One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.161809_2026-01-22.161809_qNN5KW/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/2026/01/22/peak-motifs.2026-01-22.161809_2026-01-22.161809_qNN5KW/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift1 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift1 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=18; shift=1; ncol=19; -hhcaaCCACCAACCAmhw ; Alignment reference a 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434

positions_7nt_m4_shift1 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/12; ncol2=18; w=0; offset=0; strand=D; shift=1; score= 1; -hhcaaCCACCAACCAmhw ; cor=; Ncor= a 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434

positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)
; positions_7nt_m4 versus positions_7nt_m5_rc; m=2/12; ncol2=18; w=0; offset=0; strand=R; shift=1; score=0.964218; -hhhaacCACCAACCAchw ; cor=; Ncor= a 0 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 0 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 0 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 0 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457

positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_7nt_m4 versus positions_6nt_m1; m=3/12; ncol2=16; w=0; offset=2; strand=D; shift=3; score=0.841103; ---hhacCACCAACCAChw ; cor=; Ncor= a 0 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; positions_7nt_m4 versus oligos_6nt_mkv3_m1; m=4/12; ncol2=16; w=0; offset=2; strand=D; shift=3; score=0.827668; ---hhwccACCAACCAchw ; cor=; Ncor= a 0 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m4 versus positions_7nt_m1; m=5/12; ncol2=17; w=0; offset=2; strand=D; shift=3; score=0.783318; ---hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; positions_7nt_m4 versus positions_6nt_m3_rc; m=6/12; ncol2=18; w=-1; offset=-1; strand=R; shift=0; score=0.778993; hwCCAACCACCAactahw- ; cor=; Ncor= a 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 454 299 361 0 c 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 237 364 243 0 g 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 103 105 143 0 t 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441 232 258 279 0

oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)
; positions_7nt_m4 versus oligos_7nt_mkv4_m1; m=7/12; ncol2=16; w=0; offset=3; strand=D; shift=4; score=0.703651; ----hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_7nt_m4 versus positions_6nt_m4; m=8/12; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.687324; whhcyACCAACCACcaamw ; cor=; Ncor= a 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 562 502 c 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 435 366 g 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 157 216 t 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258 379 449

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_7nt_m4 versus positions_7nt_m2_rc; m=9/12; ncol2=23; w=0; offset=1; strand=R; shift=2; score=0.586854; --wwwhyyACCAACCACCA ; cor=; Ncor= a 0 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 c 0 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 g 0 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 t 0 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117

oligos_7nt_mkv4_m3_shift7 (oligos_7nt_mkv4_m3)
; positions_7nt_m4 versus oligos_7nt_mkv4_m3; m=10/12; ncol2=12; w=0; offset=6; strand=D; shift=7; score=0.516119; -------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581

oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)
; positions_7nt_m4 versus oligos_6nt_mkv3_m5; m=11/12; ncol2=11; w=0; offset=6; strand=D; shift=7; score=0.480039; -------waCCAAACaww- ; cor=; Ncor= a 0 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 c 0 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 g 0 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 t 0 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0

oligos_7nt_mkv4_m2_shift5 (oligos_7nt_mkv4_m2)
; positions_7nt_m4 versus oligos_7nt_mkv4_m2; m=12/12; ncol2=11; w=0; offset=4; strand=D; shift=5; score=0.477142; -----wmCAACAACha--- ; cor=; Ncor= a 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 0 0 0 c 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 0 0 0 g 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 0 0 0 t 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wyCACCTAACww ; Alignment reference a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wyCACCTAACww ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307

positions_7nt_m3_shift2 (positions_7nt_m3)
; positions_6nt_m5 versus positions_7nt_m3; m=2/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.90842; --yyTACCTAAChw ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m5 versus positions_6nt_m2; m=3/8; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.838102; -wyyTACCTAAChw ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299

oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; positions_6nt_m5 versus oligos_6nt_mkv3_m3; m=4/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.782481; --whcACCTAACta ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; positions_6nt_m5 versus oligos_7nt_mkv4_m4; m=5/8; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.732165; wwtktACCTAACmw ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; positions_6nt_m5 versus oligos_6nt_mkv3_m2; m=6/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.62239; wwygTACCTAACta ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; positions_6nt_m5 versus oligos_6nt_mkv3_m5; m=7/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.615731; ----waCCAAACaw ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; positions_6nt_m5 versus oligos_7nt_mkv4_m5; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=3; score=0.533733; ---hmACCAAACcC ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -wyyTACCTAAChw ; Alignment reference a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -wyyTACCTAAChw ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299

positions_7nt_m3_shift2 (positions_7nt_m3)
; positions_6nt_m2 versus positions_7nt_m3; m=2/8; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.92307; --yyTACCTAAChw ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; positions_6nt_m2 versus oligos_7nt_mkv4_m4; m=3/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.856322; wwtktACCTAACmw ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m2 versus positions_6nt_m5; m=4/8; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.838102; --wyCACCTAACww ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=5/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.751885; wwygTACCTAACta ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167

oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; positions_6nt_m2 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=15; w=0; offset=1; strand=D; shift=2; score=0.695545; --whcACCTAACta ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; positions_6nt_m2 versus oligos_6nt_mkv3_m5; m=7/8; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.563866; ----waCCAAACaw ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; positions_6nt_m2 versus oligos_7nt_mkv4_m5; m=8/8; ncol2=15; w=0; offset=2; strand=D; shift=3; score=0.475052; ---hmACCAAACcC ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift7 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=7; ncol=18; -------wmCAACAACha ; Alignment reference a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615

oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/10; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------wmCAACAACha ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615

oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=2/10; ncol2=12; w=-1; offset=-1; strand=D; shift=6; score=0.83876; ------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1; m=3/10; ncol2=16; w=-4; offset=-4; strand=D; shift=3; score=0.583549; ---hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659

positions_6nt_m1_shift2 (positions_6nt_m1)
; oligos_7nt_mkv4_m2 versus positions_6nt_m1; m=4/10; ncol2=16; w=-5; offset=-5; strand=D; shift=2; score=0.570603; --hhacCACCAACCAChw ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=5/10; ncol2=16; w=-5; offset=-5; strand=D; shift=2; score=0.568631; --hhwccACCAACCAchw ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717

positions_7nt_m1_shift2 (positions_7nt_m1)
; oligos_7nt_mkv4_m2 versus positions_7nt_m1; m=6/10; ncol2=17; w=-5; offset=-5; strand=D; shift=2; score=0.533663; --hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527

positions_6nt_m3_rc_shift6 (positions_6nt_m3_rc)
; oligos_7nt_mkv4_m2 versus positions_6nt_m3_rc; m=7/10; ncol2=18; w=-1; offset=-1; strand=R; shift=6; score=0.49493; ------hwCCAACCACCA ; cor=; Ncor= a 0 0 0 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 c 0 0 0 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 g 0 0 0 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 t 0 0 0 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; oligos_7nt_mkv4_m2 versus positions_7nt_m5_rc; m=8/10; ncol2=18; w=-7; offset=-7; strand=R; shift=0; score=0.494442; hhhaacCACCAACCAchw ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457

positions_7nt_m4_shift3 (positions_7nt_m4)
; oligos_7nt_mkv4_m2 versus positions_7nt_m4; m=9/10; ncol2=18; w=-4; offset=-4; strand=D; shift=3; score=0.477142; ---hhcaaCCACCAACCA ; cor=; Ncor= a 0 0 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 c 0 0 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 g 0 0 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 t 0 0 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121

positions_6nt_m4_shift2 (positions_6nt_m4)
; oligos_7nt_mkv4_m2 versus positions_6nt_m4; m=10/10; ncol2=19; w=-5; offset=-5; strand=D; shift=2; score=0.470105; --whhcyACCAACCACca ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift2 ; 13 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=17; shift=2; ncol=19; --hmwcCACCAACCACcwm ; Alignment reference a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 682 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 675 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 227 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527 516

positions_7nt_m1_shift2 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/12; ncol2=17; w=0; offset=0; strand=D; shift=2; score= 1; --hmwcCACCAACCACcwm ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 682 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 675 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 227 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527 516

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=2/12; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.932332; --hhacCACCAACCAChw- ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 0 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 0 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 0 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527 0

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; positions_7nt_m1 versus oligos_6nt_mkv3_m1; m=3/12; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.930735; --hhwccACCAACCAchw- ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 0 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 0 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 0 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717 0

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; positions_7nt_m1 versus oligos_7nt_mkv4_m1; m=4/12; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.923963; ---hhycaCCAACCACcwh ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 796 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 781 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 283 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659 716

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_7nt_m1 versus positions_6nt_m4; m=5/12; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.851798; --whhcyACCAACCACcaa ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; positions_7nt_m1 versus positions_7nt_m5_rc; m=6/12; ncol2=18; w=-2; offset=-2; strand=R; shift=0; score=0.826227; hhhaacCACCAACCAchw- ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 0 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 0 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 0 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457 0

positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m1 versus positions_7nt_m4; m=7/12; ncol2=18; w=-2; offset=-2; strand=D; shift=0; score=0.783318; hhcaaCCACCAACCAmhw- ; cor=; Ncor= a 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 0 c 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 0 g 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 0 t 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434 0

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; positions_7nt_m1 versus positions_7nt_m2_rc; m=8/12; ncol2=23; w=-1; offset=-1; strand=R; shift=1; score=0.68817; -wwwhyyACCAACCACCAa ; cor=; Ncor= a 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 617 c 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 169 g 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 60 t 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117 148

positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)
; positions_7nt_m1 versus positions_6nt_m3_rc; m=9/12; ncol2=18; w=0; offset=1; strand=R; shift=3; score=0.612166; ---hwCCAACCACCAacta ; cor=; Ncor= a 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 454 c 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 237 g 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 103 t 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441 232

oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; positions_7nt_m1 versus oligos_7nt_mkv4_m3; m=10/12; ncol2=12; w=0; offset=4; strand=D; shift=6; score=0.607415; ------hwcCAACtAChw- ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 0 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 0 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 0 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581 0

oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)
; positions_7nt_m1 versus oligos_7nt_mkv4_m2; m=11/12; ncol2=11; w=0; offset=5; strand=D; shift=7; score=0.533663; -------wmCAACAACha- ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 0 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 0 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 0 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615 0

oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)
; positions_7nt_m1 versus oligos_6nt_mkv3_m5; m=12/12; ncol2=11; w=0; offset=4; strand=D; shift=6; score=0.472099; ------waCCAAACaww-- ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; wwtktACCTAACmwh ; Alignment reference a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wwtktACCTAACmwh ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_7nt_mkv4_m4 versus positions_6nt_m2; m=2/8; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.856322; -wyyTACCTAAChw- ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m2; m=3/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.85478; wwygTACCTAACtac ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182

positions_7nt_m3_shift2 (positions_7nt_m3)
; oligos_7nt_mkv4_m4 versus positions_7nt_m3; m=4/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.790477; --yyTACCTAAChw- ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0

positions_6nt_m5_shift2 (positions_6nt_m5)
; oligos_7nt_mkv4_m4 versus positions_6nt_m5; m=5/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.732165; --wyCACCTAACww- ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0

oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.709282; --whcACCTAACtam ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m5; m=7/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.585309; ----waCCAAACaww ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m5; m=8/8; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.497266; ---hmACCAAACcCt ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=15; shift=2; ncol=17; --whcACCTAACtamww ; Alignment reference a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 366 364 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 247 230 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 131 132 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256 343 361

oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score= 1; --whcACCTAACtamww ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 366 364 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 247 230 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 131 132 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256 343 361

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2; m=2/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.823032; wwygTACCTAACtachw ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 254 256 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 194 154 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 97 99 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182 228 264

positions_6nt_m5_shift2 (positions_6nt_m5)
; oligos_6nt_mkv3_m3 versus positions_6nt_m5; m=3/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.782481; --wyCACCTAACww--- ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 0 0 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 0 0 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 0 0 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0 0 0

positions_7nt_m3_shift2 (positions_7nt_m3)
; oligos_6nt_mkv3_m3 versus positions_7nt_m3; m=4/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.742358; --yyTACCTAAChw--- ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 0 0 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 0 0 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 0 0 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0 0 0

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m4; m=5/8; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.709282; wwtktACCTAACmwh-- ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 0 0 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 0 0 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 0 0 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280 0 0

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_6nt_mkv3_m3 versus positions_6nt_m2; m=6/8; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.695545; -wyyTACCTAAChw--- ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 0 0 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 0 0 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 0 0 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0 0 0

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m5; m=7/8; ncol2=15; w=0; offset=1; strand=D; shift=3; score=0.625443; ---hmACCAAACcCtah ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 290 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 205 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 99 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191 207

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m5; m=8/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.56566; ----waCCAAACaww-- ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift3 ; 14 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=16; shift=3; ncol=19; ---hhwccACCAACCAchw ; Alignment reference a 0 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/13; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---hhwccACCAACCAchw ; cor=; Ncor= a 0 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717

positions_6nt_m1_shift3 (positions_6nt_m1)
; oligos_6nt_mkv3_m1 versus positions_6nt_m1; m=2/13; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.991892; ---hhacCACCAACCAChw ; cor=; Ncor= a 0 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527

positions_7nt_m1_shift3 (positions_7nt_m1)
; oligos_6nt_mkv3_m1 versus positions_7nt_m1; m=3/13; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.930735; ---hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527

positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)
; oligos_6nt_mkv3_m1 versus positions_7nt_m5_rc; m=4/13; ncol2=18; w=-2; offset=-2; strand=R; shift=1; score=0.87543; -hhhaacCACCAACCAchw ; cor=; Ncor= a 0 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 0 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 0 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 0 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457

oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=5/13; ncol2=16; w=0; offset=1; strand=D; shift=4; score=0.868516; ----hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659

positions_7nt_m4_shift1 (positions_7nt_m4)
; oligos_6nt_mkv3_m1 versus positions_7nt_m4; m=6/13; ncol2=18; w=-2; offset=-2; strand=D; shift=1; score=0.827668; -hhcaaCCACCAACCAmhw ; cor=; Ncor= a 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434

positions_6nt_m4_shift3 (positions_6nt_m4)
; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=7/13; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.806797; ---whhcyACCAACCACca ; cor=; Ncor= a 0 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 c 0 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 g 0 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 t 0 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218

oligos_7nt_mkv4_m3_shift7 (oligos_7nt_mkv4_m3)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m3; m=8/13; ncol2=12; w=0; offset=4; strand=D; shift=7; score=0.659882; -------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; oligos_6nt_mkv3_m1 versus positions_7nt_m2_rc; m=9/13; ncol2=23; w=-1; offset=-1; strand=R; shift=2; score=0.652279; --wwwhyyACCAACCACCA ; cor=; Ncor= a 0 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 c 0 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 g 0 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 t 0 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; oligos_6nt_mkv3_m1 versus positions_6nt_m3_rc; m=10/13; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.584338; hwCCAACCACCAactahw- ; cor=; Ncor= a 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 454 299 361 0 c 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 237 364 243 0 g 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 103 105 143 0 t 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441 232 258 279 0

oligos_7nt_mkv4_m2_shift8 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=11/13; ncol2=11; w=0; offset=5; strand=D; shift=8; score=0.568631; --------wmCAACAACha ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615

oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m5; m=12/13; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.526422; -------waCCAAACaww- ; cor=; Ncor= a 0 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 c 0 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 g 0 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 t 0 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0

oligos_7nt_mkv4_m5_shift6 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5; m=13/13; ncol2=15; w=0; offset=3; strand=D; shift=6; score=0.521736; ------hmACCAAACcCta ; cor=; Ncor= a 0 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 c 0 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 g 0 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 t 0 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift2 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --yyTACCTAAChw ; Alignment reference a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301

positions_7nt_m3_shift2 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --yyTACCTAAChw ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_7nt_m3 versus positions_6nt_m2; m=2/8; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.92307; -wyyTACCTAAChw ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_7nt_m3 versus positions_6nt_m5; m=3/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.90842; --wyCACCTAACww ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; positions_7nt_m3 versus oligos_7nt_mkv4_m4; m=4/8; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.790477; wwtktACCTAACmw ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264

oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; positions_7nt_m3 versus oligos_6nt_mkv3_m3; m=5/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.742358; --whcACCTAACta ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; positions_7nt_m3 versus oligos_6nt_mkv3_m2; m=6/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.694032; wwygTACCTAACta ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; positions_7nt_m3 versus oligos_6nt_mkv3_m5; m=7/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.607839; ----waCCAAACaw ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; positions_7nt_m3 versus oligos_7nt_mkv4_m5; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=3; score=0.504957; ---hmACCAAACcC ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift6 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=6; ncol=17; ------waCCAAACaww ; Alignment reference a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358

oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/15; ncol2=11; w=0; offset=0; strand=D; shift=6; score= 1; ------waCCAAACaww ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358

oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m5; m=2/15; ncol2=15; w=-1; offset=-1; strand=D; shift=5; score=0.634182; -----hmACCAAACcCt ; cor=; Ncor= a 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 c 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 g 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 t 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480

