One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.143635_2026-01-05.143635_7Pttt5/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.143635_2026-01-05.143635_7Pttt5/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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; arCCAATCas ; Alignment reference a 530 502 33 3 1751 1878 1 42 661 368 c 459 378 1833 1694 5 1 1 1830 456 552 g 466 591 10 137 91 0 0 2 468 620 t 426 410 5 47 34 2 1879 7 296 341

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; arCCAATCas ; cor=; Ncor= a 530 502 33 3 1751 1878 1 42 661 368 c 459 378 1833 1694 5 1 1 1830 456 552 g 466 591 10 137 91 0 0 2 468 620 t 426 410 5 47 34 2 1879 7 296 341

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---ssCGCCCCCGss ; Alignment reference a 0 0 0 822 797 140 134 125 124 251 160 229 301 869 851 c 0 0 0 2390 2593 5515 77 5372 5289 4635 5291 5214 340 2643 2394 g 0 0 0 1827 1714 197 5517 269 270 776 312 306 4912 1645 1779 t 0 0 0 907 842 94 218 180 263 284 183 197 393 789 922

oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCCCGss ; cor=; Ncor= a 0 0 0 822 797 140 134 125 124 251 160 229 301 869 851 c 0 0 0 2390 2593 5515 77 5372 5289 4635 5291 5214 340 2643 2394 g 0 0 0 1827 1714 197 5517 269 270 776 312 306 4912 1645 1779 t 0 0 0 907 842 94 218 180 263 284 183 197 393 789 922

oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.84461; ---ssCGCCCTCGss ; cor=; Ncor= a 0 0 0 614 644 137 111 73 95 81 160 95 225 620 666 c 0 0 0 1713 1603 3918 132 3911 3880 3920 294 3889 583 1666 1533 g 0 0 0 1252 1346 154 3906 225 256 215 312 253 3208 1402 1303 t 0 0 0 755 741 125 185 125 103 118 3568 97 318 646 832

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m1; m=3/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.506416; ssCCCCGCCCcs--- ; cor=; Ncor= a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 0 0 0 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 0 0 0 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 0 0 0 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=21; shift=0; ncol=21; wwataTTTTTTAAAAAArwww ; Alignment reference a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 479 501 519 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 215 265 259 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 278 312 254 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340 511 405 451

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/6; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; wwataTTTTTTAAAAAArwww ; cor=; Ncor= a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 479 501 519 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 215 265 259 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 278 312 254 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340 511 405 451

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m5 versus positions_6nt_m1; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.915236; wwwtaTTTTTTAAAAAAtaww ; cor=; Ncor= a 378 351 555 174 693 119 138 110 117 97 157 864 908 896 860 831 834 218 709 286 357 c 169 219 141 143 96 89 79 70 60 57 52 50 60 52 84 76 83 116 96 144 198 g 218 198 143 96 116 82 73 85 51 61 50 54 58 60 70 80 89 95 145 142 219 t 360 357 286 712 220 835 835 860 897 910 866 157 99 117 111 138 119 696 175 553 351

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_6nt_m5 versus positions_6nt_m4_rc; m=3/6; ncol2=20; w=0; offset=0; strand=R; shift=0; score=0.867484; wwwTaTTTTTTAAAatatww- ; cor=; Ncor= a 842 810 1374 330 1751 236 291 270 296 210 326 1852 1956 1890 1812 485 1729 534 845 828 0 c 451 503 326 301 210 146 150 147 155 156 138 190 207 230 210 276 259 317 496 513 0 g 533 448 318 215 231 155 199 182 138 156 180 173 185 180 248 246 312 314 544 471 0 t 866 931 674 1846 500 2155 2052 2093 2103 2170 2048 477 344 392 422 1685 392 1527 807 880 0

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_6nt_m5 versus positions_7nt_m2; m=4/6; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.613544; ----twTTTTTAAAAAwa--- ; cor=; Ncor= a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 0 0 0 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 0 0 0 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 0 0 0 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473 0 0 0

positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_6nt_m5 versus positions_7nt_m4; m=5/6; ncol2=13; w=0; offset=5; strand=D; shift=5; score=0.490783; -----wwATTTAAAAawa--- ; cor=; Ncor= a 0 0 0 0 0 1735 1597 4823 578 396 489 5430 5219 5261 4994 3843 1881 2208 0 0 0 c 0 0 0 0 0 1216 1567 393 201 166 151 191 343 267 342 662 1368 1315 0 0 0 g 0 0 0 0 0 1407 1031 363 210 302 169 222 245 197 252 868 1247 1240 0 0 0 t 0 0 0 0 0 1957 2120 736 5326 5451 5506 472 508 590 727 942 1819 1552 0 0 0

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_6nt_m5 versus positions_7nt_m1_rc; m=6/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.402025; -ttTTTTTTTtt--------- ; cor=; Ncor= a 0 3570 3674 583 633 846 902 751 512 572 3543 4212 0 0 0 0 0 0 0 0 0 c 0 3048 3335 251 463 714 816 704 504 344 3821 3876 0 0 0 0 0 0 0 0 0 g 0 3929 3679 399 734 1199 1535 1243 608 317 3301 2357 0 0 0 0 0 0 0 0 0 t 0 7797 7656 17111 16514 15585 15091 15646 16720 17111 7679 7899 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; csCCCCTCCCcc ; Alignment reference a 1745 1414 258 355 274 278 639 130 248 291 1813 1626 c 3917 3878 9331 9149 9520 9607 376 9691 9817 9565 4393 4352 g 2521 2732 428 401 339 206 840 386 251 275 1794 2613 t 2453 2612 619 731 503 545 8781 429 320 505 2636 2045

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; csCCCCTCCCcc ; cor=; Ncor= a 1745 1414 258 355 274 278 639 130 248 291 1813 1626 c 3917 3878 9331 9149 9520 9607 376 9691 9817 9565 4393 4352 g 2521 2732 428 401 339 206 840 386 251 275 1794 2613 t 2453 2612 619 731 503 545 8781 429 320 505 2636 2045

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.878603; ssCCCCGCCCcs ; cor=; Ncor= a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---ssCGCCCTCGss ; Alignment reference a 0 0 0 614 644 137 111 73 95 81 160 95 225 620 666 c 0 0 0 1713 1603 3918 132 3911 3880 3920 294 3889 583 1666 1533 g 0 0 0 1252 1346 154 3906 225 256 215 312 253 3208 1402 1303 t 0 0 0 755 741 125 185 125 103 118 3568 97 318 646 832

oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCTCGss ; cor=; Ncor= a 0 0 0 614 644 137 111 73 95 81 160 95 225 620 666 c 0 0 0 1713 1603 3918 132 3911 3880 3920 294 3889 583 1666 1533 g 0 0 0 1252 1346 154 3906 225 256 215 312 253 3208 1402 1303 t 0 0 0 755 741 125 185 125 103 118 3568 97 318 646 832

oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.84461; ---ssCGCCCCCGss ; cor=; Ncor= a 0 0 0 822 797 140 134 125 124 251 160 229 301 869 851 c 0 0 0 2390 2593 5515 77 5372 5289 4635 5291 5214 340 2643 2394 g 0 0 0 1827 1714 197 5517 269 270 776 312 306 4912 1645 1779 t 0 0 0 907 842 94 218 180 263 284 183 197 393 789 922

