One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/11/peak-motifs.2026-04-11.085654_2026-04-11.085654_7Ssqcb/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/2026/04/11/peak-motifs.2026-04-11.085654_2026-04-11.085654_7Ssqcb/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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=22; shift=0; ncol=22; yrcATtTGCATATGCAwATgyr ; Alignment reference a 21 47 8 115 7 41 6 19 7 149 9 140 9 11 28 143 87 124 18 36 41 56 c 54 26 104 20 29 14 14 3 140 3 11 4 3 7 115 2 22 5 12 17 51 34 g 34 51 17 12 5 22 2 115 7 3 4 12 3 141 3 14 14 29 20 103 26 54 t 56 41 36 18 124 88 143 28 11 10 141 9 150 6 19 6 42 7 115 9 47 21

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; yrcATtTGCATATGCAwATgyr ; cor=; Ncor= a 21 47 8 115 7 41 6 19 7 149 9 140 9 11 28 143 87 124 18 36 41 56 c 54 26 104 20 29 14 14 3 140 3 11 4 3 7 115 2 22 5 12 17 51 34 g 34 51 17 12 5 22 2 115 7 3 4 12 3 141 3 14 14 29 20 103 26 54 t 56 41 36 18 124 88 143 28 11 10 141 9 150 6 19 6 42 7 115 9 47 21

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; dyads_m2 versus oligos_6nt_mkv3_m1; m=2/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.979759; yryaTwTGCATATGCAwAtryr ; cor=; Ncor= a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -amaAAACAAAGcma ; Alignment reference a 0 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 0 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 0 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 0 155 126 106 82 26 9 29 11 16 28 39 84 128 141

oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -amaAAACAAAGcma ; cor=; Ncor= a 0 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 0 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 0 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 0 155 126 106 82 26 9 29 11 16 28 39 84 128 141

dyads_m4_shift0 (dyads_m4)
; oligos_6nt_mkv3_m5 versus dyads_m4; m=2/2; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.847994; waAAAAACAAAGGmm ; cor=; Ncor= a 219 204 417 458 419 452 483 82 507 504 500 107 77 178 188 c 79 120 66 23 21 23 18 385 11 18 12 26 53 150 140 g 107 130 39 41 37 38 20 47 16 17 7 373 373 122 109 t 138 89 21 21 66 30 22 29 9 4 24 37 40 93 106

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; waAAAAACAAAGGmm ; Alignment reference a 219 204 417 458 419 452 483 82 507 504 500 107 77 178 188 c 79 120 66 23 21 23 18 385 11 18 12 26 53 150 140 g 107 130 39 41 37 38 20 47 16 17 7 373 373 122 109 t 138 89 21 21 66 30 22 29 9 4 24 37 40 93 106

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; waAAAAACAAAGGmm ; cor=; Ncor= a 219 204 417 458 419 452 483 82 507 504 500 107 77 178 188 c 79 120 66 23 21 23 18 385 11 18 12 26 53 150 140 g 107 130 39 41 37 38 20 47 16 17 7 373 373 122 109 t 138 89 21 21 66 30 22 29 9 4 24 37 40 93 106

oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)
; dyads_m4 versus oligos_6nt_mkv3_m5; m=2/2; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.847994; -amaAAACAAAGcma ; cor=; Ncor= a 0 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 0 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 0 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 0 155 126 106 82 26 9 29 11 16 28 39 84 128 141

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --ccCCCCACCCCcc ; Alignment reference a 0 0 238 226 62 65 35 22 821 29 28 29 113 220 281 c 0 0 512 445 912 984 1089 1100 109 1080 1067 1076 895 515 438 g 0 0 228 269 95 80 43 44 171 55 65 49 94 241 255 t 0 0 217 255 126 66 28 29 94 31 35 41 93 219 221

oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --ccCCCCACCCCcc ; cor=; Ncor= a 0 0 238 226 62 65 35 22 821 29 28 29 113 220 281 c 0 0 512 445 912 984 1089 1100 109 1080 1067 1076 895 515 438 g 0 0 228 269 95 80 43 44 171 55 65 49 94 241 255 t 0 0 217 255 126 66 28 29 94 31 35 41 93 219 221

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m2 versus dyads_m3; m=2/2; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.826722; ccCCCCCCmCCCCcc ; cor=; Ncor= a 176 184 81 86 38 46 54 67 562 38 40 37 52 224 254 c 550 497 828 830 945 953 954 944 300 963 985 973 970 526 458 g 177 212 119 92 75 67 58 50 144 74 47 54 57 194 215 t 211 221 86 106 56 48 48 53 108 39 42 50 35 170 187

