One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.180941_2026-01-25.180941_K9UVGH/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.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift5 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m4_shift5 (oligos_6-8nt_m4)
; oligos_6-8nt_m4; m=0 (reference); ncol1=12; shift=5; ncol=17; -----cvCACTCACccw ; Alignment reference a 0 0 0 0 0 116 153 37 516 8 44 7 512 11 93 146 166 c 0 0 0 0 0 270 157 494 19 574 31 550 11 554 345 226 145 g 0 0 0 0 0 74 151 29 20 4 15 7 22 13 38 103 116 t 0 0 0 0 0 134 133 34 39 8 504 30 49 16 118 119 167

oligos_6-8nt_m4_shift5 (oligos_6-8nt_m4)
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----cvCACTCACccw ; cor=; Ncor= a 0 0 0 0 0 116 153 37 516 8 44 7 512 11 93 146 166 c 0 0 0 0 0 270 157 494 19 574 31 550 11 554 345 226 145 g 0 0 0 0 0 74 151 29 20 4 15 7 22 13 38 103 116 t 0 0 0 0 0 134 133 34 39 8 504 30 49 16 118 119 167

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m4 versus oligos_6-8nt_m2; m=2/2; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.524398; acaCACrCACACACrca ; cor=; Ncor= a 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 c 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 g 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 t 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; wyGAACTGAAww ; Alignment reference a 180 137 54 512 533 48 27 16 505 495 202 182 c 100 167 35 38 8 468 22 11 22 20 108 95 g 132 122 441 9 15 19 21 531 26 26 114 140 t 159 145 41 12 15 36 501 13 18 30 147 154

oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m10 versus oligos_6-8nt_m10; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wyGAACTGAAww ; cor=; Ncor= a 180 137 54 512 533 48 27 16 505 495 202 182 c 100 167 35 38 8 468 22 11 22 20 108 95 g 132 122 441 9 15 19 21 531 26 26 114 140 t 159 145 41 12 15 36 501 13 18 30 147 154

oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)
; oligos_6-8nt_m10 versus oligos_6-8nt_m9; m=2/2; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.617511; --waAATGAAaw ; cor=; Ncor= a 0 0 145 194 429 429 0 0 429 429 202 160 c 0 0 76 70 0 0 0 0 0 0 64 68 g 0 0 93 92 0 0 0 429 0 0 62 75 t 0 0 115 73 0 0 429 0 0 0 101 126

One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m1_shift1 (positions_6-8nt_m1)
; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -kyCGCCGCyg ; Alignment reference a 0 107 85 0 1 0 0 0 0 88 108 c 0 88 148 448 4 448 448 1 448 166 110 g 0 137 102 0 434 0 0 443 0 68 137 t 0 116 113 0 9 0 0 4 0 126 93

positions_6-8nt_m1_shift1 (positions_6-8nt_m1)
; positions_6-8nt_m1 versus positions_6-8nt_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -kyCGCCGCyg ; cor=; Ncor= a 0 107 85 0 1 0 0 0 0 88 108 c 0 88 148 448 4 448 448 1 448 166 110 g 0 137 102 0 434 0 0 443 0 68 137 t 0 116 113 0 9 0 0 4 0 126 93

dyads_m8_shift0 (dyads_m8)
; positions_6-8nt_m1 versus dyads_m8; m=2/2; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.692085; bkCCGCCGmc- ; cor=; Ncor= a 87 109 0 1 13 30 1 1 152 102 0 c 157 92 503 502 24 447 502 4 147 191 0 g 130 162 0 0 430 0 0 487 97 91 0 t 129 140 0 0 36 26 0 11 107 119 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; tctCTCTCTCTCTCTCTCtc ; Alignment reference a 147 126 110 69 83 58 83 52 77 38 89 43 95 40 102 40 111 49 172 114 c 288 819 185 1046 137 1080 140 1116 114 1144 91 1135 101 1130 88 1123 108 1068 219 817 g 259 146 212 84 186 81 180 60 137 47 135 40 163 44 149 48 137 76 208 164 t 614 217 801 109 902 89 905 80 980 79 993 90 949 94 969 97 952 115 709 213

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; tctCTCTCTCTCTCTCTCtc ; cor=; Ncor= a 147 126 110 69 83 58 83 52 77 38 89 43 95 40 102 40 111 49 172 114 c 288 819 185 1046 137 1080 140 1116 114 1144 91 1135 101 1130 88 1123 108 1068 219 817 g 259 146 212 84 186 81 180 60 137 47 135 40 163 44 149 48 137 76 208 164 t 614 217 801 109 902 89 905 80 980 79 993 90 949 94 969 97 952 115 709 213

dyads_m7_rc_shift0 (dyads_m7_rc)
; dyads_m2 versus dyads_m7_rc; m=2/3; ncol2=21; w=0; offset=0; strand=R; shift=0; score=0.943064; tcTCTCTCTCTCtCTCTCyc ; cor=; Ncor= a 83 70 59 30 58 27 51 26 61 27 52 27 89 27 77 34 63 36 95 90 c 207 616 108 783 70 821 100 820 72 824 73 797 227 819 57 807 75 761 293 540 g 196 107 130 62 120 39 91 39 84 34 94 48 142 29 87 27 89 57 110 129 t 448 141 637 59 686 47 692 49 717 49 715 62 476 59 713 66 707 80 436 175

oligos_6-8nt_m7_rc_shift4 (oligos_6-8nt_m7_rc)
; dyads_m2 versus oligos_6-8nt_m7_rc; m=3/3; ncol2=16; w=0; offset=4; strand=R; shift=4; score=0.775122; ----tctCTCkCTCTCTCtc ; cor=; Ncor= a 0 0 0 0 134 131 100 41 59 35 95 34 91 35 76 32 81 53 155 112 c 0 0 0 0 261 776 115 1072 119 1086 117 1119 65 1123 54 1096 83 1005 225 738 g 0 0 0 0 248 164 199 53 103 58 508 26 83 27 124 43 97 76 228 166 t 0 0 0 0 594 166 823 71 956 58 517 58 998 52 983 66 976 103 629 221

