One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/20/peak-motifs.2026-01-20.211306_2026-01-20.211306_nF5eNg/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/2026/01/20/peak-motifs.2026-01-20.211306_2026-01-20.211306_nF5eNg/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCATTTTCdw ; Alignment reference a 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 1486 1386 0 570 249 167 284 177 0 2144 1436 t 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCATTTTCdw ; cor=; Ncor= a 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 1486 1386 0 570 249 167 284 177 0 2144 1436 t 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.812531; wtCATCTTCww ; cor=; Ncor= a 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 3502 3276 315 740 910 167 771 708 180 3110 3631 t 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m1; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.810163; wwCTTTTTCtw ; cor=; Ncor= a 2616 2559 0 274 830 534 995 634 40 2033 2673 c 1413 1247 8225 132 234 716 232 96 8186 1241 1292 g 1363 1524 1 570 235 236 243 94 0 1974 1409 t 2834 2896 0 7250 6927 6740 6756 7402 0 2978 2852

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m5; m=4/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.713466; wtCgTCTTCww ; cor=; Ncor= a 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift1 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=10; shift=1; ncol=11; -wtACCTTCww ; Alignment reference a 0 1413 1065 4440 0 0 129 547 0 1226 1412 c 0 902 1088 0 4461 4429 26 66 4461 785 755 g 0 926 510 4 0 32 393 45 0 863 782 t 0 1220 1798 17 0 0 3913 3803 0 1587 1512

oligos_6nt_mkv4_m4_shift1 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wtACCTTCww ; cor=; Ncor= a 0 1413 1065 4440 0 0 129 547 0 1226 1412 c 0 902 1088 0 4461 4429 26 66 4461 785 755 g 0 926 510 4 0 32 393 45 0 863 782 t 0 1220 1798 17 0 0 3913 3803 0 1587 1512

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m3; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.638133; wtCATCTTCww ; cor=; Ncor= a 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 3502 3276 315 740 910 167 771 708 180 3110 3631 t 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340

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=12; shift=0; ncol=12; wwTATATATAww ; Alignment reference a 3195 5290 612 10376 477 10476 604 10546 636 10313 3057 5091 c 1797 1368 459 295 377 285 315 280 373 296 1965 1597 g 1597 1965 296 373 280 315 285 377 295 459 1368 1797 t 5091 3057 10313 636 10546 604 10476 477 10376 612 5290 3195

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwTATATATAww ; cor=; Ncor= a 3195 5290 612 10376 477 10476 604 10546 636 10313 3057 5091 c 1797 1368 459 295 377 285 315 280 373 296 1965 1597 g 1597 1965 296 373 280 315 285 377 295 459 1368 1797 t 5091 3057 10313 636 10546 604 10476 477 10376 612 5290 3195

oligos_6nt_mkv4_m2_rc_shift2 (oligos_6nt_mkv4_m2_rc)
; positions_7nt_m3 versus oligos_6nt_mkv4_m2_rc; m=2/2; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.601278; --wwTATGTAww ; cor=; Ncor= a 0 0 823 1062 0 2788 0 0 0 2788 784 948 c 0 0 449 366 0 0 88 0 0 0 589 442 g 0 0 427 549 0 0 0 2788 0 0 399 551 t 0 0 1089 811 2788 0 2700 0 2788 0 1016 847

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift4 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift4 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwCTTTTTCtw ; Alignment reference a 0 0 0 0 2616 2559 0 274 830 534 995 634 40 2033 2673 c 0 0 0 0 1413 1247 8225 132 234 716 232 96 8186 1241 1292 g 0 0 0 0 1363 1524 1 570 235 236 243 94 0 1974 1409 t 0 0 0 0 2834 2896 0 7250 6927 6740 6756 7402 0 2978 2852

oligos_7nt_mkv5_m1_shift4 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wwCTTTTTCtw ; cor=; Ncor= a 0 0 0 0 2616 2559 0 274 830 534 995 634 40 2033 2673 c 0 0 0 0 1413 1247 8225 132 234 716 232 96 8186 1241 1292 g 0 0 0 0 1363 1524 1 570 235 236 243 94 0 1974 1409 t 0 0 0 0 2834 2896 0 7250 6927 6740 6756 7402 0 2978 2852

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m2; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.810163; ----wwCATTTTCdw ; cor=; Ncor= a 0 0 0 0 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 0 0 0 0 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 0 0 0 0 1486 1386 0 570 249 167 284 177 0 2144 1436 t 0 0 0 0 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m5; m=3/5; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.732268; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 0 0 0 0 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 0 0 0 0 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 0 0 0 0 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m1 versus dyads_m1_rc; m=4/5; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.581893; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2245 1776 1386 439 395 604 341 262 825 415 284 6063 2256 c 0 0 1181 2623 4030 295 7026 497 262 7192 432 229 6868 531 1133 g 0 0 1426 1320 685 354 207 327 249 256 321 359 256 422 1645 t 0 0 3128 2261 1879 6892 352 6552 7128 270 6402 6977 572 964 2946

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m1 versus dyads_m2_rc; m=5/5; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.517014; ywTTTTCTTCTTCAw ; cor=; Ncor= a 773 1002 265 124 249 113 111 265 113 116 260 131 97 2566 966 c 1103 617 179 568 125 128 2903 197 60 2873 139 132 2985 200 503 g 531 501 175 130 132 122 97 147 90 113 148 117 138 203 609 t 1081 1368 2869 2666 2982 3125 377 2879 3225 386 2941 3108 268 519 1410

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift4 ; 7 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=11; shift=4; ncol=15; ----wtCATCTTCww ; Alignment reference a 0 0 0 0 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 0 0 0 0 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 0 0 0 0 3502 3276 315 740 910 167 771 708 180 3110 3631 t 0 0 0 0 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 0 0 0 0 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 0 0 0 0 3502 3276 315 740 910 167 771 708 180 3110 3631 t 0 0 0 0 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m5; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.896294; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 0 0 0 0 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 0 0 0 0 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 0 0 0 0 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.812531; ----wwCATTTTCdw ; cor=; Ncor= a 0 0 0 0 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 0 0 0 0 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 0 0 0 0 1486 1386 0 570 249 167 284 177 0 2144 1436 t 0 0 0 0 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894

oligos_6nt_mkv4_m4_shift5 (oligos_6nt_mkv4_m4)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m4; m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.638133; -----wtACCTTCww ; cor=; Ncor= a 0 0 0 0 0 1413 1065 4440 0 0 129 547 0 1226 1412 c 0 0 0 0 0 902 1088 0 4461 4429 26 66 4461 785 755 g 0 0 0 0 0 926 510 4 0 32 393 45 0 863 782 t 0 0 0 0 0 1220 1798 17 0 0 3913 3803 0 1587 1512

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m3 versus dyads_m1_rc; m=5/6; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.632058; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2245 1776 1386 439 395 604 341 262 825 415 284 6063 2256 c 0 0 1181 2623 4030 295 7026 497 262 7192 432 229 6868 531 1133 g 0 0 1426 1320 685 354 207 327 249 256 321 359 256 422 1645 t 0 0 3128 2261 1879 6892 352 6552 7128 270 6402 6977 572 964 2946

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m3 versus dyads_m2_rc; m=6/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.54107; ywTTTTCTTCTTCAw ; cor=; Ncor= a 773 1002 265 124 249 113 111 265 113 116 260 131 97 2566 966 c 1103 617 179 568 125 128 2903 197 60 2873 139 132 2985 200 503 g 531 501 175 130 132 122 97 147 90 113 148 117 138 203 609 t 1081 1368 2869 2666 2982 3125 377 2879 3225 386 2941 3108 268 519 1410

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift9 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift9 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=20; shift=9; ncol=29; ---------aaAAAArAAAAAAAwAaaaa ; Alignment reference a 0 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 c 0 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 g 0 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 t 0 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238

positions_7nt_m1_shift9 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/8; ncol2=20; w=0; offset=0; strand=D; shift=9; score= 1; ---------aaAAAArAAAAAAAwAaaaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 c 0 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 g 0 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 t 0 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238

positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=2/8; ncol2=24; w=-3; offset=-3; strand=D; shift=6; score=0.751424; ------wawmAAAAArAAAAAAwAAAAAa ; cor=; Ncor= a 0 0 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 c 0 0 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 g 0 0 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 t 0 0 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342

positions_6nt_m4_shift5 (positions_6nt_m4)
; positions_7nt_m1 versus positions_6nt_m4; m=3/8; ncol2=24; w=-4; offset=-4; strand=D; shift=5; score=0.739564; -----aaAAAwAAAAArAAAAAAwAwAwa ; cor=; Ncor= a 0 0 0 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 0 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 0 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 0 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423

positions_6nt_m5_shift5 (positions_6nt_m5)
; positions_7nt_m1 versus positions_6nt_m5; m=4/8; ncol2=24; w=-4; offset=-4; strand=D; shift=5; score=0.707842; -----aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271

positions_6nt_m2_shift8 (positions_6nt_m2)
; positions_7nt_m1 versus positions_6nt_m2; m=5/8; ncol2=24; w=-1; offset=-1; strand=D; shift=8; score=0.69947; --------awrAAAAwAAAAArAAAAAAw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 c 0 0 0 0 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 g 0 0 0 0 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 t 0 0 0 0 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809

positions_7nt_m2_shift9 (positions_7nt_m2)
; positions_7nt_m1 versus positions_7nt_m2; m=6/8; ncol2=24; w=0; offset=0; strand=D; shift=9; score=0.623834; ---------waaAAAgAAAAAAATTTTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 108 66 c 0 0 0 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 58 52 g 0 0 0 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 45 16 t 0 0 0 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613 611 688