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ccCCCCCCmCCCCcc ; Alignment reference a 176 184 81 86 38 46 54 67 562 38 40 37 52 224 254 c 550 497 828 830 945 953 954 944 300 963 985 973 970 526 458 g 177 212 119 92 75 67 58 50 144 74 47 54 57 194 215 t 211 221 86 106 56 48 48 53 108 39 42 50 35 170 187

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ccCCCCCCmCCCCcc ; cor=; Ncor= a 176 184 81 86 38 46 54 67 562 38 40 37 52 224 254 c 550 497 828 830 945 953 954 944 300 963 985 973 970 526 458 g 177 212 119 92 75 67 58 50 144 74 47 54 57 194 215 t 211 221 86 106 56 48 48 53 108 39 42 50 35 170 187

oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; dyads_m3 versus oligos_6nt_mkv3_m2; m=2/2; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.826722; --ccCCCCACCCCcc ; cor=; Ncor= a 0 0 238 226 62 65 35 22 821 29 28 29 113 220 281 c 0 0 512 445 912 984 1089 1100 109 1080 1067 1076 895 515 438 g 0 0 228 269 95 80 43 44 171 55 65 49 94 241 255 t 0 0 217 255 126 66 28 29 94 31 35 41 93 219 221

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; yhcaTTTGCATaAcAAwgsmm ; Alignment reference a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/5; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; yhcaTTTGCATaAcAAwgsmm ; cor=; Ncor= a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170

dyads_m5_shift0 (dyads_m5)
; oligos_6nt_mkv3_m3 versus dyads_m5; m=2/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.839592; bhcATTTGCATawcAAWGcaa ; cor=; Ncor= a 36 59 36 174 7 17 39 27 10 215 8 140 143 21 200 206 59 34 45 133 91 c 57 67 129 11 6 17 4 10 210 1 4 23 17 149 12 3 2 16 106 33 52 g 56 31 19 10 4 8 5 180 0 1 2 27 6 34 1 7 7 159 55 35 46 t 74 66 39 28 206 181 175 6 3 6 209 33 57 19 10 7 155 14 17 22 34

dyads_m1_rc_shift0 (dyads_m1_rc)
; oligos_6nt_mkv3_m3 versus dyads_m1_rc; m=3/5; ncol2=21; w=0; offset=0; strand=R; shift=0; score=0.704769; bdcaTtTgCATTktcATGCaa ; cor=; Ncor= a 49 59 39 139 11 29 20 18 8 199 2 41 26 35 50 202 12 11 24 100 75 c 56 37 113 36 20 20 13 30 192 1 3 3 24 27 120 4 7 7 151 37 47 g 58 59 37 21 12 31 19 149 5 2 8 12 113 25 17 4 8 182 18 30 51 t 59 67 33 26 179 142 170 25 17 20 209 166 59 135 35 12 195 22 29 55 49

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.670864; yryaTwTGCATATGCAwAtry ; cor=; Ncor= a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142

oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m4; m=5/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.421007; ---atTTACATAws------- ; cor=; Ncor= a 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 0 0 0 0 0 0 0 c 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 0 0 0 0 0 0 0 g 0 0 0 267 182 29 23 187 29 15 56 43 199 301 0 0 0 0 0 0 0 t 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---atTTACATAws ; Alignment reference a 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 c 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 g 0 0 0 267 182 29 23 187 29 15 56 43 199 301 t 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285

oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---atTTACATAws ; cor=; Ncor= a 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 c 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 g 0 0 0 267 182 29 23 187 29 15 56 43 199 301 t 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m3; m=2/2; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.421007; yhcaTTTGCATaAc ; cor=; Ncor= a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; bhcATTTGCATawcAAWGcaaayc ; Alignment reference a 36 59 36 174 7 17 39 27 10 215 8 140 143 21 200 206 59 34 45 133 91 119 46 55 c 57 67 129 11 6 17 4 10 210 1 4 23 17 149 12 3 2 16 106 33 52 35 57 71 g 56 31 19 10 4 8 5 180 0 1 2 27 6 34 1 7 7 159 55 35 46 28 54 53 t 74 66 39 28 206 181 175 6 3 6 209 33 57 19 10 7 155 14 17 22 34 41 66 44

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; bhcATTTGCATawcAAWGcaaayc ; cor=; Ncor= a 36 59 36 174 7 17 39 27 10 215 8 140 143 21 200 206 59 34 45 133 91 119 46 55 c 57 67 129 11 6 17 4 10 210 1 4 23 17 149 12 3 2 16 106 33 52 35 57 71 g 56 31 19 10 4 8 5 180 0 1 2 27 6 34 1 7 7 159 55 35 46 28 54 53 t 74 66 39 28 206 181 175 6 3 6 209 33 57 19 10 7 155 14 17 22 34 41 66 44