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m7_shift5 (oligos_6-8nt_m7)
; oligos_6-8nt_m7; m=0 (reference); ncol1=16; shift=5; ncol=21; -----gaGAGAGAGmGAGaga ; Alignment reference a 0 0 0 0 0 221 629 103 976 66 983 52 998 58 517 58 956 71 823 166 594 c 0 0 0 0 0 166 228 76 97 43 124 27 83 26 508 58 103 53 199 164 248 g 0 0 0 0 0 738 225 1005 83 1096 54 1123 65 1119 117 1086 119 1072 115 776 261 t 0 0 0 0 0 112 155 53 81 32 76 35 91 34 95 35 59 41 100 131 134

oligos_6-8nt_m7_shift5 (oligos_6-8nt_m7)
; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=5; score= 1; -----gaGAGAGAGmGAGaga ; cor=; Ncor= a 0 0 0 0 0 221 629 103 976 66 983 52 998 58 517 58 956 71 823 166 594 c 0 0 0 0 0 166 228 76 97 43 124 27 83 26 508 58 103 53 199 164 248 g 0 0 0 0 0 738 225 1005 83 1096 54 1123 65 1119 117 1086 119 1072 115 776 261 t 0 0 0 0 0 112 155 53 81 32 76 35 91 34 95 35 59 41 100 131 134

dyads_m2_rc_shift5 (dyads_m2_rc)
; oligos_6-8nt_m7 versus dyads_m2_rc; m=2/3; ncol2=20; w=0; offset=0; strand=R; shift=5; score=0.775122; -----gaGAGAGAGAGAGAGA ; cor=; Ncor= a 0 0 0 0 0 213 709 115 952 97 969 94 949 90 993 79 980 80 905 89 902 c 0 0 0 0 0 164 208 76 137 48 149 44 163 40 135 47 137 60 180 81 186 g 0 0 0 0 0 817 219 1068 108 1123 88 1130 101 1135 91 1144 114 1116 140 1080 137 t 0 0 0 0 0 114 172 49 111 40 102 40 95 43 89 38 77 52 83 58 83

dyads_m7_shift0 (dyads_m7)
; oligos_6-8nt_m7 versus dyads_m7; m=3/3; ncol2=21; w=-5; offset=-5; strand=D; shift=0; score=0.727151; agrGAGAGaGAGAGAGAGAga ; cor=; Ncor= a 437 175 436 80 707 66 713 59 476 62 715 49 717 49 692 47 686 59 637 141 448 c 154 129 110 57 89 27 87 29 142 48 94 34 84 39 91 39 120 62 130 107 196 g 206 540 293 761 75 807 57 819 227 797 73 824 72 820 100 821 70 783 108 616 207 t 137 90 95 36 63 34 77 27 89 27 52 27 61 26 51 27 58 30 59 70 83

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; wwrAAAATATAAATAAww ; Alignment reference a 137 127 94 278 307 301 315 59 303 64 303 269 314 37 302 257 152 141 c 62 68 28 22 17 11 9 25 11 17 13 24 11 31 18 24 47 57 g 62 68 184 15 17 8 10 11 20 14 10 16 11 20 13 18 56 43 t 96 94 51 42 16 37 23 262 23 262 31 48 21 269 24 58 102 116

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwrAAAATATAAATAAww ; cor=; Ncor= a 137 127 94 278 307 301 315 59 303 64 303 269 314 37 302 257 152 141 c 62 68 28 22 17 11 9 25 11 17 13 24 11 31 18 24 47 57 g 62 68 184 15 17 8 10 11 20 14 10 16 11 20 13 18 56 43 t 96 94 51 42 16 37 23 262 23 262 31 48 21 269 24 58 102 116

oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)
; dyads_m3 versus oligos_6-8nt_m6; m=2/3; ncol2=13; w=0; offset=5; strand=D; shift=5; score=0.616398; -----wwaATAAATAAww ; cor=; Ncor= a 0 0 0 0 0 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 0 0 0 0 0 205 174 85 76 46 25 47 38 47 22 66 185 183 g 0 0 0 0 0 191 175 100 91 18 20 34 22 30 25 55 181 171 t 0 0 0 0 0 373 317 200 160 1021 64 90 60 1037 47 156 322 394

dyads_m10_rc_shift6 (dyads_m10_rc)
; dyads_m3 versus dyads_m10_rc; m=3/3; ncol2=12; w=0; offset=6; strand=R; shift=6; score=0.531102; ------wwTTAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 418 350 107 59 879 910 896 57 882 839 404 329 c 0 0 0 0 0 0 144 143 25 25 27 25 15 52 35 27 145 166 g 0 0 0 0 0 0 146 157 34 37 23 14 22 18 23 29 138 118 t 0 0 0 0 0 0 277 335 819 864 56 36 52 858 45 90 298 372

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=24; shift=0; ncol=24; caCACACACACACAmmmACAmmma ; Alignment reference a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 27 328 163 146 107 188 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 316 22 143 143 158 55 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 29 29 48 68 72 96 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21 30 23 48 45 65 63

dyads_m6_shift0 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; caCACACACACACAmmmACAmmma ; cor=; Ncor= a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 27 328 163 146 107 188 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 316 22 143 143 158 55 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 29 29 48 68 72 96 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21 30 23 48 45 65 63

dyads_m5_shift0 (dyads_m5)
; dyads_m6 versus dyads_m5; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.834672; caCrCACACACAmmCACAmmmAca ; cor=; Ncor= a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 136 100 132 237 56 153 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 120 147 115 23 162 49 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 30 42 37 41 50 72 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16 32 29 34 17 50 44

dyads_m1_shift0 (dyads_m1)
; dyads_m6 versus dyads_m1; m=3/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.741009; caCrCACACACACACAcac----- ; cor=; Ncor= a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 200 0 0 0 0 0 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 722 0 0 0 0 0 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 188 0 0 0 0 0 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181 239 0 0 0 0 0

oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; dyads_m6 versus oligos_6-8nt_m2; m=4/4; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.664136; -acaCACrCACACACrca------ ; cor=; Ncor= a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 0 0 0 0 0 0 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 0 0 0 0 0 0 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 0 0 0 0 0 0 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148 0 0 0 0 0 0

