One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/04/peak-motifs.2026-01-04.174100_2026-01-04.174100_XQSs9H/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/04/peak-motifs.2026-01-04.174100_2026-01-04.174100_XQSs9H/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----atTTACATAws ; Alignment reference a 0 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 c 0 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 g 0 0 0 0 267 182 29 23 187 29 15 56 43 199 301 t 0 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285

oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----atTTACATAws ; cor=; Ncor= a 0 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 c 0 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 g 0 0 0 0 267 182 29 23 187 29 15 56 43 199 301 t 0 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=2/4; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.540618; aydcATtTGCATaws ; cor=; Ncor= a 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 c 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 g 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 t 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2; m=3/4; ncol2=20; w=-4; offset=-4; strand=D; shift=0; score=0.431971; yyhcATTTGCATaAc ; cor=; Ncor= a 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 c 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 g 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 t 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83

oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m3; m=4/4; ncol2=21; w=-3; offset=-3; strand=D; shift=1; score=0.421007; -yhcaTTTGCATaAc ; cor=; Ncor= a 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 c 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 g 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 t 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift1 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=24; shift=1; ncol=25; -ydyaTtTgCATATGcAaAtryayr ; Alignment reference a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 78 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 48 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 63 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73 53

positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -ydyaTtTgCATATGcAaAtryayr ; cor=; Ncor= a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 78 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 48 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 63 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73 53

positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)
; positions_7nt_m2 versus positions_6nt_m1_rc; m=2/11; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.974523; -ydyatwTGCATATGCAwatryayr ; cor=; Ncor= a 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 208 c 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 160 g 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 191 t 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203 155

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; positions_7nt_m2 versus oligos_6nt_mkv3_m1; m=3/11; ncol2=22; w=0; offset=0; strand=D; shift=1; score=0.904976; -yryaTwTGCATATGCAwAtryr-- ; cor=; Ncor= a 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 0 c 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 0 g 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 0 t 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0 0

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; positions_7nt_m2 versus positions_7nt_m5_rc; m=4/11; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.834352; gyrtatgygCATATGCAaATryry- ; cor=; Ncor= a 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 0 c 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 0 g 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 0 t 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87 0

positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_7nt_m2 versus positions_6nt_m3; m=5/11; ncol2=24; w=0; offset=1; strand=D; shift=2; score=0.808804; --rywtaTGCATwTGCATAtgyrya ; cor=; Ncor= a 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 104 c 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 46 g 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 70 t 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78 72

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_7nt_m2 versus positions_6nt_m4; m=6/11; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.763838; rywywyaTgcAwATGCATATgcay- ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 0 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 0 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 0 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258 0

positions_6nt_m2_shift3 (positions_6nt_m2)
; positions_7nt_m2 versus positions_6nt_m2; m=7/11; ncol2=24; w=0; offset=2; strand=D; shift=3; score=0.69061; ---tataTGCATwTGCATAwsaawr ; cor=; Ncor= a 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 c 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 g 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 t 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63

oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)
; positions_7nt_m2 versus oligos_6nt_mkv3_m3; m=8/11; ncol2=21; w=0; offset=0; strand=D; shift=1; score=0.612591; -yhcaTTTGCATaAcAAwgsmm--- ; cor=; Ncor= a 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 0 0 0 c 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 0 0 0 g 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 0 0 0 t 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170 0 0 0

oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)
; positions_7nt_m2 versus oligos_7nt_mkv4_m1; m=9/11; ncol2=16; w=0; offset=7; strand=D; shift=8; score=0.587516; --------tswtATGCAaATghrt- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 0 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 0 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 0 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328 0

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; positions_7nt_m2 versus oligos_7nt_mkv4_m2; m=10/11; ncol2=20; w=-1; offset=-1; strand=D; shift=0; score=0.534886; yyhcATTTGCATaAcAAwrg----- ; cor=; Ncor= a 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 0 0 0 0 0 c 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 0 0 0 0 0 g 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 0 0 0 0 0 t 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99 0 0 0 0 0

oligos_7nt_mkv4_m3_rc_shift2 (oligos_7nt_mkv4_m3_rc)
; positions_7nt_m2 versus oligos_7nt_mkv4_m3_rc; m=11/11; ncol2=12; w=0; offset=1; strand=R; shift=2; score=0.400754; --wcATTwGCATaw----------- ; cor=; Ncor= a 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 0 0 0 0 0 c 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 0 0 0 0 0 g 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 0 0 0 0 0 t 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift8 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift8 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=15; shift=8; ncol=23; --------ttTGCATrACAAwrg ; Alignment reference a 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 c 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 g 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 t 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84

oligos_7nt_mkv4_m4_shift8 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=8; score= 1; --------ttTGCATrACAAwrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 c 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 g 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 t 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84

oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m2; m=2/10; ncol2=20; w=-5; offset=-5; strand=D; shift=3; score=0.710397; ---yyhcATTTGCATaAcAAwrg ; cor=; Ncor= a 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 c 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 g 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 t 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m3; m=3/10; ncol2=21; w=-4; offset=-4; strand=D; shift=4; score=0.66298; ----yhcaTTTGCATaAcAAwgs ; cor=; Ncor= a 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 c 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 g 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 t 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; oligos_7nt_mkv4_m4 versus positions_7nt_m4_rc; m=4/10; ncol2=22; w=-7; offset=-7; strand=R; shift=1; score=0.643849; -ryytkcATTTGCATracAAwrg ; cor=; Ncor= a 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 c 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 g 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 t 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; oligos_7nt_mkv4_m4 versus positions_7nt_m1_rc; m=5/10; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.588495; -rmytbcATTTGCATaAcAAwrg ; cor=; Ncor= a 0 180 174 139 109 146 128 453 25 66 84 82 39 645 25 409 489 36 576 583 353 180 146 c 0 138 184 185 162 170 314 67 24 92 17 34 603 4 22 59 20 444 33 22 32 61 132 g 0 202 152 154 136 168 87 61 12 39 8 531 7 3 11 116 11 108 16 39 42 365 307 t 0 139 149 181 252 175 130 78 598 462 550 12 10 7 601 75 139 71 34 15 232 53 74

positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)
; oligos_7nt_mkv4_m4 versus positions_7nt_m3_rc; m=6/10; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.542374; kbywTTgTTaTGCAtAAcAAwrv ; cor=; Ncor= a 35 25 26 51 12 9 22 33 11 111 5 13 4 155 34 138 115 17 131 129 73 43 44 c 35 46 73 30 9 13 27 10 13 14 3 3 147 4 8 5 10 102 14 18 13 26 51 g 43 52 26 12 18 14 101 10 5 8 4 147 3 3 14 13 10 27 13 9 30 72 46 t 54 44 42 74 128 131 17 114 138 34 155 4 13 5 111 11 32 21 9 11 51 26 26

positions_6nt_m2_shift0 (positions_6nt_m2)
; oligos_7nt_mkv4_m4 versus positions_6nt_m2; m=7/10; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.524228; tataTGCATwTGCATAwsaawrk ; cor=; Ncor= a 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 c 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 g 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 t 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89

oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=8/10; ncol2=16; w=-5; offset=-5; strand=R; shift=3; score=0.426856; ---aydcATtTGCATawsa---- ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0

positions_6nt_m5_shift14 (positions_6nt_m5)
; oligos_7nt_mkv4_m4 versus positions_6nt_m5; m=9/10; ncol2=11; w=0; offset=6; strand=D; shift=14; score=0.416607; --------------waACAAAGg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 295 332 1009 3 971 932 943 25 174 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 132 233 7 969 13 43 15 13 158 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 217 220 5 16 14 26 6 950 625 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 387 246 10 43 33 30 67 43 74

oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m3_rc; m=10/10; ncol2=12; w=-3; offset=-3; strand=R; shift=5; score= 0.4033; -----wcATTwGCATaw------ ; cor=; Ncor= a 0 0 0 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 c 0 0 0 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 g 0 0 0 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 t 0 0 0 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift4 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift4 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=22; shift=4; ncol=26; ----cywTTgtyATGCAAATgmarry ; Alignment reference a 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 226 176 c 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 176 241 g 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 231 173 t 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192 201 244

positions_7nt_m4_shift4 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/11; ncol2=22; w=0; offset=0; strand=D; shift=4; score= 1; ----cywTTgtyATGCAAATgmarry ; cor=; Ncor= a 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 226 176 c 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 176 241 g 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 231 173 t 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192 201 244

positions_7nt_m1_shift2 (positions_7nt_m1)
; positions_7nt_m4 versus positions_7nt_m1; m=2/11; ncol2=24; w=-2; offset=-2; strand=D; shift=2; score=0.887848; --kbcywTTgTtATGCAAATgvarky ; cor=; Ncor= a 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 149 139 c 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 152 202 g 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 184 138 t 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139 174 180

oligos_7nt_mkv4_m2_rc_shift4 (oligos_7nt_mkv4_m2_rc)
; positions_7nt_m4 versus oligos_7nt_mkv4_m2_rc; m=3/11; ncol2=20; w=0; offset=0; strand=R; shift=4; score=0.886146; ----cywTTgTtATGCAAATgdrr-- ; cor=; Ncor= a 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 0 0 c 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 0 0 g 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 0 0 t 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177 0 0

positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)
; positions_7nt_m4 versus positions_6nt_m2_rc; m=4/11; ncol2=24; w=-1; offset=-1; strand=R; shift=3; score=0.790398; ---ymywttswTATGCAwATGCAtat ; cor=; Ncor= a 0 0 0 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 c 0 0 0 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 g 0 0 0 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 t 0 0 0 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107

oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)
; positions_7nt_m4 versus oligos_6nt_mkv3_m3_rc; m=5/11; ncol2=21; w=-2; offset=-2; strand=R; shift=2; score=0.756027; --kkscwTTgTtATGCAAAtgdr--- ; cor=; Ncor= a 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 0 0 c 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 0 0 g 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 0 0 t 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0 0 0

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m4 versus positions_7nt_m3; m=6/11; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.693357; ---kbywTTgTTaTGCAtAAcAAwrv ; cor=; Ncor= a 0 0 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 42 44 c 0 0 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 26 52 g 0 0 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 73 46 t 0 0 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51 26 25

oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)
; positions_7nt_m4 versus oligos_7nt_mkv4_m1; m=7/11; ncol2=16; w=0; offset=4; strand=D; shift=8; score=0.67214; --------tswtATGCAaATghrt-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 0 0 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 0 0 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 0 0 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328 0 0

positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)
; positions_7nt_m4 versus positions_6nt_m3_rc; m=8/11; ncol2=24; w=0; offset=0; strand=R; shift=4; score=0.649787; ----atryrcaTATGCAwATGCAtaw ; cor=; Ncor= a 0 0 0 0 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 186 109 c 0 0 0 0 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 20 61 g 0 0 0 0 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 60 39 t 0 0 0 0 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192 26 83

oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)
; positions_7nt_m4 versus oligos_7nt_mkv4_m4_rc; m=9/11; ncol2=15; w=0; offset=0; strand=R; shift=4; score=0.643849; ----cywTTGTyATGCAaa------- ; cor=; Ncor= a 0 0 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 0 0 0 0 c 0 0 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 0 0 0 0 g 0 0 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 0 0 0 0 t 0 0 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0 0 0 0 0

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_7nt_m4 versus positions_6nt_m4; m=10/11; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.594288; rywywyaTgcAwATGCATATgcay-- ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 0 0 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 0 0 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 0 0 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258 0 0

oligos_7nt_mkv4_m3_shift10 (oligos_7nt_mkv4_m3)
; positions_7nt_m4 versus oligos_7nt_mkv4_m3; m=11/11; ncol2=12; w=0; offset=6; strand=D; shift=10; score=0.486311; ----------wtATGCwAATgw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift8 ; 17 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=16; shift=8; ncol=24; --------tswtATGCAaATghrt ; Alignment reference a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328

oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/16; ncol2=16; w=0; offset=0; strand=D; shift=8; score= 1; --------tswtATGCAaATghrt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328

oligos_7nt_mkv4_m2_rc_shift4 (oligos_7nt_mkv4_m2_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2_rc; m=2/16; ncol2=20; w=-4; offset=-4; strand=R; shift=4; score=0.73538; ----cywTTgTtATGCAAATgdrr ; cor=; Ncor= a 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 c 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 g 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 t 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177

oligos_7nt_mkv4_m3_shift10 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=3/16; ncol2=12; w=0; offset=2; strand=D; shift=10; score=0.678024; ----------wtATGCwAATgw-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 0 0 c 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 0 0 g 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 0 0 t 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210 0 0

positions_7nt_m4_shift4 (positions_7nt_m4)
; oligos_7nt_mkv4_m1 versus positions_7nt_m4; m=4/16; ncol2=22; w=-4; offset=-4; strand=D; shift=4; score=0.67214; ----cywTTgtyATGCAAATgmar ; cor=; Ncor= a 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 c 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 g 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 t 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192

oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m3_rc; m=5/16; ncol2=21; w=-6; offset=-6; strand=R; shift=2; score=0.624737; --kkscwTTgTtATGCAAAtgdr- ; cor=; Ncor= a 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 c 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 g 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 t 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; oligos_7nt_mkv4_m1 versus positions_7nt_m5_rc; m=6/16; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.608165; gyrtatgygCATATGCAaATryry ; cor=; Ncor= a 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 c 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 g 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 t 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87

positions_7nt_m1_shift2 (positions_7nt_m1)
; oligos_7nt_mkv4_m1 versus positions_7nt_m1; m=7/16; ncol2=24; w=-6; offset=-6; strand=D; shift=2; score=0.606349; --kbcywTTgTtATGCAAATgvar ; cor=; Ncor= a 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 c 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 g 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 t 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139

positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)
; oligos_7nt_mkv4_m1 versus positions_6nt_m2_rc; m=8/16; ncol2=24; w=-5; offset=-5; strand=R; shift=3; score=0.59599; ---ymywttswTATGCAwATGCAt ; cor=; Ncor= a 0 0 0 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 c 0 0 0 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 g 0 0 0 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 t 0 0 0 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218

positions_6nt_m4_shift0 (positions_6nt_m4)
; oligos_7nt_mkv4_m1 versus positions_6nt_m4; m=9/16; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.587517; rywywyaTgcAwATGCATATgcay ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258

positions_7nt_m2_shift1 (positions_7nt_m2)
; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=10/16; ncol2=24; w=-7; offset=-7; strand=D; shift=1; score=0.587516; -ydyaTtTgCATATGcAaAtryay ; cor=; Ncor= a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73

positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)
; oligos_7nt_mkv4_m1 versus positions_6nt_m3_rc; m=11/16; ncol2=24; w=-4; offset=-4; strand=R; shift=4; score=0.572169; ----atryrcaTATGCAwATGCAt ; cor=; Ncor= a 0 0 0 0 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 c 0 0 0 0 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 g 0 0 0 0 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 t 0 0 0 0 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=12/16; ncol2=22; w=-7; offset=-7; strand=D; shift=1; score=0.562498; -yryaTwTGCATATGCAwAtryr- ; cor=; Ncor= a 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 c 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 g 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 t 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0

positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)
; oligos_7nt_mkv4_m1 versus positions_6nt_m1_rc; m=13/16; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.558261; -ydyatwTGCATATGCAwatryay ; cor=; Ncor= a 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 c 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 g 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 t 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203

oligos_6nt_mkv3_m4_rc_shift9 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=14/16; ncol2=11; w=0; offset=1; strand=R; shift=9; score=0.540618; ---------swTATGTAAat---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 285 390 75 983 38 66 47 1100 1045 559 257 0 0 0 0 c 0 0 0 0 0 0 0 0 0 301 199 43 56 15 29 187 23 29 182 267 0 0 0 0 g 0 0 0 0 0 0 0 0 0 324 227 47 77 34 1038 41 41 61 227 212 0 0 0 0 t 0 0 0 0 0 0 0 0 0 286 380 1031 80 1109 63 921 32 61 228 460 0 0 0 0

positions_7nt_m3_shift3 (positions_7nt_m3)
; oligos_7nt_mkv4_m1 versus positions_7nt_m3; m=15/16; ncol2=24; w=-5; offset=-5; strand=D; shift=3; score=0.471159; ---kbywTTgTTaTGCAtAAcAAw ; cor=; Ncor= a 0 0 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 c 0 0 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 g 0 0 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 t 0 0 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51

oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=16/16; ncol2=15; w=-4; offset=-4; strand=R; shift=4; score=0.426856; ----cywTTGTyATGCAaa----- ; cor=; Ncor= a 0 0 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 0 0 c 0 0 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 0 0 g 0 0 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 0 0 t 0 0 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift3 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift3 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=24; shift=3; ncol=27; ---ryryATtTGCATATGcrcatayrc ; Alignment reference a 0 0 0 87 51 104 26 223 16 69 9 28 21 282 12 268 18 24 45 124 51 212 36 190 52 85 55 c 0 0 0 56 98 54 174 31 40 26 45 7 264 7 23 8 17 37 191 18 166 19 49 34 79 78 124 g 0 0 0 110 49 83 26 34 11 64 14 261 14 15 8 29 7 225 19 152 30 50 36 67 43 105 60 t 0 0 0 62 117 74 89 27 248 156 247 19 16 11 272 10 273 29 60 21 68 34 194 24 141 47 76

positions_7nt_m5_shift3 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---ryryATtTGCATATGcrcatayrc ; cor=; Ncor= a 0 0 0 87 51 104 26 223 16 69 9 28 21 282 12 268 18 24 45 124 51 212 36 190 52 85 55 c 0 0 0 56 98 54 174 31 40 26 45 7 264 7 23 8 17 37 191 18 166 19 49 34 79 78 124 g 0 0 0 110 49 83 26 34 11 64 14 261 14 15 8 29 7 225 19 152 30 50 36 67 43 105 60 t 0 0 0 62 117 74 89 27 248 156 247 19 16 11 272 10 273 29 60 21 68 34 194 24 141 47 76

oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; positions_7nt_m5 versus oligos_6nt_mkv3_m1; m=2/9; ncol2=22; w=0; offset=1; strand=D; shift=4; score=0.837737; ----yryaTwTGCATATGCAwAtryr- ; cor=; Ncor= a 0 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 c 0 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 g 0 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 t 0 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_7nt_m5 versus positions_7nt_m2_rc; m=3/9; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.834352; --yrtryaTtTgCATATGcAaAtrhr- ; cor=; Ncor= a 0 0 53 73 37 65 19 153 12 59 7 30 10 215 14 206 13 15 47 207 136 185 29 66 62 85 0 c 0 0 63 58 58 31 129 43 38 16 20 5 202 2 18 7 7 11 163 4 31 9 19 29 72 47 0 g 0 0 48 77 44 91 31 20 6 33 3 160 12 10 6 18 4 200 5 21 20 38 39 126 38 70 0 t 0 0 78 34 103 55 63 26 186 134 212 47 18 15 204 11 218 16 27 10 55 10 155 21 70 40 0