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; dyads_m5 versus oligos_6nt_mkv3_m3; m=2/3; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.839592; yhcaTTTGCATaAcAAwgsmm--- ; cor=; Ncor= a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 0 0 0 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 0 0 0 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 0 0 0 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170 0 0 0

dyads_m1_rc_shift0 (dyads_m1_rc)
; dyads_m5 versus dyads_m1_rc; m=3/3; ncol2=21; w=0; offset=0; strand=R; shift=0; score=0.686023; bdcaTtTgCATTktcATGCaa--- ; cor=; Ncor= a 49 59 39 139 11 29 20 18 8 199 2 41 26 35 50 202 12 11 24 100 75 0 0 0 c 56 37 113 36 20 20 13 30 192 1 3 3 24 27 120 4 7 7 151 37 47 0 0 0 g 58 59 37 21 12 31 19 149 5 2 8 12 113 25 17 4 8 182 18 30 51 0 0 0 t 59 67 33 26 179 142 170 25 17 20 209 166 59 135 35 12 195 22 29 55 49 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m1_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift3 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=21; shift=3; ncol=24; ---ttGCATgamAATGcAaAtghv ; Alignment reference a 0 0 0 49 55 29 22 195 12 35 135 59 166 209 20 17 25 170 142 179 26 33 67 59 c 0 0 0 51 30 18 182 8 4 17 25 113 12 8 2 5 149 19 31 12 21 37 59 58 g 0 0 0 47 37 151 7 7 4 120 27 24 3 3 1 192 30 13 20 20 36 113 37 56 t 0 0 0 75 100 24 11 12 202 50 35 26 41 2 199 8 18 20 29 11 139 39 59 49

dyads_m1_shift3 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/3; ncol2=21; w=0; offset=0; strand=D; shift=3; score= 1; ---ttGCATgamAATGcAaAtghv ; cor=; Ncor= a 0 0 0 49 55 29 22 195 12 35 135 59 166 209 20 17 25 170 142 179 26 33 67 59 c 0 0 0 51 30 18 182 8 4 17 25 113 12 8 2 5 149 19 31 12 21 37 59 58 g 0 0 0 47 37 151 7 7 4 120 27 24 3 3 1 192 30 13 20 20 36 113 37 56 t 0 0 0 75 100 24 11 12 202 50 35 26 41 2 199 8 18 20 29 11 139 39 59 49

oligos_6nt_mkv3_m3_rc_shift3 (oligos_6nt_mkv3_m3_rc)
; dyads_m1 versus oligos_6nt_mkv3_m3_rc; m=2/3; ncol2=21; w=0; offset=0; strand=R; shift=3; score=0.704769; ---kkscwTTgTtATGCAAAtgdr ; cor=; Ncor= a 0 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 c 0 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 g 0 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 t 0 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141

dyads_m5_rc_shift0 (dyads_m5_rc)
; dyads_m1 versus dyads_m5_rc; m=3/3; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.686023; grtttgCWTTgwtATGCAAATgdv ; cor=; Ncor= a 44 66 41 34 22 17 14 155 7 10 19 57 33 209 6 3 6 175 181 206 28 39 66 74 c 53 54 28 46 35 55 159 7 7 1 34 6 27 2 1 0 180 5 8 4 10 19 31 56 g 71 57 35 52 33 106 16 2 3 12 149 17 23 4 1 210 10 4 17 6 11 129 67 57 t 55 46 119 91 133 45 34 59 206 200 21 143 140 8 215 10 27 39 17 7 174 36 59 36

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=22; shift=0; ncol=22; yryaTwTGCATATGCAwAtryr ; Alignment reference a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; yryaTwTGCATATGCAwAtryr ; cor=; Ncor= a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_6nt_mkv3_m1 versus dyads_m2_rc; m=2/3; ncol2=22; w=0; offset=0; strand=R; shift=0; score=0.979759; yrcATwTGCATATGCAaATgyr ; cor=; Ncor= a 21 47 9 115 7 42 6 19 6 150 9 141 10 11 28 143 88 124 18 36 41 56 c 54 26 103 20 29 14 14 3 141 3 12 4 3 7 115 2 22 5 12 17 51 34 g 34 51 17 12 5 22 2 115 7 3 4 11 3 140 3 14 14 29 20 104 26 54 t 56 41 36 18 124 87 143 28 11 9 140 9 149 7 19 6 41 7 115 8 47 21

