One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/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.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 4 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=19; shift=0; ncol=19; wwTTAAAAATAAwAwAAww ; Alignment reference a 2672 2970 1245 1203 6314 6426 6472 6485 6583 1534 6431 6166 2090 6267 2064 6133 6149 3291 2951 c 1240 1182 763 370 394 426 344 374 319 436 413 694 447 374 582 483 424 1112 1285 g 1132 1118 458 464 399 404 348 322 407 412 421 356 405 497 481 420 447 1138 1146 t 2995 2769 5573 6002 932 783 875 858 730 5657 774 823 5097 901 4912 1003 1019 2498 2657

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAATAAwAwAAww ; cor=; Ncor= a 2672 2970 1245 1203 6314 6426 6472 6485 6583 1534 6431 6166 2090 6267 2064 6133 6149 3291 2951 c 1240 1182 763 370 394 426 344 374 319 436 413 694 447 374 582 483 424 1112 1285 g 1132 1118 458 464 399 404 348 322 407 412 421 356 405 497 481 420 447 1138 1146 t 2995 2769 5573 6002 932 783 875 858 730 5657 774 823 5097 901 4912 1003 1019 2498 2657

oligos_7nt_mkv5_m1_rc_shift1 (oligos_7nt_mkv5_m1_rc)
; positions_6nt_m2 versus oligos_7nt_mkv5_m1_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.519322; -wwTAAAAATaw------- ; cor=; Ncor= a 0 17108 17001 2963 43003 43712 46328 44355 44861 2303 19148 18363 0 0 0 0 0 0 0 c 0 7532 9367 1846 1548 1899 1128 1831 1880 2187 8367 10772 0 0 0 0 0 0 0 g 0 9121 8249 1972 2302 2434 1549 1606 1691 1930 10974 7692 0 0 0 0 0 0 0 t 0 17323 16467 44303 4231 3039 2079 3292 2652 44664 12595 14257 0 0 0 0 0 0 0

positions_6nt_m4_shift4 (positions_6nt_m4)
; positions_6nt_m2 versus positions_6nt_m4; m=3/3; ncol2=19; w=0; offset=4; strand=D; shift=4; score=0.497609; ----wwAAATAAAATATAT ; cor=; Ncor= a 0 0 0 0 2282 2364 4799 4622 4691 969 4661 4793 4661 4881 845 4741 916 4692 714 c 0 0 0 0 825 883 319 352 278 388 298 342 346 261 395 336 453 343 270 g 0 0 0 0 1158 953 339 347 379 461 394 344 279 333 317 476 311 446 287 t 0 0 0 0 1821 1886 629 765 738 4268 733 607 800 611 4529 533 4406 605 4815

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift2 ; 3 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=24; shift=2; ncol=26; --ssGCaGCaGCtGGCAGCCaGCass ; Alignment reference a 0 0 222 202 61 53 604 48 48 574 37 43 101 51 46 65 637 36 75 67 585 37 60 589 162 170 c 0 0 282 231 117 711 106 67 731 120 94 732 110 81 117 701 83 115 675 703 94 81 674 129 270 306 g 0 0 258 299 679 98 94 755 97 107 715 81 98 732 683 114 107 708 104 92 127 736 129 120 334 271 t 0 0 138 168 43 38 96 30 24 99 54 44 591 36 54 20 73 41 46 38 94 46 37 62 134 153

positions_7nt_m4_shift2 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/2; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssGCaGCaGCtGGCAGCCaGCass ; cor=; Ncor= a 0 0 222 202 61 53 604 48 48 574 37 43 101 51 46 65 637 36 75 67 585 37 60 589 162 170 c 0 0 282 231 117 711 106 67 731 120 94 732 110 81 117 701 83 115 675 703 94 81 674 129 270 306 g 0 0 258 299 679 98 94 755 97 107 715 81 98 732 683 114 107 708 104 92 127 736 129 120 334 271 t 0 0 138 168 43 38 96 30 24 99 54 44 591 36 54 20 73 41 46 38 94 46 37 62 134 153

positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc)
; positions_7nt_m4 versus positions_7nt_m2_rc; m=2/2; ncol2=17; w=-2; offset=-2; strand=R; shift=0; score=0.408051; ssmGGCaGCaGCcGCsg--------- ; cor=; Ncor= a 1669 1154 4429 545 351 365 4889 201 307 4742 183 289 732 532 276 1343 1120 0 0 0 0 0 0 0 0 0 c 3068 2741 2968 1559 609 7972 1812 378 7995 1984 395 8122 6225 484 7956 3252 2169 0 0 0 0 0 0 0 0 0 g 3287 4452 1183 6692 7926 607 1838 8326 705 1924 8372 539 1600 7776 624 3157 4709 0 0 0 0 0 0 0 0 0 t 1138 815 582 366 276 218 623 257 155 512 212 212 605 370 306 1410 1164 0 0 0 0 0 0 0 0 0

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_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCGGCCGss ; Alignment reference 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_6nt_mkv4_m3_shift1 (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=1; score= 1; -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_6nt_mkv4_m1_rc_shift1 (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=1; score=0.834572; -ssCGgGCGss ; cor=; Ncor= a 0 4947 4683 299 578 2555 1754 481 479 3890 4776 c 0 14594 11798 33918 3296 7014 3580 34376 1055 15785 10762 g 0 11879 16452 1737 32366 24740 30153 645 34656 11482 16270 t 0 5045 3532 511 225 2156 978 963 275 5308 4657

oligos_7nt_mkv5_m4_shift1 (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=1; score=0.704516; -ssCGGCtGCG ; cor=; Ncor= a 0 3074 2716 794 792 558 414 775 469 594 1166 c 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 g 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 t 0 3174 2677 661 677 766 270 13594 392 622 1300

oligos_7nt_mkv5_m5_shift1 (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=1; score=0.647188; -ssCGGCCCGs ; cor=; Ncor= a 0 4639 4281 1031 1932 605 439 520 1420 1087 4604 c 0 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 g 0 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 t 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=-1; offset=-1; strand=D; shift=0; score=0.473197; csGCgGCtGCt ; cor=; Ncor= a 1164 1410 306 370 605 212 212 512 155 257 623 c 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 g 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 t 1120 1343 276 532 732 289 183 4742 307 201 4889

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wtATTTAAww ; Alignment reference a 9973 5592 26183 960 4053 989 25397 21809 9547 9082 c 4145 5185 76 479 520 102 164 1423 4827 4536 g 5742 3536 517 486 1822 74 99 470 3538 4670 t 7203 12750 287 25138 20668 25898 1403 3361 9151 8775

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wtATTTAAww ; cor=; Ncor= a 9973 5592 26183 960 4053 989 25397 21809 9547 9082 c 4145 5185 76 479 520 102 164 1423 4827 4536 g 5742 3536 517 486 1822 74 99 470 3538 4670 t 7203 12750 287 25138 20668 25898 1403 3361 9151 8775

