One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.113808_2025-01-05.113808_VVhoIi/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/2025/01/05/peak-motifs.2025-01-05.113808_2025-01-05.113808_VVhoIi/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift2 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --vaAACCACAGmm ; Alignment reference a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271

positions_7nt_m4_shift2 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --vaAACCACAGmm ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_7nt_m4 versus positions_6nt_m4; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.974019; --swaACCACAgmm ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; positions_7nt_m4 versus oligos_6nt_mkv3_m1; m=3/5; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.878464; -amaAACCACAkmm ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; positions_7nt_m4 versus oligos_7nt_mkv4_m2; m=4/5; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.789614; mrraAACCACAaam ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; positions_7nt_m4 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.785828; --smAACCGCAGcs ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=13; shift=2; ncol=15; --smAACCGCAGcss ; Alignment reference a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 183 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 207 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 258 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112 152

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --smAACCGCAGcss ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 183 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 207 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 258 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112 152

positions_7nt_m4_shift2 (positions_7nt_m4)
; oligos_7nt_mkv4_m5 versus positions_7nt_m4; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.785828; --vaAACCACAGmm- ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 0 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 0 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 0 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271 0

positions_6nt_m4_shift2 (positions_6nt_m4)
; oligos_7nt_mkv4_m5 versus positions_6nt_m4; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.751018; --swaACCACAgmm- ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 0 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 0 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 0 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340 0

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.646899; -amaAACCACAkmm- ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 0 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 0 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 0 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377 0

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=5/5; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.574546; mrraAACCACAaam- ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 0 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 0 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 0 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift2 ; 6 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=12; shift=2; ncol=14; --swaACCACAgmm ; Alignment reference a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --swaACCACAgmm ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340

positions_7nt_m4_shift2 (positions_7nt_m4)
; positions_6nt_m4 versus positions_7nt_m4; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.974019; --vaAACCACAGmm ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; positions_6nt_m4 versus oligos_6nt_mkv3_m1; m=3/5; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.888438; -amaAACCACAkmm ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; positions_6nt_m4 versus oligos_7nt_mkv4_m2; m=4/5; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.797032; mrraAACCACAaam ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; positions_6nt_m4 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.751018; --smAACCGCAGcs ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -sgaTGACTCAtmc ; Alignment reference a 0 321 329 733 19 19 1272 86 63 52 1282 102 389 311 c 0 355 287 246 9 37 16 961 19 1246 33 338 392 448 g 0 367 437 298 15 1242 26 224 12 32 19 317 252 314 t 0 312 302 78 1312 57 41 84 1261 25 21 598 322 282

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -sgaTGACTCAtmc ; cor=; Ncor= a 0 321 329 733 19 19 1272 86 63 52 1282 102 389 311 c 0 355 287 246 9 37 16 961 19 1246 33 338 392 448 g 0 367 437 298 15 1242 26 224 12 32 19 317 252 314 t 0 312 302 78 1312 57 41 84 1261 25 21 598 322 282

oligos_6nt_mkv3_m4_rc_shift0 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=2/2; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.813097; gsggTGACTCAgcs ; cor=; Ncor= a 199 193 188 186 23 6 880 26 28 28 907 52 210 223 c 237 294 125 142 19 19 19 766 26 895 22 203 482 311 g 326 286 441 587 24 912 42 131 22 24 25 535 133 251 t 204 193 212 51 900 29 25 43 890 19 12 176 141 181

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift3 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift3 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---bgswGTCTGGsy ; Alignment reference a 0 0 0 415 494 355 991 22 37 16 22 142 31 538 483 c 0 0 0 597 522 856 212 22 16 2158 25 37 64 606 631 g 0 0 0 638 665 578 224 2167 17 44 45 2036 2068 735 503 t 0 0 0 579 548 440 802 18 2159 11 2137 14 66 350 612

positions_6nt_m3_shift3 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/9; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---bgswGTCTGGsy ; cor=; Ncor= a 0 0 0 415 494 355 991 22 37 16 22 142 31 538 483 c 0 0 0 597 522 856 212 22 16 2158 25 37 64 606 631 g 0 0 0 638 665 578 224 2167 17 44 45 2036 2068 735 503 t 0 0 0 579 548 440 802 18 2159 11 2137 14 66 350 612

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; positions_6nt_m3 versus positions_6nt_m1_rc; m=2/9; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.905409; ---gbCTGTCTGGsy ; cor=; Ncor= a 0 0 0 451 466 126 143 10 49 13 43 121 112 598 510 c 0 0 0 687 694 2263 97 62 103 2611 40 33 286 921 699 g 0 0 0 1040 722 242 41 2642 189 103 19 2570 1975 847 584 t 0 0 0 576 872 123 2473 40 2413 27 2652 30 381 388 961

positions_7nt_m3_rc_shift3 (positions_7nt_m3_rc)
; positions_6nt_m3 versus positions_7nt_m3_rc; m=3/9; ncol2=13; w=0; offset=0; strand=R; shift=3; score=0.84911; ---stsTGTCTGGct ; cor=; Ncor= a 0 0 0 389 365 218 61 21 27 21 18 106 65 285 383 c 0 0 0 526 435 705 107 33 39 1931 36 39 126 1106 496 g 0 0 0 663 495 874 49 1942 54 52 29 1865 1523 441 427 t 0 0 0 443 726 224 1804 25 1901 17 1938 11 307 189 715

positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)
; positions_6nt_m3 versus positions_7nt_m1_rc; m=4/9; ncol2=13; w=0; offset=0; strand=R; shift=3; score=0.837763; ---gkCTGTCTGGct ; cor=; Ncor= a 0 0 0 318 367 133 57 15 26 13 21 122 71 328 387 c 0 0 0 518 510 1573 116 22 68 2029 56 45 173 1076 514 g 0 0 0 820 547 263 49 2041 111 43 25 1914 1577 475 395 t 0 0 0 436 668 123 1870 14 1887 7 1990 11 271 213 796

positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)
; positions_6nt_m3 versus positions_7nt_m5_rc; m=5/9; ncol2=13; w=0; offset=0; strand=R; shift=3; score=0.836571; ---sbCTGTCTGGsy ; cor=; Ncor= a 0 0 0 438 459 116 141 9 47 11 43 115 110 569 500 c 0 0 0 665 670 2181 91 62 86 2512 37 31 285 850 676 g 0 0 0 983 666 234 40 2541 138 102 20 2476 1882 853 566 t 0 0 0 566 857 121 2380 40 2381 27 2552 30 375 380 910

positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)
; positions_6nt_m3 versus positions_6nt_m2_rc; m=6/9; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.835624; ---byCTGTCTrGrc ; cor=; Ncor= a 0 0 0 199 207 59 70 8 11 15 13 701 18 365 217 c 0 0 0 330 299 945 24 13 24 1087 37 30 48 283 465 g 0 0 0 314 271 66 10 1100 46 14 12 374 1033 323 198 t 0 0 0 292 358 65 1031 14 1054 19 1073 30 36 164 255

positions_6nt_m5_rc_shift3 (positions_6nt_m5_rc)
; positions_6nt_m3 versus positions_6nt_m5_rc; m=7/9; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.809238; ---syCTGTCTGcck ; cor=; Ncor= a 0 0 0 432 413 166 81 18 32 15 35 56 146 551 407 c 0 0 0 657 652 2029 115 66 64 2459 31 118 1394 912 598 g 0 0 0 920 581 277 26 2443 61 60 24 2341 477 617 645 t 0 0 0 559 922 96 2346 41 2411 34 2478 53 551 488 918

oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)
; positions_6nt_m3 versus oligos_6nt_mkv3_m2_rc; m=8/9; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.710063; ysygtCTGTCTGgst ; cor=; Ncor= a 354 390 324 287 301 131 59 13 24 18 19 101 112 447 387 c 635 852 734 456 417 1751 111 38 71 2134 51 48 283 781 547 g 560 617 437 1157 443 278 44 2197 82 102 39 2094 1431 725 494 t 719 409 773 368 1107 108 2054 20 2091 14 2159 25 442 315 840

positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_6nt_m3 versus positions_7nt_m2; m=9/9; ncol2=12; w=0; offset=2; strand=D; shift=5; score=0.505857; -----cwGTCTAGAC ; cor=; Ncor= a 0 0 0 0 0 199 259 12 39 23 8 837 12 772 23 c 0 0 0 0 0 297 120 29 34 865 63 14 22 77 858 g 0 0 0 0 0 215 157 858 77 22 14 63 865 34 29 t 0 0 0 0 0 211 386 23 772 12 837 8 23 39 12

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -amaAACCACAkmm ; Alignment reference a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -amaAACCACAkmm ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=2/5; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.90298; mrraAACCACAaam ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223

positions_6nt_m4_shift2 (positions_6nt_m4)
; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=3/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.888438; --swaACCACAgmm ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340

positions_7nt_m4_shift2 (positions_7nt_m4)
; oligos_6nt_mkv3_m1 versus positions_7nt_m4; m=4/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.878464; --vaAACCACAGmm ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=13; w=0; offset=1; strand=D; shift=2; score=0.646899; --smAACCGCAGcs ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; sagCCAGACAsas ; Alignment reference a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m3 versus positions_7nt_m1; m=2/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.969526; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m3 versus positions_7nt_m5; m=3/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.95136; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m3 versus positions_6nt_m1; m=4/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.878592; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; positions_7nt_m3 versus positions_6nt_m3_rc; m=5/8; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.84911; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_7nt_m3 versus positions_6nt_m5; m=6/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.825892; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_7nt_m3 versus positions_6nt_m2; m=7/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.791197; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_7nt_m3 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.714236; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; smAAGGTCAGrs ; Alignment reference a 184 236 523 682 20 16 27 8 707 37 214 171 c 196 228 70 21 14 30 40 716 4 65 180 232 g 240 184 116 37 700 690 47 23 18 603 233 205 t 140 112 51 20 26 24 646 13 31 55 133 152

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; smAAGGTCAGrs ; cor=; Ncor= a 184 236 523 682 20 16 27 8 707 37 214 171 c 196 228 70 21 14 30 40 716 4 65 180 232 g 240 184 116 37 700 690 47 23 18 603 233 205 t 140 112 51 20 26 24 646 13 31 55 133 152

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; srsCCAGACAGvs ; Alignment reference a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m5 versus positions_7nt_m1; m=2/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.992523; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m5 versus positions_7nt_m3; m=3/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.95136; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m5 versus positions_6nt_m1; m=4/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.922919; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_7nt_m5 versus positions_6nt_m5; m=5/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.872269; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_7nt_m5 versus positions_6nt_m2; m=6/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.838925; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; positions_7nt_m5 versus positions_6nt_m3_rc; m=7/8; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.836571; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_7nt_m5 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.743321; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; gsgcTGAGTCAccsc ; Alignment reference a 216 181 141 176 12 19 890 43 25 29 900 51 212 193 204 c 222 251 133 535 25 24 22 131 42 912 24 587 441 286 326 g 342 311 482 203 22 895 26 766 19 19 19 142 125 294 237 t 186 223 210 52 907 28 28 26 880 6 23 186 188 193 199

