAAAwa ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106

oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m7; m=2/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.810852; ----awAAAGAAAwa ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3; m=3/8; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.758775; ---wwAAAACAAwa- ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 0 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 0 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 0 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105 0

oligos_6nt_mkv3_m8_shift5 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m8; m=4/8; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.694663; -----waAATAAAww ; cor=; Ncor= a 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243

oligos_8nt_mkv5_m2_shift6 (oligos_8nt_mkv5_m2)
; oligos_6nt_mkv3_m3 versus oligos_8nt_mkv5_m2; m=5/8; ncol2=12; w=0; offset=2; strand=D; shift=6; score=0.530269; ------awACAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 342 269 724 58 715 701 721 710 707 c 0 0 0 0 0 0 141 114 12 631 36 22 20 25 7 g 0 0 0 0 0 0 107 130 17 31 5 22 20 19 23 t 0 0 0 0 0 0 182 259 19 52 16 27 11 18 35

dyads_m1_rc_shift1 (dyads_m1_rc)
; oligos_6nt_mkv3_m3 versus dyads_m1_rc; m=6/8; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.49661; -wwtTAAAATAAATA ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m3 versus dyads_m3; m=7/8; ncol2=17; w=-4; offset=-4; strand=D; shift=0; score=0.487234; wwtTAAAAATAaAwA ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53

dyads_m8_shift0 (dyads_m8)
; oligos_6nt_mkv3_m3 versus dyads_m8; m=8/8; ncol2=19; w=-4; offset=-4; strand=D; shift=0; score=0.456461; wwTTAAAAAgAAAwA ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m9_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)
; oligos_7nt_mkv4_m9; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwGAAAAGAAww ; Alignment reference a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229

oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)
; oligos_7nt_mkv4_m9 versus oligos_7nt_mkv4_m9; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwGAAAAGAAww ; cor=; Ncor= a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229

oligos_7nt_mkv4_m10_shift3 (oligos_7nt_mkv4_m10)
; oligos_7nt_mkv4_m9 versus oligos_7nt_mkv4_m10; m=2/5; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.684567; ---rwAAAGGAAwr ; cor=; Ncor= a 0 0 0 124 131 360 335 349 5 8 362 363 125 133 c 0 0 0 59 70 1 9 14 18 2 1 3 48 60 g 0 0 0 104 72 8 3 1 353 354 3 1 82 97 t 0 0 0 94 108 12 34 17 5 17 15 14 126 91

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m9 versus oligos_7nt_mkv4_m3; m=3/5; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.680525; ---wwAAAACAAwa ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105

oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)
; oligos_7nt_mkv4_m9 versus oligos_6nt_mkv3_m7; m=4/5; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.639937; ----awAAAGAAAw ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192

dyads_m8_shift0 (dyads_m8)
; oligos_7nt_mkv4_m9 versus dyads_m8; m=5/5; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.445276; wwTTAAAAAgAAAw ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m7_shift4 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=11; shift=4; ncol=15; ----awAAAGAAAwa ; Alignment reference a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134

oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----awAAAGAAAwa ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m3; m=2/9; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.810852; ----awAAACAAAwa ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106

oligos_7nt_mkv4_m10_shift4 (oligos_7nt_mkv4_m10)
; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m10; m=3/9; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.803425; ----rwAAAGGAAwr ; cor=; Ncor= a 0 0 0 0 124 131 360 335 349 5 8 362 363 125 133 c 0 0 0 0 59 70 1 9 14 18 2 1 3 48 60 g 0 0 0 0 104 72 8 3 1 353 354 3 1 82 97 t 0 0 0 0 94 108 12 34 17 5 17 15 14 126 91

oligos_6nt_mkv3_m8_shift5 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m8; m=4/9; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.696352; -----waAATAAAww ; cor=; Ncor= a 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243

oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)
; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m9; m=5/9; ncol2=12; w=-2; offset=-2; strand=D; shift=2; score=0.639937; --wwGAAAAGAAww- ; cor=; Ncor= a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 0 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 0 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 0 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229 0

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m3; m=6/9; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.585048; ---wwAAAACAAwa- ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 0 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 0 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 0 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105 0

dyads_m8_shift0 (dyads_m8)
; oligos_6nt_mkv3_m7 versus dyads_m8; m=7/9; ncol2=19; w=-4; offset=-4; strand=D; shift=0; score=0.502309; wwTTAAAAAgAAAwA ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25

dyads_m1_rc_shift1 (dyads_m1_rc)
; oligos_6nt_mkv3_m7 versus dyads_m1_rc; m=8/9; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.485719; -wwtTAAAATAAATA ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m7 versus dyads_m3; m=9/9; ncol2=17; w=-4; offset=-4; strand=D; shift=0; score=0.474527; wwtTAAAAATAaAwA ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; wvACTTCTyw ; Alignment reference a 122 98 370 4 1 7 4 4 66 106 c 93 98 2 377 8 2 377 3 113 86 g 59 101 7 2 49 7 1 17 93 73 t 110 87 5 1 326 368 2 360 112 119

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wvACTTCTyw ; cor=; Ncor= a 122 98 370 4 1 7 4 4 66 106 c 93 98 2 377 8 2 377 3 113 86 g 59 101 7 2 49 7 1 17 93 73 t 110 87 5 1 326 368 2 360 112 119

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ysAGGCTGGwg ; Alignment reference a 0 0 0 243 225 922 20 60 65 147 36 37 378 236 c 0 0 0 324 355 15 9 33 939 23 6 16 167 253 g 0 0 0 197 305 69 989 929 26 54 1007 960 218 324 t 0 0 0 297 176 55 43 39 31 837 12 48 298 248

oligos_7nt_mkv4_m2_shift3 (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=3; score= 1; ---ysAGGCTGGwg ; cor=; Ncor= a 0 0 0 243 225 922 20 60 65 147 36 37 378 236 c 0 0 0 324 355 15 9 33 939 23 6 16 167 253 g 0 0 0 197 305 69 989 929 26 54 1007 960 218 324 t 0 0 0 297 176 55 43 39 31 837 12 48 298 248

oligos_6nt_mkv3_m1_rc_shift3 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1_rc; m=2/4; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.844796; ---ssaGGCTGGGs ; cor=; Ncor= a 0 0 0 221 157 679 85 25 18 33 15 134 93 257 c 0 0 0 372 375 75 24 101 973 56 30 32 44 288 g 0 0 0 272 387 113 904 884 29 77 954 835 797 317 t 0 0 0 165 111 163 17 20 10 864 31 29 96 168

dyads_m5_shift0 (dyads_m5)
; oligos_7nt_mkv4_m2 versus dyads_m5; m=3/4; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.421038; wrCCCAGGCwg--- ; cor=; Ncor= a 324 319 38 75 54 1069 40 43 96 314 268 0 0 0 c 297 249 1011 1060 1087 42 30 82 970 268 286 0 0 0 g 257 372 108 20 38 40 1101 1042 60 191 368 0 0 0 t 338 276 59 61 37 65 45 49 90 443 294 0 0 0

dyads_m4_rc_shift0 (dyads_m4_rc)
; oligos_7nt_mkv4_m2 versus dyads_m4_rc; m=4/4; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.408711; wrGCCAGGCts--- ; cor=; Ncor= a 279 384 33 40 26 821 27 38 99 253 241 0 0 0 c 265 125 63 975 1026 65 32 24 862 244 275 0 0 0 g 263 332 947 32 26 67 1006 1013 71 200 315 0 0 0 t 292 258 56 52 21 146 34 24 67 402 268 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; mwGGGATTAyw ; Alignment reference a 146 179 32 28 16 530 47 24 537 102 296 c 214 50 3 3 9 9 43 8 8 210 70 g 94 42 515 508 518 13 16 15 8 77 57 t 120 303 24 35 31 22 468 527 21 185 151

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; mwGGGATTAyw ; cor=; Ncor= a 146 179 32 28 16 530 47 24 537 102 296 c 214 50 3 3 9 9 43 8 8 210 70 g 94 42 515 508 518 13 16 15 8 77 57 t 120 303 24 35 31 22 468 527 21 185 151

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; --awACAAAAACwa ; Alignment reference a 0 0 342 269 724 58 715 701 721 710 707 68 350 333 c 0 0 141 114 12 631 36 22 20 25 7 556 126 125 g 0 0 107 130 17 31 5 22 20 19 23 41 42 136 t 0 0 182 259 19 52 16 27 11 18 35 107 254 178

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; --awACAAAAACwa ; cor=; Ncor= a 0 0 342 269 724 58 715 701 721 710 707 68 350 333 c 0 0 141 114 12 631 36 22 20 25 7 556 126 125 g 0 0 107 130 17 31 5 22 20 19 23 41 42 136 t 0 0 182 259 19 52 16 27 11 18 35 107 254 178

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_8nt_mkv5_m2 versus oligos_6nt_mkv3_m3; m=2/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.530269; awAAACAAAwa--- ; cor=; Ncor= a 241 206 491 476 514 7 487 480 473 182 248 0 0 0 c 87 92 2 3 0 484 2 4 13 95 74 0 0 0 g 82 62 8 0 2 7 18 0 6 58 91 0 0 0 t 109 159 18 40 3 21 12 35 27 184 106 0 0 0

oligos_7nt_mkv4_m3_shift5 (oligos_7nt_mkv4_m3)
; oligos_8nt_mkv5_m2 versus oligos_7nt_mkv4_m3; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=5; score=0.51026; -----wwAAAACAA ; cor=; Ncor= a 0 0 0 0 0 177 170 446 413 423 453 7 424 443 c 0 0 0 0 0 92 84 2 7 3 2 446 5 2 g 0 0 0 0 0 56 72 3 9 5 2 2 18 1 t 0 0 0 0 0 135 134 9 31 29 3 5 13 14

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---waAAATTAwh ; Alignment reference a 0 0 0 289 323 642 644 648 1 3 649 204 192 c 0 0 0 67 92 0 4 0 0 1 0 112 175 g 0 0 0 117 106 3 0 0 0 0 0 161 110 t 0 0 0 176 128 4 1 1 648 645 0 172 172

oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---waAAATTAwh ; cor=; Ncor= a 0 0 0 289 323 642 644 648 1 3 649 204 192 c 0 0 0 67 92 0 4 0 0 1 0 112 175 g 0 0 0 117 106 3 0 0 0 0 0 161 110 t 0 0 0 176 128 4 1 1 648 645 0 172 172

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=2; score=0.878001; --wwAAAATTAkm ; cor=; Ncor= a 0 0 173 222 462 442 432 481 7 5 482 121 163 c 0 0 110 54 4 5 2 5 2 6 3 73 138 g 0 0 57 71 5 2 2 1 3 0 0 133 68 t 0 0 149 142 18 40 53 2 477 478 4 162 120

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m4 versus dyads_m3; m=3/3; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.412785; wwtTAAAAATAaA ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 c 66 52 65 21 26 17 8 15 8 20 8 77 23 g 55 57 25 18 14 13 12 6 16 13 15 25 23 t 193 190 315 396 60 57 24 43 31 438 29 108 64

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 4 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; mwCCCCryCTChm ; Alignment reference a 334 322 54 48 61 88 351 205 19 62 19 324 310 c 304 280 963 925 983 870 227 336 1090 75 1079 340 319 g 274 247 64 57 44 46 305 220 28 57 33 108 266 t 240 303 71 122 64 148 269 391 15 958 21 380 257

dyads_m7_shift0 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; mwCCCCryCTChm ; cor=; Ncor= a 334 322 54 48 61 88 351 205 19 62 19 324 310 c 304 280 963 925 983 870 227 336 1090 75 1079 340 319 g 274 247 64 57 44 46 305 220 28 57 33 108 266 t 240 303 71 122 64 148 269 391 15 958 21 380 257

oligos_8nt_mkv5_m1_shift2 (oligos_8nt_mkv5_m1)
; dyads_m7 versus oligos_8nt_mkv5_m1; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.560024; --ytCCTCCTCCy ; cor=; Ncor= a 0 0 131 116 7 13 49 11 20 48 28 22 120 c 0 0 193 137 509 518 22 495 512 18 477 505 169 g 0 0 95 119 21 13 68 23 9 58 38 17 70 t 0 0 143 190 25 18 423 33 21 438 19 18 203

dyads_m9_shift0 (dyads_m9)
; dyads_m7 versus dyads_m9; m=3/3; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.405579; cygCCCcCCTCcs ; cor=; Ncor= a 23 10 14 9 9 7 15 7 8 12 7 21 5 c 78 66 28 111 99 118 89 113 117 14 118 87 90 g 22 29 81 10 12 5 28 13 9 18 12 24 42 t 21 39 21 14 24 14 12 11 10 100 7 12 7

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=3; ncol=13; ---mgCCTCCCrr ; Alignment reference a 0 0 0 240 142 7 13 29 8 8 8 275 248 c 0 0 0 290 190 791 791 13 785 772 751 190 211 g 0 0 0 143 343 30 24 65 37 45 69 228 264 t 0 0 0 172 170 17 17 738 15 20 17 152 122

oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---mgCCTCCCrr ; cor=; Ncor= a 0 0 0 240 142 7 13 29 8 8 8 275 248 c 0 0 0 290 190 791 791 13 785 772 751 190 211 g 0 0 0 143 343 30 24 65 37 45 69 228 264 t 0 0 0 172 170 17 17 738 15 20 17 152 122

oligos_8nt_mkv5_m1_shift0 (oligos_8nt_mkv5_m1)
; oligos_6nt_mkv3_m5 versus oligos_8nt_mkv5_m1; m=2/2; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.551962; ytCCTCCTCCys- ; cor=; Ncor= a 131 116 7 13 49 11 20 48 28 22 120 114 0 c 193 137 509 518 22 495 512 18 477 505 169 171 0 g 95 119 21 13 68 23 9 58 38 17 70 143 0 t 143 190 25 18 423 33 21 438 19 18 203 134 0