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_7nt_m5 versus positions_6nt_m1; m=4/9; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.828727; --yrtryatwTGCATATGCAwatrhr- ; cor=; Ncor= a 0 0 155 203 127 185 94 316 70 228 27 68 53 646 43 603 40 43 123 606 299 437 135 238 189 218 0 c 0 0 191 167 166 128 274 151 172 74 57 19 579 8 45 20 21 35 509 14 119 35 115 127 183 168 0 g 0 0 160 200 144 228 124 114 36 113 13 505 41 21 22 44 10 586 18 58 69 172 153 244 144 188 0 t 0 0 208 144 277 173 222 133 436 299 617 122 41 39 604 47 643 50 64 36 227 70 311 105 198 140 0

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; positions_7nt_m5 versus positions_6nt_m4_rc; m=5/9; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.812705; ---rtgcATATGCATwTgcAtrwrwry ; cor=; Ncor= a 0 0 0 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 232 205 242 163 c 0 0 0 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 168 183 160 208 g 0 0 0 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 209 158 208 165 t 0 0 0 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193 145 208 144 218

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; positions_7nt_m5 versus positions_6nt_m3_rc; m=6/9; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.71384; -atryrcaTATGCAwATGCAtawry-- ; cor=; Ncor= a 0 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 186 109 101 63 0 0 c 0 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 20 61 51 77 0 0 g 0 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 60 39 81 61 0 0 t 0 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192 26 83 59 91 0 0

oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)
; positions_7nt_m5 versus oligos_7nt_mkv4_m1_rc; m=7/9; ncol2=16; w=0; offset=0; strand=R; shift=3; score=0.608165; ---aydcATtTGCATawsa-------- ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0 0 0 0 0

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m5 versus positions_6nt_m2_rc; m=8/9; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.596399; ymywttswTATGCAwATGCAtata--- ; cor=; Ncor= a 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 108 0 0 0 c 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 79 0 0 0 g 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 81 0 0 0 t 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107 73 0 0 0

oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)
; positions_7nt_m5 versus oligos_7nt_mkv4_m3_rc; m=9/9; ncol2=12; w=0; offset=2; strand=R; shift=5; score=0.408597; -----wcATTwGCATaw---------- ; cor=; Ncor= a 0 0 0 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift3 ; 13 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=20; shift=3; ncol=23; ---yyhcATTTGCATaAcAAwrg ; Alignment reference a 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 c 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 g 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 t 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99

oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/12; ncol2=20; w=0; offset=0; strand=D; shift=3; score= 1; ---yyhcATTTGCATaAcAAwrg ; cor=; Ncor= a 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 c 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 g 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 t 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; oligos_7nt_mkv4_m2 versus positions_7nt_m4_rc; m=2/12; ncol2=22; w=-2; offset=-2; strand=R; shift=1; score=0.886146; -ryytkcATTTGCATracAAwrg ; cor=; Ncor= a 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 c 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 g 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 t 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3; m=3/12; ncol2=21; w=0; offset=1; strand=D; shift=4; score=0.853034; ----yhcaTTTGCATaAcAAwgs ; cor=; Ncor= a 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 c 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 g 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 t 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; oligos_7nt_mkv4_m2 versus positions_7nt_m1_rc; m=4/12; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.82711; -rmytbcATTTGCATaAcAAwrg ; cor=; Ncor= a 0 180 174 139 109 146 128 453 25 66 84 82 39 645 25 409 489 36 576 583 353 180 146 c 0 138 184 185 162 170 314 67 24 92 17 34 603 4 22 59 20 444 33 22 32 61 132 g 0 202 152 154 136 168 87 61 12 39 8 531 7 3 11 116 11 108 16 39 42 365 307 t 0 139 149 181 252 175 130 78 598 462 550 12 10 7 601 75 139 71 34 15 232 53 74

oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1_rc; m=5/12; ncol2=16; w=0; offset=0; strand=R; shift=3; score=0.73538; ---aydcATtTGCATawsa---- ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0

oligos_7nt_mkv4_m4_shift8 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m4; m=6/12; ncol2=15; w=0; offset=5; strand=D; shift=8; score=0.710397; --------ttTGCATrACAAwrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 c 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 g 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 t 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84

positions_6nt_m2_shift0 (positions_6nt_m2)
; oligos_7nt_mkv4_m2 versus positions_6nt_m2; m=7/12; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.696222; tataTGCATwTGCATAwsaawrk ; cor=; Ncor= a 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 c 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 g 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 t 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89

positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)
; oligos_7nt_mkv4_m2 versus positions_7nt_m3_rc; m=8/12; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.66181; kbywTTgTTaTGCAtAAcAAwrv ; cor=; Ncor= a 35 25 26 51 12 9 22 33 11 111 5 13 4 155 34 138 115 17 131 129 73 43 44 c 35 46 73 30 9 13 27 10 13 14 3 3 147 4 8 5 10 102 14 18 13 26 51 g 43 52 26 12 18 14 101 10 5 8 4 147 3 3 14 13 10 27 13 9 30 72 46 t 54 44 42 74 128 131 17 114 138 34 155 4 13 5 111 11 32 21 9 11 51 26 26

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; oligos_7nt_mkv4_m2 versus positions_6nt_m4_rc; m=9/12; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.617762; ---rtgcATATGCATwTgcAtrw ; cor=; Ncor= a 0 0 0 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 c 0 0 0 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 g 0 0 0 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 t 0 0 0 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193

oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3_rc; m=10/12; ncol2=12; w=0; offset=2; strand=R; shift=5; score=0.538597; -----wcATTwGCATaw------ ; cor=; Ncor= a 0 0 0 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 c 0 0 0 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 g 0 0 0 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 t 0 0 0 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0

positions_7nt_m2_shift4 (positions_7nt_m2)
; oligos_7nt_mkv4_m2 versus positions_7nt_m2; m=11/12; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.534886; ----ydyaTtTgCATATGcAaAt ; cor=; Ncor= a 0 0 0 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 c 0 0 0 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 g 0 0 0 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 t 0 0 0 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153

oligos_6nt_mkv3_m4_shift7 (oligos_6nt_mkv3_m4)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4; m=12/12; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.431971; -------atTTACATAws----- ; cor=; Ncor= a 0 0 0 0 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 0 0 0 0 0 c 0 0 0 0 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 0 0 0 0 0 g 0 0 0 0 0 0 0 267 182 29 23 187 29 15 56 43 199 301 0 0 0 0 0 t 0 0 0 0 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; amaAAACAAAGcma ; Alignment reference a 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 155 126 106 82 26 9 29 11 16 28 39 84 128 141

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; amaAAACAAAGcma ; cor=; Ncor= a 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 155 126 106 82 26 9 29 11 16 28 39 84 128 141

positions_6nt_m5_shift3 (positions_6nt_m5)
; oligos_6nt_mkv3_m5 versus positions_6nt_m5; m=2/2; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.672958; ---waACAAAGgam ; cor=; Ncor= a 0 0 0 295 332 1009 3 971 932 943 25 174 304 327 c 0 0 0 132 233 7 969 13 43 15 13 158 252 272 g 0 0 0 217 220 5 16 14 26 6 950 625 230 221 t 0 0 0 387 246 10 43 33 30 67 43 74 245 211

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift2 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=24; shift=2; ncol=26; --rywtaTGCATwTGCATAtgyryat ; Alignment reference a 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 104 57 c 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 46 64 g 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 70 58 t 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78 72 113

positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --rywtaTGCATwTGCATAtgyryat ; cor=; Ncor= a 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 104 57 c 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 46 64 g 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 70 58 t 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78 72 113

positions_6nt_m2_shift3 (positions_6nt_m2)
; positions_6nt_m3 versus positions_6nt_m2; m=2/9; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.862118; ---tataTGCATwTGCATAwsaawrk ; cor=; Ncor= a 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 c 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 g 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 t 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89

positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)
; positions_6nt_m3 versus positions_6nt_m1_rc; m=3/9; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.840163; -ydyatwTGCATATGCAwatryayr- ; cor=; Ncor= a 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 208 0 c 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 160 0 g 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 191 0 t 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203 155 0

positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_6nt_m3 versus positions_7nt_m2; m=4/9; ncol2=24; w=-1; offset=-1; strand=D; shift=1; score=0.808804; -ydyaTtTgCATATGcAaAtryayr- ; cor=; Ncor= a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 78 0 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 48 0 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 63 0 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73 53 0

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=5/9; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.787578; rywywyaTgcAwATGCATATgcay-- ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 0 0 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 0 0 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 0 0 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258 0 0

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; positions_6nt_m3 versus oligos_6nt_mkv3_m1; m=6/9; ncol2=22; w=-1; offset=-1; strand=D; shift=1; score=0.74558; -yryaTwTGCATATGCAwAtryr--- ; cor=; Ncor= a 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 0 0 c 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 0 0 g 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 0 0 t 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0 0 0

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; positions_6nt_m3 versus positions_7nt_m5_rc; m=7/9; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.71384; gyrtatgygCATATGCAaATryry-- ; cor=; Ncor= a 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 0 0 c 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 0 0 g 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 0 0 t 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87 0 0

positions_7nt_m4_rc_shift4 (positions_7nt_m4_rc)
; positions_6nt_m3 versus positions_7nt_m4_rc; m=8/9; ncol2=22; w=0; offset=2; strand=R; shift=4; score=0.649787; ----ryytkcATTTGCATracAAwrg ; cor=; Ncor= a 0 0 0 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 c 0 0 0 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 g 0 0 0 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 t 0 0 0 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130

oligos_7nt_mkv4_m1_rc_shift6 (oligos_7nt_mkv4_m1_rc)
; positions_6nt_m3 versus oligos_7nt_mkv4_m1_rc; m=9/9; ncol2=16; w=0; offset=4; strand=R; shift=6; score=0.572169; ------aydcATtTGCATawsa---- ; cor=; Ncor= a 0 0 0 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 c 0 0 0 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 g 0 0 0 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 t 0 0 0 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=24; shift=2; ncol=26; --yrtryatwTGCATATGCAwatrhr ; Alignment reference a 0 0 155 203 127 185 94 316 70 228 27 68 53 646 43 603 40 43 123 606 299 437 135 238 189 218 c 0 0 191 167 166 128 274 151 172 74 57 19 579 8 45 20 21 35 509 14 119 35 115 127 183 168 g 0 0 160 200 144 228 124 114 36 113 13 505 41 21 22 44 10 586 18 58 69 172 153 244 144 188 t 0 0 208 144 277 173 222 133 436 299 617 122 41 39 604 47 643 50 64 36 227 70 311 105 198 140

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --yrtryatwTGCATATGCAwatrhr ; cor=; Ncor= a 0 0 155 203 127 185 94 316 70 228 27 68 53 646 43 603 40 43 123 606 299 437 135 238 189 218 c 0 0 191 167 166 128 274 151 172 74 57 19 579 8 45 20 21 35 509 14 119 35 115 127 183 168 g 0 0 160 200 144 228 124 114 36 113 13 505 41 21 22 44 10 586 18 58 69 172 153 244 144 188 t 0 0 208 144 277 173 222 133 436 299 617 122 41 39 604 47 643 50 64 36 227 70 311 105 198 140

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_6nt_m1 versus positions_7nt_m2_rc; m=2/8; ncol2=24; w=0; offset=0; strand=R; shift=2; score=0.974523; --yrtryaTtTgCATATGcAaAtrhr ; cor=; Ncor= a 0 0 53 73 37 65 19 153 12 59 7 30 10 215 14 206 13 15 47 207 136 185 29 66 62 85 c 0 0 63 58 58 31 129 43 38 16 20 5 202 2 18 7 7 11 163 4 31 9 19 29 72 47 g 0 0 48 77 44 91 31 20 6 33 3 160 12 10 6 18 4 200 5 21 20 38 39 126 38 70 t 0 0 78 34 103 55 63 26 186 134 212 47 18 15 204 11 218 16 27 10 55 10 155 21 70 40

oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; positions_6nt_m1 versus oligos_6nt_mkv3_m1; m=3/8; ncol2=22; w=0; offset=2; strand=D; shift=4; score=0.908114; ----yryaTwTGCATATGCAwAtryr ; cor=; Ncor= a 0 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 0 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 0 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 0 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; positions_6nt_m1 versus positions_6nt_m3_rc; m=4/8; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.840163; -atryrcaTATGCAwATGCAtawry- ; cor=; Ncor= a 0 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 186 109 101 63 0 c 0 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 20 61 51 77 0 g 0 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 60 39 81 61 0 t 0 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192 26 83 59 91 0

positions_7nt_m5_shift3 (positions_7nt_m5)
; positions_6nt_m1 versus positions_7nt_m5; m=5/8; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.828727; ---ryryATtTGCATATGcrcatayr ; cor=; Ncor= a 0 0 0 87 51 104 26 223 16 69 9 28 21 282 12 268 18 24 45 124 51 212 36 190 52 85 c 0 0 0 56 98 54 174 31 40 26 45 7 264 7 23 8 17 37 191 18 166 19 49 34 79 78 g 0 0 0 110 49 83 26 34 11 64 14 261 14 15 8 29 7 225 19 152 30 50 36 67 43 105 t 0 0 0 62 117 74 89 27 248 156 247 19 16 11 272 10 273 29 60 21 68 34 194 24 141 47

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; positions_6nt_m1 versus positions_6nt_m4_rc; m=6/8; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.794258; ---rtgcATATGCATwTgcAtrwrwr ; cor=; Ncor= a 0 0 0 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 232 205 242 c 0 0 0 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 168 183 160 g 0 0 0 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 209 158 208 t 0 0 0 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193 145 208 144

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_6nt_m1 versus positions_6nt_m2_rc; m=7/8; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.741229; ymywttswTATGCAwATGCAtata-- ; cor=; Ncor= a 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 108 0 0 c 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 79 0 0 g 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 81 0 0 t 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107 73 0 0

oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)
; positions_6nt_m1 versus oligos_7nt_mkv4_m1_rc; m=8/8; ncol2=16; w=0; offset=1; strand=R; shift=3; score=0.558261; ---aydcATtTGCATawsa------- ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0 0 0 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; ccCCCCCaCCCCccc ; Alignment reference a 226 200 93 53 52 38 48 668 45 52 41 64 168 275 216 c 495 461 803 916 950 983 972 201 983 966 954 934 656 428 483 g 182 251 103 68 67 63 56 154 51 56 66 67 155 215 214 t 212 203 116 78 46 31 39 92 36 41 54 50 136 197 202

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ccCCCCCaCCCCccc ; cor=; Ncor= a 226 200 93 53 52 38 48 668 45 52 41 64 168 275 216 c 495 461 803 916 950 983 972 201 983 966 954 934 656 428 483 g 182 251 103 68 67 63 56 154 51 56 66 67 155 215 214 t 212 203 116 78 46 31 39 92 36 41 54 50 136 197 202

