One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.180905_2026-01-25.180905_kvVFaU/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.2026-01-25.180905_2026-01-25.180905_kvVFaU/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift0 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=19; shift=0; ncol=19; yyCTCyyyctcyyyCTCyy ; Alignment reference a 423 426 86 69 71 289 396 357 312 460 340 339 370 446 82 87 73 327 428 c 885 617 2072 75 2103 638 923 700 1137 411 1132 664 925 592 2073 77 2116 646 869 g 320 424 71 36 48 457 372 343 423 351 372 477 325 372 68 38 31 478 363 t 628 789 27 2076 34 872 565 856 384 1034 412 776 636 846 33 2054 36 805 596

dyads_m7_shift0 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; yyCTCyyyctcyyyCTCyy ; cor=; Ncor= a 423 426 86 69 71 289 396 357 312 460 340 339 370 446 82 87 73 327 428 c 885 617 2072 75 2103 638 923 700 1137 411 1132 664 925 592 2073 77 2116 646 869 g 320 424 71 36 48 457 372 343 423 351 372 477 325 372 68 38 31 478 363 t 628 789 27 2076 34 872 565 856 384 1034 412 776 636 846 33 2054 36 805 596

oligos_6-8nt_m8_rc_shift0 (oligos_6-8nt_m8_rc)
; dyads_m7 versus oligos_6-8nt_m8_rc; m=2/4; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.596904; ctCTCkCTCTCTct----- ; cor=; Ncor= a 267 348 82 91 40 141 63 143 48 129 42 123 212 308 0 0 0 0 0 c 1205 385 1907 146 1989 156 1996 89 1997 83 1923 165 1198 461 0 0 0 0 0 g 337 498 86 176 80 1215 46 140 70 213 92 160 356 454 0 0 0 0 0 t 408 986 142 1804 108 705 112 1845 102 1792 160 1769 451 994 0 0 0 0 0

dyads_m2_shift3 (dyads_m2)
; dyads_m7 versus dyads_m2; m=3/4; ncol2=17; w=0; offset=3; strand=D; shift=3; score=0.592435; ---tccCTCTCyCTCTCyc ; cor=; Ncor= a 0 0 0 133 107 47 51 65 16 31 24 54 61 57 14 41 26 73 152 c 0 0 0 248 507 595 798 81 909 52 848 568 780 87 891 39 824 589 474 g 0 0 0 189 177 111 65 83 27 48 51 105 59 78 34 73 83 74 170 t 0 0 0 431 210 248 87 772 49 870 78 274 101 779 62 848 68 265 205

oligos_6-8nt_m7_shift7 (oligos_6-8nt_m7)
; dyads_m7 versus oligos_6-8nt_m7; m=4/4; ncol2=13; w=0; offset=7; strand=D; shift=7; score=0.42833; -------ycTCCTCCTCst ; cor=; Ncor= a 0 0 0 0 0 0 0 289 345 227 135 82 113 42 91 103 41 137 419 c 0 0 0 0 0 0 0 776 845 190 1522 1682 64 1782 1639 37 1774 518 423 g 0 0 0 0 0 0 0 408 486 193 166 119 60 64 140 59 76 1088 425 t 0 0 0 0 0 0 0 495 292 1358 145 85 1731 80 98 1769 77 225 701

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=14; shift=0; ncol=14; acgCACTCACctay ; Alignment reference a 336 229 199 113 1001 22 76 27 984 29 222 165 328 216 c 276 407 193 832 26 1046 54 1004 36 1030 616 238 274 376 g 243 206 572 77 45 26 33 31 43 36 106 132 242 243 t 264 277 155 97 47 25 956 57 56 24 175 584 275 284

oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4)
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; acgCACTCACctay ; cor=; Ncor= a 336 229 199 113 1001 22 76 27 984 29 222 165 328 216 c 276 407 193 832 26 1046 54 1004 36 1030 616 238 274 376 g 243 206 572 77 45 26 33 31 43 36 106 132 242 243 t 264 277 155 97 47 25 956 57 56 24 175 584 275 284

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; gyCGCCGCCGcc ; Alignment reference a 394 275 67 76 73 57 54 68 61 101 418 352 c 311 600 1501 24 1551 1549 27 1519 1558 83 634 660 g 617 420 65 1583 54 19 1622 84 26 1483 360 307 t 423 450 112 62 67 120 42 74 100 78 333 426

dyads_m6_shift0 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gyCGCCGCCGcc ; cor=; Ncor= a 394 275 67 76 73 57 54 68 61 101 418 352 c 311 600 1501 24 1551 1549 27 1519 1558 83 634 660 g 617 420 65 1583 54 19 1622 84 26 1483 360 307 t 423 450 112 62 67 120 42 74 100 78 333 426

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m8_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m8_shift5 (oligos_6-8nt_m8)
; oligos_6-8nt_m8; m=0 (reference); ncol1=14; shift=5; ncol=19; -----agAGAGAGmGAGag ; Alignment reference a 0 0 0 0 0 994 451 1769 160 1792 102 1845 112 705 108 1804 142 986 408 c 0 0 0 0 0 454 356 160 92 213 70 140 46 1215 80 176 86 498 337 g 0 0 0 0 0 461 1198 165 1923 83 1997 89 1996 156 1989 146 1907 385 1205 t 0 0 0 0 0 308 212 123 42 129 48 143 63 141 40 91 82 348 267

oligos_6-8nt_m8_shift5 (oligos_6-8nt_m8)
; oligos_6-8nt_m8 versus oligos_6-8nt_m8; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----agAGAGAGmGAGag ; cor=; Ncor= a 0 0 0 0 0 994 451 1769 160 1792 102 1845 112 705 108 1804 142 986 408 c 0 0 0 0 0 454 356 160 92 213 70 140 46 1215 80 176 86 498 337 g 0 0 0 0 0 461 1198 165 1923 83 1997 89 1996 156 1989 146 1907 385 1205 t 0 0 0 0 0 308 212 123 42 129 48 143 63 141 40 91 82 348 267

dyads_m2_rc_shift5 (dyads_m2_rc)
; oligos_6-8nt_m8 versus dyads_m2_rc; m=2/3; ncol2=17; w=0; offset=0; strand=R; shift=5; score=0.716906; -----agrGAGAGrGAGAG ; cor=; Ncor= a 0 0 0 0 0 401 205 265 68 848 62 779 101 274 78 870 49 772 87 c 0 0 0 0 0 199 170 74 83 73 34 78 59 105 51 48 27 83 65 g 0 0 0 0 0 245 474 589 824 39 891 87 780 568 848 52 909 81 798 t 0 0 0 0 0 156 152 73 26 41 14 57 61 54 24 31 16 65 51

dyads_m7_rc_shift0 (dyads_m7_rc)
; oligos_6-8nt_m8 versus dyads_m7_rc; m=3/3; ncol2=19; w=-5; offset=-5; strand=R; shift=0; score=0.596904; rrGAGrrrgagrrrGAGrr ; cor=; Ncor= a 596 805 36 2054 33 846 636 776 412 1034 384 856 565 872 34 2076 27 789 628 c 363 478 31 38 68 372 325 477 372 351 423 343 372 457 48 36 71 424 320 g 869 646 2116 77 2073 592 925 664 1132 411 1137 700 923 638 2103 75 2072 617 885 t 428 327 73 87 82 446 370 339 340 460 312 357 396 289 71 69 86 426 423

