One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181000_2026-01-25.181000_CpuIe4/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.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift0 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=15; shift=0; ncol=15; caACAACAACAACaa ; Alignment reference a 402 1160 1712 121 1977 1815 113 1873 1935 114 1945 1797 180 1186 1022 c 1180 397 102 1947 85 86 1907 101 54 1968 101 87 1746 340 343 g 375 354 352 78 98 260 101 126 189 67 101 255 127 398 550 t 291 337 82 102 88 87 127 148 70 99 101 109 195 324 333

dyads_m7_shift0 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; caACAACAACAACaa ; cor=; Ncor= a 402 1160 1712 121 1977 1815 113 1873 1935 114 1945 1797 180 1186 1022 c 1180 397 102 1947 85 86 1907 101 54 1968 101 87 1746 340 343 g 375 354 352 78 98 260 101 126 189 67 101 255 127 398 550 t 291 337 82 102 88 87 127 148 70 99 101 109 195 324 333

oligos_6-8nt_m7_shift1 (oligos_6-8nt_m7)
; dyads_m7 versus oligos_6-8nt_m7; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.655874; -arCAGCAACArc-- ; cor=; Ncor= a 0 1735 940 65 3364 470 66 3269 2481 137 3332 1238 599 0 0 c 0 628 697 3365 59 110 3433 122 169 3309 65 529 1847 0 0 g 0 690 1497 105 81 2932 61 130 833 90 81 1330 621 0 0 t 0 535 454 53 84 76 28 67 105 52 110 491 521 0 0

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; smCAAGGAgm ; Alignment reference a 257 283 0 1090 1115 0 0 1114 212 318 c 298 337 1103 1 1 0 0 0 223 316 g 316 253 1 7 2 1118 1112 3 419 279 t 247 245 14 20 0 0 6 1 264 205

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; smCAAGGAgm ; cor=; Ncor= a 257 283 0 1090 1115 0 0 1114 212 318 c 298 337 1103 1 1 0 0 0 223 316 g 316 253 1 7 2 1118 1112 3 419 279 t 247 245 14 20 0 0 6 1 264 205

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=20; shift=0; ncol=20; gcrGCAGCAGCAGCAGCrrc ; Alignment reference a 434 299 847 186 93 1630 155 75 1640 182 66 1631 230 107 1561 263 137 921 503 299 c 352 1081 196 189 1727 85 86 1750 70 73 1750 74 76 1668 85 107 1556 203 345 1053 g 898 334 700 1501 88 146 1664 86 138 1663 91 142 1586 98 188 1503 147 630 883 318 t 286 256 227 94 62 109 65 59 122 52 63 123 78 97 136 97 130 216 239 300

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/2; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; gcrGCAGCAGCAGCAGCrrc ; cor=; Ncor= a 434 299 847 186 93 1630 155 75 1640 182 66 1631 230 107 1561 263 137 921 503 299 c 352 1081 196 189 1727 85 86 1750 70 73 1750 74 76 1668 85 107 1556 203 345 1053 g 898 334 700 1501 88 146 1664 86 138 1663 91 142 1586 98 188 1503 147 630 883 318 t 286 256 227 94 62 109 65 59 122 52 63 123 78 97 136 97 130 216 239 300

oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; dyads_m1 versus oligos_6-8nt_m7; m=2/2; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.516214; --arCAGCAACArc------ ; cor=; Ncor= a 0 0 1735 940 65 3364 470 66 3269 2481 137 3332 1238 599 0 0 0 0 0 0 c 0 0 628 697 3365 59 110 3433 122 169 3309 65 529 1847 0 0 0 0 0 0 g 0 0 690 1497 105 81 2932 61 130 833 90 81 1330 621 0 0 0 0 0 0 t 0 0 535 454 53 84 76 28 67 105 52 110 491 521 0 0 0 0 0 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=10; shift=0; ncol=10; gyACTCAChc ; Alignment reference a 224 199 938 0 3 69 906 0 253 218 c 227 295 0 935 11 766 19 923 289 299 g 263 118 0 3 0 3 3 4 140 192 t 224 326 0 0 924 100 10 11 256 229

oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m6 versus oligos_6-8nt_m6; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; gyACTCAChc ; cor=; Ncor= a 224 199 938 0 3 69 906 0 253 218 c 227 295 0 935 11 766 19 923 289 299 g 263 118 0 3 0 3 3 4 140 192 t 224 326 0 0 924 100 10 11 256 229

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m9_shift1 (oligos_6-8nt_m9)
; oligos_6-8nt_m9; m=0 (reference); ncol1=11; shift=1; ncol=12; -ctCCCTCTCyc ; Alignment reference a 0 663 699 92 206 224 211 67 97 58 630 753 c 0 1705 928 3668 2848 3367 155 3713 116 3769 1224 1621 g 0 830 1002 125 388 197 240 107 155 103 915 822 t 0 847 1416 160 603 257 3439 158 3677 115 1276 849

oligos_6-8nt_m9_shift1 (oligos_6-8nt_m9)
; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -ctCCCTCTCyc ; cor=; Ncor= a 0 663 699 92 206 224 211 67 97 58 630 753 c 0 1705 928 3668 2848 3367 155 3713 116 3769 1224 1621 g 0 830 1002 125 388 197 240 107 155 103 915 822 t 0 847 1416 160 603 257 3439 158 3677 115 1276 849

oligos_6-8nt_m8_shift1 (oligos_6-8nt_m8)
; oligos_6-8nt_m9 versus oligos_6-8nt_m8; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.709051; -cbCTCTCCCtc ; cor=; Ncor= a 0 771 701 108 155 94 158 79 156 194 1015 646 c 0 1663 1103 3887 116 3844 138 3643 3109 3671 904 1769 g 0 795 1185 74 218 132 245 288 360 206 912 914 t 0 999 1239 159 3739 158 3687 218 603 157 1397 899

