One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/20/peak-motifs.2026-01-20.203458_2026-01-20.203458_7G23ig/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.2026-01-20.203458_2026-01-20.203458_7G23ig/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift3 ; 7 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; ---awAAAwAAAAArAAAAAtAwAaaw ; Alignment reference a 0 0 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 949 c 0 0 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 311 g 0 0 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 373 t 0 0 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545 693

positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---awAAAwAAAAArAAAAAtAwAaaw ; cor=; Ncor= a 0 0 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 949 c 0 0 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 311 g 0 0 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 373 t 0 0 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545 693

positions_6nt_m3_shift3 (positions_6nt_m3)
; positions_6nt_m1 versus positions_6nt_m3; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.847487; ---waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 0 0 0 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 0 0 0 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 0 0 0 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 0 0 0 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m1 versus positions_6nt_m5; m=3/6; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.821827; --waatAAAAArAAgAAAAAtAtawa- ; cor=; Ncor= a 0 0 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 0 c 0 0 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 0 g 0 0 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 0 t 0 0 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338 0

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m1 versus positions_6nt_m4; m=4/6; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.743864; --wwAAAgAAAAtTgAAAAAtAtaww- ; cor=; Ncor= a 0 0 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 0 c 0 0 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 0 g 0 0 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 0 t 0 0 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239 0

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=5/6; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.707016; wawrAAAAwAAAAArAAAAAttww--- ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 0 0 0 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 0 0 0 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 0 0 0 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353 0 0 0

positions_7nt_m1_shift12 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=6/6; ncol2=13; w=0; offset=9; strand=D; shift=12; score= 0.4535; ------------waAAAAAATATww-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift4 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCgTCTTCww ; Alignment reference a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.90113; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017

oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.782597; ----wtCTTCgTCww ; cor=; Ncor= a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m5; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.763399; ----wtCTTCATCww ; cor=; Ncor= a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604

positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)
; oligos_7nt_mkv5_m2 versus positions_7nt_m3_rc; m=5/7; ncol2=11; w=0; offset=1; strand=R; shift=5; score=0.664251; -----whTTCTTCTw ; cor=; Ncor= a 0 0 0 0 0 2882 2748 788 817 306 425 816 275 297 3724 c 0 0 0 0 0 1860 3369 455 294 10639 324 237 10656 234 1544 g 0 0 0 0 0 2095 1905 547 268 19 541 293 33 873 1683 t 0 0 0 0 0 4127 2942 9174 9585 0 9674 9618 0 9560 4013

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m2 versus dyads_m1_rc; m=6/7; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.654786; --tycTCTTCTTCAw ; cor=; Ncor= a 0 0 1917 1805 1296 405 337 531 248 256 652 374 351 5500 2182 c 0 0 1211 2643 3860 345 6870 392 151 7118 356 275 6529 574 1188 g 0 0 1477 1165 715 359 225 294 257 209 297 326 355 510 1482 t 0 0 3181 2173 1915 6677 354 6569 7130 203 6481 6811 551 1202 2934

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m2 versus dyads_m2_rc; m=7/7; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.561658; ywTTTTCTTCTTCAw ; cor=; Ncor= a 879 1028 460 266 324 107 127 250 146 115 257 204 134 2728 1086 c 1222 746 318 655 177 150 3373 169 88 3365 115 162 3340 212 600 g 525 680 350 231 202 156 93 179 115 152 176 96 157 288 692 t 1303 1475 2801 2777 3226 3516 336 3331 3580 297 3381 3467 298 701 1551

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=24; shift=2; ncol=26; --wwAAAgAAAAtTgAAAAAtAtaww ; Alignment reference a 0 0 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 c 0 0 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 g 0 0 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 t 0 0 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --wwAAAgAAAAtTgAAAAAtAtaww ; cor=; Ncor= a 0 0 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 c 0 0 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 g 0 0 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 t 0 0 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239

positions_6nt_m3_shift2 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.843609; --waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 0 0 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 0 0 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 0 0 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 0 0 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m4 versus positions_6nt_m5; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.775674; --waatAAAAArAAgAAAAAtAtawa ; cor=; Ncor= a 0 0 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 0 0 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 0 0 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 0 0 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338

positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m4 versus positions_6nt_m1; m=4/6; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.743864; ---awAAAwAAAAArAAAAAtAwAaa ; cor=; Ncor= a 0 0 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 c 0 0 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 g 0 0 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 t 0 0 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m4 versus positions_6nt_m2; m=5/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.636447; wawrAAAAwAAAAArAAAAAttww-- ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 0 0 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 0 0 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 0 0 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353 0 0

positions_7nt_m1_shift12 (positions_7nt_m1)
; positions_6nt_m4 versus positions_7nt_m1; m=6/6; ncol2=13; w=0; offset=10; strand=D; shift=12; score=0.445873; ------------waAAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 c 0 0 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 g 0 0 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift4 ; 9 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; ----wtCTTCATCww ; Alignment reference a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCTTCATCww ; cor=; Ncor= a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604

oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m4; m=2/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.904573; ----wtCTTCgTCww ; cor=; Ncor= a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m2; m=3/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.763399; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m3; m=4/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.755783; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m5 versus dyads_m1_rc; m=5/8; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.646801; --tycTCTTCTTCAw ; cor=; Ncor= a 0 0 1917 1805 1296 405 337 531 248 256 652 374 351 5500 2182 c 0 0 1211 2643 3860 345 6870 392 151 7118 356 275 6529 574 1188 g 0 0 1477 1165 715 359 225 294 257 209 297 326 355 510 1482 t 0 0 3181 2173 1915 6677 354 6569 7130 203 6481 6811 551 1202 2934

positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)
; oligos_7nt_mkv5_m5 versus positions_7nt_m3_rc; m=6/8; ncol2=11; w=0; offset=1; strand=R; shift=5; score=0.619928; -----whTTCTTCTw ; cor=; Ncor= a 0 0 0 0 0 2882 2748 788 817 306 425 816 275 297 3724 c 0 0 0 0 0 1860 3369 455 294 10639 324 237 10656 234 1544 g 0 0 0 0 0 2095 1905 547 268 19 541 293 33 873 1683 t 0 0 0 0 0 4127 2942 9174 9585 0 9674 9618 0 9560 4013

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m5 versus dyads_m2_rc; m=7/8; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.550569; ywTTTTCTTCTTCAw ; cor=; Ncor= a 879 1028 460 266 324 107 127 250 146 115 257 204 134 2728 1086 c 1222 746 318 655 177 150 3373 169 88 3365 115 162 3340 212 600 g 525 680 350 231 202 156 93 179 115 152 176 96 157 288 692 t 1303 1475 2801 2777 3226 3516 336 3331 3580 297 3381 3467 298 701 1551

oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m1; m=8/8; ncol2=10; w=-2; offset=-2; strand=D; shift=2; score=0.433572; --wtACCTTCww--- ; cor=; Ncor= a 0 0 1356 1041 4217 0 0 121 349 10 1289 1317 0 0 0 c 0 0 843 996 0 4217 4196 31 51 4207 718 682 0 0 0 g 0 0 880 549 0 0 21 403 34 0 822 728 0 0 0 t 0 0 1138 1631 0 0 0 3662 3783 0 1388 1490 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; wyCAAATCww ; Alignment reference a 1251 925 0 3929 3916 3933 0 0 1193 1263 c 611 1105 3933 0 0 0 0 3933 900 667 g 831 614 0 0 0 0 0 0 615 755 t 1240 1289 0 4 17 0 3933 0 1225 1248

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; wyCAAATCww ; cor=; Ncor= a 1251 925 0 3929 3916 3933 0 0 1193 1263 c 611 1105 3933 0 0 0 0 3933 900 667 g 831 614 0 0 0 0 0 0 615 755 t 1240 1289 0 4 17 0 3933 0 1225 1248

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 1623 970 292 2418 658 291 2446 649 237 2567 563 244 2618 511 206 2517 577 254 2370 672 579 1585 c 334 462 2419 145 274 2592 144 259 2643 116 300 2662 100 256 2660 118 271 2571 163 306 1694 404 g 527 1191 174 299 2041 133 327 2098 98 297 2137 71 284 2250 83 300 2117 90 338 1908 319 554 t 728 589 327 350 239 196 295 206 234 232 212 235 210 195 263 277 247 297 341 326 620 669

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 1623 970 292 2418 658 291 2446 649 237 2567 563 244 2618 511 206 2517 577 254 2370 672 579 1585 c 334 462 2419 145 274 2592 144 259 2643 116 300 2662 100 256 2660 118 271 2571 163 306 1694 404 g 527 1191 174 299 2041 133 327 2098 98 297 2137 71 284 2250 83 300 2117 90 338 1908 319 554 t 728 589 327 350 239 196 295 206 234 232 212 235 210 195 263 277 247 297 341 326 620 669

dyads_m5_shift0 (dyads_m5)
; dyads_m4 versus dyads_m5; m=2/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.977229; arCAgCAgCAgCAsCAgCAgca ; cor=; Ncor= a 1267 688 223 1885 500 195 2033 426 158 1970 406 139 2019 476 118 2007 398 194 1896 580 427 1164 c 276 434 1844 100 239 1924 63 242 2052 75 228 2027 61 1000 2100 57 271 1959 104 231 1268 280 g 353 845 110 182 1480 126 176 1570 83 211 1603 49 168 746 38 185 1577 64 197 1410 223 448 t 509 438 228 238 186 160 133 167 112 149 168 190 157 183 149 156 159 188 208 184 487 513

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 8 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; rwTGAAGAAGAgra ; Alignment reference a 2215 2934 1202 551 6811 6481 203 7130 6569 354 6677 1915 2173 3181 c 1181 1482 510 355 326 297 209 257 294 225 359 715 1165 1477 g 2711 1188 574 6529 275 356 7118 151 392 6870 345 3860 2643 1211 t 1679 2182 5500 351 374 652 256 248 531 337 405 1296 1805 1917

