One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/04/peak-motifs.2026-01-04.215525_2026-01-04.215525_0oPAHx/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/2026/01/04/peak-motifs.2026-01-04.215525_2026-01-04.215525_0oPAHx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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=12; shift=0; ncol=12; ggcGTGGGAGgs ; Alignment reference a 2570 2849 1268 337 568 145 164 220 12227 416 2583 2989 c 3388 3118 9371 778 833 206 183 381 437 783 3075 3594 g 5177 6121 1784 12478 1543 13403 13190 13126 791 12196 5915 5045 t 2739 1786 1451 281 10930 120 337 147 419 479 2301 2246

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ggcGTGGGAGgs ; cor=; Ncor= a 2570 2849 1268 337 568 145 164 220 12227 416 2583 2989 c 3388 3118 9371 778 833 206 183 381 437 783 3075 3594 g 5177 6121 1784 12478 1543 13403 13190 13126 791 12196 5915 5045 t 2739 1786 1451 281 10930 120 337 147 419 479 2301 2246

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_6nt_m2 versus positions_7nt_m1_rc; m=2/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.885444; -gbGTGGGAGsg ; cor=; Ncor= a 0 3410 3149 300 129 640 536 370 14713 421 3027 3551 c 0 4335 5070 240 1327 639 565 889 1226 591 4773 4315 g 0 7798 4929 17216 127 16331 15005 16085 425 16306 6009 6794 t 0 2303 4698 90 16263 236 1740 502 1482 528 4037 3186

positions_7nt_m3_rc_shift1 (positions_7nt_m3_rc)
; positions_6nt_m2 versus positions_7nt_m3_rc; m=3/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.788202; -scGGGGGAGsg ; cor=; Ncor= a 0 2230 2354 40 129 168 144 23 13917 21 2236 2713 c 0 4161 5991 677 1327 1177 804 79 601 450 3899 3582 g 0 6267 3111 13819 12415 13001 13356 14209 0 14069 5906 6412 t 0 1946 3148 68 733 258 300 293 86 64 2563 1897

oligos_7nt_mkv5_m4_rc_shift1 (oligos_7nt_mkv5_m4_rc)
; positions_6nt_m2 versus oligos_7nt_mkv5_m4_rc; m=4/5; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.780342; -gkGTGGGAGtg ; cor=; Ncor= a 0 2671 2600 230 716 173 202 202 10576 233 845 2107 c 0 2557 2422 665 346 140 133 274 349 267 830 2815 g 0 5494 4163 11386 951 12049 11737 11859 939 11812 2417 5377 t 0 1807 3344 248 10516 167 457 194 665 217 8437 2230

oligos_6nt_mkv4_m3_rc_shift1 (oligos_6nt_mkv4_m3_rc)
; positions_6nt_m2 versus oligos_6nt_mkv4_m3_rc; m=5/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.556046; -ggGTGGGGGCG ; cor=; Ncor= a 0 2346 1759 883 774 148 208 257 244 253 1067 370 c 0 2704 2868 1599 1373 403 736 855 917 258 9472 451 g 0 5491 4991 8885 258 11296 10390 10498 10294 11275 385 10748 t 0 1412 2335 586 9548 106 619 343 498 167 1029 384

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=13; shift=2; ncol=15; --ssCGCCCCCGCss ; Alignment reference a 0 0 1639 1696 411 561 362 406 436 500 324 528 258 2056 1549 c 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 6569 g 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 4939 t 0 0 2101 1642 335 1182 605 392 492 357 330 747 281 1939 2438

oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --ssCGCCCCCGCss ; cor=; Ncor= a 0 0 1639 1696 411 561 362 406 436 500 324 528 258 2056 1549 c 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 6569 g 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 4939 t 0 0 2101 1642 335 1182 605 392 492 357 330 747 281 1939 2438

oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m3; m=2/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.86575; --csCGCCCCCACcc ; cor=; Ncor= a 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 0 0 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m1; m=3/6; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.830938; scCCCGCCCCCGCss ; cor=; Ncor= a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297

oligos_7nt_mkv5_m2_rc_shift2 (oligos_7nt_mkv5_m2_rc)
; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m2_rc; m=4/6; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.776781; --ssCGCTCCCGss- ; cor=; Ncor= a 0 0 1754 1578 618 395 167 351 179 158 443 472 1756 2096 0 c 0 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 1011 6164 5906 0 g 0 0 4172 4237 1161 12203 402 1002 620 419 530 12339 4864 4325 0 t 0 0 2367 2161 499 653 219 11132 280 259 453 632 1670 2127 0

positions_7nt_m3_shift2 (positions_7nt_m3)
; oligos_6nt_mkv4_m4 versus positions_7nt_m3; m=5/6; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.650343; --csCTCCCCCgs-- ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 0 0 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 0 0 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 0 0 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230 0 0

oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)
; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m5; m=6/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.648816; --ssCGCCTGCGss- ; cor=; Ncor= a 0 0 1597 1425 401 287 157 261 363 104 262 374 1481 1652 0 c 0 0 4045 4144 9963 544 10297 10359 1094 790 9872 787 4537 4102 0 g 0 0 3786 4240 639 10070 699 589 646 10269 928 9719 3632 3885 0 t 0 0 1922 1541 347 449 197 141 9247 187 288 470 1700 1711 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 3 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=10; shift=0; ncol=10; gsAGGTGGgg ; Alignment reference a 1603 1318 8061 8 14 0 71 25 1762 1735 c 1844 2118 68 748 0 2 98 29 1871 1813 g 3577 3681 0 7245 8122 0 7964 7994 3130 3246 t 1116 1023 11 139 4 8138 7 92 1377 1346

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; gsAGGTGGgg ; cor=; Ncor= a 1603 1318 8061 8 14 0 71 25 1762 1735 c 1844 2118 68 748 0 2 98 29 1871 1813 g 3577 3681 0 7245 8122 0 7964 7994 3130 3246 t 1116 1023 11 139 4 8138 7 92 1377 1346

oligos_7nt_mkv5_m4_rc_shift2 (oligos_7nt_mkv5_m4_rc)
; positions_6nt_m1 versus oligos_7nt_mkv5_m4_rc; m=2/2; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.40379; --gkGTGGGA ; cor=; Ncor= a 0 0 2671 2600 230 716 173 202 202 10576 c 0 0 2557 2422 665 346 140 133 274 349 g 0 0 5494 4163 11386 951 12049 11737 11859 939 t 0 0 1807 3344 248 10516 167 457 194 665

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; sgGGTGCACCcs ; Alignment reference a 922 1241 118 104 282 59 136 4261 72 259 992 993 c 1770 1137 165 470 289 183 4930 476 4662 4766 1938 1623 g 1623 1938 4766 4662 476 4930 183 289 470 165 1137 1770 t 993 992 259 72 4261 136 59 282 104 118 1241 922

positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; sgGGTGCACCcs ; cor=; Ncor= a 922 1241 118 104 282 59 136 4261 72 259 992 993 c 1770 1137 165 470 289 183 4930 476 4662 4766 1938 1623 g 1623 1938 4766 4662 476 4930 183 289 470 165 1137 1770 t 993 992 259 72 4261 136 59 282 104 118 1241 922

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wtATTTTTAww ; Alignment reference a 6128 5376 17701 1060 1433 672 1169 1446 17563 6843 7102 c 3509 5122 1136 776 461 394 651 977 1147 3654 3601 g 4469 3873 1162 808 801 418 730 773 1002 3673 3889 t 7500 7235 1607 18962 18911 20122 19056 18410 1894 7436 7014