positions_6nt_m5_shift4 (positions_6nt_m5)
; oligos_6nt_mkv3_m5 versus positions_6nt_m5; m=3/15; ncol2=12; w=-2; offset=-2; strand=D; shift=4; score=0.615731; ----wyCACCTAACww- ; cor=; Ncor= a 0 0 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 c 0 0 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 g 0 0 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 t 0 0 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0

positions_7nt_m3_shift4 (positions_7nt_m3)
; oligos_6nt_mkv3_m5 versus positions_7nt_m3; m=4/15; ncol2=12; w=-2; offset=-2; strand=D; shift=4; score=0.607839; ----yyTACCTAAChw- ; cor=; Ncor= a 0 0 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 c 0 0 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 g 0 0 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 t 0 0 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0

oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m4; m=5/15; ncol2=15; w=-4; offset=-4; strand=D; shift=2; score=0.585309; --wwtktACCTAACmwh ; cor=; Ncor= a 0 0 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 c 0 0 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 g 0 0 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 t 0 0 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m3; m=6/15; ncol2=15; w=-2; offset=-2; strand=D; shift=4; score=0.56566; ----whcACCTAACtam ; cor=; Ncor= a 0 0 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 c 0 0 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 g 0 0 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 t 0 0 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256

positions_6nt_m2_shift3 (positions_6nt_m2)
; oligos_6nt_mkv3_m5 versus positions_6nt_m2; m=7/15; ncol2=13; w=-3; offset=-3; strand=D; shift=3; score=0.563866; ---wyyTACCTAAChw- ; cor=; Ncor= a 0 0 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 c 0 0 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 g 0 0 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 t 0 0 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m1; m=8/15; ncol2=16; w=-4; offset=-4; strand=D; shift=2; score=0.526422; --hhwccACCAACCAch ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727

positions_6nt_m1_shift2 (positions_6nt_m1)
; oligos_6nt_mkv3_m5 versus positions_6nt_m1; m=9/15; ncol2=16; w=-4; offset=-4; strand=D; shift=2; score=0.511326; --hhacCACCAACCACh ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m1; m=10/15; ncol2=16; w=-3; offset=-3; strand=D; shift=3; score=0.499606; ---hhycaCCAACCACc ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526

positions_7nt_m4_shift0 (positions_7nt_m4)
; oligos_6nt_mkv3_m5 versus positions_7nt_m4; m=11/15; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.480039; hhcaaCCACCAACCAmh ; cor=; Ncor= a 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 c 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 g 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 t 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414

oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m2; m=12/15; ncol2=17; w=-4; offset=-4; strand=D; shift=2; score=0.477432; --wwygTACCTAACtac ; cor=; Ncor= a 0 0 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 c 0 0 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 g 0 0 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 t 0 0 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182

positions_7nt_m1_shift2 (positions_7nt_m1)
; oligos_6nt_mkv3_m5 versus positions_7nt_m1; m=13/15; ncol2=17; w=-4; offset=-4; strand=D; shift=2; score=0.472099; --hmwcCACCAACCACc ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; oligos_6nt_mkv3_m5 versus positions_7nt_m5_rc; m=14/15; ncol2=18; w=-6; offset=-6; strand=R; shift=0; score=0.462941; hhhaacCACCAACCAch ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435

positions_6nt_m4_shift2 (positions_6nt_m4)
; oligos_6nt_mkv3_m5 versus positions_6nt_m4; m=15/15; ncol2=19; w=-4; offset=-4; strand=D; shift=2; score=0.425921; --whhcyACCAACCACc ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; wwygTACCTAACtachw ; Alignment reference a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 254 256 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 194 154 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 97 99 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182 228 264

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; wwygTACCTAACtachw ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 254 256 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 194 154 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 97 99 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182 228 264

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m4; m=2/7; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.85478; wwtktACCTAACmwh-- ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 0 0 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 0 0 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 0 0 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280 0 0

oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3; m=3/7; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.823032; --whcACCTAACtamww ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 366 364 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 247 230 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 131 132 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256 343 361

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=4/7; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.751885; -wyyTACCTAAChw--- ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 0 0 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 0 0 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 0 0 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0 0 0

positions_7nt_m3_shift2 (positions_7nt_m3)
; oligos_6nt_mkv3_m2 versus positions_7nt_m3; m=5/7; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.694032; --yyTACCTAAChw--- ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 0 0 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 0 0 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 0 0 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0 0 0

positions_6nt_m5_shift2 (positions_6nt_m5)
; oligos_6nt_mkv3_m2 versus positions_6nt_m5; m=6/7; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.62239; --wyCACCTAACww--- ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 0 0 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 0 0 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 0 0 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0 0 0

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m5; m=7/7; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.477432; ----waCCAAACaww-- ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift1 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=18; shift=1; ncol=19; -wdtagtTGGTGGTTGGwd ; Alignment reference a 0 279 258 232 441 96 121 96 58 35 41 79 33 52 58 76 105 269 280 c 0 143 105 103 119 53 52 73 18 10 34 15 16 38 13 23 69 101 131 g 0 243 364 237 230 691 172 57 885 889 17 848 951 83 67 863 740 227 357 t 0 361 299 454 236 186 681 800 65 92 934 84 26 853 888 64 112 429 258

positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/11; ncol2=18; w=0; offset=0; strand=D; shift=1; score= 1; -wdtagtTGGTGGTTGGwd ; cor=; Ncor= a 0 279 258 232 441 96 121 96 58 35 41 79 33 52 58 76 105 269 280 c 0 143 105 103 119 53 52 73 18 10 34 15 16 38 13 23 69 101 131 g 0 243 364 237 230 691 172 57 885 889 17 848 951 83 67 863 740 227 357 t 0 361 299 454 236 186 681 800 65 92 934 84 26 853 888 64 112 429 258

positions_7nt_m4_rc_shift0 (positions_7nt_m4_rc)
; positions_6nt_m3 versus positions_7nt_m4_rc; m=2/11; ncol2=18; w=-1; offset=-1; strand=R; shift=0; score=0.778993; wdkTGGTTGGTGGttgdd- ; cor=; Ncor= a 434 414 293 121 111 64 62 101 63 34 64 204 202 262 228 240 438 446 0 c 202 155 75 86 47 27 49 42 16 17 32 45 79 104 80 107 216 165 0 g 376 428 461 97 1198 1276 84 107 1413 1312 26 1119 1096 254 260 907 428 402 0 t 520 535 703 1228 176 165 1337 1282 40 169 1410 164 155 912 964 278 450 519 0

positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_6nt_m3 versus positions_7nt_m2; m=3/11; ncol2=23; w=0; offset=0; strand=D; shift=1; score=0.75956; -wdtwgtTGGTGGTTGGTr ; cor=; Ncor= a 0 282 273 240 370 152 148 117 108 77 35 71 30 30 63 49 67 110 486 c 0 147 99 94 118 58 60 66 33 16 33 8 14 19 9 11 40 36 72 g 0 227 311 189 218 567 169 99 736 734 23 828 907 49 46 891 792 93 262 t 0 338 311 471 288 217 617 712 117 167 903 87 43 896 876 43 95 755 174

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_6nt_m3 versus positions_7nt_m5; m=4/11; ncol2=18; w=-1; offset=-1; strand=D; shift=0; score=0.714303; wdgTGGTTGGTGgttddd- ; cor=; Ncor= a 457 435 214 112 138 38 39 87 83 55 110 232 274 370 305 535 466 522 0 c 193 142 51 98 28 11 39 20 15 29 30 56 118 143 110 187 234 204 0 g 371 504 1055 67 1321 1502 69 76 1538 1386 75 1216 1013 300 327 478 445 444 0 t 634 574 335 1378 168 104 1508 1472 19 185 1440 151 250 842 913 455 510 485 0

positions_6nt_m4_rc_shift4 (positions_6nt_m4_rc)
; positions_6nt_m3 versus positions_6nt_m4_rc; m=5/11; ncol2=19; w=0; offset=3; strand=R; shift=4; score=0.644865; ----wkttgGTGGTTGGTr ; cor=; Ncor= a 0 0 0 0 449 379 258 218 204 132 55 98 36 38 87 76 84 159 600 c 0 0 0 0 216 157 107 116 57 34 63 14 14 25 15 10 52 44 112 g 0 0 0 0 366 435 271 168 1040 1090 30 1265 1434 85 58 1397 1257 141 507 t 0 0 0 0 502 562 897 1031 232 277 1385 156 49 1385 1373 50 140 1189 314

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; positions_6nt_m3 versus positions_6nt_m1_rc; m=6/11; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.622578; wdGTGGTTGGTGgtdd--- ; cor=; Ncor= a 527 523 220 126 179 47 63 111 93 77 176 274 325 495 507 548 0 0 0 c 257 174 53 110 34 16 49 27 13 50 50 78 148 165 203 277 0 0 0 g 431 641 1411 86 1580 1838 88 116 1887 1598 107 1462 1250 359 591 579 0 0 0 t 799 676 330 1692 221 113 1814 1760 21 289 1681 200 291 995 713 610 0 0 0

positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)
; positions_6nt_m3 versus positions_7nt_m1_rc; m=7/11; ncol2=17; w=0; offset=2; strand=R; shift=3; score=0.612166; ---kwgGTGGTTGGTGgwk ; cor=; Ncor= a 0 0 0 516 527 357 222 113 173 49 52 131 73 92 191 312 376 587 524 c 0 0 0 227 286 117 55 108 29 9 47 24 22 58 57 88 171 223 238 g 0 0 0 675 399 1146 1432 77 1662 1934 98 120 1975 1625 121 1472 1222 464 645 t 0 0 0 682 888 480 391 1802 236 108 1903 1825 30 325 1731 228 331 826 693

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; positions_6nt_m3 versus oligos_6nt_mkv3_m1_rc; m=8/11; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.584338; wdgTGGTTGGTggwdd--- ; cor=; Ncor= a 717 727 328 143 242 55 53 123 125 106 325 553 579 784 701 750 0 0 0 c 371 227 82 149 37 18 50 31 16 66 117 181 289 305 330 395 0 0 0 g 566 895 1800 108 2201 2541 105 113 2566 2229 200 1575 1370 604 783 724 0 0 0 t 1085 890 529 2339 259 125 2531 2472 32 338 2097 430 501 1046 925 870 0 0 0

oligos_7nt_mkv4_m1_rc_shift6 (oligos_7nt_mkv4_m1_rc)
; positions_6nt_m3 versus oligos_7nt_mkv4_m1_rc; m=9/11; ncol2=16; w=0; offset=5; strand=R; shift=6; score=0.573674; ------dwgGTGGTTGGtg ; cor=; Ncor= a 0 0 0 0 0 0 716 659 526 225 83 204 47 42 111 143 200 398 522 c 0 0 0 0 0 0 283 372 148 26 124 31 15 61 28 20 107 131 179 g 0 0 0 0 0 0 781 432 1318 1973 52 2111 2429 97 118 2387 1909 322 1523 t 0 0 0 0 0 0 796 1113 584 352 2317 230 85 2376 2319 26 360 1725 352

oligos_7nt_mkv4_m3_rc_shift7 (oligos_7nt_mkv4_m3_rc)
; positions_6nt_m3 versus oligos_7nt_mkv4_m3_rc; m=10/11; ncol2=12; w=0; offset=6; strand=R; shift=7; score=0.569444; -------wdGTaGTTGgwd ; cor=; Ncor= a 0 0 0 0 0 0 0 581 682 63 99 1332 36 73 59 92 300 647 663 c 0 0 0 0 0 0 0 346 188 24 39 54 20 41 61 12 225 233 253 g 0 0 0 0 0 0 0 368 689 1991 69 462 2082 107 46 2043 1319 398 701 t 0 0 0 0 0 0 0 888 624 105 1976 335 45 1962 2017 36 339 905 566

oligos_7nt_mkv4_m2_rc_shift7 (oligos_7nt_mkv4_m2_rc)
; positions_6nt_m3 versus oligos_7nt_mkv4_m2_rc; m=11/11; ncol2=11; w=0; offset=6; strand=R; shift=7; score=0.49493; -------tdGTTGTTGkw- ; cor=; Ncor= a 0 0 0 0 0 0 0 615 793 38 126 305 50 120 99 54 586 745 0 c 0 0 0 0 0 0 0 456 199 12 83 55 25 94 34 20 395 311 0 g 0 0 0 0 0 0 0 385 790 2587 57 413 2567 299 66 2567 846 489 0 t 0 0 0 0 0 0 0 1195 869 14 2385 1878 9 2138 2452 10 824 1106 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; ggaGGAGGAGrw ; Alignment reference a 203 198 515 49 41 728 38 61 764 56 270 312 c 104 135 156 20 19 46 12 28 42 14 137 110 g 346 362 35 773 776 9 790 752 9 752 285 145 t 204 162 151 15 21 74 17 16 42 35 165 290

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ggaGGAGGAGrw ; cor=; Ncor= a 203 198 515 49 41 728 38 61 764 56 270 312 c 104 135 156 20 19 46 12 28 42 14 137 110 g 346 362 35 773 776 9 790 752 9 752 285 145 t 204 162 151 15 21 74 17 16 42 35 165 290

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift2 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=19; shift=2; ncol=21; --whhcyACCAACCACcaamw ; Alignment reference a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 562 502 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 435 366 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 157 216 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258 379 449

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/12; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --whhcyACCAACCACcaamw ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 562 502 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 435 366 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 157 216 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258 379 449

positions_7nt_m1_shift2 (positions_7nt_m1)
; positions_6nt_m4 versus positions_7nt_m1; m=2/12; ncol2=17; w=0; offset=0; strand=D; shift=2; score=0.851798; --hmwcCACCAACCACcwm-- ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 682 0 0 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 675 0 0 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 227 0 0 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527 516 0 0

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; positions_6nt_m4 versus positions_7nt_m2_rc; m=3/12; ncol2=23; w=-1; offset=-1; strand=R; shift=1; score=0.814221; -wwwhyyACCAACCACCAacw ; cor=; Ncor= a 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 617 217 288 c 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 169 567 218 g 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 60 58 118 t 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117 148 152 370

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; positions_6nt_m4 versus oligos_7nt_mkv4_m1; m=4/12; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.810789; ---hhycaCCAACCACcwh-- ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 796 0 0 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 781 0 0 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 283 0 0 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659 716 0 0

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; positions_6nt_m4 versus oligos_6nt_mkv3_m1; m=5/12; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.806797; --hhwccACCAACCAchw--- ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 0 0 0 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 0 0 0 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 0 0 0 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717 0 0 0

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m4 versus positions_6nt_m1; m=6/12; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.786113; --hhacCACCAACCAChw--- ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 0 0 0 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 0 0 0 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 0 0 0 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527 0 0 0

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; positions_6nt_m4 versus positions_7nt_m5_rc; m=7/12; ncol2=18; w=-2; offset=-2; strand=R; shift=0; score=0.703732; hhhaacCACCAACCAchw--- ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 0 0 0 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 0 0 0 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 0 0 0 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457 0 0 0

positions_7nt_m4_shift3 (positions_7nt_m4)
; positions_6nt_m4 versus positions_7nt_m4; m=8/12; ncol2=18; w=0; offset=1; strand=D; shift=3; score=0.687324; ---hhcaaCCACCAACCAmhw ; cor=; Ncor= a 0 0 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 0 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 0 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 0 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434

positions_6nt_m3_rc_shift6 (positions_6nt_m3_rc)
; positions_6nt_m4 versus positions_6nt_m3_rc; m=9/12; ncol2=18; w=0; offset=4; strand=R; shift=6; score=0.644865; ------hwCCAACCACCAact ; cor=; Ncor= a 0 0 0 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 c 0 0 0 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 g 0 0 0 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 t 0 0 0 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441

oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; positions_6nt_m4 versus oligos_7nt_mkv4_m3; m=10/12; ncol2=12; w=0; offset=4; strand=D; shift=6; score=0.545567; ------hwcCAACtAChw--- ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 0 0 0 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 0 0 0 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 0 0 0 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581 0 0 0

oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)
; positions_6nt_m4 versus oligos_7nt_mkv4_m2; m=11/12; ncol2=11; w=0; offset=5; strand=D; shift=7; score=0.470105; -------wmCAACAACha--- ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 0 0 0 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 0 0 0 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 0 0 0 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615 0 0 0

oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)
; positions_6nt_m4 versus oligos_6nt_mkv3_m5; m=12/12; ncol2=11; w=0; offset=4; strand=D; shift=6; score=0.425921; ------waCCAAACaww---- ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 0 0 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 0 0 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 0 0 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift5 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=15; shift=5; ncol=20; -----hmACCAAACcCtahh ; Alignment reference a 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 290 227 c 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 205 234 g 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 99 94 t 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191 207 246

oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=5; score= 1; -----hmACCAAACcCtahh ; cor=; Ncor= a 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 290 227 c 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 205 234 g 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 99 94 t 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191 207 246

oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m5; m=2/10; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.634182; ------waCCAAACaww--- ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 0 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 0 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 0 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0 0