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/7; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rwTGAAGAAGAgra ; cor=; Ncor= a 2215 2934 1202 551 6811 6481 203 7130 6569 354 6677 1915 2173 3181 c 1181 1482 510 355 326 297 209 257 294 225 359 715 1165 1477 g 2711 1188 574 6529 275 356 7118 151 392 6870 345 3860 2643 1211 t 1679 2182 5500 351 374 652 256 248 531 337 405 1296 1805 1917

dyads_m2_shift0 (dyads_m2)
; dyads_m1 versus dyads_m2; m=2/7; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.796852; rwTGAAGAAGAAAA ; cor=; Ncor= a 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 c 508 692 288 157 96 176 152 115 179 93 156 202 231 350 g 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 t 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460

oligos_7nt_mkv5_m4_rc_shift1 (oligos_7nt_mkv5_m4_rc)
; dyads_m1 versus oligos_7nt_mkv5_m4_rc; m=3/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.663988; -wwGAcGAAGaw-- ; cor=; Ncor= a 0 5489 4297 626 12435 2734 701 12970 12061 696 6081 4341 0 0 c 0 2303 2466 227 310 8183 712 233 478 308 2349 2608 0 0 g 0 2035 2304 12307 312 924 11896 123 282 12074 2146 2100 0 0 t 0 3699 4459 366 469 1685 217 200 705 448 2950 4477 0 0

positions_7nt_m3_shift3 (positions_7nt_m3)
; dyads_m1 versus positions_7nt_m3; m=4/7; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.654798; ---rwAGAAGAAdw ; cor=; Ncor= a 0 0 0 3117 4013 9560 0 9618 9674 0 9585 9174 2942 4127 c 0 0 0 2025 1683 873 33 293 541 19 268 547 1905 2095 g 0 0 0 3089 1544 234 10656 237 324 10639 294 455 3369 1860 t 0 0 0 2733 3724 297 275 816 425 306 817 788 2748 2882

oligos_7nt_mkv5_m2_rc_shift1 (oligos_7nt_mkv5_m2_rc)
; dyads_m1 versus oligos_7nt_mkv5_m2_rc; m=5/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.654786; -wwGAAGAcGaw-- ; cor=; Ncor= a 0 5614 4675 585 13471 12556 699 13044 2734 902 5854 4369 0 0 c 0 2518 2478 368 220 478 251 376 8653 515 2330 2858 0 0 g 0 2143 2511 12995 213 335 12751 325 1080 12049 2637 2236 0 0 t 0 3843 4454 170 214 749 417 373 1651 652 3297 4655 0 0

oligos_7nt_mkv5_m5_rc_shift1 (oligos_7nt_mkv5_m5_rc)
; dyads_m1 versus oligos_7nt_mkv5_m5_rc; m=6/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.646801; -wwGATGAAGaw-- ; cor=; Ncor= a 0 6604 5467 390 14356 2734 838 15746 14454 376 7546 5577 0 0 c 0 3301 3192 125 881 770 195 556 749 380 3159 3207 0 0 g 0 2658 2717 16021 894 924 15831 534 569 15934 2683 2531 0 0 t 0 4676 5863 703 1108 12811 375 403 1467 549 3851 5924 0 0

oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)
; dyads_m1 versus oligos_7nt_mkv5_m3_rc; m=7/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.636713; -wwGAAGATGaw-- ; cor=; Ncor= a 0 7017 6069 454 16471 15340 217 15158 2734 1062 7400 5817 0 0 c 0 3430 2974 162 617 705 190 967 811 296 3172 3556 0 0 g 0 2783 3102 17035 514 654 16847 875 1080 16280 3356 2643 0 0 t 0 4936 6021 515 564 1467 912 1166 13541 528 4238 6150 0 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; wwCTTACCaw ; Alignment reference a 1014 1018 33 288 56 3508 0 0 1270 991 c 540 791 3440 107 7 0 3503 3444 503 660 g 760 616 35 526 9 0 0 41 862 726 t 1194 1083 0 2587 3436 0 5 23 873 1131

oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wwCTTACCaw ; cor=; Ncor= a 1014 1018 33 288 56 3508 0 0 1270 991 c 540 791 3440 107 7 0 3503 3444 503 660 g 760 616 35 526 9 0 0 41 862 726 t 1194 1083 0 2587 3436 0 5 23 873 1131

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---rwAGAAGAAdw ; Alignment reference a 0 0 0 3117 4013 9560 0 9618 9674 0 9585 9174 2942 4127 c 0 0 0 2025 1683 873 33 293 541 19 268 547 1905 2095 g 0 0 0 3089 1544 234 10656 237 324 10639 294 455 3369 1860 t 0 0 0 2733 3724 297 275 816 425 306 817 788 2748 2882

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---rwAGAAGAAdw ; cor=; Ncor= a 0 0 0 3117 4013 9560 0 9618 9674 0 9585 9174 2942 4127 c 0 0 0 2025 1683 873 33 293 541 19 268 547 1905 2095 g 0 0 0 3089 1544 234 10656 237 324 10639 294 455 3369 1860 t 0 0 0 2733 3724 297 275 816 425 306 817 788 2748 2882

oligos_7nt_mkv5_m2_rc_shift4 (oligos_7nt_mkv5_m2_rc)
; positions_7nt_m3 versus oligos_7nt_mkv5_m2_rc; m=2/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.664251; ----wwGAAGAcGa ; cor=; Ncor= a 0 0 0 0 5614 4675 585 13471 12556 699 13044 2734 902 5854 c 0 0 0 0 2518 2478 368 220 478 251 376 8653 515 2330 g 0 0 0 0 2143 2511 12995 213 335 12751 325 1080 12049 2637 t 0 0 0 0 3843 4454 170 214 749 417 373 1651 652 3297

dyads_m1_shift0 (dyads_m1)
; positions_7nt_m3 versus dyads_m1; m=3/7; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.654798; rwTGAAGAAGAgra ; cor=; Ncor= a 2215 2934 1202 551 6811 6481 203 7130 6569 354 6677 1915 2173 3181 c 1181 1482 510 355 326 297 209 257 294 225 359 715 1165 1477 g 2711 1188 574 6529 275 356 7118 151 392 6870 345 3860 2643 1211 t 1679 2182 5500 351 374 652 256 248 531 337 405 1296 1805 1917

oligos_7nt_mkv5_m4_rc_shift4 (oligos_7nt_mkv5_m4_rc)
; positions_7nt_m3 versus oligos_7nt_mkv5_m4_rc; m=4/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.649407; ----wwGAcGAAGa ; cor=; Ncor= a 0 0 0 0 5489 4297 626 12435 2734 701 12970 12061 696 6081 c 0 0 0 0 2303 2466 227 310 8183 712 233 478 308 2349 g 0 0 0 0 2035 2304 12307 312 924 11896 123 282 12074 2146 t 0 0 0 0 3699 4459 366 469 1685 217 200 705 448 2950

oligos_7nt_mkv5_m3_rc_shift4 (oligos_7nt_mkv5_m3_rc)
; positions_7nt_m3 versus oligos_7nt_mkv5_m3_rc; m=5/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.637895; ----wwGAAGATGa ; cor=; Ncor= a 0 0 0 0 7017 6069 454 16471 15340 217 15158 2734 1062 7400 c 0 0 0 0 3430 2974 162 617 705 190 967 811 296 3172 g 0 0 0 0 2783 3102 17035 514 654 16847 875 1080 16280 3356 t 0 0 0 0 4936 6021 515 564 1467 912 1166 13541 528 4238

oligos_7nt_mkv5_m5_rc_shift4 (oligos_7nt_mkv5_m5_rc)
; positions_7nt_m3 versus oligos_7nt_mkv5_m5_rc; m=6/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.619928; ----wwGATGAAGa ; cor=; Ncor= a 0 0 0 0 6604 5467 390 14356 2734 838 15746 14454 376 7546 c 0 0 0 0 3301 3192 125 881 770 195 556 749 380 3159 g 0 0 0 0 2658 2717 16021 894 924 15831 534 569 15934 2683 t 0 0 0 0 4676 5863 703 1108 12811 375 403 1467 549 3851

dyads_m2_shift0 (dyads_m2)
; positions_7nt_m3 versus dyads_m2; m=7/7; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.59615; rwTGAAGAAGAAAA ; cor=; Ncor= a 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 c 508 692 288 157 96 176 152 115 179 93 156 202 231 350 g 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 t 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 7 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; waAAAwAAAAArAAAAAAtAwaww ; Alignment reference a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m3 versus positions_6nt_m1; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.847487; awAAAwAAAAArAAAAAtAwAaaw ; cor=; Ncor= a 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 949 c 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 311 g 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 373 t 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545 693

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.843609; wwAAAgAAAAtTgAAAAAtAtaww ; cor=; Ncor= a 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 c 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 g 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 t 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m3 versus positions_6nt_m5; m=4/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.82257; waatAAAAArAAgAAAAAtAtawa ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m3 versus positions_6nt_m2; m=5/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.747678; wawrAAAAwAAAAArAAAAAttww ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353

positions_7nt_m1_shift10 (positions_7nt_m1)
; positions_6nt_m3 versus positions_7nt_m1; m=6/6; ncol2=13; w=0; offset=10; strand=D; shift=10; score=0.495597; ----------waAAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift1 ; 4 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; -wtACCTTCww ; Alignment reference a 0 1356 1041 4217 0 0 121 349 10 1289 1317 c 0 843 996 0 4217 4196 31 51 4207 718 682 g 0 880 549 0 0 21 403 34 0 822 728 t 0 1138 1631 0 0 0 3662 3783 0 1388 1490

oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wtACCTTCww ; cor=; Ncor= a 0 1356 1041 4217 0 0 121 349 10 1289 1317 c 0 843 996 0 4217 4196 31 51 4207 718 682 g 0 880 549 0 0 21 403 34 0 822 728 t 0 1138 1631 0 0 0 3662 3783 0 1388 1490

