One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/08/peak-motifs.2026-01-08.110552_2026-01-08.110552_itajwi/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/08/peak-motifs.2026-01-08.110552_2026-01-08.110552_itajwi/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift11 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift11 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------scAGAGGGCAsy ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 c 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 g 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 t 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125

oligos_6nt_mkv4_m4_shift11 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------scAGAGGGCAsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 c 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 g 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 t 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125

oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m1; m=2/8; ncol2=14; w=-2; offset=-2; strand=D; shift=9; score=0.738757; ---------caCyAGAGGGCGsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561

oligos_6nt_mkv4_m1_rc_shift10 (oligos_6nt_mkv4_m1_rc)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m1_rc; m=3/8; ncol2=13; w=-1; offset=-1; strand=R; shift=10; score=0.707585; ----------rscAGGGGGCGsb ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 c 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 g 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 t 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082

oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)
; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m2_rc; m=4/8; ncol2=14; w=-2; offset=-2; strand=R; shift=9; score=0.602327; ---------srGcAGGGGGCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 c 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 g 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 t 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890

positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)
; oligos_6nt_mkv4_m4 versus positions_7nt_m4_rc; m=5/8; ncol2=24; w=-6; offset=-6; strand=R; shift=5; score=0.461479; -----yggCCACyAGrGGGCAGC ; cor=; Ncor= a 0 0 0 0 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 c 0 0 0 0 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 g 0 0 0 0 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 t 0 0 0 0 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324

positions_6nt_m4_shift0 (positions_6nt_m4)
; oligos_6nt_mkv4_m4 versus positions_6nt_m4; m=6/8; ncol2=24; w=-11; offset=-11; strand=D; shift=0; score=0.405609; msbaGgkGsCAGCAGAGGGCGCy ; cor=; Ncor= a 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 c 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 g 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 t 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212

positions_6nt_m3_shift6 (positions_6nt_m3)
; oligos_6nt_mkv4_m4 versus positions_6nt_m3; m=7/8; ncol2=24; w=-5; offset=-5; strand=D; shift=6; score=0.400843; ------sgCCAGCAGAGGGCGCC ; cor=; Ncor= a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110

positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)
; oligos_6nt_mkv4_m4 versus positions_6nt_m1_rc; m=8/8; ncol2=24; w=-7; offset=-7; strand=R; shift=4; score=0.40069; ----gyGGCCACyAGRGGGCGCt ; cor=; Ncor= a 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 c 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 g 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 t 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift6 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift6 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=24; shift=6; ncol=30; ------rscAGGGGGCGCTGCCaCCtmsys ; Alignment reference a 0 0 0 0 0 0 231 76 66 494 12 78 36 29 33 22 53 13 20 26 27 44 327 21 36 53 206 94 102 87 c 0 0 0 0 0 0 147 246 359 42 28 42 69 46 64 523 24 547 105 51 477 446 81 490 515 152 197 161 211 169 g 0 0 0 0 0 0 174 225 120 58 569 490 447 518 507 22 536 59 54 540 50 88 154 74 44 63 141 318 156 303 t 0 0 0 0 0 0 79 84 86 37 22 21 79 38 27 64 18 12 452 14 77 53 69 46 36 363 87 58 162 72

positions_6nt_m5_shift6 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------rscAGGGGGCGCTGCCaCCtmsys ; cor=; Ncor= a 0 0 0 0 0 0 231 76 66 494 12 78 36 29 33 22 53 13 20 26 27 44 327 21 36 53 206 94 102 87 c 0 0 0 0 0 0 147 246 359 42 28 42 69 46 64 523 24 547 105 51 477 446 81 490 515 152 197 161 211 169 g 0 0 0 0 0 0 174 225 120 58 569 490 447 518 507 22 536 59 54 540 50 88 154 74 44 63 141 318 156 303 t 0 0 0 0 0 0 79 84 86 37 22 21 79 38 27 64 18 12 452 14 77 53 69 46 36 363 87 58 162 72

positions_6nt_m2_rc_shift5 (positions_6nt_m2_rc)
; positions_6nt_m5 versus positions_6nt_m2_rc; m=2/8; ncol2=24; w=-1; offset=-1; strand=R; shift=5; score=0.769472; -----cscCtGGtGGCGCTGCCaCCaGss- ; cor=; Ncor= a 0 0 0 0 0 32 59 21 20 48 4 9 19 7 16 12 15 8 14 8 15 16 125 7 14 136 11 42 39 0 c 0 0 0 0 0 127 71 147 179 23 18 30 43 18 28 184 22 204 41 7 191 184 31 183 198 41 42 84 69 0 g 0 0 0 0 0 50 77 58 28 25 213 197 30 211 192 16 190 20 19 222 22 28 59 33 24 32 173 88 88 0 t 0 0 0 0 0 34 36 17 16 147 8 7 151 7 7 31 16 11 169 6 15 15 28 20 7 34 17 29 47 0

positions_7nt_m3_rc_shift3 (positions_7nt_m3_rc)
; positions_6nt_m5 versus positions_7nt_m3_rc; m=3/8; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.584707; ---gcCaCCAGGGGGCGCCccckGscs--- ; cor=; Ncor= a 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 99 69 103 97 60 104 113 106 0 0 0 c 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 509 473 502 110 130 310 393 319 0 0 0 g 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 133 132 110 230 531 284 110 224 0 0 0 t 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112 32 99 58 336 52 75 157 124 0 0 0

oligos_6nt_mkv4_m1_rc_shift6 (oligos_6nt_mkv4_m1_rc)
; positions_6nt_m5 versus oligos_6nt_mkv4_m1_rc; m=4/8; ncol2=13; w=0; offset=0; strand=R; shift=6; score=0.501418; ------rscAGGGGGCGsb----------- ; cor=; Ncor= a 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0 0 0 0 0 0 0

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; positions_6nt_m5 versus positions_6nt_m1_rc; m=5/8; ncol2=24; w=-6; offset=-6; strand=R; shift=0; score=0.497444; gyGGCCACyAGRGGGCGCtgccgs------ ; cor=; Ncor= a 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 81 255 218 182 0 0 0 0 0 0 c 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 625 454 194 411 0 0 0 0 0 0 g 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 183 270 596 393 0 0 0 0 0 0 t 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75 290 200 171 193 0 0 0 0 0 0

oligos_7nt_mkv5_m2_rc_shift5 (oligos_7nt_mkv5_m2_rc)
; positions_6nt_m5 versus oligos_7nt_mkv5_m2_rc; m=6/8; ncol2=14; w=-1; offset=-1; strand=R; shift=5; score=0.475997; -----srGcAGGGGGCGss----------- ; cor=; Ncor= a 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0 0 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv5_m1_shift5 (oligos_7nt_mkv5_m1)
; positions_6nt_m5 versus oligos_7nt_mkv5_m1; m=7/8; ncol2=14; w=-1; offset=-1; strand=D; shift=5; score=0.42372; -----caCyAGAGGGCGsy----------- ; cor=; Ncor= a 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv5_m3_rc_shift7 (oligos_7nt_mkv5_m3_rc)
; positions_6nt_m5 versus oligos_7nt_mkv5_m3_rc; m=8/8; ncol2=12; w=0; offset=1; strand=R; shift=7; score=0.422979; -------ssAGGTGGCGsy----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 847 1148 6438 56 446 323 47 75 430 1016 1004 972 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 2951 2842 365 120 127 482 113 97 5895 314 3116 2510 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 2875 1916 272 7035 6653 1055 7070 7005 484 5673 2356 1618 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 594 1361 192 56 41 5407 37 90 458 264 791 2167 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift5 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=24; shift=5; ncol=29; -----gsctcTGCTGCCCyCTrGTGGccr ; Alignment reference a 0 0 0 0 0 249 341 169 250 281 97 324 60 70 52 89 15 478 31 9 62 1013 44 101 4 115 228 432 838 c 0 0 0 0 0 435 612 1237 235 1223 160 133 1389 294 20 1741 1869 1397 580 1889 106 142 356 138 10 84 1072 782 302 g 0 0 0 0 0 844 508 186 310 219 194 1355 394 29 1789 47 11 18 26 13 42 573 1468 59 1909 1620 191 317 570 t 0 0 0 0 0 401 468 337 1134 206 1478 117 86 1536 68 52 34 36 1292 18 1719 201 61 1631 6 110 438 398 219

positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/13; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----gsctcTGCTGCCCyCTrGTGGccr ; cor=; Ncor= a 0 0 0 0 0 249 341 169 250 281 97 324 60 70 52 89 15 478 31 9 62 1013 44 101 4 115 228 432 838 c 0 0 0 0 0 435 612 1237 235 1223 160 133 1389 294 20 1741 1869 1397 580 1889 106 142 356 138 10 84 1072 782 302 g 0 0 0 0 0 844 508 186 310 219 194 1355 394 29 1789 47 11 18 26 13 42 573 1468 59 1909 1620 191 317 570 t 0 0 0 0 0 401 468 337 1134 206 1478 117 86 1536 68 52 34 36 1292 18 1719 201 61 1631 6 110 438 398 219

positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)
; positions_7nt_m4 versus positions_7nt_m1_rc; m=2/13; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.921854; -----gsctcTGCTGCCmCCTgsTGGccr ; cor=; Ncor= a 0 0 0 0 0 257 247 179 231 225 63 244 44 42 49 63 8 1103 12 30 109 282 77 117 13 69 233 417 698 c 0 0 0 0 0 443 584 1163 169 1163 156 102 1359 316 25 1657 1760 575 1355 1724 74 146 975 135 21 81 1023 699 306 g 0 0 0 0 0 721 521 178 270 224 153 1361 319 40 1672 42 5 58 38 15 50 1196 697 60 1747 1540 166 359 576 t 0 0 0 0 0 381 450 282 1132 190 1430 95 80 1404 56 40 29 66 397 33 1569 178 53 1490 21 112 380 327 222

positions_7nt_m5_rc_shift6 (positions_7nt_m5_rc)
; positions_7nt_m4 versus positions_7nt_m5_rc; m=3/13; ncol2=24; w=0; offset=1; strand=R; shift=6; score=0.862568; ------scycTGCTGCCmCCTrGTGGccr ; cor=; Ncor= a 0 0 0 0 0 0 279 268 283 313 64 291 39 34 45 90 12 1136 10 26 100 893 44 102 6 67 198 355 748 c 0 0 0 0 0 0 558 733 558 1003 141 107 1284 243 20 1500 1649 436 1261 1614 111 112 210 110 8 55 978 753 243 g 0 0 0 0 0 0 507 268 314 179 168 1205 274 55 1586 53 6 52 24 11 48 498 1395 64 1665 1481 165 281 477 t 0 0 0 0 0 0 341 416 530 190 1312 82 88 1353 34 42 18 61 390 34 1426 182 36 1409 6 82 344 296 217

positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_7nt_m4 versus positions_6nt_m1; m=4/13; ncol2=24; w=0; offset=1; strand=D; shift=6; score=0.706671; ------scggcaGCGCCCYCTrGTGGCCr ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 58 94 126 482 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 51 899 836 203 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 998 74 108 359 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9 72 112 109 135

positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)
; positions_7nt_m4 versus positions_6nt_m3_rc; m=5/13; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.655757; ----rstmgaGGGCGCCCTCTGCTGGcs- ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 32 30 111 126 0 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 29 27 337 267 0 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 596 581 89 174 0 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556 17 36 137 107 0

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; positions_7nt_m4 versus positions_7nt_m2_rc; m=6/13; ncol2=24; w=-2; offset=-2; strand=R; shift=3; score=0.605706; ---sgsCygstGGCGCCCTCTGCTGgc-- ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 9 62 68 0 0 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 52 95 272 0 0 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 469 304 96 0 0 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425 14 83 108 0 0

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_7nt_m4 versus positions_6nt_m4_rc; m=7/13; ncol2=24; w=-5; offset=-5; strand=R; shift=0; score=0.526055; srGCGCCCTCTGCTGsCmcCtvsk----- ; cor=; Ncor= a 106 212 38 53 46 26 24 43 25 14 15 76 15 30 9 49 20 372 91 60 60 256 82 112 0 0 0 0 0 c 264 176 91 546 36 579 642 680 122 718 42 37 649 85 27 453 690 229 453 618 80 196 244 189 0 0 0 0 0 g 254 274 564 78 659 117 46 28 60 30 32 643 104 31 734 226 25 94 154 55 114 227 331 213 0 0 0 0 0 t 155 117 86 102 38 57 67 28 572 17 690 23 11 633 9 51 44 84 81 46 525 100 122 265 0 0 0 0 0

oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)
; positions_7nt_m4 versus oligos_7nt_mkv5_m1_rc; m=8/13; ncol2=14; w=0; offset=6; strand=R; shift=11; score=0.498802; -----------rsCGCCCTCTrGtg---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 386 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 829 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 3571 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570 561 0 0 0 0

oligos_6nt_mkv4_m2_rc_shift16 (oligos_6nt_mkv4_m2_rc)
; positions_7nt_m4 versus oligos_6nt_mkv4_m2_rc; m=9/13; ncol2=12; w=0; offset=11; strand=R; shift=16; score=0.474813; ----------------cmTCTAGTGGym- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 433 1560 84 76 103 3794 96 199 64 203 979 1293 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3266 2209 649 4682 217 121 247 203 39 202 1801 1581 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 598 617 123 105 41 647 4527 182 4781 4349 902 1003 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 653 564 4094 87 4589 388 80 4366 66 196 1268 1073 0

oligos_6nt_mkv4_m4_rc_shift11 (oligos_6nt_mkv4_m4_rc)
; positions_7nt_m4 versus oligos_6nt_mkv4_m4_rc; m=10/13; ncol2=12; w=0; offset=6; strand=R; shift=11; score=0.461479; -----------rsTGCCCTCTgs------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2125 930 432 120 248 130 670 234 52 248 1904 958 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1795 3466 864 320 7303 7701 7160 733 7646 361 1647 2899 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2692 2480 278 7403 371 93 77 128 285 111 3185 2983 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1576 1312 6614 345 266 264 281 7093 205 7468 1452 1348 0 0 0 0 0 0

oligos_7nt_mkv5_m5_rc_shift17 (oligos_7nt_mkv5_m5_rc)
; positions_7nt_m4 versus oligos_7nt_mkv5_m5_rc; m=11/13; ncol2=12; w=0; offset=12; strand=R; shift=17; score=0.450852; -----------------myCTAGTGGTcr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1419 404 63 94 3163 71 141 34 77 324 854 1557 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1517 1562 3793 195 118 122 173 39 124 585 1239 744 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 599 479 81 48 488 3760 139 3889 3692 240 999 1041 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 480 1570 78 3678 246 62 3562 53 122 2866 923 673

oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)
; positions_7nt_m4 versus oligos_6nt_mkv4_m1; m=12/13; ncol2=13; w=0; offset=6; strand=D; shift=11; score=0.411561; -----------vsCGCCCCCTgsy----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083 0 0 0 0 0

oligos_7nt_mkv5_m4_rc_shift8 (oligos_7nt_mkv5_m4_rc)
; positions_7nt_m4 versus oligos_7nt_mkv5_m4_rc; m=13/13; ncol2=11; w=0; offset=3; strand=R; shift=8; score=0.403846; --------gsTGCTGCCvc---------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1338 1302 116 455 130 211 218 177 73 1827 864 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1634 2749 570 191 6393 418 180 6332 6400 1915 2798 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 2302 1947 232 6156 252 356 6417 204 337 2001 1690 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 1645 921 6001 117 144 5934 104 206 109 1176 1567 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift11 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=14; shift=11; ncol=25; -----------ssCGCCCCCTgCys ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849

oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/13; ncol2=14; w=0; offset=0; strand=D; shift=11; score= 1; -----------ssCGCCCCCTgCys ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849

oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=2/13; ncol2=13; w=0; offset=0; strand=D; shift=11; score=0.901385; -----------vsCGCCCCCTgsy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 0 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 0 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 0 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083 0

oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m1_rc; m=3/13; ncol2=14; w=0; offset=0; strand=R; shift=11; score=0.810143; -----------rsCGCCCTCTrGtg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 386 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 829 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 3571 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570 561

oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=4/13; ncol2=12; w=0; offset=0; strand=D; shift=11; score=0.747688; -----------rsCGCCACCTss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 0 0 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847 0 0

oligos_6nt_mkv4_m4_rc_shift11 (oligos_6nt_mkv4_m4_rc)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m4_rc; m=5/13; ncol2=12; w=0; offset=0; strand=R; shift=11; score=0.602327; -----------rsTGCCCTCTgs-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2125 930 432 120 248 130 670 234 52 248 1904 958 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1795 3466 864 320 7303 7701 7160 733 7646 361 1647 2899 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2692 2480 278 7403 371 93 77 128 285 111 3185 2983 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1576 1312 6614 345 266 264 281 7093 205 7468 1452 1348 0 0

positions_7nt_m3_shift3 (positions_7nt_m3)
; oligos_7nt_mkv5_m2 versus positions_7nt_m3; m=6/13; ncol2=24; w=-8; offset=-8; strand=D; shift=3; score=0.519493; ---sgsCmgggGGCGCCCCCTGGtG ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 15 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 62 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 682 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518 14

positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)
; oligos_7nt_mkv5_m2 versus positions_6nt_m3_rc; m=7/13; ncol2=24; w=-7; offset=-7; strand=R; shift=4; score=0.494956; ----rstmgaGGGCGCCCTCTGCTG ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 32 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 29 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 596 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556 17

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; oligos_7nt_mkv5_m2 versus positions_7nt_m2_rc; m=8/13; ncol2=24; w=-8; offset=-8; strand=R; shift=3; score=0.492998; ---sgsCygstGGCGCCCTCTGCTG ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 9 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 52 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 469 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425 14

positions_6nt_m4_rc_shift10 (positions_6nt_m4_rc)
; oligos_7nt_mkv5_m2 versus positions_6nt_m4_rc; m=9/13; ncol2=24; w=-1; offset=-1; strand=R; shift=10; score=0.487623; ----------srGCGCCCTCTGCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 106 212 38 53 46 26 24 43 25 14 15 76 15 30 9 c 0 0 0 0 0 0 0 0 0 0 264 176 91 546 36 579 642 680 122 718 42 37 649 85 27 g 0 0 0 0 0 0 0 0 0 0 254 274 564 78 659 117 46 28 60 30 32 643 104 31 734 t 0 0 0 0 0 0 0 0 0 0 155 117 86 102 38 57 67 28 572 17 690 23 11 633 9

positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)
; oligos_7nt_mkv5_m2 versus positions_6nt_m5_rc; m=10/13; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.475997; srskaGGtGGCAGCGCCCCCTgsy- ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 0 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 0 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 0 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231 0

positions_6nt_m1_shift6 (positions_6nt_m1)
; oligos_7nt_mkv5_m2 versus positions_6nt_m1; m=11/13; ncol2=24; w=-5; offset=-5; strand=D; shift=6; score=0.448004; ------scggcaGCGCCCYCTrGTG ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_7nt_mkv5_m2 versus positions_6nt_m2; m=12/13; ncol2=24; w=-10; offset=-10; strand=D; shift=1; score=0.438686; -ssCtGGtGGCAGCGCCaCCaGgsg ; cor=; Ncor= a 0 47 29 17 34 7 20 28 15 15 6 169 11 16 31 7 7 151 7 8 147 16 17 36 34 c 0 88 88 173 32 24 33 59 28 22 222 19 20 190 16 192 211 30 197 213 25 28 58 77 50 g 0 69 84 42 41 198 183 31 184 191 7 41 204 22 184 28 18 43 30 18 23 179 147 71 127 t 0 39 42 11 136 14 7 125 16 15 8 14 8 15 12 16 7 19 9 4 48 20 21 59 32

positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)
; oligos_7nt_mkv5_m2 versus positions_7nt_m1_rc; m=13/13; ncol2=24; w=-6; offset=-6; strand=R; shift=5; score=0.438432; -----gsctcTGCTGCCmCCTgsTG ; cor=; Ncor= a 0 0 0 0 0 257 247 179 231 225 63 244 44 42 49 63 8 1103 12 30 109 282 77 117 13 c 0 0 0 0 0 443 584 1163 169 1163 156 102 1359 316 25 1657 1760 575 1355 1724 74 146 975 135 21 g 0 0 0 0 0 721 521 178 270 224 153 1361 319 40 1672 42 5 58 38 15 50 1196 697 60 1747 t 0 0 0 0 0 381 450 282 1132 190 1430 95 80 1404 56 40 29 66 397 33 1569 178 53 1490 21