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; yacATACATACat ; Alignment reference a 178 415 124 623 23 757 44 752 26 759 57 392 190 c 235 120 466 43 79 15 669 13 85 16 555 113 203 g 110 138 66 79 9 22 28 27 21 16 40 181 108 t 290 140 157 68 702 19 72 21 681 22 161 127 312

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; yacATACATACat ; cor=; Ncor= a 178 415 124 623 23 757 44 752 26 759 57 392 190 c 235 120 466 43 79 15 669 13 85 16 555 113 203 g 110 138 66 79 9 22 28 27 21 16 40 181 108 t 290 140 157 68 702 19 72 21 681 22 161 127 312

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=19; shift=0; ncol=19; caCrCACACACACACAcac ; Alignment reference a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 200 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 722 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 188 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181 239

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; caCrCACACACACACAcac ; cor=; Ncor= a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 200 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 722 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 188 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181 239

oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; dyads_m1 versus oligos_6-8nt_m2; m=2/4; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.863815; -acaCACrCACACACrca- ; cor=; Ncor= a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 0 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 0 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 0 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148 0

dyads_m6_shift0 (dyads_m6)
; dyads_m1 versus dyads_m6; m=3/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.741009; caCACACACACACAmmmAC ; cor=; Ncor= a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 27 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 316 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 29 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21 30

dyads_m5_shift0 (dyads_m5)
; dyads_m1 versus dyads_m5; m=4/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.727367; caCrCACACACAmmCACAm ; cor=; Ncor= a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 136 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 120 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 30 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16 32

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)
; oligos_6-8nt_m6; m=0 (reference); ncol1=13; shift=5; ncol=18; -----wwaATAAATAAww ; Alignment reference a 0 0 0 0 0 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 0 0 0 0 0 205 174 85 76 46 25 47 38 47 22 66 185 183 g 0 0 0 0 0 191 175 100 91 18 20 34 22 30 25 55 181 171 t 0 0 0 0 0 373 317 200 160 1021 64 90 60 1037 47 156 322 394

oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)
; oligos_6-8nt_m6 versus oligos_6-8nt_m6; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=5; score= 1; -----wwaATAAATAAww ; cor=; Ncor= a 0 0 0 0 0 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 0 0 0 0 0 205 174 85 76 46 25 47 38 47 22 66 185 183 g 0 0 0 0 0 191 175 100 91 18 20 34 22 30 25 55 181 171 t 0 0 0 0 0 373 317 200 160 1021 64 90 60 1037 47 156 322 394

dyads_m10_rc_shift6 (dyads_m10_rc)
; oligos_6-8nt_m6 versus dyads_m10_rc; m=2/3; ncol2=12; w=0; offset=1; strand=R; shift=6; score=0.816681; ------wwTTAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 418 350 107 59 879 910 896 57 882 839 404 329 c 0 0 0 0 0 0 144 143 25 25 27 25 15 52 35 27 145 166 g 0 0 0 0 0 0 146 157 34 37 23 14 22 18 23 29 138 118 t 0 0 0 0 0 0 277 335 819 864 56 36 52 858 45 90 298 372

dyads_m3_shift0 (dyads_m3)
; oligos_6-8nt_m6 versus dyads_m3; m=3/3; ncol2=18; w=-5; offset=-5; strand=D; shift=0; score=0.616398; wwrAAAATATAAATAAww ; cor=; Ncor= a 137 127 94 278 307 301 315 59 303 64 303 269 314 37 302 257 152 141 c 62 68 28 22 17 11 9 25 11 17 13 24 11 31 18 24 47 57 g 62 68 184 15 17 8 10 11 20 14 10 16 11 20 13 18 56 43 t 96 94 51 42 16 37 23 262 23 262 31 48 21 269 24 58 102 116

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 4 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; wwTTATTTAAww ; Alignment reference a 372 298 90 45 858 52 36 56 864 819 335 277 c 118 138 29 23 18 22 14 23 37 34 157 146 g 166 145 27 35 52 15 25 27 25 25 143 144 t 329 404 839 882 57 896 910 879 59 107 350 418

dyads_m10_shift0 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwTTATTTAAww ; cor=; Ncor= a 372 298 90 45 858 52 36 56 864 819 335 277 c 118 138 29 23 18 22 14 23 37 34 157 146 g 166 145 27 35 52 15 25 27 25 25 143 144 t 329 404 839 882 57 896 910 879 59 107 350 418

oligos_6-8nt_m6_rc_shift0 (oligos_6-8nt_m6_rc)
; dyads_m10 versus oligos_6-8nt_m6_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.816681; wwTTATTTATtw ; cor=; Ncor= a 394 322 156 47 1037 60 90 64 1021 160 200 317 c 171 181 55 25 30 22 34 20 18 91 100 175 g 183 185 66 22 47 38 47 25 46 76 85 174 t 404 464 875 1058 38 1032 981 1043 67 825 767 486

dyads_m3_rc_shift0 (dyads_m3_rc)
; dyads_m10 versus dyads_m3_rc; m=3/3; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.531102; wwTTATTTATAT ; cor=; Ncor= a 116 102 58 24 269 21 48 31 262 23 262 23 c 43 56 18 13 20 11 16 10 14 20 11 10 g 57 47 24 18 31 11 24 13 17 11 25 9 t 141 152 257 302 37 314 269 303 64 303 59 315

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

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; gcgGCAGCAGCggc ; Alignment reference a 185 155 186 46 36 710 52 36 698 45 47 190 217 207 c 198 355 60 78 769 37 18 783 29 39 741 42 205 353 g 311 185 549 707 49 91 775 33 94 763 38 576 304 163 t 176 175 75 39 16 32 25 18 49 23 44 62 144 147

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; gcgGCAGCAGCggc ; cor=; Ncor= a 185 155 186 46 36 710 52 36 698 45 47 190 217 207 c 198 355 60 78 769 37 18 783 29 39 741 42 205 353 g 311 185 549 707 49 91 775 33 94 763 38 576 304 163 t 176 175 75 39 16 32 25 18 49 23 44 62 144 147

