One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/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.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m7_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift2 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=22; shift=2; ncol=24; --acrCACACACACAmamACACac ; Alignment reference a 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 1627 150 1026 343 c 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 58 1570 276 1013 g 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 182 108 388 287 t 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95 73 112 250 297

dyads_m7_shift2 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/6; ncol2=22; w=0; offset=0; strand=D; shift=2; score= 1; --acrCACACACACAmamACACac ; cor=; Ncor= a 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 1627 150 1026 343 c 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 58 1570 276 1013 g 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 182 108 388 287 t 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95 73 112 250 297

dyads_m10_shift1 (dyads_m10)
; dyads_m7 versus dyads_m10; m=2/6; ncol2=24; w=-1; offset=-1; strand=D; shift=1; score=0.88003; -caCACACACACACAmmmACAmAc ; cor=; Ncor= a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 1173 107 1153 509 994 307 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 65 1159 75 630 152 647 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 137 68 124 127 160 223 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168 46 87 69 155 115 244

dyads_m5_shift0 (dyads_m5)
; dyads_m7 versus dyads_m5; m=3/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.878265; acrCACACACACACACAcACACac ; cor=; Ncor= a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 2079 129 1987 200 1528 413 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 118 2171 137 2019 279 1453 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 322 135 371 216 537 410 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264 159 243 183 243 334 402

dyads_m3_shift3 (dyads_m3)
; dyads_m7 versus dyads_m3; m=4/6; ncol2=17; w=0; offset=1; strand=D; shift=3; score=0.725947; ---camACACACACACACac---- ; cor=; Ncor= a 0 0 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 0 0 0 0 c 0 0 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 0 0 0 0 g 0 0 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 0 0 0 0 t 0 0 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094 0 0 0 0

oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)
; dyads_m7 versus oligos_6-8nt_m6; m=5/6; ncol2=13; w=0; offset=3; strand=D; shift=5; score=0.529442; -----caCACrCACAsac------ ; cor=; Ncor= a 0 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 0 0 0 0 0 0 c 0 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 0 0 0 0 0 0 g 0 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 0 0 0 0 0 0 t 0 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293 0 0 0 0 0 0

positions_6-8nt_m5_shift6 (positions_6-8nt_m5)
; dyads_m7 versus positions_6-8nt_m5; m=6/6; ncol2=10; w=0; offset=4; strand=D; shift=6; score=0.432557; ------acACACACac-------- ; cor=; Ncor= a 0 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923 0 0 0 0 0 0 0 0

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; cwGCTGTTCbt ; Alignment reference a 1119 1580 265 201 323 171 331 210 244 1268 1256 c 1859 1305 313 4982 184 366 573 314 5164 1404 1326 g 1235 1059 4588 214 189 4990 326 127 68 1403 1378 t 1334 1603 381 150 4851 20 4317 4896 71 1472 1587

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; cwGCTGTTCbt ; cor=; Ncor= a 1119 1580 265 201 323 171 331 210 244 1268 1256 c 1859 1305 313 4982 184 366 573 314 5164 1404 1326 g 1235 1059 4588 214 189 4990 326 127 68 1403 1378 t 1334 1603 381 150 4851 20 4317 4896 71 1472 1587

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3)
; oligos_6-8nt_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -taTAyATAya ; Alignment reference a 0 895 2049 0 4182 0 3711 0 4165 587 1979 c 0 906 617 18 13 2833 183 20 21 1092 536 g 0 647 983 11 0 216 198 121 9 588 802 t 0 1747 546 4166 0 1146 103 4054 0 1928 878

oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -taTAyATAya ; cor=; Ncor= a 0 895 2049 0 4182 0 3711 0 4165 587 1979 c 0 906 617 18 13 2833 183 20 21 1092 536 g 0 647 983 11 0 216 198 121 9 588 802 t 0 1747 546 4166 0 1146 103 4054 0 1928 878

positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; oligos_6-8nt_m3 versus positions_6-8nt_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.661109; atGTATATACa ; cor=; Ncor= a 807 495 208 74 1968 106 1824 55 1915 120 882 c 335 394 64 60 26 131 47 59 59 1716 337 g 466 337 1716 59 59 47 131 26 60 64 394 t 500 882 120 1915 55 1824 106 1968 74 208 495

oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; oligos_6-8nt_m3 versus oligos_6-8nt_m2; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.606888; --atAGATACw ; cor=; Ncor= a 0 0 1041 447 2425 0 2382 0 2537 17 987 c 0 0 427 578 80 52 35 1 25 2256 411 g 0 0 614 435 50 2021 86 46 0 86 412 t 0 0 487 1109 14 496 66 2522 7 210 759

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; oligos_6-8nt_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --atAGATACww ; Alignment reference a 0 0 1041 447 2425 0 2382 0 2537 17 987 715 c 0 0 427 578 80 52 35 1 25 2256 411 627 g 0 0 614 435 50 2021 86 46 0 86 412 500 t 0 0 487 1109 14 496 66 2522 7 210 759 727

oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --atAGATACww ; cor=; Ncor= a 0 0 1041 447 2425 0 2382 0 2537 17 987 715 c 0 0 427 578 80 52 35 1 25 2256 411 627 g 0 0 614 435 50 2021 86 46 0 86 412 500 t 0 0 487 1109 14 496 66 2522 7 210 759 727

positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; oligos_6-8nt_m2 versus positions_6-8nt_m1; m=2/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.644263; atGTATATACat ; cor=; Ncor= a 807 495 208 74 1968 106 1824 55 1915 120 882 500 c 335 394 64 60 26 131 47 59 59 1716 337 466 g 466 337 1716 59 59 47 131 26 60 64 394 335 t 500 882 120 1915 55 1824 106 1968 74 208 495 807

oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3)
; oligos_6-8nt_m2 versus oligos_6-8nt_m3; m=3/3; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.606888; -taTAyATAya- ; cor=; Ncor= a 0 895 2049 0 4182 0 3711 0 4165 587 1979 0 c 0 906 617 18 13 2833 183 20 21 1092 536 0 g 0 647 983 11 0 216 198 121 9 588 802 0 t 0 1747 546 4166 0 1146 103 4054 0 1928 878 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; positions_6-8nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; atGTATATACat ; Alignment reference a 807 495 208 74 1968 106 1824 55 1915 120 882 500 c 335 394 64 60 26 131 47 59 59 1716 337 466 g 466 337 1716 59 59 47 131 26 60 64 394 335 t 500 882 120 1915 55 1824 106 1968 74 208 495 807

positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; atGTATATACat ; cor=; Ncor= a 807 495 208 74 1968 106 1824 55 1915 120 882 500 c 335 394 64 60 26 131 47 59 59 1716 337 466 g 466 337 1716 59 59 47 131 26 60 64 394 335 t 500 882 120 1915 55 1824 106 1968 74 208 495 807

oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3)
; positions_6-8nt_m1 versus oligos_6-8nt_m3; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.661109; -taTAyATAya- ; cor=; Ncor= a 0 895 2049 0 4182 0 3711 0 4165 587 1979 0 c 0 906 617 18 13 2833 183 20 21 1092 536 0 g 0 647 983 11 0 216 198 121 9 588 802 0 t 0 1747 546 4166 0 1146 103 4054 0 1928 878 0

oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; positions_6-8nt_m1 versus oligos_6-8nt_m2; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.644263; --atAGATACww ; cor=; Ncor= a 0 0 1041 447 2425 0 2382 0 2537 17 987 715 c 0 0 427 578 80 52 35 1 25 2256 411 627 g 0 0 614 435 50 2021 86 46 0 86 412 500 t 0 0 487 1109 14 496 66 2522 7 210 759 727

One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 2 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; ykCCGCCGmc ; Alignment reference a 548 654 27 1 38 175 3 5 936 635 c 886 469 2794 2820 105 2497 2826 20 751 1028 g 680 845 0 9 2468 5 3 2751 542 514 t 718 864 11 2 221 155 0 56 603 655

dyads_m8_shift0 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ykCCGCCGmc ; cor=; Ncor= a 548 654 27 1 38 175 3 5 936 635 c 886 469 2794 2820 105 2497 2826 20 751 1028 g 680 845 0 9 2468 5 3 2751 542 514 t 718 864 11 2 221 155 0 56 603 655

One-to-n matrix alignment; reference matrix: positions_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m2_shift0 (positions_6-8nt_m2)
; positions_6-8nt_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; caCATGCAGay ; Alignment reference a 1371 1740 163 4758 329 227 200 5164 57 1739 1305 c 1649 1421 5011 481 328 360 5175 213 212 1442 1486 g 1381 1298 360 283 399 4957 284 181 5370 1259 1325 t 1417 1359 284 296 4762 274 159 260 179 1378 1702

positions_6-8nt_m2_shift0 (positions_6-8nt_m2)
; positions_6-8nt_m2 versus positions_6-8nt_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; caCATGCAGay ; cor=; Ncor= a 1371 1740 163 4758 329 227 200 5164 57 1739 1305 c 1649 1421 5011 481 328 360 5175 213 212 1442 1486 g 1381 1298 360 283 399 4957 284 181 5370 1259 1325 t 1417 1359 284 296 4762 274 159 260 179 1378 1702

