One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/20/peak-motifs.2026-01-20.210349_2026-01-20.210349_A3dhoj/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/2026/01/20/peak-motifs.2026-01-20.210349_2026-01-20.210349_A3dhoj/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; aaAAAwAAAAAArAAAAAwAwaww ; Alignment reference a 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 c 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 g 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 t 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; aaAAAwAAAAAArAAAAAwAwaww ; cor=; Ncor= a 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 c 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 g 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 t 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m3 versus positions_6nt_m2; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.836857; awwAAAAAArAArAAAAATtrAww ; cor=; Ncor= a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m3 versus positions_6nt_m5; m=3/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.762517; wwcAAgAAAAATTgAAAAtAtAaw ; cor=; Ncor= a 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 418 93 400 103 355 217 193 c 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 22 28 30 54 58 79 85 g 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 31 58 33 55 33 99 90 t 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31 46 338 54 305 71 122 149

positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m3 versus positions_6nt_m1; m=4/4; ncol2=24; w=0; offset=3; strand=D; shift=3; score=0.690936; ---aawAAAAAArAAAAAtwrAAA ; cor=; Ncor= a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121

One-to-n matrix alignment; reference matrix: dyads_m2_shift3 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift3 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=16; shift=3; ncol=19; ---rwTGAAGAAGAAAAwr ; Alignment reference a 0 0 0 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 c 0 0 0 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 g 0 0 0 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 t 0 0 0 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939

dyads_m2_shift3 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---rwTGAAGAAGAAAAwr ; cor=; Ncor= a 0 0 0 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 c 0 0 0 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 g 0 0 0 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 t 0 0 0 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939

dyads_m1_shift3 (dyads_m1)
; dyads_m2 versus dyads_m1; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.79331; ---rwTGAAGAAGAgrw-- ; cor=; Ncor= a 0 0 0 2508 3180 1191 615 7656 7194 253 7954 7268 382 7609 2093 2552 3563 0 0 c 0 0 0 1335 1865 503 344 383 323 236 286 350 304 393 824 1390 1682 0 0 g 0 0 0 3037 1317 597 7506 317 456 8046 248 532 7730 358 4437 2882 1305 0 0 t 0 0 0 1935 2453 6524 350 459 842 280 327 665 399 455 1461 1991 2265 0 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; dyads_m2 versus positions_7nt_m1; m=3/8; ncol2=11; w=0; offset=5; strand=D; shift=8; score=0.610159; --------arAAGAAAAwr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 c 0 0 0 0 0 0 0 0 1325 966 0 142 0 16 12 22 38 1130 961 g 0 0 0 0 0 0 0 0 1191 1626 4 27 6134 15 25 33 20 1161 1570 t 0 0 0 0 0 0 0 0 1422 1510 103 20 0 190 317 481 83 1877 1467

oligos_7nt_mkv5_m4_rc_shift4 (oligos_7nt_mkv5_m4_rc)
; dyads_m2 versus oligos_7nt_mkv5_m4_rc; m=4/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.558147; ----wwGAAGAcGaw---- ; cor=; Ncor= a 0 0 0 0 6416 5378 638 15672 14662 975 15134 3061 961 6653 5088 0 0 0 0 c 0 0 0 0 3123 2925 455 263 539 337 421 10212 628 2804 3319 0 0 0 0 g 0 0 0 0 2492 2832 15095 212 363 14556 409 1230 14034 3061 2513 0 0 0 0 t 0 0 0 0 4379 5275 222 263 846 542 446 1907 787 3892 5490 0 0 0 0

oligos_7nt_mkv5_m5_rc_shift4 (oligos_7nt_mkv5_m5_rc)
; dyads_m2 versus oligos_7nt_mkv5_m5_rc; m=5/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.541564; ----wwGAAGATGaw---- ; cor=; Ncor= a 0 0 0 0 8243 7079 507 19633 18202 314 17960 3061 1388 8590 6945 0 0 0 0 c 0 0 0 0 4251 3597 195 804 877 202 1127 905 350 3828 4195 0 0 0 0 g 0 0 0 0 3291 3683 20466 613 764 20057 1090 1230 19285 4034 3067 0 0 0 0 t 0 0 0 0 5909 7335 526 644 1851 1121 1517 16498 671 5242 7487 0 0 0 0

oligos_7nt_mkv5_m3_rc_shift4 (oligos_7nt_mkv5_m3_rc)
; dyads_m2 versus oligos_7nt_mkv5_m3_rc; m=6/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.516166; ----wmGAAAAAGww---- ; cor=; Ncor= a 0 0 0 0 2941 3259 0 8015 7297 7168 7311 7755 0 3048 3057 0 0 0 0 c 0 0 0 0 1609 2286 0 126 255 275 321 608 0 1660 1566 0 0 0 0 g 0 0 0 0 1418 1337 8803 79 265 822 299 161 8832 1390 1440 0 0 0 0 t 0 0 0 0 2880 1966 45 628 1031 583 917 324 16 2750 2785 0 0 0 0

positions_6nt_m2_shift0 (positions_6nt_m2)
; dyads_m2 versus positions_6nt_m2; m=7/8; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.481831; awwAAAAAArAArAAAAAT ; cor=; Ncor= a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657

positions_6nt_m1_shift3 (positions_6nt_m1)
; dyads_m2 versus positions_6nt_m1; m=8/8; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.479229; ---aawAAAAAArAAAAAt ; cor=; Ncor= a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift1 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=1; ncol=11; -wtACCTTCww ; Alignment reference a 0 1620 1193 5087 0 0 152 472 30 1516 1564 c 0 1023 1264 0 5087 5057 36 60 5057 829 867 g 0 1085 594 0 0 30 461 48 0 1010 941 t 0 1359 2036 0 0 0 4438 4507 0 1732 1715

oligos_6nt_mkv4_m2_shift1 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wtACCTTCww ; cor=; Ncor= a 0 1620 1193 5087 0 0 152 472 30 1516 1564 c 0 1023 1264 0 5087 5057 36 60 5057 829 867 g 0 1085 594 0 0 30 461 48 0 1010 941 t 0 1359 2036 0 0 0 4438 4507 0 1732 1715

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m5; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.642827; wtCATCTTCww ; cor=; Ncor= a 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=22; shift=0; ncol=22; arCAgCAgCAGCAGCAgCAgca ; Alignment reference a 2015 1195 372 2975 825 360 3010 804 329 3184 701 291 3234 661 279 3060 711 299 2872 830 644 1936 c 467 522 2931 184 318 3134 194 305 3169 119 315 3282 129 268 3244 156 330 3137 222 348 2106 497 g 605 1545 227 345 2488 183 366 2579 132 329 2714 79 304 2811 116 325 2605 158 403 2412 417 638 t 866 691 423 449 322 276 383 265 323 321 223 301 286 213 314 412 307 359 456 363 786 882

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; arCAgCAgCAGCAGCAgCAgca ; cor=; Ncor= a 2015 1195 372 2975 825 360 3010 804 329 3184 701 291 3234 661 279 3060 711 299 2872 830 644 1936 c 467 522 2931 184 318 3134 194 305 3169 119 315 3282 129 268 3244 156 330 3137 222 348 2106 497 g 605 1545 227 345 2488 183 366 2579 132 329 2714 79 304 2811 116 325 2605 158 403 2412 417 638 t 866 691 423 449 322 276 383 265 323 321 223 301 286 213 314 412 307 359 456 363 786 882

dyads_m5_shift0 (dyads_m5)
; dyads_m4 versus dyads_m5; m=2/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.977653; arCAgCAgCAGCAsCAgCAgca ; cor=; Ncor= a 1560 927 265 2307 663 218 2509 557 210 2464 508 142 2467 625 155 2364 529 228 2312 655 553 1474 c 349 478 2295 92 306 2397 82 312 2485 78 268 2531 76 1159 2574 70 276 2404 107 311 1582 335 g 417 1064 126 266 1743 155 183 1891 97 238 2021 67 180 958 48 254 1943 89 219 1744 267 480 t 626 483 266 287 240 182 178 192 160 172 155 212 229 210 175 264 204 231 314 242 550 663