oligos_6nt_mkv3_m3_rc_shift1 (oligos_6nt_mkv3_m3_rc)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=3/3; ncol2=21; w=0; offset=1; strand=R; shift=1; score=0.670864; -kkscwTTgTtATGCAAAtgdr ; cor=; Ncor= a 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 c 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 g 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 t 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; yhcaTTTGCATaAcAAwgsmm ; Alignment reference a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/5; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; yhcaTTTGCATaAcAAwgsmm ; cor=; Ncor= a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170
dyads_m5_shift0 (dyads_m5)				; oligos_6nt_mkv3_m3 versus dyads_m5; m=2/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.839592; bhcATTTGCATawcAAWGcaa ; cor=; Ncor= a 36 59 36 174 7 17 39 27 10 215 8 140 143 21 200 206 59 34 45 133 91 c 57 67 129 11 6 17 4 10 210 1 4 23 17 149 12 3 2 16 106 33 52 g 56 31 19 10 4 8 5 180 0 1 2 27 6 34 1 7 7 159 55 35 46 t 74 66 39 28 206 181 175 6 3 6 209 33 57 19 10 7 155 14 17 22 34
dyads_m1_rc_shift0 (dyads_m1_rc)				; oligos_6nt_mkv3_m3 versus dyads_m1_rc; m=3/5; ncol2=21; w=0; offset=0; strand=R; shift=0; score=0.704769; bdcaTtTgCATTktcATGCaa ; cor=; Ncor= a 49 59 39 139 11 29 20 18 8 199 2 41 26 35 50 202 12 11 24 100 75 c 56 37 113 36 20 20 13 30 192 1 3 3 24 27 120 4 7 7 151 37 47 g 58 59 37 21 12 31 19 149 5 2 8 12 113 25 17 4 8 182 18 30 51 t 59 67 33 26 179 142 170 25 17 20 209 166 59 135 35 12 195 22 29 55 49
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.670864; yryaTwTGCATATGCAwAtry ; cor=; Ncor= a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m4; m=5/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.421007; ---atTTACATAws------- ; cor=; Ncor= a 0 0 0 460 228 61 32 921 63 1109 80 1031 380 286 0 0 0 0 0 0 0 c 0 0 0 212 227 61 41 41 1038 34 77 47 227 324 0 0 0 0 0 0 0 g 0 0 0 267 182 29 23 187 29 15 56 43 199 301 0 0 0 0 0 0 0 t 0 0 0 257 559 1045 1100 47 66 38 983 75 390 285 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; bhcATTTGCATawcAAWGcaaayc ; Alignment reference a 36 59 36 174 7 17 39 27 10 215 8 140 143 21 200 206 59 34 45 133 91 119 46 55 c 57 67 129 11 6 17 4 10 210 1 4 23 17 149 12 3 2 16 106 33 52 35 57 71 g 56 31 19 10 4 8 5 180 0 1 2 27 6 34 1 7 7 159 55 35 46 28 54 53 t 74 66 39 28 206 181 175 6 3 6 209 33 57 19 10 7 155 14 17 22 34 41 66 44
dyads_m5_shift0 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; bhcATTTGCATawcAAWGcaaayc ; cor=; Ncor= a 36 59 36 174 7 17 39 27 10 215 8 140 143 21 200 206 59 34 45 133 91 119 46 55 c 57 67 129 11 6 17 4 10 210 1 4 23 17 149 12 3 2 16 106 33 52 35 57 71 g 56 31 19 10 4 8 5 180 0 1 2 27 6 34 1 7 7 159 55 35 46 28 54 53 t 74 66 39 28 206 181 175 6 3 6 209 33 57 19 10 7 155 14 17 22 34 41 66 44
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; dyads_m5 versus oligos_6nt_mkv3_m3; m=2/3; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.839592; yhcaTTTGCATaAcAAwgsmm--- ; cor=; Ncor= a 141 209 180 501 47 82 96 99 42 766 25 519 544 55 658 688 459 195 178 270 218 0 0 0 c 223 205 311 89 38 104 22 40 726 12 29 59 32 501 49 31 39 58 219 216 233 0 0 0 g 189 146 126 96 24 45 8 633 9 5 13 123 28 148 24 43 42 485 306 181 169 0 0 0 t 237 230 173 104 681 559 664 18 13 7 723 89 186 86 59 28 250 52 87 123 170 0 0 0
dyads_m1_rc_shift0 (dyads_m1_rc)				; dyads_m5 versus dyads_m1_rc; m=3/3; ncol2=21; w=0; offset=0; strand=R; shift=0; score=0.686023; bdcaTtTgCATTktcATGCaa--- ; cor=; Ncor= a 49 59 39 139 11 29 20 18 8 199 2 41 26 35 50 202 12 11 24 100 75 0 0 0 c 56 37 113 36 20 20 13 30 192 1 3 3 24 27 120 4 7 7 151 37 47 0 0 0 g 58 59 37 21 12 31 19 149 5 2 8 12 113 25 17 4 8 182 18 30 51 0 0 0 t 59 67 33 26 179 142 170 25 17 20 209 166 59 135 35 12 195 22 29 55 49 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift3 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=21; shift=3; ncol=24; ---ttGCATgamAATGcAaAtghv ; Alignment reference a 0 0 0 49 55 29 22 195 12 35 135 59 166 209 20 17 25 170 142 179 26 33 67 59 c 0 0 0 51 30 18 182 8 4 17 25 113 12 8 2 5 149 19 31 12 21 37 59 58 g 0 0 0 47 37 151 7 7 4 120 27 24 3 3 1 192 30 13 20 20 36 113 37 56 t 0 0 0 75 100 24 11 12 202 50 35 26 41 2 199 8 18 20 29 11 139 39 59 49
dyads_m1_shift3 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/3; ncol2=21; w=0; offset=0; strand=D; shift=3; score= 1; ---ttGCATgamAATGcAaAtghv ; cor=; Ncor= a 0 0 0 49 55 29 22 195 12 35 135 59 166 209 20 17 25 170 142 179 26 33 67 59 c 0 0 0 51 30 18 182 8 4 17 25 113 12 8 2 5 149 19 31 12 21 37 59 58 g 0 0 0 47 37 151 7 7 4 120 27 24 3 3 1 192 30 13 20 20 36 113 37 56 t 0 0 0 75 100 24 11 12 202 50 35 26 41 2 199 8 18 20 29 11 139 39 59 49
oligos_6nt_mkv3_m3_rc_shift3 (oligos_6nt_mkv3_m3_rc)				; dyads_m1 versus oligos_6nt_mkv3_m3_rc; m=2/3; ncol2=21; w=0; offset=0; strand=R; shift=3; score=0.704769; ---kkscwTTgTtATGCAAAtgdr ; cor=; Ncor= a 0 0 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 c 0 0 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 g 0 0 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 t 0 0 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141
dyads_m5_rc_shift0 (dyads_m5_rc)				; dyads_m1 versus dyads_m5_rc; m=3/3; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.686023; grtttgCWTTgwtATGCAAATgdv ; cor=; Ncor= a 44 66 41 34 22 17 14 155 7 10 19 57 33 209 6 3 6 175 181 206 28 39 66 74 c 53 54 28 46 35 55 159 7 7 1 34 6 27 2 1 0 180 5 8 4 10 19 31 56 g 71 57 35 52 33 106 16 2 3 12 149 17 23 4 1 210 10 4 17 6 11 129 67 57 t 55 46 119 91 133 45 34 59 206 200 21 143 140 8 215 10 27 39 17 7 174 36 59 36

