One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.180830_2026-01-25.180830_qbHDLg/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/2026/01/25/peak-motifs.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=24; shift=0; ncol=24; gaGgAGGAGrAGGAGraGGAGarg ; Alignment reference a 295 606 121 281 832 180 129 1025 66 639 855 170 145 1056 64 706 824 145 135 992 67 709 477 282 c 225 201 164 119 113 116 89 75 81 128 89 95 75 48 87 128 92 102 113 70 96 143 204 251 g 572 206 846 757 171 845 961 59 1034 398 185 911 961 53 1031 349 207 930 932 70 1007 296 335 535 t 131 210 92 66 107 82 44 64 42 58 94 47 42 66 41 40 100 46 43 91 53 75 207 155

dyads_m6_shift0 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/2; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; gaGgAGGAGrAGGAGraGGAGarg ; cor=; Ncor= a 295 606 121 281 832 180 129 1025 66 639 855 170 145 1056 64 706 824 145 135 992 67 709 477 282 c 225 201 164 119 113 116 89 75 81 128 89 95 75 48 87 128 92 102 113 70 96 143 204 251 g 572 206 846 757 171 845 961 59 1034 398 185 911 961 53 1031 349 207 930 932 70 1007 296 335 535 t 131 210 92 66 107 82 44 64 42 58 94 47 42 66 41 40 100 46 43 91 53 75 207 155

dyads_m2_rc_shift4 (dyads_m2_rc)
; dyads_m6 versus dyads_m2_rc; m=2/2; ncol2=20; w=0; offset=4; strand=R; shift=4; score=0.626234; ----rrGAGGrrgagrrrGAGGar ; cor=; Ncor= a 0 0 0 0 1585 1389 169 4429 173 668 1888 1371 1009 2173 884 1363 1656 1434 210 4444 177 586 1796 1278 c 0 0 0 0 975 1100 165 156 171 222 1017 1053 881 846 1148 886 926 1166 182 168 160 264 1070 1095 g 0 0 0 0 1309 1678 4543 97 4383 3770 1269 1716 2366 866 2137 2034 1370 1613 4473 94 4399 3863 1198 1791 t 0 0 0 0 1068 770 60 255 210 277 763 797 681 1052 768 654 985 724 72 231 201 224 873 773

One-to-n matrix alignment; reference matrix: positions_6-8nt_m9_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m9_shift0 (positions_6-8nt_m9)
; positions_6-8nt_m9; m=0 (reference); ncol1=16; shift=0; ncol=16; cacayACACACAcaca ; Alignment reference a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 6009 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 1837 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 2611 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485 1808

positions_6-8nt_m9_shift0 (positions_6-8nt_m9)
; positions_6-8nt_m9 versus positions_6-8nt_m9; m=1/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cacayACACACAcaca ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 6009 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 1837 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 2611 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485 1808

positions_6-8nt_m1_shift2 (positions_6-8nt_m1)
; positions_6-8nt_m9 versus positions_6-8nt_m1; m=2/6; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.796752; --cacACACACACac- ; cor=; Ncor= a 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 0 c 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 0 g 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 0 t 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658 0

dyads_m5_shift0 (dyads_m5)
; positions_6-8nt_m9 versus dyads_m5; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.635106; caCACACACACAcACA ; cor=; Ncor= a 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 2640 122 2660 c 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 111 2736 61 g 350 612 146 295 93 255 94 174 86 169 103 193 148 255 78 291 t 464 374 262 227 187 168 152 158 167 126 163 122 299 112 182 106

oligos_6-8nt_m9_shift3 (oligos_6-8nt_m9)
; positions_6-8nt_m9 versus oligos_6-8nt_m9; m=4/6; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.568799; ---acACGCACAGmc- ; cor=; Ncor= a 0 0 0 1384 821 3178 101 379 143 3350 100 3337 166 1253 879 0 c 0 0 0 784 1438 137 3303 106 3263 126 3388 84 673 959 1029 0 g 0 0 0 896 710 176 106 3060 102 98 106 72 2546 702 863 0 t 0 0 0 576 671 149 130 95 132 66 46 147 255 726 869 0

dyads_m9_shift0 (dyads_m9)
; positions_6-8nt_m9 versus dyads_m9; m=5/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.531503; mmCACAcAmACAaCAA ; cor=; Ncor= a 171 230 98 478 46 485 130 410 148 501 39 494 377 112 403 443 c 219 159 401 31 479 34 373 104 360 24 487 33 115 392 94 45 g 89 110 26 37 19 26 37 32 30 30 20 23 50 35 19 58 t 85 65 39 18 20 19 24 18 26 9 18 14 22 25 48 18

oligos_6-8nt_m5_shift3 (oligos_6-8nt_m5)
; positions_6-8nt_m9 versus oligos_6-8nt_m5; m=6/6; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.438942; ---ryACTCAChc--- ; cor=; Ncor= a 0 0 0 697 469 2269 0 10 104 2121 0 680 544 0 0 0 c 0 0 0 513 822 12 2285 25 2062 75 2253 605 793 0 0 0 g 0 0 0 595 268 0 4 2 5 9 7 347 405 0 0 0 t 0 0 0 484 730 8 0 2252 118 84 29 657 547 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; oligos_6-8nt_m2; m=0 (reference); ncol1=10; shift=1; ncol=11; -taTAyATAya ; Alignment reference a 0 1169 2442 22 5307 41 4480 0 5276 775 2347 c 0 1153 833 22 28 3410 284 22 34 1429 799 g 0 898 1329 19 0 312 363 142 8 751 1024 t 0 2115 731 5272 0 1572 208 5171 17 2380 1165

oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -taTAyATAya ; cor=; Ncor= a 0 1169 2442 22 5307 41 4480 0 5276 775 2347 c 0 1153 833 22 28 3410 284 22 34 1429 799 g 0 898 1329 19 0 312 363 142 8 751 1024 t 0 2115 731 5272 0 1572 208 5171 17 2380 1165

positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; oligos_6-8nt_m2 versus positions_6-8nt_m6; m=2/6; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.73231; -yaTACATAyA ; cor=; Ncor= a 0 1372 2593 207 5369 349 4978 138 5350 577 4374 c 0 1476 804 383 132 4165 159 427 148 3341 308 g 0 811 1299 134 140 280 357 146 112 367 580 t 0 2077 1040 5012 95 942 242 5025 126 1451 474

positions_6-8nt_m4_shift1 (positions_6-8nt_m4)
; oligos_6-8nt_m2 versus positions_6-8nt_m4; m=3/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.647762; -yaTACATATG ; cor=; Ncor= a 0 996 1897 264 3886 456 3858 281 3905 190 822 c 0 1142 659 321 142 3081 98 195 129 368 155 g 0 646 1040 159 304 155 368 129 195 98 3081 t 0 1730 918 3770 182 822 190 3909 285 3858 456

oligos_6-8nt_m3_shift2 (oligos_6-8nt_m3)
; oligos_6-8nt_m2 versus oligos_6-8nt_m3; m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.621195; --atAGATACw ; cor=; Ncor= a 0 0 1239 519 3086 11 2979 0 3234 30 1203 c 0 0 563 739 96 127 61 1 19 2879 573 g 0 0 810 569 62 2371 119 42 0 96 585 t 0 0 647 1432 15 750 100 3216 6 254 898

positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; oligos_6-8nt_m2 versus positions_6-8nt_m3; m=5/6; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.582425; wtgTATATATA ; cor=; Ncor= a 1359 785 624 244 3013 239 3015 190 2964 243 2934 c 552 611 180 237 81 244 108 233 99 209 131 g 719 561 2409 131 209 99 233 108 244 81 237 t 916 1589 333 2934 243 2964 190 3015 239 3013 244

positions_6-8nt_m7_shift1 (positions_6-8nt_m7)
; oligos_6-8nt_m2 versus positions_6-8nt_m7; m=6/6; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.578017; -yaTAcATATg ; cor=; Ncor= a 0 643 1432 162 2736 239 2611 135 2787 98 774 c 0 809 406 220 97 2046 86 143 70 330 114 g 0 410 737 109 162 100 288 105 103 77 1975 t 0 1240 527 2611 107 717 117 2719 142 2597 239

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m3_shift4 (oligos_6-8nt_m3)
; oligos_6-8nt_m3; m=0 (reference); ncol1=10; shift=4; ncol=14; ----atAGATACww ; Alignment reference a 0 0 0 0 1239 519 3086 11 2979 0 3234 30 1203 884 c 0 0 0 0 563 739 96 127 61 1 19 2879 573 801 g 0 0 0 0 810 569 62 2371 119 42 0 96 585 661 t 0 0 0 0 647 1432 15 750 100 3216 6 254 898 913

oligos_6-8nt_m3_shift4 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----atAGATACww ; cor=; Ncor= a 0 0 0 0 1239 519 3086 11 2979 0 3234 30 1203 884 c 0 0 0 0 563 739 96 127 61 1 19 2879 573 801 g 0 0 0 0 810 569 62 2371 119 42 0 96 585 661 t 0 0 0 0 647 1432 15 750 100 3216 6 254 898 913

oligos_6-8nt_m2_shift3 (oligos_6-8nt_m2)
; oligos_6-8nt_m3 versus oligos_6-8nt_m2; m=2/4; ncol2=10; w=-1; offset=-1; strand=D; shift=3; score=0.621195; ---taTAyATAya- ; cor=; Ncor= a 0 0 0 1169 2442 22 5307 41 4480 0 5276 775 2347 0 c 0 0 0 1153 833 22 28 3410 284 22 34 1429 799 0 g 0 0 0 898 1329 19 0 312 363 142 8 751 1024 0 t 0 0 0 2115 731 5272 0 1572 208 5171 17 2380 1165 0

positions_6-8nt_m6_shift3 (positions_6-8nt_m6)
; oligos_6-8nt_m3 versus positions_6-8nt_m6; m=3/4; ncol2=13; w=-1; offset=-1; strand=D; shift=3; score=0.583758; ---yaTACATAyAT ; cor=; Ncor= a 0 0 0 1372 2593 207 5369 349 4978 138 5350 577 4374 413 c 0 0 0 1476 804 383 132 4165 159 427 148 3341 308 699 g 0 0 0 811 1299 134 140 280 357 146 112 367 580 360 t 0 0 0 2077 1040 5012 95 942 242 5025 126 1451 474 4264

positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; oligos_6-8nt_m3 versus positions_6-8nt_m3; m=4/4; ncol2=14; w=-4; offset=-4; strand=D; shift=0; score=0.562369; wtgTATATATAcaw ; cor=; Ncor= a 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 c 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 g 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 t 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m9_shift3 (oligos_6-8nt_m9)
; oligos_6-8nt_m9; m=0 (reference); ncol1=12; shift=3; ncol=15; ---acACGCACAGmc ; Alignment reference a 0 0 0 1384 821 3178 101 379 143 3350 100 3337 166 1253 879 c 0 0 0 784 1438 137 3303 106 3263 126 3388 84 673 959 1029 g 0 0 0 896 710 176 106 3060 102 98 106 72 2546 702 863 t 0 0 0 576 671 149 130 95 132 66 46 147 255 726 869

oligos_6-8nt_m9_shift3 (oligos_6-8nt_m9)
; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---acACGCACAGmc ; cor=; Ncor= a 0 0 0 1384 821 3178 101 379 143 3350 100 3337 166 1253 879 c 0 0 0 784 1438 137 3303 106 3263 126 3388 84 673 959 1029 g 0 0 0 896 710 176 106 3060 102 98 106 72 2546 702 863 t 0 0 0 576 671 149 130 95 132 66 46 147 255 726 869

positions_6-8nt_m1_shift2 (positions_6-8nt_m1)
; oligos_6-8nt_m9 versus positions_6-8nt_m1; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=2; score=0.683406; --cacACACACACac ; cor=; Ncor= a 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 c 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 g 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 t 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658

positions_6-8nt_m9_shift0 (positions_6-8nt_m9)
; oligos_6-8nt_m9 versus positions_6-8nt_m9; m=3/3; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.568799; cacayACACACAcac ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485

