One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift5 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=24; shift=5; ncol=29; -----ssCCGCCCCGCGCsGCyGCCvvss ; Alignment reference a 0 0 0 0 0 210 182 59 113 74 58 65 48 80 46 66 54 59 106 41 54 116 57 54 85 619 619 214 232 c 0 0 0 0 0 872 778 1390 1392 201 1462 1355 1403 1409 288 1551 278 1539 450 312 1492 597 324 1486 1356 485 608 722 652 g 0 0 0 0 0 518 607 283 213 1393 221 290 276 217 1386 134 1395 149 1155 1360 180 346 1320 185 269 546 456 664 674 t 0 0 0 0 0 198 231 66 80 130 57 88 71 92 78 47 71 51 87 85 72 739 97 73 88 148 115 198 240

positions_6nt_m4_shift5 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCCGCCCCGCGCsGCyGCCvvss ; cor=; Ncor= a 0 0 0 0 0 210 182 59 113 74 58 65 48 80 46 66 54 59 106 41 54 116 57 54 85 619 619 214 232 c 0 0 0 0 0 872 778 1390 1392 201 1462 1355 1403 1409 288 1551 278 1539 450 312 1492 597 324 1486 1356 485 608 722 652 g 0 0 0 0 0 518 607 283 213 1393 221 290 276 217 1386 134 1395 149 1155 1360 180 346 1320 185 269 546 456 664 674 t 0 0 0 0 0 198 231 66 80 130 57 88 71 92 78 47 71 51 87 85 72 739 97 73 88 148 115 198 240

positions_6nt_m1_rc_shift5 (positions_6nt_m1_rc)
; positions_6nt_m4 versus positions_6nt_m1_rc; m=2/4; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.730689; -----ssGCGCCCssCGCgCCGCCCCgss ; cor=; Ncor= a 0 0 0 0 0 706 859 266 435 312 206 269 264 397 226 399 268 275 285 235 453 218 308 261 269 354 287 721 712 c 0 0 0 0 0 3477 3230 1400 5534 1301 5568 5192 5280 1853 2018 5492 1550 6016 1706 5343 5009 1279 5445 4938 5062 5242 1689 3188 2998 g 0 0 0 0 0 2370 2344 5266 908 5083 1151 1378 1372 4440 4716 1083 4917 709 4709 1380 1392 5209 1131 1538 1468 1246 4844 2674 2722 t 0 0 0 0 0 644 764 265 320 501 272 358 281 507 237 223 462 197 497 239 343 491 313 460 398 355 377 614 765

positions_7nt_m2_rc_shift14 (positions_7nt_m2_rc)
; positions_6nt_m4 versus positions_7nt_m2_rc; m=3/4; ncol2=17; w=0; offset=9; strand=R; shift=14; score=0.482816; --------------ssGCGGCtGCCaaGc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 959 1094 209 344 458 146 171 371 132 163 254 3365 3536 222 702 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2440 1943 406 4923 534 392 5231 829 446 5311 4753 992 1161 349 3541 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1792 1987 5171 386 4544 5210 400 1012 5186 357 731 1354 978 5220 1200 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 789 956 194 327 444 232 178 3768 216 149 242 269 305 189 537

positions_7nt_m4_rc_shift0 (positions_7nt_m4_rc)
; positions_6nt_m4 versus positions_7nt_m4_rc; m=4/4; ncol2=24; w=-5; offset=-5; strand=R; shift=0; score=0.477205; sssGCCGCsGCCGCCCgCCGCCss----- ; cor=; Ncor= a 703 780 457 322 306 338 243 277 377 240 264 272 330 200 227 342 291 279 479 308 269 312 724 684 0 0 0 0 0 c 3075 3417 1952 1550 5745 5433 1415 5980 2131 1651 5592 5706 1340 5784 5217 5293 1645 5434 5053 1520 5630 5313 3052 3269 0 0 0 0 0 g 2905 2349 4566 5115 1008 1173 5329 857 4494 5102 1266 932 5185 1133 1531 1362 4981 1372 1397 4995 1142 1295 2614 2629 0 0 0 0 0 t 667 804 375 363 291 406 363 236 348 357 228 440 495 233 375 353 433 265 421 527 309 430 960 768 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift5 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift5 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=14; shift=5; ncol=19; -----awAcATATATgTwt ; Alignment reference a 0 0 0 0 0 4863 3175 10539 1420 11163 1114 9757 1021 9453 467 2247 619 4059 3027 c 0 0 0 0 0 1852 2994 433 8000 252 922 573 847 709 316 531 607 1970 2456 g 0 0 0 0 0 2456 1970 607 531 316 709 847 573 922 252 8000 433 2994 1852 t 0 0 0 0 0 3027 4059 619 2247 467 9453 1021 9757 1114 11163 1420 10539 3175 4863

positions_6nt_m3_shift5 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----awAcATATATgTwt ; cor=; Ncor= a 0 0 0 0 0 4863 3175 10539 1420 11163 1114 9757 1021 9453 467 2247 619 4059 3027 c 0 0 0 0 0 1852 2994 433 8000 252 922 573 847 709 316 531 607 1970 2456 g 0 0 0 0 0 2456 1970 607 531 316 709 847 573 922 252 8000 433 2994 1852 t 0 0 0 0 0 3027 4059 619 2247 467 9453 1021 9757 1114 11163 1420 10539 3175 4863

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_6nt_m3 versus positions_7nt_m5; m=2/2; ncol2=22; w=-5; offset=-5; strand=D; shift=0; score=0.458881; wwAtAAAATATATATTTTa ; cor=; Ncor= a 1389 1414 2767 685 2780 2834 2804 2961 524 2961 505 2863 407 2823 456 631 518 604 2568 c 505 627 234 290 222 251 247 193 271 200 289 201 291 242 250 178 255 254 318 g 661 529 246 317 254 255 178 250 242 291 201 290 201 271 193 247 251 223 289 t 1304 1289 612 2567 603 519 630 455 2822 407 2864 505 2960 523 2960 2803 2835 2778 684

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; ssCtGGGCaGGGCass ; Alignment reference a 1487 1329 301 711 204 419 324 435 5875 299 426 415 511 4441 1191 1602 c 2788 2612 7584 1001 530 653 562 7570 1059 504 595 388 7306 1482 2673 2255 g 3118 3383 722 1240 7798 7309 7721 635 1084 7754 7491 7786 717 1897 3729 3561 t 1437 1506 223 5878 298 449 223 190 812 273 318 241 296 1010 1237 1412

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/1; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; ssCtGGGCaGGGCass ; cor=; Ncor= a 1487 1329 301 711 204 419 324 435 5875 299 426 415 511 4441 1191 1602 c 2788 2612 7584 1001 530 653 562 7570 1059 504 595 388 7306 1482 2673 2255 g 3118 3383 722 1240 7798 7309 7721 635 1084 7754 7491 7786 717 1897 3729 3561 t 1437 1506 223 5878 298 449 223 190 812 273 318 241 296 1010 1237 1412

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift6 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift6 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=6; ncol=16; ------ssCGGCCGss ; Alignment reference a 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 c 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 g 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 t 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509

oligos_6nt_mkv4_m3_shift6 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/5; ncol2=10; w=0; offset=0; strand=D; shift=6; score= 1; ------ssCGGCCGss ; cor=; Ncor= a 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 c 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 g 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 t 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509

oligos_6nt_mkv4_m1_rc_shift6 (oligos_6nt_mkv4_m1_rc)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m1_rc; m=2/5; ncol2=10; w=0; offset=0; strand=R; shift=6; score=0.834572; ------ssCGgGCGss ; cor=; Ncor= a 0 0 0 0 0 0 4947 4683 299 578 2555 1754 481 479 3890 4776 c 0 0 0 0 0 0 14594 11798 33918 3296 7014 3580 34376 1055 15785 10762 g 0 0 0 0 0 0 11879 16452 1737 32366 24740 30153 645 34656 11482 16270 t 0 0 0 0 0 0 5045 3532 511 225 2156 978 963 275 5308 4657

oligos_7nt_mkv5_m4_shift6 (oligos_7nt_mkv5_m4)
; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m4; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=6; score=0.704516; ------ssCGGCtGCG ; cor=; Ncor= a 0 0 0 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 c 0 0 0 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 g 0 0 0 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 t 0 0 0 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300

oligos_7nt_mkv5_m5_shift6 (oligos_7nt_mkv5_m5)
; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m5; m=4/5; ncol2=11; w=0; offset=0; strand=D; shift=6; score=0.647188; ------ssCGGCCCGs ; cor=; Ncor= a 0 0 0 0 0 0 4639 4281 1031 1932 605 439 520 1420 1087 4604 c 0 0 0 0 0 0 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 g 0 0 0 0 0 0 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 t 0 0 0 0 0 0 4981 4908 1051 1848 902 439 1025 1276 1104 4225

positions_7nt_m2_shift0 (positions_7nt_m2)
; oligos_6nt_mkv4_m3 versus positions_7nt_m2; m=5/5; ncol2=17; w=-6; offset=-6; strand=D; shift=0; score=0.454447; ssgCttGGCaGCCGCs ; cor=; Ncor= a 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 c 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 g 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 t 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---ssGCsssCGCssCCGCCGCCCsss ; Alignment reference a 0 0 0 802 856 267 381 404 407 324 350 262 282 289 255 301 273 285 242 461 306 239 273 354 375 616 844 c 0 0 0 3405 3346 1438 5816 1878 1947 2464 5825 1064 6177 1879 4755 5278 5715 1244 5592 5313 1226 5862 5254 5064 1872 3657 2652 g 0 0 0 2531 2397 5415 962 4744 4749 4377 959 5765 718 4853 2118 1498 1129 5544 1394 1302 5427 1030 1477 1598 4789 2557 3077 t 0 0 0 694 833 312 273 406 329 267 298 341 255 411 304 355 315 359 204 356 473 301 428 416 396 602 859