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; ssCGmGCGss ; Alignment reference a 939 868 129 23 3008 225 134 56 711 869 c 2230 2010 5567 92 1676 354 5736 179 2555 1968 g 2030 2497 262 5750 859 5372 81 5756 1921 2357 t 870 694 111 204 526 118 118 78 882 875

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; ssCGmGCGss ; cor=; Ncor= a 939 868 129 23 3008 225 134 56 711 869 c 2230 2010 5567 92 1676 354 5736 179 2555 1968 g 2030 2497 262 5750 859 5372 81 5756 1921 2357 t 870 694 111 204 526 118 118 78 882 875

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift9 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=14; shift=9; ncol=23; ---------caCyAGAGGGCGsy ; Alignment reference a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561

oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/15; ncol2=14; w=0; offset=0; strand=D; shift=9; score= 1; ---------caCyAGAGGGCGsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561

oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m2_rc; m=2/15; ncol2=14; w=0; offset=0; strand=R; shift=9; score=0.810143; ---------srGcAGGGGGCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 c 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 g 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 t 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890

oligos_6nt_mkv4_m1_rc_shift10 (oligos_6nt_mkv4_m1_rc)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1_rc; m=3/15; ncol2=13; w=0; offset=1; strand=R; shift=10; score=0.805128; ----------rscAGGGGGCGsb ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 c 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 g 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 t 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082

oligos_6nt_mkv4_m4_shift11 (oligos_6nt_mkv4_m4)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m4; m=4/15; ncol2=12; w=0; offset=2; strand=D; shift=11; score=0.738757; -----------scAGAGGGCAsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 c 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 g 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 t 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125

oligos_7nt_mkv5_m3_rc_shift11 (oligos_7nt_mkv5_m3_rc)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m3_rc; m=5/15; ncol2=12; w=0; offset=2; strand=R; shift=11; score=0.645417; -----------ssAGGTGGCGsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 847 1148 6438 56 446 323 47 75 430 1016 1004 972 c 0 0 0 0 0 0 0 0 0 0 0 2951 2842 365 120 127 482 113 97 5895 314 3116 2510 g 0 0 0 0 0 0 0 0 0 0 0 2875 1916 272 7035 6653 1055 7070 7005 484 5673 2356 1618 t 0 0 0 0 0 0 0 0 0 0 0 594 1361 192 56 41 5407 37 90 458 264 791 2167

positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)
; oligos_7nt_mkv5_m1 versus positions_6nt_m1_rc; m=6/15; ncol2=24; w=-5; offset=-5; strand=R; shift=4; score=0.551646; ----gyGGCCACyAGRGGGCGCt ; cor=; Ncor= a 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 c 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 g 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 t 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795

positions_6nt_m3_shift6 (positions_6nt_m3)
; oligos_7nt_mkv5_m1 versus positions_6nt_m3; m=7/15; ncol2=24; w=-3; offset=-3; strand=D; shift=6; score=0.509096; ------sgCCAGCAGAGGGCGCC ; cor=; Ncor= a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110

positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)
; oligos_7nt_mkv5_m1 versus positions_7nt_m3_rc; m=8/15; ncol2=24; w=-2; offset=-2; strand=R; shift=7; score=0.500673; -------gcCaCCAGGGGGCGCC ; cor=; Ncor= a 0 0 0 0 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 c 0 0 0 0 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 g 0 0 0 0 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 t 0 0 0 0 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112

positions_7nt_m2_shift7 (positions_7nt_m2)
; oligos_7nt_mkv5_m1 versus positions_7nt_m2; m=9/15; ncol2=24; w=-2; offset=-2; strand=D; shift=7; score=0.500175; -------gcCAGCAGAGGGCGCC ; cor=; Ncor= a 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 c 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 g 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 t 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60

positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)
; oligos_7nt_mkv5_m1 versus positions_7nt_m4_rc; m=10/15; ncol2=24; w=-4; offset=-4; strand=R; shift=5; score=0.498802; -----yggCCACyAGrGGGCAGC ; cor=; Ncor= a 0 0 0 0 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 c 0 0 0 0 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 g 0 0 0 0 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 t 0 0 0 0 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324

positions_6nt_m4_shift0 (positions_6nt_m4)
; oligos_7nt_mkv5_m1 versus positions_6nt_m4; m=11/15; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.496932; msbaGgkGsCAGCAGAGGGCGCy ; cor=; Ncor= a 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 c 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 g 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 t 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212

oligos_6nt_mkv4_m2_shift6 (oligos_6nt_mkv4_m2)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m2; m=12/15; ncol2=12; w=-3; offset=-3; strand=D; shift=6; score=0.474054; ------krCCACTAGAkg----- ; cor=; Ncor= a 0 0 0 0 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 653 0 0 0 0 0 c 0 0 0 0 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 598 0 0 0 0 0 g 0 0 0 0 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 3266 0 0 0 0 0 t 0 0 0 0 0 0 1293 979 203 64 199 96 3794 103 76 84 1560 433 0 0 0 0 0

positions_7nt_m5_shift4 (positions_7nt_m5)
; oligos_7nt_mkv5_m1 versus positions_7nt_m5; m=13/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.43053; ----ryggCCACyAGGkGGCAGC ; cor=; Ncor= a 0 0 0 0 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 c 0 0 0 0 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 g 0 0 0 0 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 t 0 0 0 0 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291

positions_6nt_m5_shift10 (positions_6nt_m5)
; oligos_7nt_mkv5_m1 versus positions_6nt_m5; m=14/15; ncol2=24; w=0; offset=1; strand=D; shift=10; score=0.42372; ----------rscAGGGGGCGCT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 231 76 66 494 12 78 36 29 33 22 53 13 20 c 0 0 0 0 0 0 0 0 0 0 147 246 359 42 28 42 69 46 64 523 24 547 105 g 0 0 0 0 0 0 0 0 0 0 174 225 120 58 569 490 447 518 507 22 536 59 54 t 0 0 0 0 0 0 0 0 0 0 79 84 86 37 22 21 79 38 27 64 18 12 452

positions_7nt_m1_shift5 (positions_7nt_m1)
; oligos_7nt_mkv5_m1 versus positions_7nt_m1; m=15/15; ncol2=24; w=-4; offset=-4; strand=D; shift=5; score=0.412872; -----yggCCAscAGGkGGCAGC ; cor=; Ncor= a 0 0 0 0 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 c 0 0 0 0 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 g 0 0 0 0 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 t 0 0 0 0 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift6 ; 15 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=24; shift=6; ncol=30; ------scggcaGCGCCCYCTrGTGGCCrc ; Alignment reference a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 58 94 126 482 260 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 51 899 836 203 368 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 998 74 108 359 284 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9 72 112 109 135 267

positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/14; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------scggcaGCGCCCYCTrGTGGCCrc ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 58 94 126 482 260 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 51 899 836 203 368 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 998 74 108 359 284 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9 72 112 109 135 267

positions_7nt_m5_rc_shift6 (positions_7nt_m5_rc)
; positions_6nt_m1 versus positions_7nt_m5_rc; m=2/14; ncol2=24; w=0; offset=0; strand=R; shift=6; score=0.717491; ------scycTGCTGCCmCCTrGTGGccry ; cor=; Ncor= a 0 0 0 0 0 0 279 268 283 313 64 291 39 34 45 90 12 1136 10 26 100 893 44 102 6 67 198 355 748 380 c 0 0 0 0 0 0 558 733 558 1003 141 107 1284 243 20 1500 1649 436 1261 1614 111 112 210 110 8 55 978 753 243 501 g 0 0 0 0 0 0 507 268 314 179 168 1205 274 55 1586 53 6 52 24 11 48 498 1395 64 1665 1481 165 281 477 359 t 0 0 0 0 0 0 341 416 530 190 1312 82 88 1353 34 42 18 61 390 34 1426 182 36 1409 6 82 344 296 217 445

positions_7nt_m4_shift5 (positions_7nt_m4)
; positions_6nt_m1 versus positions_7nt_m4; m=3/14; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.706671; -----gsctcTGCTGCCCyCTrGTGGccr- ; cor=; Ncor= a 0 0 0 0 0 249 341 169 250 281 97 324 60 70 52 89 15 478 31 9 62 1013 44 101 4 115 228 432 838 0 c 0 0 0 0 0 435 612 1237 235 1223 160 133 1389 294 20 1741 1869 1397 580 1889 106 142 356 138 10 84 1072 782 302 0 g 0 0 0 0 0 844 508 186 310 219 194 1355 394 29 1789 47 11 18 26 13 42 573 1468 59 1909 1620 191 317 570 0 t 0 0 0 0 0 401 468 337 1134 206 1478 117 86 1536 68 52 34 36 1292 18 1719 201 61 1631 6 110 438 398 219 0

positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)
; positions_6nt_m1 versus positions_6nt_m3_rc; m=4/14; ncol2=24; w=-2; offset=-2; strand=R; shift=4; score=0.693247; ----rstmgaGGGCGCCCTCTGCTGGcs-- ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 32 30 111 126 0 0 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 29 27 337 267 0 0 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 596 581 89 174 0 0 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556 17 36 137 107 0 0

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_6nt_m1 versus positions_7nt_m3; m=5/14; ncol2=24; w=-3; offset=-3; strand=D; shift=3; score=0.650383; ---sgsCmgggGGCGCCCCCTGGtGgc--- ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 15 67 104 0 0 0 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 62 119 394 0 0 0 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 682 494 134 0 0 0 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518 14 93 141 0 0 0

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; positions_6nt_m1 versus positions_7nt_m2_rc; m=6/14; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.621257; ---sgsCygstGGCGCCCTCTGCTGgc--- ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 9 62 68 0 0 0 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 52 95 272 0 0 0 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 469 304 96 0 0 0 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425 14 83 108 0 0 0

positions_6nt_m4_rc_shift10 (positions_6nt_m4_rc)
; positions_6nt_m1 versus positions_6nt_m4_rc; m=7/14; ncol2=24; w=0; offset=4; strand=R; shift=10; score=0.557373; ----------srGCGCCCTCTGCTGsCmcC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 106 212 38 53 46 26 24 43 25 14 15 76 15 30 9 49 20 372 91 60 c 0 0 0 0 0 0 0 0 0 0 264 176 91 546 36 579 642 680 122 718 42 37 649 85 27 453 690 229 453 618 g 0 0 0 0 0 0 0 0 0 0 254 274 564 78 659 117 46 28 60 30 32 643 104 31 734 226 25 94 154 55 t 0 0 0 0 0 0 0 0 0 0 155 117 86 102 38 57 67 28 572 17 690 23 11 633 9 51 44 84 81 46

oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)
; positions_6nt_m1 versus oligos_7nt_mkv5_m1_rc; m=8/14; ncol2=14; w=0; offset=5; strand=R; shift=11; score=0.551646; -----------rsCGCCCTCTrGtg----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 386 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 829 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 3571 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570 561 0 0 0 0 0

positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)
; positions_6nt_m1 versus positions_6nt_m5_rc; m=9/14; ncol2=24; w=-6; offset=-6; strand=R; shift=0; score=0.497444; srskaGGtGGCAGCGCCCCCTgsy------ ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 0 0 0 0 0 0 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 0 0 0 0 0 0 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 0 0 0 0 0 0 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231 0 0 0 0 0 0

oligos_6nt_mkv4_m2_rc_shift16 (oligos_6nt_mkv4_m2_rc)
; positions_6nt_m1 versus oligos_6nt_mkv4_m2_rc; m=10/14; ncol2=12; w=0; offset=10; strand=R; shift=16; score=0.457888; ----------------cmTCTAGTGGym-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 433 1560 84 76 103 3794 96 199 64 203 979 1293 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3266 2209 649 4682 217 121 247 203 39 202 1801 1581 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 598 617 123 105 41 647 4527 182 4781 4349 902 1003 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 653 564 4094 87 4589 388 80 4366 66 196 1268 1073 0 0

oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)
; positions_6nt_m1 versus oligos_6nt_mkv4_m1; m=11/14; ncol2=13; w=0; offset=5; strand=D; shift=11; score=0.453174; -----------vsCGCCCCCTgsy------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083 0 0 0 0 0 0

oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)
; positions_6nt_m1 versus oligos_7nt_mkv5_m2; m=12/14; ncol2=14; w=0; offset=5; strand=D; shift=11; score=0.448004; -----------ssCGCCCCCTgCys----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849 0 0 0 0 0

oligos_7nt_mkv5_m5_rc_shift17 (oligos_7nt_mkv5_m5_rc)
; positions_6nt_m1 versus oligos_7nt_mkv5_m5_rc; m=13/14; ncol2=12; w=0; offset=11; strand=R; shift=17; score=0.420613; -----------------myCTAGTGGTcr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1419 404 63 94 3163 71 141 34 77 324 854 1557 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1517 1562 3793 195 118 122 173 39 124 585 1239 744 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 599 479 81 48 488 3760 139 3889 3692 240 999 1041 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 480 1570 78 3678 246 62 3562 53 122 2866 923 673 0

oligos_6nt_mkv4_m4_rc_shift11 (oligos_6nt_mkv4_m4_rc)
; positions_6nt_m1 versus oligos_6nt_mkv4_m4_rc; m=14/14; ncol2=12; w=0; offset=5; strand=R; shift=11; score=0.40069; -----------rsTGCCCTCTgs------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2125 930 432 120 248 130 670 234 52 248 1904 958 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1795 3466 864 320 7303 7701 7160 733 7646 361 1647 2899 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2692 2480 278 7403 371 93 77 128 285 111 3185 2983 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1576 1312 6614 345 266 264 281 7093 205 7468 1452 1348 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift3 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---sgsCmgggGGCGCCCCCTGGtGgc ; Alignment reference a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 15 67 104 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 62 119 394 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 682 494 134 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518 14 93 141

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---sgsCmgggGGCGCCCCCTGGtGgc ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 15 67 104 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 62 119 394 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 682 494 134 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518 14 93 141

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; positions_7nt_m3 versus positions_7nt_m2_rc; m=2/10; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.861902; ---sgsCygstGGCGCCCTCTGCTGgc ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 9 62 68 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 52 95 272 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 469 304 96 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425 14 83 108

positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)
; positions_7nt_m3 versus positions_6nt_m3_rc; m=3/10; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.801001; ----rstmgaGGGCGCCCTCTGCTGGc ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 32 30 111 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 29 27 337 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 596 581 89 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556 17 36 137

positions_6nt_m1_shift6 (positions_6nt_m1)
; positions_7nt_m3 versus positions_6nt_m1; m=4/10; ncol2=24; w=0; offset=3; strand=D; shift=6; score=0.650383; ------scggcaGCGCCCYCTrGTGGC ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 58 94 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 51 899 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 998 74 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9 72 112

positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)
; positions_7nt_m3 versus positions_6nt_m5_rc; m=5/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.584707; srskaGGtGGCAGCGCCCCCTgsy--- ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 0 0 0 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 0 0 0 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 0 0 0 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231 0 0 0

oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)
; positions_7nt_m3 versus oligos_7nt_mkv5_m2; m=6/10; ncol2=14; w=0; offset=8; strand=D; shift=11; score=0.519493; -----------ssCGCCCCCTgCys-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 0 0 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849 0 0

oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)
; positions_7nt_m3 versus oligos_7nt_mkv5_m1_rc; m=7/10; ncol2=14; w=0; offset=8; strand=R; shift=11; score=0.500673; -----------rsCGCCCTCTrGtg-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 386 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 829 0 0 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 3571 0 0 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570 561 0 0

oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)
; positions_7nt_m3 versus oligos_6nt_mkv4_m1; m=8/10; ncol2=13; w=0; offset=8; strand=D; shift=11; score=0.493783; -----------vsCGCCCCCTgsy--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083 0 0 0

positions_6nt_m4_rc_shift10 (positions_6nt_m4_rc)
; positions_7nt_m3 versus positions_6nt_m4_rc; m=9/10; ncol2=24; w=0; offset=7; strand=R; shift=10; score=0.446625; ----------srGCGCCCTCTGCTGsC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 106 212 38 53 46 26 24 43 25 14 15 76 15 30 9 49 20 c 0 0 0 0 0 0 0 0 0 0 264 176 91 546 36 579 642 680 122 718 42 37 649 85 27 453 690 g 0 0 0 0 0 0 0 0 0 0 254 274 564 78 659 117 46 28 60 30 32 643 104 31 734 226 25 t 0 0 0 0 0 0 0 0 0 0 155 117 86 102 38 57 67 28 572 17 690 23 11 633 9 51 44

oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)
; positions_7nt_m3 versus oligos_7nt_mkv5_m3; m=10/10; ncol2=12; w=0; offset=8; strand=D; shift=11; score=0.416373; -----------rsCGCCACCTss---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847 0 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; ssTGGCCAss ; Alignment reference a 1127 907 5 40 86 75 6 5550 855 1383 c 1716 1666 197 112 4 5597 5604 10 2334 1536 g 1536 2334 10 5604 5597 4 112 197 1666 1716 t 1383 855 5550 6 75 86 40 5 907 1127

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; ssTGGCCAss ; cor=; Ncor= a 1127 907 5 40 86 75 6 5550 855 1383 c 1716 1666 197 112 4 5597 5604 10 2334 1536 g 1536 2334 10 5604 5597 4 112 197 1666 1716 t 1383 855 5550 6 75 86 40 5 907 1127