One-to-n matrix alignment; reference matrix: positions_6-8nt_m7_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m7_shift0 (positions_6-8nt_m7)
; positions_6-8nt_m7; m=0 (reference); ncol1=16; shift=0; ncol=16; yaTAcATATgTAyata ; Alignment reference a 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 1964 617 1409 c 809 406 220 97 2046 86 143 70 330 114 189 96 1269 245 540 449 g 410 737 109 162 100 288 105 103 77 1975 86 196 316 552 371 563 t 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060 341 1574 681

positions_6-8nt_m7_shift0 (positions_6-8nt_m7)
; positions_6-8nt_m7 versus positions_6-8nt_m7; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; yaTAcATATgTAyata ; cor=; Ncor= a 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 1964 617 1409 c 809 406 220 97 2046 86 143 70 330 114 189 96 1269 245 540 449 g 410 737 109 162 100 288 105 103 77 1975 86 196 316 552 371 563 t 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060 341 1574 681

positions_6-8nt_m4_shift0 (positions_6-8nt_m4)
; positions_6-8nt_m7 versus positions_6-8nt_m4; m=2/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.86183; yaTACATATGTAtr-- ; cor=; Ncor= a 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 1731 0 0 c 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 645 0 0 g 646 1040 159 304 155 368 129 195 98 3081 142 321 659 1142 0 0 t 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896 996 0 0

positions_6-8nt_m6_shift0 (positions_6-8nt_m6)
; positions_6-8nt_m7 versus positions_6-8nt_m6; m=3/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.688951; yaTACATAyATay--- ; cor=; Ncor= a 1372 2593 207 5369 349 4978 138 5350 577 4374 413 2946 1162 0 0 0 c 1476 804 383 132 4165 159 427 148 3341 308 699 767 1560 0 0 0 g 811 1299 134 140 280 357 146 112 367 580 360 894 829 0 0 0 t 2077 1040 5012 95 942 242 5025 126 1451 474 4264 1129 2185 0 0 0

positions_6-8nt_m3_shift1 (positions_6-8nt_m3)
; positions_6-8nt_m7 versus positions_6-8nt_m3; m=4/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.624273; -wtgTATATATAcaw- ; cor=; Ncor= a 0 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 0 c 0 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 0 g 0 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 0 t 0 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359 0

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; positions_6-8nt_m7 versus oligos_6-8nt_m2; m=5/5; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.578017; taTAyATAya------ ; cor=; Ncor= a 1169 2442 22 5307 41 4480 0 5276 775 2347 0 0 0 0 0 0 c 1153 833 22 28 3410 284 22 34 1429 799 0 0 0 0 0 0 g 898 1329 19 0 312 363 142 8 751 1024 0 0 0 0 0 0 t 2115 731 5272 0 1572 208 5171 17 2380 1165 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m1_shift2 (positions_6-8nt_m1)
; positions_6-8nt_m1; m=0 (reference); ncol1=13; shift=2; ncol=15; --cacACACACACac ; Alignment reference a 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 c 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 g 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 t 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658

positions_6-8nt_m1_shift2 (positions_6-8nt_m1)
; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --cacACACACACac ; cor=; Ncor= a 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 c 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 g 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 t 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658

positions_6-8nt_m9_shift0 (positions_6-8nt_m9)
; positions_6-8nt_m1 versus positions_6-8nt_m9; m=2/5; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.796752; cacayACACACAcac ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485

oligos_6-8nt_m9_shift3 (oligos_6-8nt_m9)
; positions_6-8nt_m1 versus oligos_6-8nt_m9; m=3/5; ncol2=12; w=0; offset=1; strand=D; shift=3; score=0.683406; ---acACGCACAGmc ; cor=; Ncor= a 0 0 0 1384 821 3178 101 379 143 3350 100 3337 166 1253 879 c 0 0 0 784 1438 137 3303 106 3263 126 3388 84 673 959 1029 g 0 0 0 896 710 176 106 3060 102 98 106 72 2546 702 863 t 0 0 0 576 671 149 130 95 132 66 46 147 255 726 869

dyads_m5_shift2 (dyads_m5)
; positions_6-8nt_m1 versus dyads_m5; m=4/5; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.530786; --caCACACACACAc ; cor=; Ncor= a 0 0 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 c 0 0 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 g 0 0 350 612 146 295 93 255 94 174 86 169 103 193 148 t 0 0 464 374 262 227 187 168 152 158 167 126 163 122 299

dyads_m9_shift2 (dyads_m9)
; positions_6-8nt_m1 versus dyads_m9; m=5/5; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.491871; --mmCACAcAmACAa ; cor=; Ncor= a 0 0 171 230 98 478 46 485 130 410 148 501 39 494 377 c 0 0 219 159 401 31 479 34 373 104 360 24 487 33 115 g 0 0 89 110 26 37 19 26 37 32 30 30 20 23 50 t 0 0 85 65 39 18 20 19 24 18 26 9 18 14 22

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wdCTTATCAwy ; Alignment reference a 1552 1425 321 244 254 5019 231 242 4563 1456 1274 c 1306 1269 4583 131 284 251 257 4875 246 1352 1572 g 1029 1415 306 131 254 156 186 137 436 1275 955 t 1668 1446 345 5049 4763 129 4881 301 310 1472 1754

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wdCTTATCAwy ; cor=; Ncor= a 1552 1425 321 244 254 5019 231 242 4563 1456 1274 c 1306 1269 4583 131 284 251 257 4875 246 1352 1572 g 1029 1415 306 131 254 156 186 137 436 1275 955 t 1668 1446 345 5049 4763 129 4881 301 310 1472 1754

oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m1 versus oligos_6-8nt_m10; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.639081; twCTTGTCsw- ; cor=; Ncor= a 376 467 0 0 133 41 6 23 281 493 0 c 402 384 1629 12 38 1 0 1606 534 349 0 g 299 355 0 3 14 1587 0 0 452 324 0 t 552 423 0 1614 1444 0 1623 0 362 463 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; tvGACACCwa ; Alignment reference a 360 467 8 1456 0 1408 4 1 380 502 c 315 407 6 3 1301 26 1484 1449 300 327 g 315 430 1347 3 29 1 0 3 342 301 t 498 184 127 26 158 53 0 35 466 358

oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m6 versus oligos_6-8nt_m6; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; tvGACACCwa ; cor=; Ncor= a 360 467 8 1456 0 1408 4 1 380 502 c 315 407 6 3 1301 26 1484 1449 300 327 g 315 430 1347 3 29 1 0 3 342 301 t 498 184 127 26 158 53 0 35 466 358

dyads_m8_shift0 (dyads_m8)
; oligos_6-8nt_m6 versus dyads_m8; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.762343; ykGCCACCrm ; cor=; Ncor= a 536 670 67 33 0 2893 0 0 886 857 c 837 665 49 2834 2835 0 2896 2885 527 828 g 619 804 2757 3 1 0 0 1 782 661 t 904 757 23 26 60 3 0 10 701 550

One-to-n matrix alignment; reference matrix: dyads_m9_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift4 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=24; shift=4; ncol=28; ----mmCACAcAmACAaCAACAACAmmm ; Alignment reference a 0 0 0 0 171 230 98 478 46 485 130 410 148 501 39 494 377 112 403 443 61 446 424 65 447 187 175 243 c 0 0 0 0 219 159 401 31 479 34 373 104 360 24 487 33 115 392 94 45 446 60 67 425 42 281 225 156 g 0 0 0 0 89 110 26 37 19 26 37 32 30 30 20 23 50 35 19 58 31 33 51 36 40 59 79 95 t 0 0 0 0 85 65 39 18 20 19 24 18 26 9 18 14 22 25 48 18 26 25 22 38 35 37 85 70

dyads_m9_shift4 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----mmCACAcAmACAaCAACAACAmmm ; cor=; Ncor= a 0 0 0 0 171 230 98 478 46 485 130 410 148 501 39 494 377 112 403 443 61 446 424 65 447 187 175 243 c 0 0 0 0 219 159 401 31 479 34 373 104 360 24 487 33 115 392 94 45 446 60 67 425 42 281 225 156 g 0 0 0 0 89 110 26 37 19 26 37 32 30 30 20 23 50 35 19 58 31 33 51 36 40 59 79 95 t 0 0 0 0 85 65 39 18 20 19 24 18 26 9 18 14 22 25 48 18 26 25 22 38 35 37 85 70

positions_6-8nt_m9_shift4 (positions_6-8nt_m9)
; dyads_m9 versus positions_6-8nt_m9; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.531503; ----cacayACACACAcaca-------- ; cor=; Ncor= a 0 0 0 0 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 6009 0 0 0 0 0 0 0 0 c 0 0 0 0 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 1837 0 0 0 0 0 0 0 0 g 0 0 0 0 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 2611 0 0 0 0 0 0 0 0 t 0 0 0 0 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485 1808 0 0 0 0 0 0 0 0

dyads_m5_shift0 (dyads_m5)
; dyads_m9 versus dyads_m5; m=3/4; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.528148; caCACACACACAcACACAcACAca---- ; cor=; Ncor= a 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 2640 122 2660 159 2544 693 2368 235 2237 450 1624 0 0 0 0 c 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 111 2736 61 2639 150 1871 158 2429 208 1754 429 0 0 0 0 g 350 612 146 295 93 255 94 174 86 169 103 193 148 255 78 291 139 271 220 407 186 413 450 665 0 0 0 0 t 464 374 262 227 187 168 152 158 167 126 163 122 299 112 182 106 181 153 334 185 268 260 464 400 0 0 0 0

positions_6-8nt_m1_shift4 (positions_6-8nt_m1)
; dyads_m9 versus positions_6-8nt_m1; m=4/4; ncol2=13; w=0; offset=0; strand=D; shift=4; score=0.491871; ----cacACACACACac----------- ; cor=; Ncor= a 0 0 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m2_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)
; positions_6-8nt_m2; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwaAAATAAAAcAtww ; Alignment reference a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445

positions_6-8nt_m2_shift2 (positions_6-8nt_m2)
; positions_6-8nt_m2 versus positions_6-8nt_m2; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=2; score= 1; --wwaAAATAAAAcAtww ; cor=; Ncor= a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445

positions_6-8nt_m8_shift2 (positions_6-8nt_m8)
; positions_6-8nt_m2 versus positions_6-8nt_m8; m=2/7; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.977127; --wwwAAATAAAAcAtww ; cor=; Ncor= a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397

positions_6-8nt_m10_shift2 (positions_6-8nt_m10)
; positions_6-8nt_m2 versus positions_6-8nt_m10; m=3/7; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.89587; --waaAAATAAAAcmaa- ; cor=; Ncor= a 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 0 c 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 0 g 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 0 t 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319 0

positions_6-8nt_m5_shift2 (positions_6-8nt_m5)
; positions_6-8nt_m2 versus positions_6-8nt_m5; m=4/7; ncol2=18; w=0; offset=0; strand=D; shift=2; score=0.826184; --waaAAATAAAAmAAAa ; cor=; Ncor= a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287

dyads_m3_shift1 (dyads_m3)
; positions_6-8nt_m2 versus dyads_m3; m=5/7; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.732167; -wwgAAAATAAAATwa-- ; cor=; Ncor= a 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 0 0 c 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 0 0 g 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 0 0 t 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934 0 0

dyads_m4_shift0 (dyads_m4)
; positions_6-8nt_m2 versus dyads_m4; m=6/7; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.52713; wwtATAAATAAAAATAAA ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206

oligos_6-8nt_m7_shift4 (oligos_6-8nt_m7)
; positions_6-8nt_m2 versus oligos_6-8nt_m7; m=7/7; ncol2=10; w=0; offset=2; strand=D; shift=4; score=0.438558; ----waAATGAAaw---- ; cor=; Ncor= a 0 0 0 0 747 1105 2596 2596 0 0 2579 2596 1120 908 0 0 0 0 c 0 0 0 0 538 506 0 0 0 0 0 0 401 416 0 0 0 0 g 0 0 0 0 598 535 0 0 0 2596 0 0 437 491 0 0 0 0 t 0 0 0 0 713 450 0 0 2596 0 17 0 638 781 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 7 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; wwtATAAATAAAAATAAAAtww ; Alignment reference a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 577 569 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 220 259 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 232 221 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887 448 428

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; wwtATAAATAAAAATAAAAtww ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 577 569 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 220 259 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 232 221 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887 448 428

positions_6-8nt_m5_shift2 (positions_6-8nt_m5)
; dyads_m4 versus positions_6-8nt_m5; m=2/6; ncol2=18; w=0; offset=2; strand=D; shift=2; score=0.632294; --waaAAATAAAAmAAAawa-- ; cor=; Ncor= a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 2199 2034 0 0 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 895 1062 0 0 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 869 938 0 0 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287 1335 1264 0 0

dyads_m3_shift7 (dyads_m3)
; dyads_m4 versus dyads_m3; m=3/6; ncol2=15; w=0; offset=7; strand=D; shift=7; score=0.570362; -------wwgAAAATAAAATwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 c 0 0 0 0 0 0 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 g 0 0 0 0 0 0 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 t 0 0 0 0 0 0 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934

positions_6-8nt_m8_shift2 (positions_6-8nt_m8)
; dyads_m4 versus positions_6-8nt_m8; m=4/6; ncol2=16; w=0; offset=2; strand=D; shift=2; score=0.548859; --wwwAAATAAAAcAtww---- ; cor=; Ncor= a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 0 0 0 0 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 0 0 0 0 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 0 0 0 0 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397 0 0 0 0

positions_6-8nt_m10_shift8 (positions_6-8nt_m10)
; dyads_m4 versus positions_6-8nt_m10; m=5/6; ncol2=15; w=0; offset=8; strand=D; shift=8; score=0.527705; --------waaAAATAAAAcma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 c 0 0 0 0 0 0 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 g 0 0 0 0 0 0 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 t 0 0 0 0 0 0 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276

positions_6-8nt_m2_shift2 (positions_6-8nt_m2)
; dyads_m4 versus positions_6-8nt_m2; m=6/6; ncol2=16; w=0; offset=2; strand=D; shift=2; score=0.52713; --wwaAAATAAAAcAtww---- ; cor=; Ncor= a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 0 0 0 0 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 0 0 0 0 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 0 0 0 0 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; ytCCTCyyyctcyyCCTCyy ; Alignment reference a 773 873 224 201 231 72 724 985 654 768 1052 681 797 763 277 210 255 60 770 1068 c 1791 1198 3863 4399 94 4473 1613 1370 2034 2137 866 2366 1716 1269 3770 4383 97 4543 1678 1309 g 1095 1070 264 160 168 182 1166 926 886 1148 846 881 1053 1017 222 171 156 165 1100 975 t 1278 1796 586 177 4444 210 1434 1656 1363 884 2173 1009 1371 1888 668 173 4429 169 1389 1585