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---ssGCsssCGCssCCGCCGCCCsss ; cor=; Ncor= a 0 0 0 802 856 267 381 404 407 324 350 262 282 289 255 301 273 285 242 461 306 239 273 354 375 616 844 c 0 0 0 3405 3346 1438 5816 1878 1947 2464 5825 1064 6177 1879 4755 5278 5715 1244 5592 5313 1226 5862 5254 5064 1872 3657 2652 g 0 0 0 2531 2397 5415 962 4744 4749 4377 959 5765 718 4853 2118 1498 1129 5544 1394 1302 5427 1030 1477 1598 4789 2557 3077 t 0 0 0 694 833 312 273 406 329 267 298 341 255 411 304 355 315 359 204 356 473 301 428 416 396 602 859

positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)
; positions_7nt_m1 versus positions_7nt_m4_rc; m=2/4; ncol2=24; w=0; offset=2; strand=R; shift=5; score=0.673942; -----sssGCCGCsGCCGCCCgCCGCC ; cor=; Ncor= a 0 0 0 0 0 703 780 457 322 306 338 243 277 377 240 264 272 330 200 227 342 291 279 479 308 269 312 c 0 0 0 0 0 3075 3417 1952 1550 5745 5433 1415 5980 2131 1651 5592 5706 1340 5784 5217 5293 1645 5434 5053 1520 5630 5313 g 0 0 0 0 0 2905 2349 4566 5115 1008 1173 5329 857 4494 5102 1266 932 5185 1133 1531 1362 4981 1372 1397 4995 1142 1295 t 0 0 0 0 0 667 804 375 363 291 406 363 236 348 357 228 440 495 233 375 353 433 265 421 527 309 430

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=3/4; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.548696; sscGGGGCGGcGCGssGGGCGCss--- ; cor=; Ncor= a 765 614 377 355 398 460 313 491 343 239 497 197 462 223 237 507 281 358 272 501 320 265 764 644 0 0 0 c 2722 2674 4844 1246 1468 1538 1131 5209 1392 1380 4709 709 4917 1083 4716 4440 1372 1378 1151 5083 908 5266 2344 2370 0 0 0 g 2998 3188 1689 5242 5062 4938 5445 1279 5009 5343 1706 6016 1550 5492 2018 1853 5280 5192 5568 1301 5534 1400 3230 3477 0 0 0 t 712 721 287 354 269 261 308 218 453 235 285 275 268 399 226 397 264 269 206 312 435 266 859 706 0 0 0

oligos_7nt_mkv5_m2_shift8 (oligos_7nt_mkv5_m2)
; positions_7nt_m1 versus oligos_7nt_mkv5_m2; m=4/4; ncol2=12; w=0; offset=5; strand=D; shift=8; score=0.427293; --------ssCGCCCCCgss------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift9 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift9 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=9; ncol=21; ---------ssCGGCtGCGss ; Alignment reference a 0 0 0 0 0 0 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 2755 2976 c 0 0 0 0 0 0 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 8024 8987 g 0 0 0 0 0 0 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 10068 8620 t 0 0 0 0 0 0 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156

oligos_7nt_mkv5_m4_shift9 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=9; score= 1; ---------ssCGGCtGCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 2755 2976 c 0 0 0 0 0 0 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 8024 8987 g 0 0 0 0 0 0 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 10068 8620 t 0 0 0 0 0 0 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156

oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m2_rc; m=2/5; ncol2=12; w=0; offset=0; strand=R; shift=9; score=0.769998; ---------sscGGGGGCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4129 3726 2803 934 971 1176 1050 1304 1150 586 3673 4289 c 0 0 0 0 0 0 0 0 0 12013 11652 24236 3252 4931 6244 5120 2236 34377 1285 13293 11270 g 0 0 0 0 0 0 0 0 0 16802 17815 7154 31669 29983 28599 29928 32573 575 34228 16148 17323 t 0 0 0 0 0 0 0 0 0 4002 3753 2753 1091 1061 927 848 833 844 847 3832 4064

oligos_6nt_mkv4_m3_shift9 (oligos_6nt_mkv4_m3)
; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m3; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=9; score=0.704516; ---------ssCGGCCGss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 0 0 c 0 0 0 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 0 0 g 0 0 0 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 0 0 t 0 0 0 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509 0 0

positions_7nt_m2_rc_shift8 (positions_7nt_m2_rc)
; oligos_7nt_mkv5_m4 versus positions_7nt_m2_rc; m=4/5; ncol2=17; w=-1; offset=-1; strand=R; shift=8; score=0.567909; --------ssGCGGCtGCCaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 959 1094 209 344 458 146 171 371 132 163 254 3365 3536 c 0 0 0 0 0 0 0 0 2440 1943 406 4923 534 392 5231 829 446 5311 4753 992 1161 g 0 0 0 0 0 0 0 0 1792 1987 5171 386 4544 5210 400 1012 5186 357 731 1354 978 t 0 0 0 0 0 0 0 0 789 956 194 327 444 232 178 3768 216 149 242 269 305

positions_7nt_m4_shift0 (positions_7nt_m4)
; oligos_7nt_mkv5_m4 versus positions_7nt_m4; m=5/5; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.419536; ssGGCGGcGGGCGGCsGCGGC ; cor=; Ncor= a 768 960 430 309 527 421 265 433 353 375 233 495 440 228 357 348 236 363 406 291 363 c 2629 2614 1295 1142 4995 1397 1372 4981 1362 1531 1133 5185 932 1266 5102 4494 857 5329 1173 1008 5115 g 3269 3052 5313 5630 1520 5053 5434 1645 5293 5217 5784 1340 5706 5592 1651 2131 5980 1415 5433 5745 1550 t 684 724 312 269 308 479 279 291 342 227 200 330 272 264 240 377 277 243 338 306 322

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGCCCtCgss ; Alignment reference a 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCtCgss ; cor=; Ncor= a 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.897996; ssCGCCCCCgss ; cor=; Ncor= a 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m1; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.687685; ssCGCcCGss-- ; cor=; Ncor= a 4657 5308 275 963 978 2156 225 511 3532 5045 0 0 c 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 0 0 g 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 0 0 t 4776 3890 479 481 1754 2555 578 299 4683 4947 0 0

oligos_6nt_mkv4_m2_rc_shift0 (oligos_6nt_mkv4_m2_rc)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m2_rc; m=4/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.621952; ssCGCkCGss-- ; cor=; Ncor= a 3169 3720 418 645 450 2156 388 484 2384 3853 0 0 c 11847 8031 24381 692 24633 3792 25572 2251 11678 8780 0 0 g 7796 11936 1475 24686 978 7014 457 23151 8999 10187 0 0 t 3804 2929 342 593 555 13654 199 730 3555 3796 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 3 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=22; shift=0; ncol=22; wwAtAAAATATATATTTTaTww ; Alignment reference a 1389 1414 2767 685 2780 2834 2804 2961 524 2961 505 2863 407 2823 456 631 518 604 2568 613 1289 1304 c 505 627 234 290 222 251 247 193 271 200 289 201 291 242 250 178 255 254 318 246 530 661 g 661 529 246 317 254 255 178 250 242 291 201 290 201 271 193 247 251 223 289 234 625 505 t 1304 1289 612 2567 603 519 630 455 2822 407 2864 505 2960 523 2960 2803 2835 2778 684 2766 1415 1389

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; wwAtAAAATATATATTTTaTww ; cor=; Ncor= a 1389 1414 2767 685 2780 2834 2804 2961 524 2961 505 2863 407 2823 456 631 518 604 2568 613 1289 1304 c 505 627 234 290 222 251 247 193 271 200 289 201 291 242 250 178 255 254 318 246 530 661 g 661 529 246 317 254 255 178 250 242 291 201 290 201 271 193 247 251 223 289 234 625 505 t 1304 1289 612 2567 603 519 630 455 2822 407 2864 505 2960 523 2960 2803 2835 2778 684 2766 1415 1389

positions_6nt_m3_shift5 (positions_6nt_m3)
; positions_7nt_m5 versus positions_6nt_m3; m=2/2; ncol2=14; w=0; offset=5; strand=D; shift=5; score=0.458881; -----awAcATATATgTwt--- ; cor=; Ncor= a 0 0 0 0 0 4863 3175 10539 1420 11163 1114 9757 1021 9453 467 2247 619 4059 3027 0 0 0 c 0 0 0 0 0 1852 2994 433 8000 252 922 573 847 709 316 531 607 1970 2456 0 0 0 g 0 0 0 0 0 2456 1970 607 531 316 709 847 573 922 252 8000 433 2994 1852 0 0 0 t 0 0 0 0 0 3027 4059 619 2247 467 9453 1021 9757 1114 11163 1420 10539 3175 4863 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; ssGCCCaGCCtGGCaGGCtGGCss ; Alignment reference a 164 231 61 55 75 54 670 22 49 47 110 43 41 72 607 67 57 50 104 34 55 86 189 167 c 374 321 108 827 759 845 145 86 814 853 165 115 140 803 164 120 134 831 138 111 135 771 301 354 g 376 323 800 122 140 113 145 909 154 105 165 849 835 148 179 800 803 130 170 853 807 140 352 356 t 137 176 82 47 77 39 91 34 34 46 611 44 35 28 101 64 57 40 639 53 54 54 209 174

