One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/01/13/peak-motifs.2025-01-13.043824_2025-01-13.043824_m2sY0P/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/2025/01/13/peak-motifs.2025-01-13.043824_2025-01-13.043824_m2sY0P/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=19; shift=0; ncol=19; dwrGAAGAAGAgAAArwww ; Alignment reference a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 64 51 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 15 14 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 16 31 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67 51 50

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; dwrGAAGAAGAgAAArwww ; cor=; Ncor= a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 64 51 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 15 14 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 16 31 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67 51 50

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/4; ncol2=17; w=0; offset=2; strand=D; shift=2; score=0.649901; --wwaCTAAGAGAAAgtww ; cor=; Ncor= a 0 0 54 60 91 22 18 125 133 15 135 17 120 127 109 22 34 58 56 c 0 0 27 18 10 103 2 3 1 3 4 5 9 4 4 9 5 19 20 g 0 0 11 14 19 4 3 6 1 115 2 114 5 2 11 90 11 15 20 t 0 0 54 54 26 17 123 12 11 13 5 10 12 13 22 25 96 54 50

dyads_test_vs_ctrl_m1_shift3 (dyads_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m1; m=3/4; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.598889; ---dwAGAArATGAAGaw- ; cor=; Ncor= a 0 0 0 198 292 515 40 526 408 231 454 124 40 538 518 75 342 293 0 c 0 0 0 57 64 10 17 19 13 13 31 22 11 7 8 15 47 52 0 g 0 0 0 149 60 14 500 14 135 313 29 22 498 9 10 450 59 57 0 t 0 0 0 191 179 56 38 36 39 38 81 427 46 41 59 55 147 193 0

oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=4/4; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.589079; --wwTAGAAGAGAATww-- ; cor=; Ncor= a 0 0 111 122 28 219 25 226 228 20 247 40 234 234 46 114 108 0 0 c 0 0 31 26 8 5 16 9 6 4 4 7 2 2 10 32 38 0 0 g 0 0 37 39 12 16 203 8 11 218 2 195 12 11 19 38 29 0 0 t 0 0 84 76 215 23 19 20 18 21 10 21 15 16 188 79 88 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wwGAAATCww ; Alignment reference a 126 134 0 324 318 329 9 0 118 137 c 47 56 0 2 5 3 0 345 42 40 g 39 47 345 2 0 1 0 0 62 40 t 133 108 0 17 22 12 336 0 123 128

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wwGAAATCww ; cor=; Ncor= a 126 134 0 324 318 329 9 0 118 137 c 47 56 0 2 5 3 0 345 42 40 g 39 47 345 2 0 1 0 0 62 40 t 133 108 0 17 22 12 336 0 123 128

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3)
; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; wwGCTawdwwdwAGAww ; Alignment reference a 245 243 36 55 45 193 197 169 161 155 167 164 535 28 527 246 207 c 72 72 12 497 13 145 109 119 132 131 123 150 12 16 12 62 77 g 91 65 516 8 24 126 131 158 131 139 152 127 12 507 17 79 90 t 199 227 43 47 525 143 170 161 183 182 165 166 48 56 51 220 233

dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3)
; dyads_test_vs_ctrl_m3 versus dyads_test_vs_ctrl_m3; m=1/1; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; wwGCTawdwwdwAGAww ; cor=; Ncor= a 245 243 36 55 45 193 197 169 161 155 167 164 535 28 527 246 207 c 72 72 12 497 13 145 109 119 132 131 123 150 12 16 12 62 77 g 91 65 516 8 24 126 131 158 131 139 152 127 12 507 17 79 90 t 199 227 43 47 525 143 170 161 183 182 165 166 48 56 51 220 233