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2; m=2/2; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.843935; -ccCCCCACCCCcc- ; cor=; Ncor= a 0 238 226 62 65 35 22 821 29 28 29 113 220 281 0 c 0 512 445 912 984 1089 1100 109 1080 1067 1076 895 515 438 0 g 0 228 269 95 80 43 44 171 55 65 49 94 241 255 0 t 0 217 255 126 66 28 29 94 31 35 41 93 219 221 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift3 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=22; shift=3; ncol=25; ---yryaTwTGCATATGCAwAtryr ; Alignment reference a 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/10; ncol2=22; w=0; offset=0; strand=D; shift=3; score= 1; ---yryaTwTGCATATGCAwAtryr ; cor=; Ncor= a 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=2/10; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.908114; ---ydyatwTGCATATGCAwatrya ; cor=; Ncor= a 0 0 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 c 0 0 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 g 0 0 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 t 0 0 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127

positions_7nt_m2_shift3 (positions_7nt_m2)
; oligos_6nt_mkv3_m1 versus positions_7nt_m2; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.904976; ---ydyaTtTgCATATGcAaAtrya ; cor=; Ncor= a 0 0 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 c 0 0 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 g 0 0 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 t 0 0 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37

positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)
; oligos_6nt_mkv3_m1 versus positions_7nt_m5_rc; m=4/10; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.837737; --gyrtatgygCATATGCAaATryr ; cor=; Ncor= a 0 0 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 c 0 0 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 g 0 0 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 t 0 0 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51

positions_6nt_m4_shift2 (positions_6nt_m4)
; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=5/10; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.763228; --rywywyaTgcAwATGCATATgca ; cor=; Ncor= a 0 0 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 c 0 0 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 g 0 0 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 t 0 0 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; oligos_6nt_mkv3_m1 versus positions_6nt_m3_rc; m=6/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.74558; atryrcaTATGCAwATGCAtawry- ; cor=; Ncor= a 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 186 109 101 63 0 c 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 20 61 51 77 0 g 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 60 39 81 61 0 t 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192 26 83 59 91 0

oligos_6nt_mkv3_m3_rc_shift4 (oligos_6nt_mkv3_m3_rc)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=7/10; ncol2=21; w=0; offset=1; strand=R; shift=4; score=0.670864; ----kkscwTTgTtATGCAAAtgdr ; cor=; Ncor= a 0 0 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 c 0 0 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 g 0 0 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 t 0 0 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141

positions_6nt_m2_shift5 (positions_6nt_m2)
; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=8/10; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.646122; -----tataTGCATwTGCATAwsaa ; cor=; Ncor= a 0 0 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 c 0 0 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 g 0 0 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 t 0 0 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44

oligos_7nt_mkv4_m1_shift10 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=9/10; ncol2=16; w=0; offset=7; strand=D; shift=10; score=0.562498; ----------tswtATGCAaATghr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 c 0 0 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 g 0 0 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 t 0 0 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201

oligos_7nt_mkv4_m3_shift12 (oligos_7nt_mkv4_m3)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m3; m=10/10; ncol2=12; w=0; offset=9; strand=D; shift=12; score=0.424616; ------------wtATGCwAATgw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 0 c 0 0 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 0 g 0 0 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 0 t 0 0 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -ccCCCCACCCCcc ; Alignment reference a 0 238 226 62 65 35 22 821 29 28 29 113 220 281 c 0 512 445 912 984 1089 1100 109 1080 1067 1076 895 515 438 g 0 228 269 95 80 43 44 171 55 65 49 94 241 255 t 0 217 255 126 66 28 29 94 31 35 41 93 219 221

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -ccCCCCACCCCcc ; cor=; Ncor= a 0 238 226 62 65 35 22 821 29 28 29 113 220 281 c 0 512 445 912 984 1089 1100 109 1080 1067 1076 895 515 438 g 0 228 269 95 80 43 44 171 55 65 49 94 241 255 t 0 217 255 126 66 28 29 94 31 35 41 93 219 221

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5; m=2/2; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.843935; ccCCCCCaCCCCcc ; cor=; Ncor= a 226 200 93 53 52 38 48 668 45 52 41 64 168 275 c 495 461 803 916 950 983 972 201 983 966 954 934 656 428 g 182 251 103 68 67 63 56 154 51 56 66 67 155 215 t 212 203 116 78 46 31 39 92 36 41 54 50 136 197

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift4 ; 15 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=21; shift=4; ncol=25; ----yhcaTTTGCATaAcAAwgsmm ; Alignment reference a 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/14; ncol2=21; w=0; offset=0; strand=D; shift=4; score= 1; ----yhcaTTTGCATaAcAAwgsmm ; cor=; Ncor= a 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; oligos_6nt_mkv3_m3 versus positions_7nt_m1_rc; m=2/14; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.87051; -rmytbcATTTGCATaAcAAwrgvm ; cor=; Ncor= a 0 180 174 139 109 146 128 453 25 66 84 82 39 645 25 409 489 36 576 583 353 180 146 219 181 c 0 138 184 185 162 170 314 67 24 92 17 34 603 4 22 59 20 444 33 22 32 61 132 178 187 g 0 202 152 154 136 168 87 61 12 39 8 531 7 3 11 116 11 108 16 39 42 365 307 165 151 t 0 139 149 181 252 175 130 78 598 462 550 12 10 7 601 75 139 71 34 15 232 53 74 97 140

oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2; m=3/14; ncol2=20; w=-1; offset=-1; strand=D; shift=3; score=0.853034; ---yyhcATTTGCATaAcAAwrg-- ; cor=; Ncor= a 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 0 0 c 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 0 0 g 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 0 0 t 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99 0 0

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; oligos_6nt_mkv3_m3 versus positions_7nt_m4_rc; m=4/14; ncol2=22; w=-3; offset=-3; strand=R; shift=1; score=0.756027; -ryytkcATTTGCATracAAwrg-- ; cor=; Ncor= a 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 0 0 c 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 0 0 g 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 0 0 t 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130 0 0

oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=5/14; ncol2=22; w=0; offset=0; strand=D; shift=4; score=0.670864; ----yryaTwTGCATATGCAwAtry ; cor=; Ncor= a 0 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 c 0 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 g 0 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 t 0 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142

oligos_7nt_mkv4_m4_shift8 (oligos_7nt_mkv4_m4)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m4; m=6/14; ncol2=15; w=0; offset=4; strand=D; shift=8; score=0.66298; --------ttTGCATrACAAwrg-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 0 0 c 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 0 0 g 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 0 0 t 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84 0 0

positions_6nt_m2_shift0 (positions_6nt_m2)
; oligos_6nt_mkv3_m3 versus positions_6nt_m2; m=7/14; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.662096; tataTGCATwTGCATAwsaawrkr- ; cor=; Ncor= a 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 112 0 c 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 79 0 g 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 88 0 t 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89 62 0

positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)
; oligos_6nt_mkv3_m3 versus positions_7nt_m3_rc; m=8/14; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.649065; kbywTTgTTaTGCAtAAcAAwrvm- ; cor=; Ncor= a 35 25 26 51 12 9 22 33 11 111 5 13 4 155 34 138 115 17 131 129 73 43 44 54 0 c 35 46 73 30 9 13 27 10 13 14 3 3 147 4 8 5 10 102 14 18 13 26 51 43 0 g 43 52 26 12 18 14 101 10 5 8 4 147 3 3 14 13 10 27 13 9 30 72 46 35 0 t 54 44 42 74 128 131 17 114 138 34 155 4 13 5 111 11 32 21 9 11 51 26 26 35 0

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; oligos_6nt_mkv3_m3 versus positions_6nt_m4_rc; m=9/14; ncol2=24; w=-1; offset=-1; strand=R; shift=3; score=0.628309; ---rtgcATATGCATwTgcAtrwrw ; cor=; Ncor= a 0 0 0 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 232 205 c 0 0 0 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 168 183 g 0 0 0 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 209 158 t 0 0 0 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193 145 208

oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m1_rc; m=10/14; ncol2=16; w=-1; offset=-1; strand=R; shift=3; score=0.624737; ---aydcATtTGCATawsa------ ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0 0 0

positions_7nt_m2_shift4 (positions_7nt_m2)
; oligos_6nt_mkv3_m3 versus positions_7nt_m2; m=11/14; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.612591; ----ydyaTtTgCATATGcAaAtry ; cor=; Ncor= a 0 0 0 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 c 0 0 0 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 g 0 0 0 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 t 0 0 0 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65

oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3_rc; m=12/14; ncol2=12; w=0; offset=1; strand=R; shift=5; score=0.50804; -----wcATTwGCATaw-------- ; cor=; Ncor= a 0 0 0 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 0 0 c 0 0 0 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 0 0 g 0 0 0 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 0 0 t 0 0 0 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0 0 0

positions_6nt_m5_shift14 (positions_6nt_m5)
; oligos_6nt_mkv3_m3 versus positions_6nt_m5; m=13/14; ncol2=11; w=0; offset=10; strand=D; shift=14; score=0.43353; --------------waACAAAGgam ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 295 332 1009 3 971 932 943 25 174 304 327 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 132 233 7 969 13 43 15 13 158 252 272 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 217 220 5 16 14 26 6 950 625 230 221 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 387 246 10 43 33 30 67 43 74 245 211

oligos_6nt_mkv3_m4_shift7 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m4; m=14/14; ncol2=11; w=0; offset=3; strand=D; shift=7; score=0.421007; -------atTTACATAws------- ; cor=; Ncor= a 0 0 0 0 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 267 182 29 23 187 29 15 56 43 199 301 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift3 ; 15 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift3 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=24; shift=3; ncol=27; ---tataTGCATwTGCATAwsaawrkr ; Alignment reference a 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 112 c 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 79 g 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 88 t 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89 62

positions_6nt_m2_shift3 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/14; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---tataTGCATwTGCATAwsaawrkr ; cor=; Ncor= a 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 112 c 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 79 g 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 88 t 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89 62

positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_6nt_m2 versus positions_6nt_m3; m=2/14; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.862118; --rywtaTGCATwTGCATAtgyryat- ; cor=; Ncor= a 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 104 57 0 c 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 46 64 0 g 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 70 58 0 t 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78 72 113 0

positions_7nt_m4_rc_shift4 (positions_7nt_m4_rc)
; positions_6nt_m2 versus positions_7nt_m4_rc; m=3/14; ncol2=22; w=0; offset=1; strand=R; shift=4; score=0.790398; ----ryytkcATTTGCATracAAwrg- ; cor=; Ncor= a 0 0 0 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 0 c 0 0 0 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 0 g 0 0 0 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 0 t 0 0 0 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130 0

positions_7nt_m1_rc_shift4 (positions_7nt_m1_rc)
; positions_6nt_m2 versus positions_7nt_m1_rc; m=4/14; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.750894; ----rmytbcATTTGCATaAcAAwrgv ; cor=; Ncor= a 0 0 0 0 180 174 139 109 146 128 453 25 66 84 82 39 645 25 409 489 36 576 583 353 180 146 219 c 0 0 0 0 138 184 185 162 170 314 67 24 92 17 34 603 4 22 59 20 444 33 22 32 61 132 178 g 0 0 0 0 202 152 154 136 168 87 61 12 39 8 531 7 3 11 116 11 108 16 39 42 365 307 165 t 0 0 0 0 139 149 181 252 175 130 78 598 462 550 12 10 7 601 75 139 71 34 15 232 53 74 97

positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)
; positions_6nt_m2 versus positions_6nt_m1_rc; m=5/14; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.741229; -ydyatwTGCATATGCAwatryayr-- ; cor=; Ncor= a 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 208 0 0 c 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 160 0 0 g 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 191 0 0 t 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203 155 0 0

positions_7nt_m3_rc_shift3 (positions_7nt_m3_rc)
; positions_6nt_m2 versus positions_7nt_m3_rc; m=6/14; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.702386; ---kbywTTgTTaTGCAtAAcAAwrvm ; cor=; Ncor= a 0 0 0 35 25 26 51 12 9 22 33 11 111 5 13 4 155 34 138 115 17 131 129 73 43 44 54 c 0 0 0 35 46 73 30 9 13 27 10 13 14 3 3 147 4 8 5 10 102 14 18 13 26 51 43 g 0 0 0 43 52 26 12 18 14 101 10 5 8 4 147 3 3 14 13 10 27 13 9 30 72 46 35 t 0 0 0 54 44 42 74 128 131 17 114 138 34 155 4 13 5 111 11 32 21 9 11 51 26 26 35

oligos_7nt_mkv4_m2_shift6 (oligos_7nt_mkv4_m2)
; positions_6nt_m2 versus oligos_7nt_mkv4_m2; m=7/14; ncol2=20; w=0; offset=3; strand=D; shift=6; score=0.696222; ------yyhcATTTGCATaAcAAwrg- ; cor=; Ncor= a 0 0 0 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 0 c 0 0 0 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 0 g 0 0 0 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 0 t 0 0 0 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99 0

positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_6nt_m2 versus positions_7nt_m2; m=8/14; ncol2=24; w=-2; offset=-2; strand=D; shift=1; score=0.69061; -ydyaTtTgCATATGcAaAtryayr-- ; cor=; Ncor= a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 78 0 0 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 48 0 0 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 63 0 0 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73 53 0 0

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_6nt_m2 versus positions_6nt_m4_rc; m=9/14; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.680178; rtgcATATGCATwTgcAtrwrwry--- ; cor=; Ncor= a 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 232 205 242 163 0 0 0 c 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 168 183 160 208 0 0 0 g 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 209 158 208 165 0 0 0 t 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193 145 208 144 218 0 0 0

oligos_6nt_mkv3_m3_shift7 (oligos_6nt_mkv3_m3)
; positions_6nt_m2 versus oligos_6nt_mkv3_m3; m=10/14; ncol2=21; w=0; offset=4; strand=D; shift=7; score=0.662096; -------yhcaTTTGCATaAcAAwgsm ; cor=; Ncor= a 0 0 0 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 c 0 0 0 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 g 0 0 0 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 t 0 0 0 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; positions_6nt_m2 versus oligos_6nt_mkv3_m1; m=11/14; ncol2=22; w=-2; offset=-2; strand=D; shift=1; score=0.646122; -yryaTwTGCATATGCAwAtryr---- ; cor=; Ncor= a 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 0 0 0 c 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 0 0 0 g 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 0 0 0 t 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0 0 0 0

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; positions_6nt_m2 versus positions_7nt_m5_rc; m=12/14; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.596399; gyrtatgygCATATGCAaATryry--- ; cor=; Ncor= a 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 0 0 0 c 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 0 0 0 g 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 0 0 0 t 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87 0 0 0

oligos_7nt_mkv4_m1_rc_shift6 (oligos_7nt_mkv4_m1_rc)
; positions_6nt_m2 versus oligos_7nt_mkv4_m1_rc; m=13/14; ncol2=16; w=0; offset=3; strand=R; shift=6; score=0.59599; ------aydcATtTGCATawsa----- ; cor=; Ncor= a 0 0 0 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 0 c 0 0 0 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 0 g 0 0 0 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 0 t 0 0 0 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0 0

oligos_7nt_mkv4_m4_shift11 (oligos_7nt_mkv4_m4)
; positions_6nt_m2 versus oligos_7nt_mkv4_m4; m=14/14; ncol2=15; w=0; offset=8; strand=D; shift=11; score=0.524228; -----------ttTGCATrACAAwrg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 0 c 0 0 0 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 0 g 0 0 0 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 0 t 0 0 0 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift11 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------wtATGCwAATgw ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 c 0 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 g 0 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 t 0 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210

oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/10; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------wtATGCwAATgw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 c 0 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 g 0 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 t 0 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210

oligos_7nt_mkv4_m1_shift9 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=2/10; ncol2=16; w=-2; offset=-2; strand=D; shift=9; score=0.678024; ---------tswtATGCAaATgh ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 c 0 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 g 0 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 t 0 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293

oligos_7nt_mkv4_m2_rc_shift5 (oligos_7nt_mkv4_m2_rc)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2_rc; m=3/10; ncol2=20; w=-6; offset=-6; strand=R; shift=5; score=0.538597; -----cywTTgTtATGCAAATgd ; cor=; Ncor= a 0 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 c 0 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 g 0 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 t 0 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192

oligos_6nt_mkv3_m3_rc_shift3 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3_rc; m=4/10; ncol2=21; w=-8; offset=-8; strand=R; shift=3; score=0.50804; ---kkscwTTgTtATGCAAAtgd ; cor=; Ncor= a 0 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 c 0 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 g 0 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 t 0 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209

positions_7nt_m4_shift5 (positions_7nt_m4)
; oligos_7nt_mkv4_m3 versus positions_7nt_m4; m=5/10; ncol2=22; w=-6; offset=-6; strand=D; shift=5; score=0.486311; -----cywTTgtyATGCAAATgm ; cor=; Ncor= a 0 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 c 0 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 g 0 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 t 0 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163

positions_7nt_m1_shift3 (positions_7nt_m1)
; oligos_7nt_mkv4_m3 versus positions_7nt_m1; m=6/10; ncol2=24; w=-8; offset=-8; strand=D; shift=3; score=0.444909; ---kbcywTTgTtATGCAAATgv ; cor=; Ncor= a 0 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 c 0 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 g 0 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 t 0 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m1; m=7/10; ncol2=22; w=-9; offset=-9; strand=D; shift=2; score=0.424616; --yryaTwTGCATATGCAwAtry ; cor=; Ncor= a 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 c 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 g 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 t 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142

positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)
; oligos_7nt_mkv4_m3 versus positions_7nt_m5_rc; m=8/10; ncol2=24; w=-10; offset=-10; strand=R; shift=1; score=0.408597; -gyrtatgygCATATGCAaATry ; cor=; Ncor= a 0 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 c 0 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 g 0 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 t 0 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104

oligos_7nt_mkv4_m4_rc_shift5 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m4_rc; m=9/10; ncol2=15; w=-6; offset=-6; strand=R; shift=5; score= 0.4033; -----cywTTGTyATGCAaa--- ; cor=; Ncor= a 0 0 0 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 c 0 0 0 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 g 0 0 0 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 t 0 0 0 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0

positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc)
; oligos_7nt_mkv4_m3 versus positions_7nt_m2_rc; m=10/10; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.400754; yrtryaTtTgCATATGcAaAtrh ; cor=; Ncor= a 53 73 37 65 19 153 12 59 7 30 10 215 14 206 13 15 47 207 136 185 29 66 62 c 63 58 58 31 129 43 38 16 20 5 202 2 18 7 7 11 163 4 31 9 19 29 72 g 48 77 44 91 31 20 6 33 3 160 12 10 6 18 4 200 5 21 20 38 39 126 38 t 78 34 103 55 63 26 186 134 212 47 18 15 204 11 218 16 27 10 55 10 155 21 70

