One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204211_2025-11-26.204211_jXQ2u1/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/2025/11/26/peak-motifs.2025-11-26.204211_2025-11-26.204211_jXQ2u1/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift7 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift7 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=12; shift=7; ncol=19; -------dcCTGGAAGgrv ; Alignment reference a 0 0 0 0 0 0 0 2579 2037 358 383 309 283 8593 8768 275 1335 2726 2447 c 0 0 0 0 0 0 0 1802 3444 8870 470 175 419 456 385 155 1402 2135 2680 g 0 0 0 0 0 0 0 2443 2271 363 545 9074 8596 429 260 8769 5618 2471 2745 t 0 0 0 0 0 0 0 2919 1991 152 8345 185 445 265 330 544 1388 2411 1871

positions_7nt_m5_shift7 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=7; score= 1; -------dcCTGGAAGgrv ; cor=; Ncor= a 0 0 0 0 0 0 0 2579 2037 358 383 309 283 8593 8768 275 1335 2726 2447 c 0 0 0 0 0 0 0 1802 3444 8870 470 175 419 456 385 155 1402 2135 2680 g 0 0 0 0 0 0 0 2443 2271 363 545 9074 8596 429 260 8769 5618 2471 2745 t 0 0 0 0 0 0 0 2919 1991 152 8345 185 445 265 330 544 1388 2411 1871

positions_6nt_m5_rc_shift8 (positions_6nt_m5_rc)
; positions_7nt_m5 versus positions_6nt_m5_rc; m=2/4; ncol2=11; w=0; offset=1; strand=R; shift=8; score=0.868925; --------ccTGGAAGgdr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2012 2006 58 173 66 8253 8261 105 1436 2249 2768 c 0 0 0 0 0 0 0 0 2916 3332 309 152 77 129 298 400 1141 1928 1856 g 0 0 0 0 0 0 0 0 1943 2108 144 8477 8320 142 121 8001 5294 2321 2550 t 0 0 0 0 0 0 0 0 1965 1390 8325 34 373 312 156 330 965 2338 1662

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_7nt_m5 versus positions_7nt_m2_rc; m=3/4; ncol2=17; w=-5; offset=-5; strand=R; shift=2; score=0.560059; --smrGGTCCTGGcaGggs ; cor=; Ncor= a 0 0 1271 1662 1897 340 222 408 123 139 249 222 435 1444 4184 340 997 1284 1510 c 0 0 2372 2063 489 315 303 405 5930 5917 436 246 432 3932 688 459 1285 1441 1711 g 0 0 1716 1603 3731 5543 5772 401 308 261 414 5685 5296 695 831 5412 3482 2183 2142 t 0 0 1149 1180 391 310 211 5294 147 191 5409 355 345 437 805 297 744 1600 1145

positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc)
; positions_7nt_m5 versus positions_7nt_m1_rc; m=4/4; ncol2=19; w=-7; offset=-7; strand=R; shift=0; score=0.493384; bsccAGGTCCTGGcaGgks ; cor=; Ncor= a 1547 1307 1217 1221 5945 254 192 893 133 144 210 437 668 1746 4296 600 1391 1429 1788 c 1892 2103 3460 4621 313 201 272 412 6717 6776 427 354 759 3991 850 767 1549 1654 1917 g 1923 2203 1518 823 757 6614 6573 402 267 136 259 5821 5230 910 950 5353 3211 2228 2244 t 1907 1656 1074 604 254 200 232 5562 152 213 6373 657 612 622 1173 549 1118 1958 1320

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift3 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=19; shift=3; ncol=22; ---smcCtgCCAGGACCTggsv ; Alignment reference a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 1907 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 1923 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 1892 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307 1547

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/11; ncol2=19; w=0; offset=0; strand=D; shift=3; score= 1; ---smcCtgCCAGGACCTggsv ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 1907 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 1923 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 1892 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307 1547

positions_7nt_m2_shift3 (positions_7nt_m2)
; positions_7nt_m1 versus positions_7nt_m2; m=2/11; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.833426; ---sccCtgCCAGGACCyks-- ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 0 0 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 0 0 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 0 0 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271 0 0

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; positions_7nt_m1 versus positions_6nt_m1_rc; m=3/11; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.825277; ---sscctgscAGGTCCTGgar ; cor=; Ncor= a 0 0 0 1308 1478 1082 822 1238 772 949 1042 5395 160 216 994 155 137 195 391 796 3096 2133 c 0 0 0 1787 1883 3077 3724 1158 1188 1910 4229 296 160 231 312 5992 6069 366 311 803 1565 1441 g 0 0 0 1980 1775 1288 1142 1177 3433 2820 780 552 6055 5890 353 263 158 250 5381 4312 1103 1649 t 0 0 0 1454 1393 1082 841 2956 1136 850 478 286 154 192 4870 119 165 5718 446 618 765 1306

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m1 versus positions_6nt_m2_rc; m=4/11; ncol2=23; w=-3; offset=-3; strand=R; shift=0; score=0.81466; csggccCtgCCAGGACCTgsss ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 1312 1517 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 1992 1846 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 1812 1802 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160 1384 1335

oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)
; positions_7nt_m1 versus oligos_7nt_mkv5_m1; m=5/11; ncol2=16; w=0; offset=3; strand=D; shift=6; score=0.806823; ------cttcCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846

positions_7nt_m4_shift8 (positions_7nt_m4)
; positions_7nt_m1 versus positions_7nt_m4; m=6/11; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.691461; --------kcmAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276

positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_7nt_m1 versus positions_6nt_m4; m=7/11; ncol2=14; w=0; offset=3; strand=D; shift=6; score=0.669833; ------cytCCAGGACCyks-- ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 0 0 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 0 0 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 0 0 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991 0 0

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; positions_7nt_m1 versus oligos_6nt_mkv4_m1; m=8/11; ncol2=13; w=0; offset=5; strand=D; shift=8; score=0.665139; --------kcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 0 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 0 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 0 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340 0

positions_7nt_m3_shift8 (positions_7nt_m3)
; positions_7nt_m1 versus positions_7nt_m3; m=9/11; ncol2=12; w=0; offset=5; strand=D; shift=8; score=0.556459; --------ssCAGGgCCTgs-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 0 0 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 0 0 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 0 0 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581 0 0

positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)
; positions_7nt_m1 versus positions_7nt_m5_rc; m=10/11; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.493384; ---bycCTTCCAGgh------- ; cor=; Ncor= a 0 0 0 1871 2411 1388 544 330 265 445 185 8345 152 1991 2919 0 0 0 0 0 0 0 c 0 0 0 2745 2471 5618 8769 260 429 8596 9074 545 363 2271 2443 0 0 0 0 0 0 0 g 0 0 0 2680 2135 1402 155 385 456 419 175 470 8870 3444 1802 0 0 0 0 0 0 0 t 0 0 0 2447 2726 1335 275 8768 8593 283 309 383 358 2037 2579 0 0 0 0 0 0 0

positions_6nt_m5_shift3 (positions_6nt_m5)
; positions_7nt_m1 versus positions_6nt_m5; m=11/11; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.417174; ---yhcCTTCCAgg-------- ; cor=; Ncor= a 0 0 0 1662 2338 965 330 156 312 373 34 8325 1390 1965 0 0 0 0 0 0 0 0 c 0 0 0 2550 2321 5294 8001 121 142 8320 8477 144 2108 1943 0 0 0 0 0 0 0 0 g 0 0 0 1856 1928 1141 400 298 129 77 152 309 3332 2916 0 0 0 0 0 0 0 0 t 0 0 0 2768 2249 1436 105 8261 8253 66 173 58 2006 2012 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 10 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=23; shift=0; ncol=23; sssscAGGTCCTGGcaGggccsg ; Alignment reference a 1257 1335 1384 1160 1016 4969 209 178 671 121 133 191 324 632 1550 3455 550 1129 920 1166 1389 1488 1447 c 2046 1802 1812 2263 4096 412 198 305 381 5977 6046 441 364 864 3454 956 856 1211 1125 2939 2856 1788 1612 g 1991 1846 1992 2022 869 835 5925 5821 450 256 167 360 5389 4424 872 1078 4580 3201 3194 1486 1300 1899 2050 t 1206 1517 1312 1055 519 284 168 196 4998 146 154 5508 423 580 624 1011 514 959 1261 909 955 1325 1391

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/9; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; sssscAGGTCCTGGcaGggccsg ; cor=; Ncor= a 1257 1335 1384 1160 1016 4969 209 178 671 121 133 191 324 632 1550 3455 550 1129 920 1166 1389 1488 1447 c 2046 1802 1812 2263 4096 412 198 305 381 5977 6046 441 364 864 3454 956 856 1211 1125 2939 2856 1788 1612 g 1991 1846 1992 2022 869 835 5925 5821 450 256 167 360 5389 4424 872 1078 4580 3201 3194 1486 1300 1899 2050 t 1206 1517 1312 1055 519 284 168 196 4998 146 154 5508 423 580 624 1011 514 959 1261 909 955 1325 1391

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_6nt_m2 versus positions_7nt_m1_rc; m=2/9; ncol2=19; w=0; offset=1; strand=R; shift=1; score=0.81466; -bsccAGGTCCTGGcaGgks--- ; cor=; Ncor= a 0 1547 1307 1217 1221 5945 254 192 893 133 144 210 437 668 1746 4296 600 1391 1429 1788 0 0 0 c 0 1892 2103 3460 4621 313 201 272 412 6717 6776 427 354 759 3991 850 767 1549 1654 1917 0 0 0 g 0 1923 2203 1518 823 757 6614 6573 402 267 136 259 5821 5230 910 950 5353 3211 2228 2244 0 0 0 t 0 1907 1656 1074 604 254 200 232 5562 152 213 6373 657 612 622 1173 549 1118 1958 1320 0 0 0

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=3/9; ncol2=20; w=0; offset=0; strand=D; shift=0; score=0.73824; cytcCAGGACCTgscaggss--- ; cor=; Ncor= a 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 841 1082 1393 1454 0 0 0 c 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 1142 1288 1775 1980 0 0 0 g 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 3724 3077 1883 1787 0 0 0 t 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238 822 1082 1478 1308 0 0 0

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; positions_6nt_m2 versus positions_7nt_m2_rc; m=4/9; ncol2=17; w=0; offset=3; strand=R; shift=3; score=0.687453; ---smrGGTCCTGGcaGggs--- ; cor=; Ncor= a 0 0 0 1271 1662 1897 340 222 408 123 139 249 222 435 1444 4184 340 997 1284 1510 0 0 0 c 0 0 0 2372 2063 489 315 303 405 5930 5917 436 246 432 3932 688 459 1285 1441 1711 0 0 0 g 0 0 0 1716 1603 3731 5543 5772 401 308 261 414 5685 5296 695 831 5412 3482 2183 2142 0 0 0 t 0 0 0 1149 1180 391 310 211 5294 147 191 5409 355 345 437 805 297 744 1600 1145 0 0 0

oligos_7nt_mkv5_m1_rc_shift1 (oligos_7nt_mkv5_m1_rc)
; positions_6nt_m2 versus oligos_7nt_mkv5_m1_rc; m=5/9; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.665179; -tscCAGGTCCTGgaag------ ; cor=; Ncor= a 0 1846 1413 1181 1103 6930 208 232 1058 155 196 215 673 881 4400 2829 1369 0 0 0 0 0 0 c 0 1950 2294 4240 5632 242 200 263 362 7328 7489 399 482 964 1625 1588 1840 0 0 0 0 0 0 g 0 1913 2388 1442 653 576 7373 7256 323 307 125 233 6024 5385 1061 1975 3521 0 0 0 0 0 0 t 0 2249 1863 1095 570 210 177 207 6215 168 148 7111 779 728 872 1566 1228 0 0 0 0 0 0

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; positions_6nt_m2 versus positions_7nt_m4_rc; m=6/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.564804; -tbcCAGGTCCTkgm-------- ; cor=; Ncor= a 0 2276 1836 1578 1511 9319 211 226 1554 193 176 153 1205 2010 2913 0 0 0 0 0 0 0 0 c 0 2467 2810 5330 7194 200 224 275 256 9622 9697 379 1374 2432 3184 0 0 0 0 0 0 0 0 g 0 2234 2766 1692 768 440 9497 9379 281 201 88 201 3753 3581 1965 0 0 0 0 0 0 0 0 t 0 3206 2771 1583 710 224 251 303 8092 167 222 9450 3851 2160 2121 0 0 0 0 0 0 0 0