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_test_vs_ctrl_m1_shift3 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=3; ncol=18; ---dwAGAArATGAAGaw ; Alignment reference a 0 0 0 198 292 515 40 526 408 231 454 124 40 538 518 75 342 293 c 0 0 0 57 64 10 17 19 13 13 31 22 11 7 8 15 47 52 g 0 0 0 149 60 14 500 14 135 313 29 22 498 9 10 450 59 57 t 0 0 0 191 179 56 38 36 39 38 81 427 46 41 59 55 147 193

dyads_test_vs_ctrl_m1_shift3 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=3; score= 1; ---dwAGAArATGAAGaw ; cor=; Ncor= a 0 0 0 198 292 515 40 526 408 231 454 124 40 538 518 75 342 293 c 0 0 0 57 64 10 17 19 13 13 31 22 11 7 8 15 47 52 g 0 0 0 149 60 14 500 14 135 313 29 22 498 9 10 450 59 57 t 0 0 0 191 179 56 38 36 39 38 81 427 46 41 59 55 147 193

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/3; ncol2=19; w=-3; offset=-3; strand=D; shift=0; score=0.598889; dwrGAAGAAGAgAAArww ; cor=; Ncor= a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 64 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 15 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 16 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67 51

dyads_test_vs_ctrl_m2_shift3 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m2; m=3/3; ncol2=20; w=0; offset=0; strand=D; shift=3; score=0.552693; ---wwAGAwbmwrawkyw ; cor=; Ncor= a 0 0 0 249 244 607 29 614 253 119 246 216 174 285 260 125 165 213 c 0 0 0 72 92 13 12 14 111 178 203 116 103 128 104 162 201 120 g 0 0 0 130 83 17 629 16 101 193 111 127 264 130 103 219 105 108 t 0 0 0 242 274 56 23 49 228 203 133 234 152 150 226 187 222 252

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATGGTTCAww ; Alignment reference a 113 102 264 17 14 30 18 18 25 239 124 118 c 35 28 6 6 3 14 2 7 237 10 32 48 g 35 45 4 0 256 224 5 1 11 13 48 40 t 111 119 20 271 21 26 269 268 21 32 90 88

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwATGGTTCAww ; cor=; Ncor= a 113 102 264 17 14 30 18 18 25 239 124 118 c 35 28 6 6 3 14 2 7 237 10 32 48 g 35 45 4 0 256 224 5 1 11 13 48 40 t 111 119 20 271 21 26 269 268 21 32 90 88

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/2; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.74379; -wwTGGTTCww- ; cor=; Ncor= a 0 136 150 59 15 2 52 48 15 137 150 0 c 0 43 51 6 19 1 13 15 369 39 44 0 g 0 57 49 9 349 382 17 18 2 58 64 0 t 0 154 140 316 7 5 308 309 4 156 132 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; wwgATAAGAGAATww ; Alignment reference a 83 91 48 190 24 203 204 15 209 18 198 201 36 87 94 c 26 23 11 12 6 8 6 8 3 6 8 7 6 25 25 g 29 29 141 9 11 5 6 190 4 186 4 4 8 44 29 t 92 87 30 19 189 14 14 17 14 20 20 18 180 74 82

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wwgATAAGAGAATww ; cor=; Ncor= a 83 91 48 190 24 203 204 15 209 18 198 201 36 87 94 c 26 23 11 12 6 8 6 8 3 6 8 7 6 25 25 g 29 29 141 9 11 5 6 190 4 186 4 4 8 44 29 t 92 87 30 19 189 14 14 17 14 20 20 18 180 74 82

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.815929; wwTAGAAGAGAATww ; cor=; Ncor= a 111 122 28 219 25 226 228 20 247 40 234 234 46 114 108 c 31 26 8 5 16 9 6 4 4 7 2 2 10 32 38 g 37 39 12 16 203 8 11 218 2 195 12 11 19 38 29 t 84 76 215 23 19 20 18 21 10 21 15 16 188 79 88

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=3/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.67672; wwaCTAAGAGAAAgt ; cor=; Ncor= a 54 60 91 22 18 125 133 15 135 17 120 127 109 22 34 c 27 18 10 103 2 3 1 3 4 5 9 4 4 9 5 g 11 14 19 4 3 6 1 115 2 114 5 2 11 90 11 t 54 54 26 17 123 12 11 13 5 10 12 13 22 25 96