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

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; awwAAAAAArAArAAAAATtrAww ; Alignment reference a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; awwAAAAAArAArAAAAATtrAww ; cor=; Ncor= a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m2 versus positions_6nt_m3; m=2/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.836857; aaAAAwAAAAAArAAAAAwAwaww ; cor=; Ncor= a 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 c 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 g 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 t 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=3/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.702738; aawAAAAAArAAAAAtwrAAAAaw ; cor=; Ncor= a 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 934 609 545 c 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 65 116 163 g 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 87 196 205 t 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121 139 304 312

dyads_m2_shift3 (dyads_m2)
; positions_6nt_m2 versus dyads_m2; m=4/5; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.481831; ---rwTGAAGAAGAAAAwr----- ; cor=; Ncor= a 0 0 0 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 0 0 0 0 0 c 0 0 0 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 0 0 0 0 0 g 0 0 0 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 0 0 0 0 0 t 0 0 0 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939 0 0 0 0 0

positions_6nt_m5_shift7 (positions_6nt_m5)
; positions_6nt_m2 versus positions_6nt_m5; m=5/5; ncol2=24; w=0; offset=7; strand=D; shift=7; score=0.463518; -------wwcAAgAAAAATTgAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 c 0 0 0 0 0 0 0 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 g 0 0 0 0 0 0 0 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 t 0 0 0 0 0 0 0 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; twyttcAATTTTTCAAAAATTgtw ; Alignment reference a 104 130 92 75 61 84 356 371 54 55 40 44 16 50 348 384 343 341 355 29 45 76 110 120 c 97 78 197 43 50 223 25 14 14 19 23 9 17 341 31 32 28 31 18 32 32 84 67 61 g 92 95 41 38 42 57 26 31 10 31 25 36 14 24 25 4 33 36 25 25 29 219 99 90 t 152 142 115 289 292 81 38 29 367 340 357 356 398 30 41 25 41 37 47 359 339 66 169 174

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/1; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; twyttcAATTTTTCAAAAATTgtw ; cor=; Ncor= a 104 130 92 75 61 84 356 371 54 55 40 44 16 50 348 384 343 341 355 29 45 76 110 120 c 97 78 197 43 50 223 25 14 14 19 23 9 17 341 31 32 28 31 18 32 32 84 67 61 g 92 95 41 38 42 57 26 31 10 31 25 36 14 24 25 4 33 36 25 25 29 219 99 90 t 152 142 115 289 292 81 38 29 367 340 357 356 398 30 41 25 41 37 47 359 339 66 169 174

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift3 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---wwAAAAAATww ; Alignment reference a 0 0 0 1639 1626 4221 4141 4150 4118 4136 4221 0 1499 1413 c 0 0 0 632 719 0 0 0 0 0 0 0 717 924 g 0 0 0 804 792 0 0 0 0 0 0 0 767 771 t 0 0 0 1146 1084 0 80 71 103 85 0 4221 1238 1113

positions_7nt_m2_shift3 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---wwAAAAAATww ; cor=; Ncor= a 0 0 0 1639 1626 4221 4141 4150 4118 4136 4221 0 1499 1413 c 0 0 0 632 719 0 0 0 0 0 0 0 717 924 g 0 0 0 804 792 0 0 0 0 0 0 0 767 771 t 0 0 0 1146 1084 0 80 71 103 85 0 4221 1238 1113

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=2/2; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.401125; arAAGAAAAwr--- ; cor=; Ncor= a 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 0 0 0 c 1325 966 0 142 0 16 12 22 38 1130 961 0 0 0 g 1191 1626 4 27 6134 15 25 33 20 1161 1570 0 0 0 t 1422 1510 103 20 0 190 317 481 83 1877 1467 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCATTTTCkw ; Alignment reference a 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 1696 1556 19 608 288 202 288 197 3 2426 1602 t 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCATTTTCkw ; cor=; Ncor= a 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 1696 1556 19 608 288 202 288 197 3 2426 1602 t 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m5; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.815937; wtCATCTTCww ; cor=; Ncor= a 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.807876; wwCTTTTTCkw ; cor=; Ncor= a 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 1566 1660 0 608 321 275 255 126 0 2286 1609 t 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m5; m=4/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.786472; wwCCTTTTCww ; cor=; Ncor= a 3669 3687 628 274 921 408 593 644 387 3107 3323 c 2141 1709 10184 10818 368 1230 685 302 11222 2431 1929 g 2361 2356 366 578 532 452 565 446 29 2140 2441 t 3566 3985 559 67 9916 9647 9894 10345 99 4059 4044

oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4; m=5/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.71162; wtCgTCTTCww ; cor=; Ncor= a 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416

positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)
; oligos_7nt_mkv5_m2 versus positions_7nt_m1_rc; m=6/6; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.50812; --ywTTTTCTT ; cor=; Ncor= a 0 0 1467 1877 83 481 317 190 0 20 103 c 0 0 1570 1161 20 33 25 15 6134 27 4 g 0 0 961 1130 38 22 12 16 0 142 0 t 0 0 2136 1966 5993 5598 5780 5913 0 5945 6027

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift4 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwCTTTTTCkw ; Alignment reference a 0 0 0 0 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 0 0 0 0 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 0 0 0 0 1566 1660 0 608 321 275 255 126 0 2286 1609 t 0 0 0 0 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wwCTTTTTCkw ; cor=; Ncor= a 0 0 0 0 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 0 0 0 0 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 0 0 0 0 1566 1660 0 608 321 275 255 126 0 2286 1609 t 0 0 0 0 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.807876; ----wwCATTTTCkw ; cor=; Ncor= a 0 0 0 0 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 0 0 0 0 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 0 0 0 0 1696 1556 19 608 288 202 288 197 3 2426 1602 t 0 0 0 0 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109

oligos_6nt_mkv4_m5_shift4 (oligos_6nt_mkv4_m5)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m5; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.790763; ----wwCCTTTTCww ; cor=; Ncor= a 0 0 0 0 3669 3687 628 274 921 408 593 644 387 3107 3323 c 0 0 0 0 2141 1709 10184 10818 368 1230 685 302 11222 2431 1929 g 0 0 0 0 2361 2356 366 578 532 452 565 446 29 2140 2441 t 0 0 0 0 3566 3985 559 67 9916 9647 9894 10345 99 4059 4044

oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.730628; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 0 0 0 0 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 0 0 0 0 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 0 0 0 0 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m3 versus dyads_m1_rc; m=5/7; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.577915; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2265 1991 1461 455 399 665 327 280 842 459 350 6524 2453 c 0 0 1305 2882 4437 358 7730 532 248 8046 456 317 7506 597 1317 g 0 0 1682 1390 824 393 304 350 286 236 323 383 344 503 1865 t 0 0 3563 2552 2093 7609 382 7268 7954 253 7194 7656 615 1191 3180

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m3 versus dyads_m2_rc; m=6/7; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.516166; ywTTTTCTTCTTCAw ; cor=; Ncor= a 939 1178 542 249 355 144 125 298 148 139 303 241 117 3139 1217 c 1373 779 366 683 177 163 3759 230 71 3716 166 170 3768 241 668 g 652 759 409 247 210 180 118 191 122 124 212 119 171 314 875 t 1410 1658 3057 3195 3632 3887 372 3655 4033 395 3693 3844 318 680 1614

positions_7nt_m1_rc_shift6 (positions_7nt_m1_rc)
; oligos_7nt_mkv5_m3 versus positions_7nt_m1_rc; m=7/7; ncol2=11; w=0; offset=2; strand=R; shift=6; score=0.511579; ------ywTTTTCTT ; cor=; Ncor= a 0 0 0 0 0 0 1467 1877 83 481 317 190 0 20 103 c 0 0 0 0 0 0 1570 1161 20 33 25 15 6134 27 4 g 0 0 0 0 0 0 961 1130 38 22 12 16 0 142 0 t 0 0 0 0 0 0 2136 1966 5993 5598 5780 5913 0 5945 6027

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -wtACCACCrw ; Alignment reference a 0 2258 1421 7086 66 20 6561 54 41 2678 2268 c 0 1641 1810 112 7388 6800 84 7393 7144 917 1738 g 0 1721 873 249 86 258 651 65 272 2189 1381 t 0 2037 3553 210 117 579 361 145 200 1873 2270

oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wtACCACCrw ; cor=; Ncor= a 0 2258 1421 7086 66 20 6561 54 41 2678 2268 c 0 1641 1810 112 7388 6800 84 7393 7144 917 1738 g 0 1721 873 249 86 258 651 65 272 2189 1381 t 0 2037 3553 210 117 579 361 145 200 1873 2270

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv4_m1 versus dyads_m3; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.832528; wyCACCACCaw ; cor=; Ncor= a 6200 3626 964 14042 1130 494 14275 1153 621 6604 4388 c 1988 3901 12334 222 12112 13973 152 11870 13558 2093 3267 g 2906 3047 546 394 864 281 288 984 381 2740 3247 t 4055 4575 1305 491 1043 401 434 1142 589 3712 4247