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift1 ; 4 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=17; shift=1; ncol=18; -acaCACrCACACACrca ; Alignment reference a 0 1034 338 1335 112 1823 67 1084 69 1905 43 1829 38 1801 116 1065 268 1105 c 0 356 1288 220 1843 61 1956 90 1963 40 1991 54 1977 83 1749 184 1253 296 g 0 405 217 340 74 125 48 810 42 118 41 167 44 149 127 643 292 484 t 0 350 302 250 116 136 74 161 71 82 70 95 86 112 153 253 332 260

oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -acaCACrCACACACrca ; cor=; Ncor= a 0 1034 338 1335 112 1823 67 1084 69 1905 43 1829 38 1801 116 1065 268 1105 c 0 356 1288 220 1843 61 1956 90 1963 40 1991 54 1977 83 1749 184 1253 296 g 0 405 217 340 74 125 48 810 42 118 41 167 44 149 127 643 292 484 t 0 350 302 250 116 136 74 161 71 82 70 95 86 112 153 253 332 260

dyads_m1_shift2 (dyads_m1)
; oligos_6-8nt_m2 versus dyads_m1; m=2/3; ncol2=17; w=0; offset=1; strand=D; shift=2; score=0.858366; --caCACACACACACAma ; cor=; Ncor= a 0 0 463 1507 253 2185 135 2382 121 2369 144 2349 109 2337 156 2176 726 1475 c 0 0 1577 336 2171 129 2446 80 2448 76 2367 84 2382 79 2360 164 1447 389 g 0 0 288 553 115 272 47 186 62 207 97 213 86 238 106 274 263 558 t 0 0 434 366 223 176 134 114 131 110 154 116 185 108 140 148 326 340

dyads_m5_shift0 (dyads_m5)
; oligos_6-8nt_m2 versus dyads_m5; m=3/3; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.663638; caCACACACACACAmmmA ; cor=; Ncor= a 139 405 100 566 43 657 42 650 75 634 59 683 30 651 259 328 280 590 c 434 111 571 57 662 22 660 29 613 51 639 22 683 32 357 259 353 47 g 70 134 34 76 15 43 20 46 25 47 22 36 15 41 68 100 51 79 t 108 101 46 52 31 29 29 26 38 19 31 10 23 27 67 64 67 35

One-to-n matrix alignment; reference matrix: dyads_m4_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift1 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=21; shift=1; ncol=22; -wwwAAAATATAAATAAAAwww ; Alignment reference a 0 254 244 168 484 510 504 500 111 510 98 529 488 539 88 515 458 463 446 163 229 220 c 0 89 89 55 36 28 25 31 44 26 38 23 30 26 42 29 45 39 46 56 88 116 g 0 89 99 64 35 37 19 32 17 44 34 25 26 18 26 26 37 28 34 42 109 87 t 0 203 203 348 80 60 87 72 463 55 465 58 91 52 479 65 95 105 109 374 209 212

dyads_m4_shift1 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/3; ncol2=21; w=0; offset=0; strand=D; shift=1; score= 1; -wwwAAAATATAAATAAAAwww ; cor=; Ncor= a 0 254 244 168 484 510 504 500 111 510 98 529 488 539 88 515 458 463 446 163 229 220 c 0 89 89 55 36 28 25 31 44 26 38 23 30 26 42 29 45 39 46 56 88 116 g 0 89 99 64 35 37 19 32 17 44 34 25 26 18 26 26 37 28 34 42 109 87 t 0 203 203 348 80 60 87 72 463 55 465 58 91 52 479 65 95 105 109 374 209 212

dyads_m9_shift0 (dyads_m9)
; dyads_m4 versus dyads_m9; m=2/3; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.667957; wwAAtAAAAATAAATAaww--- ; cor=; Ncor= a 474 514 834 903 287 911 916 966 928 992 171 1029 966 1026 183 1004 797 491 446 0 0 0 c 193 202 100 87 93 64 63 72 71 54 77 50 61 49 75 42 111 183 196 0 0 0 g 193 167 94 65 66 101 53 42 38 66 42 48 33 46 61 50 80 182 175 0 0 0 t 344 321 176 149 758 128 172 124 167 92 914 77 144 83 885 108 216 348 387 0 0 0

oligos_6-8nt_m3_shift6 (oligos_6-8nt_m3)
; dyads_m4 versus oligos_6-8nt_m3; m=3/3; ncol2=13; w=0; offset=5; strand=D; shift=6; score=0.520655; ------wwaATAAATAAww--- ; cor=; Ncor= a 0 0 0 0 0 0 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 0 0 0 c 0 0 0 0 0 0 423 379 194 186 84 59 90 76 107 49 150 395 415 0 0 0 g 0 0 0 0 0 0 386 352 185 227 50 42 62 55 61 55 132 371 357 0 0 0 t 0 0 0 0 0 0 772 694 453 339 2110 127 186 121 2142 112 291 702 790 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 3 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; ykGCCACCrv ; Alignment reference a 176 193 19 7 0 866 0 0 272 236 c 246 210 15 856 862 0 867 867 169 251 g 192 222 822 2 1 0 0 0 223 218 t 253 242 11 2 4 1 0 0 203 162

dyads_m8_shift0 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ykGCCACCrv ; cor=; Ncor= a 176 193 19 7 0 866 0 0 272 236 c 246 210 15 856 862 0 867 867 169 251 g 192 222 822 2 1 0 0 0 223 218 t 253 242 11 2 4 1 0 0 203 162

dyads_m10_shift0 (dyads_m10)
; dyads_m8 versus dyads_m10; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.776732; ccACCACCam ; cor=; Ncor= a 190 149 854 1 1 825 2 2 331 254 c 344 366 15 878 775 30 874 853 171 293 g 186 158 0 0 19 1 0 3 177 177 t 160 207 11 1 85 24 4 22 201 156

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=11; shift=0; ncol=11; agAAGAAGAag ; Alignment reference a 927 628 2374 2345 13 2445 2419 27 2141 910 646 c 584 653 121 135 52 71 74 82 231 539 681 g 586 1057 185 160 2588 150 161 2523 203 649 968 t 653 412 70 110 97 84 96 118 175 652 455

oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)
; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; agAAGAAGAag ; cor=; Ncor= a 927 628 2374 2345 13 2445 2419 27 2141 910 646 c 584 653 121 135 52 71 74 82 231 539 681 g 586 1057 185 160 2588 150 161 2523 203 649 968 t 653 412 70 110 97 84 96 118 175 652 455