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/2; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ssGCCCaGCCtGGCaGGCtGGCss ; cor=; Ncor= a 164 231 61 55 75 54 670 22 49 47 110 43 41 72 607 67 57 50 104 34 55 86 189 167 c 374 321 108 827 759 845 145 86 814 853 165 115 140 803 164 120 134 831 138 111 135 771 301 354 g 376 323 800 122 140 113 145 909 154 105 165 849 835 148 179 800 803 130 170 853 807 140 352 356 t 137 176 82 47 77 39 91 34 34 46 611 44 35 28 101 64 57 40 639 53 54 54 209 174

positions_6nt_m5_shift8 (positions_6nt_m5)
; positions_6nt_m2 versus positions_6nt_m5; m=2/2; ncol2=24; w=0; offset=8; strand=D; shift=8; score=0.410938; --------sscGGCaGGCkGGCaG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 182 166 123 97 43 44 633 47 43 73 129 44 68 76 657 36 c 0 0 0 0 0 0 0 0 430 390 798 103 132 922 182 116 134 953 145 120 111 829 170 116 g 0 0 0 0 0 0 0 0 433 499 183 914 971 187 279 980 976 127 303 984 977 252 261 998 t 0 0 0 0 0 0 0 0 146 136 87 77 45 38 97 48 38 38 614 43 35 34 103 41

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ssCGGAGCGss ; Alignment reference a 4147 4438 1172 1364 367 21283 250 1459 1420 4414 4612 c 10528 8928 24624 1253 1638 3017 484 25020 3468 9858 8095 g 9825 11285 1860 24938 26377 3567 27654 1289 21877 10412 11854 t 4085 3934 929 1030 203 718 197 817 1820 3901 4024

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGAGCGss ; cor=; Ncor= a 4147 4438 1172 1364 367 21283 250 1459 1420 4414 4612 c 10528 8928 24624 1253 1638 3017 484 25020 3468 9858 8095 g 9825 11285 1860 24938 26377 3567 27654 1289 21877 10412 11854 t 4085 3934 929 1030 203 718 197 817 1820 3901 4024

oligos_6nt_mkv4_m2_shift1 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m2; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.666897; -ssCGmGCGss ; cor=; Ncor= a 0 3796 3555 730 199 13654 555 593 342 2929 3804 c 0 10187 8999 23151 457 7014 978 24686 1475 11936 7796 g 0 8780 11678 2251 25572 3792 24633 692 24381 8031 11847 t 0 3853 2384 484 388 2156 450 645 418 3720 3169

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ssCGGCCCGss ; Alignment reference a 4639 4281 1031 1932 605 439 520 1420 1087 4604 5305 c 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 12535 g 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 13556 t 4981 4908 1051 1848 902 439 1025 1276 1104 4225 4493

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGCCCGss ; cor=; Ncor= a 4639 4281 1031 1932 605 439 520 1420 1087 4604 5305 c 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 12535 g 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 13556 t 4981 4908 1051 1848 902 439 1025 1276 1104 4225 4493

oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m1; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.664204; -ssCGCcCGss ; cor=; Ncor= a 0 4657 5308 275 963 978 2156 225 511 3532 5045 c 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 g 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 t 0 4776 3890 479 481 1754 2555 578 299 4683 4947

oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m3; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.647188; ssCGGCCGss- ; cor=; Ncor= a 4509 4870 250 351 978 1754 268 576 3846 4128 0 c 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 0 g 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 0 t 4128 3846 576 268 1754 978 351 250 4870 4509 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift5 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift5 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=5; ncol=17; -----ssCGCCCCCgss ; Alignment reference a 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129

oligos_7nt_mkv5_m2_shift5 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCGCCCCCgss ; cor=; Ncor= a 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129

oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=5; score=0.897996; -----ssCGCCCtCgss ; cor=; Ncor= a 0 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 0 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 0 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 0 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061

oligos_7nt_mkv5_m4_rc_shift5 (oligos_7nt_mkv5_m4_rc)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4_rc; m=3/5; ncol2=12; w=0; offset=0; strand=R; shift=5; score=0.769998; -----ssCGCaGCCGss ; cor=; Ncor= a 0 0 0 0 0 3156 2892 1300 622 392 13594 270 766 677 661 2677 3174 c 0 0 0 0 0 8620 10068 18188 1084 21556 5423 1136 21088 20646 1509 11960 8643 g 0 0 0 0 0 8987 8024 3085 21439 1322 3947 21919 1327 1624 20775 6386 8848 t 0 0 0 0 0 2976 2755 1166 594 469 775 414 558 792 794 2716 3074

oligos_6nt_mkv4_m1_shift5 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=4/5; ncol2=10; w=0; offset=0; strand=D; shift=5; score=0.650901; -----ssCGCcCGss-- ; cor=; Ncor= a 0 0 0 0 0 4657 5308 275 963 978 2156 225 511 3532 5045 0 0 c 0 0 0 0 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 0 0 g 0 0 0 0 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 0 0 t 0 0 0 0 0 4776 3890 479 481 1754 2555 578 299 4683 4947 0 0

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_7nt_mkv5_m2 versus positions_7nt_m1; m=5/5; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.427293; ssGCsssCGCssCCGCC ; cor=; Ncor= a 802 856 267 381 404 407 324 350 262 282 289 255 301 273 285 242 461 c 3405 3346 1438 5816 1878 1947 2464 5825 1064 6177 1879 4755 5278 5715 1244 5592 5313 g 2531 2397 5415 962 4744 4749 4377 959 5765 718 4853 2118 1498 1129 5544 1394 1302 t 694 833 312 273 406 329 267 298 341 255 411 304 355 315 359 204 356

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --ssCGmGCGss ; Alignment reference a 0 0 3796 3555 730 199 13654 555 593 342 2929 3804 c 0 0 10187 8999 23151 457 7014 978 24686 1475 11936 7796 g 0 0 8780 11678 2251 25572 3792 24633 692 24381 8031 11847 t 0 0 3853 2384 484 388 2156 450 645 418 3720 3169

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ssCGmGCGss ; cor=; Ncor= a 0 0 3796 3555 730 199 13654 555 593 342 2929 3804 c 0 0 10187 8999 23151 457 7014 978 24686 1475 11936 7796 g 0 0 8780 11678 2251 25572 3792 24633 692 24381 8031 11847 t 0 0 3853 2384 484 388 2156 450 645 418 3720 3169

oligos_6nt_mkv4_m1_rc_shift2 (oligos_6nt_mkv4_m1_rc)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m1_rc; m=2/4; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.92327; --ssCGgGCGss ; cor=; Ncor= a 0 0 4947 4683 299 578 2555 1754 481 479 3890 4776 c 0 0 14594 11798 33918 3296 7014 3580 34376 1055 15785 10762 g 0 0 11879 16452 1737 32366 24740 30153 645 34656 11482 16270 t 0 0 5045 3532 511 225 2156 978 963 275 5308 4657

oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m5; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.666897; -ssCGGAGCGss ; cor=; Ncor= a 0 4147 4438 1172 1364 367 21283 250 1459 1420 4414 4612 c 0 10528 8928 24624 1253 1638 3017 484 25020 3468 9858 8095 g 0 9825 11285 1860 24938 26377 3567 27654 1289 21877 10412 11854 t 0 4085 3934 929 1030 203 718 197 817 1820 3901 4024

oligos_7nt_mkv5_m3_rc_shift0 (oligos_7nt_mkv5_m3_rc)
; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m3_rc; m=4/4; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.621952; sscGaGGGCGss ; cor=; Ncor= a 3061 2835 1667 307 12452 361 704 824 668 383 2703 2875 c 7016 6666 14070 950 4922 2131 3586 1112 19580 614 8452 6340 g 8592 9655 4274 19765 2890 18433 16303 18867 620 19833 7499 9671 t 2608 2121 1266 255 1013 352 684 474 409 447 2623 2391

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; ssgCttGGCaGCCGCss ; Alignment reference a 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 789 c 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 1792 g 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 2440 t 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094 959

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; ssgCttGGCaGCCGCss ; cor=; Ncor= a 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 789 c 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 1792 g 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 2440 t 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094 959