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCATCTTCww ; Alignment reference a 0 0 0 0 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 0 0 0 0 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 0 0 0 0 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 0 0 0 0 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 0 0 0 0 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 0 0 0 0 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 0 0 0 0 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243

oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m4; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.895607; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 0 0 0 0 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 0 0 0 0 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 0 0 0 0 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m2; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.815937; ----wwCATTTTCkw ; cor=; Ncor= a 0 0 0 0 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 0 0 0 0 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 0 0 0 0 1696 1556 19 608 288 202 288 197 3 2426 1602 t 0 0 0 0 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109

oligos_6nt_mkv4_m2_shift5 (oligos_6nt_mkv4_m2)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m2; m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.642827; -----wtACCTTCww ; cor=; Ncor= a 0 0 0 0 0 1620 1193 5087 0 0 152 472 30 1516 1564 c 0 0 0 0 0 1023 1264 0 5087 5057 36 60 5057 829 867 g 0 0 0 0 0 1085 594 0 0 30 461 48 0 1010 941 t 0 0 0 0 0 1359 2036 0 0 0 4438 4507 0 1732 1715

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m5 versus dyads_m1_rc; m=5/6; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.630353; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2265 1991 1461 455 399 665 327 280 842 459 350 6524 2453 c 0 0 1305 2882 4437 358 7730 532 248 8046 456 317 7506 597 1317 g 0 0 1682 1390 824 393 304 350 286 236 323 383 344 503 1865 t 0 0 3563 2552 2093 7609 382 7268 7954 253 7194 7656 615 1191 3180

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m5 versus dyads_m2_rc; m=6/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.541564; ywTTTTCTTCTTCAw ; cor=; Ncor= a 939 1178 542 249 355 144 125 298 148 139 303 241 117 3139 1217 c 1373 779 366 683 177 163 3759 230 71 3716 166 170 3768 241 668 g 652 759 409 247 210 180 118 191 122 124 212 119 171 314 875 t 1410 1658 3057 3195 3632 3887 372 3655 4033 395 3693 3844 318 680 1614

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wyCACCACCaw ; Alignment reference a 6200 3626 964 14042 1130 494 14275 1153 621 6604 4388 c 1988 3901 12334 222 12112 13973 152 11870 13558 2093 3267 g 2906 3047 546 394 864 281 288 984 381 2740 3247 t 4055 4575 1305 491 1043 401 434 1142 589 3712 4247

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wyCACCACCaw ; cor=; Ncor= a 6200 3626 964 14042 1130 494 14275 1153 621 6604 4388 c 1988 3901 12334 222 12112 13973 152 11870 13558 2093 3267 g 2906 3047 546 394 864 281 288 984 381 2740 3247 t 4055 4575 1305 491 1043 401 434 1142 589 3712 4247

oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; dyads_m3 versus oligos_6nt_mkv4_m1; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.832528; -wtACCACCrw ; cor=; Ncor= a 0 2258 1421 7086 66 20 6561 54 41 2678 2268 c 0 1641 1810 112 7388 6800 84 7393 7144 917 1738 g 0 1721 873 249 86 258 651 65 272 2189 1381 t 0 2037 3553 210 117 579 361 145 200 1873 2270

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; wwCTTACCaw ; Alignment reference a 1126 1203 31 300 82 3909 0 0 1501 1143 c 634 801 3859 196 20 0 3892 3828 580 742 g 878 656 19 583 0 0 2 64 909 800 t 1271 1249 0 2830 3807 0 15 17 919 1224

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wwCTTACCaw ; cor=; Ncor= a 1126 1203 31 300 82 3909 0 0 1501 1143 c 634 801 3859 196 20 0 3892 3828 580 742 g 878 656 19 583 0 0 2 64 909 800 t 1271 1249 0 2830 3807 0 15 17 919 1224

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift7 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift7 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=24; shift=7; ncol=31; -------wwcAAgAAAAATTgAAAAtAtAaw ; Alignment reference a 0 0 0 0 0 0 0 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 418 93 400 103 355 217 193 c 0 0 0 0 0 0 0 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 22 28 30 54 58 79 85 g 0 0 0 0 0 0 0 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 31 58 33 55 33 99 90 t 0 0 0 0 0 0 0 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31 46 338 54 305 71 122 149

positions_6nt_m5_shift7 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=7; score= 1; -------wwcAAgAAAAATTgAAAAtAtAaw ; cor=; Ncor= a 0 0 0 0 0 0 0 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 418 93 400 103 355 217 193 c 0 0 0 0 0 0 0 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 22 28 30 54 58 79 85 g 0 0 0 0 0 0 0 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 31 58 33 55 33 99 90 t 0 0 0 0 0 0 0 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31 46 338 54 305 71 122 149

positions_6nt_m3_shift7 (positions_6nt_m3)
; positions_6nt_m5 versus positions_6nt_m3; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=7; score=0.762517; -------aaAAAwAAAAAArAAAAAwAwaww ; cor=; Ncor= a 0 0 0 0 0 0 0 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 c 0 0 0 0 0 0 0 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 g 0 0 0 0 0 0 0 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 t 0 0 0 0 0 0 0 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477

positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m5 versus positions_6nt_m1; m=3/4; ncol2=24; w=-4; offset=-4; strand=D; shift=3; score=0.614597; ---aawAAAAAArAAAAAtwrAAAAaw---- ; cor=; Ncor= a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 934 609 545 0 0 0 0 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 65 116 163 0 0 0 0 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 87 196 205 0 0 0 0 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121 139 304 312 0 0 0 0

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m5 versus positions_6nt_m2; m=4/4; ncol2=24; w=-7; offset=-7; strand=D; shift=0; score=0.463518; awwAAAAAArAArAAAAATtrAww------- ; cor=; Ncor= a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 0 0 0 0 0 0 0 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 0 0 0 0 0 0 0 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 0 0 0 0 0 0 0 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCAAAAACdw ; Alignment reference a 2594 2593 0 6319 6247 5636 6003 7074 0 1946 2256 c 1117 1447 7395 127 166 470 215 94 7428 1212 1323 g 1499 1359 0 386 347 356 275 87 0 2133 1657 t 2218 2029 33 596 668 966 935 173 0 2137 2192

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCAAAAACdw ; cor=; Ncor= a 2594 2593 0 6319 6247 5636 6003 7074 0 1946 2256 c 1117 1447 7395 127 166 470 215 94 7428 1212 1323 g 1499 1359 0 386 347 356 275 87 0 2133 1657 t 2218 2029 33 596 668 966 935 173 0 2137 2192

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; wwTACATAww ; Alignment reference a 774 1144 0 2961 0 2758 0 2961 845 1174 c 604 425 0 0 2961 3 0 0 641 451 g 497 633 0 0 0 200 0 0 420 491 t 1086 759 2961 0 0 0 2961 0 1055 845

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; wwTACATAww ; cor=; Ncor= a 774 1144 0 2961 0 2758 0 2961 845 1174 c 604 425 0 0 2961 3 0 0 641 451 g 497 633 0 0 0 200 0 0 420 491 t 1086 759 2961 0 0 0 2961 0 1055 845

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; rwTGAAGAAGAgrw ; Alignment reference a 2508 3180 1191 615 7656 7194 253 7954 7268 382 7609 2093 2552 3563 c 1335 1865 503 344 383 323 236 286 350 304 393 824 1390 1682 g 3037 1317 597 7506 317 456 8046 248 532 7730 358 4437 2882 1305 t 1935 2453 6524 350 459 842 280 327 665 399 455 1461 1991 2265

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rwTGAAGAAGAgrw ; cor=; Ncor= a 2508 3180 1191 615 7656 7194 253 7954 7268 382 7609 2093 2552 3563 c 1335 1865 503 344 383 323 236 286 350 304 393 824 1390 1682 g 3037 1317 597 7506 317 456 8046 248 532 7730 358 4437 2882 1305 t 1935 2453 6524 350 459 842 280 327 665 399 455 1461 1991 2265

dyads_m2_shift0 (dyads_m2)
; dyads_m1 versus dyads_m2; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.79331; rwTGAAGAAGAAAA ; cor=; Ncor= a 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 c 597 875 314 171 119 212 124 122 191 118 180 210 247 409 g 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 t 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542

oligos_7nt_mkv5_m4_rc_shift1 (oligos_7nt_mkv5_m4_rc)
; dyads_m1 versus oligos_7nt_mkv5_m4_rc; m=3/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.648505; -wwGAAGAcGaw-- ; cor=; Ncor= a 0 6416 5378 638 15672 14662 975 15134 3061 961 6653 5088 0 0 c 0 3123 2925 455 263 539 337 421 10212 628 2804 3319 0 0 g 0 2492 2832 15095 212 363 14556 409 1230 14034 3061 2513 0 0 t 0 4379 5275 222 263 846 542 446 1907 787 3892 5490 0 0