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift12 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift12 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=12; ncol=24; ------------ssCGGCtGCGss ; Alignment reference a 0 0 0 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 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 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 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156

oligos_7nt_mkv5_m4_shift12 (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=12; score= 1; ------------ssCGGCtGCGss ; cor=; Ncor= a 0 0 0 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 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 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 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156

oligos_7nt_mkv5_m2_rc_shift12 (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=12; score=0.769998; ------------sscGGGGGCGss ; cor=; Ncor= a 0 0 0 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 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 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 0 0 0 4002 3753 2753 1091 1061 927 848 833 844 847 3832 4064

oligos_6nt_mkv4_m3_shift12 (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=12; score=0.704516; ------------ssCGGCCGss-- ; cor=; Ncor= a 0 0 0 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 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 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 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509 0 0

positions_7nt_m2_shift11 (positions_7nt_m2)
; oligos_7nt_mkv5_m4 versus positions_7nt_m2; m=4/5; ncol2=17; w=-1; offset=-1; strand=D; shift=11; score=0.593243; -----------csGCgGCtGCtGC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 c 0 0 0 0 0 0 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 g 0 0 0 0 0 0 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 t 0 0 0 0 0 0 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351

positions_6nt_m1_shift0 (positions_6nt_m1)
; oligos_7nt_mkv5_m4 versus positions_6nt_m1; m=5/5; ncol2=24; w=-12; offset=-12; strand=D; shift=0; score=0.437508; ssGGmGCCGCsCGGCkGCtGCGss ; cor=; Ncor= a 203 277 101 76 857 77 89 106 81 75 72 90 87 63 79 139 47 38 130 45 97 84 222 220 c 788 691 231 325 483 216 1352 1299 200 1360 1172 1344 238 220 1452 400 252 1557 438 232 1437 255 692 676 g 609 604 1416 1347 368 1442 299 287 1402 306 463 284 1401 1463 218 513 1433 170 433 1459 190 1359 712 707 t 205 233 57 57 97 70 65 113 122 64 98 87 79 59 56 753 73 40 804 69 81 107 179 202

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift4 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=4; ncol=16; ----ssCGCCCtCgss ; Alignment reference a 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCGCCCtCgss ; cor=; Ncor= a 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=4; score=0.897996; ----ssCGCCCCCgss ; cor=; Ncor= a 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129

oligos_6nt_mkv4_m1_shift4 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m1; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.687685; ----ssCGCcCGss-- ; cor=; Ncor= a 0 0 0 0 4657 5308 275 963 978 2156 225 511 3532 5045 0 0 c 0 0 0 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 0 0 g 0 0 0 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 0 0 t 0 0 0 0 4776 3890 479 481 1754 2555 578 299 4683 4947 0 0

oligos_6nt_mkv4_m2_rc_shift4 (oligos_6nt_mkv4_m2_rc)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m2_rc; m=4/5; ncol2=10; w=0; offset=0; strand=R; shift=4; score=0.621952; ----ssCGCkCGss-- ; cor=; Ncor= a 0 0 0 0 3169 3720 418 645 450 2156 388 484 2384 3853 0 0 c 0 0 0 0 11847 8031 24381 692 24633 3792 25572 2251 11678 8780 0 0 g 0 0 0 0 7796 11936 1475 24686 978 7014 457 23151 8999 10187 0 0 t 0 0 0 0 3804 2929 342 593 555 13654 199 730 3555 3796 0 0

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_7nt_mkv5_m3 versus positions_7nt_m1; m=5/5; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.420301; sssCcCCGCCCsCgCC ; cor=; Ncor= a 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 c 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 g 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 t 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift7 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift7 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=7; ncol=18; -------wtATTTTTAww ; Alignment reference a 0 0 0 0 0 0 0 14257 12595 44664 2652 3292 2079 3039 4231 44303 16467 17323 c 0 0 0 0 0 0 0 7692 10974 1930 1691 1606 1549 2434 2302 1972 8249 9121 g 0 0 0 0 0 0 0 10772 8367 2187 1880 1831 1128 1899 1548 1846 9367 7532 t 0 0 0 0 0 0 0 18363 19148 2303 44861 44355 46328 43712 43003 2963 17001 17108

oligos_7nt_mkv5_m1_shift7 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------wtATTTTTAww ; cor=; Ncor= a 0 0 0 0 0 0 0 14257 12595 44664 2652 3292 2079 3039 4231 44303 16467 17323 c 0 0 0 0 0 0 0 7692 10974 1930 1691 1606 1549 2434 2302 1972 8249 9121 g 0 0 0 0 0 0 0 10772 8367 2187 1880 1831 1128 1899 1548 1846 9367 7532 t 0 0 0 0 0 0 0 18363 19148 2303 44861 44355 46328 43712 43003 2963 17001 17108

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; oligos_7nt_mkv5_m1 versus positions_6nt_m2_rc; m=2/2; ncol2=19; w=-7; offset=-7; strand=R; shift=0; score=0.519322; wwTTwTwTTATTTTTAAw ; cor=; Ncor= a 2657 2498 1019 1003 4912 901 5097 823 774 5657 730 858 875 783 932 6002 5573 2769 c 1146 1138 447 420 481 497 405 356 421 412 407 322 348 404 399 464 458 1118 g 1285 1112 424 483 582 374 447 694 413 436 319 374 344 426 394 370 763 1182 t 2951 3291 6149 6133 2064 6267 2090 6166 6431 1534 6583 6485 6472 6426 6314 1203 1245 2970

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_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; ssCsCCGCCCCGCsCCCGCCbCss ; Alignment reference a 718 584 303 319 210 457 299 248 206 186 282 228 319 296 200 243 291 334 233 301 408 213 650 654 c 3670 3512 6043 2175 6008 5586 1441 6128 5526 5734 6024 1706 6092 2047 5882 5822 6046 1483 5842 5901 2481 6108 3598 3380 g 2425 2574 937 4508 1091 1182 5254 929 1375 1317 921 5262 845 4788 1173 1114 901 5161 1250 990 2106 944 2347 2624 t 771 914 301 582 275 359 590 279 477 347 357 388 328 453 329 405 346 606 259 392 2589 319 989 926

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ssCsCCGCCCCGCsCCCGCCbCss ; cor=; Ncor= a 718 584 303 319 210 457 299 248 206 186 282 228 319 296 200 243 291 334 233 301 408 213 650 654 c 3670 3512 6043 2175 6008 5586 1441 6128 5526 5734 6024 1706 6092 2047 5882 5822 6046 1483 5842 5901 2481 6108 3598 3380 g 2425 2574 937 4508 1091 1182 5254 929 1375 1317 921 5262 845 4788 1173 1114 901 5161 1250 990 2106 944 2347 2624 t 771 914 301 582 275 359 590 279 477 347 357 388 328 453 329 405 346 606 259 392 2589 319 989 926