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m2 versus positions_7nt_m3; m=2/5; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.640703; ssgCttGGCAGCAGCCA ; cor=; Ncor= a 217 233 144 45 92 73 53 53 71 743 43 64 755 45 72 46 764 c 320 282 172 868 161 150 84 109 858 121 65 859 114 72 835 886 92 g 304 319 565 96 140 199 851 831 91 85 905 96 92 890 98 79 116 t 215 222 175 47 663 634 68 63 36 107 43 37 95 49 51 45 84

oligos_7nt_mkv5_m4_rc_shift4 (oligos_7nt_mkv5_m4_rc)
; positions_7nt_m2 versus oligos_7nt_mkv5_m4_rc; m=3/5; ncol2=12; w=0; offset=4; strand=R; shift=4; score=0.567909; ----ssCGCaGCCGss- ; cor=; Ncor= a 0 0 0 0 3156 2892 1300 622 392 13594 270 766 677 661 2677 3174 0 c 0 0 0 0 8620 10068 18188 1084 21556 5423 1136 21088 20646 1509 11960 8643 0 g 0 0 0 0 8987 8024 3085 21439 1322 3947 21919 1327 1624 20775 6386 8848 0 t 0 0 0 0 2976 2755 1166 594 469 775 414 558 792 794 2716 3074 0

positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)
; positions_7nt_m2 versus positions_6nt_m4_rc; m=4/5; ncol2=24; w=0; offset=2; strand=R; shift=2; score=0.482816; --ssbbGGCrGCsGCGC ; cor=; Ncor= a 0 0 240 198 115 148 88 73 97 739 72 85 87 51 71 47 78 c 0 0 674 664 456 546 269 185 1320 346 180 1360 1155 149 1395 134 1386 g 0 0 652 722 608 485 1356 1486 324 597 1492 312 450 1539 278 1551 288 t 0 0 232 214 619 619 85 54 57 116 54 41 106 59 54 66 46

oligos_6nt_mkv4_m3_shift6 (oligos_6nt_mkv4_m3)
; positions_7nt_m2 versus oligos_6nt_mkv4_m3; m=5/5; ncol2=10; w=0; offset=6; strand=D; shift=6; score=0.454447; ------ssCGGCCGss- ; cor=; Ncor= a 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 0 c 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 0 g 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 0 t 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCGCcCGss ; Alignment reference a 0 4657 5308 275 963 978 2156 225 511 3532 5045 c 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 g 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 t 0 4776 3890 479 481 1754 2555 578 299 4683 4947

oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ssCGCcCGss ; cor=; Ncor= a 0 4657 5308 275 963 978 2156 225 511 3532 5045 c 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 g 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 t 0 4776 3890 479 481 1754 2555 578 299 4683 4947

oligos_6nt_mkv4_m2_rc_shift1 (oligos_6nt_mkv4_m2_rc)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m2_rc; m=2/6; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.92327; -ssCGCkCGss ; cor=; Ncor= a 0 3169 3720 418 645 450 2156 388 484 2384 3853 c 0 11847 8031 24381 692 24633 3792 25572 2251 11678 8780 g 0 7796 11936 1475 24686 978 7014 457 23151 8999 10187 t 0 3804 2929 342 593 555 13654 199 730 3555 3796

oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m3; m=3/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.834572; -ssCGGCCGss ; cor=; Ncor= a 0 4509 4870 250 351 978 1754 268 576 3846 4128 c 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 g 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 t 0 4128 3846 576 268 1754 978 351 250 4870 4509

oligos_7nt_mkv5_m3_shift1 (oligos_7nt_mkv5_m3)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m3; m=4/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.687685; -ssCGCCCtCg ; cor=; Ncor= a 0 2391 2623 447 409 474 684 352 1013 255 1266 c 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 g 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 t 0 2875 2703 383 668 824 704 361 12452 307 1667

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m5; m=5/6; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.664204; ssCGGCCCGss ; cor=; Ncor= a 4639 4281 1031 1932 605 439 520 1420 1087 4604 5305 c 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 12535 g 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 13556 t 4981 4908 1051 1848 902 439 1025 1276 1104 4225 4493

oligos_7nt_mkv5_m2_shift1 (oligos_7nt_mkv5_m2)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m2; m=6/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.650901; -ssCGCCCCCg ; cor=; Ncor= a 0 4064 3832 847 844 833 848 927 1061 1091 2753 c 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 g 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 t 0 4289 3673 586 1150 1304 1050 1176 971 934 2803

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift8 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift8 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=24; shift=8; ncol=32; --------sscGGCaGGCkGGCaGCtGGGCss ; Alignment reference a 0 0 0 0 0 0 0 0 182 166 123 97 43 44 633 47 43 73 129 44 68 76 657 36 36 101 44 82 43 89 203 148 c 0 0 0 0 0 0 0 0 430 390 798 103 132 922 182 116 134 953 145 120 111 829 170 116 980 188 121 135 116 900 375 385 g 0 0 0 0 0 0 0 0 433 499 183 914 971 187 279 980 976 127 303 984 977 252 261 998 150 250 980 903 988 148 397 473 t 0 0 0 0 0 0 0 0 146 136 87 77 45 38 97 48 38 38 614 43 35 34 103 41 25 652 46 71 44 54 216 185

positions_6nt_m5_shift8 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/2; ncol2=24; w=0; offset=0; strand=D; shift=8; score= 1; --------sscGGCaGGCkGGCaGCtGGGCss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 182 166 123 97 43 44 633 47 43 73 129 44 68 76 657 36 36 101 44 82 43 89 203 148 c 0 0 0 0 0 0 0 0 430 390 798 103 132 922 182 116 134 953 145 120 111 829 170 116 980 188 121 135 116 900 375 385 g 0 0 0 0 0 0 0 0 433 499 183 914 971 187 279 980 976 127 303 984 977 252 261 998 150 250 980 903 988 148 397 473 t 0 0 0 0 0 0 0 0 146 136 87 77 45 38 97 48 38 38 614 43 35 34 103 41 25 652 46 71 44 54 216 185

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m5 versus positions_6nt_m2; m=2/2; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.410938; ssGCCCaGCCtGGCaGGCtGGCss-------- ; cor=; Ncor= a 164 231 61 55 75 54 670 22 49 47 110 43 41 72 607 67 57 50 104 34 55 86 189 167 0 0 0 0 0 0 0 0 c 374 321 108 827 759 845 145 86 814 853 165 115 140 803 164 120 134 831 138 111 135 771 301 354 0 0 0 0 0 0 0 0 g 376 323 800 122 140 113 145 909 154 105 165 849 835 148 179 800 803 130 170 853 807 140 352 356 0 0 0 0 0 0 0 0 t 137 176 82 47 77 39 91 34 34 46 611 44 35 28 101 64 57 40 639 53 54 54 209 174 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; sscGGGGCGGcGCGssGGGCGCss ; Alignment reference a 765 614 377 355 398 460 313 491 343 239 497 197 462 223 237 507 281 358 272 501 320 265 764 644 c 2722 2674 4844 1246 1468 1538 1131 5209 1392 1380 4709 709 4917 1083 4716 4440 1372 1378 1151 5083 908 5266 2344 2370 g 2998 3188 1689 5242 5062 4938 5445 1279 5009 5343 1706 6016 1550 5492 2018 1853 5280 5192 5568 1301 5534 1400 3230 3477 t 712 721 287 354 269 261 308 218 453 235 285 275 268 399 226 397 264 269 206 312 435 266 859 706

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; sscGGGGCGGcGCGssGGGCGCss ; cor=; Ncor= a 765 614 377 355 398 460 313 491 343 239 497 197 462 223 237 507 281 358 272 501 320 265 764 644 c 2722 2674 4844 1246 1468 1538 1131 5209 1392 1380 4709 709 4917 1083 4716 4440 1372 1378 1151 5083 908 5266 2344 2370 g 2998 3188 1689 5242 5062 4938 5445 1279 5009 5343 1706 6016 1550 5492 2018 1853 5280 5192 5568 1301 5534 1400 3230 3477 t 712 721 287 354 269 261 308 218 453 235 285 275 268 399 226 397 264 269 206 312 435 266 859 706

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_6nt_m1 versus positions_6nt_m4_rc; m=2/3; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.730689; ssbbGGCrGCsGCGCGGGGCGGss ; cor=; Ncor= a 240 198 115 148 88 73 97 739 72 85 87 51 71 47 78 92 71 88 57 130 80 66 231 198 c 674 664 456 546 269 185 1320 346 180 1360 1155 149 1395 134 1386 217 276 290 221 1393 213 283 607 518 g 652 722 608 485 1356 1486 324 597 1492 312 450 1539 278 1551 288 1409 1403 1355 1462 201 1392 1390 778 872 t 232 214 619 619 85 54 57 116 54 41 106 59 54 66 46 80 48 65 58 74 113 59 182 210

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=3/3; ncol2=24; w=0; offset=3; strand=D; shift=3; score=0.548696; ---ssGCsssCGCssCCGCCGCCC ; cor=; Ncor= a 0 0 0 802 856 267 381 404 407 324 350 262 282 289 255 301 273 285 242 461 306 239 273 354 c 0 0 0 3405 3346 1438 5816 1878 1947 2464 5825 1064 6177 1879 4755 5278 5715 1244 5592 5313 1226 5862 5254 5064 g 0 0 0 2531 2397 5415 962 4744 4749 4377 959 5765 718 4853 2118 1498 1129 5544 1394 1302 5427 1030 1477 1598 t 0 0 0 694 833 312 273 406 329 267 298 341 255 411 304 355 315 359 204 356 473 301 428 416