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; positions_7nt_m1 versus positions_6nt_m3_rc; m=7/8; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.448297; wwTATTTTTgAAAAATAAAAAAww----- ; cor=; Ncor= a 154 171 48 403 43 75 88 57 51 108 347 377 342 372 393 82 361 374 371 359 346 381 182 201 0 0 0 0 0 c 67 63 26 8 31 29 12 39 11 38 23 18 18 23 22 15 19 14 35 19 26 29 53 38 0 0 0 0 0 g 58 77 33 12 23 19 24 26 30 250 20 8 34 22 13 27 44 25 13 38 11 11 93 67 0 0 0 0 0 t 181 149 353 37 363 337 336 338 368 64 70 57 66 43 32 336 36 47 41 44 77 39 132 154 0 0 0 0 0

dyads_m2_shift6 (dyads_m2)
; positions_7nt_m1 versus dyads_m2; m=8/8; ncol2=16; w=-3; offset=-3; strand=D; shift=6; score=0.404983; ------rwTGAAGAAGAAAAwr------- ; cor=; Ncor= a 0 0 0 0 0 0 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 1368 1081 0 0 0 0 0 0 0 c 0 0 0 0 0 0 451 609 203 138 117 148 113 90 147 97 122 132 130 175 501 531 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 617 1103 0 0 0 0 0 0 0 t 0 0 0 0 0 0 771 966 2566 97 131 260 116 113 265 111 113 249 124 265 1002 773 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift8 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift8 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=24; shift=8; ncol=32; --------awrAAAAwAAAAArAAAAAAwtwa ; Alignment reference a 0 0 0 0 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 c 0 0 0 0 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 g 0 0 0 0 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 t 0 0 0 0 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333

positions_6nt_m2_shift8 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=8; score= 1; --------awrAAAAwAAAAArAAAAAAwtwa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 c 0 0 0 0 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 g 0 0 0 0 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 t 0 0 0 0 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333

positions_6nt_m4_shift10 (positions_6nt_m4)
; positions_6nt_m2 versus positions_6nt_m4; m=2/7; ncol2=24; w=0; offset=2; strand=D; shift=10; score=0.789622; ----------aaAAAwAAAAArAAAAAAwAwA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 c 0 0 0 0 0 0 0 0 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 g 0 0 0 0 0 0 0 0 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 t 0 0 0 0 0 0 0 0 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234

positions_6nt_m1_shift8 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=3/7; ncol2=24; w=0; offset=0; strand=D; shift=8; score=0.77517; --------wawmAAAAArAAAAAAwAAAAAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 0 0 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 0 0 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 0 0 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426

positions_6nt_m5_shift8 (positions_6nt_m5)
; positions_6nt_m2 versus positions_6nt_m5; m=4/7; ncol2=24; w=0; offset=0; strand=D; shift=8; score=0.763774; --------aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271

positions_7nt_m1_shift9 (positions_7nt_m1)
; positions_6nt_m2 versus positions_7nt_m1; m=5/7; ncol2=20; w=0; offset=1; strand=D; shift=9; score=0.69947; ---------aaAAAArAAAAAAAwAaaaa--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 0 0 0 c 0 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 0 0 0 g 0 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 0 0 0 t 0 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238 0 0 0

positions_7nt_m2_shift14 (positions_7nt_m2)
; positions_6nt_m2 versus positions_7nt_m2; m=6/7; ncol2=24; w=0; offset=6; strand=D; shift=14; score=0.476052; --------------waaAAAgAAAAAAATTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; positions_6nt_m2 versus positions_6nt_m3_rc; m=7/7; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.401179; wwTATTTTTgAAAAATAAAAAAww-------- ; cor=; Ncor= a 154 171 48 403 43 75 88 57 51 108 347 377 342 372 393 82 361 374 371 359 346 381 182 201 0 0 0 0 0 0 0 0 c 67 63 26 8 31 29 12 39 11 38 23 18 18 23 22 15 19 14 35 19 26 29 53 38 0 0 0 0 0 0 0 0 g 58 77 33 12 23 19 24 26 30 250 20 8 34 22 13 27 44 25 13 38 11 11 93 67 0 0 0 0 0 0 0 0 t 181 149 353 37 363 337 336 338 368 64 70 57 66 43 32 336 36 47 41 44 77 39 132 154 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; hwTCACCAACww ; Alignment reference a 1546 1748 228 165 5278 497 189 5463 4966 411 2184 1747 c 1704 876 193 5050 131 4559 5304 73 236 4744 970 984 g 739 969 161 173 120 255 105 113 173 247 1047 1087 t 1749 2145 5156 350 209 427 140 89 363 336 1537 1920

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; hwTCACCAACww ; cor=; Ncor= a 1546 1748 228 165 5278 497 189 5463 4966 411 2184 1747 c 1704 876 193 5050 131 4559 5304 73 236 4744 970 984 g 739 969 161 173 120 255 105 113 173 247 1047 1087 t 1749 2145 5156 350 209 427 140 89 363 336 1537 1920

dyads_m3_shift1 (dyads_m3)
; dyads_m4 versus dyads_m3; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.726799; -wyCACCACCaw ; cor=; Ncor= a 0 4742 2988 811 11135 897 436 11313 936 533 5230 3469 c 0 1595 3050 9888 209 9608 11108 128 9552 10753 1751 2556 g 0 2236 2395 417 287 662 199 269 654 267 2078 2602 t 0 3500 3640 957 442 906 330 363 931 520 3014 3446

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; waAATATCww ; Alignment reference a 1664 1720 4865 4865 0 4865 0 0 1739 1488 c 874 1155 0 0 0 0 0 4865 975 953 g 948 989 0 0 0 0 0 0 710 840 t 1379 1001 0 0 4865 0 4865 0 1441 1584

oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; waAATATCww ; cor=; Ncor= a 1664 1720 4865 4865 0 4865 0 0 1739 1488 c 874 1155 0 0 0 0 0 4865 975 953 g 948 989 0 0 0 0 0 0 710 840 t 1379 1001 0 0 4865 0 4865 0 1441 1584

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift1 ; 3 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; -wtACCACCdw ; Alignment reference a 0 1928 1475 6342 90 28 5762 61 30 2366 2059 c 0 1546 1409 123 6725 6040 86 6735 6435 802 1620 g 0 1549 808 252 74 276 590 62 271 1955 1208 t 0 1964 3295 270 98 643 549 129 251 1864 2100

oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wtACCACCdw ; cor=; Ncor= a 0 1928 1475 6342 90 28 5762 61 30 2366 2059 c 0 1546 1409 123 6725 6040 86 6735 6435 802 1620 g 0 1549 808 252 74 276 590 62 271 1955 1208 t 0 1964 3295 270 98 643 549 129 251 1864 2100

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv4_m1 versus dyads_m3; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.821767; wyCACCACCaw ; cor=; Ncor= a 4742 2988 811 11135 897 436 11313 936 533 5230 3469 c 1595 3050 9888 209 9608 11108 128 9552 10753 1751 2556 g 2236 2395 417 287 662 199 269 654 267 2078 2602 t 3500 3640 957 442 906 330 363 931 520 3014 3446

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift4 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=24; shift=4; ncol=28; ----aamAArAAAAAwAAAAAArAAraw ; Alignment reference a 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271

positions_6nt_m5_shift4 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271

positions_6nt_m4_shift4 (positions_6nt_m4)
; positions_6nt_m5 versus positions_6nt_m4; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.872785; ----aaAAAwAAAAArAAAAAAwAwAwa ; cor=; Ncor= a 0 0 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423

positions_6nt_m1_shift4 (positions_6nt_m1)
; positions_6nt_m5 versus positions_6nt_m1; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.815046; ----wawmAAAAArAAAAAAwAAAAAaa ; cor=; Ncor= a 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_6nt_m5 versus positions_6nt_m2; m=4/6; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.763774; ----awrAAAAwAAAAArAAAAAAwtwa ; cor=; Ncor= a 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 c 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 g 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 t 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333

positions_7nt_m1_shift8 (positions_7nt_m1)
; positions_6nt_m5 versus positions_7nt_m1; m=5/6; ncol2=20; w=0; offset=4; strand=D; shift=8; score=0.707842; --------aaAAAArAAAAAAAwAaaaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 c 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 g 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 t 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; positions_6nt_m5 versus positions_6nt_m3_rc; m=6/6; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.512378; wwTATTTTTgAAAAATAAAAAAww---- ; cor=; Ncor= a 154 171 48 403 43 75 88 57 51 108 347 377 342 372 393 82 361 374 371 359 346 381 182 201 0 0 0 0 c 67 63 26 8 31 29 12 39 11 38 23 18 18 23 22 15 19 14 35 19 26 29 53 38 0 0 0 0 g 58 77 33 12 23 19 24 26 30 250 20 8 34 22 13 27 44 25 13 38 11 11 93 67 0 0 0 0 t 181 149 353 37 363 337 336 338 368 64 70 57 66 43 32 336 36 47 41 44 77 39 132 154 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift6 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift6 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=24; shift=6; ncol=30; ------waaAAAgAAAAAAATTTTTTThww ; Alignment reference a 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 108 66 83 235 272 274 c 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 58 52 38 274 119 140 g 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 45 16 21 104 119 90 t 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613 611 688 680 209 312 318

positions_7nt_m2_shift6 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------waaAAAgAAAAAAATTTTTTThww ; cor=; Ncor= a 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 108 66 83 235 272 274 c 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 58 52 38 274 119 140 g 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 45 16 21 104 119 90 t 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613 611 688 680 209 312 318

positions_7nt_m1_shift6 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=2/4; ncol2=20; w=0; offset=0; strand=D; shift=6; score=0.623834; ------aaAAAArAAAAAAAwAaaaa---- ; cor=; Ncor= a 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 0 0 0 0 c 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 0 0 0 0 g 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 0 0 0 0 t 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238 0 0 0 0

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_7nt_m2 versus positions_6nt_m2; m=3/4; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.476052; awrAAAAwAAAAArAAAAAAwtwa------ ; cor=; Ncor= a 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 0 0 0 0 0 0 c 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 0 0 0 0 0 0 g 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 0 0 0 0 0 0 t 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333 0 0 0 0 0 0

positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_7nt_m2 versus positions_6nt_m4; m=4/4; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.467977; -aaAAAwAAAAArAAAAAAwAwAwa----- ; cor=; Ncor= a 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 0 0 0 0 0 c 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 0 0 0 0 0 g 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 0 0 0 0 0 t 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; wwTACATAww ; Alignment reference a 847 1016 0 2788 0 2700 0 2788 811 1089 c 551 399 0 0 2788 0 0 0 549 427 g 442 589 0 0 0 88 0 0 366 449 t 948 784 2788 0 0 0 2788 0 1062 823

oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wwTACATAww ; cor=; Ncor= a 847 1016 0 2788 0 2700 0 2788 811 1089 c 551 399 0 0 2788 0 0 0 549 427 g 442 589 0 0 0 88 0 0 366 449 t 948 784 2788 0 0 0 2788 0 1062 823

positions_7nt_m3_shift0 (positions_7nt_m3)
; oligos_6nt_mkv4_m2 versus positions_7nt_m3; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.601278; wwTATATATA ; cor=; Ncor= a 3195 5290 612 10376 477 10476 604 10546 636 10313 c 1797 1368 459 295 377 285 315 280 373 296 g 1597 1965 296 373 280 315 285 377 295 459 t 5091 3057 10313 636 10546 604 10476 477 10376 612