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_6nt_m5 versus positions_7nt_m1; m=2/3; ncol2=24; w=0; offset=1; strand=D; shift=1; score= 0.6663; -sssCcCCGCCCsCgCCGCCcCss ; cor=; Ncor= a 0 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 307 311 296 369 454 434 900 c 0 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 1844 7761 7216 6517 7462 2951 4289 g 0 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 6863 1255 1679 2315 1398 5777 3620 t 0 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400 732 419 555 545 432 584 937

oligos_7nt_mkv5_m2_shift8 (oligos_7nt_mkv5_m2)
; positions_6nt_m5 versus oligos_7nt_mkv5_m2; m=3/3; ncol2=12; w=0; offset=8; strand=D; shift=8; score=0.428076; --------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 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 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 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

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=24; shift=1; ncol=25; -sssCcCCGCCCsCgCCGCCcCsss ; Alignment reference a 0 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 307 311 296 369 454 434 900 878 c 0 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 1844 7761 7216 6517 7462 2951 4289 4584 g 0 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 6863 1255 1679 2315 1398 5777 3620 3245 t 0 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400 732 419 555 545 432 584 937 1039

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -sssCcCCGCCCsCgCCGCCcCsss ; cor=; Ncor= a 0 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 307 311 296 369 454 434 900 878 c 0 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 1844 7761 7216 6517 7462 2951 4289 4584 g 0 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 6863 1255 1679 2315 1398 5777 3620 3245 t 0 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400 732 419 555 545 432 584 937 1039

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_7nt_m1 versus positions_6nt_m5; m=2/4; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score= 0.6663; ssCsCCGCCCCGCsCCCGCCbCss- ; cor=; Ncor= a 718 584 303 319 210 457 299 248 206 186 282 228 319 296 200 243 291 334 233 301 408 213 650 654 0 c 3670 3512 6043 2175 6008 5586 1441 6128 5526 5734 6024 1706 6092 2047 5882 5822 6046 1483 5842 5901 2481 6108 3598 3380 0 g 2425 2574 937 4508 1091 1182 5254 929 1375 1317 921 5262 845 4788 1173 1114 901 5161 1250 990 2106 944 2347 2624 0 t 771 914 301 582 275 359 590 279 477 347 357 388 328 453 329 405 346 606 259 392 2589 319 989 926 0

oligos_7nt_mkv5_m2_shift5 (oligos_7nt_mkv5_m2)
; positions_7nt_m1 versus oligos_7nt_mkv5_m2; m=3/4; ncol2=12; w=0; offset=4; strand=D; shift=5; score=0.433443; -----ssCGCCCCCgss-------- ; cor=; Ncor= a 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 0 0 0 0 0 0 0 0 c 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 0 0 0 0 0 0 0 0 g 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 0 0 0 0 0 0 0 0 t 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129 0 0 0 0 0 0 0 0

oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)
; positions_7nt_m1 versus oligos_7nt_mkv5_m3; m=4/4; ncol2=12; w=0; offset=4; strand=D; shift=5; score=0.420301; -----ssCGCCCtCgss-------- ; cor=; Ncor= a 0 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 0 0 0 0 0 0 0 0 c 0 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 0 0 0 0 0 0 0 0 g 0 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 0 0 0 0 0 0 0 0 t 0 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift4 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=19; shift=4; ncol=23; ----wwAAATAAAATATATgTww ; Alignment reference a 0 0 0 0 2282 2364 4799 4622 4691 969 4661 4793 4661 4881 845 4741 916 4692 714 1348 744 2186 1862 c 0 0 0 0 825 883 319 352 278 388 298 342 346 261 395 336 453 343 270 457 424 887 1120 g 0 0 0 0 1158 953 339 347 379 461 394 344 279 333 317 476 311 446 287 3149 318 1225 932 t 0 0 0 0 1821 1886 629 765 738 4268 733 607 800 611 4529 533 4406 605 4815 1132 4600 1788 2172

positions_6nt_m4_shift4 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=4; score= 1; ----wwAAATAAAATATATgTww ; cor=; Ncor= a 0 0 0 0 2282 2364 4799 4622 4691 969 4661 4793 4661 4881 845 4741 916 4692 714 1348 744 2186 1862 c 0 0 0 0 825 883 319 352 278 388 298 342 346 261 395 336 453 343 270 457 424 887 1120 g 0 0 0 0 1158 953 339 347 379 461 394 344 279 333 317 476 311 446 287 3149 318 1225 932 t 0 0 0 0 1821 1886 629 765 738 4268 733 607 800 611 4529 533 4406 605 4815 1132 4600 1788 2172

positions_7nt_m3_shift6 (positions_7nt_m3)
; positions_6nt_m4 versus positions_7nt_m3; m=2/3; ncol2=18; w=0; offset=2; strand=D; shift=6; score=0.605906; ------wwATAAAATATTTTATw ; cor=; Ncor= a 0 0 0 0 0 0 2170 2070 4605 879 4647 4499 4507 4696 526 4788 692 853 829 702 4261 773 2031 c 0 0 0 0 0 0 786 1049 296 375 293 344 394 254 404 279 358 246 328 352 482 321 847 g 0 0 0 0 0 0 1094 845 322 482 353 327 244 357 278 403 254 395 346 292 374 296 1048 t 0 0 0 0 0 0 1946 2032 773 4260 703 826 851 689 4788 526 4692 4502 4493 4650 879 4606 2070

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m4 versus positions_6nt_m2; m=3/3; ncol2=19; w=-4; offset=-4; strand=D; shift=0; score=0.497609; wwTTAAAAATAAwAwAAww---- ; cor=; Ncor= a 2672 2970 1245 1203 6314 6426 6472 6485 6583 1534 6431 6166 2090 6267 2064 6133 6149 3291 2951 0 0 0 0 c 1240 1182 763 370 394 426 344 374 319 436 413 694 447 374 582 483 424 1112 1285 0 0 0 0 g 1132 1118 458 464 399 404 348 322 407 412 421 356 405 497 481 420 447 1138 1146 0 0 0 0 t 2995 2769 5573 6002 932 783 875 858 730 5657 774 823 5097 901 4912 1003 1019 2498 2657 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift9 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift9 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=17; shift=9; ncol=26; ---------csGCgGCtGCtGCCkss ; Alignment reference a 0 0 0 0 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 366 582 815 1138 c 0 0 0 0 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 6692 1183 4452 3287 g 0 0 0 0 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 1559 2968 2741 3068 t 0 0 0 0 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351 545 4429 1154 1669

positions_7nt_m2_shift9 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=9; score= 1; ---------csGCgGCtGCtGCCkss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 366 582 815 1138 c 0 0 0 0 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 6692 1183 4452 3287 g 0 0 0 0 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 1559 2968 2741 3068 t 0 0 0 0 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351 545 4429 1154 1669