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wtATTTTTAww ; cor=; Ncor= a 6128 5376 17701 1060 1433 672 1169 1446 17563 6843 7102 c 3509 5122 1136 776 461 394 651 977 1147 3654 3601 g 4469 3873 1162 808 801 418 730 773 1002 3673 3889 t 7500 7235 1607 18962 18911 20122 19056 18410 1894 7436 7014

positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)
; oligos_7nt_mkv5_m3 versus positions_6nt_m4_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.539443; --wwTTTTATT ; cor=; Ncor= a 0 0 6507 7045 1610 1062 896 1358 20991 1571 1729 c 0 0 5167 4585 1025 614 896 1444 1522 775 748 g 0 0 5690 5133 1034 749 752 896 1883 732 1449 t 0 0 8367 8968 22062 23306 23187 22033 1335 22653 21805

positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)
; oligos_7nt_mkv5_m3 versus positions_6nt_m3_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.531555; --wwTTTTATG ; cor=; Ncor= a 0 0 4386 4365 901 321 523 1018 13878 923 1104 c 0 0 3424 3278 490 247 395 712 1260 238 675 g 0 0 3791 3615 595 365 285 727 993 612 12502 t 0 0 5200 5543 14815 15868 15598 14344 670 15028 2520

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=11; shift=0; ncol=11; ssGCGGAGCss ; Alignment reference a 2477 1752 736 77 179 169 11341 264 412 1936 2079 c 5049 6877 2288 14466 487 1016 2434 575 13567 5116 4692 g 5416 4352 10937 72 14039 13418 580 13692 492 5302 5971 t 1905 1866 886 232 142 244 492 316 376 2493 2105

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssGCGGAGCss ; cor=; Ncor= a 2477 1752 736 77 179 169 11341 264 412 1936 2079 c 5049 6877 2288 14466 487 1016 2434 575 13567 5116 4692 g 5416 4352 10937 72 14039 13418 580 13692 492 5302 5971 t 1905 1866 886 232 142 244 492 316 376 2493 2105

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift1 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -ssCGGGAGCGss ; Alignment reference a 0 2127 1670 632 453 259 280 11132 219 653 499 2161 2367 c 0 4325 4864 12339 530 419 620 1002 402 12203 1161 4237 4172 g 0 5906 6164 1011 13028 13618 13375 1969 13666 1203 12176 6478 6161 t 0 2096 1756 472 443 158 179 351 167 395 618 1578 1754

oligos_7nt_mkv5_m2_shift1 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ssCGGGAGCGss ; cor=; Ncor= a 0 2127 1670 632 453 259 280 11132 219 653 499 2161 2367 c 0 4325 4864 12339 530 419 620 1002 402 12203 1161 4237 4172 g 0 5906 6164 1011 13028 13618 13375 1969 13666 1203 12176 6478 6161 t 0 2096 1756 472 443 158 179 351 167 395 618 1578 1754

oligos_6nt_mkv4_m4_rc_shift0 (oligos_6nt_mkv4_m4_rc)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m4_rc; m=2/6; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.776781; ssGCGGGGGCGss ; cor=; Ncor= a 2438 1939 281 747 330 357 492 392 605 1182 335 1642 2101 c 4939 4320 540 14001 543 1519 2460 1466 950 13422 627 4310 4766 g 6569 7180 14416 219 14298 13119 12107 13231 13578 330 14122 7847 6989 t 1549 2056 258 528 324 500 436 406 362 561 411 1696 1639

oligos_6nt_mkv4_m3_rc_shift0 (oligos_6nt_mkv4_m3_rc)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m3_rc; m=3/6; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.680305; ggGTGGGGGCGsg ; cor=; Ncor= a 2346 1759 883 774 148 208 257 244 253 1067 370 1380 1696 c 2704 2868 1599 1373 403 736 855 917 258 9472 451 3198 2970 g 5491 4991 8885 258 11296 10390 10498 10294 11275 385 10748 5219 5711 t 1412 2335 586 9548 106 619 343 498 167 1029 384 2156 1576

oligos_7nt_mkv5_m1_rc_shift0 (oligos_7nt_mkv5_m1_rc)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m1_rc; m=4/6; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.652068; ssGCGGGGGCGGG ; cor=; Ncor= a 3297 2823 789 1951 833 683 1033 806 577 1644 658 615 941 c 6544 5424 2095 15021 1471 1482 2810 1616 1507 17496 1250 1788 2558 g 8891 9971 17333 2358 18105 18248 16584 18085 18454 853 18449 18012 16891 t 2334 2848 849 1736 657 653 639 559 528 1073 709 651 676

positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)
; oligos_7nt_mkv5_m2 versus positions_7nt_m3_rc; m=5/6; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.561411; scGGGGGAGsg-- ; cor=; Ncor= a 2230 2354 40 129 168 144 23 13917 21 2236 2713 0 0 c 4161 5991 677 1327 1177 804 79 601 450 3899 3582 0 0 g 6267 3111 13819 12415 13001 13356 14209 0 14069 5906 6412 0 0 t 1946 3148 68 733 258 300 293 86 64 2563 1897 0 0

oligos_6nt_mkv4_m5_rc_shift4 (oligos_6nt_mkv4_m5_rc)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m5_rc; m=6/6; ncol2=10; w=0; offset=3; strand=R; shift=4; score=0.486627; ----ggGAGGGGv ; cor=; Ncor= a 0 0 0 0 3246 3103 0 15970 0 0 0 0 4405 c 0 0 0 0 3162 1903 0 0 79 16 19 0 4432 g 0 0 0 0 7745 8600 15970 0 15891 15952 15950 15969 5099 t 0 0 0 0 1817 2364 0 0 0 2 1 1 2034

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift3 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---csCTCCCCCgs ; Alignment reference a 0 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 c 0 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 g 0 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 t 0 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---csCTCCCCCgs ; cor=; Ncor= a 0 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 c 0 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 g 0 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 t 0 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m3 versus positions_7nt_m1; m=2/9; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.819946; ---csCTCCCACvc ; cor=; Ncor= a 0 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410

positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)
; positions_7nt_m3 versus positions_6nt_m2_rc; m=3/9; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.788202; ---scCTCCCACgc ; cor=; Ncor= a 0 0 0 2246 2301 479 419 147 337 120 10930 281 1451 1786 c 0 0 0 5045 5915 12196 791 13126 13190 13403 1543 12478 1784 6121 g 0 0 0 3594 3075 783 437 381 183 206 833 778 9371 3118 t 0 0 0 2989 2583 416 12227 220 164 145 568 337 1268 2849

oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)
; positions_7nt_m3 versus oligos_7nt_mkv5_m4; m=4/9; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score= 0.7442; --ccaCTCCCACmc ; cor=; Ncor= a 0 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671

oligos_6nt_mkv4_m3_shift3 (oligos_6nt_mkv4_m3)
; positions_7nt_m3 versus oligos_6nt_mkv4_m3; m=5/9; ncol2=13; w=0; offset=0; strand=D; shift=3; score=0.666241; ---csCGCCCCCAC ; cor=; Ncor= a 0 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 c 0 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 g 0 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 t 0 0 0 1696 1380 370 1067 253 244 257 208 148 774 883

oligos_6nt_mkv4_m4_shift3 (oligos_6nt_mkv4_m4)
; positions_7nt_m3 versus oligos_6nt_mkv4_m4; m=6/9; ncol2=13; w=0; offset=0; strand=D; shift=3; score=0.650343; ---ssCGCCCCCGC ; cor=; Ncor= a 0 0 0 1639 1696 411 561 362 406 436 500 324 528 258 c 0 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 g 0 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 t 0 0 0 2101 1642 335 1182 605 392 492 357 330 747 281

oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)
; positions_7nt_m3 versus oligos_7nt_mkv5_m1; m=7/9; ncol2=15; w=-2; offset=-2; strand=D; shift=1; score=0.561926; -scCCCGCCCCCGC ; cor=; Ncor= a 0 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 c 0 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 g 0 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 t 0 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789

oligos_7nt_mkv5_m2_rc_shift1 (oligos_7nt_mkv5_m2_rc)
; positions_7nt_m3 versus oligos_7nt_mkv5_m2_rc; m=8/9; ncol2=12; w=-2; offset=-2; strand=R; shift=1; score=0.561411; -ssCGCTCCCGss- ; cor=; Ncor= a 0 1754 1578 618 395 167 351 179 158 443 472 1756 2096 0 c 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 1011 6164 5906 0 g 0 4172 4237 1161 12203 402 1002 620 419 530 12339 4864 4325 0 t 0 2367 2161 499 653 219 11132 280 259 453 632 1670 2127 0