oligos_7nt_mkv5_m5_rc_shift1 (oligos_7nt_mkv5_m5_rc)
; dyads_m1 versus oligos_7nt_mkv5_m5_rc; m=4/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.630353; -wwGAAGATGaw-- ; cor=; Ncor= a 0 8243 7079 507 19633 18202 314 17960 3061 1388 8590 6945 0 0 c 0 4251 3597 195 804 877 202 1127 905 350 3828 4195 0 0 g 0 3291 3683 20466 613 764 20057 1090 1230 19285 4034 3067 0 0 t 0 5909 7335 526 644 1851 1121 1517 16498 671 5242 7487 0 0

oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)
; dyads_m1 versus oligos_7nt_mkv5_m3_rc; m=5/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.577915; -wmGAAAAAGww-- ; cor=; Ncor= a 0 2941 3259 0 8015 7297 7168 7311 7755 0 3048 3057 0 0 c 0 1609 2286 0 126 255 275 321 608 0 1660 1566 0 0 g 0 1418 1337 8803 79 265 822 299 161 8832 1390 1440 0 0 t 0 2880 1966 45 628 1031 583 917 324 16 2750 2785 0 0

positions_7nt_m1_shift2 (positions_7nt_m1)
; dyads_m1 versus positions_7nt_m1; m=6/6; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.568404; --arAAGAAAAwr- ; cor=; Ncor= a 0 0 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 0 c 0 0 1325 966 0 142 0 16 12 22 38 1130 961 0 g 0 0 1191 1626 4 27 6134 15 25 33 20 1161 1570 0 t 0 0 1422 1510 103 20 0 190 317 481 83 1877 1467 0

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=22; shift=0; ncol=22; arCAgCAgCAGCAsCAgCAgca ; Alignment reference a 1560 927 265 2307 663 218 2509 557 210 2464 508 142 2467 625 155 2364 529 228 2312 655 553 1474 c 349 478 2295 92 306 2397 82 312 2485 78 268 2531 76 1159 2574 70 276 2404 107 311 1582 335 g 417 1064 126 266 1743 155 183 1891 97 238 2021 67 180 958 48 254 1943 89 219 1744 267 480 t 626 483 266 287 240 182 178 192 160 172 155 212 229 210 175 264 204 231 314 242 550 663

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; arCAgCAgCAGCAsCAgCAgca ; cor=; Ncor= a 1560 927 265 2307 663 218 2509 557 210 2464 508 142 2467 625 155 2364 529 228 2312 655 553 1474 c 349 478 2295 92 306 2397 82 312 2485 78 268 2531 76 1159 2574 70 276 2404 107 311 1582 335 g 417 1064 126 266 1743 155 183 1891 97 238 2021 67 180 958 48 254 1943 89 219 1744 267 480 t 626 483 266 287 240 182 178 192 160 172 155 212 229 210 175 264 204 231 314 242 550 663

dyads_m4_shift0 (dyads_m4)
; dyads_m5 versus dyads_m4; m=2/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.977653; arCAgCAgCAGCAGCAgCAgca ; cor=; Ncor= a 2015 1195 372 2975 825 360 3010 804 329 3184 701 291 3234 661 279 3060 711 299 2872 830 644 1936 c 467 522 2931 184 318 3134 194 305 3169 119 315 3282 129 268 3244 156 330 3137 222 348 2106 497 g 605 1545 227 345 2488 183 366 2579 132 329 2714 79 304 2811 116 325 2605 158 403 2412 417 638 t 866 691 423 449 322 276 383 265 323 321 223 301 286 213 314 412 307 359 456 363 786 882

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---aawAAAAAArAAAAAtwrAAAAaw ; Alignment reference a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 934 609 545 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 65 116 163 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 87 196 205 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121 139 304 312

positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---aawAAAAAArAAAAAtwrAAAAaw ; cor=; Ncor= a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 934 609 545 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 65 116 163 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 87 196 205 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121 139 304 312

positions_6nt_m2_shift3 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=2/5; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.702738; ---awwAAAAAArAArAAAAATtrAww ; cor=; Ncor= a 0 0 0 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 c 0 0 0 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 g 0 0 0 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 t 0 0 0 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m1 versus positions_6nt_m3; m=3/5; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.690936; aaAAAwAAAAAArAAAAAwAwaww--- ; cor=; Ncor= a 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 0 0 0 c 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 0 0 0 g 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 0 0 0 t 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477 0 0 0

positions_6nt_m5_shift7 (positions_6nt_m5)
; positions_6nt_m1 versus positions_6nt_m5; m=4/5; ncol2=24; w=0; offset=4; strand=D; shift=7; score=0.614597; -------wwcAAgAAAAATTgAAAAtA ; cor=; Ncor= a 0 0 0 0 0 0 0 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 418 93 400 c 0 0 0 0 0 0 0 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 22 28 30 g 0 0 0 0 0 0 0 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 31 58 33 t 0 0 0 0 0 0 0 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31 46 338 54

dyads_m2_shift3 (dyads_m2)
; positions_6nt_m1 versus dyads_m2; m=5/5; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.479229; ---rwTGAAGAAGAAAAwr-------- ; cor=; Ncor= a 0 0 0 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 0 0 0 0 0 0 0 0 c 0 0 0 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 0 0 0 0 0 0 0 0 g 0 0 0 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 0 0 0 0 0 0 0 0 t 0 0 0 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 5 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=11; shift=0; ncol=11; wwCCTTTTCww ; Alignment reference a 3669 3687 628 274 921 408 593 644 387 3107 3323 c 2141 1709 10184 10818 368 1230 685 302 11222 2431 1929 g 2361 2356 366 578 532 452 565 446 29 2140 2441 t 3566 3985 559 67 9916 9647 9894 10345 99 4059 4044

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCCTTTTCww ; cor=; Ncor= a 3669 3687 628 274 921 408 593 644 387 3107 3323 c 2141 1709 10184 10818 368 1230 685 302 11222 2431 1929 g 2361 2356 366 578 532 452 565 446 29 2140 2441 t 3566 3985 559 67 9916 9647 9894 10345 99 4059 4044

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m3; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.790763; wwCTTTTTCkw ; cor=; Ncor= a 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 1566 1660 0 608 321 275 255 126 0 2286 1609 t 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m2; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.786472; wwCATTTTCkw ; cor=; Ncor= a 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 1696 1556 19 608 288 202 288 197 3 2426 1602 t 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109

positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)
; oligos_6nt_mkv4_m5 versus positions_7nt_m1_rc; m=4/4; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.502181; --ywTTTTCTT ; cor=; Ncor= a 0 0 1467 1877 83 481 317 190 0 20 103 c 0 0 1570 1161 20 33 25 15 6134 27 4 g 0 0 961 1130 38 22 12 16 0 142 0 t 0 0 2136 1966 5993 5598 5780 5913 0 5945 6027

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCgTCTTCww ; Alignment reference a 0 0 0 0 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 0 0 0 0 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 0 0 0 0 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 0 0 0 0 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416

oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 0 0 0 0 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 0 0 0 0 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 0 0 0 0 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m5; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.895607; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 0 0 0 0 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 0 0 0 0 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 0 0 0 0 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.730628; ----wwCTTTTTCkw ; cor=; Ncor= a 0 0 0 0 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 0 0 0 0 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 0 0 0 0 1566 1660 0 608 321 275 255 126 0 2286 1609 t 0 0 0 0 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m2; m=4/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.71162; ----wwCATTTTCkw ; cor=; Ncor= a 0 0 0 0 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 0 0 0 0 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 0 0 0 0 1696 1556 19 608 288 202 288 197 3 2426 1602 t 0 0 0 0 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m4 versus dyads_m1_rc; m=5/6; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.648505; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2265 1991 1461 455 399 665 327 280 842 459 350 6524 2453 c 0 0 1305 2882 4437 358 7730 532 248 8046 456 317 7506 597 1317 g 0 0 1682 1390 824 393 304 350 286 236 323 383 344 503 1865 t 0 0 3563 2552 2093 7609 382 7268 7954 253 7194 7656 615 1191 3180

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m4 versus dyads_m2_rc; m=6/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.558147; ywTTTTCTTCTTCAw ; cor=; Ncor= a 939 1178 542 249 355 144 125 298 148 139 303 241 117 3139 1217 c 1373 779 366 683 177 163 3759 230 71 3716 166 170 3768 241 668 g 652 759 409 247 210 180 118 191 122 124 212 119 171 314 875 t 1410 1658 3057 3195 3632 3887 372 3655 4033 395 3693 3844 318 680 1614