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift4 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m6_shift4 (oligos_6-8nt_m6)
; oligos_6-8nt_m6; m=0 (reference); ncol1=13; shift=4; ncol=17; ----caCACrCACAsac ; Alignment reference a 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 c 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 g 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 t 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293

oligos_6-8nt_m6_shift4 (oligos_6-8nt_m6)
; oligos_6-8nt_m6 versus oligos_6-8nt_m6; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=4; score= 1; ----caCACrCACAsac ; cor=; Ncor= a 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 c 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 g 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 t 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293

positions_6-8nt_m5_shift5 (positions_6-8nt_m5)
; oligos_6-8nt_m6 versus positions_6-8nt_m5; m=2/7; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.68515; -----acACACACac-- ; cor=; Ncor= a 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 0 0 c 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 0 0 g 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 0 0 t 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923 0 0

dyads_m3_shift0 (dyads_m3)
; oligos_6-8nt_m6 versus dyads_m3; m=3/7; ncol2=17; w=-4; offset=-4; strand=D; shift=0; score=0.684689; camACACACACACACac ; cor=; Ncor= a 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 c 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 g 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 t 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094

oligos_6-8nt_m7_shift5 (oligos_6-8nt_m7)
; oligos_6-8nt_m6 versus oligos_6-8nt_m7; m=4/7; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.576116; -----ayACTCAChc-- ; cor=; Ncor= a 0 0 0 0 0 642 415 2030 0 9 69 1838 0 629 490 0 0 c 0 0 0 0 0 482 777 14 2059 34 1918 92 2033 527 732 0 0 g 0 0 0 0 0 499 224 4 4 0 4 6 4 301 333 0 0 t 0 0 0 0 0 440 647 15 0 2020 72 127 26 606 508 0 0

dyads_m7_shift1 (dyads_m7)
; oligos_6-8nt_m6 versus dyads_m7; m=5/7; ncol2=22; w=-3; offset=-3; strand=D; shift=1; score=0.529442; -acrCACACACACAmam ; cor=; Ncor= a 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 c 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 g 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 t 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198

dyads_m10_shift0 (dyads_m10)
; oligos_6-8nt_m6 versus dyads_m10; m=6/7; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.480294; caCACACACACACAmmm ; cor=; Ncor= a 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 c 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 g 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 t 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168

dyads_m5_shift3 (dyads_m5)
; oligos_6-8nt_m6 versus dyads_m5; m=7/7; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.476988; ---acrCACACACACAC ; cor=; Ncor= a 0 0 0 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 c 0 0 0 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 g 0 0 0 498 291 828 71 237 75 151 60 149 73 153 110 177 53 t 0 0 0 431 398 288 210 179 149 160 129 117 120 118 258 103 139

One-to-n matrix alignment; reference matrix: positions_6-8nt_m4_shift9 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m4_shift9 (positions_6-8nt_m4)
; positions_6-8nt_m4; m=0 (reference); ncol1=12; shift=9; ncol=21; ---------wwAATAATAAww ; Alignment reference a 0 0 0 0 0 0 0 0 0 2260 2331 5328 5299 723 5275 5253 631 5235 5243 2150 2257 c 0 0 0 0 0 0 0 0 0 934 1129 123 92 337 100 119 399 124 137 1086 991 g 0 0 0 0 0 0 0 0 0 1004 801 121 97 127 122 104 194 117 127 767 866 t 0 0 0 0 0 0 0 0 0 1546 1483 172 256 4557 247 268 4520 268 237 1741 1630

positions_6-8nt_m4_shift9 (positions_6-8nt_m4)
; positions_6-8nt_m4 versus positions_6-8nt_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=9; score= 1; ---------wwAATAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2260 2331 5328 5299 723 5275 5253 631 5235 5243 2150 2257 c 0 0 0 0 0 0 0 0 0 934 1129 123 92 337 100 119 399 124 137 1086 991 g 0 0 0 0 0 0 0 0 0 1004 801 121 97 127 122 104 194 117 127 767 866 t 0 0 0 0 0 0 0 0 0 1546 1483 172 256 4557 247 268 4520 268 237 1741 1630

dyads_m2_shift0 (dyads_m2)
; positions_6-8nt_m4 versus dyads_m2; m=2/2; ncol2=21; w=-9; offset=-9; strand=D; shift=0; score=0.402991; wwrAAAATAtAAATAAAAtww ; cor=; Ncor= a 427 352 272 825 897 886 901 171 872 231 892 866 889 149 857 850 891 806 215 418 413 c 167 169 88 66 36 38 33 66 48 61 48 53 44 81 57 57 39 52 79 168 189 g 155 207 549 53 56 32 36 52 68 68 38 37 46 71 58 47 29 47 64 179 171 t 317 338 157 122 77 110 96 777 78 706 88 110 87 765 94 112 107 161 708 301 293

One-to-n matrix alignment; reference matrix: positions_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; positions_6-8nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wwCGTCAAcr ; Alignment reference a 246 282 0 0 0 0 809 964 223 279 c 211 209 983 0 0 983 6 9 288 214 g 243 208 0 983 0 0 29 5 232 265 t 283 284 0 0 983 0 139 5 240 225

positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; positions_6-8nt_m3 versus positions_6-8nt_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wwCGTCAAcr ; cor=; Ncor= a 246 282 0 0 0 0 809 964 223 279 c 211 209 983 0 0 983 6 9 288 214 g 243 208 0 983 0 0 29 5 232 265 t 283 284 0 0 983 0 139 5 240 225

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)
; oligos_6-8nt_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waAATGAAaw ; Alignment reference a 700 1027 2381 2381 0 0 2381 2381 1101 836 c 482 452 0 0 0 0 0 0 337 368 g 529 495 0 0 0 2381 0 0 374 440 t 670 407 0 0 2381 0 0 0 569 737

oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)
; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; waAATGAAaw ; cor=; Ncor= a 700 1027 2381 2381 0 0 2381 2381 1101 836 c 482 452 0 0 0 0 0 0 337 368 g 529 495 0 0 0 2381 0 0 374 440 t 670 407 0 0 2381 0 0 0 569 737

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 7 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; acrCACACACACACACAcACACac ; Alignment reference a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 2079 129 1987 200 1528 413 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 118 2171 137 2019 279 1453 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 322 135 371 216 537 410 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264 159 243 183 243 334 402

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; acrCACACACACACACAcACACac ; cor=; Ncor= a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 2079 129 1987 200 1528 413 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 118 2171 137 2019 279 1453 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 322 135 371 216 537 410 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264 159 243 183 243 334 402

dyads_m10_shift1 (dyads_m10)
; dyads_m5 versus dyads_m10; m=2/6; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.883573; -caCACACACACACAmmmACAmAc ; cor=; Ncor= a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 1173 107 1153 509 994 307 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 65 1159 75 630 152 647 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 137 68 124 127 160 223 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168 46 87 69 155 115 244

dyads_m7_shift2 (dyads_m7)
; dyads_m5 versus dyads_m7; m=3/6; ncol2=22; w=0; offset=2; strand=D; shift=2; score=0.878265; --acrCACACACACAmamACACac ; cor=; Ncor= a 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 1627 150 1026 343 c 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 58 1570 276 1013 g 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 182 108 388 287 t 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95 73 112 250 297

dyads_m3_shift1 (dyads_m3)
; dyads_m5 versus dyads_m3; m=4/6; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.690974; -camACACACACACACac------ ; cor=; Ncor= a 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 0 0 0 0 0 0 c 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 0 0 0 0 0 0 g 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 0 0 0 0 0 0 t 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094 0 0 0 0 0 0

oligos_6-8nt_m6_shift1 (oligos_6-8nt_m6)
; dyads_m5 versus oligos_6-8nt_m6; m=5/6; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.476988; -caCACrCACAsac---------- ; cor=; Ncor= a 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 0 0 0 0 0 0 0 0 0 0 c 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 0 0 0 0 0 0 0 0 0 0 g 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 0 0 0 0 0 0 0 0 0 0 t 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293 0 0 0 0 0 0 0 0 0 0

positions_6-8nt_m5_shift2 (positions_6-8nt_m5)
; dyads_m5 versus positions_6-8nt_m5; m=6/6; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.400579; --acACACACac------------ ; cor=; Ncor= a 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 1164 365 0 1 0 5 0 10 898 737 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 646 1173 0 156 69 187 50 47 920 923 0 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; tvGACACCta ; Alignment reference a 343 490 6 1351 0 1234 5 2 314 480 c 267 353 7 2 1177 40 1367 1339 306 342 g 316 401 1252 3 33 1 2 13 294 238 t 461 143 122 31 177 112 13 33 473 327