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwAGAwbmwrawkywGAAww ; Alignment reference a 249 244 607 29 614 253 119 246 216 174 285 260 125 165 213 30 584 611 259 302 c 72 92 13 12 14 111 178 203 116 103 128 104 162 201 120 10 18 13 76 90 g 130 83 17 629 16 101 193 111 127 264 130 103 219 105 108 610 20 9 122 71 t 242 274 56 23 49 228 203 133 234 152 150 226 187 222 252 43 71 60 236 230

dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m2; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; wwAGAwbmwrawkywGAAww ; cor=; Ncor= a 249 244 607 29 614 253 119 246 216 174 285 260 125 165 213 30 584 611 259 302 c 72 92 13 12 14 111 178 203 116 103 128 104 162 201 120 10 18 13 76 90 g 130 83 17 629 16 101 193 111 127 264 130 103 219 105 108 610 20 9 122 71 t 242 274 56 23 49 228 203 133 234 152 150 226 187 222 252 43 71 60 236 230

dyads_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m1; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.552693; dwAGAArATGAAGaw----- ; cor=; Ncor= a 198 292 515 40 526 408 231 454 124 40 538 518 75 342 293 0 0 0 0 0 c 57 64 10 17 19 13 13 31 22 11 7 8 15 47 52 0 0 0 0 0 g 149 60 14 500 14 135 313 29 22 498 9 10 450 59 57 0 0 0 0 0 t 191 179 56 38 36 39 38 81 427 46 41 59 55 147 193 0 0 0 0 0

dyads_test_vs_ctrl_m4_shift0 (dyads_test_vs_ctrl_m4)
; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m4; m=3/3; ncol2=29; w=0; offset=0; strand=D; shift=0; score=0.530846; wwAGAwtatrawtywdvahy ; cor=; Ncor= a 210 200 472 48 472 195 126 198 136 151 189 275 139 127 175 213 221 190 186 127 c 65 98 17 24 22 80 133 119 105 102 118 5 121 165 108 9 143 139 144 149 g 110 90 21 426 27 131 129 108 114 194 123 18 139 117 88 183 172 98 13 128 t 177 174 52 64 41 156 174 137 207 115 132 264 163 153 191 157 26 135 219 158

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCTACTAGww ; Alignment reference a 241 216 33 24 557 56 24 562 71 226 247 c 76 77 523 4 17 492 11 4 32 100 62 g 59 96 16 5 19 20 3 9 457 68 71 t 248 235 52 591 31 56 586 49 64 230 244

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCTACTAGww ; cor=; Ncor= a 241 216 33 24 557 56 24 562 71 226 247 c 76 77 523 4 17 492 11 4 32 100 62 g 59 96 16 5 19 20 3 9 457 68 71 t 248 235 52 591 31 56 586 49 64 230 244

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5)
; dyads_test_vs_ctrl_m5; m=0 (reference); ncol1=29; shift=0; ncol=29; wwcTTvdwwkwtdmrdtmkwwdwmgAAww ; Alignment reference a 170 161 62 59 61 146 131 163 164 41 125 108 128 255 247 176 112 135 108 151 168 146 191 200 73 350 350 164 186 c 56 60 297 18 21 160 87 76 109 14 80 107 7 122 12 11 102 123 80 86 97 66 9 187 24 21 24 54 49 g 58 56 25 21 17 121 117 84 13 163 89 110 156 23 155 133 103 95 128 74 73 123 81 19 300 17 22 87 58 t 169 176 69 355 354 26 118 130 167 235 159 128 162 53 39 133 136 100 137 142 115 118 172 47 56 65 57 148 160

dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5)
; dyads_test_vs_ctrl_m5 versus dyads_test_vs_ctrl_m5; m=1/1; ncol2=29; w=0; offset=0; strand=D; shift=0; score= 1; wwcTTvdwwkwtdmrdtmkwwdwmgAAww ; cor=; Ncor= a 170 161 62 59 61 146 131 163 164 41 125 108 128 255 247 176 112 135 108 151 168 146 191 200 73 350 350 164 186 c 56 60 297 18 21 160 87 76 109 14 80 107 7 122 12 11 102 123 80 86 97 66 9 187 24 21 24 54 49 g 58 56 25 21 17 121 117 84 13 163 89 110 156 23 155 133 103 95 128 74 73 123 81 19 300 17 22 87 58 t 169 176 69 355 354 26 118 130 167 235 159 128 162 53 39 133 136 100 137 142 115 118 172 47 56 65 57 148 160

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=2; ncol=17; --wwTAGAAGAGAATww ; Alignment reference a 0 0 111 122 28 219 25 226 228 20 247 40 234 234 46 114 108 c 0 0 31 26 8 5 16 9 6 4 4 7 2 2 10 32 38 g 0 0 37 39 12 16 203 8 11 218 2 195 12 11 19 38 29 t 0 0 84 76 215 23 19 20 18 21 10 21 15 16 188 79 88

oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=2; score= 1; --wwTAGAAGAGAATww ; cor=; Ncor= a 0 0 111 122 28 219 25 226 228 20 247 40 234 234 46 114 108 c 0 0 31 26 8 5 16 9 6 4 4 7 2 2 10 32 38 g 0 0 37 39 12 16 203 8 11 218 2 195 12 11 19 38 29 t 0 0 84 76 215 23 19 20 18 21 10 21 15 16 188 79 88

oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.815929; --wwgATAAGAGAATww ; cor=; Ncor= a 0 0 83 91 48 190 24 203 204 15 209 18 198 201 36 87 94 c 0 0 26 23 11 12 6 8 6 8 3 6 8 7 6 25 25 g 0 0 29 29 141 9 11 5 6 190 4 186 4 4 8 44 29 t 0 0 92 87 30 19 189 14 14 17 14 20 20 18 180 74 82

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.589079; dwrGAAGAAGAgAAArw ; cor=; Ncor= a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; wwcaAGATTCTACTTww ; Alignment reference a 46 50 28 84 107 13 104 12 10 6 10 104 8 19 17 42 45 c 22 13 64 10 0 2 3 1 3 103 1 5 100 11 11 20 14 g 12 16 12 9 4 96 2 6 5 4 2 5 1 1 4 14 20 t 44 45 20 21 13 13 15 105 106 11 111 10 15 93 92 48 45

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/1; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; wwcaAGATTCTACTTww ; cor=; Ncor= a 46 50 28 84 107 13 104 12 10 6 10 104 8 19 17 42 45 c 22 13 64 10 0 2 3 1 3 103 1 5 100 11 11 20 14 g 12 16 12 9 4 96 2 6 5 4 2 5 1 1 4 14 20 t 44 45 20 21 13 13 15 105 106 11 111 10 15 93 92 48 45

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=2; ncol=19; --wwaCTAAGAGAAAgtww ; Alignment reference a 0 0 54 60 91 22 18 125 133 15 135 17 120 127 109 22 34 58 56 c 0 0 27 18 10 103 2 3 1 3 4 5 9 4 4 9 5 19 20 g 0 0 11 14 19 4 3 6 1 115 2 114 5 2 11 90 11 15 20 t 0 0 54 54 26 17 123 12 11 13 5 10 12 13 22 25 96 54 50

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=2; score= 1; --wwaCTAAGAGAAAgtww ; cor=; Ncor= a 0 0 54 60 91 22 18 125 133 15 135 17 120 127 109 22 34 58 56 c 0 0 27 18 10 103 2 3 1 3 4 5 9 4 4 9 5 19 20 g 0 0 11 14 19 4 3 6 1 115 2 114 5 2 11 90 11 15 20 t 0 0 54 54 26 17 123 12 11 13 5 10 12 13 22 25 96 54 50

oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.67672; --wwgATAAGAGAATww-- ; cor=; Ncor= a 0 0 83 91 48 190 24 203 204 15 209 18 198 201 36 87 94 0 0 c 0 0 26 23 11 12 6 8 6 8 3 6 8 7 6 25 25 0 0 g 0 0 29 29 141 9 11 5 6 190 4 186 4 4 8 44 29 0 0 t 0 0 92 87 30 19 189 14 14 17 14 20 20 18 180 74 82 0 0