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gsgcTGAGTCAccsc ; cor=; Ncor= a 216 181 141 176 12 19 890 43 25 29 900 51 212 193 204 c 222 251 133 535 25 24 22 131 42 912 24 587 441 286 326 g 342 311 482 203 22 895 26 766 19 19 19 142 125 294 237 t 186 223 210 52 907 28 28 26 880 6 23 186 188 193 199

oligos_7nt_mkv4_m1_rc_shift1 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=2/2; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.813097; -gkaTGAGTCAtcs- ; cor=; Ncor= a 0 282 322 598 21 25 1261 84 41 57 1312 78 302 312 0 c 0 314 252 317 19 32 12 224 26 1242 15 298 437 367 0 g 0 448 392 338 33 1246 19 961 16 37 9 246 287 355 0 t 0 311 389 102 1282 52 63 86 1272 19 19 733 329 321 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -rsCCAGACAGvc ; Alignment reference a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_6nt_m1 versus positions_6nt_m5; m=2/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.943319; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_6nt_m1 versus positions_7nt_m5; m=3/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.922919; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=4/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.917141; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=5/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.908434; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; positions_6nt_m1 versus positions_6nt_m3_rc; m=6/8; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.905409; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_6nt_m1 versus positions_7nt_m3; m=7/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.878592; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_6nt_m1 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.79253; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; sagCCAGACAGmc ; Alignment reference a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m1 versus positions_7nt_m5; m=2/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.992523; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m1 versus positions_7nt_m3; m=3/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.969526; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=4/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.917141; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_7nt_m1 versus positions_6nt_m5; m=5/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.862102; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; positions_7nt_m1 versus positions_6nt_m3_rc; m=6/8; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.837763; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_7nt_m1 versus positions_6nt_m2; m=7/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.834296; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_7nt_m1 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.739905; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; mrraAACCACAaam ; Alignment reference a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; mrraAACCACAaam ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=2/5; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.90298; -amaAACCACAkmm ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377

positions_6nt_m4_shift2 (positions_6nt_m4)
; oligos_7nt_mkv4_m2 versus positions_6nt_m4; m=3/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.797032; --swaACCACAgmm ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340

positions_7nt_m4_shift2 (positions_7nt_m4)
; oligos_7nt_mkv4_m2 versus positions_7nt_m4; m=4/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.789614; --vaAACCACAGmm ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.574546; --smAACCGCAGcs ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -mggCAGACAGrs ; Alignment reference a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m5 versus positions_6nt_m1; m=2/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.943319; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_6nt_m5 versus positions_7nt_m5; m=3/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.872269; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_6nt_m5 versus positions_7nt_m1; m=4/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.862102; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_6nt_m5 versus positions_7nt_m3; m=5/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.825892; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m5 versus positions_6nt_m2; m=6/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.820431; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; positions_6nt_m5 versus positions_6nt_m3_rc; m=7/8; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.809238; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_6nt_m5 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.760585; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; kgwttgCTTTGATctkk ; Alignment reference a 210 205 347 149 105 163 27 13 27 12 40 799 68 140 151 151 187 c 193 223 145 132 121 188 798 27 22 8 56 17 24 434 104 209 193 g 229 259 177 169 192 369 28 8 26 10 753 29 21 223 54 232 230 t 272 217 235 454 486 184 51 856 829 874 55 59 791 107 595 312 294

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/2; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; kgwttgCTTTGATctkk ; cor=; Ncor= a 210 205 347 149 105 163 27 13 27 12 40 799 68 140 151 151 187 c 193 223 145 132 121 188 798 27 22 8 56 17 24 434 104 209 193 g 229 259 177 169 192 369 28 8 26 10 753 29 21 223 54 232 230 t 272 217 235 454 486 184 51 856 829 874 55 59 791 107 595 312 294

oligos_7nt_mkv4_m3_rc_shift3 (oligos_7nt_mkv4_m3_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3_rc; m=2/2; ncol2=15; w=0; offset=3; strand=R; shift=3; score=0.749779; ---kbcCTTTGATcTtk ; cor=; Ncor= a 0 0 0 209 127 152 32 18 12 7 34 818 56 115 77 100 162 c 0 0 0 180 235 432 784 24 31 6 86 14 24 513 79 165 183 g 0 0 0 246 247 136 36 5 27 12 739 26 18 205 26 185 238 t 0 0 0 269 295 184 52 857 834 879 45 46 806 71 722 454 321

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift2 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --cwGTCTAGACwg ; Alignment reference a 0 0 199 259 12 39 23 8 837 12 772 23 386 211 c 0 0 297 120 29 34 865 63 14 22 77 858 157 215 g 0 0 215 157 858 77 22 14 63 865 34 29 120 297 t 0 0 211 386 23 772 12 837 8 23 39 12 259 199

positions_7nt_m2_shift2 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --cwGTCTAGACwg ; cor=; Ncor= a 0 0 199 259 12 39 23 8 837 12 772 23 386 211 c 0 0 297 120 29 34 865 63 14 22 77 858 157 215 g 0 0 215 157 858 77 22 14 63 865 34 29 120 297 t 0 0 211 386 23 772 12 837 8 23 39 12 259 199

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_7nt_m2 versus positions_6nt_m2; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=4; score=0.591618; ----gyCyAGACAG ; cor=; Ncor= a 0 0 0 0 255 164 36 30 1073 19 1054 14 1031 65 c 0 0 0 0 198 323 1033 374 12 14 46 1100 10 66 g 0 0 0 0 465 283 48 30 37 1087 24 13 24 945 t 0 0 0 0 217 365 18 701 13 15 11 8 70 59

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_7nt_m2 versus positions_6nt_m3; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.505857; bgswGTCTGGsy-- ; cor=; Ncor= a 415 494 355 991 22 37 16 22 142 31 538 483 0 0 c 597 522 856 212 22 16 2158 25 37 64 606 631 0 0 g 638 665 578 224 2167 17 44 45 2036 2068 735 503 0 0 t 579 548 440 802 18 2159 11 2137 14 66 350 612 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -ascCAGACAGacrsr ; Alignment reference a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 773 409 719 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 437 617 560 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 734 852 635 t 0 387 447 112 101 19 18 24 13 59 131 301 287 324 390 354

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ascCAGACAGacrsr ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 773 409 719 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 437 617 560 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 734 852 635 t 0 387 447 112 101 19 18 24 13 59 131 301 287 324 390 354