oligos_7nt_mkv5_m4_shift10 (oligos_7nt_mkv5_m4)
; positions_7nt_m2 versus oligos_7nt_mkv5_m4; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=10; score=0.593243; ----------ssCGGCtGCGss---- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m2 versus positions_6nt_m1; m=3/5; ncol2=24; w=-8; offset=-8; strand=D; shift=1; score=0.48742; -ssGGmGCCGCsCGGCkGCtGCGss- ; cor=; Ncor= a 0 203 277 101 76 857 77 89 106 81 75 72 90 87 63 79 139 47 38 130 45 97 84 222 220 0 c 0 788 691 231 325 483 216 1352 1299 200 1360 1172 1344 238 220 1452 400 252 1557 438 232 1437 255 692 676 0 g 0 609 604 1416 1347 368 1442 299 287 1402 306 463 284 1401 1463 218 513 1433 170 433 1459 190 1359 712 707 0 t 0 205 233 57 57 97 70 65 113 122 64 98 87 79 59 56 753 73 40 804 69 81 107 179 202 0

oligos_6nt_mkv4_m3_shift10 (oligos_6nt_mkv4_m3)
; positions_7nt_m2 versus oligos_6nt_mkv4_m3; m=4/5; ncol2=10; w=0; offset=1; strand=D; shift=10; score=0.473197; ----------ssCGGCCGss------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509 0 0 0 0 0 0

positions_7nt_m4_rc_shift0 (positions_7nt_m4_rc)
; positions_7nt_m2 versus positions_7nt_m4_rc; m=5/5; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.408051; sstGCtGGCTGCCaGCtGCtGCss-- ; cor=; Ncor= a 153 134 62 37 46 94 38 46 41 73 20 54 36 591 44 54 99 24 30 96 38 43 168 138 0 0 c 271 334 120 129 736 127 92 104 708 107 114 683 732 98 81 715 107 97 755 94 98 679 299 258 0 0 g 306 270 129 674 81 94 703 675 115 83 701 117 81 110 732 94 120 731 67 106 711 117 231 282 0 0 t 170 162 589 60 37 585 67 75 36 637 65 46 51 101 43 37 574 48 48 604 53 61 202 222 0 0

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: positions_7nt_m3_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift2 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=18; shift=2; ncol=20; --wwATAAAATATTTTATww ; Alignment reference a 0 0 2170 2070 4605 879 4647 4499 4507 4696 526 4788 692 853 829 702 4261 773 2031 1953 c 0 0 786 1049 296 375 293 344 394 254 404 279 358 246 328 352 482 321 847 1095 g 0 0 1094 845 322 482 353 327 244 357 278 403 254 395 346 292 374 296 1048 785 t 0 0 1946 2032 773 4260 703 826 851 689 4788 526 4692 4502 4493 4650 879 4606 2070 2163

positions_7nt_m3_shift2 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/2; ncol2=18; w=0; offset=0; strand=D; shift=2; score= 1; --wwATAAAATATTTTATww ; cor=; Ncor= a 0 0 2170 2070 4605 879 4647 4499 4507 4696 526 4788 692 853 829 702 4261 773 2031 1953 c 0 0 786 1049 296 375 293 344 394 254 404 279 358 246 328 352 482 321 847 1095 g 0 0 1094 845 322 482 353 327 244 357 278 403 254 395 346 292 374 296 1048 785 t 0 0 1946 2032 773 4260 703 826 851 689 4788 526 4692 4502 4493 4650 879 4606 2070 2163

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_7nt_m3 versus positions_6nt_m4; m=2/2; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.605906; wwAAATAAAATATATgTww- ; cor=; Ncor= a 2282 2364 4799 4622 4691 969 4661 4793 4661 4881 845 4741 916 4692 714 1348 744 2186 1862 0 c 825 883 319 352 278 388 298 342 346 261 395 336 453 343 270 457 424 887 1120 0 g 1158 953 339 347 379 461 394 344 279 333 317 476 311 446 287 3149 318 1225 932 0 t 1821 1886 629 765 738 4268 733 607 800 611 4529 533 4406 605 4815 1132 4600 1788 2172 0

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_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: oligos_7nt_mkv5_m2_shift8 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift8 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=8; ncol=20; --------ssCGCCCCCgss ; Alignment reference a 0 0 0 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129

oligos_7nt_mkv5_m2_shift8 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=8; score= 1; --------ssCGCCCCCgss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129

oligos_7nt_mkv5_m3_shift8 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=2/6; ncol2=12; w=0; offset=0; strand=D; shift=8; score=0.897996; --------ssCGCCCtCgss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 0 0 0 0 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 0 0 0 0 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 0 0 0 0 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061

oligos_7nt_mkv5_m4_rc_shift8 (oligos_7nt_mkv5_m4_rc)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4_rc; m=3/6; ncol2=12; w=0; offset=0; strand=R; shift=8; score=0.769998; --------ssCGCaGCCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 3156 2892 1300 622 392 13594 270 766 677 661 2677 3174 c 0 0 0 0 0 0 0 0 8620 10068 18188 1084 21556 5423 1136 21088 20646 1509 11960 8643 g 0 0 0 0 0 0 0 0 8987 8024 3085 21439 1322 3947 21919 1327 1624 20775 6386 8848 t 0 0 0 0 0 0 0 0 2976 2755 1166 594 469 775 414 558 792 794 2716 3074

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=4/6; ncol2=10; w=0; offset=0; strand=D; shift=8; score=0.650901; --------ssCGCcCGss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4657 5308 275 963 978 2156 225 511 3532 5045 0 0 c 0 0 0 0 0 0 0 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 0 0 g 0 0 0 0 0 0 0 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 0 0 t 0 0 0 0 0 0 0 0 4776 3890 479 481 1754 2555 578 299 4683 4947 0 0

positions_7nt_m1_shift4 (positions_7nt_m1)
; oligos_7nt_mkv5_m2 versus positions_7nt_m1; m=5/6; ncol2=24; w=-4; offset=-4; strand=D; shift=4; score=0.433443; ----sssCcCCGCCCsCgCC ; cor=; Ncor= a 0 0 0 0 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 c 0 0 0 0 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 g 0 0 0 0 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 t 0 0 0 0 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400

positions_6nt_m5_shift0 (positions_6nt_m5)
; oligos_7nt_mkv5_m2 versus positions_6nt_m5; m=6/6; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.428076; ssCsCCGCCCCGCsCCCGCC ; cor=; Ncor= a 718 584 303 319 210 457 299 248 206 186 282 228 319 296 200 243 291 334 233 301 c 3670 3512 6043 2175 6008 5586 1441 6128 5526 5734 6024 1706 6092 2047 5882 5822 6046 1483 5842 5901 g 2425 2574 937 4508 1091 1182 5254 929 1375 1317 921 5262 845 4788 1173 1114 901 5161 1250 990 t 771 914 301 582 275 359 590 279 477 347 357 388 328 453 329 405 346 606 259 392