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift1 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=24; shift=1; ncol=25; -kbywTTgTTaTGCAtAAcAAwrvm ; Alignment reference a 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 42 44 54 c 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 26 52 43 g 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 73 46 35 t 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51 26 25 35

positions_7nt_m3_shift1 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -kbywTTgTTaTGCAtAAcAAwrvm ; cor=; Ncor= a 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 42 44 54 c 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 26 52 43 g 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 73 46 35 t 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51 26 25 35

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m3 versus positions_7nt_m1; m=2/8; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.735252; kbcywTTgTtATGCAAATgvarky- ; cor=; Ncor= a 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 149 139 0 c 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 152 202 0 g 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 184 138 0 t 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139 174 180 0

positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)
; positions_7nt_m3 versus positions_6nt_m2_rc; m=3/8; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.702386; -ymywttswTATGCAwATGCAtata ; cor=; Ncor= a 0 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 108 c 0 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 79 g 0 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 81 t 0 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107 73

positions_7nt_m4_shift2 (positions_7nt_m4)
; positions_7nt_m3 versus positions_7nt_m4; m=4/8; ncol2=22; w=0; offset=1; strand=D; shift=2; score=0.693357; --cywTTgtyATGCAAATgmarry- ; cor=; Ncor= a 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 226 176 0 c 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 176 241 0 g 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 231 173 0 t 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192 201 244 0

oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)
; positions_7nt_m3 versus oligos_7nt_mkv4_m2_rc; m=5/8; ncol2=20; w=0; offset=1; strand=R; shift=2; score=0.66181; --cywTTgTtATGCAAATgdrr--- ; cor=; Ncor= a 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 0 0 0 c 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 0 0 0 g 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 0 0 0 t 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177 0 0 0

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; positions_7nt_m3 versus oligos_6nt_mkv3_m3_rc; m=6/8; ncol2=21; w=-1; offset=-1; strand=R; shift=0; score=0.649065; kkscwTTgTtATGCAAAtgdr---- ; cor=; Ncor= a 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 0 0 0 c 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 0 0 0 g 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 0 0 0 t 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0 0 0 0

oligos_7nt_mkv4_m4_rc_shift2 (oligos_7nt_mkv4_m4_rc)
; positions_7nt_m3 versus oligos_7nt_mkv4_m4_rc; m=7/8; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.542374; --cywTTGTyATGCAaa-------- ; cor=; Ncor= a 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 0 0 0 0 0 c 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 0 0 0 0 0 g 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 0 0 0 0 0 t 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0 0 0 0 0 0

oligos_7nt_mkv4_m1_shift6 (oligos_7nt_mkv4_m1)
; positions_7nt_m3 versus oligos_7nt_mkv4_m1; m=8/8; ncol2=16; w=0; offset=5; strand=D; shift=6; score=0.471159; ------tswtATGCAaATghrt--- ; cor=; Ncor= a 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 0 0 0 c 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 0 0 0 g 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 0 0 0 t 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift2 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift2 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=24; shift=2; ncol=26; --kbcywTTgTtATGCAAATgvarky ; Alignment reference a 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 149 139 c 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 152 202 g 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 184 138 t 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139 174 180

positions_7nt_m1_shift2 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --kbcywTTgTtATGCAAATgvarky ; cor=; Ncor= a 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 149 139 c 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 152 202 g 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 184 138 t 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139 174 180

positions_7nt_m4_shift4 (positions_7nt_m4)
; positions_7nt_m1 versus positions_7nt_m4; m=2/10; ncol2=22; w=0; offset=2; strand=D; shift=4; score=0.887848; ----cywTTgtyATGCAAATgmarry ; cor=; Ncor= a 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 226 176 c 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 176 241 g 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 231 173 t 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192 201 244

oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)
; positions_7nt_m1 versus oligos_6nt_mkv3_m3_rc; m=3/10; ncol2=21; w=0; offset=0; strand=R; shift=2; score=0.87051; --kkscwTTgTtATGCAAAtgdr--- ; cor=; Ncor= a 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 0 0 c 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 0 0 g 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 0 0 t 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0 0 0

oligos_7nt_mkv4_m2_rc_shift4 (oligos_7nt_mkv4_m2_rc)
; positions_7nt_m1 versus oligos_7nt_mkv4_m2_rc; m=4/10; ncol2=20; w=0; offset=2; strand=R; shift=4; score=0.82711; ----cywTTgTtATGCAAATgdrr-- ; cor=; Ncor= a 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 0 0 c 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 0 0 g 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 0 0 t 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177 0 0

positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)
; positions_7nt_m1 versus positions_6nt_m2_rc; m=5/10; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.750894; ---ymywttswTATGCAwATGCAtat ; cor=; Ncor= a 0 0 0 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 c 0 0 0 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 g 0 0 0 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 t 0 0 0 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m1 versus positions_7nt_m3; m=6/10; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.735252; ---kbywTTgTTaTGCAtAAcAAwrv ; cor=; Ncor= a 0 0 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 42 44 c 0 0 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 26 52 g 0 0 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 73 46 t 0 0 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51 26 25

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_7nt_m1 versus positions_6nt_m4; m=7/10; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.607428; rywywyaTgcAwATGCATATgcay-- ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 0 0 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 0 0 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 0 0 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258 0 0

oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)
; positions_7nt_m1 versus oligos_7nt_mkv4_m1; m=8/10; ncol2=16; w=0; offset=6; strand=D; shift=8; score=0.606349; --------tswtATGCAaATghrt-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 0 0 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 0 0 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 0 0 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328 0 0

oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)
; positions_7nt_m1 versus oligos_7nt_mkv4_m4_rc; m=9/10; ncol2=15; w=0; offset=2; strand=R; shift=4; score=0.588495; ----cywTTGTyATGCAaa------- ; cor=; Ncor= a 0 0 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 0 0 0 0 c 0 0 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 0 0 0 0 g 0 0 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 0 0 0 0 t 0 0 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0 0 0 0 0

oligos_7nt_mkv4_m3_shift10 (oligos_7nt_mkv4_m3)
; positions_7nt_m1 versus oligos_7nt_mkv4_m3; m=10/10; ncol2=12; w=0; offset=8; strand=D; shift=10; score=0.444909; ----------wtATGCwAATgw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift10 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift10 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=11; shift=10; ncol=21; ----------waACAAAGgam ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 295 332 1009 3 971 932 943 25 174 304 327 c 0 0 0 0 0 0 0 0 0 0 132 233 7 969 13 43 15 13 158 252 272 g 0 0 0 0 0 0 0 0 0 0 217 220 5 16 14 26 6 950 625 230 221 t 0 0 0 0 0 0 0 0 0 0 387 246 10 43 33 30 67 43 74 245 211

positions_6nt_m5_shift10 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=10; score= 1; ----------waACAAAGgam ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 295 332 1009 3 971 932 943 25 174 304 327 c 0 0 0 0 0 0 0 0 0 0 132 233 7 969 13 43 15 13 158 252 272 g 0 0 0 0 0 0 0 0 0 0 217 220 5 16 14 26 6 950 625 230 221 t 0 0 0 0 0 0 0 0 0 0 387 246 10 43 33 30 67 43 74 245 211

oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)
; positions_6nt_m5 versus oligos_6nt_mkv3_m5; m=2/4; ncol2=14; w=-3; offset=-3; strand=D; shift=7; score=0.672958; -------amaAAACAAAGcma ; cor=; Ncor= a 0 0 0 0 0 0 0 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 0 0 0 0 0 0 0 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 0 0 0 0 0 0 0 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 0 0 0 0 0 0 0 155 126 106 82 26 9 29 11 16 28 39 84 128 141

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; positions_6nt_m5 versus oligos_6nt_mkv3_m3; m=3/4; ncol2=21; w=-10; offset=-10; strand=D; shift=0; score=0.43353; yhcaTTTGCATaAcAAwgsmm ; cor=; Ncor= a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170

oligos_7nt_mkv4_m4_shift4 (oligos_7nt_mkv4_m4)
; positions_6nt_m5 versus oligos_7nt_mkv4_m4; m=4/4; ncol2=15; w=-6; offset=-6; strand=D; shift=4; score=0.416607; ----ttTGCATrACAAwrg-- ; cor=; Ncor= a 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 0 0 c 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 0 0 g 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 0 0 t 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift3 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift3 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---rywywyaTgcAwATGCATATgcay ; Alignment reference a 0 0 0 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 c 0 0 0 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 g 0 0 0 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 t 0 0 0 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258

positions_6nt_m4_shift3 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/12; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---rywywyaTgcAwATGCATATgcay ; cor=; Ncor= a 0 0 0 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 c 0 0 0 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 g 0 0 0 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 t 0 0 0 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258

positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)
; positions_6nt_m4 versus positions_7nt_m5_rc; m=2/12; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.812705; ---gyrtatgygCATATGCAaATryry ; cor=; Ncor= a 0 0 0 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 c 0 0 0 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 g 0 0 0 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 t 0 0 0 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87

positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)
; positions_6nt_m4 versus positions_6nt_m1_rc; m=3/12; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.794258; ----ydyatwTGCATATGCAwatryay ; cor=; Ncor= a 0 0 0 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 c 0 0 0 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 g 0 0 0 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 t 0 0 0 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203

positions_6nt_m3_shift5 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=4/12; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.787578; -----rywtaTGCATwTGCATAtgyry ; cor=; Ncor= a 0 0 0 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 c 0 0 0 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 g 0 0 0 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 t 0 0 0 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_6nt_m4 versus positions_7nt_m2; m=5/12; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.763838; ----ydyaTtTgCATATGcAaAtryay ; cor=; Ncor= a 0 0 0 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 c 0 0 0 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 g 0 0 0 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 t 0 0 0 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73

oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; positions_6nt_m4 versus oligos_6nt_mkv3_m1; m=6/12; ncol2=22; w=0; offset=1; strand=D; shift=4; score=0.763228; ----yryaTwTGCATATGCAwAtryr- ; cor=; Ncor= a 0 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 c 0 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 g 0 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 t 0 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_6nt_m4 versus positions_6nt_m2_rc; m=7/12; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.680178; ymywttswTATGCAwATGCAtata--- ; cor=; Ncor= a 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 108 0 0 0 c 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 79 0 0 0 g 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 81 0 0 0 t 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107 73 0 0 0

oligos_6nt_mkv3_m3_rc_shift5 (oligos_6nt_mkv3_m3_rc)
; positions_6nt_m4 versus oligos_6nt_mkv3_m3_rc; m=8/12; ncol2=21; w=0; offset=2; strand=R; shift=5; score=0.628309; -----kkscwTTgTtATGCAAAtgdr- ; cor=; Ncor= a 0 0 0 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 c 0 0 0 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 g 0 0 0 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 t 0 0 0 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0

oligos_7nt_mkv4_m2_rc_shift7 (oligos_7nt_mkv4_m2_rc)
; positions_6nt_m4 versus oligos_7nt_mkv4_m2_rc; m=9/12; ncol2=20; w=0; offset=4; strand=R; shift=7; score=0.617762; -------cywTTgTtATGCAAATgdrr ; cor=; Ncor= a 0 0 0 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 c 0 0 0 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 g 0 0 0 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 t 0 0 0 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177

positions_7nt_m1_shift5 (positions_7nt_m1)
; positions_6nt_m4 versus positions_7nt_m1; m=10/12; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.607428; -----kbcywTTgTtATGCAAATgvar ; cor=; Ncor= a 0 0 0 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 c 0 0 0 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 g 0 0 0 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 t 0 0 0 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139

positions_7nt_m4_shift7 (positions_7nt_m4)
; positions_6nt_m4 versus positions_7nt_m4; m=11/12; ncol2=22; w=0; offset=4; strand=D; shift=7; score=0.594288; -------cywTTgtyATGCAAATgmar ; cor=; Ncor= a 0 0 0 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 c 0 0 0 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 g 0 0 0 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 t 0 0 0 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192