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=24; shift=5; ncol=29; -----ssGGCGGcGGGCGGCsGCGGCsss ; Alignment reference a 0 0 0 0 0 768 960 430 309 527 421 265 433 353 375 233 495 440 228 357 348 236 363 406 291 363 375 804 667 c 0 0 0 0 0 2629 2614 1295 1142 4995 1397 1372 4981 1362 1531 1133 5185 932 1266 5102 4494 857 5329 1173 1008 5115 4566 2349 2905 g 0 0 0 0 0 3269 3052 5313 5630 1520 5053 5434 1645 5293 5217 5784 1340 5706 5592 1651 2131 5980 1415 5433 5745 1550 1952 3417 3075 t 0 0 0 0 0 684 724 312 269 308 479 279 291 342 227 200 330 272 264 240 377 277 243 338 306 322 457 780 703

positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----ssGGCGGcGGGCGGCsGCGGCsss ; cor=; Ncor= a 0 0 0 0 0 768 960 430 309 527 421 265 433 353 375 233 495 440 228 357 348 236 363 406 291 363 375 804 667 c 0 0 0 0 0 2629 2614 1295 1142 4995 1397 1372 4981 1362 1531 1133 5185 932 1266 5102 4494 857 5329 1173 1008 5115 4566 2349 2905 g 0 0 0 0 0 3269 3052 5313 5630 1520 5053 5434 1645 5293 5217 5784 1340 5706 5592 1651 2131 5980 1415 5433 5745 1550 1952 3417 3075 t 0 0 0 0 0 684 724 312 269 308 479 279 291 342 227 200 330 272 264 240 377 277 243 338 306 322 457 780 703

positions_7nt_m1_rc_shift7 (positions_7nt_m1_rc)
; positions_7nt_m4 versus positions_7nt_m1_rc; m=2/4; ncol2=24; w=0; offset=2; strand=R; shift=7; score=0.673942; -------sssGGGCGGCGGssGCGsssGC ; cor=; Ncor= a 0 0 0 0 0 0 0 859 602 396 416 428 301 473 356 204 359 315 355 304 411 255 341 298 267 329 406 273 312 c 0 0 0 0 0 0 0 3077 2557 4789 1598 1477 1030 5427 1302 1394 5544 1129 1498 2118 4853 718 5765 959 4377 4749 4744 962 5415 g 0 0 0 0 0 0 0 2652 3657 1872 5064 5254 5862 1226 5313 5592 1244 5715 5278 4755 1879 6177 1064 5825 2464 1947 1878 5816 1438 t 0 0 0 0 0 0 0 844 616 375 354 273 239 306 461 242 285 273 301 255 289 282 262 350 324 407 404 381 267

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_7nt_m4 versus positions_6nt_m4_rc; m=3/4; ncol2=24; w=-5; offset=-5; strand=R; shift=0; score=0.477205; ssbbGGCrGCsGCGCGGGGCGGss----- ; cor=; Ncor= a 240 198 115 148 88 73 97 739 72 85 87 51 71 47 78 92 71 88 57 130 80 66 231 198 0 0 0 0 0 c 674 664 456 546 269 185 1320 346 180 1360 1155 149 1395 134 1386 217 276 290 221 1393 213 283 607 518 0 0 0 0 0 g 652 722 608 485 1356 1486 324 597 1492 312 450 1539 278 1551 288 1409 1403 1355 1462 201 1392 1390 778 872 0 0 0 0 0 t 232 214 619 619 85 54 57 116 54 41 106 59 54 66 46 80 48 65 58 74 113 59 182 210 0 0 0 0 0

oligos_7nt_mkv5_m4_shift14 (oligos_7nt_mkv5_m4)
; positions_7nt_m4 versus oligos_7nt_mkv5_m4; m=4/4; ncol2=12; w=0; offset=9; strand=D; shift=14; score=0.419536; --------------ssCGGCtGCGss--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 2755 2976 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 8024 8987 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 10068 8620 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 3 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=22; shift=0; ncol=22; ssgCttGGCAGCAGCCAGCass ; Alignment reference a 217 233 144 45 92 73 53 53 71 743 43 64 755 45 72 46 764 54 55 711 182 196 c 320 282 172 868 161 150 84 109 858 121 65 859 114 72 835 886 92 83 858 134 337 329 g 304 319 565 96 140 199 851 831 91 85 905 96 92 890 98 79 116 868 111 115 361 325 t 215 222 175 47 663 634 68 63 36 107 43 37 95 49 51 45 84 51 32 96 176 206

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; ssgCttGGCAGCAGCCAGCass ; cor=; Ncor= a 217 233 144 45 92 73 53 53 71 743 43 64 755 45 72 46 764 54 55 711 182 196 c 320 282 172 868 161 150 84 109 858 121 65 859 114 72 835 886 92 83 858 134 337 329 g 304 319 565 96 140 199 851 831 91 85 905 96 92 890 98 79 116 868 111 115 361 325 t 215 222 175 47 663 634 68 63 36 107 43 37 95 49 51 45 84 51 32 96 176 206

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m3 versus positions_7nt_m2; m=2/2; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.640703; ssgCttGGCaGCCGCss----- ; cor=; Ncor= a 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 789 0 0 0 0 0 c 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 1792 0 0 0 0 0 g 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 2440 0 0 0 0 0 t 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094 959 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wtATTTTTAww ; Alignment reference a 14257 12595 44664 2652 3292 2079 3039 4231 44303 16467 17323 c 7692 10974 1930 1691 1606 1549 2434 2302 1972 8249 9121 g 10772 8367 2187 1880 1831 1128 1899 1548 1846 9367 7532 t 18363 19148 2303 44861 44355 46328 43712 43003 2963 17001 17108

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wtATTTTTAww ; cor=; Ncor= a 14257 12595 44664 2652 3292 2079 3039 4231 44303 16467 17323 c 7692 10974 1930 1691 1606 1549 2434 2302 1972 8249 9121 g 10772 8367 2187 1880 1831 1128 1899 1548 1846 9367 7532 t 18363 19148 2303 44861 44355 46328 43712 43003 2963 17001 17108

