One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/11/25/peak-motifs.2025-11-25.163900_2025-11-25.163900_NWtK8i/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/2025/11/25/peak-motifs.2025-11-25.163900_2025-11-25.163900_NWtK8i/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift2 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift2 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssccaGGTCCTGcCAGGaCCykgs ; Alignment reference a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 196 245 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 248 306 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 390 313 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365 209 179

positions_6nt_m2_shift2 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssccaGGTCCTGcCAGGaCCykgs ; cor=; Ncor= a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 196 245 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 248 306 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 390 313 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365 209 179

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.961589; --ssccaGGtCCTGcCAGGACCTgss ; cor=; Ncor= a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m2 versus positions_6nt_m3; m=3/11; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.815372; sskgscAGGTCCTGsCAGGacybr-- ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 0 0 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 0 0 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 0 0 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282 0 0

positions_6nt_m4_shift3 (positions_6nt_m4)
; positions_6nt_m2 versus positions_6nt_m4; m=4/11; ncol2=21; w=0; offset=1; strand=D; shift=3; score=0.799923; ---kcmAGGACCTGcCAGGACyyk-- ; cor=; Ncor= a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 0 0 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 0 0 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 0 0 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324 0 0

positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)
; positions_6nt_m2 versus positions_7nt_m1_rc; m=5/11; ncol2=19; w=0; offset=0; strand=R; shift=2; score=0.667982; --ksccAGGTCCTGGcaggks----- ; cor=; Ncor= a 0 0 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 1273 0 0 0 0 0 c 0 0 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 1371 0 0 0 0 0 g 0 0 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 1507 0 0 0 0 0 t 0 0 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470 1004 0 0 0 0 0

positions_7nt_m2_shift8 (positions_7nt_m2)
; positions_6nt_m2 versus positions_7nt_m2; m=6/11; ncol2=18; w=0; offset=6; strand=D; shift=8; score=0.644947; --------smsCtgCCAGGACCykss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915

positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)
; positions_6nt_m2 versus positions_7nt_m4_rc; m=7/11; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.565337; --tbcCAGGTCCTGsma--------- ; cor=; Ncor= a 0 0 1398 1120 1041 781 5554 160 149 1077 136 121 126 330 939 1868 2080 0 0 0 0 0 0 0 0 0 c 0 0 1538 1681 3078 4759 185 150 217 337 5902 5966 341 290 2429 1993 1335 0 0 0 0 0 0 0 0 0 g 0 0 1482 1882 1208 416 406 5860 5792 271 153 92 152 5249 2091 1189 1473 0 0 0 0 0 0 0 0 0 t 0 0 1887 1622 978 349 160 135 147 4620 114 126 5686 436 846 1255 1417 0 0 0 0 0 0 0 0 0

positions_7nt_m3_rc_shift8 (positions_7nt_m3_rc)
; positions_6nt_m2 versus positions_7nt_m3_rc; m=8/11; ncol2=16; w=0; offset=6; strand=R; shift=8; score=0.564903; --------smcCTgCCAGGACyyk-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 c 0 0 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 g 0 0 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 t 0 0 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0

oligos_6nt_mkv4_m1_rc_shift3 (oligos_6nt_mkv4_m1_rc)
; positions_6nt_m2 versus oligos_6nt_mkv4_m1_rc; m=9/11; ncol2=15; w=0; offset=1; strand=R; shift=3; score=0.556851; ---sccAGGTCCTGgcag-------- ; cor=; Ncor= a 0 0 0 1252 1316 1177 5293 187 168 987 105 102 132 360 734 1561 2432 985 0 0 0 0 0 0 0 0 c 0 0 0 1809 2513 4056 303 151 189 288 6262 6311 333 240 970 3486 1302 1388 0 0 0 0 0 0 0 0 g 0 0 0 1973 1541 754 761 6148 6120 307 166 107 191 5608 4168 834 1295 3254 0 0 0 0 0 0 0 0 t 0 0 0 1614 1278 661 291 162 171 5066 115 128 5992 440 776 767 1619 1021 0 0 0 0 0 0 0 0

oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)
; positions_6nt_m2 versus oligos_7nt_mkv5_m1_rc; m=10/11; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.556443; --tscCAGGTCCTGGaag-------- ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 0 0 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 0 0 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 0 0 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0 0 0 0 0 0

positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)
; positions_6nt_m2 versus positions_7nt_m5_rc; m=11/11; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.555952; --tbcCAGGTCCTGkma--------- ; cor=; Ncor= a 0 0 1393 1091 1058 802 5458 163 175 1056 111 118 115 334 946 1777 2134 0 0 0 0 0 0 0 0 0 c 0 0 1444 1618 2922 4547 150 118 175 271 5735 5792 240 270 1156 1918 1219 0 0 0 0 0 0 0 0 0 g 0 0 1372 1833 1155 399 342 5695 5621 239 163 89 116 5071 2112 1273 1297 0 0 0 0 0 0 0 0 0 t 0 0 1907 1574 981 368 166 140 145 4550 107 117 5645 441 1902 1148 1466 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; ycCTCCTCcb ; Alignment reference a 1015 744 58 57 166 45 77 29 870 781 c 1542 1801 4845 34 4786 4796 36 4960 1771 1592 g 1145 1235 87 332 25 152 357 12 1183 1372 t 1304 1226 16 4583 29 13 4536 5 1182 1261

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ycCTCCTCcb ; cor=; Ncor= a 1015 744 58 57 166 45 77 29 870 781 c 1542 1801 4845 34 4786 4796 36 4960 1771 1592 g 1145 1235 87 332 25 152 357 12 1183 1372 t 1304 1226 16 4583 29 13 4536 5 1182 1261

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift7 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift7 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=7; ncol=18; -------tcCTGGAAGrr ; Alignment reference a 0 0 0 0 0 0 0 1255 1201 172 173 194 111 4862 4822 97 1386 1485 c 0 0 0 0 0 0 0 948 1980 4959 253 115 81 135 194 122 1180 1147 g 0 0 0 0 0 0 0 1161 1083 146 312 4977 4760 121 130 4813 1469 1402 t 0 0 0 0 0 0 0 1986 1086 73 4612 64 398 232 204 318 1315 1316

oligos_7nt_mkv5_m5_shift7 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------tcCTGGAAGrr ; cor=; Ncor= a 0 0 0 0 0 0 0 1255 1201 172 173 194 111 4862 4822 97 1386 1485 c 0 0 0 0 0 0 0 948 1980 4959 253 115 81 135 194 122 1180 1147 g 0 0 0 0 0 0 0 1161 1083 146 312 4977 4760 121 130 4813 1469 1402 t 0 0 0 0 0 0 0 1986 1086 73 4612 64 398 232 204 318 1315 1316

positions_7nt_m3_shift3 (positions_7nt_m3)
; oligos_7nt_mkv5_m5 versus positions_7nt_m3; m=2/5; ncol2=16; w=-4; offset=-4; strand=D; shift=3; score=0.540431; ---mrrGTCCTGGcAGgk ; cor=; Ncor= a 0 0 0 1181 1555 1896 179 193 80 111 120 121 190 856 2849 298 946 870 c 0 0 0 1252 877 295 123 187 3859 3869 178 98 231 2804 420 325 1038 812 g 0 0 0 956 1230 1589 3680 198 139 83 135 3729 3563 312 371 3264 1488 1295 t 0 0 0 785 512 394 192 3596 96 111 3741 226 190 202 534 287 702 1197

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; oligos_7nt_mkv5_m5 versus positions_7nt_m2_rc; m=3/5; ncol2=18; w=-6; offset=-6; strand=R; shift=1; score= 0.4754; -ssmrGGTCCTGGcaGsk ; cor=; Ncor= a 0 915 987 1240 1472 234 162 313 80 89 136 143 317 1142 2681 398 1017 914 c 0 1466 1791 1466 310 204 196 282 4481 4453 331 154 360 2859 596 604 1275 1059 g 0 1358 1227 971 2798 4190 4346 282 185 164 270 4279 3883 490 772 3488 1745 1595 t 0 1099 833 1161 258 210 134 3961 92 132 4101 262 278 347 789 348 801 1270

positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc)
; oligos_7nt_mkv5_m5 versus positions_7nt_m1_rc; m=4/5; ncol2=19; w=-7; offset=-7; strand=R; shift=0; score=0.446516; ksccAGGTCCTGGcaggk ; cor=; Ncor= a 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 c 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 g 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 t 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470

oligos_7nt_mkv5_m1_rc_shift0 (oligos_7nt_mkv5_m1_rc)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m1_rc; m=5/5; ncol2=16; w=-7; offset=-7; strand=R; shift=0; score=0.402914; tscCAGGTCCTGGaag-- ; cor=; Ncor= a 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 c 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 g 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 t 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift9 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift9 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------ctgcCAGGACCTggs ; Alignment reference a 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 c 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 g 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 t 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252

oligos_6nt_mkv4_m1_shift9 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score= 1; ---------ctgcCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 c 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 g 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 t 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252

oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1; m=2/11; ncol2=16; w=0; offset=0; strand=D; shift=9; score=0.913917; ---------cttCCAGGACCTGgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 c 0 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 g 0 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 t 0 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862

positions_7nt_m5_shift10 (positions_7nt_m5)
; oligos_6nt_mkv4_m1 versus positions_7nt_m5; m=3/11; ncol2=15; w=0; offset=1; strand=D; shift=10; score=0.853916; ----------tkmCAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 c 0 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 g 0 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 t 0 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091

positions_7nt_m4_shift10 (positions_7nt_m4)
; oligos_6nt_mkv4_m1 versus positions_7nt_m4; m=4/11; ncol2=15; w=0; offset=1; strand=D; shift=10; score=0.851069; ----------tksCAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 c 0 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 g 0 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 t 0 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120

positions_7nt_m1_shift6 (positions_7nt_m1)
; oligos_6nt_mkv4_m1 versus positions_7nt_m1; m=5/11; ncol2=19; w=-3; offset=-3; strand=D; shift=6; score=0.781424; ------smcctgCCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 c 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 g 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 t 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938

positions_7nt_m2_shift6 (positions_7nt_m2)
; oligos_6nt_mkv4_m1 versus positions_7nt_m2; m=6/11; ncol2=18; w=-3; offset=-3; strand=D; shift=6; score=0.767207; ------smsCtgCCAGGACCykss ; cor=; Ncor= a 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915

positions_7nt_m3_rc_shift6 (positions_7nt_m3_rc)
; oligos_6nt_mkv4_m1 versus positions_7nt_m3_rc; m=7/11; ncol2=16; w=-3; offset=-3; strand=R; shift=6; score=0.630754; ------smcCTgCCAGGACyyk-- ; cor=; Ncor= a 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 c 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 g 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 t 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; oligos_6nt_mkv4_m1 versus positions_6nt_m4_rc; m=8/11; ncol2=21; w=-6; offset=-6; strand=R; shift=3; score=0.587739; ---mrrGTCCTGgCAGGTCCTkgm ; cor=; Ncor= a 0 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 90 88 168 253 303 c 0 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 933 107 176 238 342 g 0 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 57 88 426 403 274 t 0 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60 71 868 381 257 232

positions_6nt_m1_shift0 (positions_6nt_m1)
; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=9/11; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.578048; ssccaGGtCCTGcCAGGACCTgss ; cor=; Ncor= a 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157

positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)
; oligos_6nt_mkv4_m1 versus positions_6nt_m3_rc; m=10/11; ncol2=24; w=-6; offset=-6; strand=R; shift=3; score=0.57632; ---yvrgtCCTGsCAGGACCTgsc ; cor=; Ncor= a 0 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 c 0 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 g 0 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 t 0 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195

positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)
; oligos_6nt_mkv4_m1 versus positions_6nt_m2_rc; m=11/11; ncol2=24; w=-8; offset=-8; strand=R; shift=1; score=0.556851; -scmrGGtCCTGgCAGGACCtggs ; cor=; Ncor= a 0 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 c 0 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 g 0 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 t 0 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift3 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift3 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=21; shift=3; ncol=24; ---kcmAGGACCTGcCAGGACyyk ; Alignment reference a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324

positions_6nt_m4_shift3 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/11; ncol2=21; w=0; offset=0; strand=D; shift=3; score= 1; ---kcmAGGACCTGcCAGGACyyk ; cor=; Ncor= a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=2/11; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.808129; sskgscAGGTCCTGsCAGGacybr ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282

positions_6nt_m2_shift2 (positions_6nt_m2)
; positions_6nt_m4 versus positions_6nt_m2; m=3/11; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.799923; --ssccaGGTCCTGcCAGGaCCyk ; cor=; Ncor= a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m4 versus positions_6nt_m1; m=4/11; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.782281; --ssccaGGtCCTGcCAGGACCTg ; cor=; Ncor= a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148

positions_7nt_m3_rc_shift8 (positions_7nt_m3_rc)
; positions_6nt_m4 versus positions_7nt_m3_rc; m=5/11; ncol2=16; w=0; offset=5; strand=R; shift=8; score=0.664718; --------smcCTgCCAGGACyyk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 c 0 0 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 g 0 0 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 t 0 0 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181

positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)
; positions_6nt_m4 versus positions_7nt_m1_rc; m=6/11; ncol2=19; w=-1; offset=-1; strand=R; shift=2; score=0.629275; --ksccAGGTCCTGGcaggks--- ; cor=; Ncor= a 0 0 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 1273 0 0 0 c 0 0 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 1371 0 0 0 g 0 0 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 1507 0 0 0 t 0 0 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470 1004 0 0 0