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m3; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.637629; wtCATCTTCww ; cor=; Ncor= a 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 3556 3172 296 811 967 190 705 617 162 2974 3430 t 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017

oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m5; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.433572; ---wtCTTCAT ; cor=; Ncor= a 0 0 0 5924 3851 549 1467 403 375 12811 1108 c 0 0 0 2531 2683 15934 569 534 15831 924 894 g 0 0 0 3207 3159 380 749 556 195 770 881 t 0 0 0 5577 7546 376 14454 15746 838 2734 14356

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 2141 2006 0 5232 5181 4614 4999 5877 0 1660 1894 c 855 1321 6077 104 142 381 153 63 6135 978 1085 g 1344 1145 0 354 291 330 220 52 0 1855 1279 t 1795 1663 58 445 521 810 763 143 0 1642 1877

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 2141 2006 0 5232 5181 4614 4999 5877 0 1660 1894 c 855 1321 6077 104 142 381 153 63 6135 978 1085 g 1344 1145 0 354 291 330 220 52 0 1855 1279 t 1795 1663 58 445 521 810 763 143 0 1642 1877

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; waatAAAAArAAgAAAAAtAtawa ; Alignment reference a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; waatAAAAArAAgAAAAAtAtawa ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m5 versus positions_6nt_m3; m=2/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.82257; waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m5 versus positions_6nt_m1; m=3/7; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.821827; -awAAAwAAAAArAAAAAtAwAaa ; cor=; Ncor= a 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 c 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 g 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 t 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m5 versus positions_6nt_m4; m=4/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.775674; wwAAAgAAAAtTgAAAAAtAtaww ; cor=; Ncor= a 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 c 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 g 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 t 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m5 versus positions_6nt_m2; m=5/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.714927; wawrAAAAwAAAAArAAAAAttww ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353

dyads_m2_shift3 (dyads_m2)
; positions_6nt_m5 versus dyads_m2; m=6/7; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.494839; ---rwTGAAGAAGAAAAwr----- ; cor=; Ncor= a 0 0 0 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 1475 1303 0 0 0 0 0 c 0 0 0 508 692 288 157 96 176 152 115 179 93 156 202 231 350 680 525 0 0 0 0 0 g 0 0 0 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 746 1222 0 0 0 0 0 t 0 0 0 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460 1028 879 0 0 0 0 0

positions_7nt_m1_shift10 (positions_7nt_m1)
; positions_6nt_m5 versus positions_7nt_m1; m=7/7; ncol2=13; w=0; offset=10; strand=D; shift=10; score=0.447824; ----------waAAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift10 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift10 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=13; shift=10; ncol=23; ----------waAAAAAATATww ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376

positions_7nt_m1_shift10 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=10; score= 1; ----------waAAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376

positions_7nt_m2_shift10 (positions_7nt_m2)
; positions_7nt_m1 versus positions_7nt_m2; m=2/7; ncol2=12; w=0; offset=0; strand=D; shift=10; score=0.769202; ----------wwAAAAAATTaw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2739 2445 7484 7224 7025 7185 6976 7618 175 1005 3233 2574 0 c 0 0 0 0 0 0 0 0 0 0 1323 1466 74 164 202 180 198 86 138 645 1528 1426 0 g 0 0 0 0 0 0 0 0 0 0 1490 1647 107 179 253 205 141 159 100 643 1378 1415 0 t 0 0 0 0 0 0 0 0 0 0 2379 2373 266 364 451 361 616 68 7518 5638 1792 2516 0

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_7nt_m1 versus positions_6nt_m3; m=3/7; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.495597; waAAAwAAAAArAAAAAAtAwaw ; cor=; Ncor= a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=4/7; ncol2=24; w=-9; offset=-9; strand=D; shift=1; score= 0.4535; -awAAAwAAAAArAAAAAtAwAa ; cor=; Ncor= a 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 c 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 g 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 t 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_7nt_m1 versus positions_6nt_m5; m=5/7; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.447824; waatAAAAArAAgAAAAAtAtaw ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_7nt_m1 versus positions_6nt_m4; m=6/7; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.445873; wwAAAgAAAAtTgAAAAAtAtaw ; cor=; Ncor= a 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 c 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 g 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 t 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_7nt_m1 versus positions_6nt_m2; m=7/7; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.402095; wawrAAAAwAAAAArAAAAAttw ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322

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 5228 3128 854 11897 908 407 12081 935 578 5485 3696 c 1681 3417 10385 198 10315 11823 104 10045 11376 1711 2848 g 2669 2503 447 293 733 219 265 867 352 2530 2758 t 3226 3756 1118 416 848 355 354 957 498 3078 3502

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 5228 3128 854 11897 908 407 12081 935 578 5485 3696 c 1681 3417 10385 198 10315 11823 104 10045 11376 1711 2848 g 2669 2503 447 293 733 219 265 867 352 2530 2758 t 3226 3756 1118 416 848 355 354 957 498 3078 3502

oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)
; dyads_m3 versus oligos_6nt_mkv4_m3; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.832415; -wtACCACCrw ; cor=; Ncor= a 0 1957 1207 6105 32 13 5679 69 33 2313 1915 c 0 1485 1492 72 6326 5826 65 6272 6075 719 1501 g 0 1467 753 195 74 207 530 91 259 1997 1271 t 0 1644 3101 181 121 507 279 121 186 1524 1866

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 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 1475 1303 c 0 0 0 508 692 288 157 96 176 152 115 179 93 156 202 231 350 680 525 g 0 0 0 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 746 1222 t 0 0 0 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460 1028 879

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 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 1475 1303 c 0 0 0 508 692 288 157 96 176 152 115 179 93 156 202 231 350 680 525 g 0 0 0 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 746 1222 t 0 0 0 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460 1028 879

dyads_m1_shift3 (dyads_m1)
; dyads_m2 versus dyads_m1; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.796852; ---rwTGAAGAAGAgra-- ; cor=; Ncor= a 0 0 0 2215 2934 1202 551 6811 6481 203 7130 6569 354 6677 1915 2173 3181 0 0 c 0 0 0 1181 1482 510 355 326 297 209 257 294 225 359 715 1165 1477 0 0 g 0 0 0 2711 1188 574 6529 275 356 7118 151 392 6870 345 3860 2643 1211 0 0 t 0 0 0 1679 2182 5500 351 374 652 256 248 531 337 405 1296 1805 1917 0 0

positions_7nt_m3_shift6 (positions_7nt_m3)
; dyads_m2 versus positions_7nt_m3; m=3/8; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.59615; ------rwAGAAGAAdw-- ; cor=; Ncor= a 0 0 0 0 0 0 3117 4013 9560 0 9618 9674 0 9585 9174 2942 4127 0 0 c 0 0 0 0 0 0 2025 1683 873 33 293 541 19 268 547 1905 2095 0 0 g 0 0 0 0 0 0 3089 1544 234 10656 237 324 10639 294 455 3369 1860 0 0 t 0 0 0 0 0 0 2733 3724 297 275 816 425 306 817 788 2748 2882 0 0

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=0.568034; ----wwGAcGAAGaw---- ; cor=; Ncor= a 0 0 0 0 5489 4297 626 12435 2734 701 12970 12061 696 6081 4341 0 0 0 0 c 0 0 0 0 2303 2466 227 310 8183 712 233 478 308 2349 2608 0 0 0 0 g 0 0 0 0 2035 2304 12307 312 924 11896 123 282 12074 2146 2100 0 0 0 0 t 0 0 0 0 3699 4459 366 469 1685 217 200 705 448 2950 4477 0 0 0 0

oligos_7nt_mkv5_m2_rc_shift4 (oligos_7nt_mkv5_m2_rc)
; dyads_m2 versus oligos_7nt_mkv5_m2_rc; m=5/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.561658; ----wwGAAGAcGaw---- ; cor=; Ncor= a 0 0 0 0 5614 4675 585 13471 12556 699 13044 2734 902 5854 4369 0 0 0 0 c 0 0 0 0 2518 2478 368 220 478 251 376 8653 515 2330 2858 0 0 0 0 g 0 0 0 0 2143 2511 12995 213 335 12751 325 1080 12049 2637 2236 0 0 0 0 t 0 0 0 0 3843 4454 170 214 749 417 373 1651 652 3297 4655 0 0 0 0

oligos_7nt_mkv5_m5_rc_shift4 (oligos_7nt_mkv5_m5_rc)
; dyads_m2 versus oligos_7nt_mkv5_m5_rc; m=6/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.550569; ----wwGATGAAGaw---- ; cor=; Ncor= a 0 0 0 0 6604 5467 390 14356 2734 838 15746 14454 376 7546 5577 0 0 0 0 c 0 0 0 0 3301 3192 125 881 770 195 556 749 380 3159 3207 0 0 0 0 g 0 0 0 0 2658 2717 16021 894 924 15831 534 569 15934 2683 2531 0 0 0 0 t 0 0 0 0 4676 5863 703 1108 12811 375 403 1467 549 3851 5924 0 0 0 0

oligos_7nt_mkv5_m3_rc_shift4 (oligos_7nt_mkv5_m3_rc)
; dyads_m2 versus oligos_7nt_mkv5_m3_rc; m=7/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.545972; ----wwGAAGATGaw---- ; cor=; Ncor= a 0 0 0 0 7017 6069 454 16471 15340 217 15158 2734 1062 7400 5817 0 0 0 0 c 0 0 0 0 3430 2974 162 617 705 190 967 811 296 3172 3556 0 0 0 0 g 0 0 0 0 2783 3102 17035 514 654 16847 875 1080 16280 3356 2643 0 0 0 0 t 0 0 0 0 4936 6021 515 564 1467 912 1166 13541 528 4238 6150 0 0 0 0