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; positions_7nt_m3 versus oligos_6nt_mkv4_m5; m=9/9; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.409377; sbCCCCTCcc---- ; cor=; Ncor= a 2541 2034 1 1 2 0 0 0 2364 1817 0 0 0 0 c 5634 5099 15969 15950 15952 15891 0 15970 8600 7745 0 0 0 0 g 4124 4432 0 19 16 79 0 0 1903 3162 0 0 0 0 t 3671 4405 0 0 0 0 15970 0 3103 3246 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGCCTGCGss ; Alignment reference a 1597 1425 401 287 157 261 363 104 262 374 1481 1652 c 4045 4144 9963 544 10297 10359 1094 790 9872 787 4537 4102 g 3786 4240 639 10070 699 589 646 10269 928 9719 3632 3885 t 1922 1541 347 449 197 141 9247 187 288 470 1700 1711

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCTGCGss ; cor=; Ncor= a 1597 1425 401 287 157 261 363 104 262 374 1481 1652 c 4045 4144 9963 544 10297 10359 1094 790 9872 787 4537 4102 g 3786 4240 639 10070 699 589 646 10269 928 9719 3632 3885 t 1922 1541 347 449 197 141 9247 187 288 470 1700 1711

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m4; m=2/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.648816; ssCGCCCCCGCs ; cor=; Ncor= a 1639 1696 411 561 362 406 436 500 324 528 258 2056 c 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 g 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 t 2101 1642 335 1182 605 392 492 357 330 747 281 1939

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ssGTGCGCACss ; Alignment reference a 1191 1096 128 207 178 222 465 51 4928 56 1488 724 c 1944 1843 270 705 139 5164 373 5856 384 5770 1797 2365 g 2365 1797 5770 384 5856 373 5164 139 705 270 1843 1944 t 724 1488 56 4928 51 465 222 178 207 128 1096 1191

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssGTGCGCACss ; cor=; Ncor= a 1191 1096 128 207 178 222 465 51 4928 56 1488 724 c 1944 1843 270 705 139 5164 373 5856 384 5770 1797 2365 g 2365 1797 5770 384 5856 373 5164 139 705 270 1843 1944 t 724 1488 56 4928 51 465 222 178 207 128 1096 1191

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCATAAAAww ; Alignment reference a 4879 5694 2520 15028 670 14344 15598 15868 14815 5543 5200 c 3935 3936 12502 612 993 727 285 365 595 3615 3791 g 3774 2732 675 238 1260 712 395 247 490 3278 3424 t 4213 4439 1104 923 13878 1018 523 321 901 4365 4386

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCATAAAAww ; cor=; Ncor= a 4879 5694 2520 15028 670 14344 15598 15868 14815 5543 5200 c 3935 3936 12502 612 993 727 285 365 595 3615 3791 g 3774 2732 675 238 1260 712 395 247 490 3278 3424 t 4213 4439 1104 923 13878 1018 523 321 901 4365 4386

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.865214; aaAATAAAAww ; cor=; Ncor= a 8675 10232 21805 22653 1335 22033 23187 23306 22062 8968 8367 c 4672 4882 1449 732 1883 896 752 749 1034 5133 5690 g 6067 4843 748 775 1522 1444 896 614 1025 4585 5167 t 6317 5774 1729 1571 20991 1358 896 1062 1610 7045 6507

oligos_7nt_mkv5_m3_rc_shift2 (oligos_7nt_mkv5_m3_rc)
; positions_6nt_m3 versus oligos_7nt_mkv5_m3_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.531555; --wwTAAAAAT ; cor=; Ncor= a 0 0 7014 7436 1894 18410 19056 20122 18911 18962 1607 c 0 0 3889 3673 1002 773 730 418 801 808 1162 g 0 0 3601 3654 1147 977 651 394 461 776 1136 t 0 0 7102 6843 17563 1446 1169 672 1433 1060 17701

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 2 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=10; shift=0; ncol=10; baCAGATGyk ; Alignment reference a 1918 2705 52 8511 37 8770 0 437 1672 1903 c 2260 2180 8300 103 792 2 353 97 2322 2061 g 2398 2121 111 146 7173 14 0 8183 1999 2484 t 2216 1786 329 32 790 6 8439 75 2799 2344

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; baCAGATGyk ; cor=; Ncor= a 1918 2705 52 8511 37 8770 0 437 1672 1903 c 2260 2180 8300 103 792 2 353 97 2322 2061 g 2398 2121 111 146 7173 14 0 8183 1999 2484 t 2216 1786 329 32 790 6 8439 75 2799 2344

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --csCGCCCCCACcc ; Alignment reference a 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 0 0 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346

oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --csCGCCCCCACcc ; cor=; Ncor= a 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 0 0 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346

oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m4; m=2/8; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.86575; --ssCGCCCCCGCss ; cor=; Ncor= a 0 0 1639 1696 411 561 362 406 436 500 324 528 258 2056 1549 c 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 6569 g 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 4939 t 0 0 2101 1642 335 1182 605 392 492 357 330 747 281 1939 2438

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m1; m=3/8; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.751795; scCCCGCCCCCGCss ; cor=; Ncor= a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297

oligos_7nt_mkv5_m2_rc_shift2 (oligos_7nt_mkv5_m2_rc)
; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m2_rc; m=4/8; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.680305; --ssCGCTCCCGss- ; cor=; Ncor= a 0 0 1754 1578 618 395 167 351 179 158 443 472 1756 2096 0 c 0 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 1011 6164 5906 0 g 0 0 4172 4237 1161 12203 402 1002 620 419 530 12339 4864 4325 0 t 0 0 2367 2161 499 653 219 11132 280 259 453 632 1670 2127 0

positions_7nt_m3_shift2 (positions_7nt_m3)
; oligos_6nt_mkv4_m3 versus positions_7nt_m3; m=5/8; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.666241; --csCTCCCCCgs-- ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 0 0 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 0 0 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 0 0 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230 0 0

oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m4; m=6/8; ncol2=12; w=0; offset=1; strand=D; shift=3; score=0.661522; ---ccaCTCCCACmc ; cor=; Ncor= a 0 0 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 0 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 0 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 0 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671

positions_7nt_m1_shift4 (positions_7nt_m1)
; oligos_6nt_mkv4_m3 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.629712; ----csCTCCCACvc ; cor=; Ncor= a 0 0 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410

positions_6nt_m2_rc_shift4 (positions_6nt_m2_rc)
; oligos_6nt_mkv4_m3 versus positions_6nt_m2_rc; m=8/8; ncol2=12; w=0; offset=2; strand=R; shift=4; score=0.556046; ----scCTCCCACgc ; cor=; Ncor= a 0 0 0 0 2246 2301 479 419 147 337 120 10930 281 1451 1786 c 0 0 0 0 5045 5915 12196 791 13126 13190 13403 1543 12478 1784 6121 g 0 0 0 0 3594 3075 783 437 381 183 206 833 778 9371 3118 t 0 0 0 0 2989 2583 416 12227 220 164 145 568 337 1268 2849