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; positions_6nt_m4 versus positions_7nt_m2_rc; m=7/11; ncol2=18; w=0; offset=0; strand=R; shift=3; score=0.610907; ---ssmrGGTCCTGGcaGsks--- ; cor=; Ncor= a 0 0 0 915 987 1240 1472 234 162 313 80 89 136 143 317 1142 2681 398 1017 914 1143 0 0 0 c 0 0 0 1466 1791 1466 310 204 196 282 4481 4453 331 154 360 2859 596 604 1275 1059 1235 0 0 0 g 0 0 0 1358 1227 971 2798 4190 4346 282 185 164 270 4279 3883 490 772 3488 1745 1595 1529 0 0 0 t 0 0 0 1099 833 1161 258 210 134 3961 92 132 4101 262 278 347 789 348 801 1270 931 0 0 0

oligos_6nt_mkv4_m1_rc_shift3 (oligos_6nt_mkv4_m1_rc)
; positions_6nt_m4 versus oligos_6nt_mkv4_m1_rc; m=8/11; ncol2=15; w=0; offset=0; strand=R; shift=3; score=0.587739; ---sccAGGTCCTGgcag------ ; cor=; Ncor= a 0 0 0 1252 1316 1177 5293 187 168 987 105 102 132 360 734 1561 2432 985 0 0 0 0 0 0 c 0 0 0 1809 2513 4056 303 151 189 288 6262 6311 333 240 970 3486 1302 1388 0 0 0 0 0 0 g 0 0 0 1973 1541 754 761 6148 6120 307 166 107 191 5608 4168 834 1295 3254 0 0 0 0 0 0 t 0 0 0 1614 1278 661 291 162 171 5066 115 128 5992 440 776 767 1619 1021 0 0 0 0 0 0

positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_6nt_m4 versus positions_7nt_m5; m=9/11; ncol2=15; w=-1; offset=-1; strand=D; shift=2; score=0.549186; --tkmCAGGACCTGgva------- ; cor=; Ncor= a 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 0 0 0 0 0 0 0 c 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 0 0 0 0 0 0 0 g 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 0 0 0 0 0 0 0 t 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393 0 0 0 0 0 0 0

positions_7nt_m4_shift2 (positions_7nt_m4)
; positions_6nt_m4 versus positions_7nt_m4; m=10/11; ncol2=15; w=-1; offset=-1; strand=D; shift=2; score=0.545308; --tksCAGGACCTGgva------- ; cor=; Ncor= a 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 0 0 0 0 0 0 0 c 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 0 0 0 0 0 0 0 g 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 0 0 0 0 0 0 0 t 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398 0 0 0 0 0 0 0

oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)
; positions_6nt_m4 versus oligos_7nt_mkv5_m1_rc; m=11/11; ncol2=16; w=-1; offset=-1; strand=R; shift=2; score=0.522145; --tscCAGGTCCTGGaag------ ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0 0 0 0

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; mgAGACCAsv ; Alignment reference a 721 660 2498 7 2679 18 9 2502 484 744 c 763 601 132 54 6 2610 2462 39 692 732 g 569 1007 25 2530 6 3 159 140 879 747 t 648 433 46 110 10 70 71 20 646 478

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; mgAGACCAsv ; cor=; Ncor= a 721 660 2498 7 2679 18 9 2502 484 744 c 763 601 132 54 6 2610 2462 39 692 732 g 569 1007 25 2530 6 3 159 140 879 747 t 648 433 46 110 10 70 71 20 646 478

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 12 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=24; shift=0; ncol=24; sskgscAGGTCCTGsCAGGacybr ; Alignment reference a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; sskgscAGGTCCTGsCAGGacybr ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282

positions_6nt_m2_shift2 (positions_6nt_m2)
; positions_6nt_m3 versus positions_6nt_m2; m=2/11; ncol2=24; w=0; offset=2; strand=D; shift=2; score=0.815372; --ssccaGGTCCTGcCAGGaCCyk ; cor=; Ncor= a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365

positions_6nt_m4_shift3 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=3/11; ncol2=21; w=0; offset=3; strand=D; shift=3; score=0.808129; ---kcmAGGACCTGcCAGGACyyk ; cor=; Ncor= a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m3 versus positions_6nt_m1; m=4/11; ncol2=24; w=0; offset=2; strand=D; shift=2; score=0.779591; --ssccaGGtCCTGcCAGGACCTg ; cor=; Ncor= a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148

positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)
; positions_6nt_m3 versus positions_7nt_m1_rc; m=5/11; ncol2=19; w=0; offset=2; strand=R; shift=2; score=0.705577; --ksccAGGTCCTGGcaggks--- ; cor=; Ncor= a 0 0 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 1273 0 0 0 c 0 0 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 1371 0 0 0 g 0 0 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 1507 0 0 0 t 0 0 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470 1004 0 0 0

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; positions_6nt_m3 versus positions_7nt_m2_rc; m=6/11; ncol2=18; w=0; offset=3; strand=R; shift=3; score=0.627027; ---ssmrGGTCCTGGcaGsks--- ; cor=; Ncor= a 0 0 0 915 987 1240 1472 234 162 313 80 89 136 143 317 1142 2681 398 1017 914 1143 0 0 0 c 0 0 0 1466 1791 1466 310 204 196 282 4481 4453 331 154 360 2859 596 604 1275 1059 1235 0 0 0 g 0 0 0 1358 1227 971 2798 4190 4346 282 185 164 270 4279 3883 490 772 3488 1745 1595 1529 0 0 0 t 0 0 0 1099 833 1161 258 210 134 3961 92 132 4101 262 278 347 789 348 801 1270 931 0 0 0

oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)
; positions_6nt_m3 versus oligos_7nt_mkv5_m1_rc; m=7/11; ncol2=16; w=0; offset=2; strand=R; shift=2; score=0.581076; --tscCAGGTCCTGGaag------ ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0 0 0 0

positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)
; positions_6nt_m3 versus positions_7nt_m4_rc; m=8/11; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.580644; --tbcCAGGTCCTGsma------- ; cor=; Ncor= a 0 0 1398 1120 1041 781 5554 160 149 1077 136 121 126 330 939 1868 2080 0 0 0 0 0 0 0 c 0 0 1538 1681 3078 4759 185 150 217 337 5902 5966 341 290 2429 1993 1335 0 0 0 0 0 0 0 g 0 0 1482 1882 1208 416 406 5860 5792 271 153 92 152 5249 2091 1189 1473 0 0 0 0 0 0 0 t 0 0 1887 1622 978 349 160 135 147 4620 114 126 5686 436 846 1255 1417 0 0 0 0 0 0 0

oligos_6nt_mkv4_m1_rc_shift3 (oligos_6nt_mkv4_m1_rc)
; positions_6nt_m3 versus oligos_6nt_mkv4_m1_rc; m=9/11; ncol2=15; w=0; offset=3; strand=R; shift=3; score=0.57632; ---sccAGGTCCTGgcag------ ; cor=; Ncor= a 0 0 0 1252 1316 1177 5293 187 168 987 105 102 132 360 734 1561 2432 985 0 0 0 0 0 0 c 0 0 0 1809 2513 4056 303 151 189 288 6262 6311 333 240 970 3486 1302 1388 0 0 0 0 0 0 g 0 0 0 1973 1541 754 761 6148 6120 307 166 107 191 5608 4168 834 1295 3254 0 0 0 0 0 0 t 0 0 0 1614 1278 661 291 162 171 5066 115 128 5992 440 776 767 1619 1021 0 0 0 0 0 0

positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)
; positions_6nt_m3 versus positions_7nt_m5_rc; m=10/11; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.574713; --tbcCAGGTCCTGkma------- ; cor=; Ncor= a 0 0 1393 1091 1058 802 5458 163 175 1056 111 118 115 334 946 1777 2134 0 0 0 0 0 0 0 c 0 0 1444 1618 2922 4547 150 118 175 271 5735 5792 240 270 1156 1918 1219 0 0 0 0 0 0 0 g 0 0 1372 1833 1155 399 342 5695 5621 239 163 89 116 5071 2112 1273 1297 0 0 0 0 0 0 0 t 0 0 1907 1574 981 368 166 140 145 4550 107 117 5645 441 1902 1148 1466 0 0 0 0 0 0 0

positions_7nt_m3_shift5 (positions_7nt_m3)
; positions_6nt_m3 versus positions_7nt_m3; m=11/11; ncol2=16; w=0; offset=5; strand=D; shift=5; score=0.550542; -----mrrGTCCTGGcAGgks--- ; cor=; Ncor= a 0 0 0 0 0 1181 1555 1896 179 193 80 111 120 121 190 856 2849 298 946 870 984 0 0 0 c 0 0 0 0 0 1252 877 295 123 187 3859 3869 178 98 231 2804 420 325 1038 812 1089 0 0 0 g 0 0 0 0 0 956 1230 1589 3680 198 139 83 135 3729 3563 312 371 3264 1488 1295 1272 0 0 0 t 0 0 0 0 0 785 512 394 192 3596 96 111 3741 226 190 202 534 287 702 1197 829 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; ssAGCTGCsg ; Alignment reference a 946 795 3701 42 51 43 97 8 906 870 c 1088 1552 365 47 4131 326 24 4202 1215 995 g 1441 1236 134 4088 38 279 4106 6 1249 1434 t 772 664 47 70 27 3599 20 31 877 948

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssAGCTGCsg ; cor=; Ncor= a 946 795 3701 42 51 43 97 8 906 870 c 1088 1552 365 47 4131 326 24 4202 1215 995 g 1441 1236 134 4088 38 279 4106 6 1249 1434 t 772 664 47 70 27 3599 20 31 877 948

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=12; shift=0; ncol=12; wwATTTTTAwww ; Alignment reference a 2840 2634 8491 518 616 540 489 727 8627 4700 3603 3277 c 1404 2014 262 322 249 227 418 398 251 1131 1444 1747 g 2013 1362 378 313 418 295 386 257 310 1188 1470 1524 t 3379 3626 505 8483 8353 8574 8343 8254 448 2617 3119 3088

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwATTTTTAwww ; cor=; Ncor= a 2840 2634 8491 518 616 540 489 727 8627 4700 3603 3277 c 1404 2014 262 322 249 227 418 398 251 1131 1444 1747 g 2013 1362 378 313 418 295 386 257 310 1188 1470 1524 t 3379 3626 505 8483 8353 8574 8343 8254 448 2617 3119 3088

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssccaGGtCCTGcCAGGACCTgss ; Alignment reference a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157

positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssccaGGtCCTGcCAGGACCTgss ; cor=; Ncor= a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157

positions_6nt_m2_shift2 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.961589; --ssccaGGTCCTGcCAGGaCCykgs ; cor=; Ncor= a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 196 245 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 248 306 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 390 313 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365 209 179

positions_6nt_m4_shift3 (positions_6nt_m4)
; positions_6nt_m1 versus positions_6nt_m4; m=3/11; ncol2=21; w=0; offset=1; strand=D; shift=3; score=0.782281; ---kcmAGGACCTGcCAGGACyyk-- ; cor=; Ncor= a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 0 0 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 0 0 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 0 0 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324 0 0

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m1 versus positions_6nt_m3; m=4/11; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.779591; sskgscAGGTCCTGsCAGGacybr-- ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 0 0 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 0 0 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 0 0 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282 0 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=5/11; ncol2=19; w=0; offset=6; strand=D; shift=8; score=0.644624; --------smcctgCCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 c 0 0 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 g 0 0 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 t 0 0 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938

positions_7nt_m2_shift8 (positions_7nt_m2)
; positions_6nt_m1 versus positions_7nt_m2; m=6/11; ncol2=18; w=0; offset=6; strand=D; shift=8; score=0.643196; --------smsCtgCCAGGACCykss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915

oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)
; positions_6nt_m1 versus oligos_6nt_mkv4_m1; m=7/11; ncol2=15; w=0; offset=9; strand=D; shift=11; score=0.578048; -----------ctgcCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 c 0 0 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 g 0 0 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 t 0 0 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252

positions_7nt_m3_rc_shift8 (positions_7nt_m3_rc)
; positions_6nt_m1 versus positions_7nt_m3_rc; m=8/11; ncol2=16; w=0; offset=6; strand=R; shift=8; score=0.570875; --------smcCTgCCAGGACyyk-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 c 0 0 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 g 0 0 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 t 0 0 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0

positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)
; positions_6nt_m1 versus positions_7nt_m4_rc; m=9/11; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.550744; --tbcCAGGTCCTGsma--------- ; cor=; Ncor= a 0 0 1398 1120 1041 781 5554 160 149 1077 136 121 126 330 939 1868 2080 0 0 0 0 0 0 0 0 0 c 0 0 1538 1681 3078 4759 185 150 217 337 5902 5966 341 290 2429 1993 1335 0 0 0 0 0 0 0 0 0 g 0 0 1482 1882 1208 416 406 5860 5792 271 153 92 152 5249 2091 1189 1473 0 0 0 0 0 0 0 0 0 t 0 0 1887 1622 978 349 160 135 147 4620 114 126 5686 436 846 1255 1417 0 0 0 0 0 0 0 0 0

positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)
; positions_6nt_m1 versus positions_7nt_m5_rc; m=10/11; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.539793; --tbcCAGGTCCTGkma--------- ; cor=; Ncor= a 0 0 1393 1091 1058 802 5458 163 175 1056 111 118 115 334 946 1777 2134 0 0 0 0 0 0 0 0 0 c 0 0 1444 1618 2922 4547 150 118 175 271 5735 5792 240 270 1156 1918 1219 0 0 0 0 0 0 0 0 0 g 0 0 1372 1833 1155 399 342 5695 5621 239 163 89 116 5071 2112 1273 1297 0 0 0 0 0 0 0 0 0 t 0 0 1907 1574 981 368 166 140 145 4550 107 117 5645 441 1902 1148 1466 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)
; positions_6nt_m1 versus oligos_7nt_mkv5_m1_rc; m=11/11; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.535571; --tscCAGGTCCTGGaag-------- ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 0 0 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 0 0 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 0 0 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift5 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift5 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=16; shift=5; ncol=21; -----mrrGTCCTGGcAGgks ; Alignment reference a 0 0 0 0 0 1181 1555 1896 179 193 80 111 120 121 190 856 2849 298 946 870 984 c 0 0 0 0 0 1252 877 295 123 187 3859 3869 178 98 231 2804 420 325 1038 812 1089 g 0 0 0 0 0 956 1230 1589 3680 198 139 83 135 3729 3563 312 371 3264 1488 1295 1272 t 0 0 0 0 0 785 512 394 192 3596 96 111 3741 226 190 202 534 287 702 1197 829

positions_7nt_m3_shift5 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/12; ncol2=16; w=0; offset=0; strand=D; shift=5; score= 1; -----mrrGTCCTGGcAGgks ; cor=; Ncor= a 0 0 0 0 0 1181 1555 1896 179 193 80 111 120 121 190 856 2849 298 946 870 984 c 0 0 0 0 0 1252 877 295 123 187 3859 3869 178 98 231 2804 420 325 1038 812 1089 g 0 0 0 0 0 956 1230 1589 3680 198 139 83 135 3729 3563 312 371 3264 1488 1295 1272 t 0 0 0 0 0 785 512 394 192 3596 96 111 3741 226 190 202 534 287 702 1197 829