positions_6-8nt_m2_rc_shift0 (positions_6-8nt_m2_rc)
; oligos_6-8nt_m9 versus positions_6-8nt_m2_rc; m=3/3; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.583727; thTCCCTCym-- ; cor=; Ncor= a 141 161 13 50 2 0 4 38 128 167 0 0 c 151 206 5 594 641 641 7 599 161 192 0 0 g 131 110 0 0 0 3 0 2 152 135 0 0 t 221 167 626 0 1 0 633 5 203 150 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m1_shift3 (positions_6-8nt_m1)
; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=3; ncol=13; ---aaAAAAAAaa ; Alignment reference a 0 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 0 449 427 0 12 10 7 9 0 535 501

positions_6-8nt_m1_shift3 (positions_6-8nt_m1)
; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---aaAAAAAAaa ; cor=; Ncor= a 0 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 0 449 427 0 12 10 7 9 0 535 501

dyads_m10_shift1 (dyads_m10)
; positions_6-8nt_m1 versus dyads_m10; m=2/4; ncol2=12; w=-2; offset=-2; strand=D; shift=1; score= 0.5906; -wwATAAATAAww ; cor=; Ncor= a 0 747 726 1680 198 1754 1628 1767 109 1714 1534 805 669 c 0 344 353 47 86 47 52 40 116 50 93 295 349 g 0 319 252 81 53 34 45 25 54 56 60 284 257 t 0 486 565 88 1559 61 171 64 1617 76 209 512 621

dyads_m8_shift3 (dyads_m8)
; positions_6-8nt_m1 versus dyads_m8; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.586329; ---aaAAAAaaAA ; cor=; Ncor= a 0 0 0 1899 2016 4485 4686 4719 4562 2114 2094 4517 4701 c 0 0 0 1094 1124 243 175 173 200 1052 1157 234 157 g 0 0 0 1067 1059 234 141 99 155 912 992 219 140 t 0 0 0 1101 962 199 159 170 244 1083 918 191 163

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; positions_6-8nt_m1 versus oligos_6-8nt_m1; m=4/4; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.570437; aartAAACAAAwa ; cor=; Ncor= a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 823 c 472 561 318 319 47 92 71 2039 74 102 90 512 538 g 479 560 1116 266 41 72 36 70 102 65 70 433 460 t 563 565 353 1288 85 128 56 218 86 93 109 674 567

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 5 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; aartAAACAAAwa ; Alignment reference a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 823 c 472 561 318 319 47 92 71 2039 74 102 90 512 538 g 479 560 1116 266 41 72 36 70 102 65 70 433 460 t 563 565 353 1288 85 128 56 218 86 93 109 674 567

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; aartAAACAAAwa ; cor=; Ncor= a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 823 c 472 561 318 319 47 92 71 2039 74 102 90 512 538 g 479 560 1116 266 41 72 36 70 102 65 70 433 460 t 563 565 353 1288 85 128 56 218 86 93 109 674 567

dyads_m10_shift0 (dyads_m10)
; oligos_6-8nt_m1 versus dyads_m10; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.675986; wwATAAATAAww- ; cor=; Ncor= a 747 726 1680 198 1754 1628 1767 109 1714 1534 805 669 0 c 344 353 47 86 47 52 40 116 50 93 295 349 0 g 319 252 81 53 34 45 25 54 56 60 284 257 0 t 486 565 88 1559 61 171 64 1617 76 209 512 621 0

positions_6-8nt_m1_shift3 (positions_6-8nt_m1)
; oligos_6-8nt_m1 versus positions_6-8nt_m1; m=3/4; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.570437; ---aaAAAAAAaa ; cor=; Ncor= a 0 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 0 449 427 0 12 10 7 9 0 535 501

dyads_m8_shift1 (dyads_m8)
; oligos_6-8nt_m1 versus dyads_m8; m=4/4; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.565596; -aaAAAAaaAAAA ; cor=; Ncor= a 0 1899 2016 4485 4686 4719 4562 2114 2094 4517 4701 4638 4429 c 0 1094 1124 243 175 173 200 1052 1157 234 157 199 252 g 0 1067 1059 234 141 99 155 912 992 219 140 146 202 t 0 1101 962 199 159 170 244 1083 918 191 163 178 278

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m5_shift1 (oligos_6-8nt_m5)
; oligos_6-8nt_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -acACrCACACac ; Alignment reference a 0 890 379 1837 61 584 50 1945 46 1992 53 1025 395 c 0 441 1182 95 1966 77 1977 109 2009 30 1969 356 950 g 0 452 321 81 57 1360 53 43 45 53 51 432 406 t 0 346 247 116 45 108 49 32 29 54 56 316 378

oligos_6-8nt_m5_shift1 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -acACrCACACac ; cor=; Ncor= a 0 890 379 1837 61 584 50 1945 46 1992 53 1025 395 c 0 441 1182 95 1966 77 1977 109 2009 30 1969 356 950 g 0 452 321 81 57 1360 53 43 45 53 51 432 406 t 0 346 247 116 45 108 49 32 29 54 56 316 378

dyads_m2_shift0 (dyads_m2)
; oligos_6-8nt_m5 versus dyads_m2; m=2/2; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.769679; caCACACACACAc ; cor=; Ncor= a 721 1836 255 3189 162 3283 245 3181 197 3352 188 3209 664 c 1980 697 3329 219 3480 192 3319 251 3353 151 3364 213 1985 g 605 832 152 325 136 271 183 319 187 261 177 300 645 t 636 577 206 209 164 196 195 191 205 178 213 220 648

One-to-n matrix alignment; reference matrix: dyads_m8_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m8_shift1 (dyads_m8)
; dyads_m8; m=0 (reference); ncol1=14; shift=1; ncol=15; -aaAAAAaaAAAAaa ; Alignment reference a 0 1899 2016 4485 4686 4719 4562 2114 2094 4517 4701 4638 4429 2025 2008 c 0 1094 1124 243 175 173 200 1052 1157 234 157 199 252 1002 1057 g 0 1067 1059 234 141 99 155 912 992 219 140 146 202 963 977 t 0 1101 962 199 159 170 244 1083 918 191 163 178 278 1171 1119

dyads_m8_shift1 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -aaAAAAaaAAAAaa ; cor=; Ncor= a 0 1899 2016 4485 4686 4719 4562 2114 2094 4517 4701 4638 4429 2025 2008 c 0 1094 1124 243 175 173 200 1052 1157 234 157 199 252 1002 1057 g 0 1067 1059 234 141 99 155 912 992 219 140 146 202 963 977 t 0 1101 962 199 159 170 244 1083 918 191 163 178 278 1171 1119

positions_6-8nt_m1_shift1 (positions_6-8nt_m1)
; dyads_m8 versus positions_6-8nt_m1; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.586329; -aaAAAAAAaa---- ; cor=; Ncor= a 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 0 0 0 0 c 0 497 454 0 0 0 0 0 0 384 419 0 0 0 0 g 0 434 419 0 0 0 0 0 0 382 393 0 0 0 0 t 0 449 427 0 12 10 7 9 0 535 501 0 0 0 0