positions_6nt_m5_shift0 (positions_6nt_m5)
; dyads_m2 versus positions_6nt_m5; m=8/8; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.494839; waatAAAAArAAgAAAAAt ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift12 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift12 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=12; shift=12; ncol=24; ------------wwAAAAAATTaw ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 2739 2445 7484 7224 7025 7185 6976 7618 175 1005 3233 2574 c 0 0 0 0 0 0 0 0 0 0 0 0 1323 1466 74 164 202 180 198 86 138 645 1528 1426 g 0 0 0 0 0 0 0 0 0 0 0 0 1490 1647 107 179 253 205 141 159 100 643 1378 1415 t 0 0 0 0 0 0 0 0 0 0 0 0 2379 2373 266 364 451 361 616 68 7518 5638 1792 2516

positions_7nt_m2_shift12 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=12; score= 1; ------------wwAAAAAATTaw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2739 2445 7484 7224 7025 7185 6976 7618 175 1005 3233 2574 c 0 0 0 0 0 0 0 0 0 0 0 0 1323 1466 74 164 202 180 198 86 138 645 1528 1426 g 0 0 0 0 0 0 0 0 0 0 0 0 1490 1647 107 179 253 205 141 159 100 643 1378 1415 t 0 0 0 0 0 0 0 0 0 0 0 0 2379 2373 266 364 451 361 616 68 7518 5638 1792 2516

positions_7nt_m1_shift12 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=12; score=0.769202; ------------waAAAAAATATw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 c 0 0 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 g 0 0 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 t 0 0 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_7nt_m2 versus positions_6nt_m2; m=3/3; ncol2=24; w=-12; offset=-12; strand=D; shift=0; score=0.414088; wawrAAAAwAAAAArAAAAAttww ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 8 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; wawrAAAAwAAAAArAAAAAttww ; Alignment reference a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wawrAAAAwAAAAArAAAAAttww ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m2 versus positions_6nt_m3; m=2/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.747678; waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m2 versus positions_6nt_m5; m=3/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.714927; waatAAAAArAAgAAAAAtAtawa ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338

positions_6nt_m1_shift3 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=4/7; ncol2=24; w=0; offset=3; strand=D; shift=3; score=0.707016; ---awAAAwAAAAArAAAAAtAwA ; cor=; Ncor= a 0 0 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 c 0 0 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 g 0 0 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 t 0 0 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m2 versus positions_6nt_m4; m=5/7; ncol2=24; w=0; offset=2; strand=D; shift=2; score=0.636447; --wwAAAgAAAAtTgAAAAAtAta ; cor=; Ncor= a 0 0 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 c 0 0 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 g 0 0 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 t 0 0 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109

positions_7nt_m2_shift12 (positions_7nt_m2)
; positions_6nt_m2 versus positions_7nt_m2; m=6/7; ncol2=12; w=0; offset=12; strand=D; shift=12; score=0.414088; ------------wwAAAAAATTaw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2739 2445 7484 7224 7025 7185 6976 7618 175 1005 3233 2574 c 0 0 0 0 0 0 0 0 0 0 0 0 1323 1466 74 164 202 180 198 86 138 645 1528 1426 g 0 0 0 0 0 0 0 0 0 0 0 0 1490 1647 107 179 253 205 141 159 100 643 1378 1415 t 0 0 0 0 0 0 0 0 0 0 0 0 2379 2373 266 364 451 361 616 68 7518 5638 1792 2516

positions_7nt_m1_shift10 (positions_7nt_m1)
; positions_6nt_m2 versus positions_7nt_m1; m=7/7; ncol2=13; w=0; offset=10; strand=D; shift=10; score=0.402095; ----------waAAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift4 ; 8 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; ----wtCTTCgTCww ; Alignment reference a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489

oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCTTCgTCww ; cor=; Ncor= a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m5; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.904573; ----wtCTTCATCww ; cor=; Ncor= a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m2; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.782597; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.761648; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m4 versus dyads_m1_rc; m=5/7; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.663988; --tycTCTTCTTCAw ; cor=; Ncor= a 0 0 1917 1805 1296 405 337 531 248 256 652 374 351 5500 2182 c 0 0 1211 2643 3860 345 6870 392 151 7118 356 275 6529 574 1188 g 0 0 1477 1165 715 359 225 294 257 209 297 326 355 510 1482 t 0 0 3181 2173 1915 6677 354 6569 7130 203 6481 6811 551 1202 2934

positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)
; oligos_7nt_mkv5_m4 versus positions_7nt_m3_rc; m=6/7; ncol2=11; w=0; offset=1; strand=R; shift=5; score=0.649407; -----whTTCTTCTw ; cor=; Ncor= a 0 0 0 0 0 2882 2748 788 817 306 425 816 275 297 3724 c 0 0 0 0 0 1860 3369 455 294 10639 324 237 10656 234 1544 g 0 0 0 0 0 2095 1905 547 268 19 541 293 33 873 1683 t 0 0 0 0 0 4127 2942 9174 9585 0 9674 9618 0 9560 4013

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m4 versus dyads_m2_rc; m=7/7; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.568034; ywTTTTCTTCTTCAw ; cor=; Ncor= a 879 1028 460 266 324 107 127 250 146 115 257 204 134 2728 1086 c 1222 746 318 655 177 150 3373 169 88 3365 115 162 3340 212 600 g 525 680 350 231 202 156 93 179 115 152 176 96 157 288 692 t 1303 1475 2801 2777 3226 3516 336 3331 3580 297 3381 3467 298 701 1551

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift4 ; 9 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; ----wtCATCTTCww ; Alignment reference a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017

oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017

oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=2/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.90113; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614

oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=3/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.761648; ----wtCTTCgTCww ; cor=; Ncor= a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489

oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m5; m=4/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.755783; ----wtCTTCATCww ; cor=; Ncor= a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604

positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)
; oligos_7nt_mkv5_m3 versus positions_7nt_m3_rc; m=5/8; ncol2=11; w=0; offset=1; strand=R; shift=5; score=0.637895; -----whTTCTTCTw ; cor=; Ncor= a 0 0 0 0 0 2882 2748 788 817 306 425 816 275 297 3724 c 0 0 0 0 0 1860 3369 455 294 10639 324 237 10656 234 1544 g 0 0 0 0 0 2095 1905 547 268 19 541 293 33 873 1683 t 0 0 0 0 0 4127 2942 9174 9585 0 9674 9618 0 9560 4013

oligos_6nt_mkv4_m1_shift5 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m1; m=6/8; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.637629; -----wtACCTTCww ; cor=; Ncor= a 0 0 0 0 0 1356 1041 4217 0 0 121 349 10 1289 1317 c 0 0 0 0 0 843 996 0 4217 4196 31 51 4207 718 682 g 0 0 0 0 0 880 549 0 0 21 403 34 0 822 728 t 0 0 0 0 0 1138 1631 0 0 0 3662 3783 0 1388 1490

dyads_m1_rc_shift2 (dyads_m1_rc)
; oligos_7nt_mkv5_m3 versus dyads_m1_rc; m=7/8; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.636713; --tycTCTTCTTCAw ; cor=; Ncor= a 0 0 1917 1805 1296 405 337 531 248 256 652 374 351 5500 2182 c 0 0 1211 2643 3860 345 6870 392 151 7118 356 275 6529 574 1188 g 0 0 1477 1165 715 359 225 294 257 209 297 326 355 510 1482 t 0 0 3181 2173 1915 6677 354 6569 7130 203 6481 6811 551 1202 2934

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv5_m3 versus dyads_m2_rc; m=8/8; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.545972; ywTTTTCTTCTTCAw ; cor=; Ncor= a 879 1028 460 266 324 107 127 250 146 115 257 204 134 2728 1086 c 1222 746 318 655 177 150 3373 169 88 3365 115 162 3340 212 600 g 525 680 350 231 202 156 93 179 115 152 176 96 157 288 692 t 1303 1475 2801 2777 3226 3516 336 3331 3580 297 3381 3467 298 701 1551

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 1267 688 223 1885 500 195 2033 426 158 1970 406 139 2019 476 118 2007 398 194 1896 580 427 1164 c 276 434 1844 100 239 1924 63 242 2052 75 228 2027 61 1000 2100 57 271 1959 104 231 1268 280 g 353 845 110 182 1480 126 176 1570 83 211 1603 49 168 746 38 185 1577 64 197 1410 223 448 t 509 438 228 238 186 160 133 167 112 149 168 190 157 183 149 156 159 188 208 184 487 513

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 1267 688 223 1885 500 195 2033 426 158 1970 406 139 2019 476 118 2007 398 194 1896 580 427 1164 c 276 434 1844 100 239 1924 63 242 2052 75 228 2027 61 1000 2100 57 271 1959 104 231 1268 280 g 353 845 110 182 1480 126 176 1570 83 211 1603 49 168 746 38 185 1577 64 197 1410 223 448 t 509 438 228 238 186 160 133 167 112 149 168 190 157 183 149 156 159 188 208 184 487 513

dyads_m4_shift0 (dyads_m4)
; dyads_m5 versus dyads_m4; m=2/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.977229; arCAgCAgCAgCAGCAgCAgca ; cor=; Ncor= a 1623 970 292 2418 658 291 2446 649 237 2567 563 244 2618 511 206 2517 577 254 2370 672 579 1585 c 334 462 2419 145 274 2592 144 259 2643 116 300 2662 100 256 2660 118 271 2571 163 306 1694 404 g 527 1191 174 299 2041 133 327 2098 98 297 2137 71 284 2250 83 300 2117 90 338 1908 319 554 t 728 589 327 350 239 196 295 206 234 232 212 235 210 195 263 277 247 297 341 326 620 669

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=11; shift=0; ncol=11; wwCCTTTTCww ; Alignment reference a 3393 3268 970 149 697 279 492 491 266 3179 3206 c 2341 1736 7909 10894 241 1069 541 200 11086 2343 1854 g 2233 2303 671 342 418 380 572 273 39 1785 2247 t 3456 4116 1873 38 10067 9695 9818 10459 32 4116 4116