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCAAAAACdw ; Alignment reference a 2466 2570 0 5817 5809 5343 5519 6573 0 1811 2247 c 1014 1213 6874 129 176 403 251 94 6912 1013 1129 g 1238 1212 1 408 283 304 281 92 0 1910 1481 t 2194 1917 37 558 644 862 861 153 0 2178 2055

oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCAAAAACdw ; cor=; Ncor= a 2466 2570 0 5817 5809 5343 5519 6573 0 1811 2247 c 1014 1213 6874 129 176 403 251 94 6912 1013 1129 g 1238 1212 1 408 283 304 281 92 0 1910 1481 t 2194 1917 37 558 644 862 861 153 0 2178 2055

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift8 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift8 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=24; shift=8; ncol=32; --------wwTTTTTTATTTTTcAAAAATAww ; Alignment reference a 0 0 0 0 0 0 0 0 154 132 39 77 44 41 47 36 336 32 43 66 57 70 64 368 338 336 337 363 37 353 149 181 c 0 0 0 0 0 0 0 0 67 93 11 11 38 13 25 44 27 13 22 34 8 20 250 30 26 24 19 23 12 33 77 58 g 0 0 0 0 0 0 0 0 38 53 29 26 19 35 14 19 15 22 23 18 18 23 38 11 39 12 29 31 8 26 63 67 t 0 0 0 0 0 0 0 0 201 182 381 346 359 371 374 361 82 393 372 342 377 347 108 51 57 88 75 43 403 48 171 154

positions_6nt_m3_shift8 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=8; score= 1; --------wwTTTTTTATTTTTcAAAAATAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 154 132 39 77 44 41 47 36 336 32 43 66 57 70 64 368 338 336 337 363 37 353 149 181 c 0 0 0 0 0 0 0 0 67 93 11 11 38 13 25 44 27 13 22 34 8 20 250 30 26 24 19 23 12 33 77 58 g 0 0 0 0 0 0 0 0 38 53 29 26 19 35 14 19 15 22 23 18 18 23 38 11 39 12 29 31 8 26 63 67 t 0 0 0 0 0 0 0 0 201 182 381 346 359 371 374 361 82 393 372 342 377 347 108 51 57 88 75 43 403 48 171 154

positions_6nt_m5_rc_shift4 (positions_6nt_m5_rc)
; positions_6nt_m3 versus positions_6nt_m5_rc; m=2/5; ncol2=24; w=-4; offset=-4; strand=R; shift=4; score=0.512378; ----wtyTTyTTTTTTwTTTTTyTTktt---- ; cor=; Ncor= a 0 0 0 0 271 239 123 85 63 86 109 56 61 99 57 54 509 63 39 54 36 62 111 86 49 152 247 264 0 0 0 0 c 0 0 0 0 199 168 502 41 33 547 60 41 64 44 63 40 139 43 51 55 48 64 558 38 65 126 173 185 0 0 0 0 g 0 0 0 0 132 144 72 51 49 74 52 55 33 36 42 44 55 36 28 34 20 27 65 42 32 386 164 105 0 0 0 0 t 0 0 0 0 463 514 368 888 920 358 844 913 907 886 903 927 362 923 947 922 961 912 331 899 919 401 481 511 0 0 0 0

positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)
; positions_6nt_m3 versus positions_6nt_m1_rc; m=3/5; ncol2=24; w=-6; offset=-6; strand=R; shift=2; score=0.497511; --ttTTTTTwTTTTTTyTTTTTkwtw------ ; cor=; Ncor= a 0 0 426 342 129 134 170 134 134 813 88 73 106 53 95 98 162 121 82 88 145 201 256 864 441 479 0 0 0 0 0 0 c 0 0 243 253 93 95 72 77 76 128 90 53 67 70 89 88 799 75 95 116 127 114 228 151 250 259 0 0 0 0 0 0 g 0 0 219 253 118 57 57 59 47 85 50 40 51 44 39 51 66 59 46 39 107 120 610 160 225 195 0 0 0 0 0 0 t 0 0 889 929 1437 1491 1478 1507 1520 751 1549 1611 1553 1610 1554 1540 750 1522 1554 1534 1398 1342 683 602 861 844 0 0 0 0 0 0

positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)
; positions_6nt_m3 versus positions_7nt_m1_rc; m=4/5; ncol2=20; w=-5; offset=-5; strand=R; shift=3; score=0.448297; ---ttttTwTTTTTTTyTTTTtt--------- ; cor=; Ncor= a 0 0 0 1238 1317 1194 834 432 3420 251 270 353 297 284 260 281 670 523 525 517 808 1282 1369 0 0 0 0 0 0 0 0 0 c 0 0 0 969 1044 693 545 391 360 166 219 194 215 263 159 171 2752 338 320 505 462 1024 997 0 0 0 0 0 0 0 0 0 g 0 0 0 896 794 674 492 267 217 133 124 125 126 151 142 133 332 273 230 252 473 682 783 0 0 0 0 0 0 0 0 0 t 0 0 0 2608 2556 3150 3840 4621 1714 5161 5098 5039 5073 5013 5150 5126 1957 4577 4636 4437 3968 2723 2562 0 0 0 0 0 0 0 0 0

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_6nt_m3 versus positions_6nt_m2_rc; m=5/5; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.401179; twawTTTTTTyTTTTTwTTTTywt-------- ; cor=; Ncor= a 333 374 797 809 114 112 63 114 50 111 151 117 100 88 115 84 744 87 95 90 91 160 356 324 0 0 0 0 0 0 0 0 c 249 238 116 98 65 46 58 49 63 64 705 85 77 82 38 67 160 60 76 83 99 620 245 250 0 0 0 0 0 0 0 0 g 196 204 92 74 49 59 41 62 54 66 64 50 49 52 59 46 51 55 39 57 36 133 134 168 0 0 0 0 0 0 0 0 t 556 518 329 353 1106 1117 1172 1109 1167 1093 414 1082 1108 1112 1122 1137 379 1132 1124 1104 1108 421 599 592 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift6 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=24; shift=6; ncol=30; ------wawmAAAAArAAAAAAwAAAAAaa ; Alignment reference a 0 0 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426

positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------wawmAAAAArAAAAAAwAAAAAaa ; cor=; Ncor= a 0 0 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426

positions_6nt_m5_shift6 (positions_6nt_m5)
; positions_6nt_m1 versus positions_6nt_m5; m=2/7; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.815046; ------aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271

positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_6nt_m1 versus positions_6nt_m4; m=3/7; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.806598; ------aaAAAwAAAAArAAAAAAwAwAwa ; cor=; Ncor= a 0 0 0 0 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 0 0 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 0 0 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 0 0 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423

positions_6nt_m2_shift6 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=4/7; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.77517; ------awrAAAAwAAAAArAAAAAAwtwa ; cor=; Ncor= a 0 0 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 c 0 0 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 g 0 0 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 t 0 0 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333

positions_7nt_m1_shift9 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=5/7; ncol2=20; w=0; offset=3; strand=D; shift=9; score=0.751424; ---------aaAAAArAAAAAAAwAaaaa- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 0 c 0 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 0 g 0 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 0 t 0 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238 0

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; positions_6nt_m1 versus positions_6nt_m3_rc; m=6/7; ncol2=24; w=-6; offset=-6; strand=R; shift=0; score=0.497511; wwTATTTTTgAAAAATAAAAAAww------ ; cor=; Ncor= a 154 171 48 403 43 75 88 57 51 108 347 377 342 372 393 82 361 374 371 359 346 381 182 201 0 0 0 0 0 0 c 67 63 26 8 31 29 12 39 11 38 23 18 18 23 22 15 19 14 35 19 26 29 53 38 0 0 0 0 0 0 g 58 77 33 12 23 19 24 26 30 250 20 8 34 22 13 27 44 25 13 38 11 11 93 67 0 0 0 0 0 0 t 181 149 353 37 363 337 336 338 368 64 70 57 66 43 32 336 36 47 41 44 77 39 132 154 0 0 0 0 0 0

dyads_m2_shift6 (dyads_m2)
; positions_6nt_m1 versus dyads_m2; m=7/7; ncol2=16; w=0; offset=0; strand=D; shift=6; score=0.485995; ------rwTGAAGAAGAAAAwr-------- ; cor=; Ncor= a 0 0 0 0 0 0 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 1368 1081 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 451 609 203 138 117 148 113 90 147 97 122 132 130 175 501 531 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 617 1103 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 771 966 2566 97 131 260 116 113 265 111 113 249 124 265 1002 773 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; rwTGAAGAAGAAAAwr ; Alignment reference a 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 1368 1081 c 451 609 203 138 117 148 113 90 147 97 122 132 130 175 501 531 g 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 617 1103 t 771 966 2566 97 131 260 116 113 265 111 113 249 124 265 1002 773