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; positions_6nt_m2 versus positions_6nt_m4_rc; m=7/9; ncol2=14; w=0; offset=3; strand=R; shift=3; score=0.561044; ---smrGGTCCTGGarg------ ; cor=; Ncor= a 0 0 0 1991 2653 3555 425 296 587 145 172 211 453 1046 5177 3446 1658 0 0 0 0 0 0 c 0 0 0 3865 3395 1015 365 275 393 9701 9897 516 350 1190 2286 2163 2381 0 0 0 0 0 0 g 0 0 0 2706 2413 4902 9284 9606 445 385 217 396 9180 7332 1691 2763 4782 0 0 0 0 0 0 t 0 0 0 1899 2000 989 387 284 9036 230 175 9338 478 893 1307 2089 1640 0 0 0 0 0 0

oligos_6nt_mkv4_m1_rc_shift2 (oligos_6nt_mkv4_m1_rc)
; positions_6nt_m2 versus oligos_6nt_mkv4_m1_rc; m=8/9; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.551534; --sccAGGTCCTGgm-------- ; cor=; Ncor= a 0 0 2340 2240 2413 9738 324 318 1648 199 227 203 626 2358 3553 0 0 0 0 0 0 0 0 c 0 0 3399 4645 6622 510 263 344 458 11530 11661 494 499 2853 3802 0 0 0 0 0 0 0 0 g 0 0 3540 2879 1662 1576 11398 11320 480 347 155 237 10356 4729 2606 0 0 0 0 0 0 0 0 t 0 0 2995 2510 1577 450 289 292 9688 198 231 11340 793 2334 2313 0 0 0 0 0 0 0 0

positions_7nt_m3_rc_shift3 (positions_7nt_m3_rc)
; positions_6nt_m2 versus positions_7nt_m3_rc; m=9/9; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.462316; ---scAGGcCCTGss-------- ; cor=; Ncor= a 0 0 0 2581 2801 10238 283 462 2056 365 223 358 200 2317 3105 0 0 0 0 0 0 0 0 c 0 0 0 4801 5562 1319 267 324 8473 11782 12519 608 223 3798 4129 0 0 0 0 0 0 0 0 g 0 0 0 3419 3279 1125 12541 12150 522 583 350 543 12741 4770 3801 0 0 0 0 0 0 0 0 t 0 0 0 2524 1683 643 234 389 2274 595 233 11816 161 2440 2290 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift8 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift8 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=14; shift=8; ncol=22; --------kcmAGGACCTGgva ; Alignment reference a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276

positions_7nt_m4_shift8 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/9; ncol2=14; w=0; offset=0; strand=D; shift=8; score= 1; --------kcmAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; positions_7nt_m4 versus oligos_6nt_mkv4_m1; m=2/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score=0.884892; --------kcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 0 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 0 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 0 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340 0

oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)
; positions_7nt_m4 versus oligos_7nt_mkv5_m1; m=3/9; ncol2=16; w=-2; offset=-2; strand=D; shift=6; score=0.831405; ------cttcCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846

positions_7nt_m3_rc_shift9 (positions_7nt_m3_rc)
; positions_7nt_m4 versus positions_7nt_m3_rc; m=4/9; ncol2=12; w=0; offset=1; strand=R; shift=9; score=0.761131; ---------scAGGcCCTGss- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2581 2801 10238 283 462 2056 365 223 358 200 2317 3105 0 c 0 0 0 0 0 0 0 0 0 4801 5562 1319 267 324 8473 11782 12519 608 223 3798 4129 0 g 0 0 0 0 0 0 0 0 0 3419 3279 1125 12541 12150 522 583 350 543 12741 4770 3801 0 t 0 0 0 0 0 0 0 0 0 2524 1683 643 234 389 2274 595 233 11816 161 2440 2290 0

positions_6nt_m4_rc_shift9 (positions_6nt_m4_rc)
; positions_7nt_m4 versus positions_6nt_m4_rc; m=5/9; ncol2=14; w=0; offset=1; strand=R; shift=9; score=0.695681; ---------smrGGTCCTGGar ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1991 2653 3555 425 296 587 145 172 211 453 1046 5177 3446 c 0 0 0 0 0 0 0 0 0 3865 3395 1015 365 275 393 9701 9897 516 350 1190 2286 2163 g 0 0 0 0 0 0 0 0 0 2706 2413 4902 9284 9606 445 385 217 396 9180 7332 1691 2763 t 0 0 0 0 0 0 0 0 0 1899 2000 989 387 284 9036 230 175 9338 478 893 1307 2089

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m4 versus positions_7nt_m1; m=6/9; ncol2=19; w=-5; offset=-5; strand=D; shift=3; score=0.691461; ---smcCtgCCAGGACCTggsv ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 1907 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 1923 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 1892 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307 1547

positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_7nt_m4 versus positions_6nt_m1; m=7/9; ncol2=20; w=-2; offset=-2; strand=D; shift=6; score=0.644377; ------cytcCAGGACCTgsca ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m4 versus positions_6nt_m2_rc; m=8/9; ncol2=23; w=-8; offset=-8; strand=R; shift=0; score=0.564804; csggccCtgCCAGGACCTgsss ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 1312 1517 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 1992 1846 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 1812 1802 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160 1384 1335

positions_7nt_m2_rc_shift9 (positions_7nt_m2_rc)
; positions_7nt_m4 versus positions_7nt_m2_rc; m=9/9; ncol2=17; w=0; offset=1; strand=R; shift=9; score=0.550391; ---------smrGGTCCTGGca ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1271 1662 1897 340 222 408 123 139 249 222 435 1444 4184 c 0 0 0 0 0 0 0 0 0 2372 2063 489 315 303 405 5930 5917 436 246 432 3932 688 g 0 0 0 0 0 0 0 0 0 1716 1603 3731 5543 5772 401 308 261 414 5685 5296 695 831 t 0 0 0 0 0 0 0 0 0 1149 1180 391 310 211 5294 147 191 5409 355 345 437 805

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---ssCGCCCGss ; Alignment reference a 0 0 0 1806 2332 74 338 540 779 116 239 1410 1961 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 4445 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 t 0 0 0 1774 1470 183 127 771 862 417 104 1979 1836

oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/7; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCGss ; cor=; Ncor= a 0 0 0 1806 2332 74 338 540 779 116 239 1410 1961 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 4445 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 t 0 0 0 1774 1470 183 127 771 862 417 104 1979 1836

oligos_6nt_mkv4_m4_rc_shift3 (oligos_6nt_mkv4_m4_rc)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m4_rc; m=2/7; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.918767; ---ssCGCtCGss ; cor=; Ncor= a 0 0 0 1221 1423 122 198 198 779 137 176 888 1250 c 0 0 0 3711 2634 8231 109 7735 1429 8312 499 3676 2949 g 0 0 0 2593 3710 333 8356 540 2060 265 7910 3001 3301 t 0 0 0 1286 1044 125 148 338 4543 97 226 1246 1311

oligos_6nt_mkv4_m5_shift3 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m5; m=3/7; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.848843; ---ssCGGCCGss ; cor=; Ncor= a 0 0 0 1948 2212 83 178 540 771 127 225 1522 1604 c 0 0 0 6090 3685 13210 1890 1429 11164 11709 386 6485 4262 g 0 0 0 4262 6485 386 11709 11164 1429 1890 13210 3685 6090 t 0 0 0 1604 1522 225 127 771 540 178 83 2212 1948

oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m3; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.708768; ---ssCGCCCTCs ; cor=; Ncor= a 0 0 0 1616 1521 171 314 374 268 321 694 182 1687 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 4290 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 3033 t 0 0 0 1984 2017 191 358 485 548 530 8084 306 2132

oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m4; m=5/7; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.694484; ---ssCGCCCCCs ; cor=; Ncor= a 0 0 0 2483 1951 136 314 459 504 831 694 633 2720 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 5263 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 5303 t 0 0 0 2689 2068 142 198 640 812 1227 847 639 2913

oligos_7nt_mkv5_m5_rc_shift3 (oligos_7nt_mkv5_m5_rc)
; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m5_rc; m=6/7; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.659628; ---ssCGCCtGCG ; cor=; Ncor= a 0 0 0 848 842 216 197 211 216 239 138 126 172 c 0 0 0 2250 2036 5467 168 5218 5040 1110 535 5592 417 g 0 0 0 2142 2553 349 5660 563 867 1024 5381 357 5443 t 0 0 0 990 799 198 205 238 107 3857 176 155 198

positions_6nt_m3_shift0 (positions_6nt_m3)
; oligos_6nt_mkv4_m2 versus positions_6nt_m3; m=7/7; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.559785; ssCCCCGCCCss- ; cor=; Ncor= a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 0 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 0 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 0 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353 0

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift8 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift8 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=12; shift=8; ncol=20; --------ssCAGGgCCTgs ; Alignment reference a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581

positions_7nt_m3_shift8 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/9; ncol2=12; w=0; offset=0; strand=D; shift=8; score= 1; --------ssCAGGgCCTgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; positions_7nt_m3 versus oligos_6nt_mkv4_m1; m=2/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score=0.838354; --------kcCAGGACCTgg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240

positions_7nt_m4_rc_shift7 (positions_7nt_m4_rc)
; positions_7nt_m3 versus positions_7nt_m4_rc; m=3/9; ncol2=14; w=-1; offset=-1; strand=R; shift=7; score=0.761131; -------tbcCAGGTCCTkg ; cor=; Ncor= a 0 0 0 0 0 0 0 2276 1836 1578 1511 9319 211 226 1554 193 176 153 1205 2010 c 0 0 0 0 0 0 0 2467 2810 5330 7194 200 224 275 256 9622 9697 379 1374 2432 g 0 0 0 0 0 0 0 2234 2766 1692 768 440 9497 9379 281 201 88 201 3753 3581 t 0 0 0 0 0 0 0 3206 2771 1583 710 224 251 303 8092 167 222 9450 3851 2160

positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_7nt_m3 versus positions_6nt_m4; m=4/9; ncol2=14; w=-2; offset=-2; strand=D; shift=6; score=0.713192; ------cytCCAGGACCyks ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991

oligos_7nt_mkv5_m1_rc_shift7 (oligos_7nt_mkv5_m1_rc)
; positions_7nt_m3 versus oligos_7nt_mkv5_m1_rc; m=5/9; ncol2=16; w=-1; offset=-1; strand=R; shift=7; score=0.652662; -------tscCAGGTCCTGg ; cor=; Ncor= a 0 0 0 0 0 0 0 1846 1413 1181 1103 6930 208 232 1058 155 196 215 673 881 c 0 0 0 0 0 0 0 1950 2294 4240 5632 242 200 263 362 7328 7489 399 482 964 g 0 0 0 0 0 0 0 1913 2388 1442 653 576 7373 7256 323 307 125 233 6024 5385 t 0 0 0 0 0 0 0 2249 1863 1095 570 210 177 207 6215 168 148 7111 779 728

positions_7nt_m2_shift3 (positions_7nt_m2)
; positions_7nt_m3 versus positions_7nt_m2; m=6/9; ncol2=17; w=-5; offset=-5; strand=D; shift=3; score=0.569261; ---sccCtgCCAGGACCyks ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m3 versus positions_7nt_m1; m=7/9; ncol2=19; w=-5; offset=-5; strand=D; shift=3; score=0.556459; ---smcCtgCCAGGACCTgg ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217

positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_7nt_m3 versus positions_6nt_m1; m=8/9; ncol2=20; w=-2; offset=-2; strand=D; shift=6; score=0.531533; ------cytcCAGGACCTgs ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m3 versus positions_6nt_m2_rc; m=9/9; ncol2=23; w=-8; offset=-8; strand=R; shift=0; score=0.462316; csggccCtgCCAGGACCTgs ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160

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; wwATTTTTAww ; Alignment reference a 4985 4732 15517 917 898 746 692 1285 15283 5478 5734 c 2543 3859 535 697 523 554 835 948 591 3043 3304 g 3776 2848 846 668 675 488 647 620 824 3436 2668 t 6334 6199 740 15356 15542 15850 15464 14785 940 5681 5932

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; wwATTTTTAww ; cor=; Ncor= a 4985 4732 15517 917 898 746 692 1285 15283 5478 5734 c 2543 3859 535 697 523 554 835 948 591 3043 3304 g 3776 2848 846 668 675 488 647 620 824 3436 2668 t 6334 6199 740 15356 15542 15850 15464 14785 940 5681 5932

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 6 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=12; shift=0; ncol=12; ssCCCCGCCCss ; Alignment reference a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCCCCGCCCss ; cor=; Ncor= a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353

oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)
; positions_6nt_m3 versus oligos_6nt_mkv4_m2; m=2/5; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.559785; ---ssCGCCCGs ; cor=; Ncor= a 0 0 0 1806 2332 74 338 540 779 116 239 1410 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 t 0 0 0 1774 1470 183 127 771 862 417 104 1979

oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; positions_6nt_m3 versus oligos_7nt_mkv5_m4; m=3/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.548442; ---ssCGCCCCC ; cor=; Ncor= a 0 0 0 2483 1951 136 314 459 504 831 694 633 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 t 0 0 0 2689 2068 142 198 640 812 1227 847 639

oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; positions_6nt_m3 versus oligos_7nt_mkv5_m3; m=4/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.520265; ---ssCGCCCTC ; cor=; Ncor= a 0 0 0 1616 1521 171 314 374 268 321 694 182 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 t 0 0 0 1984 2017 191 358 485 548 530 8084 306

oligos_6nt_mkv4_m4_rc_shift3 (oligos_6nt_mkv4_m4_rc)
; positions_6nt_m3 versus oligos_6nt_mkv4_m4_rc; m=5/5; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.494136; ---ssCGCtCGs ; cor=; Ncor= a 0 0 0 1221 1423 122 198 198 779 137 176 888 c 0 0 0 3711 2634 8231 109 7735 1429 8312 499 3676 g 0 0 0 2593 3710 333 8356 540 2060 265 7910 3001 t 0 0 0 1286 1044 125 148 338 4543 97 226 1246

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGCaGGCGss ; Alignment reference a 937 961 198 155 176 3857 107 238 205 198 799 990 c 2196 1854 5443 357 5381 1024 867 563 5660 349 2553 2142 g 2227 2599 417 5592 535 1110 5040 5218 168 5467 2036 2250 t 870 816 172 126 138 239 216 211 197 216 842 848

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCaGGCGss ; cor=; Ncor= a 937 961 198 155 176 3857 107 238 205 198 799 990 c 2196 1854 5443 357 5381 1024 867 563 5660 349 2553 2142 g 2227 2599 417 5592 535 1110 5040 5218 168 5467 2036 2250 t 870 816 172 126 138 239 216 211 197 216 842 848

oligos_6nt_mkv4_m2_rc_shift2 (oligos_6nt_mkv4_m2_rc)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m2_rc; m=2/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.659628; --ssCGGGCGss ; cor=; Ncor= a 0 0 1836 1979 104 417 862 771 127 183 1470 1774 c 0 0 4946 4175 12376 1244 2060 1406 12562 356 5360 4038 g 0 0 4445 5624 469 11411 9487 10471 161 12575 4026 5570 t 0 0 1961 1410 239 116 779 540 338 74 2332 1806

oligos_7nt_mkv5_m4_rc_shift1 (oligos_7nt_mkv5_m4_rc)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m4_rc; m=3/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.649591; -ssGGGGGCGss ; cor=; Ncor= a 0 2419 2913 639 847 1227 812 640 198 142 2068 2689 c 0 5073 5303 1187 1364 1781 1243 889 15620 248 4880 4812 g 0 6483 5263 13740 13294 12360 13640 14211 67 15673 7300 6215 t 0 2224 2720 633 694 831 504 459 314 136 1951 2483