One-to-n matrix alignment; reference matrix: dyads_m5_shift1 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift1 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -wrCCCAGGCwg ; Alignment reference a 0 324 319 38 75 54 1069 40 43 96 314 268 c 0 297 249 1011 1060 1087 42 30 82 970 268 286 g 0 257 372 108 20 38 40 1101 1042 60 191 368 t 0 338 276 59 61 37 65 45 49 90 443 294

dyads_m5_shift1 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wrCCCAGGCwg ; cor=; Ncor= a 0 324 319 38 75 54 1069 40 43 96 314 268 c 0 297 249 1011 1060 1087 42 30 82 970 268 286 g 0 257 372 108 20 38 40 1101 1042 60 191 368 t 0 338 276 59 61 37 65 45 49 90 443 294

dyads_m4_rc_shift1 (dyads_m4_rc)
; dyads_m5 versus dyads_m4_rc; m=2/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.825588; -wrGCCAGGCts ; cor=; Ncor= a 0 279 384 33 40 26 821 27 38 99 253 241 c 0 265 125 63 975 1026 65 32 24 862 244 275 g 0 263 332 947 32 26 67 1006 1013 71 200 315 t 0 292 258 56 52 21 146 34 24 67 402 268

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; dyads_m5 versus oligos_6nt_mkv3_m2_rc; m=3/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.801627; -ddGCCAGGctb ; cor=; Ncor= a 0 253 318 18 39 16 708 14 34 117 234 196 c 0 204 128 32 851 894 59 35 11 637 170 258 g 0 241 272 884 32 29 85 893 895 81 198 251 t 0 262 242 26 38 21 108 18 20 125 358 255

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; dyads_m5 versus oligos_6nt_mkv3_m1; m=4/7; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.738918; -msCCCAGCCts ; cor=; Ncor= a 0 323 168 96 29 31 864 10 20 17 163 111 c 0 286 317 797 835 954 77 29 884 904 113 387 g 0 232 288 44 32 30 56 973 101 24 75 375 t 0 189 257 93 134 15 33 18 25 85 679 157

oligos_7nt_mkv4_m7_rc_shift0 (oligos_7nt_mkv4_m7_rc)
; dyads_m5 versus oligos_7nt_mkv4_m7_rc; m=5/7; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.738641; twGGCCAGGCtg ; cor=; Ncor= a 121 173 65 22 28 17 526 15 19 70 145 123 c 171 113 42 73 608 637 57 40 27 518 124 149 g 153 155 550 570 26 32 67 626 635 53 153 254 t 246 250 34 26 29 5 41 10 10 50 269 165

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; dyads_m5 versus oligos_6nt_mkv3_m10; m=6/7; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.618718; wdGCCAAGGhk- ; cor=; Ncor= a 217 196 80 16 11 504 534 17 37 170 156 0 c 94 104 59 595 609 57 40 6 6 183 149 0 g 144 180 461 9 6 43 24 607 584 101 164 0 t 186 161 41 21 15 37 43 11 14 187 172 0

oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)
; dyads_m5 versus oligos_7nt_mkv4_m2; m=7/7; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.421038; ----ysAGGCTG ; cor=; Ncor= a 0 0 0 0 243 225 922 20 60 65 147 36 c 0 0 0 0 324 355 15 9 33 939 23 6 g 0 0 0 0 197 305 69 989 929 26 54 1007 t 0 0 0 0 297 176 55 43 39 31 837 12

One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m8_shift0 (dyads_m8)
; dyads_m8; m=0 (reference); ncol1=19; shift=0; ncol=19; wwTTAAAAAgAAAwAawww ; Alignment reference a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 150 59 91 86 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 15 20 18 30 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 20 22 42 29 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25 36 120 70 76

dyads_m8_shift0 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/8; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAAgAAAwAawww ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 150 59 91 86 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 15 20 18 30 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 20 22 42 29 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25 36 120 70 76

dyads_m3_shift0 (dyads_m3)
; dyads_m8 versus dyads_m3; m=2/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.810782; wwtTAAAAATAaAwAww-- ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 227 255 0 0 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 60 66 0 0 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 53 59 0 0 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53 170 130 0 0

dyads_m1_rc_shift1 (dyads_m1_rc)
; dyads_m8 versus dyads_m1_rc; m=3/8; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.654387; -wwtTAAAATAAATAww-- ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 152 199 0 0 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 61 55 0 0 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 74 59 0 0 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58 146 120 0 0

oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)
; dyads_m8 versus oligos_6nt_mkv3_m7; m=4/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.502309; ----awAAAGAAAwa---- ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 0 0 0 0 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 0 0 0 0 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 0 0 0 0 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134 0 0 0 0

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; dyads_m8 versus oligos_6nt_mkv3_m3; m=5/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.456461; ----awAAACAAAwa---- ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 0 0 0 0 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 0 0 0 0 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 0 0 0 0 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106 0 0 0 0

oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)
; dyads_m8 versus oligos_7nt_mkv4_m9; m=6/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.445276; --wwGAAAAGAAww----- ; cor=; Ncor= a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 0 0 0 0 0 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 0 0 0 0 0 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 0 0 0 0 0 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229 0 0 0 0 0

oligos_6nt_mkv3_m8_shift9 (oligos_6nt_mkv3_m8)
; dyads_m8 versus oligos_6nt_mkv3_m8; m=7/8; ncol2=10; w=0; offset=9; strand=D; shift=9; score=0.42076; ---------waAATAAAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; dyads_m8 versus oligos_7nt_mkv4_m3; m=8/8; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.417143; ---wwAAAACAAwa----- ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 0 0 0 0 0 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 0 0 0 0 0 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 0 0 0 0 0 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift9 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m8_shift9 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=9; ncol=19; ---------waAATAAAww ; Alignment reference a 0 0 0 0 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243

oligos_6nt_mkv3_m8_shift9 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=9; score= 1; ---------waAATAAAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243

oligos_6nt_mkv3_m7_shift8 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m7; m=2/6; ncol2=11; w=-1; offset=-1; strand=D; shift=8; score=0.696352; --------awAAAGAAAwa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 c 0 0 0 0 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 g 0 0 0 0 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 t 0 0 0 0 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134

oligos_6nt_mkv3_m3_shift8 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m3; m=3/6; ncol2=11; w=-1; offset=-1; strand=D; shift=8; score=0.694663; --------awAAACAAAwa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 c 0 0 0 0 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 g 0 0 0 0 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 t 0 0 0 0 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106

dyads_m1_rc_shift5 (dyads_m1_rc)
; oligos_6nt_mkv3_m8 versus dyads_m1_rc; m=4/6; ncol2=16; w=-4; offset=-4; strand=R; shift=5; score=0.538029; -----wwtTAAAATAAATA ; cor=; Ncor= a 0 0 0 0 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 c 0 0 0 0 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 g 0 0 0 0 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 t 0 0 0 0 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58

dyads_m3_shift4 (dyads_m3)
; oligos_6nt_mkv3_m8 versus dyads_m3; m=5/6; ncol2=17; w=-5; offset=-5; strand=D; shift=4; score=0.501902; ----wwtTAAAAATAaAwA ; cor=; Ncor= a 0 0 0 0 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 c 0 0 0 0 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 g 0 0 0 0 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 t 0 0 0 0 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53

dyads_m8_shift0 (dyads_m8)
; oligos_6nt_mkv3_m8 versus dyads_m8; m=6/6; ncol2=19; w=-9; offset=-9; strand=D; shift=0; score=0.42076; wwTTAAAAAgAAAwAawww ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 150 59 91 86 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 15 20 18 30 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 20 22 42 29 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25 36 120 70 76

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m10_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=11; shift=1; ncol=12; -wdGCCAAGGhk ; Alignment reference a 0 217 196 80 16 11 504 534 17 37 170 156 c 0 94 104 59 595 609 57 40 6 6 183 149 g 0 144 180 461 9 6 43 24 607 584 101 164 t 0 186 161 41 21 15 37 43 11 14 187 172

oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wdGCCAAGGhk ; cor=; Ncor= a 0 217 196 80 16 11 504 534 17 37 170 156 c 0 94 104 59 595 609 57 40 6 6 183 149 g 0 144 180 461 9 6 43 24 607 584 101 164 t 0 186 161 41 21 15 37 43 11 14 187 172

dyads_m5_shift2 (dyads_m5)
; oligos_6nt_mkv3_m10 versus dyads_m5; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.618718; --wrCCCAGGCw ; cor=; Ncor= a 0 0 324 319 38 75 54 1069 40 43 96 314 c 0 0 297 249 1011 1060 1087 42 30 82 970 268 g 0 0 257 372 108 20 38 40 1101 1042 60 191 t 0 0 338 276 59 61 37 65 45 49 90 443

positions_6nt_m1_shift0 (positions_6nt_m1)
; oligos_6nt_mkv3_m10 versus positions_6nt_m1; m=3/3; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.579298; wvAGCCAArr-- ; cor=; Ncor= a 112 106 383 3 4 1 361 367 110 156 0 0 c 90 105 25 0 413 402 4 42 89 65 0 0 g 74 148 10 416 1 16 54 3 151 118 0 0 t 144 61 2 1 2 1 1 8 70 81 0 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; msCCCAGCCtss ; Alignment reference a 323 168 96 29 31 864 10 20 17 163 111 165 c 286 317 797 835 954 77 29 884 904 113 387 272 g 232 288 44 32 30 56 973 101 24 75 375 372 t 189 257 93 134 15 33 18 25 85 679 157 221

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; msCCCAGCCtss ; cor=; Ncor= a 323 168 96 29 31 864 10 20 17 163 111 165 c 286 317 797 835 954 77 29 884 904 113 387 272 g 232 288 44 32 30 56 973 101 24 75 375 372 t 189 257 93 134 15 33 18 25 85 679 157 221

oligos_7nt_mkv4_m2_rc_shift1 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.844796; -cwCCAGCCTsr ; cor=; Ncor= a 0 248 298 48 12 837 31 39 43 55 176 297 c 0 324 218 960 1007 54 26 929 989 69 305 197 g 0 253 167 16 6 23 939 33 9 15 355 324 t 0 236 378 37 36 147 65 60 20 922 225 243

dyads_m5_shift0 (dyads_m5)
; oligos_6nt_mkv3_m1 versus dyads_m5; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.738918; wrCCCAGGCwg- ; cor=; Ncor= a 324 319 38 75 54 1069 40 43 96 314 268 0 c 297 249 1011 1060 1087 42 30 82 970 268 286 0 g 257 372 108 20 38 40 1101 1042 60 191 368 0 t 338 276 59 61 37 65 45 49 90 443 294 0

One-to-n matrix alignment; reference matrix: dyads_m1_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift2 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwTATTTATTTTAaww ; Alignment reference a 0 0 120 146 58 298 43 83 20 351 18 33 23 34 370 277 167 145 c 0 0 59 74 19 25 26 13 8 15 12 4 8 14 11 23 33 60 g 0 0 55 61 14 16 26 33 7 18 13 16 20 19 12 25 54 53 t 0 0 199 152 342 94 338 304 398 49 390 380 382 366 40 108 179 175

dyads_m1_shift2 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=2; score= 1; --wwTATTTATTTTAaww ; cor=; Ncor= a 0 0 120 146 58 298 43 83 20 351 18 33 23 34 370 277 167 145 c 0 0 59 74 19 25 26 13 8 15 12 4 8 14 11 23 33 60 g 0 0 55 61 14 16 26 33 7 18 13 16 20 19 12 25 54 53 t 0 0 199 152 342 94 338 304 398 49 390 380 382 366 40 108 179 175

dyads_m3_rc_shift2 (dyads_m3_rc)
; dyads_m1 versus dyads_m3_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.835959; --wwTwTtTATTTTTAaw ; cor=; Ncor= a 0 0 130 170 53 317 64 108 29 438 31 43 24 57 60 396 315 190 c 0 0 59 53 22 27 23 25 15 13 16 6 12 13 14 18 25 57 g 0 0 66 60 22 32 23 77 8 20 8 15 8 17 26 21 65 52 t 0 0 255 227 413 134 400 300 458 39 455 446 466 423 410 75 105 211

dyads_m8_rc_shift0 (dyads_m8_rc)
; dyads_m1 versus dyads_m8_rc; m=3/8; ncol2=19; w=-2; offset=-2; strand=R; shift=0; score=0.654387; wwwtTwTTTcTTTTTAAw ; cor=; Ncor= a 76 70 120 36 25 136 12 33 32 40 13 12 8 23 11 193 156 78 c 29 42 22 20 14 9 10 6 10 119 4 6 14 3 2 5 7 25 g 30 18 20 15 10 9 5 16 12 14 3 8 1 5 7 5 11 25 t 86 91 59 150 172 67 194 166 167 48 201 195 198 190 201 18 47 93