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; positions_7nt_m3 versus positions_7nt_m2_rc; m=2/12; ncol2=18; w=-2; offset=-2; strand=R; shift=3; score=0.837466; ---ssmrGGTCCTGGcaGsks ; cor=; Ncor= a 0 0 0 915 987 1240 1472 234 162 313 80 89 136 143 317 1142 2681 398 1017 914 1143 c 0 0 0 1466 1791 1466 310 204 196 282 4481 4453 331 154 360 2859 596 604 1275 1059 1235 g 0 0 0 1358 1227 971 2798 4190 4346 282 185 164 270 4279 3883 490 772 3488 1745 1595 1529 t 0 0 0 1099 833 1161 258 210 134 3961 92 132 4101 262 278 347 789 348 801 1270 931

positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)
; positions_7nt_m3 versus positions_7nt_m1_rc; m=3/12; ncol2=19; w=-3; offset=-3; strand=R; shift=2; score=0.753606; --ksccAGGTCCTGGcaggks ; cor=; Ncor= a 0 0 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 1273 c 0 0 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 1371 g 0 0 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 1507 t 0 0 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470 1004

positions_6nt_m4_rc_shift5 (positions_6nt_m4_rc)
; positions_7nt_m3 versus positions_6nt_m4_rc; m=4/12; ncol2=21; w=0; offset=0; strand=R; shift=5; score=0.664718; -----mrrGTCCTGgCAGGTC ; cor=; Ncor= a 0 0 0 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 c 0 0 0 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 g 0 0 0 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 t 0 0 0 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60

oligos_6nt_mkv4_m1_rc_shift3 (oligos_6nt_mkv4_m1_rc)
; positions_7nt_m3 versus oligos_6nt_mkv4_m1_rc; m=5/12; ncol2=15; w=-2; offset=-2; strand=R; shift=3; score=0.630754; ---sccAGGTCCTGgcag--- ; cor=; Ncor= a 0 0 0 1252 1316 1177 5293 187 168 987 105 102 132 360 734 1561 2432 985 0 0 0 c 0 0 0 1809 2513 4056 303 151 189 288 6262 6311 333 240 970 3486 1302 1388 0 0 0 g 0 0 0 1973 1541 754 761 6148 6120 307 166 107 191 5608 4168 834 1295 3254 0 0 0 t 0 0 0 1614 1278 661 291 162 171 5066 115 128 5992 440 776 767 1619 1021 0 0 0

oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)
; positions_7nt_m3 versus oligos_7nt_mkv5_m1_rc; m=6/12; ncol2=16; w=-3; offset=-3; strand=R; shift=2; score=0.571239; --tscCAGGTCCTGGaag--- ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; positions_7nt_m3 versus positions_6nt_m1_rc; m=7/12; ncol2=24; w=-2; offset=-2; strand=R; shift=3; score=0.570875; ---sscAGGTCCTGgCAGGaC ; cor=; Ncor= a 0 0 0 157 195 148 654 59 35 119 46 21 46 44 97 133 801 25 64 580 102 c 0 0 0 289 329 606 68 65 86 94 791 881 64 35 196 725 45 16 93 98 673 g 0 0 0 283 242 106 130 753 765 78 74 24 49 763 566 55 63 888 737 131 119 t 0 0 0 226 189 95 103 78 69 664 44 29 796 113 96 42 46 26 61 146 61

positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)
; positions_7nt_m3 versus positions_6nt_m2_rc; m=8/12; ncol2=24; w=-2; offset=-2; strand=R; shift=3; score=0.564903; ---scmrGGtCCTGgCAGGAC ; cor=; Ncor= a 0 0 0 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 c 0 0 0 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 g 0 0 0 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 t 0 0 0 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_7nt_m3 versus positions_6nt_m3; m=9/12; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.550542; sskgscAGGTCCTGsCAGGac ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93

oligos_7nt_mkv5_m5_shift9 (oligos_7nt_mkv5_m5)
; positions_7nt_m3 versus oligos_7nt_mkv5_m5; m=10/12; ncol2=11; w=0; offset=4; strand=D; shift=9; score=0.540431; ---------tcCTGGAAGrr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1255 1201 172 173 194 111 4862 4822 97 1386 1485 0 c 0 0 0 0 0 0 0 0 0 948 1980 4959 253 115 81 135 194 122 1180 1147 0 g 0 0 0 0 0 0 0 0 0 1161 1083 146 312 4977 4760 121 130 4813 1469 1402 0 t 0 0 0 0 0 0 0 0 0 1986 1086 73 4612 64 398 232 204 318 1315 1316 0

positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)
; positions_7nt_m3 versus positions_7nt_m5_rc; m=11/12; ncol2=15; w=-3; offset=-3; strand=R; shift=2; score=0.506642; --tbcCAGGTCCTGkma---- ; cor=; Ncor= a 0 0 1393 1091 1058 802 5458 163 175 1056 111 118 115 334 946 1777 2134 0 0 0 0 c 0 0 1444 1618 2922 4547 150 118 175 271 5735 5792 240 270 1156 1918 1219 0 0 0 0 g 0 0 1372 1833 1155 399 342 5695 5621 239 163 89 116 5071 2112 1273 1297 0 0 0 0 t 0 0 1907 1574 981 368 166 140 145 4550 107 117 5645 441 1902 1148 1466 0 0 0 0

positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)
; positions_7nt_m3 versus positions_7nt_m4_rc; m=12/12; ncol2=15; w=-3; offset=-3; strand=R; shift=2; score=0.502365; --tbcCAGGTCCTGsma---- ; cor=; Ncor= a 0 0 1398 1120 1041 781 5554 160 149 1077 136 121 126 330 939 1868 2080 0 0 0 0 c 0 0 1538 1681 3078 4759 185 150 217 337 5902 5966 341 290 2429 1993 1335 0 0 0 0 g 0 0 1482 1882 1208 416 406 5860 5792 271 153 92 152 5249 2091 1189 1473 0 0 0 0 t 0 0 1887 1622 978 349 160 135 147 4620 114 126 5686 436 846 1255 1417 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift9 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift9 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------tkmCAGGACCTGgva ; Alignment reference a 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393

positions_7nt_m5_shift9 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score= 1; ---------tkmCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393

positions_7nt_m4_shift9 (positions_7nt_m4)
; positions_7nt_m5 versus positions_7nt_m4; m=2/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score=0.992438; ---------tksCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398

oligos_7nt_mkv5_m1_shift8 (oligos_7nt_mkv5_m1)
; positions_7nt_m5 versus oligos_7nt_mkv5_m1; m=3/11; ncol2=16; w=-1; offset=-1; strand=D; shift=8; score= 0.9065; --------cttCCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; positions_7nt_m5 versus oligos_6nt_mkv4_m1; m=4/11; ncol2=15; w=-1; offset=-1; strand=D; shift=8; score=0.853916; --------ctgcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 0 c 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 0 g 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 0 t 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252 0

positions_7nt_m1_shift5 (positions_7nt_m1)
; positions_7nt_m5 versus positions_7nt_m1; m=5/11; ncol2=19; w=-4; offset=-4; strand=D; shift=5; score=0.762596; -----smcctgCCAGGACCTggsm ; cor=; Ncor= a 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076

positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_7nt_m5 versus positions_7nt_m2; m=6/11; ncol2=18; w=-4; offset=-4; strand=D; shift=5; score=0.629259; -----smsCtgCCAGGACCykss- ; cor=; Ncor= a 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 0 c 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 0 g 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 0 t 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915 0

positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)
; positions_7nt_m5 versus positions_6nt_m3_rc; m=7/11; ncol2=24; w=-7; offset=-7; strand=R; shift=2; score=0.574713; --yvrgtCCTGsCAGGACCTgscm ; cor=; Ncor= a 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 365 c 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 297 g 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 262 t 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195 230

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m5 versus positions_6nt_m2_rc; m=8/11; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.555952; scmrGGtCCTGgCAGGACCtggss ; cor=; Ncor= a 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 242 c 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 292 g 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 275 t 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173 234

positions_6nt_m4_shift10 (positions_6nt_m4)
; positions_7nt_m5 versus positions_6nt_m4; m=9/11; ncol2=21; w=0; offset=1; strand=D; shift=10; score=0.549186; ----------kcmAGGACCTGcCA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 c 0 0 0 0 0 0 0 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 g 0 0 0 0 0 0 0 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 t 0 0 0 0 0 0 0 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; positions_7nt_m5 versus positions_6nt_m1_rc; m=10/11; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.539793; sscAGGTCCTGgCAGGaCCtggss ; cor=; Ncor= a 157 195 148 654 59 35 119 46 21 46 44 97 133 801 25 64 580 102 114 144 122 207 221 237 c 289 329 606 68 65 86 94 791 881 64 35 196 725 45 16 93 98 673 676 137 118 231 262 270 g 283 242 106 130 753 765 78 74 24 49 763 566 55 63 888 737 131 119 101 92 583 328 290 247 t 226 189 95 103 78 69 664 44 29 796 113 96 42 46 26 61 146 61 64 582 132 189 182 201

positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)
; positions_7nt_m5 versus positions_7nt_m3_rc; m=11/11; ncol2=16; w=-4; offset=-4; strand=R; shift=5; score=0.506642; -----smcCTgCCAGGACyyk--- ; cor=; Ncor= a 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 0 c 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 0 g 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 0 t 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; avTGGACCAyw ; Alignment reference a 883 908 143 158 209 2778 154 137 2714 523 876 c 677 769 80 35 212 55 2529 2527 100 914 647 g 732 786 131 2711 2323 55 64 105 85 745 712 t 698 527 2636 86 246 102 243 221 91 808 755

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; avTGGACCAyw ; cor=; Ncor= a 883 908 143 158 209 2778 154 137 2714 523 876 c 677 769 80 35 212 55 2529 2527 100 914 647 g 732 786 131 2711 2323 55 64 105 85 745 712 t 698 527 2636 86 246 102 243 221 91 808 755

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift6 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift6 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=19; shift=6; ncol=25; ------smcctgCCAGGACCTggsm ; Alignment reference a 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076

positions_7nt_m1_shift6 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/12; ncol2=19; w=0; offset=0; strand=D; shift=6; score= 1; ------smcctgCCAGGACCTggsm ; cor=; Ncor= a 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076

positions_7nt_m2_shift6 (positions_7nt_m2)
; positions_7nt_m1 versus positions_7nt_m2; m=2/12; ncol2=18; w=0; offset=0; strand=D; shift=6; score=0.878094; ------smsCtgCCAGGACCykss- ; cor=; Ncor= a 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 0 c 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 0 g 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 0 t 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915 0

oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)
; positions_7nt_m1 versus oligos_7nt_mkv5_m1; m=3/12; ncol2=16; w=0; offset=3; strand=D; shift=9; score=0.81887; ---------cttCCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086

oligos_6nt_mkv4_m1_shift9 (oligos_6nt_mkv4_m1)
; positions_7nt_m1 versus oligos_6nt_mkv4_m1; m=4/12; ncol2=15; w=0; offset=3; strand=D; shift=9; score=0.781424; ---------ctgcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 0 c 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 0 g 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 0 t 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252 0

positions_7nt_m5_shift10 (positions_7nt_m5)
; positions_7nt_m1 versus positions_7nt_m5; m=5/12; ncol2=15; w=0; offset=4; strand=D; shift=10; score=0.762596; ----------tkmCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393

positions_7nt_m4_shift10 (positions_7nt_m4)
; positions_7nt_m1 versus positions_7nt_m4; m=6/12; ncol2=15; w=0; offset=4; strand=D; shift=10; score=0.75964; ----------tksCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398

positions_7nt_m3_rc_shift6 (positions_7nt_m3_rc)
; positions_7nt_m1 versus positions_7nt_m3_rc; m=7/12; ncol2=16; w=0; offset=0; strand=R; shift=6; score=0.753606; ------smcCTgCCAGGACyyk--- ; cor=; Ncor= a 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 0 c 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 0 g 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 0 t 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0 0

positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)
; positions_7nt_m1 versus positions_6nt_m3_rc; m=8/12; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.705577; ---yvrgtCCTGsCAGGACCTgscm ; cor=; Ncor= a 0 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 365 c 0 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 297 g 0 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 262 t 0 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195 230

positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)
; positions_7nt_m1 versus positions_6nt_m2_rc; m=9/12; ncol2=24; w=-5; offset=-5; strand=R; shift=1; score=0.667982; -scmrGGtCCTGgCAGGACCtggss ; cor=; Ncor= a 0 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 242 c 0 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 292 g 0 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 275 t 0 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173 234

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=10/12; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.644624; ssccaGGtCCTGcCAGGACCTgss- ; cor=; Ncor= a 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 0 c 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 0 g 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 0 t 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157 0

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; positions_7nt_m1 versus positions_6nt_m4_rc; m=11/12; ncol2=21; w=-3; offset=-3; strand=R; shift=3; score=0.629275; ---mrrGTCCTGgCAGGTCCTkgm- ; cor=; Ncor= a 0 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 90 88 168 253 303 0 c 0 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 933 107 176 238 342 0 g 0 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 57 88 426 403 274 0 t 0 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60 71 868 381 257 232 0

oligos_7nt_mkv5_m5_rc_shift7 (oligos_7nt_mkv5_m5_rc)
; positions_7nt_m1 versus oligos_7nt_mkv5_m5_rc; m=12/12; ncol2=11; w=0; offset=1; strand=R; shift=7; score=0.446516; -------yyCTTCCAGga------- ; cor=; Ncor= a 0 0 0 0 0 0 0 1316 1315 318 204 232 398 64 4612 73 1086 1986 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1402 1469 4813 130 121 4760 4977 312 146 1083 1161 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1147 1180 122 194 135 81 115 253 4959 1980 948 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 1485 1386 97 4822 4862 111 194 173 172 1201 1255 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; ssCGCCCGss ; Alignment reference a 924 1162 169 253 158 289 158 211 819 1163 c 3163 2279 6381 241 5982 5906 5883 628 2801 2379 g 2043 2851 458 6433 764 606 755 6116 2528 2657 t 1014 852 136 217 240 343 348 189 996 945

oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCGss ; cor=; Ncor= a 924 1162 169 253 158 289 158 211 819 1163 c 3163 2279 6381 241 5982 5906 5883 628 2801 2379 g 2043 2851 458 6433 764 606 755 6116 2528 2657 t 1014 852 136 217 240 343 348 189 996 945