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; tvGACACCta ; cor=; Ncor= a 343 490 6 1351 0 1234 5 2 314 480 c 267 353 7 2 1177 40 1367 1339 306 342 g 316 401 1252 3 33 1 2 13 294 238 t 461 143 122 31 177 112 13 33 473 327

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 1393 1372 362 3626 251 256 3765 3938 248 1372 1131 c 869 823 352 169 143 135 177 58 116 884 928 g 992 1088 466 196 3588 3657 112 99 3597 784 1201 t 919 890 2993 182 191 125 119 78 212 1133 913

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 1393 1372 362 3626 251 256 3765 3938 248 1372 1131 c 869 823 352 169 143 135 177 58 116 884 928 g 992 1088 466 196 3588 3657 112 99 3597 784 1201 t 919 890 2993 182 191 125 119 78 212 1133 913

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 2 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; wwCTTATCAwy ; Alignment reference a 1315 1240 278 206 228 4297 201 236 3918 1294 1114 c 1116 1072 3945 98 226 225 219 4132 183 1139 1306 g 856 1159 258 116 171 128 150 120 403 1091 780 t 1485 1301 291 4352 4147 122 4202 284 268 1248 1572

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCTTATCAwy ; cor=; Ncor= a 1315 1240 278 206 228 4297 201 236 3918 1294 1114 c 1116 1072 3945 98 226 225 219 4132 183 1139 1306 g 856 1159 258 116 171 128 150 120 403 1091 780 t 1485 1301 291 4352 4147 122 4202 284 268 1248 1572

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; gcrGCAGCAGCAGca ; Alignment reference a 722 543 969 213 135 2681 180 126 2607 225 131 2678 326 562 1446 c 567 1412 256 219 2785 88 78 2767 103 91 2789 96 111 1601 455 g 1306 606 1613 2544 135 199 2774 125 221 2742 117 164 2556 486 645 t 515 549 272 134 55 142 78 92 179 52 73 172 117 461 564

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/1; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gcrGCAGCAGCAGca ; cor=; Ncor= a 722 543 969 213 135 2681 180 126 2607 225 131 2678 326 562 1446 c 567 1412 256 219 2785 88 78 2767 103 91 2789 96 111 1601 455 g 1306 606 1613 2544 135 199 2774 125 221 2742 117 164 2556 486 645 t 515 549 272 134 55 142 78 92 179 52 73 172 117 461 564

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m7_shift1 (oligos_6-8nt_m7)
; oligos_6-8nt_m7; m=0 (reference); ncol1=10; shift=1; ncol=11; -ayACTCAChc ; Alignment reference a 0 642 415 2030 0 9 69 1838 0 629 490 c 0 482 777 14 2059 34 1918 92 2033 527 732 g 0 499 224 4 4 0 4 6 4 301 333 t 0 440 647 15 0 2020 72 127 26 606 508

oligos_6-8nt_m7_shift1 (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=1; score= 1; -ayACTCAChc ; cor=; Ncor= a 0 642 415 2030 0 9 69 1838 0 629 490 c 0 482 777 14 2059 34 1918 92 2033 527 732 g 0 499 224 4 4 0 4 6 4 301 333 t 0 440 647 15 0 2020 72 127 26 606 508

positions_6-8nt_m5_shift1 (positions_6-8nt_m5)
; oligos_6-8nt_m7 versus positions_6-8nt_m5; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.754717; -acACACACac ; cor=; Ncor= a 0 3234 818 5808 0 5705 0 5739 0 3405 906 c 0 764 3452 0 5651 34 5616 19 5751 585 3242 g 0 1164 365 0 1 0 5 0 10 898 737 t 0 646 1173 0 156 69 187 50 47 920 923

oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m7 versus oligos_6-8nt_m6; m=3/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.576116; caCACrCACAs ; cor=; Ncor= a 1205 3191 667 5998 113 2198 176 6219 77 6071 509 c 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 g 914 1368 531 199 144 3808 151 140 139 219 2126 t 1117 993 453 291 149 378 137 114 100 227 760

One-to-n matrix alignment; reference matrix: dyads_m9_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift3 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=17; shift=3; ncol=20; ---agrGAGAGAGAGAGrga ; Alignment reference a 0 0 0 1657 610 1459 259 2892 258 2908 225 2732 196 2915 150 2821 221 1338 635 1635 c 0 0 0 567 464 338 225 234 97 234 90 266 91 205 86 241 119 426 447 622 g 0 0 0 702 1976 1356 2812 153 2993 149 3025 284 3045 182 3108 200 2952 1465 1993 798 t 0 0 0 494 370 267 124 141 72 129 80 138 88 118 76 158 128 191 345 365

dyads_m9_shift3 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---agrGAGAGAGAGAGrga ; cor=; Ncor= a 0 0 0 1657 610 1459 259 2892 258 2908 225 2732 196 2915 150 2821 221 1338 635 1635 c 0 0 0 567 464 338 225 234 97 234 90 266 91 205 86 241 119 426 447 622 g 0 0 0 702 1976 1356 2812 153 2993 149 3025 284 3045 182 3108 200 2952 1465 1993 798 t 0 0 0 494 370 267 124 141 72 129 80 138 88 118 76 158 128 191 345 365

dyads_m1_shift2 (dyads_m1)
; dyads_m9 versus dyads_m1; m=2/3; ncol2=18; w=-1; offset=-1; strand=D; shift=2; score=0.912603; --gaGrGAGAGrGAGAGrga ; cor=; Ncor= a 0 0 507 1361 325 1047 182 2307 112 2255 163 1039 186 2322 100 2276 243 1032 549 1258 c 0 0 356 421 229 206 121 159 78 161 118 227 78 113 63 155 171 293 347 481 g 0 0 1582 565 1992 1321 2365 191 2500 202 2356 1348 2413 223 2511 190 2177 1252 1561 676 t 0 0 323 421 222 194 100 111 78 150 131 154 91 110 94 147 177 191 311 353

dyads_m6_rc_shift0 (dyads_m6_rc)
; dyads_m9 versus dyads_m6_rc; m=3/3; ncol2=19; w=-3; offset=-3; strand=R; shift=0; score=0.620492; rrGAGarrgagrgrGAGrr- ; cor=; Ncor= a 1831 2667 133 6137 125 2777 1833 2549 1318 3293 1319 2791 1689 2808 130 6193 132 2608 1889 0 c 1115 1300 150 154 217 1050 955 1355 1026 986 1196 989 1075 1289 154 132 214 1168 1006 0 g 2699 1894 6387 292 6302 1702 3039 1896 3531 1345 3414 1985 2924 1861 6363 282 6311 1785 2778 0 t 1262 1046 237 324 263 1378 1080 1107 1032 1283 978 1142 1219 949 260 300 250 1346 1234 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift1 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=17; shift=1; ncol=18; -camACACACACACACac ; Alignment reference a 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 c 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 g 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 t 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094

dyads_m3_shift1 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/6; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -camACACACACACACac ; cor=; Ncor= a 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 c 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 g 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 t 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094

dyads_m7_shift0 (dyads_m7)
; dyads_m3 versus dyads_m7; m=2/6; ncol2=22; w=-1; offset=-1; strand=D; shift=0; score=0.725947; acrCACACACACAmamAC ; cor=; Ncor= a 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 c 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 g 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 t 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95

dyads_m5_shift0 (dyads_m5)
; dyads_m3 versus dyads_m5; m=3/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.690974; acrCACACACACACACAc ; cor=; Ncor= a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264

dyads_m10_shift1 (dyads_m10)
; dyads_m3 versus dyads_m10; m=4/6; ncol2=24; w=0; offset=0; strand=D; shift=1; score=0.687919; -caCACACACACACAmmm ; cor=; Ncor= a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168

oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)
; dyads_m3 versus oligos_6-8nt_m6; m=5/6; ncol2=13; w=0; offset=4; strand=D; shift=5; score=0.684689; -----caCACrCACAsac ; cor=; Ncor= a 0 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 c 0 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 g 0 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 t 0 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293

positions_6-8nt_m5_shift8 (positions_6-8nt_m5)
; dyads_m3 versus positions_6-8nt_m5; m=6/6; ncol2=10; w=0; offset=7; strand=D; shift=8; score=0.564274; --------acACACACac ; cor=; Ncor= a 0 0 0 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 c 0 0 0 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 g 0 0 0 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 t 0 0 0 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923