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=24; shift=1; ncol=25; -ssCtGGtGGCAGCGCCaCCaGgsg ; Alignment reference a 0 47 29 17 34 7 20 28 15 15 6 169 11 16 31 7 7 151 7 8 147 16 17 36 34 c 0 88 88 173 32 24 33 59 28 22 222 19 20 190 16 192 211 30 197 213 25 28 58 77 50 g 0 69 84 42 41 198 183 31 184 191 7 41 204 22 184 28 18 43 30 18 23 179 147 71 127 t 0 39 42 11 136 14 7 125 16 15 8 14 8 15 12 16 7 19 9 4 48 20 21 59 32

positions_6nt_m2_shift1 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -ssCtGGtGGCAGCGCCaCCaGgsg ; cor=; Ncor= a 0 47 29 17 34 7 20 28 15 15 6 169 11 16 31 7 7 151 7 8 147 16 17 36 34 c 0 88 88 173 32 24 33 59 28 22 222 19 20 190 16 192 211 30 197 213 25 28 58 77 50 g 0 69 84 42 41 198 183 31 184 191 7 41 204 22 184 28 18 43 30 18 23 179 147 71 127 t 0 39 42 11 136 14 7 125 16 15 8 14 8 15 12 16 7 19 9 4 48 20 21 59 32

positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)
; positions_6nt_m2 versus positions_6nt_m5_rc; m=2/4; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.769472; srskaGGtGGCAGCGCCCCCTgsy- ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 0 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 0 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 0 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231 0

oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)
; positions_6nt_m2 versus oligos_7nt_mkv5_m2; m=3/4; ncol2=14; w=0; offset=10; strand=D; shift=11; score=0.438686; -----------ssCGCCCCCTgCys ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849

oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)
; positions_6nt_m2 versus oligos_7nt_mkv5_m3; m=4/4; ncol2=12; w=0; offset=10; strand=D; shift=11; score=0.406395; -----------rsCGCCACCTss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 0 0 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift7 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift7 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=24; shift=7; ncol=31; -------gcCAGCAGAGGGCGCCascrGscs ; Alignment reference a 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 52 106 283 58 74 94 110 c 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 304 334 46 76 147 256 203 g 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 142 68 146 383 284 99 144 t 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36 46 36 69 27 39 95 87

positions_7nt_m2_shift7 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=7; score= 1; -------gcCAGCAGAGGGCGCCascrGscs ; cor=; Ncor= a 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 52 106 283 58 74 94 110 c 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 304 334 46 76 147 256 203 g 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 142 68 146 383 284 99 144 t 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36 46 36 69 27 39 95 87

positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)
; positions_7nt_m2 versus positions_7nt_m3_rc; m=2/10; ncol2=24; w=0; offset=0; strand=R; shift=7; score=0.861902; -------gcCaCCAGGGGGCGCCccckGscs ; cor=; Ncor= a 0 0 0 0 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 99 69 103 97 60 104 113 106 c 0 0 0 0 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 509 473 502 110 130 310 393 319 g 0 0 0 0 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 133 132 110 230 531 284 110 224 t 0 0 0 0 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112 32 99 58 336 52 75 157 124

positions_6nt_m3_shift6 (positions_6nt_m3)
; positions_7nt_m2 versus positions_6nt_m3; m=3/10; ncol2=24; w=-1; offset=-1; strand=D; shift=6; score=0.819642; ------sgCCAGCAGAGGGCGCCCtckasy- ; cor=; Ncor= a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 109 70 93 74 275 104 94 0 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 470 102 387 97 166 325 349 0 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 72 129 102 211 168 174 59 0 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110 23 373 92 292 65 71 172 0

positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)
; positions_7nt_m2 versus positions_6nt_m1_rc; m=4/10; ncol2=24; w=-3; offset=-3; strand=R; shift=4; score=0.621257; ----gyGGCCACyAGRGGGCGCtgccgs--- ; cor=; Ncor= a 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 81 255 218 182 0 0 0 c 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 625 454 194 411 0 0 0 g 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 183 270 596 393 0 0 0 t 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75 290 200 171 193 0 0 0

positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)
; positions_7nt_m2 versus positions_7nt_m4_rc; m=5/10; ncol2=24; w=-2; offset=-2; strand=R; shift=5; score=0.605706; -----yggCCACyAGrGGGCAGCAgagsc-- ; cor=; Ncor= a 0 0 0 0 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 401 0 0 c 0 0 0 0 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 844 0 0 g 0 0 0 0 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 435 0 0 t 0 0 0 0 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341 249 0 0

positions_7nt_m1_shift5 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=6/10; ncol2=24; w=-2; offset=-2; strand=D; shift=5; score=0.600212; -----yggCCAscAGGkGGCAGCAgagsc-- ; cor=; Ncor= a 0 0 0 0 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 381 0 0 c 0 0 0 0 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 721 0 0 g 0 0 0 0 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 443 0 0 t 0 0 0 0 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247 257 0 0

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_7nt_m2 versus positions_6nt_m4; m=7/10; ncol2=24; w=-7; offset=-7; strand=D; shift=0; score=0.507662; msbaGgkGsCAGCAGAGGGCGCys------- ; cor=; Ncor= a 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 155 0 0 0 0 0 0 0 c 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 254 0 0 0 0 0 0 0 g 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 264 0 0 0 0 0 0 0 t 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212 106 0 0 0 0 0 0 0

oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)
; positions_7nt_m2 versus oligos_7nt_mkv5_m1; m=8/10; ncol2=14; w=0; offset=2; strand=D; shift=9; score=0.500175; ---------caCyAGAGGGCGsy-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0 0 0 0

oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)
; positions_7nt_m2 versus oligos_7nt_mkv5_m2_rc; m=9/10; ncol2=14; w=0; offset=2; strand=R; shift=9; score=0.492998; ---------srGcAGGGGGCGss-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0 0 0 0 0 0 0 0

oligos_6nt_mkv4_m1_rc_shift10 (oligos_6nt_mkv4_m1_rc)
; positions_7nt_m2 versus oligos_6nt_mkv4_m1_rc; m=10/10; ncol2=13; w=0; offset=3; strand=R; shift=10; score=0.444065; ----------rscAGGGGGCGsb-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -ygACCACTAGrk ; Alignment reference a 0 673 923 2866 122 53 3562 62 246 3678 78 1570 480 c 0 1041 999 240 3692 3889 139 3760 488 48 81 479 599 g 0 744 1239 585 124 39 173 122 118 195 3793 1562 1517 t 0 1557 854 324 77 34 141 71 3163 94 63 404 1419

oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ygACCACTAGrk ; cor=; Ncor= a 0 673 923 2866 122 53 3562 62 246 3678 78 1570 480 c 0 1041 999 240 3692 3889 139 3760 488 48 81 479 599 g 0 744 1239 585 124 39 173 122 118 195 3793 1562 1517 t 0 1557 854 324 77 34 141 71 3163 94 63 404 1419

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m2; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.792288; --krCCACTAGAk ; cor=; Ncor= a 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 c 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 g 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 t 0 0 1293 979 203 64 199 96 3794 103 76 84 1560

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; oligos_7nt_mkv5_m5 versus positions_7nt_m4_rc; m=3/5; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.450852; -yggCCACyAGrG ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 t 0 838 432 228 115 4 101 44 1013 62 9 31 478

positions_7nt_m5_shift0 (positions_7nt_m5)
; oligos_7nt_mkv5_m5 versus positions_7nt_m5; m=4/5; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.447532; ryggCCACyAGGk ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 t 380 748 355 198 67 6 102 44 893 100 26 10 1136

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; oligos_7nt_mkv5_m5 versus positions_6nt_m1_rc; m=5/5; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.420613; gyGGCCACyAGRG ; cor=; Ncor= a 267 135 109 112 72 9 960 20 98 1030 9 806 23 c 284 359 108 74 998 1147 37 940 399 43 16 21 33 g 368 203 836 899 51 16 129 202 86 77 1146 337 877 t 260 482 126 94 58 7 53 17 596 29 8 15 246

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift1 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=24; shift=1; ncol=25; -yggCCAscAGGkGGCAGCAgagsc ; Alignment reference a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 381 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 721 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 443 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247 257

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -yggCCAscAGGkGGCAGCAgagsc ; cor=; Ncor= a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 381 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 721 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 443 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247 257

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; positions_7nt_m1 versus positions_7nt_m4_rc; m=2/10; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.921854; -yggCCACyAGrGGGCAGCAgagsc ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 401 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 844 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 435 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341 249

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m1 versus positions_7nt_m5; m=3/10; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.868363; ryggCCACyAGGkGGCAGCAgrgs- ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 416 341 0 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 268 507 0 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 733 558 0 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283 268 279 0

positions_7nt_m2_shift3 (positions_7nt_m2)
; positions_7nt_m1 versus positions_7nt_m2; m=4/10; ncol2=24; w=0; offset=2; strand=D; shift=3; score=0.600212; ---gcCAGCAGAGGGCGCCascrGs ; cor=; Ncor= a 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 52 106 283 58 74 c 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 304 334 46 76 147 g 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 142 68 146 383 284 t 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36 46 36 69 27 39

positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_7nt_m1 versus positions_6nt_m4; m=5/10; ncol2=24; w=0; offset=5; strand=D; shift=6; score=0.558979; ------msbaGgkGsCAGCAGAGGG ; cor=; Ncor= a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26

oligos_7nt_mkv5_m2_rc_shift5 (oligos_7nt_mkv5_m2_rc)
; positions_7nt_m1 versus oligos_7nt_mkv5_m2_rc; m=6/10; ncol2=14; w=0; offset=4; strand=R; shift=5; score=0.438432; -----srGcAGGGGGCGss------ ; cor=; Ncor= a 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 0 0 0 0 0 c 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 0 0 0 0 0 g 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 0 0 0 0 0 t 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0 0 0 0 0 0

oligos_6nt_mkv4_m1_rc_shift6 (oligos_6nt_mkv4_m1_rc)
; positions_7nt_m1 versus oligos_6nt_mkv4_m1_rc; m=7/10; ncol2=13; w=0; offset=5; strand=R; shift=6; score=0.42638; ------rscAGGGGGCGsb------ ; cor=; Ncor= a 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 0 c 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 0 g 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 0 t 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0 0

oligos_7nt_mkv5_m3_rc_shift7 (oligos_7nt_mkv5_m3_rc)
; positions_7nt_m1 versus oligos_7nt_mkv5_m3_rc; m=8/10; ncol2=12; w=0; offset=6; strand=R; shift=7; score=0.422176; -------ssAGGTGGCGsy------ ; cor=; Ncor= a 0 0 0 0 0 0 0 847 1148 6438 56 446 323 47 75 430 1016 1004 972 0 0 0 0 0 0 c 0 0 0 0 0 0 0 2951 2842 365 120 127 482 113 97 5895 314 3116 2510 0 0 0 0 0 0 g 0 0 0 0 0 0 0 2875 1916 272 7035 6653 1055 7070 7005 484 5673 2356 1618 0 0 0 0 0 0 t 0 0 0 0 0 0 0 594 1361 192 56 41 5407 37 90 458 264 791 2167 0 0 0 0 0 0

oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)
; positions_7nt_m1 versus oligos_7nt_mkv5_m4; m=9/10; ncol2=11; w=0; offset=10; strand=D; shift=11; score=0.41522; -----------gbGGCAGCAsc--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338 0 0 0

oligos_7nt_mkv5_m1_shift5 (oligos_7nt_mkv5_m1)
; positions_7nt_m1 versus oligos_7nt_mkv5_m1; m=10/10; ncol2=14; w=0; offset=4; strand=D; shift=5; score=0.412872; -----caCyAGAGGGCGsy------ ; cor=; Ncor= a 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 0 c 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 0 g 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 0 t 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift6 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift6 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=24; shift=6; ncol=30; ------sgCCAGCAGAGGGCGCCCtckasy ; Alignment reference a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 109 70 93 74 275 104 94 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 470 102 387 97 166 325 349 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 72 129 102 211 168 174 59 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110 23 373 92 292 65 71 172

positions_6nt_m3_shift6 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------sgCCAGCAGAGGGCGCCCtckasy ; cor=; Ncor= a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 109 70 93 74 275 104 94 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 470 102 387 97 166 325 349 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 72 129 102 211 168 174 59 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110 23 373 92 292 65 71 172

positions_7nt_m2_shift7 (positions_7nt_m2)
; positions_6nt_m3 versus positions_7nt_m2; m=2/10; ncol2=24; w=0; offset=1; strand=D; shift=7; score=0.819642; -------gcCAGCAGAGGGCGCCascrGsc ; cor=; Ncor= a 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 52 106 283 58 74 94 c 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 304 334 46 76 147 256 g 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 142 68 146 383 284 99 t 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36 46 36 69 27 39 95

positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)
; positions_6nt_m3 versus positions_7nt_m3_rc; m=3/10; ncol2=24; w=0; offset=1; strand=R; shift=7; score=0.801001; -------gcCaCCAGGGGGCGCCccckGsc ; cor=; Ncor= a 0 0 0 0 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 99 69 103 97 60 104 113 c 0 0 0 0 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 509 473 502 110 130 310 393 g 0 0 0 0 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 133 132 110 230 531 284 110 t 0 0 0 0 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112 32 99 58 336 52 75 157

positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)
; positions_6nt_m3 versus positions_6nt_m1_rc; m=4/10; ncol2=24; w=-2; offset=-2; strand=R; shift=4; score=0.693247; ----gyGGCCACyAGRGGGCGCtgccgs-- ; cor=; Ncor= a 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 81 255 218 182 0 0 c 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 625 454 194 411 0 0 g 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 183 270 596 393 0 0 t 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75 290 200 171 193 0 0

positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)
; positions_6nt_m3 versus positions_7nt_m4_rc; m=5/10; ncol2=24; w=-1; offset=-1; strand=R; shift=5; score=0.655757; -----yggCCACyAGrGGGCAGCAgagsc- ; cor=; Ncor= a 0 0 0 0 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 401 0 c 0 0 0 0 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 844 0 g 0 0 0 0 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 435 0 t 0 0 0 0 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341 249 0

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=6/10; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.537819; msbaGgkGsCAGCAGAGGGCGCys------ ; cor=; Ncor= a 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 155 0 0 0 0 0 0 c 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 254 0 0 0 0 0 0 g 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 264 0 0 0 0 0 0 t 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212 106 0 0 0 0 0 0

oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)
; positions_6nt_m3 versus oligos_7nt_mkv5_m1; m=7/10; ncol2=14; w=0; offset=3; strand=D; shift=9; score=0.509096; ---------caCyAGAGGGCGsy------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0 0 0

oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)
; positions_6nt_m3 versus oligos_7nt_mkv5_m2_rc; m=8/10; ncol2=14; w=0; offset=3; strand=R; shift=9; score=0.494956; ---------srGcAGGGGGCGss------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0 0 0 0 0 0 0

oligos_6nt_mkv4_m1_rc_shift10 (oligos_6nt_mkv4_m1_rc)
; positions_6nt_m3 versus oligos_6nt_mkv4_m1_rc; m=9/10; ncol2=13; w=0; offset=4; strand=R; shift=10; score=0.451881; ----------rscAGGGGGCGsb------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0 0 0

oligos_6nt_mkv4_m4_shift11 (oligos_6nt_mkv4_m4)
; positions_6nt_m3 versus oligos_6nt_mkv4_m4; m=10/10; ncol2=12; w=0; offset=5; strand=D; shift=11; score=0.400843; -----------scAGAGGGCAsy------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift11 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------rsCGCCACCTss ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847

oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/9; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------rsCGCCACCTss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847

oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m1; m=2/9; ncol2=13; w=0; offset=0; strand=D; shift=11; score=0.830838; -----------vsCGCCCCCTgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952

oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=3/9; ncol2=14; w=0; offset=0; strand=D; shift=11; score=0.747688; -----------ssCGCCCCCTgC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396

oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m1_rc; m=4/9; ncol2=14; w=0; offset=0; strand=R; shift=11; score=0.645417; -----------rsCGCCCTCTrG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277

positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)
; oligos_7nt_mkv5_m3 versus positions_6nt_m5_rc; m=5/9; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.422979; srskaGGtGGCAGCGCCCCCTgs ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76

positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)
; oligos_7nt_mkv5_m3 versus positions_7nt_m1_rc; m=6/9; ncol2=24; w=-6; offset=-6; strand=R; shift=5; score=0.422176; -----gsctcTGCTGCCmCCTgs ; cor=; Ncor= a 0 0 0 0 0 257 247 179 231 225 63 244 44 42 49 63 8 1103 12 30 109 282 77 c 0 0 0 0 0 443 584 1163 169 1163 156 102 1359 316 25 1657 1760 575 1355 1724 74 146 975 g 0 0 0 0 0 721 521 178 270 224 153 1361 319 40 1672 42 5 58 38 15 50 1196 697 t 0 0 0 0 0 381 450 282 1132 190 1430 95 80 1404 56 40 29 66 397 33 1569 178 53

positions_7nt_m3_shift3 (positions_7nt_m3)
; oligos_7nt_mkv5_m3 versus positions_7nt_m3; m=7/9; ncol2=24; w=-8; offset=-8; strand=D; shift=3; score=0.416373; ---sgsCmgggGGCGCCCCCTGG ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10

positions_7nt_m5_rc_shift6 (positions_7nt_m5_rc)
; oligos_7nt_mkv5_m3 versus positions_7nt_m5_rc; m=8/9; ncol2=24; w=-5; offset=-5; strand=R; shift=6; score=0.407699; ------scycTGCTGCCmCCTrG ; cor=; Ncor= a 0 0 0 0 0 0 279 268 283 313 64 291 39 34 45 90 12 1136 10 26 100 893 44 c 0 0 0 0 0 0 558 733 558 1003 141 107 1284 243 20 1500 1649 436 1261 1614 111 112 210 g 0 0 0 0 0 0 507 268 314 179 168 1205 274 55 1586 53 6 52 24 11 48 498 1395 t 0 0 0 0 0 0 341 416 530 190 1312 82 88 1353 34 42 18 61 390 34 1426 182 36

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_7nt_mkv5_m3 versus positions_6nt_m2; m=9/9; ncol2=24; w=-10; offset=-10; strand=D; shift=1; score=0.406395; -ssCtGGtGGCAGCGCCaCCaGg ; cor=; Ncor= a 0 47 29 17 34 7 20 28 15 15 6 169 11 16 31 7 7 151 7 8 147 16 17 c 0 88 88 173 32 24 33 59 28 22 222 19 20 190 16 192 211 30 197 213 25 28 58 g 0 69 84 42 41 198 183 31 184 191 7 41 204 22 184 28 18 43 30 18 23 179 147 t 0 39 42 11 136 14 7 125 16 15 8 14 8 15 12 16 7 19 9 4 48 20 21