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m1; m=3/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.479746; ssCCCCGCCCcs--- ; cor=; Ncor= a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 0 0 0 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 0 0 0 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 0 0 0 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; rrGAACAATGgvr ; Alignment reference a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rrGAACAATGgvr ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_6nt_m2 versus positions_7nt_m3; m=2/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.986676; rrGAACAATGGvr ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; positions_6nt_m2 versus oligos_6nt_mkv4_m2; m=3/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.785374; --raACAATGGmr ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554

positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_6nt_m2 versus positions_7nt_m5; m=4/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.660265; --rmACAATAGma ; cor=; Ncor= a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595

positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_6nt_m2 versus positions_6nt_m3; m=5/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.581529; --rrACAAAGrv- ; cor=; Ncor= a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 0 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 0 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 0 t 0 0 909 1067 0 96 35 165 52 77 790 764 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift9 ; 4 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=11; shift=9; ncol=20; ---------aaAAAAAAAaa ; Alignment reference a 0 0 0 0 0 0 0 0 0 7899 7679 17111 16720 15646 15091 15585 16514 17111 7656 7797 c 0 0 0 0 0 0 0 0 0 2357 3301 317 608 1243 1535 1199 734 399 3679 3929 g 0 0 0 0 0 0 0 0 0 3876 3821 344 504 704 816 714 463 251 3335 3048 t 0 0 0 0 0 0 0 0 0 4212 3543 572 512 751 902 846 633 583 3674 3570

positions_7nt_m1_shift9 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=9; score= 1; ---------aaAAAAAAAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 7899 7679 17111 16720 15646 15091 15585 16514 17111 7656 7797 c 0 0 0 0 0 0 0 0 0 2357 3301 317 608 1243 1535 1199 734 399 3679 3929 g 0 0 0 0 0 0 0 0 0 3876 3821 344 504 704 816 714 463 251 3335 3048 t 0 0 0 0 0 0 0 0 0 4212 3543 572 512 751 902 846 633 583 3674 3570

positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_7nt_m1 versus positions_6nt_m4; m=2/3; ncol2=20; w=-8; offset=-8; strand=D; shift=1; score=0.424402; -wwatatTTTAAAAAAtAww ; cor=; Ncor= a 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 1846 674 931 c 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 215 318 448 g 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 301 326 503 t 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751 330 1374 810

positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)
; positions_7nt_m1 versus positions_6nt_m5_rc; m=3/3; ncol2=21; w=-9; offset=-9; strand=R; shift=0; score=0.402025; wwwyTTTTTTAAAAAAtatw ; cor=; Ncor= a 451 405 511 340 159 137 138 123 128 210 1143 1227 1216 1142 1144 1141 296 991 367 491 c 254 312 278 491 119 97 97 80 83 70 74 73 55 113 102 97 154 135 184 254 g 259 265 215 227 93 106 86 76 75 70 67 63 71 85 102 104 136 169 191 277 t 519 501 479 425 1112 1143 1162 1204 1197 1133 199 120 141 143 135 141 897 188 741 461

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --wyATTTTTAww ; Alignment reference a 0 0 2293 2082 7650 373 328 325 305 641 7627 3145 2826 c 0 0 1790 2642 481 308 321 261 358 513 489 1573 1732 g 0 0 1902 1778 426 358 333 446 327 391 399 1765 1712 t 0 0 3172 2655 600 8118 8175 8125 8167 7612 642 2674 2887

oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wyATTTTTAww ; cor=; Ncor= a 0 0 2293 2082 7650 373 328 325 305 641 7627 3145 2826 c 0 0 1790 2642 481 308 321 261 358 513 489 1573 1732 g 0 0 1902 1778 426 358 333 446 327 391 399 1765 1712 t 0 0 3172 2655 600 8118 8175 8125 8167 7612 642 2674 2887

positions_7nt_m4_rc_shift3 (positions_7nt_m4_rc)
; oligos_7nt_mkv5_m5 versus positions_7nt_m4_rc; m=2/4; ncol2=13; w=0; offset=1; strand=R; shift=3; score=0.582372; ---twtTTTTAAA ; cor=; Ncor= a 0 0 0 1552 1819 942 727 590 508 472 5506 5451 5326 c 0 0 0 1240 1247 868 252 197 245 222 169 302 210 g 0 0 0 1315 1368 662 342 267 343 191 151 166 201 t 0 0 0 2208 1881 3843 4994 5261 5219 5430 489 396 578

positions_7nt_m2_shift3 (positions_7nt_m2)
; oligos_7nt_mkv5_m5 versus positions_7nt_m2; m=3/4; ncol2=14; w=0; offset=1; strand=D; shift=3; score=0.544235; ---twTTTTTAAA ; cor=; Ncor= a 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 c 0 0 0 1202 1274 487 351 237 204 257 292 253 246 g 0 0 0 1268 1268 490 352 246 253 293 260 206 238 t 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; oligos_7nt_mkv5_m5 versus positions_6nt_m4_rc; m=4/4; ncol2=20; w=-2; offset=-2; strand=R; shift=0; score=0.408712; wwwTaTTTTTTAA ; cor=; Ncor= a 842 810 1374 330 1751 236 291 270 296 210 326 1852 1956 c 451 503 326 301 210 146 150 147 155 156 138 190 207 g 533 448 318 215 231 155 199 182 138 156 180 173 185 t 866 931 674 1846 500 2155 2052 2093 2103 2170 2048 477 344

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -aaCAAAAGAma ; Alignment reference a 0 2009 2725 172 5975 5911 5797 5868 69 4635 1927 2011 c 0 1327 1166 5662 94 180 189 144 377 706 1704 1595 g 0 1568 1107 171 157 162 102 187 5589 740 1339 1413 t 0 1540 1446 439 218 191 356 245 409 363 1474 1425

oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -aaCAAAAGAma ; cor=; Ncor= a 0 2009 2725 172 5975 5911 5797 5868 69 4635 1927 2011 c 0 1327 1166 5662 94 180 189 144 377 706 1704 1595 g 0 1568 1107 171 157 162 102 187 5589 740 1339 1413 t 0 1540 1446 439 218 191 356 245 409 363 1474 1425

positions_7nt_m5_shift0 (positions_7nt_m5)
; oligos_6nt_mkv4_m5 versus positions_7nt_m5; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.621087; rmACAATAGma- ; cor=; Ncor= a 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 0 c 1216 1846 245 6259 207 284 481 113 297 1858 1748 0 g 1863 1719 156 277 52 344 292 1092 6169 1771 1669 0 t 1694 1190 210 209 128 248 5856 306 242 1392 1595 0

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; rrGAACAATGGvr ; Alignment reference a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rrGAACAATGGvr ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_7nt_m3 versus positions_6nt_m2; m=2/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.986676; rrGAACAATGgvr ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; positions_7nt_m3 versus oligos_6nt_mkv4_m2; m=3/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.774337; --raACAATGGmr ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554

positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_7nt_m3 versus positions_7nt_m5; m=4/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.675389; --rmACAATAGma ; cor=; Ncor= a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595

positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_7nt_m3 versus positions_6nt_m3; m=5/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.559665; --rrACAAAGrv- ; cor=; Ncor= a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 0 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 0 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 0 t 0 0 909 1067 0 96 35 165 52 77 790 764 0

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift5 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=13; shift=5; ncol=18; -----wwATTTAAAAawa ; Alignment reference a 0 0 0 0 0 1735 1597 4823 578 396 489 5430 5219 5261 4994 3843 1881 2208 c 0 0 0 0 0 1216 1567 393 201 166 151 191 343 267 342 662 1368 1315 g 0 0 0 0 0 1407 1031 363 210 302 169 222 245 197 252 868 1247 1240 t 0 0 0 0 0 1957 2120 736 5326 5451 5506 472 508 590 727 942 1819 1552

positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=5; score= 1; -----wwATTTAAAAawa ; cor=; Ncor= a 0 0 0 0 0 1735 1597 4823 578 396 489 5430 5219 5261 4994 3843 1881 2208 c 0 0 0 0 0 1216 1567 393 201 166 151 191 343 267 342 662 1368 1315 g 0 0 0 0 0 1407 1031 363 210 302 169 222 245 197 252 868 1247 1240 t 0 0 0 0 0 1957 2120 736 5326 5451 5506 472 508 590 727 942 1819 1552

positions_7nt_m2_rc_shift4 (positions_7nt_m2_rc)
; positions_7nt_m4 versus positions_7nt_m2_rc; m=2/6; ncol2=14; w=-1; offset=-1; strand=R; shift=4; score=0.79293; ----twTTTTTAAAAAwa ; cor=; Ncor= a 0 0 0 0 1473 1487 710 444 388 336 657 4715 5132 5052 4777 4230 1893 1979 c 0 0 0 0 1203 1276 488 350 238 206 260 293 253 246 352 490 1268 1268 g 0 0 0 0 1267 1266 494 353 246 253 292 257 204 237 351 487 1274 1202 t 0 0 0 0 1979 1893 4230 4775 5050 5127 4713 657 333 387 442 715 1487 1473

oligos_7nt_mkv5_m5_rc_shift8 (oligos_7nt_mkv5_m5_rc)
; positions_7nt_m4 versus oligos_7nt_mkv5_m5_rc; m=3/6; ncol2=11; w=0; offset=3; strand=R; shift=8; score=0.582372; --------wwTAAAAATr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2887 2674 642 7612 8167 8125 8175 8118 600 2655 c 0 0 0 0 0 0 0 0 1712 1765 399 391 327 446 333 358 426 1778 g 0 0 0 0 0 0 0 0 1732 1573 489 513 358 261 321 308 481 2642 t 0 0 0 0 0 0 0 0 2826 3145 7627 641 305 325 328 373 7650 2082