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 7 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=15; shift=0; ncol=15; scCCCGCCCCCGCss ; Alignment reference a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; scCCCGCCCCCGCss ; cor=; Ncor= a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297

oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m4; m=2/6; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.830938; --ssCGCCCCCGCss ; cor=; Ncor= a 0 0 1639 1696 411 561 362 406 436 500 324 528 258 2056 1549 c 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 6569 g 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 4939 t 0 0 2101 1642 335 1182 605 392 492 357 330 747 281 1939 2438

oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m3; m=3/6; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.751795; --csCGCCCCCACcc ; cor=; Ncor= a 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 0 0 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346

oligos_7nt_mkv5_m2_rc_shift2 (oligos_7nt_mkv5_m2_rc)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m2_rc; m=4/6; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.652068; --ssCGCTCCCGss- ; cor=; Ncor= a 0 0 1754 1578 618 395 167 351 179 158 443 472 1756 2096 0 c 0 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 1011 6164 5906 0 g 0 0 4172 4237 1161 12203 402 1002 620 419 530 12339 4864 4325 0 t 0 0 2367 2161 499 653 219 11132 280 259 453 632 1670 2127 0

positions_7nt_m3_shift2 (positions_7nt_m3)
; oligos_7nt_mkv5_m1 versus positions_7nt_m3; m=5/6; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.561926; --csCTCCCCCgs-- ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 0 0 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 0 0 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 0 0 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230 0 0

oligos_6nt_mkv4_m5_shift5 (oligos_6nt_mkv4_m5)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m5; m=6/6; ncol2=10; w=0; offset=5; strand=D; shift=5; score=0.475063; -----sbCCCCTCcc ; cor=; Ncor= a 0 0 0 0 0 2541 2034 1 1 2 0 0 0 2364 1817 c 0 0 0 0 0 5634 5099 15969 15950 15952 15891 0 15970 8600 7745 g 0 0 0 0 0 4124 4432 0 19 16 79 0 0 1903 3162 t 0 0 0 0 0 3671 4405 0 0 0 0 15970 0 3103 3246

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=1; ncol=13; -ccaCTCCCACmc ; Alignment reference a 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671

oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ccaCTCCCACmc ; cor=; Ncor= a 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671

positions_7nt_m1_shift2 (positions_7nt_m1)
; oligos_7nt_mkv5_m4 versus positions_7nt_m1; m=2/6; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.881581; --csCTCCCACvc ; cor=; Ncor= a 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410

positions_6nt_m2_rc_shift2 (positions_6nt_m2_rc)
; oligos_7nt_mkv5_m4 versus positions_6nt_m2_rc; m=3/6; ncol2=12; w=0; offset=1; strand=R; shift=2; score=0.780342; --scCTCCCACgc ; cor=; Ncor= a 0 0 2246 2301 479 419 147 337 120 10930 281 1451 1786 c 0 0 5045 5915 12196 791 13126 13190 13403 1543 12478 1784 6121 g 0 0 3594 3075 783 437 381 183 206 833 778 9371 3118 t 0 0 2989 2583 416 12227 220 164 145 568 337 1268 2849

positions_7nt_m3_shift2 (positions_7nt_m3)
; oligos_7nt_mkv5_m4 versus positions_7nt_m3; m=4/6; ncol2=11; w=0; offset=1; strand=D; shift=2; score= 0.7442; --csCTCCCCCgs ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230

oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m3; m=5/6; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.661522; csCGCCCCCACcc ; cor=; Ncor= a 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346

positions_6nt_m1_rc_shift5 (positions_6nt_m1_rc)
; oligos_7nt_mkv5_m4 versus positions_6nt_m1_rc; m=6/6; ncol2=10; w=0; offset=4; strand=R; shift=5; score=0.40379; -----ccCCACCT ; cor=; Ncor= a 0 0 0 0 0 1346 1377 92 7 8138 4 139 11 c 0 0 0 0 0 3246 3130 7994 7964 0 8122 7245 0 g 0 0 0 0 0 1813 1871 29 98 2 0 748 68 t 0 0 0 0 0 1735 1762 25 71 0 14 8 8061

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift0 ; 2 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=17; shift=0; ncol=17; ssgCtGGGCAGGGCass ; Alignment reference a 728 729 327 165 327 138 224 197 194 3071 106 207 178 223 2189 583 703 c 1243 1291 675 3547 452 237 351 272 3556 399 206 241 175 3523 786 1121 1180 g 1709 1600 2827 403 705 3757 3443 3644 388 561 3827 3677 3757 339 808 1936 1697 t 570 630 421 135 2766 118 232 137 112 219 111 125 140 165 467 610 670

oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/1; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; ssgCtGGGCAGGGCass ; cor=; Ncor= a 728 729 327 165 327 138 224 197 194 3071 106 207 178 223 2189 583 703 c 1243 1291 675 3547 452 237 351 272 3556 399 206 241 175 3523 786 1121 1180 g 1709 1600 2827 403 705 3757 3443 3644 388 561 3827 3677 3757 339 808 1936 1697 t 570 630 421 135 2766 118 232 137 112 219 111 125 140 165 467 610 670

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; waTATATATAtw ; Alignment reference a 5022 8469 1770 14881 1412 15210 1453 15086 1281 14491 4068 7749 c 3357 2455 1876 777 1881 658 1753 691 2138 933 4078 2943 g 2940 4070 934 2131 697 1748 660 1880 779 1876 2453 3355 t 7751 4076 14490 1281 15080 1454 15204 1413 14872 1770 8471 5023

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; waTATATATAtw ; cor=; Ncor= a 5022 8469 1770 14881 1412 15210 1453 15086 1281 14491 4068 7749 c 3357 2455 1876 777 1881 658 1753 691 2138 933 4078 2943 g 2940 4070 934 2131 697 1748 660 1880 779 1876 2453 3355 t 7751 4076 14490 1281 15080 1454 15204 1413 14872 1770 8471 5023

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift5 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=10; shift=5; ncol=15; -----sbCCCCTCcc ; Alignment reference a 0 0 0 0 0 2541 2034 1 1 2 0 0 0 2364 1817 c 0 0 0 0 0 5634 5099 15969 15950 15952 15891 0 15970 8600 7745 g 0 0 0 0 0 4124 4432 0 19 16 79 0 0 1903 3162 t 0 0 0 0 0 3671 4405 0 0 0 0 15970 0 3103 3246

oligos_6nt_mkv4_m5_shift5 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----sbCCCCTCcc ; cor=; Ncor= a 0 0 0 0 0 2541 2034 1 1 2 0 0 0 2364 1817 c 0 0 0 0 0 5634 5099 15969 15950 15952 15891 0 15970 8600 7745 g 0 0 0 0 0 4124 4432 0 19 16 79 0 0 1903 3162 t 0 0 0 0 0 3671 4405 0 0 0 0 15970 0 3103 3246

oligos_7nt_mkv5_m2_rc_shift6 (oligos_7nt_mkv5_m2_rc)
; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m2_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=6; score=0.486627; ------ssCGCTCCC ; cor=; Ncor= a 0 0 0 0 0 0 1754 1578 618 395 167 351 179 158 443 c 0 0 0 0 0 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 g 0 0 0 0 0 0 4172 4237 1161 12203 402 1002 620 419 530 t 0 0 0 0 0 0 2367 2161 499 653 219 11132 280 259 453

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m1; m=3/4; ncol2=15; w=-5; offset=-5; strand=D; shift=0; score=0.475063; scCCCGCCCCCGCss ; cor=; Ncor= a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297

positions_7nt_m3_shift8 (positions_7nt_m3)
; oligos_6nt_mkv4_m5 versus positions_7nt_m3; m=4/4; ncol2=11; w=0; offset=3; strand=D; shift=8; score=0.409377; --------csCTCCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1897 2563 64 86 293 300 258 c 0 0 0 0 0 0 0 0 6412 5906 14069 0 14209 13356 13001 g 0 0 0 0 0 0 0 0 3582 3899 450 601 79 804 1177 t 0 0 0 0 0 0 0 0 2713 2236 21 13917 23 144 168

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; aaAATAAAAww ; Alignment reference a 8675 10232 21805 22653 1335 22033 23187 23306 22062 8968 8367 c 4672 4882 1449 732 1883 896 752 749 1034 5133 5690 g 6067 4843 748 775 1522 1444 896 614 1025 4585 5167 t 6317 5774 1729 1571 20991 1358 896 1062 1610 7045 6507