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift5 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=24; shift=5; ncol=29; -----ssCCGCCCCGCGCsGCyGCCvvss ; Alignment reference a 0 0 0 0 0 210 182 59 113 74 58 65 48 80 46 66 54 59 106 41 54 116 57 54 85 619 619 214 232 c 0 0 0 0 0 872 778 1390 1392 201 1462 1355 1403 1409 288 1551 278 1539 450 312 1492 597 324 1486 1356 485 608 722 652 g 0 0 0 0 0 518 607 283 213 1393 221 290 276 217 1386 134 1395 149 1155 1360 180 346 1320 185 269 546 456 664 674 t 0 0 0 0 0 198 231 66 80 130 57 88 71 92 78 47 71 51 87 85 72 739 97 73 88 148 115 198 240
positions_6nt_m4_shift5 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCCGCCCCGCGCsGCyGCCvvss ; cor=; Ncor= a 0 0 0 0 0 210 182 59 113 74 58 65 48 80 46 66 54 59 106 41 54 116 57 54 85 619 619 214 232 c 0 0 0 0 0 872 778 1390 1392 201 1462 1355 1403 1409 288 1551 278 1539 450 312 1492 597 324 1486 1356 485 608 722 652 g 0 0 0 0 0 518 607 283 213 1393 221 290 276 217 1386 134 1395 149 1155 1360 180 346 1320 185 269 546 456 664 674 t 0 0 0 0 0 198 231 66 80 130 57 88 71 92 78 47 71 51 87 85 72 739 97 73 88 148 115 198 240
positions_6nt_m1_rc_shift5 (positions_6nt_m1_rc)				; positions_6nt_m4 versus positions_6nt_m1_rc; m=2/4; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.730689; -----ssGCGCCCssCGCgCCGCCCCgss ; cor=; Ncor= a 0 0 0 0 0 706 859 266 435 312 206 269 264 397 226 399 268 275 285 235 453 218 308 261 269 354 287 721 712 c 0 0 0 0 0 3477 3230 1400 5534 1301 5568 5192 5280 1853 2018 5492 1550 6016 1706 5343 5009 1279 5445 4938 5062 5242 1689 3188 2998 g 0 0 0 0 0 2370 2344 5266 908 5083 1151 1378 1372 4440 4716 1083 4917 709 4709 1380 1392 5209 1131 1538 1468 1246 4844 2674 2722 t 0 0 0 0 0 644 764 265 320 501 272 358 281 507 237 223 462 197 497 239 343 491 313 460 398 355 377 614 765
positions_7nt_m2_rc_shift14 (positions_7nt_m2_rc)				; positions_6nt_m4 versus positions_7nt_m2_rc; m=3/4; ncol2=17; w=0; offset=9; strand=R; shift=14; score=0.482816; --------------ssGCGGCtGCCaaGc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 959 1094 209 344 458 146 171 371 132 163 254 3365 3536 222 702 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2440 1943 406 4923 534 392 5231 829 446 5311 4753 992 1161 349 3541 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1792 1987 5171 386 4544 5210 400 1012 5186 357 731 1354 978 5220 1200 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 789 956 194 327 444 232 178 3768 216 149 242 269 305 189 537
positions_7nt_m4_rc_shift0 (positions_7nt_m4_rc)				; positions_6nt_m4 versus positions_7nt_m4_rc; m=4/4; ncol2=24; w=-5; offset=-5; strand=R; shift=0; score=0.477205; sssGCCGCsGCCGCCCgCCGCCss----- ; cor=; Ncor= a 703 780 457 322 306 338 243 277 377 240 264 272 330 200 227 342 291 279 479 308 269 312 724 684 0 0 0 0 0 c 3075 3417 1952 1550 5745 5433 1415 5980 2131 1651 5592 5706 1340 5784 5217 5293 1645 5434 5053 1520 5630 5313 3052 3269 0 0 0 0 0 g 2905 2349 4566 5115 1008 1173 5329 857 4494 5102 1266 932 5185 1133 1531 1362 4981 1372 1397 4995 1142 1295 2614 2629 0 0 0 0 0 t 667 804 375 363 291 406 363 236 348 357 228 440 495 233 375 353 433 265 421 527 309 430 960 768 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m3_shift6 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=6; ncol=16; ------ssCGGCCGss ; Alignment reference a 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 c 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 g 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 t 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509
oligos_6nt_mkv4_m3_shift6 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/5; ncol2=10; w=0; offset=0; strand=D; shift=6; score= 1; ------ssCGGCCGss ; cor=; Ncor= a 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 c 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 g 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 t 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509
oligos_6nt_mkv4_m1_rc_shift6 (oligos_6nt_mkv4_m1_rc)				; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m1_rc; m=2/5; ncol2=10; w=0; offset=0; strand=R; shift=6; score=0.834572; ------ssCGgGCGss ; cor=; Ncor= a 0 0 0 0 0 0 4947 4683 299 578 2555 1754 481 479 3890 4776 c 0 0 0 0 0 0 14594 11798 33918 3296 7014 3580 34376 1055 15785 10762 g 0 0 0 0 0 0 11879 16452 1737 32366 24740 30153 645 34656 11482 16270 t 0 0 0 0 0 0 5045 3532 511 225 2156 978 963 275 5308 4657
oligos_7nt_mkv5_m4_shift6 (oligos_7nt_mkv5_m4)				; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m4; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=6; score=0.704516; ------ssCGGCtGCG ; cor=; Ncor= a 0 0 0 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 c 0 0 0 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 g 0 0 0 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 t 0 0 0 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300
oligos_7nt_mkv5_m5_shift6 (oligos_7nt_mkv5_m5)				; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m5; m=4/5; ncol2=11; w=0; offset=0; strand=D; shift=6; score=0.647188; ------ssCGGCCCGs ; cor=; Ncor= a 0 0 0 0 0 0 4639 4281 1031 1932 605 439 520 1420 1087 4604 c 0 0 0 0 0 0 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 g 0 0 0 0 0 0 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 t 0 0 0 0 0 0 4981 4908 1051 1848 902 439 1025 1276 1104 4225
positions_7nt_m2_shift0 (positions_7nt_m2)				; oligos_6nt_mkv4_m3 versus positions_7nt_m2; m=5/5; ncol2=17; w=-6; offset=-6; strand=D; shift=0; score=0.454447; ssgCttGGCaGCCGCs ; cor=; Ncor= a 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 c 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 g 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 t 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---ssGCsssCGCssCCGCCGCCCsss ; Alignment reference a 0 0 0 802 856 267 381 404 407 324 350 262 282 289 255 301 273 285 242 461 306 239 273 354 375 616 844 c 0 0 0 3405 3346 1438 5816 1878 1947 2464 5825 1064 6177 1879 4755 5278 5715 1244 5592 5313 1226 5862 5254 5064 1872 3657 2652 g 0 0 0 2531 2397 5415 962 4744 4749 4377 959 5765 718 4853 2118 1498 1129 5544 1394 1302 5427 1030 1477 1598 4789 2557 3077 t 0 0 0 694 833 312 273 406 329 267 298 341 255 411 304 355 315 359 204 356 473 301 428 416 396 602 859
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---ssGCsssCGCssCCGCCGCCCsss ; cor=; Ncor= a 0 0 0 802 856 267 381 404 407 324 350 262 282 289 255 301 273 285 242 461 306 239 273 354 375 616 844 c 0 0 0 3405 3346 1438 5816 1878 1947 2464 5825 1064 6177 1879 4755 5278 5715 1244 5592 5313 1226 5862 5254 5064 1872 3657 2652 g 0 0 0 2531 2397 5415 962 4744 4749 4377 959 5765 718 4853 2118 1498 1129 5544 1394 1302 5427 1030 1477 1598 4789 2557 3077 t 0 0 0 694 833 312 273 406 329 267 298 341 255 411 304 355 315 359 204 356 473 301 428 416 396 602 859
positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)				; positions_7nt_m1 versus positions_7nt_m4_rc; m=2/4; ncol2=24; w=0; offset=2; strand=R; shift=5; score=0.673942; -----sssGCCGCsGCCGCCCgCCGCC ; cor=; Ncor= a 0 0 0 0 0 703 780 457 322 306 338 243 277 377 240 264 272 330 200 227 342 291 279 479 308 269 312 c 0 0 0 0 0 3075 3417 1952 1550 5745 5433 1415 5980 2131 1651 5592 5706 1340 5784 5217 5293 1645 5434 5053 1520 5630 5313 g 0 0 0 0 0 2905 2349 4566 5115 1008 1173 5329 857 4494 5102 1266 932 5185 1133 1531 1362 4981 1372 1397 4995 1142 1295 t 0 0 0 0 0 667 804 375 363 291 406 363 236 348 357 228 440 495 233 375 353 433 265 421 527 309 430
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=3/4; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.548696; sscGGGGCGGcGCGssGGGCGCss--- ; cor=; Ncor= a 765 614 377 355 398 460 313 491 343 239 497 197 462 223 237 507 281 358 272 501 320 265 764 644 0 0 0 c 2722 2674 4844 1246 1468 1538 1131 5209 1392 1380 4709 709 4917 1083 4716 4440 1372 1378 1151 5083 908 5266 2344 2370 0 0 0 g 2998 3188 1689 5242 5062 4938 5445 1279 5009 5343 1706 6016 1550 5492 2018 1853 5280 5192 5568 1301 5534 1400 3230 3477 0 0 0 t 712 721 287 354 269 261 308 218 453 235 285 275 268 399 226 397 264 269 206 312 435 266 859 706 0 0 0
oligos_7nt_mkv5_m2_shift8 (oligos_7nt_mkv5_m2)				; positions_7nt_m1 versus oligos_7nt_mkv5_m2; m=4/4; ncol2=12; w=0; offset=5; strand=D; shift=8; score=0.427293; --------ssCGCCCCCgss------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift9 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=9; ncol=21; ---------ssCGGCtGCGss ; Alignment reference a 0 0 0 0 0 0 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 2755 2976 c 0 0 0 0 0 0 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 8024 8987 g 0 0 0 0 0 0 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 10068 8620 t 0 0 0 0 0 0 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156
oligos_7nt_mkv5_m4_shift9 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=9; score= 1; ---------ssCGGCtGCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 2755 2976 c 0 0 0 0 0 0 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 8024 8987 g 0 0 0 0 0 0 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 10068 8620 t 0 0 0 0 0 0 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156
oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m2_rc; m=2/5; ncol2=12; w=0; offset=0; strand=R; shift=9; score=0.769998; ---------sscGGGGGCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4129 3726 2803 934 971 1176 1050 1304 1150 586 3673 4289 c 0 0 0 0 0 0 0 0 0 12013 11652 24236 3252 4931 6244 5120 2236 34377 1285 13293 11270 g 0 0 0 0 0 0 0 0 0 16802 17815 7154 31669 29983 28599 29928 32573 575 34228 16148 17323 t 0 0 0 0 0 0 0 0 0 4002 3753 2753 1091 1061 927 848 833 844 847 3832 4064
oligos_6nt_mkv4_m3_shift9 (oligos_6nt_mkv4_m3)				; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m3; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=9; score=0.704516; ---------ssCGGCCGss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 0 0 c 0 0 0 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 0 0 g 0 0 0 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 0 0 t 0 0 0 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509 0 0
positions_7nt_m2_rc_shift8 (positions_7nt_m2_rc)				; oligos_7nt_mkv5_m4 versus positions_7nt_m2_rc; m=4/5; ncol2=17; w=-1; offset=-1; strand=R; shift=8; score=0.567909; --------ssGCGGCtGCCaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 959 1094 209 344 458 146 171 371 132 163 254 3365 3536 c 0 0 0 0 0 0 0 0 2440 1943 406 4923 534 392 5231 829 446 5311 4753 992 1161 g 0 0 0 0 0 0 0 0 1792 1987 5171 386 4544 5210 400 1012 5186 357 731 1354 978 t 0 0 0 0 0 0 0 0 789 956 194 327 444 232 178 3768 216 149 242 269 305
positions_7nt_m4_shift0 (positions_7nt_m4)				; oligos_7nt_mkv5_m4 versus positions_7nt_m4; m=5/5; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.419536; ssGGCGGcGGGCGGCsGCGGC ; cor=; Ncor= a 768 960 430 309 527 421 265 433 353 375 233 495 440 228 357 348 236 363 406 291 363 c 2629 2614 1295 1142 4995 1397 1372 4981 1362 1531 1133 5185 932 1266 5102 4494 857 5329 1173 1008 5115 g 3269 3052 5313 5630 1520 5053 5434 1645 5293 5217 5784 1340 5706 5592 1651 2131 5980 1415 5433 5745 1550 t 684 724 312 269 308 479 279 291 342 227 200 330 272 264 240 377 277 243 338 306 322