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=12; shift=0; ncol=12; wbGAACTGAAaa ; Alignment reference a 348 238 100 1025 1049 82 58 29 974 1039 365 335 c 215 322 51 68 20 958 49 31 72 20 240 236 g 262 286 961 18 46 34 42 1044 68 37 265 284 t 313 292 26 27 23 64 989 34 24 42 268 283

oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m10 versus oligos_6-8nt_m10; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wbGAACTGAAaa ; cor=; Ncor= a 348 238 100 1025 1049 82 58 29 974 1039 365 335 c 215 322 51 68 20 958 49 31 72 20 240 236 g 262 286 961 18 46 34 42 1044 68 37 265 284 t 313 292 26 27 23 64 989 34 24 42 268 283

One-to-n matrix alignment; reference matrix: dyads_m2_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift3 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=17; shift=3; ncol=20; ---tccCTCTCyCTCTCyct ; Alignment reference a 0 0 0 133 107 47 51 65 16 31 24 54 61 57 14 41 26 73 152 156 c 0 0 0 248 507 595 798 81 909 52 848 568 780 87 891 39 824 589 474 245 g 0 0 0 189 177 111 65 83 27 48 51 105 59 78 34 73 83 74 170 199 t 0 0 0 431 210 248 87 772 49 870 78 274 101 779 62 848 68 265 205 401

dyads_m2_shift3 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---tccCTCTCyCTCTCyct ; cor=; Ncor= a 0 0 0 133 107 47 51 65 16 31 24 54 61 57 14 41 26 73 152 156 c 0 0 0 248 507 595 798 81 909 52 848 568 780 87 891 39 824 589 474 245 g 0 0 0 189 177 111 65 83 27 48 51 105 59 78 34 73 83 74 170 199 t 0 0 0 431 210 248 87 772 49 870 78 274 101 779 62 848 68 265 205 401

oligos_6-8nt_m8_rc_shift6 (oligos_6-8nt_m8_rc)
; dyads_m2 versus oligos_6-8nt_m8_rc; m=2/3; ncol2=14; w=0; offset=3; strand=R; shift=6; score=0.716906; ------ctCTCkCTCTCTct ; cor=; Ncor= a 0 0 0 0 0 0 267 348 82 91 40 141 63 143 48 129 42 123 212 308 c 0 0 0 0 0 0 1205 385 1907 146 1989 156 1996 89 1997 83 1923 165 1198 461 g 0 0 0 0 0 0 337 498 86 176 80 1215 46 140 70 213 92 160 356 454 t 0 0 0 0 0 0 408 986 142 1804 108 705 112 1845 102 1792 160 1769 451 994

dyads_m7_shift0 (dyads_m7)
; dyads_m2 versus dyads_m7; m=3/3; ncol2=19; w=-3; offset=-3; strand=D; shift=0; score=0.592435; yyCTCyyyctcyyyCTCyy- ; cor=; Ncor= a 423 426 86 69 71 289 396 357 312 460 340 339 370 446 82 87 73 327 428 0 c 885 617 2072 75 2103 638 923 700 1137 411 1132 664 925 592 2073 77 2116 646 869 0 g 320 424 71 36 48 457 372 343 423 351 372 477 325 372 68 38 31 478 363 0 t 628 789 27 2076 34 872 565 856 384 1034 412 776 636 846 33 2054 36 805 596 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift0 ; 2 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=12; shift=0; ncol=12; vmaATCGATtkb ; Alignment reference a 458 571 1111 1593 40 41 81 1641 90 308 349 402 c 446 480 201 48 36 1597 41 44 32 139 360 455 g 454 362 141 30 44 41 1598 36 48 201 481 447 t 403 348 308 90 1641 82 41 40 1591 1113 571 457

oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m6 versus oligos_6-8nt_m6; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; vmaATCGATtkb ; cor=; Ncor= a 458 571 1111 1593 40 41 81 1641 90 308 349 402 c 446 480 201 48 36 1597 41 44 32 139 360 455 g 454 362 141 30 44 41 1598 36 48 201 481 447 t 403 348 308 90 1641 82 41 40 1591 1113 571 457

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 4 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; caCACACACACACAmmmACAmmma ; Alignment reference a 139 405 100 566 43 657 42 650 75 634 59 683 30 651 259 328 280 590 66 584 313 258 227 333 c 434 111 571 57 662 22 660 29 613 51 639 22 683 32 357 259 353 47 593 63 267 304 273 147 g 70 134 34 76 15 43 20 46 25 47 22 36 15 41 68 100 51 79 43 57 94 114 130 168 t 108 101 46 52 31 29 29 26 38 19 31 10 23 27 67 64 67 35 49 47 77 75 121 103

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; caCACACACACACAmmmACAmmma ; cor=; Ncor= a 139 405 100 566 43 657 42 650 75 634 59 683 30 651 259 328 280 590 66 584 313 258 227 333 c 434 111 571 57 662 22 660 29 613 51 639 22 683 32 357 259 353 47 593 63 267 304 273 147 g 70 134 34 76 15 43 20 46 25 47 22 36 15 41 68 100 51 79 43 57 94 114 130 168 t 108 101 46 52 31 29 29 26 38 19 31 10 23 27 67 64 67 35 49 47 77 75 121 103

dyads_m1_shift0 (dyads_m1)
; dyads_m5 versus dyads_m1; m=2/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.699449; caCACACACACACAmac------- ; cor=; Ncor= a 463 1507 253 2185 135 2382 121 2369 144 2349 109 2337 156 2176 726 1475 458 0 0 0 0 0 0 0 c 1577 336 2171 129 2446 80 2448 76 2367 84 2382 79 2360 164 1447 389 1466 0 0 0 0 0 0 0 g 288 553 115 272 47 186 62 207 97 213 86 238 106 274 263 558 379 0 0 0 0 0 0 0 t 434 366 223 176 134 114 131 110 154 116 185 108 140 148 326 340 459 0 0 0 0 0 0 0

oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; dyads_m5 versus oligos_6-8nt_m2; m=3/3; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.663638; -acaCACrCACACACrca------ ; cor=; Ncor= a 0 1034 338 1335 112 1823 67 1084 69 1905 43 1829 38 1801 116 1065 268 1105 0 0 0 0 0 0 c 0 356 1288 220 1843 61 1956 90 1963 40 1991 54 1977 83 1749 184 1253 296 0 0 0 0 0 0 g 0 405 217 340 74 125 48 810 42 118 41 167 44 149 127 643 292 484 0 0 0 0 0 0 t 0 350 302 250 116 136 74 161 71 82 70 95 86 112 153 253 332 260 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift1 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=17; shift=1; ncol=18; -caCACACACACACAmac ; Alignment reference a 0 463 1507 253 2185 135 2382 121 2369 144 2349 109 2337 156 2176 726 1475 458 c 0 1577 336 2171 129 2446 80 2448 76 2367 84 2382 79 2360 164 1447 389 1466 g 0 288 553 115 272 47 186 62 207 97 213 86 238 106 274 263 558 379 t 0 434 366 223 176 134 114 131 110 154 116 185 108 140 148 326 340 459

dyads_m1_shift1 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -caCACACACACACAmac ; cor=; Ncor= a 0 463 1507 253 2185 135 2382 121 2369 144 2349 109 2337 156 2176 726 1475 458 c 0 1577 336 2171 129 2446 80 2448 76 2367 84 2382 79 2360 164 1447 389 1466 g 0 288 553 115 272 47 186 62 207 97 213 86 238 106 274 263 558 379 t 0 434 366 223 176 134 114 131 110 154 116 185 108 140 148 326 340 459