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; acGACGACka ; Alignment reference a 137 92 0 416 1 1 422 1 87 166 c 105 178 5 3 413 2 0 399 75 66 g 94 86 393 1 8 369 2 12 158 103 t 92 72 30 8 6 56 4 16 108 93

oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8 versus oligos_6-8nt_m8; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; acGACGACka ; cor=; Ncor= a 137 92 0 416 1 1 422 1 87 166 c 105 178 5 3 413 2 0 399 75 66 g 94 86 393 1 8 369 2 12 158 103 t 92 72 30 8 6 56 4 16 108 93

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=15; shift=0; ncol=15; aacAAACAACAAAaa ; Alignment reference a 188 200 106 394 423 436 54 451 441 49 452 444 399 196 229 c 121 98 287 61 31 24 388 17 15 410 17 23 56 107 85 g 90 123 50 26 18 23 19 10 28 19 15 17 20 82 83 t 101 79 57 19 28 17 39 22 16 22 16 16 25 115 103

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; aacAAACAACAAAaa ; cor=; Ncor= a 188 200 106 394 423 436 54 451 441 49 452 444 399 196 229 c 121 98 287 61 31 24 388 17 15 410 17 23 56 107 85 g 90 123 50 26 18 23 19 10 28 19 15 17 20 82 83 t 101 79 57 19 28 17 39 22 16 22 16 16 25 115 103

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; bkCCGCCGmc ; Alignment reference a 87 109 0 1 13 30 1 1 152 102 c 157 92 503 502 24 447 502 4 147 191 g 130 162 0 0 430 0 0 487 97 91 t 129 140 0 0 36 26 0 11 107 119

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; bkCCGCCGmc ; cor=; Ncor= a 87 109 0 1 13 30 1 1 152 102 c 157 92 503 502 24 447 502 4 147 191 g 130 162 0 0 430 0 0 487 97 91 t 129 140 0 0 36 26 0 11 107 119

positions_6-8nt_m1_shift1 (positions_6-8nt_m1)
; dyads_m8 versus positions_6-8nt_m1; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.692085; -kyCGCCGCy ; cor=; Ncor= a 0 107 85 0 1 0 0 0 0 88 c 0 88 148 448 4 448 448 1 448 166 g 0 137 102 0 434 0 0 443 0 68 t 0 116 113 0 9 0 0 4 0 126

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift0 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=21; shift=0; ncol=21; agrGAGAGaGAGAGAGAGAga ; Alignment reference a 437 175 436 80 707 66 713 59 476 62 715 49 717 49 692 47 686 59 637 141 448 c 154 129 110 57 89 27 87 29 142 48 94 34 84 39 91 39 120 62 130 107 196 g 206 540 293 761 75 807 57 819 227 797 73 824 72 820 100 821 70 783 108 616 207 t 137 90 95 36 63 34 77 27 89 27 52 27 61 26 51 27 58 30 59 70 83

dyads_m7_shift0 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/3; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; agrGAGAGaGAGAGAGAGAga ; cor=; Ncor= a 437 175 436 80 707 66 713 59 476 62 715 49 717 49 692 47 686 59 637 141 448 c 154 129 110 57 89 27 87 29 142 48 94 34 84 39 91 39 120 62 130 107 196 g 206 540 293 761 75 807 57 819 227 797 73 824 72 820 100 821 70 783 108 616 207 t 137 90 95 36 63 34 77 27 89 27 52 27 61 26 51 27 58 30 59 70 83

dyads_m2_rc_shift1 (dyads_m2_rc)
; dyads_m7 versus dyads_m2_rc; m=2/3; ncol2=20; w=0; offset=1; strand=R; shift=1; score=0.943064; -gaGAGAGAGAGAGAGAGaga ; cor=; Ncor= a 0 213 709 115 952 97 969 94 949 90 993 79 980 80 905 89 902 109 801 217 614 c 0 164 208 76 137 48 149 44 163 40 135 47 137 60 180 81 186 84 212 146 259 g 0 817 219 1068 108 1123 88 1130 101 1135 91 1144 114 1116 140 1080 137 1046 185 819 288 t 0 114 172 49 111 40 102 40 95 43 89 38 77 52 83 58 83 69 110 126 147

oligos_6-8nt_m7_shift5 (oligos_6-8nt_m7)
; dyads_m7 versus oligos_6-8nt_m7; m=3/3; ncol2=16; w=0; offset=5; strand=D; shift=5; score=0.727151; -----gaGAGAGAGmGAGaga ; cor=; Ncor= a 0 0 0 0 0 221 629 103 976 66 983 52 998 58 517 58 956 71 823 166 594 c 0 0 0 0 0 166 228 76 97 43 124 27 83 26 508 58 103 53 199 164 248 g 0 0 0 0 0 738 225 1005 83 1096 54 1123 65 1119 117 1086 119 1072 115 776 261 t 0 0 0 0 0 112 155 53 81 32 76 35 91 34 95 35 59 41 100 131 134

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)
; oligos_6-8nt_m9; m=0 (reference); ncol1=10; shift=2; ncol=12; --waAATGAAaw ; Alignment reference a 0 0 145 194 429 429 0 0 429 429 202 160 c 0 0 76 70 0 0 0 0 0 0 64 68 g 0 0 93 92 0 0 0 429 0 0 62 75 t 0 0 115 73 0 0 429 0 0 0 101 126

oligos_6-8nt_m9_shift2 (oligos_6-8nt_m9)
; oligos_6-8nt_m9 versus oligos_6-8nt_m9; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --waAATGAAaw ; cor=; Ncor= a 0 0 145 194 429 429 0 0 429 429 202 160 c 0 0 76 70 0 0 0 0 0 0 64 68 g 0 0 93 92 0 0 0 429 0 0 62 75 t 0 0 115 73 0 0 429 0 0 0 101 126

oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10)
; oligos_6-8nt_m9 versus oligos_6-8nt_m10; m=2/2; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.617511; wyGAACTGAAww ; cor=; Ncor= a 180 137 54 512 533 48 27 16 505 495 202 182 c 100 167 35 38 8 468 22 11 22 20 108 95 g 132 122 441 9 15 19 21 531 26 26 114 140 t 159 145 41 12 15 36 501 13 18 30 147 154

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

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; caCrCACACACAmmCACAmmmAca ; Alignment reference a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 136 100 132 237 56 153 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 120 147 115 23 162 49 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 30 42 37 41 50 72 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16 32 29 34 17 50 44