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_7nt_m4 versus positions_6nt_m4; m=4/6; ncol2=20; w=-3; offset=-3; strand=D; shift=2; score=0.506448; --wwatatTTTAAAAAAt ; cor=; Ncor= a 0 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 c 0 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 g 0 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 t 0 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_7nt_m4 versus positions_6nt_m5; m=5/6; ncol2=21; w=-5; offset=-5; strand=D; shift=0; score=0.490783; wwataTTTTTTAAAAAAr ; cor=; Ncor= a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; positions_7nt_m4 versus positions_6nt_m1_rc; m=6/6; ncol2=22; w=-5; offset=-5; strand=R; shift=0; score=0.462626; wwwtaTTTTTTAAAAAAt ; cor=; Ncor= a 380 351 553 175 696 119 138 111 117 99 157 866 910 897 860 835 835 220 c 169 219 142 145 95 89 80 70 60 58 54 50 61 51 85 73 82 116 g 216 198 144 96 116 83 76 84 52 60 50 52 57 60 70 79 89 96 t 360 357 286 709 218 834 831 860 896 908 864 157 97 117 110 138 119 693

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; waTAATkAkw ; Alignment reference a 1994 2133 27 6476 6418 66 813 6153 1626 1940 c 1233 1415 10 42 101 300 258 112 1613 1527 g 1659 1535 38 101 117 86 3913 140 1725 1521 t 1848 1651 6659 115 98 6282 1750 329 1770 1746

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; waTAATkAkw ; cor=; Ncor= a 1994 2133 27 6476 6418 66 813 6153 1626 1940 c 1233 1415 10 42 101 300 258 112 1613 1527 g 1659 1535 38 101 117 86 3913 140 1725 1521 t 1848 1651 6659 115 98 6282 1750 329 1770 1746

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCCCCGCCCcs ; Alignment reference a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCCCCGCCCcs ; cor=; Ncor= a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m4; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.878603; csCCCCTCCCcc ; cor=; Ncor= a 1745 1414 258 355 274 278 639 130 248 291 1813 1626 c 3917 3878 9331 9149 9520 9607 376 9691 9817 9565 4393 4352 g 2521 2732 428 401 339 206 840 386 251 275 1794 2613 t 2453 2612 619 731 503 545 8781 429 320 505 2636 2045

oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m3; m=3/4; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.506416; ---ssCGCCCCC ; cor=; Ncor= a 0 0 0 822 797 140 134 125 124 251 160 229 c 0 0 0 2390 2593 5515 77 5372 5289 4635 5291 5214 g 0 0 0 1827 1714 197 5517 269 270 776 312 306 t 0 0 0 907 842 94 218 180 263 284 183 197

oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m4; m=4/4; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.479746; ---ssCGCCCTC ; cor=; Ncor= a 0 0 0 614 644 137 111 73 95 81 160 95 c 0 0 0 1713 1603 3918 132 3911 3880 3920 294 3889 g 0 0 0 1252 1346 154 3906 225 256 215 312 253 t 0 0 0 755 741 125 185 125 103 118 3568 97

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --rmACAATAGma ; Alignment reference a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595

positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --rmACAATAGma ; cor=; Ncor= a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; positions_7nt_m5 versus oligos_6nt_mkv4_m2; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.858138; --raACAATGGmr ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m5 versus positions_7nt_m3; m=3/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.675389; rrGAACAATGGvr ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_7nt_m5 versus positions_6nt_m2; m=4/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.660265; rrGAACAATGgvr ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161

oligos_6nt_mkv4_m5_shift3 (oligos_6nt_mkv4_m5)
; positions_7nt_m5 versus oligos_6nt_mkv4_m5; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.621087; ---aaCAAAAGAm ; cor=; Ncor= a 0 0 0 2009 2725 172 5975 5911 5797 5868 69 4635 1927 c 0 0 0 1327 1166 5662 94 180 189 144 377 706 1704 g 0 0 0 1568 1107 171 157 162 102 187 5589 740 1339 t 0 0 0 1540 1446 439 218 191 356 245 409 363 1474

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=22; shift=0; ncol=22; wwwtaTTTTTTAAAAAAtawww ; Alignment reference a 378 351 555 174 693 119 138 110 117 97 157 864 908 896 860 831 834 218 709 286 357 360 c 169 219 141 143 96 89 79 70 60 57 52 50 60 52 84 76 83 116 96 144 198 216 g 218 198 143 96 116 82 73 85 51 61 50 54 58 60 70 80 89 95 145 142 219 169 t 360 357 286 712 220 835 835 860 897 910 866 157 99 117 111 138 119 696 175 553 351 380

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/5; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; wwwtaTTTTTTAAAAAAtawww ; cor=; Ncor= a 378 351 555 174 693 119 138 110 117 97 157 864 908 896 860 831 834 218 709 286 357 360 c 169 219 141 143 96 89 79 70 60 57 52 50 60 52 84 76 83 116 96 144 198 216 g 218 198 143 96 116 82 73 85 51 61 50 54 58 60 70 80 89 95 145 142 219 169 t 360 357 286 712 220 835 835 860 897 910 866 157 99 117 111 138 119 696 175 553 351 380

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m1 versus positions_6nt_m5; m=2/5; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.915236; wwataTTTTTTAAAAAArwww- ; cor=; Ncor= a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 479 501 519 0 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 215 265 259 0 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 278 312 254 0 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340 511 405 451 0

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_6nt_m1 versus positions_6nt_m4_rc; m=3/5; ncol2=20; w=0; offset=0; strand=R; shift=0; score=0.837051; wwwTaTTTTTTAAAatatww-- ; cor=; Ncor= a 842 810 1374 330 1751 236 291 270 296 210 326 1852 1956 1890 1812 485 1729 534 845 828 0 0 c 451 503 326 301 210 146 150 147 155 156 138 190 207 230 210 276 259 317 496 513 0 0 g 533 448 318 215 231 155 199 182 138 156 180 173 185 180 248 246 312 314 544 471 0 0 t 866 931 674 1846 500 2155 2052 2093 2103 2170 2048 477 344 392 422 1685 392 1527 807 880 0 0

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_6nt_m1 versus positions_7nt_m2; m=4/5; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.575641; ----twTTTTTAAAAAwa---- ; cor=; Ncor= a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 0 0 0 0 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 0 0 0 0 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 0 0 0 0 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473 0 0 0 0

positions_7nt_m4_rc_shift4 (positions_7nt_m4_rc)
; positions_6nt_m1 versus positions_7nt_m4_rc; m=5/5; ncol2=13; w=0; offset=4; strand=R; shift=4; score=0.462626; ----twtTTTTAAATww----- ; cor=; Ncor= a 0 0 0 0 1552 1819 942 727 590 508 472 5506 5451 5326 736 2120 1957 0 0 0 0 0 c 0 0 0 0 1240 1247 868 252 197 245 222 169 302 210 363 1031 1407 0 0 0 0 0 g 0 0 0 0 1315 1368 662 342 267 343 191 151 166 201 393 1567 1216 0 0 0 0 0 t 0 0 0 0 2208 1881 3843 4994 5261 5219 5430 489 396 578 4823 1597 1735 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=14; shift=4; ncol=18; ----twTTTTTAAAAAwa ; Alignment reference a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=4; score= 1; ----twTTTTTAAAAAwa ; cor=; Ncor= a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473

positions_7nt_m4_rc_shift4 (positions_7nt_m4_rc)
; positions_7nt_m2 versus positions_7nt_m4_rc; m=2/6; ncol2=13; w=0; offset=0; strand=R; shift=4; score=0.79293; ----twtTTTTAAATww- ; cor=; Ncor= a 0 0 0 0 1552 1819 942 727 590 508 472 5506 5451 5326 736 2120 1957 0 c 0 0 0 0 1240 1247 868 252 197 245 222 169 302 210 363 1031 1407 0 g 0 0 0 0 1315 1368 662 342 267 343 191 151 166 201 393 1567 1216 0 t 0 0 0 0 2208 1881 3843 4994 5261 5219 5430 489 396 578 4823 1597 1735 0