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/2; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; ytCCTCyyyctcyyCCTCyy ; cor=; Ncor= a 773 873 224 201 231 72 724 985 654 768 1052 681 797 763 277 210 255 60 770 1068 c 1791 1198 3863 4399 94 4473 1613 1370 2034 2137 866 2366 1716 1269 3770 4383 97 4543 1678 1309 g 1095 1070 264 160 168 182 1166 926 886 1148 846 881 1053 1017 222 171 156 165 1100 975 t 1278 1796 586 177 4444 210 1434 1656 1363 884 2173 1009 1371 1888 668 173 4429 169 1389 1585

dyads_m6_rc_shift0 (dyads_m6_rc)
; dyads_m2 versus dyads_m6_rc; m=2/2; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.626234; cytCTCCtyCTCCTyCTCCT ; cor=; Ncor= a 155 207 75 53 91 43 46 100 40 41 66 42 47 94 58 42 64 44 82 107 c 535 335 296 1007 70 932 930 207 349 1031 53 961 911 185 398 1034 59 961 845 171 g 251 204 143 96 70 113 102 92 128 87 48 75 95 89 128 81 75 89 116 113 t 282 477 709 67 992 135 145 824 706 64 1056 145 170 855 639 66 1025 129 180 832

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8; m=0 (reference); ncol1=11; shift=0; ncol=11; arTAGGAAGwr ; Alignment reference a 1613 1509 422 4272 283 274 4456 4610 261 1534 1315 c 1026 1014 477 210 173 174 206 74 142 1092 1105 g 1163 1321 558 234 4248 4331 130 124 4291 972 1399 t 1120 1078 3465 206 218 143 130 114 228 1324 1103

oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8 versus oligos_6-8nt_m8; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; arTAGGAAGwr ; cor=; Ncor= a 1613 1509 422 4272 283 274 4456 4610 261 1534 1315 c 1026 1014 477 210 173 174 206 74 142 1092 1105 g 1163 1321 558 234 4248 4331 130 124 4291 972 1399 t 1120 1078 3465 206 218 143 130 114 228 1324 1103

One-to-n matrix alignment; reference matrix: positions_6-8nt_m3_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m3_shift1 (positions_6-8nt_m3)
; positions_6-8nt_m3; m=0 (reference); ncol1=14; shift=1; ncol=15; -wtgTATATATAcaw ; Alignment reference a 0 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 c 0 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 g 0 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 t 0 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359

positions_6-8nt_m3_shift1 (positions_6-8nt_m3)
; positions_6-8nt_m3 versus positions_6-8nt_m3; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wtgTATATATAcaw ; cor=; Ncor= a 0 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 c 0 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 g 0 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 t 0 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359

positions_6-8nt_m6_rc_shift1 (positions_6-8nt_m6_rc)
; positions_6-8nt_m3 versus positions_6-8nt_m6_rc; m=2/5; ncol2=13; w=0; offset=0; strand=R; shift=1; score=0.655709; -rtATrTATGTAtr- ; cor=; Ncor= a 0 2185 1129 4264 474 1451 126 5025 242 942 95 5012 1040 2077 0 c 0 829 894 360 580 367 112 146 357 280 140 134 1299 811 0 g 0 1560 767 699 308 3341 148 427 159 4165 132 383 804 1476 0 t 0 1162 2946 413 4374 577 5350 138 4978 349 5369 207 2593 1372 0

positions_6-8nt_m7_shift0 (positions_6-8nt_m7)
; positions_6-8nt_m3 versus positions_6-8nt_m7; m=3/5; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.624273; yaTAcATATgTAyat ; cor=; Ncor= a 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 1964 617 c 809 406 220 97 2046 86 143 70 330 114 189 96 1269 245 540 g 410 737 109 162 100 288 105 103 77 1975 86 196 316 552 371 t 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060 341 1574

oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; positions_6-8nt_m3 versus oligos_6-8nt_m2; m=4/5; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.582425; --taTAyATAya--- ; cor=; Ncor= a 0 0 1169 2442 22 5307 41 4480 0 5276 775 2347 0 0 0 c 0 0 1153 833 22 28 3410 284 22 34 1429 799 0 0 0 g 0 0 898 1329 19 0 312 363 142 8 751 1024 0 0 0 t 0 0 2115 731 5272 0 1572 208 5171 17 2380 1165 0 0 0

oligos_6-8nt_m3_rc_shift1 (oligos_6-8nt_m3_rc)
; positions_6-8nt_m3 versus oligos_6-8nt_m3_rc; m=5/5; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.562369; -wwGTATCTat---- ; cor=; Ncor= a 0 913 898 254 6 3216 100 750 15 1432 647 0 0 0 0 c 0 661 585 96 0 42 119 2371 62 569 810 0 0 0 0 g 0 801 573 2879 19 1 61 127 96 739 563 0 0 0 0 t 0 884 1203 30 3234 0 2979 11 3086 519 1239 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m10_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m10; m=0 (reference); ncol1=10; shift=0; ncol=10; twCTTGTCsw ; Alignment reference a 376 467 0 0 133 41 6 23 281 493 c 402 384 1629 12 38 1 0 1606 534 349 g 299 355 0 3 14 1587 0 0 452 324 t 552 423 0 1614 1444 0 1623 0 362 463

oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m10 versus oligos_6-8nt_m10; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; twCTTGTCsw ; cor=; Ncor= a 376 467 0 0 133 41 6 23 281 493 c 402 384 1629 12 38 1 0 1606 534 349 g 299 355 0 3 14 1587 0 0 452 324 t 552 423 0 1614 1444 0 1623 0 362 463

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m10 versus oligos_6-8nt_m1; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.639081; wdCTTATCAw ; cor=; Ncor= a 1552 1425 321 244 254 5019 231 242 4563 1456 c 1306 1269 4583 131 284 251 257 4875 246 1352 g 1029 1415 306 131 254 156 186 137 436 1275 t 1668 1446 345 5049 4763 129 4881 301 310 1472

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; gcrGCAGCAGCAGca ; Alignment reference a 923 698 1357 282 171 3630 224 152 3547 278 159 3620 434 693 1924 c 782 1989 341 318 3794 117 111 3783 140 132 3806 132 153 2260 625 g 1802 836 2122 3445 172 261 3762 160 288 3718 157 206 3468 663 874 t 703 687 390 165 73 202 113 115 235 82 88 252 155 594 787

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/1; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gcrGCAGCAGCAGca ; cor=; Ncor= a 923 698 1357 282 171 3630 224 152 3547 278 159 3620 434 693 1924 c 782 1989 341 318 3794 117 111 3783 140 132 3806 132 153 2260 625 g 1802 836 2122 3445 172 261 3762 160 288 3718 157 206 3468 663 874 t 703 687 390 165 73 202 113 115 235 82 88 252 155 594 787

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4)
; oligos_6-8nt_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ymGCTGTTCbt ; Alignment reference a 1035 1494 312 212 190 184 320 271 212 1064 1187 c 1605 1286 397 4586 159 251 228 342 4828 1391 1230 g 1188 1067 3947 237 180 4672 351 37 33 1368 1230 t 1288 1269 460 81 4587 9 4217 4466 43 1293 1469

oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4)
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ymGCTGTTCbt ; cor=; Ncor= a 1035 1494 312 212 190 184 320 271 212 1064 1187 c 1605 1286 397 4586 159 251 228 342 4828 1391 1230 g 1188 1067 3947 237 180 4672 351 37 33 1368 1230 t 1288 1269 460 81 4587 9 4217 4466 43 1293 1469

One-to-n matrix alignment; reference matrix: positions_6-8nt_m6_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; positions_6-8nt_m6; m=0 (reference); ncol1=13; shift=1; ncol=14; -yaTACATAyATay ; Alignment reference a 0 1372 2593 207 5369 349 4978 138 5350 577 4374 413 2946 1162 c 0 1476 804 383 132 4165 159 427 148 3341 308 699 767 1560 g 0 811 1299 134 140 280 357 146 112 367 580 360 894 829 t 0 2077 1040 5012 95 942 242 5025 126 1451 474 4264 1129 2185

positions_6-8nt_m6_shift1 (positions_6-8nt_m6)
; positions_6-8nt_m6 versus positions_6-8nt_m6; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -yaTACATAyATay ; cor=; Ncor= a 0 1372 2593 207 5369 349 4978 138 5350 577 4374 413 2946 1162 c 0 1476 804 383 132 4165 159 427 148 3341 308 699 767 1560 g 0 811 1299 134 140 280 357 146 112 367 580 360 894 829 t 0 2077 1040 5012 95 942 242 5025 126 1451 474 4264 1129 2185

positions_6-8nt_m4_shift1 (positions_6-8nt_m4)
; positions_6-8nt_m6 versus positions_6-8nt_m4; m=2/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.771151; -yaTACATATGTAt ; cor=; Ncor= a 0 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 c 0 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 g 0 646 1040 159 304 155 368 129 195 98 3081 142 321 659 t 0 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896

oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; positions_6-8nt_m6 versus oligos_6-8nt_m2; m=3/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.73231; -taTAyATAya--- ; cor=; Ncor= a 0 1169 2442 22 5307 41 4480 0 5276 775 2347 0 0 0 c 0 1153 833 22 28 3410 284 22 34 1429 799 0 0 0 g 0 898 1329 19 0 312 363 142 8 751 1024 0 0 0 t 0 2115 731 5272 0 1572 208 5171 17 2380 1165 0 0 0

positions_6-8nt_m7_shift1 (positions_6-8nt_m7)
; positions_6-8nt_m6 versus positions_6-8nt_m7; m=4/6; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.688951; -yaTAcATATgTAy ; cor=; Ncor= a 0 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 c 0 809 406 220 97 2046 86 143 70 330 114 189 96 1269 g 0 410 737 109 162 100 288 105 103 77 1975 86 196 316 t 0 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060

positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; positions_6-8nt_m6 versus positions_6-8nt_m3; m=5/6; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.655709; wtgTATATATAcaw ; cor=; Ncor= a 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 c 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 g 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 t 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359

oligos_6-8nt_m3_shift2 (oligos_6-8nt_m3)
; positions_6-8nt_m6 versus oligos_6-8nt_m3; m=6/6; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.583758; --atAGATACww-- ; cor=; Ncor= a 0 0 1239 519 3086 11 2979 0 3234 30 1203 884 0 0 c 0 0 563 739 96 127 61 1 19 2879 573 801 0 0 g 0 0 810 569 62 2371 119 42 0 96 585 661 0 0 t 0 0 647 1432 15 750 100 3216 6 254 898 913 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m5_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m5_shift2 (positions_6-8nt_m5)
; positions_6-8nt_m5; m=0 (reference); ncol1=18; shift=2; ncol=20; --waaAAATAAAAmAAAawa ; Alignment reference a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 2199 2034 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 895 1062 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 869 938 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287 1335 1264

positions_6-8nt_m5_shift2 (positions_6-8nt_m5)
; positions_6-8nt_m5 versus positions_6-8nt_m5; m=1/6; ncol2=18; w=0; offset=0; strand=D; shift=2; score= 1; --waaAAATAAAAmAAAawa ; cor=; Ncor= a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 2199 2034 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 895 1062 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 869 938 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287 1335 1264

positions_6-8nt_m2_shift2 (positions_6-8nt_m2)
; positions_6-8nt_m5 versus positions_6-8nt_m2; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.826184; --wwaAAATAAAAcAtww-- ; cor=; Ncor= a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 0 0 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 0 0 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 0 0 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445 0 0

positions_6-8nt_m8_shift2 (positions_6-8nt_m8)
; positions_6-8nt_m5 versus positions_6-8nt_m8; m=3/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.797811; --wwwAAATAAAAcAtww-- ; cor=; Ncor= a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 0 0 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 0 0 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 0 0 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397 0 0

positions_6-8nt_m10_shift2 (positions_6-8nt_m10)
; positions_6-8nt_m5 versus positions_6-8nt_m10; m=4/6; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.768016; --waaAAATAAAAcmaa--- ; cor=; Ncor= a 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 0 0 0 c 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 0 0 0 g 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 0 0 0 t 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319 0 0 0

dyads_m3_shift1 (dyads_m3)
; positions_6-8nt_m5 versus dyads_m3; m=5/6; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.638908; -wwgAAAATAAAATwa---- ; cor=; Ncor= a 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 0 0 0 0 c 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 0 0 0 0 g 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 0 0 0 0 t 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934 0 0 0 0

dyads_m4_shift0 (dyads_m4)
; positions_6-8nt_m5 versus dyads_m4; m=6/6; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.632294; wwtATAAATAAAAATAAAAt ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887