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.649901; dwrGAAGAAGAgAAArwww ; cor=; Ncor= a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 64 51 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 15 14 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 16 31 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67 51 50

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -wwGAACCAww ; Alignment reference a 0 132 156 4 309 308 5 7 316 140 154 c 0 64 58 2 18 17 382 349 9 49 57 g 0 44 39 369 15 13 1 19 6 51 43 t 0 150 137 15 48 52 2 15 59 150 136

oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wwGAACCAww ; cor=; Ncor= a 0 132 156 4 309 308 5 7 316 140 154 c 0 64 58 2 18 17 382 349 9 49 57 g 0 44 39 369 15 13 1 19 6 51 43 t 0 150 137 15 48 52 2 15 59 150 136

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=2/2; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.74379; wwTGAACCATw ; cor=; Ncor= a 88 90 32 21 268 269 26 21 271 20 119 c 40 48 13 11 1 5 224 256 0 4 45 g 48 32 10 237 7 2 14 3 6 6 28 t 118 124 239 25 18 18 30 14 17 264 102

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; wwACTCTACgcww ; Alignment reference a 67 79 185 20 8 16 9 175 31 40 30 74 72 c 42 32 9 155 3 176 5 5 149 17 141 31 32 g 29 26 7 8 3 5 5 8 8 110 10 17 37 t 71 72 8 26 195 12 190 21 21 42 28 87 68

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wwACTCTACgcww ; cor=; Ncor= a 67 79 185 20 8 16 9 175 31 40 30 74 72 c 42 32 9 155 3 176 5 5 149 17 141 31 32 g 29 26 7 8 3 5 5 8 8 110 10 17 37 t 71 72 8 26 195 12 190 21 21 42 28 87 68

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_test_vs_ctrl_m4_shift0 (dyads_test_vs_ctrl_m4)
; dyads_test_vs_ctrl_m4; m=0 (reference); ncol1=29; shift=0; ncol=29; wwAGAwtatrawtywdvahywrrdAGAww ; Alignment reference a 210 200 472 48 472 195 126 198 136 151 189 275 139 127 175 213 221 190 186 127 209 214 181 224 447 75 451 183 215 c 65 98 17 24 22 80 133 119 105 102 118 5 121 165 108 9 143 139 144 149 105 9 101 13 16 28 28 65 61 g 110 90 21 426 27 131 129 108 114 194 123 18 139 117 88 183 172 98 13 128 11 205 172 144 28 416 26 115 84 t 177 174 52 64 41 156 174 137 207 115 132 264 163 153 191 157 26 135 219 158 237 134 108 181 71 43 57 199 202

dyads_test_vs_ctrl_m4_shift0 (dyads_test_vs_ctrl_m4)
; dyads_test_vs_ctrl_m4 versus dyads_test_vs_ctrl_m4; m=1/2; ncol2=29; w=0; offset=0; strand=D; shift=0; score= 1; wwAGAwtatrawtywdvahywrrdAGAww ; cor=; Ncor= a 210 200 472 48 472 195 126 198 136 151 189 275 139 127 175 213 221 190 186 127 209 214 181 224 447 75 451 183 215 c 65 98 17 24 22 80 133 119 105 102 118 5 121 165 108 9 143 139 144 149 105 9 101 13 16 28 28 65 61 g 110 90 21 426 27 131 129 108 114 194 123 18 139 117 88 183 172 98 13 128 11 205 172 144 28 416 26 115 84 t 177 174 52 64 41 156 174 137 207 115 132 264 163 153 191 157 26 135 219 158 237 134 108 181 71 43 57 199 202

dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m4 versus dyads_test_vs_ctrl_m2; m=2/2; ncol2=20; w=0; offset=0; strand=D; shift=0; score=0.530846; wwAGAwbmwrawkywGAAww--------- ; cor=; Ncor= a 249 244 607 29 614 253 119 246 216 174 285 260 125 165 213 30 584 611 259 302 0 0 0 0 0 0 0 0 0 c 72 92 13 12 14 111 178 203 116 103 128 104 162 201 120 10 18 13 76 90 0 0 0 0 0 0 0 0 0 g 130 83 17 629 16 101 193 111 127 264 130 103 219 105 108 610 20 9 122 71 0 0 0 0 0 0 0 0 0 t 242 274 56 23 49 228 203 133 234 152 150 226 187 222 252 43 71 60 236 230 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=19; shift=0; ncol=19; dwrGAAGAAGAgAAArwww ; Alignment reference a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 64 51 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 15 14 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 16 31 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67 51 50
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; dwrGAAGAAGAgAAArwww ; cor=; Ncor= a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 64 51 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 15 14 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 16 31 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67 51 50
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/4; ncol2=17; w=0; offset=2; strand=D; shift=2; score=0.649901; --wwaCTAAGAGAAAgtww ; cor=; Ncor= a 0 0 54 60 91 22 18 125 133 15 135 17 120 127 109 22 34 58 56 c 0 0 27 18 10 103 2 3 1 3 4 5 9 4 4 9 5 19 20 g 0 0 11 14 19 4 3 6 1 115 2 114 5 2 11 90 11 15 20 t 0 0 54 54 26 17 123 12 11 13 5 10 12 13 22 25 96 54 50
dyads_test_vs_ctrl_m1_shift3 (dyads_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m1; m=3/4; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.598889; ---dwAGAArATGAAGaw- ; cor=; Ncor= a 0 0 0 198 292 515 40 526 408 231 454 124 40 538 518 75 342 293 0 c 0 0 0 57 64 10 17 19 13 13 31 22 11 7 8 15 47 52 0 g 0 0 0 149 60 14 500 14 135 313 29 22 498 9 10 450 59 57 0 t 0 0 0 191 179 56 38 36 39 38 81 427 46 41 59 55 147 193 0
oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=4/4; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.589079; --wwTAGAAGAGAATww-- ; cor=; Ncor= a 0 0 111 122 28 219 25 226 228 20 247 40 234 234 46 114 108 0 0 c 0 0 31 26 8 5 16 9 6 4 4 7 2 2 10 32 38 0 0 g 0 0 37 39 12 16 203 8 11 218 2 195 12 11 19 38 29 0 0 t 0 0 84 76 215 23 19 20 18 21 10 21 15 16 188 79 88 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_test_vs_ctrl_m1_shift3 (dyads_test_vs_ctrl_m1)				; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=3; ncol=18; ---dwAGAArATGAAGaw ; Alignment reference a 0 0 0 198 292 515 40 526 408 231 454 124 40 538 518 75 342 293 c 0 0 0 57 64 10 17 19 13 13 31 22 11 7 8 15 47 52 g 0 0 0 149 60 14 500 14 135 313 29 22 498 9 10 450 59 57 t 0 0 0 191 179 56 38 36 39 38 81 427 46 41 59 55 147 193
dyads_test_vs_ctrl_m1_shift3 (dyads_test_vs_ctrl_m1)				; dyads_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=3; score= 1; ---dwAGAArATGAAGaw ; cor=; Ncor= a 0 0 0 198 292 515 40 526 408 231 454 124 40 538 518 75 342 293 c 0 0 0 57 64 10 17 19 13 13 31 22 11 7 8 15 47 52 g 0 0 0 149 60 14 500 14 135 313 29 22 498 9 10 450 59 57 t 0 0 0 191 179 56 38 36 39 38 81 427 46 41 59 55 147 193
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; dyads_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/3; ncol2=19; w=-3; offset=-3; strand=D; shift=0; score=0.598889; dwrGAAGAAGAgAAArww ; cor=; Ncor= a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 64 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 15 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 16 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67 51
dyads_test_vs_ctrl_m2_shift3 (dyads_test_vs_ctrl_m2)				; dyads_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m2; m=3/3; ncol2=20; w=0; offset=0; strand=D; shift=3; score=0.552693; ---wwAGAwbmwrawkyw ; cor=; Ncor= a 0 0 0 249 244 607 29 614 253 119 246 216 174 285 260 125 165 213 c 0 0 0 72 92 13 12 14 111 178 203 116 103 128 104 162 201 120 g 0 0 0 130 83 17 629 16 101 193 111 127 264 130 103 219 105 108 t 0 0 0 242 274 56 23 49 228 203 133 234 152 150 226 187 222 252