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; ssGGmGCCGCsCGGCkGCtGCGss ; Alignment reference a 203 277 101 76 857 77 89 106 81 75 72 90 87 63 79 139 47 38 130 45 97 84 222 220 c 788 691 231 325 483 216 1352 1299 200 1360 1172 1344 238 220 1452 400 252 1557 438 232 1437 255 692 676 g 609 604 1416 1347 368 1442 299 287 1402 306 463 284 1401 1463 218 513 1433 170 433 1459 190 1359 712 707 t 205 233 57 57 97 70 65 113 122 64 98 87 79 59 56 753 73 40 804 69 81 107 179 202

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; ssGGmGCCGCsCGGCkGCtGCGss ; cor=; Ncor= a 203 277 101 76 857 77 89 106 81 75 72 90 87 63 79 139 47 38 130 45 97 84 222 220 c 788 691 231 325 483 216 1352 1299 200 1360 1172 1344 238 220 1452 400 252 1557 438 232 1437 255 692 676 g 609 604 1416 1347 368 1442 299 287 1402 306 463 284 1401 1463 218 513 1433 170 433 1459 190 1359 712 707 t 205 233 57 57 97 70 65 113 122 64 98 87 79 59 56 753 73 40 804 69 81 107 179 202

positions_7nt_m2_shift8 (positions_7nt_m2)
; positions_6nt_m1 versus positions_7nt_m2; m=2/3; ncol2=17; w=0; offset=8; strand=D; shift=8; score=0.48742; --------csGCgGCtGCtGCCks ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 366 582 815 c 0 0 0 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 6692 1183 4452 g 0 0 0 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 1559 2968 2741 t 0 0 0 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351 545 4429 1154

oligos_7nt_mkv5_m4_shift12 (oligos_7nt_mkv5_m4)
; positions_6nt_m1 versus oligos_7nt_mkv5_m4; m=3/3; ncol2=12; w=0; offset=12; strand=D; shift=12; score=0.437508; ------------ssCGGCtGCGss ; cor=; Ncor= a 0 0 0 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 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 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 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 2 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=24; shift=0; ncol=24; sgGCCtGGCaGCCaGCtGGCtGss ; Alignment reference a 170 173 48 42 60 86 34 50 44 542 38 56 41 530 33 41 104 33 42 40 92 41 110 150 c 298 199 95 645 670 124 92 105 658 108 99 629 701 113 70 681 136 79 114 674 106 79 310 255 g 242 274 625 91 57 97 668 645 106 81 639 115 60 113 705 76 134 681 623 80 99 670 258 280 t 125 189 67 57 48 528 41 35 27 104 59 35 33 79 27 37 461 42 56 41 538 45 157 150

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/1; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; sgGCCtGGCaGCCaGCtGGCtGss ; cor=; Ncor= a 170 173 48 42 60 86 34 50 44 542 38 56 41 530 33 41 104 33 42 40 92 41 110 150 c 298 199 95 645 670 124 92 105 658 108 99 629 701 113 70 681 136 79 114 674 106 79 310 255 g 242 274 625 91 57 97 668 645 106 81 639 115 60 113 705 76 134 681 623 80 99 670 258 280 t 125 189 67 57 48 528 41 35 27 104 59 35 33 79 27 37 461 42 56 41 538 45 157 150

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=19; shift=0; ncol=19; wwTTAAAAATAAwAwAAww ; Alignment reference a 2672 2970 1245 1203 6314 6426 6472 6485 6583 1534 6431 6166 2090 6267 2064 6133 6149 3291 2951 c 1240 1182 763 370 394 426 344 374 319 436 413 694 447 374 582 483 424 1112 1285 g 1132 1118 458 464 399 404 348 322 407 412 421 356 405 497 481 420 447 1138 1146 t 2995 2769 5573 6002 932 783 875 858 730 5657 774 823 5097 901 4912 1003 1019 2498 2657
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAATAAwAwAAww ; cor=; Ncor= a 2672 2970 1245 1203 6314 6426 6472 6485 6583 1534 6431 6166 2090 6267 2064 6133 6149 3291 2951 c 1240 1182 763 370 394 426 344 374 319 436 413 694 447 374 582 483 424 1112 1285 g 1132 1118 458 464 399 404 348 322 407 412 421 356 405 497 481 420 447 1138 1146 t 2995 2769 5573 6002 932 783 875 858 730 5657 774 823 5097 901 4912 1003 1019 2498 2657
oligos_7nt_mkv5_m1_rc_shift1 (oligos_7nt_mkv5_m1_rc)				; positions_6nt_m2 versus oligos_7nt_mkv5_m1_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.519322; -wwTAAAAATaw------- ; cor=; Ncor= a 0 17108 17001 2963 43003 43712 46328 44355 44861 2303 19148 18363 0 0 0 0 0 0 0 c 0 7532 9367 1846 1548 1899 1128 1831 1880 2187 8367 10772 0 0 0 0 0 0 0 g 0 9121 8249 1972 2302 2434 1549 1606 1691 1930 10974 7692 0 0 0 0 0 0 0 t 0 17323 16467 44303 4231 3039 2079 3292 2652 44664 12595 14257 0 0 0 0 0 0 0
positions_6nt_m4_shift4 (positions_6nt_m4)				; positions_6nt_m2 versus positions_6nt_m4; m=3/3; ncol2=19; w=0; offset=4; strand=D; shift=4; score=0.497609; ----wwAAATAAAATATAT ; cor=; Ncor= a 0 0 0 0 2282 2364 4799 4622 4691 969 4661 4793 4661 4881 845 4741 916 4692 714 c 0 0 0 0 825 883 319 352 278 388 298 342 346 261 395 336 453 343 270 g 0 0 0 0 1158 953 339 347 379 461 394 344 279 333 317 476 311 446 287 t 0 0 0 0 1821 1886 629 765 738 4268 733 607 800 611 4529 533 4406 605 4815

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCGGCCGss ; Alignment reference 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_6nt_mkv4_m3_shift1 (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=1; score= 1; -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_6nt_mkv4_m1_rc_shift1 (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=1; score=0.834572; -ssCGgGCGss ; cor=; Ncor= a 0 4947 4683 299 578 2555 1754 481 479 3890 4776 c 0 14594 11798 33918 3296 7014 3580 34376 1055 15785 10762 g 0 11879 16452 1737 32366 24740 30153 645 34656 11482 16270 t 0 5045 3532 511 225 2156 978 963 275 5308 4657
oligos_7nt_mkv5_m4_shift1 (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=1; score=0.704516; -ssCGGCtGCG ; cor=; Ncor= a 0 3074 2716 794 792 558 414 775 469 594 1166 c 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 g 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 t 0 3174 2677 661 677 766 270 13594 392 622 1300
oligos_7nt_mkv5_m5_shift1 (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=1; score=0.647188; -ssCGGCCCGs ; cor=; Ncor= a 0 4639 4281 1031 1932 605 439 520 1420 1087 4604 c 0 15820 13706 32008 3533 3658 32581 31692 30617 2714 13014 g 0 10449 12994 1799 28576 30724 2430 2652 2576 30984 14046 t 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=-1; offset=-1; strand=D; shift=0; score=0.473197; csGCgGCtGCt ; cor=; Ncor= a 1164 1410 306 370 605 212 212 512 155 257 623 c 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 g 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 t 1120 1343 276 532 732 289 183 4742 307 201 4889