oligos_7nt_mkv4_m1_shift11 (oligos_7nt_mkv4_m1)
; positions_6nt_m4 versus oligos_7nt_mkv4_m1; m=12/12; ncol2=16; w=0; offset=8; strand=D; shift=11; score=0.587517; -----------tswtATGCAaATghrt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 c 0 0 0 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 g 0 0 0 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 t 0 0 0 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----atTTACATAws ; Alignment reference a 0 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 c 0 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 g 0 0 0 0 267 182 29 23 187 29 15 56 43 199 301 t 0 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----atTTACATAws ; cor=; Ncor= a 0 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 c 0 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 g 0 0 0 0 267 182 29 23 187 29 15 56 43 199 301 t 0 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=2/4; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.540618; aydcATtTGCATaws ; cor=; Ncor= a 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 c 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 g 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 t 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2; m=3/4; ncol2=20; w=-4; offset=-4; strand=D; shift=0; score=0.431971; yyhcATTTGCATaAc ; cor=; Ncor= a 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 c 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 g 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 t 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m3; m=4/4; ncol2=21; w=-3; offset=-3; strand=D; shift=1; score=0.421007; -yhcaTTTGCATaAc ; cor=; Ncor= a 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 c 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 g 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 t 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=24; shift=1; ncol=25; -ydyaTtTgCATATGcAaAtryayr ; Alignment reference a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 78 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 48 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 63 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73 53
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -ydyaTtTgCATATGcAaAtryayr ; cor=; Ncor= a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 78 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 48 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 63 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73 53
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)				; positions_7nt_m2 versus positions_6nt_m1_rc; m=2/11; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.974523; -ydyatwTGCATATGCAwatryayr ; cor=; Ncor= a 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 208 c 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 160 g 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 191 t 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203 155
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; positions_7nt_m2 versus oligos_6nt_mkv3_m1; m=3/11; ncol2=22; w=0; offset=0; strand=D; shift=1; score=0.904976; -yryaTwTGCATATGCAwAtryr-- ; cor=; Ncor= a 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 0 c 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 0 g 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 0 t 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0 0
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; positions_7nt_m2 versus positions_7nt_m5_rc; m=4/11; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.834352; gyrtatgygCATATGCAaATryry- ; cor=; Ncor= a 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 0 c 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 0 g 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 0 t 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87 0
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_7nt_m2 versus positions_6nt_m3; m=5/11; ncol2=24; w=0; offset=1; strand=D; shift=2; score=0.808804; --rywtaTGCATwTGCATAtgyrya ; cor=; Ncor= a 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 104 c 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 46 g 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 70 t 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78 72
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_7nt_m2 versus positions_6nt_m4; m=6/11; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.763838; rywywyaTgcAwATGCATATgcay- ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 0 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 0 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 0 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258 0
positions_6nt_m2_shift3 (positions_6nt_m2)				; positions_7nt_m2 versus positions_6nt_m2; m=7/11; ncol2=24; w=0; offset=2; strand=D; shift=3; score=0.69061; ---tataTGCATwTGCATAwsaawr ; cor=; Ncor= a 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 c 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 g 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 t 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)				; positions_7nt_m2 versus oligos_6nt_mkv3_m3; m=8/11; ncol2=21; w=0; offset=0; strand=D; shift=1; score=0.612591; -yhcaTTTGCATaAcAAwgsmm--- ; cor=; Ncor= a 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 0 0 0 c 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 0 0 0 g 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 0 0 0 t 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170 0 0 0
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)				; positions_7nt_m2 versus oligos_7nt_mkv4_m1; m=9/11; ncol2=16; w=0; offset=7; strand=D; shift=8; score=0.587516; --------tswtATGCAaATghrt- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 0 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 0 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 0 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328 0
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; positions_7nt_m2 versus oligos_7nt_mkv4_m2; m=10/11; ncol2=20; w=-1; offset=-1; strand=D; shift=0; score=0.534886; yyhcATTTGCATaAcAAwrg----- ; cor=; Ncor= a 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 0 0 0 0 0 c 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 0 0 0 0 0 g 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 0 0 0 0 0 t 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99 0 0 0 0 0
oligos_7nt_mkv4_m3_rc_shift2 (oligos_7nt_mkv4_m3_rc)				; positions_7nt_m2 versus oligos_7nt_mkv4_m3_rc; m=11/11; ncol2=12; w=0; offset=1; strand=R; shift=2; score=0.400754; --wcATTwGCATaw----------- ; cor=; Ncor= a 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 0 0 0 0 0 c 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 0 0 0 0 0 g 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 0 0 0 0 0 t 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift8 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=15; shift=8; ncol=23; --------ttTGCATrACAAwrg ; Alignment reference a 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 c 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 g 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 t 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84
oligos_7nt_mkv4_m4_shift8 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=8; score= 1; --------ttTGCATrACAAwrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 c 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 g 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 t 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m2; m=2/10; ncol2=20; w=-5; offset=-5; strand=D; shift=3; score=0.710397; ---yyhcATTTGCATaAcAAwrg ; cor=; Ncor= a 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 c 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 g 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 t 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m3; m=3/10; ncol2=21; w=-4; offset=-4; strand=D; shift=4; score=0.66298; ----yhcaTTTGCATaAcAAwgs ; cor=; Ncor= a 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 c 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 g 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 t 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; oligos_7nt_mkv4_m4 versus positions_7nt_m4_rc; m=4/10; ncol2=22; w=-7; offset=-7; strand=R; shift=1; score=0.643849; -ryytkcATTTGCATracAAwrg ; cor=; Ncor= a 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 c 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 g 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 t 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; oligos_7nt_mkv4_m4 versus positions_7nt_m1_rc; m=5/10; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.588495; -rmytbcATTTGCATaAcAAwrg ; cor=; Ncor= a 0 180 174 139 109 146 128 453 25 66 84 82 39 645 25 409 489 36 576 583 353 180 146 c 0 138 184 185 162 170 314 67 24 92 17 34 603 4 22 59 20 444 33 22 32 61 132 g 0 202 152 154 136 168 87 61 12 39 8 531 7 3 11 116 11 108 16 39 42 365 307 t 0 139 149 181 252 175 130 78 598 462 550 12 10 7 601 75 139 71 34 15 232 53 74
positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)				; oligos_7nt_mkv4_m4 versus positions_7nt_m3_rc; m=6/10; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.542374; kbywTTgTTaTGCAtAAcAAwrv ; cor=; Ncor= a 35 25 26 51 12 9 22 33 11 111 5 13 4 155 34 138 115 17 131 129 73 43 44 c 35 46 73 30 9 13 27 10 13 14 3 3 147 4 8 5 10 102 14 18 13 26 51 g 43 52 26 12 18 14 101 10 5 8 4 147 3 3 14 13 10 27 13 9 30 72 46 t 54 44 42 74 128 131 17 114 138 34 155 4 13 5 111 11 32 21 9 11 51 26 26
positions_6nt_m2_shift0 (positions_6nt_m2)				; oligos_7nt_mkv4_m4 versus positions_6nt_m2; m=7/10; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.524228; tataTGCATwTGCATAwsaawrk ; cor=; Ncor= a 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 c 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 g 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 t 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89
oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=8/10; ncol2=16; w=-5; offset=-5; strand=R; shift=3; score=0.426856; ---aydcATtTGCATawsa---- ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0
positions_6nt_m5_shift14 (positions_6nt_m5)				; oligos_7nt_mkv4_m4 versus positions_6nt_m5; m=9/10; ncol2=11; w=0; offset=6; strand=D; shift=14; score=0.416607; --------------waACAAAGg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 295 332 1009 3 971 932 943 25 174 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 132 233 7 969 13 43 15 13 158 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 217 220 5 16 14 26 6 950 625 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 387 246 10 43 33 30 67 43 74
oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m3_rc; m=10/10; ncol2=12; w=-3; offset=-3; strand=R; shift=5; score= 0.4033; -----wcATTwGCATaw------ ; cor=; Ncor= a 0 0 0 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 c 0 0 0 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 g 0 0 0 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 t 0 0 0 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift4 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=22; shift=4; ncol=26; ----cywTTgtyATGCAAATgmarry ; Alignment reference a 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 226 176 c 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 176 241 g 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 231 173 t 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192 201 244
positions_7nt_m4_shift4 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/11; ncol2=22; w=0; offset=0; strand=D; shift=4; score= 1; ----cywTTgtyATGCAAATgmarry ; cor=; Ncor= a 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 226 176 c 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 176 241 g 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 231 173 t 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192 201 244
positions_7nt_m1_shift2 (positions_7nt_m1)				; positions_7nt_m4 versus positions_7nt_m1; m=2/11; ncol2=24; w=-2; offset=-2; strand=D; shift=2; score=0.887848; --kbcywTTgTtATGCAAATgvarky ; cor=; Ncor= a 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 149 139 c 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 152 202 g 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 184 138 t 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139 174 180
oligos_7nt_mkv4_m2_rc_shift4 (oligos_7nt_mkv4_m2_rc)				; positions_7nt_m4 versus oligos_7nt_mkv4_m2_rc; m=3/11; ncol2=20; w=0; offset=0; strand=R; shift=4; score=0.886146; ----cywTTgTtATGCAAATgdrr-- ; cor=; Ncor= a 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 0 0 c 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 0 0 g 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 0 0 t 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177 0 0
positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)				; positions_7nt_m4 versus positions_6nt_m2_rc; m=4/11; ncol2=24; w=-1; offset=-1; strand=R; shift=3; score=0.790398; ---ymywttswTATGCAwATGCAtat ; cor=; Ncor= a 0 0 0 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 c 0 0 0 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 g 0 0 0 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 t 0 0 0 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107
oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)				; positions_7nt_m4 versus oligos_6nt_mkv3_m3_rc; m=5/11; ncol2=21; w=-2; offset=-2; strand=R; shift=2; score=0.756027; --kkscwTTgTtATGCAAAtgdr--- ; cor=; Ncor= a 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 0 0 c 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 0 0 g 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 0 0 t 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m4 versus positions_7nt_m3; m=6/11; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.693357; ---kbywTTgTTaTGCAtAAcAAwrv ; cor=; Ncor= a 0 0 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 42 44 c 0 0 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 26 52 g 0 0 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 73 46 t 0 0 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51 26 25
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)				; positions_7nt_m4 versus oligos_7nt_mkv4_m1; m=7/11; ncol2=16; w=0; offset=4; strand=D; shift=8; score=0.67214; --------tswtATGCAaATghrt-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 0 0 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 0 0 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 0 0 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328 0 0
positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)				; positions_7nt_m4 versus positions_6nt_m3_rc; m=8/11; ncol2=24; w=0; offset=0; strand=R; shift=4; score=0.649787; ----atryrcaTATGCAwATGCAtaw ; cor=; Ncor= a 0 0 0 0 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 186 109 c 0 0 0 0 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 20 61 g 0 0 0 0 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 60 39 t 0 0 0 0 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192 26 83
oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)				; positions_7nt_m4 versus oligos_7nt_mkv4_m4_rc; m=9/11; ncol2=15; w=0; offset=0; strand=R; shift=4; score=0.643849; ----cywTTGTyATGCAaa------- ; cor=; Ncor= a 0 0 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 0 0 0 0 c 0 0 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 0 0 0 0 g 0 0 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 0 0 0 0 t 0 0 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0 0 0 0 0
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_7nt_m4 versus positions_6nt_m4; m=10/11; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.594288; rywywyaTgcAwATGCATATgcay-- ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 0 0 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 0 0 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 0 0 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258 0 0
oligos_7nt_mkv4_m3_shift10 (oligos_7nt_mkv4_m3)				; positions_7nt_m4 versus oligos_7nt_mkv4_m3; m=11/11; ncol2=12; w=0; offset=6; strand=D; shift=10; score=0.486311; ----------wtATGCwAATgw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=16; shift=8; ncol=24; --------tswtATGCAaATghrt ; Alignment reference a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/16; ncol2=16; w=0; offset=0; strand=D; shift=8; score= 1; --------tswtATGCAaATghrt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328
oligos_7nt_mkv4_m2_rc_shift4 (oligos_7nt_mkv4_m2_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2_rc; m=2/16; ncol2=20; w=-4; offset=-4; strand=R; shift=4; score=0.73538; ----cywTTgTtATGCAAATgdrr ; cor=; Ncor= a 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 c 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 g 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 t 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177
oligos_7nt_mkv4_m3_shift10 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=3/16; ncol2=12; w=0; offset=2; strand=D; shift=10; score=0.678024; ----------wtATGCwAATgw-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 0 0 c 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 0 0 g 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 0 0 t 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210 0 0
positions_7nt_m4_shift4 (positions_7nt_m4)				; oligos_7nt_mkv4_m1 versus positions_7nt_m4; m=4/16; ncol2=22; w=-4; offset=-4; strand=D; shift=4; score=0.67214; ----cywTTgtyATGCAAATgmar ; cor=; Ncor= a 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 c 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 g 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 t 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192
oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m3_rc; m=5/16; ncol2=21; w=-6; offset=-6; strand=R; shift=2; score=0.624737; --kkscwTTgTtATGCAAAtgdr- ; cor=; Ncor= a 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 c 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 g 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 t 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; oligos_7nt_mkv4_m1 versus positions_7nt_m5_rc; m=6/16; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.608165; gyrtatgygCATATGCAaATryry ; cor=; Ncor= a 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 c 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 g 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 t 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87
positions_7nt_m1_shift2 (positions_7nt_m1)				; oligos_7nt_mkv4_m1 versus positions_7nt_m1; m=7/16; ncol2=24; w=-6; offset=-6; strand=D; shift=2; score=0.606349; --kbcywTTgTtATGCAAATgvar ; cor=; Ncor= a 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 c 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 g 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 t 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139
positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)				; oligos_7nt_mkv4_m1 versus positions_6nt_m2_rc; m=8/16; ncol2=24; w=-5; offset=-5; strand=R; shift=3; score=0.59599; ---ymywttswTATGCAwATGCAt ; cor=; Ncor= a 0 0 0 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 c 0 0 0 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 g 0 0 0 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 t 0 0 0 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218
positions_6nt_m4_shift0 (positions_6nt_m4)				; oligos_7nt_mkv4_m1 versus positions_6nt_m4; m=9/16; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.587517; rywywyaTgcAwATGCATATgcay ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258
positions_7nt_m2_shift1 (positions_7nt_m2)				; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=10/16; ncol2=24; w=-7; offset=-7; strand=D; shift=1; score=0.587516; -ydyaTtTgCATATGcAaAtryay ; cor=; Ncor= a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73
positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)				; oligos_7nt_mkv4_m1 versus positions_6nt_m3_rc; m=11/16; ncol2=24; w=-4; offset=-4; strand=R; shift=4; score=0.572169; ----atryrcaTATGCAwATGCAt ; cor=; Ncor= a 0 0 0 0 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 c 0 0 0 0 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 g 0 0 0 0 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 t 0 0 0 0 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=12/16; ncol2=22; w=-7; offset=-7; strand=D; shift=1; score=0.562498; -yryaTwTGCATATGCAwAtryr- ; cor=; Ncor= a 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 c 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 g 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 t 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)				; oligos_7nt_mkv4_m1 versus positions_6nt_m1_rc; m=13/16; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.558261; -ydyatwTGCATATGCAwatryay ; cor=; Ncor= a 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 c 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 g 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 t 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203
oligos_6nt_mkv3_m4_rc_shift9 (oligos_6nt_mkv3_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=14/16; ncol2=11; w=0; offset=1; strand=R; shift=9; score=0.540618; ---------swTATGTAAat---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 285 390 75 983 38 66 47 1100 1045 559 257 0 0 0 0 c 0 0 0 0 0 0 0 0 0 301 199 43 56 15 29 187 23 29 182 267 0 0 0 0 g 0 0 0 0 0 0 0 0 0 324 227 47 77 34 1038 41 41 61 227 212 0 0 0 0 t 0 0 0 0 0 0 0 0 0 286 380 1031 80 1109 63 921 32 61 228 460 0 0 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)				; oligos_7nt_mkv4_m1 versus positions_7nt_m3; m=15/16; ncol2=24; w=-5; offset=-5; strand=D; shift=3; score=0.471159; ---kbywTTgTTaTGCAtAAcAAw ; cor=; Ncor= a 0 0 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 c 0 0 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 g 0 0 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 t 0 0 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51
oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=16/16; ncol2=15; w=-4; offset=-4; strand=R; shift=4; score=0.426856; ----cywTTGTyATGCAaa----- ; cor=; Ncor= a 0 0 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 0 0 c 0 0 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 0 0 g 0 0 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 0 0 t 0 0 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m5_shift3 (positions_7nt_m5)				; positions_7nt_m5; m=0 (reference); ncol1=24; shift=3; ncol=27; ---ryryATtTGCATATGcrcatayrc ; Alignment reference a 0 0 0 87 51 104 26 223 16 69 9 28 21 282 12 268 18 24 45 124 51 212 36 190 52 85 55 c 0 0 0 56 98 54 174 31 40 26 45 7 264 7 23 8 17 37 191 18 166 19 49 34 79 78 124 g 0 0 0 110 49 83 26 34 11 64 14 261 14 15 8 29 7 225 19 152 30 50 36 67 43 105 60 t 0 0 0 62 117 74 89 27 248 156 247 19 16 11 272 10 273 29 60 21 68 34 194 24 141 47 76
positions_7nt_m5_shift3 (positions_7nt_m5)				; positions_7nt_m5 versus positions_7nt_m5; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---ryryATtTGCATATGcrcatayrc ; cor=; Ncor= a 0 0 0 87 51 104 26 223 16 69 9 28 21 282 12 268 18 24 45 124 51 212 36 190 52 85 55 c 0 0 0 56 98 54 174 31 40 26 45 7 264 7 23 8 17 37 191 18 166 19 49 34 79 78 124 g 0 0 0 110 49 83 26 34 11 64 14 261 14 15 8 29 7 225 19 152 30 50 36 67 43 105 60 t 0 0 0 62 117 74 89 27 248 156 247 19 16 11 272 10 273 29 60 21 68 34 194 24 141 47 76
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; positions_7nt_m5 versus oligos_6nt_mkv3_m1; m=2/9; ncol2=22; w=0; offset=1; strand=D; shift=4; score=0.837737; ----yryaTwTGCATATGCAwAtryr- ; cor=; Ncor= a 0 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 c 0 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 g 0 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 t 0 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_7nt_m5 versus positions_7nt_m2_rc; m=3/9; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.834352; --yrtryaTtTgCATATGcAaAtrhr- ; cor=; Ncor= a 0 0 53 73 37 65 19 153 12 59 7 30 10 215 14 206 13 15 47 207 136 185 29 66 62 85 0 c 0 0 63 58 58 31 129 43 38 16 20 5 202 2 18 7 7 11 163 4 31 9 19 29 72 47 0 g 0 0 48 77 44 91 31 20 6 33 3 160 12 10 6 18 4 200 5 21 20 38 39 126 38 70 0 t 0 0 78 34 103 55 63 26 186 134 212 47 18 15 204 11 218 16 27 10 55 10 155 21 70 40 0
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_7nt_m5 versus positions_6nt_m1; m=4/9; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.828727; --yrtryatwTGCATATGCAwatrhr- ; cor=; Ncor= a 0 0 155 203 127 185 94 316 70 228 27 68 53 646 43 603 40 43 123 606 299 437 135 238 189 218 0 c 0 0 191 167 166 128 274 151 172 74 57 19 579 8 45 20 21 35 509 14 119 35 115 127 183 168 0 g 0 0 160 200 144 228 124 114 36 113 13 505 41 21 22 44 10 586 18 58 69 172 153 244 144 188 0 t 0 0 208 144 277 173 222 133 436 299 617 122 41 39 604 47 643 50 64 36 227 70 311 105 198 140 0
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; positions_7nt_m5 versus positions_6nt_m4_rc; m=5/9; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.812705; ---rtgcATATGCATwTgcAtrwrwry ; cor=; Ncor= a 0 0 0 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 232 205 242 163 c 0 0 0 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 168 183 160 208 g 0 0 0 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 209 158 208 165 t 0 0 0 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193 145 208 144 218
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; positions_7nt_m5 versus positions_6nt_m3_rc; m=6/9; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.71384; -atryrcaTATGCAwATGCAtawry-- ; cor=; Ncor= a 0 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 186 109 101 63 0 0 c 0 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 20 61 51 77 0 0 g 0 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 60 39 81 61 0 0 t 0 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192 26 83 59 91 0 0
oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)				; positions_7nt_m5 versus oligos_7nt_mkv4_m1_rc; m=7/9; ncol2=16; w=0; offset=0; strand=R; shift=3; score=0.608165; ---aydcATtTGCATawsa-------- ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0 0 0 0 0
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m5 versus positions_6nt_m2_rc; m=8/9; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.596399; ymywttswTATGCAwATGCAtata--- ; cor=; Ncor= a 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 108 0 0 0 c 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 79 0 0 0 g 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 81 0 0 0 t 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107 73 0 0 0
oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)				; positions_7nt_m5 versus oligos_7nt_mkv4_m3_rc; m=9/9; ncol2=12; w=0; offset=2; strand=R; shift=5; score=0.408597; -----wcATTwGCATaw---------- ; cor=; Ncor= a 0 0 0 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0 0 0 0 0