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_7nt_m2 versus positions_6nt_m5; m=3/6; ncol2=21; w=-4; offset=-4; strand=D; shift=0; score=0.613544; wwataTTTTTTAAAAAAr ; cor=; Ncor= a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_7nt_m2 versus positions_6nt_m4; m=4/6; ncol2=20; w=-2; offset=-2; strand=D; shift=2; score=0.577384; --wwatatTTTAAAAAAt ; cor=; Ncor= a 0 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 c 0 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 g 0 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 t 0 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m2 versus positions_6nt_m1; m=5/6; ncol2=22; w=-4; offset=-4; strand=D; shift=0; score=0.575641; wwwtaTTTTTTAAAAAAt ; cor=; Ncor= a 378 351 555 174 693 119 138 110 117 97 157 864 908 896 860 831 834 218 c 169 219 141 143 96 89 79 70 60 57 52 50 60 52 84 76 83 116 g 218 198 143 96 116 82 73 85 51 61 50 54 58 60 70 80 89 95 t 360 357 286 712 220 835 835 860 897 910 866 157 99 117 111 138 119 696

oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)
; positions_7nt_m2 versus oligos_7nt_mkv5_m5; m=6/6; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.544235; ---wyATTTTTAww---- ; cor=; Ncor= a 0 0 0 2293 2082 7650 373 328 325 305 641 7627 3145 2826 0 0 0 0 c 0 0 0 1790 2642 481 308 321 261 358 513 489 1573 1732 0 0 0 0 g 0 0 0 1902 1778 426 358 333 446 327 391 399 1765 1712 0 0 0 0 t 0 0 0 3172 2655 600 8118 8175 8125 8167 7612 642 2674 2887 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --raACAATGGmr ; Alignment reference a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --raACAATGGmr ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554

positions_7nt_m5_shift2 (positions_7nt_m5)
; oligos_6nt_mkv4_m2 versus positions_7nt_m5; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.858138; --rmACAATAGma ; cor=; Ncor= a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595

positions_6nt_m2_shift0 (positions_6nt_m2)
; oligos_6nt_mkv4_m2 versus positions_6nt_m2; m=3/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.785374; rrGAACAATGgvr ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161

positions_7nt_m3_shift0 (positions_7nt_m3)
; oligos_6nt_mkv4_m2 versus positions_7nt_m3; m=4/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.774337; rrGAACAATGGvr ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549

positions_6nt_m3_shift2 (positions_6nt_m3)
; oligos_6nt_mkv4_m2 versus positions_6nt_m3; m=5/5; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.690755; --rrACAAAGrv- ; cor=; Ncor= a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 0 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 0 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 0 t 0 0 909 1067 0 96 35 165 52 77 790 764 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 2 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; ssACTTCCGss ; Alignment reference a 1162 1043 4719 135 167 121 71 265 298 1192 1149 c 1823 2210 443 5412 374 354 5586 5241 316 1665 1778 g 1588 1495 462 235 150 321 179 192 5001 1875 1630 t 1406 1231 355 197 5288 5183 143 281 364 1247 1422

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssACTTCCGss ; cor=; Ncor= a 1162 1043 4719 135 167 121 71 265 298 1192 1149 c 1823 2210 443 5412 374 354 5586 5241 316 1665 1778 g 1588 1495 462 235 150 321 179 192 5001 1875 1630 t 1406 1231 355 197 5288 5183 143 281 364 1247 1422

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift2 ; 8 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=20; shift=2; ncol=22; --wwatatTTTAAAAAAtAwww ; Alignment reference a 0 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 1846 674 931 866 c 0 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 215 318 448 533 g 0 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 301 326 503 451 t 0 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751 330 1374 810 842

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/7; ncol2=20; w=0; offset=0; strand=D; shift=2; score= 1; --wwatatTTTAAAAAAtAwww ; cor=; Ncor= a 0 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 1846 674 931 866 c 0 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 215 318 448 533 g 0 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 301 326 503 451 t 0 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751 330 1374 810 842

positions_6nt_m5_rc_shift1 (positions_6nt_m5_rc)
; positions_6nt_m4 versus positions_6nt_m5_rc; m=2/7; ncol2=21; w=-1; offset=-1; strand=R; shift=1; score=0.867484; -wwwyTTTTTTAAAAAAtatww ; cor=; Ncor= a 0 451 405 511 340 159 137 138 123 128 210 1143 1227 1216 1142 1144 1141 296 991 367 491 478 c 0 254 312 278 491 119 97 97 80 83 70 74 73 55 113 102 97 154 135 184 254 278 g 0 259 265 215 227 93 106 86 76 75 70 67 63 71 85 102 104 136 169 191 277 232 t 0 519 501 479 425 1112 1143 1162 1204 1197 1133 199 120 141 143 135 141 897 188 741 461 495

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; positions_6nt_m4 versus positions_6nt_m1_rc; m=3/7; ncol2=22; w=-2; offset=-2; strand=R; shift=0; score=0.837051; wwwtaTTTTTTAAAAAAtawww ; cor=; Ncor= a 380 351 553 175 696 119 138 111 117 99 157 866 910 897 860 835 835 220 712 286 357 360 c 169 219 142 145 95 89 80 70 60 58 54 50 61 51 85 73 82 116 96 143 198 218 g 216 198 144 96 116 83 76 84 52 60 50 52 57 60 70 79 89 96 143 141 219 169 t 360 357 286 709 218 834 831 860 896 908 864 157 97 117 110 138 119 693 174 555 351 378

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_6nt_m4 versus positions_7nt_m2; m=4/7; ncol2=14; w=0; offset=2; strand=D; shift=4; score=0.577384; ----twTTTTTAAAAAwa---- ; cor=; Ncor= a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 0 0 0 0 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 0 0 0 0 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 0 0 0 0 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473 0 0 0 0

positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_6nt_m4 versus positions_7nt_m4; m=5/7; ncol2=13; w=0; offset=3; strand=D; shift=5; score=0.506448; -----wwATTTAAAAawa---- ; cor=; Ncor= a 0 0 0 0 0 1735 1597 4823 578 396 489 5430 5219 5261 4994 3843 1881 2208 0 0 0 0 c 0 0 0 0 0 1216 1567 393 201 166 151 191 343 267 342 662 1368 1315 0 0 0 0 g 0 0 0 0 0 1407 1031 363 210 302 169 222 245 197 252 868 1247 1240 0 0 0 0 t 0 0 0 0 0 1957 2120 736 5326 5451 5506 472 508 590 727 942 1819 1552 0 0 0 0

positions_7nt_m1_shift10 (positions_7nt_m1)
; positions_6nt_m4 versus positions_7nt_m1; m=6/7; ncol2=11; w=0; offset=8; strand=D; shift=10; score=0.424402; ----------aaAAAAAAAaa- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 7899 7679 17111 16720 15646 15091 15585 16514 17111 7656 7797 0 c 0 0 0 0 0 0 0 0 0 0 2357 3301 317 608 1243 1535 1199 734 399 3679 3929 0 g 0 0 0 0 0 0 0 0 0 0 3876 3821 344 504 704 816 714 463 251 3335 3048 0 t 0 0 0 0 0 0 0 0 0 0 4212 3543 572 512 751 902 846 633 583 3674 3570 0

oligos_7nt_mkv5_m5_rc_shift9 (oligos_7nt_mkv5_m5_rc)
; positions_6nt_m4 versus oligos_7nt_mkv5_m5_rc; m=7/7; ncol2=11; w=0; offset=7; strand=R; shift=9; score=0.408712; ---------wwTAAAAATrw-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2887 2674 642 7612 8167 8125 8175 8118 600 2655 3172 0 0 c 0 0 0 0 0 0 0 0 0 1712 1765 399 391 327 446 333 358 426 1778 1902 0 0 g 0 0 0 0 0 0 0 0 0 1732 1573 489 513 358 261 321 308 481 2642 1790 0 0 t 0 0 0 0 0 0 0 0 0 2826 3145 7627 641 305 325 328 373 7650 2082 2293 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --rrACAAAGrv ; Alignment reference a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 t 0 0 909 1067 0 96 35 165 52 77 790 764

positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --rrACAAAGrv ; cor=; Ncor= a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 t 0 0 909 1067 0 96 35 165 52 77 790 764