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift5 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift5 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=11; shift=5; ncol=16; -----arAAGAAAAwr ; Alignment reference a 0 0 0 0 0 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 c 0 0 0 0 0 1325 966 0 142 0 16 12 22 38 1130 961 g 0 0 0 0 0 1191 1626 4 27 6134 15 25 33 20 1161 1570 t 0 0 0 0 0 1422 1510 103 20 0 190 317 481 83 1877 1467

positions_7nt_m1_shift5 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----arAAGAAAAwr ; cor=; Ncor= a 0 0 0 0 0 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 c 0 0 0 0 0 1325 966 0 142 0 16 12 22 38 1130 961 g 0 0 0 0 0 1191 1626 4 27 6134 15 25 33 20 1161 1570 t 0 0 0 0 0 1422 1510 103 20 0 190 317 481 83 1877 1467

dyads_m2_shift0 (dyads_m2)
; positions_7nt_m1 versus dyads_m2; m=2/7; ncol2=16; w=-5; offset=-5; strand=D; shift=0; score=0.610159; rwTGAAGAAGAAAAwr ; cor=; Ncor= a 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 c 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 g 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 t 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939

dyads_m1_shift3 (dyads_m1)
; positions_7nt_m1 versus dyads_m1; m=3/7; ncol2=14; w=-2; offset=-2; strand=D; shift=3; score=0.568404; ---rwTGAAGAAGAgr ; cor=; Ncor= a 0 0 0 2508 3180 1191 615 7656 7194 253 7954 7268 382 7609 2093 2552 c 0 0 0 1335 1865 503 344 383 323 236 286 350 304 393 824 1390 g 0 0 0 3037 1317 597 7506 317 456 8046 248 532 7730 358 4437 2882 t 0 0 0 1935 2453 6524 350 459 842 280 327 665 399 455 1461 1991

oligos_7nt_mkv5_m3_rc_shift7 (oligos_7nt_mkv5_m3_rc)
; positions_7nt_m1 versus oligos_7nt_mkv5_m3_rc; m=4/7; ncol2=11; w=0; offset=2; strand=R; shift=7; score=0.511579; -------wmGAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 2941 3259 0 8015 7297 7168 7311 7755 0 c 0 0 0 0 0 0 0 1609 2286 0 126 255 275 321 608 0 g 0 0 0 0 0 0 0 1418 1337 8803 79 265 822 299 161 8832 t 0 0 0 0 0 0 0 2880 1966 45 628 1031 583 917 324 16

oligos_7nt_mkv5_m2_rc_shift7 (oligos_7nt_mkv5_m2_rc)
; positions_7nt_m1 versus oligos_7nt_mkv5_m2_rc; m=5/7; ncol2=11; w=0; offset=2; strand=R; shift=7; score=0.50812; -------wmGAAAATG ; cor=; Ncor= a 0 0 0 0 0 0 0 3109 2760 0 7653 6998 6779 8000 83 228 c 0 0 0 0 0 0 0 1602 2426 3 197 288 202 288 608 19 g 0 0 0 0 0 0 0 1376 1460 8602 200 221 602 232 161 8454 t 0 0 0 0 0 0 0 2617 2058 99 654 1197 1121 184 7852 3

oligos_6nt_mkv4_m5_rc_shift7 (oligos_6nt_mkv4_m5_rc)
; positions_7nt_m1 versus oligos_6nt_mkv4_m5_rc; m=6/7; ncol2=11; w=0; offset=2; strand=R; shift=7; score=0.502181; -------wwGAAAAGG ; cor=; Ncor= a 0 0 0 0 0 0 0 4044 4059 99 10345 9894 9647 9916 67 559 c 0 0 0 0 0 0 0 2441 2140 29 446 565 452 532 578 366 g 0 0 0 0 0 0 0 1929 2431 11222 302 685 1230 368 10818 10184 t 0 0 0 0 0 0 0 3323 3107 387 644 593 408 921 274 628

positions_7nt_m2_shift8 (positions_7nt_m2)
; positions_7nt_m1 versus positions_7nt_m2; m=7/7; ncol2=11; w=0; offset=3; strand=D; shift=8; score=0.401125; --------wwAAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1639 1626 4221 4141 4150 4118 4136 4221 c 0 0 0 0 0 0 0 0 632 719 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 804 792 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 1146 1084 0 80 71 103 85 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; aaAAAwAAAAAArAAAAAwAwaww ; Alignment reference a 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 c 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 g 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 t 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; aaAAAwAAAAAArAAAAAwAwaww ; cor=; Ncor= a 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 c 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 g 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 t 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m3 versus positions_6nt_m2; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.836857; awwAAAAAArAArAAAAATtrAww ; cor=; Ncor= a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m3 versus positions_6nt_m5; m=3/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.762517; wwcAAgAAAAATTgAAAAtAtAaw ; cor=; Ncor= a 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 418 93 400 103 355 217 193 c 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 22 28 30 54 58 79 85 g 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 31 58 33 55 33 99 90 t 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31 46 338 54 305 71 122 149
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m3 versus positions_6nt_m1; m=4/4; ncol2=24; w=0; offset=3; strand=D; shift=3; score=0.690936; ---aawAAAAAArAAAAAtwrAAA ; cor=; Ncor= a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift3 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=16; shift=3; ncol=19; ---rwTGAAGAAGAAAAwr ; Alignment reference a 0 0 0 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 c 0 0 0 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 g 0 0 0 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 t 0 0 0 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939
dyads_m2_shift3 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---rwTGAAGAAGAAAAwr ; cor=; Ncor= a 0 0 0 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 c 0 0 0 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 g 0 0 0 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 t 0 0 0 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939
dyads_m1_shift3 (dyads_m1)				; dyads_m2 versus dyads_m1; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.79331; ---rwTGAAGAAGAgrw-- ; cor=; Ncor= a 0 0 0 2508 3180 1191 615 7656 7194 253 7954 7268 382 7609 2093 2552 3563 0 0 c 0 0 0 1335 1865 503 344 383 323 236 286 350 304 393 824 1390 1682 0 0 g 0 0 0 3037 1317 597 7506 317 456 8046 248 532 7730 358 4437 2882 1305 0 0 t 0 0 0 1935 2453 6524 350 459 842 280 327 665 399 455 1461 1991 2265 0 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; dyads_m2 versus positions_7nt_m1; m=3/8; ncol2=11; w=0; offset=5; strand=D; shift=8; score=0.610159; --------arAAGAAAAwr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 c 0 0 0 0 0 0 0 0 1325 966 0 142 0 16 12 22 38 1130 961 g 0 0 0 0 0 0 0 0 1191 1626 4 27 6134 15 25 33 20 1161 1570 t 0 0 0 0 0 0 0 0 1422 1510 103 20 0 190 317 481 83 1877 1467
oligos_7nt_mkv5_m4_rc_shift4 (oligos_7nt_mkv5_m4_rc)				; dyads_m2 versus oligos_7nt_mkv5_m4_rc; m=4/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.558147; ----wwGAAGAcGaw---- ; cor=; Ncor= a 0 0 0 0 6416 5378 638 15672 14662 975 15134 3061 961 6653 5088 0 0 0 0 c 0 0 0 0 3123 2925 455 263 539 337 421 10212 628 2804 3319 0 0 0 0 g 0 0 0 0 2492 2832 15095 212 363 14556 409 1230 14034 3061 2513 0 0 0 0 t 0 0 0 0 4379 5275 222 263 846 542 446 1907 787 3892 5490 0 0 0 0
oligos_7nt_mkv5_m5_rc_shift4 (oligos_7nt_mkv5_m5_rc)				; dyads_m2 versus oligos_7nt_mkv5_m5_rc; m=5/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.541564; ----wwGAAGATGaw---- ; cor=; Ncor= a 0 0 0 0 8243 7079 507 19633 18202 314 17960 3061 1388 8590 6945 0 0 0 0 c 0 0 0 0 4251 3597 195 804 877 202 1127 905 350 3828 4195 0 0 0 0 g 0 0 0 0 3291 3683 20466 613 764 20057 1090 1230 19285 4034 3067 0 0 0 0 t 0 0 0 0 5909 7335 526 644 1851 1121 1517 16498 671 5242 7487 0 0 0 0
oligos_7nt_mkv5_m3_rc_shift4 (oligos_7nt_mkv5_m3_rc)				; dyads_m2 versus oligos_7nt_mkv5_m3_rc; m=6/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.516166; ----wmGAAAAAGww---- ; cor=; Ncor= a 0 0 0 0 2941 3259 0 8015 7297 7168 7311 7755 0 3048 3057 0 0 0 0 c 0 0 0 0 1609 2286 0 126 255 275 321 608 0 1660 1566 0 0 0 0 g 0 0 0 0 1418 1337 8803 79 265 822 299 161 8832 1390 1440 0 0 0 0 t 0 0 0 0 2880 1966 45 628 1031 583 917 324 16 2750 2785 0 0 0 0
positions_6nt_m2_shift0 (positions_6nt_m2)				; dyads_m2 versus positions_6nt_m2; m=7/8; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.481831; awwAAAAAArAArAAAAAT ; cor=; Ncor= a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657
positions_6nt_m1_shift3 (positions_6nt_m1)				; dyads_m2 versus positions_6nt_m1; m=8/8; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.479229; ---aawAAAAAArAAAAAt ; cor=; Ncor= a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; awwAAAAAArAArAAAAATtrAww ; Alignment reference a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; awwAAAAAArAArAAAAATtrAww ; cor=; Ncor= a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m2 versus positions_6nt_m3; m=2/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.836857; aaAAAwAAAAAArAAAAAwAwaww ; cor=; Ncor= a 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 c 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 g 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 t 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=3/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.702738; aawAAAAAArAAAAAtwrAAAAaw ; cor=; Ncor= a 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 934 609 545 c 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 65 116 163 g 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 87 196 205 t 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121 139 304 312
dyads_m2_shift3 (dyads_m2)				; positions_6nt_m2 versus dyads_m2; m=4/5; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.481831; ---rwTGAAGAAGAAAAwr----- ; cor=; Ncor= a 0 0 0 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 0 0 0 0 0 c 0 0 0 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 0 0 0 0 0 g 0 0 0 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 0 0 0 0 0 t 0 0 0 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939 0 0 0 0 0
positions_6nt_m5_shift7 (positions_6nt_m5)				; positions_6nt_m2 versus positions_6nt_m5; m=5/5; ncol2=24; w=0; offset=7; strand=D; shift=7; score=0.463518; -------wwcAAgAAAAATTgAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 c 0 0 0 0 0 0 0 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 g 0 0 0 0 0 0 0 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 t 0 0 0 0 0 0 0 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCATTTTCkw ; Alignment reference a 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 1696 1556 19 608 288 202 288 197 3 2426 1602 t 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCATTTTCkw ; cor=; Ncor= a 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 1696 1556 19 608 288 202 288 197 3 2426 1602 t 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m5; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.815937; wtCATCTTCww ; cor=; Ncor= a 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.807876; wwCTTTTTCkw ; cor=; Ncor= a 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 1566 1660 0 608 321 275 255 126 0 2286 1609 t 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m5; m=4/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.786472; wwCCTTTTCww ; cor=; Ncor= a 3669 3687 628 274 921 408 593 644 387 3107 3323 c 2141 1709 10184 10818 368 1230 685 302 11222 2431 1929 g 2361 2356 366 578 532 452 565 446 29 2140 2441 t 3566 3985 559 67 9916 9647 9894 10345 99 4059 4044
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4; m=5/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.71162; wtCgTCTTCww ; cor=; Ncor= a 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416
positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)				; oligos_7nt_mkv5_m2 versus positions_7nt_m1_rc; m=6/6; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.50812; --ywTTTTCTT ; cor=; Ncor= a 0 0 1467 1877 83 481 317 190 0 20 103 c 0 0 1570 1161 20 33 25 15 6134 27 4 g 0 0 961 1130 38 22 12 16 0 142 0 t 0 0 2136 1966 5993 5598 5780 5913 0 5945 6027