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m3; m=3/10; ncol2=15; w=-1; offset=-1; strand=D; shift=4; score=0.625443; ----whcACCTAACtamww- ; cor=; Ncor= a 0 0 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 366 364 0 c 0 0 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 247 230 0 g 0 0 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 131 132 0 t 0 0 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256 343 361 0

positions_6nt_m5_shift4 (positions_6nt_m5)
; oligos_7nt_mkv4_m5 versus positions_6nt_m5; m=4/10; ncol2=12; w=-1; offset=-1; strand=D; shift=4; score=0.533733; ----wyCACCTAACww---- ; cor=; Ncor= a 0 0 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 0 0 0 c 0 0 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 0 0 0 g 0 0 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 0 0 0 t 0 0 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0 0 0 0

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1; m=5/10; ncol2=16; w=-3; offset=-3; strand=D; shift=2; score=0.521736; --hhwccACCAACCAchw-- ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 0 0 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 0 0 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 0 0 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717 0 0

positions_6nt_m1_shift2 (positions_6nt_m1)
; oligos_7nt_mkv4_m5 versus positions_6nt_m1; m=6/10; ncol2=16; w=-3; offset=-3; strand=D; shift=2; score=0.516779; --hhacCACCAACCAChw-- ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 0 0 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 0 0 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 0 0 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527 0 0

positions_7nt_m3_shift4 (positions_7nt_m3)
; oligos_7nt_mkv4_m5 versus positions_7nt_m3; m=7/10; ncol2=12; w=-1; offset=-1; strand=D; shift=4; score=0.504957; ----yyTACCTAAChw---- ; cor=; Ncor= a 0 0 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 0 0 0 c 0 0 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 0 0 0 g 0 0 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 0 0 0 t 0 0 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0 0 0 0

oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m4; m=8/10; ncol2=15; w=-3; offset=-3; strand=D; shift=2; score=0.497266; --wwtktACCTAACmwh--- ; cor=; Ncor= a 0 0 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 0 0 0 c 0 0 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 0 0 0 g 0 0 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 0 0 0 t 0 0 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280 0 0 0

positions_6nt_m2_shift3 (positions_6nt_m2)
; oligos_7nt_mkv4_m5 versus positions_6nt_m2; m=9/10; ncol2=13; w=-2; offset=-2; strand=D; shift=3; score=0.475052; ---wyyTACCTAAChw---- ; cor=; Ncor= a 0 0 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 0 0 0 c 0 0 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 0 0 0 g 0 0 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 0 0 0 t 0 0 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0 0 0 0

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; oligos_7nt_mkv4_m5 versus positions_7nt_m5_rc; m=10/10; ncol2=18; w=-5; offset=-5; strand=R; shift=0; score=0.469162; hhhaacCACCAACCAchw-- ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 0 0 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 0 0 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 0 0 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift3 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=16; shift=3; ncol=19; ---hhycaCCAACCACcwh ; Alignment reference a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 796 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 781 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 283 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659 716

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/12; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---hhycaCCAACCACcwh ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 796 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 781 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 283 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659 716

positions_7nt_m1_shift2 (positions_7nt_m1)
; oligos_7nt_mkv4_m1 versus positions_7nt_m1; m=2/12; ncol2=17; w=-1; offset=-1; strand=D; shift=2; score=0.923963; --hmwcCACCAACCACcwm ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 682 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 675 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 227 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527 516

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/12; ncol2=16; w=-1; offset=-1; strand=D; shift=2; score=0.868516; --hhwccACCAACCAchw- ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 0 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 0 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 0 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717 0

positions_6nt_m1_shift2 (positions_6nt_m1)
; oligos_7nt_mkv4_m1 versus positions_6nt_m1; m=4/12; ncol2=16; w=-1; offset=-1; strand=D; shift=2; score=0.853953; --hhacCACCAACCAChw- ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 0 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 0 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 0 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527 0

positions_6nt_m4_shift2 (positions_6nt_m4)
; oligos_7nt_mkv4_m1 versus positions_6nt_m4; m=5/12; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.810789; --whhcyACCAACCACcaa ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; oligos_7nt_mkv4_m1 versus positions_7nt_m5_rc; m=6/12; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.754519; hhhaacCACCAACCAchw- ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 0 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 0 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 0 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457 0

positions_7nt_m4_shift0 (positions_7nt_m4)
; oligos_7nt_mkv4_m1 versus positions_7nt_m4; m=7/12; ncol2=18; w=-3; offset=-3; strand=D; shift=0; score=0.703651; hhcaaCCACCAACCAmhw- ; cor=; Ncor= a 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 0 c 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 0 g 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 0 t 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434 0

oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=8/12; ncol2=12; w=0; offset=3; strand=D; shift=6; score=0.668909; ------hwcCAACtAChw- ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 0 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 0 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 0 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581 0

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; oligos_7nt_mkv4_m1 versus positions_7nt_m2_rc; m=9/12; ncol2=23; w=-2; offset=-2; strand=R; shift=1; score=0.659126; -wwwhyyACCAACCACCAa ; cor=; Ncor= a 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 617 c 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 169 g 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 60 t 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117 148

oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=10/12; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.583549; -------wmCAACAACha- ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 0 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 0 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 0 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615 0

positions_6nt_m3_rc_shift6 (positions_6nt_m3_rc)
; oligos_7nt_mkv4_m1 versus positions_6nt_m3_rc; m=11/12; ncol2=18; w=0; offset=3; strand=R; shift=6; score=0.573674; ------hwCCAACCACCAa ; cor=; Ncor= a 0 0 0 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 681 c 0 0 0 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 172 g 0 0 0 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 52 t 0 0 0 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96 121

oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m5; m=12/12; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.499606; ------waCCAAACaww-- ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift6 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=6; ncol=18; ------hwcCAACtAChw ; Alignment reference a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581

oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/11; ncol2=12; w=0; offset=0; strand=D; shift=6; score= 1; ------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581

oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2; m=2/11; ncol2=11; w=0; offset=1; strand=D; shift=7; score=0.83876; -------wmCAACAACha ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=3/11; ncol2=16; w=-3; offset=-3; strand=D; shift=3; score=0.668909; ---hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m1; m=4/11; ncol2=16; w=-4; offset=-4; strand=D; shift=2; score=0.659882; --hhwccACCAACCAchw ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717

positions_6nt_m1_shift2 (positions_6nt_m1)
; oligos_7nt_mkv4_m3 versus positions_6nt_m1; m=5/11; ncol2=16; w=-4; offset=-4; strand=D; shift=2; score=0.648354; --hhacCACCAACCAChw ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527

positions_7nt_m1_shift2 (positions_7nt_m1)
; oligos_7nt_mkv4_m3 versus positions_7nt_m1; m=6/11; ncol2=17; w=-4; offset=-4; strand=D; shift=2; score=0.607415; --hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527

positions_6nt_m3_rc_shift6 (positions_6nt_m3_rc)
; oligos_7nt_mkv4_m3 versus positions_6nt_m3_rc; m=7/11; ncol2=18; w=0; offset=0; strand=R; shift=6; score=0.569444; ------hwCCAACCACCA ; cor=; Ncor= a 0 0 0 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 c 0 0 0 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 g 0 0 0 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 t 0 0 0 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; oligos_7nt_mkv4_m3 versus positions_7nt_m5_rc; m=8/11; ncol2=18; w=-6; offset=-6; strand=R; shift=0; score=0.566665; hhhaacCACCAACCAchw ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457

positions_6nt_m4_shift2 (positions_6nt_m4)
; oligos_7nt_mkv4_m3 versus positions_6nt_m4; m=9/11; ncol2=19; w=-4; offset=-4; strand=D; shift=2; score=0.545567; --whhcyACCAACCACca ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218

positions_7nt_m4_shift0 (positions_7nt_m4)
; oligos_7nt_mkv4_m3 versus positions_7nt_m4; m=10/11; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.516119; hhcaaCCACCAACCAmhw ; cor=; Ncor= a 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; oligos_7nt_mkv4_m3 versus positions_7nt_m2_rc; m=11/11; ncol2=23; w=-5; offset=-5; strand=R; shift=1; score=0.445559; -wwwhyyACCAACCACCA ; cor=; Ncor= a 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 c 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 g 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 t 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift6 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift6 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=18; shift=6; ncol=24; ------wdgTGGTTGGTGgttddd ; Alignment reference a 0 0 0 0 0 0 457 435 214 112 138 38 39 87 83 55 110 232 274 370 305 535 466 522 c 0 0 0 0 0 0 193 142 51 98 28 11 39 20 15 29 30 56 118 143 110 187 234 204 g 0 0 0 0 0 0 371 504 1055 67 1321 1502 69 76 1538 1386 75 1216 1013 300 327 478 445 444 t 0 0 0 0 0 0 634 574 335 1378 168 104 1508 1472 19 185 1440 151 250 842 913 455 510 485

positions_7nt_m5_shift6 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/13; ncol2=18; w=0; offset=0; strand=D; shift=6; score= 1; ------wdgTGGTTGGTGgttddd ; cor=; Ncor= a 0 0 0 0 0 0 457 435 214 112 138 38 39 87 83 55 110 232 274 370 305 535 466 522 c 0 0 0 0 0 0 193 142 51 98 28 11 39 20 15 29 30 56 118 143 110 187 234 204 g 0 0 0 0 0 0 371 504 1055 67 1321 1502 69 76 1538 1386 75 1216 1013 300 327 478 445 444 t 0 0 0 0 0 0 634 574 335 1378 168 104 1508 1472 19 185 1440 151 250 842 913 455 510 485

positions_7nt_m4_rc_shift6 (positions_7nt_m4_rc)
; positions_7nt_m5 versus positions_7nt_m4_rc; m=2/13; ncol2=18; w=0; offset=0; strand=R; shift=6; score=0.964218; ------wdkTGGTTGGTGGttgdd ; cor=; Ncor= a 0 0 0 0 0 0 434 414 293 121 111 64 62 101 63 34 64 204 202 262 228 240 438 446 c 0 0 0 0 0 0 202 155 75 86 47 27 49 42 16 17 32 45 79 104 80 107 216 165 g 0 0 0 0 0 0 376 428 461 97 1198 1276 84 107 1413 1312 26 1119 1096 254 260 907 428 402 t 0 0 0 0 0 0 520 535 703 1228 176 165 1337 1282 40 169 1410 164 155 912 964 278 450 519

positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)
; positions_7nt_m5 versus positions_6nt_m1_rc; m=3/13; ncol2=16; w=0; offset=0; strand=R; shift=6; score=0.882809; ------wdGTGGTTGGTGgtdd-- ; cor=; Ncor= a 0 0 0 0 0 0 527 523 220 126 179 47 63 111 93 77 176 274 325 495 507 548 0 0 c 0 0 0 0 0 0 257 174 53 110 34 16 49 27 13 50 50 78 148 165 203 277 0 0 g 0 0 0 0 0 0 431 641 1411 86 1580 1838 88 116 1887 1598 107 1462 1250 359 591 579 0 0 t 0 0 0 0 0 0 799 676 330 1692 221 113 1814 1760 21 289 1681 200 291 995 713 610 0 0

oligos_6nt_mkv3_m1_rc_shift6 (oligos_6nt_mkv3_m1_rc)
; positions_7nt_m5 versus oligos_6nt_mkv3_m1_rc; m=4/13; ncol2=16; w=0; offset=0; strand=R; shift=6; score=0.87543; ------wdgTGGTTGGTggwdd-- ; cor=; Ncor= a 0 0 0 0 0 0 717 727 328 143 242 55 53 123 125 106 325 553 579 784 701 750 0 0 c 0 0 0 0 0 0 371 227 82 149 37 18 50 31 16 66 117 181 289 305 330 395 0 0 g 0 0 0 0 0 0 566 895 1800 108 2201 2541 105 113 2566 2229 200 1575 1370 604 783 724 0 0 t 0 0 0 0 0 0 1085 890 529 2339 259 125 2531 2472 32 338 2097 430 501 1046 925 870 0 0

positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)
; positions_7nt_m5 versus positions_7nt_m1_rc; m=5/13; ncol2=17; w=-1; offset=-1; strand=R; shift=5; score=0.826227; -----kwgGTGGTTGGTGgwkd-- ; cor=; Ncor= a 0 0 0 0 0 516 527 357 222 113 173 49 52 131 73 92 191 312 376 587 524 552 0 0 c 0 0 0 0 0 227 286 117 55 108 29 9 47 24 22 58 57 88 171 223 238 297 0 0 g 0 0 0 0 0 675 399 1146 1432 77 1662 1934 98 120 1975 1625 121 1472 1222 464 645 593 0 0 t 0 0 0 0 0 682 888 480 391 1802 236 108 1903 1825 30 325 1731 228 331 826 693 658 0 0

oligos_7nt_mkv4_m1_rc_shift5 (oligos_7nt_mkv4_m1_rc)
; positions_7nt_m5 versus oligos_7nt_mkv4_m1_rc; m=6/13; ncol2=16; w=-1; offset=-1; strand=R; shift=5; score=0.754519; -----dwgGTGGTTGGtgrdd--- ; cor=; Ncor= a 0 0 0 0 0 716 659 526 225 83 204 47 42 111 143 200 398 522 761 811 691 0 0 0 c 0 0 0 0 0 283 372 148 26 124 31 15 61 28 20 107 131 179 362 329 310 0 0 0 g 0 0 0 0 0 781 432 1318 1973 52 2111 2429 97 118 2387 1909 322 1523 813 649 767 0 0 0 t 0 0 0 0 0 796 1113 584 352 2317 230 85 2376 2319 26 360 1725 352 640 787 808 0 0 0

positions_6nt_m3_shift7 (positions_6nt_m3)
; positions_7nt_m5 versus positions_6nt_m3; m=7/13; ncol2=18; w=0; offset=1; strand=D; shift=7; score=0.714303; -------wdtagtTGGTGGTTGGw ; cor=; Ncor= a 0 0 0 0 0 0 0 279 258 232 441 96 121 96 58 35 41 79 33 52 58 76 105 269 c 0 0 0 0 0 0 0 143 105 103 119 53 52 73 18 10 34 15 16 38 13 23 69 101 g 0 0 0 0 0 0 0 243 364 237 230 691 172 57 885 889 17 848 951 83 67 863 740 227 t 0 0 0 0 0 0 0 361 299 454 236 186 681 800 65 92 934 84 26 853 888 64 112 429

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; positions_7nt_m5 versus positions_6nt_m4_rc; m=8/13; ncol2=19; w=-3; offset=-3; strand=R; shift=3; score=0.703732; ---wkttgGTGGTTGGTrgddw-- ; cor=; Ncor= a 0 0 0 449 379 258 218 204 132 55 98 36 38 87 76 84 159 600 353 456 416 440 0 0 c 0 0 0 216 157 107 116 57 34 63 14 14 25 15 10 52 44 112 205 183 180 230 0 0 g 0 0 0 366 435 271 168 1040 1090 30 1265 1434 85 58 1397 1257 141 507 634 473 418 349 0 0 t 0 0 0 502 562 897 1031 232 277 1385 156 49 1385 1373 50 140 1189 314 341 421 519 514 0 0