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift3 ; 5 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=11; shift=3; ncol=14; ---ssCGCCCTCss ; Alignment reference a 0 0 0 1616 1521 171 314 374 268 321 694 182 1687 1615 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 4290 4261 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 3033 3246 t 0 0 0 1984 2017 191 358 485 548 530 8084 306 2132 2020

oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCTCss ; cor=; Ncor= a 0 0 0 1616 1521 171 314 374 268 321 694 182 1687 1615 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 4290 4261 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 3033 3246 t 0 0 0 1984 2017 191 358 485 548 530 8084 306 2132 2020

oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.862237; ---ssCGCCCCCss ; cor=; Ncor= a 0 0 0 2483 1951 136 314 459 504 831 694 633 2720 2224 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 5263 6483 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 5303 5073 t 0 0 0 2689 2068 142 198 640 812 1227 847 639 2913 2419

oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m2; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.708768; ---ssCGCCCGss- ; cor=; Ncor= a 0 0 0 1806 2332 74 338 540 779 116 239 1410 1961 0 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 4445 0 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 0 t 0 0 0 1774 1470 183 127 771 862 417 104 1979 1836 0

positions_6nt_m3_shift0 (positions_6nt_m3)
; oligos_7nt_mkv5_m3 versus positions_6nt_m3; m=4/4; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.520265; ssCCCCGCCCss-- ; cor=; Ncor= a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 0 0 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 0 0 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 0 0 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift8 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=13; shift=8; ncol=21; --------kcCAGGACCTggs ; Alignment reference a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score= 1; --------kcCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340

positions_7nt_m4_shift8 (positions_7nt_m4)
; oligos_6nt_mkv4_m1 versus positions_7nt_m4; m=2/9; ncol2=14; w=0; offset=0; strand=D; shift=8; score=0.884892; --------kcmAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836

positions_7nt_m3_shift8 (positions_7nt_m3)
; oligos_6nt_mkv4_m1 versus positions_7nt_m3; m=3/9; ncol2=12; w=0; offset=0; strand=D; shift=8; score=0.838354; --------ssCAGGgCCTgs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 0 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 0 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 0 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581 0

oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1; m=4/9; ncol2=16; w=-2; offset=-2; strand=D; shift=6; score=0.787897; ------cttcCAGGACCTGgs ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413

positions_6nt_m4_shift6 (positions_6nt_m4)
; oligos_6nt_mkv4_m1 versus positions_6nt_m4; m=5/9; ncol2=14; w=-2; offset=-2; strand=D; shift=6; score=0.746841; ------cytCCAGGACCyks- ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 0 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 0 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 0 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991 0

positions_7nt_m1_shift3 (positions_7nt_m1)
; oligos_6nt_mkv4_m1 versus positions_7nt_m1; m=6/9; ncol2=19; w=-5; offset=-5; strand=D; shift=3; score=0.665139; ---smcCtgCCAGGACCTggs ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307

positions_6nt_m1_shift6 (positions_6nt_m1)
; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=7/9; ncol2=20; w=-2; offset=-2; strand=D; shift=6; score=0.629132; ------cytcCAGGACCTgsc ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772

positions_7nt_m2_shift3 (positions_7nt_m2)
; oligos_6nt_mkv4_m1 versus positions_7nt_m2; m=8/9; ncol2=17; w=-5; offset=-5; strand=D; shift=3; score=0.598292; ---sccCtgCCAGGACCyks- ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 0 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 0 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 0 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271 0

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; oligos_6nt_mkv4_m1 versus positions_6nt_m2_rc; m=9/9; ncol2=23; w=-8; offset=-8; strand=R; shift=0; score=0.551534; csggccCtgCCAGGACCTgss ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 1312 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 1992 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 1812 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160 1384

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; ssCGGaGCss ; Alignment reference a 1366 1555 36 61 157 5981 346 190 993 1134 c 3516 2385 8617 411 833 1811 406 8241 2810 2599 g 2601 3739 117 8296 7541 481 7814 168 3718 3769 t 1320 1124 33 35 272 530 237 204 1282 1301

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; ssCGGaGCss ; cor=; Ncor= a 1366 1555 36 61 157 5981 346 190 993 1134 c 3516 2385 8617 411 833 1811 406 8241 2810 2599 g 2601 3739 117 8296 7541 481 7814 168 3718 3769 t 1320 1124 33 35 272 530 237 204 1282 1301

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; ssCGGCCGss ; Alignment reference a 1948 2212 83 178 540 771 127 225 1522 1604 c 6090 3685 13210 1890 1429 11164 11709 386 6485 4262 g 4262 6485 386 11709 11164 1429 1890 13210 3685 6090 t 1604 1522 225 127 771 540 178 83 2212 1948

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGCCGss ; cor=; Ncor= a 1948 2212 83 178 540 771 127 225 1522 1604 c 6090 3685 13210 1890 1429 11164 11709 386 6485 4262 g 4262 6485 386 11709 11164 1429 1890 13210 3685 6090 t 1604 1522 225 127 771 540 178 83 2212 1948

oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m2; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.848843; ssCGCCCGss ; cor=; Ncor= a 1806 2332 74 338 540 779 116 239 1410 1961 c 5570 4026 12575 161 10471 9487 11411 469 5624 4445 g 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 t 1774 1470 183 127 771 862 417 104 1979 1836

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m4; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.719752; ssCGaGCGss ; cor=; Ncor= a 1311 1246 226 97 4543 338 148 125 1044 1286 c 3301 3001 7910 265 2060 540 8356 333 3710 2593 g 2949 3676 499 8312 1429 7735 109 8231 2634 3711 t 1250 888 176 137 779 198 198 122 1423 1221

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift6 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=16; shift=6; ncol=22; ------cttcCAGGACCTGgsa ; Alignment reference a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846

oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=6; score= 1; ------cttcCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846

positions_7nt_m4_shift8 (positions_7nt_m4)
; oligos_7nt_mkv5_m1 versus positions_7nt_m4; m=2/9; ncol2=14; w=0; offset=2; strand=D; shift=8; score=0.831405; --------kcmAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276

positions_6nt_m4_shift6 (positions_6nt_m4)
; oligos_7nt_mkv5_m1 versus positions_6nt_m4; m=3/9; ncol2=14; w=0; offset=0; strand=D; shift=6; score=0.810239; ------cytCCAGGACCyks-- ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 0 0 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 0 0 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 0 0 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991 0 0

positions_7nt_m1_shift3 (positions_7nt_m1)
; oligos_7nt_mkv5_m1 versus positions_7nt_m1; m=4/9; ncol2=19; w=-3; offset=-3; strand=D; shift=3; score=0.806823; ---smcCtgCCAGGACCTggsv ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 1907 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 1923 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 1892 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307 1547

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1; m=5/9; ncol2=13; w=0; offset=2; strand=D; shift=8; score=0.787897; --------kcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 0 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 0 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 0 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340 0

positions_6nt_m1_shift6 (positions_6nt_m1)
; oligos_7nt_mkv5_m1 versus positions_6nt_m1; m=6/9; ncol2=20; w=0; offset=0; strand=D; shift=6; score=0.779526; ------cytcCAGGACCTgsca ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; oligos_7nt_mkv5_m1 versus positions_6nt_m2_rc; m=7/9; ncol2=23; w=-6; offset=-6; strand=R; shift=0; score=0.665179; csggccCtgCCAGGACCTgsss ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 1312 1517 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 1992 1846 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 1812 1802 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160 1384 1335

positions_7nt_m3_rc_shift9 (positions_7nt_m3_rc)
; oligos_7nt_mkv5_m1 versus positions_7nt_m3_rc; m=8/9; ncol2=12; w=0; offset=3; strand=R; shift=9; score=0.652662; ---------scAGGcCCTGss- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2581 2801 10238 283 462 2056 365 223 358 200 2317 3105 0 c 0 0 0 0 0 0 0 0 0 4801 5562 1319 267 324 8473 11782 12519 608 223 3798 4129 0 g 0 0 0 0 0 0 0 0 0 3419 3279 1125 12541 12150 522 583 350 543 12741 4770 3801 0 t 0 0 0 0 0 0 0 0 0 2524 1683 643 234 389 2274 595 233 11816 161 2440 2290 0

positions_7nt_m2_shift3 (positions_7nt_m2)
; oligos_7nt_mkv5_m1 versus positions_7nt_m2; m=9/9; ncol2=17; w=-3; offset=-3; strand=D; shift=3; score=0.628351; ---sccCtgCCAGGACCyks-- ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 0 0 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 0 0 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 0 0 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 5 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=10; shift=0; ncol=10; ssCGaGCGss ; Alignment reference a 1311 1246 226 97 4543 338 148 125 1044 1286 c 3301 3001 7910 265 2060 540 8356 333 3710 2593 g 2949 3676 499 8312 1429 7735 109 8231 2634 3711 t 1250 888 176 137 779 198 198 122 1423 1221

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssCGaGCGss ; cor=; Ncor= a 1311 1246 226 97 4543 338 148 125 1044 1286 c 3301 3001 7910 265 2060 540 8356 333 3710 2593 g 2949 3676 499 8312 1429 7735 109 8231 2634 3711 t 1250 888 176 137 779 198 198 122 1423 1221

oligos_6nt_mkv4_m2_rc_shift0 (oligos_6nt_mkv4_m2_rc)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m2_rc; m=2/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.918767; ssCGGGCGss ; cor=; Ncor= a 1836 1979 104 417 862 771 127 183 1470 1774 c 4946 4175 12376 1244 2060 1406 12562 356 5360 4038 g 4445 5624 469 11411 9487 10471 161 12575 4026 5570 t 1961 1410 239 116 779 540 338 74 2332 1806

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m5; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.719752; ssCGGCCGss ; cor=; Ncor= a 1948 2212 83 178 540 771 127 225 1522 1604 c 6090 3685 13210 1890 1429 11164 11709 386 6485 4262 g 4262 6485 386 11709 11164 1429 1890 13210 3685 6090 t 1604 1522 225 127 771 540 178 83 2212 1948

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; oligos_6nt_mkv4_m4 versus positions_6nt_m3_rc; m=4/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.494136; -ssGGGCGGG ; cor=; Ncor= a 0 2353 2789 540 390 393 753 676 495 714 c 0 5764 4467 1149 1452 818 14208 883 1396 1529 g 0 6144 6579 14123 13910 14583 113 13846 13674 13410 t 0 1881 2307 330 390 348 1068 737 577 489

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 5 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=11; shift=0; ncol=11; yhcCTTCCAgg ; Alignment reference a 1662 2338 965 330 156 312 373 34 8325 1390 1965 c 2550 2321 5294 8001 121 142 8320 8477 144 2108 1943 g 1856 1928 1141 400 298 129 77 152 309 3332 2916 t 2768 2249 1436 105 8261 8253 66 173 58 2006 2012

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; yhcCTTCCAgg ; cor=; Ncor= a 1662 2338 965 330 156 312 373 34 8325 1390 1965 c 2550 2321 5294 8001 121 142 8320 8477 144 2108 1943 g 1856 1928 1141 400 298 129 77 152 309 3332 2916 t 2768 2249 1436 105 8261 8253 66 173 58 2006 2012

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; positions_6nt_m5 versus positions_7nt_m5_rc; m=2/4; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.868925; bycCTTCCAGg ; cor=; Ncor= a 1871 2411 1388 544 330 265 445 185 8345 152 1991 c 2745 2471 5618 8769 260 429 8596 9074 545 363 2271 g 2680 2135 1402 155 385 456 419 175 470 8870 3444 t 2447 2726 1335 275 8768 8593 283 309 383 358 2037

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_6nt_m5 versus positions_7nt_m2; m=3/4; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.48442; sccCtgCCAGG ; cor=; Ncor= a 1145 1600 744 297 805 437 345 355 5409 191 147 c 2142 2183 3482 5412 831 695 5296 5685 414 261 308 g 1711 1441 1285 459 688 3932 432 246 436 5917 5930 t 1510 1284 997 340 4184 1444 435 222 249 139 123

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_6nt_m5 versus positions_7nt_m1; m=4/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.417174; smcCtgCCAGG ; cor=; Ncor= a 1320 1958 1118 549 1173 622 612 657 6373 213 152 c 2244 2228 3211 5353 950 910 5230 5821 259 136 267 g 1917 1654 1549 767 850 3991 759 354 427 6776 6717 t 1788 1429 1391 600 4296 1746 668 437 210 144 133

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 10 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=20; shift=0; ncol=20; cytcCAGGACCTgscaggss ; Alignment reference a 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 841 1082 1393 1454 c 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 1142 1288 1775 1980 g 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 3724 3077 1883 1787 t 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238 822 1082 1478 1308

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/9; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; cytcCAGGACCTgscaggss ; cor=; Ncor= a 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 841 1082 1393 1454 c 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 1142 1288 1775 1980 g 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 3724 3077 1883 1787 t 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238 822 1082 1478 1308

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_6nt_m1 versus positions_7nt_m1_rc; m=2/9; ncol2=19; w=0; offset=1; strand=R; shift=1; score=0.825277; -bsccAGGTCCTGGcaGgks ; cor=; Ncor= a 0 1547 1307 1217 1221 5945 254 192 893 133 144 210 437 668 1746 4296 600 1391 1429 1788 c 0 1892 2103 3460 4621 313 201 272 412 6717 6776 427 354 759 3991 850 767 1549 1654 1917 g 0 1923 2203 1518 823 757 6614 6573 402 267 136 259 5821 5230 910 950 5353 3211 2228 2244 t 0 1907 1656 1074 604 254 200 232 5562 152 213 6373 657 612 622 1173 549 1118 1958 1320