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; dyads_m1 versus oligos_6-8nt_m2; m=2/3; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.858366; acaCACrCACACACrca- ; cor=; Ncor= a 1034 338 1335 112 1823 67 1084 69 1905 43 1829 38 1801 116 1065 268 1105 0 c 356 1288 220 1843 61 1956 90 1963 40 1991 54 1977 83 1749 184 1253 296 0 g 405 217 340 74 125 48 810 42 118 41 167 44 149 127 643 292 484 0 t 350 302 250 116 136 74 161 71 82 70 95 86 112 153 253 332 260 0

dyads_m5_shift1 (dyads_m5)
; dyads_m1 versus dyads_m5; m=3/3; ncol2=24; w=0; offset=0; strand=D; shift=1; score=0.699449; -caCACACACACACAmmm ; cor=; Ncor= a 0 139 405 100 566 43 657 42 650 75 634 59 683 30 651 259 328 280 c 0 434 111 571 57 662 22 660 29 613 51 639 22 683 32 357 259 353 g 0 70 134 34 76 15 43 20 46 25 47 22 36 15 41 68 100 51 t 0 108 101 46 52 31 29 29 26 38 19 31 10 23 27 67 64 67

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=14; shift=0; ncol=14; awAAACAACAAAwa ; Alignment reference a 564 466 1031 1172 1230 69 1218 1246 81 1214 1205 1086 499 552 c 244 275 184 71 63 1122 52 58 1137 49 72 149 285 261 g 327 276 92 60 38 53 49 45 57 59 64 68 240 277 t 265 383 93 97 69 156 81 51 125 78 59 97 376 310

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; awAAACAACAAAwa ; cor=; Ncor= a 564 466 1031 1172 1230 69 1218 1246 81 1214 1205 1086 499 552 c 244 275 184 71 63 1122 52 58 1137 49 72 149 285 261 g 327 276 92 60 38 53 49 45 57 59 64 68 240 277 t 265 383 93 97 69 156 81 51 125 78 59 97 376 310

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=13; shift=0; ncol=13; yacATACATACay ; Alignment reference a 369 779 261 1181 60 1506 98 1520 74 1495 114 760 369 c 463 269 899 117 140 40 1356 20 154 34 1112 236 418 g 223 300 164 188 24 51 46 40 35 51 91 356 258 t 572 279 303 141 1403 30 127 47 1364 47 310 275 582

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; yacATACATACay ; cor=; Ncor= a 369 779 261 1181 60 1506 98 1520 74 1495 114 760 369 c 463 269 899 117 140 40 1356 20 154 34 1112 236 418 g 223 300 164 188 24 51 46 40 35 51 91 356 258 t 572 279 303 141 1403 30 127 47 1364 47 310 275 582

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; ccACCACCam ; Alignment reference a 190 149 854 1 1 825 2 2 331 254 c 344 366 15 878 775 30 874 853 171 293 g 186 158 0 0 19 1 0 3 177 177 t 160 207 11 1 85 24 4 22 201 156

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; ccACCACCam ; cor=; Ncor= a 190 149 854 1 1 825 2 2 331 254 c 344 366 15 878 775 30 874 853 171 293 g 186 158 0 0 19 1 0 3 177 177 t 160 207 11 1 85 24 4 22 201 156

dyads_m8_shift0 (dyads_m8)
; dyads_m10 versus dyads_m8; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.776732; ykGCCACCrv ; cor=; Ncor= a 176 193 19 7 0 866 0 0 272 236 c 246 210 15 856 862 0 867 867 169 251 g 192 222 822 2 1 0 0 0 223 218 t 253 242 11 2 4 1 0 0 203 162

One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift0 ; 2 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=10; shift=0; ncol=10; rtATAGGAww ; Alignment reference a 170 118 470 0 527 4 9 441 146 185 c 110 78 26 1 3 18 0 4 98 104 g 138 114 34 14 4 489 429 35 128 95 t 116 224 4 519 0 23 96 54 162 150

positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; rtATAGGAww ; cor=; Ncor= a 170 118 470 0 527 4 9 441 146 185 c 110 78 26 1 3 18 0 4 98 104 g 138 114 34 14 4 489 429 35 128 95 t 116 224 4 519 0 23 96 54 162 150

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; gcrGCAGCAGCAGCrgc ; Alignment reference a 289 237 421 104 64 1087 97 66 1017 96 52 1099 112 83 456 316 256 c 247 651 126 109 1163 52 42 1174 65 48 1203 55 47 1121 95 267 653 g 586 220 674 1058 73 126 1156 54 171 1154 50 104 1123 60 665 581 231 t 214 228 115 65 36 71 41 42 83 38 31 78 54 72 120 172 196

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/1; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; gcrGCAGCAGCAGCrgc ; cor=; Ncor= a 289 237 421 104 64 1087 97 66 1017 96 52 1099 112 83 456 316 256 c 247 651 126 109 1163 52 42 1174 65 48 1203 55 47 1121 95 267 653 g 586 220 674 1058 73 126 1156 54 171 1154 50 104 1123 60 665 581 231 t 214 228 115 65 36 71 41 42 83 38 31 78 54 72 120 172 196

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=19; shift=0; ncol=19; wwAAtAAAAATAAATAaww ; Alignment reference a 474 514 834 903 287 911 916 966 928 992 171 1029 966 1026 183 1004 797 491 446 c 193 202 100 87 93 64 63 72 71 54 77 50 61 49 75 42 111 183 196 g 193 167 94 65 66 101 53 42 38 66 42 48 33 46 61 50 80 182 175 t 344 321 176 149 758 128 172 124 167 92 914 77 144 83 885 108 216 348 387

dyads_m9_shift0 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; wwAAtAAAAATAAATAaww ; cor=; Ncor= a 474 514 834 903 287 911 916 966 928 992 171 1029 966 1026 183 1004 797 491 446 c 193 202 100 87 93 64 63 72 71 54 77 50 61 49 75 42 111 183 196 g 193 167 94 65 66 101 53 42 38 66 42 48 33 46 61 50 80 182 175 t 344 321 176 149 758 128 172 124 167 92 914 77 144 83 885 108 216 348 387

dyads_m4_shift1 (dyads_m4)
; dyads_m9 versus dyads_m4; m=2/3; ncol2=21; w=0; offset=1; strand=D; shift=1; score=0.667957; -wwwAAAATATAAATAAAA ; cor=; Ncor= a 0 254 244 168 484 510 504 500 111 510 98 529 488 539 88 515 458 463 446 c 0 89 89 55 36 28 25 31 44 26 38 23 30 26 42 29 45 39 46 g 0 89 99 64 35 37 19 32 17 44 34 25 26 18 26 26 37 28 34 t 0 203 203 348 80 60 87 72 463 55 465 58 91 52 479 65 95 105 109

oligos_6-8nt_m3_shift6 (oligos_6-8nt_m3)
; dyads_m9 versus oligos_6-8nt_m3; m=3/3; ncol2=13; w=0; offset=6; strand=D; shift=6; score=0.636779; ------wwaATAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 c 0 0 0 0 0 0 423 379 194 186 84 59 90 76 107 49 150 395 415 g 0 0 0 0 0 0 386 352 185 227 50 42 62 55 61 55 132 371 357 t 0 0 0 0 0 0 772 694 453 339 2110 127 186 121 2142 112 291 702 790