One-to-n matrix alignment; reference matrix: dyads_m3_shift7 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift7 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=15; shift=7; ncol=22; -------wwgAAAATAAAATwa ; Alignment reference a 0 0 0 0 0 0 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 c 0 0 0 0 0 0 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 g 0 0 0 0 0 0 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 t 0 0 0 0 0 0 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934

dyads_m3_shift7 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=7; score= 1; -------wwgAAAATAAAATwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 c 0 0 0 0 0 0 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 g 0 0 0 0 0 0 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 t 0 0 0 0 0 0 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934

positions_6-8nt_m10_shift8 (positions_6-8nt_m10)
; dyads_m3 versus positions_6-8nt_m10; m=2/6; ncol2=15; w=0; offset=1; strand=D; shift=8; score=0.793627; --------waaAAATAAAAcma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 c 0 0 0 0 0 0 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 g 0 0 0 0 0 0 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 t 0 0 0 0 0 0 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276

positions_6-8nt_m2_shift8 (positions_6-8nt_m2)
; dyads_m3 versus positions_6-8nt_m2; m=3/6; ncol2=16; w=0; offset=1; strand=D; shift=8; score=0.732167; --------wwaAAATAAAAcAt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 c 0 0 0 0 0 0 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 g 0 0 0 0 0 0 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 t 0 0 0 0 0 0 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681

positions_6-8nt_m8_shift8 (positions_6-8nt_m8)
; dyads_m3 versus positions_6-8nt_m8; m=4/6; ncol2=16; w=0; offset=1; strand=D; shift=8; score=0.689867; --------wwwAAATAAAAcAt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 c 0 0 0 0 0 0 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 g 0 0 0 0 0 0 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 t 0 0 0 0 0 0 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633

positions_6-8nt_m5_shift8 (positions_6-8nt_m5)
; dyads_m3 versus positions_6-8nt_m5; m=5/6; ncol2=18; w=0; offset=1; strand=D; shift=8; score=0.638908; --------waaAAATAAAAmAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 c 0 0 0 0 0 0 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 g 0 0 0 0 0 0 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 t 0 0 0 0 0 0 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479

dyads_m4_shift0 (dyads_m4)
; dyads_m3 versus dyads_m4; m=6/6; ncol2=22; w=-7; offset=-7; strand=D; shift=0; score=0.570362; wwtATAAATAAAAATAAAAtww ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 577 569 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 220 259 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 232 221 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887 448 428

One-to-n matrix alignment; reference matrix: positions_6-8nt_m8_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m8_shift2 (positions_6-8nt_m8)
; positions_6-8nt_m8; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwwAAATAAAAcAtww ; Alignment reference a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397

positions_6-8nt_m8_shift2 (positions_6-8nt_m8)
; positions_6-8nt_m8 versus positions_6-8nt_m8; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=2; score= 1; --wwwAAATAAAAcAtww ; cor=; Ncor= a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397

positions_6-8nt_m2_shift2 (positions_6-8nt_m2)
; positions_6-8nt_m8 versus positions_6-8nt_m2; m=2/7; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.977127; --wwaAAATAAAAcAtww ; cor=; Ncor= a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445

positions_6-8nt_m10_shift2 (positions_6-8nt_m10)
; positions_6-8nt_m8 versus positions_6-8nt_m10; m=3/7; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.866979; --waaAAATAAAAcmaa- ; cor=; Ncor= a 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 0 c 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 0 g 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 0 t 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319 0

positions_6-8nt_m5_shift2 (positions_6-8nt_m5)
; positions_6-8nt_m8 versus positions_6-8nt_m5; m=4/7; ncol2=18; w=0; offset=0; strand=D; shift=2; score=0.797811; --waaAAATAAAAmAAAa ; cor=; Ncor= a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287

dyads_m3_shift1 (dyads_m3)
; positions_6-8nt_m8 versus dyads_m3; m=5/7; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.689867; -wwgAAAATAAAATwa-- ; cor=; Ncor= a 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 0 0 c 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 0 0 g 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 0 0 t 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934 0 0

dyads_m4_shift0 (dyads_m4)
; positions_6-8nt_m8 versus dyads_m4; m=6/7; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.548859; wwtATAAATAAAAATAAA ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206

oligos_6-8nt_m7_shift4 (oligos_6-8nt_m7)
; positions_6-8nt_m8 versus oligos_6-8nt_m7; m=7/7; ncol2=10; w=0; offset=2; strand=D; shift=4; score=0.442381; ----waAATGAAaw---- ; cor=; Ncor= a 0 0 0 0 747 1105 2596 2596 0 0 2579 2596 1120 908 0 0 0 0 c 0 0 0 0 538 506 0 0 0 0 0 0 401 416 0 0 0 0 g 0 0 0 0 598 535 0 0 0 2596 0 0 437 491 0 0 0 0 t 0 0 0 0 713 450 0 0 2596 0 17 0 638 781 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift0 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; ygCCGCCGmc ; Alignment reference a 516 670 7 1 41 29 3 4 730 692 c 903 398 2819 2827 22 2775 2826 0 961 1043 g 624 1071 0 2 2713 1 2 2816 573 474 t 789 693 6 2 56 27 1 12 568 623

dyads_m7_shift0 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ygCCGCCGmc ; cor=; Ncor= a 516 670 7 1 41 29 3 4 730 692 c 903 398 2819 2827 22 2775 2826 0 961 1043 g 624 1071 0 2 2713 1 2 2816 573 474 t 789 693 6 2 56 27 1 12 568 623

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift0 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=10; shift=0; ncol=10; cyACCACCam ; Alignment reference a 602 536 2893 8 8 2785 15 14 1108 864 c 1091 1126 49 2954 2635 82 2941 2828 537 944 g 676 526 3 0 53 2 1 24 616 611 t 599 780 23 6 272 99 11 102 707 549

dyads_m10_shift0 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; cyACCACCam ; cor=; Ncor= a 602 536 2893 8 8 2785 15 14 1108 864 c 1091 1126 49 2954 2635 82 2941 2828 537 944 g 676 526 3 0 53 2 1 24 616 611 t 599 780 23 6 272 99 11 102 707 549

dyads_m8_shift0 (dyads_m8)
; dyads_m10 versus dyads_m8; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.775485; ykGCCACCrm ; cor=; Ncor= a 536 670 67 33 0 2893 0 0 886 857 c 837 665 49 2834 2835 0 2896 2885 527 828 g 619 804 2757 3 1 0 0 1 782 661 t 904 757 23 26 60 3 0 10 701 550

One-to-n matrix alignment; reference matrix: positions_6-8nt_m4_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)
; positions_6-8nt_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; yaTACATATGTAtr ; Alignment reference a 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 1731 c 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 645 g 646 1040 159 304 155 368 129 195 98 3081 142 321 659 1142 t 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896 996

positions_6-8nt_m4_shift0 (positions_6-8nt_m4)
; positions_6-8nt_m4 versus positions_6-8nt_m4; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; yaTACATATGTAtr ; cor=; Ncor= a 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 1731 c 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 645 g 646 1040 159 304 155 368 129 195 98 3081 142 321 659 1142 t 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896 996

positions_6-8nt_m7_shift0 (positions_6-8nt_m7)
; positions_6-8nt_m4 versus positions_6-8nt_m7; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.86183; yaTAcATATgTAya ; cor=; Ncor= a 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 1964 c 809 406 220 97 2046 86 143 70 330 114 189 96 1269 245 g 410 737 109 162 100 288 105 103 77 1975 86 196 316 552 t 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060 341

positions_6-8nt_m6_shift0 (positions_6-8nt_m6)
; positions_6-8nt_m4 versus positions_6-8nt_m6; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.771151; yaTACATAyATay- ; cor=; Ncor= a 1372 2593 207 5369 349 4978 138 5350 577 4374 413 2946 1162 0 c 1476 804 383 132 4165 159 427 148 3341 308 699 767 1560 0 g 811 1299 134 140 280 357 146 112 367 580 360 894 829 0 t 2077 1040 5012 95 942 242 5025 126 1451 474 4264 1129 2185 0

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; positions_6-8nt_m4 versus oligos_6-8nt_m2; m=4/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.647762; taTAyATAya---- ; cor=; Ncor= a 1169 2442 22 5307 41 4480 0 5276 775 2347 0 0 0 0 c 1153 833 22 28 3410 284 22 34 1429 799 0 0 0 0 g 898 1329 19 0 312 363 142 8 751 1024 0 0 0 0 t 2115 731 5272 0 1572 208 5171 17 2380 1165 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m8_shift0 (dyads_m8)
; dyads_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; ykGCCACCrm ; Alignment reference a 536 670 67 33 0 2893 0 0 886 857 c 837 665 49 2834 2835 0 2896 2885 527 828 g 619 804 2757 3 1 0 0 1 782 661 t 904 757 23 26 60 3 0 10 701 550

dyads_m8_shift0 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ykGCCACCrm ; cor=; Ncor= a 536 670 67 33 0 2893 0 0 886 857 c 837 665 49 2834 2835 0 2896 2885 527 828 g 619 804 2757 3 1 0 0 1 782 661 t 904 757 23 26 60 3 0 10 701 550

dyads_m10_shift0 (dyads_m10)
; dyads_m8 versus dyads_m10; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.775485; cyACCACCam ; cor=; Ncor= a 602 536 2893 8 8 2785 15 14 1108 864 c 1091 1126 49 2954 2635 82 2941 2828 537 944 g 676 526 3 0 53 2 1 24 616 611 t 599 780 23 6 272 99 11 102 707 549

oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; dyads_m8 versus oligos_6-8nt_m6; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.762343; tvGACACCwa ; cor=; Ncor= a 360 467 8 1456 0 1408 4 1 380 502 c 315 407 6 3 1301 26 1484 1449 300 327 g 315 430 1347 3 29 1 0 3 342 301 t 498 184 127 26 158 53 0 35 466 358

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; caCACACACACAcACACAcACAca ; Alignment reference a 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 2640 122 2660 159 2544 693 2368 235 2237 450 1624 c 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 111 2736 61 2639 150 1871 158 2429 208 1754 429 g 350 612 146 295 93 255 94 174 86 169 103 193 148 255 78 291 139 271 220 407 186 413 450 665 t 464 374 262 227 187 168 152 158 167 126 163 122 299 112 182 106 181 153 334 185 268 260 464 400

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; caCACACACACAcACACAcACAca ; cor=; Ncor= a 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 2640 122 2660 159 2544 693 2368 235 2237 450 1624 c 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 111 2736 61 2639 150 1871 158 2429 208 1754 429 g 350 612 146 295 93 255 94 174 86 169 103 193 148 255 78 291 139 271 220 407 186 413 450 665 t 464 374 262 227 187 168 152 158 167 126 163 122 299 112 182 106 181 153 334 185 268 260 464 400

positions_6-8nt_m9_shift0 (positions_6-8nt_m9)
; dyads_m5 versus positions_6-8nt_m9; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.635106; cacayACACACAcaca-------- ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 6009 0 0 0 0 0 0 0 0 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 1837 0 0 0 0 0 0 0 0 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 2611 0 0 0 0 0 0 0 0 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485 1808 0 0 0 0 0 0 0 0

positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; dyads_m5 versus positions_6-8nt_m1; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.530786; cacACACACACac----------- ; cor=; Ncor= a 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 0 0 0 0 0 0 0 0 0 0 0 c 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 0 0 0 0 0 0 0 0 0 0 0 g 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 0 0 0 0 0 0 0 0 0 0 0 t 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658 0 0 0 0 0 0 0 0 0 0 0

dyads_m9_shift4 (dyads_m9)
; dyads_m5 versus dyads_m9; m=4/4; ncol2=24; w=0; offset=4; strand=D; shift=4; score=0.528148; ----mmCACAcAmACAaCAACAAC ; cor=; Ncor= a 0 0 0 0 171 230 98 478 46 485 130 410 148 501 39 494 377 112 403 443 61 446 424 65 c 0 0 0 0 219 159 401 31 479 34 373 104 360 24 487 33 115 392 94 45 446 60 67 425 g 0 0 0 0 89 110 26 37 19 26 37 32 30 30 20 23 50 35 19 58 31 33 51 36 t 0 0 0 0 85 65 39 18 20 19 24 18 26 9 18 14 22 25 48 18 26 25 22 38