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCCTTTTCww ; cor=; Ncor= a 3393 3268 970 149 697 279 492 491 266 3179 3206 c 2341 1736 7909 10894 241 1069 541 200 11086 2343 1854 g 2233 2303 671 342 418 380 572 273 39 1785 2247 t 3456 4116 1873 38 10067 9695 9818 10459 32 4116 4116

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -wtACCACCrw ; Alignment reference a 0 1957 1207 6105 32 13 5679 69 33 2313 1915 c 0 1485 1492 72 6326 5826 65 6272 6075 719 1501 g 0 1467 753 195 74 207 530 91 259 1997 1271 t 0 1644 3101 181 121 507 279 121 186 1524 1866

oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wtACCACCrw ; cor=; Ncor= a 0 1957 1207 6105 32 13 5679 69 33 2313 1915 c 0 1485 1492 72 6326 5826 65 6272 6075 719 1501 g 0 1467 753 195 74 207 530 91 259 1997 1271 t 0 1644 3101 181 121 507 279 121 186 1524 1866

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv4_m3 versus dyads_m3; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.832415; wyCACCACCaw ; cor=; Ncor= a 5228 3128 854 11897 908 407 12081 935 578 5485 3696 c 1681 3417 10385 198 10315 11823 104 10045 11376 1711 2848 g 2669 2503 447 293 733 219 265 867 352 2530 2758 t 3226 3756 1118 416 848 355 354 957 498 3078 3502

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; ---awAAAwAAAAArAAAAAtAwAaaw ; Alignment reference a 0 0 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 949 c 0 0 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 311 g 0 0 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 373 t 0 0 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545 693
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---awAAAwAAAAArAAAAAtAwAaaw ; cor=; Ncor= a 0 0 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 949 c 0 0 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 311 g 0 0 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 373 t 0 0 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545 693
positions_6nt_m3_shift3 (positions_6nt_m3)				; positions_6nt_m1 versus positions_6nt_m3; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.847487; ---waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 0 0 0 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 0 0 0 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 0 0 0 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 0 0 0 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m1 versus positions_6nt_m5; m=3/6; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.821827; --waatAAAAArAAgAAAAAtAtawa- ; cor=; Ncor= a 0 0 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 0 c 0 0 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 0 g 0 0 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 0 t 0 0 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338 0
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m1 versus positions_6nt_m4; m=4/6; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.743864; --wwAAAgAAAAtTgAAAAAtAtaww- ; cor=; Ncor= a 0 0 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 0 c 0 0 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 0 g 0 0 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 0 t 0 0 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239 0
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=5/6; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.707016; wawrAAAAwAAAAArAAAAAttww--- ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 0 0 0 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 0 0 0 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 0 0 0 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353 0 0 0
positions_7nt_m1_shift12 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=6/6; ncol2=13; w=0; offset=9; strand=D; shift=12; score= 0.4535; ------------waAAAAAATATww-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCgTCTTCww ; Alignment reference a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.90113; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.782597; ----wtCTTCgTCww ; cor=; Ncor= a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m5; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.763399; ----wtCTTCATCww ; cor=; Ncor= a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604
positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)				; oligos_7nt_mkv5_m2 versus positions_7nt_m3_rc; m=5/7; ncol2=11; w=0; offset=1; strand=R; shift=5; score=0.664251; -----whTTCTTCTw ; cor=; Ncor= a 0 0 0 0 0 2882 2748 788 817 306 425 816 275 297 3724 c 0 0 0 0 0 1860 3369 455 294 10639 324 237 10656 234 1544 g 0 0 0 0 0 2095 1905 547 268 19 541 293 33 873 1683 t 0 0 0 0 0 4127 2942 9174 9585 0 9674 9618 0 9560 4013
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m2 versus dyads_m1_rc; m=6/7; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.654786; --tycTCTTCTTCAw ; cor=; Ncor= a 0 0 1917 1805 1296 405 337 531 248 256 652 374 351 5500 2182 c 0 0 1211 2643 3860 345 6870 392 151 7118 356 275 6529 574 1188 g 0 0 1477 1165 715 359 225 294 257 209 297 326 355 510 1482 t 0 0 3181 2173 1915 6677 354 6569 7130 203 6481 6811 551 1202 2934
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m2 versus dyads_m2_rc; m=7/7; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.561658; ywTTTTCTTCTTCAw ; cor=; Ncor= a 879 1028 460 266 324 107 127 250 146 115 257 204 134 2728 1086 c 1222 746 318 655 177 150 3373 169 88 3365 115 162 3340 212 600 g 525 680 350 231 202 156 93 179 115 152 176 96 157 288 692 t 1303 1475 2801 2777 3226 3516 336 3331 3580 297 3381 3467 298 701 1551

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=24; shift=2; ncol=26; --wwAAAgAAAAtTgAAAAAtAtaww ; Alignment reference a 0 0 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 c 0 0 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 g 0 0 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 t 0 0 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --wwAAAgAAAAtTgAAAAAtAtaww ; cor=; Ncor= a 0 0 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 c 0 0 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 g 0 0 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 t 0 0 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239
positions_6nt_m3_shift2 (positions_6nt_m3)				; positions_6nt_m4 versus positions_6nt_m3; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.843609; --waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 0 0 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 0 0 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 0 0 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 0 0 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m4 versus positions_6nt_m5; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.775674; --waatAAAAArAAgAAAAAtAtawa ; cor=; Ncor= a 0 0 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 0 0 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 0 0 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 0 0 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m4 versus positions_6nt_m1; m=4/6; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.743864; ---awAAAwAAAAArAAAAAtAwAaa ; cor=; Ncor= a 0 0 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 c 0 0 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 g 0 0 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 t 0 0 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m4 versus positions_6nt_m2; m=5/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.636447; wawrAAAAwAAAAArAAAAAttww-- ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 0 0 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 0 0 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 0 0 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353 0 0
positions_7nt_m1_shift12 (positions_7nt_m1)				; positions_6nt_m4 versus positions_7nt_m1; m=6/6; ncol2=13; w=0; offset=10; strand=D; shift=12; score=0.445873; ------------waAAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 c 0 0 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 g 0 0 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0