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; wwgATAAGAGAATww ; Alignment reference a 83 91 48 190 24 203 204 15 209 18 198 201 36 87 94 c 26 23 11 12 6 8 6 8 3 6 8 7 6 25 25 g 29 29 141 9 11 5 6 190 4 186 4 4 8 44 29 t 92 87 30 19 189 14 14 17 14 20 20 18 180 74 82
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wwgATAAGAGAATww ; cor=; Ncor= a 83 91 48 190 24 203 204 15 209 18 198 201 36 87 94 c 26 23 11 12 6 8 6 8 3 6 8 7 6 25 25 g 29 29 141 9 11 5 6 190 4 186 4 4 8 44 29 t 92 87 30 19 189 14 14 17 14 20 20 18 180 74 82
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.815929; wwTAGAAGAGAATww ; cor=; Ncor= a 111 122 28 219 25 226 228 20 247 40 234 234 46 114 108 c 31 26 8 5 16 9 6 4 4 7 2 2 10 32 38 g 37 39 12 16 203 8 11 218 2 195 12 11 19 38 29 t 84 76 215 23 19 20 18 21 10 21 15 16 188 79 88
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=3/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.67672; wwaCTAAGAGAAAgt ; cor=; Ncor= a 54 60 91 22 18 125 133 15 135 17 120 127 109 22 34 c 27 18 10 103 2 3 1 3 4 5 9 4 4 9 5 g 11 14 19 4 3 6 1 115 2 114 5 2 11 90 11 t 54 54 26 17 123 12 11 13 5 10 12 13 22 25 96

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)				; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwAGAwbmwrawkywGAAww ; Alignment reference a 249 244 607 29 614 253 119 246 216 174 285 260 125 165 213 30 584 611 259 302 c 72 92 13 12 14 111 178 203 116 103 128 104 162 201 120 10 18 13 76 90 g 130 83 17 629 16 101 193 111 127 264 130 103 219 105 108 610 20 9 122 71 t 242 274 56 23 49 228 203 133 234 152 150 226 187 222 252 43 71 60 236 230
dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)				; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m2; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; wwAGAwbmwrawkywGAAww ; cor=; Ncor= a 249 244 607 29 614 253 119 246 216 174 285 260 125 165 213 30 584 611 259 302 c 72 92 13 12 14 111 178 203 116 103 128 104 162 201 120 10 18 13 76 90 g 130 83 17 629 16 101 193 111 127 264 130 103 219 105 108 610 20 9 122 71 t 242 274 56 23 49 228 203 133 234 152 150 226 187 222 252 43 71 60 236 230
dyads_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1)				; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m1; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.552693; dwAGAArATGAAGaw----- ; cor=; Ncor= a 198 292 515 40 526 408 231 454 124 40 538 518 75 342 293 0 0 0 0 0 c 57 64 10 17 19 13 13 31 22 11 7 8 15 47 52 0 0 0 0 0 g 149 60 14 500 14 135 313 29 22 498 9 10 450 59 57 0 0 0 0 0 t 191 179 56 38 36 39 38 81 427 46 41 59 55 147 193 0 0 0 0 0
dyads_test_vs_ctrl_m4_shift0 (dyads_test_vs_ctrl_m4)				; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m4; m=3/3; ncol2=29; w=0; offset=0; strand=D; shift=0; score=0.530846; wwAGAwtatrawtywdvahy ; cor=; Ncor= a 210 200 472 48 472 195 126 198 136 151 189 275 139 127 175 213 221 190 186 127 c 65 98 17 24 22 80 133 119 105 102 118 5 121 165 108 9 143 139 144 149 g 110 90 21 426 27 131 129 108 114 194 123 18 139 117 88 183 172 98 13 128 t 177 174 52 64 41 156 174 137 207 115 132 264 163 153 191 157 26 135 219 158