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; dyads_m8 versus oligos_6-8nt_m1; m=3/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.565596; aartAAACAAAwa-- ; cor=; Ncor= a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 823 0 0 c 472 561 318 319 47 92 71 2039 74 102 90 512 538 0 0 g 479 560 1116 266 41 72 36 70 102 65 70 433 460 0 0 t 563 565 353 1288 85 128 56 218 86 93 109 674 567 0 0

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=23; shift=0; ncol=23; ctCCTCCTCCTCCwCCTCCwCcw ; Alignment reference a 83 150 35 45 91 20 35 103 15 37 93 14 26 294 33 49 102 25 43 321 44 92 162 c 331 83 502 514 22 549 539 26 552 524 14 569 540 36 536 483 21 532 504 44 479 309 110 g 137 140 76 57 67 49 42 57 47 51 63 38 51 81 46 64 76 51 61 79 66 146 142 t 96 274 34 31 467 29 31 461 33 35 477 26 30 236 32 51 448 39 39 203 58 100 233

dyads_m9_shift0 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/2; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; ctCCTCCTCCTCCwCCTCCwCcw ; cor=; Ncor= a 83 150 35 45 91 20 35 103 15 37 93 14 26 294 33 49 102 25 43 321 44 92 162 c 331 83 502 514 22 549 539 26 552 524 14 569 540 36 536 483 21 532 504 44 479 309 110 g 137 140 76 57 67 49 42 57 47 51 63 38 51 81 46 64 76 51 61 79 66 146 142 t 96 274 34 31 467 29 31 461 33 35 477 26 30 236 32 51 448 39 39 203 58 100 233

dyads_m3_rc_shift0 (dyads_m3_rc)
; dyads_m9 versus dyads_m3_rc; m=2/2; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.717252; stcCTCCTCCTCCTCstc----- ; cor=; Ncor= a 212 313 146 103 138 41 58 118 58 76 96 28 92 161 70 131 308 228 0 0 0 0 0 c 639 217 1012 1201 53 1279 1256 70 1263 1249 50 1359 1185 86 1081 493 267 682 0 0 0 0 0 g 422 284 187 141 78 106 131 108 117 128 102 66 158 132 170 731 318 306 0 0 0 0 0 t 247 706 175 75 1251 94 75 1224 82 67 1272 67 85 1141 199 165 627 304 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift0 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATAAATAAww ; Alignment reference a 747 726 1680 198 1754 1628 1767 109 1714 1534 805 669 c 344 353 47 86 47 52 40 116 50 93 295 349 g 319 252 81 53 34 45 25 54 56 60 284 257 t 486 565 88 1559 61 171 64 1617 76 209 512 621

dyads_m10_shift0 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAATAAww ; cor=; Ncor= a 747 726 1680 198 1754 1628 1767 109 1714 1534 805 669 c 344 353 47 86 47 52 40 116 50 93 295 349 g 319 252 81 53 34 45 25 54 56 60 284 257 t 486 565 88 1559 61 171 64 1617 76 209 512 621

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; dyads_m10 versus oligos_6-8nt_m1; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.675986; aartAAACAAAw ; cor=; Ncor= a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 c 472 561 318 319 47 92 71 2039 74 102 90 512 g 479 560 1116 266 41 72 36 70 102 65 70 433 t 563 565 353 1288 85 128 56 218 86 93 109 674

oligos_6-8nt_m4_shift1 (oligos_6-8nt_m4)
; dyads_m10 versus oligos_6-8nt_m4; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.621792; -wrTAyATAya- ; cor=; Ncor= a 0 607 949 20 2377 126 1841 4 2324 446 933 0 c 0 502 392 33 21 1426 149 26 27 617 437 0 g 0 435 630 16 0 211 229 55 21 360 449 0 t 0 855 428 2330 1 636 180 2314 27 976 580 0

positions_6-8nt_m1_shift2 (positions_6-8nt_m1)
; dyads_m10 versus positions_6-8nt_m1; m=4/4; ncol2=10; w=0; offset=2; strand=D; shift=2; score= 0.5906; --aaAAAAAAaa ; cor=; Ncor= a 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 449 427 0 12 10 7 9 0 535 501

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m4_shift1 (oligos_6-8nt_m4)
; oligos_6-8nt_m4; m=0 (reference); ncol1=10; shift=1; ncol=11; -wrTAyATAya ; Alignment reference a 0 607 949 20 2377 126 1841 4 2324 446 933 c 0 502 392 33 21 1426 149 26 27 617 437 g 0 435 630 16 0 211 229 55 21 360 449 t 0 855 428 2330 1 636 180 2314 27 976 580

oligos_6-8nt_m4_shift1 (oligos_6-8nt_m4)
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wrTAyATAya ; cor=; Ncor= a 0 607 949 20 2377 126 1841 4 2324 446 933 c 0 502 392 33 21 1426 149 26 27 617 437 g 0 435 630 16 0 211 229 55 21 360 449 t 0 855 428 2330 1 636 180 2314 27 976 580

dyads_m10_shift0 (dyads_m10)
; oligos_6-8nt_m4 versus dyads_m10; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.621792; wwATAAATAAw ; cor=; Ncor= a 747 726 1680 198 1754 1628 1767 109 1714 1534 805 c 344 353 47 86 47 52 40 116 50 93 295 g 319 252 81 53 34 45 25 54 56 60 284 t 486 565 88 1559 61 171 64 1617 76 209 512