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; positions_6nt_m1 versus oligos_7nt_mkv5_m1; m=3/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.779526; cttcCAGGACCTGgsa---- ; cor=; Ncor= a 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 0 0 0 0 c 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 0 0 0 0 g 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 0 0 0 0 t 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846 0 0 0 0

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=4/9; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.73824; sssscAGGTCCTGGcaGggc ; cor=; Ncor= a 1257 1335 1384 1160 1016 4969 209 178 671 121 133 191 324 632 1550 3455 550 1129 920 1166 c 2046 1802 1812 2263 4096 412 198 305 381 5977 6046 441 364 864 3454 956 856 1211 1125 2939 g 1991 1846 1992 2022 869 835 5925 5821 450 256 167 360 5389 4424 872 1078 4580 3201 3194 1486 t 1206 1517 1312 1055 519 284 168 196 4998 146 154 5508 423 580 624 1011 514 959 1261 909

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m1 versus positions_6nt_m4; m=5/9; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.65467; cytCCAGGACCyks------ ; cor=; Ncor= a 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 0 0 0 0 0 0 c 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 0 0 0 0 0 0 g 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 0 0 0 0 0 0 t 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991 0 0 0 0 0 0

positions_7nt_m4_shift2 (positions_7nt_m4)
; positions_6nt_m1 versus positions_7nt_m4; m=6/9; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.644377; --kcmAGGACCTGgva---- ; cor=; Ncor= a 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 0 0 0 0 c 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 0 0 0 0 g 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 0 0 0 0 t 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276 0 0 0 0

oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)
; positions_6nt_m1 versus oligos_6nt_mkv4_m1; m=7/9; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.629132; --kcCAGGACCTggs----- ; cor=; Ncor= a 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 0 0 0 0 0 c 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 0 0 0 0 0 g 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 0 0 0 0 0 t 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340 0 0 0 0 0

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; positions_6nt_m1 versus positions_7nt_m2_rc; m=8/9; ncol2=17; w=0; offset=3; strand=R; shift=3; score=0.628411; ---smrGGTCCTGGcaGggs ; cor=; Ncor= a 0 0 0 1271 1662 1897 340 222 408 123 139 249 222 435 1444 4184 340 997 1284 1510 c 0 0 0 2372 2063 489 315 303 405 5930 5917 436 246 432 3932 688 459 1285 1441 1711 g 0 0 0 1716 1603 3731 5543 5772 401 308 261 414 5685 5296 695 831 5412 3482 2183 2142 t 0 0 0 1149 1180 391 310 211 5294 147 191 5409 355 345 437 805 297 744 1600 1145

positions_7nt_m3_shift2 (positions_7nt_m3)
; positions_6nt_m1 versus positions_7nt_m3; m=9/9; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.531533; --ssCAGGgCCTgs------ ; cor=; Ncor= a 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 0 0 0 0 0 0 c 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 0 0 0 0 0 0 g 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 0 0 0 0 0 0 t 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift3 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift3 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=17; shift=3; ncol=20; ---sccCtgCCAGGACCyks ; Alignment reference a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271

positions_7nt_m2_shift3 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/11; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---sccCtgCCAGGACCyks ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=2/11; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.833426; ---smcCtgCCAGGACCTgg ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217

positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_7nt_m2 versus positions_6nt_m4; m=3/11; ncol2=14; w=0; offset=3; strand=D; shift=6; score=0.773224; ------cytCCAGGACCyks ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m2 versus positions_6nt_m2_rc; m=4/11; ncol2=23; w=-3; offset=-3; strand=R; shift=0; score=0.687453; csggccCtgCCAGGACCTgs ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; positions_7nt_m2 versus positions_6nt_m1_rc; m=5/11; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.628411; ---sscctgscAGGTCCTGg ; cor=; Ncor= a 0 0 0 1308 1478 1082 822 1238 772 949 1042 5395 160 216 994 155 137 195 391 796 c 0 0 0 1787 1883 3077 3724 1158 1188 1910 4229 296 160 231 312 5992 6069 366 311 803 g 0 0 0 1980 1775 1288 1142 1177 3433 2820 780 552 6055 5890 353 263 158 250 5381 4312 t 0 0 0 1454 1393 1082 841 2956 1136 850 478 286 154 192 4870 119 165 5718 446 618

oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)
; positions_7nt_m2 versus oligos_7nt_mkv5_m1; m=6/11; ncol2=16; w=0; offset=3; strand=D; shift=6; score=0.628351; ------cttcCAGGACCTGg ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; positions_7nt_m2 versus oligos_6nt_mkv4_m1; m=7/11; ncol2=13; w=0; offset=5; strand=D; shift=8; score=0.598292; --------kcCAGGACCTgg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240

positions_7nt_m3_shift8 (positions_7nt_m3)
; positions_7nt_m2 versus positions_7nt_m3; m=8/11; ncol2=12; w=0; offset=5; strand=D; shift=8; score=0.569261; --------ssCAGGgCCTgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581

positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)
; positions_7nt_m2 versus positions_7nt_m5_rc; m=9/11; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.560059; ---bycCTTCCAGgh----- ; cor=; Ncor= a 0 0 0 1871 2411 1388 544 330 265 445 185 8345 152 1991 2919 0 0 0 0 0 c 0 0 0 2745 2471 5618 8769 260 429 8596 9074 545 363 2271 2443 0 0 0 0 0 g 0 0 0 2680 2135 1402 155 385 456 419 175 470 8870 3444 1802 0 0 0 0 0 t 0 0 0 2447 2726 1335 275 8768 8593 283 309 383 358 2037 2579 0 0 0 0 0

positions_7nt_m4_rc_shift7 (positions_7nt_m4_rc)
; positions_7nt_m2 versus positions_7nt_m4_rc; m=10/11; ncol2=14; w=0; offset=4; strand=R; shift=7; score=0.550391; -------tbcCAGGTCCTkg ; cor=; Ncor= a 0 0 0 0 0 0 0 2276 1836 1578 1511 9319 211 226 1554 193 176 153 1205 2010 c 0 0 0 0 0 0 0 2467 2810 5330 7194 200 224 275 256 9622 9697 379 1374 2432 g 0 0 0 0 0 0 0 2234 2766 1692 768 440 9497 9379 281 201 88 201 3753 3581 t 0 0 0 0 0 0 0 3206 2771 1583 710 224 251 303 8092 167 222 9450 3851 2160

positions_6nt_m5_shift3 (positions_6nt_m5)
; positions_7nt_m2 versus positions_6nt_m5; m=11/11; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.48442; ---yhcCTTCCAgg------ ; cor=; Ncor= a 0 0 0 1662 2338 965 330 156 312 373 34 8325 1390 1965 0 0 0 0 0 0 c 0 0 0 2550 2321 5294 8001 121 142 8320 8477 144 2108 1943 0 0 0 0 0 0 g 0 0 0 1856 1928 1141 400 298 129 77 152 309 3332 2916 0 0 0 0 0 0 t 0 0 0 2768 2249 1436 105 8261 8253 66 173 58 2006 2012 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift3 ; 6 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=11; shift=3; ncol=14; ---ssCGCCCCCss ; Alignment reference a 0 0 0 2483 1951 136 314 459 504 831 694 633 2720 2224 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 5263 6483 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 5303 5073 t 0 0 0 2689 2068 142 198 640 812 1227 847 639 2913 2419

oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCCCss ; cor=; Ncor= a 0 0 0 2483 1951 136 314 459 504 831 694 633 2720 2224 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 5263 6483 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 5303 5073 t 0 0 0 2689 2068 142 198 640 812 1227 847 639 2913 2419

oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.862237; ---ssCGCCCTCss ; cor=; Ncor= a 0 0 0 1616 1521 171 314 374 268 321 694 182 1687 1615 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 4290 4261 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 3033 3246 t 0 0 0 1984 2017 191 358 485 548 530 8084 306 2132 2020

oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)
; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m2; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.694484; ---ssCGCCCGss- ; cor=; Ncor= a 0 0 0 1806 2332 74 338 540 779 116 239 1410 1961 0 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 4445 0 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 0 t 0 0 0 1774 1470 183 127 771 862 417 104 1979 1836 0

oligos_7nt_mkv5_m5_rc_shift3 (oligos_7nt_mkv5_m5_rc)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m5_rc; m=4/5; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.649591; ---ssCGCCtGCGs ; cor=; Ncor= a 0 0 0 848 842 216 197 211 216 239 138 126 172 816 c 0 0 0 2250 2036 5467 168 5218 5040 1110 535 5592 417 2599 g 0 0 0 2142 2553 349 5660 563 867 1024 5381 357 5443 1854 t 0 0 0 990 799 198 205 238 107 3857 176 155 198 961

positions_6nt_m3_shift0 (positions_6nt_m3)
; oligos_7nt_mkv5_m4 versus positions_6nt_m3; m=5/5; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.548442; ssCCCCGCCCss-- ; cor=; Ncor= a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 0 0 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 0 0 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 0 0 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift6 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=14; shift=6; ncol=20; ------cytCCAGGACCyks ; Alignment reference a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991

positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/9; ncol2=14; w=0; offset=0; strand=D; shift=6; score= 1; ------cytCCAGGACCyks ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991

oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)
; positions_6nt_m4 versus oligos_7nt_mkv5_m1; m=2/9; ncol2=16; w=0; offset=0; strand=D; shift=6; score=0.810239; ------cttcCAGGACCTGg ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181

positions_7nt_m2_shift3 (positions_7nt_m2)
; positions_6nt_m4 versus positions_7nt_m2; m=3/9; ncol2=17; w=-3; offset=-3; strand=D; shift=3; score=0.773224; ---sccCtgCCAGGACCyks ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; positions_6nt_m4 versus oligos_6nt_mkv4_m1; m=4/9; ncol2=13; w=0; offset=2; strand=D; shift=8; score=0.746841; --------kcCAGGACCTgg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240

positions_7nt_m3_shift8 (positions_7nt_m3)
; positions_6nt_m4 versus positions_7nt_m3; m=5/9; ncol2=12; w=0; offset=2; strand=D; shift=8; score=0.713192; --------ssCAGGgCCTgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581

positions_7nt_m4_rc_shift7 (positions_7nt_m4_rc)
; positions_6nt_m4 versus positions_7nt_m4_rc; m=6/9; ncol2=14; w=0; offset=1; strand=R; shift=7; score=0.695681; -------tbcCAGGTCCTkg ; cor=; Ncor= a 0 0 0 0 0 0 0 2276 1836 1578 1511 9319 211 226 1554 193 176 153 1205 2010 c 0 0 0 0 0 0 0 2467 2810 5330 7194 200 224 275 256 9622 9697 379 1374 2432 g 0 0 0 0 0 0 0 2234 2766 1692 768 440 9497 9379 281 201 88 201 3753 3581 t 0 0 0 0 0 0 0 3206 2771 1583 710 224 251 303 8092 167 222 9450 3851 2160

positions_7nt_m1_shift3 (positions_7nt_m1)
; positions_6nt_m4 versus positions_7nt_m1; m=7/9; ncol2=19; w=-3; offset=-3; strand=D; shift=3; score=0.669833; ---smcCtgCCAGGACCTgg ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217

positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_6nt_m4 versus positions_6nt_m1; m=8/9; ncol2=20; w=0; offset=0; strand=D; shift=6; score=0.65467; ------cytcCAGGACCTgs ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_6nt_m4 versus positions_6nt_m2_rc; m=9/9; ncol2=23; w=-6; offset=-6; strand=R; shift=0; score=0.561044; csggccCtgCCAGGACCTgs ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m5_shift7 (positions_7nt_m5)				; positions_7nt_m5; m=0 (reference); ncol1=12; shift=7; ncol=19; -------dcCTGGAAGgrv ; Alignment reference a 0 0 0 0 0 0 0 2579 2037 358 383 309 283 8593 8768 275 1335 2726 2447 c 0 0 0 0 0 0 0 1802 3444 8870 470 175 419 456 385 155 1402 2135 2680 g 0 0 0 0 0 0 0 2443 2271 363 545 9074 8596 429 260 8769 5618 2471 2745 t 0 0 0 0 0 0 0 2919 1991 152 8345 185 445 265 330 544 1388 2411 1871
positions_7nt_m5_shift7 (positions_7nt_m5)				; positions_7nt_m5 versus positions_7nt_m5; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=7; score= 1; -------dcCTGGAAGgrv ; cor=; Ncor= a 0 0 0 0 0 0 0 2579 2037 358 383 309 283 8593 8768 275 1335 2726 2447 c 0 0 0 0 0 0 0 1802 3444 8870 470 175 419 456 385 155 1402 2135 2680 g 0 0 0 0 0 0 0 2443 2271 363 545 9074 8596 429 260 8769 5618 2471 2745 t 0 0 0 0 0 0 0 2919 1991 152 8345 185 445 265 330 544 1388 2411 1871
positions_6nt_m5_rc_shift8 (positions_6nt_m5_rc)				; positions_7nt_m5 versus positions_6nt_m5_rc; m=2/4; ncol2=11; w=0; offset=1; strand=R; shift=8; score=0.868925; --------ccTGGAAGgdr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2012 2006 58 173 66 8253 8261 105 1436 2249 2768 c 0 0 0 0 0 0 0 0 2916 3332 309 152 77 129 298 400 1141 1928 1856 g 0 0 0 0 0 0 0 0 1943 2108 144 8477 8320 142 121 8001 5294 2321 2550 t 0 0 0 0 0 0 0 0 1965 1390 8325 34 373 312 156 330 965 2338 1662
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_7nt_m5 versus positions_7nt_m2_rc; m=3/4; ncol2=17; w=-5; offset=-5; strand=R; shift=2; score=0.560059; --smrGGTCCTGGcaGggs ; cor=; Ncor= a 0 0 1271 1662 1897 340 222 408 123 139 249 222 435 1444 4184 340 997 1284 1510 c 0 0 2372 2063 489 315 303 405 5930 5917 436 246 432 3932 688 459 1285 1441 1711 g 0 0 1716 1603 3731 5543 5772 401 308 261 414 5685 5296 695 831 5412 3482 2183 2142 t 0 0 1149 1180 391 310 211 5294 147 191 5409 355 345 437 805 297 744 1600 1145
positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc)				; positions_7nt_m5 versus positions_7nt_m1_rc; m=4/4; ncol2=19; w=-7; offset=-7; strand=R; shift=0; score=0.493384; bsccAGGTCCTGGcaGgks ; cor=; Ncor= a 1547 1307 1217 1221 5945 254 192 893 133 144 210 437 668 1746 4296 600 1391 1429 1788 c 1892 2103 3460 4621 313 201 272 412 6717 6776 427 354 759 3991 850 767 1549 1654 1917 g 1923 2203 1518 823 757 6614 6573 402 267 136 259 5821 5230 910 950 5353 3211 2228 2244 t 1907 1656 1074 604 254 200 232 5562 152 213 6373 657 612 622 1173 549 1118 1958 1320