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; rwTGAAGAAGAAAAwr ; cor=; Ncor= a 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 1368 1081 c 451 609 203 138 117 148 113 90 147 97 122 132 130 175 501 531 g 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 617 1103 t 771 966 2566 97 131 260 116 113 265 111 113 249 124 265 1002 773

dyads_m1_shift0 (dyads_m1)
; dyads_m2 versus dyads_m1; m=2/7; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.776471; rwTGAAGAAGAgrw-- ; cor=; Ncor= a 2373 2946 964 572 6977 6402 270 7128 6552 352 6892 1879 2261 3128 0 0 c 1108 1645 422 256 359 321 256 249 327 207 354 685 1320 1426 0 0 g 2715 1133 531 6868 229 432 7192 262 497 7026 295 4030 2623 1181 0 0 t 1784 2256 6063 284 415 825 262 341 604 395 439 1386 1776 2245 0 0

oligos_7nt_mkv5_m5_rc_shift1 (oligos_7nt_mkv5_m5_rc)
; dyads_m2 versus oligos_7nt_mkv5_m5_rc; m=3/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.55693; -wwGAAGAcGaw---- ; cor=; Ncor= a 0 5560 4613 571 13781 12950 912 13346 2670 809 5995 4611 0 0 0 0 c 0 2696 2583 418 228 423 267 353 8881 551 2326 2701 0 0 0 0 g 0 2105 2489 13240 214 261 12727 345 1191 12395 2590 2251 0 0 0 0 t 0 4069 4745 201 207 796 524 386 1688 675 3519 4867 0 0 0 0

oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)
; dyads_m2 versus oligos_7nt_mkv5_m3_rc; m=4/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.54107; -wwGAAGATGaw---- ; cor=; Ncor= a 0 7340 6289 502 17361 16087 261 15990 2670 1207 7892 6371 0 0 0 0 c 0 3631 3110 180 708 771 167 910 740 315 3276 3502 0 0 0 0 g 0 2840 3166 18082 540 677 17792 948 1191 17107 3402 2857 0 0 0 0 t 0 5415 6661 462 617 1691 1006 1378 14625 597 4656 6496 0 0 0 0

oligos_7nt_mkv5_m1_rc_shift1 (oligos_7nt_mkv5_m1_rc)
; dyads_m2 versus oligos_7nt_mkv5_m1_rc; m=5/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.517014; -waGAAAAAGww---- ; cor=; Ncor= a 0 2852 2978 0 7402 6756 6740 6927 7250 0 2896 2834 0 0 0 0 c 0 1409 1974 0 94 243 236 235 570 1 1524 1363 0 0 0 0 g 0 1292 1241 8186 96 232 716 234 132 8225 1247 1413 0 0 0 0 t 0 2673 2033 40 634 995 534 830 274 0 2559 2616 0 0 0 0

positions_6nt_m1_shift0 (positions_6nt_m1)
; dyads_m2 versus positions_6nt_m1; m=6/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.485995; wawmAAAAArAAAAAA ; cor=; Ncor= a 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 c 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 g 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 t 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88

positions_7nt_m1_shift3 (positions_7nt_m1)
; dyads_m2 versus positions_7nt_m1; m=7/7; ncol2=20; w=0; offset=3; strand=D; shift=3; score=0.404983; ---aaAAAArAAAAAA ; cor=; Ncor= a 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 c 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 g 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 t 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=20; shift=0; ncol=20; arCAgCAgCAGCAGCAgCar ; Alignment reference a 1851 1179 390 2707 792 289 2721 776 279 2982 669 232 3041 612 224 2860 696 302 1807 1186 c 485 529 2696 189 298 2919 221 290 3022 140 276 3094 129 261 3095 154 361 2819 462 517 g 599 1305 185 365 2289 187 403 2363 104 285 2624 88 264 2681 109 329 2329 169 621 1275 t 785 707 449 459 341 325 375 291 315 313 151 306 286 166 292 377 334 430 830 742

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/1; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; arCAgCAgCAGCAGCAgCar ; cor=; Ncor= a 1851 1179 390 2707 792 289 2721 776 279 2982 669 232 3041 612 224 2860 696 302 1807 1186 c 485 529 2696 189 298 2919 221 290 3022 140 276 3094 129 261 3095 154 361 2819 462 517 g 599 1305 185 365 2289 187 403 2363 104 285 2624 88 264 2681 109 329 2329 169 621 1275 t 785 707 449 459 341 325 375 291 315 313 151 306 286 166 292 377 334 430 830 742

One-to-n matrix alignment; reference matrix: dyads_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift1 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wyCACCACCaw ; Alignment reference a 0 4742 2988 811 11135 897 436 11313 936 533 5230 3469 c 0 1595 3050 9888 209 9608 11108 128 9552 10753 1751 2556 g 0 2236 2395 417 287 662 199 269 654 267 2078 2602 t 0 3500 3640 957 442 906 330 363 931 520 3014 3446

dyads_m3_shift1 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wyCACCACCaw ; cor=; Ncor= a 0 4742 2988 811 11135 897 436 11313 936 533 5230 3469 c 0 1595 3050 9888 209 9608 11108 128 9552 10753 1751 2556 g 0 2236 2395 417 287 662 199 269 654 267 2078 2602 t 0 3500 3640 957 442 906 330 363 931 520 3014 3446

oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)
; dyads_m3 versus oligos_6nt_mkv4_m1; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.821767; --wtACCACCdw ; cor=; Ncor= a 0 0 1928 1475 6342 90 28 5762 61 30 2366 2059 c 0 0 1546 1409 123 6725 6040 86 6735 6435 802 1620 g 0 0 1549 808 252 74 276 590 62 271 1955 1208 t 0 0 1964 3295 270 98 643 549 129 251 1864 2100

dyads_m4_shift0 (dyads_m4)
; dyads_m3 versus dyads_m4; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.726799; hwTCACCAACww ; cor=; Ncor= a 1546 1748 228 165 5278 497 189 5463 4966 411 2184 1747 c 1704 876 193 5050 131 4559 5304 73 236 4744 970 984 g 739 969 161 173 120 255 105 113 173 247 1047 1087 t 1749 2145 5156 350 209 427 140 89 363 336 1537 1920

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift4 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCgTCTTCww ; Alignment reference a 0 0 0 0 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 0 0 0 0 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 0 0 0 0 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 0 0 0 0 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 0 0 0 0 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 0 0 0 0 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 0 0 0 0 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m3; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.896294; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 0 0 0 0 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 0 0 0 0 3502 3276 315 740 910 167 771 708 180 3110 3631 t 0 0 0 0 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340

oligos_7nt_mkv5_m1_shift4 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m1; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.732268; ----wwCTTTTTCtw ; cor=; Ncor= a 0 0 0 0 2616 2559 0 274 830 534 995 634 40 2033 2673 c 0 0 0 0 1413 1247 8225 132 234 716 232 96 8186 1241 1292 g 0 0 0 0 1363 1524 1 570 235 236 243 94 0 1974 1409 t 0 0 0 0 2834 2896 0 7250 6927 6740 6756 7402 0 2978 2852

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m2; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.713466; ----wwCATTTTCdw ; cor=; Ncor= a 0 0 0 0 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 0 0 0 0 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 0 0 0 0 1486 1386 0 570 249 167 284 177 0 2144 1436 t 0 0 0 0 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m5 versus dyads_m1_rc; m=5/7; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.649507; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2245 1776 1386 439 395 604 341 262 825 415 284 6063 2256 c 0 0 1181 2623 4030 295 7026 497 262 7192 432 229 6868 531 1133 g 0 0 1426 1320 685 354 207 327 249 256 321 359 256 422 1645 t 0 0 3128 2261 1879 6892 352 6552 7128 270 6402 6977 572 964 2946

oligos_6nt_mkv4_m5_rc_shift5 (oligos_6nt_mkv4_m5_rc)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m5_rc; m=6/7; ncol2=10; w=0; offset=1; strand=R; shift=5; score=0.640181; -----wwGTTTTCww ; cor=; Ncor= a 0 0 0 0 0 1381 1343 0 0 27 8 2 0 1570 1440 c 0 0 0 0 0 931 929 0 0 0 0 0 4612 955 757 g 0 0 0 0 0 796 766 4612 0 0 0 0 0 642 727 t 0 0 0 0 0 1504 1574 0 4612 4585 4604 4610 0 1445 1688

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m5 versus dyads_m2_rc; m=7/7; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.55693; ywTTTTCTTCTTCAw ; cor=; Ncor= a 773 1002 265 124 249 113 111 265 113 116 260 131 97 2566 966 c 1103 617 179 568 125 128 2903 197 60 2873 139 132 2985 200 503 g 531 501 175 130 132 122 97 147 90 113 148 117 138 203 609 t 1081 1368 2869 2666 2982 3125 377 2879 3225 386 2941 3108 268 519 1410

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; rwTGAAGAAGAgrw ; Alignment reference a 2373 2946 964 572 6977 6402 270 7128 6552 352 6892 1879 2261 3128 c 1108 1645 422 256 359 321 256 249 327 207 354 685 1320 1426 g 2715 1133 531 6868 229 432 7192 262 497 7026 295 4030 2623 1181 t 1784 2256 6063 284 415 825 262 341 604 395 439 1386 1776 2245

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rwTGAAGAAGAgrw ; cor=; Ncor= a 2373 2946 964 572 6977 6402 270 7128 6552 352 6892 1879 2261 3128 c 1108 1645 422 256 359 321 256 249 327 207 354 685 1320 1426 g 2715 1133 531 6868 229 432 7192 262 497 7026 295 4030 2623 1181 t 1784 2256 6063 284 415 825 262 341 604 395 439 1386 1776 2245

dyads_m2_shift0 (dyads_m2)
; dyads_m1 versus dyads_m2; m=2/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.776471; rwTGAAGAAGAAAA ; cor=; Ncor= a 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 c 451 609 203 138 117 148 113 90 147 97 122 132 130 175 g 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 t 771 966 2566 97 131 260 116 113 265 111 113 249 124 265

oligos_7nt_mkv5_m5_rc_shift1 (oligos_7nt_mkv5_m5_rc)
; dyads_m1 versus oligos_7nt_mkv5_m5_rc; m=3/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.649507; -wwGAAGAcGaw-- ; cor=; Ncor= a 0 5560 4613 571 13781 12950 912 13346 2670 809 5995 4611 0 0 c 0 2696 2583 418 228 423 267 353 8881 551 2326 2701 0 0 g 0 2105 2489 13240 214 261 12727 345 1191 12395 2590 2251 0 0 t 0 4069 4745 201 207 796 524 386 1688 675 3519 4867 0 0

oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)
; dyads_m1 versus oligos_7nt_mkv5_m3_rc; m=4/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.632058; -wwGAAGATGaw-- ; cor=; Ncor= a 0 7340 6289 502 17361 16087 261 15990 2670 1207 7892 6371 0 0 c 0 3631 3110 180 708 771 167 910 740 315 3276 3502 0 0 g 0 2840 3166 18082 540 677 17792 948 1191 17107 3402 2857 0 0 t 0 5415 6661 462 617 1691 1006 1378 14625 597 4656 6496 0 0

oligos_7nt_mkv5_m1_rc_shift1 (oligos_7nt_mkv5_m1_rc)
; dyads_m1 versus oligos_7nt_mkv5_m1_rc; m=5/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.581893; -waGAAAAAGww-- ; cor=; Ncor= a 0 2852 2978 0 7402 6756 6740 6927 7250 0 2896 2834 0 0 c 0 1409 1974 0 94 243 236 235 570 1 1524 1363 0 0 g 0 1292 1241 8186 96 232 716 234 132 8225 1247 1413 0 0 t 0 2673 2033 40 634 995 534 830 274 0 2559 2616 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=24; shift=2; ncol=26; --aaAAAwAAAAArAAAAAAwAwAwa ; Alignment reference a 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --aaAAAwAAAAArAAAAAAwAwAwa ; cor=; Ncor= a 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m4 versus positions_6nt_m5; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.872785; --aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m4 versus positions_6nt_m1; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.806598; --wawmAAAAArAAAAAAwAAAAAaa ; cor=; Ncor= a 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m4 versus positions_6nt_m2; m=4/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.789622; awrAAAAwAAAAArAAAAAAwtwa-- ; cor=; Ncor= a 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 0 0 c 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 0 0 g 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 0 0 t 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333 0 0

positions_7nt_m1_shift6 (positions_7nt_m1)
; positions_6nt_m4 versus positions_7nt_m1; m=5/6; ncol2=20; w=0; offset=4; strand=D; shift=6; score=0.739564; ------aaAAAArAAAAAAAwAaaaa ; cor=; Ncor= a 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 c 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 g 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 t 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238

positions_7nt_m2_shift7 (positions_7nt_m2)
; positions_6nt_m4 versus positions_7nt_m2; m=6/6; ncol2=24; w=0; offset=5; strand=D; shift=7; score=0.467977; -------waaAAAgAAAAAAATTTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 108 c 0 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 58 g 0 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 45 t 0 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613 611