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m5 versus positions_7nt_m2; m=9/13; ncol2=23; w=-6; offset=-6; strand=D; shift=0; score=0.63824; wdtwgtTGGTGGTTGGTrrdwww- ; cor=; Ncor= a 282 273 240 370 152 148 117 108 77 35 71 30 30 63 49 67 110 486 254 314 273 297 289 0 c 147 99 94 118 58 60 66 33 16 33 8 14 19 9 11 40 36 72 140 120 112 129 144 0 g 227 311 189 218 567 169 99 736 734 23 828 907 49 46 891 792 93 262 368 286 242 230 244 0 t 338 311 471 288 217 617 712 117 167 903 87 43 896 876 43 95 755 174 232 274 367 338 317 0

oligos_7nt_mkv4_m3_rc_shift6 (oligos_7nt_mkv4_m3_rc)
; positions_7nt_m5 versus oligos_7nt_mkv4_m3_rc; m=10/13; ncol2=12; w=0; offset=0; strand=R; shift=6; score=0.566665; ------wdGTaGTTGgwd------ ; cor=; Ncor= a 0 0 0 0 0 0 581 682 63 99 1332 36 73 59 92 300 647 663 0 0 0 0 0 0 c 0 0 0 0 0 0 346 188 24 39 54 20 41 61 12 225 233 253 0 0 0 0 0 0 g 0 0 0 0 0 0 368 689 1991 69 462 2082 107 46 2043 1319 398 701 0 0 0 0 0 0 t 0 0 0 0 0 0 888 624 105 1976 335 45 1962 2017 36 339 905 566 0 0 0 0 0 0

oligos_7nt_mkv4_m2_rc_shift6 (oligos_7nt_mkv4_m2_rc)
; positions_7nt_m5 versus oligos_7nt_mkv4_m2_rc; m=11/13; ncol2=11; w=0; offset=0; strand=R; shift=6; score=0.494442; ------tdGTTGTTGkw------- ; cor=; Ncor= a 0 0 0 0 0 0 615 793 38 126 305 50 120 99 54 586 745 0 0 0 0 0 0 0 c 0 0 0 0 0 0 456 199 12 83 55 25 94 34 20 395 311 0 0 0 0 0 0 0 g 0 0 0 0 0 0 385 790 2587 57 413 2567 299 66 2567 846 489 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1195 869 14 2385 1878 9 2138 2452 10 824 1106 0 0 0 0 0 0 0

oligos_7nt_mkv4_m5_rc_shift4 (oligos_7nt_mkv4_m5_rc)
; positions_7nt_m5 versus oligos_7nt_mkv4_m5_rc; m=12/13; ncol2=15; w=-2; offset=-2; strand=R; shift=4; score=0.469162; ----ddtaGgGTTTGGTkd----- ; cor=; Ncor= a 0 0 0 0 246 207 191 480 60 100 47 28 17 67 44 25 48 189 212 0 0 0 0 0 c 0 0 0 0 94 99 74 63 41 47 26 11 14 8 11 12 18 70 86 0 0 0 0 0 g 0 0 0 0 234 205 181 67 598 536 657 93 32 22 717 733 18 255 276 0 0 0 0 0 t 0 0 0 0 227 290 355 191 102 118 71 669 738 704 29 31 717 287 227 0 0 0 0 0

oligos_6nt_mkv3_m5_rc_shift7 (oligos_6nt_mkv3_m5_rc)
; positions_7nt_m5 versus oligos_6nt_mkv3_m5_rc; m=13/13; ncol2=11; w=0; offset=1; strand=R; shift=7; score=0.462941; -------wwtGTTTGGtw------ ; cor=; Ncor= a 0 0 0 0 0 0 0 358 447 174 21 85 58 157 30 6 247 412 0 0 0 0 0 0 c 0 0 0 0 0 0 0 192 178 60 6 32 20 37 23 7 156 145 0 0 0 0 0 0 g 0 0 0 0 0 0 0 226 321 255 1316 91 22 14 1292 1325 150 330 0 0 0 0 0 0 t 0 0 0 0 0 0 0 569 399 856 2 1137 1245 1137 0 7 792 458 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=23; shift=0; ncol=23; wdtwgtTGGTGGTTGGTrrdwww ; Alignment reference a 282 273 240 370 152 148 117 108 77 35 71 30 30 63 49 67 110 486 254 314 273 297 289 c 147 99 94 118 58 60 66 33 16 33 8 14 19 9 11 40 36 72 140 120 112 129 144 g 227 311 189 218 567 169 99 736 734 23 828 907 49 46 891 792 93 262 368 286 242 230 244 t 338 311 471 288 217 617 712 117 167 903 87 43 896 876 43 95 755 174 232 274 367 338 317

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/10; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; wdtwgtTGGTGGTTGGTrrdwww ; cor=; Ncor= a 282 273 240 370 152 148 117 108 77 35 71 30 30 63 49 67 110 486 254 314 273 297 289 c 147 99 94 118 58 60 66 33 16 33 8 14 19 9 11 40 36 72 140 120 112 129 144 g 227 311 189 218 567 169 99 736 734 23 828 907 49 46 891 792 93 262 368 286 242 230 244 t 338 311 471 288 217 617 712 117 167 903 87 43 896 876 43 95 755 174 232 274 367 338 317

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; positions_7nt_m2 versus positions_6nt_m4_rc; m=2/10; ncol2=19; w=0; offset=3; strand=R; shift=3; score=0.814221; ---wkttgGTGGTTGGTrgddw- ; cor=; Ncor= a 0 0 0 449 379 258 218 204 132 55 98 36 38 87 76 84 159 600 353 456 416 440 0 c 0 0 0 216 157 107 116 57 34 63 14 14 25 15 10 52 44 112 205 183 180 230 0 g 0 0 0 366 435 271 168 1040 1090 30 1265 1434 85 58 1397 1257 141 507 634 473 418 349 0 t 0 0 0 502 562 897 1031 232 277 1385 156 49 1385 1373 50 140 1189 314 341 421 519 514 0

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_7nt_m2 versus positions_6nt_m3; m=3/10; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.75956; wdtagtTGGTGGTTGGwd----- ; cor=; Ncor= a 279 258 232 441 96 121 96 58 35 41 79 33 52 58 76 105 269 280 0 0 0 0 0 c 143 105 103 119 53 52 73 18 10 34 15 16 38 13 23 69 101 131 0 0 0 0 0 g 243 364 237 230 691 172 57 885 889 17 848 951 83 67 863 740 227 357 0 0 0 0 0 t 361 299 454 236 186 681 800 65 92 934 84 26 853 888 64 112 429 258 0 0 0 0 0

positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)
; positions_7nt_m2 versus positions_7nt_m1_rc; m=4/10; ncol2=17; w=0; offset=5; strand=R; shift=5; score=0.68817; -----kwgGTGGTTGGTGgwkd- ; cor=; Ncor= a 0 0 0 0 0 516 527 357 222 113 173 49 52 131 73 92 191 312 376 587 524 552 0 c 0 0 0 0 0 227 286 117 55 108 29 9 47 24 22 58 57 88 171 223 238 297 0 g 0 0 0 0 0 675 399 1146 1432 77 1662 1934 98 120 1975 1625 121 1472 1222 464 645 593 0 t 0 0 0 0 0 682 888 480 391 1802 236 108 1903 1825 30 325 1731 228 331 826 693 658 0

oligos_7nt_mkv4_m1_rc_shift5 (oligos_7nt_mkv4_m1_rc)
; positions_7nt_m2 versus oligos_7nt_mkv4_m1_rc; m=5/10; ncol2=16; w=0; offset=5; strand=R; shift=5; score=0.659126; -----dwgGTGGTTGGtgrdd-- ; cor=; Ncor= a 0 0 0 0 0 716 659 526 225 83 204 47 42 111 143 200 398 522 761 811 691 0 0 c 0 0 0 0 0 283 372 148 26 124 31 15 61 28 20 107 131 179 362 329 310 0 0 g 0 0 0 0 0 781 432 1318 1973 52 2111 2429 97 118 2387 1909 322 1523 813 649 767 0 0 t 0 0 0 0 0 796 1113 584 352 2317 230 85 2376 2319 26 360 1725 352 640 787 808 0 0

oligos_6nt_mkv3_m1_rc_shift6 (oligos_6nt_mkv3_m1_rc)
; positions_7nt_m2 versus oligos_6nt_mkv3_m1_rc; m=6/10; ncol2=16; w=0; offset=6; strand=R; shift=6; score=0.652279; ------wdgTGGTTGGTggwdd- ; cor=; Ncor= a 0 0 0 0 0 0 717 727 328 143 242 55 53 123 125 106 325 553 579 784 701 750 0 c 0 0 0 0 0 0 371 227 82 149 37 18 50 31 16 66 117 181 289 305 330 395 0 g 0 0 0 0 0 0 566 895 1800 108 2201 2541 105 113 2566 2229 200 1575 1370 604 783 724 0 t 0 0 0 0 0 0 1085 890 529 2339 259 125 2531 2472 32 338 2097 430 501 1046 925 870 0

positions_7nt_m5_shift6 (positions_7nt_m5)
; positions_7nt_m2 versus positions_7nt_m5; m=7/10; ncol2=18; w=0; offset=6; strand=D; shift=6; score=0.63824; ------wdgTGGTTGGTGgttdd ; cor=; Ncor= a 0 0 0 0 0 0 457 435 214 112 138 38 39 87 83 55 110 232 274 370 305 535 466 c 0 0 0 0 0 0 193 142 51 98 28 11 39 20 15 29 30 56 118 143 110 187 234 g 0 0 0 0 0 0 371 504 1055 67 1321 1502 69 76 1538 1386 75 1216 1013 300 327 478 445 t 0 0 0 0 0 0 634 574 335 1378 168 104 1508 1472 19 185 1440 151 250 842 913 455 510

positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)
; positions_7nt_m2 versus positions_6nt_m1_rc; m=8/10; ncol2=16; w=0; offset=6; strand=R; shift=6; score=0.632779; ------wdGTGGTTGGTGgtdd- ; cor=; Ncor= a 0 0 0 0 0 0 527 523 220 126 179 47 63 111 93 77 176 274 325 495 507 548 0 c 0 0 0 0 0 0 257 174 53 110 34 16 49 27 13 50 50 78 148 165 203 277 0 g 0 0 0 0 0 0 431 641 1411 86 1580 1838 88 116 1887 1598 107 1462 1250 359 591 579 0 t 0 0 0 0 0 0 799 676 330 1692 221 113 1814 1760 21 289 1681 200 291 995 713 610 0

positions_7nt_m4_rc_shift6 (positions_7nt_m4_rc)
; positions_7nt_m2 versus positions_7nt_m4_rc; m=9/10; ncol2=18; w=0; offset=6; strand=R; shift=6; score=0.586854; ------wdkTGGTTGGTGGttgd ; cor=; Ncor= a 0 0 0 0 0 0 434 414 293 121 111 64 62 101 63 34 64 204 202 262 228 240 438 c 0 0 0 0 0 0 202 155 75 86 47 27 49 42 16 17 32 45 79 104 80 107 216 g 0 0 0 0 0 0 376 428 461 97 1198 1276 84 107 1413 1312 26 1119 1096 254 260 907 428 t 0 0 0 0 0 0 520 535 703 1228 176 165 1337 1282 40 169 1410 164 155 912 964 278 450

oligos_7nt_mkv4_m3_rc_shift6 (oligos_7nt_mkv4_m3_rc)
; positions_7nt_m2 versus oligos_7nt_mkv4_m3_rc; m=10/10; ncol2=12; w=0; offset=6; strand=R; shift=6; score=0.445559; ------wdGTaGTTGgwd----- ; cor=; Ncor= a 0 0 0 0 0 0 581 682 63 99 1332 36 73 59 92 300 647 663 0 0 0 0 0 c 0 0 0 0 0 0 346 188 24 39 54 20 41 61 12 225 233 253 0 0 0 0 0 g 0 0 0 0 0 0 368 689 1991 69 462 2082 107 46 2043 1319 398 701 0 0 0 0 0 t 0 0 0 0 0 0 888 624 105 1976 335 45 1962 2017 36 339 905 566 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift3 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=16; shift=3; ncol=19; ---hhacCACCAACCAChw ; Alignment reference a 0 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527

positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/13; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---hhacCACCAACCAChw ; cor=; Ncor= a 0 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; positions_6nt_m1 versus oligos_6nt_mkv3_m1; m=2/13; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.991892; ---hhwccACCAACCAchw ; cor=; Ncor= a 0 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=3/13; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.932332; ---hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527

positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)
; positions_6nt_m1 versus positions_7nt_m5_rc; m=4/13; ncol2=18; w=-2; offset=-2; strand=R; shift=1; score=0.882809; -hhhaacCACCAACCAchw ; cor=; Ncor= a 0 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 0 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 0 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 0 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457

oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)
; positions_6nt_m1 versus oligos_7nt_mkv4_m1; m=5/13; ncol2=16; w=0; offset=1; strand=D; shift=4; score=0.853953; ----hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659

positions_7nt_m4_shift1 (positions_7nt_m4)
; positions_6nt_m1 versus positions_7nt_m4; m=6/13; ncol2=18; w=-2; offset=-2; strand=D; shift=1; score=0.841103; -hhcaaCCACCAACCAmhw ; cor=; Ncor= a 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434

positions_6nt_m4_shift3 (positions_6nt_m4)
; positions_6nt_m1 versus positions_6nt_m4; m=7/13; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.786113; ---whhcyACCAACCACca ; cor=; Ncor= a 0 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 c 0 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 g 0 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 t 0 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218

oligos_7nt_mkv4_m3_shift7 (oligos_7nt_mkv4_m3)
; positions_6nt_m1 versus oligos_7nt_mkv4_m3; m=8/13; ncol2=12; w=0; offset=4; strand=D; shift=7; score=0.648354; -------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_6nt_m1 versus positions_7nt_m2_rc; m=9/13; ncol2=23; w=-1; offset=-1; strand=R; shift=2; score=0.632779; --wwwhyyACCAACCACCA ; cor=; Ncor= a 0 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 c 0 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 g 0 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 t 0 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; positions_6nt_m1 versus positions_6nt_m3_rc; m=10/13; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.622578; hwCCAACCACCAactahw- ; cor=; Ncor= a 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 454 299 361 0 c 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 237 364 243 0 g 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 103 105 143 0 t 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441 232 258 279 0

oligos_7nt_mkv4_m2_shift8 (oligos_7nt_mkv4_m2)
; positions_6nt_m1 versus oligos_7nt_mkv4_m2; m=11/13; ncol2=11; w=0; offset=5; strand=D; shift=8; score=0.570603; --------wmCAACAACha ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615

oligos_7nt_mkv4_m5_shift6 (oligos_7nt_mkv4_m5)
; positions_6nt_m1 versus oligos_7nt_mkv4_m5; m=12/13; ncol2=15; w=0; offset=3; strand=D; shift=6; score=0.516779; ------hmACCAAACcCta ; cor=; Ncor= a 0 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 c 0 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 g 0 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 t 0 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191

oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)
; positions_6nt_m1 versus oligos_6nt_mkv3_m5; m=13/13; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.511326; -------waCCAAACaww- ; cor=; Ncor= a 0 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 c 0 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 g 0 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 t 0 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift1 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=18; shift=1; ncol=19; -hhcaaCCACCAACCAmhw ; Alignment reference a 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434
positions_7nt_m4_shift1 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/12; ncol2=18; w=0; offset=0; strand=D; shift=1; score= 1; -hhcaaCCACCAACCAmhw ; cor=; Ncor= a 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434
positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)				; positions_7nt_m4 versus positions_7nt_m5_rc; m=2/12; ncol2=18; w=0; offset=0; strand=R; shift=1; score=0.964218; -hhhaacCACCAACCAchw ; cor=; Ncor= a 0 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 0 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 0 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 0 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_7nt_m4 versus positions_6nt_m1; m=3/12; ncol2=16; w=0; offset=2; strand=D; shift=3; score=0.841103; ---hhacCACCAACCAChw ; cor=; Ncor= a 0 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; positions_7nt_m4 versus oligos_6nt_mkv3_m1; m=4/12; ncol2=16; w=0; offset=2; strand=D; shift=3; score=0.827668; ---hhwccACCAACCAchw ; cor=; Ncor= a 0 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m4 versus positions_7nt_m1; m=5/12; ncol2=17; w=0; offset=2; strand=D; shift=3; score=0.783318; ---hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)				; positions_7nt_m4 versus positions_6nt_m3_rc; m=6/12; ncol2=18; w=-1; offset=-1; strand=R; shift=0; score=0.778993; hwCCAACCACCAactahw- ; cor=; Ncor= a 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 454 299 361 0 c 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 237 364 243 0 g 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 103 105 143 0 t 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441 232 258 279 0
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)				; positions_7nt_m4 versus oligos_7nt_mkv4_m1; m=7/12; ncol2=16; w=0; offset=3; strand=D; shift=4; score=0.703651; ----hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_7nt_m4 versus positions_6nt_m4; m=8/12; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.687324; whhcyACCAACCACcaamw ; cor=; Ncor= a 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 562 502 c 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 435 366 g 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 157 216 t 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258 379 449
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_7nt_m4 versus positions_7nt_m2_rc; m=9/12; ncol2=23; w=0; offset=1; strand=R; shift=2; score=0.586854; --wwwhyyACCAACCACCA ; cor=; Ncor= a 0 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 c 0 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 g 0 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 t 0 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117
oligos_7nt_mkv4_m3_shift7 (oligos_7nt_mkv4_m3)				; positions_7nt_m4 versus oligos_7nt_mkv4_m3; m=10/12; ncol2=12; w=0; offset=6; strand=D; shift=7; score=0.516119; -------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581
oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)				; positions_7nt_m4 versus oligos_6nt_mkv3_m5; m=11/12; ncol2=11; w=0; offset=6; strand=D; shift=7; score=0.480039; -------waCCAAACaww- ; cor=; Ncor= a 0 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 c 0 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 g 0 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 t 0 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0
oligos_7nt_mkv4_m2_shift5 (oligos_7nt_mkv4_m2)				; positions_7nt_m4 versus oligos_7nt_mkv4_m2; m=12/12; ncol2=11; w=0; offset=4; strand=D; shift=5; score=0.477142; -----wmCAACAACha--- ; cor=; Ncor= a 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 0 0 0 c 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 0 0 0 g 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 0 0 0 t 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wyCACCTAACww ; Alignment reference a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wyCACCTAACww ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307
positions_7nt_m3_shift2 (positions_7nt_m3)				; positions_6nt_m5 versus positions_7nt_m3; m=2/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.90842; --yyTACCTAAChw ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m5 versus positions_6nt_m2; m=3/8; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.838102; -wyyTACCTAAChw ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; positions_6nt_m5 versus oligos_6nt_mkv3_m3; m=4/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.782481; --whcACCTAACta ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; positions_6nt_m5 versus oligos_7nt_mkv4_m4; m=5/8; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.732165; wwtktACCTAACmw ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; positions_6nt_m5 versus oligos_6nt_mkv3_m2; m=6/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.62239; wwygTACCTAACta ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; positions_6nt_m5 versus oligos_6nt_mkv3_m5; m=7/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.615731; ----waCCAAACaw ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; positions_6nt_m5 versus oligos_7nt_mkv4_m5; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=3; score=0.533733; ---hmACCAAACcC ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -wyyTACCTAAChw ; Alignment reference a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -wyyTACCTAAChw ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299
positions_7nt_m3_shift2 (positions_7nt_m3)				; positions_6nt_m2 versus positions_7nt_m3; m=2/8; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.92307; --yyTACCTAAChw ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; positions_6nt_m2 versus oligos_7nt_mkv4_m4; m=3/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.856322; wwtktACCTAACmw ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m2 versus positions_6nt_m5; m=4/8; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.838102; --wyCACCTAACww ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=5/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.751885; wwygTACCTAACta ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; positions_6nt_m2 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=15; w=0; offset=1; strand=D; shift=2; score=0.695545; --whcACCTAACta ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; positions_6nt_m2 versus oligos_6nt_mkv3_m5; m=7/8; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.563866; ----waCCAAACaw ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; positions_6nt_m2 versus oligos_7nt_mkv4_m5; m=8/8; ncol2=15; w=0; offset=2; strand=D; shift=3; score=0.475052; ---hmACCAAACcC ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=7; ncol=18; -------wmCAACAACha ; Alignment reference a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615
oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/10; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------wmCAACAACha ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=2/10; ncol2=12; w=-1; offset=-1; strand=D; shift=6; score=0.83876; ------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1; m=3/10; ncol2=16; w=-4; offset=-4; strand=D; shift=3; score=0.583549; ---hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659
positions_6nt_m1_shift2 (positions_6nt_m1)				; oligos_7nt_mkv4_m2 versus positions_6nt_m1; m=4/10; ncol2=16; w=-5; offset=-5; strand=D; shift=2; score=0.570603; --hhacCACCAACCAChw ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=5/10; ncol2=16; w=-5; offset=-5; strand=D; shift=2; score=0.568631; --hhwccACCAACCAchw ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717
positions_7nt_m1_shift2 (positions_7nt_m1)				; oligos_7nt_mkv4_m2 versus positions_7nt_m1; m=6/10; ncol2=17; w=-5; offset=-5; strand=D; shift=2; score=0.533663; --hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527
positions_6nt_m3_rc_shift6 (positions_6nt_m3_rc)				; oligos_7nt_mkv4_m2 versus positions_6nt_m3_rc; m=7/10; ncol2=18; w=-1; offset=-1; strand=R; shift=6; score=0.49493; ------hwCCAACCACCA ; cor=; Ncor= a 0 0 0 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 c 0 0 0 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 g 0 0 0 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 t 0 0 0 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; oligos_7nt_mkv4_m2 versus positions_7nt_m5_rc; m=8/10; ncol2=18; w=-7; offset=-7; strand=R; shift=0; score=0.494442; hhhaacCACCAACCAchw ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457
positions_7nt_m4_shift3 (positions_7nt_m4)				; oligos_7nt_mkv4_m2 versus positions_7nt_m4; m=9/10; ncol2=18; w=-4; offset=-4; strand=D; shift=3; score=0.477142; ---hhcaaCCACCAACCA ; cor=; Ncor= a 0 0 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 c 0 0 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 g 0 0 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 t 0 0 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121
positions_6nt_m4_shift2 (positions_6nt_m4)				; oligos_7nt_mkv4_m2 versus positions_6nt_m4; m=10/10; ncol2=19; w=-5; offset=-5; strand=D; shift=2; score=0.470105; --whhcyACCAACCACca ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift2 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=17; shift=2; ncol=19; --hmwcCACCAACCACcwm ; Alignment reference a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 682 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 675 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 227 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527 516
positions_7nt_m1_shift2 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/12; ncol2=17; w=0; offset=0; strand=D; shift=2; score= 1; --hmwcCACCAACCACcwm ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 682 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 675 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 227 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527 516
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=2/12; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.932332; --hhacCACCAACCAChw- ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 0 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 0 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 0 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527 0
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; positions_7nt_m1 versus oligos_6nt_mkv3_m1; m=3/12; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.930735; --hhwccACCAACCAchw- ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 0 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 0 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 0 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717 0
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; positions_7nt_m1 versus oligos_7nt_mkv4_m1; m=4/12; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.923963; ---hhycaCCAACCACcwh ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 796 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 781 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 283 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659 716
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_7nt_m1 versus positions_6nt_m4; m=5/12; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.851798; --whhcyACCAACCACcaa ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; positions_7nt_m1 versus positions_7nt_m5_rc; m=6/12; ncol2=18; w=-2; offset=-2; strand=R; shift=0; score=0.826227; hhhaacCACCAACCAchw- ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 0 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 0 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 0 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457 0
positions_7nt_m4_shift0 (positions_7nt_m4)				; positions_7nt_m1 versus positions_7nt_m4; m=7/12; ncol2=18; w=-2; offset=-2; strand=D; shift=0; score=0.783318; hhcaaCCACCAACCAmhw- ; cor=; Ncor= a 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 0 c 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 0 g 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 0 t 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434 0
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; positions_7nt_m1 versus positions_7nt_m2_rc; m=8/12; ncol2=23; w=-1; offset=-1; strand=R; shift=1; score=0.68817; -wwwhyyACCAACCACCAa ; cor=; Ncor= a 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 617 c 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 169 g 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 60 t 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117 148
positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)				; positions_7nt_m1 versus positions_6nt_m3_rc; m=9/12; ncol2=18; w=0; offset=1; strand=R; shift=3; score=0.612166; ---hwCCAACCACCAacta ; cor=; Ncor= a 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 454 c 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 237 g 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 103 t 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441 232
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; positions_7nt_m1 versus oligos_7nt_mkv4_m3; m=10/12; ncol2=12; w=0; offset=4; strand=D; shift=6; score=0.607415; ------hwcCAACtAChw- ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 0 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 0 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 0 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581 0
oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)				; positions_7nt_m1 versus oligos_7nt_mkv4_m2; m=11/12; ncol2=11; w=0; offset=5; strand=D; shift=7; score=0.533663; -------wmCAACAACha- ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 0 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 0 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 0 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615 0
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)				; positions_7nt_m1 versus oligos_6nt_mkv3_m5; m=12/12; ncol2=11; w=0; offset=4; strand=D; shift=6; score=0.472099; ------waCCAAACaww-- ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; wwtktACCTAACmwh ; Alignment reference a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wwtktACCTAACmwh ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_7nt_mkv4_m4 versus positions_6nt_m2; m=2/8; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.856322; -wyyTACCTAAChw- ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m2; m=3/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.85478; wwygTACCTAACtac ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182
positions_7nt_m3_shift2 (positions_7nt_m3)				; oligos_7nt_mkv4_m4 versus positions_7nt_m3; m=4/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.790477; --yyTACCTAAChw- ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0
positions_6nt_m5_shift2 (positions_6nt_m5)				; oligos_7nt_mkv4_m4 versus positions_6nt_m5; m=5/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.732165; --wyCACCTAACww- ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.709282; --whcACCTAACtam ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m5; m=7/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.585309; ----waCCAAACaww ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m5; m=8/8; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.497266; ---hmACCAAACcCt ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=15; shift=2; ncol=17; --whcACCTAACtamww ; Alignment reference a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 366 364 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 247 230 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 131 132 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256 343 361
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score= 1; --whcACCTAACtamww ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 366 364 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 247 230 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 131 132 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256 343 361
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2; m=2/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.823032; wwygTACCTAACtachw ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 254 256 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 194 154 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 97 99 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182 228 264
positions_6nt_m5_shift2 (positions_6nt_m5)				; oligos_6nt_mkv3_m3 versus positions_6nt_m5; m=3/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.782481; --wyCACCTAACww--- ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 0 0 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 0 0 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 0 0 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0 0 0
positions_7nt_m3_shift2 (positions_7nt_m3)				; oligos_6nt_mkv3_m3 versus positions_7nt_m3; m=4/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.742358; --yyTACCTAAChw--- ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 0 0 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 0 0 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 0 0 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0 0 0
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m4; m=5/8; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.709282; wwtktACCTAACmwh-- ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 0 0 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 0 0 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 0 0 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280 0 0
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_6nt_mkv3_m3 versus positions_6nt_m2; m=6/8; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.695545; -wyyTACCTAAChw--- ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 0 0 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 0 0 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 0 0 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0 0 0
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m5; m=7/8; ncol2=15; w=0; offset=1; strand=D; shift=3; score=0.625443; ---hmACCAAACcCtah ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 290 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 205 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 99 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191 207
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m5; m=8/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.56566; ----waCCAAACaww-- ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 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=16; shift=3; ncol=19; ---hhwccACCAACCAchw ; Alignment reference a 0 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/13; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---hhwccACCAACCAchw ; cor=; Ncor= a 0 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717
positions_6nt_m1_shift3 (positions_6nt_m1)				; oligos_6nt_mkv3_m1 versus positions_6nt_m1; m=2/13; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.991892; ---hhacCACCAACCAChw ; cor=; Ncor= a 0 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527
positions_7nt_m1_shift3 (positions_7nt_m1)				; oligos_6nt_mkv3_m1 versus positions_7nt_m1; m=3/13; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.930735; ---hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527
positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)				; oligos_6nt_mkv3_m1 versus positions_7nt_m5_rc; m=4/13; ncol2=18; w=-2; offset=-2; strand=R; shift=1; score=0.87543; -hhhaacCACCAACCAchw ; cor=; Ncor= a 0 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 0 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 0 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 0 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=5/13; ncol2=16; w=0; offset=1; strand=D; shift=4; score=0.868516; ----hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659
positions_7nt_m4_shift1 (positions_7nt_m4)				; oligos_6nt_mkv3_m1 versus positions_7nt_m4; m=6/13; ncol2=18; w=-2; offset=-2; strand=D; shift=1; score=0.827668; -hhcaaCCACCAACCAmhw ; cor=; Ncor= a 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434
positions_6nt_m4_shift3 (positions_6nt_m4)				; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=7/13; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.806797; ---whhcyACCAACCACca ; cor=; Ncor= a 0 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 c 0 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 g 0 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 t 0 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218
oligos_7nt_mkv4_m3_shift7 (oligos_7nt_mkv4_m3)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m3; m=8/13; ncol2=12; w=0; offset=4; strand=D; shift=7; score=0.659882; -------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; oligos_6nt_mkv3_m1 versus positions_7nt_m2_rc; m=9/13; ncol2=23; w=-1; offset=-1; strand=R; shift=2; score=0.652279; --wwwhyyACCAACCACCA ; cor=; Ncor= a 0 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 c 0 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 g 0 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 t 0 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)				; oligos_6nt_mkv3_m1 versus positions_6nt_m3_rc; m=10/13; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.584338; hwCCAACCACCAactahw- ; cor=; Ncor= a 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 454 299 361 0 c 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 237 364 243 0 g 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 103 105 143 0 t 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441 232 258 279 0
oligos_7nt_mkv4_m2_shift8 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=11/13; ncol2=11; w=0; offset=5; strand=D; shift=8; score=0.568631; --------wmCAACAACha ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615
oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m5; m=12/13; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.526422; -------waCCAAACaww- ; cor=; Ncor= a 0 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 c 0 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 g 0 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 t 0 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0
oligos_7nt_mkv4_m5_shift6 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5; m=13/13; ncol2=15; w=0; offset=3; strand=D; shift=6; score=0.521736; ------hmACCAAACcCta ; cor=; Ncor= a 0 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 c 0 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 g 0 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 t 0 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift2 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --yyTACCTAAChw ; Alignment reference a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301
positions_7nt_m3_shift2 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --yyTACCTAAChw ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_7nt_m3 versus positions_6nt_m2; m=2/8; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.92307; -wyyTACCTAAChw ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_7nt_m3 versus positions_6nt_m5; m=3/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.90842; --wyCACCTAACww ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; positions_7nt_m3 versus oligos_7nt_mkv4_m4; m=4/8; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.790477; wwtktACCTAACmw ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; positions_7nt_m3 versus oligos_6nt_mkv3_m3; m=5/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.742358; --whcACCTAACta ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; positions_7nt_m3 versus oligos_6nt_mkv3_m2; m=6/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.694032; wwygTACCTAACta ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; positions_7nt_m3 versus oligos_6nt_mkv3_m5; m=7/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.607839; ----waCCAAACaw ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; positions_7nt_m3 versus oligos_7nt_mkv4_m5; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=3; score=0.504957; ---hmACCAAACcC ; cor=; Ncor= a 0 0 0 227 287 717 31 29 704 738 669 71 118 102 c 0 0 0 276 255 18 733 717 22 32 93 657 536 598 g 0 0 0 86 70 18 12 11 8 14 11 26 47 41 t 0 0 0 212 189 48 25 44 67 17 28 47 100 60