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; oligos_6-8nt_m7; m=0 (reference); ncol1=10; shift=2; ncol=12; --waAATGAAaw ; Alignment reference a 0 0 747 1105 2596 2596 0 0 2579 2596 1120 908 c 0 0 538 506 0 0 0 0 0 0 401 416 g 0 0 598 535 0 0 0 2596 0 0 437 491 t 0 0 713 450 0 0 2596 0 17 0 638 781

oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --waAATGAAaw ; cor=; Ncor= a 0 0 747 1105 2596 2596 0 0 2579 2596 1120 908 c 0 0 538 506 0 0 0 0 0 0 401 416 g 0 0 598 535 0 0 0 2596 0 0 437 491 t 0 0 713 450 0 0 2596 0 17 0 638 781

positions_6-8nt_m8_shift0 (positions_6-8nt_m8)
; oligos_6-8nt_m7 versus positions_6-8nt_m8; m=2/3; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.442381; wwwAAATAAAAc ; cor=; Ncor= a 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 c 792 757 586 114 157 154 310 151 197 190 245 2186 g 832 925 545 129 87 138 193 123 110 140 165 415 t 1386 1198 2295 218 291 237 3781 269 290 357 363 993

positions_6-8nt_m2_shift0 (positions_6-8nt_m2)
; oligos_6-8nt_m7 versus positions_6-8nt_m2; m=3/3; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.438558; wwaAAATAAAAc ; cor=; Ncor= a 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 c 901 832 545 143 140 193 316 137 201 184 248 2350 g 922 995 498 125 95 152 222 155 132 136 156 458 t 1443 1293 898 263 297 248 4031 246 313 337 372 1047

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m5_shift3 (oligos_6-8nt_m5)
; oligos_6-8nt_m5; m=0 (reference); ncol1=10; shift=3; ncol=13; ---ryACTCAChc ; Alignment reference a 0 0 0 697 469 2269 0 10 104 2121 0 680 544 c 0 0 0 513 822 12 2285 25 2062 75 2253 605 793 g 0 0 0 595 268 0 4 2 5 9 7 347 405 t 0 0 0 484 730 8 0 2252 118 84 29 657 547

oligos_6-8nt_m5_shift3 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---ryACTCAChc ; cor=; Ncor= a 0 0 0 697 469 2269 0 10 104 2121 0 680 544 c 0 0 0 513 822 12 2285 25 2062 75 2253 605 793 g 0 0 0 595 268 0 4 2 5 9 7 347 405 t 0 0 0 484 730 8 0 2252 118 84 29 657 547

positions_6-8nt_m9_shift0 (positions_6-8nt_m9)
; oligos_6-8nt_m5 versus positions_6-8nt_m9; m=2/2; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.438942; cacayACACACAc ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908

One-to-n matrix alignment; reference matrix: positions_6-8nt_m10_shift8 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m10_shift8 (positions_6-8nt_m10)
; positions_6-8nt_m10; m=0 (reference); ncol1=15; shift=8; ncol=23; --------waaAAATAAAAcmaa ; Alignment reference a 0 0 0 0 0 0 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 c 0 0 0 0 0 0 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 g 0 0 0 0 0 0 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 t 0 0 0 0 0 0 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319

positions_6-8nt_m10_shift8 (positions_6-8nt_m10)
; positions_6-8nt_m10 versus positions_6-8nt_m10; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=8; score= 1; --------waaAAATAAAAcmaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 c 0 0 0 0 0 0 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 g 0 0 0 0 0 0 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 t 0 0 0 0 0 0 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319

positions_6-8nt_m2_shift8 (positions_6-8nt_m2)
; positions_6-8nt_m10 versus positions_6-8nt_m2; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=8; score=0.89587; --------wwaAAATAAAAcAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 c 0 0 0 0 0 0 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 g 0 0 0 0 0 0 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 t 0 0 0 0 0 0 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371

positions_6-8nt_m8_shift8 (positions_6-8nt_m8)
; positions_6-8nt_m10 versus positions_6-8nt_m8; m=3/6; ncol2=16; w=0; offset=0; strand=D; shift=8; score=0.866979; --------wwwAAATAAAAcAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 c 0 0 0 0 0 0 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 g 0 0 0 0 0 0 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 t 0 0 0 0 0 0 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276

dyads_m3_shift7 (dyads_m3)
; positions_6-8nt_m10 versus dyads_m3; m=4/6; ncol2=15; w=-1; offset=-1; strand=D; shift=7; score=0.793627; -------wwgAAAATAAAATwa- ; cor=; Ncor= a 0 0 0 0 0 0 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 0 c 0 0 0 0 0 0 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 0 g 0 0 0 0 0 0 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 0 t 0 0 0 0 0 0 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934 0

positions_6-8nt_m5_shift8 (positions_6-8nt_m5)
; positions_6-8nt_m10 versus positions_6-8nt_m5; m=5/6; ncol2=18; w=0; offset=0; strand=D; shift=8; score=0.768016; --------waaAAATAAAAmAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 c 0 0 0 0 0 0 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 g 0 0 0 0 0 0 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 t 0 0 0 0 0 0 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457

dyads_m4_shift0 (dyads_m4)
; positions_6-8nt_m10 versus dyads_m4; m=6/6; ncol2=22; w=-8; offset=-8; strand=D; shift=0; score=0.527705; wwtATAAATAAAAATAAAAtww- ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 577 569 0 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 220 259 0 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 232 221 0 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887 448 428 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m9_shift0 (positions_6-8nt_m9)				; positions_6-8nt_m9; m=0 (reference); ncol1=16; shift=0; ncol=16; cacayACACACAcaca ; Alignment reference a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 6009 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 1837 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 2611 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485 1808
positions_6-8nt_m9_shift0 (positions_6-8nt_m9)				; positions_6-8nt_m9 versus positions_6-8nt_m9; m=1/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cacayACACACAcaca ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 6009 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 1837 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 2611 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485 1808
positions_6-8nt_m1_shift2 (positions_6-8nt_m1)				; positions_6-8nt_m9 versus positions_6-8nt_m1; m=2/6; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.796752; --cacACACACACac- ; cor=; Ncor= a 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 0 c 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 0 g 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 0 t 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658 0
dyads_m5_shift0 (dyads_m5)				; positions_6-8nt_m9 versus dyads_m5; m=3/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.635106; caCACACACACAcACA ; cor=; Ncor= a 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 2640 122 2660 c 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 111 2736 61 g 350 612 146 295 93 255 94 174 86 169 103 193 148 255 78 291 t 464 374 262 227 187 168 152 158 167 126 163 122 299 112 182 106
oligos_6-8nt_m9_shift3 (oligos_6-8nt_m9)				; positions_6-8nt_m9 versus oligos_6-8nt_m9; m=4/6; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.568799; ---acACGCACAGmc- ; cor=; Ncor= a 0 0 0 1384 821 3178 101 379 143 3350 100 3337 166 1253 879 0 c 0 0 0 784 1438 137 3303 106 3263 126 3388 84 673 959 1029 0 g 0 0 0 896 710 176 106 3060 102 98 106 72 2546 702 863 0 t 0 0 0 576 671 149 130 95 132 66 46 147 255 726 869 0
dyads_m9_shift0 (dyads_m9)				; positions_6-8nt_m9 versus dyads_m9; m=5/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.531503; mmCACAcAmACAaCAA ; cor=; Ncor= a 171 230 98 478 46 485 130 410 148 501 39 494 377 112 403 443 c 219 159 401 31 479 34 373 104 360 24 487 33 115 392 94 45 g 89 110 26 37 19 26 37 32 30 30 20 23 50 35 19 58 t 85 65 39 18 20 19 24 18 26 9 18 14 22 25 48 18
oligos_6-8nt_m5_shift3 (oligos_6-8nt_m5)				; positions_6-8nt_m9 versus oligos_6-8nt_m5; m=6/6; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.438942; ---ryACTCAChc--- ; cor=; Ncor= a 0 0 0 697 469 2269 0 10 104 2121 0 680 544 0 0 0 c 0 0 0 513 822 12 2285 25 2062 75 2253 605 793 0 0 0 g 0 0 0 595 268 0 4 2 5 9 7 347 405 0 0 0 t 0 0 0 484 730 8 0 2252 118 84 29 657 547 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; oligos_6-8nt_m2; m=0 (reference); ncol1=10; shift=1; ncol=11; -taTAyATAya ; Alignment reference a 0 1169 2442 22 5307 41 4480 0 5276 775 2347 c 0 1153 833 22 28 3410 284 22 34 1429 799 g 0 898 1329 19 0 312 363 142 8 751 1024 t 0 2115 731 5272 0 1572 208 5171 17 2380 1165
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -taTAyATAya ; cor=; Ncor= a 0 1169 2442 22 5307 41 4480 0 5276 775 2347 c 0 1153 833 22 28 3410 284 22 34 1429 799 g 0 898 1329 19 0 312 363 142 8 751 1024 t 0 2115 731 5272 0 1572 208 5171 17 2380 1165
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; oligos_6-8nt_m2 versus positions_6-8nt_m6; m=2/6; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.73231; -yaTACATAyA ; cor=; Ncor= a 0 1372 2593 207 5369 349 4978 138 5350 577 4374 c 0 1476 804 383 132 4165 159 427 148 3341 308 g 0 811 1299 134 140 280 357 146 112 367 580 t 0 2077 1040 5012 95 942 242 5025 126 1451 474
positions_6-8nt_m4_shift1 (positions_6-8nt_m4)				; oligos_6-8nt_m2 versus positions_6-8nt_m4; m=3/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.647762; -yaTACATATG ; cor=; Ncor= a 0 996 1897 264 3886 456 3858 281 3905 190 822 c 0 1142 659 321 142 3081 98 195 129 368 155 g 0 646 1040 159 304 155 368 129 195 98 3081 t 0 1730 918 3770 182 822 190 3909 285 3858 456
oligos_6-8nt_m3_shift2 (oligos_6-8nt_m3)				; oligos_6-8nt_m2 versus oligos_6-8nt_m3; m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.621195; --atAGATACw ; cor=; Ncor= a 0 0 1239 519 3086 11 2979 0 3234 30 1203 c 0 0 563 739 96 127 61 1 19 2879 573 g 0 0 810 569 62 2371 119 42 0 96 585 t 0 0 647 1432 15 750 100 3216 6 254 898
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)				; oligos_6-8nt_m2 versus positions_6-8nt_m3; m=5/6; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.582425; wtgTATATATA ; cor=; Ncor= a 1359 785 624 244 3013 239 3015 190 2964 243 2934 c 552 611 180 237 81 244 108 233 99 209 131 g 719 561 2409 131 209 99 233 108 244 81 237 t 916 1589 333 2934 243 2964 190 3015 239 3013 244
positions_6-8nt_m7_shift1 (positions_6-8nt_m7)				; oligos_6-8nt_m2 versus positions_6-8nt_m7; m=6/6; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.578017; -yaTAcATATg ; cor=; Ncor= a 0 643 1432 162 2736 239 2611 135 2787 98 774 c 0 809 406 220 97 2046 86 143 70 330 114 g 0 410 737 109 162 100 288 105 103 77 1975 t 0 1240 527 2611 107 717 117 2719 142 2597 239