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; bcTGAGGACAgr ; Alignment reference a 920 945 244 141 3677 219 198 3463 299 3673 864 1209 c 1067 1247 276 152 76 58 152 213 3531 230 1000 760 g 1079 1019 243 3750 213 3736 3692 170 216 113 1357 1155 t 1088 943 3391 111 188 141 112 308 108 138 933 1030

oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; bcTGAGGACAgr ; cor=; Ncor= a 920 945 244 141 3677 219 198 3463 299 3673 864 1209 c 1067 1247 276 152 76 58 152 213 3531 230 1000 760 g 1079 1019 243 3750 213 3736 3692 170 216 113 1357 1155 t 1088 943 3391 111 188 141 112 308 108 138 933 1030

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift6 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift6 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=18; shift=6; ncol=24; ------smsCtgCCAGGACCykss ; Alignment reference a 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915

positions_7nt_m2_shift6 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/12; ncol2=18; w=0; offset=0; strand=D; shift=6; score= 1; ------smsCtgCCAGGACCykss ; cor=; Ncor= a 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915

positions_7nt_m1_shift6 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=2/12; ncol2=19; w=0; offset=0; strand=D; shift=6; score=0.878094; ------smcctgCCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 c 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 g 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 t 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938

positions_7nt_m3_rc_shift6 (positions_7nt_m3_rc)
; positions_7nt_m2 versus positions_7nt_m3_rc; m=3/12; ncol2=16; w=0; offset=0; strand=R; shift=6; score=0.837466; ------smcCTgCCAGGACyyk-- ; cor=; Ncor= a 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 c 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 g 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 t 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0

oligos_6nt_mkv4_m1_shift9 (oligos_6nt_mkv4_m1)
; positions_7nt_m2 versus oligos_6nt_mkv4_m1; m=4/12; ncol2=15; w=0; offset=3; strand=D; shift=9; score=0.767207; ---------ctgcCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 c 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 g 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 t 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252

oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)
; positions_7nt_m2 versus oligos_7nt_mkv5_m1; m=5/12; ncol2=16; w=0; offset=3; strand=D; shift=9; score=0.696804; ---------cttCCAGGACCTGgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 c 0 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 g 0 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 t 0 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_7nt_m2 versus positions_6nt_m2; m=6/12; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.644947; ssccaGGTCCTGcCAGGaCCykgs ; cor=; Ncor= a 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 196 245 c 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 248 306 g 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 390 313 t 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365 209 179

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m2 versus positions_6nt_m1; m=7/12; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.643196; ssccaGGtCCTGcCAGGACCTgss ; cor=; Ncor= a 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157

positions_7nt_m5_shift10 (positions_7nt_m5)
; positions_7nt_m2 versus positions_7nt_m5; m=8/12; ncol2=15; w=0; offset=4; strand=D; shift=10; score=0.629259; ----------tkmCAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 c 0 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 g 0 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 t 0 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091

positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)
; positions_7nt_m2 versus positions_6nt_m3_rc; m=9/12; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.627027; ---yvrgtCCTGsCAGGACCTgsc ; cor=; Ncor= a 0 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 c 0 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 g 0 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 t 0 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195

positions_7nt_m4_shift10 (positions_7nt_m4)
; positions_7nt_m2 versus positions_7nt_m4; m=10/12; ncol2=15; w=0; offset=4; strand=D; shift=10; score=0.62602; ----------tksCAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 c 0 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 g 0 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 t 0 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120

positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)
; positions_7nt_m2 versus positions_6nt_m4_rc; m=11/12; ncol2=21; w=-3; offset=-3; strand=R; shift=3; score=0.610907; ---mrrGTCCTGgCAGGTCCTkgm ; cor=; Ncor= a 0 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 90 88 168 253 303 c 0 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 933 107 176 238 342 g 0 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 57 88 426 403 274 t 0 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60 71 868 381 257 232

oligos_7nt_mkv5_m5_rc_shift7 (oligos_7nt_mkv5_m5_rc)
; positions_7nt_m2 versus oligos_7nt_mkv5_m5_rc; m=12/12; ncol2=11; w=0; offset=1; strand=R; shift=7; score= 0.4754; -------yyCTTCCAGga------ ; cor=; Ncor= a 0 0 0 0 0 0 0 1316 1315 318 204 232 398 64 4612 73 1086 1986 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1402 1469 4813 130 121 4760 4977 312 146 1083 1161 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1147 1180 122 194 135 81 115 253 4959 1980 948 0 0 0 0 0 0 t 0 0 0 0 0 0 0 1485 1386 97 4822 4862 111 194 173 172 1201 1255 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift9 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift9 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------tksCAGGACCTGgva ; Alignment reference a 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398

positions_7nt_m4_shift9 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score= 1; ---------tksCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398

positions_7nt_m5_shift9 (positions_7nt_m5)
; positions_7nt_m4 versus positions_7nt_m5; m=2/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score=0.992438; ---------tkmCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393

oligos_7nt_mkv5_m1_shift8 (oligos_7nt_mkv5_m1)
; positions_7nt_m4 versus oligos_7nt_mkv5_m1; m=3/11; ncol2=16; w=-1; offset=-1; strand=D; shift=8; score=0.904242; --------cttCCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; positions_7nt_m4 versus oligos_6nt_mkv4_m1; m=4/11; ncol2=15; w=-1; offset=-1; strand=D; shift=8; score=0.851069; --------ctgcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 0 c 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 0 g 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 0 t 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252 0

positions_7nt_m1_shift5 (positions_7nt_m1)
; positions_7nt_m4 versus positions_7nt_m1; m=5/11; ncol2=19; w=-4; offset=-4; strand=D; shift=5; score=0.75964; -----smcctgCCAGGACCTggsm ; cor=; Ncor= a 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076

positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_7nt_m4 versus positions_7nt_m2; m=6/11; ncol2=18; w=-4; offset=-4; strand=D; shift=5; score=0.62602; -----smsCtgCCAGGACCykss- ; cor=; Ncor= a 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 0 c 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 0 g 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 0 t 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915 0

positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)
; positions_7nt_m4 versus positions_6nt_m3_rc; m=7/11; ncol2=24; w=-7; offset=-7; strand=R; shift=2; score=0.580644; --yvrgtCCTGsCAGGACCTgscm ; cor=; Ncor= a 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 365 c 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 297 g 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 262 t 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195 230

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m4 versus positions_6nt_m2_rc; m=8/11; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.565337; scmrGGtCCTGgCAGGACCtggss ; cor=; Ncor= a 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 242 c 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 292 g 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 275 t 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173 234

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; positions_7nt_m4 versus positions_6nt_m1_rc; m=9/11; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.550744; sscAGGTCCTGgCAGGaCCtggss ; cor=; Ncor= a 157 195 148 654 59 35 119 46 21 46 44 97 133 801 25 64 580 102 114 144 122 207 221 237 c 289 329 606 68 65 86 94 791 881 64 35 196 725 45 16 93 98 673 676 137 118 231 262 270 g 283 242 106 130 753 765 78 74 24 49 763 566 55 63 888 737 131 119 101 92 583 328 290 247 t 226 189 95 103 78 69 664 44 29 796 113 96 42 46 26 61 146 61 64 582 132 189 182 201

positions_6nt_m4_shift10 (positions_6nt_m4)
; positions_7nt_m4 versus positions_6nt_m4; m=10/11; ncol2=21; w=0; offset=1; strand=D; shift=10; score=0.545308; ----------kcmAGGACCTGcCA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 c 0 0 0 0 0 0 0 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 g 0 0 0 0 0 0 0 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 t 0 0 0 0 0 0 0 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81

positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)
; positions_7nt_m4 versus positions_7nt_m3_rc; m=11/11; ncol2=16; w=-4; offset=-4; strand=R; shift=5; score=0.502365; -----smcCTgCCAGGACyyk--- ; cor=; Ncor= a 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 0 c 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 0 g 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 0 t 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 2 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; yvTGGACAbr ; Alignment reference a 652 848 25 73 50 2788 4 2632 494 870 c 785 728 157 118 57 16 2763 39 826 614 g 575 803 48 2651 2546 9 12 178 731 753 t 847 480 2629 17 206 46 80 10 808 622

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; yvTGGACAbr ; cor=; Ncor= a 652 848 25 73 50 2788 4 2632 494 870 c 785 728 157 118 57 16 2763 39 826 614 g 575 803 48 2651 2546 9 12 178 731 753 t 847 480 2629 17 206 46 80 10 808 622

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift8 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift8 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=16; shift=8; ncol=24; --------cttCCAGGACCTGgsa ; Alignment reference a 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086

oligos_7nt_mkv5_m1_shift8 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/12; ncol2=16; w=0; offset=0; strand=D; shift=8; score= 1; --------cttCCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086

oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1; m=2/12; ncol2=15; w=0; offset=0; strand=D; shift=8; score=0.913917; --------ctgcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 0 c 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 0 g 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 0 t 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252 0

positions_7nt_m5_shift9 (positions_7nt_m5)
; oligos_7nt_mkv5_m1 versus positions_7nt_m5; m=3/12; ncol2=15; w=0; offset=1; strand=D; shift=9; score= 0.9065; ---------tkmCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393

positions_7nt_m4_shift9 (positions_7nt_m4)
; oligos_7nt_mkv5_m1 versus positions_7nt_m4; m=4/12; ncol2=15; w=0; offset=1; strand=D; shift=9; score=0.904242; ---------tksCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398

positions_7nt_m1_shift5 (positions_7nt_m1)
; oligos_7nt_mkv5_m1 versus positions_7nt_m1; m=5/12; ncol2=19; w=-3; offset=-3; strand=D; shift=5; score=0.81887; -----smcctgCCAGGACCTggsm ; cor=; Ncor= a 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076

positions_7nt_m2_shift5 (positions_7nt_m2)
; oligos_7nt_mkv5_m1 versus positions_7nt_m2; m=6/12; ncol2=18; w=-3; offset=-3; strand=D; shift=5; score=0.696804; -----smsCtgCCAGGACCykss- ; cor=; Ncor= a 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 0 c 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 0 g 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 0 t 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915 0

positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)
; oligos_7nt_mkv5_m1 versus positions_6nt_m3_rc; m=7/12; ncol2=24; w=-6; offset=-6; strand=R; shift=2; score=0.581076; --yvrgtCCTGsCAGGACCTgscm ; cor=; Ncor= a 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 365 c 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 297 g 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 262 t 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195 230

positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)
; oligos_7nt_mkv5_m1 versus positions_7nt_m3_rc; m=8/12; ncol2=16; w=-3; offset=-3; strand=R; shift=5; score=0.571239; -----smcCTgCCAGGACyyk--- ; cor=; Ncor= a 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 0 c 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 0 g 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 0 t 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0 0

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; oligos_7nt_mkv5_m1 versus positions_6nt_m2_rc; m=9/12; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.556443; scmrGGtCCTGgCAGGACCtggss ; cor=; Ncor= a 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 242 c 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 292 g 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 275 t 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173 234

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; oligos_7nt_mkv5_m1 versus positions_6nt_m1_rc; m=10/12; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.535571; sscAGGTCCTGgCAGGaCCtggss ; cor=; Ncor= a 157 195 148 654 59 35 119 46 21 46 44 97 133 801 25 64 580 102 114 144 122 207 221 237 c 289 329 606 68 65 86 94 791 881 64 35 196 725 45 16 93 98 673 676 137 118 231 262 270 g 283 242 106 130 753 765 78 74 24 49 763 566 55 63 888 737 131 119 101 92 583 328 290 247 t 226 189 95 103 78 69 664 44 29 796 113 96 42 46 26 61 146 61 64 582 132 189 182 201

positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)
; oligos_7nt_mkv5_m1 versus positions_6nt_m4_rc; m=11/12; ncol2=21; w=-6; offset=-6; strand=R; shift=2; score=0.522145; --mrrGTCCTGgCAGGTCCTkgm- ; cor=; Ncor= a 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 90 88 168 253 303 0 c 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 933 107 176 238 342 0 g 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 57 88 426 403 274 0 t 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60 71 868 381 257 232 0