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift7 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m7_shift7 (oligos_6-8nt_m7)
; oligos_6-8nt_m7; m=0 (reference); ncol1=13; shift=7; ncol=20; -------ycTCCTCCTCstc ; Alignment reference a 0 0 0 0 0 0 0 289 345 227 135 82 113 42 91 103 41 137 419 337 c 0 0 0 0 0 0 0 776 845 190 1522 1682 64 1782 1639 37 1774 518 423 780 g 0 0 0 0 0 0 0 408 486 193 166 119 60 64 140 59 76 1088 425 383 t 0 0 0 0 0 0 0 495 292 1358 145 85 1731 80 98 1769 77 225 701 468

oligos_6-8nt_m7_shift7 (oligos_6-8nt_m7)
; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=7; score= 1; -------ycTCCTCCTCstc ; cor=; Ncor= a 0 0 0 0 0 0 0 289 345 227 135 82 113 42 91 103 41 137 419 337 c 0 0 0 0 0 0 0 776 845 190 1522 1682 64 1782 1639 37 1774 518 423 780 g 0 0 0 0 0 0 0 408 486 193 166 119 60 64 140 59 76 1088 425 383 t 0 0 0 0 0 0 0 495 292 1358 145 85 1731 80 98 1769 77 225 701 468

dyads_m7_shift0 (dyads_m7)
; oligos_6-8nt_m7 versus dyads_m7; m=2/2; ncol2=19; w=-7; offset=-7; strand=D; shift=0; score=0.42833; yyCTCyyyctcyyyCTCyy- ; cor=; Ncor= a 423 426 86 69 71 289 396 357 312 460 340 339 370 446 82 87 73 327 428 0 c 885 617 2072 75 2103 638 923 700 1137 411 1132 664 925 592 2073 77 2116 646 869 0 g 320 424 71 36 48 457 372 343 423 351 372 477 325 372 68 38 31 478 363 0 t 628 789 27 2076 34 872 565 856 384 1034 412 776 636 846 33 2054 36 805 596 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift6 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m3_shift6 (oligos_6-8nt_m3)
; oligos_6-8nt_m3; m=0 (reference); ncol1=13; shift=6; ncol=19; ------wwaATAAATAAww ; Alignment reference a 0 0 0 0 0 0 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 c 0 0 0 0 0 0 423 379 194 186 84 59 90 76 107 49 150 395 415 g 0 0 0 0 0 0 386 352 185 227 50 42 62 55 61 55 132 371 357 t 0 0 0 0 0 0 772 694 453 339 2110 127 186 121 2142 112 291 702 790

oligos_6-8nt_m3_shift6 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=6; score= 1; ------wwaATAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 c 0 0 0 0 0 0 423 379 194 186 84 59 90 76 107 49 150 395 415 g 0 0 0 0 0 0 386 352 185 227 50 42 62 55 61 55 132 371 357 t 0 0 0 0 0 0 772 694 453 339 2110 127 186 121 2142 112 291 702 790

dyads_m9_shift0 (dyads_m9)
; oligos_6-8nt_m3 versus dyads_m9; m=2/3; ncol2=19; w=-6; offset=-6; strand=D; shift=0; score=0.636779; wwAAtAAAAATAAATAaww ; cor=; Ncor= a 474 514 834 903 287 911 916 966 928 992 171 1029 966 1026 183 1004 797 491 446 c 193 202 100 87 93 64 63 72 71 54 77 50 61 49 75 42 111 183 196 g 193 167 94 65 66 101 53 42 38 66 42 48 33 46 61 50 80 182 175 t 344 321 176 149 758 128 172 124 167 92 914 77 144 83 885 108 216 348 387

dyads_m4_shift1 (dyads_m4)
; oligos_6-8nt_m3 versus dyads_m4; m=3/3; ncol2=21; w=-5; offset=-5; strand=D; shift=1; score=0.520655; -wwwAAAATATAAATAAAA ; cor=; Ncor= a 0 254 244 168 484 510 504 500 111 510 98 529 488 539 88 515 458 463 446 c 0 89 89 55 36 28 25 31 44 26 38 23 30 26 42 29 45 39 46 g 0 89 99 64 35 37 19 32 17 44 34 25 26 18 26 26 37 28 34 t 0 203 203 348 80 60 87 72 463 55 465 58 91 52 479 65 95 105 109

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift0 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=19; shift=0; ncol=19; yyCTCyyyctcyyyCTCyy ; Alignment reference a 423 426 86 69 71 289 396 357 312 460 340 339 370 446 82 87 73 327 428 c 885 617 2072 75 2103 638 923 700 1137 411 1132 664 925 592 2073 77 2116 646 869 g 320 424 71 36 48 457 372 343 423 351 372 477 325 372 68 38 31 478 363 t 628 789 27 2076 34 872 565 856 384 1034 412 776 636 846 33 2054 36 805 596
dyads_m7_shift0 (dyads_m7)				; dyads_m7 versus dyads_m7; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; yyCTCyyyctcyyyCTCyy ; cor=; Ncor= a 423 426 86 69 71 289 396 357 312 460 340 339 370 446 82 87 73 327 428 c 885 617 2072 75 2103 638 923 700 1137 411 1132 664 925 592 2073 77 2116 646 869 g 320 424 71 36 48 457 372 343 423 351 372 477 325 372 68 38 31 478 363 t 628 789 27 2076 34 872 565 856 384 1034 412 776 636 846 33 2054 36 805 596
oligos_6-8nt_m8_rc_shift0 (oligos_6-8nt_m8_rc)				; dyads_m7 versus oligos_6-8nt_m8_rc; m=2/4; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.596904; ctCTCkCTCTCTct----- ; cor=; Ncor= a 267 348 82 91 40 141 63 143 48 129 42 123 212 308 0 0 0 0 0 c 1205 385 1907 146 1989 156 1996 89 1997 83 1923 165 1198 461 0 0 0 0 0 g 337 498 86 176 80 1215 46 140 70 213 92 160 356 454 0 0 0 0 0 t 408 986 142 1804 108 705 112 1845 102 1792 160 1769 451 994 0 0 0 0 0
dyads_m2_shift3 (dyads_m2)				; dyads_m7 versus dyads_m2; m=3/4; ncol2=17; w=0; offset=3; strand=D; shift=3; score=0.592435; ---tccCTCTCyCTCTCyc ; cor=; Ncor= a 0 0 0 133 107 47 51 65 16 31 24 54 61 57 14 41 26 73 152 c 0 0 0 248 507 595 798 81 909 52 848 568 780 87 891 39 824 589 474 g 0 0 0 189 177 111 65 83 27 48 51 105 59 78 34 73 83 74 170 t 0 0 0 431 210 248 87 772 49 870 78 274 101 779 62 848 68 265 205
oligos_6-8nt_m7_shift7 (oligos_6-8nt_m7)				; dyads_m7 versus oligos_6-8nt_m7; m=4/4; ncol2=13; w=0; offset=7; strand=D; shift=7; score=0.42833; -------ycTCCTCCTCst ; cor=; Ncor= a 0 0 0 0 0 0 0 289 345 227 135 82 113 42 91 103 41 137 419 c 0 0 0 0 0 0 0 776 845 190 1522 1682 64 1782 1639 37 1774 518 423 g 0 0 0 0 0 0 0 408 486 193 166 119 60 64 140 59 76 1088 425 t 0 0 0 0 0 0 0 495 292 1358 145 85 1731 80 98 1769 77 225 701