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; ----wtCTTCATCww ; Alignment reference a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCTTCATCww ; cor=; Ncor= a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m4; m=2/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.904573; ----wtCTTCgTCww ; cor=; Ncor= a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m2; m=3/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.763399; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m3; m=4/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.755783; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m5 versus dyads_m1_rc; m=5/8; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.646801; --tycTCTTCTTCAw ; cor=; Ncor= a 0 0 1917 1805 1296 405 337 531 248 256 652 374 351 5500 2182 c 0 0 1211 2643 3860 345 6870 392 151 7118 356 275 6529 574 1188 g 0 0 1477 1165 715 359 225 294 257 209 297 326 355 510 1482 t 0 0 3181 2173 1915 6677 354 6569 7130 203 6481 6811 551 1202 2934
positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)				; oligos_7nt_mkv5_m5 versus positions_7nt_m3_rc; m=6/8; ncol2=11; w=0; offset=1; strand=R; shift=5; score=0.619928; -----whTTCTTCTw ; cor=; Ncor= a 0 0 0 0 0 2882 2748 788 817 306 425 816 275 297 3724 c 0 0 0 0 0 1860 3369 455 294 10639 324 237 10656 234 1544 g 0 0 0 0 0 2095 1905 547 268 19 541 293 33 873 1683 t 0 0 0 0 0 4127 2942 9174 9585 0 9674 9618 0 9560 4013
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m5 versus dyads_m2_rc; m=7/8; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.550569; ywTTTTCTTCTTCAw ; cor=; Ncor= a 879 1028 460 266 324 107 127 250 146 115 257 204 134 2728 1086 c 1222 746 318 655 177 150 3373 169 88 3365 115 162 3340 212 600 g 525 680 350 231 202 156 93 179 115 152 176 96 157 288 692 t 1303 1475 2801 2777 3226 3516 336 3331 3580 297 3381 3467 298 701 1551
oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m1; m=8/8; ncol2=10; w=-2; offset=-2; strand=D; shift=2; score=0.433572; --wtACCTTCww--- ; cor=; Ncor= a 0 0 1356 1041 4217 0 0 121 349 10 1289 1317 0 0 0 c 0 0 843 996 0 4217 4196 31 51 4207 718 682 0 0 0 g 0 0 880 549 0 0 21 403 34 0 822 728 0 0 0 t 0 0 1138 1631 0 0 0 3662 3783 0 1388 1490 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; rwTGAAGAAGAgra ; Alignment reference a 2215 2934 1202 551 6811 6481 203 7130 6569 354 6677 1915 2173 3181 c 1181 1482 510 355 326 297 209 257 294 225 359 715 1165 1477 g 2711 1188 574 6529 275 356 7118 151 392 6870 345 3860 2643 1211 t 1679 2182 5500 351 374 652 256 248 531 337 405 1296 1805 1917
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/7; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rwTGAAGAAGAgra ; cor=; Ncor= a 2215 2934 1202 551 6811 6481 203 7130 6569 354 6677 1915 2173 3181 c 1181 1482 510 355 326 297 209 257 294 225 359 715 1165 1477 g 2711 1188 574 6529 275 356 7118 151 392 6870 345 3860 2643 1211 t 1679 2182 5500 351 374 652 256 248 531 337 405 1296 1805 1917
dyads_m2_shift0 (dyads_m2)				; dyads_m1 versus dyads_m2; m=2/7; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.796852; rwTGAAGAAGAAAA ; cor=; Ncor= a 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 c 508 692 288 157 96 176 152 115 179 93 156 202 231 350 g 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 t 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460
oligos_7nt_mkv5_m4_rc_shift1 (oligos_7nt_mkv5_m4_rc)				; dyads_m1 versus oligos_7nt_mkv5_m4_rc; m=3/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.663988; -wwGAcGAAGaw-- ; cor=; Ncor= a 0 5489 4297 626 12435 2734 701 12970 12061 696 6081 4341 0 0 c 0 2303 2466 227 310 8183 712 233 478 308 2349 2608 0 0 g 0 2035 2304 12307 312 924 11896 123 282 12074 2146 2100 0 0 t 0 3699 4459 366 469 1685 217 200 705 448 2950 4477 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)				; dyads_m1 versus positions_7nt_m3; m=4/7; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.654798; ---rwAGAAGAAdw ; cor=; Ncor= a 0 0 0 3117 4013 9560 0 9618 9674 0 9585 9174 2942 4127 c 0 0 0 2025 1683 873 33 293 541 19 268 547 1905 2095 g 0 0 0 3089 1544 234 10656 237 324 10639 294 455 3369 1860 t 0 0 0 2733 3724 297 275 816 425 306 817 788 2748 2882
oligos_7nt_mkv5_m2_rc_shift1 (oligos_7nt_mkv5_m2_rc)				; dyads_m1 versus oligos_7nt_mkv5_m2_rc; m=5/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.654786; -wwGAAGAcGaw-- ; cor=; Ncor= a 0 5614 4675 585 13471 12556 699 13044 2734 902 5854 4369 0 0 c 0 2518 2478 368 220 478 251 376 8653 515 2330 2858 0 0 g 0 2143 2511 12995 213 335 12751 325 1080 12049 2637 2236 0 0 t 0 3843 4454 170 214 749 417 373 1651 652 3297 4655 0 0
oligos_7nt_mkv5_m5_rc_shift1 (oligos_7nt_mkv5_m5_rc)				; dyads_m1 versus oligos_7nt_mkv5_m5_rc; m=6/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.646801; -wwGATGAAGaw-- ; cor=; Ncor= a 0 6604 5467 390 14356 2734 838 15746 14454 376 7546 5577 0 0 c 0 3301 3192 125 881 770 195 556 749 380 3159 3207 0 0 g 0 2658 2717 16021 894 924 15831 534 569 15934 2683 2531 0 0 t 0 4676 5863 703 1108 12811 375 403 1467 549 3851 5924 0 0
oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)				; dyads_m1 versus oligos_7nt_mkv5_m3_rc; m=7/7; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.636713; -wwGAAGATGaw-- ; cor=; Ncor= a 0 7017 6069 454 16471 15340 217 15158 2734 1062 7400 5817 0 0 c 0 3430 2974 162 617 705 190 967 811 296 3172 3556 0 0 g 0 2783 3102 17035 514 654 16847 875 1080 16280 3356 2643 0 0 t 0 4936 6021 515 564 1467 912 1166 13541 528 4238 6150 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---rwAGAAGAAdw ; Alignment reference a 0 0 0 3117 4013 9560 0 9618 9674 0 9585 9174 2942 4127 c 0 0 0 2025 1683 873 33 293 541 19 268 547 1905 2095 g 0 0 0 3089 1544 234 10656 237 324 10639 294 455 3369 1860 t 0 0 0 2733 3724 297 275 816 425 306 817 788 2748 2882
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---rwAGAAGAAdw ; cor=; Ncor= a 0 0 0 3117 4013 9560 0 9618 9674 0 9585 9174 2942 4127 c 0 0 0 2025 1683 873 33 293 541 19 268 547 1905 2095 g 0 0 0 3089 1544 234 10656 237 324 10639 294 455 3369 1860 t 0 0 0 2733 3724 297 275 816 425 306 817 788 2748 2882
oligos_7nt_mkv5_m2_rc_shift4 (oligos_7nt_mkv5_m2_rc)				; positions_7nt_m3 versus oligos_7nt_mkv5_m2_rc; m=2/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.664251; ----wwGAAGAcGa ; cor=; Ncor= a 0 0 0 0 5614 4675 585 13471 12556 699 13044 2734 902 5854 c 0 0 0 0 2518 2478 368 220 478 251 376 8653 515 2330 g 0 0 0 0 2143 2511 12995 213 335 12751 325 1080 12049 2637 t 0 0 0 0 3843 4454 170 214 749 417 373 1651 652 3297
dyads_m1_shift0 (dyads_m1)				; positions_7nt_m3 versus dyads_m1; m=3/7; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.654798; rwTGAAGAAGAgra ; cor=; Ncor= a 2215 2934 1202 551 6811 6481 203 7130 6569 354 6677 1915 2173 3181 c 1181 1482 510 355 326 297 209 257 294 225 359 715 1165 1477 g 2711 1188 574 6529 275 356 7118 151 392 6870 345 3860 2643 1211 t 1679 2182 5500 351 374 652 256 248 531 337 405 1296 1805 1917
oligos_7nt_mkv5_m4_rc_shift4 (oligos_7nt_mkv5_m4_rc)				; positions_7nt_m3 versus oligos_7nt_mkv5_m4_rc; m=4/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.649407; ----wwGAcGAAGa ; cor=; Ncor= a 0 0 0 0 5489 4297 626 12435 2734 701 12970 12061 696 6081 c 0 0 0 0 2303 2466 227 310 8183 712 233 478 308 2349 g 0 0 0 0 2035 2304 12307 312 924 11896 123 282 12074 2146 t 0 0 0 0 3699 4459 366 469 1685 217 200 705 448 2950
oligos_7nt_mkv5_m3_rc_shift4 (oligos_7nt_mkv5_m3_rc)				; positions_7nt_m3 versus oligos_7nt_mkv5_m3_rc; m=5/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.637895; ----wwGAAGATGa ; cor=; Ncor= a 0 0 0 0 7017 6069 454 16471 15340 217 15158 2734 1062 7400 c 0 0 0 0 3430 2974 162 617 705 190 967 811 296 3172 g 0 0 0 0 2783 3102 17035 514 654 16847 875 1080 16280 3356 t 0 0 0 0 4936 6021 515 564 1467 912 1166 13541 528 4238
oligos_7nt_mkv5_m5_rc_shift4 (oligos_7nt_mkv5_m5_rc)				; positions_7nt_m3 versus oligos_7nt_mkv5_m5_rc; m=6/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.619928; ----wwGATGAAGa ; cor=; Ncor= a 0 0 0 0 6604 5467 390 14356 2734 838 15746 14454 376 7546 c 0 0 0 0 3301 3192 125 881 770 195 556 749 380 3159 g 0 0 0 0 2658 2717 16021 894 924 15831 534 569 15934 2683 t 0 0 0 0 4676 5863 703 1108 12811 375 403 1467 549 3851
dyads_m2_shift0 (dyads_m2)				; positions_7nt_m3 versus dyads_m2; m=7/7; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.59615; rwTGAAGAAGAAAA ; cor=; Ncor= a 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 c 508 692 288 157 96 176 152 115 179 93 156 202 231 350 g 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 t 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460

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; waAAAwAAAAArAAAAAAtAwaww ; Alignment reference a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m3 versus positions_6nt_m1; m=2/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.847487; awAAAwAAAAArAAAAAtAwAaaw ; cor=; Ncor= a 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 949 c 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 311 g 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 373 t 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545 693
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m3 versus positions_6nt_m4; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.843609; wwAAAgAAAAtTgAAAAAtAtaww ; cor=; Ncor= a 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 c 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 g 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 t 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m3 versus positions_6nt_m5; m=4/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.82257; waatAAAAArAAgAAAAAtAtawa ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m3 versus positions_6nt_m2; m=5/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.747678; wawrAAAAwAAAAArAAAAAttww ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353
positions_7nt_m1_shift10 (positions_7nt_m1)				; positions_6nt_m3 versus positions_7nt_m1; m=6/6; ncol2=13; w=0; offset=10; strand=D; shift=10; score=0.495597; ----------waAAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0

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; -wtACCTTCww ; Alignment reference a 0 1356 1041 4217 0 0 121 349 10 1289 1317 c 0 843 996 0 4217 4196 31 51 4207 718 682 g 0 880 549 0 0 21 403 34 0 822 728 t 0 1138 1631 0 0 0 3662 3783 0 1388 1490
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wtACCTTCww ; cor=; Ncor= a 0 1356 1041 4217 0 0 121 349 10 1289 1317 c 0 843 996 0 4217 4196 31 51 4207 718 682 g 0 880 549 0 0 21 403 34 0 822 728 t 0 1138 1631 0 0 0 3662 3783 0 1388 1490
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m3; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.637629; wtCATCTTCww ; cor=; Ncor= a 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 3556 3172 296 811 967 190 705 617 162 2974 3430 t 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017
oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m5; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.433572; ---wtCTTCAT ; cor=; Ncor= a 0 0 0 5924 3851 549 1467 403 375 12811 1108 c 0 0 0 2531 2683 15934 569 534 15831 924 894 g 0 0 0 3207 3159 380 749 556 195 770 881 t 0 0 0 5577 7546 376 14454 15746 838 2734 14356