One-to-n matrix alignment; reference matrix: dyads_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift2 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=18; shift=2; ncol=20; --gaGrGAGAGrGAGAGrga ; Alignment reference a 0 0 507 1361 325 1047 182 2307 112 2255 163 1039 186 2322 100 2276 243 1032 549 1258 c 0 0 356 421 229 206 121 159 78 161 118 227 78 113 63 155 171 293 347 481 g 0 0 1582 565 1992 1321 2365 191 2500 202 2356 1348 2413 223 2511 190 2177 1252 1561 676 t 0 0 323 421 222 194 100 111 78 150 131 154 91 110 94 147 177 191 311 353

dyads_m1_shift2 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=2; score= 1; --gaGrGAGAGrGAGAGrga ; cor=; Ncor= a 0 0 507 1361 325 1047 182 2307 112 2255 163 1039 186 2322 100 2276 243 1032 549 1258 c 0 0 356 421 229 206 121 159 78 161 118 227 78 113 63 155 171 293 347 481 g 0 0 1582 565 1992 1321 2365 191 2500 202 2356 1348 2413 223 2511 190 2177 1252 1561 676 t 0 0 323 421 222 194 100 111 78 150 131 154 91 110 94 147 177 191 311 353

dyads_m9_shift3 (dyads_m9)
; dyads_m1 versus dyads_m9; m=2/3; ncol2=17; w=0; offset=1; strand=D; shift=3; score=0.912603; ---agrGAGAGAGAGAGrga ; cor=; Ncor= a 0 0 0 1657 610 1459 259 2892 258 2908 225 2732 196 2915 150 2821 221 1338 635 1635 c 0 0 0 567 464 338 225 234 97 234 90 266 91 205 86 241 119 426 447 622 g 0 0 0 702 1976 1356 2812 153 2993 149 3025 284 3045 182 3108 200 2952 1465 1993 798 t 0 0 0 494 370 267 124 141 72 129 80 138 88 118 76 158 128 191 345 365

dyads_m6_rc_shift0 (dyads_m6_rc)
; dyads_m1 versus dyads_m6_rc; m=3/3; ncol2=19; w=-2; offset=-2; strand=R; shift=0; score=0.665382; rrGAGarrgagrgrGAGrr- ; cor=; Ncor= a 1831 2667 133 6137 125 2777 1833 2549 1318 3293 1319 2791 1689 2808 130 6193 132 2608 1889 0 c 1115 1300 150 154 217 1050 955 1355 1026 986 1196 989 1075 1289 154 132 214 1168 1006 0 g 2699 1894 6387 292 6302 1702 3039 1896 3531 1345 3414 1985 2924 1861 6363 282 6311 1785 2778 0 t 1262 1046 237 324 263 1378 1080 1107 1032 1283 978 1142 1219 949 260 300 250 1346 1234 0

One-to-n matrix alignment; reference matrix: dyads_m10_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift1 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=24; shift=1; ncol=25; -caCACACACACACAmmmACAmAca ; Alignment reference a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 1173 107 1153 509 994 307 654 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 65 1159 75 630 152 647 233 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 137 68 124 127 160 223 329 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168 46 87 69 155 115 244 205

dyads_m10_shift1 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -caCACACACACACAmmmACAmAca ; cor=; Ncor= a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 1173 107 1153 509 994 307 654 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 65 1159 75 630 152 647 233 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 137 68 124 127 160 223 329 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168 46 87 69 155 115 244 205

dyads_m5_shift0 (dyads_m5)
; dyads_m10 versus dyads_m5; m=2/5; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.883573; acrCACACACACACACAcACACac- ; cor=; Ncor= a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 2079 129 1987 200 1528 413 0 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 118 2171 137 2019 279 1453 0 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 322 135 371 216 537 410 0 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264 159 243 183 243 334 402 0

dyads_m7_shift2 (dyads_m7)
; dyads_m10 versus dyads_m7; m=3/5; ncol2=22; w=0; offset=1; strand=D; shift=2; score=0.88003; --acrCACACACACAmamACACac- ; cor=; Ncor= a 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 1627 150 1026 343 0 c 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 58 1570 276 1013 0 g 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 182 108 388 287 0 t 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95 73 112 250 297 0

dyads_m3_shift1 (dyads_m3)
; dyads_m10 versus dyads_m3; m=4/5; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.687919; -camACACACACACACac------- ; cor=; Ncor= a 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 0 0 0 0 0 0 0 c 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 0 0 0 0 0 0 0 g 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 0 0 0 0 0 0 0 t 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094 0 0 0 0 0 0 0

oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)
; dyads_m10 versus oligos_6-8nt_m6; m=5/5; ncol2=13; w=0; offset=4; strand=D; shift=5; score=0.480294; -----caCACrCACAsac------- ; cor=; Ncor= a 0 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 0 0 0 0 0 0 0 c 0 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 0 0 0 0 0 0 0 g 0 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 0 0 0 0 0 0 0 t 0 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293 0 0 0 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=21; shift=0; ncol=21; wwrAAAATAtAAATAAAAtww ; Alignment reference a 427 352 272 825 897 886 901 171 872 231 892 866 889 149 857 850 891 806 215 418 413 c 167 169 88 66 36 38 33 66 48 61 48 53 44 81 57 57 39 52 79 168 189 g 155 207 549 53 56 32 36 52 68 68 38 37 46 71 58 47 29 47 64 179 171 t 317 338 157 122 77 110 96 777 78 706 88 110 87 765 94 112 107 161 708 301 293

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/2; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; wwrAAAATAtAAATAAAAtww ; cor=; Ncor= a 427 352 272 825 897 886 901 171 872 231 892 866 889 149 857 850 891 806 215 418 413 c 167 169 88 66 36 38 33 66 48 61 48 53 44 81 57 57 39 52 79 168 189 g 155 207 549 53 56 32 36 52 68 68 38 37 46 71 58 47 29 47 64 179 171 t 317 338 157 122 77 110 96 777 78 706 88 110 87 765 94 112 107 161 708 301 293

positions_6-8nt_m4_shift9 (positions_6-8nt_m4)
; dyads_m2 versus positions_6-8nt_m4; m=2/2; ncol2=12; w=0; offset=9; strand=D; shift=9; score=0.402991; ---------wwAATAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2260 2331 5328 5299 723 5275 5253 631 5235 5243 2150 2257 c 0 0 0 0 0 0 0 0 0 934 1129 123 92 337 100 119 399 124 137 1086 991 g 0 0 0 0 0 0 0 0 0 1004 801 121 97 127 122 104 194 117 127 767 866 t 0 0 0 0 0 0 0 0 0 1546 1483 172 256 4557 247 268 4520 268 237 1741 1630

One-to-n matrix alignment; reference matrix: positions_6-8nt_m5_shift7 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m5_shift7 (positions_6-8nt_m5)
; positions_6-8nt_m5; m=0 (reference); ncol1=10; shift=7; ncol=17; -------acACACACac ; Alignment reference a 0 0 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 c 0 0 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 g 0 0 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 t 0 0 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923

positions_6-8nt_m5_shift7 (positions_6-8nt_m5)
; positions_6-8nt_m5 versus positions_6-8nt_m5; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=7; score= 1; -------acACACACac ; cor=; Ncor= a 0 0 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 c 0 0 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 g 0 0 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 t 0 0 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923

oligos_6-8nt_m7_shift7 (oligos_6-8nt_m7)
; positions_6-8nt_m5 versus oligos_6-8nt_m7; m=2/6; ncol2=10; w=0; offset=0; strand=D; shift=7; score=0.754717; -------ayACTCAChc ; cor=; Ncor= a 0 0 0 0 0 0 0 642 415 2030 0 9 69 1838 0 629 490 c 0 0 0 0 0 0 0 482 777 14 2059 34 1918 92 2033 527 732 g 0 0 0 0 0 0 0 499 224 4 4 0 4 6 4 301 333 t 0 0 0 0 0 0 0 440 647 15 0 2020 72 127 26 606 508

oligos_6-8nt_m6_shift6 (oligos_6-8nt_m6)
; positions_6-8nt_m5 versus oligos_6-8nt_m6; m=3/6; ncol2=13; w=-1; offset=-1; strand=D; shift=6; score=0.68515; ------caCACrCACAs ; cor=; Ncor= a 0 0 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 c 0 0 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 g 0 0 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 t 0 0 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760

dyads_m3_shift0 (dyads_m3)
; positions_6-8nt_m5 versus dyads_m3; m=4/6; ncol2=17; w=-7; offset=-7; strand=D; shift=0; score=0.564274; camACACACACACACac ; cor=; Ncor= a 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 c 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 g 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 t 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094

dyads_m7_shift3 (dyads_m7)
; positions_6-8nt_m5 versus dyads_m7; m=5/6; ncol2=22; w=-4; offset=-4; strand=D; shift=3; score=0.432557; ---acrCACACACACAm ; cor=; Ncor= a 0 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 c 0 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 g 0 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 t 0 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136

dyads_m5_shift5 (dyads_m5)
; positions_6-8nt_m5 versus dyads_m5; m=6/6; ncol2=24; w=-2; offset=-2; strand=D; shift=5; score=0.400579; -----acrCACACACAC ; cor=; Ncor= a 0 0 0 0 0 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 c 0 0 0 0 0 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 g 0 0 0 0 0 498 291 828 71 237 75 151 60 149 73 153 110 t 0 0 0 0 0 431 398 288 210 179 149 160 129 117 120 118 258