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=2; ncol=17; --wwTAGAAGAGAATww ; Alignment reference a 0 0 111 122 28 219 25 226 228 20 247 40 234 234 46 114 108 c 0 0 31 26 8 5 16 9 6 4 4 7 2 2 10 32 38 g 0 0 37 39 12 16 203 8 11 218 2 195 12 11 19 38 29 t 0 0 84 76 215 23 19 20 18 21 10 21 15 16 188 79 88
oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=2; score= 1; --wwTAGAAGAGAATww ; cor=; Ncor= a 0 0 111 122 28 219 25 226 228 20 247 40 234 234 46 114 108 c 0 0 31 26 8 5 16 9 6 4 4 7 2 2 10 32 38 g 0 0 37 39 12 16 203 8 11 218 2 195 12 11 19 38 29 t 0 0 84 76 215 23 19 20 18 21 10 21 15 16 188 79 88
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.815929; --wwgATAAGAGAATww ; cor=; Ncor= a 0 0 83 91 48 190 24 203 204 15 209 18 198 201 36 87 94 c 0 0 26 23 11 12 6 8 6 8 3 6 8 7 6 25 25 g 0 0 29 29 141 9 11 5 6 190 4 186 4 4 8 44 29 t 0 0 92 87 30 19 189 14 14 17 14 20 20 18 180 74 82
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.589079; dwrGAAGAAGAgAAArw ; cor=; Ncor= a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=2; ncol=19; --wwaCTAAGAGAAAgtww ; Alignment reference a 0 0 54 60 91 22 18 125 133 15 135 17 120 127 109 22 34 58 56 c 0 0 27 18 10 103 2 3 1 3 4 5 9 4 4 9 5 19 20 g 0 0 11 14 19 4 3 6 1 115 2 114 5 2 11 90 11 15 20 t 0 0 54 54 26 17 123 12 11 13 5 10 12 13 22 25 96 54 50
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=2; score= 1; --wwaCTAAGAGAAAgtww ; cor=; Ncor= a 0 0 54 60 91 22 18 125 133 15 135 17 120 127 109 22 34 58 56 c 0 0 27 18 10 103 2 3 1 3 4 5 9 4 4 9 5 19 20 g 0 0 11 14 19 4 3 6 1 115 2 114 5 2 11 90 11 15 20 t 0 0 54 54 26 17 123 12 11 13 5 10 12 13 22 25 96 54 50
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=2; score=0.67672; --wwgATAAGAGAATww-- ; cor=; Ncor= a 0 0 83 91 48 190 24 203 204 15 209 18 198 201 36 87 94 0 0 c 0 0 26 23 11 12 6 8 6 8 3 6 8 7 6 25 25 0 0 g 0 0 29 29 141 9 11 5 6 190 4 186 4 4 8 44 29 0 0 t 0 0 92 87 30 19 189 14 14 17 14 20 20 18 180 74 82 0 0
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.649901; dwrGAAGAAGAgAAArwww ; cor=; Ncor= a 53 73 58 17 122 128 14 132 132 12 136 32 111 127 124 41 62 64 51 c 11 20 19 1 5 0 3 2 3 2 3 5 5 2 3 7 6 15 14 g 37 9 44 108 8 6 116 5 2 123 0 88 15 10 8 84 11 16 31 t 45 44 25 20 11 12 13 7 9 9 7 21 15 7 11 14 67 51 50