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_6nt_mkv3_m2 versus positions_6nt_m1; m=2/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.79253; -rsCCAGACAGvc--- ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 0 0 0 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 0 0 0 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 0 0 0 t 0 510 598 112 121 43 13 49 10 143 126 466 451 0 0 0

positions_6nt_m5_shift1 (positions_6nt_m5)
; oligos_6nt_mkv3_m2 versus positions_6nt_m5; m=3/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.760585; -mggCAGACAGrs--- ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 0 0 0 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 0 0 0 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 0 0 0 t 0 407 551 146 56 35 15 32 18 81 166 413 432 0 0 0

positions_7nt_m5_shift0 (positions_7nt_m5)
; oligos_6nt_mkv3_m2 versus positions_7nt_m5; m=4/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.743321; srsCCAGACAGvs--- ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 0 0 0 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 0 0 0 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 0 0 0 t 504 500 569 110 115 43 11 47 9 141 116 459 438 0 0 0

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_6nt_mkv3_m2 versus positions_7nt_m1; m=5/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.739905; sagCCAGACAGmc--- ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 0 0 0 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 0 0 0 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 0 0 0 t 392 387 328 71 122 21 13 26 15 57 133 367 318 0 0 0

positions_7nt_m3_shift0 (positions_7nt_m3)
; oligos_6nt_mkv3_m2 versus positions_7nt_m3; m=6/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.714236; sagCCAGACAsas--- ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 0 0 0 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 0 0 0 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 0 0 0 t 417 383 285 65 106 18 21 27 21 61 218 365 389 0 0 0

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=7/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.712256; -gyCyAGACAGrv--- ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 0 0 0 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 0 0 0 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 0 0 0 t 0 217 365 18 701 13 15 11 8 70 59 207 199 0 0 0

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; oligos_6nt_mkv3_m2 versus positions_6nt_m3_rc; m=8/8; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.710063; -rsCCAGACwscv--- ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 0 0 0 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 0 0 0 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 0 0 0 t 0 483 538 31 142 22 16 37 22 991 355 494 415 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; amaAgATCAAAGgvm ; Alignment reference a 288 321 454 722 71 806 46 45 879 834 857 52 184 295 269 c 219 238 185 26 205 18 26 739 12 27 5 36 136 247 246 g 198 183 165 79 513 24 14 86 6 31 24 784 432 235 180 t 199 162 100 77 115 56 818 34 7 12 18 32 152 127 209

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; amaAgATCAAAGgvm ; cor=; Ncor= a 288 321 454 722 71 806 46 45 879 834 857 52 184 295 269 c 219 238 185 26 205 18 26 739 12 27 5 36 136 247 246 g 198 183 165 79 513 24 14 86 6 31 24 784 432 235 180 t 199 162 100 77 115 56 818 34 7 12 18 32 152 127 209

oligos_6nt_mkv3_m3_rc_shift1 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3_rc; m=2/2; ncol2=17; w=0; offset=1; strand=R; shift=1; score=0.749779; -mmagATCAAAGcaa ; cor=; Ncor= a 0 294 312 595 107 791 59 55 874 829 856 51 184 486 454 c 0 230 232 54 223 21 29 753 10 26 8 28 369 192 169 g 0 193 209 104 434 24 17 56 8 22 27 798 188 121 132 t 0 187 151 151 140 68 799 40 12 27 13 27 163 105 149

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 2 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=12; shift=0; ncol=12; wawGTAAACAra ; Alignment reference a 460 501 580 184 89 1233 1163 1232 40 1239 403 497 c 237 297 141 58 59 37 62 47 1167 39 313 266 g 254 301 209 1042 51 37 78 14 33 19 334 258 t 379 231 400 46 1131 23 27 37 90 33 280 309

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wawGTAAACAra ; cor=; Ncor= a 460 501 580 184 89 1233 1163 1232 40 1239 403 497 c 237 297 141 58 59 37 62 47 1167 39 313 266 g 254 301 209 1042 51 37 78 14 33 19 334 258 t 379 231 400 46 1131 23 27 37 90 33 280 309

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift2 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift2 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --gyCyAGACAGrv ; Alignment reference a 0 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 0 217 365 18 701 13 15 11 8 70 59 207 199

positions_6nt_m2_shift2 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/9; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --gyCyAGACAGrv ; cor=; Ncor= a 0 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 0 217 365 18 701 13 15 11 8 70 59 207 199

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=2/9; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.908434; --rsCCAGACAGvc ; cor=; Ncor= a 0 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 0 510 598 112 121 43 13 49 10 143 126 466 451

positions_7nt_m5_shift1 (positions_7nt_m5)
; positions_6nt_m2 versus positions_7nt_m5; m=3/9; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.838925; -srsCCAGACAGvs ; cor=; Ncor= a 0 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 0 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 0 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 0 504 500 569 110 115 43 11 47 9 141 116 459 438

positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)
; positions_6nt_m2 versus positions_6nt_m3_rc; m=4/9; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.835624; --rsCCAGACwscv ; cor=; Ncor= a 0 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 0 483 538 31 142 22 16 37 22 991 355 494 415

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_6nt_m2 versus positions_7nt_m1; m=5/9; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.834296; -sagCCAGACAGmc ; cor=; Ncor= a 0 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 0 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 0 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 0 392 387 328 71 122 21 13 26 15 57 133 367 318

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m2 versus positions_6nt_m5; m=6/9; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.820431; --mggCAGACAGrs ; cor=; Ncor= a 0 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 0 407 551 146 56 35 15 32 18 81 166 413 432

positions_7nt_m3_shift1 (positions_7nt_m3)
; positions_6nt_m2 versus positions_7nt_m3; m=7/9; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.791197; -sagCCAGACAsas ; cor=; Ncor= a 0 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 0 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 0 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 0 417 383 285 65 106 18 21 27 21 61 218 365 389

oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=8/9; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.712256; --ascCAGACAGac ; cor=; Ncor= a 0 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 0 387 447 112 101 19 18 24 13 59 131 301 287