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; caCrCACACACAmmCACAmmmAca ; cor=; Ncor= a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 136 100 132 237 56 153 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 120 147 115 23 162 49 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 30 42 37 41 50 72 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16 32 29 34 17 50 44

dyads_m6_shift0 (dyads_m6)
; dyads_m5 versus dyads_m6; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.834672; caCACACACACACAmmmACAmmma ; cor=; Ncor= a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 27 328 163 146 107 188 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 316 22 143 143 158 55 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 29 29 48 68 72 96 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21 30 23 48 45 65 63

dyads_m1_shift0 (dyads_m1)
; dyads_m5 versus dyads_m1; m=3/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.727367; caCrCACACACACACAcac----- ; cor=; Ncor= a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 200 0 0 0 0 0 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 722 0 0 0 0 0 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 188 0 0 0 0 0 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181 239 0 0 0 0 0

oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; dyads_m5 versus oligos_6-8nt_m2; m=4/4; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.632955; -acaCACrCACACACrca------ ; cor=; Ncor= a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 0 0 0 0 0 0 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 0 0 0 0 0 0 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 0 0 0 0 0 0 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; ykCTTTTCyy ; Alignment reference a 92 123 0 0 0 9 1 0 102 117 c 168 84 511 0 0 0 0 511 145 140 g 83 166 0 0 0 0 0 0 123 116 t 168 138 0 511 511 502 510 0 141 138

dyads_m9_shift0 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ykCTTTTCyy ; cor=; Ncor= a 92 123 0 0 0 9 1 0 102 117 c 168 84 511 0 0 0 0 511 145 140 g 83 166 0 0 0 0 0 0 123 116 t 168 138 0 511 511 502 510 0 141 138

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift1 ; 6 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 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148

oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -acaCACrCACACACrca ; cor=; Ncor= a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148

dyads_m1_shift0 (dyads_m1)
; oligos_6-8nt_m2 versus dyads_m1; m=2/5; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.863815; caCrCACACACACACAca ; cor=; Ncor= a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181

dyads_m6_shift0 (dyads_m6)
; oligos_6-8nt_m2 versus dyads_m6; m=3/5; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.664136; caCACACACACACAmmmA ; cor=; Ncor= a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21

dyads_m5_shift0 (dyads_m5)
; oligos_6-8nt_m2 versus dyads_m5; m=4/5; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.632955; caCrCACACACAmmCACA ; cor=; Ncor= a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16

oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)
; oligos_6-8nt_m2 versus oligos_6-8nt_m4; m=5/5; ncol2=12; w=0; offset=5; strand=D; shift=6; score=0.524398; ------cvCACTCACccw ; cor=; Ncor= a 0 0 0 0 0 0 116 153 37 516 8 44 7 512 11 93 146 166 c 0 0 0 0 0 0 270 157 494 19 574 31 550 11 554 345 226 145 g 0 0 0 0 0 0 74 151 29 20 4 15 7 22 13 38 103 116 t 0 0 0 0 0 0 134 133 34 39 8 504 30 49 16 118 119 167

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=14; shift=0; ncol=14; wygaATCGATtcgw ; Alignment reference a 150 135 100 346 500 15 17 13 517 41 114 79 141 169 c 131 157 107 66 18 18 525 10 18 7 42 283 129 120 g 119 130 283 42 7 18 12 527 18 15 67 107 160 129 t 167 145 77 113 42 516 13 17 14 504 344 98 137 149

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wygaATCGATtcgw ; cor=; Ncor= a 150 135 100 346 500 15 17 13 517 41 114 79 141 169 c 131 157 107 66 18 18 525 10 18 7 42 283 129 120 g 119 130 283 42 7 18 12 527 18 15 67 107 160 129 t 167 145 77 113 42 516 13 17 14 504 344 98 137 149

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift0 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; tctCTCTCTCTCTCTCTCtc ; Alignment reference a 147 126 110 69 83 58 83 52 77 38 89 43 95 40 102 40 111 49 172 114 c 288 819 185 1046 137 1080 140 1116 114 1144 91 1135 101 1130 88 1123 108 1068 219 817 g 259 146 212 84 186 81 180 60 137 47 135 40 163 44 149 48 137 76 208 164 t 614 217 801 109 902 89 905 80 980 79 993 90 949 94 969 97 952 115 709 213
dyads_m2_shift0 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; tctCTCTCTCTCTCTCTCtc ; cor=; Ncor= a 147 126 110 69 83 58 83 52 77 38 89 43 95 40 102 40 111 49 172 114 c 288 819 185 1046 137 1080 140 1116 114 1144 91 1135 101 1130 88 1123 108 1068 219 817 g 259 146 212 84 186 81 180 60 137 47 135 40 163 44 149 48 137 76 208 164 t 614 217 801 109 902 89 905 80 980 79 993 90 949 94 969 97 952 115 709 213
dyads_m7_rc_shift0 (dyads_m7_rc)				; dyads_m2 versus dyads_m7_rc; m=2/3; ncol2=21; w=0; offset=0; strand=R; shift=0; score=0.943064; tcTCTCTCTCTCtCTCTCyc ; cor=; Ncor= a 83 70 59 30 58 27 51 26 61 27 52 27 89 27 77 34 63 36 95 90 c 207 616 108 783 70 821 100 820 72 824 73 797 227 819 57 807 75 761 293 540 g 196 107 130 62 120 39 91 39 84 34 94 48 142 29 87 27 89 57 110 129 t 448 141 637 59 686 47 692 49 717 49 715 62 476 59 713 66 707 80 436 175
oligos_6-8nt_m7_rc_shift4 (oligos_6-8nt_m7_rc)				; dyads_m2 versus oligos_6-8nt_m7_rc; m=3/3; ncol2=16; w=0; offset=4; strand=R; shift=4; score=0.775122; ----tctCTCkCTCTCTCtc ; cor=; Ncor= a 0 0 0 0 134 131 100 41 59 35 95 34 91 35 76 32 81 53 155 112 c 0 0 0 0 261 776 115 1072 119 1086 117 1119 65 1123 54 1096 83 1005 225 738 g 0 0 0 0 248 164 199 53 103 58 508 26 83 27 124 43 97 76 228 166 t 0 0 0 0 594 166 823 71 956 58 517 58 998 52 983 66 976 103 629 221