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; aaAATAAAAww ; cor=; Ncor= a 8675 10232 21805 22653 1335 22033 23187 23306 22062 8968 8367 c 4672 4882 1449 732 1883 896 752 749 1034 5133 5690 g 6067 4843 748 775 1522 1444 896 614 1025 4585 5167 t 6317 5774 1729 1571 20991 1358 896 1062 1610 7045 6507

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.865214; wwCATAAAAww ; cor=; Ncor= a 4879 5694 2520 15028 670 14344 15598 15868 14815 5543 5200 c 3935 3936 12502 612 993 727 285 365 595 3615 3791 g 3774 2732 675 238 1260 712 395 247 490 3278 3424 t 4213 4439 1104 923 13878 1018 523 321 901 4365 4386

oligos_7nt_mkv5_m3_rc_shift2 (oligos_7nt_mkv5_m3_rc)
; positions_6nt_m4 versus oligos_7nt_mkv5_m3_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.539443; --wwTAAAAAT ; cor=; Ncor= a 0 0 7014 7436 1894 18410 19056 20122 18911 18962 1607 c 0 0 3889 3673 1002 773 730 418 801 808 1162 g 0 0 3601 3654 1147 977 651 394 461 776 1136 t 0 0 7102 6843 17563 1446 1169 672 1433 1060 17701

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift2 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --csCTCCCACvc ; Alignment reference a 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410

positions_7nt_m1_shift2 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --csCTCCCACvc ; cor=; Ncor= a 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410

positions_6nt_m2_rc_shift2 (positions_6nt_m2_rc)
; positions_7nt_m1 versus positions_6nt_m2_rc; m=2/5; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.885444; --scCTCCCACgc ; cor=; Ncor= a 0 0 2246 2301 479 419 147 337 120 10930 281 1451 1786 c 0 0 5045 5915 12196 791 13126 13190 13403 1543 12478 1784 6121 g 0 0 3594 3075 783 437 381 183 206 833 778 9371 3118 t 0 0 2989 2583 416 12227 220 164 145 568 337 1268 2849

oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; positions_7nt_m1 versus oligos_7nt_mkv5_m4; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.881581; -ccaCTCCCACmc ; cor=; Ncor= a 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671

positions_7nt_m3_shift2 (positions_7nt_m3)
; positions_7nt_m1 versus positions_7nt_m3; m=4/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.819946; --csCTCCCCCgs ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230

oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; positions_7nt_m1 versus oligos_6nt_mkv4_m3; m=5/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.629712; csCGCCCCCACcc ; cor=; Ncor= a 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; ggcGTGGGAGgs ; Alignment reference a 2570 2849 1268 337 568 145 164 220 12227 416 2583 2989 c 3388 3118 9371 778 833 206 183 381 437 783 3075 3594 g 5177 6121 1784 12478 1543 13403 13190 13126 791 12196 5915 5045 t 2739 1786 1451 281 10930 120 337 147 419 479 2301 2246
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ggcGTGGGAGgs ; cor=; Ncor= a 2570 2849 1268 337 568 145 164 220 12227 416 2583 2989 c 3388 3118 9371 778 833 206 183 381 437 783 3075 3594 g 5177 6121 1784 12478 1543 13403 13190 13126 791 12196 5915 5045 t 2739 1786 1451 281 10930 120 337 147 419 479 2301 2246
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_6nt_m2 versus positions_7nt_m1_rc; m=2/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.885444; -gbGTGGGAGsg ; cor=; Ncor= a 0 3410 3149 300 129 640 536 370 14713 421 3027 3551 c 0 4335 5070 240 1327 639 565 889 1226 591 4773 4315 g 0 7798 4929 17216 127 16331 15005 16085 425 16306 6009 6794 t 0 2303 4698 90 16263 236 1740 502 1482 528 4037 3186
positions_7nt_m3_rc_shift1 (positions_7nt_m3_rc)				; positions_6nt_m2 versus positions_7nt_m3_rc; m=3/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.788202; -scGGGGGAGsg ; cor=; Ncor= a 0 2230 2354 40 129 168 144 23 13917 21 2236 2713 c 0 4161 5991 677 1327 1177 804 79 601 450 3899 3582 g 0 6267 3111 13819 12415 13001 13356 14209 0 14069 5906 6412 t 0 1946 3148 68 733 258 300 293 86 64 2563 1897
oligos_7nt_mkv5_m4_rc_shift1 (oligos_7nt_mkv5_m4_rc)				; positions_6nt_m2 versus oligos_7nt_mkv5_m4_rc; m=4/5; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.780342; -gkGTGGGAGtg ; cor=; Ncor= a 0 2671 2600 230 716 173 202 202 10576 233 845 2107 c 0 2557 2422 665 346 140 133 274 349 267 830 2815 g 0 5494 4163 11386 951 12049 11737 11859 939 11812 2417 5377 t 0 1807 3344 248 10516 167 457 194 665 217 8437 2230
oligos_6nt_mkv4_m3_rc_shift1 (oligos_6nt_mkv4_m3_rc)				; positions_6nt_m2 versus oligos_6nt_mkv4_m3_rc; m=5/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.556046; -ggGTGGGGGCG ; cor=; Ncor= a 0 2346 1759 883 774 148 208 257 244 253 1067 370 c 0 2704 2868 1599 1373 403 736 855 917 258 9472 451 g 0 5491 4991 8885 258 11296 10390 10498 10294 11275 385 10748 t 0 1412 2335 586 9548 106 619 343 498 167 1029 384

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=13; shift=2; ncol=15; --ssCGCCCCCGCss ; Alignment reference a 0 0 1639 1696 411 561 362 406 436 500 324 528 258 2056 1549 c 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 6569 g 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 4939 t 0 0 2101 1642 335 1182 605 392 492 357 330 747 281 1939 2438
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --ssCGCCCCCGCss ; cor=; Ncor= a 0 0 1639 1696 411 561 362 406 436 500 324 528 258 2056 1549 c 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 6569 g 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 4939 t 0 0 2101 1642 335 1182 605 392 492 357 330 747 281 1939 2438
oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m3; m=2/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.86575; --csCGCCCCCACcc ; cor=; Ncor= a 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 0 0 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m1; m=3/6; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.830938; scCCCGCCCCCGCss ; cor=; Ncor= a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297
oligos_7nt_mkv5_m2_rc_shift2 (oligos_7nt_mkv5_m2_rc)				; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m2_rc; m=4/6; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.776781; --ssCGCTCCCGss- ; cor=; Ncor= a 0 0 1754 1578 618 395 167 351 179 158 443 472 1756 2096 0 c 0 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 1011 6164 5906 0 g 0 0 4172 4237 1161 12203 402 1002 620 419 530 12339 4864 4325 0 t 0 0 2367 2161 499 653 219 11132 280 259 453 632 1670 2127 0
positions_7nt_m3_shift2 (positions_7nt_m3)				; oligos_6nt_mkv4_m4 versus positions_7nt_m3; m=5/6; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.650343; --csCTCCCCCgs-- ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 0 0 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 0 0 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 0 0 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230 0 0
oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)				; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m5; m=6/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.648816; --ssCGCCTGCGss- ; cor=; Ncor= a 0 0 1597 1425 401 287 157 261 363 104 262 374 1481 1652 0 c 0 0 4045 4144 9963 544 10297 10359 1094 790 9872 787 4537 4102 0 g 0 0 3786 4240 639 10070 699 589 646 10269 928 9719 3632 3885 0 t 0 0 1922 1541 347 449 197 141 9247 187 288 470 1700 1711 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wtATTTTTAww ; Alignment reference a 6128 5376 17701 1060 1433 672 1169 1446 17563 6843 7102 c 3509 5122 1136 776 461 394 651 977 1147 3654 3601 g 4469 3873 1162 808 801 418 730 773 1002 3673 3889 t 7500 7235 1607 18962 18911 20122 19056 18410 1894 7436 7014
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wtATTTTTAww ; cor=; Ncor= a 6128 5376 17701 1060 1433 672 1169 1446 17563 6843 7102 c 3509 5122 1136 776 461 394 651 977 1147 3654 3601 g 4469 3873 1162 808 801 418 730 773 1002 3673 3889 t 7500 7235 1607 18962 18911 20122 19056 18410 1894 7436 7014
positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)				; oligos_7nt_mkv5_m3 versus positions_6nt_m4_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.539443; --wwTTTTATT ; cor=; Ncor= a 0 0 6507 7045 1610 1062 896 1358 20991 1571 1729 c 0 0 5167 4585 1025 614 896 1444 1522 775 748 g 0 0 5690 5133 1034 749 752 896 1883 732 1449 t 0 0 8367 8968 22062 23306 23187 22033 1335 22653 21805
positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)				; oligos_7nt_mkv5_m3 versus positions_6nt_m3_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.531555; --wwTTTTATG ; cor=; Ncor= a 0 0 4386 4365 901 321 523 1018 13878 923 1104 c 0 0 3424 3278 490 247 395 712 1260 238 675 g 0 0 3791 3615 595 365 285 727 993 612 12502 t 0 0 5200 5543 14815 15868 15598 14344 670 15028 2520