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=6; ncol=17; ------waCCAAACaww ; Alignment reference a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/15; ncol2=11; w=0; offset=0; strand=D; shift=6; score= 1; ------waCCAAACaww ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m5; m=2/15; ncol2=15; w=-1; offset=-1; strand=D; shift=5; score=0.634182; -----hmACCAAACcCt ; cor=; Ncor= a 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 c 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 g 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 t 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480
positions_6nt_m5_shift4 (positions_6nt_m5)				; oligos_6nt_mkv3_m5 versus positions_6nt_m5; m=3/15; ncol2=12; w=-2; offset=-2; strand=D; shift=4; score=0.615731; ----wyCACCTAACww- ; cor=; Ncor= a 0 0 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 c 0 0 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 g 0 0 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 t 0 0 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0
positions_7nt_m3_shift4 (positions_7nt_m3)				; oligos_6nt_mkv3_m5 versus positions_7nt_m3; m=4/15; ncol2=12; w=-2; offset=-2; strand=D; shift=4; score=0.607839; ----yyTACCTAAChw- ; cor=; Ncor= a 0 0 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 c 0 0 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 g 0 0 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 t 0 0 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m4; m=5/15; ncol2=15; w=-4; offset=-4; strand=D; shift=2; score=0.585309; --wwtktACCTAACmwh ; cor=; Ncor= a 0 0 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 c 0 0 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 g 0 0 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 t 0 0 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m3; m=6/15; ncol2=15; w=-2; offset=-2; strand=D; shift=4; score=0.56566; ----whcACCTAACtam ; cor=; Ncor= a 0 0 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 c 0 0 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 g 0 0 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 t 0 0 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256
positions_6nt_m2_shift3 (positions_6nt_m2)				; oligos_6nt_mkv3_m5 versus positions_6nt_m2; m=7/15; ncol2=13; w=-3; offset=-3; strand=D; shift=3; score=0.563866; ---wyyTACCTAAChw- ; cor=; Ncor= a 0 0 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 c 0 0 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 g 0 0 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 t 0 0 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m1; m=8/15; ncol2=16; w=-4; offset=-4; strand=D; shift=2; score=0.526422; --hhwccACCAACCAch ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727
positions_6nt_m1_shift2 (positions_6nt_m1)				; oligos_6nt_mkv3_m5 versus positions_6nt_m1; m=9/15; ncol2=16; w=-4; offset=-4; strand=D; shift=2; score=0.511326; --hhacCACCAACCACh ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m1; m=10/15; ncol2=16; w=-3; offset=-3; strand=D; shift=3; score=0.499606; ---hhycaCCAACCACc ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526
positions_7nt_m4_shift0 (positions_7nt_m4)				; oligos_6nt_mkv3_m5 versus positions_7nt_m4; m=11/15; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.480039; hhcaaCCACCAACCAmh ; cor=; Ncor= a 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 c 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 g 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 t 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m2; m=12/15; ncol2=17; w=-4; offset=-4; strand=D; shift=2; score=0.477432; --wwygTACCTAACtac ; cor=; Ncor= a 0 0 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 c 0 0 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 g 0 0 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 t 0 0 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182
positions_7nt_m1_shift2 (positions_7nt_m1)				; oligos_6nt_mkv3_m5 versus positions_7nt_m1; m=13/15; ncol2=17; w=-4; offset=-4; strand=D; shift=2; score=0.472099; --hmwcCACCAACCACc ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; oligos_6nt_mkv3_m5 versus positions_7nt_m5_rc; m=14/15; ncol2=18; w=-6; offset=-6; strand=R; shift=0; score=0.462941; hhhaacCACCAACCAch ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435
positions_6nt_m4_shift2 (positions_6nt_m4)				; oligos_6nt_mkv3_m5 versus positions_6nt_m4; m=15/15; ncol2=19; w=-4; offset=-4; strand=D; shift=2; score=0.425921; --whhcyACCAACCACc ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; wwygTACCTAACtachw ; Alignment reference a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 254 256 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 194 154 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 97 99 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182 228 264
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; wwygTACCTAACtachw ; cor=; Ncor= a 243 247 175 167 48 692 65 33 48 743 669 38 183 441 170 254 256 c 146 158 219 157 82 29 638 698 30 12 66 672 137 120 353 194 154 g 133 122 97 263 23 11 27 21 11 3 9 8 55 45 68 97 99 t 251 246 282 186 620 41 43 21 684 15 29 55 398 167 182 228 264
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m4; m=2/7; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.85478; wwtktACCTAACmwh-- ; cor=; Ncor= a 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 0 0 c 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 0 0 g 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 0 0 t 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280 0 0
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3; m=3/7; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.823032; --whcACCTAACtamww ; cor=; Ncor= a 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 366 364 c 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 247 230 g 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 131 132 t 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256 343 361
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=4/7; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.751885; -wyyTACCTAAChw--- ; cor=; Ncor= a 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 0 0 c 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 0 0 g 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 0 0 t 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0 0 0
positions_7nt_m3_shift2 (positions_7nt_m3)				; oligos_6nt_mkv3_m2 versus positions_7nt_m3; m=5/7; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.694032; --yyTACCTAAChw--- ; cor=; Ncor= a 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 0 0 c 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 0 0 g 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 0 0 t 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0 0 0
positions_6nt_m5_shift2 (positions_6nt_m5)				; oligos_6nt_mkv3_m2 versus positions_6nt_m5; m=6/7; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.62239; --wyCACCTAACww--- ; cor=; Ncor= a 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 0 0 c 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 0 0 g 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 0 0 t 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0 0 0
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m5; m=7/7; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.477432; ----waCCAAACaww-- ; cor=; Ncor= a 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 c 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 g 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 t 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=18; shift=1; ncol=19; -wdtagtTGGTGGTTGGwd ; Alignment reference a 0 279 258 232 441 96 121 96 58 35 41 79 33 52 58 76 105 269 280 c 0 143 105 103 119 53 52 73 18 10 34 15 16 38 13 23 69 101 131 g 0 243 364 237 230 691 172 57 885 889 17 848 951 83 67 863 740 227 357 t 0 361 299 454 236 186 681 800 65 92 934 84 26 853 888 64 112 429 258
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/11; ncol2=18; w=0; offset=0; strand=D; shift=1; score= 1; -wdtagtTGGTGGTTGGwd ; cor=; Ncor= a 0 279 258 232 441 96 121 96 58 35 41 79 33 52 58 76 105 269 280 c 0 143 105 103 119 53 52 73 18 10 34 15 16 38 13 23 69 101 131 g 0 243 364 237 230 691 172 57 885 889 17 848 951 83 67 863 740 227 357 t 0 361 299 454 236 186 681 800 65 92 934 84 26 853 888 64 112 429 258
positions_7nt_m4_rc_shift0 (positions_7nt_m4_rc)				; positions_6nt_m3 versus positions_7nt_m4_rc; m=2/11; ncol2=18; w=-1; offset=-1; strand=R; shift=0; score=0.778993; wdkTGGTTGGTGGttgdd- ; cor=; Ncor= a 434 414 293 121 111 64 62 101 63 34 64 204 202 262 228 240 438 446 0 c 202 155 75 86 47 27 49 42 16 17 32 45 79 104 80 107 216 165 0 g 376 428 461 97 1198 1276 84 107 1413 1312 26 1119 1096 254 260 907 428 402 0 t 520 535 703 1228 176 165 1337 1282 40 169 1410 164 155 912 964 278 450 519 0
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_6nt_m3 versus positions_7nt_m2; m=3/11; ncol2=23; w=0; offset=0; strand=D; shift=1; score=0.75956; -wdtwgtTGGTGGTTGGTr ; cor=; Ncor= a 0 282 273 240 370 152 148 117 108 77 35 71 30 30 63 49 67 110 486 c 0 147 99 94 118 58 60 66 33 16 33 8 14 19 9 11 40 36 72 g 0 227 311 189 218 567 169 99 736 734 23 828 907 49 46 891 792 93 262 t 0 338 311 471 288 217 617 712 117 167 903 87 43 896 876 43 95 755 174
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_6nt_m3 versus positions_7nt_m5; m=4/11; ncol2=18; w=-1; offset=-1; strand=D; shift=0; score=0.714303; wdgTGGTTGGTGgttddd- ; cor=; Ncor= a 457 435 214 112 138 38 39 87 83 55 110 232 274 370 305 535 466 522 0 c 193 142 51 98 28 11 39 20 15 29 30 56 118 143 110 187 234 204 0 g 371 504 1055 67 1321 1502 69 76 1538 1386 75 1216 1013 300 327 478 445 444 0 t 634 574 335 1378 168 104 1508 1472 19 185 1440 151 250 842 913 455 510 485 0
positions_6nt_m4_rc_shift4 (positions_6nt_m4_rc)				; positions_6nt_m3 versus positions_6nt_m4_rc; m=5/11; ncol2=19; w=0; offset=3; strand=R; shift=4; score=0.644865; ----wkttgGTGGTTGGTr ; cor=; Ncor= a 0 0 0 0 449 379 258 218 204 132 55 98 36 38 87 76 84 159 600 c 0 0 0 0 216 157 107 116 57 34 63 14 14 25 15 10 52 44 112 g 0 0 0 0 366 435 271 168 1040 1090 30 1265 1434 85 58 1397 1257 141 507 t 0 0 0 0 502 562 897 1031 232 277 1385 156 49 1385 1373 50 140 1189 314
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; positions_6nt_m3 versus positions_6nt_m1_rc; m=6/11; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.622578; wdGTGGTTGGTGgtdd--- ; cor=; Ncor= a 527 523 220 126 179 47 63 111 93 77 176 274 325 495 507 548 0 0 0 c 257 174 53 110 34 16 49 27 13 50 50 78 148 165 203 277 0 0 0 g 431 641 1411 86 1580 1838 88 116 1887 1598 107 1462 1250 359 591 579 0 0 0 t 799 676 330 1692 221 113 1814 1760 21 289 1681 200 291 995 713 610 0 0 0
positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)				; positions_6nt_m3 versus positions_7nt_m1_rc; m=7/11; ncol2=17; w=0; offset=2; strand=R; shift=3; score=0.612166; ---kwgGTGGTTGGTGgwk ; cor=; Ncor= a 0 0 0 516 527 357 222 113 173 49 52 131 73 92 191 312 376 587 524 c 0 0 0 227 286 117 55 108 29 9 47 24 22 58 57 88 171 223 238 g 0 0 0 675 399 1146 1432 77 1662 1934 98 120 1975 1625 121 1472 1222 464 645 t 0 0 0 682 888 480 391 1802 236 108 1903 1825 30 325 1731 228 331 826 693
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; positions_6nt_m3 versus oligos_6nt_mkv3_m1_rc; m=8/11; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.584338; wdgTGGTTGGTggwdd--- ; cor=; Ncor= a 717 727 328 143 242 55 53 123 125 106 325 553 579 784 701 750 0 0 0 c 371 227 82 149 37 18 50 31 16 66 117 181 289 305 330 395 0 0 0 g 566 895 1800 108 2201 2541 105 113 2566 2229 200 1575 1370 604 783 724 0 0 0 t 1085 890 529 2339 259 125 2531 2472 32 338 2097 430 501 1046 925 870 0 0 0
oligos_7nt_mkv4_m1_rc_shift6 (oligos_7nt_mkv4_m1_rc)				; positions_6nt_m3 versus oligos_7nt_mkv4_m1_rc; m=9/11; ncol2=16; w=0; offset=5; strand=R; shift=6; score=0.573674; ------dwgGTGGTTGGtg ; cor=; Ncor= a 0 0 0 0 0 0 716 659 526 225 83 204 47 42 111 143 200 398 522 c 0 0 0 0 0 0 283 372 148 26 124 31 15 61 28 20 107 131 179 g 0 0 0 0 0 0 781 432 1318 1973 52 2111 2429 97 118 2387 1909 322 1523 t 0 0 0 0 0 0 796 1113 584 352 2317 230 85 2376 2319 26 360 1725 352
oligos_7nt_mkv4_m3_rc_shift7 (oligos_7nt_mkv4_m3_rc)				; positions_6nt_m3 versus oligos_7nt_mkv4_m3_rc; m=10/11; ncol2=12; w=0; offset=6; strand=R; shift=7; score=0.569444; -------wdGTaGTTGgwd ; cor=; Ncor= a 0 0 0 0 0 0 0 581 682 63 99 1332 36 73 59 92 300 647 663 c 0 0 0 0 0 0 0 346 188 24 39 54 20 41 61 12 225 233 253 g 0 0 0 0 0 0 0 368 689 1991 69 462 2082 107 46 2043 1319 398 701 t 0 0 0 0 0 0 0 888 624 105 1976 335 45 1962 2017 36 339 905 566
oligos_7nt_mkv4_m2_rc_shift7 (oligos_7nt_mkv4_m2_rc)				; positions_6nt_m3 versus oligos_7nt_mkv4_m2_rc; m=11/11; ncol2=11; w=0; offset=6; strand=R; shift=7; score=0.49493; -------tdGTTGTTGkw- ; cor=; Ncor= a 0 0 0 0 0 0 0 615 793 38 126 305 50 120 99 54 586 745 0 c 0 0 0 0 0 0 0 456 199 12 83 55 25 94 34 20 395 311 0 g 0 0 0 0 0 0 0 385 790 2587 57 413 2567 299 66 2567 846 489 0 t 0 0 0 0 0 0 0 1195 869 14 2385 1878 9 2138 2452 10 824 1106 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=19; shift=2; ncol=21; --whhcyACCAACCACcaamw ; Alignment reference a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 562 502 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 435 366 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 157 216 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258 379 449
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/12; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --whhcyACCAACCACcaamw ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 562 502 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 435 366 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 157 216 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258 379 449
positions_7nt_m1_shift2 (positions_7nt_m1)				; positions_6nt_m4 versus positions_7nt_m1; m=2/12; ncol2=17; w=0; offset=0; strand=D; shift=2; score=0.851798; --hmwcCACCAACCACcwm-- ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 682 0 0 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 675 0 0 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 227 0 0 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527 516 0 0
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; positions_6nt_m4 versus positions_7nt_m2_rc; m=3/12; ncol2=23; w=-1; offset=-1; strand=R; shift=1; score=0.814221; -wwwhyyACCAACCACCAacw ; cor=; Ncor= a 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 617 217 288 c 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 169 567 218 g 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 60 58 118 t 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117 148 152 370
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; positions_6nt_m4 versus oligos_7nt_mkv4_m1; m=4/12; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.810789; ---hhycaCCAACCACcwh-- ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 796 0 0 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 781 0 0 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 283 0 0 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659 716 0 0
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; positions_6nt_m4 versus oligos_6nt_mkv3_m1; m=5/12; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.806797; --hhwccACCAACCAchw--- ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 0 0 0 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 0 0 0 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 0 0 0 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717 0 0 0
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m4 versus positions_6nt_m1; m=6/12; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.786113; --hhacCACCAACCAChw--- ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 0 0 0 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 0 0 0 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 0 0 0 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527 0 0 0
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; positions_6nt_m4 versus positions_7nt_m5_rc; m=7/12; ncol2=18; w=-2; offset=-2; strand=R; shift=0; score=0.703732; hhhaacCACCAACCAchw--- ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 0 0 0 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 0 0 0 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 0 0 0 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457 0 0 0
positions_7nt_m4_shift3 (positions_7nt_m4)				; positions_6nt_m4 versus positions_7nt_m4; m=8/12; ncol2=18; w=0; offset=1; strand=D; shift=3; score=0.687324; ---hhcaaCCACCAACCAmhw ; cor=; Ncor= a 0 0 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 0 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 0 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 0 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434