oligos_7nt_mkv5_m5_rc_shift6 (oligos_7nt_mkv5_m5_rc)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m5_rc; m=12/12; ncol2=11; w=-2; offset=-2; strand=R; shift=6; score=0.402914; ------yyCTTCCAGga------- ; cor=; Ncor= a 0 0 0 0 0 0 1316 1315 318 204 232 398 64 4612 73 1086 1986 0 0 0 0 0 0 0 c 0 0 0 0 0 0 1402 1469 4813 130 121 4760 4977 312 146 1083 1161 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1147 1180 122 194 135 81 115 253 4959 1980 948 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1485 1386 97 4822 4862 111 194 173 172 1201 1255 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift2 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssccaGGTCCTGcCAGGaCCykgs ; Alignment reference a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 196 245 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 248 306 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 390 313 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365 209 179
positions_6nt_m2_shift2 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssccaGGTCCTGcCAGGaCCykgs ; cor=; Ncor= a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 196 245 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 248 306 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 390 313 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365 209 179
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.961589; --ssccaGGtCCTGcCAGGACCTgss ; cor=; Ncor= a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m2 versus positions_6nt_m3; m=3/11; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.815372; sskgscAGGTCCTGsCAGGacybr-- ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 0 0 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 0 0 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 0 0 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282 0 0
positions_6nt_m4_shift3 (positions_6nt_m4)				; positions_6nt_m2 versus positions_6nt_m4; m=4/11; ncol2=21; w=0; offset=1; strand=D; shift=3; score=0.799923; ---kcmAGGACCTGcCAGGACyyk-- ; cor=; Ncor= a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 0 0 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 0 0 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 0 0 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324 0 0
positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)				; positions_6nt_m2 versus positions_7nt_m1_rc; m=5/11; ncol2=19; w=0; offset=0; strand=R; shift=2; score=0.667982; --ksccAGGTCCTGGcaggks----- ; cor=; Ncor= a 0 0 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 1273 0 0 0 0 0 c 0 0 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 1371 0 0 0 0 0 g 0 0 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 1507 0 0 0 0 0 t 0 0 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470 1004 0 0 0 0 0
positions_7nt_m2_shift8 (positions_7nt_m2)				; positions_6nt_m2 versus positions_7nt_m2; m=6/11; ncol2=18; w=0; offset=6; strand=D; shift=8; score=0.644947; --------smsCtgCCAGGACCykss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915
positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)				; positions_6nt_m2 versus positions_7nt_m4_rc; m=7/11; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.565337; --tbcCAGGTCCTGsma--------- ; cor=; Ncor= a 0 0 1398 1120 1041 781 5554 160 149 1077 136 121 126 330 939 1868 2080 0 0 0 0 0 0 0 0 0 c 0 0 1538 1681 3078 4759 185 150 217 337 5902 5966 341 290 2429 1993 1335 0 0 0 0 0 0 0 0 0 g 0 0 1482 1882 1208 416 406 5860 5792 271 153 92 152 5249 2091 1189 1473 0 0 0 0 0 0 0 0 0 t 0 0 1887 1622 978 349 160 135 147 4620 114 126 5686 436 846 1255 1417 0 0 0 0 0 0 0 0 0
positions_7nt_m3_rc_shift8 (positions_7nt_m3_rc)				; positions_6nt_m2 versus positions_7nt_m3_rc; m=8/11; ncol2=16; w=0; offset=6; strand=R; shift=8; score=0.564903; --------smcCTgCCAGGACyyk-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 c 0 0 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 g 0 0 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 t 0 0 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0
oligos_6nt_mkv4_m1_rc_shift3 (oligos_6nt_mkv4_m1_rc)				; positions_6nt_m2 versus oligos_6nt_mkv4_m1_rc; m=9/11; ncol2=15; w=0; offset=1; strand=R; shift=3; score=0.556851; ---sccAGGTCCTGgcag-------- ; cor=; Ncor= a 0 0 0 1252 1316 1177 5293 187 168 987 105 102 132 360 734 1561 2432 985 0 0 0 0 0 0 0 0 c 0 0 0 1809 2513 4056 303 151 189 288 6262 6311 333 240 970 3486 1302 1388 0 0 0 0 0 0 0 0 g 0 0 0 1973 1541 754 761 6148 6120 307 166 107 191 5608 4168 834 1295 3254 0 0 0 0 0 0 0 0 t 0 0 0 1614 1278 661 291 162 171 5066 115 128 5992 440 776 767 1619 1021 0 0 0 0 0 0 0 0
oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)				; positions_6nt_m2 versus oligos_7nt_mkv5_m1_rc; m=10/11; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.556443; --tscCAGGTCCTGGaag-------- ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 0 0 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 0 0 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 0 0 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0 0 0 0 0 0
positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)				; positions_6nt_m2 versus positions_7nt_m5_rc; m=11/11; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.555952; --tbcCAGGTCCTGkma--------- ; cor=; Ncor= a 0 0 1393 1091 1058 802 5458 163 175 1056 111 118 115 334 946 1777 2134 0 0 0 0 0 0 0 0 0 c 0 0 1444 1618 2922 4547 150 118 175 271 5735 5792 240 270 1156 1918 1219 0 0 0 0 0 0 0 0 0 g 0 0 1372 1833 1155 399 342 5695 5621 239 163 89 116 5071 2112 1273 1297 0 0 0 0 0 0 0 0 0 t 0 0 1907 1574 981 368 166 140 145 4550 107 117 5645 441 1902 1148 1466 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift7 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=7; ncol=18; -------tcCTGGAAGrr ; Alignment reference a 0 0 0 0 0 0 0 1255 1201 172 173 194 111 4862 4822 97 1386 1485 c 0 0 0 0 0 0 0 948 1980 4959 253 115 81 135 194 122 1180 1147 g 0 0 0 0 0 0 0 1161 1083 146 312 4977 4760 121 130 4813 1469 1402 t 0 0 0 0 0 0 0 1986 1086 73 4612 64 398 232 204 318 1315 1316
oligos_7nt_mkv5_m5_shift7 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------tcCTGGAAGrr ; cor=; Ncor= a 0 0 0 0 0 0 0 1255 1201 172 173 194 111 4862 4822 97 1386 1485 c 0 0 0 0 0 0 0 948 1980 4959 253 115 81 135 194 122 1180 1147 g 0 0 0 0 0 0 0 1161 1083 146 312 4977 4760 121 130 4813 1469 1402 t 0 0 0 0 0 0 0 1986 1086 73 4612 64 398 232 204 318 1315 1316
positions_7nt_m3_shift3 (positions_7nt_m3)				; oligos_7nt_mkv5_m5 versus positions_7nt_m3; m=2/5; ncol2=16; w=-4; offset=-4; strand=D; shift=3; score=0.540431; ---mrrGTCCTGGcAGgk ; cor=; Ncor= a 0 0 0 1181 1555 1896 179 193 80 111 120 121 190 856 2849 298 946 870 c 0 0 0 1252 877 295 123 187 3859 3869 178 98 231 2804 420 325 1038 812 g 0 0 0 956 1230 1589 3680 198 139 83 135 3729 3563 312 371 3264 1488 1295 t 0 0 0 785 512 394 192 3596 96 111 3741 226 190 202 534 287 702 1197
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; oligos_7nt_mkv5_m5 versus positions_7nt_m2_rc; m=3/5; ncol2=18; w=-6; offset=-6; strand=R; shift=1; score= 0.4754; -ssmrGGTCCTGGcaGsk ; cor=; Ncor= a 0 915 987 1240 1472 234 162 313 80 89 136 143 317 1142 2681 398 1017 914 c 0 1466 1791 1466 310 204 196 282 4481 4453 331 154 360 2859 596 604 1275 1059 g 0 1358 1227 971 2798 4190 4346 282 185 164 270 4279 3883 490 772 3488 1745 1595 t 0 1099 833 1161 258 210 134 3961 92 132 4101 262 278 347 789 348 801 1270
positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc)				; oligos_7nt_mkv5_m5 versus positions_7nt_m1_rc; m=4/5; ncol2=19; w=-7; offset=-7; strand=R; shift=0; score=0.446516; ksccAGGTCCTGGcaggk ; cor=; Ncor= a 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 c 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 g 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 t 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470
oligos_7nt_mkv5_m1_rc_shift0 (oligos_7nt_mkv5_m1_rc)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m1_rc; m=5/5; ncol2=16; w=-7; offset=-7; strand=R; shift=0; score=0.402914; tscCAGGTCCTGGaag-- ; cor=; Ncor= a 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 c 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 g 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 t 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m1_shift9 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------ctgcCAGGACCTggs ; Alignment reference a 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 c 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 g 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 t 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252
oligos_6nt_mkv4_m1_shift9 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score= 1; ---------ctgcCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 c 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 g 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 t 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1; m=2/11; ncol2=16; w=0; offset=0; strand=D; shift=9; score=0.913917; ---------cttCCAGGACCTGgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 c 0 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 g 0 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 t 0 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862
positions_7nt_m5_shift10 (positions_7nt_m5)				; oligos_6nt_mkv4_m1 versus positions_7nt_m5; m=3/11; ncol2=15; w=0; offset=1; strand=D; shift=10; score=0.853916; ----------tkmCAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 c 0 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 g 0 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 t 0 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091
positions_7nt_m4_shift10 (positions_7nt_m4)				; oligos_6nt_mkv4_m1 versus positions_7nt_m4; m=4/11; ncol2=15; w=0; offset=1; strand=D; shift=10; score=0.851069; ----------tksCAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 c 0 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 g 0 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 t 0 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120
positions_7nt_m1_shift6 (positions_7nt_m1)				; oligos_6nt_mkv4_m1 versus positions_7nt_m1; m=5/11; ncol2=19; w=-3; offset=-3; strand=D; shift=6; score=0.781424; ------smcctgCCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 c 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 g 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 t 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938
positions_7nt_m2_shift6 (positions_7nt_m2)				; oligos_6nt_mkv4_m1 versus positions_7nt_m2; m=6/11; ncol2=18; w=-3; offset=-3; strand=D; shift=6; score=0.767207; ------smsCtgCCAGGACCykss ; cor=; Ncor= a 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915
positions_7nt_m3_rc_shift6 (positions_7nt_m3_rc)				; oligos_6nt_mkv4_m1 versus positions_7nt_m3_rc; m=7/11; ncol2=16; w=-3; offset=-3; strand=R; shift=6; score=0.630754; ------smcCTgCCAGGACyyk-- ; cor=; Ncor= a 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 c 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 g 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 t 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; oligos_6nt_mkv4_m1 versus positions_6nt_m4_rc; m=8/11; ncol2=21; w=-6; offset=-6; strand=R; shift=3; score=0.587739; ---mrrGTCCTGgCAGGTCCTkgm ; cor=; Ncor= a 0 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 90 88 168 253 303 c 0 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 933 107 176 238 342 g 0 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 57 88 426 403 274 t 0 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60 71 868 381 257 232
positions_6nt_m1_shift0 (positions_6nt_m1)				; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=9/11; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.578048; ssccaGGtCCTGcCAGGACCTgss ; cor=; Ncor= a 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157
positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)				; oligos_6nt_mkv4_m1 versus positions_6nt_m3_rc; m=10/11; ncol2=24; w=-6; offset=-6; strand=R; shift=3; score=0.57632; ---yvrgtCCTGsCAGGACCTgsc ; cor=; Ncor= a 0 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 c 0 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 g 0 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 t 0 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195
positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)				; oligos_6nt_mkv4_m1 versus positions_6nt_m2_rc; m=11/11; ncol2=24; w=-8; offset=-8; strand=R; shift=1; score=0.556851; -scmrGGtCCTGgCAGGACCtggs ; cor=; Ncor= a 0 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 c 0 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 g 0 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 t 0 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift3 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=21; shift=3; ncol=24; ---kcmAGGACCTGcCAGGACyyk ; Alignment reference a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324
positions_6nt_m4_shift3 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/11; ncol2=21; w=0; offset=0; strand=D; shift=3; score= 1; ---kcmAGGACCTGcCAGGACyyk ; cor=; Ncor= a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m4 versus positions_6nt_m3; m=2/11; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.808129; sskgscAGGTCCTGsCAGGacybr ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282
positions_6nt_m2_shift2 (positions_6nt_m2)				; positions_6nt_m4 versus positions_6nt_m2; m=3/11; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.799923; --ssccaGGTCCTGcCAGGaCCyk ; cor=; Ncor= a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m4 versus positions_6nt_m1; m=4/11; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.782281; --ssccaGGtCCTGcCAGGACCTg ; cor=; Ncor= a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148
positions_7nt_m3_rc_shift8 (positions_7nt_m3_rc)				; positions_6nt_m4 versus positions_7nt_m3_rc; m=5/11; ncol2=16; w=0; offset=5; strand=R; shift=8; score=0.664718; --------smcCTgCCAGGACyyk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 c 0 0 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 g 0 0 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 t 0 0 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181
positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)				; positions_6nt_m4 versus positions_7nt_m1_rc; m=6/11; ncol2=19; w=-1; offset=-1; strand=R; shift=2; score=0.629275; --ksccAGGTCCTGGcaggks--- ; cor=; Ncor= a 0 0 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 1273 0 0 0 c 0 0 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 1371 0 0 0 g 0 0 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 1507 0 0 0 t 0 0 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470 1004 0 0 0