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=20; shift=3; ncol=23; ---yyhcATTTGCATaAcAAwrg ; Alignment reference a 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 c 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 g 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 t 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/12; ncol2=20; w=0; offset=0; strand=D; shift=3; score= 1; ---yyhcATTTGCATaAcAAwrg ; cor=; Ncor= a 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 c 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 g 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 t 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; oligos_7nt_mkv4_m2 versus positions_7nt_m4_rc; m=2/12; ncol2=22; w=-2; offset=-2; strand=R; shift=1; score=0.886146; -ryytkcATTTGCATracAAwrg ; cor=; Ncor= a 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 c 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 g 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 t 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3; m=3/12; ncol2=21; w=0; offset=1; strand=D; shift=4; score=0.853034; ----yhcaTTTGCATaAcAAwgs ; cor=; Ncor= a 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 c 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 g 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 t 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; oligos_7nt_mkv4_m2 versus positions_7nt_m1_rc; m=4/12; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.82711; -rmytbcATTTGCATaAcAAwrg ; cor=; Ncor= a 0 180 174 139 109 146 128 453 25 66 84 82 39 645 25 409 489 36 576 583 353 180 146 c 0 138 184 185 162 170 314 67 24 92 17 34 603 4 22 59 20 444 33 22 32 61 132 g 0 202 152 154 136 168 87 61 12 39 8 531 7 3 11 116 11 108 16 39 42 365 307 t 0 139 149 181 252 175 130 78 598 462 550 12 10 7 601 75 139 71 34 15 232 53 74
oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1_rc; m=5/12; ncol2=16; w=0; offset=0; strand=R; shift=3; score=0.73538; ---aydcATtTGCATawsa---- ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0
oligos_7nt_mkv4_m4_shift8 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m4; m=6/12; ncol2=15; w=0; offset=5; strand=D; shift=8; score=0.710397; --------ttTGCATrACAAwrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 c 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 g 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 t 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84
positions_6nt_m2_shift0 (positions_6nt_m2)				; oligos_7nt_mkv4_m2 versus positions_6nt_m2; m=7/12; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.696222; tataTGCATwTGCATAwsaawrk ; cor=; Ncor= a 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 c 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 g 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 t 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89
positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)				; oligos_7nt_mkv4_m2 versus positions_7nt_m3_rc; m=8/12; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.66181; kbywTTgTTaTGCAtAAcAAwrv ; cor=; Ncor= a 35 25 26 51 12 9 22 33 11 111 5 13 4 155 34 138 115 17 131 129 73 43 44 c 35 46 73 30 9 13 27 10 13 14 3 3 147 4 8 5 10 102 14 18 13 26 51 g 43 52 26 12 18 14 101 10 5 8 4 147 3 3 14 13 10 27 13 9 30 72 46 t 54 44 42 74 128 131 17 114 138 34 155 4 13 5 111 11 32 21 9 11 51 26 26
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; oligos_7nt_mkv4_m2 versus positions_6nt_m4_rc; m=9/12; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.617762; ---rtgcATATGCATwTgcAtrw ; cor=; Ncor= a 0 0 0 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 c 0 0 0 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 g 0 0 0 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 t 0 0 0 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193
oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3_rc; m=10/12; ncol2=12; w=0; offset=2; strand=R; shift=5; score=0.538597; -----wcATTwGCATaw------ ; cor=; Ncor= a 0 0 0 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 c 0 0 0 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 g 0 0 0 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 t 0 0 0 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0
positions_7nt_m2_shift4 (positions_7nt_m2)				; oligos_7nt_mkv4_m2 versus positions_7nt_m2; m=11/12; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.534886; ----ydyaTtTgCATATGcAaAt ; cor=; Ncor= a 0 0 0 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 c 0 0 0 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 g 0 0 0 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 t 0 0 0 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153
oligos_6nt_mkv3_m4_shift7 (oligos_6nt_mkv3_m4)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4; m=12/12; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.431971; -------atTTACATAws----- ; cor=; Ncor= a 0 0 0 0 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 0 0 0 0 0 c 0 0 0 0 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 0 0 0 0 0 g 0 0 0 0 0 0 0 267 182 29 23 187 29 15 56 43 199 301 0 0 0 0 0 t 0 0 0 0 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=24; shift=2; ncol=26; --rywtaTGCATwTGCATAtgyryat ; Alignment reference a 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 104 57 c 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 46 64 g 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 70 58 t 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78 72 113
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --rywtaTGCATwTGCATAtgyryat ; cor=; Ncor= a 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 104 57 c 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 46 64 g 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 70 58 t 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78 72 113
positions_6nt_m2_shift3 (positions_6nt_m2)				; positions_6nt_m3 versus positions_6nt_m2; m=2/9; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.862118; ---tataTGCATwTGCATAwsaawrk ; cor=; Ncor= a 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 c 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 g 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 t 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)				; positions_6nt_m3 versus positions_6nt_m1_rc; m=3/9; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.840163; -ydyatwTGCATATGCAwatryayr- ; cor=; Ncor= a 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 208 0 c 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 160 0 g 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 191 0 t 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203 155 0
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_6nt_m3 versus positions_7nt_m2; m=4/9; ncol2=24; w=-1; offset=-1; strand=D; shift=1; score=0.808804; -ydyaTtTgCATATGcAaAtryayr- ; cor=; Ncor= a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 78 0 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 48 0 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 63 0 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73 53 0
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m3 versus positions_6nt_m4; m=5/9; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.787578; rywywyaTgcAwATGCATATgcay-- ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 0 0 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 0 0 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 0 0 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258 0 0
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; positions_6nt_m3 versus oligos_6nt_mkv3_m1; m=6/9; ncol2=22; w=-1; offset=-1; strand=D; shift=1; score=0.74558; -yryaTwTGCATATGCAwAtryr--- ; cor=; Ncor= a 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 0 0 c 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 0 0 g 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 0 0 t 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0 0 0
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; positions_6nt_m3 versus positions_7nt_m5_rc; m=7/9; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.71384; gyrtatgygCATATGCAaATryry-- ; cor=; Ncor= a 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 0 0 c 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 0 0 g 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 0 0 t 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87 0 0
positions_7nt_m4_rc_shift4 (positions_7nt_m4_rc)				; positions_6nt_m3 versus positions_7nt_m4_rc; m=8/9; ncol2=22; w=0; offset=2; strand=R; shift=4; score=0.649787; ----ryytkcATTTGCATracAAwrg ; cor=; Ncor= a 0 0 0 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 c 0 0 0 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 g 0 0 0 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 t 0 0 0 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130
oligos_7nt_mkv4_m1_rc_shift6 (oligos_7nt_mkv4_m1_rc)				; positions_6nt_m3 versus oligos_7nt_mkv4_m1_rc; m=9/9; ncol2=16; w=0; offset=4; strand=R; shift=6; score=0.572169; ------aydcATtTGCATawsa---- ; cor=; Ncor= a 0 0 0 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 c 0 0 0 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 g 0 0 0 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 t 0 0 0 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=24; shift=2; ncol=26; --yrtryatwTGCATATGCAwatrhr ; Alignment reference a 0 0 155 203 127 185 94 316 70 228 27 68 53 646 43 603 40 43 123 606 299 437 135 238 189 218 c 0 0 191 167 166 128 274 151 172 74 57 19 579 8 45 20 21 35 509 14 119 35 115 127 183 168 g 0 0 160 200 144 228 124 114 36 113 13 505 41 21 22 44 10 586 18 58 69 172 153 244 144 188 t 0 0 208 144 277 173 222 133 436 299 617 122 41 39 604 47 643 50 64 36 227 70 311 105 198 140
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --yrtryatwTGCATATGCAwatrhr ; cor=; Ncor= a 0 0 155 203 127 185 94 316 70 228 27 68 53 646 43 603 40 43 123 606 299 437 135 238 189 218 c 0 0 191 167 166 128 274 151 172 74 57 19 579 8 45 20 21 35 509 14 119 35 115 127 183 168 g 0 0 160 200 144 228 124 114 36 113 13 505 41 21 22 44 10 586 18 58 69 172 153 244 144 188 t 0 0 208 144 277 173 222 133 436 299 617 122 41 39 604 47 643 50 64 36 227 70 311 105 198 140
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_6nt_m1 versus positions_7nt_m2_rc; m=2/8; ncol2=24; w=0; offset=0; strand=R; shift=2; score=0.974523; --yrtryaTtTgCATATGcAaAtrhr ; cor=; Ncor= a 0 0 53 73 37 65 19 153 12 59 7 30 10 215 14 206 13 15 47 207 136 185 29 66 62 85 c 0 0 63 58 58 31 129 43 38 16 20 5 202 2 18 7 7 11 163 4 31 9 19 29 72 47 g 0 0 48 77 44 91 31 20 6 33 3 160 12 10 6 18 4 200 5 21 20 38 39 126 38 70 t 0 0 78 34 103 55 63 26 186 134 212 47 18 15 204 11 218 16 27 10 55 10 155 21 70 40
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; positions_6nt_m1 versus oligos_6nt_mkv3_m1; m=3/8; ncol2=22; w=0; offset=2; strand=D; shift=4; score=0.908114; ----yryaTwTGCATATGCAwAtryr ; cor=; Ncor= a 0 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 0 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 0 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 0 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; positions_6nt_m1 versus positions_6nt_m3_rc; m=4/8; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.840163; -atryrcaTATGCAwATGCAtawry- ; cor=; Ncor= a 0 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 186 109 101 63 0 c 0 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 20 61 51 77 0 g 0 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 60 39 81 61 0 t 0 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192 26 83 59 91 0
positions_7nt_m5_shift3 (positions_7nt_m5)				; positions_6nt_m1 versus positions_7nt_m5; m=5/8; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.828727; ---ryryATtTGCATATGcrcatayr ; cor=; Ncor= a 0 0 0 87 51 104 26 223 16 69 9 28 21 282 12 268 18 24 45 124 51 212 36 190 52 85 c 0 0 0 56 98 54 174 31 40 26 45 7 264 7 23 8 17 37 191 18 166 19 49 34 79 78 g 0 0 0 110 49 83 26 34 11 64 14 261 14 15 8 29 7 225 19 152 30 50 36 67 43 105 t 0 0 0 62 117 74 89 27 248 156 247 19 16 11 272 10 273 29 60 21 68 34 194 24 141 47
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; positions_6nt_m1 versus positions_6nt_m4_rc; m=6/8; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.794258; ---rtgcATATGCATwTgcAtrwrwr ; cor=; Ncor= a 0 0 0 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 232 205 242 c 0 0 0 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 168 183 160 g 0 0 0 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 209 158 208 t 0 0 0 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193 145 208 144
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_6nt_m1 versus positions_6nt_m2_rc; m=7/8; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.741229; ymywttswTATGCAwATGCAtata-- ; cor=; Ncor= a 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 108 0 0 c 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 79 0 0 g 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 81 0 0 t 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107 73 0 0
oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)				; positions_6nt_m1 versus oligos_7nt_mkv4_m1_rc; m=8/8; ncol2=16; w=0; offset=1; strand=R; shift=3; score=0.558261; ---aydcATtTGCATawsa------- ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=22; shift=3; ncol=25; ---yryaTwTGCATATGCAwAtryr ; Alignment reference a 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/10; ncol2=22; w=0; offset=0; strand=D; shift=3; score= 1; ---yryaTwTGCATATGCAwAtryr ; cor=; Ncor= a 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=2/10; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.908114; ---ydyatwTGCATATGCAwatrya ; cor=; Ncor= a 0 0 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 c 0 0 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 g 0 0 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 t 0 0 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127
positions_7nt_m2_shift3 (positions_7nt_m2)				; oligos_6nt_mkv3_m1 versus positions_7nt_m2; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.904976; ---ydyaTtTgCATATGcAaAtrya ; cor=; Ncor= a 0 0 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 c 0 0 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 g 0 0 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 t 0 0 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37
positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)				; oligos_6nt_mkv3_m1 versus positions_7nt_m5_rc; m=4/10; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.837737; --gyrtatgygCATATGCAaATryr ; cor=; Ncor= a 0 0 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 c 0 0 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 g 0 0 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 t 0 0 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51
positions_6nt_m4_shift2 (positions_6nt_m4)				; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=5/10; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.763228; --rywywyaTgcAwATGCATATgca ; cor=; Ncor= a 0 0 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 c 0 0 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 g 0 0 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 t 0 0 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)				; oligos_6nt_mkv3_m1 versus positions_6nt_m3_rc; m=6/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.74558; atryrcaTATGCAwATGCAtawry- ; cor=; Ncor= a 113 72 78 40 78 33 176 22 216 10 21 18 260 85 222 7 27 39 244 32 186 109 101 63 0 c 58 70 43 97 35 162 30 44 17 16 9 242 3 36 16 15 8 209 13 44 20 61 51 77 0 g 64 46 118 41 124 35 31 12 31 5 239 7 16 22 36 9 236 18 21 24 60 39 81 61 0 t 57 104 53 114 55 62 55 214 28 261 23 25 13 149 18 261 21 26 14 192 26 83 59 91 0
oligos_6nt_mkv3_m3_rc_shift4 (oligos_6nt_mkv3_m3_rc)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=7/10; ncol2=21; w=0; offset=1; strand=R; shift=4; score=0.670864; ----kkscwTTgTtATGCAAAtgdr ; cor=; Ncor= a 0 0 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 c 0 0 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 g 0 0 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 t 0 0 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141
positions_6nt_m2_shift5 (positions_6nt_m2)				; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=8/10; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.646122; -----tataTGCATwTGCATAwsaa ; cor=; Ncor= a 0 0 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 c 0 0 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 g 0 0 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 t 0 0 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44
oligos_7nt_mkv4_m1_shift10 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=9/10; ncol2=16; w=0; offset=7; strand=D; shift=10; score=0.562498; ----------tswtATGCAaATghr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 c 0 0 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 g 0 0 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 t 0 0 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201
oligos_7nt_mkv4_m3_shift12 (oligos_7nt_mkv4_m3)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m3; m=10/10; ncol2=12; w=0; offset=9; strand=D; shift=12; score=0.424616; ------------wtATGCwAATgw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 0 c 0 0 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 0 g 0 0 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 0 t 0 0 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210 0