positions_6nt_m3_rc_shift6 (positions_6nt_m3_rc)				; positions_6nt_m4 versus positions_6nt_m3_rc; m=9/12; ncol2=18; w=0; offset=4; strand=R; shift=6; score=0.644865; ------hwCCAACCACCAact ; cor=; Ncor= a 0 0 0 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 c 0 0 0 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 g 0 0 0 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 t 0 0 0 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; positions_6nt_m4 versus oligos_7nt_mkv4_m3; m=10/12; ncol2=12; w=0; offset=4; strand=D; shift=6; score=0.545567; ------hwcCAACtAChw--- ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 0 0 0 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 0 0 0 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 0 0 0 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581 0 0 0
oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)				; positions_6nt_m4 versus oligos_7nt_mkv4_m2; m=11/12; ncol2=11; w=0; offset=5; strand=D; shift=7; score=0.470105; -------wmCAACAACha--- ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 0 0 0 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 0 0 0 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 0 0 0 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615 0 0 0
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)				; positions_6nt_m4 versus oligos_6nt_mkv3_m5; m=12/12; ncol2=11; w=0; offset=4; strand=D; shift=6; score=0.425921; ------waCCAAACaww---- ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 0 0 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 0 0 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 0 0 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=15; shift=5; ncol=20; -----hmACCAAACcCtahh ; Alignment reference a 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 290 227 c 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 205 234 g 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 99 94 t 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191 207 246
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=5; score= 1; -----hmACCAAACcCtahh ; cor=; Ncor= a 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 290 227 c 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 205 234 g 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 99 94 t 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191 207 246
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m5; m=2/10; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.634182; ------waCCAAACaww--- ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 0 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 0 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 0 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0 0
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m3; m=3/10; ncol2=15; w=-1; offset=-1; strand=D; shift=4; score=0.625443; ----whcACCTAACtamww- ; cor=; Ncor= a 0 0 0 0 311 288 143 995 91 27 112 1049 964 54 246 602 293 366 364 0 c 0 0 0 0 263 285 632 17 908 1022 49 15 75 934 164 170 425 247 230 0 g 0 0 0 0 142 177 48 24 40 19 24 4 21 13 80 60 113 131 132 0 t 0 0 0 0 371 337 264 51 48 19 902 19 27 86 597 255 256 343 361 0
positions_6nt_m5_shift4 (positions_6nt_m5)				; oligos_7nt_mkv4_m5 versus positions_6nt_m5; m=4/10; ncol2=12; w=-1; offset=-1; strand=D; shift=4; score=0.533733; ----wyCACCTAACww---- ; cor=; Ncor= a 0 0 0 0 294 239 73 1009 88 21 150 1011 949 58 352 364 0 0 0 0 c 0 0 0 0 245 333 782 1 908 989 30 12 65 877 255 258 0 0 0 0 g 0 0 0 0 130 142 26 9 15 11 19 0 7 13 110 107 0 0 0 0 t 0 0 0 0 367 322 155 17 25 15 837 13 15 88 319 307 0 0 0 0
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1; m=5/10; ncol2=16; w=-3; offset=-3; strand=D; shift=2; score=0.521736; --hhwccACCAACCAchw-- ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 0 0 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 0 0 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 0 0 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717 0 0
positions_6nt_m1_shift2 (positions_6nt_m1)				; oligos_7nt_mkv4_m5 versus positions_6nt_m1; m=6/10; ncol2=16; w=-3; offset=-3; strand=D; shift=2; score=0.516779; --hhacCACCAACCAChw-- ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 0 0 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 0 0 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 0 0 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527 0 0
positions_7nt_m3_shift4 (positions_7nt_m3)				; oligos_7nt_mkv4_m5 versus positions_7nt_m3; m=7/10; ncol2=12; w=-1; offset=-1; strand=D; shift=4; score=0.504957; ----yyTACCTAAChw---- ; cor=; Ncor= a 0 0 0 0 247 250 73 1004 104 23 104 1022 978 70 374 429 0 0 0 0 c 0 0 0 0 265 271 125 13 894 992 30 13 55 896 264 216 0 0 0 0 g 0 0 0 0 136 196 26 12 19 13 12 4 6 7 98 109 0 0 0 0 t 0 0 0 0 407 338 831 26 38 27 909 16 16 82 319 301 0 0 0 0
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m4; m=8/10; ncol2=15; w=-3; offset=-3; strand=D; shift=2; score=0.497266; --wwtktACCTAACmwh--- ; cor=; Ncor= a 0 0 311 297 181 190 119 904 74 17 93 927 873 54 278 416 314 0 0 0 c 0 0 182 199 175 205 154 20 815 906 33 11 56 845 374 172 243 0 0 0 g 0 0 174 159 90 310 51 10 30 14 15 4 12 5 75 110 125 0 0 0 t 0 0 295 307 516 257 638 28 43 25 821 20 21 58 235 264 280 0 0 0
positions_6nt_m2_shift3 (positions_6nt_m2)				; oligos_7nt_mkv4_m5 versus positions_6nt_m2; m=9/10; ncol2=13; w=-2; offset=-2; strand=D; shift=3; score=0.475052; ---wyyTACCTAAChw---- ; cor=; Ncor= a 0 0 0 340 242 250 69 997 103 23 103 1013 972 70 371 425 0 0 0 0 c 0 0 0 209 264 269 124 13 886 983 30 13 55 887 263 215 0 0 0 0 g 0 0 0 162 134 194 25 11 19 13 11 4 5 7 96 107 0 0 0 0 t 0 0 0 335 406 333 828 25 38 27 902 16 14 82 316 299 0 0 0 0
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; oligos_7nt_mkv4_m5 versus positions_7nt_m5_rc; m=10/10; ncol2=18; w=-5; offset=-5; strand=R; shift=0; score=0.469162; hhhaacCACCAACCAchw-- ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 0 0 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 0 0 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 0 0 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=16; shift=3; ncol=19; ---hhycaCCAACCACcwh ; Alignment reference a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 796 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 781 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 283 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659 716
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/12; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---hhycaCCAACCACcwh ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 796 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 781 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 283 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659 716
positions_7nt_m1_shift2 (positions_7nt_m1)				; oligos_7nt_mkv4_m1 versus positions_7nt_m1; m=2/12; ncol2=17; w=-1; offset=-1; strand=D; shift=2; score=0.923963; --hmwcCACCAACCACcwm ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 682 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 675 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 227 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527 516
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/12; ncol2=16; w=-1; offset=-1; strand=D; shift=2; score=0.868516; --hhwccACCAACCAchw- ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 0 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 0 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 0 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717 0
positions_6nt_m1_shift2 (positions_6nt_m1)				; oligos_7nt_mkv4_m1 versus positions_6nt_m1; m=4/12; ncol2=16; w=-1; offset=-1; strand=D; shift=2; score=0.853953; --hhacCACCAACCAChw- ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 0 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 0 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 0 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527 0
positions_6nt_m4_shift2 (positions_6nt_m4)				; oligos_7nt_mkv4_m1 versus positions_6nt_m4; m=5/12; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.810789; --whhcyACCAACCACcaa ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 897 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 271 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 107 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218 258
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; oligos_7nt_mkv4_m1 versus positions_7nt_m5_rc; m=6/12; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.754519; hhhaacCACCAACCAchw- ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 0 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 0 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 0 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457 0
positions_7nt_m4_shift0 (positions_7nt_m4)				; oligos_7nt_mkv4_m1 versus positions_7nt_m4; m=7/12; ncol2=18; w=-3; offset=-3; strand=D; shift=0; score=0.703651; hhcaaCCACCAACCAmhw- ; cor=; Ncor= a 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 0 c 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 0 g 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 0 t 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434 0
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=8/12; ncol2=12; w=0; offset=3; strand=D; shift=6; score=0.668909; ------hwcCAACtAChw- ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 0 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 0 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 0 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581 0
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; oligos_7nt_mkv4_m1 versus positions_7nt_m2_rc; m=9/12; ncol2=23; w=-2; offset=-2; strand=R; shift=1; score=0.659126; -wwwhyyACCAACCACCAa ; cor=; Ncor= a 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 617 c 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 169 g 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 60 t 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117 148
oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=10/12; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.583549; -------wmCAACAACha- ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 0 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 0 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 0 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615 0
positions_6nt_m3_rc_shift6 (positions_6nt_m3_rc)				; oligos_7nt_mkv4_m1 versus positions_6nt_m3_rc; m=11/12; ncol2=18; w=0; offset=3; strand=R; shift=6; score=0.573674; ------hwCCAACCACCAa ; cor=; Ncor= a 0 0 0 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 681 c 0 0 0 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 172 g 0 0 0 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 52 t 0 0 0 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96 121
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m5; m=12/12; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.499606; ------waCCAAACaww-- ; cor=; Ncor= a 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 0 c 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 0 g 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 0 t 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=6; ncol=18; ------hwcCAACtAChw ; Alignment reference a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/11; ncol2=12; w=0; offset=0; strand=D; shift=6; score= 1; ------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581
oligos_7nt_mkv4_m2_shift7 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2; m=2/11; ncol2=11; w=0; offset=1; strand=D; shift=7; score=0.83876; -------wmCAACAACha ; cor=; Ncor= a 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=3/11; ncol2=16; w=-3; offset=-3; strand=D; shift=3; score=0.668909; ---hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m1; m=4/11; ncol2=16; w=-4; offset=-4; strand=D; shift=2; score=0.659882; --hhwccACCAACCAchw ; cor=; Ncor= a 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717
positions_6nt_m1_shift2 (positions_6nt_m1)				; oligos_7nt_mkv4_m3 versus positions_6nt_m1; m=5/11; ncol2=16; w=-4; offset=-4; strand=D; shift=2; score=0.648354; --hhacCACCAACCAChw ; cor=; Ncor= a 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527
positions_7nt_m1_shift2 (positions_7nt_m1)				; oligos_7nt_mkv4_m3 versus positions_7nt_m1; m=6/11; ncol2=17; w=-4; offset=-4; strand=D; shift=2; score=0.607415; --hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527
positions_6nt_m3_rc_shift6 (positions_6nt_m3_rc)				; oligos_7nt_mkv4_m3 versus positions_6nt_m3_rc; m=7/11; ncol2=18; w=0; offset=0; strand=R; shift=6; score=0.569444; ------hwCCAACCACCA ; cor=; Ncor= a 0 0 0 0 0 0 258 429 112 64 888 853 26 84 934 92 65 800 c 0 0 0 0 0 0 357 227 740 863 67 83 951 848 17 889 885 57 g 0 0 0 0 0 0 131 101 69 23 13 38 16 15 34 10 18 73 t 0 0 0 0 0 0 280 269 105 76 58 52 33 79 41 35 58 96
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; oligos_7nt_mkv4_m3 versus positions_7nt_m5_rc; m=8/11; ncol2=18; w=-6; offset=-6; strand=R; shift=0; score=0.566665; hhhaacCACCAACCAchw ; cor=; Ncor= a 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457
positions_6nt_m4_shift2 (positions_6nt_m4)				; oligos_7nt_mkv4_m3 versus positions_6nt_m4; m=9/11; ncol2=19; w=-4; offset=-4; strand=D; shift=2; score=0.545567; --whhcyACCAACCACca ; cor=; Ncor= a 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 c 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 g 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 t 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218
positions_7nt_m4_shift0 (positions_7nt_m4)				; oligos_7nt_mkv4_m3 versus positions_7nt_m4; m=10/11; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.516119; hhcaaCCACCAACCAmhw ; cor=; Ncor= a 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; oligos_7nt_mkv4_m3 versus positions_7nt_m2_rc; m=11/11; ncol2=23; w=-5; offset=-5; strand=R; shift=1; score=0.445559; -wwwhyyACCAACCACCA ; cor=; Ncor= a 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 c 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 g 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 t 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m5_shift6 (positions_7nt_m5)				; positions_7nt_m5; m=0 (reference); ncol1=18; shift=6; ncol=24; ------wdgTGGTTGGTGgttddd ; Alignment reference a 0 0 0 0 0 0 457 435 214 112 138 38 39 87 83 55 110 232 274 370 305 535 466 522 c 0 0 0 0 0 0 193 142 51 98 28 11 39 20 15 29 30 56 118 143 110 187 234 204 g 0 0 0 0 0 0 371 504 1055 67 1321 1502 69 76 1538 1386 75 1216 1013 300 327 478 445 444 t 0 0 0 0 0 0 634 574 335 1378 168 104 1508 1472 19 185 1440 151 250 842 913 455 510 485
positions_7nt_m5_shift6 (positions_7nt_m5)				; positions_7nt_m5 versus positions_7nt_m5; m=1/13; ncol2=18; w=0; offset=0; strand=D; shift=6; score= 1; ------wdgTGGTTGGTGgttddd ; cor=; Ncor= a 0 0 0 0 0 0 457 435 214 112 138 38 39 87 83 55 110 232 274 370 305 535 466 522 c 0 0 0 0 0 0 193 142 51 98 28 11 39 20 15 29 30 56 118 143 110 187 234 204 g 0 0 0 0 0 0 371 504 1055 67 1321 1502 69 76 1538 1386 75 1216 1013 300 327 478 445 444 t 0 0 0 0 0 0 634 574 335 1378 168 104 1508 1472 19 185 1440 151 250 842 913 455 510 485
positions_7nt_m4_rc_shift6 (positions_7nt_m4_rc)				; positions_7nt_m5 versus positions_7nt_m4_rc; m=2/13; ncol2=18; w=0; offset=0; strand=R; shift=6; score=0.964218; ------wdkTGGTTGGTGGttgdd ; cor=; Ncor= a 0 0 0 0 0 0 434 414 293 121 111 64 62 101 63 34 64 204 202 262 228 240 438 446 c 0 0 0 0 0 0 202 155 75 86 47 27 49 42 16 17 32 45 79 104 80 107 216 165 g 0 0 0 0 0 0 376 428 461 97 1198 1276 84 107 1413 1312 26 1119 1096 254 260 907 428 402 t 0 0 0 0 0 0 520 535 703 1228 176 165 1337 1282 40 169 1410 164 155 912 964 278 450 519
positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)				; positions_7nt_m5 versus positions_6nt_m1_rc; m=3/13; ncol2=16; w=0; offset=0; strand=R; shift=6; score=0.882809; ------wdGTGGTTGGTGgtdd-- ; cor=; Ncor= a 0 0 0 0 0 0 527 523 220 126 179 47 63 111 93 77 176 274 325 495 507 548 0 0 c 0 0 0 0 0 0 257 174 53 110 34 16 49 27 13 50 50 78 148 165 203 277 0 0 g 0 0 0 0 0 0 431 641 1411 86 1580 1838 88 116 1887 1598 107 1462 1250 359 591 579 0 0 t 0 0 0 0 0 0 799 676 330 1692 221 113 1814 1760 21 289 1681 200 291 995 713 610 0 0