One-to-n matrix alignment; reference matrix: positions_6-8nt_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)
; positions_6-8nt_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --krGAGGGAda ; Alignment reference a 0 0 150 203 5 633 0 1 0 626 167 221 c 0 0 135 152 2 0 3 0 0 0 110 131 g 0 0 192 161 599 7 641 641 594 5 206 151 t 0 0 167 128 38 4 0 2 50 13 161 141

positions_6-8nt_m2_shift2 (positions_6-8nt_m2)
; positions_6-8nt_m2 versus positions_6-8nt_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --krGAGGGAda ; cor=; Ncor= a 0 0 150 203 5 633 0 1 0 626 167 221 c 0 0 135 152 2 0 3 0 0 0 110 131 g 0 0 192 161 599 7 641 641 594 5 206 151 t 0 0 167 128 38 4 0 2 50 13 161 141

oligos_6-8nt_m9_rc_shift0 (oligos_6-8nt_m9_rc)
; positions_6-8nt_m2 versus oligos_6-8nt_m9_rc; m=2/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.583727; grGAGAGGGag- ; cor=; Ncor= a 849 1276 115 3677 158 3439 257 603 160 1416 847 0 c 822 915 103 155 107 240 197 388 125 1002 830 0 g 1621 1224 3769 116 3713 155 3367 2848 3668 928 1705 0 t 753 630 58 97 67 211 224 206 92 699 663 0

oligos_6-8nt_m8_rc_shift4 (oligos_6-8nt_m8_rc)
; positions_6-8nt_m2 versus oligos_6-8nt_m8_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.454866; ----gaGGGAGA ; cor=; Ncor= a 0 0 0 0 899 1397 157 603 218 3687 158 3739 c 0 0 0 0 914 912 206 360 288 245 132 218 g 0 0 0 0 1769 904 3671 3109 3643 138 3844 116 t 0 0 0 0 646 1015 194 156 79 158 94 155

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=14; shift=0; ncol=14; caCACACACACAca ; Alignment reference a 721 1836 255 3189 162 3283 245 3181 197 3352 188 3209 664 1817 c 1980 697 3329 219 3480 192 3319 251 3353 151 3364 213 1985 736 g 605 832 152 325 136 271 183 319 187 261 177 300 645 805 t 636 577 206 209 164 196 195 191 205 178 213 220 648 584

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; caCACACACACAca ; cor=; Ncor= a 721 1836 255 3189 162 3283 245 3181 197 3352 188 3209 664 1817 c 1980 697 3329 219 3480 192 3319 251 3353 151 3364 213 1985 736 g 605 832 152 325 136 271 183 319 187 261 177 300 645 805 t 636 577 206 209 164 196 195 191 205 178 213 220 648 584

oligos_6-8nt_m5_shift1 (oligos_6-8nt_m5)
; dyads_m2 versus oligos_6-8nt_m5; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.769679; -acACrCACACac- ; cor=; Ncor= a 0 890 379 1837 61 584 50 1945 46 1992 53 1025 395 0 c 0 441 1182 95 1966 77 1977 109 2009 30 1969 356 950 0 g 0 452 321 81 57 1360 53 43 45 53 51 432 406 0 t 0 346 247 116 45 108 49 32 29 54 56 316 378 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m8_shift0 ; 4 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; cbCTCTCCCtc ; Alignment reference a 771 701 108 155 94 158 79 156 194 1015 646 c 1663 1103 3887 116 3844 138 3643 3109 3671 904 1769 g 795 1185 74 218 132 245 288 360 206 912 914 t 999 1239 159 3739 158 3687 218 603 157 1397 899

oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8 versus oligos_6-8nt_m8; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; cbCTCTCCCtc ; cor=; Ncor= a 771 701 108 155 94 158 79 156 194 1015 646 c 1663 1103 3887 116 3844 138 3643 3109 3671 904 1769 g 795 1185 74 218 132 245 288 360 206 912 914 t 999 1239 159 3739 158 3687 218 603 157 1397 899

oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)
; oligos_6-8nt_m8 versus oligos_6-8nt_m9; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.709051; ctCCCTCTCyc ; cor=; Ncor= a 663 699 92 206 224 211 67 97 58 630 753 c 1705 928 3668 2848 3367 155 3713 116 3769 1224 1621 g 830 1002 125 388 197 240 107 155 103 915 822 t 847 1416 160 603 257 3439 158 3677 115 1276 849

positions_6-8nt_m2_rc_shift3 (positions_6-8nt_m2_rc)
; oligos_6-8nt_m8 versus positions_6-8nt_m2_rc; m=3/3; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.454866; ---thTCCCTC ; cor=; Ncor= a 0 0 0 141 161 13 50 2 0 4 38 c 0 0 0 151 206 5 594 641 641 7 599 g 0 0 0 131 110 0 0 0 3 0 2 t 0 0 0 221 167 626 0 1 0 633 5

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; mmAACACAAmh ; Alignment reference a 949 1129 2938 3059 158 3134 181 2999 2977 1051 889 c 973 884 251 176 2965 128 2938 207 224 880 938 g 723 818 114 116 111 72 190 134 123 712 756 t 807 621 149 101 218 118 143 112 128 809 869

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; mmAACACAAmh ; cor=; Ncor= a 949 1129 2938 3059 158 3134 181 2999 2977 1051 889 c 973 884 251 176 2965 128 2938 207 224 880 938 g 723 818 114 116 111 72 190 134 123 712 756 t 807 621 149 101 218 118 143 112 128 809 869

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ysGCCACCGvc ; Alignment reference a 1043 968 245 116 102 4214 194 169 464 1384 988 c 1522 1537 191 4462 4566 104 4303 4341 268 1303 1645 g 1118 1415 4246 192 164 376 170 179 3917 1269 1141 t 1255 1018 256 168 106 244 271 249 289 982 1164