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m3_shift4 (oligos_6-8nt_m3)				; oligos_6-8nt_m3; m=0 (reference); ncol1=10; shift=4; ncol=14; ----atAGATACww ; Alignment reference a 0 0 0 0 1239 519 3086 11 2979 0 3234 30 1203 884 c 0 0 0 0 563 739 96 127 61 1 19 2879 573 801 g 0 0 0 0 810 569 62 2371 119 42 0 96 585 661 t 0 0 0 0 647 1432 15 750 100 3216 6 254 898 913
oligos_6-8nt_m3_shift4 (oligos_6-8nt_m3)				; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----atAGATACww ; cor=; Ncor= a 0 0 0 0 1239 519 3086 11 2979 0 3234 30 1203 884 c 0 0 0 0 563 739 96 127 61 1 19 2879 573 801 g 0 0 0 0 810 569 62 2371 119 42 0 96 585 661 t 0 0 0 0 647 1432 15 750 100 3216 6 254 898 913
oligos_6-8nt_m2_shift3 (oligos_6-8nt_m2)				; oligos_6-8nt_m3 versus oligos_6-8nt_m2; m=2/4; ncol2=10; w=-1; offset=-1; strand=D; shift=3; score=0.621195; ---taTAyATAya- ; cor=; Ncor= a 0 0 0 1169 2442 22 5307 41 4480 0 5276 775 2347 0 c 0 0 0 1153 833 22 28 3410 284 22 34 1429 799 0 g 0 0 0 898 1329 19 0 312 363 142 8 751 1024 0 t 0 0 0 2115 731 5272 0 1572 208 5171 17 2380 1165 0
positions_6-8nt_m6_shift3 (positions_6-8nt_m6)				; oligos_6-8nt_m3 versus positions_6-8nt_m6; m=3/4; ncol2=13; w=-1; offset=-1; strand=D; shift=3; score=0.583758; ---yaTACATAyAT ; cor=; Ncor= a 0 0 0 1372 2593 207 5369 349 4978 138 5350 577 4374 413 c 0 0 0 1476 804 383 132 4165 159 427 148 3341 308 699 g 0 0 0 811 1299 134 140 280 357 146 112 367 580 360 t 0 0 0 2077 1040 5012 95 942 242 5025 126 1451 474 4264
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)				; oligos_6-8nt_m3 versus positions_6-8nt_m3; m=4/4; ncol2=14; w=-4; offset=-4; strand=D; shift=0; score=0.562369; wtgTATATATAcaw ; cor=; Ncor= a 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 c 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 g 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 t 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m9_shift3 (oligos_6-8nt_m9)				; oligos_6-8nt_m9; m=0 (reference); ncol1=12; shift=3; ncol=15; ---acACGCACAGmc ; Alignment reference a 0 0 0 1384 821 3178 101 379 143 3350 100 3337 166 1253 879 c 0 0 0 784 1438 137 3303 106 3263 126 3388 84 673 959 1029 g 0 0 0 896 710 176 106 3060 102 98 106 72 2546 702 863 t 0 0 0 576 671 149 130 95 132 66 46 147 255 726 869
oligos_6-8nt_m9_shift3 (oligos_6-8nt_m9)				; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---acACGCACAGmc ; cor=; Ncor= a 0 0 0 1384 821 3178 101 379 143 3350 100 3337 166 1253 879 c 0 0 0 784 1438 137 3303 106 3263 126 3388 84 673 959 1029 g 0 0 0 896 710 176 106 3060 102 98 106 72 2546 702 863 t 0 0 0 576 671 149 130 95 132 66 46 147 255 726 869
positions_6-8nt_m1_shift2 (positions_6-8nt_m1)				; oligos_6-8nt_m9 versus positions_6-8nt_m1; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=2; score=0.683406; --cacACACACACac ; cor=; Ncor= a 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 c 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 g 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 t 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658
positions_6-8nt_m9_shift0 (positions_6-8nt_m9)				; oligos_6-8nt_m9 versus positions_6-8nt_m9; m=3/3; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.568799; cacayACACACAcac ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m7_shift0 (positions_6-8nt_m7)				; positions_6-8nt_m7; m=0 (reference); ncol1=16; shift=0; ncol=16; yaTAcATATgTAyata ; Alignment reference a 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 1964 617 1409 c 809 406 220 97 2046 86 143 70 330 114 189 96 1269 245 540 449 g 410 737 109 162 100 288 105 103 77 1975 86 196 316 552 371 563 t 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060 341 1574 681
positions_6-8nt_m7_shift0 (positions_6-8nt_m7)				; positions_6-8nt_m7 versus positions_6-8nt_m7; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; yaTAcATATgTAyata ; cor=; Ncor= a 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 1964 617 1409 c 809 406 220 97 2046 86 143 70 330 114 189 96 1269 245 540 449 g 410 737 109 162 100 288 105 103 77 1975 86 196 316 552 371 563 t 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060 341 1574 681
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)				; positions_6-8nt_m7 versus positions_6-8nt_m4; m=2/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.86183; yaTACATATGTAtr-- ; cor=; Ncor= a 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 1731 0 0 c 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 645 0 0 g 646 1040 159 304 155 368 129 195 98 3081 142 321 659 1142 0 0 t 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896 996 0 0
positions_6-8nt_m6_shift0 (positions_6-8nt_m6)				; positions_6-8nt_m7 versus positions_6-8nt_m6; m=3/5; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.688951; yaTACATAyATay--- ; cor=; Ncor= a 1372 2593 207 5369 349 4978 138 5350 577 4374 413 2946 1162 0 0 0 c 1476 804 383 132 4165 159 427 148 3341 308 699 767 1560 0 0 0 g 811 1299 134 140 280 357 146 112 367 580 360 894 829 0 0 0 t 2077 1040 5012 95 942 242 5025 126 1451 474 4264 1129 2185 0 0 0
positions_6-8nt_m3_shift1 (positions_6-8nt_m3)				; positions_6-8nt_m7 versus positions_6-8nt_m3; m=4/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.624273; -wtgTATATATAcaw- ; cor=; Ncor= a 0 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 0 c 0 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 0 g 0 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 0 t 0 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359 0
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; positions_6-8nt_m7 versus oligos_6-8nt_m2; m=5/5; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.578017; taTAyATAya------ ; cor=; Ncor= a 1169 2442 22 5307 41 4480 0 5276 775 2347 0 0 0 0 0 0 c 1153 833 22 28 3410 284 22 34 1429 799 0 0 0 0 0 0 g 898 1329 19 0 312 363 142 8 751 1024 0 0 0 0 0 0 t 2115 731 5272 0 1572 208 5171 17 2380 1165 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m1_shift2 (positions_6-8nt_m1)				; positions_6-8nt_m1; m=0 (reference); ncol1=13; shift=2; ncol=15; --cacACACACACac ; Alignment reference a 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 c 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 g 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 t 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658
positions_6-8nt_m1_shift2 (positions_6-8nt_m1)				; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --cacACACACACac ; cor=; Ncor= a 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 c 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 g 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 t 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658
positions_6-8nt_m9_shift0 (positions_6-8nt_m9)				; positions_6-8nt_m1 versus positions_6-8nt_m9; m=2/5; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.796752; cacayACACACAcac ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485
oligos_6-8nt_m9_shift3 (oligos_6-8nt_m9)				; positions_6-8nt_m1 versus oligos_6-8nt_m9; m=3/5; ncol2=12; w=0; offset=1; strand=D; shift=3; score=0.683406; ---acACGCACAGmc ; cor=; Ncor= a 0 0 0 1384 821 3178 101 379 143 3350 100 3337 166 1253 879 c 0 0 0 784 1438 137 3303 106 3263 126 3388 84 673 959 1029 g 0 0 0 896 710 176 106 3060 102 98 106 72 2546 702 863 t 0 0 0 576 671 149 130 95 132 66 46 147 255 726 869
dyads_m5_shift2 (dyads_m5)				; positions_6-8nt_m1 versus dyads_m5; m=4/5; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.530786; --caCACACACACAc ; cor=; Ncor= a 0 0 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 c 0 0 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 g 0 0 350 612 146 295 93 255 94 174 86 169 103 193 148 t 0 0 464 374 262 227 187 168 152 158 167 126 163 122 299
dyads_m9_shift2 (dyads_m9)				; positions_6-8nt_m1 versus dyads_m9; m=5/5; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.491871; --mmCACAcAmACAa ; cor=; Ncor= a 0 0 171 230 98 478 46 485 130 410 148 501 39 494 377 c 0 0 219 159 401 31 479 34 373 104 360 24 487 33 115 g 0 0 89 110 26 37 19 26 37 32 30 30 20 23 50 t 0 0 85 65 39 18 20 19 24 18 26 9 18 14 22