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; waatAAAAArAAgAAAAAtAtawa ; Alignment reference a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; waatAAAAArAAgAAAAAtAtawa ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m5 versus positions_6nt_m3; m=2/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.82257; waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m5 versus positions_6nt_m1; m=3/7; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.821827; -awAAAwAAAAArAAAAAtAwAaa ; cor=; Ncor= a 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 1169 c 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 272 g 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 340 t 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514 545
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m5 versus positions_6nt_m4; m=4/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.775674; wwAAAgAAAAtTgAAAAAtAtaww ; cor=; Ncor= a 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 363 c 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 114 g 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 152 t 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251 239
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m5 versus positions_6nt_m2; m=5/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.714927; wawrAAAAwAAAAArAAAAAttww ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353
dyads_m2_shift3 (dyads_m2)				; positions_6nt_m5 versus dyads_m2; m=6/7; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.494839; ---rwTGAAGAAGAAAAwr----- ; cor=; Ncor= a 0 0 0 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 1475 1303 0 0 0 0 0 c 0 0 0 508 692 288 157 96 176 152 115 179 93 156 202 231 350 680 525 0 0 0 0 0 g 0 0 0 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 746 1222 0 0 0 0 0 t 0 0 0 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460 1028 879 0 0 0 0 0
positions_7nt_m1_shift10 (positions_7nt_m1)				; positions_6nt_m5 versus positions_7nt_m1; m=7/7; ncol2=13; w=0; offset=10; strand=D; shift=10; score=0.447824; ----------waAAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift10 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=13; shift=10; ncol=23; ----------waAAAAAATATww ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376
positions_7nt_m1_shift10 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=10; score= 1; ----------waAAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376
positions_7nt_m2_shift10 (positions_7nt_m2)				; positions_7nt_m1 versus positions_7nt_m2; m=2/7; ncol2=12; w=0; offset=0; strand=D; shift=10; score=0.769202; ----------wwAAAAAATTaw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2739 2445 7484 7224 7025 7185 6976 7618 175 1005 3233 2574 0 c 0 0 0 0 0 0 0 0 0 0 1323 1466 74 164 202 180 198 86 138 645 1528 1426 0 g 0 0 0 0 0 0 0 0 0 0 1490 1647 107 179 253 205 141 159 100 643 1378 1415 0 t 0 0 0 0 0 0 0 0 0 0 2379 2373 266 364 451 361 616 68 7518 5638 1792 2516 0
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_7nt_m1 versus positions_6nt_m3; m=3/7; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.495597; waAAAwAAAAArAAAAAAtAwaw ; cor=; Ncor= a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=4/7; ncol2=24; w=-9; offset=-9; strand=D; shift=1; score= 0.4535; -awAAAwAAAAArAAAAAtAwAa ; cor=; Ncor= a 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 1368 c 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 216 g 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 228 t 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387 514
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_7nt_m1 versus positions_6nt_m5; m=5/7; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.447824; waatAAAAArAAgAAAAAtAtaw ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_7nt_m1 versus positions_6nt_m4; m=6/7; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.445873; wwAAAgAAAAtTgAAAAAtAtaw ; cor=; Ncor= a 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 338 c 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 124 g 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 155 t 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109 251
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_7nt_m1 versus positions_6nt_m2; m=7/7; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.402095; wawrAAAAwAAAAArAAAAAttw ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322

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 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 1475 1303 c 0 0 0 508 692 288 157 96 176 152 115 179 93 156 202 231 350 680 525 g 0 0 0 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 746 1222 t 0 0 0 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460 1028 879
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 1232 1551 701 298 3467 3381 297 3580 3331 336 3516 3226 2777 2801 1475 1303 c 0 0 0 508 692 288 157 96 176 152 115 179 93 156 202 231 350 680 525 g 0 0 0 1319 600 212 3340 162 115 3365 88 169 3373 150 177 655 318 746 1222 t 0 0 0 870 1086 2728 134 204 257 115 146 250 127 107 324 266 460 1028 879
dyads_m1_shift3 (dyads_m1)				; dyads_m2 versus dyads_m1; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.796852; ---rwTGAAGAAGAgra-- ; cor=; Ncor= a 0 0 0 2215 2934 1202 551 6811 6481 203 7130 6569 354 6677 1915 2173 3181 0 0 c 0 0 0 1181 1482 510 355 326 297 209 257 294 225 359 715 1165 1477 0 0 g 0 0 0 2711 1188 574 6529 275 356 7118 151 392 6870 345 3860 2643 1211 0 0 t 0 0 0 1679 2182 5500 351 374 652 256 248 531 337 405 1296 1805 1917 0 0
positions_7nt_m3_shift6 (positions_7nt_m3)				; dyads_m2 versus positions_7nt_m3; m=3/8; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.59615; ------rwAGAAGAAdw-- ; cor=; Ncor= a 0 0 0 0 0 0 3117 4013 9560 0 9618 9674 0 9585 9174 2942 4127 0 0 c 0 0 0 0 0 0 2025 1683 873 33 293 541 19 268 547 1905 2095 0 0 g 0 0 0 0 0 0 3089 1544 234 10656 237 324 10639 294 455 3369 1860 0 0 t 0 0 0 0 0 0 2733 3724 297 275 816 425 306 817 788 2748 2882 0 0
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=0.568034; ----wwGAcGAAGaw---- ; cor=; Ncor= a 0 0 0 0 5489 4297 626 12435 2734 701 12970 12061 696 6081 4341 0 0 0 0 c 0 0 0 0 2303 2466 227 310 8183 712 233 478 308 2349 2608 0 0 0 0 g 0 0 0 0 2035 2304 12307 312 924 11896 123 282 12074 2146 2100 0 0 0 0 t 0 0 0 0 3699 4459 366 469 1685 217 200 705 448 2950 4477 0 0 0 0
oligos_7nt_mkv5_m2_rc_shift4 (oligos_7nt_mkv5_m2_rc)				; dyads_m2 versus oligos_7nt_mkv5_m2_rc; m=5/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.561658; ----wwGAAGAcGaw---- ; cor=; Ncor= a 0 0 0 0 5614 4675 585 13471 12556 699 13044 2734 902 5854 4369 0 0 0 0 c 0 0 0 0 2518 2478 368 220 478 251 376 8653 515 2330 2858 0 0 0 0 g 0 0 0 0 2143 2511 12995 213 335 12751 325 1080 12049 2637 2236 0 0 0 0 t 0 0 0 0 3843 4454 170 214 749 417 373 1651 652 3297 4655 0 0 0 0
oligos_7nt_mkv5_m5_rc_shift4 (oligos_7nt_mkv5_m5_rc)				; dyads_m2 versus oligos_7nt_mkv5_m5_rc; m=6/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.550569; ----wwGATGAAGaw---- ; cor=; Ncor= a 0 0 0 0 6604 5467 390 14356 2734 838 15746 14454 376 7546 5577 0 0 0 0 c 0 0 0 0 3301 3192 125 881 770 195 556 749 380 3159 3207 0 0 0 0 g 0 0 0 0 2658 2717 16021 894 924 15831 534 569 15934 2683 2531 0 0 0 0 t 0 0 0 0 4676 5863 703 1108 12811 375 403 1467 549 3851 5924 0 0 0 0
oligos_7nt_mkv5_m3_rc_shift4 (oligos_7nt_mkv5_m3_rc)				; dyads_m2 versus oligos_7nt_mkv5_m3_rc; m=7/8; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.545972; ----wwGAAGATGaw---- ; cor=; Ncor= a 0 0 0 0 7017 6069 454 16471 15340 217 15158 2734 1062 7400 5817 0 0 0 0 c 0 0 0 0 3430 2974 162 617 705 190 967 811 296 3172 3556 0 0 0 0 g 0 0 0 0 2783 3102 17035 514 654 16847 875 1080 16280 3356 2643 0 0 0 0 t 0 0 0 0 4936 6021 515 564 1467 912 1166 13541 528 4238 6150 0 0 0 0
positions_6nt_m5_shift0 (positions_6nt_m5)				; dyads_m2 versus positions_6nt_m5; m=8/8; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.494839; waatAAAAArAAgAAAAAt ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift12 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=12; shift=12; ncol=24; ------------wwAAAAAATTaw ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 2739 2445 7484 7224 7025 7185 6976 7618 175 1005 3233 2574 c 0 0 0 0 0 0 0 0 0 0 0 0 1323 1466 74 164 202 180 198 86 138 645 1528 1426 g 0 0 0 0 0 0 0 0 0 0 0 0 1490 1647 107 179 253 205 141 159 100 643 1378 1415 t 0 0 0 0 0 0 0 0 0 0 0 0 2379 2373 266 364 451 361 616 68 7518 5638 1792 2516
positions_7nt_m2_shift12 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=12; score= 1; ------------wwAAAAAATTaw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2739 2445 7484 7224 7025 7185 6976 7618 175 1005 3233 2574 c 0 0 0 0 0 0 0 0 0 0 0 0 1323 1466 74 164 202 180 198 86 138 645 1528 1426 g 0 0 0 0 0 0 0 0 0 0 0 0 1490 1647 107 179 253 205 141 159 100 643 1378 1415 t 0 0 0 0 0 0 0 0 0 0 0 0 2379 2373 266 364 451 361 616 68 7518 5638 1792 2516
positions_7nt_m1_shift12 (positions_7nt_m1)				; positions_7nt_m2 versus positions_7nt_m1; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=12; score=0.769202; ------------waAAAAAATATw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 c 0 0 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 g 0 0 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 t 0 0 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_7nt_m2 versus positions_6nt_m2; m=3/3; ncol2=24; w=-12; offset=-12; strand=D; shift=0; score=0.414088; wawrAAAAwAAAAArAAAAAttww ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353