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_6nt_m2 versus positions_7nt_m2; m=9/9; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.591618; cwGTCTAGACwg-- ; cor=; Ncor= a 199 259 12 39 23 8 837 12 772 23 386 211 0 0 c 297 120 29 34 865 63 14 22 77 858 157 215 0 0 g 215 157 858 77 22 14 63 865 34 29 120 297 0 0 t 211 386 23 772 12 837 8 23 39 12 259 199 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift2 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --vaAACCACAGmm ; Alignment reference a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271
positions_7nt_m4_shift2 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --vaAACCACAGmm ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_7nt_m4 versus positions_6nt_m4; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.974019; --swaACCACAgmm ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; positions_7nt_m4 versus oligos_6nt_mkv3_m1; m=3/5; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.878464; -amaAACCACAkmm ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; positions_7nt_m4 versus oligos_7nt_mkv4_m2; m=4/5; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.789614; mrraAACCACAaam ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; positions_7nt_m4 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.785828; --smAACCGCAGcs ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=13; shift=2; ncol=15; --smAACCGCAGcss ; Alignment reference a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 183 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 207 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 258 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112 152
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --smAACCGCAGcss ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 183 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 207 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 258 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112 152
positions_7nt_m4_shift2 (positions_7nt_m4)				; oligos_7nt_mkv4_m5 versus positions_7nt_m4; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.785828; --vaAACCACAGmm- ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 0 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 0 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 0 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271 0
positions_6nt_m4_shift2 (positions_6nt_m4)				; oligos_7nt_mkv4_m5 versus positions_6nt_m4; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.751018; --swaACCACAgmm- ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 0 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 0 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 0 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340 0
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.646899; -amaAACCACAkmm- ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 0 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 0 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 0 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377 0
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=5/5; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.574546; mrraAACCACAaam- ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 0 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 0 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 0 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --swaACCACAgmm ; Alignment reference a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --swaACCACAgmm ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340
positions_7nt_m4_shift2 (positions_7nt_m4)				; positions_6nt_m4 versus positions_7nt_m4; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.974019; --vaAACCACAGmm ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; positions_6nt_m4 versus oligos_6nt_mkv3_m1; m=3/5; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.888438; -amaAACCACAkmm ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; positions_6nt_m4 versus oligos_7nt_mkv4_m2; m=4/5; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.797032; mrraAACCACAaam ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; positions_6nt_m4 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.751018; --smAACCGCAGcs ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift3 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---bgswGTCTGGsy ; Alignment reference a 0 0 0 415 494 355 991 22 37 16 22 142 31 538 483 c 0 0 0 597 522 856 212 22 16 2158 25 37 64 606 631 g 0 0 0 638 665 578 224 2167 17 44 45 2036 2068 735 503 t 0 0 0 579 548 440 802 18 2159 11 2137 14 66 350 612
positions_6nt_m3_shift3 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/9; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---bgswGTCTGGsy ; cor=; Ncor= a 0 0 0 415 494 355 991 22 37 16 22 142 31 538 483 c 0 0 0 597 522 856 212 22 16 2158 25 37 64 606 631 g 0 0 0 638 665 578 224 2167 17 44 45 2036 2068 735 503 t 0 0 0 579 548 440 802 18 2159 11 2137 14 66 350 612
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; positions_6nt_m3 versus positions_6nt_m1_rc; m=2/9; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.905409; ---gbCTGTCTGGsy ; cor=; Ncor= a 0 0 0 451 466 126 143 10 49 13 43 121 112 598 510 c 0 0 0 687 694 2263 97 62 103 2611 40 33 286 921 699 g 0 0 0 1040 722 242 41 2642 189 103 19 2570 1975 847 584 t 0 0 0 576 872 123 2473 40 2413 27 2652 30 381 388 961
positions_7nt_m3_rc_shift3 (positions_7nt_m3_rc)				; positions_6nt_m3 versus positions_7nt_m3_rc; m=3/9; ncol2=13; w=0; offset=0; strand=R; shift=3; score=0.84911; ---stsTGTCTGGct ; cor=; Ncor= a 0 0 0 389 365 218 61 21 27 21 18 106 65 285 383 c 0 0 0 526 435 705 107 33 39 1931 36 39 126 1106 496 g 0 0 0 663 495 874 49 1942 54 52 29 1865 1523 441 427 t 0 0 0 443 726 224 1804 25 1901 17 1938 11 307 189 715
positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)				; positions_6nt_m3 versus positions_7nt_m1_rc; m=4/9; ncol2=13; w=0; offset=0; strand=R; shift=3; score=0.837763; ---gkCTGTCTGGct ; cor=; Ncor= a 0 0 0 318 367 133 57 15 26 13 21 122 71 328 387 c 0 0 0 518 510 1573 116 22 68 2029 56 45 173 1076 514 g 0 0 0 820 547 263 49 2041 111 43 25 1914 1577 475 395 t 0 0 0 436 668 123 1870 14 1887 7 1990 11 271 213 796
positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)				; positions_6nt_m3 versus positions_7nt_m5_rc; m=5/9; ncol2=13; w=0; offset=0; strand=R; shift=3; score=0.836571; ---sbCTGTCTGGsy ; cor=; Ncor= a 0 0 0 438 459 116 141 9 47 11 43 115 110 569 500 c 0 0 0 665 670 2181 91 62 86 2512 37 31 285 850 676 g 0 0 0 983 666 234 40 2541 138 102 20 2476 1882 853 566 t 0 0 0 566 857 121 2380 40 2381 27 2552 30 375 380 910
positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)				; positions_6nt_m3 versus positions_6nt_m2_rc; m=6/9; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.835624; ---byCTGTCTrGrc ; cor=; Ncor= a 0 0 0 199 207 59 70 8 11 15 13 701 18 365 217 c 0 0 0 330 299 945 24 13 24 1087 37 30 48 283 465 g 0 0 0 314 271 66 10 1100 46 14 12 374 1033 323 198 t 0 0 0 292 358 65 1031 14 1054 19 1073 30 36 164 255
positions_6nt_m5_rc_shift3 (positions_6nt_m5_rc)				; positions_6nt_m3 versus positions_6nt_m5_rc; m=7/9; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.809238; ---syCTGTCTGcck ; cor=; Ncor= a 0 0 0 432 413 166 81 18 32 15 35 56 146 551 407 c 0 0 0 657 652 2029 115 66 64 2459 31 118 1394 912 598 g 0 0 0 920 581 277 26 2443 61 60 24 2341 477 617 645 t 0 0 0 559 922 96 2346 41 2411 34 2478 53 551 488 918
oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)				; positions_6nt_m3 versus oligos_6nt_mkv3_m2_rc; m=8/9; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.710063; ysygtCTGTCTGgst ; cor=; Ncor= a 354 390 324 287 301 131 59 13 24 18 19 101 112 447 387 c 635 852 734 456 417 1751 111 38 71 2134 51 48 283 781 547 g 560 617 437 1157 443 278 44 2197 82 102 39 2094 1431 725 494 t 719 409 773 368 1107 108 2054 20 2091 14 2159 25 442 315 840
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_6nt_m3 versus positions_7nt_m2; m=9/9; ncol2=12; w=0; offset=2; strand=D; shift=5; score=0.505857; -----cwGTCTAGAC ; cor=; Ncor= a 0 0 0 0 0 199 259 12 39 23 8 837 12 772 23 c 0 0 0 0 0 297 120 29 34 865 63 14 22 77 858 g 0 0 0 0 0 215 157 858 77 22 14 63 865 34 29 t 0 0 0 0 0 211 386 23 772 12 837 8 23 39 12