oligos_6nt_mkv3_m8_rc_shift4 (oligos_6nt_mkv3_m8_rc)
; dyads_m1 versus oligos_6nt_mkv3_m8_rc; m=4/8; ncol2=10; w=0; offset=2; strand=R; shift=4; score=0.538029; ----wwTTTATTtw---- ; cor=; Ncor= a 0 0 0 0 243 231 2 4 0 852 1 5 154 254 0 0 0 0 c 0 0 0 0 156 137 0 0 1 0 0 4 143 146 0 0 0 0 g 0 0 0 0 125 124 11 8 1 0 2 1 157 133 0 0 0 0 t 0 0 0 0 328 360 839 840 850 0 849 842 398 319 0 0 0 0

oligos_6nt_mkv3_m3_rc_shift4 (oligos_6nt_mkv3_m3_rc)
; dyads_m1 versus oligos_6nt_mkv3_m3_rc; m=5/8; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.49661; ----twTTTGTTTwt--- ; cor=; Ncor= a 0 0 0 0 106 184 27 35 12 21 3 40 18 159 109 0 0 0 c 0 0 0 0 91 58 6 0 18 7 2 0 8 62 82 0 0 0 g 0 0 0 0 74 95 13 4 2 484 0 3 2 92 87 0 0 0 t 0 0 0 0 248 182 473 480 487 7 514 476 491 206 241 0 0 0

oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)
; dyads_m1 versus oligos_7nt_mkv4_m3_rc; m=6/8; ncol2=11; w=0; offset=3; strand=R; shift=5; score=0.490823; -----twTTGTTTTww-- ; cor=; Ncor= a 0 0 0 0 0 105 128 14 13 5 3 29 31 9 134 135 0 0 c 0 0 0 0 0 65 62 1 18 2 2 5 9 3 72 56 0 0 g 0 0 0 0 0 90 76 2 5 446 2 3 7 2 84 92 0 0 t 0 0 0 0 0 200 194 443 424 7 453 423 413 446 170 177 0 0

oligos_6nt_mkv3_m7_rc_shift4 (oligos_6nt_mkv3_m7_rc)
; dyads_m1 versus oligos_6nt_mkv3_m7_rc; m=7/8; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.485719; ----twTTTCTTTwt--- ; cor=; Ncor= a 0 0 0 0 134 192 5 32 16 21 8 34 23 159 116 0 0 0 c 0 0 0 0 119 90 2 2 2 536 4 4 3 123 110 0 0 0 g 0 0 0 0 74 73 4 3 2 2 26 2 3 75 83 0 0 0 t 0 0 0 0 239 211 555 529 546 7 528 526 537 209 257 0 0 0

oligos_6nt_mkv3_m6_rc_shift2 (oligos_6nt_mkv3_m6_rc)
; dyads_m1 versus oligos_6nt_mkv3_m6_rc; m=8/8; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.452458; --twTATGTAtw------ ; cor=; Ncor= a 0 0 93 157 5 387 3 54 4 395 88 165 0 0 0 0 0 0 c 0 0 73 54 0 6 24 2 3 5 77 51 0 0 0 0 0 0 g 0 0 48 95 4 10 2 349 1 2 58 75 0 0 0 0 0 0 t 0 0 194 102 399 5 379 3 400 6 185 117 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; csCCCACCyc ; Alignment reference a 129 141 16 35 3 515 5 5 144 116 c 251 180 576 575 638 14 610 613 174 224 g 120 199 57 37 18 123 43 45 154 165 t 166 146 17 19 7 14 8 3 194 161

dyads_m6_shift0 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; csCCCACCyc ; cor=; Ncor= a 129 141 16 35 3 515 5 5 144 116 c 251 180 576 575 638 14 610 613 174 224 g 120 199 57 37 18 123 43 45 154 165 t 166 146 17 19 7 14 8 3 194 161

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=12; shift=0; ncol=12; gwgACAGAGcma ; Alignment reference a 190 297 123 718 21 724 17 714 17 175 234 292 c 161 122 119 19 713 16 18 18 28 321 200 127 g 273 135 481 35 26 30 730 23 722 108 167 183 t 165 235 66 17 29 19 24 34 22 185 188 187

oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gwgACAGAGcma ; cor=; Ncor= a 190 297 123 718 21 724 17 714 17 175 234 292 c 161 122 119 19 713 16 18 18 28 321 200 127 g 273 135 481 35 26 30 730 23 722 108 167 183 t 165 235 66 17 29 19 24 34 22 185 188 187

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m7_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m7_shift0 (oligos_7nt_mkv4_m7)
; oligos_7nt_mkv4_m7; m=0 (reference); ncol1=12; shift=0; ncol=12; caGCCTGGCCwa ; Alignment reference a 165 269 50 10 10 41 5 29 26 34 250 246 c 254 153 53 635 626 67 32 26 570 550 155 153 g 149 124 518 27 40 57 637 608 73 42 113 171 t 123 145 70 19 15 526 17 28 22 65 173 121

oligos_7nt_mkv4_m7_shift0 (oligos_7nt_mkv4_m7)
; oligos_7nt_mkv4_m7 versus oligos_7nt_mkv4_m7; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; caGCCTGGCCwa ; cor=; Ncor= a 165 269 50 10 10 41 5 29 26 34 250 246 c 254 153 53 635 626 67 32 26 570 550 155 153 g 149 124 518 27 40 57 637 608 73 42 113 171 t 123 145 70 19 15 526 17 28 22 65 173 121

dyads_m4_shift0 (dyads_m4)
; oligos_7nt_mkv4_m7 versus dyads_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.869559; saGCCTGGCyw- ; cor=; Ncor= a 268 402 67 24 34 146 21 52 56 258 292 0 c 315 200 71 1013 1006 67 26 32 947 332 263 0 g 275 244 862 24 32 65 1026 975 63 125 265 0 t 241 253 99 38 27 821 26 40 33 384 279 0

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m7 versus oligos_6nt_mkv3_m2; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.865174; vagCCTGGChh- ; cor=; Ncor= a 255 358 125 20 18 108 21 38 26 242 262 0 c 251 198 81 895 893 85 29 32 884 272 241 0 g 258 170 637 11 35 59 894 851 32 128 204 0 t 196 234 117 34 14 708 16 39 18 318 253 0

dyads_m5_rc_shift0 (dyads_m5_rc)
; oligos_7nt_mkv4_m7 versus dyads_m5_rc; m=4/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.738641; cwGCCTGGGyw- ; cor=; Ncor= a 294 443 90 49 45 65 37 61 59 276 338 0 c 368 191 60 1042 1101 40 38 20 108 372 257 0 g 286 268 970 82 30 42 1087 1060 1011 249 297 0 t 268 314 96 43 40 1069 54 75 38 319 324 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift3 ; 9 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; ---wwAAAACAAwa ; Alignment reference a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---wwAAAACAAwa ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3; m=2/8; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.758775; ----awAAACAAAw ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184

oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m9; m=3/8; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.680525; --wwGAAAAGAAww ; cor=; Ncor= a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229

oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m7; m=4/8; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.585048; ----awAAAGAAAw ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192

oligos_8nt_mkv5_m2_shift0 (oligos_8nt_mkv5_m2)
; oligos_7nt_mkv4_m3 versus oligos_8nt_mkv5_m2; m=5/8; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.51026; awACAAAAACwa-- ; cor=; Ncor= a 342 269 724 58 715 701 721 710 707 68 350 333 0 0 c 141 114 12 631 36 22 20 25 7 556 126 125 0 0 g 107 130 17 31 5 22 20 19 23 41 42 136 0 0 t 182 259 19 52 16 27 11 18 35 107 254 178 0 0

dyads_m1_rc_shift1 (dyads_m1_rc)
; oligos_7nt_mkv4_m3 versus dyads_m1_rc; m=6/8; ncol2=16; w=-2; offset=-2; strand=R; shift=1; score=0.490823; -wwtTAAAATAAAT ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298

dyads_m3_shift0 (dyads_m3)
; oligos_7nt_mkv4_m3 versus dyads_m3; m=7/8; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.455372; wwtTAAAAATAaAw ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317

dyads_m8_shift0 (dyads_m8)
; oligos_7nt_mkv4_m3 versus dyads_m8; m=8/8; ncol2=19; w=-3; offset=-3; strand=D; shift=0; score=0.417143; wwTTAAAAAgAAAw ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136

One-to-n matrix alignment; reference matrix: dyads_m4_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift3 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---saGCCTGGCyw ; Alignment reference a 0 0 0 268 402 67 24 34 146 21 52 56 258 292 c 0 0 0 315 200 71 1013 1006 67 26 32 947 332 263 g 0 0 0 275 244 862 24 32 65 1026 975 63 125 265 t 0 0 0 241 253 99 38 27 821 26 40 33 384 279

dyads_m4_shift3 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---saGCCTGGCyw ; cor=; Ncor= a 0 0 0 268 402 67 24 34 146 21 52 56 258 292 c 0 0 0 315 200 71 1013 1006 67 26 32 947 332 263 g 0 0 0 275 244 862 24 32 65 1026 975 63 125 265 t 0 0 0 241 253 99 38 27 821 26 40 33 384 279

oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)
; dyads_m4 versus oligos_6nt_mkv3_m2; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.995191; ---vagCCTGGChh ; cor=; Ncor= a 0 0 0 255 358 125 20 18 108 21 38 26 242 262 c 0 0 0 251 198 81 895 893 85 29 32 884 272 241 g 0 0 0 258 170 637 11 35 59 894 851 32 128 204 t 0 0 0 196 234 117 34 14 708 16 39 18 318 253

oligos_7nt_mkv4_m7_shift3 (oligos_7nt_mkv4_m7)
; dyads_m4 versus oligos_7nt_mkv4_m7; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.869559; ---caGCCTGGCCw ; cor=; Ncor= a 0 0 0 165 269 50 10 10 41 5 29 26 34 250 c 0 0 0 254 153 53 635 626 67 32 26 570 550 155 g 0 0 0 149 124 518 27 40 57 637 608 73 42 113 t 0 0 0 123 145 70 19 15 526 17 28 22 65 173

dyads_m5_rc_shift3 (dyads_m5_rc)
; dyads_m4 versus dyads_m5_rc; m=4/5; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.825588; ---cwGCCTGGGyw ; cor=; Ncor= a 0 0 0 294 443 90 49 45 65 37 61 59 276 338 c 0 0 0 368 191 60 1042 1101 40 38 20 108 372 257 g 0 0 0 286 268 970 82 30 42 1087 1060 1011 249 297 t 0 0 0 268 314 96 43 40 1069 54 75 38 319 324

oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)
; dyads_m4 versus oligos_7nt_mkv4_m2_rc; m=5/5; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.408711; cwCCAGCCTsr--- ; cor=; Ncor= a 248 298 48 12 837 31 39 43 55 176 297 0 0 0 c 324 218 960 1007 54 26 929 989 69 305 197 0 0 0 g 253 167 16 6 23 939 33 9 15 355 324 0 0 0 t 236 378 37 36 147 65 60 20 922 225 243 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 2 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; wwCAGCATCwy ; Alignment reference a 205 209 21 613 42 34 587 37 40 265 148 c 146 138 611 9 23 579 36 33 572 116 185 g 147 99 10 7 560 17 14 43 35 62 103 t 170 222 26 39 43 38 31 555 21 225 232

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCAGCATCwy ; cor=; Ncor= a 205 209 21 613 42 34 587 37 40 265 148 c 146 138 611 9 23 579 36 33 572 116 185 g 147 99 10 7 560 17 14 43 35 62 103 t 170 222 26 39 43 38 31 555 21 225 232

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; ccCCtCCCCcccCCCmgCCCyCcs ; Alignment reference a 25 20 11 18 15 5 16 21 14 11 15 17 7 11 7 78 10 7 7 11 15 17 24 23 c 92 92 142 131 47 139 130 134 135 120 112 117 152 148 156 53 42 148 147 131 69 129 79 75 g 34 46 21 21 32 16 25 17 18 26 37 24 13 16 15 35 117 25 18 21 36 30 43 57 t 38 31 15 19 95 29 18 17 22 32 25 31 17 14 11 23 20 9 17 26 69 13 43 34

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/2; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ccCCtCCCCcccCCCmgCCCyCcs ; cor=; Ncor= a 25 20 11 18 15 5 16 21 14 11 15 17 7 11 7 78 10 7 7 11 15 17 24 23 c 92 92 142 131 47 139 130 134 135 120 112 117 152 148 156 53 42 148 147 131 69 129 79 75 g 34 46 21 21 32 16 25 17 18 26 37 24 13 16 15 35 117 25 18 21 36 30 43 57 t 38 31 15 19 95 29 18 17 22 32 25 31 17 14 11 23 20 9 17 26 69 13 43 34

dyads_m9_shift1 (dyads_m9)
; dyads_m2 versus dyads_m9; m=2/2; ncol2=23; w=0; offset=1; strand=D; shift=1; score=0.701505; -cygCCCcCCTCcsCCtCCCtcms ; cor=; Ncor= a 0 23 10 14 9 9 7 15 7 8 12 7 21 5 6 3 12 4 3 3 30 33 45 15 c 0 78 66 28 111 99 118 89 113 117 14 118 87 90 108 118 25 115 123 121 29 87 43 64 g 0 22 29 81 10 12 5 28 13 9 18 12 24 42 6 8 16 16 11 11 26 12 21 44 t 0 21 39 21 14 24 14 12 11 10 100 7 12 7 24 15 91 9 7 9 59 12 35 21

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; wwAAGGCAAwa ; Alignment reference a 123 94 296 322 7 25 8 300 292 98 142 c 62 64 6 9 7 1 317 10 9 58 64 g 71 63 5 1 320 311 1 8 13 58 54 t 88 123 37 12 10 7 18 26 30 130 84