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift1 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -ssCGGGAGCGss ; Alignment reference a 0 2127 1670 632 453 259 280 11132 219 653 499 2161 2367 c 0 4325 4864 12339 530 419 620 1002 402 12203 1161 4237 4172 g 0 5906 6164 1011 13028 13618 13375 1969 13666 1203 12176 6478 6161 t 0 2096 1756 472 443 158 179 351 167 395 618 1578 1754
oligos_7nt_mkv5_m2_shift1 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ssCGGGAGCGss ; cor=; Ncor= a 0 2127 1670 632 453 259 280 11132 219 653 499 2161 2367 c 0 4325 4864 12339 530 419 620 1002 402 12203 1161 4237 4172 g 0 5906 6164 1011 13028 13618 13375 1969 13666 1203 12176 6478 6161 t 0 2096 1756 472 443 158 179 351 167 395 618 1578 1754
oligos_6nt_mkv4_m4_rc_shift0 (oligos_6nt_mkv4_m4_rc)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m4_rc; m=2/6; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.776781; ssGCGGGGGCGss ; cor=; Ncor= a 2438 1939 281 747 330 357 492 392 605 1182 335 1642 2101 c 4939 4320 540 14001 543 1519 2460 1466 950 13422 627 4310 4766 g 6569 7180 14416 219 14298 13119 12107 13231 13578 330 14122 7847 6989 t 1549 2056 258 528 324 500 436 406 362 561 411 1696 1639
oligos_6nt_mkv4_m3_rc_shift0 (oligos_6nt_mkv4_m3_rc)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m3_rc; m=3/6; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.680305; ggGTGGGGGCGsg ; cor=; Ncor= a 2346 1759 883 774 148 208 257 244 253 1067 370 1380 1696 c 2704 2868 1599 1373 403 736 855 917 258 9472 451 3198 2970 g 5491 4991 8885 258 11296 10390 10498 10294 11275 385 10748 5219 5711 t 1412 2335 586 9548 106 619 343 498 167 1029 384 2156 1576
oligos_7nt_mkv5_m1_rc_shift0 (oligos_7nt_mkv5_m1_rc)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m1_rc; m=4/6; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.652068; ssGCGGGGGCGGG ; cor=; Ncor= a 3297 2823 789 1951 833 683 1033 806 577 1644 658 615 941 c 6544 5424 2095 15021 1471 1482 2810 1616 1507 17496 1250 1788 2558 g 8891 9971 17333 2358 18105 18248 16584 18085 18454 853 18449 18012 16891 t 2334 2848 849 1736 657 653 639 559 528 1073 709 651 676
positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)				; oligos_7nt_mkv5_m2 versus positions_7nt_m3_rc; m=5/6; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.561411; scGGGGGAGsg-- ; cor=; Ncor= a 2230 2354 40 129 168 144 23 13917 21 2236 2713 0 0 c 4161 5991 677 1327 1177 804 79 601 450 3899 3582 0 0 g 6267 3111 13819 12415 13001 13356 14209 0 14069 5906 6412 0 0 t 1946 3148 68 733 258 300 293 86 64 2563 1897 0 0
oligos_6nt_mkv4_m5_rc_shift4 (oligos_6nt_mkv4_m5_rc)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m5_rc; m=6/6; ncol2=10; w=0; offset=3; strand=R; shift=4; score=0.486627; ----ggGAGGGGv ; cor=; Ncor= a 0 0 0 0 3246 3103 0 15970 0 0 0 0 4405 c 0 0 0 0 3162 1903 0 0 79 16 19 0 4432 g 0 0 0 0 7745 8600 15970 0 15891 15952 15950 15969 5099 t 0 0 0 0 1817 2364 0 0 0 2 1 1 2034

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---csCTCCCCCgs ; Alignment reference a 0 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 c 0 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 g 0 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 t 0 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---csCTCCCCCgs ; cor=; Ncor= a 0 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 c 0 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 g 0 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 t 0 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m3 versus positions_7nt_m1; m=2/9; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.819946; ---csCTCCCACvc ; cor=; Ncor= a 0 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410
positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)				; positions_7nt_m3 versus positions_6nt_m2_rc; m=3/9; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.788202; ---scCTCCCACgc ; cor=; Ncor= a 0 0 0 2246 2301 479 419 147 337 120 10930 281 1451 1786 c 0 0 0 5045 5915 12196 791 13126 13190 13403 1543 12478 1784 6121 g 0 0 0 3594 3075 783 437 381 183 206 833 778 9371 3118 t 0 0 0 2989 2583 416 12227 220 164 145 568 337 1268 2849
oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)				; positions_7nt_m3 versus oligos_7nt_mkv5_m4; m=4/9; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score= 0.7442; --ccaCTCCCACmc ; cor=; Ncor= a 0 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671
oligos_6nt_mkv4_m3_shift3 (oligos_6nt_mkv4_m3)				; positions_7nt_m3 versus oligos_6nt_mkv4_m3; m=5/9; ncol2=13; w=0; offset=0; strand=D; shift=3; score=0.666241; ---csCGCCCCCAC ; cor=; Ncor= a 0 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 c 0 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 g 0 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 t 0 0 0 1696 1380 370 1067 253 244 257 208 148 774 883
oligos_6nt_mkv4_m4_shift3 (oligos_6nt_mkv4_m4)				; positions_7nt_m3 versus oligos_6nt_mkv4_m4; m=6/9; ncol2=13; w=0; offset=0; strand=D; shift=3; score=0.650343; ---ssCGCCCCCGC ; cor=; Ncor= a 0 0 0 1639 1696 411 561 362 406 436 500 324 528 258 c 0 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 g 0 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 t 0 0 0 2101 1642 335 1182 605 392 492 357 330 747 281
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)				; positions_7nt_m3 versus oligos_7nt_mkv5_m1; m=7/9; ncol2=15; w=-2; offset=-2; strand=D; shift=1; score=0.561926; -scCCCGCCCCCGC ; cor=; Ncor= a 0 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 c 0 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 g 0 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 t 0 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789
oligos_7nt_mkv5_m2_rc_shift1 (oligos_7nt_mkv5_m2_rc)				; positions_7nt_m3 versus oligos_7nt_mkv5_m2_rc; m=8/9; ncol2=12; w=-2; offset=-2; strand=R; shift=1; score=0.561411; -ssCGCTCCCGss- ; cor=; Ncor= a 0 1754 1578 618 395 167 351 179 158 443 472 1756 2096 0 c 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 1011 6164 5906 0 g 0 4172 4237 1161 12203 402 1002 620 419 530 12339 4864 4325 0 t 0 2367 2161 499 653 219 11132 280 259 453 632 1670 2127 0
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; positions_7nt_m3 versus oligos_6nt_mkv4_m5; m=9/9; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.409377; sbCCCCTCcc---- ; cor=; Ncor= a 2541 2034 1 1 2 0 0 0 2364 1817 0 0 0 0 c 5634 5099 15969 15950 15952 15891 0 15970 8600 7745 0 0 0 0 g 4124 4432 0 19 16 79 0 0 1903 3162 0 0 0 0 t 3671 4405 0 0 0 0 15970 0 3103 3246 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCATAAAAww ; Alignment reference a 4879 5694 2520 15028 670 14344 15598 15868 14815 5543 5200 c 3935 3936 12502 612 993 727 285 365 595 3615 3791 g 3774 2732 675 238 1260 712 395 247 490 3278 3424 t 4213 4439 1104 923 13878 1018 523 321 901 4365 4386
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCATAAAAww ; cor=; Ncor= a 4879 5694 2520 15028 670 14344 15598 15868 14815 5543 5200 c 3935 3936 12502 612 993 727 285 365 595 3615 3791 g 3774 2732 675 238 1260 712 395 247 490 3278 3424 t 4213 4439 1104 923 13878 1018 523 321 901 4365 4386
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m3 versus positions_6nt_m4; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.865214; aaAATAAAAww ; cor=; Ncor= a 8675 10232 21805 22653 1335 22033 23187 23306 22062 8968 8367 c 4672 4882 1449 732 1883 896 752 749 1034 5133 5690 g 6067 4843 748 775 1522 1444 896 614 1025 4585 5167 t 6317 5774 1729 1571 20991 1358 896 1062 1610 7045 6507
oligos_7nt_mkv5_m3_rc_shift2 (oligos_7nt_mkv5_m3_rc)				; positions_6nt_m3 versus oligos_7nt_mkv5_m3_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.531555; --wwTAAAAAT ; cor=; Ncor= a 0 0 7014 7436 1894 18410 19056 20122 18911 18962 1607 c 0 0 3889 3673 1002 773 730 418 801 808 1162 g 0 0 3601 3654 1147 977 651 394 461 776 1136 t 0 0 7102 6843 17563 1446 1169 672 1433 1060 17701