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift12 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=12; ncol=24; ------------ssCGGCtGCGss ; Alignment reference a 0 0 0 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 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 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 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156
oligos_7nt_mkv5_m4_shift12 (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=12; score= 1; ------------ssCGGCtGCGss ; cor=; Ncor= a 0 0 0 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 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 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 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156
oligos_7nt_mkv5_m2_rc_shift12 (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=12; score=0.769998; ------------sscGGGGGCGss ; cor=; Ncor= a 0 0 0 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 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 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 0 0 0 4002 3753 2753 1091 1061 927 848 833 844 847 3832 4064
oligos_6nt_mkv4_m3_shift12 (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=12; score=0.704516; ------------ssCGGCCGss-- ; cor=; Ncor= a 0 0 0 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 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 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 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509 0 0
positions_7nt_m2_shift11 (positions_7nt_m2)				; oligos_7nt_mkv5_m4 versus positions_7nt_m2; m=4/5; ncol2=17; w=-1; offset=-1; strand=D; shift=11; score=0.593243; -----------csGCgGCtGCtGC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 c 0 0 0 0 0 0 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 g 0 0 0 0 0 0 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 t 0 0 0 0 0 0 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351
positions_6nt_m1_shift0 (positions_6nt_m1)				; oligos_7nt_mkv5_m4 versus positions_6nt_m1; m=5/5; ncol2=24; w=-12; offset=-12; strand=D; shift=0; score=0.437508; ssGGmGCCGCsCGGCkGCtGCGss ; cor=; Ncor= a 203 277 101 76 857 77 89 106 81 75 72 90 87 63 79 139 47 38 130 45 97 84 222 220 c 788 691 231 325 483 216 1352 1299 200 1360 1172 1344 238 220 1452 400 252 1557 438 232 1437 255 692 676 g 609 604 1416 1347 368 1442 299 287 1402 306 463 284 1401 1463 218 513 1433 170 433 1459 190 1359 712 707 t 205 233 57 57 97 70 65 113 122 64 98 87 79 59 56 753 73 40 804 69 81 107 179 202

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=4; ncol=16; ----ssCGCCCtCgss ; Alignment reference a 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCGCCCtCgss ; cor=; Ncor= a 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=4; score=0.897996; ----ssCGCCCCCgss ; cor=; Ncor= a 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129
oligos_6nt_mkv4_m1_shift4 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m1; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.687685; ----ssCGCcCGss-- ; cor=; Ncor= a 0 0 0 0 4657 5308 275 963 978 2156 225 511 3532 5045 0 0 c 0 0 0 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 0 0 g 0 0 0 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 0 0 t 0 0 0 0 4776 3890 479 481 1754 2555 578 299 4683 4947 0 0
oligos_6nt_mkv4_m2_rc_shift4 (oligos_6nt_mkv4_m2_rc)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m2_rc; m=4/5; ncol2=10; w=0; offset=0; strand=R; shift=4; score=0.621952; ----ssCGCkCGss-- ; cor=; Ncor= a 0 0 0 0 3169 3720 418 645 450 2156 388 484 2384 3853 0 0 c 0 0 0 0 11847 8031 24381 692 24633 3792 25572 2251 11678 8780 0 0 g 0 0 0 0 7796 11936 1475 24686 978 7014 457 23151 8999 10187 0 0 t 0 0 0 0 3804 2929 342 593 555 13654 199 730 3555 3796 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_7nt_mkv5_m3 versus positions_7nt_m1; m=5/5; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.420301; sssCcCCGCCCsCgCC ; cor=; Ncor= a 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 c 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 g 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 t 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400