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m7_shift5 (oligos_6-8nt_m7)				; oligos_6-8nt_m7; m=0 (reference); ncol1=16; shift=5; ncol=21; -----gaGAGAGAGmGAGaga ; Alignment reference a 0 0 0 0 0 221 629 103 976 66 983 52 998 58 517 58 956 71 823 166 594 c 0 0 0 0 0 166 228 76 97 43 124 27 83 26 508 58 103 53 199 164 248 g 0 0 0 0 0 738 225 1005 83 1096 54 1123 65 1119 117 1086 119 1072 115 776 261 t 0 0 0 0 0 112 155 53 81 32 76 35 91 34 95 35 59 41 100 131 134
oligos_6-8nt_m7_shift5 (oligos_6-8nt_m7)				; oligos_6-8nt_m7 versus oligos_6-8nt_m7; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=5; score= 1; -----gaGAGAGAGmGAGaga ; cor=; Ncor= a 0 0 0 0 0 221 629 103 976 66 983 52 998 58 517 58 956 71 823 166 594 c 0 0 0 0 0 166 228 76 97 43 124 27 83 26 508 58 103 53 199 164 248 g 0 0 0 0 0 738 225 1005 83 1096 54 1123 65 1119 117 1086 119 1072 115 776 261 t 0 0 0 0 0 112 155 53 81 32 76 35 91 34 95 35 59 41 100 131 134
dyads_m2_rc_shift5 (dyads_m2_rc)				; oligos_6-8nt_m7 versus dyads_m2_rc; m=2/3; ncol2=20; w=0; offset=0; strand=R; shift=5; score=0.775122; -----gaGAGAGAGAGAGAGA ; cor=; Ncor= a 0 0 0 0 0 213 709 115 952 97 969 94 949 90 993 79 980 80 905 89 902 c 0 0 0 0 0 164 208 76 137 48 149 44 163 40 135 47 137 60 180 81 186 g 0 0 0 0 0 817 219 1068 108 1123 88 1130 101 1135 91 1144 114 1116 140 1080 137 t 0 0 0 0 0 114 172 49 111 40 102 40 95 43 89 38 77 52 83 58 83
dyads_m7_shift0 (dyads_m7)				; oligos_6-8nt_m7 versus dyads_m7; m=3/3; ncol2=21; w=-5; offset=-5; strand=D; shift=0; score=0.727151; agrGAGAGaGAGAGAGAGAga ; cor=; Ncor= a 437 175 436 80 707 66 713 59 476 62 715 49 717 49 692 47 686 59 637 141 448 c 154 129 110 57 89 27 87 29 142 48 94 34 84 39 91 39 120 62 130 107 196 g 206 540 293 761 75 807 57 819 227 797 73 824 72 820 100 821 70 783 108 616 207 t 137 90 95 36 63 34 77 27 89 27 52 27 61 26 51 27 58 30 59 70 83

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift0 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; wwrAAAATATAAATAAww ; Alignment reference a 137 127 94 278 307 301 315 59 303 64 303 269 314 37 302 257 152 141 c 62 68 28 22 17 11 9 25 11 17 13 24 11 31 18 24 47 57 g 62 68 184 15 17 8 10 11 20 14 10 16 11 20 13 18 56 43 t 96 94 51 42 16 37 23 262 23 262 31 48 21 269 24 58 102 116
dyads_m3_shift0 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwrAAAATATAAATAAww ; cor=; Ncor= a 137 127 94 278 307 301 315 59 303 64 303 269 314 37 302 257 152 141 c 62 68 28 22 17 11 9 25 11 17 13 24 11 31 18 24 47 57 g 62 68 184 15 17 8 10 11 20 14 10 16 11 20 13 18 56 43 t 96 94 51 42 16 37 23 262 23 262 31 48 21 269 24 58 102 116
oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)				; dyads_m3 versus oligos_6-8nt_m6; m=2/3; ncol2=13; w=0; offset=5; strand=D; shift=5; score=0.616398; -----wwaATAAATAAww ; cor=; Ncor= a 0 0 0 0 0 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 0 0 0 0 0 205 174 85 76 46 25 47 38 47 22 66 185 183 g 0 0 0 0 0 191 175 100 91 18 20 34 22 30 25 55 181 171 t 0 0 0 0 0 373 317 200 160 1021 64 90 60 1037 47 156 322 394
dyads_m10_rc_shift6 (dyads_m10_rc)				; dyads_m3 versus dyads_m10_rc; m=3/3; ncol2=12; w=0; offset=6; strand=R; shift=6; score=0.531102; ------wwTTAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 418 350 107 59 879 910 896 57 882 839 404 329 c 0 0 0 0 0 0 144 143 25 25 27 25 15 52 35 27 145 166 g 0 0 0 0 0 0 146 157 34 37 23 14 22 18 23 29 138 118 t 0 0 0 0 0 0 277 335 819 864 56 36 52 858 45 90 298 372