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=21; shift=4; ncol=25; ----yhcaTTTGCATaAcAAwgsmm ; Alignment reference a 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/14; ncol2=21; w=0; offset=0; strand=D; shift=4; score= 1; ----yhcaTTTGCATaAcAAwgsmm ; cor=; Ncor= a 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; oligos_6nt_mkv3_m3 versus positions_7nt_m1_rc; m=2/14; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.87051; -rmytbcATTTGCATaAcAAwrgvm ; cor=; Ncor= a 0 180 174 139 109 146 128 453 25 66 84 82 39 645 25 409 489 36 576 583 353 180 146 219 181 c 0 138 184 185 162 170 314 67 24 92 17 34 603 4 22 59 20 444 33 22 32 61 132 178 187 g 0 202 152 154 136 168 87 61 12 39 8 531 7 3 11 116 11 108 16 39 42 365 307 165 151 t 0 139 149 181 252 175 130 78 598 462 550 12 10 7 601 75 139 71 34 15 232 53 74 97 140
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2; m=3/14; ncol2=20; w=-1; offset=-1; strand=D; shift=3; score=0.853034; ---yyhcATTTGCATaAcAAwrg-- ; cor=; Ncor= a 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 0 0 c 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 0 0 g 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 0 0 t 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99 0 0
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; oligos_6nt_mkv3_m3 versus positions_7nt_m4_rc; m=4/14; ncol2=22; w=-3; offset=-3; strand=R; shift=1; score=0.756027; -ryytkcATTTGCATracAAwrg-- ; cor=; Ncor= a 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 0 0 c 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 0 0 g 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 0 0 t 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130 0 0
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=5/14; ncol2=22; w=0; offset=0; strand=D; shift=4; score=0.670864; ----yryaTwTGCATATGCAwAtry ; cor=; Ncor= a 0 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 c 0 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 g 0 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 t 0 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142
oligos_7nt_mkv4_m4_shift8 (oligos_7nt_mkv4_m4)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m4; m=6/14; ncol2=15; w=0; offset=4; strand=D; shift=8; score=0.66298; --------ttTGCATrACAAwrg-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 0 0 c 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 0 0 g 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 0 0 t 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84 0 0
positions_6nt_m2_shift0 (positions_6nt_m2)				; oligos_6nt_mkv3_m3 versus positions_6nt_m2; m=7/14; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.662096; tataTGCATwTGCATAwsaawrkr- ; cor=; Ncor= a 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 112 0 c 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 79 0 g 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 88 0 t 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89 62 0
positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)				; oligos_6nt_mkv3_m3 versus positions_7nt_m3_rc; m=8/14; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.649065; kbywTTgTTaTGCAtAAcAAwrvm- ; cor=; Ncor= a 35 25 26 51 12 9 22 33 11 111 5 13 4 155 34 138 115 17 131 129 73 43 44 54 0 c 35 46 73 30 9 13 27 10 13 14 3 3 147 4 8 5 10 102 14 18 13 26 51 43 0 g 43 52 26 12 18 14 101 10 5 8 4 147 3 3 14 13 10 27 13 9 30 72 46 35 0 t 54 44 42 74 128 131 17 114 138 34 155 4 13 5 111 11 32 21 9 11 51 26 26 35 0
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; oligos_6nt_mkv3_m3 versus positions_6nt_m4_rc; m=9/14; ncol2=24; w=-1; offset=-1; strand=R; shift=3; score=0.628309; ---rtgcATATGCATwTgcAtrwrw ; cor=; Ncor= a 0 0 0 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 232 205 c 0 0 0 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 168 183 g 0 0 0 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 209 158 t 0 0 0 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193 145 208
oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m1_rc; m=10/14; ncol2=16; w=-1; offset=-1; strand=R; shift=3; score=0.624737; ---aydcATtTGCATawsa------ ; cor=; Ncor= a 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 0 0 c 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 0 0 g 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 0 0 t 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0 0 0
positions_7nt_m2_shift4 (positions_7nt_m2)				; oligos_6nt_mkv3_m3 versus positions_7nt_m2; m=11/14; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.612591; ----ydyaTtTgCATATGcAaAtry ; cor=; Ncor= a 0 0 0 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 c 0 0 0 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 g 0 0 0 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 t 0 0 0 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65
oligos_7nt_mkv4_m3_rc_shift5 (oligos_7nt_mkv4_m3_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3_rc; m=12/14; ncol2=12; w=0; offset=1; strand=R; shift=5; score=0.50804; -----wcATTwGCATaw-------- ; cor=; Ncor= a 0 0 0 0 0 210 177 618 12 15 448 40 26 699 17 271 235 0 0 0 0 0 0 0 0 c 0 0 0 0 0 171 258 35 5 39 50 23 688 16 14 131 120 0 0 0 0 0 0 0 0 g 0 0 0 0 0 141 120 34 10 44 18 630 8 7 15 154 79 0 0 0 0 0 0 0 0 t 0 0 0 0 0 210 177 45 705 634 216 39 10 10 686 176 298 0 0 0 0 0 0 0 0
positions_6nt_m5_shift14 (positions_6nt_m5)				; oligos_6nt_mkv3_m3 versus positions_6nt_m5; m=13/14; ncol2=11; w=0; offset=10; strand=D; shift=14; score=0.43353; --------------waACAAAGgam ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 295 332 1009 3 971 932 943 25 174 304 327 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 132 233 7 969 13 43 15 13 158 252 272 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 217 220 5 16 14 26 6 950 625 230 221 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 387 246 10 43 33 30 67 43 74 245 211
oligos_6nt_mkv3_m4_shift7 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m4; m=14/14; ncol2=11; w=0; offset=3; strand=D; shift=7; score=0.421007; -------atTTACATAws------- ; cor=; Ncor= a 0 0 0 0 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 267 182 29 23 187 29 15 56 43 199 301 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift3 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=24; shift=3; ncol=27; ---tataTGCATwTGCATAwsaawrkr ; Alignment reference a 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 112 c 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 79 g 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 88 t 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89 62
positions_6nt_m2_shift3 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/14; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---tataTGCATwTGCATAwsaawrkr ; cor=; Ncor= a 0 0 0 73 107 44 218 15 26 23 309 18 134 24 25 33 315 23 232 155 70 159 195 86 95 85 112 c 0 0 0 81 70 61 40 29 35 271 8 24 29 13 19 273 3 16 20 45 124 68 48 68 52 73 79 g 0 0 0 79 84 22 37 23 233 14 13 20 32 3 277 11 12 20 56 38 95 42 54 50 131 94 88 t 0 0 0 108 80 214 46 274 47 33 11 279 146 301 20 24 11 282 33 103 52 72 44 137 63 89 62
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_6nt_m2 versus positions_6nt_m3; m=2/14; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.862118; --rywtaTGCATwTGCATAtgyryat- ; cor=; Ncor= a 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 104 57 0 c 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 46 64 0 g 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 70 58 0 t 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78 72 113 0
positions_7nt_m4_rc_shift4 (positions_7nt_m4_rc)				; positions_6nt_m2 versus positions_7nt_m4_rc; m=3/14; ncol2=22; w=0; offset=1; strand=R; shift=4; score=0.790398; ----ryytkcATTTGCATracAAwrg- ; cor=; Ncor= a 0 0 0 0 244 201 192 119 163 131 636 18 116 80 79 63 802 40 253 524 108 624 643 291 245 199 0 c 0 0 0 0 173 231 213 181 175 470 59 22 77 16 41 741 7 21 78 77 466 62 50 93 96 197 0 g 0 0 0 0 241 176 199 150 285 95 69 9 38 11 670 7 4 8 374 42 159 53 82 98 364 308 0 t 0 0 0 0 176 226 230 384 211 138 70 785 603 727 44 23 21 765 129 191 101 95 59 352 129 130 0
positions_7nt_m1_rc_shift4 (positions_7nt_m1_rc)				; positions_6nt_m2 versus positions_7nt_m1_rc; m=4/14; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.750894; ----rmytbcATTTGCATaAcAAwrgv ; cor=; Ncor= a 0 0 0 0 180 174 139 109 146 128 453 25 66 84 82 39 645 25 409 489 36 576 583 353 180 146 219 c 0 0 0 0 138 184 185 162 170 314 67 24 92 17 34 603 4 22 59 20 444 33 22 32 61 132 178 g 0 0 0 0 202 152 154 136 168 87 61 12 39 8 531 7 3 11 116 11 108 16 39 42 365 307 165 t 0 0 0 0 139 149 181 252 175 130 78 598 462 550 12 10 7 601 75 139 71 34 15 232 53 74 97
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)				; positions_6nt_m2 versus positions_6nt_m1_rc; m=5/14; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.741229; -ydyatwTGCATATGCAwatryayr-- ; cor=; Ncor= a 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 208 0 0 c 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 160 0 0 g 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 191 0 0 t 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203 155 0 0
positions_7nt_m3_rc_shift3 (positions_7nt_m3_rc)				; positions_6nt_m2 versus positions_7nt_m3_rc; m=6/14; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.702386; ---kbywTTgTTaTGCAtAAcAAwrvm ; cor=; Ncor= a 0 0 0 35 25 26 51 12 9 22 33 11 111 5 13 4 155 34 138 115 17 131 129 73 43 44 54 c 0 0 0 35 46 73 30 9 13 27 10 13 14 3 3 147 4 8 5 10 102 14 18 13 26 51 43 g 0 0 0 43 52 26 12 18 14 101 10 5 8 4 147 3 3 14 13 10 27 13 9 30 72 46 35 t 0 0 0 54 44 42 74 128 131 17 114 138 34 155 4 13 5 111 11 32 21 9 11 51 26 26 35
oligos_7nt_mkv4_m2_shift6 (oligos_7nt_mkv4_m2)				; positions_6nt_m2 versus oligos_7nt_mkv4_m2; m=7/14; ncol2=20; w=0; offset=3; strand=D; shift=6; score=0.696222; ------yyhcATTTGCATaAcAAwrg- ; cor=; Ncor= a 0 0 0 0 0 0 177 143 192 159 530 32 74 97 95 43 731 30 446 536 49 635 665 270 225 181 0 c 0 0 0 0 0 0 203 197 191 360 74 22 99 18 38 698 10 20 75 34 491 48 24 48 85 183 0 g 0 0 0 0 0 0 183 171 152 104 75 12 43 8 609 5 4 15 144 19 134 24 38 48 363 294 0 t 0 0 0 0 0 0 194 246 222 134 78 691 541 634 15 11 12 692 92 168 83 50 30 391 84 99 0
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_6nt_m2 versus positions_7nt_m2; m=8/14; ncol2=24; w=-2; offset=-2; strand=D; shift=1; score=0.69061; -ydyaTtTgCATATGcAaAtryayr-- ; cor=; Ncor= a 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 78 0 0 c 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 48 0 0 g 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 63 0 0 t 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73 53 0 0
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_6nt_m2 versus positions_6nt_m4_rc; m=9/14; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.680178; rtgcATATGCATwTgcAtrwrwry--- ; cor=; Ncor= a 258 119 161 118 516 44 516 18 42 35 681 79 327 90 140 186 528 100 201 233 232 205 242 163 0 0 0 c 140 181 74 419 60 89 51 41 24 669 13 79 50 72 86 390 58 110 99 187 168 183 160 208 0 0 0 g 197 105 370 80 90 24 70 13 646 9 49 57 132 50 440 56 107 85 349 141 209 158 208 165 0 0 0 t 159 349 149 137 88 597 117 682 42 41 11 539 245 542 88 122 61 459 105 193 145 208 144 218 0 0 0
oligos_6nt_mkv3_m3_shift7 (oligos_6nt_mkv3_m3)				; positions_6nt_m2 versus oligos_6nt_mkv3_m3; m=10/14; ncol2=21; w=0; offset=4; strand=D; shift=7; score=0.662096; -------yhcaTTTGCATaAcAAwgsm ; cor=; Ncor= a 0 0 0 0 0 0 0 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 c 0 0 0 0 0 0 0 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 g 0 0 0 0 0 0 0 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 t 0 0 0 0 0 0 0 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; positions_6nt_m2 versus oligos_6nt_mkv3_m1; m=11/14; ncol2=22; w=-2; offset=-2; strand=D; shift=1; score=0.646122; -yryaTwTGCATATGCAwAtryr---- ; cor=; Ncor= a 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 0 0 0 c 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 0 0 0 g 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 0 0 0 t 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0 0 0 0
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; positions_6nt_m2 versus positions_7nt_m5_rc; m=12/14; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.596399; gyrtatgygCATATGCAaATryry--- ; cor=; Ncor= a 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 0 0 0 c 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 0 0 0 g 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 0 0 0 t 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87 0 0 0
oligos_7nt_mkv4_m1_rc_shift6 (oligos_7nt_mkv4_m1_rc)				; positions_6nt_m2 versus oligos_7nt_mkv4_m1_rc; m=13/14; ncol2=16; w=0; offset=3; strand=R; shift=6; score=0.59599; ------aydcATtTGCATawsa----- ; cor=; Ncor= a 0 0 0 0 0 0 328 201 293 156 898 19 193 86 102 55 1043 61 667 279 200 472 0 0 0 0 0 c 0 0 0 0 0 0 235 295 204 594 63 35 79 55 37 991 14 41 84 102 332 237 0 0 0 0 0 g 0 0 0 0 0 0 271 203 278 129 70 17 90 11 931 10 11 24 163 70 343 137 0 0 0 0 0 t 0 0 0 0 0 0 259 394 318 214 62 1022 731 941 23 37 25 967 179 642 218 247 0 0 0 0 0
oligos_7nt_mkv4_m4_shift11 (oligos_7nt_mkv4_m4)				; positions_6nt_m2 versus oligos_7nt_mkv4_m4; m=14/14; ncol2=15; w=0; offset=8; strand=D; shift=11; score=0.524228; -----------ttTGCATrACAAwrg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 0 c 0 0 0 0 0 0 0 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 0 g 0 0 0 0 0 0 0 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 0 t 0 0 0 0 0 0 0 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------wtATGCwAATgw ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 c 0 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 g 0 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 t 0 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210
oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/10; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------wtATGCwAATgw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 c 0 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 g 0 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 t 0 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210
oligos_7nt_mkv4_m1_shift9 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=2/10; ncol2=16; w=-2; offset=-2; strand=D; shift=9; score=0.678024; ---------tswtATGCAaATgh ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 c 0 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 g 0 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 t 0 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293
oligos_7nt_mkv4_m2_rc_shift5 (oligos_7nt_mkv4_m2_rc)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2_rc; m=3/10; ncol2=20; w=-6; offset=-6; strand=R; shift=5; score=0.538597; -----cywTTgTtATGCAAATgd ; cor=; Ncor= a 0 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 c 0 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 g 0 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 t 0 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192
oligos_6nt_mkv3_m3_rc_shift3 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3_rc; m=4/10; ncol2=21; w=-8; offset=-8; strand=R; shift=3; score=0.50804; ---kkscwTTgTtATGCAAAtgd ; cor=; Ncor= a 0 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 c 0 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 g 0 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 t 0 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209
positions_7nt_m4_shift5 (positions_7nt_m4)				; oligos_7nt_mkv4_m3 versus positions_7nt_m4; m=5/10; ncol2=22; w=-6; offset=-6; strand=D; shift=5; score=0.486311; -----cywTTgtyATGCAAATgm ; cor=; Ncor= a 0 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 c 0 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 g 0 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 t 0 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163
positions_7nt_m1_shift3 (positions_7nt_m1)				; oligos_7nt_mkv4_m3 versus positions_7nt_m1; m=6/10; ncol2=24; w=-8; offset=-8; strand=D; shift=3; score=0.444909; ---kbcywTTgTtATGCAAATgv ; cor=; Ncor= a 0 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 c 0 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 g 0 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 t 0 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m1; m=7/10; ncol2=22; w=-9; offset=-9; strand=D; shift=2; score=0.424616; --yryaTwTGCATATGCAwAtry ; cor=; Ncor= a 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 c 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 g 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 t 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142
positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)				; oligos_7nt_mkv4_m3 versus positions_7nt_m5_rc; m=8/10; ncol2=24; w=-10; offset=-10; strand=R; shift=1; score=0.408597; -gyrtatgygCATATGCAaATry ; cor=; Ncor= a 0 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 c 0 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 g 0 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 t 0 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104
oligos_7nt_mkv4_m4_rc_shift5 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m4_rc; m=9/10; ncol2=15; w=-6; offset=-6; strand=R; shift=5; score= 0.4033; -----cywTTGTyATGCAaa--- ; cor=; Ncor= a 0 0 0 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 c 0 0 0 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 g 0 0 0 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 t 0 0 0 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0
positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc)				; oligos_7nt_mkv4_m3 versus positions_7nt_m2_rc; m=10/10; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.400754; yrtryaTtTgCATATGcAaAtrh ; cor=; Ncor= a 53 73 37 65 19 153 12 59 7 30 10 215 14 206 13 15 47 207 136 185 29 66 62 c 63 58 58 31 129 43 38 16 20 5 202 2 18 7 7 11 163 4 31 9 19 29 72 g 48 77 44 91 31 20 6 33 3 160 12 10 6 18 4 200 5 21 20 38 39 126 38 t 78 34 103 55 63 26 186 134 212 47 18 15 204 11 218 16 27 10 55 10 155 21 70