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=10; shift=0; ncol=10; wwGAAAACww ; Alignment reference a 1688 1445 0 4610 4604 4585 4612 0 1574 1504 c 727 642 0 0 0 0 0 4612 766 796 g 757 955 4612 0 0 0 0 0 929 931 t 1440 1570 0 2 8 27 0 0 1343 1381

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wwGAAAACww ; cor=; Ncor= a 1688 1445 0 4610 4604 4585 4612 0 1574 1504 c 727 642 0 0 0 0 0 4612 766 796 g 757 955 4612 0 0 0 0 0 929 931 t 1440 1570 0 2 8 27 0 0 1343 1381

oligos_7nt_mkv5_m5_rc_shift0 (oligos_7nt_mkv5_m5_rc)
; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m5_rc; m=2/2; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.640181; wwGAAGAcGa ; cor=; Ncor= a 5560 4613 571 13781 12950 912 13346 2670 809 5995 c 2696 2583 418 228 423 267 353 8881 551 2326 g 2105 2489 13240 214 261 12727 345 1191 12395 2590 t 4069 4745 201 207 796 524 386 1688 675 3519

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCATTTTCdw ; Alignment reference a 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 1486 1386 0 570 249 167 284 177 0 2144 1436 t 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCATTTTCdw ; cor=; Ncor= a 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 1486 1386 0 570 249 167 284 177 0 2144 1436 t 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.812531; wtCATCTTCww ; cor=; Ncor= a 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 3502 3276 315 740 910 167 771 708 180 3110 3631 t 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m1; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.810163; wwCTTTTTCtw ; cor=; Ncor= a 2616 2559 0 274 830 534 995 634 40 2033 2673 c 1413 1247 8225 132 234 716 232 96 8186 1241 1292 g 1363 1524 1 570 235 236 243 94 0 1974 1409 t 2834 2896 0 7250 6927 6740 6756 7402 0 2978 2852
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m5; m=4/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.713466; wtCgTCTTCww ; cor=; Ncor= a 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m1_shift4 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwCTTTTTCtw ; Alignment reference a 0 0 0 0 2616 2559 0 274 830 534 995 634 40 2033 2673 c 0 0 0 0 1413 1247 8225 132 234 716 232 96 8186 1241 1292 g 0 0 0 0 1363 1524 1 570 235 236 243 94 0 1974 1409 t 0 0 0 0 2834 2896 0 7250 6927 6740 6756 7402 0 2978 2852
oligos_7nt_mkv5_m1_shift4 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wwCTTTTTCtw ; cor=; Ncor= a 0 0 0 0 2616 2559 0 274 830 534 995 634 40 2033 2673 c 0 0 0 0 1413 1247 8225 132 234 716 232 96 8186 1241 1292 g 0 0 0 0 1363 1524 1 570 235 236 243 94 0 1974 1409 t 0 0 0 0 2834 2896 0 7250 6927 6740 6756 7402 0 2978 2852
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m2; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.810163; ----wwCATTTTCdw ; cor=; Ncor= a 0 0 0 0 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 0 0 0 0 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 0 0 0 0 1486 1386 0 570 249 167 284 177 0 2144 1436 t 0 0 0 0 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m5; m=3/5; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.732268; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 0 0 0 0 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 0 0 0 0 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 0 0 0 0 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m1 versus dyads_m1_rc; m=4/5; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.581893; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2245 1776 1386 439 395 604 341 262 825 415 284 6063 2256 c 0 0 1181 2623 4030 295 7026 497 262 7192 432 229 6868 531 1133 g 0 0 1426 1320 685 354 207 327 249 256 321 359 256 422 1645 t 0 0 3128 2261 1879 6892 352 6552 7128 270 6402 6977 572 964 2946
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m1 versus dyads_m2_rc; m=5/5; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.517014; ywTTTTCTTCTTCAw ; cor=; Ncor= a 773 1002 265 124 249 113 111 265 113 116 260 131 97 2566 966 c 1103 617 179 568 125 128 2903 197 60 2873 139 132 2985 200 503 g 531 501 175 130 132 122 97 147 90 113 148 117 138 203 609 t 1081 1368 2869 2666 2982 3125 377 2879 3225 386 2941 3108 268 519 1410

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=11; shift=4; ncol=15; ----wtCATCTTCww ; Alignment reference a 0 0 0 0 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 0 0 0 0 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 0 0 0 0 3502 3276 315 740 910 167 771 708 180 3110 3631 t 0 0 0 0 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 0 0 0 0 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 0 0 0 0 3502 3276 315 740 910 167 771 708 180 3110 3631 t 0 0 0 0 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m5; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.896294; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 0 0 0 0 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 0 0 0 0 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 0 0 0 0 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.812531; ----wwCATTTTCdw ; cor=; Ncor= a 0 0 0 0 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 0 0 0 0 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 0 0 0 0 1486 1386 0 570 249 167 284 177 0 2144 1436 t 0 0 0 0 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894
oligos_6nt_mkv4_m4_shift5 (oligos_6nt_mkv4_m4)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m4; m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.638133; -----wtACCTTCww ; cor=; Ncor= a 0 0 0 0 0 1413 1065 4440 0 0 129 547 0 1226 1412 c 0 0 0 0 0 902 1088 0 4461 4429 26 66 4461 785 755 g 0 0 0 0 0 926 510 4 0 32 393 45 0 863 782 t 0 0 0 0 0 1220 1798 17 0 0 3913 3803 0 1587 1512
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m3 versus dyads_m1_rc; m=5/6; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.632058; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2245 1776 1386 439 395 604 341 262 825 415 284 6063 2256 c 0 0 1181 2623 4030 295 7026 497 262 7192 432 229 6868 531 1133 g 0 0 1426 1320 685 354 207 327 249 256 321 359 256 422 1645 t 0 0 3128 2261 1879 6892 352 6552 7128 270 6402 6977 572 964 2946
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m3 versus dyads_m2_rc; m=6/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.54107; ywTTTTCTTCTTCAw ; cor=; Ncor= a 773 1002 265 124 249 113 111 265 113 116 260 131 97 2566 966 c 1103 617 179 568 125 128 2903 197 60 2873 139 132 2985 200 503 g 531 501 175 130 132 122 97 147 90 113 148 117 138 203 609 t 1081 1368 2869 2666 2982 3125 377 2879 3225 386 2941 3108 268 519 1410