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m6_shift0 (dyads_m6)				; dyads_m6; m=0 (reference); ncol1=24; shift=0; ncol=24; caCACACACACACAmmmACAmmma ; Alignment reference a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 27 328 163 146 107 188 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 316 22 143 143 158 55 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 29 29 48 68 72 96 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21 30 23 48 45 65 63
dyads_m6_shift0 (dyads_m6)				; dyads_m6 versus dyads_m6; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; caCACACACACACAmmmACAmmma ; cor=; Ncor= a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 27 328 163 146 107 188 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 316 22 143 143 158 55 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 29 29 48 68 72 96 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21 30 23 48 45 65 63
dyads_m5_shift0 (dyads_m5)				; dyads_m6 versus dyads_m5; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.834672; caCrCACACACAmmCACAmmmAca ; cor=; Ncor= a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 136 100 132 237 56 153 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 120 147 115 23 162 49 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 30 42 37 41 50 72 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16 32 29 34 17 50 44
dyads_m1_shift0 (dyads_m1)				; dyads_m6 versus dyads_m1; m=3/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.741009; caCrCACACACACACAcac----- ; cor=; Ncor= a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 200 0 0 0 0 0 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 722 0 0 0 0 0 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 188 0 0 0 0 0 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181 239 0 0 0 0 0
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; dyads_m6 versus oligos_6-8nt_m2; m=4/4; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.664136; -acaCACrCACACACrca------ ; cor=; Ncor= a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 0 0 0 0 0 0 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 0 0 0 0 0 0 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 0 0 0 0 0 0 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift0 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=19; shift=0; ncol=19; caCrCACACACACACAcac ; Alignment reference a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 200 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 722 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 188 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181 239
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; caCrCACACACACACAcac ; cor=; Ncor= a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 200 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 722 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 188 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181 239
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; dyads_m1 versus oligos_6-8nt_m2; m=2/4; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.863815; -acaCACrCACACACrca- ; cor=; Ncor= a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 0 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 0 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 0 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148 0
dyads_m6_shift0 (dyads_m6)				; dyads_m1 versus dyads_m6; m=3/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.741009; caCACACACACACAmmmAC ; cor=; Ncor= a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 27 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 316 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 29 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21 30
dyads_m5_shift0 (dyads_m5)				; dyads_m1 versus dyads_m5; m=4/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.727367; caCrCACACACAmmCACAm ; cor=; Ncor= a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 136 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 120 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 30 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16 32

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)				; oligos_6-8nt_m6; m=0 (reference); ncol1=13; shift=5; ncol=18; -----wwaATAAATAAww ; Alignment reference a 0 0 0 0 0 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 0 0 0 0 0 205 174 85 76 46 25 47 38 47 22 66 185 183 g 0 0 0 0 0 191 175 100 91 18 20 34 22 30 25 55 181 171 t 0 0 0 0 0 373 317 200 160 1021 64 90 60 1037 47 156 322 394
oligos_6-8nt_m6_shift5 (oligos_6-8nt_m6)				; oligos_6-8nt_m6 versus oligos_6-8nt_m6; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=5; score= 1; -----wwaATAAATAAww ; cor=; Ncor= a 0 0 0 0 0 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 0 0 0 0 0 205 174 85 76 46 25 47 38 47 22 66 185 183 g 0 0 0 0 0 191 175 100 91 18 20 34 22 30 25 55 181 171 t 0 0 0 0 0 373 317 200 160 1021 64 90 60 1037 47 156 322 394
dyads_m10_rc_shift6 (dyads_m10_rc)				; oligos_6-8nt_m6 versus dyads_m10_rc; m=2/3; ncol2=12; w=0; offset=1; strand=R; shift=6; score=0.816681; ------wwTTAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 418 350 107 59 879 910 896 57 882 839 404 329 c 0 0 0 0 0 0 144 143 25 25 27 25 15 52 35 27 145 166 g 0 0 0 0 0 0 146 157 34 37 23 14 22 18 23 29 138 118 t 0 0 0 0 0 0 277 335 819 864 56 36 52 858 45 90 298 372
dyads_m3_shift0 (dyads_m3)				; oligos_6-8nt_m6 versus dyads_m3; m=3/3; ncol2=18; w=-5; offset=-5; strand=D; shift=0; score=0.616398; wwrAAAATATAAATAAww ; cor=; Ncor= a 137 127 94 278 307 301 315 59 303 64 303 269 314 37 302 257 152 141 c 62 68 28 22 17 11 9 25 11 17 13 24 11 31 18 24 47 57 g 62 68 184 15 17 8 10 11 20 14 10 16 11 20 13 18 56 43 t 96 94 51 42 16 37 23 262 23 262 31 48 21 269 24 58 102 116

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m10_shift0 (dyads_m10)				; dyads_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; wwTTATTTAAww ; Alignment reference a 372 298 90 45 858 52 36 56 864 819 335 277 c 118 138 29 23 18 22 14 23 37 34 157 146 g 166 145 27 35 52 15 25 27 25 25 143 144 t 329 404 839 882 57 896 910 879 59 107 350 418
dyads_m10_shift0 (dyads_m10)				; dyads_m10 versus dyads_m10; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwTTATTTAAww ; cor=; Ncor= a 372 298 90 45 858 52 36 56 864 819 335 277 c 118 138 29 23 18 22 14 23 37 34 157 146 g 166 145 27 35 52 15 25 27 25 25 143 144 t 329 404 839 882 57 896 910 879 59 107 350 418
oligos_6-8nt_m6_rc_shift0 (oligos_6-8nt_m6_rc)				; dyads_m10 versus oligos_6-8nt_m6_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.816681; wwTTATTTATtw ; cor=; Ncor= a 394 322 156 47 1037 60 90 64 1021 160 200 317 c 171 181 55 25 30 22 34 20 18 91 100 175 g 183 185 66 22 47 38 47 25 46 76 85 174 t 404 464 875 1058 38 1032 981 1043 67 825 767 486
dyads_m3_rc_shift0 (dyads_m3_rc)				; dyads_m10 versus dyads_m3_rc; m=3/3; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.531102; wwTTATTTATAT ; cor=; Ncor= a 116 102 58 24 269 21 48 31 262 23 262 23 c 43 56 18 13 20 11 16 10 14 20 11 10 g 57 47 24 18 31 11 24 13 17 11 25 9 t 141 152 257 302 37 314 269 303 64 303 59 315