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; positions_6nt_m3 versus oligos_6nt_mkv4_m2; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.690755; --raACAATGGm ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m3 versus positions_6nt_m2; m=3/4; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.581529; rrGAACAATGgv ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 t 923 1192 498 225 68 167 85 88 4191 154 677 929

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_6nt_m3 versus positions_7nt_m3; m=4/4; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.559665; rrGAACAATGGv ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 c 574 386 118 109 73 2248 48 66 87 98 165 711 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 t 456 555 223 122 42 133 78 27 2100 70 188 447

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---ssCGCCCCCGss ; Alignment reference a 0 0 0 822 797 140 134 125 124 251 160 229 301 869 851 c 0 0 0 2390 2593 5515 77 5372 5289 4635 5291 5214 340 2643 2394 g 0 0 0 1827 1714 197 5517 269 270 776 312 306 4912 1645 1779 t 0 0 0 907 842 94 218 180 263 284 183 197 393 789 922
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCCCGss ; cor=; Ncor= a 0 0 0 822 797 140 134 125 124 251 160 229 301 869 851 c 0 0 0 2390 2593 5515 77 5372 5289 4635 5291 5214 340 2643 2394 g 0 0 0 1827 1714 197 5517 269 270 776 312 306 4912 1645 1779 t 0 0 0 907 842 94 218 180 263 284 183 197 393 789 922
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.84461; ---ssCGCCCTCGss ; cor=; Ncor= a 0 0 0 614 644 137 111 73 95 81 160 95 225 620 666 c 0 0 0 1713 1603 3918 132 3911 3880 3920 294 3889 583 1666 1533 g 0 0 0 1252 1346 154 3906 225 256 215 312 253 3208 1402 1303 t 0 0 0 755 741 125 185 125 103 118 3568 97 318 646 832
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m1; m=3/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.506416; ssCCCCGCCCcs--- ; cor=; Ncor= a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 0 0 0 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 0 0 0 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 0 0 0 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=21; shift=0; ncol=21; wwataTTTTTTAAAAAArwww ; Alignment reference a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 479 501 519 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 215 265 259 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 278 312 254 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340 511 405 451
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/6; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; wwataTTTTTTAAAAAArwww ; cor=; Ncor= a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 479 501 519 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 215 265 259 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 278 312 254 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340 511 405 451
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m5 versus positions_6nt_m1; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.915236; wwwtaTTTTTTAAAAAAtaww ; cor=; Ncor= a 378 351 555 174 693 119 138 110 117 97 157 864 908 896 860 831 834 218 709 286 357 c 169 219 141 143 96 89 79 70 60 57 52 50 60 52 84 76 83 116 96 144 198 g 218 198 143 96 116 82 73 85 51 61 50 54 58 60 70 80 89 95 145 142 219 t 360 357 286 712 220 835 835 860 897 910 866 157 99 117 111 138 119 696 175 553 351
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_6nt_m5 versus positions_6nt_m4_rc; m=3/6; ncol2=20; w=0; offset=0; strand=R; shift=0; score=0.867484; wwwTaTTTTTTAAAatatww- ; cor=; Ncor= a 842 810 1374 330 1751 236 291 270 296 210 326 1852 1956 1890 1812 485 1729 534 845 828 0 c 451 503 326 301 210 146 150 147 155 156 138 190 207 230 210 276 259 317 496 513 0 g 533 448 318 215 231 155 199 182 138 156 180 173 185 180 248 246 312 314 544 471 0 t 866 931 674 1846 500 2155 2052 2093 2103 2170 2048 477 344 392 422 1685 392 1527 807 880 0
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_6nt_m5 versus positions_7nt_m2; m=4/6; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.613544; ----twTTTTTAAAAAwa--- ; cor=; Ncor= a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 0 0 0 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 0 0 0 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 0 0 0 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473 0 0 0
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_6nt_m5 versus positions_7nt_m4; m=5/6; ncol2=13; w=0; offset=5; strand=D; shift=5; score=0.490783; -----wwATTTAAAAawa--- ; cor=; Ncor= a 0 0 0 0 0 1735 1597 4823 578 396 489 5430 5219 5261 4994 3843 1881 2208 0 0 0 c 0 0 0 0 0 1216 1567 393 201 166 151 191 343 267 342 662 1368 1315 0 0 0 g 0 0 0 0 0 1407 1031 363 210 302 169 222 245 197 252 868 1247 1240 0 0 0 t 0 0 0 0 0 1957 2120 736 5326 5451 5506 472 508 590 727 942 1819 1552 0 0 0
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_6nt_m5 versus positions_7nt_m1_rc; m=6/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.402025; -ttTTTTTTTtt--------- ; cor=; Ncor= a 0 3570 3674 583 633 846 902 751 512 572 3543 4212 0 0 0 0 0 0 0 0 0 c 0 3048 3335 251 463 714 816 704 504 344 3821 3876 0 0 0 0 0 0 0 0 0 g 0 3929 3679 399 734 1199 1535 1243 608 317 3301 2357 0 0 0 0 0 0 0 0 0 t 0 7797 7656 17111 16514 15585 15091 15646 16720 17111 7679 7899 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---ssCGCCCTCGss ; Alignment reference a 0 0 0 614 644 137 111 73 95 81 160 95 225 620 666 c 0 0 0 1713 1603 3918 132 3911 3880 3920 294 3889 583 1666 1533 g 0 0 0 1252 1346 154 3906 225 256 215 312 253 3208 1402 1303 t 0 0 0 755 741 125 185 125 103 118 3568 97 318 646 832
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCTCGss ; cor=; Ncor= a 0 0 0 614 644 137 111 73 95 81 160 95 225 620 666 c 0 0 0 1713 1603 3918 132 3911 3880 3920 294 3889 583 1666 1533 g 0 0 0 1252 1346 154 3906 225 256 215 312 253 3208 1402 1303 t 0 0 0 755 741 125 185 125 103 118 3568 97 318 646 832
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.84461; ---ssCGCCCCCGss ; cor=; Ncor= a 0 0 0 822 797 140 134 125 124 251 160 229 301 869 851 c 0 0 0 2390 2593 5515 77 5372 5289 4635 5291 5214 340 2643 2394 g 0 0 0 1827 1714 197 5517 269 270 776 312 306 4912 1645 1779 t 0 0 0 907 842 94 218 180 263 284 183 197 393 789 922
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m1; m=3/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.479746; ssCCCCGCCCcs--- ; cor=; Ncor= a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 0 0 0 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 0 0 0 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 0 0 0 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; rrGAACAATGgvr ; Alignment reference a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rrGAACAATGgvr ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_6nt_m2 versus positions_7nt_m3; m=2/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.986676; rrGAACAATGGvr ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; positions_6nt_m2 versus oligos_6nt_mkv4_m2; m=3/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.785374; --raACAATGGmr ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_6nt_m2 versus positions_7nt_m5; m=4/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.660265; --rmACAATAGma ; cor=; Ncor= a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_6nt_m2 versus positions_6nt_m3; m=5/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.581529; --rrACAAAGrv- ; cor=; Ncor= a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 0 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 0 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 0 t 0 0 909 1067 0 96 35 165 52 77 790 764 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift9 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=11; shift=9; ncol=20; ---------aaAAAAAAAaa ; Alignment reference a 0 0 0 0 0 0 0 0 0 7899 7679 17111 16720 15646 15091 15585 16514 17111 7656 7797 c 0 0 0 0 0 0 0 0 0 2357 3301 317 608 1243 1535 1199 734 399 3679 3929 g 0 0 0 0 0 0 0 0 0 3876 3821 344 504 704 816 714 463 251 3335 3048 t 0 0 0 0 0 0 0 0 0 4212 3543 572 512 751 902 846 633 583 3674 3570
positions_7nt_m1_shift9 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=9; score= 1; ---------aaAAAAAAAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 7899 7679 17111 16720 15646 15091 15585 16514 17111 7656 7797 c 0 0 0 0 0 0 0 0 0 2357 3301 317 608 1243 1535 1199 734 399 3679 3929 g 0 0 0 0 0 0 0 0 0 3876 3821 344 504 704 816 714 463 251 3335 3048 t 0 0 0 0 0 0 0 0 0 4212 3543 572 512 751 902 846 633 583 3674 3570
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_7nt_m1 versus positions_6nt_m4; m=2/3; ncol2=20; w=-8; offset=-8; strand=D; shift=1; score=0.424402; -wwatatTTTAAAAAAtAww ; cor=; Ncor= a 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 1846 674 931 c 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 215 318 448 g 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 301 326 503 t 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751 330 1374 810
positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)				; positions_7nt_m1 versus positions_6nt_m5_rc; m=3/3; ncol2=21; w=-9; offset=-9; strand=R; shift=0; score=0.402025; wwwyTTTTTTAAAAAAtatw ; cor=; Ncor= a 451 405 511 340 159 137 138 123 128 210 1143 1227 1216 1142 1144 1141 296 991 367 491 c 254 312 278 491 119 97 97 80 83 70 74 73 55 113 102 97 154 135 184 254 g 259 265 215 227 93 106 86 76 75 70 67 63 71 85 102 104 136 169 191 277 t 519 501 479 425 1112 1143 1162 1204 1197 1133 199 120 141 143 135 141 897 188 741 461