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m8_shift5 (oligos_6-8nt_m8)				; oligos_6-8nt_m8; m=0 (reference); ncol1=14; shift=5; ncol=19; -----agAGAGAGmGAGag ; Alignment reference a 0 0 0 0 0 994 451 1769 160 1792 102 1845 112 705 108 1804 142 986 408 c 0 0 0 0 0 454 356 160 92 213 70 140 46 1215 80 176 86 498 337 g 0 0 0 0 0 461 1198 165 1923 83 1997 89 1996 156 1989 146 1907 385 1205 t 0 0 0 0 0 308 212 123 42 129 48 143 63 141 40 91 82 348 267
oligos_6-8nt_m8_shift5 (oligos_6-8nt_m8)				; oligos_6-8nt_m8 versus oligos_6-8nt_m8; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----agAGAGAGmGAGag ; cor=; Ncor= a 0 0 0 0 0 994 451 1769 160 1792 102 1845 112 705 108 1804 142 986 408 c 0 0 0 0 0 454 356 160 92 213 70 140 46 1215 80 176 86 498 337 g 0 0 0 0 0 461 1198 165 1923 83 1997 89 1996 156 1989 146 1907 385 1205 t 0 0 0 0 0 308 212 123 42 129 48 143 63 141 40 91 82 348 267
dyads_m2_rc_shift5 (dyads_m2_rc)				; oligos_6-8nt_m8 versus dyads_m2_rc; m=2/3; ncol2=17; w=0; offset=0; strand=R; shift=5; score=0.716906; -----agrGAGAGrGAGAG ; cor=; Ncor= a 0 0 0 0 0 401 205 265 68 848 62 779 101 274 78 870 49 772 87 c 0 0 0 0 0 199 170 74 83 73 34 78 59 105 51 48 27 83 65 g 0 0 0 0 0 245 474 589 824 39 891 87 780 568 848 52 909 81 798 t 0 0 0 0 0 156 152 73 26 41 14 57 61 54 24 31 16 65 51
dyads_m7_rc_shift0 (dyads_m7_rc)				; oligos_6-8nt_m8 versus dyads_m7_rc; m=3/3; ncol2=19; w=-5; offset=-5; strand=R; shift=0; score=0.596904; rrGAGrrrgagrrrGAGrr ; cor=; Ncor= a 596 805 36 2054 33 846 636 776 412 1034 384 856 565 872 34 2076 27 789 628 c 363 478 31 38 68 372 325 477 372 351 423 343 372 457 48 36 71 424 320 g 869 646 2116 77 2073 592 925 664 1132 411 1137 700 923 638 2103 75 2072 617 885 t 428 327 73 87 82 446 370 339 340 460 312 357 396 289 71 69 86 426 423

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=17; shift=1; ncol=18; -acaCACrCACACACrca ; Alignment reference a 0 1034 338 1335 112 1823 67 1084 69 1905 43 1829 38 1801 116 1065 268 1105 c 0 356 1288 220 1843 61 1956 90 1963 40 1991 54 1977 83 1749 184 1253 296 g 0 405 217 340 74 125 48 810 42 118 41 167 44 149 127 643 292 484 t 0 350 302 250 116 136 74 161 71 82 70 95 86 112 153 253 332 260
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -acaCACrCACACACrca ; cor=; Ncor= a 0 1034 338 1335 112 1823 67 1084 69 1905 43 1829 38 1801 116 1065 268 1105 c 0 356 1288 220 1843 61 1956 90 1963 40 1991 54 1977 83 1749 184 1253 296 g 0 405 217 340 74 125 48 810 42 118 41 167 44 149 127 643 292 484 t 0 350 302 250 116 136 74 161 71 82 70 95 86 112 153 253 332 260
dyads_m1_shift2 (dyads_m1)				; oligos_6-8nt_m2 versus dyads_m1; m=2/3; ncol2=17; w=0; offset=1; strand=D; shift=2; score=0.858366; --caCACACACACACAma ; cor=; Ncor= a 0 0 463 1507 253 2185 135 2382 121 2369 144 2349 109 2337 156 2176 726 1475 c 0 0 1577 336 2171 129 2446 80 2448 76 2367 84 2382 79 2360 164 1447 389 g 0 0 288 553 115 272 47 186 62 207 97 213 86 238 106 274 263 558 t 0 0 434 366 223 176 134 114 131 110 154 116 185 108 140 148 326 340
dyads_m5_shift0 (dyads_m5)				; oligos_6-8nt_m2 versus dyads_m5; m=3/3; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.663638; caCACACACACACAmmmA ; cor=; Ncor= a 139 405 100 566 43 657 42 650 75 634 59 683 30 651 259 328 280 590 c 434 111 571 57 662 22 660 29 613 51 639 22 683 32 357 259 353 47 g 70 134 34 76 15 43 20 46 25 47 22 36 15 41 68 100 51 79 t 108 101 46 52 31 29 29 26 38 19 31 10 23 27 67 64 67 35