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=22; shift=0; ncol=22; yryaTwTGCATATGCAwAtryr ; Alignment reference a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; yryaTwTGCATATGCAwAtryr ; cor=; Ncor= a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_6nt_mkv3_m1 versus dyads_m2_rc; m=2/3; ncol2=22; w=0; offset=0; strand=R; shift=0; score=0.979759; yrcATwTGCATATGCAaATgyr ; cor=; Ncor= a 21 47 9 115 7 42 6 19 6 150 9 141 10 11 28 143 88 124 18 36 41 56 c 54 26 103 20 29 14 14 3 141 3 12 4 3 7 115 2 22 5 12 17 51 34 g 34 51 17 12 5 22 2 115 7 3 4 11 3 140 3 14 14 29 20 104 26 54 t 56 41 36 18 124 87 143 28 11 9 140 9 149 7 19 6 41 7 115 8 47 21
oligos_6nt_mkv3_m3_rc_shift1 (oligos_6nt_mkv3_m3_rc)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=3/3; ncol2=21; w=0; offset=1; strand=R; shift=1; score=0.670864; -kkscwTTgTtATGCAAAtgdr ; cor=; Ncor= a 0 170 123 87 52 250 28 59 86 186 89 723 7 13 18 664 559 681 104 173 230 237 c 0 169 181 306 485 42 43 24 148 28 123 13 5 9 633 8 45 24 96 126 146 189 g 0 233 216 219 58 39 31 49 501 32 59 29 12 726 40 22 104 38 89 311 205 223 t 0 218 270 178 195 459 688 658 55 544 519 25 766 42 99 96 82 47 501 180 209 141