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift11 ; 15 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=13; shift=11; ncol=24; -----------vsCGCCCCCTgsy ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083

oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/14; ncol2=13; w=0; offset=0; strand=D; shift=11; score= 1; -----------vsCGCCCCCTgsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083

oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m2; m=2/14; ncol2=14; w=0; offset=0; strand=D; shift=11; score=0.901385; -----------ssCGCCCCCTgCy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563

oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m3; m=3/14; ncol2=12; w=0; offset=0; strand=D; shift=11; score=0.830838; -----------rsCGCCACCTss- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 0 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 0 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 0 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847 0

oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1_rc; m=4/14; ncol2=14; w=0; offset=0; strand=R; shift=11; score=0.805128; -----------rsCGCCCTCTrGt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570

oligos_6nt_mkv4_m4_rc_shift11 (oligos_6nt_mkv4_m4_rc)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m4_rc; m=5/14; ncol2=12; w=0; offset=0; strand=R; shift=11; score=0.707585; -----------rsTGCCCTCTgs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2125 930 432 120 248 130 670 234 52 248 1904 958 0 c 0 0 0 0 0 0 0 0 0 0 0 1795 3466 864 320 7303 7701 7160 733 7646 361 1647 2899 0 g 0 0 0 0 0 0 0 0 0 0 0 2692 2480 278 7403 371 93 77 128 285 111 3185 2983 0 t 0 0 0 0 0 0 0 0 0 0 0 1576 1312 6614 345 266 264 281 7093 205 7468 1452 1348 0

positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)
; oligos_6nt_mkv4_m1 versus positions_6nt_m5_rc; m=6/14; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.501418; srskaGGtGGCAGCGCCCCCTgsy ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231

positions_7nt_m3_shift3 (positions_7nt_m3)
; oligos_6nt_mkv4_m1 versus positions_7nt_m3; m=7/14; ncol2=24; w=-8; offset=-8; strand=D; shift=3; score=0.493783; ---sgsCmgggGGCGCCCCCTGGt ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518

positions_6nt_m1_shift6 (positions_6nt_m1)
; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=8/14; ncol2=24; w=-5; offset=-5; strand=D; shift=6; score=0.453174; ------scggcaGCGCCCYCTrGT ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960

positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)
; oligos_6nt_mkv4_m1 versus positions_6nt_m3_rc; m=9/14; ncol2=24; w=-7; offset=-7; strand=R; shift=4; score=0.451881; ----rstmgaGGGCGCCCTCTGCT ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556

positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)
; oligos_6nt_mkv4_m1 versus positions_7nt_m2_rc; m=10/14; ncol2=24; w=-8; offset=-8; strand=R; shift=3; score=0.444065; ---sgsCygstGGCGCCCTCTGCT ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425

positions_6nt_m4_rc_shift10 (positions_6nt_m4_rc)
; oligos_6nt_mkv4_m1 versus positions_6nt_m4_rc; m=11/14; ncol2=24; w=-1; offset=-1; strand=R; shift=10; score=0.440807; ----------srGCGCCCTCTGCT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 106 212 38 53 46 26 24 43 25 14 15 76 15 30 c 0 0 0 0 0 0 0 0 0 0 264 176 91 546 36 579 642 680 122 718 42 37 649 85 g 0 0 0 0 0 0 0 0 0 0 254 274 564 78 659 117 46 28 60 30 32 643 104 31 t 0 0 0 0 0 0 0 0 0 0 155 117 86 102 38 57 67 28 572 17 690 23 11 633

positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)
; oligos_6nt_mkv4_m1 versus positions_7nt_m1_rc; m=12/14; ncol2=24; w=-6; offset=-6; strand=R; shift=5; score=0.42638; -----gsctcTGCTGCCmCCTgsT ; cor=; Ncor= a 0 0 0 0 0 257 247 179 231 225 63 244 44 42 49 63 8 1103 12 30 109 282 77 117 c 0 0 0 0 0 443 584 1163 169 1163 156 102 1359 316 25 1657 1760 575 1355 1724 74 146 975 135 g 0 0 0 0 0 721 521 178 270 224 153 1361 319 40 1672 42 5 58 38 15 50 1196 697 60 t 0 0 0 0 0 381 450 282 1132 190 1430 95 80 1404 56 40 29 66 397 33 1569 178 53 1490

positions_7nt_m4_shift5 (positions_7nt_m4)
; oligos_6nt_mkv4_m1 versus positions_7nt_m4; m=13/14; ncol2=24; w=-6; offset=-6; strand=D; shift=5; score=0.411561; -----gsctcTGCTGCCCyCTrGT ; cor=; Ncor= a 0 0 0 0 0 249 341 169 250 281 97 324 60 70 52 89 15 478 31 9 62 1013 44 101 c 0 0 0 0 0 435 612 1237 235 1223 160 133 1389 294 20 1741 1869 1397 580 1889 106 142 356 138 g 0 0 0 0 0 844 508 186 310 219 194 1355 394 29 1789 47 11 18 26 13 42 573 1468 59 t 0 0 0 0 0 401 468 337 1134 206 1478 117 86 1536 68 52 34 36 1292 18 1719 201 61 1631

positions_7nt_m5_rc_shift6 (positions_7nt_m5_rc)
; oligos_6nt_mkv4_m1 versus positions_7nt_m5_rc; m=14/14; ncol2=24; w=-5; offset=-5; strand=R; shift=6; score=0.402675; ------scycTGCTGCCmCCTrGT ; cor=; Ncor= a 0 0 0 0 0 0 279 268 283 313 64 291 39 34 45 90 12 1136 10 26 100 893 44 102 c 0 0 0 0 0 0 558 733 558 1003 141 107 1284 243 20 1500 1649 436 1261 1614 111 112 210 110 g 0 0 0 0 0 0 507 268 314 179 168 1205 274 55 1586 53 6 52 24 11 48 498 1395 64 t 0 0 0 0 0 0 341 416 530 190 1312 82 88 1353 34 42 18 61 390 34 1426 182 36 1409

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --krCCACTAGAkg ; Alignment reference a 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 653 c 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 598 g 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 3266 t 0 0 1293 979 203 64 199 96 3794 103 76 84 1560 433

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --krCCACTAGAkg ; cor=; Ncor= a 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 653 c 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 598 g 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 3266 t 0 0 1293 979 203 64 199 96 3794 103 76 84 1560 433

oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)
; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m5; m=2/6; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.792288; -ygACCACTAGrk- ; cor=; Ncor= a 0 673 923 2866 122 53 3562 62 246 3678 78 1570 480 0 c 0 1041 999 240 3692 3889 139 3760 488 48 81 479 599 0 g 0 744 1239 585 124 39 173 122 118 195 3793 1562 1517 0 t 0 1557 854 324 77 34 141 71 3163 94 63 404 1419 0

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; oligos_6nt_mkv4_m2 versus positions_7nt_m4_rc; m=3/6; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.474813; -yggCCACyAGrGG ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15

oligos_7nt_mkv5_m1_shift5 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m1; m=4/6; ncol2=14; w=0; offset=3; strand=D; shift=5; score=0.474054; -----caCyAGAGG ; cor=; Ncor= a 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 c 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 g 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 t 0 0 0 0 0 386 654 203 2492 107 47 155 637 112

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; oligos_6nt_mkv4_m2 versus positions_6nt_m1_rc; m=5/6; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.457888; gyGGCCACyAGRGG ; cor=; Ncor= a 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 c 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 g 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 t 260 482 126 94 58 7 53 17 596 29 8 15 246 10

positions_7nt_m5_shift0 (positions_7nt_m5)
; oligos_6nt_mkv4_m2 versus positions_7nt_m5; m=6/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.435969; ryggCCACyAGGkG ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift6 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=24; shift=6; ncol=30; ------msbaGgkGsCAGCAGAGGGCGCys ; Alignment reference a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 155 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 254 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 264 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212 106

positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/13; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------msbaGgkGsCAGCAGAGGGCGCys ; cor=; Ncor= a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 155 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 254 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 264 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212 106

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_6nt_m4 versus positions_7nt_m1; m=2/13; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.558979; -yggCCAscAGGkGGCAGCAgagsc----- ; cor=; Ncor= a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 381 0 0 0 0 0 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 721 0 0 0 0 0 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 443 0 0 0 0 0 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247 257 0 0 0 0 0

positions_6nt_m1_rc_shift10 (positions_6nt_m1_rc)
; positions_6nt_m4 versus positions_6nt_m1_rc; m=3/13; ncol2=24; w=0; offset=4; strand=R; shift=10; score=0.557373; ----------gyGGCCACyAGRGGGCGCtg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 c 0 0 0 0 0 0 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 g 0 0 0 0 0 0 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 t 0 0 0 0 0 0 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75

positions_6nt_m3_shift12 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=4/13; ncol2=24; w=0; offset=6; strand=D; shift=12; score=0.537819; ------------sgCCAGCAGAGGGCGCCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 109 c 0 0 0 0 0 0 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 470 g 0 0 0 0 0 0 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 72 t 0 0 0 0 0 0 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110 23

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; positions_6nt_m4 versus positions_7nt_m4_rc; m=5/13; ncol2=24; w=-5; offset=-5; strand=R; shift=1; score=0.526055; -yggCCACyAGrGGGCAGCAgagsc----- ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 401 0 0 0 0 0 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 844 0 0 0 0 0 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 435 0 0 0 0 0 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341 249 0 0 0 0 0

positions_7nt_m2_shift13 (positions_7nt_m2)
; positions_6nt_m4 versus positions_7nt_m2; m=6/13; ncol2=24; w=0; offset=7; strand=D; shift=13; score=0.507662; -------------gcCAGCAGAGGGCGCCa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 c 0 0 0 0 0 0 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 g 0 0 0 0 0 0 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 t 0 0 0 0 0 0 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_6nt_m4 versus positions_7nt_m5; m=7/13; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.501293; ryggCCACyAGGkGGCAGCAgrgs------ ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 416 341 0 0 0 0 0 0 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 268 507 0 0 0 0 0 0 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 733 558 0 0 0 0 0 0 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283 268 279 0 0 0 0 0 0

oligos_7nt_mkv5_m1_shift15 (oligos_7nt_mkv5_m1)
; positions_6nt_m4 versus oligos_7nt_mkv5_m1; m=8/13; ncol2=14; w=0; offset=9; strand=D; shift=15; score=0.496932; ---------------caCyAGAGGGCGsy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0

oligos_7nt_mkv5_m2_rc_shift15 (oligos_7nt_mkv5_m2_rc)
; positions_6nt_m4 versus oligos_7nt_mkv5_m2_rc; m=9/13; ncol2=14; w=0; offset=9; strand=R; shift=15; score=0.487623; ---------------srGcAGGGGGCGss- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0

positions_7nt_m3_rc_shift13 (positions_7nt_m3_rc)
; positions_6nt_m4 versus positions_7nt_m3_rc; m=10/13; ncol2=24; w=0; offset=7; strand=R; shift=13; score=0.446625; -------------gcCaCCAGGGGGCGCCc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 99 c 0 0 0 0 0 0 0 0 0 0 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 509 g 0 0 0 0 0 0 0 0 0 0 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 133 t 0 0 0 0 0 0 0 0 0 0 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112 32

oligos_6nt_mkv4_m1_rc_shift16 (oligos_6nt_mkv4_m1_rc)
; positions_6nt_m4 versus oligos_6nt_mkv4_m1_rc; m=11/13; ncol2=13; w=0; offset=10; strand=R; shift=16; score=0.440807; ----------------rscAGGGGGCGsb- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0

oligos_6nt_mkv4_m4_shift17 (oligos_6nt_mkv4_m4)
; positions_6nt_m4 versus oligos_6nt_mkv4_m4; m=12/13; ncol2=12; w=0; offset=11; strand=D; shift=17; score=0.405609; -----------------scAGAGGGCAsy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125 0

oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)
; positions_6nt_m4 versus oligos_7nt_mkv5_m4; m=13/13; ncol2=11; w=0; offset=5; strand=D; shift=11; score=0.401116; -----------gbGGCAGCAsc-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift11 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=11; ncol=22; -----------gbGGCAGCAsc ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338

oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=11; score= 1; -----------gbGGCAGCAsc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338

positions_7nt_m5_shift0 (positions_7nt_m5)
; oligos_7nt_mkv5_m4 versus positions_7nt_m5; m=2/5; ncol2=24; w=-11; offset=-11; strand=D; shift=0; score=0.421428; ryggCCACyAGGkGGCAGCAgr ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283

positions_7nt_m1_shift1 (positions_7nt_m1)
; oligos_7nt_mkv5_m4 versus positions_7nt_m1; m=3/5; ncol2=24; w=-10; offset=-10; strand=D; shift=1; score=0.41522; -yggCCAscAGGkGGCAGCAga ; cor=; Ncor= a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; oligos_7nt_mkv5_m4 versus positions_7nt_m4_rc; m=4/5; ncol2=24; w=-10; offset=-10; strand=R; shift=1; score=0.403846; -yggCCACyAGrGGGCAGCAga ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250

positions_6nt_m4_shift6 (positions_6nt_m4)
; oligos_7nt_mkv5_m4 versus positions_6nt_m4; m=5/5; ncol2=24; w=-5; offset=-5; strand=D; shift=6; score=0.401116; ------msbaGgkGsCAGCAGA ; cor=; Ncor= a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; ryggCCACyAGGkGGCAGCAgrgs ; Alignment reference a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 416 341 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 268 507 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 733 558 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283 268 279

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ryggCCACyAGGkGGCAGCAgrgs ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 416 341 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 268 507 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 733 558 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283 268 279

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m5 versus positions_7nt_m1; m=2/11; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.868363; -yggCCAscAGGkGGCAGCAgags ; cor=; Ncor= a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; positions_7nt_m5 versus positions_7nt_m4_rc; m=3/11; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.862568; -yggCCACyAGrGGGCAGCAgags ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; positions_7nt_m5 versus positions_6nt_m1_rc; m=4/11; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.717491; gyGGCCACyAGRGGGCGCtgccgs ; cor=; Ncor= a 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 81 255 218 182 c 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 625 454 194 411 g 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 183 270 596 393 t 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75 290 200 171 193

positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_7nt_m5 versus positions_6nt_m4; m=5/11; ncol2=24; w=0; offset=6; strand=D; shift=6; score=0.501293; ------msbaGgkGsCAGCAGAGG ; cor=; Ncor= a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24

oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)
; positions_7nt_m5 versus oligos_7nt_mkv5_m5; m=6/11; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.447532; -ygACCACTAGrk----------- ; cor=; Ncor= a 0 673 923 2866 122 53 3562 62 246 3678 78 1570 480 0 0 0 0 0 0 0 0 0 0 0 c 0 1041 999 240 3692 3889 139 3760 488 48 81 479 599 0 0 0 0 0 0 0 0 0 0 0 g 0 744 1239 585 124 39 173 122 118 195 3793 1562 1517 0 0 0 0 0 0 0 0 0 0 0 t 0 1557 854 324 77 34 141 71 3163 94 63 404 1419 0 0 0 0 0 0 0 0 0 0 0

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; positions_7nt_m5 versus oligos_6nt_mkv4_m2; m=7/11; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.435969; --krCCACTAGAkg---------- ; cor=; Ncor= a 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 653 0 0 0 0 0 0 0 0 0 0 c 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 598 0 0 0 0 0 0 0 0 0 0 g 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 3266 0 0 0 0 0 0 0 0 0 0 t 0 0 1293 979 203 64 199 96 3794 103 76 84 1560 433 0 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv5_m1_shift5 (oligos_7nt_mkv5_m1)
; positions_7nt_m5 versus oligos_7nt_mkv5_m1; m=8/11; ncol2=14; w=0; offset=5; strand=D; shift=5; score=0.43053; -----caCyAGAGGGCGsy----- ; cor=; Ncor= a 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 c 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 g 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 t 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0

oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)
; positions_7nt_m5 versus oligos_7nt_mkv5_m4; m=9/11; ncol2=11; w=0; offset=11; strand=D; shift=11; score=0.421428; -----------gbGGCAGCAsc-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 0 0 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338 0 0

oligos_7nt_mkv5_m3_rc_shift7 (oligos_7nt_mkv5_m3_rc)
; positions_7nt_m5 versus oligos_7nt_mkv5_m3_rc; m=10/11; ncol2=12; w=0; offset=7; strand=R; shift=7; score=0.407699; -------ssAGGTGGCGsy----- ; cor=; Ncor= a 0 0 0 0 0 0 0 847 1148 6438 56 446 323 47 75 430 1016 1004 972 0 0 0 0 0 c 0 0 0 0 0 0 0 2951 2842 365 120 127 482 113 97 5895 314 3116 2510 0 0 0 0 0 g 0 0 0 0 0 0 0 2875 1916 272 7035 6653 1055 7070 7005 484 5673 2356 1618 0 0 0 0 0 t 0 0 0 0 0 0 0 594 1361 192 56 41 5407 37 90 458 264 791 2167 0 0 0 0 0