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift1 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=24; shift=1; ncol=25; -kbywTTgTTaTGCAtAAcAAwrvm ; Alignment reference a 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 42 44 54 c 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 26 52 43 g 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 73 46 35 t 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51 26 25 35
positions_7nt_m3_shift1 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -kbywTTgTTaTGCAtAAcAAwrvm ; cor=; Ncor= a 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 42 44 54 c 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 26 52 43 g 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 73 46 35 t 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51 26 25 35
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m3 versus positions_7nt_m1; m=2/8; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.735252; kbcywTTgTtATGCAAATgvarky- ; cor=; Ncor= a 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 149 139 0 c 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 152 202 0 g 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 184 138 0 t 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139 174 180 0
positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)				; positions_7nt_m3 versus positions_6nt_m2_rc; m=3/8; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.702386; -ymywttswTATGCAwATGCAtata ; cor=; Ncor= a 0 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 108 c 0 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 79 g 0 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 81 t 0 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107 73
positions_7nt_m4_shift2 (positions_7nt_m4)				; positions_7nt_m3 versus positions_7nt_m4; m=4/8; ncol2=22; w=0; offset=1; strand=D; shift=2; score=0.693357; --cywTTgtyATGCAAATgmarry- ; cor=; Ncor= a 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 226 176 0 c 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 176 241 0 g 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 231 173 0 t 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192 201 244 0
oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)				; positions_7nt_m3 versus oligos_7nt_mkv4_m2_rc; m=5/8; ncol2=20; w=0; offset=1; strand=R; shift=2; score=0.66181; --cywTTgTtATGCAAATgdrr--- ; cor=; Ncor= a 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 0 0 0 c 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 0 0 0 g 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 0 0 0 t 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177 0 0 0
oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)				; positions_7nt_m3 versus oligos_6nt_mkv3_m3_rc; m=6/8; ncol2=21; w=-1; offset=-1; strand=R; shift=0; score=0.649065; kkscwTTgTtATGCAAAtgdr---- ; cor=; Ncor= a 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 0 0 0 c 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 0 0 0 g 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 0 0 0 t 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0 0 0 0
oligos_7nt_mkv4_m4_rc_shift2 (oligos_7nt_mkv4_m4_rc)				; positions_7nt_m3 versus oligos_7nt_mkv4_m4_rc; m=7/8; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.542374; --cywTTGTyATGCAaa-------- ; cor=; Ncor= a 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 0 0 0 0 0 c 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 0 0 0 0 0 g 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 0 0 0 0 0 t 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0 0 0 0 0 0
oligos_7nt_mkv4_m1_shift6 (oligos_7nt_mkv4_m1)				; positions_7nt_m3 versus oligos_7nt_mkv4_m1; m=8/8; ncol2=16; w=0; offset=5; strand=D; shift=6; score=0.471159; ------tswtATGCAaATghrt--- ; cor=; Ncor= a 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 0 0 0 c 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 0 0 0 g 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 0 0 0 t 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift2 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=24; shift=2; ncol=26; --kbcywTTgTtATGCAAATgvarky ; Alignment reference a 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 149 139 c 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 152 202 g 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 184 138 t 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139 174 180
positions_7nt_m1_shift2 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --kbcywTTgTtATGCAAATgvarky ; cor=; Ncor= a 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 149 139 c 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 152 202 g 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 184 138 t 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139 174 180
positions_7nt_m4_shift4 (positions_7nt_m4)				; positions_7nt_m1 versus positions_7nt_m4; m=2/10; ncol2=22; w=0; offset=2; strand=D; shift=4; score=0.887848; ----cywTTgtyATGCAAATgmarry ; cor=; Ncor= a 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 226 176 c 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 176 241 g 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 231 173 t 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192 201 244
oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)				; positions_7nt_m1 versus oligos_6nt_mkv3_m3_rc; m=3/10; ncol2=21; w=0; offset=0; strand=R; shift=2; score=0.87051; --kkscwTTgTtATGCAAAtgdr--- ; cor=; Ncor= a 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 0 0 c 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 0 0 g 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 0 0 t 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0 0 0
oligos_7nt_mkv4_m2_rc_shift4 (oligos_7nt_mkv4_m2_rc)				; positions_7nt_m1 versus oligos_7nt_mkv4_m2_rc; m=4/10; ncol2=20; w=0; offset=2; strand=R; shift=4; score=0.82711; ----cywTTgTtATGCAAATgdrr-- ; cor=; Ncor= a 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 0 0 c 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 0 0 g 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 0 0 t 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177 0 0
positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)				; positions_7nt_m1 versus positions_6nt_m2_rc; m=5/10; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.750894; ---ymywttswTATGCAwATGCAtat ; cor=; Ncor= a 0 0 0 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 c 0 0 0 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 g 0 0 0 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 t 0 0 0 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m1 versus positions_7nt_m3; m=6/10; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.735252; ---kbywTTgTTaTGCAtAAcAAwrv ; cor=; Ncor= a 0 0 0 35 26 26 51 11 9 21 32 11 111 5 13 4 155 34 138 114 17 131 128 74 42 44 c 0 0 0 35 46 72 30 9 13 27 10 13 14 3 3 147 4 8 5 10 101 14 18 12 26 52 g 0 0 0 43 51 26 13 18 14 102 10 5 8 4 147 3 3 14 13 10 27 13 9 30 73 46 t 0 0 0 54 44 43 73 129 131 17 115 138 34 155 4 13 5 111 11 33 22 9 12 51 26 25
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_7nt_m1 versus positions_6nt_m4; m=7/10; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.607428; rywywyaTgcAwATGCATATgcay-- ; cor=; Ncor= a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 0 0 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 0 0 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 0 0 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258 0 0
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)				; positions_7nt_m1 versus oligos_7nt_mkv4_m1; m=8/10; ncol2=16; w=0; offset=6; strand=D; shift=8; score=0.606349; --------tswtATGCAaATghrt-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 0 0 c 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 0 0 g 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 0 0 t 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328 0 0
oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)				; positions_7nt_m1 versus oligos_7nt_mkv4_m4_rc; m=9/10; ncol2=15; w=0; offset=2; strand=R; shift=4; score=0.588495; ----cywTTGTyATGCAaa------- ; cor=; Ncor= a 0 0 0 0 84 79 390 10 19 49 28 61 651 11 10 34 493 301 451 0 0 0 0 0 0 0 c 0 0 0 0 283 328 34 17 7 60 6 379 10 11 14 528 30 84 59 0 0 0 0 0 0 0 g 0 0 0 0 148 75 39 15 18 548 18 63 2 10 610 44 40 150 81 0 0 0 0 0 0 0 t 0 0 0 0 170 203 222 643 641 28 633 182 22 653 51 79 122 150 94 0 0 0 0 0 0 0
oligos_7nt_mkv4_m3_shift10 (oligos_7nt_mkv4_m3)				; positions_7nt_m1 versus oligos_7nt_mkv4_m3; m=10/10; ncol2=12; w=0; offset=8; strand=D; shift=10; score=0.444909; ----------wtATGCwAATgw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 298 176 686 10 10 39 216 634 705 45 177 210 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 79 154 15 7 8 630 18 44 10 34 120 141 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 120 131 14 16 688 23 50 39 5 35 258 171 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 235 271 17 699 26 40 448 15 12 618 177 210 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift10 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=11; shift=10; ncol=21; ----------waACAAAGgam ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 295 332 1009 3 971 932 943 25 174 304 327 c 0 0 0 0 0 0 0 0 0 0 132 233 7 969 13 43 15 13 158 252 272 g 0 0 0 0 0 0 0 0 0 0 217 220 5 16 14 26 6 950 625 230 221 t 0 0 0 0 0 0 0 0 0 0 387 246 10 43 33 30 67 43 74 245 211
positions_6nt_m5_shift10 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=10; score= 1; ----------waACAAAGgam ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 295 332 1009 3 971 932 943 25 174 304 327 c 0 0 0 0 0 0 0 0 0 0 132 233 7 969 13 43 15 13 158 252 272 g 0 0 0 0 0 0 0 0 0 0 217 220 5 16 14 26 6 950 625 230 221 t 0 0 0 0 0 0 0 0 0 0 387 246 10 43 33 30 67 43 74 245 211
oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)				; positions_6nt_m5 versus oligos_6nt_mkv3_m5; m=2/4; ncol2=14; w=-3; offset=-3; strand=D; shift=7; score=0.672958; -------amaAAACAAAGcma ; cor=; Ncor= a 0 0 0 0 0 0 0 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 0 0 0 0 0 0 0 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 0 0 0 0 0 0 0 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 0 0 0 0 0 0 0 155 126 106 82 26 9 29 11 16 28 39 84 128 141
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; positions_6nt_m5 versus oligos_6nt_mkv3_m3; m=3/4; ncol2=21; w=-10; offset=-10; strand=D; shift=0; score=0.43353; yhcaTTTGCATaAcAAwgsmm ; cor=; Ncor= a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170
oligos_7nt_mkv4_m4_shift4 (oligos_7nt_mkv4_m4)				; positions_6nt_m5 versus oligos_7nt_mkv4_m4; m=4/4; ncol2=15; w=-6; offset=-6; strand=D; shift=4; score=0.416607; ----ttTGCATrACAAwrg-- ; cor=; Ncor= a 0 0 0 0 94 150 122 79 51 653 22 182 633 28 641 643 222 203 170 0 0 c 0 0 0 0 81 150 40 44 610 10 2 63 18 548 18 15 39 75 148 0 0 g 0 0 0 0 59 84 30 528 14 11 10 379 6 60 7 17 34 328 283 0 0 t 0 0 0 0 451 301 493 34 10 11 651 61 28 49 19 10 390 79 84 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift3 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---rywywyaTgcAwATGCATATgcay ; Alignment reference a 0 0 0 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 c 0 0 0 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 g 0 0 0 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 t 0 0 0 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258
positions_6nt_m4_shift3 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/12; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---rywywyaTgcAwATGCATATgcay ; cor=; Ncor= a 0 0 0 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 c 0 0 0 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 g 0 0 0 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 t 0 0 0 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258
positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)				; positions_6nt_m4 versus positions_7nt_m5_rc; m=2/12; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.812705; ---gyrtatgygCATATGCAaATryry ; cor=; Ncor= a 0 0 0 76 47 141 24 194 34 68 21 60 29 273 10 272 11 16 19 247 156 248 27 89 74 117 62 c 0 0 0 60 105 43 67 36 50 30 152 19 225 7 29 8 15 14 261 14 64 11 34 26 83 49 110 g 0 0 0 124 78 79 34 49 19 166 18 191 37 17 8 23 7 264 7 45 26 40 31 174 54 98 56 t 0 0 0 55 85 52 190 36 212 51 124 45 24 18 268 12 282 21 28 9 69 16 223 26 104 51 87
positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)				; positions_6nt_m4 versus positions_6nt_m1_rc; m=3/12; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.794258; ----ydyatwTGCATATGCAwatryay ; cor=; Ncor= a 0 0 0 0 140 198 105 311 70 227 36 64 50 643 47 604 39 41 122 617 299 436 133 222 173 277 144 c 0 0 0 0 188 144 244 153 172 69 58 18 586 10 44 22 21 41 505 13 113 36 114 124 228 144 200 g 0 0 0 0 168 183 127 115 35 119 14 509 35 21 20 45 8 579 19 57 74 172 151 274 128 166 167 t 0 0 0 0 218 189 238 135 437 299 606 123 43 40 603 43 646 53 68 27 228 70 316 94 185 127 203
positions_6nt_m3_shift5 (positions_6nt_m3)				; positions_6nt_m4 versus positions_6nt_m3; m=4/12; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.787578; -----rywtaTGCATwTGCATAtgyry ; cor=; Ncor= a 0 0 0 0 0 91 59 83 26 192 14 26 21 261 18 149 13 25 23 261 28 214 55 62 55 114 53 c 0 0 0 0 0 61 81 39 60 24 21 18 236 9 36 22 16 7 239 5 31 12 31 35 124 41 118 g 0 0 0 0 0 77 51 61 20 44 13 209 8 15 16 36 3 242 9 16 17 44 30 162 35 97 43 t 0 0 0 0 0 63 101 109 186 32 244 39 27 7 222 85 260 18 21 10 216 22 176 33 78 40 78
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_6nt_m4 versus positions_7nt_m2; m=5/12; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.763838; ----ydyaTtTgCATATGcAaAtryay ; cor=; Ncor= a 0 0 0 0 40 70 21 155 10 55 10 27 16 218 11 204 15 18 47 212 134 186 26 63 55 103 34 c 0 0 0 0 70 38 126 39 38 20 21 5 200 4 18 6 10 12 160 3 33 6 20 31 91 44 77 g 0 0 0 0 47 72 29 19 9 31 4 163 11 7 7 18 2 202 5 20 16 38 43 129 31 58 58 t 0 0 0 0 85 62 66 29 185 136 207 47 15 13 206 14 215 10 30 7 59 12 153 19 65 37 73
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; positions_6nt_m4 versus oligos_6nt_mkv3_m1; m=6/12; ncol2=22; w=0; offset=1; strand=D; shift=4; score=0.763228; ----yryaTwTGCATATGCAwAtryr- ; cor=; Ncor= a 0 0 0 0 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 0 c 0 0 0 0 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 0 g 0 0 0 0 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 0 t 0 0 0 0 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86 0
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_6nt_m4 versus positions_6nt_m2_rc; m=7/12; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.680178; ymywttswTATGCAwATGCAtata--- ; cor=; Ncor= a 62 89 63 137 44 72 52 103 33 282 11 24 20 301 146 279 11 33 47 274 46 214 80 108 0 0 0 c 88 94 131 50 54 42 95 38 56 20 12 11 277 3 32 20 13 14 233 23 37 22 84 79 0 0 0 g 79 73 52 68 48 68 124 45 20 16 3 273 19 13 29 24 8 271 35 29 40 61 70 81 0 0 0 t 112 85 95 86 195 159 70 155 232 23 315 33 25 24 134 18 309 23 26 15 218 44 107 73 0 0 0
oligos_6nt_mkv3_m3_rc_shift5 (oligos_6nt_mkv3_m3_rc)				; positions_6nt_m4 versus oligos_6nt_mkv3_m3_rc; m=8/12; ncol2=21; w=0; offset=2; strand=R; shift=5; score=0.628309; -----kkscwTTgTtATGCAAAtgdr- ; cor=; Ncor= a 0 0 0 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 0 c 0 0 0 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 0 g 0 0 0 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 0 t 0 0 0 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141 0
oligos_7nt_mkv4_m2_rc_shift7 (oligos_7nt_mkv4_m2_rc)				; positions_6nt_m4 versus oligos_7nt_mkv4_m2_rc; m=9/12; ncol2=20; w=0; offset=4; strand=R; shift=7; score=0.617762; -------cywTTgTtATGCAAATgdrr ; cor=; Ncor= a 0 0 0 0 0 0 0 99 84 391 30 50 83 168 92 692 12 11 15 634 541 691 78 134 222 246 194 c 0 0 0 0 0 0 0 294 363 48 38 24 134 19 144 15 4 5 609 8 43 12 75 104 152 171 183 g 0 0 0 0 0 0 0 183 85 48 24 48 491 34 75 20 10 698 38 18 99 22 74 360 191 197 203 t 0 0 0 0 0 0 0 181 225 270 665 635 49 536 446 30 731 43 95 97 74 32 530 159 192 143 177
positions_7nt_m1_shift5 (positions_7nt_m1)				; positions_6nt_m4 versus positions_7nt_m1; m=10/12; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.607428; -----kbcywTTgTtATGCAAATgvar ; cor=; Ncor= a 0 0 0 0 0 140 97 74 53 232 15 34 71 139 75 601 7 10 12 550 462 598 78 130 175 252 181 c 0 0 0 0 0 151 165 307 365 42 39 16 108 11 116 11 3 7 531 8 39 12 61 87 168 136 154 g 0 0 0 0 0 187 178 132 61 32 22 33 444 20 59 22 4 603 34 17 92 24 67 314 170 162 185 t 0 0 0 0 0 181 219 146 180 353 583 576 36 489 409 25 645 39 82 84 66 25 453 128 146 109 139
positions_7nt_m4_shift7 (positions_7nt_m4)				; positions_6nt_m4 versus positions_7nt_m4; m=11/12; ncol2=22; w=0; offset=4; strand=D; shift=7; score=0.594288; -------cywTTgtyATGCAAATgmar ; cor=; Ncor= a 0 0 0 0 0 0 0 130 129 352 59 95 101 191 129 765 21 23 44 727 603 785 70 138 211 384 230 c 0 0 0 0 0 0 0 308 364 98 82 53 159 42 374 8 4 7 670 11 38 9 69 95 285 150 199 g 0 0 0 0 0 0 0 197 96 93 50 62 466 77 78 21 7 741 41 16 77 22 59 470 175 181 213 t 0 0 0 0 0 0 0 199 245 291 643 624 108 524 253 40 802 63 79 80 116 18 636 131 163 119 192
oligos_7nt_mkv4_m1_shift11 (oligos_7nt_mkv4_m1)				; positions_6nt_m4 versus oligos_7nt_mkv4_m1; m=12/12; ncol2=16; w=0; offset=8; strand=D; shift=11; score=0.587517; -----------tswtATGCAaATghrt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 247 218 642 179 967 25 37 23 941 731 1022 62 214 318 394 259 c 0 0 0 0 0 0 0 0 0 0 0 137 343 70 163 24 11 10 931 11 90 17 70 129 278 203 271 g 0 0 0 0 0 0 0 0 0 0 0 237 332 102 84 41 14 991 37 55 79 35 63 594 204 295 235 t 0 0 0 0 0 0 0 0 0 0 0 472 200 279 667 61 1043 55 102 86 193 19 898 156 293 201 328