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -amaAACCACAkmm ; Alignment reference a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -amaAACCACAkmm ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=2/5; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.90298; mrraAACCACAaam ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223
positions_6nt_m4_shift2 (positions_6nt_m4)				; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=3/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.888438; --swaACCACAgmm ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340
positions_7nt_m4_shift2 (positions_7nt_m4)				; oligos_6nt_mkv3_m1 versus positions_7nt_m4; m=4/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.878464; --vaAACCACAGmm ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=13; w=0; offset=1; strand=D; shift=2; score=0.646899; --smAACCGCAGcs ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; sagCCAGACAsas ; Alignment reference a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m3 versus positions_7nt_m1; m=2/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.969526; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_7nt_m3 versus positions_7nt_m5; m=3/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.95136; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_7nt_m3 versus positions_6nt_m1; m=4/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.878592; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; positions_7nt_m3 versus positions_6nt_m3_rc; m=5/8; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.84911; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_7nt_m3 versus positions_6nt_m5; m=6/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.825892; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_7nt_m3 versus positions_6nt_m2; m=7/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.791197; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_7nt_m3 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.714236; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_7nt_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; srsCCAGACAGvs ; Alignment reference a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_7nt_m5 versus positions_7nt_m5; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m5 versus positions_7nt_m1; m=2/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.992523; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_7nt_m5 versus positions_7nt_m3; m=3/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.95136; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_7nt_m5 versus positions_6nt_m1; m=4/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.922919; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_7nt_m5 versus positions_6nt_m5; m=5/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.872269; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_7nt_m5 versus positions_6nt_m2; m=6/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.838925; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; positions_7nt_m5 versus positions_6nt_m3_rc; m=7/8; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.836571; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_7nt_m5 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.743321; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -rsCCAGACAGvc ; Alignment reference a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_6nt_m1 versus positions_6nt_m5; m=2/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.943319; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_6nt_m1 versus positions_7nt_m5; m=3/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.922919; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=4/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.917141; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=5/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.908434; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; positions_6nt_m1 versus positions_6nt_m3_rc; m=6/8; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.905409; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_6nt_m1 versus positions_7nt_m3; m=7/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.878592; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_6nt_m1 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.79253; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; sagCCAGACAGmc ; Alignment reference a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_7nt_m1 versus positions_7nt_m5; m=2/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.992523; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_7nt_m1 versus positions_7nt_m3; m=3/8; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.969526; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=4/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.917141; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_7nt_m1 versus positions_6nt_m5; m=5/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.862102; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; positions_7nt_m1 versus positions_6nt_m3_rc; m=6/8; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.837763; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_7nt_m1 versus positions_6nt_m2; m=7/8; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.834296; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_7nt_m1 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.739905; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; mrraAACCACAaam ; Alignment reference a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; mrraAACCACAaam ; cor=; Ncor= a 326 388 300 708 1014 1059 46 44 1075 46 1057 707 416 384 c 311 234 267 152 45 28 1077 1067 22 1060 45 87 275 305 g 275 289 405 73 51 52 9 12 32 18 19 188 238 244 t 244 245 184 223 46 17 24 33 27 32 35 174 227 223
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=2/5; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.90298; -amaAACCACAkmm ; cor=; Ncor= a 0 597 535 1227 1517 1738 93 68 1802 82 1789 444 632 608 c 0 459 551 227 153 70 1774 1816 29 1787 47 276 561 591 g 0 466 470 135 195 96 37 10 70 46 35 521 379 367 t 0 421 387 354 78 39 39 49 42 28 72 702 371 377
positions_6nt_m4_shift2 (positions_6nt_m4)				; oligos_7nt_mkv4_m2 versus positions_6nt_m4; m=3/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.797032; --swaACCACAgmm ; cor=; Ncor= a 0 0 483 705 1036 1886 65 35 1831 9 1868 374 620 549 c 0 0 578 397 327 44 1865 1892 13 1934 40 204 581 701 g 0 0 516 253 430 34 12 21 116 11 49 1040 415 394 t 0 0 407 629 191 20 42 36 24 30 27 366 368 340
positions_7nt_m4_shift2 (positions_7nt_m4)				; oligos_7nt_mkv4_m2 versus positions_7nt_m4; m=4/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.789614; --vaAACCACAGmm ; cor=; Ncor= a 0 0 418 650 1378 1385 57 39 1491 26 1576 188 512 439 c 0 0 458 396 93 96 1530 1602 44 1601 23 76 470 591 g 0 0 450 247 152 148 37 6 74 22 17 1233 394 358 t 0 0 333 366 36 30 35 12 50 10 43 162 283 271
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.574546; --smAACCGCAGcs ; cor=; Ncor= a 0 0 170 233 585 635 21 19 116 5 670 30 180 125 c 0 0 232 226 100 38 754 735 32 776 62 22 410 341 g 0 0 258 157 91 118 17 29 622 8 52 728 119 222 t 0 0 140 184 24 9 8 17 30 11 16 20 91 112