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m10_shift0 ; 2 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; ryGGTCACwc ; Alignment reference a 400 301 27 8 31 34 1333 0 575 342 c 303 444 9 4 0 1382 28 1439 284 591 g 395 210 1423 1444 0 10 1 12 208 242 t 361 504 0 3 1428 33 97 8 392 284

oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m10 versus oligos_6-8nt_m10; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ryGGTCACwc ; cor=; Ncor= a 400 301 27 8 31 34 1333 0 575 342 c 303 444 9 4 0 1382 28 1439 284 591 g 395 210 1423 1444 0 10 1 12 208 242 t 361 504 0 3 1428 33 97 8 392 284

One-to-n matrix alignment; reference matrix: dyads_m6_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift1 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=19; shift=1; ncol=20; -yyCTCycyctcyytCTCyy ; Alignment reference a 0 1234 1346 250 300 260 949 1219 1142 978 1283 1032 1107 1080 1378 263 324 237 1046 1262 c 0 2778 1785 6311 282 6363 1861 2924 1985 3414 1345 3531 1896 3039 1702 6302 292 6387 1894 2699 g 0 1006 1168 214 132 154 1289 1075 989 1196 986 1026 1355 955 1050 217 154 150 1300 1115 t 0 1889 2608 132 6193 130 2808 1689 2791 1319 3293 1318 2549 1833 2777 125 6137 133 2667 1831

dyads_m6_shift1 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -yyCTCycyctcyytCTCyy ; cor=; Ncor= a 0 1234 1346 250 300 260 949 1219 1142 978 1283 1032 1107 1080 1378 263 324 237 1046 1262 c 0 2778 1785 6311 282 6363 1861 2924 1985 3414 1345 3531 1896 3039 1702 6302 292 6387 1894 2699 g 0 1006 1168 214 132 154 1289 1075 989 1196 986 1026 1355 955 1050 217 154 150 1300 1115 t 0 1889 2608 132 6193 130 2808 1689 2791 1319 3293 1318 2549 1833 2777 125 6137 133 2667 1831

dyads_m1_rc_shift0 (dyads_m1_rc)
; dyads_m6 versus dyads_m1_rc; m=2/3; ncol2=18; w=-1; offset=-1; strand=R; shift=0; score=0.665382; tcyCTCTCyCTCTCyCtc-- ; cor=; Ncor= a 353 311 191 177 147 94 110 91 154 131 150 78 111 100 194 222 421 323 0 0 c 676 1561 1252 2177 190 2511 223 2413 1348 2356 202 2500 191 2365 1321 1992 565 1582 0 0 g 481 347 293 171 155 63 113 78 227 118 161 78 159 121 206 229 421 356 0 0 t 1258 549 1032 243 2276 100 2322 186 1039 163 2255 112 2307 182 1047 325 1361 507 0 0

dyads_m9_rc_shift0 (dyads_m9_rc)
; dyads_m6 versus dyads_m9_rc; m=3/3; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.620492; tcyCTCTCTCTCTCyct--- ; cor=; Ncor= a 365 345 191 128 158 76 118 88 138 80 129 72 141 124 267 370 494 0 0 0 c 798 1993 1465 2952 200 3108 182 3045 284 3025 149 2993 153 2812 1356 1976 702 0 0 0 g 622 447 426 119 241 86 205 91 266 90 234 97 234 225 338 464 567 0 0 0 t 1635 635 1338 221 2821 150 2915 196 2732 225 2908 258 2892 259 1459 610 1657 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift2 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=22; shift=2; ncol=24; --acrCACACACACAmamACACac ; Alignment reference a 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 1627 150 1026 343 c 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 58 1570 276 1013 g 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 182 108 388 287 t 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95 73 112 250 297
dyads_m7_shift2 (dyads_m7)				; dyads_m7 versus dyads_m7; m=1/6; ncol2=22; w=0; offset=0; strand=D; shift=2; score= 1; --acrCACACACACAmamACACac ; cor=; Ncor= a 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 1627 150 1026 343 c 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 58 1570 276 1013 g 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 182 108 388 287 t 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95 73 112 250 297
dyads_m10_shift1 (dyads_m10)				; dyads_m7 versus dyads_m10; m=2/6; ncol2=24; w=-1; offset=-1; strand=D; shift=1; score=0.88003; -caCACACACACACAmmmACAmAc ; cor=; Ncor= a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 1173 107 1153 509 994 307 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 65 1159 75 630 152 647 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 137 68 124 127 160 223 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168 46 87 69 155 115 244
dyads_m5_shift0 (dyads_m5)				; dyads_m7 versus dyads_m5; m=3/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.878265; acrCACACACACACACAcACACac ; cor=; Ncor= a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 2079 129 1987 200 1528 413 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 118 2171 137 2019 279 1453 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 322 135 371 216 537 410 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264 159 243 183 243 334 402
dyads_m3_shift3 (dyads_m3)				; dyads_m7 versus dyads_m3; m=4/6; ncol2=17; w=0; offset=1; strand=D; shift=3; score=0.725947; ---camACACACACACACac---- ; cor=; Ncor= a 0 0 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 0 0 0 0 c 0 0 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 0 0 0 0 g 0 0 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 0 0 0 0 t 0 0 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094 0 0 0 0
oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)				; dyads_m7 versus oligos_6-8nt_m6; m=5/6; ncol2=13; w=0; offset=3; strand=D; shift=5; score=0.529442; -----caCACrCACAsac------ ; cor=; Ncor= a 0 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 0 0 0 0 0 0 c 0 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 0 0 0 0 0 0 g 0 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 0 0 0 0 0 0 t 0 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293 0 0 0 0 0 0
positions_6-8nt_m5_shift6 (positions_6-8nt_m5)				; dyads_m7 versus positions_6-8nt_m5; m=6/6; ncol2=10; w=0; offset=4; strand=D; shift=6; score=0.432557; ------acACACACac-------- ; cor=; Ncor= a 0 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3)				; oligos_6-8nt_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -taTAyATAya ; Alignment reference a 0 895 2049 0 4182 0 3711 0 4165 587 1979 c 0 906 617 18 13 2833 183 20 21 1092 536 g 0 647 983 11 0 216 198 121 9 588 802 t 0 1747 546 4166 0 1146 103 4054 0 1928 878
oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3)				; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -taTAyATAya ; cor=; Ncor= a 0 895 2049 0 4182 0 3711 0 4165 587 1979 c 0 906 617 18 13 2833 183 20 21 1092 536 g 0 647 983 11 0 216 198 121 9 588 802 t 0 1747 546 4166 0 1146 103 4054 0 1928 878
positions_6-8nt_m1_shift0 (positions_6-8nt_m1)				; oligos_6-8nt_m3 versus positions_6-8nt_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.661109; atGTATATACa ; cor=; Ncor= a 807 495 208 74 1968 106 1824 55 1915 120 882 c 335 394 64 60 26 131 47 59 59 1716 337 g 466 337 1716 59 59 47 131 26 60 64 394 t 500 882 120 1915 55 1824 106 1968 74 208 495
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; oligos_6-8nt_m3 versus oligos_6-8nt_m2; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.606888; --atAGATACw ; cor=; Ncor= a 0 0 1041 447 2425 0 2382 0 2537 17 987 c 0 0 427 578 80 52 35 1 25 2256 411 g 0 0 614 435 50 2021 86 46 0 86 412 t 0 0 487 1109 14 496 66 2522 7 210 759