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_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; ssCsCCGCCCCGCsCCCGCCbCss ; Alignment reference a 718 584 303 319 210 457 299 248 206 186 282 228 319 296 200 243 291 334 233 301 408 213 650 654 c 3670 3512 6043 2175 6008 5586 1441 6128 5526 5734 6024 1706 6092 2047 5882 5822 6046 1483 5842 5901 2481 6108 3598 3380 g 2425 2574 937 4508 1091 1182 5254 929 1375 1317 921 5262 845 4788 1173 1114 901 5161 1250 990 2106 944 2347 2624 t 771 914 301 582 275 359 590 279 477 347 357 388 328 453 329 405 346 606 259 392 2589 319 989 926
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ssCsCCGCCCCGCsCCCGCCbCss ; cor=; Ncor= a 718 584 303 319 210 457 299 248 206 186 282 228 319 296 200 243 291 334 233 301 408 213 650 654 c 3670 3512 6043 2175 6008 5586 1441 6128 5526 5734 6024 1706 6092 2047 5882 5822 6046 1483 5842 5901 2481 6108 3598 3380 g 2425 2574 937 4508 1091 1182 5254 929 1375 1317 921 5262 845 4788 1173 1114 901 5161 1250 990 2106 944 2347 2624 t 771 914 301 582 275 359 590 279 477 347 357 388 328 453 329 405 346 606 259 392 2589 319 989 926
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_6nt_m5 versus positions_7nt_m1; m=2/3; ncol2=24; w=0; offset=1; strand=D; shift=1; score= 0.6663; -sssCcCCGCCCsCgCCGCCcCss ; cor=; Ncor= a 0 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 307 311 296 369 454 434 900 c 0 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 1844 7761 7216 6517 7462 2951 4289 g 0 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 6863 1255 1679 2315 1398 5777 3620 t 0 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400 732 419 555 545 432 584 937
oligos_7nt_mkv5_m2_shift8 (oligos_7nt_mkv5_m2)				; positions_6nt_m5 versus oligos_7nt_mkv5_m2; m=3/3; ncol2=12; w=0; offset=8; strand=D; shift=8; score=0.428076; --------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 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 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 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=24; shift=1; ncol=25; -sssCcCCGCCCsCgCCGCCcCsss ; Alignment reference a 0 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 307 311 296 369 454 434 900 878 c 0 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 1844 7761 7216 6517 7462 2951 4289 4584 g 0 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 6863 1255 1679 2315 1398 5777 3620 3245 t 0 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400 732 419 555 545 432 584 937 1039
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -sssCcCCGCCCsCgCCGCCcCsss ; cor=; Ncor= a 0 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 307 311 296 369 454 434 900 878 c 0 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 1844 7761 7216 6517 7462 2951 4289 4584 g 0 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 6863 1255 1679 2315 1398 5777 3620 3245 t 0 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400 732 419 555 545 432 584 937 1039
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_7nt_m1 versus positions_6nt_m5; m=2/4; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score= 0.6663; ssCsCCGCCCCGCsCCCGCCbCss- ; cor=; Ncor= a 718 584 303 319 210 457 299 248 206 186 282 228 319 296 200 243 291 334 233 301 408 213 650 654 0 c 3670 3512 6043 2175 6008 5586 1441 6128 5526 5734 6024 1706 6092 2047 5882 5822 6046 1483 5842 5901 2481 6108 3598 3380 0 g 2425 2574 937 4508 1091 1182 5254 929 1375 1317 921 5262 845 4788 1173 1114 901 5161 1250 990 2106 944 2347 2624 0 t 771 914 301 582 275 359 590 279 477 347 357 388 328 453 329 405 346 606 259 392 2589 319 989 926 0
oligos_7nt_mkv5_m2_shift5 (oligos_7nt_mkv5_m2)				; positions_7nt_m1 versus oligos_7nt_mkv5_m2; m=3/4; ncol2=12; w=0; offset=4; strand=D; shift=5; score=0.433443; -----ssCGCCCCCgss-------- ; cor=; Ncor= a 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 0 0 0 0 0 0 0 0 c 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 0 0 0 0 0 0 0 0 g 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 0 0 0 0 0 0 0 0 t 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129 0 0 0 0 0 0 0 0
oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)				; positions_7nt_m1 versus oligos_7nt_mkv5_m3; m=4/4; ncol2=12; w=0; offset=4; strand=D; shift=5; score=0.420301; -----ssCGCCCtCgss-------- ; cor=; Ncor= a 0 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 0 0 0 0 0 0 0 0 c 0 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 0 0 0 0 0 0 0 0 g 0 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 0 0 0 0 0 0 0 0 t 0 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift4 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=19; shift=4; ncol=23; ----wwAAATAAAATATATgTww ; Alignment reference a 0 0 0 0 2282 2364 4799 4622 4691 969 4661 4793 4661 4881 845 4741 916 4692 714 1348 744 2186 1862 c 0 0 0 0 825 883 319 352 278 388 298 342 346 261 395 336 453 343 270 457 424 887 1120 g 0 0 0 0 1158 953 339 347 379 461 394 344 279 333 317 476 311 446 287 3149 318 1225 932 t 0 0 0 0 1821 1886 629 765 738 4268 733 607 800 611 4529 533 4406 605 4815 1132 4600 1788 2172
positions_6nt_m4_shift4 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=4; score= 1; ----wwAAATAAAATATATgTww ; cor=; Ncor= a 0 0 0 0 2282 2364 4799 4622 4691 969 4661 4793 4661 4881 845 4741 916 4692 714 1348 744 2186 1862 c 0 0 0 0 825 883 319 352 278 388 298 342 346 261 395 336 453 343 270 457 424 887 1120 g 0 0 0 0 1158 953 339 347 379 461 394 344 279 333 317 476 311 446 287 3149 318 1225 932 t 0 0 0 0 1821 1886 629 765 738 4268 733 607 800 611 4529 533 4406 605 4815 1132 4600 1788 2172
positions_7nt_m3_shift6 (positions_7nt_m3)				; positions_6nt_m4 versus positions_7nt_m3; m=2/3; ncol2=18; w=0; offset=2; strand=D; shift=6; score=0.605906; ------wwATAAAATATTTTATw ; cor=; Ncor= a 0 0 0 0 0 0 2170 2070 4605 879 4647 4499 4507 4696 526 4788 692 853 829 702 4261 773 2031 c 0 0 0 0 0 0 786 1049 296 375 293 344 394 254 404 279 358 246 328 352 482 321 847 g 0 0 0 0 0 0 1094 845 322 482 353 327 244 357 278 403 254 395 346 292 374 296 1048 t 0 0 0 0 0 0 1946 2032 773 4260 703 826 851 689 4788 526 4692 4502 4493 4650 879 4606 2070
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m4 versus positions_6nt_m2; m=3/3; ncol2=19; w=-4; offset=-4; strand=D; shift=0; score=0.497609; wwTTAAAAATAAwAwAAww---- ; cor=; Ncor= a 2672 2970 1245 1203 6314 6426 6472 6485 6583 1534 6431 6166 2090 6267 2064 6133 6149 3291 2951 0 0 0 0 c 1240 1182 763 370 394 426 344 374 319 436 413 694 447 374 582 483 424 1112 1285 0 0 0 0 g 1132 1118 458 464 399 404 348 322 407 412 421 356 405 497 481 420 447 1138 1146 0 0 0 0 t 2995 2769 5573 6002 932 783 875 858 730 5657 774 823 5097 901 4912 1003 1019 2498 2657 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift9 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=17; shift=9; ncol=26; ---------csGCgGCtGCtGCCkss ; Alignment reference a 0 0 0 0 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 366 582 815 1138 c 0 0 0 0 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 6692 1183 4452 3287 g 0 0 0 0 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 1559 2968 2741 3068 t 0 0 0 0 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351 545 4429 1154 1669
positions_7nt_m2_shift9 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=9; score= 1; ---------csGCgGCtGCtGCCkss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 366 582 815 1138 c 0 0 0 0 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 6692 1183 4452 3287 g 0 0 0 0 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 1559 2968 2741 3068 t 0 0 0 0 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351 545 4429 1154 1669
oligos_7nt_mkv5_m4_shift10 (oligos_7nt_mkv5_m4)				; positions_7nt_m2 versus oligos_7nt_mkv5_m4; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=10; score=0.593243; ----------ssCGGCtGCGss---- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_7nt_m2 versus positions_6nt_m1; m=3/5; ncol2=24; w=-8; offset=-8; strand=D; shift=1; score=0.48742; -ssGGmGCCGCsCGGCkGCtGCGss- ; cor=; Ncor= a 0 203 277 101 76 857 77 89 106 81 75 72 90 87 63 79 139 47 38 130 45 97 84 222 220 0 c 0 788 691 231 325 483 216 1352 1299 200 1360 1172 1344 238 220 1452 400 252 1557 438 232 1437 255 692 676 0 g 0 609 604 1416 1347 368 1442 299 287 1402 306 463 284 1401 1463 218 513 1433 170 433 1459 190 1359 712 707 0 t 0 205 233 57 57 97 70 65 113 122 64 98 87 79 59 56 753 73 40 804 69 81 107 179 202 0
oligos_6nt_mkv4_m3_shift10 (oligos_6nt_mkv4_m3)				; positions_7nt_m2 versus oligos_6nt_mkv4_m3; m=4/5; ncol2=10; w=0; offset=1; strand=D; shift=10; score=0.473197; ----------ssCGGCCGss------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509 0 0 0 0 0 0
positions_7nt_m4_rc_shift0 (positions_7nt_m4_rc)				; positions_7nt_m2 versus positions_7nt_m4_rc; m=5/5; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.408051; sstGCtGGCTGCCaGCtGCtGCss-- ; cor=; Ncor= a 153 134 62 37 46 94 38 46 41 73 20 54 36 591 44 54 99 24 30 96 38 43 168 138 0 0 c 271 334 120 129 736 127 92 104 708 107 114 683 732 98 81 715 107 97 755 94 98 679 299 258 0 0 g 306 270 129 674 81 94 703 675 115 83 701 117 81 110 732 94 120 731 67 106 711 117 231 282 0 0 t 170 162 589 60 37 585 67 75 36 637 65 46 51 101 43 37 574 48 48 604 53 61 202 222 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_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
oligos_7nt_mkv5_m2_shift8 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=8; ncol=20; --------ssCGCCCCCgss ; Alignment reference a 0 0 0 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129
oligos_7nt_mkv5_m2_shift8 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=8; score= 1; --------ssCGCCCCCgss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4064 3832 847 844 833 848 927 1061 1091 2753 3753 4002 c 0 0 0 0 0 0 0 0 17323 16148 34228 575 32573 29928 28599 29983 31669 7154 17815 16802 g 0 0 0 0 0 0 0 0 11270 13293 1285 34377 2236 5120 6244 4931 3252 24236 11652 12013 t 0 0 0 0 0 0 0 0 4289 3673 586 1150 1304 1050 1176 971 934 2803 3726 4129
oligos_7nt_mkv5_m3_shift8 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=2/6; ncol2=12; w=0; offset=0; strand=D; shift=8; score=0.897996; --------ssCGCCCtCgss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2391 2623 447 409 474 684 352 1013 255 1266 2121 2608 c 0 0 0 0 0 0 0 0 9671 7499 19833 620 18867 16303 18433 2890 19765 4274 9655 8592 g 0 0 0 0 0 0 0 0 6340 8452 614 19580 1112 3586 2131 4922 950 14070 6666 7016 t 0 0 0 0 0 0 0 0 2875 2703 383 668 824 704 361 12452 307 1667 2835 3061
oligos_7nt_mkv5_m4_rc_shift8 (oligos_7nt_mkv5_m4_rc)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4_rc; m=3/6; ncol2=12; w=0; offset=0; strand=R; shift=8; score=0.769998; --------ssCGCaGCCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 3156 2892 1300 622 392 13594 270 766 677 661 2677 3174 c 0 0 0 0 0 0 0 0 8620 10068 18188 1084 21556 5423 1136 21088 20646 1509 11960 8643 g 0 0 0 0 0 0 0 0 8987 8024 3085 21439 1322 3947 21919 1327 1624 20775 6386 8848 t 0 0 0 0 0 0 0 0 2976 2755 1166 594 469 775 414 558 792 794 2716 3074
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=4/6; ncol2=10; w=0; offset=0; strand=D; shift=8; score=0.650901; --------ssCGCcCGss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4657 5308 275 963 978 2156 225 511 3532 5045 0 0 c 0 0 0 0 0 0 0 0 16270 11482 34656 645 30153 24740 32366 1737 16452 11879 0 0 g 0 0 0 0 0 0 0 0 10762 15785 1055 34376 3580 7014 3296 33918 11798 14594 0 0 t 0 0 0 0 0 0 0 0 4776 3890 479 481 1754 2555 578 299 4683 4947 0 0
positions_7nt_m1_shift4 (positions_7nt_m1)				; oligos_7nt_mkv5_m2 versus positions_7nt_m1; m=5/6; ncol2=24; w=-4; offset=-4; strand=D; shift=4; score=0.433443; ----sssCcCCGCCCsCgCC ; cor=; Ncor= a 0 0 0 0 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 c 0 0 0 0 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 g 0 0 0 0 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 t 0 0 0 0 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400
positions_6nt_m5_shift0 (positions_6nt_m5)				; oligos_7nt_mkv5_m2 versus positions_6nt_m5; m=6/6; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.428076; ssCsCCGCCCCGCsCCCGCC ; cor=; Ncor= a 718 584 303 319 210 457 299 248 206 186 282 228 319 296 200 243 291 334 233 301 c 3670 3512 6043 2175 6008 5586 1441 6128 5526 5734 6024 1706 6092 2047 5882 5822 6046 1483 5842 5901 g 2425 2574 937 4508 1091 1182 5254 929 1375 1317 921 5262 845 4788 1173 1114 901 5161 1250 990 t 771 914 301 582 275 359 590 279 477 347 357 388 328 453 329 405 346 606 259 392