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; positions_6nt_m4 versus positions_7nt_m2_rc; m=7/11; ncol2=18; w=0; offset=0; strand=R; shift=3; score=0.610907; ---ssmrGGTCCTGGcaGsks--- ; cor=; Ncor= a 0 0 0 915 987 1240 1472 234 162 313 80 89 136 143 317 1142 2681 398 1017 914 1143 0 0 0 c 0 0 0 1466 1791 1466 310 204 196 282 4481 4453 331 154 360 2859 596 604 1275 1059 1235 0 0 0 g 0 0 0 1358 1227 971 2798 4190 4346 282 185 164 270 4279 3883 490 772 3488 1745 1595 1529 0 0 0 t 0 0 0 1099 833 1161 258 210 134 3961 92 132 4101 262 278 347 789 348 801 1270 931 0 0 0
oligos_6nt_mkv4_m1_rc_shift3 (oligos_6nt_mkv4_m1_rc)				; positions_6nt_m4 versus oligos_6nt_mkv4_m1_rc; m=8/11; ncol2=15; w=0; offset=0; strand=R; shift=3; score=0.587739; ---sccAGGTCCTGgcag------ ; cor=; Ncor= a 0 0 0 1252 1316 1177 5293 187 168 987 105 102 132 360 734 1561 2432 985 0 0 0 0 0 0 c 0 0 0 1809 2513 4056 303 151 189 288 6262 6311 333 240 970 3486 1302 1388 0 0 0 0 0 0 g 0 0 0 1973 1541 754 761 6148 6120 307 166 107 191 5608 4168 834 1295 3254 0 0 0 0 0 0 t 0 0 0 1614 1278 661 291 162 171 5066 115 128 5992 440 776 767 1619 1021 0 0 0 0 0 0
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_6nt_m4 versus positions_7nt_m5; m=9/11; ncol2=15; w=-1; offset=-1; strand=D; shift=2; score=0.549186; --tkmCAGGACCTGgva------- ; cor=; Ncor= a 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 0 0 0 0 0 0 0 c 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 0 0 0 0 0 0 0 g 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 0 0 0 0 0 0 0 t 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393 0 0 0 0 0 0 0
positions_7nt_m4_shift2 (positions_7nt_m4)				; positions_6nt_m4 versus positions_7nt_m4; m=10/11; ncol2=15; w=-1; offset=-1; strand=D; shift=2; score=0.545308; --tksCAGGACCTGgva------- ; cor=; Ncor= a 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 0 0 0 0 0 0 0 c 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 0 0 0 0 0 0 0 g 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 0 0 0 0 0 0 0 t 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398 0 0 0 0 0 0 0
oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)				; positions_6nt_m4 versus oligos_7nt_mkv5_m1_rc; m=11/11; ncol2=16; w=-1; offset=-1; strand=R; shift=2; score=0.522145; --tscCAGGTCCTGGaag------ ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; sskgscAGGTCCTGsCAGGacybr ; Alignment reference a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; sskgscAGGTCCTGsCAGGacybr ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282
positions_6nt_m2_shift2 (positions_6nt_m2)				; positions_6nt_m3 versus positions_6nt_m2; m=2/11; ncol2=24; w=0; offset=2; strand=D; shift=2; score=0.815372; --ssccaGGTCCTGcCAGGaCCyk ; cor=; Ncor= a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365
positions_6nt_m4_shift3 (positions_6nt_m4)				; positions_6nt_m3 versus positions_6nt_m4; m=3/11; ncol2=21; w=0; offset=3; strand=D; shift=3; score=0.808129; ---kcmAGGACCTGcCAGGACyyk ; cor=; Ncor= a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m3 versus positions_6nt_m1; m=4/11; ncol2=24; w=0; offset=2; strand=D; shift=2; score=0.779591; --ssccaGGtCCTGcCAGGACCTg ; cor=; Ncor= a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148
positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)				; positions_6nt_m3 versus positions_7nt_m1_rc; m=5/11; ncol2=19; w=0; offset=2; strand=R; shift=2; score=0.705577; --ksccAGGTCCTGGcaggks--- ; cor=; Ncor= a 0 0 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 1273 0 0 0 c 0 0 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 1371 0 0 0 g 0 0 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 1507 0 0 0 t 0 0 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470 1004 0 0 0
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; positions_6nt_m3 versus positions_7nt_m2_rc; m=6/11; ncol2=18; w=0; offset=3; strand=R; shift=3; score=0.627027; ---ssmrGGTCCTGGcaGsks--- ; cor=; Ncor= a 0 0 0 915 987 1240 1472 234 162 313 80 89 136 143 317 1142 2681 398 1017 914 1143 0 0 0 c 0 0 0 1466 1791 1466 310 204 196 282 4481 4453 331 154 360 2859 596 604 1275 1059 1235 0 0 0 g 0 0 0 1358 1227 971 2798 4190 4346 282 185 164 270 4279 3883 490 772 3488 1745 1595 1529 0 0 0 t 0 0 0 1099 833 1161 258 210 134 3961 92 132 4101 262 278 347 789 348 801 1270 931 0 0 0
oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)				; positions_6nt_m3 versus oligos_7nt_mkv5_m1_rc; m=7/11; ncol2=16; w=0; offset=2; strand=R; shift=2; score=0.581076; --tscCAGGTCCTGGaag------ ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0 0 0 0
positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)				; positions_6nt_m3 versus positions_7nt_m4_rc; m=8/11; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.580644; --tbcCAGGTCCTGsma------- ; cor=; Ncor= a 0 0 1398 1120 1041 781 5554 160 149 1077 136 121 126 330 939 1868 2080 0 0 0 0 0 0 0 c 0 0 1538 1681 3078 4759 185 150 217 337 5902 5966 341 290 2429 1993 1335 0 0 0 0 0 0 0 g 0 0 1482 1882 1208 416 406 5860 5792 271 153 92 152 5249 2091 1189 1473 0 0 0 0 0 0 0 t 0 0 1887 1622 978 349 160 135 147 4620 114 126 5686 436 846 1255 1417 0 0 0 0 0 0 0
oligos_6nt_mkv4_m1_rc_shift3 (oligos_6nt_mkv4_m1_rc)				; positions_6nt_m3 versus oligos_6nt_mkv4_m1_rc; m=9/11; ncol2=15; w=0; offset=3; strand=R; shift=3; score=0.57632; ---sccAGGTCCTGgcag------ ; cor=; Ncor= a 0 0 0 1252 1316 1177 5293 187 168 987 105 102 132 360 734 1561 2432 985 0 0 0 0 0 0 c 0 0 0 1809 2513 4056 303 151 189 288 6262 6311 333 240 970 3486 1302 1388 0 0 0 0 0 0 g 0 0 0 1973 1541 754 761 6148 6120 307 166 107 191 5608 4168 834 1295 3254 0 0 0 0 0 0 t 0 0 0 1614 1278 661 291 162 171 5066 115 128 5992 440 776 767 1619 1021 0 0 0 0 0 0
positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)				; positions_6nt_m3 versus positions_7nt_m5_rc; m=10/11; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.574713; --tbcCAGGTCCTGkma------- ; cor=; Ncor= a 0 0 1393 1091 1058 802 5458 163 175 1056 111 118 115 334 946 1777 2134 0 0 0 0 0 0 0 c 0 0 1444 1618 2922 4547 150 118 175 271 5735 5792 240 270 1156 1918 1219 0 0 0 0 0 0 0 g 0 0 1372 1833 1155 399 342 5695 5621 239 163 89 116 5071 2112 1273 1297 0 0 0 0 0 0 0 t 0 0 1907 1574 981 368 166 140 145 4550 107 117 5645 441 1902 1148 1466 0 0 0 0 0 0 0
positions_7nt_m3_shift5 (positions_7nt_m3)				; positions_6nt_m3 versus positions_7nt_m3; m=11/11; ncol2=16; w=0; offset=5; strand=D; shift=5; score=0.550542; -----mrrGTCCTGGcAGgks--- ; cor=; Ncor= a 0 0 0 0 0 1181 1555 1896 179 193 80 111 120 121 190 856 2849 298 946 870 984 0 0 0 c 0 0 0 0 0 1252 877 295 123 187 3859 3869 178 98 231 2804 420 325 1038 812 1089 0 0 0 g 0 0 0 0 0 956 1230 1589 3680 198 139 83 135 3729 3563 312 371 3264 1488 1295 1272 0 0 0 t 0 0 0 0 0 785 512 394 192 3596 96 111 3741 226 190 202 534 287 702 1197 829 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssccaGGtCCTGcCAGGACCTgss ; Alignment reference a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssccaGGtCCTGcCAGGACCTgss ; cor=; Ncor= a 0 0 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 0 0 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 0 0 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 0 0 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157
positions_6nt_m2_shift2 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.961589; --ssccaGGTCCTGcCAGGaCCykgs ; cor=; Ncor= a 0 0 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 196 245 c 0 0 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 248 306 g 0 0 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 390 313 t 0 0 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365 209 179
positions_6nt_m4_shift3 (positions_6nt_m4)				; positions_6nt_m1 versus positions_6nt_m4; m=3/11; ncol2=21; w=0; offset=1; strand=D; shift=3; score=0.782281; ---kcmAGGACCTGcCAGGACyyk-- ; cor=; Ncor= a 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 61 57 811 116 229 186 243 0 0 c 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 41 80 123 851 384 319 264 0 0 g 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 989 953 116 84 155 264 320 0 0 t 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81 60 61 101 100 383 382 324 0 0
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m1 versus positions_6nt_m3; m=4/11; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.779591; sskgscAGGTCCTGsCAGGacybr-- ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 256 240 292 0 0 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 335 320 243 0 0 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 204 299 337 0 0 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93 359 295 282 0 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=5/11; ncol2=19; w=0; offset=6; strand=D; shift=8; score=0.644624; --------smcctgCCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 c 0 0 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 g 0 0 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 t 0 0 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938
positions_7nt_m2_shift8 (positions_7nt_m2)				; positions_6nt_m1 versus positions_7nt_m2; m=6/11; ncol2=18; w=0; offset=6; strand=D; shift=8; score=0.643196; --------smsCtgCCAGGACCykss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)				; positions_6nt_m1 versus oligos_6nt_mkv4_m1; m=7/11; ncol2=15; w=0; offset=9; strand=D; shift=11; score=0.578048; -----------ctgcCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 c 0 0 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 g 0 0 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 t 0 0 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252
positions_7nt_m3_rc_shift8 (positions_7nt_m3_rc)				; positions_6nt_m1 versus positions_7nt_m3_rc; m=8/11; ncol2=16; w=0; offset=6; strand=R; shift=8; score=0.570875; --------smcCTgCCAGGACyyk-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 c 0 0 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 g 0 0 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 t 0 0 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0
positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)				; positions_6nt_m1 versus positions_7nt_m4_rc; m=9/11; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.550744; --tbcCAGGTCCTGsma--------- ; cor=; Ncor= a 0 0 1398 1120 1041 781 5554 160 149 1077 136 121 126 330 939 1868 2080 0 0 0 0 0 0 0 0 0 c 0 0 1538 1681 3078 4759 185 150 217 337 5902 5966 341 290 2429 1993 1335 0 0 0 0 0 0 0 0 0 g 0 0 1482 1882 1208 416 406 5860 5792 271 153 92 152 5249 2091 1189 1473 0 0 0 0 0 0 0 0 0 t 0 0 1887 1622 978 349 160 135 147 4620 114 126 5686 436 846 1255 1417 0 0 0 0 0 0 0 0 0
positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)				; positions_6nt_m1 versus positions_7nt_m5_rc; m=10/11; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.539793; --tbcCAGGTCCTGkma--------- ; cor=; Ncor= a 0 0 1393 1091 1058 802 5458 163 175 1056 111 118 115 334 946 1777 2134 0 0 0 0 0 0 0 0 0 c 0 0 1444 1618 2922 4547 150 118 175 271 5735 5792 240 270 1156 1918 1219 0 0 0 0 0 0 0 0 0 g 0 0 1372 1833 1155 399 342 5695 5621 239 163 89 116 5071 2112 1273 1297 0 0 0 0 0 0 0 0 0 t 0 0 1907 1574 981 368 166 140 145 4550 107 117 5645 441 1902 1148 1466 0 0 0 0 0 0 0 0 0
oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)				; positions_6nt_m1 versus oligos_7nt_mkv5_m1_rc; m=11/11; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.535571; --tscCAGGTCCTGGaag-------- ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 0 0 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 0 0 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 0 0 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift5 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=16; shift=5; ncol=21; -----mrrGTCCTGGcAGgks ; Alignment reference a 0 0 0 0 0 1181 1555 1896 179 193 80 111 120 121 190 856 2849 298 946 870 984 c 0 0 0 0 0 1252 877 295 123 187 3859 3869 178 98 231 2804 420 325 1038 812 1089 g 0 0 0 0 0 956 1230 1589 3680 198 139 83 135 3729 3563 312 371 3264 1488 1295 1272 t 0 0 0 0 0 785 512 394 192 3596 96 111 3741 226 190 202 534 287 702 1197 829
positions_7nt_m3_shift5 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/12; ncol2=16; w=0; offset=0; strand=D; shift=5; score= 1; -----mrrGTCCTGGcAGgks ; cor=; Ncor= a 0 0 0 0 0 1181 1555 1896 179 193 80 111 120 121 190 856 2849 298 946 870 984 c 0 0 0 0 0 1252 877 295 123 187 3859 3869 178 98 231 2804 420 325 1038 812 1089 g 0 0 0 0 0 956 1230 1589 3680 198 139 83 135 3729 3563 312 371 3264 1488 1295 1272 t 0 0 0 0 0 785 512 394 192 3596 96 111 3741 226 190 202 534 287 702 1197 829
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; positions_7nt_m3 versus positions_7nt_m2_rc; m=2/12; ncol2=18; w=-2; offset=-2; strand=R; shift=3; score=0.837466; ---ssmrGGTCCTGGcaGsks ; cor=; Ncor= a 0 0 0 915 987 1240 1472 234 162 313 80 89 136 143 317 1142 2681 398 1017 914 1143 c 0 0 0 1466 1791 1466 310 204 196 282 4481 4453 331 154 360 2859 596 604 1275 1059 1235 g 0 0 0 1358 1227 971 2798 4190 4346 282 185 164 270 4279 3883 490 772 3488 1745 1595 1529 t 0 0 0 1099 833 1161 258 210 134 3961 92 132 4101 262 278 347 789 348 801 1270 931
positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)				; positions_7nt_m3 versus positions_7nt_m1_rc; m=3/12; ncol2=19; w=-3; offset=-3; strand=R; shift=2; score=0.753606; --ksccAGGTCCTGGcaggks ; cor=; Ncor= a 0 0 1076 938 874 815 4275 187 126 732 79 85 138 291 471 1244 2690 544 1161 978 1273 c 0 0 1287 1442 2489 3500 210 127 160 288 4825 4853 289 192 556 2867 712 689 1265 1106 1371 g 0 0 1330 1563 1034 448 514 4719 4709 262 154 85 173 4239 3700 580 758 3427 1750 1601 1507 t 0 0 1462 1212 758 392 156 122 160 3873 97 132 4555 433 428 464 995 495 979 1470 1004
positions_6nt_m4_rc_shift5 (positions_6nt_m4_rc)				; positions_7nt_m3 versus positions_6nt_m4_rc; m=4/12; ncol2=21; w=0; offset=0; strand=R; shift=5; score=0.664718; -----mrrGTCCTGgCAGGTC ; cor=; Ncor= a 0 0 0 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 c 0 0 0 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 g 0 0 0 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 t 0 0 0 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60
oligos_6nt_mkv4_m1_rc_shift3 (oligos_6nt_mkv4_m1_rc)				; positions_7nt_m3 versus oligos_6nt_mkv4_m1_rc; m=5/12; ncol2=15; w=-2; offset=-2; strand=R; shift=3; score=0.630754; ---sccAGGTCCTGgcag--- ; cor=; Ncor= a 0 0 0 1252 1316 1177 5293 187 168 987 105 102 132 360 734 1561 2432 985 0 0 0 c 0 0 0 1809 2513 4056 303 151 189 288 6262 6311 333 240 970 3486 1302 1388 0 0 0 g 0 0 0 1973 1541 754 761 6148 6120 307 166 107 191 5608 4168 834 1295 3254 0 0 0 t 0 0 0 1614 1278 661 291 162 171 5066 115 128 5992 440 776 767 1619 1021 0 0 0
oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)				; positions_7nt_m3 versus oligos_7nt_mkv5_m1_rc; m=6/12; ncol2=16; w=-3; offset=-3; strand=R; shift=2; score=0.571239; --tscCAGGTCCTGGaag--- ; cor=; Ncor= a 0 0 1086 862 822 717 4129 122 119 728 87 65 127 314 462 2649 1865 789 0 0 0 c 0 0 1108 1283 2344 3320 149 103 119 205 4434 4505 230 151 472 1023 876 934 0 0 0 g 0 0 1138 1454 856 364 352 4408 4381 198 112 64 127 3860 3512 560 1084 2305 0 0 0 t 0 0 1398 1131 708 329 100 97 111 3599 97 96 4246 405 284 498 905 702 0 0 0
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; positions_7nt_m3 versus positions_6nt_m1_rc; m=7/12; ncol2=24; w=-2; offset=-2; strand=R; shift=3; score=0.570875; ---sscAGGTCCTGgCAGGaC ; cor=; Ncor= a 0 0 0 157 195 148 654 59 35 119 46 21 46 44 97 133 801 25 64 580 102 c 0 0 0 289 329 606 68 65 86 94 791 881 64 35 196 725 45 16 93 98 673 g 0 0 0 283 242 106 130 753 765 78 74 24 49 763 566 55 63 888 737 131 119 t 0 0 0 226 189 95 103 78 69 664 44 29 796 113 96 42 46 26 61 146 61
positions_6nt_m2_rc_shift3 (positions_6nt_m2_rc)				; positions_7nt_m3 versus positions_6nt_m2_rc; m=8/12; ncol2=24; w=-2; offset=-2; strand=R; shift=3; score=0.564903; ---scmrGGtCCTGgCAGGAC ; cor=; Ncor= a 0 0 0 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 c 0 0 0 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 g 0 0 0 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 t 0 0 0 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_7nt_m3 versus positions_6nt_m3; m=9/12; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.550542; sskgscAGGTCCTGsCAGGac ; cor=; Ncor= a 248 212 230 195 219 167 861 44 44 140 30 18 29 42 139 152 907 41 90 689 164 c 335 381 262 274 395 771 78 67 73 88 1009 1095 63 57 541 896 83 39 117 122 758 g 344 337 297 462 352 105 133 969 972 66 68 15 55 935 348 62 64 1028 865 183 139 t 227 224 365 223 188 111 82 74 65 860 47 26 1007 120 126 44 100 46 82 160 93
oligos_7nt_mkv5_m5_shift9 (oligos_7nt_mkv5_m5)				; positions_7nt_m3 versus oligos_7nt_mkv5_m5; m=10/12; ncol2=11; w=0; offset=4; strand=D; shift=9; score=0.540431; ---------tcCTGGAAGrr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1255 1201 172 173 194 111 4862 4822 97 1386 1485 0 c 0 0 0 0 0 0 0 0 0 948 1980 4959 253 115 81 135 194 122 1180 1147 0 g 0 0 0 0 0 0 0 0 0 1161 1083 146 312 4977 4760 121 130 4813 1469 1402 0 t 0 0 0 0 0 0 0 0 0 1986 1086 73 4612 64 398 232 204 318 1315 1316 0
positions_7nt_m5_rc_shift2 (positions_7nt_m5_rc)				; positions_7nt_m3 versus positions_7nt_m5_rc; m=11/12; ncol2=15; w=-3; offset=-3; strand=R; shift=2; score=0.506642; --tbcCAGGTCCTGkma---- ; cor=; Ncor= a 0 0 1393 1091 1058 802 5458 163 175 1056 111 118 115 334 946 1777 2134 0 0 0 0 c 0 0 1444 1618 2922 4547 150 118 175 271 5735 5792 240 270 1156 1918 1219 0 0 0 0 g 0 0 1372 1833 1155 399 342 5695 5621 239 163 89 116 5071 2112 1273 1297 0 0 0 0 t 0 0 1907 1574 981 368 166 140 145 4550 107 117 5645 441 1902 1148 1466 0 0 0 0
positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)				; positions_7nt_m3 versus positions_7nt_m4_rc; m=12/12; ncol2=15; w=-3; offset=-3; strand=R; shift=2; score=0.502365; --tbcCAGGTCCTGsma---- ; cor=; Ncor= a 0 0 1398 1120 1041 781 5554 160 149 1077 136 121 126 330 939 1868 2080 0 0 0 0 c 0 0 1538 1681 3078 4759 185 150 217 337 5902 5966 341 290 2429 1993 1335 0 0 0 0 g 0 0 1482 1882 1208 416 406 5860 5792 271 153 92 152 5249 2091 1189 1473 0 0 0 0 t 0 0 1887 1622 978 349 160 135 147 4620 114 126 5686 436 846 1255 1417 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m5_shift9 (positions_7nt_m5)				; positions_7nt_m5; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------tkmCAGGACCTGgva ; Alignment reference a 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393
positions_7nt_m5_shift9 (positions_7nt_m5)				; positions_7nt_m5 versus positions_7nt_m5; m=1/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score= 1; ---------tkmCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393
positions_7nt_m4_shift9 (positions_7nt_m4)				; positions_7nt_m5 versus positions_7nt_m4; m=2/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score=0.992438; ---------tksCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398
oligos_7nt_mkv5_m1_shift8 (oligos_7nt_mkv5_m1)				; positions_7nt_m5 versus oligos_7nt_mkv5_m1; m=3/11; ncol2=16; w=-1; offset=-1; strand=D; shift=8; score= 0.9065; --------cttCCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; positions_7nt_m5 versus oligos_6nt_mkv4_m1; m=4/11; ncol2=15; w=-1; offset=-1; strand=D; shift=8; score=0.853916; --------ctgcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 0 c 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 0 g 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 0 t 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252 0
positions_7nt_m1_shift5 (positions_7nt_m1)				; positions_7nt_m5 versus positions_7nt_m1; m=5/11; ncol2=19; w=-4; offset=-4; strand=D; shift=5; score=0.762596; -----smcctgCCAGGACCTggsm ; cor=; Ncor= a 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_7nt_m5 versus positions_7nt_m2; m=6/11; ncol2=18; w=-4; offset=-4; strand=D; shift=5; score=0.629259; -----smsCtgCCAGGACCykss- ; cor=; Ncor= a 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 0 c 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 0 g 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 0 t 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915 0
positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)				; positions_7nt_m5 versus positions_6nt_m3_rc; m=7/11; ncol2=24; w=-7; offset=-7; strand=R; shift=2; score=0.574713; --yvrgtCCTGsCAGGACCTgscm ; cor=; Ncor= a 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 365 c 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 297 g 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 262 t 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195 230
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m5 versus positions_6nt_m2_rc; m=8/11; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.555952; scmrGGtCCTGgCAGGACCtggss ; cor=; Ncor= a 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 242 c 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 292 g 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 275 t 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173 234
positions_6nt_m4_shift10 (positions_6nt_m4)				; positions_7nt_m5 versus positions_6nt_m4; m=9/11; ncol2=21; w=0; offset=1; strand=D; shift=10; score=0.549186; ----------kcmAGGACCTGcCA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 c 0 0 0 0 0 0 0 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 g 0 0 0 0 0 0 0 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 t 0 0 0 0 0 0 0 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; positions_7nt_m5 versus positions_6nt_m1_rc; m=10/11; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.539793; sscAGGTCCTGgCAGGaCCtggss ; cor=; Ncor= a 157 195 148 654 59 35 119 46 21 46 44 97 133 801 25 64 580 102 114 144 122 207 221 237 c 289 329 606 68 65 86 94 791 881 64 35 196 725 45 16 93 98 673 676 137 118 231 262 270 g 283 242 106 130 753 765 78 74 24 49 763 566 55 63 888 737 131 119 101 92 583 328 290 247 t 226 189 95 103 78 69 664 44 29 796 113 96 42 46 26 61 146 61 64 582 132 189 182 201
positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)				; positions_7nt_m5 versus positions_7nt_m3_rc; m=11/11; ncol2=16; w=-4; offset=-4; strand=R; shift=5; score=0.506642; -----smcCTgCCAGGACyyk--- ; cor=; Ncor= a 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 0 c 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 0 g 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 0 t 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift6 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=19; shift=6; ncol=25; ------smcctgCCAGGACCTggsm ; Alignment reference a 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076
positions_7nt_m1_shift6 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/12; ncol2=19; w=0; offset=0; strand=D; shift=6; score= 1; ------smcctgCCAGGACCTggsm ; cor=; Ncor= a 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076
positions_7nt_m2_shift6 (positions_7nt_m2)				; positions_7nt_m1 versus positions_7nt_m2; m=2/12; ncol2=18; w=0; offset=0; strand=D; shift=6; score=0.878094; ------smsCtgCCAGGACCykss- ; cor=; Ncor= a 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 0 c 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 0 g 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 0 t 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915 0
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)				; positions_7nt_m1 versus oligos_7nt_mkv5_m1; m=3/12; ncol2=16; w=0; offset=3; strand=D; shift=9; score=0.81887; ---------cttCCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086
oligos_6nt_mkv4_m1_shift9 (oligos_6nt_mkv4_m1)				; positions_7nt_m1 versus oligos_6nt_mkv4_m1; m=4/12; ncol2=15; w=0; offset=3; strand=D; shift=9; score=0.781424; ---------ctgcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 0 c 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 0 g 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 0 t 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252 0
positions_7nt_m5_shift10 (positions_7nt_m5)				; positions_7nt_m1 versus positions_7nt_m5; m=5/12; ncol2=15; w=0; offset=4; strand=D; shift=10; score=0.762596; ----------tkmCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393
positions_7nt_m4_shift10 (positions_7nt_m4)				; positions_7nt_m1 versus positions_7nt_m4; m=6/12; ncol2=15; w=0; offset=4; strand=D; shift=10; score=0.75964; ----------tksCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398
positions_7nt_m3_rc_shift6 (positions_7nt_m3_rc)				; positions_7nt_m1 versus positions_7nt_m3_rc; m=7/12; ncol2=16; w=0; offset=0; strand=R; shift=6; score=0.753606; ------smcCTgCCAGGACyyk--- ; cor=; Ncor= a 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 0 c 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 0 g 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 0 t 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0 0
positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)				; positions_7nt_m1 versus positions_6nt_m3_rc; m=8/12; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.705577; ---yvrgtCCTGsCAGGACCTgscm ; cor=; Ncor= a 0 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 365 c 0 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 297 g 0 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 262 t 0 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195 230
positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)				; positions_7nt_m1 versus positions_6nt_m2_rc; m=9/12; ncol2=24; w=-5; offset=-5; strand=R; shift=1; score=0.667982; -scmrGGtCCTGgCAGGACCtggss ; cor=; Ncor= a 0 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 242 c 0 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 292 g 0 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 275 t 0 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173 234
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=10/12; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.644624; ssccaGGtCCTGcCAGGACCTgss- ; cor=; Ncor= a 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 0 c 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 0 g 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 0 t 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157 0
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; positions_7nt_m1 versus positions_6nt_m4_rc; m=11/12; ncol2=21; w=-3; offset=-3; strand=R; shift=3; score=0.629275; ---mrrGTCCTGgCAGGTCCTkgm- ; cor=; Ncor= a 0 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 90 88 168 253 303 0 c 0 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 933 107 176 238 342 0 g 0 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 57 88 426 403 274 0 t 0 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60 71 868 381 257 232 0
oligos_7nt_mkv5_m5_rc_shift7 (oligos_7nt_mkv5_m5_rc)				; positions_7nt_m1 versus oligos_7nt_mkv5_m5_rc; m=12/12; ncol2=11; w=0; offset=1; strand=R; shift=7; score=0.446516; -------yyCTTCCAGga------- ; cor=; Ncor= a 0 0 0 0 0 0 0 1316 1315 318 204 232 398 64 4612 73 1086 1986 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1402 1469 4813 130 121 4760 4977 312 146 1083 1161 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1147 1180 122 194 135 81 115 253 4959 1980 948 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 1485 1386 97 4822 4862 111 194 173 172 1201 1255 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift6 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=18; shift=6; ncol=24; ------smsCtgCCAGGACCykss ; Alignment reference a 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915
positions_7nt_m2_shift6 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/12; ncol2=18; w=0; offset=0; strand=D; shift=6; score= 1; ------smsCtgCCAGGACCykss ; cor=; Ncor= a 0 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 c 0 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 g 0 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 t 0 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915
positions_7nt_m1_shift6 (positions_7nt_m1)				; positions_7nt_m2 versus positions_7nt_m1; m=2/12; ncol2=19; w=0; offset=0; strand=D; shift=6; score=0.878094; ------smcctgCCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 c 0 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 g 0 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 t 0 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938
positions_7nt_m3_rc_shift6 (positions_7nt_m3_rc)				; positions_7nt_m2 versus positions_7nt_m3_rc; m=3/12; ncol2=16; w=0; offset=0; strand=R; shift=6; score=0.837466; ------smcCTgCCAGGACyyk-- ; cor=; Ncor= a 0 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 c 0 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 g 0 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 t 0 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0