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m9_shift4 (dyads_m9)				; dyads_m9; m=0 (reference); ncol1=24; shift=4; ncol=28; ----mmCACAcAmACAaCAACAACAmmm ; Alignment reference a 0 0 0 0 171 230 98 478 46 485 130 410 148 501 39 494 377 112 403 443 61 446 424 65 447 187 175 243 c 0 0 0 0 219 159 401 31 479 34 373 104 360 24 487 33 115 392 94 45 446 60 67 425 42 281 225 156 g 0 0 0 0 89 110 26 37 19 26 37 32 30 30 20 23 50 35 19 58 31 33 51 36 40 59 79 95 t 0 0 0 0 85 65 39 18 20 19 24 18 26 9 18 14 22 25 48 18 26 25 22 38 35 37 85 70
dyads_m9_shift4 (dyads_m9)				; dyads_m9 versus dyads_m9; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----mmCACAcAmACAaCAACAACAmmm ; cor=; Ncor= a 0 0 0 0 171 230 98 478 46 485 130 410 148 501 39 494 377 112 403 443 61 446 424 65 447 187 175 243 c 0 0 0 0 219 159 401 31 479 34 373 104 360 24 487 33 115 392 94 45 446 60 67 425 42 281 225 156 g 0 0 0 0 89 110 26 37 19 26 37 32 30 30 20 23 50 35 19 58 31 33 51 36 40 59 79 95 t 0 0 0 0 85 65 39 18 20 19 24 18 26 9 18 14 22 25 48 18 26 25 22 38 35 37 85 70
positions_6-8nt_m9_shift4 (positions_6-8nt_m9)				; dyads_m9 versus positions_6-8nt_m9; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.531503; ----cacayACACACAcaca-------- ; cor=; Ncor= a 0 0 0 0 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 6009 0 0 0 0 0 0 0 0 c 0 0 0 0 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 1837 0 0 0 0 0 0 0 0 g 0 0 0 0 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 2611 0 0 0 0 0 0 0 0 t 0 0 0 0 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485 1808 0 0 0 0 0 0 0 0
dyads_m5_shift0 (dyads_m5)				; dyads_m9 versus dyads_m5; m=3/4; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.528148; caCACACACACAcACACAcACAca---- ; cor=; Ncor= a 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 2640 122 2660 159 2544 693 2368 235 2237 450 1624 0 0 0 0 c 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 111 2736 61 2639 150 1871 158 2429 208 1754 429 0 0 0 0 g 350 612 146 295 93 255 94 174 86 169 103 193 148 255 78 291 139 271 220 407 186 413 450 665 0 0 0 0 t 464 374 262 227 187 168 152 158 167 126 163 122 299 112 182 106 181 153 334 185 268 260 464 400 0 0 0 0
positions_6-8nt_m1_shift4 (positions_6-8nt_m1)				; dyads_m9 versus positions_6-8nt_m1; m=4/4; ncol2=13; w=0; offset=0; strand=D; shift=4; score=0.491871; ----cacACACACACac----------- ; cor=; Ncor= a 0 0 0 0 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)				; positions_6-8nt_m2; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwaAAATAAAAcAtww ; Alignment reference a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)				; positions_6-8nt_m2 versus positions_6-8nt_m2; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=2; score= 1; --wwaAAATAAAAcAtww ; cor=; Ncor= a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445
positions_6-8nt_m8_shift2 (positions_6-8nt_m8)				; positions_6-8nt_m2 versus positions_6-8nt_m8; m=2/7; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.977127; --wwwAAATAAAAcAtww ; cor=; Ncor= a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397
positions_6-8nt_m10_shift2 (positions_6-8nt_m10)				; positions_6-8nt_m2 versus positions_6-8nt_m10; m=3/7; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.89587; --waaAAATAAAAcmaa- ; cor=; Ncor= a 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 0 c 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 0 g 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 0 t 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319 0
positions_6-8nt_m5_shift2 (positions_6-8nt_m5)				; positions_6-8nt_m2 versus positions_6-8nt_m5; m=4/7; ncol2=18; w=0; offset=0; strand=D; shift=2; score=0.826184; --waaAAATAAAAmAAAa ; cor=; Ncor= a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287
dyads_m3_shift1 (dyads_m3)				; positions_6-8nt_m2 versus dyads_m3; m=5/7; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.732167; -wwgAAAATAAAATwa-- ; cor=; Ncor= a 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 0 0 c 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 0 0 g 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 0 0 t 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934 0 0
dyads_m4_shift0 (dyads_m4)				; positions_6-8nt_m2 versus dyads_m4; m=6/7; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.52713; wwtATAAATAAAAATAAA ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206
oligos_6-8nt_m7_shift4 (oligos_6-8nt_m7)				; positions_6-8nt_m2 versus oligos_6-8nt_m7; m=7/7; ncol2=10; w=0; offset=2; strand=D; shift=4; score=0.438558; ----waAATGAAaw---- ; cor=; Ncor= a 0 0 0 0 747 1105 2596 2596 0 0 2579 2596 1120 908 0 0 0 0 c 0 0 0 0 538 506 0 0 0 0 0 0 401 416 0 0 0 0 g 0 0 0 0 598 535 0 0 0 2596 0 0 437 491 0 0 0 0 t 0 0 0 0 713 450 0 0 2596 0 17 0 638 781 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift0 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=22; shift=0; ncol=22; wwtATAAATAAAAATAAAAtww ; Alignment reference a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 577 569 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 220 259 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 232 221 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887 448 428
dyads_m4_shift0 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; wwtATAAATAAAAATAAAAtww ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 577 569 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 220 259 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 232 221 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887 448 428
positions_6-8nt_m5_shift2 (positions_6-8nt_m5)				; dyads_m4 versus positions_6-8nt_m5; m=2/6; ncol2=18; w=0; offset=2; strand=D; shift=2; score=0.632294; --waaAAATAAAAmAAAawa-- ; cor=; Ncor= a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 2199 2034 0 0 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 895 1062 0 0 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 869 938 0 0 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287 1335 1264 0 0
dyads_m3_shift7 (dyads_m3)				; dyads_m4 versus dyads_m3; m=3/6; ncol2=15; w=0; offset=7; strand=D; shift=7; score=0.570362; -------wwgAAAATAAAATwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 c 0 0 0 0 0 0 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 g 0 0 0 0 0 0 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 t 0 0 0 0 0 0 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934
positions_6-8nt_m8_shift2 (positions_6-8nt_m8)				; dyads_m4 versus positions_6-8nt_m8; m=4/6; ncol2=16; w=0; offset=2; strand=D; shift=2; score=0.548859; --wwwAAATAAAAcAtww---- ; cor=; Ncor= a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 0 0 0 0 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 0 0 0 0 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 0 0 0 0 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397 0 0 0 0
positions_6-8nt_m10_shift8 (positions_6-8nt_m10)				; dyads_m4 versus positions_6-8nt_m10; m=5/6; ncol2=15; w=0; offset=8; strand=D; shift=8; score=0.527705; --------waaAAATAAAAcma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 c 0 0 0 0 0 0 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 g 0 0 0 0 0 0 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 t 0 0 0 0 0 0 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)				; dyads_m4 versus positions_6-8nt_m2; m=6/6; ncol2=16; w=0; offset=2; strand=D; shift=2; score=0.52713; --wwaAAATAAAAcAtww---- ; cor=; Ncor= a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 0 0 0 0 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 0 0 0 0 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 0 0 0 0 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m3_shift1 (positions_6-8nt_m3)				; positions_6-8nt_m3; m=0 (reference); ncol1=14; shift=1; ncol=15; -wtgTATATATAcaw ; Alignment reference a 0 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 c 0 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 g 0 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 t 0 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359
positions_6-8nt_m3_shift1 (positions_6-8nt_m3)				; positions_6-8nt_m3 versus positions_6-8nt_m3; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wtgTATATATAcaw ; cor=; Ncor= a 0 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 c 0 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 g 0 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 t 0 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359
positions_6-8nt_m6_rc_shift1 (positions_6-8nt_m6_rc)				; positions_6-8nt_m3 versus positions_6-8nt_m6_rc; m=2/5; ncol2=13; w=0; offset=0; strand=R; shift=1; score=0.655709; -rtATrTATGTAtr- ; cor=; Ncor= a 0 2185 1129 4264 474 1451 126 5025 242 942 95 5012 1040 2077 0 c 0 829 894 360 580 367 112 146 357 280 140 134 1299 811 0 g 0 1560 767 699 308 3341 148 427 159 4165 132 383 804 1476 0 t 0 1162 2946 413 4374 577 5350 138 4978 349 5369 207 2593 1372 0
positions_6-8nt_m7_shift0 (positions_6-8nt_m7)				; positions_6-8nt_m3 versus positions_6-8nt_m7; m=3/5; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.624273; yaTAcATATgTAyat ; cor=; Ncor= a 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 1964 617 c 809 406 220 97 2046 86 143 70 330 114 189 96 1269 245 540 g 410 737 109 162 100 288 105 103 77 1975 86 196 316 552 371 t 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060 341 1574
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; positions_6-8nt_m3 versus oligos_6-8nt_m2; m=4/5; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.582425; --taTAyATAya--- ; cor=; Ncor= a 0 0 1169 2442 22 5307 41 4480 0 5276 775 2347 0 0 0 c 0 0 1153 833 22 28 3410 284 22 34 1429 799 0 0 0 g 0 0 898 1329 19 0 312 363 142 8 751 1024 0 0 0 t 0 0 2115 731 5272 0 1572 208 5171 17 2380 1165 0 0 0
oligos_6-8nt_m3_rc_shift1 (oligos_6-8nt_m3_rc)				; positions_6-8nt_m3 versus oligos_6-8nt_m3_rc; m=5/5; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.562369; -wwGTATCTat---- ; cor=; Ncor= a 0 913 898 254 6 3216 100 750 15 1432 647 0 0 0 0 c 0 661 585 96 0 42 119 2371 62 569 810 0 0 0 0 g 0 801 573 2879 19 1 61 127 96 739 563 0 0 0 0 t 0 884 1203 30 3234 0 2979 11 3086 519 1239 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; positions_6-8nt_m6; m=0 (reference); ncol1=13; shift=1; ncol=14; -yaTACATAyATay ; Alignment reference a 0 1372 2593 207 5369 349 4978 138 5350 577 4374 413 2946 1162 c 0 1476 804 383 132 4165 159 427 148 3341 308 699 767 1560 g 0 811 1299 134 140 280 357 146 112 367 580 360 894 829 t 0 2077 1040 5012 95 942 242 5025 126 1451 474 4264 1129 2185
positions_6-8nt_m6_shift1 (positions_6-8nt_m6)				; positions_6-8nt_m6 versus positions_6-8nt_m6; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -yaTACATAyATay ; cor=; Ncor= a 0 1372 2593 207 5369 349 4978 138 5350 577 4374 413 2946 1162 c 0 1476 804 383 132 4165 159 427 148 3341 308 699 767 1560 g 0 811 1299 134 140 280 357 146 112 367 580 360 894 829 t 0 2077 1040 5012 95 942 242 5025 126 1451 474 4264 1129 2185
positions_6-8nt_m4_shift1 (positions_6-8nt_m4)				; positions_6-8nt_m6 versus positions_6-8nt_m4; m=2/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.771151; -yaTACATATGTAt ; cor=; Ncor= a 0 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 c 0 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 g 0 646 1040 159 304 155 368 129 195 98 3081 142 321 659 t 0 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; positions_6-8nt_m6 versus oligos_6-8nt_m2; m=3/6; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.73231; -taTAyATAya--- ; cor=; Ncor= a 0 1169 2442 22 5307 41 4480 0 5276 775 2347 0 0 0 c 0 1153 833 22 28 3410 284 22 34 1429 799 0 0 0 g 0 898 1329 19 0 312 363 142 8 751 1024 0 0 0 t 0 2115 731 5272 0 1572 208 5171 17 2380 1165 0 0 0
positions_6-8nt_m7_shift1 (positions_6-8nt_m7)				; positions_6-8nt_m6 versus positions_6-8nt_m7; m=4/6; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.688951; -yaTAcATATgTAy ; cor=; Ncor= a 0 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 c 0 809 406 220 97 2046 86 143 70 330 114 189 96 1269 g 0 410 737 109 162 100 288 105 103 77 1975 86 196 316 t 0 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)				; positions_6-8nt_m6 versus positions_6-8nt_m3; m=5/6; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.655709; wtgTATATATAcaw ; cor=; Ncor= a 1359 785 624 244 3013 239 3015 190 2964 243 2934 333 1589 916 c 552 611 180 237 81 244 108 233 99 209 131 2409 561 719 g 719 561 2409 131 209 99 233 108 244 81 237 180 611 552 t 916 1589 333 2934 243 2964 190 3015 239 3013 244 624 785 1359
oligos_6-8nt_m3_shift2 (oligos_6-8nt_m3)				; positions_6-8nt_m6 versus oligos_6-8nt_m3; m=6/6; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.583758; --atAGATACww-- ; cor=; Ncor= a 0 0 1239 519 3086 11 2979 0 3234 30 1203 884 0 0 c 0 0 563 739 96 127 61 1 19 2879 573 801 0 0 g 0 0 810 569 62 2371 119 42 0 96 585 661 0 0 t 0 0 647 1432 15 750 100 3216 6 254 898 913 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m5_shift2 (positions_6-8nt_m5)				; positions_6-8nt_m5; m=0 (reference); ncol1=18; shift=2; ncol=20; --waaAAATAAAAmAAAawa ; Alignment reference a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 2199 2034 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 895 1062 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 869 938 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287 1335 1264
positions_6-8nt_m5_shift2 (positions_6-8nt_m5)				; positions_6-8nt_m5 versus positions_6-8nt_m5; m=1/6; ncol2=18; w=0; offset=0; strand=D; shift=2; score= 1; --waaAAATAAAAmAAAawa ; cor=; Ncor= a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 2199 2034 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 895 1062 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 869 938 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287 1335 1264
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)				; positions_6-8nt_m5 versus positions_6-8nt_m2; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.826184; --wwaAAATAAAAcAtww-- ; cor=; Ncor= a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 0 0 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 0 0 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 0 0 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445 0 0
positions_6-8nt_m8_shift2 (positions_6-8nt_m8)				; positions_6-8nt_m5 versus positions_6-8nt_m8; m=3/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.797811; --wwwAAATAAAAcAtww-- ; cor=; Ncor= a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 0 0 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 0 0 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 0 0 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397 0 0
positions_6-8nt_m10_shift2 (positions_6-8nt_m10)				; positions_6-8nt_m5 versus positions_6-8nt_m10; m=4/6; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.768016; --waaAAATAAAAcmaa--- ; cor=; Ncor= a 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 0 0 0 c 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 0 0 0 g 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 0 0 0 t 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319 0 0 0
dyads_m3_shift1 (dyads_m3)				; positions_6-8nt_m5 versus dyads_m3; m=5/6; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.638908; -wwgAAAATAAAATwa---- ; cor=; Ncor= a 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 0 0 0 0 c 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 0 0 0 0 g 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 0 0 0 0 t 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934 0 0 0 0
dyads_m4_shift0 (dyads_m4)				; positions_6-8nt_m5 versus dyads_m4; m=6/6; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.632294; wwtATAAATAAAAATAAAAt ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift7 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=15; shift=7; ncol=22; -------wwgAAAATAAAATwa ; Alignment reference a 0 0 0 0 0 0 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 c 0 0 0 0 0 0 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 g 0 0 0 0 0 0 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 t 0 0 0 0 0 0 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934
dyads_m3_shift7 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=7; score= 1; -------wwgAAAATAAAATwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 c 0 0 0 0 0 0 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 g 0 0 0 0 0 0 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 t 0 0 0 0 0 0 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934
positions_6-8nt_m10_shift8 (positions_6-8nt_m10)				; dyads_m3 versus positions_6-8nt_m10; m=2/6; ncol2=15; w=0; offset=1; strand=D; shift=8; score=0.793627; --------waaAAATAAAAcma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 c 0 0 0 0 0 0 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 g 0 0 0 0 0 0 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 t 0 0 0 0 0 0 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276
positions_6-8nt_m2_shift8 (positions_6-8nt_m2)				; dyads_m3 versus positions_6-8nt_m2; m=3/6; ncol2=16; w=0; offset=1; strand=D; shift=8; score=0.732167; --------wwaAAATAAAAcAt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 c 0 0 0 0 0 0 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 g 0 0 0 0 0 0 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 t 0 0 0 0 0 0 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681
positions_6-8nt_m8_shift8 (positions_6-8nt_m8)				; dyads_m3 versus positions_6-8nt_m8; m=4/6; ncol2=16; w=0; offset=1; strand=D; shift=8; score=0.689867; --------wwwAAATAAAAcAt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 c 0 0 0 0 0 0 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 g 0 0 0 0 0 0 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 t 0 0 0 0 0 0 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633
positions_6-8nt_m5_shift8 (positions_6-8nt_m5)				; dyads_m3 versus positions_6-8nt_m5; m=5/6; ncol2=18; w=0; offset=1; strand=D; shift=8; score=0.638908; --------waaAAATAAAAmAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 c 0 0 0 0 0 0 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 g 0 0 0 0 0 0 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 t 0 0 0 0 0 0 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479
dyads_m4_shift0 (dyads_m4)				; dyads_m3 versus dyads_m4; m=6/6; ncol2=22; w=-7; offset=-7; strand=D; shift=0; score=0.570362; wwtATAAATAAAAATAAAAtww ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 577 569 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 220 259 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 232 221 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887 448 428