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --wyATTTTTAww ; Alignment reference a 0 0 2293 2082 7650 373 328 325 305 641 7627 3145 2826 c 0 0 1790 2642 481 308 321 261 358 513 489 1573 1732 g 0 0 1902 1778 426 358 333 446 327 391 399 1765 1712 t 0 0 3172 2655 600 8118 8175 8125 8167 7612 642 2674 2887
oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wyATTTTTAww ; cor=; Ncor= a 0 0 2293 2082 7650 373 328 325 305 641 7627 3145 2826 c 0 0 1790 2642 481 308 321 261 358 513 489 1573 1732 g 0 0 1902 1778 426 358 333 446 327 391 399 1765 1712 t 0 0 3172 2655 600 8118 8175 8125 8167 7612 642 2674 2887
positions_7nt_m4_rc_shift3 (positions_7nt_m4_rc)				; oligos_7nt_mkv5_m5 versus positions_7nt_m4_rc; m=2/4; ncol2=13; w=0; offset=1; strand=R; shift=3; score=0.582372; ---twtTTTTAAA ; cor=; Ncor= a 0 0 0 1552 1819 942 727 590 508 472 5506 5451 5326 c 0 0 0 1240 1247 868 252 197 245 222 169 302 210 g 0 0 0 1315 1368 662 342 267 343 191 151 166 201 t 0 0 0 2208 1881 3843 4994 5261 5219 5430 489 396 578
positions_7nt_m2_shift3 (positions_7nt_m2)				; oligos_7nt_mkv5_m5 versus positions_7nt_m2; m=3/4; ncol2=14; w=0; offset=1; strand=D; shift=3; score=0.544235; ---twTTTTTAAA ; cor=; Ncor= a 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 c 0 0 0 1202 1274 487 351 237 204 257 292 253 246 g 0 0 0 1268 1268 490 352 246 253 293 260 206 238 t 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; oligos_7nt_mkv5_m5 versus positions_6nt_m4_rc; m=4/4; ncol2=20; w=-2; offset=-2; strand=R; shift=0; score=0.408712; wwwTaTTTTTTAA ; cor=; Ncor= a 842 810 1374 330 1751 236 291 270 296 210 326 1852 1956 c 451 503 326 301 210 146 150 147 155 156 138 190 207 g 533 448 318 215 231 155 199 182 138 156 180 173 185 t 866 931 674 1846 500 2155 2052 2093 2103 2170 2048 477 344

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; rrGAACAATGGvr ; Alignment reference a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rrGAACAATGGvr ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_7nt_m3 versus positions_6nt_m2; m=2/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.986676; rrGAACAATGgvr ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; positions_7nt_m3 versus oligos_6nt_mkv4_m2; m=3/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.774337; --raACAATGGmr ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_7nt_m3 versus positions_7nt_m5; m=4/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.675389; --rmACAATAGma ; cor=; Ncor= a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_7nt_m3 versus positions_6nt_m3; m=5/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.559665; --rrACAAAGrv- ; cor=; Ncor= a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 0 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 0 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 0 t 0 0 909 1067 0 96 35 165 52 77 790 764 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=13; shift=5; ncol=18; -----wwATTTAAAAawa ; Alignment reference a 0 0 0 0 0 1735 1597 4823 578 396 489 5430 5219 5261 4994 3843 1881 2208 c 0 0 0 0 0 1216 1567 393 201 166 151 191 343 267 342 662 1368 1315 g 0 0 0 0 0 1407 1031 363 210 302 169 222 245 197 252 868 1247 1240 t 0 0 0 0 0 1957 2120 736 5326 5451 5506 472 508 590 727 942 1819 1552
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=5; score= 1; -----wwATTTAAAAawa ; cor=; Ncor= a 0 0 0 0 0 1735 1597 4823 578 396 489 5430 5219 5261 4994 3843 1881 2208 c 0 0 0 0 0 1216 1567 393 201 166 151 191 343 267 342 662 1368 1315 g 0 0 0 0 0 1407 1031 363 210 302 169 222 245 197 252 868 1247 1240 t 0 0 0 0 0 1957 2120 736 5326 5451 5506 472 508 590 727 942 1819 1552
positions_7nt_m2_rc_shift4 (positions_7nt_m2_rc)				; positions_7nt_m4 versus positions_7nt_m2_rc; m=2/6; ncol2=14; w=-1; offset=-1; strand=R; shift=4; score=0.79293; ----twTTTTTAAAAAwa ; cor=; Ncor= a 0 0 0 0 1473 1487 710 444 388 336 657 4715 5132 5052 4777 4230 1893 1979 c 0 0 0 0 1203 1276 488 350 238 206 260 293 253 246 352 490 1268 1268 g 0 0 0 0 1267 1266 494 353 246 253 292 257 204 237 351 487 1274 1202 t 0 0 0 0 1979 1893 4230 4775 5050 5127 4713 657 333 387 442 715 1487 1473
oligos_7nt_mkv5_m5_rc_shift8 (oligos_7nt_mkv5_m5_rc)				; positions_7nt_m4 versus oligos_7nt_mkv5_m5_rc; m=3/6; ncol2=11; w=0; offset=3; strand=R; shift=8; score=0.582372; --------wwTAAAAATr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2887 2674 642 7612 8167 8125 8175 8118 600 2655 c 0 0 0 0 0 0 0 0 1712 1765 399 391 327 446 333 358 426 1778 g 0 0 0 0 0 0 0 0 1732 1573 489 513 358 261 321 308 481 2642 t 0 0 0 0 0 0 0 0 2826 3145 7627 641 305 325 328 373 7650 2082
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_7nt_m4 versus positions_6nt_m4; m=4/6; ncol2=20; w=-3; offset=-3; strand=D; shift=2; score=0.506448; --wwatatTTTAAAAAAt ; cor=; Ncor= a 0 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 c 0 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 g 0 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 t 0 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_7nt_m4 versus positions_6nt_m5; m=5/6; ncol2=21; w=-5; offset=-5; strand=D; shift=0; score=0.490783; wwataTTTTTTAAAAAAr ; cor=; Ncor= a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; positions_7nt_m4 versus positions_6nt_m1_rc; m=6/6; ncol2=22; w=-5; offset=-5; strand=R; shift=0; score=0.462626; wwwtaTTTTTTAAAAAAt ; cor=; Ncor= a 380 351 553 175 696 119 138 111 117 99 157 866 910 897 860 835 835 220 c 169 219 142 145 95 89 80 70 60 58 54 50 61 51 85 73 82 116 g 216 198 144 96 116 83 76 84 52 60 50 52 57 60 70 79 89 96 t 360 357 286 709 218 834 831 860 896 908 864 157 97 117 110 138 119 693

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCCCCGCCCcs ; Alignment reference a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCCCCGCCCcs ; cor=; Ncor= a 1724 1432 382 289 362 399 639 185 228 236 1624 1312 c 3548 3270 8473 8809 8946 9017 355 9395 9145 9113 4276 4329 g 2988 3210 681 450 501 372 8090 341 474 416 2246 2802 t 1848 2196 572 560 299 320 1024 187 261 343 1962 1665
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m4; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.878603; csCCCCTCCCcc ; cor=; Ncor= a 1745 1414 258 355 274 278 639 130 248 291 1813 1626 c 3917 3878 9331 9149 9520 9607 376 9691 9817 9565 4393 4352 g 2521 2732 428 401 339 206 840 386 251 275 1794 2613 t 2453 2612 619 731 503 545 8781 429 320 505 2636 2045
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m3; m=3/4; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.506416; ---ssCGCCCCC ; cor=; Ncor= a 0 0 0 822 797 140 134 125 124 251 160 229 c 0 0 0 2390 2593 5515 77 5372 5289 4635 5291 5214 g 0 0 0 1827 1714 197 5517 269 270 776 312 306 t 0 0 0 907 842 94 218 180 263 284 183 197
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m4; m=4/4; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.479746; ---ssCGCCCTC ; cor=; Ncor= a 0 0 0 614 644 137 111 73 95 81 160 95 c 0 0 0 1713 1603 3918 132 3911 3880 3920 294 3889 g 0 0 0 1252 1346 154 3906 225 256 215 312 253 t 0 0 0 755 741 125 185 125 103 118 3568 97