oligos_6nt_mkv4_m1_rc_shift6 (oligos_6nt_mkv4_m1_rc)
; positions_7nt_m5 versus oligos_6nt_mkv4_m1_rc; m=11/11; ncol2=13; w=0; offset=6; strand=R; shift=6; score=0.402675; ------rscAGGGGGCGsb----- ; cor=; Ncor= a 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 c 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 g 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 t 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m4_shift11 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------scAGAGGGCAsy ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 c 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 g 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 t 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125
oligos_6nt_mkv4_m4_shift11 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------scAGAGGGCAsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 c 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 g 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 t 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)				; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m1; m=2/8; ncol2=14; w=-2; offset=-2; strand=D; shift=9; score=0.738757; ---------caCyAGAGGGCGsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561
oligos_6nt_mkv4_m1_rc_shift10 (oligos_6nt_mkv4_m1_rc)				; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m1_rc; m=3/8; ncol2=13; w=-1; offset=-1; strand=R; shift=10; score=0.707585; ----------rscAGGGGGCGsb ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 c 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 g 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 t 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082
oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)				; oligos_6nt_mkv4_m4 versus oligos_7nt_mkv5_m2_rc; m=4/8; ncol2=14; w=-2; offset=-2; strand=R; shift=9; score=0.602327; ---------srGcAGGGGGCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 c 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 g 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 t 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890
positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)				; oligos_6nt_mkv4_m4 versus positions_7nt_m4_rc; m=5/8; ncol2=24; w=-6; offset=-6; strand=R; shift=5; score=0.461479; -----yggCCACyAGrGGGCAGC ; cor=; Ncor= a 0 0 0 0 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 c 0 0 0 0 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 g 0 0 0 0 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 t 0 0 0 0 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324
positions_6nt_m4_shift0 (positions_6nt_m4)				; oligos_6nt_mkv4_m4 versus positions_6nt_m4; m=6/8; ncol2=24; w=-11; offset=-11; strand=D; shift=0; score=0.405609; msbaGgkGsCAGCAGAGGGCGCy ; cor=; Ncor= a 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 c 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 g 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 t 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212
positions_6nt_m3_shift6 (positions_6nt_m3)				; oligos_6nt_mkv4_m4 versus positions_6nt_m3; m=7/8; ncol2=24; w=-5; offset=-5; strand=D; shift=6; score=0.400843; ------sgCCAGCAGAGGGCGCC ; cor=; Ncor= a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110
positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)				; oligos_6nt_mkv4_m4 versus positions_6nt_m1_rc; m=8/8; ncol2=24; w=-7; offset=-7; strand=R; shift=4; score=0.40069; ----gyGGCCACyAGRGGGCGCt ; cor=; Ncor= a 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 c 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 g 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 t 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift6 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=24; shift=6; ncol=30; ------rscAGGGGGCGCTGCCaCCtmsys ; Alignment reference a 0 0 0 0 0 0 231 76 66 494 12 78 36 29 33 22 53 13 20 26 27 44 327 21 36 53 206 94 102 87 c 0 0 0 0 0 0 147 246 359 42 28 42 69 46 64 523 24 547 105 51 477 446 81 490 515 152 197 161 211 169 g 0 0 0 0 0 0 174 225 120 58 569 490 447 518 507 22 536 59 54 540 50 88 154 74 44 63 141 318 156 303 t 0 0 0 0 0 0 79 84 86 37 22 21 79 38 27 64 18 12 452 14 77 53 69 46 36 363 87 58 162 72
positions_6nt_m5_shift6 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------rscAGGGGGCGCTGCCaCCtmsys ; cor=; Ncor= a 0 0 0 0 0 0 231 76 66 494 12 78 36 29 33 22 53 13 20 26 27 44 327 21 36 53 206 94 102 87 c 0 0 0 0 0 0 147 246 359 42 28 42 69 46 64 523 24 547 105 51 477 446 81 490 515 152 197 161 211 169 g 0 0 0 0 0 0 174 225 120 58 569 490 447 518 507 22 536 59 54 540 50 88 154 74 44 63 141 318 156 303 t 0 0 0 0 0 0 79 84 86 37 22 21 79 38 27 64 18 12 452 14 77 53 69 46 36 363 87 58 162 72
positions_6nt_m2_rc_shift5 (positions_6nt_m2_rc)				; positions_6nt_m5 versus positions_6nt_m2_rc; m=2/8; ncol2=24; w=-1; offset=-1; strand=R; shift=5; score=0.769472; -----cscCtGGtGGCGCTGCCaCCaGss- ; cor=; Ncor= a 0 0 0 0 0 32 59 21 20 48 4 9 19 7 16 12 15 8 14 8 15 16 125 7 14 136 11 42 39 0 c 0 0 0 0 0 127 71 147 179 23 18 30 43 18 28 184 22 204 41 7 191 184 31 183 198 41 42 84 69 0 g 0 0 0 0 0 50 77 58 28 25 213 197 30 211 192 16 190 20 19 222 22 28 59 33 24 32 173 88 88 0 t 0 0 0 0 0 34 36 17 16 147 8 7 151 7 7 31 16 11 169 6 15 15 28 20 7 34 17 29 47 0
positions_7nt_m3_rc_shift3 (positions_7nt_m3_rc)				; positions_6nt_m5 versus positions_7nt_m3_rc; m=3/8; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.584707; ---gcCaCCAGGGGGCGCCccckGscs--- ; cor=; Ncor= a 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 99 69 103 97 60 104 113 106 0 0 0 c 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 509 473 502 110 130 310 393 319 0 0 0 g 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 133 132 110 230 531 284 110 224 0 0 0 t 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112 32 99 58 336 52 75 157 124 0 0 0
oligos_6nt_mkv4_m1_rc_shift6 (oligos_6nt_mkv4_m1_rc)				; positions_6nt_m5 versus oligos_6nt_mkv4_m1_rc; m=4/8; ncol2=13; w=0; offset=0; strand=R; shift=6; score=0.501418; ------rscAGGGGGCGsb----------- ; cor=; Ncor= a 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0 0 0 0 0 0 0
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; positions_6nt_m5 versus positions_6nt_m1_rc; m=5/8; ncol2=24; w=-6; offset=-6; strand=R; shift=0; score=0.497444; gyGGCCACyAGRGGGCGCtgccgs------ ; cor=; Ncor= a 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 81 255 218 182 0 0 0 0 0 0 c 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 625 454 194 411 0 0 0 0 0 0 g 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 183 270 596 393 0 0 0 0 0 0 t 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75 290 200 171 193 0 0 0 0 0 0
oligos_7nt_mkv5_m2_rc_shift5 (oligos_7nt_mkv5_m2_rc)				; positions_6nt_m5 versus oligos_7nt_mkv5_m2_rc; m=6/8; ncol2=14; w=-1; offset=-1; strand=R; shift=5; score=0.475997; -----srGcAGGGGGCGss----------- ; cor=; Ncor= a 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0 0 0 0 0 0 0 0 0 0 0
oligos_7nt_mkv5_m1_shift5 (oligos_7nt_mkv5_m1)				; positions_6nt_m5 versus oligos_7nt_mkv5_m1; m=7/8; ncol2=14; w=-1; offset=-1; strand=D; shift=5; score=0.42372; -----caCyAGAGGGCGsy----------- ; cor=; Ncor= a 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0 0 0 0 0 0 0
oligos_7nt_mkv5_m3_rc_shift7 (oligos_7nt_mkv5_m3_rc)				; positions_6nt_m5 versus oligos_7nt_mkv5_m3_rc; m=8/8; ncol2=12; w=0; offset=1; strand=R; shift=7; score=0.422979; -------ssAGGTGGCGsy----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 847 1148 6438 56 446 323 47 75 430 1016 1004 972 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 2951 2842 365 120 127 482 113 97 5895 314 3116 2510 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 2875 1916 272 7035 6653 1055 7070 7005 484 5673 2356 1618 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 594 1361 192 56 41 5407 37 90 458 264 791 2167 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=24; shift=5; ncol=29; -----gsctcTGCTGCCCyCTrGTGGccr ; Alignment reference a 0 0 0 0 0 249 341 169 250 281 97 324 60 70 52 89 15 478 31 9 62 1013 44 101 4 115 228 432 838 c 0 0 0 0 0 435 612 1237 235 1223 160 133 1389 294 20 1741 1869 1397 580 1889 106 142 356 138 10 84 1072 782 302 g 0 0 0 0 0 844 508 186 310 219 194 1355 394 29 1789 47 11 18 26 13 42 573 1468 59 1909 1620 191 317 570 t 0 0 0 0 0 401 468 337 1134 206 1478 117 86 1536 68 52 34 36 1292 18 1719 201 61 1631 6 110 438 398 219
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/13; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----gsctcTGCTGCCCyCTrGTGGccr ; cor=; Ncor= a 0 0 0 0 0 249 341 169 250 281 97 324 60 70 52 89 15 478 31 9 62 1013 44 101 4 115 228 432 838 c 0 0 0 0 0 435 612 1237 235 1223 160 133 1389 294 20 1741 1869 1397 580 1889 106 142 356 138 10 84 1072 782 302 g 0 0 0 0 0 844 508 186 310 219 194 1355 394 29 1789 47 11 18 26 13 42 573 1468 59 1909 1620 191 317 570 t 0 0 0 0 0 401 468 337 1134 206 1478 117 86 1536 68 52 34 36 1292 18 1719 201 61 1631 6 110 438 398 219
positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)				; positions_7nt_m4 versus positions_7nt_m1_rc; m=2/13; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.921854; -----gsctcTGCTGCCmCCTgsTGGccr ; cor=; Ncor= a 0 0 0 0 0 257 247 179 231 225 63 244 44 42 49 63 8 1103 12 30 109 282 77 117 13 69 233 417 698 c 0 0 0 0 0 443 584 1163 169 1163 156 102 1359 316 25 1657 1760 575 1355 1724 74 146 975 135 21 81 1023 699 306 g 0 0 0 0 0 721 521 178 270 224 153 1361 319 40 1672 42 5 58 38 15 50 1196 697 60 1747 1540 166 359 576 t 0 0 0 0 0 381 450 282 1132 190 1430 95 80 1404 56 40 29 66 397 33 1569 178 53 1490 21 112 380 327 222
positions_7nt_m5_rc_shift6 (positions_7nt_m5_rc)				; positions_7nt_m4 versus positions_7nt_m5_rc; m=3/13; ncol2=24; w=0; offset=1; strand=R; shift=6; score=0.862568; ------scycTGCTGCCmCCTrGTGGccr ; cor=; Ncor= a 0 0 0 0 0 0 279 268 283 313 64 291 39 34 45 90 12 1136 10 26 100 893 44 102 6 67 198 355 748 c 0 0 0 0 0 0 558 733 558 1003 141 107 1284 243 20 1500 1649 436 1261 1614 111 112 210 110 8 55 978 753 243 g 0 0 0 0 0 0 507 268 314 179 168 1205 274 55 1586 53 6 52 24 11 48 498 1395 64 1665 1481 165 281 477 t 0 0 0 0 0 0 341 416 530 190 1312 82 88 1353 34 42 18 61 390 34 1426 182 36 1409 6 82 344 296 217
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_7nt_m4 versus positions_6nt_m1; m=4/13; ncol2=24; w=0; offset=1; strand=D; shift=6; score=0.706671; ------scggcaGCGCCCYCTrGTGGCCr ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 58 94 126 482 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 51 899 836 203 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 998 74 108 359 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9 72 112 109 135
positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)				; positions_7nt_m4 versus positions_6nt_m3_rc; m=5/13; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.655757; ----rstmgaGGGCGCCCTCTGCTGGcs- ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 32 30 111 126 0 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 29 27 337 267 0 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 596 581 89 174 0 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556 17 36 137 107 0
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; positions_7nt_m4 versus positions_7nt_m2_rc; m=6/13; ncol2=24; w=-2; offset=-2; strand=R; shift=3; score=0.605706; ---sgsCygstGGCGCCCTCTGCTGgc-- ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 9 62 68 0 0 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 52 95 272 0 0 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 469 304 96 0 0 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425 14 83 108 0 0
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_7nt_m4 versus positions_6nt_m4_rc; m=7/13; ncol2=24; w=-5; offset=-5; strand=R; shift=0; score=0.526055; srGCGCCCTCTGCTGsCmcCtvsk----- ; cor=; Ncor= a 106 212 38 53 46 26 24 43 25 14 15 76 15 30 9 49 20 372 91 60 60 256 82 112 0 0 0 0 0 c 264 176 91 546 36 579 642 680 122 718 42 37 649 85 27 453 690 229 453 618 80 196 244 189 0 0 0 0 0 g 254 274 564 78 659 117 46 28 60 30 32 643 104 31 734 226 25 94 154 55 114 227 331 213 0 0 0 0 0 t 155 117 86 102 38 57 67 28 572 17 690 23 11 633 9 51 44 84 81 46 525 100 122 265 0 0 0 0 0
oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)				; positions_7nt_m4 versus oligos_7nt_mkv5_m1_rc; m=8/13; ncol2=14; w=0; offset=6; strand=R; shift=11; score=0.498802; -----------rsCGCCCTCTrGtg---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 386 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 829 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 3571 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570 561 0 0 0 0
oligos_6nt_mkv4_m2_rc_shift16 (oligos_6nt_mkv4_m2_rc)				; positions_7nt_m4 versus oligos_6nt_mkv4_m2_rc; m=9/13; ncol2=12; w=0; offset=11; strand=R; shift=16; score=0.474813; ----------------cmTCTAGTGGym- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 433 1560 84 76 103 3794 96 199 64 203 979 1293 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3266 2209 649 4682 217 121 247 203 39 202 1801 1581 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 598 617 123 105 41 647 4527 182 4781 4349 902 1003 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 653 564 4094 87 4589 388 80 4366 66 196 1268 1073 0
oligos_6nt_mkv4_m4_rc_shift11 (oligos_6nt_mkv4_m4_rc)				; positions_7nt_m4 versus oligos_6nt_mkv4_m4_rc; m=10/13; ncol2=12; w=0; offset=6; strand=R; shift=11; score=0.461479; -----------rsTGCCCTCTgs------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2125 930 432 120 248 130 670 234 52 248 1904 958 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1795 3466 864 320 7303 7701 7160 733 7646 361 1647 2899 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2692 2480 278 7403 371 93 77 128 285 111 3185 2983 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1576 1312 6614 345 266 264 281 7093 205 7468 1452 1348 0 0 0 0 0 0
oligos_7nt_mkv5_m5_rc_shift17 (oligos_7nt_mkv5_m5_rc)				; positions_7nt_m4 versus oligos_7nt_mkv5_m5_rc; m=11/13; ncol2=12; w=0; offset=12; strand=R; shift=17; score=0.450852; -----------------myCTAGTGGTcr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1419 404 63 94 3163 71 141 34 77 324 854 1557 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1517 1562 3793 195 118 122 173 39 124 585 1239 744 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 599 479 81 48 488 3760 139 3889 3692 240 999 1041 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 480 1570 78 3678 246 62 3562 53 122 2866 923 673
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)				; positions_7nt_m4 versus oligos_6nt_mkv4_m1; m=12/13; ncol2=13; w=0; offset=6; strand=D; shift=11; score=0.411561; -----------vsCGCCCCCTgsy----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083 0 0 0 0 0
oligos_7nt_mkv5_m4_rc_shift8 (oligos_7nt_mkv5_m4_rc)				; positions_7nt_m4 versus oligos_7nt_mkv5_m4_rc; m=13/13; ncol2=11; w=0; offset=3; strand=R; shift=8; score=0.403846; --------gsTGCTGCCvc---------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1338 1302 116 455 130 211 218 177 73 1827 864 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1634 2749 570 191 6393 418 180 6332 6400 1915 2798 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 2302 1947 232 6156 252 356 6417 204 337 2001 1690 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 1645 921 6001 117 144 5934 104 206 109 1176 1567 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=14; shift=11; ncol=25; -----------ssCGCCCCCTgCys ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849
oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/13; ncol2=14; w=0; offset=0; strand=D; shift=11; score= 1; -----------ssCGCCCCCTgCys ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=2/13; ncol2=13; w=0; offset=0; strand=D; shift=11; score=0.901385; -----------vsCGCCCCCTgsy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 0 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 0 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 0 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083 0
oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m1_rc; m=3/13; ncol2=14; w=0; offset=0; strand=R; shift=11; score=0.810143; -----------rsCGCCCTCTrGtg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 386 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 829 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 3571 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570 561
oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=4/13; ncol2=12; w=0; offset=0; strand=D; shift=11; score=0.747688; -----------rsCGCCACCTss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 0 0 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847 0 0
oligos_6nt_mkv4_m4_rc_shift11 (oligos_6nt_mkv4_m4_rc)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m4_rc; m=5/13; ncol2=12; w=0; offset=0; strand=R; shift=11; score=0.602327; -----------rsTGCCCTCTgs-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2125 930 432 120 248 130 670 234 52 248 1904 958 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1795 3466 864 320 7303 7701 7160 733 7646 361 1647 2899 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2692 2480 278 7403 371 93 77 128 285 111 3185 2983 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1576 1312 6614 345 266 264 281 7093 205 7468 1452 1348 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)				; oligos_7nt_mkv5_m2 versus positions_7nt_m3; m=6/13; ncol2=24; w=-8; offset=-8; strand=D; shift=3; score=0.519493; ---sgsCmgggGGCGCCCCCTGGtG ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 15 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 62 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 682 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518 14
positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)				; oligos_7nt_mkv5_m2 versus positions_6nt_m3_rc; m=7/13; ncol2=24; w=-7; offset=-7; strand=R; shift=4; score=0.494956; ----rstmgaGGGCGCCCTCTGCTG ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 32 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 29 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 596 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556 17
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; oligos_7nt_mkv5_m2 versus positions_7nt_m2_rc; m=8/13; ncol2=24; w=-8; offset=-8; strand=R; shift=3; score=0.492998; ---sgsCygstGGCGCCCTCTGCTG ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 9 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 52 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 469 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425 14
positions_6nt_m4_rc_shift10 (positions_6nt_m4_rc)				; oligos_7nt_mkv5_m2 versus positions_6nt_m4_rc; m=9/13; ncol2=24; w=-1; offset=-1; strand=R; shift=10; score=0.487623; ----------srGCGCCCTCTGCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 106 212 38 53 46 26 24 43 25 14 15 76 15 30 9 c 0 0 0 0 0 0 0 0 0 0 264 176 91 546 36 579 642 680 122 718 42 37 649 85 27 g 0 0 0 0 0 0 0 0 0 0 254 274 564 78 659 117 46 28 60 30 32 643 104 31 734 t 0 0 0 0 0 0 0 0 0 0 155 117 86 102 38 57 67 28 572 17 690 23 11 633 9
positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)				; oligos_7nt_mkv5_m2 versus positions_6nt_m5_rc; m=10/13; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.475997; srskaGGtGGCAGCGCCCCCTgsy- ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 0 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 0 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 0 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231 0
positions_6nt_m1_shift6 (positions_6nt_m1)				; oligos_7nt_mkv5_m2 versus positions_6nt_m1; m=11/13; ncol2=24; w=-5; offset=-5; strand=D; shift=6; score=0.448004; ------scggcaGCGCCCYCTrGTG ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_7nt_mkv5_m2 versus positions_6nt_m2; m=12/13; ncol2=24; w=-10; offset=-10; strand=D; shift=1; score=0.438686; -ssCtGGtGGCAGCGCCaCCaGgsg ; cor=; Ncor= a 0 47 29 17 34 7 20 28 15 15 6 169 11 16 31 7 7 151 7 8 147 16 17 36 34 c 0 88 88 173 32 24 33 59 28 22 222 19 20 190 16 192 211 30 197 213 25 28 58 77 50 g 0 69 84 42 41 198 183 31 184 191 7 41 204 22 184 28 18 43 30 18 23 179 147 71 127 t 0 39 42 11 136 14 7 125 16 15 8 14 8 15 12 16 7 19 9 4 48 20 21 59 32
positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)				; oligos_7nt_mkv5_m2 versus positions_7nt_m1_rc; m=13/13; ncol2=24; w=-6; offset=-6; strand=R; shift=5; score=0.438432; -----gsctcTGCTGCCmCCTgsTG ; cor=; Ncor= a 0 0 0 0 0 257 247 179 231 225 63 244 44 42 49 63 8 1103 12 30 109 282 77 117 13 c 0 0 0 0 0 443 584 1163 169 1163 156 102 1359 316 25 1657 1760 575 1355 1724 74 146 975 135 21 g 0 0 0 0 0 721 521 178 270 224 153 1361 319 40 1672 42 5 58 38 15 50 1196 697 60 1747 t 0 0 0 0 0 381 450 282 1132 190 1430 95 80 1404 56 40 29 66 397 33 1569 178 53 1490 21