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; wwAAGGCAAwa ; cor=; Ncor= a 123 94 296 322 7 25 8 300 292 98 142 c 62 64 6 9 7 1 317 10 9 58 64 g 71 63 5 1 320 311 1 8 13 58 54 t 88 123 37 12 10 7 18 26 30 130 84

oligos_7nt_mkv4_m8_shift0 (oligos_7nt_mkv4_m8)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m8; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.788202; wwAATGCAAww ; cor=; Ncor= a 107 124 315 330 7 29 9 317 315 127 120 c 54 38 5 5 7 1 301 5 7 62 81 g 78 52 2 9 5 316 3 3 6 39 52 t 113 138 30 8 333 6 39 27 24 124 99

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 5 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; vagCCTGGChh ; Alignment reference a 255 358 125 20 18 108 21 38 26 242 262 c 251 198 81 895 893 85 29 32 884 272 241 g 258 170 637 11 35 59 894 851 32 128 204 t 196 234 117 34 14 708 16 39 18 318 253

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; vagCCTGGChh ; cor=; Ncor= a 255 358 125 20 18 108 21 38 26 242 262 c 251 198 81 895 893 85 29 32 884 272 241 g 258 170 637 11 35 59 894 851 32 128 204 t 196 234 117 34 14 708 16 39 18 318 253

dyads_m4_shift0 (dyads_m4)
; oligos_6nt_mkv3_m2 versus dyads_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.995191; saGCCTGGCyw ; cor=; Ncor= a 268 402 67 24 34 146 21 52 56 258 292 c 315 200 71 1013 1006 67 26 32 947 332 263 g 275 244 862 24 32 65 1026 975 63 125 265 t 241 253 99 38 27 821 26 40 33 384 279

oligos_7nt_mkv4_m7_shift0 (oligos_7nt_mkv4_m7)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m7; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.865174; caGCCTGGCCw ; cor=; Ncor= a 165 269 50 10 10 41 5 29 26 34 250 c 254 153 53 635 626 67 32 26 570 550 155 g 149 124 518 27 40 57 637 608 73 42 113 t 123 145 70 19 15 526 17 28 22 65 173

dyads_m5_rc_shift0 (dyads_m5_rc)
; oligos_6nt_mkv3_m2 versus dyads_m5_rc; m=4/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.801627; cwGCCTGGGyw ; cor=; Ncor= a 294 443 90 49 45 65 37 61 59 276 338 c 368 191 60 1042 1101 40 38 20 108 372 257 g 286 268 970 82 30 42 1087 1060 1011 249 297 t 268 314 96 43 40 1069 54 75 38 319 324

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m6_shift7 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m6_shift7 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=7; ncol=17; -------waTACATAwa ; Alignment reference a 0 0 0 0 0 0 0 117 185 6 400 3 379 5 399 102 194 c 0 0 0 0 0 0 0 75 58 2 1 349 2 10 4 95 48 g 0 0 0 0 0 0 0 51 77 5 3 2 24 6 0 54 73 t 0 0 0 0 0 0 0 165 88 395 4 54 3 387 5 157 93

oligos_6nt_mkv3_m6_shift7 (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=7; score= 1; -------waTACATAwa ; cor=; Ncor= a 0 0 0 0 0 0 0 117 185 6 400 3 379 5 399 102 194 c 0 0 0 0 0 0 0 75 58 2 1 349 2 10 4 95 48 g 0 0 0 0 0 0 0 51 77 5 3 2 24 6 0 54 73 t 0 0 0 0 0 0 0 165 88 395 4 54 3 387 5 157 93

dyads_m1_rc_shift1 (dyads_m1_rc)
; oligos_6nt_mkv3_m6 versus dyads_m1_rc; m=2/3; ncol2=16; w=-6; offset=-6; strand=R; shift=1; score=0.452458; -wwtTAAAATAAATAww ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 152 199 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 61 55 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 74 59 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58 146 120

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m6 versus dyads_m3; m=3/3; ncol2=17; w=-7; offset=-7; strand=D; shift=0; score=0.440482; wwtTAAAAATAaAwAww ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 227 255 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 60 66 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 53 59 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53 170 130

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m8_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m8_shift0 (oligos_7nt_mkv4_m8)
; oligos_7nt_mkv4_m8; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAATGCAAww ; Alignment reference a 107 124 315 330 7 29 9 317 315 127 120 c 54 38 5 5 7 1 301 5 7 62 81 g 78 52 2 9 5 316 3 3 6 39 52 t 113 138 30 8 333 6 39 27 24 124 99

oligos_7nt_mkv4_m8_shift0 (oligos_7nt_mkv4_m8)
; oligos_7nt_mkv4_m8 versus oligos_7nt_mkv4_m8; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAATGCAAww ; cor=; Ncor= a 107 124 315 330 7 29 9 317 315 127 120 c 54 38 5 5 7 1 301 5 7 62 81 g 78 52 2 9 5 316 3 3 6 39 52 t 113 138 30 8 333 6 39 27 24 124 99

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m8 versus oligos_7nt_mkv4_m4; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.788202; wwAAGGCAAwa ; cor=; Ncor= a 123 94 296 322 7 25 8 300 292 98 142 c 62 64 6 9 7 1 317 10 9 58 64 g 71 63 5 1 320 311 1 8 13 58 54 t 88 123 37 12 10 7 18 26 30 130 84

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; wwtTAAAAATAaAwAww ; Alignment reference a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 227 255 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 60 66 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 53 59 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53 170 130

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/10; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; wwtTAAAAATAaAwAww ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 227 255 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 60 66 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 53 59 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53 170 130

dyads_m1_rc_shift1 (dyads_m1_rc)
; dyads_m3 versus dyads_m1_rc; m=2/10; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.835959; -wwtTAAAATAAATAww ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 152 199 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 61 55 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 74 59 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58 146 120

dyads_m8_shift0 (dyads_m8)
; dyads_m3 versus dyads_m8; m=3/10; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.810782; wwTTAAAAAgAAAwAaw ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 150 59 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 15 20 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 20 22 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25 36 120

oligos_6nt_mkv3_m8_shift5 (oligos_6nt_mkv3_m8)
; dyads_m3 versus oligos_6nt_mkv3_m8; m=4/10; ncol2=10; w=0; offset=5; strand=D; shift=5; score=0.501902; -----waAATAAAww-- ; cor=; Ncor= a 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 0 0 c 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 0 0 g 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 0 0 t 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243 0 0

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; dyads_m3 versus oligos_6nt_mkv3_m3; m=5/10; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.487234; ----awAAACAAAwa-- ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 0 0 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 0 0 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 0 0 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106 0 0

oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)
; dyads_m3 versus oligos_6nt_mkv3_m7; m=6/10; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.474527; ----awAAAGAAAwa-- ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 0 0 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 0 0 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 0 0 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134 0 0

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; dyads_m3 versus oligos_7nt_mkv4_m1; m=7/10; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.466196; --wwAAAATTAkm---- ; cor=; Ncor= a 0 0 173 222 462 442 432 481 7 5 482 121 163 0 0 0 0 c 0 0 110 54 4 5 2 5 2 6 3 73 138 0 0 0 0 g 0 0 57 71 5 2 2 1 3 0 0 133 68 0 0 0 0 t 0 0 149 142 18 40 53 2 477 478 4 162 120 0 0 0 0

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; dyads_m3 versus oligos_7nt_mkv4_m3; m=8/10; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.455372; ---wwAAAACAAwa--- ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 0 0 0 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 0 0 0 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 0 0 0 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105 0 0 0

oligos_6nt_mkv3_m6_shift7 (oligos_6nt_mkv3_m6)
; dyads_m3 versus oligos_6nt_mkv3_m6; m=9/10; ncol2=10; w=0; offset=7; strand=D; shift=7; score=0.440482; -------waTACATAwa ; cor=; Ncor= a 0 0 0 0 0 0 0 117 185 6 400 3 379 5 399 102 194 c 0 0 0 0 0 0 0 75 58 2 1 349 2 10 4 95 48 g 0 0 0 0 0 0 0 51 77 5 3 2 24 6 0 54 73 t 0 0 0 0 0 0 0 165 88 395 4 54 3 387 5 157 93

oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)
; dyads_m3 versus oligos_6nt_mkv3_m4; m=10/10; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.412785; ---waAAATTAwh---- ; cor=; Ncor= a 0 0 0 289 323 642 644 648 1 3 649 204 192 0 0 0 0 c 0 0 0 67 92 0 4 0 0 1 0 112 175 0 0 0 0 g 0 0 0 117 106 3 0 0 0 0 0 161 110 0 0 0 0 t 0 0 0 176 128 4 1 1 648 645 0 172 172 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --wwAAAATTAkm ; Alignment reference a 0 0 173 222 462 442 432 481 7 5 482 121 163 c 0 0 110 54 4 5 2 5 2 6 3 73 138 g 0 0 57 71 5 2 2 1 3 0 0 133 68 t 0 0 149 142 18 40 53 2 477 478 4 162 120

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wwAAAATTAkm ; cor=; Ncor= a 0 0 173 222 462 442 432 481 7 5 482 121 163 c 0 0 110 54 4 5 2 5 2 6 3 73 138 g 0 0 57 71 5 2 2 1 3 0 0 133 68 t 0 0 149 142 18 40 53 2 477 478 4 162 120

oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.878001; ---waAAATTAwh ; cor=; Ncor= a 0 0 0 289 323 642 644 648 1 3 649 204 192 c 0 0 0 67 92 0 4 0 0 1 0 112 175 g 0 0 0 117 106 3 0 0 0 0 0 161 110 t 0 0 0 176 128 4 1 1 648 645 0 172 172

dyads_m3_shift0 (dyads_m3)
; oligos_7nt_mkv4_m1 versus dyads_m3; m=3/3; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.466196; wwtTAAAAATAaA ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 c 66 52 65 21 26 17 8 15 8 20 8 77 23 g 55 57 25 18 14 13 12 6 16 13 15 25 23 t 193 190 315 396 60 57 24 43 31 438 29 108 64

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m10_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; oligos_7nt_mkv4_m10; m=0 (reference); ncol1=11; shift=1; ncol=12; -rwAAAGGAAwr ; Alignment reference a 0 124 131 360 335 349 5 8 362 363 125 133 c 0 59 70 1 9 14 18 2 1 3 48 60 g 0 104 72 8 3 1 353 354 3 1 82 97 t 0 94 108 12 34 17 5 17 15 14 126 91

oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m10; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -rwAAAGGAAwr ; cor=; Ncor= a 0 124 131 360 335 349 5 8 362 363 125 133 c 0 59 70 1 9 14 18 2 1 3 48 60 g 0 104 72 8 3 1 353 354 3 1 82 97 t 0 94 108 12 34 17 5 17 15 14 126 91

oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)
; oligos_7nt_mkv4_m10 versus oligos_6nt_mkv3_m7; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.803425; -awAAAGAAAwa ; cor=; Ncor= a 0 257 209 537 526 528 7 546 529 555 211 239 c 0 83 75 3 2 26 2 2 3 4 73 74 g 0 110 123 3 4 4 536 2 2 2 90 119 t 0 116 159 23 34 8 21 16 32 5 192 134

oligos_7nt_mkv4_m9_shift0 (oligos_7nt_mkv4_m9)
; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m9; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.684567; wwGAAAAGAAww ; cor=; Ncor= a 339 357 51 765 748 742 739 28 743 725 350 340 c 110 42 18 21 23 31 9 31 22 38 110 128 g 160 183 721 30 42 35 39 717 37 36 156 137 t 225 252 44 18 21 26 47 58 32 35 218 229