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=19; shift=3; ncol=22; ---smcCtgCCAGGACCTggsv ; Alignment reference a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 1907 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 1923 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 1892 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307 1547
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/11; ncol2=19; w=0; offset=0; strand=D; shift=3; score= 1; ---smcCtgCCAGGACCTggsv ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 1907 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 1923 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 1892 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307 1547
positions_7nt_m2_shift3 (positions_7nt_m2)				; positions_7nt_m1 versus positions_7nt_m2; m=2/11; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.833426; ---sccCtgCCAGGACCyks-- ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 0 0 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 0 0 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 0 0 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271 0 0
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; positions_7nt_m1 versus positions_6nt_m1_rc; m=3/11; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.825277; ---sscctgscAGGTCCTGgar ; cor=; Ncor= a 0 0 0 1308 1478 1082 822 1238 772 949 1042 5395 160 216 994 155 137 195 391 796 3096 2133 c 0 0 0 1787 1883 3077 3724 1158 1188 1910 4229 296 160 231 312 5992 6069 366 311 803 1565 1441 g 0 0 0 1980 1775 1288 1142 1177 3433 2820 780 552 6055 5890 353 263 158 250 5381 4312 1103 1649 t 0 0 0 1454 1393 1082 841 2956 1136 850 478 286 154 192 4870 119 165 5718 446 618 765 1306
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m1 versus positions_6nt_m2_rc; m=4/11; ncol2=23; w=-3; offset=-3; strand=R; shift=0; score=0.81466; csggccCtgCCAGGACCTgsss ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 1312 1517 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 1992 1846 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 1812 1802 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160 1384 1335
oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)				; positions_7nt_m1 versus oligos_7nt_mkv5_m1; m=5/11; ncol2=16; w=0; offset=3; strand=D; shift=6; score=0.806823; ------cttcCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846
positions_7nt_m4_shift8 (positions_7nt_m4)				; positions_7nt_m1 versus positions_7nt_m4; m=6/11; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.691461; --------kcmAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_7nt_m1 versus positions_6nt_m4; m=7/11; ncol2=14; w=0; offset=3; strand=D; shift=6; score=0.669833; ------cytCCAGGACCyks-- ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 0 0 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 0 0 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 0 0 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991 0 0
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; positions_7nt_m1 versus oligos_6nt_mkv4_m1; m=8/11; ncol2=13; w=0; offset=5; strand=D; shift=8; score=0.665139; --------kcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 0 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 0 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 0 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340 0
positions_7nt_m3_shift8 (positions_7nt_m3)				; positions_7nt_m1 versus positions_7nt_m3; m=9/11; ncol2=12; w=0; offset=5; strand=D; shift=8; score=0.556459; --------ssCAGGgCCTgs-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 0 0 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 0 0 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 0 0 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581 0 0
positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)				; positions_7nt_m1 versus positions_7nt_m5_rc; m=10/11; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.493384; ---bycCTTCCAGgh------- ; cor=; Ncor= a 0 0 0 1871 2411 1388 544 330 265 445 185 8345 152 1991 2919 0 0 0 0 0 0 0 c 0 0 0 2745 2471 5618 8769 260 429 8596 9074 545 363 2271 2443 0 0 0 0 0 0 0 g 0 0 0 2680 2135 1402 155 385 456 419 175 470 8870 3444 1802 0 0 0 0 0 0 0 t 0 0 0 2447 2726 1335 275 8768 8593 283 309 383 358 2037 2579 0 0 0 0 0 0 0
positions_6nt_m5_shift3 (positions_6nt_m5)				; positions_7nt_m1 versus positions_6nt_m5; m=11/11; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.417174; ---yhcCTTCCAgg-------- ; cor=; Ncor= a 0 0 0 1662 2338 965 330 156 312 373 34 8325 1390 1965 0 0 0 0 0 0 0 0 c 0 0 0 2550 2321 5294 8001 121 142 8320 8477 144 2108 1943 0 0 0 0 0 0 0 0 g 0 0 0 1856 1928 1141 400 298 129 77 152 309 3332 2916 0 0 0 0 0 0 0 0 t 0 0 0 2768 2249 1436 105 8261 8253 66 173 58 2006 2012 0 0 0 0 0 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=23; shift=0; ncol=23; sssscAGGTCCTGGcaGggccsg ; Alignment reference a 1257 1335 1384 1160 1016 4969 209 178 671 121 133 191 324 632 1550 3455 550 1129 920 1166 1389 1488 1447 c 2046 1802 1812 2263 4096 412 198 305 381 5977 6046 441 364 864 3454 956 856 1211 1125 2939 2856 1788 1612 g 1991 1846 1992 2022 869 835 5925 5821 450 256 167 360 5389 4424 872 1078 4580 3201 3194 1486 1300 1899 2050 t 1206 1517 1312 1055 519 284 168 196 4998 146 154 5508 423 580 624 1011 514 959 1261 909 955 1325 1391
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/9; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; sssscAGGTCCTGGcaGggccsg ; cor=; Ncor= a 1257 1335 1384 1160 1016 4969 209 178 671 121 133 191 324 632 1550 3455 550 1129 920 1166 1389 1488 1447 c 2046 1802 1812 2263 4096 412 198 305 381 5977 6046 441 364 864 3454 956 856 1211 1125 2939 2856 1788 1612 g 1991 1846 1992 2022 869 835 5925 5821 450 256 167 360 5389 4424 872 1078 4580 3201 3194 1486 1300 1899 2050 t 1206 1517 1312 1055 519 284 168 196 4998 146 154 5508 423 580 624 1011 514 959 1261 909 955 1325 1391
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_6nt_m2 versus positions_7nt_m1_rc; m=2/9; ncol2=19; w=0; offset=1; strand=R; shift=1; score=0.81466; -bsccAGGTCCTGGcaGgks--- ; cor=; Ncor= a 0 1547 1307 1217 1221 5945 254 192 893 133 144 210 437 668 1746 4296 600 1391 1429 1788 0 0 0 c 0 1892 2103 3460 4621 313 201 272 412 6717 6776 427 354 759 3991 850 767 1549 1654 1917 0 0 0 g 0 1923 2203 1518 823 757 6614 6573 402 267 136 259 5821 5230 910 950 5353 3211 2228 2244 0 0 0 t 0 1907 1656 1074 604 254 200 232 5562 152 213 6373 657 612 622 1173 549 1118 1958 1320 0 0 0
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=3/9; ncol2=20; w=0; offset=0; strand=D; shift=0; score=0.73824; cytcCAGGACCTgscaggss--- ; cor=; Ncor= a 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 841 1082 1393 1454 0 0 0 c 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 1142 1288 1775 1980 0 0 0 g 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 3724 3077 1883 1787 0 0 0 t 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238 822 1082 1478 1308 0 0 0
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; positions_6nt_m2 versus positions_7nt_m2_rc; m=4/9; ncol2=17; w=0; offset=3; strand=R; shift=3; score=0.687453; ---smrGGTCCTGGcaGggs--- ; cor=; Ncor= a 0 0 0 1271 1662 1897 340 222 408 123 139 249 222 435 1444 4184 340 997 1284 1510 0 0 0 c 0 0 0 2372 2063 489 315 303 405 5930 5917 436 246 432 3932 688 459 1285 1441 1711 0 0 0 g 0 0 0 1716 1603 3731 5543 5772 401 308 261 414 5685 5296 695 831 5412 3482 2183 2142 0 0 0 t 0 0 0 1149 1180 391 310 211 5294 147 191 5409 355 345 437 805 297 744 1600 1145 0 0 0
oligos_7nt_mkv5_m1_rc_shift1 (oligos_7nt_mkv5_m1_rc)				; positions_6nt_m2 versus oligos_7nt_mkv5_m1_rc; m=5/9; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.665179; -tscCAGGTCCTGgaag------ ; cor=; Ncor= a 0 1846 1413 1181 1103 6930 208 232 1058 155 196 215 673 881 4400 2829 1369 0 0 0 0 0 0 c 0 1950 2294 4240 5632 242 200 263 362 7328 7489 399 482 964 1625 1588 1840 0 0 0 0 0 0 g 0 1913 2388 1442 653 576 7373 7256 323 307 125 233 6024 5385 1061 1975 3521 0 0 0 0 0 0 t 0 2249 1863 1095 570 210 177 207 6215 168 148 7111 779 728 872 1566 1228 0 0 0 0 0 0
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; positions_6nt_m2 versus positions_7nt_m4_rc; m=6/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.564804; -tbcCAGGTCCTkgm-------- ; cor=; Ncor= a 0 2276 1836 1578 1511 9319 211 226 1554 193 176 153 1205 2010 2913 0 0 0 0 0 0 0 0 c 0 2467 2810 5330 7194 200 224 275 256 9622 9697 379 1374 2432 3184 0 0 0 0 0 0 0 0 g 0 2234 2766 1692 768 440 9497 9379 281 201 88 201 3753 3581 1965 0 0 0 0 0 0 0 0 t 0 3206 2771 1583 710 224 251 303 8092 167 222 9450 3851 2160 2121 0 0 0 0 0 0 0 0
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; positions_6nt_m2 versus positions_6nt_m4_rc; m=7/9; ncol2=14; w=0; offset=3; strand=R; shift=3; score=0.561044; ---smrGGTCCTGGarg------ ; cor=; Ncor= a 0 0 0 1991 2653 3555 425 296 587 145 172 211 453 1046 5177 3446 1658 0 0 0 0 0 0 c 0 0 0 3865 3395 1015 365 275 393 9701 9897 516 350 1190 2286 2163 2381 0 0 0 0 0 0 g 0 0 0 2706 2413 4902 9284 9606 445 385 217 396 9180 7332 1691 2763 4782 0 0 0 0 0 0 t 0 0 0 1899 2000 989 387 284 9036 230 175 9338 478 893 1307 2089 1640 0 0 0 0 0 0
oligos_6nt_mkv4_m1_rc_shift2 (oligos_6nt_mkv4_m1_rc)				; positions_6nt_m2 versus oligos_6nt_mkv4_m1_rc; m=8/9; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.551534; --sccAGGTCCTGgm-------- ; cor=; Ncor= a 0 0 2340 2240 2413 9738 324 318 1648 199 227 203 626 2358 3553 0 0 0 0 0 0 0 0 c 0 0 3399 4645 6622 510 263 344 458 11530 11661 494 499 2853 3802 0 0 0 0 0 0 0 0 g 0 0 3540 2879 1662 1576 11398 11320 480 347 155 237 10356 4729 2606 0 0 0 0 0 0 0 0 t 0 0 2995 2510 1577 450 289 292 9688 198 231 11340 793 2334 2313 0 0 0 0 0 0 0 0
positions_7nt_m3_rc_shift3 (positions_7nt_m3_rc)				; positions_6nt_m2 versus positions_7nt_m3_rc; m=9/9; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.462316; ---scAGGcCCTGss-------- ; cor=; Ncor= a 0 0 0 2581 2801 10238 283 462 2056 365 223 358 200 2317 3105 0 0 0 0 0 0 0 0 c 0 0 0 4801 5562 1319 267 324 8473 11782 12519 608 223 3798 4129 0 0 0 0 0 0 0 0 g 0 0 0 3419 3279 1125 12541 12150 522 583 350 543 12741 4770 3801 0 0 0 0 0 0 0 0 t 0 0 0 2524 1683 643 234 389 2274 595 233 11816 161 2440 2290 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift8 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=14; shift=8; ncol=22; --------kcmAGGACCTGgva ; Alignment reference a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276
positions_7nt_m4_shift8 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/9; ncol2=14; w=0; offset=0; strand=D; shift=8; score= 1; --------kcmAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; positions_7nt_m4 versus oligos_6nt_mkv4_m1; m=2/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score=0.884892; --------kcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 0 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 0 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 0 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340 0
oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)				; positions_7nt_m4 versus oligos_7nt_mkv5_m1; m=3/9; ncol2=16; w=-2; offset=-2; strand=D; shift=6; score=0.831405; ------cttcCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846
positions_7nt_m3_rc_shift9 (positions_7nt_m3_rc)				; positions_7nt_m4 versus positions_7nt_m3_rc; m=4/9; ncol2=12; w=0; offset=1; strand=R; shift=9; score=0.761131; ---------scAGGcCCTGss- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2581 2801 10238 283 462 2056 365 223 358 200 2317 3105 0 c 0 0 0 0 0 0 0 0 0 4801 5562 1319 267 324 8473 11782 12519 608 223 3798 4129 0 g 0 0 0 0 0 0 0 0 0 3419 3279 1125 12541 12150 522 583 350 543 12741 4770 3801 0 t 0 0 0 0 0 0 0 0 0 2524 1683 643 234 389 2274 595 233 11816 161 2440 2290 0
positions_6nt_m4_rc_shift9 (positions_6nt_m4_rc)				; positions_7nt_m4 versus positions_6nt_m4_rc; m=5/9; ncol2=14; w=0; offset=1; strand=R; shift=9; score=0.695681; ---------smrGGTCCTGGar ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1991 2653 3555 425 296 587 145 172 211 453 1046 5177 3446 c 0 0 0 0 0 0 0 0 0 3865 3395 1015 365 275 393 9701 9897 516 350 1190 2286 2163 g 0 0 0 0 0 0 0 0 0 2706 2413 4902 9284 9606 445 385 217 396 9180 7332 1691 2763 t 0 0 0 0 0 0 0 0 0 1899 2000 989 387 284 9036 230 175 9338 478 893 1307 2089
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m4 versus positions_7nt_m1; m=6/9; ncol2=19; w=-5; offset=-5; strand=D; shift=3; score=0.691461; ---smcCtgCCAGGACCTggsv ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 1907 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 1923 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 1892 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307 1547
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_7nt_m4 versus positions_6nt_m1; m=7/9; ncol2=20; w=-2; offset=-2; strand=D; shift=6; score=0.644377; ------cytcCAGGACCTgsca ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m4 versus positions_6nt_m2_rc; m=8/9; ncol2=23; w=-8; offset=-8; strand=R; shift=0; score=0.564804; csggccCtgCCAGGACCTgsss ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 1312 1517 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 1992 1846 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 1812 1802 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160 1384 1335
positions_7nt_m2_rc_shift9 (positions_7nt_m2_rc)				; positions_7nt_m4 versus positions_7nt_m2_rc; m=9/9; ncol2=17; w=0; offset=1; strand=R; shift=9; score=0.550391; ---------smrGGTCCTGGca ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1271 1662 1897 340 222 408 123 139 249 222 435 1444 4184 c 0 0 0 0 0 0 0 0 0 2372 2063 489 315 303 405 5930 5917 436 246 432 3932 688 g 0 0 0 0 0 0 0 0 0 1716 1603 3731 5543 5772 401 308 261 414 5685 5296 695 831 t 0 0 0 0 0 0 0 0 0 1149 1180 391 310 211 5294 147 191 5409 355 345 437 805