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=14; shift=9; ncol=23; ---------caCyAGAGGGCGsy ; Alignment reference a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/15; ncol2=14; w=0; offset=0; strand=D; shift=9; score= 1; ---------caCyAGAGGGCGsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561
oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m2_rc; m=2/15; ncol2=14; w=0; offset=0; strand=R; shift=9; score=0.810143; ---------srGcAGGGGGCGss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 c 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 g 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 t 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890
oligos_6nt_mkv4_m1_rc_shift10 (oligos_6nt_mkv4_m1_rc)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1_rc; m=3/15; ncol2=13; w=0; offset=1; strand=R; shift=10; score=0.805128; ----------rscAGGGGGCGsb ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 c 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 g 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 t 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082
oligos_6nt_mkv4_m4_shift11 (oligos_6nt_mkv4_m4)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m4; m=4/15; ncol2=12; w=0; offset=2; strand=D; shift=11; score=0.738757; -----------scAGAGGGCAsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 c 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 g 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 t 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125
oligos_7nt_mkv5_m3_rc_shift11 (oligos_7nt_mkv5_m3_rc)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m3_rc; m=5/15; ncol2=12; w=0; offset=2; strand=R; shift=11; score=0.645417; -----------ssAGGTGGCGsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 847 1148 6438 56 446 323 47 75 430 1016 1004 972 c 0 0 0 0 0 0 0 0 0 0 0 2951 2842 365 120 127 482 113 97 5895 314 3116 2510 g 0 0 0 0 0 0 0 0 0 0 0 2875 1916 272 7035 6653 1055 7070 7005 484 5673 2356 1618 t 0 0 0 0 0 0 0 0 0 0 0 594 1361 192 56 41 5407 37 90 458 264 791 2167
positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)				; oligos_7nt_mkv5_m1 versus positions_6nt_m1_rc; m=6/15; ncol2=24; w=-5; offset=-5; strand=R; shift=4; score=0.551646; ----gyGGCCACyAGRGGGCGCt ; cor=; Ncor= a 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 c 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 g 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 t 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795
positions_6nt_m3_shift6 (positions_6nt_m3)				; oligos_7nt_mkv5_m1 versus positions_6nt_m3; m=7/15; ncol2=24; w=-3; offset=-3; strand=D; shift=6; score=0.509096; ------sgCCAGCAGAGGGCGCC ; cor=; Ncor= a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110
positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)				; oligos_7nt_mkv5_m1 versus positions_7nt_m3_rc; m=8/15; ncol2=24; w=-2; offset=-2; strand=R; shift=7; score=0.500673; -------gcCaCCAGGGGGCGCC ; cor=; Ncor= a 0 0 0 0 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 c 0 0 0 0 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 g 0 0 0 0 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 t 0 0 0 0 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112
positions_7nt_m2_shift7 (positions_7nt_m2)				; oligos_7nt_mkv5_m1 versus positions_7nt_m2; m=9/15; ncol2=24; w=-2; offset=-2; strand=D; shift=7; score=0.500175; -------gcCAGCAGAGGGCGCC ; cor=; Ncor= a 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 c 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 g 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 t 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60
positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)				; oligos_7nt_mkv5_m1 versus positions_7nt_m4_rc; m=10/15; ncol2=24; w=-4; offset=-4; strand=R; shift=5; score=0.498802; -----yggCCACyAGrGGGCAGC ; cor=; Ncor= a 0 0 0 0 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 c 0 0 0 0 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 g 0 0 0 0 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 t 0 0 0 0 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324
positions_6nt_m4_shift0 (positions_6nt_m4)				; oligos_7nt_mkv5_m1 versus positions_6nt_m4; m=11/15; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.496932; msbaGgkGsCAGCAGAGGGCGCy ; cor=; Ncor= a 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 c 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 g 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 t 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212
oligos_6nt_mkv4_m2_shift6 (oligos_6nt_mkv4_m2)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m2; m=12/15; ncol2=12; w=-3; offset=-3; strand=D; shift=6; score=0.474054; ------krCCACTAGAkg----- ; cor=; Ncor= a 0 0 0 0 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 653 0 0 0 0 0 c 0 0 0 0 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 598 0 0 0 0 0 g 0 0 0 0 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 3266 0 0 0 0 0 t 0 0 0 0 0 0 1293 979 203 64 199 96 3794 103 76 84 1560 433 0 0 0 0 0
positions_7nt_m5_shift4 (positions_7nt_m5)				; oligos_7nt_mkv5_m1 versus positions_7nt_m5; m=13/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.43053; ----ryggCCACyAGGkGGCAGC ; cor=; Ncor= a 0 0 0 0 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 c 0 0 0 0 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 g 0 0 0 0 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 t 0 0 0 0 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291
positions_6nt_m5_shift10 (positions_6nt_m5)				; oligos_7nt_mkv5_m1 versus positions_6nt_m5; m=14/15; ncol2=24; w=0; offset=1; strand=D; shift=10; score=0.42372; ----------rscAGGGGGCGCT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 231 76 66 494 12 78 36 29 33 22 53 13 20 c 0 0 0 0 0 0 0 0 0 0 147 246 359 42 28 42 69 46 64 523 24 547 105 g 0 0 0 0 0 0 0 0 0 0 174 225 120 58 569 490 447 518 507 22 536 59 54 t 0 0 0 0 0 0 0 0 0 0 79 84 86 37 22 21 79 38 27 64 18 12 452
positions_7nt_m1_shift5 (positions_7nt_m1)				; oligos_7nt_mkv5_m1 versus positions_7nt_m1; m=15/15; ncol2=24; w=-4; offset=-4; strand=D; shift=5; score=0.412872; -----yggCCAscAGGkGGCAGC ; cor=; Ncor= a 0 0 0 0 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 c 0 0 0 0 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 g 0 0 0 0 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 t 0 0 0 0 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=24; shift=6; ncol=30; ------scggcaGCGCCCYCTrGTGGCCrc ; Alignment reference a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 58 94 126 482 260 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 51 899 836 203 368 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 998 74 108 359 284 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9 72 112 109 135 267
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/14; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------scggcaGCGCCCYCTrGTGGCCrc ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 58 94 126 482 260 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 51 899 836 203 368 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 998 74 108 359 284 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9 72 112 109 135 267
positions_7nt_m5_rc_shift6 (positions_7nt_m5_rc)				; positions_6nt_m1 versus positions_7nt_m5_rc; m=2/14; ncol2=24; w=0; offset=0; strand=R; shift=6; score=0.717491; ------scycTGCTGCCmCCTrGTGGccry ; cor=; Ncor= a 0 0 0 0 0 0 279 268 283 313 64 291 39 34 45 90 12 1136 10 26 100 893 44 102 6 67 198 355 748 380 c 0 0 0 0 0 0 558 733 558 1003 141 107 1284 243 20 1500 1649 436 1261 1614 111 112 210 110 8 55 978 753 243 501 g 0 0 0 0 0 0 507 268 314 179 168 1205 274 55 1586 53 6 52 24 11 48 498 1395 64 1665 1481 165 281 477 359 t 0 0 0 0 0 0 341 416 530 190 1312 82 88 1353 34 42 18 61 390 34 1426 182 36 1409 6 82 344 296 217 445
positions_7nt_m4_shift5 (positions_7nt_m4)				; positions_6nt_m1 versus positions_7nt_m4; m=3/14; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.706671; -----gsctcTGCTGCCCyCTrGTGGccr- ; cor=; Ncor= a 0 0 0 0 0 249 341 169 250 281 97 324 60 70 52 89 15 478 31 9 62 1013 44 101 4 115 228 432 838 0 c 0 0 0 0 0 435 612 1237 235 1223 160 133 1389 294 20 1741 1869 1397 580 1889 106 142 356 138 10 84 1072 782 302 0 g 0 0 0 0 0 844 508 186 310 219 194 1355 394 29 1789 47 11 18 26 13 42 573 1468 59 1909 1620 191 317 570 0 t 0 0 0 0 0 401 468 337 1134 206 1478 117 86 1536 68 52 34 36 1292 18 1719 201 61 1631 6 110 438 398 219 0
positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)				; positions_6nt_m1 versus positions_6nt_m3_rc; m=4/14; ncol2=24; w=-2; offset=-2; strand=R; shift=4; score=0.693247; ----rstmgaGGGCGCCCTCTGCTGGcs-- ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 32 30 111 126 0 0 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 29 27 337 267 0 0 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 596 581 89 174 0 0 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556 17 36 137 107 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_6nt_m1 versus positions_7nt_m3; m=5/14; ncol2=24; w=-3; offset=-3; strand=D; shift=3; score=0.650383; ---sgsCmgggGGCGCCCCCTGGtGgc--- ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 15 67 104 0 0 0 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 62 119 394 0 0 0 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 682 494 134 0 0 0 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518 14 93 141 0 0 0
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; positions_6nt_m1 versus positions_7nt_m2_rc; m=6/14; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.621257; ---sgsCygstGGCGCCCTCTGCTGgc--- ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 9 62 68 0 0 0 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 52 95 272 0 0 0 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 469 304 96 0 0 0 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425 14 83 108 0 0 0
positions_6nt_m4_rc_shift10 (positions_6nt_m4_rc)				; positions_6nt_m1 versus positions_6nt_m4_rc; m=7/14; ncol2=24; w=0; offset=4; strand=R; shift=10; score=0.557373; ----------srGCGCCCTCTGCTGsCmcC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 106 212 38 53 46 26 24 43 25 14 15 76 15 30 9 49 20 372 91 60 c 0 0 0 0 0 0 0 0 0 0 264 176 91 546 36 579 642 680 122 718 42 37 649 85 27 453 690 229 453 618 g 0 0 0 0 0 0 0 0 0 0 254 274 564 78 659 117 46 28 60 30 32 643 104 31 734 226 25 94 154 55 t 0 0 0 0 0 0 0 0 0 0 155 117 86 102 38 57 67 28 572 17 690 23 11 633 9 51 44 84 81 46
oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)				; positions_6nt_m1 versus oligos_7nt_mkv5_m1_rc; m=8/14; ncol2=14; w=0; offset=5; strand=R; shift=11; score=0.551646; -----------rsCGCCCTCTrGtg----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 386 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 829 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 3571 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570 561 0 0 0 0 0
positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)				; positions_6nt_m1 versus positions_6nt_m5_rc; m=9/14; ncol2=24; w=-6; offset=-6; strand=R; shift=0; score=0.497444; srskaGGtGGCAGCGCCCCCTgsy------ ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 0 0 0 0 0 0 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 0 0 0 0 0 0 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 0 0 0 0 0 0 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231 0 0 0 0 0 0
oligos_6nt_mkv4_m2_rc_shift16 (oligos_6nt_mkv4_m2_rc)				; positions_6nt_m1 versus oligos_6nt_mkv4_m2_rc; m=10/14; ncol2=12; w=0; offset=10; strand=R; shift=16; score=0.457888; ----------------cmTCTAGTGGym-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 433 1560 84 76 103 3794 96 199 64 203 979 1293 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3266 2209 649 4682 217 121 247 203 39 202 1801 1581 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 598 617 123 105 41 647 4527 182 4781 4349 902 1003 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 653 564 4094 87 4589 388 80 4366 66 196 1268 1073 0 0
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)				; positions_6nt_m1 versus oligos_6nt_mkv4_m1; m=11/14; ncol2=13; w=0; offset=5; strand=D; shift=11; score=0.453174; -----------vsCGCCCCCTgsy------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083 0 0 0 0 0 0
oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)				; positions_6nt_m1 versus oligos_7nt_mkv5_m2; m=12/14; ncol2=14; w=0; offset=5; strand=D; shift=11; score=0.448004; -----------ssCGCCCCCTgCys----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849 0 0 0 0 0
oligos_7nt_mkv5_m5_rc_shift17 (oligos_7nt_mkv5_m5_rc)				; positions_6nt_m1 versus oligos_7nt_mkv5_m5_rc; m=13/14; ncol2=12; w=0; offset=11; strand=R; shift=17; score=0.420613; -----------------myCTAGTGGTcr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1419 404 63 94 3163 71 141 34 77 324 854 1557 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1517 1562 3793 195 118 122 173 39 124 585 1239 744 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 599 479 81 48 488 3760 139 3889 3692 240 999 1041 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 480 1570 78 3678 246 62 3562 53 122 2866 923 673 0
oligos_6nt_mkv4_m4_rc_shift11 (oligos_6nt_mkv4_m4_rc)				; positions_6nt_m1 versus oligos_6nt_mkv4_m4_rc; m=14/14; ncol2=12; w=0; offset=5; strand=R; shift=11; score=0.40069; -----------rsTGCCCTCTgs------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2125 930 432 120 248 130 670 234 52 248 1904 958 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1795 3466 864 320 7303 7701 7160 733 7646 361 1647 2899 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2692 2480 278 7403 371 93 77 128 285 111 3185 2983 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1576 1312 6614 345 266 264 281 7093 205 7468 1452 1348 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---sgsCmgggGGCGCCCCCTGGtGgc ; Alignment reference a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 15 67 104 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 62 119 394 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 682 494 134 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518 14 93 141
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---sgsCmgggGGCGCCCCCTGGtGgc ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 15 67 104 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 62 119 394 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 682 494 134 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518 14 93 141
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; positions_7nt_m3 versus positions_7nt_m2_rc; m=2/10; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.861902; ---sgsCygstGGCGCCCTCTGCTGgc ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 9 62 68 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 52 95 272 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 469 304 96 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425 14 83 108
positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)				; positions_7nt_m3 versus positions_6nt_m3_rc; m=3/10; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.801001; ----rstmgaGGGCGCCCTCTGCTGGc ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 32 30 111 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 29 27 337 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 596 581 89 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556 17 36 137
positions_6nt_m1_shift6 (positions_6nt_m1)				; positions_7nt_m3 versus positions_6nt_m1; m=4/10; ncol2=24; w=0; offset=3; strand=D; shift=6; score=0.650383; ------scggcaGCGCCCYCTrGTGGC ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 7 58 94 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 16 51 899 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 1147 998 74 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960 9 72 112
positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)				; positions_7nt_m3 versus positions_6nt_m5_rc; m=5/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.584707; srskaGGtGGCAGCGCCCCCTgsy--- ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 0 0 0 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 0 0 0 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 0 0 0 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231 0 0 0
oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)				; positions_7nt_m3 versus oligos_7nt_mkv5_m2; m=6/10; ncol2=14; w=0; offset=8; strand=D; shift=11; score=0.519493; -----------ssCGCCCCCTgCys-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 0 0 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849 0 0
oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)				; positions_7nt_m3 versus oligos_7nt_mkv5_m1_rc; m=7/10; ncol2=14; w=0; offset=8; strand=R; shift=11; score=0.500673; -----------rsCGCCCTCTrGtg-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 386 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 829 0 0 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 3571 0 0 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570 561 0 0
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)				; positions_7nt_m3 versus oligos_6nt_mkv4_m1; m=8/10; ncol2=13; w=0; offset=8; strand=D; shift=11; score=0.493783; -----------vsCGCCCCCTgsy--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083 0 0 0
positions_6nt_m4_rc_shift10 (positions_6nt_m4_rc)				; positions_7nt_m3 versus positions_6nt_m4_rc; m=9/10; ncol2=24; w=0; offset=7; strand=R; shift=10; score=0.446625; ----------srGCGCCCTCTGCTGsC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 106 212 38 53 46 26 24 43 25 14 15 76 15 30 9 49 20 c 0 0 0 0 0 0 0 0 0 0 264 176 91 546 36 579 642 680 122 718 42 37 649 85 27 453 690 g 0 0 0 0 0 0 0 0 0 0 254 274 564 78 659 117 46 28 60 30 32 643 104 31 734 226 25 t 0 0 0 0 0 0 0 0 0 0 155 117 86 102 38 57 67 28 572 17 690 23 11 633 9 51 44
oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)				; positions_7nt_m3 versus oligos_7nt_mkv5_m3; m=10/10; ncol2=12; w=0; offset=8; strand=D; shift=11; score=0.416373; -----------rsCGCCACCTss---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=24; shift=1; ncol=25; -ssCtGGtGGCAGCGCCaCCaGgsg ; Alignment reference a 0 47 29 17 34 7 20 28 15 15 6 169 11 16 31 7 7 151 7 8 147 16 17 36 34 c 0 88 88 173 32 24 33 59 28 22 222 19 20 190 16 192 211 30 197 213 25 28 58 77 50 g 0 69 84 42 41 198 183 31 184 191 7 41 204 22 184 28 18 43 30 18 23 179 147 71 127 t 0 39 42 11 136 14 7 125 16 15 8 14 8 15 12 16 7 19 9 4 48 20 21 59 32
positions_6nt_m2_shift1 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -ssCtGGtGGCAGCGCCaCCaGgsg ; cor=; Ncor= a 0 47 29 17 34 7 20 28 15 15 6 169 11 16 31 7 7 151 7 8 147 16 17 36 34 c 0 88 88 173 32 24 33 59 28 22 222 19 20 190 16 192 211 30 197 213 25 28 58 77 50 g 0 69 84 42 41 198 183 31 184 191 7 41 204 22 184 28 18 43 30 18 23 179 147 71 127 t 0 39 42 11 136 14 7 125 16 15 8 14 8 15 12 16 7 19 9 4 48 20 21 59 32
positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)				; positions_6nt_m2 versus positions_6nt_m5_rc; m=2/4; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.769472; srskaGGtGGCAGCGCCCCCTgsy- ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 0 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 0 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 0 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231 0
oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)				; positions_6nt_m2 versus oligos_7nt_mkv5_m2; m=3/4; ncol2=14; w=0; offset=10; strand=D; shift=11; score=0.438686; -----------ssCGCCCCCTgCys ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 639 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 2106 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 4285 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563 849
oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)				; positions_6nt_m2 versus oligos_7nt_mkv5_m3; m=4/4; ncol2=12; w=0; offset=10; strand=D; shift=11; score=0.406395; -----------rsCGCCACCTss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 0 0 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift7 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=24; shift=7; ncol=31; -------gcCAGCAGAGGGCGCCascrGscs ; Alignment reference a 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 52 106 283 58 74 94 110 c 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 304 334 46 76 147 256 203 g 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 142 68 146 383 284 99 144 t 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36 46 36 69 27 39 95 87
positions_7nt_m2_shift7 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=7; score= 1; -------gcCAGCAGAGGGCGCCascrGscs ; cor=; Ncor= a 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 52 106 283 58 74 94 110 c 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 304 334 46 76 147 256 203 g 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 142 68 146 383 284 99 144 t 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36 46 36 69 27 39 95 87
positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)				; positions_7nt_m2 versus positions_7nt_m3_rc; m=2/10; ncol2=24; w=0; offset=0; strand=R; shift=7; score=0.861902; -------gcCaCCAGGGGGCGCCccckGscs ; cor=; Ncor= a 0 0 0 0 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 99 69 103 97 60 104 113 106 c 0 0 0 0 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 509 473 502 110 130 310 393 319 g 0 0 0 0 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 133 132 110 230 531 284 110 224 t 0 0 0 0 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112 32 99 58 336 52 75 157 124
positions_6nt_m3_shift6 (positions_6nt_m3)				; positions_7nt_m2 versus positions_6nt_m3; m=3/10; ncol2=24; w=-1; offset=-1; strand=D; shift=6; score=0.819642; ------sgCCAGCAGAGGGCGCCCtckasy- ; cor=; Ncor= a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 109 70 93 74 275 104 94 0 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 470 102 387 97 166 325 349 0 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 72 129 102 211 168 174 59 0 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110 23 373 92 292 65 71 172 0
positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)				; positions_7nt_m2 versus positions_6nt_m1_rc; m=4/10; ncol2=24; w=-3; offset=-3; strand=R; shift=4; score=0.621257; ----gyGGCCACyAGRGGGCGCtgccgs--- ; cor=; Ncor= a 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 81 255 218 182 0 0 0 c 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 625 454 194 411 0 0 0 g 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 183 270 596 393 0 0 0 t 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75 290 200 171 193 0 0 0
positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)				; positions_7nt_m2 versus positions_7nt_m4_rc; m=5/10; ncol2=24; w=-2; offset=-2; strand=R; shift=5; score=0.605706; -----yggCCACyAGrGGGCAGCAgagsc-- ; cor=; Ncor= a 0 0 0 0 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 401 0 0 c 0 0 0 0 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 844 0 0 g 0 0 0 0 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 435 0 0 t 0 0 0 0 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341 249 0 0
positions_7nt_m1_shift5 (positions_7nt_m1)				; positions_7nt_m2 versus positions_7nt_m1; m=6/10; ncol2=24; w=-2; offset=-2; strand=D; shift=5; score=0.600212; -----yggCCAscAGGkGGCAGCAgagsc-- ; cor=; Ncor= a 0 0 0 0 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 381 0 0 c 0 0 0 0 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 721 0 0 g 0 0 0 0 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 443 0 0 t 0 0 0 0 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247 257 0 0
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_7nt_m2 versus positions_6nt_m4; m=7/10; ncol2=24; w=-7; offset=-7; strand=D; shift=0; score=0.507662; msbaGgkGsCAGCAGAGGGCGCys------- ; cor=; Ncor= a 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 155 0 0 0 0 0 0 0 c 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 254 0 0 0 0 0 0 0 g 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 264 0 0 0 0 0 0 0 t 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212 106 0 0 0 0 0 0 0
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)				; positions_7nt_m2 versus oligos_7nt_mkv5_m1; m=8/10; ncol2=14; w=0; offset=2; strand=D; shift=9; score=0.500175; ---------caCyAGAGGGCGsy-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0 0 0 0
oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)				; positions_7nt_m2 versus oligos_7nt_mkv5_m2_rc; m=9/10; ncol2=14; w=0; offset=2; strand=R; shift=9; score=0.492998; ---------srGcAGGGGGCGss-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0 0 0 0 0 0 0 0
oligos_6nt_mkv4_m1_rc_shift10 (oligos_6nt_mkv4_m1_rc)				; positions_7nt_m2 versus oligos_6nt_mkv4_m1_rc; m=10/10; ncol2=13; w=0; offset=3; strand=R; shift=10; score=0.444065; ----------rscAGGGGGCGsb-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -ygACCACTAGrk ; Alignment reference a 0 673 923 2866 122 53 3562 62 246 3678 78 1570 480 c 0 1041 999 240 3692 3889 139 3760 488 48 81 479 599 g 0 744 1239 585 124 39 173 122 118 195 3793 1562 1517 t 0 1557 854 324 77 34 141 71 3163 94 63 404 1419
oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ygACCACTAGrk ; cor=; Ncor= a 0 673 923 2866 122 53 3562 62 246 3678 78 1570 480 c 0 1041 999 240 3692 3889 139 3760 488 48 81 479 599 g 0 744 1239 585 124 39 173 122 118 195 3793 1562 1517 t 0 1557 854 324 77 34 141 71 3163 94 63 404 1419
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m2; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.792288; --krCCACTAGAk ; cor=; Ncor= a 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 c 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 g 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 t 0 0 1293 979 203 64 199 96 3794 103 76 84 1560
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; oligos_7nt_mkv5_m5 versus positions_7nt_m4_rc; m=3/5; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.450852; -yggCCACyAGrG ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 t 0 838 432 228 115 4 101 44 1013 62 9 31 478
positions_7nt_m5_shift0 (positions_7nt_m5)				; oligos_7nt_mkv5_m5 versus positions_7nt_m5; m=4/5; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.447532; ryggCCACyAGGk ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 t 380 748 355 198 67 6 102 44 893 100 26 10 1136
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; oligos_7nt_mkv5_m5 versus positions_6nt_m1_rc; m=5/5; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.420613; gyGGCCACyAGRG ; cor=; Ncor= a 267 135 109 112 72 9 960 20 98 1030 9 806 23 c 284 359 108 74 998 1147 37 940 399 43 16 21 33 g 368 203 836 899 51 16 129 202 86 77 1146 337 877 t 260 482 126 94 58 7 53 17 596 29 8 15 246