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=23; shift=1; ncol=24; -cygCCCcCCTCcsCCtCCCtcms ; Alignment reference a 0 23 10 14 9 9 7 15 7 8 12 7 21 5 6 3 12 4 3 3 30 33 45 15 c 0 78 66 28 111 99 118 89 113 117 14 118 87 90 108 118 25 115 123 121 29 87 43 64 g 0 22 29 81 10 12 5 28 13 9 18 12 24 42 6 8 16 16 11 11 26 12 21 44 t 0 21 39 21 14 24 14 12 11 10 100 7 12 7 24 15 91 9 7 9 59 12 35 21

dyads_m9_shift1 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/3; ncol2=23; w=0; offset=0; strand=D; shift=1; score= 1; -cygCCCcCCTCcsCCtCCCtcms ; cor=; Ncor= a 0 23 10 14 9 9 7 15 7 8 12 7 21 5 6 3 12 4 3 3 30 33 45 15 c 0 78 66 28 111 99 118 89 113 117 14 118 87 90 108 118 25 115 123 121 29 87 43 64 g 0 22 29 81 10 12 5 28 13 9 18 12 24 42 6 8 16 16 11 11 26 12 21 44 t 0 21 39 21 14 24 14 12 11 10 100 7 12 7 24 15 91 9 7 9 59 12 35 21

dyads_m2_shift0 (dyads_m2)
; dyads_m9 versus dyads_m2; m=2/3; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.701505; ccCCtCCCCcccCCCmgCCCyCcs ; cor=; Ncor= a 25 20 11 18 15 5 16 21 14 11 15 17 7 11 7 78 10 7 7 11 15 17 24 23 c 92 92 142 131 47 139 130 134 135 120 112 117 152 148 156 53 42 148 147 131 69 129 79 75 g 34 46 21 21 32 16 25 17 18 26 37 24 13 16 15 35 117 25 18 21 36 30 43 57 t 38 31 15 19 95 29 18 17 22 32 25 31 17 14 11 23 20 9 17 26 69 13 43 34

dyads_m7_shift1 (dyads_m7)
; dyads_m9 versus dyads_m7; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.405579; -mwCCCCryCTChm---------- ; cor=; Ncor= a 0 334 322 54 48 61 88 351 205 19 62 19 324 310 0 0 0 0 0 0 0 0 0 0 c 0 304 280 963 925 983 870 227 336 1090 75 1079 340 319 0 0 0 0 0 0 0 0 0 0 g 0 274 247 64 57 44 46 305 220 28 57 33 108 266 0 0 0 0 0 0 0 0 0 0 t 0 240 303 71 122 64 148 269 391 15 958 21 380 257 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m1_shift2 ; 4 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; --ytCCTCCTCCys ; Alignment reference a 0 0 131 116 7 13 49 11 20 48 28 22 120 114 c 0 0 193 137 509 518 22 495 512 18 477 505 169 171 g 0 0 95 119 21 13 68 23 9 58 38 17 70 143 t 0 0 143 190 25 18 423 33 21 438 19 18 203 134

oligos_8nt_mkv5_m1_shift2 (oligos_8nt_mkv5_m1)
; oligos_8nt_mkv5_m1 versus oligos_8nt_mkv5_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ytCCTCCTCCys ; cor=; Ncor= a 0 0 131 116 7 13 49 11 20 48 28 22 120 114 c 0 0 193 137 509 518 22 495 512 18 477 505 169 171 g 0 0 95 119 21 13 68 23 9 58 38 17 70 143 t 0 0 143 190 25 18 423 33 21 438 19 18 203 134

dyads_m7_shift0 (dyads_m7)
; oligos_8nt_mkv5_m1 versus dyads_m7; m=2/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.560024; mwCCCCryCTChm- ; cor=; Ncor= a 334 322 54 48 61 88 351 205 19 62 19 324 310 0 c 304 280 963 925 983 870 227 336 1090 75 1079 340 319 0 g 274 247 64 57 44 46 305 220 28 57 33 108 266 0 t 240 303 71 122 64 148 269 391 15 958 21 380 257 0

oligos_6nt_mkv3_m5_shift5 (oligos_6nt_mkv3_m5)
; oligos_8nt_mkv5_m1 versus oligos_6nt_mkv3_m5; m=3/3; ncol2=10; w=0; offset=3; strand=D; shift=5; score=0.551962; -----mgCCTCCCr ; cor=; Ncor= a 0 0 0 0 0 240 142 7 13 29 8 8 8 275 c 0 0 0 0 0 290 190 791 791 13 785 772 751 190 g 0 0 0 0 0 143 343 30 24 65 37 45 69 228 t 0 0 0 0 0 172 170 17 17 738 15 20 17 152

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----awAAACAAAwa ; Alignment reference a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----awAAACAAAwa ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106
oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m7; m=2/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.810852; ----awAAAGAAAwa ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3; m=3/8; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.758775; ---wwAAAACAAwa- ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 0 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 0 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 0 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105 0
oligos_6nt_mkv3_m8_shift5 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m8; m=4/8; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.694663; -----waAATAAAww ; cor=; Ncor= a 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243
oligos_8nt_mkv5_m2_shift6 (oligos_8nt_mkv5_m2)				; oligos_6nt_mkv3_m3 versus oligos_8nt_mkv5_m2; m=5/8; ncol2=12; w=0; offset=2; strand=D; shift=6; score=0.530269; ------awACAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 342 269 724 58 715 701 721 710 707 c 0 0 0 0 0 0 141 114 12 631 36 22 20 25 7 g 0 0 0 0 0 0 107 130 17 31 5 22 20 19 23 t 0 0 0 0 0 0 182 259 19 52 16 27 11 18 35
dyads_m1_rc_shift1 (dyads_m1_rc)				; oligos_6nt_mkv3_m3 versus dyads_m1_rc; m=6/8; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.49661; -wwtTAAAATAAATA ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m3 versus dyads_m3; m=7/8; ncol2=17; w=-4; offset=-4; strand=D; shift=0; score=0.487234; wwtTAAAAATAaAwA ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53
dyads_m8_shift0 (dyads_m8)				; oligos_6nt_mkv3_m3 versus dyads_m8; m=8/8; ncol2=19; w=-4; offset=-4; strand=D; shift=0; score=0.456461; wwTTAAAAAgAAAwA ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)				; oligos_7nt_mkv4_m9; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwGAAAAGAAww ; Alignment reference a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229
oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)				; oligos_7nt_mkv4_m9 versus oligos_7nt_mkv4_m9; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwGAAAAGAAww ; cor=; Ncor= a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229
oligos_7nt_mkv4_m10_shift3 (oligos_7nt_mkv4_m10)				; oligos_7nt_mkv4_m9 versus oligos_7nt_mkv4_m10; m=2/5; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.684567; ---rwAAAGGAAwr ; cor=; Ncor= a 0 0 0 124 131 360 335 349 5 8 362 363 125 133 c 0 0 0 59 70 1 9 14 18 2 1 3 48 60 g 0 0 0 104 72 8 3 1 353 354 3 1 82 97 t 0 0 0 94 108 12 34 17 5 17 15 14 126 91
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m9 versus oligos_7nt_mkv4_m3; m=3/5; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.680525; ---wwAAAACAAwa ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105
oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)				; oligos_7nt_mkv4_m9 versus oligos_6nt_mkv3_m7; m=4/5; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.639937; ----awAAAGAAAw ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192
dyads_m8_shift0 (dyads_m8)				; oligos_7nt_mkv4_m9 versus dyads_m8; m=5/5; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.445276; wwTTAAAAAgAAAw ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=11; shift=4; ncol=15; ----awAAAGAAAwa ; Alignment reference a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134
oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----awAAAGAAAwa ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m3; m=2/9; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.810852; ----awAAACAAAwa ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106
oligos_7nt_mkv4_m10_shift4 (oligos_7nt_mkv4_m10)				; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m10; m=3/9; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.803425; ----rwAAAGGAAwr ; cor=; Ncor= a 0 0 0 0 124 131 360 335 349 5 8 362 363 125 133 c 0 0 0 0 59 70 1 9 14 18 2 1 3 48 60 g 0 0 0 0 104 72 8 3 1 353 354 3 1 82 97 t 0 0 0 0 94 108 12 34 17 5 17 15 14 126 91
oligos_6nt_mkv3_m8_shift5 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m8; m=4/9; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.696352; -----waAATAAAww ; cor=; Ncor= a 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243
oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)				; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m9; m=5/9; ncol2=12; w=-2; offset=-2; strand=D; shift=2; score=0.639937; --wwGAAAAGAAww- ; cor=; Ncor= a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 0 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 0 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 0 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229 0
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m3; m=6/9; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.585048; ---wwAAAACAAwa- ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 0 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 0 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 0 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105 0
dyads_m8_shift0 (dyads_m8)				; oligos_6nt_mkv3_m7 versus dyads_m8; m=7/9; ncol2=19; w=-4; offset=-4; strand=D; shift=0; score=0.502309; wwTTAAAAAgAAAwA ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25
dyads_m1_rc_shift1 (dyads_m1_rc)				; oligos_6nt_mkv3_m7 versus dyads_m1_rc; m=8/9; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.485719; -wwtTAAAATAAATA ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m7 versus dyads_m3; m=9/9; ncol2=17; w=-4; offset=-4; strand=D; shift=0; score=0.474527; wwtTAAAAATAaAwA ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ysAGGCTGGwg ; Alignment reference a 0 0 0 243 225 922 20 60 65 147 36 37 378 236 c 0 0 0 324 355 15 9 33 939 23 6 16 167 253 g 0 0 0 197 305 69 989 929 26 54 1007 960 218 324 t 0 0 0 297 176 55 43 39 31 837 12 48 298 248
oligos_7nt_mkv4_m2_shift3 (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=3; score= 1; ---ysAGGCTGGwg ; cor=; Ncor= a 0 0 0 243 225 922 20 60 65 147 36 37 378 236 c 0 0 0 324 355 15 9 33 939 23 6 16 167 253 g 0 0 0 197 305 69 989 929 26 54 1007 960 218 324 t 0 0 0 297 176 55 43 39 31 837 12 48 298 248
oligos_6nt_mkv3_m1_rc_shift3 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1_rc; m=2/4; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.844796; ---ssaGGCTGGGs ; cor=; Ncor= a 0 0 0 221 157 679 85 25 18 33 15 134 93 257 c 0 0 0 372 375 75 24 101 973 56 30 32 44 288 g 0 0 0 272 387 113 904 884 29 77 954 835 797 317 t 0 0 0 165 111 163 17 20 10 864 31 29 96 168
dyads_m5_shift0 (dyads_m5)				; oligos_7nt_mkv4_m2 versus dyads_m5; m=3/4; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.421038; wrCCCAGGCwg--- ; cor=; Ncor= a 324 319 38 75 54 1069 40 43 96 314 268 0 0 0 c 297 249 1011 1060 1087 42 30 82 970 268 286 0 0 0 g 257 372 108 20 38 40 1101 1042 60 191 368 0 0 0 t 338 276 59 61 37 65 45 49 90 443 294 0 0 0
dyads_m4_rc_shift0 (dyads_m4_rc)				; oligos_7nt_mkv4_m2 versus dyads_m4_rc; m=4/4; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.408711; wrGCCAGGCts--- ; cor=; Ncor= a 279 384 33 40 26 821 27 38 99 253 241 0 0 0 c 265 125 63 975 1026 65 32 24 862 244 275 0 0 0 g 263 332 947 32 26 67 1006 1013 71 200 315 0 0 0 t 292 258 56 52 21 146 34 24 67 402 268 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; --awACAAAAACwa ; Alignment reference a 0 0 342 269 724 58 715 701 721 710 707 68 350 333 c 0 0 141 114 12 631 36 22 20 25 7 556 126 125 g 0 0 107 130 17 31 5 22 20 19 23 41 42 136 t 0 0 182 259 19 52 16 27 11 18 35 107 254 178
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; --awACAAAAACwa ; cor=; Ncor= a 0 0 342 269 724 58 715 701 721 710 707 68 350 333 c 0 0 141 114 12 631 36 22 20 25 7 556 126 125 g 0 0 107 130 17 31 5 22 20 19 23 41 42 136 t 0 0 182 259 19 52 16 27 11 18 35 107 254 178
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_8nt_mkv5_m2 versus oligos_6nt_mkv3_m3; m=2/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.530269; awAAACAAAwa--- ; cor=; Ncor= a 241 206 491 476 514 7 487 480 473 182 248 0 0 0 c 87 92 2 3 0 484 2 4 13 95 74 0 0 0 g 82 62 8 0 2 7 18 0 6 58 91 0 0 0 t 109 159 18 40 3 21 12 35 27 184 106 0 0 0
oligos_7nt_mkv4_m3_shift5 (oligos_7nt_mkv4_m3)				; oligos_8nt_mkv5_m2 versus oligos_7nt_mkv4_m3; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=5; score=0.51026; -----wwAAAACAA ; cor=; Ncor= a 0 0 0 0 0 177 170 446 413 423 453 7 424 443 c 0 0 0 0 0 92 84 2 7 3 2 446 5 2 g 0 0 0 0 0 56 72 3 9 5 2 2 18 1 t 0 0 0 0 0 135 134 9 31 29 3 5 13 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---waAAATTAwh ; Alignment reference a 0 0 0 289 323 642 644 648 1 3 649 204 192 c 0 0 0 67 92 0 4 0 0 1 0 112 175 g 0 0 0 117 106 3 0 0 0 0 0 161 110 t 0 0 0 176 128 4 1 1 648 645 0 172 172
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---waAAATTAwh ; cor=; Ncor= a 0 0 0 289 323 642 644 648 1 3 649 204 192 c 0 0 0 67 92 0 4 0 0 1 0 112 175 g 0 0 0 117 106 3 0 0 0 0 0 161 110 t 0 0 0 176 128 4 1 1 648 645 0 172 172
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=2; score=0.878001; --wwAAAATTAkm ; cor=; Ncor= a 0 0 173 222 462 442 432 481 7 5 482 121 163 c 0 0 110 54 4 5 2 5 2 6 3 73 138 g 0 0 57 71 5 2 2 1 3 0 0 133 68 t 0 0 149 142 18 40 53 2 477 478 4 162 120
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m4 versus dyads_m3; m=3/3; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.412785; wwtTAAAAATAaA ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 c 66 52 65 21 26 17 8 15 8 20 8 77 23 g 55 57 25 18 14 13 12 6 16 13 15 25 23 t 193 190 315 396 60 57 24 43 31 438 29 108 64