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; oligos_6-8nt_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --atAGATACww ; Alignment reference a 0 0 1041 447 2425 0 2382 0 2537 17 987 715 c 0 0 427 578 80 52 35 1 25 2256 411 627 g 0 0 614 435 50 2021 86 46 0 86 412 500 t 0 0 487 1109 14 496 66 2522 7 210 759 727
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --atAGATACww ; cor=; Ncor= a 0 0 1041 447 2425 0 2382 0 2537 17 987 715 c 0 0 427 578 80 52 35 1 25 2256 411 627 g 0 0 614 435 50 2021 86 46 0 86 412 500 t 0 0 487 1109 14 496 66 2522 7 210 759 727
positions_6-8nt_m1_shift0 (positions_6-8nt_m1)				; oligos_6-8nt_m2 versus positions_6-8nt_m1; m=2/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.644263; atGTATATACat ; cor=; Ncor= a 807 495 208 74 1968 106 1824 55 1915 120 882 500 c 335 394 64 60 26 131 47 59 59 1716 337 466 g 466 337 1716 59 59 47 131 26 60 64 394 335 t 500 882 120 1915 55 1824 106 1968 74 208 495 807
oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3)				; oligos_6-8nt_m2 versus oligos_6-8nt_m3; m=3/3; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.606888; -taTAyATAya- ; cor=; Ncor= a 0 895 2049 0 4182 0 3711 0 4165 587 1979 0 c 0 906 617 18 13 2833 183 20 21 1092 536 0 g 0 647 983 11 0 216 198 121 9 588 802 0 t 0 1747 546 4166 0 1146 103 4054 0 1928 878 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m1_shift0 (positions_6-8nt_m1)				; positions_6-8nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; atGTATATACat ; Alignment reference a 807 495 208 74 1968 106 1824 55 1915 120 882 500 c 335 394 64 60 26 131 47 59 59 1716 337 466 g 466 337 1716 59 59 47 131 26 60 64 394 335 t 500 882 120 1915 55 1824 106 1968 74 208 495 807
positions_6-8nt_m1_shift0 (positions_6-8nt_m1)				; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; atGTATATACat ; cor=; Ncor= a 807 495 208 74 1968 106 1824 55 1915 120 882 500 c 335 394 64 60 26 131 47 59 59 1716 337 466 g 466 337 1716 59 59 47 131 26 60 64 394 335 t 500 882 120 1915 55 1824 106 1968 74 208 495 807
oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3)				; positions_6-8nt_m1 versus oligos_6-8nt_m3; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.661109; -taTAyATAya- ; cor=; Ncor= a 0 895 2049 0 4182 0 3711 0 4165 587 1979 0 c 0 906 617 18 13 2833 183 20 21 1092 536 0 g 0 647 983 11 0 216 198 121 9 588 802 0 t 0 1747 546 4166 0 1146 103 4054 0 1928 878 0
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; positions_6-8nt_m1 versus oligos_6-8nt_m2; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.644263; --atAGATACww ; cor=; Ncor= a 0 0 1041 447 2425 0 2382 0 2537 17 987 715 c 0 0 427 578 80 52 35 1 25 2256 411 627 g 0 0 614 435 50 2021 86 46 0 86 412 500 t 0 0 487 1109 14 496 66 2522 7 210 759 727

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m6_shift4 (oligos_6-8nt_m6)				; oligos_6-8nt_m6; m=0 (reference); ncol1=13; shift=4; ncol=17; ----caCACrCACAsac ; Alignment reference a 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 c 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 g 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 t 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293
oligos_6-8nt_m6_shift4 (oligos_6-8nt_m6)				; oligos_6-8nt_m6 versus oligos_6-8nt_m6; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=4; score= 1; ----caCACrCACAsac ; cor=; Ncor= a 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 c 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 g 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 t 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293
positions_6-8nt_m5_shift5 (positions_6-8nt_m5)				; oligos_6-8nt_m6 versus positions_6-8nt_m5; m=2/7; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.68515; -----acACACACac-- ; cor=; Ncor= a 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 0 0 c 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 0 0 g 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 0 0 t 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923 0 0
dyads_m3_shift0 (dyads_m3)				; oligos_6-8nt_m6 versus dyads_m3; m=3/7; ncol2=17; w=-4; offset=-4; strand=D; shift=0; score=0.684689; camACACACACACACac ; cor=; Ncor= a 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 c 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 g 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 t 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094
oligos_6-8nt_m7_shift5 (oligos_6-8nt_m7)				; oligos_6-8nt_m6 versus oligos_6-8nt_m7; m=4/7; ncol2=10; w=0; offset=1; strand=D; shift=5; score=0.576116; -----ayACTCAChc-- ; cor=; Ncor= a 0 0 0 0 0 642 415 2030 0 9 69 1838 0 629 490 0 0 c 0 0 0 0 0 482 777 14 2059 34 1918 92 2033 527 732 0 0 g 0 0 0 0 0 499 224 4 4 0 4 6 4 301 333 0 0 t 0 0 0 0 0 440 647 15 0 2020 72 127 26 606 508 0 0
dyads_m7_shift1 (dyads_m7)				; oligos_6-8nt_m6 versus dyads_m7; m=5/7; ncol2=22; w=-3; offset=-3; strand=D; shift=1; score=0.529442; -acrCACACACACAmam ; cor=; Ncor= a 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 c 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 g 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 t 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198
dyads_m10_shift0 (dyads_m10)				; oligos_6-8nt_m6 versus dyads_m10; m=6/7; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.480294; caCACACACACACAmmm ; cor=; Ncor= a 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 c 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 g 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 t 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168
dyads_m5_shift3 (dyads_m5)				; oligos_6-8nt_m6 versus dyads_m5; m=7/7; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.476988; ---acrCACACACACAC ; cor=; Ncor= a 0 0 0 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 c 0 0 0 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 g 0 0 0 498 291 828 71 237 75 151 60 149 73 153 110 177 53 t 0 0 0 431 398 288 210 179 149 160 129 117 120 118 258 103 139

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; acrCACACACACACACAcACACac ; Alignment reference a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 2079 129 1987 200 1528 413 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 118 2171 137 2019 279 1453 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 322 135 371 216 537 410 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264 159 243 183 243 334 402
dyads_m5_shift0 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; acrCACACACACACACAcACACac ; cor=; Ncor= a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 2079 129 1987 200 1528 413 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 118 2171 137 2019 279 1453 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 322 135 371 216 537 410 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264 159 243 183 243 334 402
dyads_m10_shift1 (dyads_m10)				; dyads_m5 versus dyads_m10; m=2/6; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.883573; -caCACACACACACAmmmACAmAc ; cor=; Ncor= a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 1173 107 1153 509 994 307 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 65 1159 75 630 152 647 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 137 68 124 127 160 223 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168 46 87 69 155 115 244
dyads_m7_shift2 (dyads_m7)				; dyads_m5 versus dyads_m7; m=3/6; ncol2=22; w=0; offset=2; strand=D; shift=2; score=0.878265; --acrCACACACACAmamACACac ; cor=; Ncor= a 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 1627 150 1026 343 c 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 58 1570 276 1013 g 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 182 108 388 287 t 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95 73 112 250 297
dyads_m3_shift1 (dyads_m3)				; dyads_m5 versus dyads_m3; m=4/6; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.690974; -camACACACACACACac------ ; cor=; Ncor= a 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 0 0 0 0 0 0 c 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 0 0 0 0 0 0 g 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 0 0 0 0 0 0 t 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094 0 0 0 0 0 0
oligos_6-8nt_m6_shift1 (oligos_6-8nt_m6)				; dyads_m5 versus oligos_6-8nt_m6; m=5/6; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.476988; -caCACrCACAsac---------- ; cor=; Ncor= a 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 0 0 0 0 0 0 0 0 0 0 c 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 0 0 0 0 0 0 0 0 0 0 g 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 0 0 0 0 0 0 0 0 0 0 t 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293 0 0 0 0 0 0 0 0 0 0
positions_6-8nt_m5_shift2 (positions_6-8nt_m5)				; dyads_m5 versus positions_6-8nt_m5; m=6/6; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.400579; --acACACACac------------ ; cor=; Ncor= a 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 1164 365 0 1 0 5 0 10 898 737 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 646 1173 0 156 69 187 50 47 920 923 0 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m7_shift1 (oligos_6-8nt_m7)				; oligos_6-8nt_m7; m=0 (reference); ncol1=10; shift=1; ncol=11; -ayACTCAChc ; Alignment reference a 0 642 415 2030 0 9 69 1838 0 629 490 c 0 482 777 14 2059 34 1918 92 2033 527 732 g 0 499 224 4 4 0 4 6 4 301 333 t 0 440 647 15 0 2020 72 127 26 606 508
oligos_6-8nt_m7_shift1 (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=1; score= 1; -ayACTCAChc ; cor=; Ncor= a 0 642 415 2030 0 9 69 1838 0 629 490 c 0 482 777 14 2059 34 1918 92 2033 527 732 g 0 499 224 4 4 0 4 6 4 301 333 t 0 440 647 15 0 2020 72 127 26 606 508
positions_6-8nt_m5_shift1 (positions_6-8nt_m5)				; oligos_6-8nt_m7 versus positions_6-8nt_m5; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.754717; -acACACACac ; cor=; Ncor= a 0 3234 818 5808 0 5705 0 5739 0 3405 906 c 0 764 3452 0 5651 34 5616 19 5751 585 3242 g 0 1164 365 0 1 0 5 0 10 898 737 t 0 646 1173 0 156 69 187 50 47 920 923
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)				; oligos_6-8nt_m7 versus oligos_6-8nt_m6; m=3/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.576116; caCACrCACAs ; cor=; Ncor= a 1205 3191 667 5998 113 2198 176 6219 77 6071 509 c 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 g 914 1368 531 199 144 3808 151 140 139 219 2126 t 1117 993 453 291 149 378 137 114 100 227 760