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwCTTTTTCkw ; Alignment reference a 0 0 0 0 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 0 0 0 0 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 0 0 0 0 1566 1660 0 608 321 275 255 126 0 2286 1609 t 0 0 0 0 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wwCTTTTTCkw ; cor=; Ncor= a 0 0 0 0 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 0 0 0 0 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 0 0 0 0 1566 1660 0 608 321 275 255 126 0 2286 1609 t 0 0 0 0 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.807876; ----wwCATTTTCkw ; cor=; Ncor= a 0 0 0 0 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 0 0 0 0 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 0 0 0 0 1696 1556 19 608 288 202 288 197 3 2426 1602 t 0 0 0 0 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109
oligos_6nt_mkv4_m5_shift4 (oligos_6nt_mkv4_m5)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m5; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.790763; ----wwCCTTTTCww ; cor=; Ncor= a 0 0 0 0 3669 3687 628 274 921 408 593 644 387 3107 3323 c 0 0 0 0 2141 1709 10184 10818 368 1230 685 302 11222 2431 1929 g 0 0 0 0 2361 2356 366 578 532 452 565 446 29 2140 2441 t 0 0 0 0 3566 3985 559 67 9916 9647 9894 10345 99 4059 4044
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.730628; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 0 0 0 0 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 0 0 0 0 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 0 0 0 0 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m3 versus dyads_m1_rc; m=5/7; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.577915; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2265 1991 1461 455 399 665 327 280 842 459 350 6524 2453 c 0 0 1305 2882 4437 358 7730 532 248 8046 456 317 7506 597 1317 g 0 0 1682 1390 824 393 304 350 286 236 323 383 344 503 1865 t 0 0 3563 2552 2093 7609 382 7268 7954 253 7194 7656 615 1191 3180
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m3 versus dyads_m2_rc; m=6/7; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.516166; ywTTTTCTTCTTCAw ; cor=; Ncor= a 939 1178 542 249 355 144 125 298 148 139 303 241 117 3139 1217 c 1373 779 366 683 177 163 3759 230 71 3716 166 170 3768 241 668 g 652 759 409 247 210 180 118 191 122 124 212 119 171 314 875 t 1410 1658 3057 3195 3632 3887 372 3655 4033 395 3693 3844 318 680 1614
positions_7nt_m1_rc_shift6 (positions_7nt_m1_rc)				; oligos_7nt_mkv5_m3 versus positions_7nt_m1_rc; m=7/7; ncol2=11; w=0; offset=2; strand=R; shift=6; score=0.511579; ------ywTTTTCTT ; cor=; Ncor= a 0 0 0 0 0 0 1467 1877 83 481 317 190 0 20 103 c 0 0 0 0 0 0 1570 1161 20 33 25 15 6134 27 4 g 0 0 0 0 0 0 961 1130 38 22 12 16 0 142 0 t 0 0 0 0 0 0 2136 1966 5993 5598 5780 5913 0 5945 6027

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCATCTTCww ; Alignment reference a 0 0 0 0 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 0 0 0 0 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 0 0 0 0 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 0 0 0 0 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 0 0 0 0 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 0 0 0 0 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 0 0 0 0 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m4; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.895607; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 0 0 0 0 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 0 0 0 0 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 0 0 0 0 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m2; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.815937; ----wwCATTTTCkw ; cor=; Ncor= a 0 0 0 0 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 0 0 0 0 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 0 0 0 0 1696 1556 19 608 288 202 288 197 3 2426 1602 t 0 0 0 0 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109
oligos_6nt_mkv4_m2_shift5 (oligos_6nt_mkv4_m2)				; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m2; m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.642827; -----wtACCTTCww ; cor=; Ncor= a 0 0 0 0 0 1620 1193 5087 0 0 152 472 30 1516 1564 c 0 0 0 0 0 1023 1264 0 5087 5057 36 60 5057 829 867 g 0 0 0 0 0 1085 594 0 0 30 461 48 0 1010 941 t 0 0 0 0 0 1359 2036 0 0 0 4438 4507 0 1732 1715
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m5 versus dyads_m1_rc; m=5/6; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.630353; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2265 1991 1461 455 399 665 327 280 842 459 350 6524 2453 c 0 0 1305 2882 4437 358 7730 532 248 8046 456 317 7506 597 1317 g 0 0 1682 1390 824 393 304 350 286 236 323 383 344 503 1865 t 0 0 3563 2552 2093 7609 382 7268 7954 253 7194 7656 615 1191 3180
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m5 versus dyads_m2_rc; m=6/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.541564; ywTTTTCTTCTTCAw ; cor=; Ncor= a 939 1178 542 249 355 144 125 298 148 139 303 241 117 3139 1217 c 1373 779 366 683 177 163 3759 230 71 3716 166 170 3768 241 668 g 652 759 409 247 210 180 118 191 122 124 212 119 171 314 875 t 1410 1658 3057 3195 3632 3887 372 3655 4033 395 3693 3844 318 680 1614