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift9 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=20; shift=9; ncol=29; ---------aaAAAArAAAAAAAwAaaaa ; Alignment reference a 0 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 c 0 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 g 0 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 t 0 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238
positions_7nt_m1_shift9 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/8; ncol2=20; w=0; offset=0; strand=D; shift=9; score= 1; ---------aaAAAArAAAAAAAwAaaaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 c 0 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 g 0 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 t 0 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=2/8; ncol2=24; w=-3; offset=-3; strand=D; shift=6; score=0.751424; ------wawmAAAAArAAAAAAwAAAAAa ; cor=; Ncor= a 0 0 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 c 0 0 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 g 0 0 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 t 0 0 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342
positions_6nt_m4_shift5 (positions_6nt_m4)				; positions_7nt_m1 versus positions_6nt_m4; m=3/8; ncol2=24; w=-4; offset=-4; strand=D; shift=5; score=0.739564; -----aaAAAwAAAAArAAAAAAwAwAwa ; cor=; Ncor= a 0 0 0 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 0 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 0 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 0 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423
positions_6nt_m5_shift5 (positions_6nt_m5)				; positions_7nt_m1 versus positions_6nt_m5; m=4/8; ncol2=24; w=-4; offset=-4; strand=D; shift=5; score=0.707842; -----aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271
positions_6nt_m2_shift8 (positions_6nt_m2)				; positions_7nt_m1 versus positions_6nt_m2; m=5/8; ncol2=24; w=-1; offset=-1; strand=D; shift=8; score=0.69947; --------awrAAAAwAAAAArAAAAAAw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 c 0 0 0 0 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 g 0 0 0 0 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 t 0 0 0 0 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809
positions_7nt_m2_shift9 (positions_7nt_m2)				; positions_7nt_m1 versus positions_7nt_m2; m=6/8; ncol2=24; w=0; offset=0; strand=D; shift=9; score=0.623834; ---------waaAAAgAAAAAAATTTTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 108 66 c 0 0 0 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 58 52 g 0 0 0 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 45 16 t 0 0 0 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613 611 688
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)				; positions_7nt_m1 versus positions_6nt_m3_rc; m=7/8; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.448297; wwTATTTTTgAAAAATAAAAAAww----- ; cor=; Ncor= a 154 171 48 403 43 75 88 57 51 108 347 377 342 372 393 82 361 374 371 359 346 381 182 201 0 0 0 0 0 c 67 63 26 8 31 29 12 39 11 38 23 18 18 23 22 15 19 14 35 19 26 29 53 38 0 0 0 0 0 g 58 77 33 12 23 19 24 26 30 250 20 8 34 22 13 27 44 25 13 38 11 11 93 67 0 0 0 0 0 t 181 149 353 37 363 337 336 338 368 64 70 57 66 43 32 336 36 47 41 44 77 39 132 154 0 0 0 0 0
dyads_m2_shift6 (dyads_m2)				; positions_7nt_m1 versus dyads_m2; m=8/8; ncol2=16; w=-3; offset=-3; strand=D; shift=6; score=0.404983; ------rwTGAAGAAGAAAAwr------- ; cor=; Ncor= a 0 0 0 0 0 0 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 1368 1081 0 0 0 0 0 0 0 c 0 0 0 0 0 0 451 609 203 138 117 148 113 90 147 97 122 132 130 175 501 531 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 617 1103 0 0 0 0 0 0 0 t 0 0 0 0 0 0 771 966 2566 97 131 260 116 113 265 111 113 249 124 265 1002 773 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift8 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=24; shift=8; ncol=32; --------awrAAAAwAAAAArAAAAAAwtwa ; Alignment reference a 0 0 0 0 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 c 0 0 0 0 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 g 0 0 0 0 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 t 0 0 0 0 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333
positions_6nt_m2_shift8 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=8; score= 1; --------awrAAAAwAAAAArAAAAAAwtwa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 c 0 0 0 0 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 g 0 0 0 0 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 t 0 0 0 0 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333
positions_6nt_m4_shift10 (positions_6nt_m4)				; positions_6nt_m2 versus positions_6nt_m4; m=2/7; ncol2=24; w=0; offset=2; strand=D; shift=10; score=0.789622; ----------aaAAAwAAAAArAAAAAAwAwA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 c 0 0 0 0 0 0 0 0 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 g 0 0 0 0 0 0 0 0 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 t 0 0 0 0 0 0 0 0 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234
positions_6nt_m1_shift8 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=3/7; ncol2=24; w=0; offset=0; strand=D; shift=8; score=0.77517; --------wawmAAAAArAAAAAAwAAAAAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 0 0 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 0 0 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 0 0 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426
positions_6nt_m5_shift8 (positions_6nt_m5)				; positions_6nt_m2 versus positions_6nt_m5; m=4/7; ncol2=24; w=0; offset=0; strand=D; shift=8; score=0.763774; --------aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271
positions_7nt_m1_shift9 (positions_7nt_m1)				; positions_6nt_m2 versus positions_7nt_m1; m=5/7; ncol2=20; w=0; offset=1; strand=D; shift=9; score=0.69947; ---------aaAAAArAAAAAAAwAaaaa--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 0 0 0 c 0 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 0 0 0 g 0 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 0 0 0 t 0 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238 0 0 0
positions_7nt_m2_shift14 (positions_7nt_m2)				; positions_6nt_m2 versus positions_7nt_m2; m=6/7; ncol2=24; w=0; offset=6; strand=D; shift=14; score=0.476052; --------------waaAAAgAAAAAAATTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)				; positions_6nt_m2 versus positions_6nt_m3_rc; m=7/7; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.401179; wwTATTTTTgAAAAATAAAAAAww-------- ; cor=; Ncor= a 154 171 48 403 43 75 88 57 51 108 347 377 342 372 393 82 361 374 371 359 346 381 182 201 0 0 0 0 0 0 0 0 c 67 63 26 8 31 29 12 39 11 38 23 18 18 23 22 15 19 14 35 19 26 29 53 38 0 0 0 0 0 0 0 0 g 58 77 33 12 23 19 24 26 30 250 20 8 34 22 13 27 44 25 13 38 11 11 93 67 0 0 0 0 0 0 0 0 t 181 149 353 37 363 337 336 338 368 64 70 57 66 43 32 336 36 47 41 44 77 39 132 154 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift4 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=24; shift=4; ncol=28; ----aamAArAAAAAwAAAAAArAAraw ; Alignment reference a 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271
positions_6nt_m5_shift4 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271
positions_6nt_m4_shift4 (positions_6nt_m4)				; positions_6nt_m5 versus positions_6nt_m4; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.872785; ----aaAAAwAAAAArAAAAAAwAwAwa ; cor=; Ncor= a 0 0 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423
positions_6nt_m1_shift4 (positions_6nt_m1)				; positions_6nt_m5 versus positions_6nt_m1; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.815046; ----wawmAAAAArAAAAAAwAAAAAaa ; cor=; Ncor= a 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_6nt_m5 versus positions_6nt_m2; m=4/6; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.763774; ----awrAAAAwAAAAArAAAAAAwtwa ; cor=; Ncor= a 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 c 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 g 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 t 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333
positions_7nt_m1_shift8 (positions_7nt_m1)				; positions_6nt_m5 versus positions_7nt_m1; m=5/6; ncol2=20; w=0; offset=4; strand=D; shift=8; score=0.707842; --------aaAAAArAAAAAAAwAaaaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 c 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 g 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 t 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)				; positions_6nt_m5 versus positions_6nt_m3_rc; m=6/6; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.512378; wwTATTTTTgAAAAATAAAAAAww---- ; cor=; Ncor= a 154 171 48 403 43 75 88 57 51 108 347 377 342 372 393 82 361 374 371 359 346 381 182 201 0 0 0 0 c 67 63 26 8 31 29 12 39 11 38 23 18 18 23 22 15 19 14 35 19 26 29 53 38 0 0 0 0 g 58 77 33 12 23 19 24 26 30 250 20 8 34 22 13 27 44 25 13 38 11 11 93 67 0 0 0 0 t 181 149 353 37 363 337 336 338 368 64 70 57 66 43 32 336 36 47 41 44 77 39 132 154 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift6 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=24; shift=6; ncol=30; ------waaAAAgAAAAAAATTTTTTThww ; Alignment reference a 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 108 66 83 235 272 274 c 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 58 52 38 274 119 140 g 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 45 16 21 104 119 90 t 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613 611 688 680 209 312 318
positions_7nt_m2_shift6 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------waaAAAgAAAAAAATTTTTTThww ; cor=; Ncor= a 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 108 66 83 235 272 274 c 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 58 52 38 274 119 140 g 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 45 16 21 104 119 90 t 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613 611 688 680 209 312 318
positions_7nt_m1_shift6 (positions_7nt_m1)				; positions_7nt_m2 versus positions_7nt_m1; m=2/4; ncol2=20; w=0; offset=0; strand=D; shift=6; score=0.623834; ------aaAAAArAAAAAAAwAaaaa---- ; cor=; Ncor= a 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 0 0 0 0 c 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 0 0 0 0 g 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 0 0 0 0 t 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238 0 0 0 0
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_7nt_m2 versus positions_6nt_m2; m=3/4; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.476052; awrAAAAwAAAAArAAAAAAwtwa------ ; cor=; Ncor= a 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 0 0 0 0 0 0 c 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 0 0 0 0 0 0 g 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 0 0 0 0 0 0 t 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333 0 0 0 0 0 0
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_7nt_m2 versus positions_6nt_m4; m=4/4; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.467977; -aaAAAwAAAAArAAAAAAwAwAwa----- ; cor=; Ncor= a 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 0 0 0 0 0 c 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 0 0 0 0 0 g 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 0 0 0 0 0 t 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift8 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=24; shift=8; ncol=32; --------wwTTTTTTATTTTTcAAAAATAww ; Alignment reference a 0 0 0 0 0 0 0 0 154 132 39 77 44 41 47 36 336 32 43 66 57 70 64 368 338 336 337 363 37 353 149 181 c 0 0 0 0 0 0 0 0 67 93 11 11 38 13 25 44 27 13 22 34 8 20 250 30 26 24 19 23 12 33 77 58 g 0 0 0 0 0 0 0 0 38 53 29 26 19 35 14 19 15 22 23 18 18 23 38 11 39 12 29 31 8 26 63 67 t 0 0 0 0 0 0 0 0 201 182 381 346 359 371 374 361 82 393 372 342 377 347 108 51 57 88 75 43 403 48 171 154
positions_6nt_m3_shift8 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=8; score= 1; --------wwTTTTTTATTTTTcAAAAATAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 154 132 39 77 44 41 47 36 336 32 43 66 57 70 64 368 338 336 337 363 37 353 149 181 c 0 0 0 0 0 0 0 0 67 93 11 11 38 13 25 44 27 13 22 34 8 20 250 30 26 24 19 23 12 33 77 58 g 0 0 0 0 0 0 0 0 38 53 29 26 19 35 14 19 15 22 23 18 18 23 38 11 39 12 29 31 8 26 63 67 t 0 0 0 0 0 0 0 0 201 182 381 346 359 371 374 361 82 393 372 342 377 347 108 51 57 88 75 43 403 48 171 154
positions_6nt_m5_rc_shift4 (positions_6nt_m5_rc)				; positions_6nt_m3 versus positions_6nt_m5_rc; m=2/5; ncol2=24; w=-4; offset=-4; strand=R; shift=4; score=0.512378; ----wtyTTyTTTTTTwTTTTTyTTktt---- ; cor=; Ncor= a 0 0 0 0 271 239 123 85 63 86 109 56 61 99 57 54 509 63 39 54 36 62 111 86 49 152 247 264 0 0 0 0 c 0 0 0 0 199 168 502 41 33 547 60 41 64 44 63 40 139 43 51 55 48 64 558 38 65 126 173 185 0 0 0 0 g 0 0 0 0 132 144 72 51 49 74 52 55 33 36 42 44 55 36 28 34 20 27 65 42 32 386 164 105 0 0 0 0 t 0 0 0 0 463 514 368 888 920 358 844 913 907 886 903 927 362 923 947 922 961 912 331 899 919 401 481 511 0 0 0 0
positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)				; positions_6nt_m3 versus positions_6nt_m1_rc; m=3/5; ncol2=24; w=-6; offset=-6; strand=R; shift=2; score=0.497511; --ttTTTTTwTTTTTTyTTTTTkwtw------ ; cor=; Ncor= a 0 0 426 342 129 134 170 134 134 813 88 73 106 53 95 98 162 121 82 88 145 201 256 864 441 479 0 0 0 0 0 0 c 0 0 243 253 93 95 72 77 76 128 90 53 67 70 89 88 799 75 95 116 127 114 228 151 250 259 0 0 0 0 0 0 g 0 0 219 253 118 57 57 59 47 85 50 40 51 44 39 51 66 59 46 39 107 120 610 160 225 195 0 0 0 0 0 0 t 0 0 889 929 1437 1491 1478 1507 1520 751 1549 1611 1553 1610 1554 1540 750 1522 1554 1534 1398 1342 683 602 861 844 0 0 0 0 0 0
positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)				; positions_6nt_m3 versus positions_7nt_m1_rc; m=4/5; ncol2=20; w=-5; offset=-5; strand=R; shift=3; score=0.448297; ---ttttTwTTTTTTTyTTTTtt--------- ; cor=; Ncor= a 0 0 0 1238 1317 1194 834 432 3420 251 270 353 297 284 260 281 670 523 525 517 808 1282 1369 0 0 0 0 0 0 0 0 0 c 0 0 0 969 1044 693 545 391 360 166 219 194 215 263 159 171 2752 338 320 505 462 1024 997 0 0 0 0 0 0 0 0 0 g 0 0 0 896 794 674 492 267 217 133 124 125 126 151 142 133 332 273 230 252 473 682 783 0 0 0 0 0 0 0 0 0 t 0 0 0 2608 2556 3150 3840 4621 1714 5161 5098 5039 5073 5013 5150 5126 1957 4577 4636 4437 3968 2723 2562 0 0 0 0 0 0 0 0 0
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_6nt_m3 versus positions_6nt_m2_rc; m=5/5; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.401179; twawTTTTTTyTTTTTwTTTTywt-------- ; cor=; Ncor= a 333 374 797 809 114 112 63 114 50 111 151 117 100 88 115 84 744 87 95 90 91 160 356 324 0 0 0 0 0 0 0 0 c 249 238 116 98 65 46 58 49 63 64 705 85 77 82 38 67 160 60 76 83 99 620 245 250 0 0 0 0 0 0 0 0 g 196 204 92 74 49 59 41 62 54 66 64 50 49 52 59 46 51 55 39 57 36 133 134 168 0 0 0 0 0 0 0 0 t 556 518 329 353 1106 1117 1172 1109 1167 1093 414 1082 1108 1112 1122 1137 379 1132 1124 1104 1108 421 599 592 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=24; shift=6; ncol=30; ------wawmAAAAArAAAAAAwAAAAAaa ; Alignment reference a 0 0 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------wawmAAAAArAAAAAAwAAAAAaa ; cor=; Ncor= a 0 0 0 0 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 0 0 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 0 0 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 0 0 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426
positions_6nt_m5_shift6 (positions_6nt_m5)				; positions_6nt_m1 versus positions_6nt_m5; m=2/7; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.815046; ------aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 0 0 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 0 0 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 0 0 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 0 0 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_6nt_m1 versus positions_6nt_m4; m=3/7; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.806598; ------aaAAAwAAAAArAAAAAAwAwAwa ; cor=; Ncor= a 0 0 0 0 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 0 0 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 0 0 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 0 0 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423
positions_6nt_m2_shift6 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=4/7; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.77517; ------awrAAAAwAAAAArAAAAAAwtwa ; cor=; Ncor= a 0 0 0 0 0 0 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 c 0 0 0 0 0 0 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 g 0 0 0 0 0 0 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 t 0 0 0 0 0 0 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333
positions_7nt_m1_shift9 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=5/7; ncol2=20; w=0; offset=3; strand=D; shift=9; score=0.751424; ---------aaAAAArAAAAAAAwAaaaa- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 0 c 0 0 0 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 0 g 0 0 0 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 0 t 0 0 0 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238 0
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)				; positions_6nt_m1 versus positions_6nt_m3_rc; m=6/7; ncol2=24; w=-6; offset=-6; strand=R; shift=0; score=0.497511; wwTATTTTTgAAAAATAAAAAAww------ ; cor=; Ncor= a 154 171 48 403 43 75 88 57 51 108 347 377 342 372 393 82 361 374 371 359 346 381 182 201 0 0 0 0 0 0 c 67 63 26 8 31 29 12 39 11 38 23 18 18 23 22 15 19 14 35 19 26 29 53 38 0 0 0 0 0 0 g 58 77 33 12 23 19 24 26 30 250 20 8 34 22 13 27 44 25 13 38 11 11 93 67 0 0 0 0 0 0 t 181 149 353 37 363 337 336 338 368 64 70 57 66 43 32 336 36 47 41 44 77 39 132 154 0 0 0 0 0 0
dyads_m2_shift6 (dyads_m2)				; positions_6nt_m1 versus dyads_m2; m=7/7; ncol2=16; w=0; offset=0; strand=D; shift=6; score=0.485995; ------rwTGAAGAAGAAAAwr-------- ; cor=; Ncor= a 0 0 0 0 0 0 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 1368 1081 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 451 609 203 138 117 148 113 90 147 97 122 132 130 175 501 531 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 617 1103 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 771 966 2566 97 131 260 116 113 265 111 113 249 124 265 1002 773 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift0 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; rwTGAAGAAGAAAAwr ; Alignment reference a 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 1368 1081 c 451 609 203 138 117 148 113 90 147 97 122 132 130 175 501 531 g 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 617 1103 t 771 966 2566 97 131 260 116 113 265 111 113 249 124 265 1002 773
dyads_m2_shift0 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; rwTGAAGAAGAAAAwr ; cor=; Ncor= a 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 1368 1081 c 451 609 203 138 117 148 113 90 147 97 122 132 130 175 501 531 g 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 617 1103 t 771 966 2566 97 131 260 116 113 265 111 113 249 124 265 1002 773
dyads_m1_shift0 (dyads_m1)				; dyads_m2 versus dyads_m1; m=2/7; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.776471; rwTGAAGAAGAgrw-- ; cor=; Ncor= a 2373 2946 964 572 6977 6402 270 7128 6552 352 6892 1879 2261 3128 0 0 c 1108 1645 422 256 359 321 256 249 327 207 354 685 1320 1426 0 0 g 2715 1133 531 6868 229 432 7192 262 497 7026 295 4030 2623 1181 0 0 t 1784 2256 6063 284 415 825 262 341 604 395 439 1386 1776 2245 0 0
oligos_7nt_mkv5_m5_rc_shift1 (oligos_7nt_mkv5_m5_rc)				; dyads_m2 versus oligos_7nt_mkv5_m5_rc; m=3/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.55693; -wwGAAGAcGaw---- ; cor=; Ncor= a 0 5560 4613 571 13781 12950 912 13346 2670 809 5995 4611 0 0 0 0 c 0 2696 2583 418 228 423 267 353 8881 551 2326 2701 0 0 0 0 g 0 2105 2489 13240 214 261 12727 345 1191 12395 2590 2251 0 0 0 0 t 0 4069 4745 201 207 796 524 386 1688 675 3519 4867 0 0 0 0
oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)				; dyads_m2 versus oligos_7nt_mkv5_m3_rc; m=4/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.54107; -wwGAAGATGaw---- ; cor=; Ncor= a 0 7340 6289 502 17361 16087 261 15990 2670 1207 7892 6371 0 0 0 0 c 0 3631 3110 180 708 771 167 910 740 315 3276 3502 0 0 0 0 g 0 2840 3166 18082 540 677 17792 948 1191 17107 3402 2857 0 0 0 0 t 0 5415 6661 462 617 1691 1006 1378 14625 597 4656 6496 0 0 0 0
oligos_7nt_mkv5_m1_rc_shift1 (oligos_7nt_mkv5_m1_rc)				; dyads_m2 versus oligos_7nt_mkv5_m1_rc; m=5/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.517014; -waGAAAAAGww---- ; cor=; Ncor= a 0 2852 2978 0 7402 6756 6740 6927 7250 0 2896 2834 0 0 0 0 c 0 1409 1974 0 94 243 236 235 570 1 1524 1363 0 0 0 0 g 0 1292 1241 8186 96 232 716 234 132 8225 1247 1413 0 0 0 0 t 0 2673 2033 40 634 995 534 830 274 0 2559 2616 0 0 0 0
positions_6nt_m1_shift0 (positions_6nt_m1)				; dyads_m2 versus positions_6nt_m1; m=6/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.485995; wawmAAAAArAAAAAA ; cor=; Ncor= a 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 c 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 g 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 t 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88
positions_7nt_m1_shift3 (positions_7nt_m1)				; dyads_m2 versus positions_7nt_m1; m=7/7; ncol2=20; w=0; offset=3; strand=D; shift=3; score=0.404983; ---aaAAAArAAAAAA ; cor=; Ncor= a 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 c 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 g 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 t 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift1 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wyCACCACCaw ; Alignment reference a 0 4742 2988 811 11135 897 436 11313 936 533 5230 3469 c 0 1595 3050 9888 209 9608 11108 128 9552 10753 1751 2556 g 0 2236 2395 417 287 662 199 269 654 267 2078 2602 t 0 3500 3640 957 442 906 330 363 931 520 3014 3446
dyads_m3_shift1 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wyCACCACCaw ; cor=; Ncor= a 0 4742 2988 811 11135 897 436 11313 936 533 5230 3469 c 0 1595 3050 9888 209 9608 11108 128 9552 10753 1751 2556 g 0 2236 2395 417 287 662 199 269 654 267 2078 2602 t 0 3500 3640 957 442 906 330 363 931 520 3014 3446
oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)				; dyads_m3 versus oligos_6nt_mkv4_m1; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.821767; --wtACCACCdw ; cor=; Ncor= a 0 0 1928 1475 6342 90 28 5762 61 30 2366 2059 c 0 0 1546 1409 123 6725 6040 86 6735 6435 802 1620 g 0 0 1549 808 252 74 276 590 62 271 1955 1208 t 0 0 1964 3295 270 98 643 549 129 251 1864 2100
dyads_m4_shift0 (dyads_m4)				; dyads_m3 versus dyads_m4; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.726799; hwTCACCAACww ; cor=; Ncor= a 1546 1748 228 165 5278 497 189 5463 4966 411 2184 1747 c 1704 876 193 5050 131 4559 5304 73 236 4744 970 984 g 739 969 161 173 120 255 105 113 173 247 1047 1087 t 1749 2145 5156 350 209 427 140 89 363 336 1537 1920