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift0 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=13; shift=0; ncol=13; mwCCCCryCTChm ; Alignment reference a 334 322 54 48 61 88 351 205 19 62 19 324 310 c 304 280 963 925 983 870 227 336 1090 75 1079 340 319 g 274 247 64 57 44 46 305 220 28 57 33 108 266 t 240 303 71 122 64 148 269 391 15 958 21 380 257
dyads_m7_shift0 (dyads_m7)				; dyads_m7 versus dyads_m7; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; mwCCCCryCTChm ; cor=; Ncor= a 334 322 54 48 61 88 351 205 19 62 19 324 310 c 304 280 963 925 983 870 227 336 1090 75 1079 340 319 g 274 247 64 57 44 46 305 220 28 57 33 108 266 t 240 303 71 122 64 148 269 391 15 958 21 380 257
oligos_8nt_mkv5_m1_shift2 (oligos_8nt_mkv5_m1)				; dyads_m7 versus oligos_8nt_mkv5_m1; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.560024; --ytCCTCCTCCy ; cor=; Ncor= a 0 0 131 116 7 13 49 11 20 48 28 22 120 c 0 0 193 137 509 518 22 495 512 18 477 505 169 g 0 0 95 119 21 13 68 23 9 58 38 17 70 t 0 0 143 190 25 18 423 33 21 438 19 18 203
dyads_m9_shift0 (dyads_m9)				; dyads_m7 versus dyads_m9; m=3/3; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.405579; cygCCCcCCTCcs ; cor=; Ncor= a 23 10 14 9 9 7 15 7 8 12 7 21 5 c 78 66 28 111 99 118 89 113 117 14 118 87 90 g 22 29 81 10 12 5 28 13 9 18 12 24 42 t 21 39 21 14 24 14 12 11 10 100 7 12 7

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift1 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -wrCCCAGGCwg ; Alignment reference a 0 324 319 38 75 54 1069 40 43 96 314 268 c 0 297 249 1011 1060 1087 42 30 82 970 268 286 g 0 257 372 108 20 38 40 1101 1042 60 191 368 t 0 338 276 59 61 37 65 45 49 90 443 294
dyads_m5_shift1 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wrCCCAGGCwg ; cor=; Ncor= a 0 324 319 38 75 54 1069 40 43 96 314 268 c 0 297 249 1011 1060 1087 42 30 82 970 268 286 g 0 257 372 108 20 38 40 1101 1042 60 191 368 t 0 338 276 59 61 37 65 45 49 90 443 294
dyads_m4_rc_shift1 (dyads_m4_rc)				; dyads_m5 versus dyads_m4_rc; m=2/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.825588; -wrGCCAGGCts ; cor=; Ncor= a 0 279 384 33 40 26 821 27 38 99 253 241 c 0 265 125 63 975 1026 65 32 24 862 244 275 g 0 263 332 947 32 26 67 1006 1013 71 200 315 t 0 292 258 56 52 21 146 34 24 67 402 268
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; dyads_m5 versus oligos_6nt_mkv3_m2_rc; m=3/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.801627; -ddGCCAGGctb ; cor=; Ncor= a 0 253 318 18 39 16 708 14 34 117 234 196 c 0 204 128 32 851 894 59 35 11 637 170 258 g 0 241 272 884 32 29 85 893 895 81 198 251 t 0 262 242 26 38 21 108 18 20 125 358 255
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; dyads_m5 versus oligos_6nt_mkv3_m1; m=4/7; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.738918; -msCCCAGCCts ; cor=; Ncor= a 0 323 168 96 29 31 864 10 20 17 163 111 c 0 286 317 797 835 954 77 29 884 904 113 387 g 0 232 288 44 32 30 56 973 101 24 75 375 t 0 189 257 93 134 15 33 18 25 85 679 157
oligos_7nt_mkv4_m7_rc_shift0 (oligos_7nt_mkv4_m7_rc)				; dyads_m5 versus oligos_7nt_mkv4_m7_rc; m=5/7; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.738641; twGGCCAGGCtg ; cor=; Ncor= a 121 173 65 22 28 17 526 15 19 70 145 123 c 171 113 42 73 608 637 57 40 27 518 124 149 g 153 155 550 570 26 32 67 626 635 53 153 254 t 246 250 34 26 29 5 41 10 10 50 269 165
oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)				; dyads_m5 versus oligos_6nt_mkv3_m10; m=6/7; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.618718; wdGCCAAGGhk- ; cor=; Ncor= a 217 196 80 16 11 504 534 17 37 170 156 0 c 94 104 59 595 609 57 40 6 6 183 149 0 g 144 180 461 9 6 43 24 607 584 101 164 0 t 186 161 41 21 15 37 43 11 14 187 172 0
oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)				; dyads_m5 versus oligos_7nt_mkv4_m2; m=7/7; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.421038; ----ysAGGCTG ; cor=; Ncor= a 0 0 0 0 243 225 922 20 60 65 147 36 c 0 0 0 0 324 355 15 9 33 939 23 6 g 0 0 0 0 197 305 69 989 929 26 54 1007 t 0 0 0 0 297 176 55 43 39 31 837 12

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m8_shift0 (dyads_m8)				; dyads_m8; m=0 (reference); ncol1=19; shift=0; ncol=19; wwTTAAAAAgAAAwAawww ; Alignment reference a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 150 59 91 86 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 15 20 18 30 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 20 22 42 29 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25 36 120 70 76
dyads_m8_shift0 (dyads_m8)				; dyads_m8 versus dyads_m8; m=1/8; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAAgAAAwAawww ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 150 59 91 86 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 15 20 18 30 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 20 22 42 29 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25 36 120 70 76
dyads_m3_shift0 (dyads_m3)				; dyads_m8 versus dyads_m3; m=2/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.810782; wwtTAAAAATAaAwAww-- ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 227 255 0 0 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 60 66 0 0 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 53 59 0 0 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53 170 130 0 0
dyads_m1_rc_shift1 (dyads_m1_rc)				; dyads_m8 versus dyads_m1_rc; m=3/8; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.654387; -wwtTAAAATAAATAww-- ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 152 199 0 0 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 61 55 0 0 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 74 59 0 0 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58 146 120 0 0
oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)				; dyads_m8 versus oligos_6nt_mkv3_m7; m=4/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.502309; ----awAAAGAAAwa---- ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 0 0 0 0 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 0 0 0 0 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 0 0 0 0 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134 0 0 0 0
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; dyads_m8 versus oligos_6nt_mkv3_m3; m=5/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.456461; ----awAAACAAAwa---- ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 0 0 0 0 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 0 0 0 0 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 0 0 0 0 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106 0 0 0 0
oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)				; dyads_m8 versus oligos_7nt_mkv4_m9; m=6/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.445276; --wwGAAAAGAAww----- ; cor=; Ncor= a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 0 0 0 0 0 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 0 0 0 0 0 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 0 0 0 0 0 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229 0 0 0 0 0
oligos_6nt_mkv3_m8_shift9 (oligos_6nt_mkv3_m8)				; dyads_m8 versus oligos_6nt_mkv3_m8; m=7/8; ncol2=10; w=0; offset=9; strand=D; shift=9; score=0.42076; ---------waAATAAAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; dyads_m8 versus oligos_7nt_mkv4_m3; m=8/8; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.417143; ---wwAAAACAAwa----- ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 0 0 0 0 0 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 0 0 0 0 0 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 0 0 0 0 0 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m8_shift9 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=9; ncol=19; ---------waAATAAAww ; Alignment reference a 0 0 0 0 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243
oligos_6nt_mkv3_m8_shift9 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=9; score= 1; ---------waAATAAAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 c 0 0 0 0 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 g 0 0 0 0 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 t 0 0 0 0 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243
oligos_6nt_mkv3_m7_shift8 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m7; m=2/6; ncol2=11; w=-1; offset=-1; strand=D; shift=8; score=0.696352; --------awAAAGAAAwa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 c 0 0 0 0 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 g 0 0 0 0 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 t 0 0 0 0 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134
oligos_6nt_mkv3_m3_shift8 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m3; m=3/6; ncol2=11; w=-1; offset=-1; strand=D; shift=8; score=0.694663; --------awAAACAAAwa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 c 0 0 0 0 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 g 0 0 0 0 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 t 0 0 0 0 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106
dyads_m1_rc_shift5 (dyads_m1_rc)				; oligos_6nt_mkv3_m8 versus dyads_m1_rc; m=4/6; ncol2=16; w=-4; offset=-4; strand=R; shift=5; score=0.538029; -----wwtTAAAATAAATA ; cor=; Ncor= a 0 0 0 0 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 c 0 0 0 0 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 g 0 0 0 0 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 t 0 0 0 0 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58
dyads_m3_shift4 (dyads_m3)				; oligos_6nt_mkv3_m8 versus dyads_m3; m=5/6; ncol2=17; w=-5; offset=-5; strand=D; shift=4; score=0.501902; ----wwtTAAAAATAaAwA ; cor=; Ncor= a 0 0 0 0 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 c 0 0 0 0 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 g 0 0 0 0 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 t 0 0 0 0 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53
dyads_m8_shift0 (dyads_m8)				; oligos_6nt_mkv3_m8 versus dyads_m8; m=6/6; ncol2=19; w=-9; offset=-9; strand=D; shift=0; score=0.42076; wwTTAAAAAgAAAwAawww ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 150 59 91 86 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 15 20 18 30 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 20 22 42 29 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25 36 120 70 76