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --csCGCCCCCACcc ; Alignment reference a 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 0 0 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346
oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/8; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --csCGCCCCCACcc ; cor=; Ncor= a 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 0 0 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m4; m=2/8; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.86575; --ssCGCCCCCGCss ; cor=; Ncor= a 0 0 1639 1696 411 561 362 406 436 500 324 528 258 2056 1549 c 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 6569 g 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 4939 t 0 0 2101 1642 335 1182 605 392 492 357 330 747 281 1939 2438
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m1; m=3/8; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.751795; scCCCGCCCCCGCss ; cor=; Ncor= a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297
oligos_7nt_mkv5_m2_rc_shift2 (oligos_7nt_mkv5_m2_rc)				; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m2_rc; m=4/8; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.680305; --ssCGCTCCCGss- ; cor=; Ncor= a 0 0 1754 1578 618 395 167 351 179 158 443 472 1756 2096 0 c 0 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 1011 6164 5906 0 g 0 0 4172 4237 1161 12203 402 1002 620 419 530 12339 4864 4325 0 t 0 0 2367 2161 499 653 219 11132 280 259 453 632 1670 2127 0
positions_7nt_m3_shift2 (positions_7nt_m3)				; oligos_6nt_mkv4_m3 versus positions_7nt_m3; m=5/8; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.666241; --csCTCCCCCgs-- ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 0 0 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 0 0 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 0 0 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230 0 0
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m4; m=6/8; ncol2=12; w=0; offset=1; strand=D; shift=3; score=0.661522; ---ccaCTCCCACmc ; cor=; Ncor= a 0 0 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 0 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 0 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 0 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671
positions_7nt_m1_shift4 (positions_7nt_m1)				; oligos_6nt_mkv4_m3 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.629712; ----csCTCCCACvc ; cor=; Ncor= a 0 0 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410
positions_6nt_m2_rc_shift4 (positions_6nt_m2_rc)				; oligos_6nt_mkv4_m3 versus positions_6nt_m2_rc; m=8/8; ncol2=12; w=0; offset=2; strand=R; shift=4; score=0.556046; ----scCTCCCACgc ; cor=; Ncor= a 0 0 0 0 2246 2301 479 419 147 337 120 10930 281 1451 1786 c 0 0 0 0 5045 5915 12196 791 13126 13190 13403 1543 12478 1784 6121 g 0 0 0 0 3594 3075 783 437 381 183 206 833 778 9371 3118 t 0 0 0 0 2989 2583 416 12227 220 164 145 568 337 1268 2849

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=15; shift=0; ncol=15; scCCCGCCCCCGCss ; Alignment reference a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; scCCCGCCCCCGCss ; cor=; Ncor= a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m4; m=2/6; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.830938; --ssCGCCCCCGCss ; cor=; Ncor= a 0 0 1639 1696 411 561 362 406 436 500 324 528 258 2056 1549 c 0 0 6989 7847 14122 330 13578 13231 12107 13119 14298 219 14416 7180 6569 g 0 0 4766 4310 627 13422 950 1466 2460 1519 543 14001 540 4320 4939 t 0 0 2101 1642 335 1182 605 392 492 357 330 747 281 1939 2438
oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m3; m=3/6; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.751795; --csCGCCCCCACcc ; cor=; Ncor= a 0 0 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 0 0 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 0 0 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 0 0 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346
oligos_7nt_mkv5_m2_rc_shift2 (oligos_7nt_mkv5_m2_rc)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m2_rc; m=4/6; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.652068; --ssCGCTCCCGss- ; cor=; Ncor= a 0 0 1754 1578 618 395 167 351 179 158 443 472 1756 2096 0 c 0 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 1011 6164 5906 0 g 0 0 4172 4237 1161 12203 402 1002 620 419 530 12339 4864 4325 0 t 0 0 2367 2161 499 653 219 11132 280 259 453 632 1670 2127 0
positions_7nt_m3_shift2 (positions_7nt_m3)				; oligos_7nt_mkv5_m1 versus positions_7nt_m3; m=5/6; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.561926; --csCTCCCCCgs-- ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 0 0 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 0 0 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 0 0 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230 0 0
oligos_6nt_mkv4_m5_shift5 (oligos_6nt_mkv4_m5)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m5; m=6/6; ncol2=10; w=0; offset=5; strand=D; shift=5; score=0.475063; -----sbCCCCTCcc ; cor=; Ncor= a 0 0 0 0 0 2541 2034 1 1 2 0 0 0 2364 1817 c 0 0 0 0 0 5634 5099 15969 15950 15952 15891 0 15970 8600 7745 g 0 0 0 0 0 4124 4432 0 19 16 79 0 0 1903 3162 t 0 0 0 0 0 3671 4405 0 0 0 0 15970 0 3103 3246

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=1; ncol=13; -ccaCTCCCACmc ; Alignment reference a 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ccaCTCCCACmc ; cor=; Ncor= a 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671
positions_7nt_m1_shift2 (positions_7nt_m1)				; oligos_7nt_mkv5_m4 versus positions_7nt_m1; m=2/6; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.881581; --csCTCCCACvc ; cor=; Ncor= a 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410
positions_6nt_m2_rc_shift2 (positions_6nt_m2_rc)				; oligos_7nt_mkv5_m4 versus positions_6nt_m2_rc; m=3/6; ncol2=12; w=0; offset=1; strand=R; shift=2; score=0.780342; --scCTCCCACgc ; cor=; Ncor= a 0 0 2246 2301 479 419 147 337 120 10930 281 1451 1786 c 0 0 5045 5915 12196 791 13126 13190 13403 1543 12478 1784 6121 g 0 0 3594 3075 783 437 381 183 206 833 778 9371 3118 t 0 0 2989 2583 416 12227 220 164 145 568 337 1268 2849
positions_7nt_m3_shift2 (positions_7nt_m3)				; oligos_7nt_mkv5_m4 versus positions_7nt_m3; m=4/6; ncol2=11; w=0; offset=1; strand=D; shift=2; score= 0.7442; --csCTCCCCCgs ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230
oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)				; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m3; m=5/6; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.661522; csCGCCCCCACcc ; cor=; Ncor= a 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346
positions_6nt_m1_rc_shift5 (positions_6nt_m1_rc)				; oligos_7nt_mkv5_m4 versus positions_6nt_m1_rc; m=6/6; ncol2=10; w=0; offset=4; strand=R; shift=5; score=0.40379; -----ccCCACCT ; cor=; Ncor= a 0 0 0 0 0 1346 1377 92 7 8138 4 139 11 c 0 0 0 0 0 3246 3130 7994 7964 0 8122 7245 0 g 0 0 0 0 0 1813 1871 29 98 2 0 748 68 t 0 0 0 0 0 1735 1762 25 71 0 14 8 8061