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=24; shift=1; ncol=25; -yggCCAscAGGkGGCAGCAgagsc ; Alignment reference a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 381 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 721 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 443 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247 257
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -yggCCAscAGGkGGCAGCAgagsc ; cor=; Ncor= a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 381 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 721 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 443 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247 257
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; positions_7nt_m1 versus positions_7nt_m4_rc; m=2/10; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.921854; -yggCCACyAGrGGGCAGCAgagsc ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 401 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 844 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 435 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341 249
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_7nt_m1 versus positions_7nt_m5; m=3/10; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.868363; ryggCCACyAGGkGGCAGCAgrgs- ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 416 341 0 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 268 507 0 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 733 558 0 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283 268 279 0
positions_7nt_m2_shift3 (positions_7nt_m2)				; positions_7nt_m1 versus positions_7nt_m2; m=4/10; ncol2=24; w=0; offset=2; strand=D; shift=3; score=0.600212; ---gcCAGCAGAGGGCGCCascrGs ; cor=; Ncor= a 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 52 106 283 58 74 c 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 304 334 46 76 147 g 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 142 68 146 383 284 t 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36 46 36 69 27 39
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_7nt_m1 versus positions_6nt_m4; m=5/10; ncol2=24; w=0; offset=5; strand=D; shift=6; score=0.558979; ------msbaGgkGsCAGCAGAGGG ; cor=; Ncor= a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26
oligos_7nt_mkv5_m2_rc_shift5 (oligos_7nt_mkv5_m2_rc)				; positions_7nt_m1 versus oligos_7nt_mkv5_m2_rc; m=6/10; ncol2=14; w=0; offset=4; strand=R; shift=5; score=0.438432; -----srGcAGGGGGCGss------ ; cor=; Ncor= a 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 0 0 0 0 0 c 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 0 0 0 0 0 g 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 0 0 0 0 0 t 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0 0 0 0 0 0
oligos_6nt_mkv4_m1_rc_shift6 (oligos_6nt_mkv4_m1_rc)				; positions_7nt_m1 versus oligos_6nt_mkv4_m1_rc; m=7/10; ncol2=13; w=0; offset=5; strand=R; shift=6; score=0.42638; ------rscAGGGGGCGsb------ ; cor=; Ncor= a 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 0 c 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 0 g 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 0 t 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0 0
oligos_7nt_mkv5_m3_rc_shift7 (oligos_7nt_mkv5_m3_rc)				; positions_7nt_m1 versus oligos_7nt_mkv5_m3_rc; m=8/10; ncol2=12; w=0; offset=6; strand=R; shift=7; score=0.422176; -------ssAGGTGGCGsy------ ; cor=; Ncor= a 0 0 0 0 0 0 0 847 1148 6438 56 446 323 47 75 430 1016 1004 972 0 0 0 0 0 0 c 0 0 0 0 0 0 0 2951 2842 365 120 127 482 113 97 5895 314 3116 2510 0 0 0 0 0 0 g 0 0 0 0 0 0 0 2875 1916 272 7035 6653 1055 7070 7005 484 5673 2356 1618 0 0 0 0 0 0 t 0 0 0 0 0 0 0 594 1361 192 56 41 5407 37 90 458 264 791 2167 0 0 0 0 0 0
oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)				; positions_7nt_m1 versus oligos_7nt_mkv5_m4; m=9/10; ncol2=11; w=0; offset=10; strand=D; shift=11; score=0.41522; -----------gbGGCAGCAsc--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338 0 0 0
oligos_7nt_mkv5_m1_shift5 (oligos_7nt_mkv5_m1)				; positions_7nt_m1 versus oligos_7nt_mkv5_m1; m=10/10; ncol2=14; w=0; offset=4; strand=D; shift=5; score=0.412872; -----caCyAGAGGGCGsy------ ; cor=; Ncor= a 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 0 c 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 0 g 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 0 t 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift6 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=24; shift=6; ncol=30; ------sgCCAGCAGAGGGCGCCCtckasy ; Alignment reference a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 109 70 93 74 275 104 94 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 470 102 387 97 166 325 349 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 72 129 102 211 168 174 59 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110 23 373 92 292 65 71 172
positions_6nt_m3_shift6 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------sgCCAGCAGAGGGCGCCCtckasy ; cor=; Ncor= a 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 109 70 93 74 275 104 94 c 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 470 102 387 97 166 325 349 g 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 72 129 102 211 168 174 59 t 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110 23 373 92 292 65 71 172
positions_7nt_m2_shift7 (positions_7nt_m2)				; positions_6nt_m3 versus positions_7nt_m2; m=2/10; ncol2=24; w=0; offset=1; strand=D; shift=7; score=0.819642; -------gcCAGCAGAGGGCGCCascrGsc ; cor=; Ncor= a 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 52 106 283 58 74 94 c 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 304 334 46 76 147 256 g 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 142 68 146 383 284 99 t 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36 46 36 69 27 39 95
positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)				; positions_6nt_m3 versus positions_7nt_m3_rc; m=3/10; ncol2=24; w=0; offset=1; strand=R; shift=7; score=0.801001; -------gcCaCCAGGGGGCGCCccckGsc ; cor=; Ncor= a 0 0 0 0 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 99 69 103 97 60 104 113 c 0 0 0 0 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 509 473 502 110 130 310 393 g 0 0 0 0 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 133 132 110 230 531 284 110 t 0 0 0 0 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112 32 99 58 336 52 75 157
positions_6nt_m1_rc_shift4 (positions_6nt_m1_rc)				; positions_6nt_m3 versus positions_6nt_m1_rc; m=4/10; ncol2=24; w=-2; offset=-2; strand=R; shift=4; score=0.693247; ----gyGGCCACyAGRGGGCGCtgccgs-- ; cor=; Ncor= a 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 81 255 218 182 0 0 c 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 625 454 194 411 0 0 g 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 183 270 596 393 0 0 t 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75 290 200 171 193 0 0
positions_7nt_m4_rc_shift5 (positions_7nt_m4_rc)				; positions_6nt_m3 versus positions_7nt_m4_rc; m=5/10; ncol2=24; w=-1; offset=-1; strand=R; shift=5; score=0.655757; -----yggCCACyAGrGGGCAGCAgagsc- ; cor=; Ncor= a 0 0 0 0 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 401 0 c 0 0 0 0 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 844 0 g 0 0 0 0 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 435 0 t 0 0 0 0 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341 249 0
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m3 versus positions_6nt_m4; m=6/10; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.537819; msbaGgkGsCAGCAGAGGGCGCys------ ; cor=; Ncor= a 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 155 0 0 0 0 0 0 c 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 254 0 0 0 0 0 0 g 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 264 0 0 0 0 0 0 t 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212 106 0 0 0 0 0 0
oligos_7nt_mkv5_m1_shift9 (oligos_7nt_mkv5_m1)				; positions_6nt_m3 versus oligos_7nt_mkv5_m1; m=7/10; ncol2=14; w=0; offset=3; strand=D; shift=9; score=0.509096; ---------caCyAGAGGGCGsy------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0 0 0
oligos_7nt_mkv5_m2_rc_shift9 (oligos_7nt_mkv5_m2_rc)				; positions_6nt_m3 versus oligos_7nt_mkv5_m2_rc; m=8/10; ncol2=14; w=0; offset=3; strand=R; shift=9; score=0.494956; ---------srGcAGGGGGCGss------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0 0 0 0 0 0 0
oligos_6nt_mkv4_m1_rc_shift10 (oligos_6nt_mkv4_m1_rc)				; positions_6nt_m3 versus oligos_6nt_mkv4_m1_rc; m=9/10; ncol2=13; w=0; offset=4; strand=R; shift=10; score=0.451881; ----------rscAGGGGGCGsb------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0 0 0
oligos_6nt_mkv4_m4_shift11 (oligos_6nt_mkv4_m4)				; positions_6nt_m3 versus oligos_6nt_mkv4_m4; m=10/10; ncol2=12; w=0; offset=5; strand=D; shift=11; score=0.400843; -----------scAGAGGGCAsy------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------rsCGCCACCTss ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847
oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/9; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------rsCGCCACCTss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m1; m=2/9; ncol2=13; w=0; offset=0; strand=D; shift=11; score=0.830838; -----------vsCGCCCCCTgs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952
oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=3/9; ncol2=14; w=0; offset=0; strand=D; shift=11; score=0.747688; -----------ssCGCCCCCTgC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396
oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m1_rc; m=4/9; ncol2=14; w=0; offset=0; strand=R; shift=11; score=0.645417; -----------rsCGCCCTCTrG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277
positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)				; oligos_7nt_mkv5_m3 versus positions_6nt_m5_rc; m=5/9; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.422979; srskaGGtGGCAGCGCCCCCTgs ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76
positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)				; oligos_7nt_mkv5_m3 versus positions_7nt_m1_rc; m=6/9; ncol2=24; w=-6; offset=-6; strand=R; shift=5; score=0.422176; -----gsctcTGCTGCCmCCTgs ; cor=; Ncor= a 0 0 0 0 0 257 247 179 231 225 63 244 44 42 49 63 8 1103 12 30 109 282 77 c 0 0 0 0 0 443 584 1163 169 1163 156 102 1359 316 25 1657 1760 575 1355 1724 74 146 975 g 0 0 0 0 0 721 521 178 270 224 153 1361 319 40 1672 42 5 58 38 15 50 1196 697 t 0 0 0 0 0 381 450 282 1132 190 1430 95 80 1404 56 40 29 66 397 33 1569 178 53
positions_7nt_m3_shift3 (positions_7nt_m3)				; oligos_7nt_mkv5_m3 versus positions_7nt_m3; m=7/9; ncol2=24; w=-8; offset=-8; strand=D; shift=3; score=0.416373; ---sgsCmgggGGCGCCCCCTGG ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10
positions_7nt_m5_rc_shift6 (positions_7nt_m5_rc)				; oligos_7nt_mkv5_m3 versus positions_7nt_m5_rc; m=8/9; ncol2=24; w=-5; offset=-5; strand=R; shift=6; score=0.407699; ------scycTGCTGCCmCCTrG ; cor=; Ncor= a 0 0 0 0 0 0 279 268 283 313 64 291 39 34 45 90 12 1136 10 26 100 893 44 c 0 0 0 0 0 0 558 733 558 1003 141 107 1284 243 20 1500 1649 436 1261 1614 111 112 210 g 0 0 0 0 0 0 507 268 314 179 168 1205 274 55 1586 53 6 52 24 11 48 498 1395 t 0 0 0 0 0 0 341 416 530 190 1312 82 88 1353 34 42 18 61 390 34 1426 182 36
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_7nt_mkv5_m3 versus positions_6nt_m2; m=9/9; ncol2=24; w=-10; offset=-10; strand=D; shift=1; score=0.406395; -ssCtGGtGGCAGCGCCaCCaGg ; cor=; Ncor= a 0 47 29 17 34 7 20 28 15 15 6 169 11 16 31 7 7 151 7 8 147 16 17 c 0 88 88 173 32 24 33 59 28 22 222 19 20 190 16 192 211 30 197 213 25 28 58 g 0 69 84 42 41 198 183 31 184 191 7 41 204 22 184 28 18 43 30 18 23 179 147 t 0 39 42 11 136 14 7 125 16 15 8 14 8 15 12 16 7 19 9 4 48 20 21

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=13; shift=11; ncol=24; -----------vsCGCCCCCTgsy ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083
oligos_6nt_mkv4_m1_shift11 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/14; ncol2=13; w=0; offset=0; strand=D; shift=11; score= 1; -----------vsCGCCCCCTgsy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2082 795 331 130 140 105 768 137 89 291 1786 627 1097 c 0 0 0 0 0 0 0 0 0 0 0 2151 2627 6132 22 7372 7268 6365 6654 7518 268 1956 3301 2282 g 0 0 0 0 0 0 0 0 0 0 0 2649 3620 414 7584 235 337 434 242 158 551 3150 3019 1437 t 0 0 0 0 0 0 0 0 0 0 0 1017 857 1022 163 152 189 332 866 134 6789 1007 952 3083
oligos_7nt_mkv5_m2_shift11 (oligos_7nt_mkv5_m2)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m2; m=2/14; ncol2=14; w=0; offset=0; strand=D; shift=11; score=0.901385; -----------ssCGCCCCCTgCy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1890 761 121 241 168 145 682 163 114 426 654 288 1018 c 0 0 0 0 0 0 0 0 0 0 0 2462 2689 7177 57 7132 6850 6021 6383 7297 798 1545 5362 2656 g 0 0 0 0 0 0 0 0 0 0 0 2541 3648 169 7298 383 591 822 537 309 1042 5136 1833 1642 t 0 0 0 0 0 0 0 0 0 0 0 986 781 412 283 196 293 354 796 159 5613 544 396 2563
oligos_7nt_mkv5_m3_shift11 (oligos_7nt_mkv5_m3)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m3; m=3/14; ncol2=12; w=0; offset=0; strand=D; shift=11; score=0.830838; -----------rsCGCCACCTss- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2167 791 264 458 90 37 5407 41 56 192 1361 594 0 c 0 0 0 0 0 0 0 0 0 0 0 1618 2356 5673 484 7005 7070 1055 6653 7035 272 1916 2875 0 g 0 0 0 0 0 0 0 0 0 0 0 2510 3116 314 5895 97 113 482 127 120 365 2842 2951 0 t 0 0 0 0 0 0 0 0 0 0 0 972 1004 1016 430 75 47 323 446 56 6438 1148 847 0
oligos_7nt_mkv5_m1_rc_shift11 (oligos_7nt_mkv5_m1_rc)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1_rc; m=4/14; ncol2=14; w=0; offset=0; strand=R; shift=11; score=0.805128; -----------rsCGCCCTCTrGt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1561 588 230 232 119 112 637 155 47 107 2492 203 654 c 0 0 0 0 0 0 0 0 0 0 0 1236 1366 4235 106 4858 4868 4480 783 5136 291 688 950 1222 g 0 0 0 0 0 0 0 0 0 0 0 1854 2684 121 4671 224 235 154 257 110 277 1598 3917 901 t 0 0 0 0 0 0 0 0 0 0 0 696 709 761 338 146 132 76 4152 54 4672 569 277 2570
oligos_6nt_mkv4_m4_rc_shift11 (oligos_6nt_mkv4_m4_rc)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m4_rc; m=5/14; ncol2=12; w=0; offset=0; strand=R; shift=11; score=0.707585; -----------rsTGCCCTCTgs- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2125 930 432 120 248 130 670 234 52 248 1904 958 0 c 0 0 0 0 0 0 0 0 0 0 0 1795 3466 864 320 7303 7701 7160 733 7646 361 1647 2899 0 g 0 0 0 0 0 0 0 0 0 0 0 2692 2480 278 7403 371 93 77 128 285 111 3185 2983 0 t 0 0 0 0 0 0 0 0 0 0 0 1576 1312 6614 345 266 264 281 7093 205 7468 1452 1348 0
positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)				; oligos_6nt_mkv4_m1 versus positions_6nt_m5_rc; m=6/14; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.501418; srskaGGtGGCAGCGCCCCCTgsy ; cor=; Ncor= a 72 162 58 87 363 36 46 69 53 77 14 452 12 18 64 27 38 79 21 22 37 86 84 79 c 303 156 318 141 63 44 74 154 88 50 540 54 59 536 22 507 518 447 490 569 58 120 225 174 g 169 211 161 197 152 515 490 81 446 477 51 105 547 24 523 64 46 69 42 28 42 359 246 147 t 87 102 94 206 53 36 21 327 44 27 26 20 13 53 22 33 29 36 78 12 494 66 76 231
positions_7nt_m3_shift3 (positions_7nt_m3)				; oligos_6nt_mkv4_m1 versus positions_7nt_m3; m=7/14; ncol2=24; w=-8; offset=-8; strand=D; shift=3; score=0.493783; ---sgsCmgggGGCGCCCCCTGGt ; cor=; Ncor= a 0 0 0 124 157 75 52 336 58 99 32 112 17 11 18 16 8 90 10 16 44 63 19 52 c 0 0 0 224 110 284 531 230 110 132 133 98 53 692 9 708 686 593 586 696 49 75 169 151 g 0 0 0 319 393 310 130 110 502 473 509 536 690 14 726 34 38 65 49 43 90 590 575 52 t 0 0 0 106 113 104 60 97 103 69 99 27 13 56 20 15 41 25 128 18 590 45 10 518
positions_6nt_m1_shift6 (positions_6nt_m1)				; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=8/14; ncol2=24; w=-5; offset=-5; strand=D; shift=6; score=0.453174; ------scggcaGCGCCCYCTrGT ; cor=; Ncor= a 0 0 0 0 0 0 193 171 200 290 75 795 21 72 63 39 10 246 15 8 29 596 17 53 c 0 0 0 0 0 0 393 596 270 183 742 92 105 895 19 1074 1138 877 337 1146 77 86 202 129 g 0 0 0 0 0 0 411 194 454 625 258 224 1000 23 1037 45 19 33 21 16 43 399 940 37 t 0 0 0 0 0 0 182 218 255 81 104 68 53 189 60 21 12 23 806 9 1030 98 20 960
positions_6nt_m3_rc_shift4 (positions_6nt_m3_rc)				; oligos_6nt_mkv4_m1 versus positions_6nt_m3_rc; m=9/14; ncol2=24; w=-7; offset=-7; strand=R; shift=4; score=0.451881; ----rstmgaGGGCGCCCTCTGCT ; cor=; Ncor= a 0 0 0 0 172 71 65 292 92 373 23 110 14 19 35 15 7 73 8 13 23 34 13 31 c 0 0 0 0 59 174 168 211 102 129 72 65 57 547 6 636 634 578 149 612 22 38 482 71 g 0 0 0 0 349 325 166 97 387 102 470 476 582 14 569 17 14 14 21 36 51 545 159 16 t 0 0 0 0 94 104 275 74 93 70 109 23 21 94 64 6 19 9 496 13 578 57 20 556
positions_7nt_m2_rc_shift3 (positions_7nt_m2_rc)				; oligos_6nt_mkv4_m1 versus positions_7nt_m2_rc; m=10/14; ncol2=24; w=-8; offset=-8; strand=R; shift=3; score=0.444065; ---sgsCygstGGCGCCCTCTGCT ; cor=; Ncor= a 0 0 0 87 95 39 27 69 36 46 36 60 6 12 25 15 7 47 6 4 16 40 9 21 c 0 0 0 144 99 284 383 146 68 142 93 33 57 448 25 480 490 462 104 502 21 31 428 69 g 0 0 0 203 256 147 76 46 334 304 101 424 462 16 459 31 14 24 32 27 46 444 95 29 t 0 0 0 110 94 74 58 283 106 52 314 27 19 68 35 18 33 11 402 11 461 29 12 425
positions_6nt_m4_rc_shift10 (positions_6nt_m4_rc)				; oligos_6nt_mkv4_m1 versus positions_6nt_m4_rc; m=11/14; ncol2=24; w=-1; offset=-1; strand=R; shift=10; score=0.440807; ----------srGCGCCCTCTGCT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 106 212 38 53 46 26 24 43 25 14 15 76 15 30 c 0 0 0 0 0 0 0 0 0 0 264 176 91 546 36 579 642 680 122 718 42 37 649 85 g 0 0 0 0 0 0 0 0 0 0 254 274 564 78 659 117 46 28 60 30 32 643 104 31 t 0 0 0 0 0 0 0 0 0 0 155 117 86 102 38 57 67 28 572 17 690 23 11 633
positions_7nt_m1_rc_shift5 (positions_7nt_m1_rc)				; oligos_6nt_mkv4_m1 versus positions_7nt_m1_rc; m=12/14; ncol2=24; w=-6; offset=-6; strand=R; shift=5; score=0.42638; -----gsctcTGCTGCCmCCTgsT ; cor=; Ncor= a 0 0 0 0 0 257 247 179 231 225 63 244 44 42 49 63 8 1103 12 30 109 282 77 117 c 0 0 0 0 0 443 584 1163 169 1163 156 102 1359 316 25 1657 1760 575 1355 1724 74 146 975 135 g 0 0 0 0 0 721 521 178 270 224 153 1361 319 40 1672 42 5 58 38 15 50 1196 697 60 t 0 0 0 0 0 381 450 282 1132 190 1430 95 80 1404 56 40 29 66 397 33 1569 178 53 1490
positions_7nt_m4_shift5 (positions_7nt_m4)				; oligos_6nt_mkv4_m1 versus positions_7nt_m4; m=13/14; ncol2=24; w=-6; offset=-6; strand=D; shift=5; score=0.411561; -----gsctcTGCTGCCCyCTrGT ; cor=; Ncor= a 0 0 0 0 0 249 341 169 250 281 97 324 60 70 52 89 15 478 31 9 62 1013 44 101 c 0 0 0 0 0 435 612 1237 235 1223 160 133 1389 294 20 1741 1869 1397 580 1889 106 142 356 138 g 0 0 0 0 0 844 508 186 310 219 194 1355 394 29 1789 47 11 18 26 13 42 573 1468 59 t 0 0 0 0 0 401 468 337 1134 206 1478 117 86 1536 68 52 34 36 1292 18 1719 201 61 1631
positions_7nt_m5_rc_shift6 (positions_7nt_m5_rc)				; oligos_6nt_mkv4_m1 versus positions_7nt_m5_rc; m=14/14; ncol2=24; w=-5; offset=-5; strand=R; shift=6; score=0.402675; ------scycTGCTGCCmCCTrGT ; cor=; Ncor= a 0 0 0 0 0 0 279 268 283 313 64 291 39 34 45 90 12 1136 10 26 100 893 44 102 c 0 0 0 0 0 0 558 733 558 1003 141 107 1284 243 20 1500 1649 436 1261 1614 111 112 210 110 g 0 0 0 0 0 0 507 268 314 179 168 1205 274 55 1586 53 6 52 24 11 48 498 1395 64 t 0 0 0 0 0 0 341 416 530 190 1312 82 88 1353 34 42 18 61 390 34 1426 182 36 1409