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift1 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=21; shift=1; ncol=22; -wwwAAAATATAAATAAAAwww ; Alignment reference a 0 254 244 168 484 510 504 500 111 510 98 529 488 539 88 515 458 463 446 163 229 220 c 0 89 89 55 36 28 25 31 44 26 38 23 30 26 42 29 45 39 46 56 88 116 g 0 89 99 64 35 37 19 32 17 44 34 25 26 18 26 26 37 28 34 42 109 87 t 0 203 203 348 80 60 87 72 463 55 465 58 91 52 479 65 95 105 109 374 209 212
dyads_m4_shift1 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/3; ncol2=21; w=0; offset=0; strand=D; shift=1; score= 1; -wwwAAAATATAAATAAAAwww ; cor=; Ncor= a 0 254 244 168 484 510 504 500 111 510 98 529 488 539 88 515 458 463 446 163 229 220 c 0 89 89 55 36 28 25 31 44 26 38 23 30 26 42 29 45 39 46 56 88 116 g 0 89 99 64 35 37 19 32 17 44 34 25 26 18 26 26 37 28 34 42 109 87 t 0 203 203 348 80 60 87 72 463 55 465 58 91 52 479 65 95 105 109 374 209 212
dyads_m9_shift0 (dyads_m9)				; dyads_m4 versus dyads_m9; m=2/3; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.667957; wwAAtAAAAATAAATAaww--- ; cor=; Ncor= a 474 514 834 903 287 911 916 966 928 992 171 1029 966 1026 183 1004 797 491 446 0 0 0 c 193 202 100 87 93 64 63 72 71 54 77 50 61 49 75 42 111 183 196 0 0 0 g 193 167 94 65 66 101 53 42 38 66 42 48 33 46 61 50 80 182 175 0 0 0 t 344 321 176 149 758 128 172 124 167 92 914 77 144 83 885 108 216 348 387 0 0 0
oligos_6-8nt_m3_shift6 (oligos_6-8nt_m3)				; dyads_m4 versus oligos_6-8nt_m3; m=3/3; ncol2=13; w=0; offset=5; strand=D; shift=6; score=0.520655; ------wwaATAAATAAww--- ; cor=; Ncor= a 0 0 0 0 0 0 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 0 0 0 c 0 0 0 0 0 0 423 379 194 186 84 59 90 76 107 49 150 395 415 0 0 0 g 0 0 0 0 0 0 386 352 185 227 50 42 62 55 61 55 132 371 357 0 0 0 t 0 0 0 0 0 0 772 694 453 339 2110 127 186 121 2142 112 291 702 790 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift3 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=17; shift=3; ncol=20; ---tccCTCTCyCTCTCyct ; Alignment reference a 0 0 0 133 107 47 51 65 16 31 24 54 61 57 14 41 26 73 152 156 c 0 0 0 248 507 595 798 81 909 52 848 568 780 87 891 39 824 589 474 245 g 0 0 0 189 177 111 65 83 27 48 51 105 59 78 34 73 83 74 170 199 t 0 0 0 431 210 248 87 772 49 870 78 274 101 779 62 848 68 265 205 401
dyads_m2_shift3 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---tccCTCTCyCTCTCyct ; cor=; Ncor= a 0 0 0 133 107 47 51 65 16 31 24 54 61 57 14 41 26 73 152 156 c 0 0 0 248 507 595 798 81 909 52 848 568 780 87 891 39 824 589 474 245 g 0 0 0 189 177 111 65 83 27 48 51 105 59 78 34 73 83 74 170 199 t 0 0 0 431 210 248 87 772 49 870 78 274 101 779 62 848 68 265 205 401
oligos_6-8nt_m8_rc_shift6 (oligos_6-8nt_m8_rc)				; dyads_m2 versus oligos_6-8nt_m8_rc; m=2/3; ncol2=14; w=0; offset=3; strand=R; shift=6; score=0.716906; ------ctCTCkCTCTCTct ; cor=; Ncor= a 0 0 0 0 0 0 267 348 82 91 40 141 63 143 48 129 42 123 212 308 c 0 0 0 0 0 0 1205 385 1907 146 1989 156 1996 89 1997 83 1923 165 1198 461 g 0 0 0 0 0 0 337 498 86 176 80 1215 46 140 70 213 92 160 356 454 t 0 0 0 0 0 0 408 986 142 1804 108 705 112 1845 102 1792 160 1769 451 994
dyads_m7_shift0 (dyads_m7)				; dyads_m2 versus dyads_m7; m=3/3; ncol2=19; w=-3; offset=-3; strand=D; shift=0; score=0.592435; yyCTCyyyctcyyyCTCyy- ; cor=; Ncor= a 423 426 86 69 71 289 396 357 312 460 340 339 370 446 82 87 73 327 428 0 c 885 617 2072 75 2103 638 923 700 1137 411 1132 664 925 592 2073 77 2116 646 869 0 g 320 424 71 36 48 457 372 343 423 351 372 477 325 372 68 38 31 478 363 0 t 628 789 27 2076 34 872 565 856 384 1034 412 776 636 846 33 2054 36 805 596 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; caCACACACACACAmmmACAmmma ; Alignment reference a 139 405 100 566 43 657 42 650 75 634 59 683 30 651 259 328 280 590 66 584 313 258 227 333 c 434 111 571 57 662 22 660 29 613 51 639 22 683 32 357 259 353 47 593 63 267 304 273 147 g 70 134 34 76 15 43 20 46 25 47 22 36 15 41 68 100 51 79 43 57 94 114 130 168 t 108 101 46 52 31 29 29 26 38 19 31 10 23 27 67 64 67 35 49 47 77 75 121 103
dyads_m5_shift0 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; caCACACACACACAmmmACAmmma ; cor=; Ncor= a 139 405 100 566 43 657 42 650 75 634 59 683 30 651 259 328 280 590 66 584 313 258 227 333 c 434 111 571 57 662 22 660 29 613 51 639 22 683 32 357 259 353 47 593 63 267 304 273 147 g 70 134 34 76 15 43 20 46 25 47 22 36 15 41 68 100 51 79 43 57 94 114 130 168 t 108 101 46 52 31 29 29 26 38 19 31 10 23 27 67 64 67 35 49 47 77 75 121 103
dyads_m1_shift0 (dyads_m1)				; dyads_m5 versus dyads_m1; m=2/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.699449; caCACACACACACAmac------- ; cor=; Ncor= a 463 1507 253 2185 135 2382 121 2369 144 2349 109 2337 156 2176 726 1475 458 0 0 0 0 0 0 0 c 1577 336 2171 129 2446 80 2448 76 2367 84 2382 79 2360 164 1447 389 1466 0 0 0 0 0 0 0 g 288 553 115 272 47 186 62 207 97 213 86 238 106 274 263 558 379 0 0 0 0 0 0 0 t 434 366 223 176 134 114 131 110 154 116 185 108 140 148 326 340 459 0 0 0 0 0 0 0
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; dyads_m5 versus oligos_6-8nt_m2; m=3/3; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.663638; -acaCACrCACACACrca------ ; cor=; Ncor= a 0 1034 338 1335 112 1823 67 1084 69 1905 43 1829 38 1801 116 1065 268 1105 0 0 0 0 0 0 c 0 356 1288 220 1843 61 1956 90 1963 40 1991 54 1977 83 1749 184 1253 296 0 0 0 0 0 0 g 0 405 217 340 74 125 48 810 42 118 41 167 44 149 127 643 292 484 0 0 0 0 0 0 t 0 350 302 250 116 136 74 161 71 82 70 95 86 112 153 253 332 260 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift1 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=17; shift=1; ncol=18; -caCACACACACACAmac ; Alignment reference a 0 463 1507 253 2185 135 2382 121 2369 144 2349 109 2337 156 2176 726 1475 458 c 0 1577 336 2171 129 2446 80 2448 76 2367 84 2382 79 2360 164 1447 389 1466 g 0 288 553 115 272 47 186 62 207 97 213 86 238 106 274 263 558 379 t 0 434 366 223 176 134 114 131 110 154 116 185 108 140 148 326 340 459
dyads_m1_shift1 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -caCACACACACACAmac ; cor=; Ncor= a 0 463 1507 253 2185 135 2382 121 2369 144 2349 109 2337 156 2176 726 1475 458 c 0 1577 336 2171 129 2446 80 2448 76 2367 84 2382 79 2360 164 1447 389 1466 g 0 288 553 115 272 47 186 62 207 97 213 86 238 106 274 263 558 379 t 0 434 366 223 176 134 114 131 110 154 116 185 108 140 148 326 340 459
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; dyads_m1 versus oligos_6-8nt_m2; m=2/3; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.858366; acaCACrCACACACrca- ; cor=; Ncor= a 1034 338 1335 112 1823 67 1084 69 1905 43 1829 38 1801 116 1065 268 1105 0 c 356 1288 220 1843 61 1956 90 1963 40 1991 54 1977 83 1749 184 1253 296 0 g 405 217 340 74 125 48 810 42 118 41 167 44 149 127 643 292 484 0 t 350 302 250 116 136 74 161 71 82 70 95 86 112 153 253 332 260 0
dyads_m5_shift1 (dyads_m5)				; dyads_m1 versus dyads_m5; m=3/3; ncol2=24; w=0; offset=0; strand=D; shift=1; score=0.699449; -caCACACACACACAmmm ; cor=; Ncor= a 0 139 405 100 566 43 657 42 650 75 634 59 683 30 651 259 328 280 c 0 434 111 571 57 662 22 660 29 613 51 639 22 683 32 357 259 353 g 0 70 134 34 76 15 43 20 46 25 47 22 36 15 41 68 100 51 t 0 108 101 46 52 31 29 29 26 38 19 31 10 23 27 67 64 67