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ysGCCACCGvc ; cor=; Ncor= a 1043 968 245 116 102 4214 194 169 464 1384 988 c 1522 1537 191 4462 4566 104 4303 4341 268 1303 1645 g 1118 1415 4246 192 164 376 170 179 3917 1269 1141 t 1255 1018 256 168 106 244 271 249 289 982 1164

dyads_m5_shift0 (dyads_m5)
; dyads_m4 versus dyads_m5; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.831308; ycGCCGCCGcc ; cor=; Ncor= a 1024 909 274 229 115 379 237 117 206 1236 982 c 1634 1767 191 4280 4573 104 4199 4626 242 1428 1816 g 1052 1179 4138 182 149 4234 287 93 4299 1198 983 t 1251 1106 358 270 124 244 238 125 214 1099 1180

dyads_m6_shift0 (dyads_m6)
; dyads_m4 versus dyads_m6; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.658834; ccACCACCac- ; cor=; Ncor= a 253 232 1338 3 1 1311 2 3 520 332 0 c 515 559 0 1335 1208 16 1332 1298 229 436 0 g 326 258 0 0 26 1 0 11 301 324 0 t 245 290 1 1 104 11 5 27 289 247 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; ccACCACCac ; Alignment reference a 253 232 1338 3 1 1311 2 3 520 332 c 515 559 0 1335 1208 16 1332 1298 229 436 g 326 258 0 0 26 1 0 11 301 324 t 245 290 1 1 104 11 5 27 289 247

dyads_m6_shift0 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ccACCACCac ; cor=; Ncor= a 253 232 1338 3 1 1311 2 3 520 332 c 515 559 0 1335 1208 16 1332 1298 229 436 g 326 258 0 0 26 1 0 11 301 324 t 245 290 1 1 104 11 5 27 289 247

dyads_m4_shift0 (dyads_m4)
; dyads_m6 versus dyads_m4; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.658834; ysGCCACCGv ; cor=; Ncor= a 1043 968 245 116 102 4214 194 169 464 1384 c 1522 1537 191 4462 4566 104 4303 4341 268 1303 g 1118 1415 4246 192 164 376 170 179 3917 1269 t 1255 1018 256 168 106 244 271 249 289 982

One-to-n matrix alignment; reference matrix: dyads_m3_shift5 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift5 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=18; shift=5; ncol=23; -----gasGAGGAGGAGGAGgas ; Alignment reference a 0 0 0 0 0 304 627 165 199 1141 85 67 1272 67 82 1224 75 94 1251 75 175 706 247 c 0 0 0 0 0 306 318 731 170 132 158 66 102 128 117 108 131 106 78 141 187 284 422 g 0 0 0 0 0 682 267 493 1081 86 1185 1359 50 1249 1263 70 1256 1279 53 1201 1012 217 639 t 0 0 0 0 0 228 308 131 70 161 92 28 96 76 58 118 58 41 138 103 146 313 212

dyads_m3_shift5 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/2; ncol2=18; w=0; offset=0; strand=D; shift=5; score= 1; -----gasGAGGAGGAGGAGgas ; cor=; Ncor= a 0 0 0 0 0 304 627 165 199 1141 85 67 1272 67 82 1224 75 94 1251 75 175 706 247 c 0 0 0 0 0 306 318 731 170 132 158 66 102 128 117 108 131 106 78 141 187 284 422 g 0 0 0 0 0 682 267 493 1081 86 1185 1359 50 1249 1263 70 1256 1279 53 1201 1012 217 639 t 0 0 0 0 0 228 308 131 70 161 92 28 96 76 58 118 58 41 138 103 146 313 212

dyads_m9_rc_shift0 (dyads_m9_rc)
; dyads_m3 versus dyads_m9_rc; m=2/2; ncol2=23; w=-5; offset=-5; strand=R; shift=0; score=0.717252; wgGwGGAGGwGGAGGAGGAGGag ; cor=; Ncor= a 233 100 58 203 39 39 448 51 32 236 30 26 477 35 33 461 31 29 467 31 34 274 96 c 142 146 66 79 61 51 76 64 46 81 51 38 63 51 47 57 42 49 67 57 76 140 137 g 110 309 479 44 504 532 21 483 536 36 540 569 14 524 552 26 539 549 22 514 502 83 331 t 162 92 44 321 43 25 102 49 33 294 26 14 93 37 15 103 35 20 91 45 35 150 83

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; wmCTTATCAby ; Alignment reference a 457 436 93 80 61 1561 55 89 1247 357 362 c 403 411 1336 67 47 42 99 1395 123 429 451 g 328 396 102 52 32 15 42 54 129 412 336 t 433 378 90 1422 1481 3 1425 83 122 423 472

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wmCTTATCAby ; cor=; Ncor= a 457 436 93 80 61 1561 55 89 1247 357 362 c 403 411 1336 67 47 42 99 1395 123 429 451 g 328 396 102 52 32 15 42 54 129 412 336 t 433 378 90 1422 1481 3 1425 83 122 423 472

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; gtAGCGTAyw ; Alignment reference a 195 154 787 39 62 6 0 813 145 244 c 186 148 10 97 618 11 0 3 209 188 g 254 185 19 591 85 794 1 1 197 180 t 182 330 1 90 52 6 816 0 266 205

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; gtAGCGTAyw ; cor=; Ncor= a 195 154 787 39 62 6 0 813 145 244 c 186 148 10 97 618 11 0 3 209 188 g 254 185 19 591 85 794 1 1 197 180 t 182 330 1 90 52 6 816 0 266 205

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

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ycGCCGCCGcc ; Alignment reference a 1024 909 274 229 115 379 237 117 206 1236 982 c 1634 1767 191 4280 4573 104 4199 4626 242 1428 1816 g 1052 1179 4138 182 149 4234 287 93 4299 1198 983 t 1251 1106 358 270 124 244 238 125 214 1099 1180

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ycGCCGCCGcc ; cor=; Ncor= a 1024 909 274 229 115 379 237 117 206 1236 982 c 1634 1767 191 4280 4573 104 4199 4626 242 1428 1816 g 1052 1179 4138 182 149 4234 287 93 4299 1198 983 t 1251 1106 358 270 124 244 238 125 214 1099 1180

dyads_m4_shift0 (dyads_m4)
; dyads_m5 versus dyads_m4; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.831308; ysGCCACCGvc ; cor=; Ncor= a 1043 968 245 116 102 4214 194 169 464 1384 988 c 1522 1537 191 4462 4566 104 4303 4341 268 1303 1645 g 1118 1415 4246 192 164 376 170 179 3917 1269 1141 t 1255 1018 256 168 106 244 271 249 289 982 1164