oligos_6nt_mkv4_m1_shift9 (oligos_6nt_mkv4_m1)				; positions_7nt_m2 versus oligos_6nt_mkv4_m1; m=4/12; ncol2=15; w=0; offset=3; strand=D; shift=9; score=0.767207; ---------ctgcCAGGACCTggs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 c 0 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 g 0 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 t 0 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)				; positions_7nt_m2 versus oligos_7nt_mkv5_m1; m=5/12; ncol2=16; w=0; offset=3; strand=D; shift=9; score=0.696804; ---------cttCCAGGACCTGgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 c 0 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 g 0 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 t 0 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_7nt_m2 versus positions_6nt_m2; m=6/12; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.644947; ssccaGGTCCTGcCAGGaCCykgs ; cor=; Ncor= a 234 173 186 134 692 65 54 133 45 18 39 36 91 112 845 39 57 699 94 111 166 192 196 245 c 275 317 406 675 97 89 95 113 863 984 57 59 584 843 70 37 97 107 780 766 456 191 248 306 g 292 296 246 106 145 779 793 77 72 14 62 816 259 44 58 942 829 120 107 81 139 295 390 313 t 242 257 205 128 109 110 101 720 63 27 885 132 109 44 70 25 60 117 62 85 282 365 209 179
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_7nt_m2 versus positions_6nt_m1; m=7/12; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.643196; ssccaGGtCCTGcCAGGACCTgss ; cor=; Ncor= a 201 182 189 132 582 64 61 146 61 26 46 42 96 113 796 29 44 664 69 78 103 95 189 226 c 247 290 328 583 92 101 119 131 737 888 63 55 566 763 49 24 74 78 765 753 130 106 242 283 g 270 262 231 118 137 676 673 98 93 16 45 725 196 35 64 881 791 94 86 65 68 606 329 289 t 237 221 207 122 144 114 102 580 64 25 801 133 97 44 46 21 46 119 35 59 654 148 195 157
positions_7nt_m5_shift10 (positions_7nt_m5)				; positions_7nt_m2 versus positions_7nt_m5; m=8/12; ncol2=15; w=0; offset=4; strand=D; shift=10; score=0.629259; ----------tkmCAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 c 0 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 g 0 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 t 0 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091
positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)				; positions_7nt_m2 versus positions_6nt_m3_rc; m=9/12; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.627027; ---yvrgtCCTGsCAGGACCTgsc ; cor=; Ncor= a 0 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 c 0 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 g 0 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 t 0 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195
positions_7nt_m4_shift10 (positions_7nt_m4)				; positions_7nt_m2 versus positions_7nt_m4; m=10/12; ncol2=15; w=0; offset=4; strand=D; shift=10; score=0.62602; ----------tksCAGGACCTGgv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 c 0 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 g 0 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 t 0 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120
positions_6nt_m4_rc_shift3 (positions_6nt_m4_rc)				; positions_7nt_m2 versus positions_6nt_m4_rc; m=11/12; ncol2=21; w=-3; offset=-3; strand=R; shift=3; score=0.610907; ---mrrGTCCTGgCAGGTCCTkgm ; cor=; Ncor= a 0 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 90 88 168 253 303 c 0 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 933 107 176 238 342 g 0 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 57 88 426 403 274 t 0 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60 71 868 381 257 232
oligos_7nt_mkv5_m5_rc_shift7 (oligos_7nt_mkv5_m5_rc)				; positions_7nt_m2 versus oligos_7nt_mkv5_m5_rc; m=12/12; ncol2=11; w=0; offset=1; strand=R; shift=7; score= 0.4754; -------yyCTTCCAGga------ ; cor=; Ncor= a 0 0 0 0 0 0 0 1316 1315 318 204 232 398 64 4612 73 1086 1986 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1402 1469 4813 130 121 4760 4977 312 146 1083 1161 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1147 1180 122 194 135 81 115 253 4959 1980 948 0 0 0 0 0 0 t 0 0 0 0 0 0 0 1485 1386 97 4822 4862 111 194 173 172 1201 1255 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift9 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------tksCAGGACCTGgva ; Alignment reference a 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398
positions_7nt_m4_shift9 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score= 1; ---------tksCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398
positions_7nt_m5_shift9 (positions_7nt_m5)				; positions_7nt_m4 versus positions_7nt_m5; m=2/11; ncol2=15; w=0; offset=0; strand=D; shift=9; score=0.992438; ---------tkmCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393
oligos_7nt_mkv5_m1_shift8 (oligos_7nt_mkv5_m1)				; positions_7nt_m4 versus oligos_7nt_mkv5_m1; m=3/11; ncol2=16; w=-1; offset=-1; strand=D; shift=8; score=0.904242; --------cttCCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; positions_7nt_m4 versus oligos_6nt_mkv4_m1; m=4/11; ncol2=15; w=-1; offset=-1; strand=D; shift=8; score=0.851069; --------ctgcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 0 c 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 0 g 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 0 t 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252 0
positions_7nt_m1_shift5 (positions_7nt_m1)				; positions_7nt_m4 versus positions_7nt_m1; m=5/11; ncol2=19; w=-4; offset=-4; strand=D; shift=5; score=0.75964; -----smcctgCCAGGACCTggsm ; cor=; Ncor= a 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_7nt_m4 versus positions_7nt_m2; m=6/11; ncol2=18; w=-4; offset=-4; strand=D; shift=5; score=0.62602; -----smsCtgCCAGGACCykss- ; cor=; Ncor= a 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 0 c 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 0 g 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 0 t 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915 0
positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)				; positions_7nt_m4 versus positions_6nt_m3_rc; m=7/11; ncol2=24; w=-7; offset=-7; strand=R; shift=2; score=0.580644; --yvrgtCCTGsCAGGACCTgscm ; cor=; Ncor= a 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 365 c 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 297 g 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 262 t 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195 230
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m4 versus positions_6nt_m2_rc; m=8/11; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.565337; scmrGGtCCTGgCAGGACCtggss ; cor=; Ncor= a 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 242 c 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 292 g 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 275 t 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173 234
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; positions_7nt_m4 versus positions_6nt_m1_rc; m=9/11; ncol2=24; w=-9; offset=-9; strand=R; shift=0; score=0.550744; sscAGGTCCTGgCAGGaCCtggss ; cor=; Ncor= a 157 195 148 654 59 35 119 46 21 46 44 97 133 801 25 64 580 102 114 144 122 207 221 237 c 289 329 606 68 65 86 94 791 881 64 35 196 725 45 16 93 98 673 676 137 118 231 262 270 g 283 242 106 130 753 765 78 74 24 49 763 566 55 63 888 737 131 119 101 92 583 328 290 247 t 226 189 95 103 78 69 664 44 29 796 113 96 42 46 26 61 146 61 64 582 132 189 182 201
positions_6nt_m4_shift10 (positions_6nt_m4)				; positions_7nt_m4 versus positions_6nt_m4; m=10/11; ncol2=21; w=0; offset=1; strand=D; shift=10; score=0.545308; ----------kcmAGGACCTGcCA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 232 257 381 868 71 60 797 47 38 54 80 117 119 909 c 0 0 0 0 0 0 0 0 0 0 274 403 426 88 57 90 93 948 1066 78 78 667 898 78 g 0 0 0 0 0 0 0 0 0 0 342 238 176 107 933 936 54 90 23 57 794 248 86 83 t 0 0 0 0 0 0 0 0 0 0 303 253 168 88 90 65 207 66 24 962 199 119 48 81
positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)				; positions_7nt_m4 versus positions_7nt_m3_rc; m=11/11; ncol2=16; w=-4; offset=-4; strand=R; shift=5; score=0.502365; -----smcCTgCCAGGACyyk--- ; cor=; Ncor= a 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 0 c 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 0 g 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 0 t 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m1_shift8 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=16; shift=8; ncol=24; --------cttCCAGGACCTGgsa ; Alignment reference a 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086
oligos_7nt_mkv5_m1_shift8 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/12; ncol2=16; w=0; offset=0; strand=D; shift=8; score= 1; --------cttCCAGGACCTGgsa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 702 905 498 284 405 4246 96 97 3599 111 97 100 329 708 1131 1398 c 0 0 0 0 0 0 0 0 2305 1084 560 3512 3860 127 64 112 198 4381 4408 352 364 856 1454 1138 g 0 0 0 0 0 0 0 0 934 876 1023 472 151 230 4505 4434 205 119 103 149 3320 2344 1283 1108 t 0 0 0 0 0 0 0 0 789 1865 2649 462 314 127 65 87 728 119 122 4129 717 822 862 1086
oligos_6nt_mkv4_m1_shift8 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1; m=2/12; ncol2=15; w=0; offset=0; strand=D; shift=8; score=0.913917; --------ctgcCAGGACCTggs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1021 1619 767 776 440 5992 128 115 5066 171 162 291 661 1278 1614 0 c 0 0 0 0 0 0 0 0 3254 1295 834 4168 5608 191 107 166 307 6120 6148 761 754 1541 1973 0 g 0 0 0 0 0 0 0 0 1388 1302 3486 970 240 333 6311 6262 288 189 151 303 4056 2513 1809 0 t 0 0 0 0 0 0 0 0 985 2432 1561 734 360 132 102 105 987 168 187 5293 1177 1316 1252 0
positions_7nt_m5_shift9 (positions_7nt_m5)				; oligos_7nt_mkv5_m1 versus positions_7nt_m5; m=3/12; ncol2=15; w=0; offset=1; strand=D; shift=9; score= 0.9065; ---------tkmCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1466 1148 1902 441 5645 117 107 4550 145 140 166 368 981 1574 1907 c 0 0 0 0 0 0 0 0 0 1297 1273 2112 5071 116 89 163 239 5621 5695 342 399 1155 1833 1372 g 0 0 0 0 0 0 0 0 0 1219 1918 1156 270 240 5792 5735 271 175 118 150 4547 2922 1618 1444 t 0 0 0 0 0 0 0 0 0 2134 1777 946 334 115 118 111 1056 175 163 5458 802 1058 1091 1393
positions_7nt_m4_shift9 (positions_7nt_m4)				; oligos_7nt_mkv5_m1 versus positions_7nt_m4; m=4/12; ncol2=15; w=0; offset=1; strand=D; shift=9; score=0.904242; ---------tksCAGGACCTGgva ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1417 1255 846 436 5686 126 114 4620 147 135 160 349 978 1622 1887 c 0 0 0 0 0 0 0 0 0 1473 1189 2091 5249 152 92 153 271 5792 5860 406 416 1208 1882 1482 g 0 0 0 0 0 0 0 0 0 1335 1993 2429 290 341 5966 5902 337 217 150 185 4759 3078 1681 1538 t 0 0 0 0 0 0 0 0 0 2080 1868 939 330 126 121 136 1077 149 160 5554 781 1041 1120 1398
positions_7nt_m1_shift5 (positions_7nt_m1)				; oligos_7nt_mkv5_m1 versus positions_7nt_m1; m=5/12; ncol2=19; w=-3; offset=-3; strand=D; shift=5; score=0.81887; -----smcctgCCAGGACCTggsm ; cor=; Ncor= a 0 0 0 0 0 1004 1470 979 495 995 464 428 433 4555 132 97 3873 160 122 156 392 758 1212 1462 c 0 0 0 0 0 1507 1601 1750 3427 758 580 3700 4239 173 85 154 262 4709 4719 514 448 1034 1563 1330 g 0 0 0 0 0 1371 1106 1265 689 712 2867 556 192 289 4853 4825 288 160 127 210 3500 2489 1442 1287 t 0 0 0 0 0 1273 978 1161 544 2690 1244 471 291 138 85 79 732 126 187 4275 815 874 938 1076
positions_7nt_m2_shift5 (positions_7nt_m2)				; oligos_7nt_mkv5_m1 versus positions_7nt_m2; m=6/12; ncol2=18; w=-3; offset=-3; strand=D; shift=5; score=0.696804; -----smsCtgCCAGGACCykss- ; cor=; Ncor= a 0 0 0 0 0 931 1270 801 348 789 347 278 262 4101 132 92 3961 134 210 258 1161 833 1099 0 c 0 0 0 0 0 1529 1595 1745 3488 772 490 3883 4279 270 164 185 282 4346 4190 2798 971 1227 1358 0 g 0 0 0 0 0 1235 1059 1275 604 596 2859 360 154 331 4453 4481 282 196 204 310 1466 1791 1466 0 t 0 0 0 0 0 1143 914 1017 398 2681 1142 317 143 136 89 80 313 162 234 1472 1240 987 915 0
positions_6nt_m3_rc_shift2 (positions_6nt_m3_rc)				; oligos_7nt_mkv5_m1 versus positions_6nt_m3_rc; m=7/12; ncol2=24; w=-6; offset=-6; strand=R; shift=2; score=0.581076; --yvrgtCCTGsCAGGACCTgscm ; cor=; Ncor= a 0 0 282 295 359 93 160 82 46 100 44 126 120 1007 26 47 860 65 74 82 111 188 223 365 c 0 0 337 299 204 139 183 865 1028 64 62 348 935 55 15 68 66 972 969 133 105 352 462 297 g 0 0 243 320 335 758 122 117 39 83 896 541 57 63 1095 1009 88 73 67 78 771 395 274 262 t 0 0 292 240 256 164 689 90 41 907 152 139 42 29 18 30 140 44 44 861 167 219 195 230
positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)				; oligos_7nt_mkv5_m1 versus positions_7nt_m3_rc; m=8/12; ncol2=16; w=-3; offset=-3; strand=R; shift=5; score=0.571239; -----smcCTgCCAGGACyyk--- ; cor=; Ncor= a 0 0 0 0 0 829 1197 702 287 534 202 190 226 3741 111 96 3596 192 394 512 785 0 0 0 c 0 0 0 0 0 1272 1295 1488 3264 371 312 3563 3729 135 83 139 198 3680 1589 1230 956 0 0 0 g 0 0 0 0 0 1089 812 1038 325 420 2804 231 98 178 3869 3859 187 123 295 877 1252 0 0 0 t 0 0 0 0 0 984 870 946 298 2849 856 190 121 120 111 80 193 179 1896 1555 1181 0 0 0
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; oligos_7nt_mkv5_m1 versus positions_6nt_m2_rc; m=9/12; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.556443; scmrGGtCCTGgCAGGACCtggss ; cor=; Ncor= a 179 209 365 282 85 62 117 60 25 70 44 109 132 885 27 63 720 101 110 109 128 205 257 242 c 313 390 295 139 81 107 120 829 942 58 44 259 816 62 14 72 77 793 779 145 106 246 296 292 g 306 248 191 456 766 780 107 97 37 70 843 584 59 57 984 863 113 95 89 97 675 406 317 275 t 245 196 192 166 111 94 699 57 39 845 112 91 36 39 18 45 133 54 65 692 134 186 173 234
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; oligos_7nt_mkv5_m1 versus positions_6nt_m1_rc; m=10/12; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.535571; sscAGGTCCTGgCAGGaCCtggss ; cor=; Ncor= a 157 195 148 654 59 35 119 46 21 46 44 97 133 801 25 64 580 102 114 144 122 207 221 237 c 289 329 606 68 65 86 94 791 881 64 35 196 725 45 16 93 98 673 676 137 118 231 262 270 g 283 242 106 130 753 765 78 74 24 49 763 566 55 63 888 737 131 119 101 92 583 328 290 247 t 226 189 95 103 78 69 664 44 29 796 113 96 42 46 26 61 146 61 64 582 132 189 182 201
positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)				; oligos_7nt_mkv5_m1 versus positions_6nt_m4_rc; m=11/12; ncol2=21; w=-6; offset=-6; strand=R; shift=2; score=0.522145; --mrrGTCCTGgCAGGTCCTkgm- ; cor=; Ncor= a 0 0 324 382 383 100 101 61 60 81 48 119 199 962 24 66 207 65 90 88 168 253 303 0 c 0 0 320 264 155 84 116 953 989 83 86 248 794 57 23 90 54 936 933 107 176 238 342 0 g 0 0 264 319 384 851 123 80 41 78 898 667 78 78 1066 948 93 90 57 88 426 403 274 0 t 0 0 243 186 229 116 811 57 61 909 119 117 80 54 38 47 797 60 71 868 381 257 232 0
oligos_7nt_mkv5_m5_rc_shift6 (oligos_7nt_mkv5_m5_rc)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m5_rc; m=12/12; ncol2=11; w=-2; offset=-2; strand=R; shift=6; score=0.402914; ------yyCTTCCAGga------- ; cor=; Ncor= a 0 0 0 0 0 0 1316 1315 318 204 232 398 64 4612 73 1086 1986 0 0 0 0 0 0 0 c 0 0 0 0 0 0 1402 1469 4813 130 121 4760 4977 312 146 1083 1161 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1147 1180 122 194 135 81 115 253 4959 1980 948 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1485 1386 97 4822 4862 111 194 173 172 1201 1255 0 0 0 0 0 0 0