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGCCCtCgss ; Alignment reference a 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCtCgss ; cor=; Ncor= a 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.897996; ssCGCCCCCgss ; cor=; Ncor= a 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m1; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.687685; ssCGCcCGss-- ; cor=; Ncor= a 4657 5308 275 963 978 2156 225 511 3532 5045 0 0 c 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 0 0 g 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 0 0 t 4776 3890 479 481 1754 2555 578 299 4683 4947 0 0
oligos_6nt_mkv4_m2_rc_shift0 (oligos_6nt_mkv4_m2_rc)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m2_rc; m=4/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.621952; ssCGCkCGss-- ; cor=; Ncor= a 3169 3720 418 645 450 2156 388 484 2384 3853 0 0 c 11847 8031 24381 692 24633 3792 25572 2251 11678 8780 0 0 g 7796 11936 1475 24686 978 7014 457 23151 8999 10187 0 0 t 3804 2929 342 593 555 13654 199 730 3555 3796 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ssCGGCCCGss ; Alignment reference a 4639 4281 1031 1932 605 439 520 1420 1087 4604 5305 c 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 12535 g 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 13556 t 4981 4908 1051 1848 902 439 1025 1276 1104 4225 4493
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGCCCGss ; cor=; Ncor= a 4639 4281 1031 1932 605 439 520 1420 1087 4604 5305 c 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 12535 g 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 13556 t 4981 4908 1051 1848 902 439 1025 1276 1104 4225 4493
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m1; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.664204; -ssCGCcCGss ; cor=; Ncor= a 0 4657 5308 275 963 978 2156 225 511 3532 5045 c 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 g 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 t 0 4776 3890 479 481 1754 2555 578 299 4683 4947
oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)				; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m3; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.647188; ssCGGCCGss- ; cor=; Ncor= a 4509 4870 250 351 978 1754 268 576 3846 4128 0 c 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 0 g 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 0 t 4128 3846 576 268 1754 978 351 250 4870 4509 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift5 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=5; ncol=17; -----ssCGCCCCCgss ; Alignment reference a 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129
oligos_7nt_mkv5_m2_shift5 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCGCCCCCgss ; cor=; Ncor= a 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129
oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=5; score=0.897996; -----ssCGCCCtCgss ; cor=; Ncor= a 0 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 0 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 0 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 0 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061
oligos_7nt_mkv5_m4_rc_shift5 (oligos_7nt_mkv5_m4_rc)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4_rc; m=3/5; ncol2=12; w=0; offset=0; strand=R; shift=5; score=0.769998; -----ssCGCaGCCGss ; cor=; Ncor= a 0 0 0 0 0 3156 2892 1300 622 392 13594 270 766 677 661 2677 3174 c 0 0 0 0 0 8620 10068 18188 1084 21556 5423 1136 21088 20646 1509 11960 8643 g 0 0 0 0 0 8987 8024 3085 21439 1322 3947 21919 1327 1624 20775 6386 8848 t 0 0 0 0 0 2976 2755 1166 594 469 775 414 558 792 794 2716 3074
oligos_6nt_mkv4_m1_shift5 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=4/5; ncol2=10; w=0; offset=0; strand=D; shift=5; score=0.650901; -----ssCGCcCGss-- ; cor=; Ncor= a 0 0 0 0 0 4657 5308 275 963 978 2156 225 511 3532 5045 0 0 c 0 0 0 0 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 0 0 g 0 0 0 0 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 0 0 t 0 0 0 0 0 4776 3890 479 481 1754 2555 578 299 4683 4947 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_7nt_mkv5_m2 versus positions_7nt_m1; m=5/5; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.427293; ssGCsssCGCssCCGCC ; cor=; Ncor= a 802 856 267 381 404 407 324 350 262 282 289 255 301 273 285 242 461 c 3405 3346 1438 5816 1878 1947 2464 5825 1064 6177 1879 4755 5278 5715 1244 5592 5313 g 2531 2397 5415 962 4744 4749 4377 959 5765 718 4853 2118 1498 1129 5544 1394 1302 t 694 833 312 273 406 329 267 298 341 255 411 304 355 315 359 204 356

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --ssCGmGCGss ; Alignment reference a 0 0 3796 3555 730 199 13654 555 593 342 2929 3804 c 0 0 10187 8999 23151 457 7014 978 24686 1475 11936 7796 g 0 0 8780 11678 2251 25572 3792 24633 692 24381 8031 11847 t 0 0 3853 2384 484 388 2156 450 645 418 3720 3169
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ssCGmGCGss ; cor=; Ncor= a 0 0 3796 3555 730 199 13654 555 593 342 2929 3804 c 0 0 10187 8999 23151 457 7014 978 24686 1475 11936 7796 g 0 0 8780 11678 2251 25572 3792 24633 692 24381 8031 11847 t 0 0 3853 2384 484 388 2156 450 645 418 3720 3169
oligos_6nt_mkv4_m1_rc_shift2 (oligos_6nt_mkv4_m1_rc)				; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m1_rc; m=2/4; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.92327; --ssCGgGCGss ; cor=; Ncor= a 0 0 4947 4683 299 578 2555 1754 481 479 3890 4776 c 0 0 14594 11798 33918 3296 7014 3580 34376 1055 15785 10762 g 0 0 11879 16452 1737 32366 24740 30153 645 34656 11482 16270 t 0 0 5045 3532 511 225 2156 978 963 275 5308 4657
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m5; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.666897; -ssCGGAGCGss ; cor=; Ncor= a 0 4147 4438 1172 1364 367 21283 250 1459 1420 4414 4612 c 0 10528 8928 24624 1253 1638 3017 484 25020 3468 9858 8095 g 0 9825 11285 1860 24938 26377 3567 27654 1289 21877 10412 11854 t 0 4085 3934 929 1030 203 718 197 817 1820 3901 4024
oligos_7nt_mkv5_m3_rc_shift0 (oligos_7nt_mkv5_m3_rc)				; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m3_rc; m=4/4; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.621952; sscGaGGGCGss ; cor=; Ncor= a 3061 2835 1667 307 12452 361 704 824 668 383 2703 2875 c 7016 6666 14070 950 4922 2131 3586 1112 19580 614 8452 6340 g 8592 9655 4274 19765 2890 18433 16303 18867 620 19833 7499 9671 t 2608 2121 1266 255 1013 352 684 474 409 447 2623 2391