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; wawrAAAAwAAAAArAAAAAttww ; Alignment reference a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wawrAAAAwAAAAArAAAAAttww ; cor=; Ncor= a 551 580 377 395 1024 1011 1033 1046 314 1057 999 987 1009 990 355 1064 1069 1052 1101 1077 252 286 482 510 c 170 159 111 108 41 47 22 59 67 26 64 60 59 39 89 35 39 32 35 36 68 81 216 196 g 208 197 149 575 88 63 79 73 137 93 66 74 72 92 621 74 67 53 45 43 99 112 220 181 t 311 304 603 162 87 119 106 62 722 64 111 119 100 119 175 67 65 103 59 84 821 761 322 353
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m2 versus positions_6nt_m3; m=2/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.747678; waAAAwAAAAArAAAAAAtAwaww ; cor=; Ncor= a 868 971 1483 1487 1525 656 1621 1643 1621 1660 1659 661 1657 1739 1742 1754 1737 1692 493 1614 566 1352 853 887 c 260 209 135 118 135 122 100 87 78 67 64 85 62 64 64 65 75 54 115 91 144 186 338 287 g 356 362 150 158 122 201 134 112 162 103 120 1016 126 91 95 54 59 109 164 157 194 184 288 332 t 532 474 248 253 234 1037 161 174 155 186 173 254 171 122 115 143 145 161 1244 154 1112 294 537 510
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m2 versus positions_6nt_m5; m=3/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.714927; waatAAAAArAAgAAAAAtAtawa ; cor=; Ncor= a 540 654 950 334 1082 1151 988 1163 1139 358 1161 1158 325 1237 1235 1098 1182 1215 292 1110 349 900 634 594 c 202 183 100 81 84 84 82 36 66 110 46 41 61 31 33 38 55 34 77 97 99 120 196 208 g 289 246 125 193 99 56 189 98 76 760 75 59 844 56 54 123 55 72 108 89 122 154 207 269 t 378 326 234 801 144 118 150 112 128 181 127 151 179 85 87 150 117 88 932 113 839 235 372 338
positions_6nt_m1_shift3 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=4/7; ncol2=24; w=0; offset=3; strand=D; shift=3; score=0.707016; ---awAAAwAAAAArAAAAAtAwA ; cor=; Ncor= a 0 0 0 1135 1014 1667 1631 1864 652 1919 1817 1875 1778 1961 668 2039 1934 1929 1900 2057 521 1918 677 1608 c 0 0 0 283 278 178 153 137 113 99 71 104 94 77 108 68 45 75 54 56 87 86 135 167 g 0 0 0 380 347 176 155 137 256 153 103 161 98 121 1088 92 67 132 78 84 169 141 198 164 t 0 0 0 528 687 305 387 188 1305 155 335 186 356 167 462 127 280 190 294 129 1549 181 1316 387
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m2 versus positions_6nt_m4; m=5/7; ncol2=24; w=0; offset=2; strand=D; shift=2; score=0.636447; --wwAAAgAAAAtTgAAAAAtAta ; cor=; Ncor= a 0 0 308 373 664 696 709 215 696 711 681 672 182 172 187 750 719 766 723 743 149 646 193 577 c 0 0 121 107 31 46 44 39 35 48 55 77 48 30 68 38 40 28 21 38 34 64 65 86 g 0 0 187 148 60 54 61 498 54 43 56 38 52 75 497 34 32 47 50 44 105 74 74 96 t 0 0 252 240 113 72 54 116 83 66 76 81 586 591 116 46 77 27 74 43 580 84 536 109
positions_7nt_m2_shift12 (positions_7nt_m2)				; positions_6nt_m2 versus positions_7nt_m2; m=6/7; ncol2=12; w=0; offset=12; strand=D; shift=12; score=0.414088; ------------wwAAAAAATTaw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2739 2445 7484 7224 7025 7185 6976 7618 175 1005 3233 2574 c 0 0 0 0 0 0 0 0 0 0 0 0 1323 1466 74 164 202 180 198 86 138 645 1528 1426 g 0 0 0 0 0 0 0 0 0 0 0 0 1490 1647 107 179 253 205 141 159 100 643 1378 1415 t 0 0 0 0 0 0 0 0 0 0 0 0 2379 2373 266 364 451 361 616 68 7518 5638 1792 2516
positions_7nt_m1_shift10 (positions_7nt_m1)				; positions_6nt_m2 versus positions_7nt_m1; m=7/7; ncol2=13; w=0; offset=10; strand=D; shift=10; score=0.402095; ----------waAAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2030 2163 4938 4951 5020 4964 5046 4921 651 4783 422 1625 1913 0 c 0 0 0 0 0 0 0 0 0 0 797 991 173 111 119 115 113 178 110 206 185 1031 1096 0 g 0 0 0 0 0 0 0 0 0 0 1088 1169 155 167 140 179 94 119 199 158 158 1089 1058 0 t 0 0 0 0 0 0 0 0 0 0 1528 1120 177 214 164 185 190 225 4483 296 4678 1698 1376 0

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; ----wtCTTCgTCww ; Alignment reference a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCTTCgTCww ; cor=; Ncor= a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m5; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.904573; ----wtCTTCATCww ; cor=; Ncor= a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m2; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.782597; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=4/7; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.761648; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m4 versus dyads_m1_rc; m=5/7; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.663988; --tycTCTTCTTCAw ; cor=; Ncor= a 0 0 1917 1805 1296 405 337 531 248 256 652 374 351 5500 2182 c 0 0 1211 2643 3860 345 6870 392 151 7118 356 275 6529 574 1188 g 0 0 1477 1165 715 359 225 294 257 209 297 326 355 510 1482 t 0 0 3181 2173 1915 6677 354 6569 7130 203 6481 6811 551 1202 2934
positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)				; oligos_7nt_mkv5_m4 versus positions_7nt_m3_rc; m=6/7; ncol2=11; w=0; offset=1; strand=R; shift=5; score=0.649407; -----whTTCTTCTw ; cor=; Ncor= a 0 0 0 0 0 2882 2748 788 817 306 425 816 275 297 3724 c 0 0 0 0 0 1860 3369 455 294 10639 324 237 10656 234 1544 g 0 0 0 0 0 2095 1905 547 268 19 541 293 33 873 1683 t 0 0 0 0 0 4127 2942 9174 9585 0 9674 9618 0 9560 4013
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m4 versus dyads_m2_rc; m=7/7; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.568034; ywTTTTCTTCTTCAw ; cor=; Ncor= a 879 1028 460 266 324 107 127 250 146 115 257 204 134 2728 1086 c 1222 746 318 655 177 150 3373 169 88 3365 115 162 3340 212 600 g 525 680 350 231 202 156 93 179 115 152 176 96 157 288 692 t 1303 1475 2801 2777 3226 3516 336 3331 3580 297 3381 3467 298 701 1551

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; ----wtCATCTTCww ; Alignment reference a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----wtCATCTTCww ; cor=; Ncor= a 0 0 0 0 6150 4238 528 13541 1166 912 1467 564 515 6021 4936 c 0 0 0 0 2643 3356 16280 1080 875 16847 654 514 17035 3102 2783 g 0 0 0 0 3556 3172 296 811 967 190 705 617 162 2974 3430 t 0 0 0 0 5817 7400 1062 2734 15158 217 15340 16471 454 6069 7017
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2; m=2/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.90113; ----wtCgTCTTCww ; cor=; Ncor= a 0 0 0 0 4655 3297 652 1651 373 417 749 214 170 4454 3843 c 0 0 0 0 2236 2637 12049 1080 325 12751 335 213 12995 2511 2143 g 0 0 0 0 2858 2330 515 8653 376 251 478 220 368 2478 2518 t 0 0 0 0 4369 5854 902 2734 13044 699 12556 13471 585 4675 5614
oligos_7nt_mkv5_m4_shift4 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=3/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.761648; ----wtCTTCgTCww ; cor=; Ncor= a 0 0 0 0 4477 2950 448 705 200 217 1685 469 366 4459 3699 c 0 0 0 0 2100 2146 12074 282 123 11896 924 312 12307 2304 2035 g 0 0 0 0 2608 2349 308 478 233 712 8183 310 227 2466 2303 t 0 0 0 0 4341 6081 696 12061 12970 701 2734 12435 626 4297 5489
oligos_7nt_mkv5_m5_shift4 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m5; m=4/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.755783; ----wtCTTCATCww ; cor=; Ncor= a 0 0 0 0 5924 3851 549 1467 403 375 12811 1108 703 5863 4676 c 0 0 0 0 2531 2683 15934 569 534 15831 924 894 16021 2717 2658 g 0 0 0 0 3207 3159 380 749 556 195 770 881 125 3192 3301 t 0 0 0 0 5577 7546 376 14454 15746 838 2734 14356 390 5467 6604
positions_7nt_m3_rc_shift5 (positions_7nt_m3_rc)				; oligos_7nt_mkv5_m3 versus positions_7nt_m3_rc; m=5/8; ncol2=11; w=0; offset=1; strand=R; shift=5; score=0.637895; -----whTTCTTCTw ; cor=; Ncor= a 0 0 0 0 0 2882 2748 788 817 306 425 816 275 297 3724 c 0 0 0 0 0 1860 3369 455 294 10639 324 237 10656 234 1544 g 0 0 0 0 0 2095 1905 547 268 19 541 293 33 873 1683 t 0 0 0 0 0 4127 2942 9174 9585 0 9674 9618 0 9560 4013
oligos_6nt_mkv4_m1_shift5 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m1; m=6/8; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.637629; -----wtACCTTCww ; cor=; Ncor= a 0 0 0 0 0 1356 1041 4217 0 0 121 349 10 1289 1317 c 0 0 0 0 0 843 996 0 4217 4196 31 51 4207 718 682 g 0 0 0 0 0 880 549 0 0 21 403 34 0 822 728 t 0 0 0 0 0 1138 1631 0 0 0 3662 3783 0 1388 1490
dyads_m1_rc_shift2 (dyads_m1_rc)				; oligos_7nt_mkv5_m3 versus dyads_m1_rc; m=7/8; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.636713; --tycTCTTCTTCAw ; cor=; Ncor= a 0 0 1917 1805 1296 405 337 531 248 256 652 374 351 5500 2182 c 0 0 1211 2643 3860 345 6870 392 151 7118 356 275 6529 574 1188 g 0 0 1477 1165 715 359 225 294 257 209 297 326 355 510 1482 t 0 0 3181 2173 1915 6677 354 6569 7130 203 6481 6811 551 1202 2934
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv5_m3 versus dyads_m2_rc; m=8/8; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.545972; ywTTTTCTTCTTCAw ; cor=; Ncor= a 879 1028 460 266 324 107 127 250 146 115 257 204 134 2728 1086 c 1222 746 318 655 177 150 3373 169 88 3365 115 162 3340 212 600 g 525 680 350 231 202 156 93 179 115 152 176 96 157 288 692 t 1303 1475 2801 2777 3226 3516 336 3331 3580 297 3381 3467 298 701 1551