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m8_shift2 (positions_6-8nt_m8)				; positions_6-8nt_m8; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwwAAATAAAAcAtww ; Alignment reference a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397
positions_6-8nt_m8_shift2 (positions_6-8nt_m8)				; positions_6-8nt_m8 versus positions_6-8nt_m8; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=2; score= 1; --wwwAAATAAAAcAtww ; cor=; Ncor= a 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 c 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 g 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 t 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)				; positions_6-8nt_m8 versus positions_6-8nt_m2; m=2/7; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.977127; --wwaAAATAAAAcAtww ; cor=; Ncor= a 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 c 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 g 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 t 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445
positions_6-8nt_m10_shift2 (positions_6-8nt_m10)				; positions_6-8nt_m8 versus positions_6-8nt_m10; m=3/7; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.866979; --waaAAATAAAAcmaa- ; cor=; Ncor= a 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 0 c 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 0 g 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 0 t 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319 0
positions_6-8nt_m5_shift2 (positions_6-8nt_m5)				; positions_6-8nt_m8 versus positions_6-8nt_m5; m=4/7; ncol2=18; w=0; offset=0; strand=D; shift=2; score=0.797811; --waaAAATAAAAmAAAa ; cor=; Ncor= a 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 2484 c 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 817 g 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 710 t 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457 1287
dyads_m3_shift1 (dyads_m3)				; positions_6-8nt_m8 versus dyads_m3; m=5/7; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.689867; -wwgAAAATAAAATwa-- ; cor=; Ncor= a 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 0 0 c 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 0 0 g 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 0 0 t 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934 0 0
dyads_m4_shift0 (dyads_m4)				; positions_6-8nt_m8 versus dyads_m4; m=6/7; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.548859; wwtATAAATAAAAATAAA ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206
oligos_6-8nt_m7_shift4 (oligos_6-8nt_m7)				; positions_6-8nt_m8 versus oligos_6-8nt_m7; m=7/7; ncol2=10; w=0; offset=2; strand=D; shift=4; score=0.442381; ----waAATGAAaw---- ; cor=; Ncor= a 0 0 0 0 747 1105 2596 2596 0 0 2579 2596 1120 908 0 0 0 0 c 0 0 0 0 538 506 0 0 0 0 0 0 401 416 0 0 0 0 g 0 0 0 0 598 535 0 0 0 2596 0 0 437 491 0 0 0 0 t 0 0 0 0 713 450 0 0 2596 0 17 0 638 781 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)				; positions_6-8nt_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; yaTACATATGTAtr ; Alignment reference a 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 1731 c 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 645 g 646 1040 159 304 155 368 129 195 98 3081 142 321 659 1142 t 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896 996
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)				; positions_6-8nt_m4 versus positions_6-8nt_m4; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; yaTACATATGTAtr ; cor=; Ncor= a 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 1731 c 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 645 g 646 1040 159 304 155 368 129 195 98 3081 142 321 659 1142 t 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896 996
positions_6-8nt_m7_shift0 (positions_6-8nt_m7)				; positions_6-8nt_m4 versus positions_6-8nt_m7; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.86183; yaTAcATATgTAya ; cor=; Ncor= a 643 1432 162 2736 239 2611 135 2787 98 774 92 2663 457 1964 c 809 406 220 97 2046 86 143 70 330 114 189 96 1269 245 g 410 737 109 162 100 288 105 103 77 1975 86 196 316 552 t 1240 527 2611 107 717 117 2719 142 2597 239 2735 147 1060 341
positions_6-8nt_m6_shift0 (positions_6-8nt_m6)				; positions_6-8nt_m4 versus positions_6-8nt_m6; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.771151; yaTACATAyATay- ; cor=; Ncor= a 1372 2593 207 5369 349 4978 138 5350 577 4374 413 2946 1162 0 c 1476 804 383 132 4165 159 427 148 3341 308 699 767 1560 0 g 811 1299 134 140 280 357 146 112 367 580 360 894 829 0 t 2077 1040 5012 95 942 242 5025 126 1451 474 4264 1129 2185 0
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; positions_6-8nt_m4 versus oligos_6-8nt_m2; m=4/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.647762; taTAyATAya---- ; cor=; Ncor= a 1169 2442 22 5307 41 4480 0 5276 775 2347 0 0 0 0 c 1153 833 22 28 3410 284 22 34 1429 799 0 0 0 0 g 898 1329 19 0 312 363 142 8 751 1024 0 0 0 0 t 2115 731 5272 0 1572 208 5171 17 2380 1165 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m8_shift0 (dyads_m8)				; dyads_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; ykGCCACCrm ; Alignment reference a 536 670 67 33 0 2893 0 0 886 857 c 837 665 49 2834 2835 0 2896 2885 527 828 g 619 804 2757 3 1 0 0 1 782 661 t 904 757 23 26 60 3 0 10 701 550
dyads_m8_shift0 (dyads_m8)				; dyads_m8 versus dyads_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ykGCCACCrm ; cor=; Ncor= a 536 670 67 33 0 2893 0 0 886 857 c 837 665 49 2834 2835 0 2896 2885 527 828 g 619 804 2757 3 1 0 0 1 782 661 t 904 757 23 26 60 3 0 10 701 550
dyads_m10_shift0 (dyads_m10)				; dyads_m8 versus dyads_m10; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.775485; cyACCACCam ; cor=; Ncor= a 602 536 2893 8 8 2785 15 14 1108 864 c 1091 1126 49 2954 2635 82 2941 2828 537 944 g 676 526 3 0 53 2 1 24 616 611 t 599 780 23 6 272 99 11 102 707 549
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)				; dyads_m8 versus oligos_6-8nt_m6; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.762343; tvGACACCwa ; cor=; Ncor= a 360 467 8 1456 0 1408 4 1 380 502 c 315 407 6 3 1301 26 1484 1449 300 327 g 315 430 1347 3 29 1 0 3 342 301 t 498 184 127 26 158 53 0 35 466 358

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; caCACACACACAcACACAcACAca ; Alignment reference a 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 2640 122 2660 159 2544 693 2368 235 2237 450 1624 c 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 111 2736 61 2639 150 1871 158 2429 208 1754 429 g 350 612 146 295 93 255 94 174 86 169 103 193 148 255 78 291 139 271 220 407 186 413 450 665 t 464 374 262 227 187 168 152 158 167 126 163 122 299 112 182 106 181 153 334 185 268 260 464 400
dyads_m5_shift0 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; caCACACACACAcACACAcACAca ; cor=; Ncor= a 523 1725 259 2405 184 2567 183 2711 137 2756 134 2696 593 2640 122 2660 159 2544 693 2368 235 2237 450 1624 c 1781 407 2451 191 2654 128 2689 75 2728 67 2718 107 2078 111 2736 61 2639 150 1871 158 2429 208 1754 429 g 350 612 146 295 93 255 94 174 86 169 103 193 148 255 78 291 139 271 220 407 186 413 450 665 t 464 374 262 227 187 168 152 158 167 126 163 122 299 112 182 106 181 153 334 185 268 260 464 400
positions_6-8nt_m9_shift0 (positions_6-8nt_m9)				; dyads_m5 versus positions_6-8nt_m9; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.635106; cacayACACACAcaca-------- ; cor=; Ncor= a 2454 6125 1654 8218 1448 10684 414 10987 373 11207 382 10654 1441 7656 1974 6009 0 0 0 0 0 0 0 0 c 5594 1857 7827 1133 6501 389 10925 273 10739 235 10835 363 7558 1308 6100 1837 0 0 0 0 0 0 0 0 g 1702 2362 1064 1665 922 752 225 631 287 490 365 706 1358 1847 1706 2611 0 0 0 0 0 0 0 0 t 2515 1921 1720 1249 3394 440 701 374 866 333 683 542 1908 1454 2485 1808 0 0 0 0 0 0 0 0
positions_6-8nt_m1_shift0 (positions_6-8nt_m1)				; dyads_m5 versus positions_6-8nt_m1; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.530786; cacACACACACac----------- ; cor=; Ncor= a 1927 5450 1618 8722 394 9190 339 9378 330 9420 390 5925 1706 0 0 0 0 0 0 0 0 0 0 0 c 5311 1494 6514 413 9285 210 9585 215 9497 136 9181 1164 5574 0 0 0 0 0 0 0 0 0 0 0 g 1318 1945 861 764 178 620 147 490 178 463 356 1813 1415 0 0 0 0 0 0 0 0 0 0 0 t 1797 1464 1360 454 496 333 282 270 348 334 426 1451 1658 0 0 0 0 0 0 0 0 0 0 0
dyads_m9_shift4 (dyads_m9)				; dyads_m5 versus dyads_m9; m=4/4; ncol2=24; w=0; offset=4; strand=D; shift=4; score=0.528148; ----mmCACAcAmACAaCAACAAC ; cor=; Ncor= a 0 0 0 0 171 230 98 478 46 485 130 410 148 501 39 494 377 112 403 443 61 446 424 65 c 0 0 0 0 219 159 401 31 479 34 373 104 360 24 487 33 115 392 94 45 446 60 67 425 g 0 0 0 0 89 110 26 37 19 26 37 32 30 30 20 23 50 35 19 58 31 33 51 36 t 0 0 0 0 85 65 39 18 20 19 24 18 26 9 18 14 22 25 48 18 26 25 22 38

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; oligos_6-8nt_m7; m=0 (reference); ncol1=10; shift=2; ncol=12; --waAATGAAaw ; Alignment reference a 0 0 747 1105 2596 2596 0 0 2579 2596 1120 908 c 0 0 538 506 0 0 0 0 0 0 401 416 g 0 0 598 535 0 0 0 2596 0 0 437 491 t 0 0 713 450 0 0 2596 0 17 0 638 781
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --waAATGAAaw ; cor=; Ncor= a 0 0 747 1105 2596 2596 0 0 2579 2596 1120 908 c 0 0 538 506 0 0 0 0 0 0 401 416 g 0 0 598 535 0 0 0 2596 0 0 437 491 t 0 0 713 450 0 0 2596 0 17 0 638 781
positions_6-8nt_m8_shift0 (positions_6-8nt_m8)				; oligos_6-8nt_m7 versus positions_6-8nt_m8; m=2/3; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.442381; wwwAAATAAAAc ; cor=; Ncor= a 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 c 792 757 586 114 157 154 310 151 197 190 245 2186 g 832 925 545 129 87 138 193 123 110 140 165 415 t 1386 1198 2295 218 291 237 3781 269 290 357 363 993
positions_6-8nt_m2_shift0 (positions_6-8nt_m2)				; oligos_6-8nt_m7 versus positions_6-8nt_m2; m=3/3; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.438558; wwaAAATAAAAc ; cor=; Ncor= a 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 c 901 832 545 143 140 193 316 137 201 184 248 2350 g 922 995 498 125 95 152 222 155 132 136 156 458 t 1443 1293 898 263 297 248 4031 246 313 337 372 1047

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m10_shift8 (positions_6-8nt_m10)				; positions_6-8nt_m10; m=0 (reference); ncol1=15; shift=8; ncol=23; --------waaAAATAAAAcmaa ; Alignment reference a 0 0 0 0 0 0 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 c 0 0 0 0 0 0 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 g 0 0 0 0 0 0 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 t 0 0 0 0 0 0 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319
positions_6-8nt_m10_shift8 (positions_6-8nt_m10)				; positions_6-8nt_m10 versus positions_6-8nt_m10; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=8; score= 1; --------waaAAATAAAAcmaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 c 0 0 0 0 0 0 0 0 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 g 0 0 0 0 0 0 0 0 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 t 0 0 0 0 0 0 0 0 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319
positions_6-8nt_m2_shift8 (positions_6-8nt_m2)				; positions_6-8nt_m10 versus positions_6-8nt_m2; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=8; score=0.89587; --------wwaAAATAAAAcAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 c 0 0 0 0 0 0 0 0 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 g 0 0 0 0 0 0 0 0 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 t 0 0 0 0 0 0 0 0 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371
positions_6-8nt_m8_shift8 (positions_6-8nt_m8)				; positions_6-8nt_m10 versus positions_6-8nt_m8; m=3/6; ncol2=16; w=0; offset=0; strand=D; shift=8; score=0.866979; --------wwwAAATAAAAcAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 c 0 0 0 0 0 0 0 0 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 g 0 0 0 0 0 0 0 0 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 t 0 0 0 0 0 0 0 0 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276
dyads_m3_shift7 (dyads_m3)				; positions_6-8nt_m10 versus dyads_m3; m=4/6; ncol2=15; w=-1; offset=-1; strand=D; shift=7; score=0.793627; -------wwgAAAATAAAATwa- ; cor=; Ncor= a 0 0 0 0 0 0 0 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 0 c 0 0 0 0 0 0 0 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 0 g 0 0 0 0 0 0 0 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 0 t 0 0 0 0 0 0 0 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934 0
positions_6-8nt_m5_shift8 (positions_6-8nt_m5)				; positions_6-8nt_m10 versus positions_6-8nt_m5; m=5/6; ncol2=18; w=0; offset=0; strand=D; shift=8; score=0.768016; --------waaAAATAAAAmAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1982 2168 3449 4724 4736 4513 906 4637 4541 4585 4420 1334 4046 4149 4272 c 0 0 0 0 0 0 0 0 938 883 536 162 167 255 438 183 275 227 254 2642 344 351 297 g 0 0 0 0 0 0 0 0 978 1029 509 138 113 217 320 164 157 141 204 462 353 319 272 t 0 0 0 0 0 0 0 0 1400 1218 804 274 282 313 3634 314 325 345 420 860 555 479 457
dyads_m4_shift0 (dyads_m4)				; positions_6-8nt_m10 versus dyads_m4; m=6/6; ncol2=22; w=-8; offset=-8; strand=D; shift=0; score=0.527705; wwtATAAATAAAAATAAAAtww- ; cor=; Ncor= a 539 656 318 1179 261 1239 1108 1259 240 1206 1100 1177 1130 1188 224 1197 1067 1104 1035 362 577 569 0 c 216 190 120 55 100 46 85 61 110 57 93 77 69 70 99 70 95 94 109 128 220 259 0 g 234 232 99 104 84 54 53 44 59 75 49 54 41 81 67 62 82 73 85 100 232 221 0 t 488 399 940 139 1032 138 231 113 1068 139 235 169 237 138 1087 148 233 206 248 887 448 428 0