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---ssCGCCCGss ; Alignment reference a 0 0 0 1806 2332 74 338 540 779 116 239 1410 1961 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 4445 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 t 0 0 0 1774 1470 183 127 771 862 417 104 1979 1836
oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/7; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCGss ; cor=; Ncor= a 0 0 0 1806 2332 74 338 540 779 116 239 1410 1961 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 4445 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 t 0 0 0 1774 1470 183 127 771 862 417 104 1979 1836
oligos_6nt_mkv4_m4_rc_shift3 (oligos_6nt_mkv4_m4_rc)				; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m4_rc; m=2/7; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.918767; ---ssCGCtCGss ; cor=; Ncor= a 0 0 0 1221 1423 122 198 198 779 137 176 888 1250 c 0 0 0 3711 2634 8231 109 7735 1429 8312 499 3676 2949 g 0 0 0 2593 3710 333 8356 540 2060 265 7910 3001 3301 t 0 0 0 1286 1044 125 148 338 4543 97 226 1246 1311
oligos_6nt_mkv4_m5_shift3 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m5; m=3/7; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.848843; ---ssCGGCCGss ; cor=; Ncor= a 0 0 0 1948 2212 83 178 540 771 127 225 1522 1604 c 0 0 0 6090 3685 13210 1890 1429 11164 11709 386 6485 4262 g 0 0 0 4262 6485 386 11709 11164 1429 1890 13210 3685 6090 t 0 0 0 1604 1522 225 127 771 540 178 83 2212 1948
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m3; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.708768; ---ssCGCCCTCs ; cor=; Ncor= a 0 0 0 1616 1521 171 314 374 268 321 694 182 1687 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 4290 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 3033 t 0 0 0 1984 2017 191 358 485 548 530 8084 306 2132
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m4; m=5/7; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.694484; ---ssCGCCCCCs ; cor=; Ncor= a 0 0 0 2483 1951 136 314 459 504 831 694 633 2720 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 5263 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 5303 t 0 0 0 2689 2068 142 198 640 812 1227 847 639 2913
oligos_7nt_mkv5_m5_rc_shift3 (oligos_7nt_mkv5_m5_rc)				; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m5_rc; m=6/7; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.659628; ---ssCGCCtGCG ; cor=; Ncor= a 0 0 0 848 842 216 197 211 216 239 138 126 172 c 0 0 0 2250 2036 5467 168 5218 5040 1110 535 5592 417 g 0 0 0 2142 2553 349 5660 563 867 1024 5381 357 5443 t 0 0 0 990 799 198 205 238 107 3857 176 155 198
positions_6nt_m3_shift0 (positions_6nt_m3)				; oligos_6nt_mkv4_m2 versus positions_6nt_m3; m=7/7; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.559785; ssCCCCGCCCss- ; cor=; Ncor= a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 0 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 0 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 0 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift8 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=12; shift=8; ncol=20; --------ssCAGGgCCTgs ; Alignment reference a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581
positions_7nt_m3_shift8 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/9; ncol2=12; w=0; offset=0; strand=D; shift=8; score= 1; --------ssCAGGgCCTgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; positions_7nt_m3 versus oligos_6nt_mkv4_m1; m=2/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score=0.838354; --------kcCAGGACCTgg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240
positions_7nt_m4_rc_shift7 (positions_7nt_m4_rc)				; positions_7nt_m3 versus positions_7nt_m4_rc; m=3/9; ncol2=14; w=-1; offset=-1; strand=R; shift=7; score=0.761131; -------tbcCAGGTCCTkg ; cor=; Ncor= a 0 0 0 0 0 0 0 2276 1836 1578 1511 9319 211 226 1554 193 176 153 1205 2010 c 0 0 0 0 0 0 0 2467 2810 5330 7194 200 224 275 256 9622 9697 379 1374 2432 g 0 0 0 0 0 0 0 2234 2766 1692 768 440 9497 9379 281 201 88 201 3753 3581 t 0 0 0 0 0 0 0 3206 2771 1583 710 224 251 303 8092 167 222 9450 3851 2160
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_7nt_m3 versus positions_6nt_m4; m=4/9; ncol2=14; w=-2; offset=-2; strand=D; shift=6; score=0.713192; ------cytCCAGGACCyks ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991
oligos_7nt_mkv5_m1_rc_shift7 (oligos_7nt_mkv5_m1_rc)				; positions_7nt_m3 versus oligos_7nt_mkv5_m1_rc; m=5/9; ncol2=16; w=-1; offset=-1; strand=R; shift=7; score=0.652662; -------tscCAGGTCCTGg ; cor=; Ncor= a 0 0 0 0 0 0 0 1846 1413 1181 1103 6930 208 232 1058 155 196 215 673 881 c 0 0 0 0 0 0 0 1950 2294 4240 5632 242 200 263 362 7328 7489 399 482 964 g 0 0 0 0 0 0 0 1913 2388 1442 653 576 7373 7256 323 307 125 233 6024 5385 t 0 0 0 0 0 0 0 2249 1863 1095 570 210 177 207 6215 168 148 7111 779 728
positions_7nt_m2_shift3 (positions_7nt_m2)				; positions_7nt_m3 versus positions_7nt_m2; m=6/9; ncol2=17; w=-5; offset=-5; strand=D; shift=3; score=0.569261; ---sccCtgCCAGGACCyks ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m3 versus positions_7nt_m1; m=7/9; ncol2=19; w=-5; offset=-5; strand=D; shift=3; score=0.556459; ---smcCtgCCAGGACCTgg ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_7nt_m3 versus positions_6nt_m1; m=8/9; ncol2=20; w=-2; offset=-2; strand=D; shift=6; score=0.531533; ------cytcCAGGACCTgs ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m3 versus positions_6nt_m2_rc; m=9/9; ncol2=23; w=-8; offset=-8; strand=R; shift=0; score=0.462316; csggccCtgCCAGGACCTgs ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCCCCGCCCss ; Alignment reference a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCCCCGCCCss ; cor=; Ncor= a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353
oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)				; positions_6nt_m3 versus oligos_6nt_mkv4_m2; m=2/5; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.559785; ---ssCGCCCGs ; cor=; Ncor= a 0 0 0 1806 2332 74 338 540 779 116 239 1410 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 t 0 0 0 1774 1470 183 127 771 862 417 104 1979
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; positions_6nt_m3 versus oligos_7nt_mkv5_m4; m=3/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.548442; ---ssCGCCCCC ; cor=; Ncor= a 0 0 0 2483 1951 136 314 459 504 831 694 633 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 t 0 0 0 2689 2068 142 198 640 812 1227 847 639
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; positions_6nt_m3 versus oligos_7nt_mkv5_m3; m=4/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.520265; ---ssCGCCCTC ; cor=; Ncor= a 0 0 0 1616 1521 171 314 374 268 321 694 182 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 t 0 0 0 1984 2017 191 358 485 548 530 8084 306
oligos_6nt_mkv4_m4_rc_shift3 (oligos_6nt_mkv4_m4_rc)				; positions_6nt_m3 versus oligos_6nt_mkv4_m4_rc; m=5/5; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.494136; ---ssCGCtCGs ; cor=; Ncor= a 0 0 0 1221 1423 122 198 198 779 137 176 888 c 0 0 0 3711 2634 8231 109 7735 1429 8312 499 3676 g 0 0 0 2593 3710 333 8356 540 2060 265 7910 3001 t 0 0 0 1286 1044 125 148 338 4543 97 226 1246

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; ssCGCaGGCGss ; Alignment reference a 937 961 198 155 176 3857 107 238 205 198 799 990 c 2196 1854 5443 357 5381 1024 867 563 5660 349 2553 2142 g 2227 2599 417 5592 535 1110 5040 5218 168 5467 2036 2250 t 870 816 172 126 138 239 216 211 197 216 842 848
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCaGGCGss ; cor=; Ncor= a 937 961 198 155 176 3857 107 238 205 198 799 990 c 2196 1854 5443 357 5381 1024 867 563 5660 349 2553 2142 g 2227 2599 417 5592 535 1110 5040 5218 168 5467 2036 2250 t 870 816 172 126 138 239 216 211 197 216 842 848
oligos_6nt_mkv4_m2_rc_shift2 (oligos_6nt_mkv4_m2_rc)				; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m2_rc; m=2/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.659628; --ssCGGGCGss ; cor=; Ncor= a 0 0 1836 1979 104 417 862 771 127 183 1470 1774 c 0 0 4946 4175 12376 1244 2060 1406 12562 356 5360 4038 g 0 0 4445 5624 469 11411 9487 10471 161 12575 4026 5570 t 0 0 1961 1410 239 116 779 540 338 74 2332 1806
oligos_7nt_mkv5_m4_rc_shift1 (oligos_7nt_mkv5_m4_rc)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m4_rc; m=3/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.649591; -ssGGGGGCGss ; cor=; Ncor= a 0 2419 2913 639 847 1227 812 640 198 142 2068 2689 c 0 5073 5303 1187 1364 1781 1243 889 15620 248 4880 4812 g 0 6483 5263 13740 13294 12360 13640 14211 67 15673 7300 6215 t 0 2224 2720 633 694 831 504 459 314 136 1951 2483

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=11; shift=3; ncol=14; ---ssCGCCCTCss ; Alignment reference a 0 0 0 1616 1521 171 314 374 268 321 694 182 1687 1615 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 4290 4261 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 3033 3246 t 0 0 0 1984 2017 191 358 485 548 530 8084 306 2132 2020
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCTCss ; cor=; Ncor= a 0 0 0 1616 1521 171 314 374 268 321 694 182 1687 1615 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 4290 4261 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 3033 3246 t 0 0 0 1984 2017 191 358 485 548 530 8084 306 2132 2020
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.862237; ---ssCGCCCCCss ; cor=; Ncor= a 0 0 0 2483 1951 136 314 459 504 831 694 633 2720 2224 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 5263 6483 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 5303 5073 t 0 0 0 2689 2068 142 198 640 812 1227 847 639 2913 2419
oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m2; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.708768; ---ssCGCCCGss- ; cor=; Ncor= a 0 0 0 1806 2332 74 338 540 779 116 239 1410 1961 0 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 4445 0 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 0 t 0 0 0 1774 1470 183 127 771 862 417 104 1979 1836 0
positions_6nt_m3_shift0 (positions_6nt_m3)				; oligos_7nt_mkv5_m3 versus positions_6nt_m3; m=4/4; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.520265; ssCCCCGCCCss-- ; cor=; Ncor= a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 0 0 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 0 0 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 0 0 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=13; shift=8; ncol=21; --------kcCAGGACCTggs ; Alignment reference a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score= 1; --------kcCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340
positions_7nt_m4_shift8 (positions_7nt_m4)				; oligos_6nt_mkv4_m1 versus positions_7nt_m4; m=2/9; ncol2=14; w=0; offset=0; strand=D; shift=8; score=0.884892; --------kcmAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836
positions_7nt_m3_shift8 (positions_7nt_m3)				; oligos_6nt_mkv4_m1 versus positions_7nt_m3; m=3/9; ncol2=12; w=0; offset=0; strand=D; shift=8; score=0.838354; --------ssCAGGgCCTgs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 0 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 0 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 0 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581 0
oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1; m=4/9; ncol2=16; w=-2; offset=-2; strand=D; shift=6; score=0.787897; ------cttcCAGGACCTGgs ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413
positions_6nt_m4_shift6 (positions_6nt_m4)				; oligos_6nt_mkv4_m1 versus positions_6nt_m4; m=5/9; ncol2=14; w=-2; offset=-2; strand=D; shift=6; score=0.746841; ------cytCCAGGACCyks- ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 0 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 0 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 0 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991 0
positions_7nt_m1_shift3 (positions_7nt_m1)				; oligos_6nt_mkv4_m1 versus positions_7nt_m1; m=6/9; ncol2=19; w=-5; offset=-5; strand=D; shift=3; score=0.665139; ---smcCtgCCAGGACCTggs ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307
positions_6nt_m1_shift6 (positions_6nt_m1)				; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=7/9; ncol2=20; w=-2; offset=-2; strand=D; shift=6; score=0.629132; ------cytcCAGGACCTgsc ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772
positions_7nt_m2_shift3 (positions_7nt_m2)				; oligos_6nt_mkv4_m1 versus positions_7nt_m2; m=8/9; ncol2=17; w=-5; offset=-5; strand=D; shift=3; score=0.598292; ---sccCtgCCAGGACCyks- ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 0 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 0 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 0 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271 0
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; oligos_6nt_mkv4_m1 versus positions_6nt_m2_rc; m=9/9; ncol2=23; w=-8; offset=-8; strand=R; shift=0; score=0.551534; csggccCtgCCAGGACCTgss ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 1312 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 1992 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 1812 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160 1384