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m5_shift5 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=10; shift=5; ncol=15; -----sbCCCCTCcc ; Alignment reference a 0 0 0 0 0 2541 2034 1 1 2 0 0 0 2364 1817 c 0 0 0 0 0 5634 5099 15969 15950 15952 15891 0 15970 8600 7745 g 0 0 0 0 0 4124 4432 0 19 16 79 0 0 1903 3162 t 0 0 0 0 0 3671 4405 0 0 0 0 15970 0 3103 3246
oligos_6nt_mkv4_m5_shift5 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----sbCCCCTCcc ; cor=; Ncor= a 0 0 0 0 0 2541 2034 1 1 2 0 0 0 2364 1817 c 0 0 0 0 0 5634 5099 15969 15950 15952 15891 0 15970 8600 7745 g 0 0 0 0 0 4124 4432 0 19 16 79 0 0 1903 3162 t 0 0 0 0 0 3671 4405 0 0 0 0 15970 0 3103 3246
oligos_7nt_mkv5_m2_rc_shift6 (oligos_7nt_mkv5_m2_rc)				; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m2_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=6; score=0.486627; ------ssCGCTCCC ; cor=; Ncor= a 0 0 0 0 0 0 1754 1578 618 395 167 351 179 158 443 c 0 0 0 0 0 0 6161 6478 12176 1203 13666 1969 13375 13618 13028 g 0 0 0 0 0 0 4172 4237 1161 12203 402 1002 620 419 530 t 0 0 0 0 0 0 2367 2161 499 653 219 11132 280 259 453
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m1; m=3/4; ncol2=15; w=-5; offset=-5; strand=D; shift=0; score=0.475063; scCCCGCCCCCGCss ; cor=; Ncor= a 2450 2321 676 651 709 1073 528 559 639 653 657 1736 849 2848 2334 c 9452 10145 16891 18012 18449 853 18454 18085 16584 18248 18105 2358 17333 9971 8891 g 5624 5125 2558 1788 1250 17496 1507 1616 2810 1482 1471 15021 2095 5424 6544 t 3540 3475 941 615 658 1644 577 806 1033 683 833 1951 789 2823 3297
positions_7nt_m3_shift8 (positions_7nt_m3)				; oligos_6nt_mkv4_m5 versus positions_7nt_m3; m=4/4; ncol2=11; w=0; offset=3; strand=D; shift=8; score=0.409377; --------csCTCCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1897 2563 64 86 293 300 258 c 0 0 0 0 0 0 0 0 6412 5906 14069 0 14209 13356 13001 g 0 0 0 0 0 0 0 0 3582 3899 450 601 79 804 1177 t 0 0 0 0 0 0 0 0 2713 2236 21 13917 23 144 168

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; aaAATAAAAww ; Alignment reference a 8675 10232 21805 22653 1335 22033 23187 23306 22062 8968 8367 c 4672 4882 1449 732 1883 896 752 749 1034 5133 5690 g 6067 4843 748 775 1522 1444 896 614 1025 4585 5167 t 6317 5774 1729 1571 20991 1358 896 1062 1610 7045 6507
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; aaAATAAAAww ; cor=; Ncor= a 8675 10232 21805 22653 1335 22033 23187 23306 22062 8968 8367 c 4672 4882 1449 732 1883 896 752 749 1034 5133 5690 g 6067 4843 748 775 1522 1444 896 614 1025 4585 5167 t 6317 5774 1729 1571 20991 1358 896 1062 1610 7045 6507
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m4 versus positions_6nt_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.865214; wwCATAAAAww ; cor=; Ncor= a 4879 5694 2520 15028 670 14344 15598 15868 14815 5543 5200 c 3935 3936 12502 612 993 727 285 365 595 3615 3791 g 3774 2732 675 238 1260 712 395 247 490 3278 3424 t 4213 4439 1104 923 13878 1018 523 321 901 4365 4386
oligos_7nt_mkv5_m3_rc_shift2 (oligos_7nt_mkv5_m3_rc)				; positions_6nt_m4 versus oligos_7nt_mkv5_m3_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.539443; --wwTAAAAAT ; cor=; Ncor= a 0 0 7014 7436 1894 18410 19056 20122 18911 18962 1607 c 0 0 3889 3673 1002 773 730 418 801 808 1162 g 0 0 3601 3654 1147 977 651 394 461 776 1136 t 0 0 7102 6843 17563 1446 1169 672 1433 1060 17701

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift2 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --csCTCCCACvc ; Alignment reference a 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410
positions_7nt_m1_shift2 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --csCTCCCACvc ; cor=; Ncor= a 0 0 3186 4037 528 1482 502 1740 236 16263 90 4698 2303 c 0 0 6794 6009 16306 425 16085 15005 16331 127 17216 4929 7798 g 0 0 4315 4773 591 1226 889 565 639 1327 240 5070 4335 t 0 0 3551 3027 421 14713 370 536 640 129 300 3149 3410
positions_6nt_m2_rc_shift2 (positions_6nt_m2_rc)				; positions_7nt_m1 versus positions_6nt_m2_rc; m=2/5; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.885444; --scCTCCCACgc ; cor=; Ncor= a 0 0 2246 2301 479 419 147 337 120 10930 281 1451 1786 c 0 0 5045 5915 12196 791 13126 13190 13403 1543 12478 1784 6121 g 0 0 3594 3075 783 437 381 183 206 833 778 9371 3118 t 0 0 2989 2583 416 12227 220 164 145 568 337 1268 2849
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; positions_7nt_m1 versus oligos_7nt_mkv5_m4; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.881581; -ccaCTCCCACmc ; cor=; Ncor= a 0 2712 2230 8437 217 665 194 457 167 10516 248 3344 1807 c 0 4747 5377 2417 11812 939 11859 11737 12049 951 11386 4163 5494 g 0 2429 2815 830 267 349 274 133 140 346 665 2422 2557 t 0 2641 2107 845 233 10576 202 202 173 716 230 2600 2671
positions_7nt_m3_shift2 (positions_7nt_m3)				; positions_7nt_m1 versus positions_7nt_m3; m=4/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.819946; --csCTCCCCCgs ; cor=; Ncor= a 0 0 1897 2563 64 86 293 300 258 733 68 3148 1946 c 0 0 6412 5906 14069 0 14209 13356 13001 12415 13819 3111 6267 g 0 0 3582 3899 450 601 79 804 1177 1327 677 5991 4161 t 0 0 2713 2236 21 13917 23 144 168 129 40 2354 2230
oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)				; positions_7nt_m1 versus oligos_6nt_mkv4_m3; m=5/5; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.629712; csCGCCCCCACcc ; cor=; Ncor= a 1576 2156 384 1029 167 498 343 619 106 9548 586 2335 1412 c 5711 5219 10748 385 11275 10294 10498 10390 11296 258 8885 4991 5491 g 2970 3198 451 9472 258 917 855 736 403 1373 1599 2868 2704 t 1696 1380 370 1067 253 244 257 208 148 774 883 1759 2346