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; ssGGmGCCGCsCGGCkGCtGCGss ; Alignment reference a 203 277 101 76 857 77 89 106 81 75 72 90 87 63 79 139 47 38 130 45 97 84 222 220 c 788 691 231 325 483 216 1352 1299 200 1360 1172 1344 238 220 1452 400 252 1557 438 232 1437 255 692 676 g 609 604 1416 1347 368 1442 299 287 1402 306 463 284 1401 1463 218 513 1433 170 433 1459 190 1359 712 707 t 205 233 57 57 97 70 65 113 122 64 98 87 79 59 56 753 73 40 804 69 81 107 179 202
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; ssGGmGCCGCsCGGCkGCtGCGss ; cor=; Ncor= a 203 277 101 76 857 77 89 106 81 75 72 90 87 63 79 139 47 38 130 45 97 84 222 220 c 788 691 231 325 483 216 1352 1299 200 1360 1172 1344 238 220 1452 400 252 1557 438 232 1437 255 692 676 g 609 604 1416 1347 368 1442 299 287 1402 306 463 284 1401 1463 218 513 1433 170 433 1459 190 1359 712 707 t 205 233 57 57 97 70 65 113 122 64 98 87 79 59 56 753 73 40 804 69 81 107 179 202
positions_7nt_m2_shift8 (positions_7nt_m2)				; positions_6nt_m1 versus positions_7nt_m2; m=2/3; ncol2=17; w=0; offset=8; strand=D; shift=8; score=0.48742; --------csGCgGCtGCtGCCks ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 366 582 815 c 0 0 0 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 6692 1183 4452 g 0 0 0 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 1559 2968 2741 t 0 0 0 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351 545 4429 1154
oligos_7nt_mkv5_m4_shift12 (oligos_7nt_mkv5_m4)				; positions_6nt_m1 versus oligos_7nt_mkv5_m4; m=3/3; ncol2=12; w=0; offset=12; strand=D; shift=12; score=0.437508; ------------ssCGGCtGCGss ; cor=; Ncor= a 0 0 0 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 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 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 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156