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; oligos_6-8nt_m7; m=0 (reference); ncol1=12; shift=2; ncol=14; --arCAGCAACArc ; Alignment reference a 0 0 1735 940 65 3364 470 66 3269 2481 137 3332 1238 599 c 0 0 628 697 3365 59 110 3433 122 169 3309 65 529 1847 g 0 0 690 1497 105 81 2932 61 130 833 90 81 1330 621 t 0 0 535 454 53 84 76 28 67 105 52 110 491 521

oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)
; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --arCAGCAACArc ; cor=; Ncor= a 0 0 1735 940 65 3364 470 66 3269 2481 137 3332 1238 599 c 0 0 628 697 3365 59 110 3433 122 169 3309 65 529 1847 g 0 0 690 1497 105 81 2932 61 130 833 90 81 1330 621 t 0 0 535 454 53 84 76 28 67 105 52 110 491 521

dyads_m7_shift1 (dyads_m7)
; oligos_6-8nt_m7 versus dyads_m7; m=2/3; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.655874; -caACAACAACAAC ; cor=; Ncor= a 0 402 1160 1712 121 1977 1815 113 1873 1935 114 1945 1797 180 c 0 1180 397 102 1947 85 86 1907 101 54 1968 101 87 1746 g 0 375 354 352 78 98 260 101 126 189 67 101 255 127 t 0 291 337 82 102 88 87 127 148 70 99 101 109 195

dyads_m1_shift0 (dyads_m1)
; oligos_6-8nt_m7 versus dyads_m1; m=3/3; ncol2=20; w=-2; offset=-2; strand=D; shift=0; score=0.516214; gcrGCAGCAGCAGC ; cor=; Ncor= a 434 299 847 186 93 1630 155 75 1640 182 66 1631 230 107 c 352 1081 196 189 1727 85 86 1750 70 73 1750 74 76 1668 g 898 334 700 1501 88 146 1664 86 138 1663 91 142 1586 98 t 286 256 227 94 62 109 65 59 122 52 63 123 78 97

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m9_shift1 (oligos_6-8nt_m9)				; oligos_6-8nt_m9; m=0 (reference); ncol1=11; shift=1; ncol=12; -ctCCCTCTCyc ; Alignment reference a 0 663 699 92 206 224 211 67 97 58 630 753 c 0 1705 928 3668 2848 3367 155 3713 116 3769 1224 1621 g 0 830 1002 125 388 197 240 107 155 103 915 822 t 0 847 1416 160 603 257 3439 158 3677 115 1276 849
oligos_6-8nt_m9_shift1 (oligos_6-8nt_m9)				; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -ctCCCTCTCyc ; cor=; Ncor= a 0 663 699 92 206 224 211 67 97 58 630 753 c 0 1705 928 3668 2848 3367 155 3713 116 3769 1224 1621 g 0 830 1002 125 388 197 240 107 155 103 915 822 t 0 847 1416 160 603 257 3439 158 3677 115 1276 849
oligos_6-8nt_m8_shift1 (oligos_6-8nt_m8)				; oligos_6-8nt_m9 versus oligos_6-8nt_m8; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.709051; -cbCTCTCCCtc ; cor=; Ncor= a 0 771 701 108 155 94 158 79 156 194 1015 646 c 0 1663 1103 3887 116 3844 138 3643 3109 3671 904 1769 g 0 795 1185 74 218 132 245 288 360 206 912 914 t 0 999 1239 159 3739 158 3687 218 603 157 1397 899
positions_6-8nt_m2_rc_shift0 (positions_6-8nt_m2_rc)				; oligos_6-8nt_m9 versus positions_6-8nt_m2_rc; m=3/3; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.583727; thTCCCTCym-- ; cor=; Ncor= a 141 161 13 50 2 0 4 38 128 167 0 0 c 151 206 5 594 641 641 7 599 161 192 0 0 g 131 110 0 0 0 3 0 2 152 135 0 0 t 221 167 626 0 1 0 633 5 203 150 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m1_shift3 (positions_6-8nt_m1)				; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=3; ncol=13; ---aaAAAAAAaa ; Alignment reference a 0 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 0 449 427 0 12 10 7 9 0 535 501
positions_6-8nt_m1_shift3 (positions_6-8nt_m1)				; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---aaAAAAAAaa ; cor=; Ncor= a 0 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 0 449 427 0 12 10 7 9 0 535 501
dyads_m10_shift1 (dyads_m10)				; positions_6-8nt_m1 versus dyads_m10; m=2/4; ncol2=12; w=-2; offset=-2; strand=D; shift=1; score= 0.5906; -wwATAAATAAww ; cor=; Ncor= a 0 747 726 1680 198 1754 1628 1767 109 1714 1534 805 669 c 0 344 353 47 86 47 52 40 116 50 93 295 349 g 0 319 252 81 53 34 45 25 54 56 60 284 257 t 0 486 565 88 1559 61 171 64 1617 76 209 512 621
dyads_m8_shift3 (dyads_m8)				; positions_6-8nt_m1 versus dyads_m8; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.586329; ---aaAAAAaaAA ; cor=; Ncor= a 0 0 0 1899 2016 4485 4686 4719 4562 2114 2094 4517 4701 c 0 0 0 1094 1124 243 175 173 200 1052 1157 234 157 g 0 0 0 1067 1059 234 141 99 155 912 992 219 140 t 0 0 0 1101 962 199 159 170 244 1083 918 191 163
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)				; positions_6-8nt_m1 versus oligos_6-8nt_m1; m=4/4; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.570437; aartAAACAAAwa ; cor=; Ncor= a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 823 c 472 561 318 319 47 92 71 2039 74 102 90 512 538 g 479 560 1116 266 41 72 36 70 102 65 70 433 460 t 563 565 353 1288 85 128 56 218 86 93 109 674 567