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=11; shift=1; ncol=12; -wdGCCAAGGhk ; Alignment reference a 0 217 196 80 16 11 504 534 17 37 170 156 c 0 94 104 59 595 609 57 40 6 6 183 149 g 0 144 180 461 9 6 43 24 607 584 101 164 t 0 186 161 41 21 15 37 43 11 14 187 172
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wdGCCAAGGhk ; cor=; Ncor= a 0 217 196 80 16 11 504 534 17 37 170 156 c 0 94 104 59 595 609 57 40 6 6 183 149 g 0 144 180 461 9 6 43 24 607 584 101 164 t 0 186 161 41 21 15 37 43 11 14 187 172
dyads_m5_shift2 (dyads_m5)				; oligos_6nt_mkv3_m10 versus dyads_m5; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.618718; --wrCCCAGGCw ; cor=; Ncor= a 0 0 324 319 38 75 54 1069 40 43 96 314 c 0 0 297 249 1011 1060 1087 42 30 82 970 268 g 0 0 257 372 108 20 38 40 1101 1042 60 191 t 0 0 338 276 59 61 37 65 45 49 90 443
positions_6nt_m1_shift0 (positions_6nt_m1)				; oligos_6nt_mkv3_m10 versus positions_6nt_m1; m=3/3; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.579298; wvAGCCAArr-- ; cor=; Ncor= a 112 106 383 3 4 1 361 367 110 156 0 0 c 90 105 25 0 413 402 4 42 89 65 0 0 g 74 148 10 416 1 16 54 3 151 118 0 0 t 144 61 2 1 2 1 1 8 70 81 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; msCCCAGCCtss ; Alignment reference a 323 168 96 29 31 864 10 20 17 163 111 165 c 286 317 797 835 954 77 29 884 904 113 387 272 g 232 288 44 32 30 56 973 101 24 75 375 372 t 189 257 93 134 15 33 18 25 85 679 157 221
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; msCCCAGCCtss ; cor=; Ncor= a 323 168 96 29 31 864 10 20 17 163 111 165 c 286 317 797 835 954 77 29 884 904 113 387 272 g 232 288 44 32 30 56 973 101 24 75 375 372 t 189 257 93 134 15 33 18 25 85 679 157 221
oligos_7nt_mkv4_m2_rc_shift1 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.844796; -cwCCAGCCTsr ; cor=; Ncor= a 0 248 298 48 12 837 31 39 43 55 176 297 c 0 324 218 960 1007 54 26 929 989 69 305 197 g 0 253 167 16 6 23 939 33 9 15 355 324 t 0 236 378 37 36 147 65 60 20 922 225 243
dyads_m5_shift0 (dyads_m5)				; oligos_6nt_mkv3_m1 versus dyads_m5; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.738918; wrCCCAGGCwg- ; cor=; Ncor= a 324 319 38 75 54 1069 40 43 96 314 268 0 c 297 249 1011 1060 1087 42 30 82 970 268 286 0 g 257 372 108 20 38 40 1101 1042 60 191 368 0 t 338 276 59 61 37 65 45 49 90 443 294 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift2 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwTATTTATTTTAaww ; Alignment reference a 0 0 120 146 58 298 43 83 20 351 18 33 23 34 370 277 167 145 c 0 0 59 74 19 25 26 13 8 15 12 4 8 14 11 23 33 60 g 0 0 55 61 14 16 26 33 7 18 13 16 20 19 12 25 54 53 t 0 0 199 152 342 94 338 304 398 49 390 380 382 366 40 108 179 175
dyads_m1_shift2 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=2; score= 1; --wwTATTTATTTTAaww ; cor=; Ncor= a 0 0 120 146 58 298 43 83 20 351 18 33 23 34 370 277 167 145 c 0 0 59 74 19 25 26 13 8 15 12 4 8 14 11 23 33 60 g 0 0 55 61 14 16 26 33 7 18 13 16 20 19 12 25 54 53 t 0 0 199 152 342 94 338 304 398 49 390 380 382 366 40 108 179 175
dyads_m3_rc_shift2 (dyads_m3_rc)				; dyads_m1 versus dyads_m3_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.835959; --wwTwTtTATTTTTAaw ; cor=; Ncor= a 0 0 130 170 53 317 64 108 29 438 31 43 24 57 60 396 315 190 c 0 0 59 53 22 27 23 25 15 13 16 6 12 13 14 18 25 57 g 0 0 66 60 22 32 23 77 8 20 8 15 8 17 26 21 65 52 t 0 0 255 227 413 134 400 300 458 39 455 446 466 423 410 75 105 211
dyads_m8_rc_shift0 (dyads_m8_rc)				; dyads_m1 versus dyads_m8_rc; m=3/8; ncol2=19; w=-2; offset=-2; strand=R; shift=0; score=0.654387; wwwtTwTTTcTTTTTAAw ; cor=; Ncor= a 76 70 120 36 25 136 12 33 32 40 13 12 8 23 11 193 156 78 c 29 42 22 20 14 9 10 6 10 119 4 6 14 3 2 5 7 25 g 30 18 20 15 10 9 5 16 12 14 3 8 1 5 7 5 11 25 t 86 91 59 150 172 67 194 166 167 48 201 195 198 190 201 18 47 93
oligos_6nt_mkv3_m8_rc_shift4 (oligos_6nt_mkv3_m8_rc)				; dyads_m1 versus oligos_6nt_mkv3_m8_rc; m=4/8; ncol2=10; w=0; offset=2; strand=R; shift=4; score=0.538029; ----wwTTTATTtw---- ; cor=; Ncor= a 0 0 0 0 243 231 2 4 0 852 1 5 154 254 0 0 0 0 c 0 0 0 0 156 137 0 0 1 0 0 4 143 146 0 0 0 0 g 0 0 0 0 125 124 11 8 1 0 2 1 157 133 0 0 0 0 t 0 0 0 0 328 360 839 840 850 0 849 842 398 319 0 0 0 0
oligos_6nt_mkv3_m3_rc_shift4 (oligos_6nt_mkv3_m3_rc)				; dyads_m1 versus oligos_6nt_mkv3_m3_rc; m=5/8; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.49661; ----twTTTGTTTwt--- ; cor=; Ncor= a 0 0 0 0 106 184 27 35 12 21 3 40 18 159 109 0 0 0 c 0 0 0 0 91 58 6 0 18 7 2 0 8 62 82 0 0 0 g 0 0 0 0 74 95 13 4 2 484 0 3 2 92 87 0 0 0 t 0 0 0 0 248 182 473 480 487 7 514 476 491 206 241 0 0 0
oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)				; dyads_m1 versus oligos_7nt_mkv4_m3_rc; m=6/8; ncol2=11; w=0; offset=3; strand=R; shift=5; score=0.490823; -----twTTGTTTTww-- ; cor=; Ncor= a 0 0 0 0 0 105 128 14 13 5 3 29 31 9 134 135 0 0 c 0 0 0 0 0 65 62 1 18 2 2 5 9 3 72 56 0 0 g 0 0 0 0 0 90 76 2 5 446 2 3 7 2 84 92 0 0 t 0 0 0 0 0 200 194 443 424 7 453 423 413 446 170 177 0 0
oligos_6nt_mkv3_m7_rc_shift4 (oligos_6nt_mkv3_m7_rc)				; dyads_m1 versus oligos_6nt_mkv3_m7_rc; m=7/8; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.485719; ----twTTTCTTTwt--- ; cor=; Ncor= a 0 0 0 0 134 192 5 32 16 21 8 34 23 159 116 0 0 0 c 0 0 0 0 119 90 2 2 2 536 4 4 3 123 110 0 0 0 g 0 0 0 0 74 73 4 3 2 2 26 2 3 75 83 0 0 0 t 0 0 0 0 239 211 555 529 546 7 528 526 537 209 257 0 0 0
oligos_6nt_mkv3_m6_rc_shift2 (oligos_6nt_mkv3_m6_rc)				; dyads_m1 versus oligos_6nt_mkv3_m6_rc; m=8/8; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.452458; --twTATGTAtw------ ; cor=; Ncor= a 0 0 93 157 5 387 3 54 4 395 88 165 0 0 0 0 0 0 c 0 0 73 54 0 6 24 2 3 5 77 51 0 0 0 0 0 0 g 0 0 48 95 4 10 2 349 1 2 58 75 0 0 0 0 0 0 t 0 0 194 102 399 5 379 3 400 6 185 117 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m7_shift0 (oligos_7nt_mkv4_m7)				; oligos_7nt_mkv4_m7; m=0 (reference); ncol1=12; shift=0; ncol=12; caGCCTGGCCwa ; Alignment reference a 165 269 50 10 10 41 5 29 26 34 250 246 c 254 153 53 635 626 67 32 26 570 550 155 153 g 149 124 518 27 40 57 637 608 73 42 113 171 t 123 145 70 19 15 526 17 28 22 65 173 121
oligos_7nt_mkv4_m7_shift0 (oligos_7nt_mkv4_m7)				; oligos_7nt_mkv4_m7 versus oligos_7nt_mkv4_m7; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; caGCCTGGCCwa ; cor=; Ncor= a 165 269 50 10 10 41 5 29 26 34 250 246 c 254 153 53 635 626 67 32 26 570 550 155 153 g 149 124 518 27 40 57 637 608 73 42 113 171 t 123 145 70 19 15 526 17 28 22 65 173 121
dyads_m4_shift0 (dyads_m4)				; oligos_7nt_mkv4_m7 versus dyads_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.869559; saGCCTGGCyw- ; cor=; Ncor= a 268 402 67 24 34 146 21 52 56 258 292 0 c 315 200 71 1013 1006 67 26 32 947 332 263 0 g 275 244 862 24 32 65 1026 975 63 125 265 0 t 241 253 99 38 27 821 26 40 33 384 279 0
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m7 versus oligos_6nt_mkv3_m2; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.865174; vagCCTGGChh- ; cor=; Ncor= a 255 358 125 20 18 108 21 38 26 242 262 0 c 251 198 81 895 893 85 29 32 884 272 241 0 g 258 170 637 11 35 59 894 851 32 128 204 0 t 196 234 117 34 14 708 16 39 18 318 253 0
dyads_m5_rc_shift0 (dyads_m5_rc)				; oligos_7nt_mkv4_m7 versus dyads_m5_rc; m=4/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.738641; cwGCCTGGGyw- ; cor=; Ncor= a 294 443 90 49 45 65 37 61 59 276 338 0 c 368 191 60 1042 1101 40 38 20 108 372 257 0 g 286 268 970 82 30 42 1087 1060 1011 249 297 0 t 268 314 96 43 40 1069 54 75 38 319 324 0

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; ---wwAAAACAAwa ; Alignment reference a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---wwAAAACAAwa ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3; m=2/8; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.758775; ----awAAACAAAw ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184
oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m9; m=3/8; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.680525; --wwGAAAAGAAww ; cor=; Ncor= a 0 0 339 357 51 765 748 742 739 28 743 725 350 340 c 0 0 110 42 18 21 23 31 9 31 22 38 110 128 g 0 0 160 183 721 30 42 35 39 717 37 36 156 137 t 0 0 225 252 44 18 21 26 47 58 32 35 218 229
oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m7; m=4/8; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.585048; ----awAAAGAAAw ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192
oligos_8nt_mkv5_m2_shift0 (oligos_8nt_mkv5_m2)				; oligos_7nt_mkv4_m3 versus oligos_8nt_mkv5_m2; m=5/8; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.51026; awACAAAAACwa-- ; cor=; Ncor= a 342 269 724 58 715 701 721 710 707 68 350 333 0 0 c 141 114 12 631 36 22 20 25 7 556 126 125 0 0 g 107 130 17 31 5 22 20 19 23 41 42 136 0 0 t 182 259 19 52 16 27 11 18 35 107 254 178 0 0
dyads_m1_rc_shift1 (dyads_m1_rc)				; oligos_7nt_mkv4_m3 versus dyads_m1_rc; m=6/8; ncol2=16; w=-2; offset=-2; strand=R; shift=1; score=0.490823; -wwtTAAAATAAAT ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298
dyads_m3_shift0 (dyads_m3)				; oligos_7nt_mkv4_m3 versus dyads_m3; m=7/8; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.455372; wwtTAAAAATAaAw ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317
dyads_m8_shift0 (dyads_m8)				; oligos_7nt_mkv4_m3 versus dyads_m8; m=8/8; ncol2=19; w=-3; offset=-3; strand=D; shift=0; score=0.417143; wwTTAAAAAgAAAw ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift3 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---saGCCTGGCyw ; Alignment reference a 0 0 0 268 402 67 24 34 146 21 52 56 258 292 c 0 0 0 315 200 71 1013 1006 67 26 32 947 332 263 g 0 0 0 275 244 862 24 32 65 1026 975 63 125 265 t 0 0 0 241 253 99 38 27 821 26 40 33 384 279
dyads_m4_shift3 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---saGCCTGGCyw ; cor=; Ncor= a 0 0 0 268 402 67 24 34 146 21 52 56 258 292 c 0 0 0 315 200 71 1013 1006 67 26 32 947 332 263 g 0 0 0 275 244 862 24 32 65 1026 975 63 125 265 t 0 0 0 241 253 99 38 27 821 26 40 33 384 279
oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)				; dyads_m4 versus oligos_6nt_mkv3_m2; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.995191; ---vagCCTGGChh ; cor=; Ncor= a 0 0 0 255 358 125 20 18 108 21 38 26 242 262 c 0 0 0 251 198 81 895 893 85 29 32 884 272 241 g 0 0 0 258 170 637 11 35 59 894 851 32 128 204 t 0 0 0 196 234 117 34 14 708 16 39 18 318 253
oligos_7nt_mkv4_m7_shift3 (oligos_7nt_mkv4_m7)				; dyads_m4 versus oligos_7nt_mkv4_m7; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.869559; ---caGCCTGGCCw ; cor=; Ncor= a 0 0 0 165 269 50 10 10 41 5 29 26 34 250 c 0 0 0 254 153 53 635 626 67 32 26 570 550 155 g 0 0 0 149 124 518 27 40 57 637 608 73 42 113 t 0 0 0 123 145 70 19 15 526 17 28 22 65 173
dyads_m5_rc_shift3 (dyads_m5_rc)				; dyads_m4 versus dyads_m5_rc; m=4/5; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.825588; ---cwGCCTGGGyw ; cor=; Ncor= a 0 0 0 294 443 90 49 45 65 37 61 59 276 338 c 0 0 0 368 191 60 1042 1101 40 38 20 108 372 257 g 0 0 0 286 268 970 82 30 42 1087 1060 1011 249 297 t 0 0 0 268 314 96 43 40 1069 54 75 38 319 324
oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)				; dyads_m4 versus oligos_7nt_mkv4_m2_rc; m=5/5; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.408711; cwCCAGCCTsr--- ; cor=; Ncor= a 248 298 48 12 837 31 39 43 55 176 297 0 0 0 c 324 218 960 1007 54 26 929 989 69 305 197 0 0 0 g 253 167 16 6 23 939 33 9 15 355 324 0 0 0 t 236 378 37 36 147 65 60 20 922 225 243 0 0 0

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; vagCCTGGChh ; Alignment reference a 255 358 125 20 18 108 21 38 26 242 262 c 251 198 81 895 893 85 29 32 884 272 241 g 258 170 637 11 35 59 894 851 32 128 204 t 196 234 117 34 14 708 16 39 18 318 253
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; vagCCTGGChh ; cor=; Ncor= a 255 358 125 20 18 108 21 38 26 242 262 c 251 198 81 895 893 85 29 32 884 272 241 g 258 170 637 11 35 59 894 851 32 128 204 t 196 234 117 34 14 708 16 39 18 318 253
dyads_m4_shift0 (dyads_m4)				; oligos_6nt_mkv3_m2 versus dyads_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.995191; saGCCTGGCyw ; cor=; Ncor= a 268 402 67 24 34 146 21 52 56 258 292 c 315 200 71 1013 1006 67 26 32 947 332 263 g 275 244 862 24 32 65 1026 975 63 125 265 t 241 253 99 38 27 821 26 40 33 384 279
oligos_7nt_mkv4_m7_shift0 (oligos_7nt_mkv4_m7)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m7; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.865174; caGCCTGGCCw ; cor=; Ncor= a 165 269 50 10 10 41 5 29 26 34 250 c 254 153 53 635 626 67 32 26 570 550 155 g 149 124 518 27 40 57 637 608 73 42 113 t 123 145 70 19 15 526 17 28 22 65 173
dyads_m5_rc_shift0 (dyads_m5_rc)				; oligos_6nt_mkv3_m2 versus dyads_m5_rc; m=4/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.801627; cwGCCTGGGyw ; cor=; Ncor= a 294 443 90 49 45 65 37 61 59 276 338 c 368 191 60 1042 1101 40 38 20 108 372 257 g 286 268 970 82 30 42 1087 1060 1011 249 297 t 268 314 96 43 40 1069 54 75 38 319 324

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m6_shift7 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=7; ncol=17; -------waTACATAwa ; Alignment reference a 0 0 0 0 0 0 0 117 185 6 400 3 379 5 399 102 194 c 0 0 0 0 0 0 0 75 58 2 1 349 2 10 4 95 48 g 0 0 0 0 0 0 0 51 77 5 3 2 24 6 0 54 73 t 0 0 0 0 0 0 0 165 88 395 4 54 3 387 5 157 93
oligos_6nt_mkv3_m6_shift7 (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=7; score= 1; -------waTACATAwa ; cor=; Ncor= a 0 0 0 0 0 0 0 117 185 6 400 3 379 5 399 102 194 c 0 0 0 0 0 0 0 75 58 2 1 349 2 10 4 95 48 g 0 0 0 0 0 0 0 51 77 5 3 2 24 6 0 54 73 t 0 0 0 0 0 0 0 165 88 395 4 54 3 387 5 157 93
dyads_m1_rc_shift1 (dyads_m1_rc)				; oligos_6nt_mkv3_m6 versus dyads_m1_rc; m=2/3; ncol2=16; w=-6; offset=-6; strand=R; shift=1; score=0.452458; -wwtTAAAATAAATAww ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 152 199 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 61 55 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 74 59 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58 146 120
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m6 versus dyads_m3; m=3/3; ncol2=17; w=-7; offset=-7; strand=D; shift=0; score=0.440482; wwtTAAAAATAaAwAww ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 227 255 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 60 66 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 53 59 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53 170 130