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; ssgCttGGCaGCCGCss ; Alignment reference a 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 789 c 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 1792 g 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 2440 t 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094 959
positions_7nt_m2_shift0 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; ssgCttGGCaGCCGCss ; cor=; Ncor= a 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 789 c 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 1792 g 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 2440 t 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094 959
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_7nt_m2 versus positions_7nt_m3; m=2/5; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.640703; ssgCttGGCAGCAGCCA ; cor=; Ncor= a 217 233 144 45 92 73 53 53 71 743 43 64 755 45 72 46 764 c 320 282 172 868 161 150 84 109 858 121 65 859 114 72 835 886 92 g 304 319 565 96 140 199 851 831 91 85 905 96 92 890 98 79 116 t 215 222 175 47 663 634 68 63 36 107 43 37 95 49 51 45 84
oligos_7nt_mkv5_m4_rc_shift4 (oligos_7nt_mkv5_m4_rc)				; positions_7nt_m2 versus oligos_7nt_mkv5_m4_rc; m=3/5; ncol2=12; w=0; offset=4; strand=R; shift=4; score=0.567909; ----ssCGCaGCCGss- ; cor=; Ncor= a 0 0 0 0 3156 2892 1300 622 392 13594 270 766 677 661 2677 3174 0 c 0 0 0 0 8620 10068 18188 1084 21556 5423 1136 21088 20646 1509 11960 8643 0 g 0 0 0 0 8987 8024 3085 21439 1322 3947 21919 1327 1624 20775 6386 8848 0 t 0 0 0 0 2976 2755 1166 594 469 775 414 558 792 794 2716 3074 0
positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)				; positions_7nt_m2 versus positions_6nt_m4_rc; m=4/5; ncol2=24; w=0; offset=2; strand=R; shift=2; score=0.482816; --ssbbGGCrGCsGCGC ; cor=; Ncor= a 0 0 240 198 115 148 88 73 97 739 72 85 87 51 71 47 78 c 0 0 674 664 456 546 269 185 1320 346 180 1360 1155 149 1395 134 1386 g 0 0 652 722 608 485 1356 1486 324 597 1492 312 450 1539 278 1551 288 t 0 0 232 214 619 619 85 54 57 116 54 41 106 59 54 66 46
oligos_6nt_mkv4_m3_shift6 (oligos_6nt_mkv4_m3)				; positions_7nt_m2 versus oligos_6nt_mkv4_m3; m=5/5; ncol2=10; w=0; offset=6; strand=D; shift=6; score=0.454447; ------ssCGGCCGss- ; cor=; Ncor= a 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 0 c 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 0 g 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 0 t 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCGCcCGss ; Alignment reference a 0 4657 5308 275 963 978 2156 225 511 3532 5045 c 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 g 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 t 0 4776 3890 479 481 1754 2555 578 299 4683 4947
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ssCGCcCGss ; cor=; Ncor= a 0 4657 5308 275 963 978 2156 225 511 3532 5045 c 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 g 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 t 0 4776 3890 479 481 1754 2555 578 299 4683 4947
oligos_6nt_mkv4_m2_rc_shift1 (oligos_6nt_mkv4_m2_rc)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m2_rc; m=2/6; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.92327; -ssCGCkCGss ; cor=; Ncor= a 0 3169 3720 418 645 450 2156 388 484 2384 3853 c 0 11847 8031 24381 692 24633 3792 25572 2251 11678 8780 g 0 7796 11936 1475 24686 978 7014 457 23151 8999 10187 t 0 3804 2929 342 593 555 13654 199 730 3555 3796
oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m3; m=3/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.834572; -ssCGGCCGss ; cor=; Ncor= a 0 4509 4870 250 351 978 1754 268 576 3846 4128 c 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 g 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 t 0 4128 3846 576 268 1754 978 351 250 4870 4509
oligos_7nt_mkv5_m3_shift1 (oligos_7nt_mkv5_m3)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m3; m=4/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.687685; -ssCGCCCtCg ; cor=; Ncor= a 0 2391 2623 447 409 474 684 352 1013 255 1266 c 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 g 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 t 0 2875 2703 383 668 824 704 361 12452 307 1667
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m5; m=5/6; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.664204; ssCGGCCCGss ; cor=; Ncor= a 4639 4281 1031 1932 605 439 520 1420 1087 4604 5305 c 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 12535 g 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 13556 t 4981 4908 1051 1848 902 439 1025 1276 1104 4225 4493
oligos_7nt_mkv5_m2_shift1 (oligos_7nt_mkv5_m2)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m2; m=6/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.650901; -ssCGCCCCCg ; cor=; Ncor= a 0 4064 3832 847 844 833 848 927 1061 1091 2753 c 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 g 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 t 0 4289 3673 586 1150 1304 1050 1176 971 934 2803

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; sscGGGGCGGcGCGssGGGCGCss ; Alignment reference a 765 614 377 355 398 460 313 491 343 239 497 197 462 223 237 507 281 358 272 501 320 265 764 644 c 2722 2674 4844 1246 1468 1538 1131 5209 1392 1380 4709 709 4917 1083 4716 4440 1372 1378 1151 5083 908 5266 2344 2370 g 2998 3188 1689 5242 5062 4938 5445 1279 5009 5343 1706 6016 1550 5492 2018 1853 5280 5192 5568 1301 5534 1400 3230 3477 t 712 721 287 354 269 261 308 218 453 235 285 275 268 399 226 397 264 269 206 312 435 266 859 706
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; sscGGGGCGGcGCGssGGGCGCss ; cor=; Ncor= a 765 614 377 355 398 460 313 491 343 239 497 197 462 223 237 507 281 358 272 501 320 265 764 644 c 2722 2674 4844 1246 1468 1538 1131 5209 1392 1380 4709 709 4917 1083 4716 4440 1372 1378 1151 5083 908 5266 2344 2370 g 2998 3188 1689 5242 5062 4938 5445 1279 5009 5343 1706 6016 1550 5492 2018 1853 5280 5192 5568 1301 5534 1400 3230 3477 t 712 721 287 354 269 261 308 218 453 235 285 275 268 399 226 397 264 269 206 312 435 266 859 706
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_6nt_m1 versus positions_6nt_m4_rc; m=2/3; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.730689; ssbbGGCrGCsGCGCGGGGCGGss ; cor=; Ncor= a 240 198 115 148 88 73 97 739 72 85 87 51 71 47 78 92 71 88 57 130 80 66 231 198 c 674 664 456 546 269 185 1320 346 180 1360 1155 149 1395 134 1386 217 276 290 221 1393 213 283 607 518 g 652 722 608 485 1356 1486 324 597 1492 312 450 1539 278 1551 288 1409 1403 1355 1462 201 1392 1390 778 872 t 232 214 619 619 85 54 57 116 54 41 106 59 54 66 46 80 48 65 58 74 113 59 182 210
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=3/3; ncol2=24; w=0; offset=3; strand=D; shift=3; score=0.548696; ---ssGCsssCGCssCCGCCGCCC ; cor=; Ncor= a 0 0 0 802 856 267 381 404 407 324 350 262 282 289 255 301 273 285 242 461 306 239 273 354 c 0 0 0 3405 3346 1438 5816 1878 1947 2464 5825 1064 6177 1879 4755 5278 5715 1244 5592 5313 1226 5862 5254 5064 g 0 0 0 2531 2397 5415 962 4744 4749 4377 959 5765 718 4853 2118 1498 1129 5544 1394 1302 5427 1030 1477 1598 t 0 0 0 694 833 312 273 406 329 267 298 341 255 411 304 355 315 359 204 356 473 301 428 416

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=24; shift=5; ncol=29; -----ssGGCGGcGGGCGGCsGCGGCsss ; Alignment reference a 0 0 0 0 0 768 960 430 309 527 421 265 433 353 375 233 495 440 228 357 348 236 363 406 291 363 375 804 667 c 0 0 0 0 0 2629 2614 1295 1142 4995 1397 1372 4981 1362 1531 1133 5185 932 1266 5102 4494 857 5329 1173 1008 5115 4566 2349 2905 g 0 0 0 0 0 3269 3052 5313 5630 1520 5053 5434 1645 5293 5217 5784 1340 5706 5592 1651 2131 5980 1415 5433 5745 1550 1952 3417 3075 t 0 0 0 0 0 684 724 312 269 308 479 279 291 342 227 200 330 272 264 240 377 277 243 338 306 322 457 780 703
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----ssGGCGGcGGGCGGCsGCGGCsss ; cor=; Ncor= a 0 0 0 0 0 768 960 430 309 527 421 265 433 353 375 233 495 440 228 357 348 236 363 406 291 363 375 804 667 c 0 0 0 0 0 2629 2614 1295 1142 4995 1397 1372 4981 1362 1531 1133 5185 932 1266 5102 4494 857 5329 1173 1008 5115 4566 2349 2905 g 0 0 0 0 0 3269 3052 5313 5630 1520 5053 5434 1645 5293 5217 5784 1340 5706 5592 1651 2131 5980 1415 5433 5745 1550 1952 3417 3075 t 0 0 0 0 0 684 724 312 269 308 479 279 291 342 227 200 330 272 264 240 377 277 243 338 306 322 457 780 703
positions_7nt_m1_rc_shift7 (positions_7nt_m1_rc)				; positions_7nt_m4 versus positions_7nt_m1_rc; m=2/4; ncol2=24; w=0; offset=2; strand=R; shift=7; score=0.673942; -------sssGGGCGGCGGssGCGsssGC ; cor=; Ncor= a 0 0 0 0 0 0 0 859 602 396 416 428 301 473 356 204 359 315 355 304 411 255 341 298 267 329 406 273 312 c 0 0 0 0 0 0 0 3077 2557 4789 1598 1477 1030 5427 1302 1394 5544 1129 1498 2118 4853 718 5765 959 4377 4749 4744 962 5415 g 0 0 0 0 0 0 0 2652 3657 1872 5064 5254 5862 1226 5313 5592 1244 5715 5278 4755 1879 6177 1064 5825 2464 1947 1878 5816 1438 t 0 0 0 0 0 0 0 844 616 375 354 273 239 306 461 242 285 273 301 255 289 282 262 350 324 407 404 381 267
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_7nt_m4 versus positions_6nt_m4_rc; m=3/4; ncol2=24; w=-5; offset=-5; strand=R; shift=0; score=0.477205; ssbbGGCrGCsGCGCGGGGCGGss----- ; cor=; Ncor= a 240 198 115 148 88 73 97 739 72 85 87 51 71 47 78 92 71 88 57 130 80 66 231 198 0 0 0 0 0 c 674 664 456 546 269 185 1320 346 180 1360 1155 149 1395 134 1386 217 276 290 221 1393 213 283 607 518 0 0 0 0 0 g 652 722 608 485 1356 1486 324 597 1492 312 450 1539 278 1551 288 1409 1403 1355 1462 201 1392 1390 778 872 0 0 0 0 0 t 232 214 619 619 85 54 57 116 54 41 106 59 54 66 46 80 48 65 58 74 113 59 182 210 0 0 0 0 0
oligos_7nt_mkv5_m4_shift14 (oligos_7nt_mkv5_m4)				; positions_7nt_m4 versus oligos_7nt_mkv5_m4; m=4/4; ncol2=12; w=0; offset=9; strand=D; shift=14; score=0.419536; --------------ssCGGCtGCGss--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 2755 2976 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 8024 8987 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 10068 8620 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156 0 0 0