oligos_6nt_mkv3_m1_rc_shift6 (oligos_6nt_mkv3_m1_rc)				; positions_7nt_m5 versus oligos_6nt_mkv3_m1_rc; m=4/13; ncol2=16; w=0; offset=0; strand=R; shift=6; score=0.87543; ------wdgTGGTTGGTggwdd-- ; cor=; Ncor= a 0 0 0 0 0 0 717 727 328 143 242 55 53 123 125 106 325 553 579 784 701 750 0 0 c 0 0 0 0 0 0 371 227 82 149 37 18 50 31 16 66 117 181 289 305 330 395 0 0 g 0 0 0 0 0 0 566 895 1800 108 2201 2541 105 113 2566 2229 200 1575 1370 604 783 724 0 0 t 0 0 0 0 0 0 1085 890 529 2339 259 125 2531 2472 32 338 2097 430 501 1046 925 870 0 0
positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)				; positions_7nt_m5 versus positions_7nt_m1_rc; m=5/13; ncol2=17; w=-1; offset=-1; strand=R; shift=5; score=0.826227; -----kwgGTGGTTGGTGgwkd-- ; cor=; Ncor= a 0 0 0 0 0 516 527 357 222 113 173 49 52 131 73 92 191 312 376 587 524 552 0 0 c 0 0 0 0 0 227 286 117 55 108 29 9 47 24 22 58 57 88 171 223 238 297 0 0 g 0 0 0 0 0 675 399 1146 1432 77 1662 1934 98 120 1975 1625 121 1472 1222 464 645 593 0 0 t 0 0 0 0 0 682 888 480 391 1802 236 108 1903 1825 30 325 1731 228 331 826 693 658 0 0
oligos_7nt_mkv4_m1_rc_shift5 (oligos_7nt_mkv4_m1_rc)				; positions_7nt_m5 versus oligos_7nt_mkv4_m1_rc; m=6/13; ncol2=16; w=-1; offset=-1; strand=R; shift=5; score=0.754519; -----dwgGTGGTTGGtgrdd--- ; cor=; Ncor= a 0 0 0 0 0 716 659 526 225 83 204 47 42 111 143 200 398 522 761 811 691 0 0 0 c 0 0 0 0 0 283 372 148 26 124 31 15 61 28 20 107 131 179 362 329 310 0 0 0 g 0 0 0 0 0 781 432 1318 1973 52 2111 2429 97 118 2387 1909 322 1523 813 649 767 0 0 0 t 0 0 0 0 0 796 1113 584 352 2317 230 85 2376 2319 26 360 1725 352 640 787 808 0 0 0
positions_6nt_m3_shift7 (positions_6nt_m3)				; positions_7nt_m5 versus positions_6nt_m3; m=7/13; ncol2=18; w=0; offset=1; strand=D; shift=7; score=0.714303; -------wdtagtTGGTGGTTGGw ; cor=; Ncor= a 0 0 0 0 0 0 0 279 258 232 441 96 121 96 58 35 41 79 33 52 58 76 105 269 c 0 0 0 0 0 0 0 143 105 103 119 53 52 73 18 10 34 15 16 38 13 23 69 101 g 0 0 0 0 0 0 0 243 364 237 230 691 172 57 885 889 17 848 951 83 67 863 740 227 t 0 0 0 0 0 0 0 361 299 454 236 186 681 800 65 92 934 84 26 853 888 64 112 429
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; positions_7nt_m5 versus positions_6nt_m4_rc; m=8/13; ncol2=19; w=-3; offset=-3; strand=R; shift=3; score=0.703732; ---wkttgGTGGTTGGTrgddw-- ; cor=; Ncor= a 0 0 0 449 379 258 218 204 132 55 98 36 38 87 76 84 159 600 353 456 416 440 0 0 c 0 0 0 216 157 107 116 57 34 63 14 14 25 15 10 52 44 112 205 183 180 230 0 0 g 0 0 0 366 435 271 168 1040 1090 30 1265 1434 85 58 1397 1257 141 507 634 473 418 349 0 0 t 0 0 0 502 562 897 1031 232 277 1385 156 49 1385 1373 50 140 1189 314 341 421 519 514 0 0
positions_7nt_m2_shift0 (positions_7nt_m2)				; positions_7nt_m5 versus positions_7nt_m2; m=9/13; ncol2=23; w=-6; offset=-6; strand=D; shift=0; score=0.63824; wdtwgtTGGTGGTTGGTrrdwww- ; cor=; Ncor= a 282 273 240 370 152 148 117 108 77 35 71 30 30 63 49 67 110 486 254 314 273 297 289 0 c 147 99 94 118 58 60 66 33 16 33 8 14 19 9 11 40 36 72 140 120 112 129 144 0 g 227 311 189 218 567 169 99 736 734 23 828 907 49 46 891 792 93 262 368 286 242 230 244 0 t 338 311 471 288 217 617 712 117 167 903 87 43 896 876 43 95 755 174 232 274 367 338 317 0
oligos_7nt_mkv4_m3_rc_shift6 (oligos_7nt_mkv4_m3_rc)				; positions_7nt_m5 versus oligos_7nt_mkv4_m3_rc; m=10/13; ncol2=12; w=0; offset=0; strand=R; shift=6; score=0.566665; ------wdGTaGTTGgwd------ ; cor=; Ncor= a 0 0 0 0 0 0 581 682 63 99 1332 36 73 59 92 300 647 663 0 0 0 0 0 0 c 0 0 0 0 0 0 346 188 24 39 54 20 41 61 12 225 233 253 0 0 0 0 0 0 g 0 0 0 0 0 0 368 689 1991 69 462 2082 107 46 2043 1319 398 701 0 0 0 0 0 0 t 0 0 0 0 0 0 888 624 105 1976 335 45 1962 2017 36 339 905 566 0 0 0 0 0 0
oligos_7nt_mkv4_m2_rc_shift6 (oligos_7nt_mkv4_m2_rc)				; positions_7nt_m5 versus oligos_7nt_mkv4_m2_rc; m=11/13; ncol2=11; w=0; offset=0; strand=R; shift=6; score=0.494442; ------tdGTTGTTGkw------- ; cor=; Ncor= a 0 0 0 0 0 0 615 793 38 126 305 50 120 99 54 586 745 0 0 0 0 0 0 0 c 0 0 0 0 0 0 456 199 12 83 55 25 94 34 20 395 311 0 0 0 0 0 0 0 g 0 0 0 0 0 0 385 790 2587 57 413 2567 299 66 2567 846 489 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1195 869 14 2385 1878 9 2138 2452 10 824 1106 0 0 0 0 0 0 0
oligos_7nt_mkv4_m5_rc_shift4 (oligos_7nt_mkv4_m5_rc)				; positions_7nt_m5 versus oligos_7nt_mkv4_m5_rc; m=12/13; ncol2=15; w=-2; offset=-2; strand=R; shift=4; score=0.469162; ----ddtaGgGTTTGGTkd----- ; cor=; Ncor= a 0 0 0 0 246 207 191 480 60 100 47 28 17 67 44 25 48 189 212 0 0 0 0 0 c 0 0 0 0 94 99 74 63 41 47 26 11 14 8 11 12 18 70 86 0 0 0 0 0 g 0 0 0 0 234 205 181 67 598 536 657 93 32 22 717 733 18 255 276 0 0 0 0 0 t 0 0 0 0 227 290 355 191 102 118 71 669 738 704 29 31 717 287 227 0 0 0 0 0
oligos_6nt_mkv3_m5_rc_shift7 (oligos_6nt_mkv3_m5_rc)				; positions_7nt_m5 versus oligos_6nt_mkv3_m5_rc; m=13/13; ncol2=11; w=0; offset=1; strand=R; shift=7; score=0.462941; -------wwtGTTTGGtw------ ; cor=; Ncor= a 0 0 0 0 0 0 0 358 447 174 21 85 58 157 30 6 247 412 0 0 0 0 0 0 c 0 0 0 0 0 0 0 192 178 60 6 32 20 37 23 7 156 145 0 0 0 0 0 0 g 0 0 0 0 0 0 0 226 321 255 1316 91 22 14 1292 1325 150 330 0 0 0 0 0 0 t 0 0 0 0 0 0 0 569 399 856 2 1137 1245 1137 0 7 792 458 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=23; shift=0; ncol=23; wdtwgtTGGTGGTTGGTrrdwww ; Alignment reference a 282 273 240 370 152 148 117 108 77 35 71 30 30 63 49 67 110 486 254 314 273 297 289 c 147 99 94 118 58 60 66 33 16 33 8 14 19 9 11 40 36 72 140 120 112 129 144 g 227 311 189 218 567 169 99 736 734 23 828 907 49 46 891 792 93 262 368 286 242 230 244 t 338 311 471 288 217 617 712 117 167 903 87 43 896 876 43 95 755 174 232 274 367 338 317
positions_7nt_m2_shift0 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/10; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; wdtwgtTGGTGGTTGGTrrdwww ; cor=; Ncor= a 282 273 240 370 152 148 117 108 77 35 71 30 30 63 49 67 110 486 254 314 273 297 289 c 147 99 94 118 58 60 66 33 16 33 8 14 19 9 11 40 36 72 140 120 112 129 144 g 227 311 189 218 567 169 99 736 734 23 828 907 49 46 891 792 93 262 368 286 242 230 244 t 338 311 471 288 217 617 712 117 167 903 87 43 896 876 43 95 755 174 232 274 367 338 317
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; positions_7nt_m2 versus positions_6nt_m4_rc; m=2/10; ncol2=19; w=0; offset=3; strand=R; shift=3; score=0.814221; ---wkttgGTGGTTGGTrgddw- ; cor=; Ncor= a 0 0 0 449 379 258 218 204 132 55 98 36 38 87 76 84 159 600 353 456 416 440 0 c 0 0 0 216 157 107 116 57 34 63 14 14 25 15 10 52 44 112 205 183 180 230 0 g 0 0 0 366 435 271 168 1040 1090 30 1265 1434 85 58 1397 1257 141 507 634 473 418 349 0 t 0 0 0 502 562 897 1031 232 277 1385 156 49 1385 1373 50 140 1189 314 341 421 519 514 0
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_7nt_m2 versus positions_6nt_m3; m=3/10; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.75956; wdtagtTGGTGGTTGGwd----- ; cor=; Ncor= a 279 258 232 441 96 121 96 58 35 41 79 33 52 58 76 105 269 280 0 0 0 0 0 c 143 105 103 119 53 52 73 18 10 34 15 16 38 13 23 69 101 131 0 0 0 0 0 g 243 364 237 230 691 172 57 885 889 17 848 951 83 67 863 740 227 357 0 0 0 0 0 t 361 299 454 236 186 681 800 65 92 934 84 26 853 888 64 112 429 258 0 0 0 0 0
positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)				; positions_7nt_m2 versus positions_7nt_m1_rc; m=4/10; ncol2=17; w=0; offset=5; strand=R; shift=5; score=0.68817; -----kwgGTGGTTGGTGgwkd- ; cor=; Ncor= a 0 0 0 0 0 516 527 357 222 113 173 49 52 131 73 92 191 312 376 587 524 552 0 c 0 0 0 0 0 227 286 117 55 108 29 9 47 24 22 58 57 88 171 223 238 297 0 g 0 0 0 0 0 675 399 1146 1432 77 1662 1934 98 120 1975 1625 121 1472 1222 464 645 593 0 t 0 0 0 0 0 682 888 480 391 1802 236 108 1903 1825 30 325 1731 228 331 826 693 658 0
oligos_7nt_mkv4_m1_rc_shift5 (oligos_7nt_mkv4_m1_rc)				; positions_7nt_m2 versus oligos_7nt_mkv4_m1_rc; m=5/10; ncol2=16; w=0; offset=5; strand=R; shift=5; score=0.659126; -----dwgGTGGTTGGtgrdd-- ; cor=; Ncor= a 0 0 0 0 0 716 659 526 225 83 204 47 42 111 143 200 398 522 761 811 691 0 0 c 0 0 0 0 0 283 372 148 26 124 31 15 61 28 20 107 131 179 362 329 310 0 0 g 0 0 0 0 0 781 432 1318 1973 52 2111 2429 97 118 2387 1909 322 1523 813 649 767 0 0 t 0 0 0 0 0 796 1113 584 352 2317 230 85 2376 2319 26 360 1725 352 640 787 808 0 0
oligos_6nt_mkv3_m1_rc_shift6 (oligos_6nt_mkv3_m1_rc)				; positions_7nt_m2 versus oligos_6nt_mkv3_m1_rc; m=6/10; ncol2=16; w=0; offset=6; strand=R; shift=6; score=0.652279; ------wdgTGGTTGGTggwdd- ; cor=; Ncor= a 0 0 0 0 0 0 717 727 328 143 242 55 53 123 125 106 325 553 579 784 701 750 0 c 0 0 0 0 0 0 371 227 82 149 37 18 50 31 16 66 117 181 289 305 330 395 0 g 0 0 0 0 0 0 566 895 1800 108 2201 2541 105 113 2566 2229 200 1575 1370 604 783 724 0 t 0 0 0 0 0 0 1085 890 529 2339 259 125 2531 2472 32 338 2097 430 501 1046 925 870 0
positions_7nt_m5_shift6 (positions_7nt_m5)				; positions_7nt_m2 versus positions_7nt_m5; m=7/10; ncol2=18; w=0; offset=6; strand=D; shift=6; score=0.63824; ------wdgTGGTTGGTGgttdd ; cor=; Ncor= a 0 0 0 0 0 0 457 435 214 112 138 38 39 87 83 55 110 232 274 370 305 535 466 c 0 0 0 0 0 0 193 142 51 98 28 11 39 20 15 29 30 56 118 143 110 187 234 g 0 0 0 0 0 0 371 504 1055 67 1321 1502 69 76 1538 1386 75 1216 1013 300 327 478 445 t 0 0 0 0 0 0 634 574 335 1378 168 104 1508 1472 19 185 1440 151 250 842 913 455 510
positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)				; positions_7nt_m2 versus positions_6nt_m1_rc; m=8/10; ncol2=16; w=0; offset=6; strand=R; shift=6; score=0.632779; ------wdGTGGTTGGTGgtdd- ; cor=; Ncor= a 0 0 0 0 0 0 527 523 220 126 179 47 63 111 93 77 176 274 325 495 507 548 0 c 0 0 0 0 0 0 257 174 53 110 34 16 49 27 13 50 50 78 148 165 203 277 0 g 0 0 0 0 0 0 431 641 1411 86 1580 1838 88 116 1887 1598 107 1462 1250 359 591 579 0 t 0 0 0 0 0 0 799 676 330 1692 221 113 1814 1760 21 289 1681 200 291 995 713 610 0
positions_7nt_m4_rc_shift6 (positions_7nt_m4_rc)				; positions_7nt_m2 versus positions_7nt_m4_rc; m=9/10; ncol2=18; w=0; offset=6; strand=R; shift=6; score=0.586854; ------wdkTGGTTGGTGGttgd ; cor=; Ncor= a 0 0 0 0 0 0 434 414 293 121 111 64 62 101 63 34 64 204 202 262 228 240 438 c 0 0 0 0 0 0 202 155 75 86 47 27 49 42 16 17 32 45 79 104 80 107 216 g 0 0 0 0 0 0 376 428 461 97 1198 1276 84 107 1413 1312 26 1119 1096 254 260 907 428 t 0 0 0 0 0 0 520 535 703 1228 176 165 1337 1282 40 169 1410 164 155 912 964 278 450
oligos_7nt_mkv4_m3_rc_shift6 (oligos_7nt_mkv4_m3_rc)				; positions_7nt_m2 versus oligos_7nt_mkv4_m3_rc; m=10/10; ncol2=12; w=0; offset=6; strand=R; shift=6; score=0.445559; ------wdGTaGTTGgwd----- ; cor=; Ncor= a 0 0 0 0 0 0 581 682 63 99 1332 36 73 59 92 300 647 663 0 0 0 0 0 c 0 0 0 0 0 0 346 188 24 39 54 20 41 61 12 225 233 253 0 0 0 0 0 g 0 0 0 0 0 0 368 689 1991 69 462 2082 107 46 2043 1319 398 701 0 0 0 0 0 t 0 0 0 0 0 0 888 624 105 1976 335 45 1962 2017 36 339 905 566 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=16; shift=3; ncol=19; ---hhacCACCAACCAChw ; Alignment reference a 0 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/13; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---hhacCACCAACCAChw ; cor=; Ncor= a 0 0 0 610 713 995 291 200 1681 289 21 1760 1814 113 221 1692 330 676 799 c 0 0 0 579 591 359 1250 1462 107 1598 1887 116 88 1838 1580 86 1411 641 431 g 0 0 0 277 203 165 148 78 50 50 13 27 49 16 34 110 53 174 257 t 0 0 0 548 507 495 325 274 176 77 93 111 63 47 179 126 220 523 527
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; positions_6nt_m1 versus oligos_6nt_mkv3_m1; m=2/13; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.991892; ---hhwccACCAACCAchw ; cor=; Ncor= a 0 0 0 870 925 1046 501 430 2097 338 32 2472 2531 125 259 2339 529 890 1085 c 0 0 0 724 783 604 1370 1575 200 2229 2566 113 105 2541 2201 108 1800 895 566 g 0 0 0 395 330 305 289 181 117 66 16 31 50 18 37 149 82 227 371 t 0 0 0 750 701 784 579 553 325 106 125 123 53 55 242 143 328 727 717
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=3/13; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.932332; ---hmwcCACCAACCACcw ; cor=; Ncor= a 0 0 0 658 693 826 331 228 1731 325 30 1825 1903 108 236 1802 391 480 888 c 0 0 0 593 645 464 1222 1472 121 1625 1975 120 98 1934 1662 77 1432 1146 399 g 0 0 0 297 238 223 171 88 57 58 22 24 47 9 29 108 55 117 286 t 0 0 0 552 524 587 376 312 191 92 73 131 52 49 173 113 222 357 527
positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)				; positions_6nt_m1 versus positions_7nt_m5_rc; m=4/13; ncol2=18; w=-2; offset=-2; strand=R; shift=1; score=0.882809; -hhhaacCACCAACCAchw ; cor=; Ncor= a 0 485 510 455 913 842 250 151 1440 185 19 1472 1508 104 168 1378 335 574 634 c 0 444 445 478 327 300 1013 1216 75 1386 1538 76 69 1502 1321 67 1055 504 371 g 0 204 234 187 110 143 118 56 30 29 15 20 39 11 28 98 51 142 193 t 0 522 466 535 305 370 274 232 110 55 83 87 39 38 138 112 214 435 457
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)				; positions_6nt_m1 versus oligos_7nt_mkv4_m1; m=5/13; ncol2=16; w=0; offset=1; strand=D; shift=4; score=0.853953; ----hhycaCCAACCACcw ; cor=; Ncor= a 0 0 0 0 808 787 640 352 1725 360 26 2319 2376 85 230 2317 352 584 1113 c 0 0 0 0 767 649 813 1523 322 1909 2387 118 97 2429 2111 52 1973 1318 432 g 0 0 0 0 310 329 362 179 131 107 20 28 61 15 31 124 26 148 372 t 0 0 0 0 691 811 761 522 398 200 143 111 42 47 204 83 225 526 659
positions_7nt_m4_shift1 (positions_7nt_m4)				; positions_6nt_m1 versus positions_7nt_m4; m=6/13; ncol2=18; w=-2; offset=-2; strand=D; shift=1; score=0.841103; -hhcaaCCACCAACCAmhw ; cor=; Ncor= a 0 519 450 278 964 912 155 164 1410 169 40 1282 1337 165 176 1228 703 535 520 c 0 402 428 907 260 254 1096 1119 26 1312 1413 107 84 1276 1198 97 461 428 376 g 0 165 216 107 80 104 79 45 32 17 16 42 49 27 47 86 75 155 202 t 0 446 438 240 228 262 202 204 64 34 63 101 62 64 111 121 293 414 434
positions_6nt_m4_shift3 (positions_6nt_m4)				; positions_6nt_m1 versus positions_6nt_m4; m=7/13; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.786113; ---whhcyACCAACCACca ; cor=; Ncor= a 0 0 0 514 519 421 341 314 1189 140 50 1373 1385 49 156 1385 277 232 1031 c 0 0 0 349 418 473 634 507 141 1257 1397 58 85 1434 1265 30 1090 1040 168 g 0 0 0 230 180 183 205 112 44 52 10 15 25 14 14 63 34 57 116 t 0 0 0 440 416 456 353 600 159 84 76 87 38 36 98 55 132 204 218
oligos_7nt_mkv4_m3_shift7 (oligos_7nt_mkv4_m3)				; positions_6nt_m1 versus oligos_7nt_mkv4_m3; m=8/13; ncol2=12; w=0; offset=4; strand=D; shift=7; score=0.648354; -------hwcCAACtAChw ; cor=; Ncor= a 0 0 0 0 0 0 0 566 905 339 36 2017 1962 45 335 1976 105 624 888 c 0 0 0 0 0 0 0 701 398 1319 2043 46 107 2082 462 69 1991 689 368 g 0 0 0 0 0 0 0 253 233 225 12 61 41 20 54 39 24 188 346 t 0 0 0 0 0 0 0 663 647 300 92 59 73 36 1332 99 63 682 581
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_6nt_m1 versus positions_7nt_m2_rc; m=9/13; ncol2=23; w=-1; offset=-1; strand=R; shift=2; score=0.632779; --wwwhyyACCAACCACCA ; cor=; Ncor= a 0 0 317 338 367 274 232 174 755 95 43 876 896 43 87 903 167 117 712 c 0 0 244 230 242 286 368 262 93 792 891 46 49 907 828 23 734 736 99 g 0 0 144 129 112 120 140 72 36 40 11 9 19 14 8 33 16 33 66 t 0 0 289 297 273 314 254 486 110 67 49 63 30 30 71 35 77 108 117
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)				; positions_6nt_m1 versus positions_6nt_m3_rc; m=10/13; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.622578; hwCCAACCACCAactahw- ; cor=; Ncor= a 258 429 112 64 888 853 26 84 934 92 65 800 681 186 236 454 299 361 0 c 357 227 740 863 67 83 951 848 17 889 885 57 172 691 230 237 364 243 0 g 131 101 69 23 13 38 16 15 34 10 18 73 52 53 119 103 105 143 0 t 280 269 105 76 58 52 33 79 41 35 58 96 121 96 441 232 258 279 0
oligos_7nt_mkv4_m2_shift8 (oligos_7nt_mkv4_m2)				; positions_6nt_m1 versus oligos_7nt_mkv4_m2; m=11/13; ncol2=11; w=0; offset=5; strand=D; shift=8; score=0.570603; --------wmCAACAACha ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1106 824 10 2452 2138 9 1878 2385 14 869 1195 c 0 0 0 0 0 0 0 0 489 846 2567 66 299 2567 413 57 2587 790 385 g 0 0 0 0 0 0 0 0 311 395 20 34 94 25 55 83 12 199 456 t 0 0 0 0 0 0 0 0 745 586 54 99 120 50 305 126 38 793 615
oligos_7nt_mkv4_m5_shift6 (oligos_7nt_mkv4_m5)				; positions_6nt_m1 versus oligos_7nt_mkv4_m5; m=12/13; ncol2=15; w=0; offset=3; strand=D; shift=6; score=0.516779; ------hmACCAAACcCta ; cor=; Ncor= a 0 0 0 0 0 0 227 287 717 31 29 704 738 669 71 118 102 191 355 c 0 0 0 0 0 0 276 255 18 733 717 22 32 93 657 536 598 67 181 g 0 0 0 0 0 0 86 70 18 12 11 8 14 11 26 47 41 63 74 t 0 0 0 0 0 0 212 189 48 25 44 67 17 28 47 100 60 480 191
oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)				; positions_6nt_m1 versus oligos_6nt_mkv3_m5; m=13/13; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.511326; -------waCCAAACaww- ; cor=; Ncor= a 0 0 0 0 0 0 0 458 792 7 0 1137 1245 1137 2 856 399 569 0 c 0 0 0 0 0 0 0 330 150 1325 1292 14 22 91 1316 255 321 226 0 g 0 0 0 0 0 0 0 145 156 7 23 37 20 32 6 60 178 192 0 t 0 0 0 0 0 0 0 412 247 6 30 157 58 85 21 174 447 358 0