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --krCCACTAGAkg ; Alignment reference a 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 653 c 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 598 g 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 3266 t 0 0 1293 979 203 64 199 96 3794 103 76 84 1560 433
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --krCCACTAGAkg ; cor=; Ncor= a 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 653 c 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 598 g 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 3266 t 0 0 1293 979 203 64 199 96 3794 103 76 84 1560 433
oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)				; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m5; m=2/6; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.792288; -ygACCACTAGrk- ; cor=; Ncor= a 0 673 923 2866 122 53 3562 62 246 3678 78 1570 480 0 c 0 1041 999 240 3692 3889 139 3760 488 48 81 479 599 0 g 0 744 1239 585 124 39 173 122 118 195 3793 1562 1517 0 t 0 1557 854 324 77 34 141 71 3163 94 63 404 1419 0
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; oligos_6nt_mkv4_m2 versus positions_7nt_m4_rc; m=3/6; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.474813; -yggCCACyAGrGG ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15
oligos_7nt_mkv5_m1_shift5 (oligos_7nt_mkv5_m1)				; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m1; m=4/6; ncol2=14; w=0; offset=3; strand=D; shift=5; score=0.474054; -----caCyAGAGG ; cor=; Ncor= a 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 c 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 g 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 t 0 0 0 0 0 386 654 203 2492 107 47 155 637 112
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; oligos_6nt_mkv4_m2 versus positions_6nt_m1_rc; m=5/6; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.457888; gyGGCCACyAGRGG ; cor=; Ncor= a 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 c 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 g 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 t 260 482 126 94 58 7 53 17 596 29 8 15 246 10
positions_7nt_m5_shift0 (positions_7nt_m5)				; oligos_6nt_mkv4_m2 versus positions_7nt_m5; m=6/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.435969; ryggCCACyAGGkG ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=24; shift=6; ncol=30; ------msbaGgkGsCAGCAGAGGGCGCys ; Alignment reference a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 155 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 254 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 264 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212 106
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/13; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------msbaGgkGsCAGCAGAGGGCGCys ; cor=; Ncor= a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 57 38 102 86 117 155 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 117 659 78 564 274 254 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 579 36 546 91 176 264 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24 26 46 53 38 212 106
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_6nt_m4 versus positions_7nt_m1; m=2/13; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.558979; -yggCCAscAGGkGGCAGCAgagsc----- ; cor=; Ncor= a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 381 0 0 0 0 0 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 721 0 0 0 0 0 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 443 0 0 0 0 0 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247 257 0 0 0 0 0
positions_6nt_m1_rc_shift10 (positions_6nt_m1_rc)				; positions_6nt_m4 versus positions_6nt_m1_rc; m=3/13; ncol2=24; w=0; offset=4; strand=R; shift=10; score=0.557373; ----------gyGGCCACyAGRGGGCGCtg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 c 0 0 0 0 0 0 0 0 0 0 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 g 0 0 0 0 0 0 0 0 0 0 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 t 0 0 0 0 0 0 0 0 0 0 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75
positions_6nt_m3_shift12 (positions_6nt_m3)				; positions_6nt_m4 versus positions_6nt_m3; m=4/13; ncol2=24; w=0; offset=6; strand=D; shift=12; score=0.537819; ------------sgCCAGCAGAGGGCGCCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 107 137 36 17 556 20 57 578 13 496 9 19 6 64 94 21 23 109 c 0 0 0 0 0 0 0 0 0 0 0 0 174 89 581 596 16 159 545 51 36 21 14 14 17 569 14 582 476 470 g 0 0 0 0 0 0 0 0 0 0 0 0 267 337 27 29 71 482 38 22 612 149 578 634 636 6 547 57 65 72 t 0 0 0 0 0 0 0 0 0 0 0 0 126 111 30 32 31 13 34 23 13 8 73 7 15 35 19 14 110 23
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; positions_6nt_m4 versus positions_7nt_m4_rc; m=5/13; ncol2=24; w=-5; offset=-5; strand=R; shift=1; score=0.526055; -yggCCACyAGrGGGCAGCAgagsc----- ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 401 0 0 0 0 0 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 844 0 0 0 0 0 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 435 0 0 0 0 0 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341 249 0 0 0 0 0
positions_7nt_m2_shift13 (positions_7nt_m2)				; positions_6nt_m4 versus positions_7nt_m2; m=6/13; ncol2=24; w=0; offset=7; strand=D; shift=13; score=0.507662; -------------gcCAGCAGAGGGCGCCa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 108 83 14 425 12 29 461 11 402 11 33 18 35 68 19 27 314 c 0 0 0 0 0 0 0 0 0 0 0 0 0 96 304 469 29 95 444 46 27 32 24 14 31 459 16 462 424 101 g 0 0 0 0 0 0 0 0 0 0 0 0 0 272 95 52 69 428 31 21 502 104 462 490 480 25 448 57 33 93 t 0 0 0 0 0 0 0 0 0 0 0 0 0 68 62 9 21 9 40 16 4 6 47 7 15 25 12 6 60 36
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_6nt_m4 versus positions_7nt_m5; m=7/13; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.501293; ryggCCACyAGGkGGCAGCAgrgs------ ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 416 341 0 0 0 0 0 0 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 268 507 0 0 0 0 0 0 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 733 558 0 0 0 0 0 0 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283 268 279 0 0 0 0 0 0
oligos_7nt_mkv5_m1_shift15 (oligos_7nt_mkv5_m1)				; positions_6nt_m4 versus oligos_7nt_mkv5_m1; m=8/13; ncol2=14; w=0; offset=9; strand=D; shift=15; score=0.496932; ---------------caCyAGAGGGCGsy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0
oligos_7nt_mkv5_m2_rc_shift15 (oligos_7nt_mkv5_m2_rc)				; positions_6nt_m4 versus oligos_7nt_mkv5_m2_rc; m=9/13; ncol2=14; w=0; offset=9; strand=R; shift=15; score=0.487623; ---------------srGcAGGGGGCGss- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 849 2563 396 544 5613 159 796 354 293 196 283 412 781 986 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4285 1642 1833 5136 1042 309 537 822 591 383 7298 169 3648 2541 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2106 2656 5362 1545 798 7297 6383 6021 6850 7132 57 7177 2689 2462 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 639 1018 288 654 426 114 163 682 145 168 241 121 761 1890 0
positions_7nt_m3_rc_shift13 (positions_7nt_m3_rc)				; positions_6nt_m4 versus positions_7nt_m3_rc; m=10/13; ncol2=24; w=0; offset=7; strand=R; shift=13; score=0.446625; -------------gcCaCCAGGGGGCGCCc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 141 93 14 518 10 45 590 18 128 25 41 15 20 56 13 27 99 c 0 0 0 0 0 0 0 0 0 0 0 0 0 134 494 682 52 575 590 90 43 49 65 38 34 726 14 690 536 509 g 0 0 0 0 0 0 0 0 0 0 0 0 0 394 119 62 151 169 75 49 696 586 593 686 708 9 692 53 98 133 t 0 0 0 0 0 0 0 0 0 0 0 0 0 104 67 15 52 19 63 44 16 10 90 8 16 18 11 17 112 32
oligos_6nt_mkv4_m1_rc_shift16 (oligos_6nt_mkv4_m1_rc)				; positions_6nt_m4 versus oligos_6nt_mkv4_m1_rc; m=11/13; ncol2=13; w=0; offset=10; strand=R; shift=16; score=0.440807; ----------------rscAGGGGGCGsb- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0
oligos_6nt_mkv4_m4_shift17 (oligos_6nt_mkv4_m4)				; positions_6nt_m4 versus oligos_6nt_mkv4_m4; m=12/13; ncol2=12; w=0; offset=11; strand=D; shift=17; score=0.405609; -----------------scAGAGGGCAsy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1348 1452 7468 205 7093 281 264 266 345 6614 1312 1576 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2983 3185 111 285 128 77 93 371 7403 278 2480 2692 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2899 1647 361 7646 733 7160 7701 7303 320 864 3466 1795 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 958 1904 248 52 234 670 130 248 120 432 930 2125 0
oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)				; positions_6nt_m4 versus oligos_7nt_mkv5_m4; m=13/13; ncol2=11; w=0; offset=5; strand=D; shift=11; score=0.401116; -----------gbGGCAGCAsc-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=11; ncol=22; -----------gbGGCAGCAsc ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338
oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=11; score= 1; -----------gbGGCAGCAsc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338
positions_7nt_m5_shift0 (positions_7nt_m5)				; oligos_7nt_mkv5_m4 versus positions_7nt_m5; m=2/5; ncol2=24; w=-11; offset=-11; strand=D; shift=0; score=0.421428; ryggCCACyAGGkGGCAGCAgr ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283
positions_7nt_m1_shift1 (positions_7nt_m1)				; oligos_7nt_mkv5_m4 versus positions_7nt_m1; m=3/5; ncol2=24; w=-10; offset=-10; strand=D; shift=1; score=0.41522; -yggCCAscAGGkGGCAGCAga ; cor=; Ncor= a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; oligos_7nt_mkv5_m4 versus positions_7nt_m4_rc; m=4/5; ncol2=24; w=-10; offset=-10; strand=R; shift=1; score=0.403846; -yggCCACyAGrGGGCAGCAga ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250
positions_6nt_m4_shift6 (positions_6nt_m4)				; oligos_7nt_mkv5_m4 versus positions_6nt_m4; m=5/5; ncol2=24; w=-5; offset=-5; strand=D; shift=6; score=0.401116; ------msbaGgkGsCAGCAGA ; cor=; Ncor= a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_7nt_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; ryggCCACyAGGkGGCAGCAgrgs ; Alignment reference a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 416 341 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 268 507 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 733 558 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283 268 279
positions_7nt_m5_shift0 (positions_7nt_m5)				; positions_7nt_m5 versus positions_7nt_m5; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ryggCCACyAGGkGGCAGCAgrgs ; cor=; Ncor= a 445 217 296 344 82 6 1409 36 182 1426 34 390 61 18 42 34 1353 88 82 1312 190 530 416 341 c 359 477 281 165 1481 1665 64 1395 498 48 11 24 52 6 53 1586 55 274 1205 168 179 314 268 507 g 501 243 753 978 55 8 110 210 112 111 1614 1261 436 1649 1500 20 243 1284 107 141 1003 558 733 558 t 380 748 355 198 67 6 102 44 893 100 26 10 1136 12 90 45 34 39 291 64 313 283 268 279
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_7nt_m5 versus positions_7nt_m1; m=2/11; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.868363; -yggCCAscAGGkGGCAGCAgags ; cor=; Ncor= a 0 222 327 380 112 21 1490 53 178 1569 33 397 66 29 40 56 1404 80 95 1430 190 1132 282 450 c 0 576 359 166 1540 1747 60 697 1196 50 15 38 58 5 42 1672 40 319 1361 153 224 270 178 521 g 0 306 699 1023 81 21 135 975 146 74 1724 1355 575 1760 1657 25 316 1359 102 156 1163 169 1163 584 t 0 698 417 233 69 13 117 77 282 109 30 12 1103 8 63 49 42 44 244 63 225 231 179 247
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; positions_7nt_m5 versus positions_7nt_m4_rc; m=3/11; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.862568; -yggCCACyAGrGGGCAGCAgags ; cor=; Ncor= a 0 219 398 438 110 6 1631 61 201 1719 18 1292 36 34 52 68 1536 86 117 1478 206 1134 337 468 c 0 570 317 191 1620 1909 59 1468 573 42 13 26 18 11 47 1789 29 394 1355 194 219 310 186 508 g 0 302 782 1072 84 10 138 356 142 106 1889 580 1397 1869 1741 20 294 1389 133 160 1223 235 1237 612 t 0 838 432 228 115 4 101 44 1013 62 9 31 478 15 89 52 70 60 324 97 281 250 169 341
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; positions_7nt_m5 versus positions_6nt_m1_rc; m=4/11; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.717491; gyGGCCACyAGRGGGCGCtgccgs ; cor=; Ncor= a 267 135 109 112 72 9 960 20 98 1030 9 806 23 12 21 60 189 53 68 104 81 255 218 182 c 284 359 108 74 998 1147 37 940 399 43 16 21 33 19 45 1037 23 1000 224 258 625 454 194 411 g 368 203 836 899 51 16 129 202 86 77 1146 337 877 1138 1074 19 895 105 92 742 183 270 596 393 t 260 482 126 94 58 7 53 17 596 29 8 15 246 10 39 63 72 21 795 75 290 200 171 193
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_7nt_m5 versus positions_6nt_m4; m=5/11; ncol2=24; w=0; offset=6; strand=D; shift=6; score=0.501293; ------msbaGgkGsCAGCAGAGG ; cor=; Ncor= a 0 0 0 0 0 0 265 122 100 525 46 81 84 44 51 9 633 11 23 690 17 572 28 67 c 0 0 0 0 0 0 213 331 227 114 55 154 94 25 226 734 31 104 643 32 30 60 28 46 g 0 0 0 0 0 0 189 244 196 80 618 453 229 690 453 27 85 649 37 42 718 122 680 642 t 0 0 0 0 0 0 112 82 256 60 60 91 372 20 49 9 30 15 76 15 14 25 43 24
oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)				; positions_7nt_m5 versus oligos_7nt_mkv5_m5; m=6/11; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.447532; -ygACCACTAGrk----------- ; cor=; Ncor= a 0 673 923 2866 122 53 3562 62 246 3678 78 1570 480 0 0 0 0 0 0 0 0 0 0 0 c 0 1041 999 240 3692 3889 139 3760 488 48 81 479 599 0 0 0 0 0 0 0 0 0 0 0 g 0 744 1239 585 124 39 173 122 118 195 3793 1562 1517 0 0 0 0 0 0 0 0 0 0 0 t 0 1557 854 324 77 34 141 71 3163 94 63 404 1419 0 0 0 0 0 0 0 0 0 0 0
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)				; positions_7nt_m5 versus oligos_6nt_mkv4_m2; m=7/11; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.435969; --krCCACTAGAkg---------- ; cor=; Ncor= a 0 0 1073 1268 196 66 4366 80 388 4589 87 4094 564 653 0 0 0 0 0 0 0 0 0 0 c 0 0 1003 902 4349 4781 182 4527 647 41 105 123 617 598 0 0 0 0 0 0 0 0 0 0 g 0 0 1581 1801 202 39 203 247 121 217 4682 649 2209 3266 0 0 0 0 0 0 0 0 0 0 t 0 0 1293 979 203 64 199 96 3794 103 76 84 1560 433 0 0 0 0 0 0 0 0 0 0
oligos_7nt_mkv5_m1_shift5 (oligos_7nt_mkv5_m1)				; positions_7nt_m5 versus oligos_7nt_mkv5_m1; m=8/11; ncol2=14; w=0; offset=5; strand=D; shift=5; score=0.43053; -----caCyAGAGGGCGsy----- ; cor=; Ncor= a 0 0 0 0 0 561 2570 277 569 4672 54 4152 76 132 146 338 761 709 696 0 0 0 0 0 c 0 0 0 0 0 3571 901 3917 1598 277 110 257 154 235 224 4671 121 2684 1854 0 0 0 0 0 g 0 0 0 0 0 829 1222 950 688 291 5136 783 4480 4868 4858 106 4235 1366 1236 0 0 0 0 0 t 0 0 0 0 0 386 654 203 2492 107 47 155 637 112 119 232 230 588 1561 0 0 0 0 0
oligos_7nt_mkv5_m4_shift11 (oligos_7nt_mkv5_m4)				; positions_7nt_m5 versus oligos_7nt_mkv5_m4; m=9/11; ncol2=11; w=0; offset=11; strand=D; shift=11; score=0.421428; -----------gbGGCAGCAsc-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1567 1176 109 206 104 5934 144 117 6001 921 1645 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1690 2001 337 204 6417 356 252 6156 232 1947 2302 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2798 1915 6400 6332 180 418 6393 191 570 2749 1634 0 0 t 0 0 0 0 0 0 0 0 0 0 0 864 1827 73 177 218 211 130 455 116 1302 1338 0 0
oligos_7nt_mkv5_m3_rc_shift7 (oligos_7nt_mkv5_m3_rc)				; positions_7nt_m5 versus oligos_7nt_mkv5_m3_rc; m=10/11; ncol2=12; w=0; offset=7; strand=R; shift=7; score=0.407699; -------ssAGGTGGCGsy----- ; cor=; Ncor= a 0 0 0 0 0 0 0 847 1148 6438 56 446 323 47 75 430 1016 1004 972 0 0 0 0 0 c 0 0 0 0 0 0 0 2951 2842 365 120 127 482 113 97 5895 314 3116 2510 0 0 0 0 0 g 0 0 0 0 0 0 0 2875 1916 272 7035 6653 1055 7070 7005 484 5673 2356 1618 0 0 0 0 0 t 0 0 0 0 0 0 0 594 1361 192 56 41 5407 37 90 458 264 791 2167 0 0 0 0 0
oligos_6nt_mkv4_m1_rc_shift6 (oligos_6nt_mkv4_m1_rc)				; positions_7nt_m5 versus oligos_6nt_mkv4_m1_rc; m=11/11; ncol2=13; w=0; offset=6; strand=R; shift=6; score=0.402675; ------rscAGGGGGCGsb----- ; cor=; Ncor= a 0 0 0 0 0 0 3083 952 1007 6789 134 866 332 189 152 163 1022 857 1017 0 0 0 0 0 c 0 0 0 0 0 0 1437 3019 3150 551 158 242 434 337 235 7584 414 3620 2649 0 0 0 0 0 g 0 0 0 0 0 0 2282 3301 1956 268 7518 6654 6365 7268 7372 22 6132 2627 2151 0 0 0 0 0 t 0 0 0 0 0 0 1097 627 1786 291 89 137 768 105 140 130 331 795 2082 0 0 0 0 0