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_7nt_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --rmACAATAGma ; Alignment reference a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_7nt_m5 versus positions_7nt_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --rmACAATAGma ; cor=; Ncor= a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; positions_7nt_m5 versus oligos_6nt_mkv4_m2; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.858138; --raACAATGGmr ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_7nt_m5 versus positions_7nt_m3; m=3/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.675389; rrGAACAATGGvr ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_7nt_m5 versus positions_6nt_m2; m=4/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.660265; rrGAACAATGgvr ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161
oligos_6nt_mkv4_m5_shift3 (oligos_6nt_mkv4_m5)				; positions_7nt_m5 versus oligos_6nt_mkv4_m5; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.621087; ---aaCAAAAGAm ; cor=; Ncor= a 0 0 0 2009 2725 172 5975 5911 5797 5868 69 4635 1927 c 0 0 0 1327 1166 5662 94 180 189 144 377 706 1704 g 0 0 0 1568 1107 171 157 162 102 187 5589 740 1339 t 0 0 0 1540 1446 439 218 191 356 245 409 363 1474

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=22; shift=0; ncol=22; wwwtaTTTTTTAAAAAAtawww ; Alignment reference a 378 351 555 174 693 119 138 110 117 97 157 864 908 896 860 831 834 218 709 286 357 360 c 169 219 141 143 96 89 79 70 60 57 52 50 60 52 84 76 83 116 96 144 198 216 g 218 198 143 96 116 82 73 85 51 61 50 54 58 60 70 80 89 95 145 142 219 169 t 360 357 286 712 220 835 835 860 897 910 866 157 99 117 111 138 119 696 175 553 351 380
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/5; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; wwwtaTTTTTTAAAAAAtawww ; cor=; Ncor= a 378 351 555 174 693 119 138 110 117 97 157 864 908 896 860 831 834 218 709 286 357 360 c 169 219 141 143 96 89 79 70 60 57 52 50 60 52 84 76 83 116 96 144 198 216 g 218 198 143 96 116 82 73 85 51 61 50 54 58 60 70 80 89 95 145 142 219 169 t 360 357 286 712 220 835 835 860 897 910 866 157 99 117 111 138 119 696 175 553 351 380
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m1 versus positions_6nt_m5; m=2/5; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.915236; wwataTTTTTTAAAAAArwww- ; cor=; Ncor= a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 479 501 519 0 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 215 265 259 0 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 278 312 254 0 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340 511 405 451 0
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_6nt_m1 versus positions_6nt_m4_rc; m=3/5; ncol2=20; w=0; offset=0; strand=R; shift=0; score=0.837051; wwwTaTTTTTTAAAatatww-- ; cor=; Ncor= a 842 810 1374 330 1751 236 291 270 296 210 326 1852 1956 1890 1812 485 1729 534 845 828 0 0 c 451 503 326 301 210 146 150 147 155 156 138 190 207 230 210 276 259 317 496 513 0 0 g 533 448 318 215 231 155 199 182 138 156 180 173 185 180 248 246 312 314 544 471 0 0 t 866 931 674 1846 500 2155 2052 2093 2103 2170 2048 477 344 392 422 1685 392 1527 807 880 0 0
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_6nt_m1 versus positions_7nt_m2; m=4/5; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.575641; ----twTTTTTAAAAAwa---- ; cor=; Ncor= a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 0 0 0 0 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 0 0 0 0 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 0 0 0 0 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473 0 0 0 0
positions_7nt_m4_rc_shift4 (positions_7nt_m4_rc)				; positions_6nt_m1 versus positions_7nt_m4_rc; m=5/5; ncol2=13; w=0; offset=4; strand=R; shift=4; score=0.462626; ----twtTTTTAAATww----- ; cor=; Ncor= a 0 0 0 0 1552 1819 942 727 590 508 472 5506 5451 5326 736 2120 1957 0 0 0 0 0 c 0 0 0 0 1240 1247 868 252 197 245 222 169 302 210 363 1031 1407 0 0 0 0 0 g 0 0 0 0 1315 1368 662 342 267 343 191 151 166 201 393 1567 1216 0 0 0 0 0 t 0 0 0 0 2208 1881 3843 4994 5261 5219 5430 489 396 578 4823 1597 1735 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=14; shift=4; ncol=18; ----twTTTTTAAAAAwa ; Alignment reference a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=4; score= 1; ----twTTTTTAAAAAwa ; cor=; Ncor= a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473
positions_7nt_m4_rc_shift4 (positions_7nt_m4_rc)				; positions_7nt_m2 versus positions_7nt_m4_rc; m=2/6; ncol2=13; w=0; offset=0; strand=R; shift=4; score=0.79293; ----twtTTTTAAATww- ; cor=; Ncor= a 0 0 0 0 1552 1819 942 727 590 508 472 5506 5451 5326 736 2120 1957 0 c 0 0 0 0 1240 1247 868 252 197 245 222 169 302 210 363 1031 1407 0 g 0 0 0 0 1315 1368 662 342 267 343 191 151 166 201 393 1567 1216 0 t 0 0 0 0 2208 1881 3843 4994 5261 5219 5430 489 396 578 4823 1597 1735 0
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_7nt_m2 versus positions_6nt_m5; m=3/6; ncol2=21; w=-4; offset=-4; strand=D; shift=0; score=0.613544; wwataTTTTTTAAAAAAr ; cor=; Ncor= a 495 461 741 188 897 141 135 143 141 120 199 1133 1197 1204 1162 1143 1112 425 c 232 277 191 169 136 104 102 85 71 63 67 70 75 76 86 106 93 227 g 278 254 184 135 154 97 102 113 55 73 74 70 83 80 97 97 119 491 t 478 491 367 991 296 1141 1144 1142 1216 1227 1143 210 128 123 138 137 159 340
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_7nt_m2 versus positions_6nt_m4; m=4/6; ncol2=20; w=-2; offset=-2; strand=D; shift=2; score=0.577384; --wwatatTTTAAAAAAt ; cor=; Ncor= a 0 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 c 0 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 g 0 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 t 0 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_7nt_m2 versus positions_6nt_m1; m=5/6; ncol2=22; w=-4; offset=-4; strand=D; shift=0; score=0.575641; wwwtaTTTTTTAAAAAAt ; cor=; Ncor= a 378 351 555 174 693 119 138 110 117 97 157 864 908 896 860 831 834 218 c 169 219 141 143 96 89 79 70 60 57 52 50 60 52 84 76 83 116 g 218 198 143 96 116 82 73 85 51 61 50 54 58 60 70 80 89 95 t 360 357 286 712 220 835 835 860 897 910 866 157 99 117 111 138 119 696
oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)				; positions_7nt_m2 versus oligos_7nt_mkv5_m5; m=6/6; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.544235; ---wyATTTTTAww---- ; cor=; Ncor= a 0 0 0 2293 2082 7650 373 328 325 305 641 7627 3145 2826 0 0 0 0 c 0 0 0 1790 2642 481 308 321 261 358 513 489 1573 1732 0 0 0 0 g 0 0 0 1902 1778 426 358 333 446 327 391 399 1765 1712 0 0 0 0 t 0 0 0 3172 2655 600 8118 8175 8125 8167 7612 642 2674 2887 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --raACAATGGmr ; Alignment reference a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --raACAATGGmr ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 1701 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 1528 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 1763 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425 1554