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCgTCTTCww ; Alignment reference a 0 0 0 0 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 0 0 0 0 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 0 0 0 0 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 0 0 0 0 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4867 3519 675 1688 386 524 796 207 201 4745 4069 c 0 0 0 0 2251 2590 12395 1191 345 12727 261 214 13240 2489 2105 g 0 0 0 0 2701 2326 551 8881 353 267 423 228 418 2583 2696 t 0 0 0 0 4611 5995 809 2670 13346 912 12950 13781 571 4613 5560
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m3; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.896294; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6496 4656 597 14625 1378 1006 1691 617 462 6661 5415 c 0 0 0 0 2857 3402 17107 1191 948 17792 677 540 18082 3166 2840 g 0 0 0 0 3502 3276 315 740 910 167 771 708 180 3110 3631 t 0 0 0 0 6371 7892 1207 2670 15990 261 16087 17361 502 6289 7340
oligos_7nt_mkv5_m1_shift4 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m1; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.732268; ----wwCTTTTTCtw ; cor=; Ncor= a 0 0 0 0 2616 2559 0 274 830 534 995 634 40 2033 2673 c 0 0 0 0 1413 1247 8225 132 234 716 232 96 8186 1241 1292 g 0 0 0 0 1363 1524 1 570 235 236 243 94 0 1974 1409 t 0 0 0 0 2834 2896 0 7250 6927 6740 6756 7402 0 2978 2852
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m2; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.713466; ----wwCATTTTCdw ; cor=; Ncor= a 0 0 0 0 2697 2318 0 7010 167 1006 1099 675 19 1983 2337 c 0 0 0 0 1110 1564 7709 132 206 469 199 154 7789 1225 1141 g 0 0 0 0 1486 1386 0 570 249 167 284 177 0 2144 1436 t 0 0 0 0 2515 2540 99 96 7186 6166 6226 6802 0 2456 2894
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m5 versus dyads_m1_rc; m=5/7; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.649507; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2245 1776 1386 439 395 604 341 262 825 415 284 6063 2256 c 0 0 1181 2623 4030 295 7026 497 262 7192 432 229 6868 531 1133 g 0 0 1426 1320 685 354 207 327 249 256 321 359 256 422 1645 t 0 0 3128 2261 1879 6892 352 6552 7128 270 6402 6977 572 964 2946
oligos_6nt_mkv4_m5_rc_shift5 (oligos_6nt_mkv4_m5_rc)				; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m5_rc; m=6/7; ncol2=10; w=0; offset=1; strand=R; shift=5; score=0.640181; -----wwGTTTTCww ; cor=; Ncor= a 0 0 0 0 0 1381 1343 0 0 27 8 2 0 1570 1440 c 0 0 0 0 0 931 929 0 0 0 0 0 4612 955 757 g 0 0 0 0 0 796 766 4612 0 0 0 0 0 642 727 t 0 0 0 0 0 1504 1574 0 4612 4585 4604 4610 0 1445 1688
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m5 versus dyads_m2_rc; m=7/7; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.55693; ywTTTTCTTCTTCAw ; cor=; Ncor= a 773 1002 265 124 249 113 111 265 113 116 260 131 97 2566 966 c 1103 617 179 568 125 128 2903 197 60 2873 139 132 2985 200 503 g 531 501 175 130 132 122 97 147 90 113 148 117 138 203 609 t 1081 1368 2869 2666 2982 3125 377 2879 3225 386 2941 3108 268 519 1410