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m9_shift0 (dyads_m9)				; dyads_m9; m=0 (reference); ncol1=19; shift=0; ncol=19; wwAAtAAAAATAAATAaww ; Alignment reference a 474 514 834 903 287 911 916 966 928 992 171 1029 966 1026 183 1004 797 491 446 c 193 202 100 87 93 64 63 72 71 54 77 50 61 49 75 42 111 183 196 g 193 167 94 65 66 101 53 42 38 66 42 48 33 46 61 50 80 182 175 t 344 321 176 149 758 128 172 124 167 92 914 77 144 83 885 108 216 348 387
dyads_m9_shift0 (dyads_m9)				; dyads_m9 versus dyads_m9; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; wwAAtAAAAATAAATAaww ; cor=; Ncor= a 474 514 834 903 287 911 916 966 928 992 171 1029 966 1026 183 1004 797 491 446 c 193 202 100 87 93 64 63 72 71 54 77 50 61 49 75 42 111 183 196 g 193 167 94 65 66 101 53 42 38 66 42 48 33 46 61 50 80 182 175 t 344 321 176 149 758 128 172 124 167 92 914 77 144 83 885 108 216 348 387
dyads_m4_shift1 (dyads_m4)				; dyads_m9 versus dyads_m4; m=2/3; ncol2=21; w=0; offset=1; strand=D; shift=1; score=0.667957; -wwwAAAATATAAATAAAA ; cor=; Ncor= a 0 254 244 168 484 510 504 500 111 510 98 529 488 539 88 515 458 463 446 c 0 89 89 55 36 28 25 31 44 26 38 23 30 26 42 29 45 39 46 g 0 89 99 64 35 37 19 32 17 44 34 25 26 18 26 26 37 28 34 t 0 203 203 348 80 60 87 72 463 55 465 58 91 52 479 65 95 105 109
oligos_6-8nt_m3_shift6 (oligos_6-8nt_m3)				; dyads_m9 versus oligos_6-8nt_m3; m=3/3; ncol2=13; w=0; offset=6; strand=D; shift=6; score=0.636779; ------wwaATAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 c 0 0 0 0 0 0 423 379 194 186 84 59 90 76 107 49 150 395 415 g 0 0 0 0 0 0 386 352 185 227 50 42 62 55 61 55 132 371 357 t 0 0 0 0 0 0 772 694 453 339 2110 127 186 121 2142 112 291 702 790

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m3_shift6 (oligos_6-8nt_m3)				; oligos_6-8nt_m3; m=0 (reference); ncol1=13; shift=6; ncol=19; ------wwaATAAATAAww ; Alignment reference a 0 0 0 0 0 0 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 c 0 0 0 0 0 0 423 379 194 186 84 59 90 76 107 49 150 395 415 g 0 0 0 0 0 0 386 352 185 227 50 42 62 55 61 55 132 371 357 t 0 0 0 0 0 0 772 694 453 339 2110 127 186 121 2142 112 291 702 790
oligos_6-8nt_m3_shift6 (oligos_6-8nt_m3)				; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=6; score= 1; ------wwaATAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 c 0 0 0 0 0 0 423 379 194 186 84 59 90 76 107 49 150 395 415 g 0 0 0 0 0 0 386 352 185 227 50 42 62 55 61 55 132 371 357 t 0 0 0 0 0 0 772 694 453 339 2110 127 186 121 2142 112 291 702 790
dyads_m9_shift0 (dyads_m9)				; oligos_6-8nt_m3 versus dyads_m9; m=2/3; ncol2=19; w=-6; offset=-6; strand=D; shift=0; score=0.636779; wwAAtAAAAATAAATAaww ; cor=; Ncor= a 474 514 834 903 287 911 916 966 928 992 171 1029 966 1026 183 1004 797 491 446 c 193 202 100 87 93 64 63 72 71 54 77 50 61 49 75 42 111 183 196 g 193 167 94 65 66 101 53 42 38 66 42 48 33 46 61 50 80 182 175 t 344 321 176 149 758 128 172 124 167 92 914 77 144 83 885 108 216 348 387
dyads_m4_shift1 (dyads_m4)				; oligos_6-8nt_m3 versus dyads_m4; m=3/3; ncol2=21; w=-5; offset=-5; strand=D; shift=1; score=0.520655; -wwwAAAATATAAATAAAA ; cor=; Ncor= a 0 254 244 168 484 510 504 500 111 510 98 529 488 539 88 515 458 463 446 c 0 89 89 55 36 28 25 31 44 26 38 23 30 26 42 29 45 39 46 g 0 89 99 64 35 37 19 32 17 44 34 25 26 18 26 26 37 28 34 t 0 203 203 348 80 60 87 72 463 55 465 58 91 52 479 65 95 105 109