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; ssCGGCCGss ; Alignment reference a 1948 2212 83 178 540 771 127 225 1522 1604 c 6090 3685 13210 1890 1429 11164 11709 386 6485 4262 g 4262 6485 386 11709 11164 1429 1890 13210 3685 6090 t 1604 1522 225 127 771 540 178 83 2212 1948
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGCCGss ; cor=; Ncor= a 1948 2212 83 178 540 771 127 225 1522 1604 c 6090 3685 13210 1890 1429 11164 11709 386 6485 4262 g 4262 6485 386 11709 11164 1429 1890 13210 3685 6090 t 1604 1522 225 127 771 540 178 83 2212 1948
oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m2; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.848843; ssCGCCCGss ; cor=; Ncor= a 1806 2332 74 338 540 779 116 239 1410 1961 c 5570 4026 12575 161 10471 9487 11411 469 5624 4445 g 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 t 1774 1470 183 127 771 862 417 104 1979 1836
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m4; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.719752; ssCGaGCGss ; cor=; Ncor= a 1311 1246 226 97 4543 338 148 125 1044 1286 c 3301 3001 7910 265 2060 540 8356 333 3710 2593 g 2949 3676 499 8312 1429 7735 109 8231 2634 3711 t 1250 888 176 137 779 198 198 122 1423 1221

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=16; shift=6; ncol=22; ------cttcCAGGACCTGgsa ; Alignment reference a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846
oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=6; score= 1; ------cttcCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846
positions_7nt_m4_shift8 (positions_7nt_m4)				; oligos_7nt_mkv5_m1 versus positions_7nt_m4; m=2/9; ncol2=14; w=0; offset=2; strand=D; shift=8; score=0.831405; --------kcmAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 c 0 0 0 0 0 0 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 g 0 0 0 0 0 0 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 t 0 0 0 0 0 0 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276
positions_6nt_m4_shift6 (positions_6nt_m4)				; oligos_7nt_mkv5_m1 versus positions_6nt_m4; m=3/9; ncol2=14; w=0; offset=0; strand=D; shift=6; score=0.810239; ------cytCCAGGACCyks-- ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 0 0 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 0 0 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 0 0 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991 0 0
positions_7nt_m1_shift3 (positions_7nt_m1)				; oligos_7nt_mkv5_m1 versus positions_7nt_m1; m=4/9; ncol2=19; w=-3; offset=-3; strand=D; shift=3; score=0.806823; ---smcCtgCCAGGACCTggsv ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 1656 1907 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 2203 1923 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 2103 1892 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217 1307 1547
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1; m=5/9; ncol2=13; w=0; offset=2; strand=D; shift=8; score=0.787897; --------kcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 0 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 0 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 0 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340 0
positions_6nt_m1_shift6 (positions_6nt_m1)				; oligos_7nt_mkv5_m1 versus positions_6nt_m1; m=6/9; ncol2=20; w=0; offset=0; strand=D; shift=6; score=0.779526; ------cytcCAGGACCTgsca ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; oligos_7nt_mkv5_m1 versus positions_6nt_m2_rc; m=7/9; ncol2=23; w=-6; offset=-6; strand=R; shift=0; score=0.665179; csggccCtgCCAGGACCTgsss ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 1312 1517 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 1992 1846 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 1812 1802 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160 1384 1335
positions_7nt_m3_rc_shift9 (positions_7nt_m3_rc)				; oligos_7nt_mkv5_m1 versus positions_7nt_m3_rc; m=8/9; ncol2=12; w=0; offset=3; strand=R; shift=9; score=0.652662; ---------scAGGcCCTGss- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2581 2801 10238 283 462 2056 365 223 358 200 2317 3105 0 c 0 0 0 0 0 0 0 0 0 4801 5562 1319 267 324 8473 11782 12519 608 223 3798 4129 0 g 0 0 0 0 0 0 0 0 0 3419 3279 1125 12541 12150 522 583 350 543 12741 4770 3801 0 t 0 0 0 0 0 0 0 0 0 2524 1683 643 234 389 2274 595 233 11816 161 2440 2290 0
positions_7nt_m2_shift3 (positions_7nt_m2)				; oligos_7nt_mkv5_m1 versus positions_7nt_m2; m=9/9; ncol2=17; w=-3; offset=-3; strand=D; shift=3; score=0.628351; ---sccCtgCCAGGACCyks-- ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 0 0 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 0 0 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 0 0 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271 0 0

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=10; shift=0; ncol=10; ssCGaGCGss ; Alignment reference a 1311 1246 226 97 4543 338 148 125 1044 1286 c 3301 3001 7910 265 2060 540 8356 333 3710 2593 g 2949 3676 499 8312 1429 7735 109 8231 2634 3711 t 1250 888 176 137 779 198 198 122 1423 1221
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssCGaGCGss ; cor=; Ncor= a 1311 1246 226 97 4543 338 148 125 1044 1286 c 3301 3001 7910 265 2060 540 8356 333 3710 2593 g 2949 3676 499 8312 1429 7735 109 8231 2634 3711 t 1250 888 176 137 779 198 198 122 1423 1221
oligos_6nt_mkv4_m2_rc_shift0 (oligos_6nt_mkv4_m2_rc)				; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m2_rc; m=2/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.918767; ssCGGGCGss ; cor=; Ncor= a 1836 1979 104 417 862 771 127 183 1470 1774 c 4946 4175 12376 1244 2060 1406 12562 356 5360 4038 g 4445 5624 469 11411 9487 10471 161 12575 4026 5570 t 1961 1410 239 116 779 540 338 74 2332 1806
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m5; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.719752; ssCGGCCGss ; cor=; Ncor= a 1948 2212 83 178 540 771 127 225 1522 1604 c 6090 3685 13210 1890 1429 11164 11709 386 6485 4262 g 4262 6485 386 11709 11164 1429 1890 13210 3685 6090 t 1604 1522 225 127 771 540 178 83 2212 1948
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; oligos_6nt_mkv4_m4 versus positions_6nt_m3_rc; m=4/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.494136; -ssGGGCGGG ; cor=; Ncor= a 0 2353 2789 540 390 393 753 676 495 714 c 0 5764 4467 1149 1452 818 14208 883 1396 1529 g 0 6144 6579 14123 13910 14583 113 13846 13674 13410 t 0 1881 2307 330 390 348 1068 737 577 489

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; yhcCTTCCAgg ; Alignment reference a 1662 2338 965 330 156 312 373 34 8325 1390 1965 c 2550 2321 5294 8001 121 142 8320 8477 144 2108 1943 g 1856 1928 1141 400 298 129 77 152 309 3332 2916 t 2768 2249 1436 105 8261 8253 66 173 58 2006 2012
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; yhcCTTCCAgg ; cor=; Ncor= a 1662 2338 965 330 156 312 373 34 8325 1390 1965 c 2550 2321 5294 8001 121 142 8320 8477 144 2108 1943 g 1856 1928 1141 400 298 129 77 152 309 3332 2916 t 2768 2249 1436 105 8261 8253 66 173 58 2006 2012
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; positions_6nt_m5 versus positions_7nt_m5_rc; m=2/4; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.868925; bycCTTCCAGg ; cor=; Ncor= a 1871 2411 1388 544 330 265 445 185 8345 152 1991 c 2745 2471 5618 8769 260 429 8596 9074 545 363 2271 g 2680 2135 1402 155 385 456 419 175 470 8870 3444 t 2447 2726 1335 275 8768 8593 283 309 383 358 2037
positions_7nt_m2_shift0 (positions_7nt_m2)				; positions_6nt_m5 versus positions_7nt_m2; m=3/4; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.48442; sccCtgCCAGG ; cor=; Ncor= a 1145 1600 744 297 805 437 345 355 5409 191 147 c 2142 2183 3482 5412 831 695 5296 5685 414 261 308 g 1711 1441 1285 459 688 3932 432 246 436 5917 5930 t 1510 1284 997 340 4184 1444 435 222 249 139 123
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_6nt_m5 versus positions_7nt_m1; m=4/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.417174; smcCtgCCAGG ; cor=; Ncor= a 1320 1958 1118 549 1173 622 612 657 6373 213 152 c 2244 2228 3211 5353 950 910 5230 5821 259 136 267 g 1917 1654 1549 767 850 3991 759 354 427 6776 6717 t 1788 1429 1391 600 4296 1746 668 437 210 144 133