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift7 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=24; shift=7; ncol=31; -------wwcAAgAAAAATTgAAAAtAtAaw ; Alignment reference a 0 0 0 0 0 0 0 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 418 93 400 103 355 217 193 c 0 0 0 0 0 0 0 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 22 28 30 54 58 79 85 g 0 0 0 0 0 0 0 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 31 58 33 55 33 99 90 t 0 0 0 0 0 0 0 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31 46 338 54 305 71 122 149
positions_6nt_m5_shift7 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=7; score= 1; -------wwcAAgAAAAATTgAAAAtAtAaw ; cor=; Ncor= a 0 0 0 0 0 0 0 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 418 93 400 103 355 217 193 c 0 0 0 0 0 0 0 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 22 28 30 54 58 79 85 g 0 0 0 0 0 0 0 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 31 58 33 55 33 99 90 t 0 0 0 0 0 0 0 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31 46 338 54 305 71 122 149
positions_6nt_m3_shift7 (positions_6nt_m3)				; positions_6nt_m5 versus positions_6nt_m3; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=7; score=0.762517; -------aaAAAwAAAAAArAAAAAwAwaww ; cor=; Ncor= a 0 0 0 0 0 0 0 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 c 0 0 0 0 0 0 0 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 g 0 0 0 0 0 0 0 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 t 0 0 0 0 0 0 0 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m5 versus positions_6nt_m1; m=3/4; ncol2=24; w=-4; offset=-4; strand=D; shift=3; score=0.614597; ---aawAAAAAArAAAAAtwrAAAAaw---- ; cor=; Ncor= a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 934 609 545 0 0 0 0 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 65 116 163 0 0 0 0 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 87 196 205 0 0 0 0 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121 139 304 312 0 0 0 0
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m5 versus positions_6nt_m2; m=4/4; ncol2=24; w=-7; offset=-7; strand=D; shift=0; score=0.463518; awwAAAAAArAArAAAAATtrAww------- ; cor=; Ncor= a 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 0 0 0 0 0 0 0 c 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 0 0 0 0 0 0 0 g 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 0 0 0 0 0 0 0 t 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift0 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; rwTGAAGAAGAgrw ; Alignment reference a 2508 3180 1191 615 7656 7194 253 7954 7268 382 7609 2093 2552 3563 c 1335 1865 503 344 383 323 236 286 350 304 393 824 1390 1682 g 3037 1317 597 7506 317 456 8046 248 532 7730 358 4437 2882 1305 t 1935 2453 6524 350 459 842 280 327 665 399 455 1461 1991 2265
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rwTGAAGAAGAgrw ; cor=; Ncor= a 2508 3180 1191 615 7656 7194 253 7954 7268 382 7609 2093 2552 3563 c 1335 1865 503 344 383 323 236 286 350 304 393 824 1390 1682 g 3037 1317 597 7506 317 456 8046 248 532 7730 358 4437 2882 1305 t 1935 2453 6524 350 459 842 280 327 665 399 455 1461 1991 2265
dyads_m2_shift0 (dyads_m2)				; dyads_m1 versus dyads_m2; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.79331; rwTGAAGAAGAAAA ; cor=; Ncor= a 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 c 597 875 314 171 119 212 124 122 191 118 180 210 247 409 g 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 t 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542
oligos_7nt_mkv5_m4_rc_shift1 (oligos_7nt_mkv5_m4_rc)				; dyads_m1 versus oligos_7nt_mkv5_m4_rc; m=3/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.648505; -wwGAAGAcGaw-- ; cor=; Ncor= a 0 6416 5378 638 15672 14662 975 15134 3061 961 6653 5088 0 0 c 0 3123 2925 455 263 539 337 421 10212 628 2804 3319 0 0 g 0 2492 2832 15095 212 363 14556 409 1230 14034 3061 2513 0 0 t 0 4379 5275 222 263 846 542 446 1907 787 3892 5490 0 0
oligos_7nt_mkv5_m5_rc_shift1 (oligos_7nt_mkv5_m5_rc)				; dyads_m1 versus oligos_7nt_mkv5_m5_rc; m=4/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.630353; -wwGAAGATGaw-- ; cor=; Ncor= a 0 8243 7079 507 19633 18202 314 17960 3061 1388 8590 6945 0 0 c 0 4251 3597 195 804 877 202 1127 905 350 3828 4195 0 0 g 0 3291 3683 20466 613 764 20057 1090 1230 19285 4034 3067 0 0 t 0 5909 7335 526 644 1851 1121 1517 16498 671 5242 7487 0 0
oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)				; dyads_m1 versus oligos_7nt_mkv5_m3_rc; m=5/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.577915; -wmGAAAAAGww-- ; cor=; Ncor= a 0 2941 3259 0 8015 7297 7168 7311 7755 0 3048 3057 0 0 c 0 1609 2286 0 126 255 275 321 608 0 1660 1566 0 0 g 0 1418 1337 8803 79 265 822 299 161 8832 1390 1440 0 0 t 0 2880 1966 45 628 1031 583 917 324 16 2750 2785 0 0
positions_7nt_m1_shift2 (positions_7nt_m1)				; dyads_m1 versus positions_7nt_m1; m=6/6; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.568404; --arAAGAAAAwr- ; cor=; Ncor= a 0 0 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 0 c 0 0 1325 966 0 142 0 16 12 22 38 1130 961 0 g 0 0 1191 1626 4 27 6134 15 25 33 20 1161 1570 0 t 0 0 1422 1510 103 20 0 190 317 481 83 1877 1467 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---aawAAAAAArAAAAAtwrAAAAaw ; Alignment reference a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 934 609 545 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 65 116 163 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 87 196 205 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121 139 304 312
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---aawAAAAAArAAAAAtwrAAAAaw ; cor=; Ncor= a 0 0 0 521 553 393 1010 1040 998 1015 1052 1022 381 1040 1073 1072 1067 989 293 311 307 942 1006 945 934 609 545 c 0 0 0 163 165 104 40 63 57 40 43 44 56 24 61 44 42 48 60 43 86 80 82 63 65 116 163 g 0 0 0 238 201 79 83 44 64 101 55 62 665 67 49 51 53 58 84 130 686 92 36 96 87 196 205 t 0 0 0 303 306 649 92 78 106 69 75 97 123 94 42 58 63 130 788 741 146 111 101 121 139 304 312
positions_6nt_m2_shift3 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=2/5; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.702738; ---awwAAAAAArAArAAAAATtrAww ; cor=; Ncor= a 0 0 0 427 350 295 721 778 773 748 775 765 241 781 810 244 813 831 742 809 788 165 166 247 636 393 379 c 0 0 0 129 136 83 46 30 43 30 37 40 39 42 35 19 38 21 42 35 31 25 50 88 88 139 134 g 0 0 0 201 193 91 98 47 30 100 59 41 577 28 32 561 37 36 75 15 67 88 115 488 78 157 168 t 0 0 0 178 256 466 70 80 89 57 64 89 78 84 58 111 47 47 76 76 49 657 604 112 133 246 254
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m1 versus positions_6nt_m3; m=3/5; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.690936; aaAAAwAAAAAArAAAAAwAwaww--- ; cor=; Ncor= a 859 920 1468 1476 1437 734 1525 1584 1645 1609 1651 1645 618 1633 1648 1693 1626 1595 544 1503 599 1201 814 864 0 0 0 c 271 215 130 105 102 121 86 83 54 53 55 39 93 35 56 31 70 87 85 105 137 156 280 242 0 0 0 g 310 306 118 117 129 186 143 102 60 87 63 97 986 117 69 95 68 95 158 121 174 225 315 318 0 0 0 t 461 460 185 203 233 860 147 132 142 152 132 120 204 116 128 82 137 124 1114 172 991 319 492 477 0 0 0
positions_6nt_m5_shift7 (positions_6nt_m5)				; positions_6nt_m1 versus positions_6nt_m5; m=4/5; ncol2=24; w=0; offset=4; strand=D; shift=7; score=0.614597; -------wwcAAgAAAAATTgAAAAtA ; cor=; Ncor= a 0 0 0 0 0 0 0 157 165 120 416 444 96 433 442 439 454 435 63 85 79 394 403 408 418 93 400 c 0 0 0 0 0 0 0 112 91 301 47 25 37 26 6 26 14 12 52 21 89 50 36 31 22 28 30 g 0 0 0 0 0 0 0 87 113 50 20 18 319 23 36 21 11 31 20 42 301 24 35 47 31 58 33 t 0 0 0 0 0 0 0 161 148 46 34 30 65 35 33 31 38 39 382 369 48 49 43 31 46 338 54
dyads_m2_shift3 (dyads_m2)				; positions_6nt_m1 versus dyads_m2; m=5/5; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.479229; ---rwTGAAGAAGAAAAwr-------- ; cor=; Ncor= a 0 0 0 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 0 0 0 0 0 0 0 0 c 0 0 0 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 0 0 0 0 0 0 0 0 g 0 0 0 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 0 0 0 0 0 0 0 0 t 0 0 0 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939 0 0 0 0 0 0 0 0