positions_7nt_m5_shift2 (positions_7nt_m5)				; oligos_6nt_mkv4_m2 versus positions_7nt_m5; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.858138; --rmACAATAGma ; cor=; Ncor= a 0 0 2380 2398 6542 408 6766 6277 524 5642 445 2132 2141 c 0 0 1216 1846 245 6259 207 284 481 113 297 1858 1748 g 0 0 1863 1719 156 277 52 344 292 1092 6169 1771 1669 t 0 0 1694 1190 210 209 128 248 5856 306 242 1392 1595
positions_6nt_m2_shift0 (positions_6nt_m2)				; oligos_6nt_mkv4_m2 versus positions_6nt_m2; m=3/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.785374; rrGAACAATGgvr ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 1324 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 1137 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 1238 t 923 1192 498 225 68 167 85 88 4191 154 677 929 1161
positions_7nt_m3_shift0 (positions_7nt_m3)				; oligos_6nt_mkv4_m2 versus positions_7nt_m3; m=4/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.774337; rrGAACAATGGvr ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 686 c 574 386 118 109 73 2248 48 66 87 98 165 711 569 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 706 t 456 555 223 122 42 133 78 27 2100 70 188 447 549
positions_6nt_m3_shift2 (positions_6nt_m3)				; oligos_6nt_mkv4_m2 versus positions_6nt_m3; m=5/5; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.690755; --rrACAAAGrv- ; cor=; Ncor= a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 0 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 0 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 0 t 0 0 909 1067 0 96 35 165 52 77 790 764 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=20; shift=2; ncol=22; --wwatatTTTAAAAAAtAwww ; Alignment reference a 0 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 1846 674 931 866 c 0 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 215 318 448 533 g 0 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 301 326 503 451 t 0 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751 330 1374 810 842
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/7; ncol2=20; w=0; offset=0; strand=D; shift=2; score= 1; --wwatatTTTAAAAAAtAwww ; cor=; Ncor= a 0 0 880 807 1527 392 1685 422 392 344 477 2048 2170 2103 2093 2052 2155 500 1846 674 931 866 c 0 0 471 544 314 312 246 248 180 185 173 180 156 138 182 199 155 231 215 318 448 533 g 0 0 513 496 317 259 276 210 230 207 190 138 156 155 147 150 146 210 301 326 503 451 t 0 0 828 845 534 1729 485 1812 1890 1956 1852 326 210 296 270 291 236 1751 330 1374 810 842
positions_6nt_m5_rc_shift1 (positions_6nt_m5_rc)				; positions_6nt_m4 versus positions_6nt_m5_rc; m=2/7; ncol2=21; w=-1; offset=-1; strand=R; shift=1; score=0.867484; -wwwyTTTTTTAAAAAAtatww ; cor=; Ncor= a 0 451 405 511 340 159 137 138 123 128 210 1143 1227 1216 1142 1144 1141 296 991 367 491 478 c 0 254 312 278 491 119 97 97 80 83 70 74 73 55 113 102 97 154 135 184 254 278 g 0 259 265 215 227 93 106 86 76 75 70 67 63 71 85 102 104 136 169 191 277 232 t 0 519 501 479 425 1112 1143 1162 1204 1197 1133 199 120 141 143 135 141 897 188 741 461 495
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; positions_6nt_m4 versus positions_6nt_m1_rc; m=3/7; ncol2=22; w=-2; offset=-2; strand=R; shift=0; score=0.837051; wwwtaTTTTTTAAAAAAtawww ; cor=; Ncor= a 380 351 553 175 696 119 138 111 117 99 157 866 910 897 860 835 835 220 712 286 357 360 c 169 219 142 145 95 89 80 70 60 58 54 50 61 51 85 73 82 116 96 143 198 218 g 216 198 144 96 116 83 76 84 52 60 50 52 57 60 70 79 89 96 143 141 219 169 t 360 357 286 709 218 834 831 860 896 908 864 157 97 117 110 138 119 693 174 555 351 378
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_6nt_m4 versus positions_7nt_m2; m=4/7; ncol2=14; w=0; offset=2; strand=D; shift=4; score=0.577384; ----twTTTTTAAAAAwa---- ; cor=; Ncor= a 0 0 0 0 1473 1487 715 442 387 333 657 4713 5127 5050 4775 4230 1893 1979 0 0 0 0 c 0 0 0 0 1202 1274 487 351 237 204 257 292 253 246 353 494 1266 1267 0 0 0 0 g 0 0 0 0 1268 1268 490 352 246 253 293 260 206 238 350 488 1276 1203 0 0 0 0 t 0 0 0 0 1979 1893 4230 4777 5052 5132 4715 657 336 388 444 710 1487 1473 0 0 0 0
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_6nt_m4 versus positions_7nt_m4; m=5/7; ncol2=13; w=0; offset=3; strand=D; shift=5; score=0.506448; -----wwATTTAAAAawa---- ; cor=; Ncor= a 0 0 0 0 0 1735 1597 4823 578 396 489 5430 5219 5261 4994 3843 1881 2208 0 0 0 0 c 0 0 0 0 0 1216 1567 393 201 166 151 191 343 267 342 662 1368 1315 0 0 0 0 g 0 0 0 0 0 1407 1031 363 210 302 169 222 245 197 252 868 1247 1240 0 0 0 0 t 0 0 0 0 0 1957 2120 736 5326 5451 5506 472 508 590 727 942 1819 1552 0 0 0 0
positions_7nt_m1_shift10 (positions_7nt_m1)				; positions_6nt_m4 versus positions_7nt_m1; m=6/7; ncol2=11; w=0; offset=8; strand=D; shift=10; score=0.424402; ----------aaAAAAAAAaa- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 7899 7679 17111 16720 15646 15091 15585 16514 17111 7656 7797 0 c 0 0 0 0 0 0 0 0 0 0 2357 3301 317 608 1243 1535 1199 734 399 3679 3929 0 g 0 0 0 0 0 0 0 0 0 0 3876 3821 344 504 704 816 714 463 251 3335 3048 0 t 0 0 0 0 0 0 0 0 0 0 4212 3543 572 512 751 902 846 633 583 3674 3570 0
oligos_7nt_mkv5_m5_rc_shift9 (oligos_7nt_mkv5_m5_rc)				; positions_6nt_m4 versus oligos_7nt_mkv5_m5_rc; m=7/7; ncol2=11; w=0; offset=7; strand=R; shift=9; score=0.408712; ---------wwTAAAAATrw-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2887 2674 642 7612 8167 8125 8175 8118 600 2655 3172 0 0 c 0 0 0 0 0 0 0 0 0 1712 1765 399 391 327 446 333 358 426 1778 1902 0 0 g 0 0 0 0 0 0 0 0 0 1732 1573 489 513 358 261 321 308 481 2642 1790 0 0 t 0 0 0 0 0 0 0 0 0 2826 3145 7627 641 305 325 328 373 7650 2082 2293 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --rrACAAAGrv ; Alignment reference a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 t 0 0 909 1067 0 96 35 165 52 77 790 764
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --rrACAAAGrv ; cor=; Ncor= a 0 0 1770 1540 4967 0 4843 4767 4767 20 1348 1619 c 0 0 793 1102 0 4871 6 28 139 51 1072 1310 g 0 0 1495 1258 0 0 83 7 9 4819 1757 1274 t 0 0 909 1067 0 96 35 165 52 77 790 764
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; positions_6nt_m3 versus oligos_6nt_mkv4_m2; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.690755; --raACAATGGm ; cor=; Ncor= a 0 0 2032 1995 6297 221 5963 5913 183 603 766 1832 c 0 0 1079 1596 78 5798 234 265 156 113 678 1754 g 0 0 1910 1628 78 210 159 264 85 5640 4593 1535 t 0 0 1525 1327 93 317 190 104 6122 190 509 1425
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m3 versus positions_6nt_m2; m=3/4; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.581529; rrGAACAATGgv ; cor=; Ncor= a 1368 1682 721 3809 4592 170 4579 4394 454 337 973 1350 c 1110 666 326 372 106 4328 110 209 88 138 753 1304 g 1459 1320 3315 454 94 195 86 169 127 4231 2457 1277 t 923 1192 498 225 68 167 85 88 4191 154 677 929
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_6nt_m3 versus positions_7nt_m3; m=4/4; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.559665; rrGAACAATGGv ; cor=; Ncor= a 681 889 226 2125 2354 54 2303 2343 269 236 210 679 c 574 386 118 109 73 2248 48 66 87 98 165 711 g 799 680 1943 154 41 75 81 74 54 2106 1947 673 t 456 555 223 122 42 133 78 27 2100 70 188 447