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift0 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; wwtTAAAAATAaAwAww ; Alignment reference a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 227 255 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 60 66 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 53 59 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53 170 130
dyads_m3_shift0 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/10; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; wwtTAAAAATAaAwAww ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 134 413 227 255 c 66 52 65 21 26 17 8 15 8 20 8 77 23 32 22 60 66 g 55 57 25 18 14 13 12 6 16 13 15 25 23 27 22 53 59 t 193 190 315 396 60 57 24 43 31 438 29 108 64 317 53 170 130
dyads_m1_rc_shift1 (dyads_m1_rc)				; dyads_m3 versus dyads_m1_rc; m=2/10; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.835959; -wwtTAAAATAAATAww ; cor=; Ncor= a 0 175 179 108 40 366 382 380 390 49 398 304 338 94 342 152 199 c 0 53 54 25 12 19 20 16 13 18 7 33 26 16 14 61 55 g 0 60 33 23 11 14 8 4 12 15 8 13 26 25 19 74 59 t 0 145 167 277 370 34 23 33 18 351 20 83 43 298 58 146 120
dyads_m8_shift0 (dyads_m8)				; dyads_m3 versus dyads_m8; m=3/10; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.810782; wwTTAAAAAgAAAwAaw ; cor=; Ncor= a 85 93 47 18 201 190 198 195 201 48 167 166 194 67 172 150 59 c 30 25 11 5 7 5 1 8 3 14 12 16 5 9 10 15 20 g 23 25 7 5 2 3 14 6 4 119 10 6 10 9 14 20 22 t 83 78 156 193 11 23 8 12 13 40 32 33 12 136 25 36 120
oligos_6nt_mkv3_m8_shift5 (oligos_6nt_mkv3_m8)				; dyads_m3 versus oligos_6nt_mkv3_m8; m=4/10; ncol2=10; w=0; offset=5; strand=D; shift=5; score=0.501902; -----waAATAAAww-- ; cor=; Ncor= a 0 0 0 0 0 319 398 842 849 0 850 840 839 360 328 0 0 c 0 0 0 0 0 133 157 1 2 0 1 8 11 124 125 0 0 g 0 0 0 0 0 146 143 4 0 0 1 0 0 137 156 0 0 t 0 0 0 0 0 254 154 5 1 852 0 4 2 231 243 0 0
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; dyads_m3 versus oligos_6nt_mkv3_m3; m=5/10; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.487234; ----awAAACAAAwa-- ; cor=; Ncor= a 0 0 0 0 241 206 491 476 514 7 487 480 473 182 248 0 0 c 0 0 0 0 87 92 2 3 0 484 2 4 13 95 74 0 0 g 0 0 0 0 82 62 8 0 2 7 18 0 6 58 91 0 0 t 0 0 0 0 109 159 18 40 3 21 12 35 27 184 106 0 0
oligos_6nt_mkv3_m7_shift4 (oligos_6nt_mkv3_m7)				; dyads_m3 versus oligos_6nt_mkv3_m7; m=6/10; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.474527; ----awAAAGAAAwa-- ; cor=; Ncor= a 0 0 0 0 257 209 537 526 528 7 546 529 555 211 239 0 0 c 0 0 0 0 83 75 3 2 26 2 2 3 4 73 74 0 0 g 0 0 0 0 110 123 3 4 4 536 2 2 2 90 119 0 0 t 0 0 0 0 116 159 23 34 8 21 16 32 5 192 134 0 0
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; dyads_m3 versus oligos_7nt_mkv4_m1; m=7/10; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.466196; --wwAAAATTAkm---- ; cor=; Ncor= a 0 0 173 222 462 442 432 481 7 5 482 121 163 0 0 0 0 c 0 0 110 54 4 5 2 5 2 6 3 73 138 0 0 0 0 g 0 0 57 71 5 2 2 1 3 0 0 133 68 0 0 0 0 t 0 0 149 142 18 40 53 2 477 478 4 162 120 0 0 0 0
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; dyads_m3 versus oligos_7nt_mkv4_m3; m=8/10; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.455372; ---wwAAAACAAwa--- ; cor=; Ncor= a 0 0 0 177 170 446 413 423 453 7 424 443 194 200 0 0 0 c 0 0 0 92 84 2 7 3 2 446 5 2 76 90 0 0 0 g 0 0 0 56 72 3 9 5 2 2 18 1 62 65 0 0 0 t 0 0 0 135 134 9 31 29 3 5 13 14 128 105 0 0 0
oligos_6nt_mkv3_m6_shift7 (oligos_6nt_mkv3_m6)				; dyads_m3 versus oligos_6nt_mkv3_m6; m=9/10; ncol2=10; w=0; offset=7; strand=D; shift=7; score=0.440482; -------waTACATAwa ; cor=; Ncor= a 0 0 0 0 0 0 0 117 185 6 400 3 379 5 399 102 194 c 0 0 0 0 0 0 0 75 58 2 1 349 2 10 4 95 48 g 0 0 0 0 0 0 0 51 77 5 3 2 24 6 0 54 73 t 0 0 0 0 0 0 0 165 88 395 4 54 3 387 5 157 93
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)				; dyads_m3 versus oligos_6nt_mkv3_m4; m=10/10; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.412785; ---waAAATTAwh---- ; cor=; Ncor= a 0 0 0 289 323 642 644 648 1 3 649 204 192 0 0 0 0 c 0 0 0 67 92 0 4 0 0 1 0 112 175 0 0 0 0 g 0 0 0 117 106 3 0 0 0 0 0 161 110 0 0 0 0 t 0 0 0 176 128 4 1 1 648 645 0 172 172 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --wwAAAATTAkm ; Alignment reference a 0 0 173 222 462 442 432 481 7 5 482 121 163 c 0 0 110 54 4 5 2 5 2 6 3 73 138 g 0 0 57 71 5 2 2 1 3 0 0 133 68 t 0 0 149 142 18 40 53 2 477 478 4 162 120
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wwAAAATTAkm ; cor=; Ncor= a 0 0 173 222 462 442 432 481 7 5 482 121 163 c 0 0 110 54 4 5 2 5 2 6 3 73 138 g 0 0 57 71 5 2 2 1 3 0 0 133 68 t 0 0 149 142 18 40 53 2 477 478 4 162 120
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.878001; ---waAAATTAwh ; cor=; Ncor= a 0 0 0 289 323 642 644 648 1 3 649 204 192 c 0 0 0 67 92 0 4 0 0 1 0 112 175 g 0 0 0 117 106 3 0 0 0 0 0 161 110 t 0 0 0 176 128 4 1 1 648 645 0 172 172
dyads_m3_shift0 (dyads_m3)				; oligos_7nt_mkv4_m1 versus dyads_m3; m=3/3; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.466196; wwtTAAAAATAaA ; cor=; Ncor= a 196 211 105 75 410 423 466 446 455 39 458 300 400 c 66 52 65 21 26 17 8 15 8 20 8 77 23 g 55 57 25 18 14 13 12 6 16 13 15 25 23 t 193 190 315 396 60 57 24 43 31 438 29 108 64

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; oligos_7nt_mkv4_m10; m=0 (reference); ncol1=11; shift=1; ncol=12; -rwAAAGGAAwr ; Alignment reference a 0 124 131 360 335 349 5 8 362 363 125 133 c 0 59 70 1 9 14 18 2 1 3 48 60 g 0 104 72 8 3 1 353 354 3 1 82 97 t 0 94 108 12 34 17 5 17 15 14 126 91
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m10; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -rwAAAGGAAwr ; cor=; Ncor= a 0 124 131 360 335 349 5 8 362 363 125 133 c 0 59 70 1 9 14 18 2 1 3 48 60 g 0 104 72 8 3 1 353 354 3 1 82 97 t 0 94 108 12 34 17 5 17 15 14 126 91
oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)				; oligos_7nt_mkv4_m10 versus oligos_6nt_mkv3_m7; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.803425; -awAAAGAAAwa ; cor=; Ncor= a 0 257 209 537 526 528 7 546 529 555 211 239 c 0 83 75 3 2 26 2 2 3 4 73 74 g 0 110 123 3 4 4 536 2 2 2 90 119 t 0 116 159 23 34 8 21 16 32 5 192 134
oligos_7nt_mkv4_m9_shift0 (oligos_7nt_mkv4_m9)				; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m9; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.684567; wwGAAAAGAAww ; cor=; Ncor= a 339 357 51 765 748 742 739 28 743 725 350 340 c 110 42 18 21 23 31 9 31 22 38 110 128 g 160 183 721 30 42 35 39 717 37 36 156 137 t 225 252 44 18 21 26 47 58 32 35 218 229

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m9_shift1 (dyads_m9)				; dyads_m9; m=0 (reference); ncol1=23; shift=1; ncol=24; -cygCCCcCCTCcsCCtCCCtcms ; Alignment reference a 0 23 10 14 9 9 7 15 7 8 12 7 21 5 6 3 12 4 3 3 30 33 45 15 c 0 78 66 28 111 99 118 89 113 117 14 118 87 90 108 118 25 115 123 121 29 87 43 64 g 0 22 29 81 10 12 5 28 13 9 18 12 24 42 6 8 16 16 11 11 26 12 21 44 t 0 21 39 21 14 24 14 12 11 10 100 7 12 7 24 15 91 9 7 9 59 12 35 21
dyads_m9_shift1 (dyads_m9)				; dyads_m9 versus dyads_m9; m=1/3; ncol2=23; w=0; offset=0; strand=D; shift=1; score= 1; -cygCCCcCCTCcsCCtCCCtcms ; cor=; Ncor= a 0 23 10 14 9 9 7 15 7 8 12 7 21 5 6 3 12 4 3 3 30 33 45 15 c 0 78 66 28 111 99 118 89 113 117 14 118 87 90 108 118 25 115 123 121 29 87 43 64 g 0 22 29 81 10 12 5 28 13 9 18 12 24 42 6 8 16 16 11 11 26 12 21 44 t 0 21 39 21 14 24 14 12 11 10 100 7 12 7 24 15 91 9 7 9 59 12 35 21
dyads_m2_shift0 (dyads_m2)				; dyads_m9 versus dyads_m2; m=2/3; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.701505; ccCCtCCCCcccCCCmgCCCyCcs ; cor=; Ncor= a 25 20 11 18 15 5 16 21 14 11 15 17 7 11 7 78 10 7 7 11 15 17 24 23 c 92 92 142 131 47 139 130 134 135 120 112 117 152 148 156 53 42 148 147 131 69 129 79 75 g 34 46 21 21 32 16 25 17 18 26 37 24 13 16 15 35 117 25 18 21 36 30 43 57 t 38 31 15 19 95 29 18 17 22 32 25 31 17 14 11 23 20 9 17 26 69 13 43 34
dyads_m7_shift1 (dyads_m7)				; dyads_m9 versus dyads_m7; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.405579; -mwCCCCryCTChm---------- ; cor=; Ncor= a 0 334 322 54 48 61 88 351 205 19 62 19 324 310 0 0 0 0 0 0 0 0 0 0 c 0 304 280 963 925 983 870 227 336 1090 75 1079 340 319 0 0 0 0 0 0 0 0 0 0 g 0 274 247 64 57 44 46 305 220 28 57 33 108 266 0 0 0 0 0 0 0 0 0 0 t 0 240 303 71 122 64 148 269 391 15 958 21 380 257 0 0 0 0 0 0 0 0 0 0

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; --ytCCTCCTCCys ; Alignment reference a 0 0 131 116 7 13 49 11 20 48 28 22 120 114 c 0 0 193 137 509 518 22 495 512 18 477 505 169 171 g 0 0 95 119 21 13 68 23 9 58 38 17 70 143 t 0 0 143 190 25 18 423 33 21 438 19 18 203 134
oligos_8nt_mkv5_m1_shift2 (oligos_8nt_mkv5_m1)				; oligos_8nt_mkv5_m1 versus oligos_8nt_mkv5_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ytCCTCCTCCys ; cor=; Ncor= a 0 0 131 116 7 13 49 11 20 48 28 22 120 114 c 0 0 193 137 509 518 22 495 512 18 477 505 169 171 g 0 0 95 119 21 13 68 23 9 58 38 17 70 143 t 0 0 143 190 25 18 423 33 21 438 19 18 203 134
dyads_m7_shift0 (dyads_m7)				; oligos_8nt_mkv5_m1 versus dyads_m7; m=2/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.560024; mwCCCCryCTChm- ; cor=; Ncor= a 334 322 54 48 61 88 351 205 19 62 19 324 310 0 c 304 280 963 925 983 870 227 336 1090 75 1079 340 319 0 g 274 247 64 57 44 46 305 220 28 57 33 108 266 0 t 240 303 71 122 64 148 269 391 15 958 21 380 257 0
oligos_6nt_mkv3_m5_shift5 (oligos_6nt_mkv3_m5)				; oligos_8nt_mkv5_m1 versus oligos_6nt_mkv3_m5; m=3/3; ncol2=10; w=0; offset=3; strand=D; shift=5; score=0.551962; -----mgCCTCCCr ; cor=; Ncor= a 0 0 0 0 0 240 142 7 13 29 8 8 8 275 c 0 0 0 0 0 290 190 791 791 13 785 772 751 190 g 0 0 0 0 0 143 343 30 24 65 37 45 69 228 t 0 0 0 0 0 172 170 17 17 738 15 20 17 152