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=20; shift=0; ncol=20; cytcCAGGACCTgscaggss ; Alignment reference a 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 841 1082 1393 1454 c 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 1142 1288 1775 1980 g 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 3724 3077 1883 1787 t 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238 822 1082 1478 1308
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/9; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; cytcCAGGACCTgscaggss ; cor=; Ncor= a 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 1136 2956 841 1082 1393 1454 c 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 3433 1177 1142 1288 1775 1980 g 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 1188 1158 3724 3077 1883 1787 t 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949 772 1238 822 1082 1478 1308
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_6nt_m1 versus positions_7nt_m1_rc; m=2/9; ncol2=19; w=0; offset=1; strand=R; shift=1; score=0.825277; -bsccAGGTCCTGGcaGgks ; cor=; Ncor= a 0 1547 1307 1217 1221 5945 254 192 893 133 144 210 437 668 1746 4296 600 1391 1429 1788 c 0 1892 2103 3460 4621 313 201 272 412 6717 6776 427 354 759 3991 850 767 1549 1654 1917 g 0 1923 2203 1518 823 757 6614 6573 402 267 136 259 5821 5230 910 950 5353 3211 2228 2244 t 0 1907 1656 1074 604 254 200 232 5562 152 213 6373 657 612 622 1173 549 1118 1958 1320
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; positions_6nt_m1 versus oligos_7nt_mkv5_m1; m=3/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.779526; cttcCAGGACCTGgsa---- ; cor=; Ncor= a 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 1863 2249 0 0 0 0 c 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 2388 1913 0 0 0 0 g 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 2294 1950 0 0 0 0 t 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181 1413 1846 0 0 0 0
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=4/9; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.73824; sssscAGGTCCTGGcaGggc ; cor=; Ncor= a 1257 1335 1384 1160 1016 4969 209 178 671 121 133 191 324 632 1550 3455 550 1129 920 1166 c 2046 1802 1812 2263 4096 412 198 305 381 5977 6046 441 364 864 3454 956 856 1211 1125 2939 g 1991 1846 1992 2022 869 835 5925 5821 450 256 167 360 5389 4424 872 1078 4580 3201 3194 1486 t 1206 1517 1312 1055 519 284 168 196 4998 146 154 5508 423 580 624 1011 514 959 1261 909
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m1 versus positions_6nt_m4; m=5/9; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.65467; cytCCAGGACCyks------ ; cor=; Ncor= a 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 0 0 0 0 0 0 c 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 0 0 0 0 0 0 g 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 0 0 0 0 0 0 t 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991 0 0 0 0 0 0
positions_7nt_m4_shift2 (positions_7nt_m4)				; positions_6nt_m1 versus positions_7nt_m4; m=6/9; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.644377; --kcmAGGACCTGgva---- ; cor=; Ncor= a 0 0 2121 2160 3851 9450 222 167 8092 303 251 224 710 1583 2771 3206 0 0 0 0 c 0 0 1965 3581 3753 201 88 201 281 9379 9497 440 768 1692 2766 2234 0 0 0 0 g 0 0 3184 2432 1374 379 9697 9622 256 275 224 200 7194 5330 2810 2467 0 0 0 0 t 0 0 2913 2010 1205 153 176 193 1554 226 211 9319 1511 1578 1836 2276 0 0 0 0
oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)				; positions_6nt_m1 versus oligos_6nt_mkv4_m1; m=7/9; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.629132; --kcCAGGACCTggs----- ; cor=; Ncor= a 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 2995 0 0 0 0 0 c 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 3540 0 0 0 0 0 g 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 3399 0 0 0 0 0 t 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240 2340 0 0 0 0 0
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; positions_6nt_m1 versus positions_7nt_m2_rc; m=8/9; ncol2=17; w=0; offset=3; strand=R; shift=3; score=0.628411; ---smrGGTCCTGGcaGggs ; cor=; Ncor= a 0 0 0 1271 1662 1897 340 222 408 123 139 249 222 435 1444 4184 340 997 1284 1510 c 0 0 0 2372 2063 489 315 303 405 5930 5917 436 246 432 3932 688 459 1285 1441 1711 g 0 0 0 1716 1603 3731 5543 5772 401 308 261 414 5685 5296 695 831 5412 3482 2183 2142 t 0 0 0 1149 1180 391 310 211 5294 147 191 5409 355 345 437 805 297 744 1600 1145
positions_7nt_m3_shift2 (positions_7nt_m3)				; positions_6nt_m1 versus positions_7nt_m3; m=9/9; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.531533; --ssCAGGgCCTgs------ ; cor=; Ncor= a 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 0 0 0 0 0 0 c 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 0 0 0 0 0 0 g 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 0 0 0 0 0 0 t 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift3 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=17; shift=3; ncol=20; ---sccCtgCCAGGACCyks ; Alignment reference a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271
positions_7nt_m2_shift3 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/11; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---sccCtgCCAGGACCyks ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_7nt_m2 versus positions_7nt_m1; m=2/11; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.833426; ---smcCtgCCAGGACCTgg ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_7nt_m2 versus positions_6nt_m4; m=3/11; ncol2=14; w=0; offset=3; strand=D; shift=6; score=0.773224; ------cytCCAGGACCyks ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m2 versus positions_6nt_m2_rc; m=4/11; ncol2=23; w=-3; offset=-3; strand=R; shift=0; score=0.687453; csggccCtgCCAGGACCTgs ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; positions_7nt_m2 versus positions_6nt_m1_rc; m=5/11; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.628411; ---sscctgscAGGTCCTGg ; cor=; Ncor= a 0 0 0 1308 1478 1082 822 1238 772 949 1042 5395 160 216 994 155 137 195 391 796 c 0 0 0 1787 1883 3077 3724 1158 1188 1910 4229 296 160 231 312 5992 6069 366 311 803 g 0 0 0 1980 1775 1288 1142 1177 3433 2820 780 552 6055 5890 353 263 158 250 5381 4312 t 0 0 0 1454 1393 1082 841 2956 1136 850 478 286 154 192 4870 119 165 5718 446 618
oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)				; positions_7nt_m2 versus oligos_7nt_mkv5_m1; m=6/11; ncol2=16; w=0; offset=3; strand=D; shift=6; score=0.628351; ------cttcCAGGACCTGg ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; positions_7nt_m2 versus oligos_6nt_mkv4_m1; m=7/11; ncol2=13; w=0; offset=5; strand=D; shift=8; score=0.598292; --------kcCAGGACCTgg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240
positions_7nt_m3_shift8 (positions_7nt_m3)				; positions_7nt_m2 versus positions_7nt_m3; m=8/11; ncol2=12; w=0; offset=5; strand=D; shift=8; score=0.569261; --------ssCAGGgCCTgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581
positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)				; positions_7nt_m2 versus positions_7nt_m5_rc; m=9/11; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.560059; ---bycCTTCCAGgh----- ; cor=; Ncor= a 0 0 0 1871 2411 1388 544 330 265 445 185 8345 152 1991 2919 0 0 0 0 0 c 0 0 0 2745 2471 5618 8769 260 429 8596 9074 545 363 2271 2443 0 0 0 0 0 g 0 0 0 2680 2135 1402 155 385 456 419 175 470 8870 3444 1802 0 0 0 0 0 t 0 0 0 2447 2726 1335 275 8768 8593 283 309 383 358 2037 2579 0 0 0 0 0
positions_7nt_m4_rc_shift7 (positions_7nt_m4_rc)				; positions_7nt_m2 versus positions_7nt_m4_rc; m=10/11; ncol2=14; w=0; offset=4; strand=R; shift=7; score=0.550391; -------tbcCAGGTCCTkg ; cor=; Ncor= a 0 0 0 0 0 0 0 2276 1836 1578 1511 9319 211 226 1554 193 176 153 1205 2010 c 0 0 0 0 0 0 0 2467 2810 5330 7194 200 224 275 256 9622 9697 379 1374 2432 g 0 0 0 0 0 0 0 2234 2766 1692 768 440 9497 9379 281 201 88 201 3753 3581 t 0 0 0 0 0 0 0 3206 2771 1583 710 224 251 303 8092 167 222 9450 3851 2160
positions_6nt_m5_shift3 (positions_6nt_m5)				; positions_7nt_m2 versus positions_6nt_m5; m=11/11; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.48442; ---yhcCTTCCAgg------ ; cor=; Ncor= a 0 0 0 1662 2338 965 330 156 312 373 34 8325 1390 1965 0 0 0 0 0 0 c 0 0 0 2550 2321 5294 8001 121 142 8320 8477 144 2108 1943 0 0 0 0 0 0 g 0 0 0 1856 1928 1141 400 298 129 77 152 309 3332 2916 0 0 0 0 0 0 t 0 0 0 2768 2249 1436 105 8261 8253 66 173 58 2006 2012 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=11; shift=3; ncol=14; ---ssCGCCCCCss ; Alignment reference a 0 0 0 2483 1951 136 314 459 504 831 694 633 2720 2224 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 5263 6483 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 5303 5073 t 0 0 0 2689 2068 142 198 640 812 1227 847 639 2913 2419
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCCCss ; cor=; Ncor= a 0 0 0 2483 1951 136 314 459 504 831 694 633 2720 2224 c 0 0 0 6215 7300 15673 67 14211 13640 12360 13294 13740 5263 6483 g 0 0 0 4812 4880 248 15620 889 1243 1781 1364 1187 5303 5073 t 0 0 0 2689 2068 142 198 640 812 1227 847 639 2913 2419
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.862237; ---ssCGCCCTCss ; cor=; Ncor= a 0 0 0 1616 1521 171 314 374 268 321 694 182 1687 1615 c 0 0 0 4423 4127 10533 181 9268 9675 9948 1000 9958 4290 4261 g 0 0 0 3119 3477 247 10289 1015 651 343 1364 696 3033 3246 t 0 0 0 1984 2017 191 358 485 548 530 8084 306 2132 2020
oligos_6nt_mkv4_m2_shift3 (oligos_6nt_mkv4_m2)				; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m2; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.694484; ---ssCGCCCGss- ; cor=; Ncor= a 0 0 0 1806 2332 74 338 540 779 116 239 1410 1961 0 c 0 0 0 5570 4026 12575 161 10471 9487 11411 469 5624 4445 0 g 0 0 0 4038 5360 356 12562 1406 2060 1244 12376 4175 4946 0 t 0 0 0 1774 1470 183 127 771 862 417 104 1979 1836 0
oligos_7nt_mkv5_m5_rc_shift3 (oligos_7nt_mkv5_m5_rc)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m5_rc; m=4/5; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.649591; ---ssCGCCtGCGs ; cor=; Ncor= a 0 0 0 848 842 216 197 211 216 239 138 126 172 816 c 0 0 0 2250 2036 5467 168 5218 5040 1110 535 5592 417 2599 g 0 0 0 2142 2553 349 5660 563 867 1024 5381 357 5443 1854 t 0 0 0 990 799 198 205 238 107 3857 176 155 198 961
positions_6nt_m3_shift0 (positions_6nt_m3)				; oligos_7nt_mkv5_m4 versus positions_6nt_m3; m=5/5; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.548442; ssCCCCGCCCss-- ; cor=; Ncor= a 2610 2402 749 489 577 737 1068 348 390 330 2307 1881 0 0 c 6033 5371 12678 13410 13674 13846 113 14583 13910 14123 6579 6144 0 0 g 4978 5426 1846 1529 1396 883 14208 818 1452 1149 4467 5764 0 0 t 2521 2943 869 714 495 676 753 393 390 540 2789 2353 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=14; shift=6; ncol=20; ------cytCCAGGACCyks ; Alignment reference a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/9; ncol2=14; w=0; offset=0; strand=D; shift=6; score= 1; ------cytCCAGGACCyks ; cor=; Ncor= a 0 0 0 0 0 0 1640 2089 1307 893 478 9338 175 230 9036 284 387 989 2000 1899 c 0 0 0 0 0 0 4782 2763 1691 7332 9180 396 217 385 445 9606 9284 4902 2413 2706 g 0 0 0 0 0 0 2381 2163 2286 1190 350 516 9897 9701 393 275 365 1015 3395 3865 t 0 0 0 0 0 0 1658 3446 5177 1046 453 211 172 145 587 296 425 3555 2653 1991
oligos_7nt_mkv5_m1_shift6 (oligos_7nt_mkv5_m1)				; positions_6nt_m4 versus oligos_7nt_mkv5_m1; m=2/9; ncol2=16; w=0; offset=0; strand=D; shift=6; score=0.810239; ------cttcCAGGACCTGg ; cor=; Ncor= a 0 0 0 0 0 0 1228 1566 872 728 779 7111 148 168 6215 207 177 210 570 1095 c 0 0 0 0 0 0 3521 1975 1061 5385 6024 233 125 307 323 7256 7373 576 653 1442 g 0 0 0 0 0 0 1840 1588 1625 964 482 399 7489 7328 362 263 200 242 5632 4240 t 0 0 0 0 0 0 1369 2829 4400 881 673 215 196 155 1058 232 208 6930 1103 1181
positions_7nt_m2_shift3 (positions_7nt_m2)				; positions_6nt_m4 versus positions_7nt_m2; m=3/9; ncol2=17; w=-3; offset=-3; strand=D; shift=3; score=0.773224; ---sccCtgCCAGGACCyks ; cor=; Ncor= a 0 0 0 1145 1600 744 297 805 437 345 355 5409 191 147 5294 211 310 391 1180 1149 c 0 0 0 2142 2183 3482 5412 831 695 5296 5685 414 261 308 401 5772 5543 3731 1603 1716 g 0 0 0 1711 1441 1285 459 688 3932 432 246 436 5917 5930 405 303 315 489 2063 2372 t 0 0 0 1510 1284 997 340 4184 1444 435 222 249 139 123 408 222 340 1897 1662 1271
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; positions_6nt_m4 versus oligos_6nt_mkv4_m1; m=4/9; ncol2=13; w=0; offset=2; strand=D; shift=8; score=0.746841; --------kcCAGGACCTgg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2313 2334 793 11340 231 198 9688 292 289 450 1577 2510 c 0 0 0 0 0 0 0 0 2606 4729 10356 237 155 347 480 11320 11398 1576 1662 2879 g 0 0 0 0 0 0 0 0 3802 2853 499 494 11661 11530 458 344 263 510 6622 4645 t 0 0 0 0 0 0 0 0 3553 2358 626 203 227 199 1648 318 324 9738 2413 2240
positions_7nt_m3_shift8 (positions_7nt_m3)				; positions_6nt_m4 versus positions_7nt_m3; m=5/9; ncol2=12; w=0; offset=2; strand=D; shift=8; score=0.713192; --------ssCAGGgCCTgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2290 2440 161 11816 233 595 2274 389 234 643 1683 2524 c 0 0 0 0 0 0 0 0 3801 4770 12741 543 350 583 522 12150 12541 1125 3279 3419 g 0 0 0 0 0 0 0 0 4129 3798 223 608 12519 11782 8473 324 267 1319 5562 4801 t 0 0 0 0 0 0 0 0 3105 2317 200 358 223 365 2056 462 283 10238 2801 2581
positions_7nt_m4_rc_shift7 (positions_7nt_m4_rc)				; positions_6nt_m4 versus positions_7nt_m4_rc; m=6/9; ncol2=14; w=0; offset=1; strand=R; shift=7; score=0.695681; -------tbcCAGGTCCTkg ; cor=; Ncor= a 0 0 0 0 0 0 0 2276 1836 1578 1511 9319 211 226 1554 193 176 153 1205 2010 c 0 0 0 0 0 0 0 2467 2810 5330 7194 200 224 275 256 9622 9697 379 1374 2432 g 0 0 0 0 0 0 0 2234 2766 1692 768 440 9497 9379 281 201 88 201 3753 3581 t 0 0 0 0 0 0 0 3206 2771 1583 710 224 251 303 8092 167 222 9450 3851 2160
positions_7nt_m1_shift3 (positions_7nt_m1)				; positions_6nt_m4 versus positions_7nt_m1; m=7/9; ncol2=19; w=-3; offset=-3; strand=D; shift=3; score=0.669833; ---smcCtgCCAGGACCTgg ; cor=; Ncor= a 0 0 0 1320 1958 1118 549 1173 622 612 657 6373 213 152 5562 232 200 254 604 1074 c 0 0 0 2244 2228 3211 5353 950 910 5230 5821 259 136 267 402 6573 6614 757 823 1518 g 0 0 0 1917 1654 1549 767 850 3991 759 354 427 6776 6717 412 272 201 313 4621 3460 t 0 0 0 1788 1429 1391 600 4296 1746 668 437 210 144 133 893 192 254 5945 1221 1217
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_6nt_m4 versus positions_6nt_m1; m=8/9; ncol2=20; w=0; offset=0; strand=D; shift=6; score=0.65467; ------cytcCAGGACCTgs ; cor=; Ncor= a 0 0 0 0 0 0 1059 1306 765 618 446 5718 165 119 4870 192 154 286 478 850 c 0 0 0 0 0 0 2836 1649 1103 4312 5381 250 158 263 353 5890 6055 552 780 2820 g 0 0 0 0 0 0 1497 1441 1565 803 311 366 6069 5992 312 231 160 296 4229 1910 t 0 0 0 0 0 0 1137 2133 3096 796 391 195 137 155 994 216 160 5395 1042 949
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_6nt_m4 versus positions_6nt_m2_rc; m=9/9; ncol2=23; w=-6; offset=-6; strand=R; shift=0; score=0.561044; csggccCtgCCAGGACCTgs ; cor=; Ncor= a 1391 1325 955 909 1261 959 514 1011 624 580 423 5508 154 146 4998 196 168 284 519 1055 c 2050 1899 1300 1486 3194 3201 4580 1078 872 4424 5389 360 167 256 450 5821 5925 835 869 2022 g 1612 1788 2856 2939 1125 1211 856 956 3454 864 364 441 6046 5977 381 305 198 412 4096 2263 t 1447 1488 1389 1166 920 1129 550 3455 1550 632 324 191 133 121 671 178 209 4969 1016 1160