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift0 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; rwTGAAGAAGAgrw ; Alignment reference a 2373 2946 964 572 6977 6402 270 7128 6552 352 6892 1879 2261 3128 c 1108 1645 422 256 359 321 256 249 327 207 354 685 1320 1426 g 2715 1133 531 6868 229 432 7192 262 497 7026 295 4030 2623 1181 t 1784 2256 6063 284 415 825 262 341 604 395 439 1386 1776 2245
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rwTGAAGAAGAgrw ; cor=; Ncor= a 2373 2946 964 572 6977 6402 270 7128 6552 352 6892 1879 2261 3128 c 1108 1645 422 256 359 321 256 249 327 207 354 685 1320 1426 g 2715 1133 531 6868 229 432 7192 262 497 7026 295 4030 2623 1181 t 1784 2256 6063 284 415 825 262 341 604 395 439 1386 1776 2245
dyads_m2_shift0 (dyads_m2)				; dyads_m1 versus dyads_m2; m=2/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.776471; rwTGAAGAAGAAAA ; cor=; Ncor= a 1098 1410 519 268 3108 2941 386 3225 2879 377 3125 2982 2666 2869 c 451 609 203 138 117 148 113 90 147 97 122 132 130 175 g 1168 503 200 2985 132 139 2873 60 197 2903 128 125 568 179 t 771 966 2566 97 131 260 116 113 265 111 113 249 124 265
oligos_7nt_mkv5_m5_rc_shift1 (oligos_7nt_mkv5_m5_rc)				; dyads_m1 versus oligos_7nt_mkv5_m5_rc; m=3/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.649507; -wwGAAGAcGaw-- ; cor=; Ncor= a 0 5560 4613 571 13781 12950 912 13346 2670 809 5995 4611 0 0 c 0 2696 2583 418 228 423 267 353 8881 551 2326 2701 0 0 g 0 2105 2489 13240 214 261 12727 345 1191 12395 2590 2251 0 0 t 0 4069 4745 201 207 796 524 386 1688 675 3519 4867 0 0
oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)				; dyads_m1 versus oligos_7nt_mkv5_m3_rc; m=4/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.632058; -wwGAAGATGaw-- ; cor=; Ncor= a 0 7340 6289 502 17361 16087 261 15990 2670 1207 7892 6371 0 0 c 0 3631 3110 180 708 771 167 910 740 315 3276 3502 0 0 g 0 2840 3166 18082 540 677 17792 948 1191 17107 3402 2857 0 0 t 0 5415 6661 462 617 1691 1006 1378 14625 597 4656 6496 0 0
oligos_7nt_mkv5_m1_rc_shift1 (oligos_7nt_mkv5_m1_rc)				; dyads_m1 versus oligos_7nt_mkv5_m1_rc; m=5/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.581893; -waGAAAAAGww-- ; cor=; Ncor= a 0 2852 2978 0 7402 6756 6740 6927 7250 0 2896 2834 0 0 c 0 1409 1974 0 94 243 236 235 570 1 1524 1363 0 0 g 0 1292 1241 8186 96 232 716 234 132 8225 1247 1413 0 0 t 0 2673 2033 40 634 995 534 830 274 0 2559 2616 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=24; shift=2; ncol=26; --aaAAAwAAAAArAAAAAAwAwAwa ; Alignment reference a 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --aaAAAwAAAAArAAAAAAwAwAwa ; cor=; Ncor= a 0 0 946 945 1567 1548 1569 680 1532 1591 1573 1585 1542 640 1597 1644 1558 1630 1621 1536 587 1513 664 1353 822 890 c 0 0 211 187 73 67 73 91 89 92 65 48 92 72 67 43 60 63 48 84 70 92 149 129 275 255 g 0 0 311 332 97 86 86 194 103 74 121 97 97 916 100 77 82 63 55 110 127 92 154 156 285 304 t 0 0 404 408 135 171 144 907 148 115 113 142 141 244 108 108 172 116 148 142 1088 175 905 234 490 423
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m4 versus positions_6nt_m5; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.872785; --aamAArAAAAAwAAAAAArAAraw ; cor=; Ncor= a 0 0 511 481 401 919 899 331 912 961 922 947 923 362 927 903 886 907 913 844 358 920 888 368 514 463 c 0 0 105 164 386 32 42 65 27 20 34 28 36 55 44 42 36 33 55 52 74 49 51 72 144 132 g 0 0 185 173 126 65 38 558 64 48 55 51 43 139 40 63 44 64 41 60 547 33 41 502 168 199 t 0 0 264 247 152 49 86 111 62 36 54 39 63 509 54 57 99 61 56 109 86 63 85 123 239 271
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m4 versus positions_6nt_m1; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.806598; --wawmAAAAArAAAAAAwAAAAAaa ; cor=; Ncor= a 0 0 844 861 602 683 1342 1398 1534 1554 1522 750 1540 1554 1610 1553 1611 1549 751 1520 1507 1478 1491 1437 929 889 c 0 0 195 225 160 610 120 107 39 46 59 66 51 39 44 51 40 50 85 47 59 57 57 118 253 219 g 0 0 259 250 151 228 114 127 116 95 75 799 88 89 70 67 53 90 128 76 77 72 95 93 253 243 t 0 0 479 441 864 256 201 145 88 82 121 162 98 95 53 106 73 88 813 134 134 170 134 129 342 426
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m4 versus positions_6nt_m2; m=4/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.789622; awrAAAAwAAAAArAAAAAAwtwa-- ; cor=; Ncor= a 592 599 421 1108 1104 1124 1132 379 1137 1122 1112 1108 1082 414 1093 1167 1109 1172 1117 1106 353 329 518 556 0 0 c 168 134 133 36 57 39 55 51 46 59 52 49 50 64 66 54 62 41 59 49 74 92 204 196 0 0 g 250 245 620 99 83 76 60 160 67 38 82 77 85 705 64 63 49 58 46 65 98 116 238 249 0 0 t 324 356 160 91 90 95 87 744 84 115 88 100 117 151 111 50 114 63 112 114 809 797 374 333 0 0
positions_7nt_m1_shift6 (positions_7nt_m1)				; positions_6nt_m4 versus positions_7nt_m1; m=5/6; ncol2=20; w=0; offset=4; strand=D; shift=6; score=0.739564; ------aaAAAArAAAAAAAwAaaaa ; cor=; Ncor= a 0 0 0 0 0 0 2562 2723 3968 4437 4636 4577 1957 5126 5150 5013 5073 5039 5098 5161 1714 4621 3840 3150 2556 2608 c 0 0 0 0 0 0 783 682 473 252 230 273 332 133 142 151 126 125 124 133 217 267 492 674 794 896 g 0 0 0 0 0 0 997 1024 462 505 320 338 2752 171 159 263 215 194 219 166 360 391 545 693 1044 969 t 0 0 0 0 0 0 1369 1282 808 517 525 523 670 281 260 284 297 353 270 251 3420 432 834 1194 1317 1238
positions_7nt_m2_shift7 (positions_7nt_m2)				; positions_6nt_m4 versus positions_7nt_m2; m=6/6; ncol2=24; w=0; offset=5; strand=D; shift=7; score=0.467977; -------waaAAAgAAAAAAATTTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 316 329 515 576 664 622 178 696 637 658 699 664 666 684 77 83 74 109 108 c 0 0 0 0 0 0 0 102 150 73 71 23 37 50 28 46 32 35 34 55 38 30 37 57 53 58 g 0 0 0 0 0 0 0 146 153 69 69 48 68 470 38 45 73 33 49 27 29 51 49 53 47 45 t 0 0 0 0 0 0 0 258 190 165 106 87 95 124 60 94 59 55 75 74 71 664 653 638 613 611