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m9_shift3 (dyads_m9)				; dyads_m9; m=0 (reference); ncol1=17; shift=3; ncol=20; ---agrGAGAGAGAGAGrga ; Alignment reference a 0 0 0 1657 610 1459 259 2892 258 2908 225 2732 196 2915 150 2821 221 1338 635 1635 c 0 0 0 567 464 338 225 234 97 234 90 266 91 205 86 241 119 426 447 622 g 0 0 0 702 1976 1356 2812 153 2993 149 3025 284 3045 182 3108 200 2952 1465 1993 798 t 0 0 0 494 370 267 124 141 72 129 80 138 88 118 76 158 128 191 345 365
dyads_m9_shift3 (dyads_m9)				; dyads_m9 versus dyads_m9; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---agrGAGAGAGAGAGrga ; cor=; Ncor= a 0 0 0 1657 610 1459 259 2892 258 2908 225 2732 196 2915 150 2821 221 1338 635 1635 c 0 0 0 567 464 338 225 234 97 234 90 266 91 205 86 241 119 426 447 622 g 0 0 0 702 1976 1356 2812 153 2993 149 3025 284 3045 182 3108 200 2952 1465 1993 798 t 0 0 0 494 370 267 124 141 72 129 80 138 88 118 76 158 128 191 345 365
dyads_m1_shift2 (dyads_m1)				; dyads_m9 versus dyads_m1; m=2/3; ncol2=18; w=-1; offset=-1; strand=D; shift=2; score=0.912603; --gaGrGAGAGrGAGAGrga ; cor=; Ncor= a 0 0 507 1361 325 1047 182 2307 112 2255 163 1039 186 2322 100 2276 243 1032 549 1258 c 0 0 356 421 229 206 121 159 78 161 118 227 78 113 63 155 171 293 347 481 g 0 0 1582 565 1992 1321 2365 191 2500 202 2356 1348 2413 223 2511 190 2177 1252 1561 676 t 0 0 323 421 222 194 100 111 78 150 131 154 91 110 94 147 177 191 311 353
dyads_m6_rc_shift0 (dyads_m6_rc)				; dyads_m9 versus dyads_m6_rc; m=3/3; ncol2=19; w=-3; offset=-3; strand=R; shift=0; score=0.620492; rrGAGarrgagrgrGAGrr- ; cor=; Ncor= a 1831 2667 133 6137 125 2777 1833 2549 1318 3293 1319 2791 1689 2808 130 6193 132 2608 1889 0 c 1115 1300 150 154 217 1050 955 1355 1026 986 1196 989 1075 1289 154 132 214 1168 1006 0 g 2699 1894 6387 292 6302 1702 3039 1896 3531 1345 3414 1985 2924 1861 6363 282 6311 1785 2778 0 t 1262 1046 237 324 263 1378 1080 1107 1032 1283 978 1142 1219 949 260 300 250 1346 1234 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift1 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=17; shift=1; ncol=18; -camACACACACACACac ; Alignment reference a 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 c 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 g 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 t 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094
dyads_m3_shift1 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/6; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -camACACACACACACac ; cor=; Ncor= a 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 c 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 g 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 t 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094
dyads_m7_shift0 (dyads_m7)				; dyads_m3 versus dyads_m7; m=2/6; ncol2=22; w=-1; offset=-1; strand=D; shift=0; score=0.725947; acrCACACACACAmamAC ; cor=; Ncor= a 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 c 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 g 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 t 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95
dyads_m5_shift0 (dyads_m5)				; dyads_m3 versus dyads_m5; m=3/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.690974; acrCACACACACACACAc ; cor=; Ncor= a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264
dyads_m10_shift1 (dyads_m10)				; dyads_m3 versus dyads_m10; m=4/6; ncol2=24; w=0; offset=0; strand=D; shift=1; score=0.687919; -caCACACACACACAmmm ; cor=; Ncor= a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168
oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)				; dyads_m3 versus oligos_6-8nt_m6; m=5/6; ncol2=13; w=0; offset=4; strand=D; shift=5; score=0.684689; -----caCACrCACAsac ; cor=; Ncor= a 0 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 c 0 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 g 0 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 t 0 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293
positions_6-8nt_m5_shift8 (positions_6-8nt_m5)				; dyads_m3 versus positions_6-8nt_m5; m=6/6; ncol2=10; w=0; offset=7; strand=D; shift=8; score=0.564274; --------acACACACac ; cor=; Ncor= a 0 0 0 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 c 0 0 0 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 g 0 0 0 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 t 0 0 0 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift2 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=18; shift=2; ncol=20; --gaGrGAGAGrGAGAGrga ; Alignment reference a 0 0 507 1361 325 1047 182 2307 112 2255 163 1039 186 2322 100 2276 243 1032 549 1258 c 0 0 356 421 229 206 121 159 78 161 118 227 78 113 63 155 171 293 347 481 g 0 0 1582 565 1992 1321 2365 191 2500 202 2356 1348 2413 223 2511 190 2177 1252 1561 676 t 0 0 323 421 222 194 100 111 78 150 131 154 91 110 94 147 177 191 311 353
dyads_m1_shift2 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=2; score= 1; --gaGrGAGAGrGAGAGrga ; cor=; Ncor= a 0 0 507 1361 325 1047 182 2307 112 2255 163 1039 186 2322 100 2276 243 1032 549 1258 c 0 0 356 421 229 206 121 159 78 161 118 227 78 113 63 155 171 293 347 481 g 0 0 1582 565 1992 1321 2365 191 2500 202 2356 1348 2413 223 2511 190 2177 1252 1561 676 t 0 0 323 421 222 194 100 111 78 150 131 154 91 110 94 147 177 191 311 353
dyads_m9_shift3 (dyads_m9)				; dyads_m1 versus dyads_m9; m=2/3; ncol2=17; w=0; offset=1; strand=D; shift=3; score=0.912603; ---agrGAGAGAGAGAGrga ; cor=; Ncor= a 0 0 0 1657 610 1459 259 2892 258 2908 225 2732 196 2915 150 2821 221 1338 635 1635 c 0 0 0 567 464 338 225 234 97 234 90 266 91 205 86 241 119 426 447 622 g 0 0 0 702 1976 1356 2812 153 2993 149 3025 284 3045 182 3108 200 2952 1465 1993 798 t 0 0 0 494 370 267 124 141 72 129 80 138 88 118 76 158 128 191 345 365
dyads_m6_rc_shift0 (dyads_m6_rc)				; dyads_m1 versus dyads_m6_rc; m=3/3; ncol2=19; w=-2; offset=-2; strand=R; shift=0; score=0.665382; rrGAGarrgagrgrGAGrr- ; cor=; Ncor= a 1831 2667 133 6137 125 2777 1833 2549 1318 3293 1319 2791 1689 2808 130 6193 132 2608 1889 0 c 1115 1300 150 154 217 1050 955 1355 1026 986 1196 989 1075 1289 154 132 214 1168 1006 0 g 2699 1894 6387 292 6302 1702 3039 1896 3531 1345 3414 1985 2924 1861 6363 282 6311 1785 2778 0 t 1262 1046 237 324 263 1378 1080 1107 1032 1283 978 1142 1219 949 260 300 250 1346 1234 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m10_shift1 (dyads_m10)				; dyads_m10; m=0 (reference); ncol1=24; shift=1; ncol=25; -caCACACACACACAmmmACAmAca ; Alignment reference a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 1173 107 1153 509 994 307 654 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 65 1159 75 630 152 647 233 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 137 68 124 127 160 223 329 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168 46 87 69 155 115 244 205
dyads_m10_shift1 (dyads_m10)				; dyads_m10 versus dyads_m10; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -caCACACACACACAmmmACAmAca ; cor=; Ncor= a 0 244 799 103 1212 72 1275 64 1262 83 1276 87 1296 55 1249 430 742 446 1173 107 1153 509 994 307 654 c 0 826 181 1206 54 1263 39 1279 44 1225 49 1254 25 1278 55 767 393 721 65 1159 75 630 152 647 233 g 0 127 271 37 89 29 55 30 74 49 60 29 68 37 63 108 172 86 137 68 124 127 160 223 329 t 0 224 170 75 66 57 52 48 41 64 36 51 32 51 54 116 114 168 46 87 69 155 115 244 205
dyads_m5_shift0 (dyads_m5)				; dyads_m10 versus dyads_m5; m=2/5; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.883573; acrCACACACACACACAcACACac- ; cor=; Ncor= a 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 2331 100 2347 95 2261 526 2079 129 1987 200 1528 413 0 c 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 67 2386 52 2376 94 1707 118 2171 137 2019 279 1453 0 g 498 291 828 71 237 75 151 60 149 73 153 110 177 53 182 81 193 181 322 135 371 216 537 410 0 t 431 398 288 210 179 149 160 129 117 120 118 258 103 139 97 126 130 264 159 243 183 243 334 402 0
dyads_m7_shift2 (dyads_m7)				; dyads_m10 versus dyads_m7; m=3/5; ncol2=22; w=0; offset=1; strand=D; shift=2; score=0.88003; --acrCACACACACAmamACACac- ; cor=; Ncor= a 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 1017 504 1580 99 1627 150 1026 343 0 c 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 477 1136 85 1685 58 1570 276 1013 0 g 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 296 102 201 61 182 108 388 287 0 t 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136 150 198 74 95 73 112 250 297 0
dyads_m3_shift1 (dyads_m3)				; dyads_m10 versus dyads_m3; m=4/5; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.687919; -camACACACACACACac------- ; cor=; Ncor= a 0 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 0 0 0 0 0 0 0 c 0 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 0 0 0 0 0 0 0 g 0 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 0 0 0 0 0 0 0 t 0 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094 0 0 0 0 0 0 0
oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)				; dyads_m10 versus oligos_6-8nt_m6; m=5/5; ncol2=13; w=0; offset=4; strand=D; shift=5; score=0.480294; -----caCACrCACAsac------- ; cor=; Ncor= a 0 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 3080 1267 0 0 0 0 0 0 0 c 0 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 1267 2856 0 0 0 0 0 0 0 g 0 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 1180 1246 0 0 0 0 0 0 0 t 0 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760 1135 1293 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m5_shift7 (positions_6-8nt_m5)				; positions_6-8nt_m5; m=0 (reference); ncol1=10; shift=7; ncol=17; -------acACACACac ; Alignment reference a 0 0 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 c 0 0 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 g 0 0 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 t 0 0 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923
positions_6-8nt_m5_shift7 (positions_6-8nt_m5)				; positions_6-8nt_m5 versus positions_6-8nt_m5; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=7; score= 1; -------acACACACac ; cor=; Ncor= a 0 0 0 0 0 0 0 3234 818 5808 0 5705 0 5739 0 3405 906 c 0 0 0 0 0 0 0 764 3452 0 5651 34 5616 19 5751 585 3242 g 0 0 0 0 0 0 0 1164 365 0 1 0 5 0 10 898 737 t 0 0 0 0 0 0 0 646 1173 0 156 69 187 50 47 920 923
oligos_6-8nt_m7_shift7 (oligos_6-8nt_m7)				; positions_6-8nt_m5 versus oligos_6-8nt_m7; m=2/6; ncol2=10; w=0; offset=0; strand=D; shift=7; score=0.754717; -------ayACTCAChc ; cor=; Ncor= a 0 0 0 0 0 0 0 642 415 2030 0 9 69 1838 0 629 490 c 0 0 0 0 0 0 0 482 777 14 2059 34 1918 92 2033 527 732 g 0 0 0 0 0 0 0 499 224 4 4 0 4 6 4 301 333 t 0 0 0 0 0 0 0 440 647 15 0 2020 72 127 26 606 508
oligos_6-8nt_m6_shift6 (oligos_6-8nt_m6)				; positions_6-8nt_m5 versus oligos_6-8nt_m6; m=3/6; ncol2=13; w=-1; offset=-1; strand=D; shift=6; score=0.68515; ------caCACrCACAs ; cor=; Ncor= a 0 0 0 0 0 0 1205 3191 667 5998 113 2198 176 6219 77 6071 509 c 0 0 0 0 0 0 3426 1110 5011 174 6256 278 6198 189 6346 145 3267 g 0 0 0 0 0 0 914 1368 531 199 144 3808 151 140 139 219 2126 t 0 0 0 0 0 0 1117 993 453 291 149 378 137 114 100 227 760
dyads_m3_shift0 (dyads_m3)				; positions_6-8nt_m5 versus dyads_m3; m=4/6; ncol2=17; w=-7; offset=-7; strand=D; shift=0; score=0.564274; camACACACACACACac ; cor=; Ncor= a 1474 3831 2188 5727 491 6251 346 6430 357 6381 265 6362 315 6207 443 4256 1058 c 3954 1256 4063 447 6342 253 6641 219 6574 186 6652 195 6539 220 6141 838 4315 g 912 1336 433 824 200 603 171 515 194 603 201 627 243 659 404 1453 1010 t 1137 1054 793 479 444 370 319 313 352 307 359 293 380 391 489 930 1094
dyads_m7_shift3 (dyads_m7)				; positions_6-8nt_m5 versus dyads_m7; m=5/6; ncol2=22; w=-4; offset=-4; strand=D; shift=3; score=0.432557; ---acrCACACACACAm ; cor=; Ncor= a 0 0 0 906 308 840 93 1677 62 1675 79 1712 80 1774 61 1727 490 c 0 0 0 339 1151 161 1728 56 1774 59 1756 69 1740 39 1766 76 1163 g 0 0 0 363 212 762 35 122 40 118 43 100 51 74 53 73 151 t 0 0 0 332 269 177 84 85 64 88 62 59 69 53 60 64 136
dyads_m5_shift5 (dyads_m5)				; positions_6-8nt_m5 versus dyads_m5; m=6/6; ncol2=24; w=-2; offset=-2; strand=D; shift=5; score=0.400579; -----acrCACACACAC ; cor=; Ncor= a 0 0 0 0 0 1325 406 1300 142 2140 147 2290 103 2354 107 2316 447 c 0 0 0 0 0 424 1583 262 2255 122 2307 77 2386 58 2378 91 1863 g 0 0 0 0 0 498 291 828 71 237 75 151 60 149 73 153 110 t 0 0 0 0 0 431 398 288 210 179 149 160 129 117 120 118 258