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -mggCAGACAGrs ; Alignment reference a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -mggCAGACAGrs ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 407 551 146 56 35 15 32 18 81 166 413 432
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m5 versus positions_6nt_m1; m=2/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.943319; -rsCCAGACAGvc ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 510 598 112 121 43 13 49 10 143 126 466 451
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_6nt_m5 versus positions_7nt_m5; m=3/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.872269; srsCCAGACAGvs ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 504 500 569 110 115 43 11 47 9 141 116 459 438
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_6nt_m5 versus positions_7nt_m1; m=4/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.862102; sagCCAGACAGmc ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 392 387 328 71 122 21 13 26 15 57 133 367 318
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_6nt_m5 versus positions_7nt_m3; m=5/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.825892; sagCCAGACAsas ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 417 383 285 65 106 18 21 27 21 61 218 365 389
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m5 versus positions_6nt_m2; m=6/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.820431; -gyCyAGACAGrv ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 217 365 18 701 13 15 11 8 70 59 207 199
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; positions_6nt_m5 versus positions_6nt_m3_rc; m=7/8; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.809238; -rsCCAGACwscv ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 483 538 31 142 22 16 37 22 991 355 494 415
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_6nt_m5 versus oligos_6nt_mkv3_m2; m=8/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.760585; -ascCAGACAGac ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 387 447 112 101 19 18 24 13 59 131 301 287