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; aartAAACAAAwa ; Alignment reference a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 823 c 472 561 318 319 47 92 71 2039 74 102 90 512 538 g 479 560 1116 266 41 72 36 70 102 65 70 433 460 t 563 565 353 1288 85 128 56 218 86 93 109 674 567
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)				; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; aartAAACAAAwa ; cor=; Ncor= a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 823 c 472 561 318 319 47 92 71 2039 74 102 90 512 538 g 479 560 1116 266 41 72 36 70 102 65 70 433 460 t 563 565 353 1288 85 128 56 218 86 93 109 674 567
dyads_m10_shift0 (dyads_m10)				; oligos_6-8nt_m1 versus dyads_m10; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.675986; wwATAAATAAww- ; cor=; Ncor= a 747 726 1680 198 1754 1628 1767 109 1714 1534 805 669 0 c 344 353 47 86 47 52 40 116 50 93 295 349 0 g 319 252 81 53 34 45 25 54 56 60 284 257 0 t 486 565 88 1559 61 171 64 1617 76 209 512 621 0
positions_6-8nt_m1_shift3 (positions_6-8nt_m1)				; oligos_6-8nt_m1 versus positions_6-8nt_m1; m=3/4; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.570437; ---aaAAAAAAaa ; cor=; Ncor= a 0 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 0 449 427 0 12 10 7 9 0 535 501
dyads_m8_shift1 (dyads_m8)				; oligos_6-8nt_m1 versus dyads_m8; m=4/4; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.565596; -aaAAAAaaAAAA ; cor=; Ncor= a 0 1899 2016 4485 4686 4719 4562 2114 2094 4517 4701 4638 4429 c 0 1094 1124 243 175 173 200 1052 1157 234 157 199 252 g 0 1067 1059 234 141 99 155 912 992 219 140 146 202 t 0 1101 962 199 159 170 244 1083 918 191 163 178 278

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m8_shift1 (dyads_m8)				; dyads_m8; m=0 (reference); ncol1=14; shift=1; ncol=15; -aaAAAAaaAAAAaa ; Alignment reference a 0 1899 2016 4485 4686 4719 4562 2114 2094 4517 4701 4638 4429 2025 2008 c 0 1094 1124 243 175 173 200 1052 1157 234 157 199 252 1002 1057 g 0 1067 1059 234 141 99 155 912 992 219 140 146 202 963 977 t 0 1101 962 199 159 170 244 1083 918 191 163 178 278 1171 1119
dyads_m8_shift1 (dyads_m8)				; dyads_m8 versus dyads_m8; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -aaAAAAaaAAAAaa ; cor=; Ncor= a 0 1899 2016 4485 4686 4719 4562 2114 2094 4517 4701 4638 4429 2025 2008 c 0 1094 1124 243 175 173 200 1052 1157 234 157 199 252 1002 1057 g 0 1067 1059 234 141 99 155 912 992 219 140 146 202 963 977 t 0 1101 962 199 159 170 244 1083 918 191 163 178 278 1171 1119
positions_6-8nt_m1_shift1 (positions_6-8nt_m1)				; dyads_m8 versus positions_6-8nt_m1; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.586329; -aaAAAAAAaa---- ; cor=; Ncor= a 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 0 0 0 0 c 0 497 454 0 0 0 0 0 0 384 419 0 0 0 0 g 0 434 419 0 0 0 0 0 0 382 393 0 0 0 0 t 0 449 427 0 12 10 7 9 0 535 501 0 0 0 0
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)				; dyads_m8 versus oligos_6-8nt_m1; m=3/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.565596; aartAAACAAAwa-- ; cor=; Ncor= a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 823 0 0 c 472 561 318 319 47 92 71 2039 74 102 90 512 538 0 0 g 479 560 1116 266 41 72 36 70 102 65 70 433 460 0 0 t 563 565 353 1288 85 128 56 218 86 93 109 674 567 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m10_shift0 (dyads_m10)				; dyads_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATAAATAAww ; Alignment reference a 747 726 1680 198 1754 1628 1767 109 1714 1534 805 669 c 344 353 47 86 47 52 40 116 50 93 295 349 g 319 252 81 53 34 45 25 54 56 60 284 257 t 486 565 88 1559 61 171 64 1617 76 209 512 621
dyads_m10_shift0 (dyads_m10)				; dyads_m10 versus dyads_m10; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAATAAww ; cor=; Ncor= a 747 726 1680 198 1754 1628 1767 109 1714 1534 805 669 c 344 353 47 86 47 52 40 116 50 93 295 349 g 319 252 81 53 34 45 25 54 56 60 284 257 t 486 565 88 1559 61 171 64 1617 76 209 512 621
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)				; dyads_m10 versus oligos_6-8nt_m1; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.675986; aartAAACAAAw ; cor=; Ncor= a 874 702 601 515 2215 2096 2225 61 2126 2128 2119 769 c 472 561 318 319 47 92 71 2039 74 102 90 512 g 479 560 1116 266 41 72 36 70 102 65 70 433 t 563 565 353 1288 85 128 56 218 86 93 109 674
oligos_6-8nt_m4_shift1 (oligos_6-8nt_m4)				; dyads_m10 versus oligos_6-8nt_m4; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.621792; -wrTAyATAya- ; cor=; Ncor= a 0 607 949 20 2377 126 1841 4 2324 446 933 0 c 0 502 392 33 21 1426 149 26 27 617 437 0 g 0 435 630 16 0 211 229 55 21 360 449 0 t 0 855 428 2330 1 636 180 2314 27 976 580 0
positions_6-8nt_m1_shift2 (positions_6-8nt_m1)				; dyads_m10 versus positions_6-8nt_m1; m=4/4; ncol2=10; w=0; offset=2; strand=D; shift=2; score= 0.5906; --aaAAAAAAaa ; cor=; Ncor= a 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 449 427 0 12 10 7 9 0 535 501