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=11; shift=0; ncol=11; wwCCTTTTCww ; Alignment reference a 3669 3687 628 274 921 408 593 644 387 3107 3323 c 2141 1709 10184 10818 368 1230 685 302 11222 2431 1929 g 2361 2356 366 578 532 452 565 446 29 2140 2441 t 3566 3985 559 67 9916 9647 9894 10345 99 4059 4044
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCCTTTTCww ; cor=; Ncor= a 3669 3687 628 274 921 408 593 644 387 3107 3323 c 2141 1709 10184 10818 368 1230 685 302 11222 2431 1929 g 2361 2356 366 578 532 452 565 446 29 2140 2441 t 3566 3985 559 67 9916 9647 9894 10345 99 4059 4044
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m3; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.790763; wwCTTTTTCkw ; cor=; Ncor= a 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 1566 1660 0 608 321 275 255 126 0 2286 1609 t 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m2; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.786472; wwCATTTTCkw ; cor=; Ncor= a 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 1696 1556 19 608 288 202 288 197 3 2426 1602 t 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109
positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)				; oligos_6nt_mkv4_m5 versus positions_7nt_m1_rc; m=4/4; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.502181; --ywTTTTCTT ; cor=; Ncor= a 0 0 1467 1877 83 481 317 190 0 20 103 c 0 0 1570 1161 20 33 25 15 6134 27 4 g 0 0 961 1130 38 22 12 16 0 142 0 t 0 0 2136 1966 5993 5598 5780 5913 0 5945 6027

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCgTCTTCww ; Alignment reference a 0 0 0 0 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 0 0 0 0 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 0 0 0 0 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 0 0 0 0 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 5490 3892 787 1907 446 542 846 263 222 5275 4379 c 0 0 0 0 2513 3061 14034 1230 409 14556 363 212 15095 2832 2492 g 0 0 0 0 3319 2804 628 10212 421 337 539 263 455 2925 3123 t 0 0 0 0 5088 6653 961 3061 15134 975 14662 15672 638 5378 6416
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m5; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.895607; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 7487 5242 671 16498 1517 1121 1851 644 526 7335 5909 c 0 0 0 0 3067 4034 19285 1230 1090 20057 764 613 20466 3683 3291 g 0 0 0 0 4195 3828 350 905 1127 202 877 804 195 3597 4251 t 0 0 0 0 6945 8590 1388 3061 17960 314 18202 19633 507 7079 8243
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.730628; ----wwCTTTTTCkw ; cor=; Ncor= a 0 0 0 0 2785 2750 16 324 917 583 1031 628 45 1966 2880 c 0 0 0 0 1440 1390 8832 161 299 822 265 79 8803 1337 1418 g 0 0 0 0 1566 1660 0 608 321 275 255 126 0 2286 1609 t 0 0 0 0 3057 3048 0 7755 7311 7168 7297 8015 0 3259 2941
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m2; m=4/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.71162; ----wwCATTTTCkw ; cor=; Ncor= a 0 0 0 0 2917 2578 3 7852 184 1121 1197 654 99 2058 2617 c 0 0 0 0 1258 1829 8454 161 232 602 221 200 8602 1460 1376 g 0 0 0 0 1696 1556 19 608 288 202 288 197 3 2426 1602 t 0 0 0 0 2833 2741 228 83 8000 6779 6998 7653 0 2760 3109
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m4 versus dyads_m1_rc; m=5/6; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.648505; --wycTCTTCTTCAw ; cor=; Ncor= a 0 0 2265 1991 1461 455 399 665 327 280 842 459 350 6524 2453 c 0 0 1305 2882 4437 358 7730 532 248 8046 456 317 7506 597 1317 g 0 0 1682 1390 824 393 304 350 286 236 323 383 344 503 1865 t 0 0 3563 2552 2093 7609 382 7268 7954 253 7194 7656 615 1191 3180
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m4 versus dyads_m2_rc; m=6/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.558147; ywTTTTCTTCTTCAw ; cor=; Ncor= a 939 1178 542 249 355 144 125 298 148 139 303 241 117 3139 1217 c 1373 779 366 683 177 163 3759 230 71 3716 166 170 3768 241 668 g 652 759 409 247 210 180 118 191 122 124 212 119 171 314 875 t 1410 1658 3057 3195 3632 3887 372 3655 4033 395 3693 3844 318 680 1614

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift5 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=11; shift=5; ncol=16; -----arAAGAAAAwr ; Alignment reference a 0 0 0 0 0 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 c 0 0 0 0 0 1325 966 0 142 0 16 12 22 38 1130 961 g 0 0 0 0 0 1191 1626 4 27 6134 15 25 33 20 1161 1570 t 0 0 0 0 0 1422 1510 103 20 0 190 317 481 83 1877 1467
positions_7nt_m1_shift5 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----arAAGAAAAwr ; cor=; Ncor= a 0 0 0 0 0 2196 2032 6027 5945 0 5913 5780 5598 5993 1966 2136 c 0 0 0 0 0 1325 966 0 142 0 16 12 22 38 1130 961 g 0 0 0 0 0 1191 1626 4 27 6134 15 25 33 20 1161 1570 t 0 0 0 0 0 1422 1510 103 20 0 190 317 481 83 1877 1467
dyads_m2_shift0 (dyads_m2)				; positions_7nt_m1 versus dyads_m2; m=2/7; ncol2=16; w=-5; offset=-5; strand=D; shift=0; score=0.610159; rwTGAAGAAGAAAAwr ; cor=; Ncor= a 1349 1614 680 318 3844 3693 395 4033 3655 372 3887 3632 3195 3057 1658 1410 c 597 875 314 171 119 212 124 122 191 118 180 210 247 409 759 652 g 1437 668 241 3768 170 166 3716 71 230 3759 163 177 683 366 779 1373 t 991 1217 3139 117 241 303 139 148 298 125 144 355 249 542 1178 939
dyads_m1_shift3 (dyads_m1)				; positions_7nt_m1 versus dyads_m1; m=3/7; ncol2=14; w=-2; offset=-2; strand=D; shift=3; score=0.568404; ---rwTGAAGAAGAgr ; cor=; Ncor= a 0 0 0 2508 3180 1191 615 7656 7194 253 7954 7268 382 7609 2093 2552 c 0 0 0 1335 1865 503 344 383 323 236 286 350 304 393 824 1390 g 0 0 0 3037 1317 597 7506 317 456 8046 248 532 7730 358 4437 2882 t 0 0 0 1935 2453 6524 350 459 842 280 327 665 399 455 1461 1991
oligos_7nt_mkv5_m3_rc_shift7 (oligos_7nt_mkv5_m3_rc)				; positions_7nt_m1 versus oligos_7nt_mkv5_m3_rc; m=4/7; ncol2=11; w=0; offset=2; strand=R; shift=7; score=0.511579; -------wmGAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 2941 3259 0 8015 7297 7168 7311 7755 0 c 0 0 0 0 0 0 0 1609 2286 0 126 255 275 321 608 0 g 0 0 0 0 0 0 0 1418 1337 8803 79 265 822 299 161 8832 t 0 0 0 0 0 0 0 2880 1966 45 628 1031 583 917 324 16
oligos_7nt_mkv5_m2_rc_shift7 (oligos_7nt_mkv5_m2_rc)				; positions_7nt_m1 versus oligos_7nt_mkv5_m2_rc; m=5/7; ncol2=11; w=0; offset=2; strand=R; shift=7; score=0.50812; -------wmGAAAATG ; cor=; Ncor= a 0 0 0 0 0 0 0 3109 2760 0 7653 6998 6779 8000 83 228 c 0 0 0 0 0 0 0 1602 2426 3 197 288 202 288 608 19 g 0 0 0 0 0 0 0 1376 1460 8602 200 221 602 232 161 8454 t 0 0 0 0 0 0 0 2617 2058 99 654 1197 1121 184 7852 3
oligos_6nt_mkv4_m5_rc_shift7 (oligos_6nt_mkv4_m5_rc)				; positions_7nt_m1 versus oligos_6nt_mkv4_m5_rc; m=6/7; ncol2=11; w=0; offset=2; strand=R; shift=7; score=0.502181; -------wwGAAAAGG ; cor=; Ncor= a 0 0 0 0 0 0 0 4044 4059 99 10345 9894 9647 9916 67 559 c 0 0 0 0 0 0 0 2441 2140 29 446 565 452 532 578 366 g 0 0 0 0 0 0 0 1929 2431 11222 302 685 1230 368 10818 10184 t 0 0 0 0 0 0 0 3323 3107 387 644 593 408 921 274 628
positions_7nt_m2_shift8 (positions_7nt_m2)				; positions_7nt_m1 versus positions_7nt_m2; m=7/7; ncol2=11; w=0; offset=3; strand=D; shift=8; score=0.401125; --------wwAAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1639 1626 4221 4141 4150 4118 4136 4221 c 0 0 0 0 0 0 0 0 632 719 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 804 792 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 1146 1084 0 80 71 103 85 0