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift0 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=21; shift=0; ncol=21; agrGAGAGaGAGAGAGAGAga ; Alignment reference a 437 175 436 80 707 66 713 59 476 62 715 49 717 49 692 47 686 59 637 141 448 c 154 129 110 57 89 27 87 29 142 48 94 34 84 39 91 39 120 62 130 107 196 g 206 540 293 761 75 807 57 819 227 797 73 824 72 820 100 821 70 783 108 616 207 t 137 90 95 36 63 34 77 27 89 27 52 27 61 26 51 27 58 30 59 70 83
dyads_m7_shift0 (dyads_m7)				; dyads_m7 versus dyads_m7; m=1/3; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; agrGAGAGaGAGAGAGAGAga ; cor=; Ncor= a 437 175 436 80 707 66 713 59 476 62 715 49 717 49 692 47 686 59 637 141 448 c 154 129 110 57 89 27 87 29 142 48 94 34 84 39 91 39 120 62 130 107 196 g 206 540 293 761 75 807 57 819 227 797 73 824 72 820 100 821 70 783 108 616 207 t 137 90 95 36 63 34 77 27 89 27 52 27 61 26 51 27 58 30 59 70 83
dyads_m2_rc_shift1 (dyads_m2_rc)				; dyads_m7 versus dyads_m2_rc; m=2/3; ncol2=20; w=0; offset=1; strand=R; shift=1; score=0.943064; -gaGAGAGAGAGAGAGAGaga ; cor=; Ncor= a 0 213 709 115 952 97 969 94 949 90 993 79 980 80 905 89 902 109 801 217 614 c 0 164 208 76 137 48 149 44 163 40 135 47 137 60 180 81 186 84 212 146 259 g 0 817 219 1068 108 1123 88 1130 101 1135 91 1144 114 1116 140 1080 137 1046 185 819 288 t 0 114 172 49 111 40 102 40 95 43 89 38 77 52 83 58 83 69 110 126 147
oligos_6-8nt_m7_shift5 (oligos_6-8nt_m7)				; dyads_m7 versus oligos_6-8nt_m7; m=3/3; ncol2=16; w=0; offset=5; strand=D; shift=5; score=0.727151; -----gaGAGAGAGmGAGaga ; cor=; Ncor= a 0 0 0 0 0 221 629 103 976 66 983 52 998 58 517 58 956 71 823 166 594 c 0 0 0 0 0 166 228 76 97 43 124 27 83 26 508 58 103 53 199 164 248 g 0 0 0 0 0 738 225 1005 83 1096 54 1123 65 1119 117 1086 119 1072 115 776 261 t 0 0 0 0 0 112 155 53 81 32 76 35 91 34 95 35 59 41 100 131 134

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; caCrCACACACAmmCACAmmmAca ; Alignment reference a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 136 100 132 237 56 153 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 120 147 115 23 162 49 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 30 42 37 41 50 72 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16 32 29 34 17 50 44
dyads_m5_shift0 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; caCrCACACACAmmCACAmmmAca ; cor=; Ncor= a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 136 100 132 237 56 153 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 120 147 115 23 162 49 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 30 42 37 41 50 72 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16 32 29 34 17 50 44
dyads_m6_shift0 (dyads_m6)				; dyads_m5 versus dyads_m6; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.834672; caCACACACACACAmmmACAmmma ; cor=; Ncor= a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 27 328 163 146 107 188 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 316 22 143 143 158 55 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 29 29 48 68 72 96 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21 30 23 48 45 65 63
dyads_m1_shift0 (dyads_m1)				; dyads_m5 versus dyads_m1; m=3/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.727367; caCrCACACACACACAcac----- ; cor=; Ncor= a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 200 0 0 0 0 0 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 722 0 0 0 0 0 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 188 0 0 0 0 0 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181 239 0 0 0 0 0
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; dyads_m5 versus oligos_6-8nt_m2; m=4/4; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.632955; -acaCACrCACACACrca------ ; cor=; Ncor= a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 0 0 0 0 0 0 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 0 0 0 0 0 0 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 0 0 0 0 0 0 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; oligos_6-8nt_m2; m=0 (reference); ncol1=17; shift=1; ncol=18; -acaCACrCACACACrca ; Alignment reference a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2)				; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -acaCACrCACACACrca ; cor=; Ncor= a 0 546 186 673 59 970 43 587 34 1020 27 1007 25 972 71 580 147 595 c 0 190 688 115 1012 34 1053 46 1064 20 1075 20 1072 45 927 108 669 151 g 0 227 116 222 32 72 24 434 21 72 18 84 21 71 78 323 162 263 t 0 194 167 147 54 81 37 90 38 45 37 46 39 69 81 146 179 148
dyads_m1_shift0 (dyads_m1)				; oligos_6-8nt_m2 versus dyads_m1; m=2/5; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.863815; caCrCACACACACACAca ; cor=; Ncor= a 252 663 156 635 104 1050 54 1164 43 1133 62 1131 53 1126 66 1045 290 707 c 720 206 958 111 1087 64 1213 32 1220 39 1158 30 1152 42 1161 75 750 170 g 173 256 91 455 49 149 17 89 29 114 58 111 45 118 55 138 153 291 t 204 224 144 148 109 86 65 64 57 63 71 77 99 63 67 91 156 181
dyads_m6_shift0 (dyads_m6)				; oligos_6-8nt_m2 versus dyads_m6; m=3/5; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.664136; caCACACACACACAmmmA ; cor=; Ncor= a 84 204 55 297 20 353 23 339 37 345 29 362 20 337 136 162 151 312 c 216 68 299 28 357 10 352 13 331 25 343 13 362 20 185 148 180 24 g 41 70 18 52 9 22 10 26 14 22 11 19 8 24 43 51 31 45 t 61 60 30 25 16 17 17 24 20 10 19 8 12 21 38 41 40 21
dyads_m5_shift0 (dyads_m5)				; oligos_6-8nt_m2 versus dyads_m5; m=4/5; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.632955; caCrCACACACAmmCACA ; cor=; Ncor= a 75 139 49 154 13 278 28 248 32 296 10 284 120 139 51 271 11 271 c 145 74 230 26 283 13 261 33 265 3 296 13 144 111 244 12 282 10 g 58 58 20 115 8 11 15 20 10 13 9 13 30 40 12 24 11 21 t 40 47 19 23 14 16 14 17 11 6 3 8 24 28 11 11 14 16
oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)				; oligos_6-8nt_m2 versus oligos_6-8nt_m4; m=5/5; ncol2=12; w=0; offset=5; strand=D; shift=6; score=0.524398; ------cvCACTCACccw ; cor=; Ncor= a 0 0 0 0 0 0 116 153 37 516 8 44 7 512 11 93 146 166 c 0 0 0 0 0 0 270 157 494 19 574 31 550 11 554 345 226 145 g 0 0 0 0 0 0 74 151 29 20 4 15 7 22 13 38 103 116 t 0 0 0 0 0 0 134 133 34 39 8 504 30 49 16 118 119 167