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m6_shift1 (dyads_m6)				; dyads_m6; m=0 (reference); ncol1=19; shift=1; ncol=20; -yyCTCycyctcyytCTCyy ; Alignment reference a 0 1234 1346 250 300 260 949 1219 1142 978 1283 1032 1107 1080 1378 263 324 237 1046 1262 c 0 2778 1785 6311 282 6363 1861 2924 1985 3414 1345 3531 1896 3039 1702 6302 292 6387 1894 2699 g 0 1006 1168 214 132 154 1289 1075 989 1196 986 1026 1355 955 1050 217 154 150 1300 1115 t 0 1889 2608 132 6193 130 2808 1689 2791 1319 3293 1318 2549 1833 2777 125 6137 133 2667 1831
dyads_m6_shift1 (dyads_m6)				; dyads_m6 versus dyads_m6; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -yyCTCycyctcyytCTCyy ; cor=; Ncor= a 0 1234 1346 250 300 260 949 1219 1142 978 1283 1032 1107 1080 1378 263 324 237 1046 1262 c 0 2778 1785 6311 282 6363 1861 2924 1985 3414 1345 3531 1896 3039 1702 6302 292 6387 1894 2699 g 0 1006 1168 214 132 154 1289 1075 989 1196 986 1026 1355 955 1050 217 154 150 1300 1115 t 0 1889 2608 132 6193 130 2808 1689 2791 1319 3293 1318 2549 1833 2777 125 6137 133 2667 1831
dyads_m1_rc_shift0 (dyads_m1_rc)				; dyads_m6 versus dyads_m1_rc; m=2/3; ncol2=18; w=-1; offset=-1; strand=R; shift=0; score=0.665382; tcyCTCTCyCTCTCyCtc-- ; cor=; Ncor= a 353 311 191 177 147 94 110 91 154 131 150 78 111 100 194 222 421 323 0 0 c 676 1561 1252 2177 190 2511 223 2413 1348 2356 202 2500 191 2365 1321 1992 565 1582 0 0 g 481 347 293 171 155 63 113 78 227 118 161 78 159 121 206 229 421 356 0 0 t 1258 549 1032 243 2276 100 2322 186 1039 163 2255 112 2307 182 1047 325 1361 507 0 0
dyads_m9_rc_shift0 (dyads_m9_rc)				; dyads_m6 versus dyads_m9_rc; m=3/3; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.620492; tcyCTCTCTCTCTCyct--- ; cor=; Ncor= a 365 345 191 128 158 76 118 88 138 80 129 72 141 124 267 370 494 0 0 0 c 798 1993 1465 2952 200 3108 182 3045 284 3025 149 2993 153 2812 1356 1976 702 0 0 0 g 622 447 426 119 241 86 205 91 266 90 234 97 234 225 338 464 567 0 0 0 t 1635 635 1338 221 2821 150 2915 196 2732 225 2908 258 2892 259 1459 610 1657 0 0 0