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift2 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --cwGTCTAGACwg ; Alignment reference a 0 0 199 259 12 39 23 8 837 12 772 23 386 211 c 0 0 297 120 29 34 865 63 14 22 77 858 157 215 g 0 0 215 157 858 77 22 14 63 865 34 29 120 297 t 0 0 211 386 23 772 12 837 8 23 39 12 259 199
positions_7nt_m2_shift2 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --cwGTCTAGACwg ; cor=; Ncor= a 0 0 199 259 12 39 23 8 837 12 772 23 386 211 c 0 0 297 120 29 34 865 63 14 22 77 858 157 215 g 0 0 215 157 858 77 22 14 63 865 34 29 120 297 t 0 0 211 386 23 772 12 837 8 23 39 12 259 199
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_7nt_m2 versus positions_6nt_m2; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=4; score=0.591618; ----gyCyAGACAG ; cor=; Ncor= a 0 0 0 0 255 164 36 30 1073 19 1054 14 1031 65 c 0 0 0 0 198 323 1033 374 12 14 46 1100 10 66 g 0 0 0 0 465 283 48 30 37 1087 24 13 24 945 t 0 0 0 0 217 365 18 701 13 15 11 8 70 59
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_7nt_m2 versus positions_6nt_m3; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.505857; bgswGTCTGGsy-- ; cor=; Ncor= a 415 494 355 991 22 37 16 22 142 31 538 483 0 0 c 597 522 856 212 22 16 2158 25 37 64 606 631 0 0 g 638 665 578 224 2167 17 44 45 2036 2068 735 503 0 0 t 579 548 440 802 18 2159 11 2137 14 66 350 612 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -ascCAGACAGacrsr ; Alignment reference a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 773 409 719 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 437 617 560 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 734 852 635 t 0 387 447 112 101 19 18 24 13 59 131 301 287 324 390 354
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ascCAGACAGacrsr ; cor=; Ncor= a 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 773 409 719 c 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 437 617 560 g 0 547 781 283 48 51 2134 71 38 111 1751 417 456 734 852 635 t 0 387 447 112 101 19 18 24 13 59 131 301 287 324 390 354
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_6nt_mkv3_m2 versus positions_6nt_m1; m=2/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.79253; -rsCCAGACAGvc--- ; cor=; Ncor= a 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 0 0 0 c 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 0 0 0 g 0 699 921 286 33 40 2611 103 62 97 2263 694 687 0 0 0 t 0 510 598 112 121 43 13 49 10 143 126 466 451 0 0 0
positions_6nt_m5_shift1 (positions_6nt_m5)				; oligos_6nt_mkv3_m2 versus positions_6nt_m5; m=3/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.760585; -mggCAGACAGrs--- ; cor=; Ncor= a 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 0 0 0 c 0 645 617 477 2341 24 60 61 2443 26 277 581 920 0 0 0 g 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 0 0 0 t 0 407 551 146 56 35 15 32 18 81 166 413 432 0 0 0
positions_7nt_m5_shift0 (positions_7nt_m5)				; oligos_6nt_mkv3_m2 versus positions_7nt_m5; m=4/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.743321; srsCCAGACAGvs--- ; cor=; Ncor= a 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 0 0 0 c 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 0 0 0 g 707 676 850 285 31 37 2512 86 62 91 2181 670 665 0 0 0 t 504 500 569 110 115 43 11 47 9 141 116 459 438 0 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_6nt_mkv3_m2 versus positions_7nt_m1; m=5/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.739905; sagCCAGACAGmc--- ; cor=; Ncor= a 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 0 0 0 c 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 0 0 0 g 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 0 0 0 t 392 387 328 71 122 21 13 26 15 57 133 367 318 0 0 0
positions_7nt_m3_shift0 (positions_7nt_m3)				; oligos_6nt_mkv3_m2 versus positions_7nt_m3; m=6/8; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.714236; sagCCAGACAsas--- ; cor=; Ncor= a 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 0 0 0 c 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 0 0 0 g 539 496 1106 126 39 36 1931 39 33 107 705 435 526 0 0 0 t 417 383 285 65 106 18 21 27 21 61 218 365 389 0 0 0
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=7/8; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.712256; -gyCyAGACAGrv--- ; cor=; Ncor= a 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 0 0 0 c 0 198 323 1033 374 12 14 46 1100 10 66 271 314 0 0 0 g 0 465 283 48 30 37 1087 24 13 24 945 299 330 0 0 0 t 0 217 365 18 701 13 15 11 8 70 59 207 199 0 0 0
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; oligos_6nt_mkv3_m2 versus positions_6nt_m3_rc; m=8/8; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.710063; -rsCCAGACwscv--- ; cor=; Ncor= a 0 612 350 66 14 2137 11 2159 18 802 440 548 579 0 0 0 c 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 0 0 0 g 0 631 606 64 37 25 2158 16 22 212 856 522 597 0 0 0 t 0 483 538 31 142 22 16 37 22 991 355 494 415 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift2 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --gyCyAGACAGrv ; Alignment reference a 0 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 0 217 365 18 701 13 15 11 8 70 59 207 199
positions_6nt_m2_shift2 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/9; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --gyCyAGACAGrv ; cor=; Ncor= a 0 0 255 164 36 30 1073 19 1054 14 1031 65 358 292 c 0 0 198 323 1033 374 12 14 46 1100 10 66 271 314 g 0 0 465 283 48 30 37 1087 24 13 24 945 299 330 t 0 0 217 365 18 701 13 15 11 8 70 59 207 199
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=2/9; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.908434; --rsCCAGACAGvc ; cor=; Ncor= a 0 0 961 388 381 30 2652 27 2413 40 2473 123 872 576 c 0 0 584 847 1975 2570 19 103 189 2642 41 242 722 1040 g 0 0 699 921 286 33 40 2611 103 62 97 2263 694 687 t 0 0 510 598 112 121 43 13 49 10 143 126 466 451
positions_7nt_m5_shift1 (positions_7nt_m5)				; positions_6nt_m2 versus positions_7nt_m5; m=3/9; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.838925; -srsCCAGACAGvs ; cor=; Ncor= a 0 628 910 380 375 30 2552 27 2381 40 2380 121 857 566 c 0 813 566 853 1882 2476 20 102 138 2541 40 234 666 983 g 0 707 676 850 285 31 37 2512 86 62 91 2181 670 665 t 0 504 500 569 110 115 43 11 47 9 141 116 459 438
positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)				; positions_6nt_m2 versus positions_6nt_m3_rc; m=4/9; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.835624; --rsCCAGACwscv ; cor=; Ncor= a 0 0 612 350 66 14 2137 11 2159 18 802 440 548 579 c 0 0 503 735 2068 2036 45 44 17 2167 224 578 665 638 g 0 0 631 606 64 37 25 2158 16 22 212 856 522 597 t 0 0 483 538 31 142 22 16 37 22 991 355 494 415
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_6nt_m2 versus positions_7nt_m1; m=5/9; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.834296; -sagCCAGACAGmc ; cor=; Ncor= a 0 464 796 213 271 11 1990 7 1887 14 1870 123 668 436 c 0 693 395 475 1577 1914 25 43 111 2041 49 263 547 820 g 0 543 514 1076 173 45 56 2029 68 22 116 1573 510 518 t 0 392 387 328 71 122 21 13 26 15 57 133 367 318
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m2 versus positions_6nt_m5; m=6/9; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.820431; --mggCAGACAGrs ; cor=; Ncor= a 0 0 918 488 551 53 2478 34 2411 41 2346 96 922 559 c 0 0 645 617 477 2341 24 60 61 2443 26 277 581 920 g 0 0 598 912 1394 118 31 2459 64 66 115 2029 652 657 t 0 0 407 551 146 56 35 15 32 18 81 166 413 432
positions_7nt_m3_shift1 (positions_7nt_m3)				; positions_6nt_m2 versus positions_7nt_m3; m=7/9; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.791197; -sagCCAGACAsas ; cor=; Ncor= a 0 437 715 189 307 11 1938 17 1901 25 1804 224 726 443 c 0 628 427 441 1523 1865 29 52 54 1942 49 874 495 663 g 0 539 496 1106 126 39 36 1931 39 33 107 705 435 526 t 0 417 383 285 65 106 18 21 27 21 61 218 365 389
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)				; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=8/9; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.712256; --ascCAGACAGac ; cor=; Ncor= a 0 0 840 315 442 25 2159 14 2091 20 2054 108 1107 368 c 0 0 494 725 1431 2094 39 102 82 2197 44 278 443 1157 g 0 0 547 781 283 48 51 2134 71 38 111 1751 417 456 t 0 0 387 447 112 101 19 18 24 13 59 131 301 287
positions_7nt_m2_shift0 (positions_7nt_m2)				; positions_6nt_m2 versus positions_7nt_m2; m=9/9; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.591618; cwGTCTAGACwg-- ; cor=; Ncor= a 199 259 12 39 23 8 837 12 772 23 386 211 0 0 c 297 120 29 34 865 63 14 22 77 858 157 215 0 0 g 215 157 858 77 22 14 63 865 34 29 120 297 0 0 t 211 386 23 772 12 837 8 23 39 12 259 199 0 0