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)				; positions_6-8nt_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --krGAGGGAda ; Alignment reference a 0 0 150 203 5 633 0 1 0 626 167 221 c 0 0 135 152 2 0 3 0 0 0 110 131 g 0 0 192 161 599 7 641 641 594 5 206 151 t 0 0 167 128 38 4 0 2 50 13 161 141
positions_6-8nt_m2_shift2 (positions_6-8nt_m2)				; positions_6-8nt_m2 versus positions_6-8nt_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --krGAGGGAda ; cor=; Ncor= a 0 0 150 203 5 633 0 1 0 626 167 221 c 0 0 135 152 2 0 3 0 0 0 110 131 g 0 0 192 161 599 7 641 641 594 5 206 151 t 0 0 167 128 38 4 0 2 50 13 161 141
oligos_6-8nt_m9_rc_shift0 (oligos_6-8nt_m9_rc)				; positions_6-8nt_m2 versus oligos_6-8nt_m9_rc; m=2/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.583727; grGAGAGGGag- ; cor=; Ncor= a 849 1276 115 3677 158 3439 257 603 160 1416 847 0 c 822 915 103 155 107 240 197 388 125 1002 830 0 g 1621 1224 3769 116 3713 155 3367 2848 3668 928 1705 0 t 753 630 58 97 67 211 224 206 92 699 663 0
oligos_6-8nt_m8_rc_shift4 (oligos_6-8nt_m8_rc)				; positions_6-8nt_m2 versus oligos_6-8nt_m8_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.454866; ----gaGGGAGA ; cor=; Ncor= a 0 0 0 0 899 1397 157 603 218 3687 158 3739 c 0 0 0 0 914 912 206 360 288 245 132 218 g 0 0 0 0 1769 904 3671 3109 3643 138 3844 116 t 0 0 0 0 646 1015 194 156 79 158 94 155

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; cbCTCTCCCtc ; Alignment reference a 771 701 108 155 94 158 79 156 194 1015 646 c 1663 1103 3887 116 3844 138 3643 3109 3671 904 1769 g 795 1185 74 218 132 245 288 360 206 912 914 t 999 1239 159 3739 158 3687 218 603 157 1397 899
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)				; oligos_6-8nt_m8 versus oligos_6-8nt_m8; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; cbCTCTCCCtc ; cor=; Ncor= a 771 701 108 155 94 158 79 156 194 1015 646 c 1663 1103 3887 116 3844 138 3643 3109 3671 904 1769 g 795 1185 74 218 132 245 288 360 206 912 914 t 999 1239 159 3739 158 3687 218 603 157 1397 899
oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)				; oligos_6-8nt_m8 versus oligos_6-8nt_m9; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.709051; ctCCCTCTCyc ; cor=; Ncor= a 663 699 92 206 224 211 67 97 58 630 753 c 1705 928 3668 2848 3367 155 3713 116 3769 1224 1621 g 830 1002 125 388 197 240 107 155 103 915 822 t 847 1416 160 603 257 3439 158 3677 115 1276 849
positions_6-8nt_m2_rc_shift3 (positions_6-8nt_m2_rc)				; oligos_6-8nt_m8 versus positions_6-8nt_m2_rc; m=3/3; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.454866; ---thTCCCTC ; cor=; Ncor= a 0 0 0 141 161 13 50 2 0 4 38 c 0 0 0 151 206 5 594 641 641 7 599 g 0 0 0 131 110 0 0 0 3 0 2 t 0 0 0 221 167 626 0 1 0 633 5

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift0 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ysGCCACCGvc ; Alignment reference a 1043 968 245 116 102 4214 194 169 464 1384 988 c 1522 1537 191 4462 4566 104 4303 4341 268 1303 1645 g 1118 1415 4246 192 164 376 170 179 3917 1269 1141 t 1255 1018 256 168 106 244 271 249 289 982 1164
dyads_m4_shift0 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ysGCCACCGvc ; cor=; Ncor= a 1043 968 245 116 102 4214 194 169 464 1384 988 c 1522 1537 191 4462 4566 104 4303 4341 268 1303 1645 g 1118 1415 4246 192 164 376 170 179 3917 1269 1141 t 1255 1018 256 168 106 244 271 249 289 982 1164
dyads_m5_shift0 (dyads_m5)				; dyads_m4 versus dyads_m5; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.831308; ycGCCGCCGcc ; cor=; Ncor= a 1024 909 274 229 115 379 237 117 206 1236 982 c 1634 1767 191 4280 4573 104 4199 4626 242 1428 1816 g 1052 1179 4138 182 149 4234 287 93 4299 1198 983 t 1251 1106 358 270 124 244 238 125 214 1099 1180
dyads_m6_shift0 (dyads_m6)				; dyads_m4 versus dyads_m6; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.658834; ccACCACCac- ; cor=; Ncor= a 253 232 1338 3 1 1311 2 3 520 332 0 c 515 559 0 1335 1208 16 1332 1298 229 436 0 g 326 258 0 0 26 1 0 11 301 324 0 t 245 290 1 1 104 11 5 27 289 247 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; oligos_6-8nt_m7; m=0 (reference); ncol1=12; shift=2; ncol=14; --arCAGCAACArc ; Alignment reference a 0 0 1735 940 65 3364 470 66 3269 2481 137 3332 1238 599 c 0 0 628 697 3365 59 110 3433 122 169 3309 65 529 1847 g 0 0 690 1497 105 81 2932 61 130 833 90 81 1330 621 t 0 0 535 454 53 84 76 28 67 105 52 110 491 521
oligos_6-8nt_m7_shift2 (oligos_6-8nt_m7)				; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --arCAGCAACArc ; cor=; Ncor= a 0 0 1735 940 65 3364 470 66 3269 2481 137 3332 1238 599 c 0 0 628 697 3365 59 110 3433 122 169 3309 65 529 1847 g 0 0 690 1497 105 81 2932 61 130 833 90 81 1330 621 t 0 0 535 454 53 84 76 28 67 105 52 110 491 521
dyads_m7_shift1 (dyads_m7)				; oligos_6-8nt_m7 versus dyads_m7; m=2/3; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.655874; -caACAACAACAAC ; cor=; Ncor= a 0 402 1160 1712 121 1977 1815 113 1873 1935 114 1945 1797 180 c 0 1180 397 102 1947 85 86 1907 101 54 1968 101 87 1746 g 0 375 354 352 78 98 260 101 126 189 67 101 255 127 t 0 291 337 82 102 88 87 127 148 70 99 101 109 195
dyads_m1_shift0 (dyads_m1)				; oligos_6-8nt_m7 versus dyads_m1; m=3/3; ncol2=20; w=-2; offset=-2; strand=D; shift=0; score=0.516214; gcrGCAGCAGCAGC ; cor=; Ncor= a 434 299 847 186 93 1630 155 75 1640 182 66 1631 230 107 c 352 1081 196 189 1727 85 86 1750 70 73 1750 74 76 1668 g 898 334 700 1501 88 146 1664 86 138 1663 91 142 1586 98 t 286 256 227 94 62 109 65 59 122 52 63 123 78 97