One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/24/peak-motifs.2026-03-24.173120_2026-03-24.173120_dVE4vB/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/2026/03/24/peak-motifs.2026-03-24.173120_2026-03-24.173120_dVE4vB/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ytCCTCCTCct ; Alignment reference a 156 153 34 30 61 25 33 46 10 161 206 c 337 183 785 839 38 790 816 31 839 358 192 g 192 217 61 24 42 76 29 43 40 205 208 t 244 376 49 36 788 38 51 809 40 205 323

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ytCCTCCTCct ; cor=; Ncor= a 156 153 34 30 61 25 33 46 10 161 206 c 337 183 785 839 38 790 816 31 839 358 192 g 192 217 61 24 42 76 29 43 40 205 208 t 244 376 49 36 788 38 51 809 40 205 323

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; kmcTGCGCAgkm ; Alignment reference a 109 129 75 18 12 8 13 10 443 58 115 126 c 106 141 297 9 12 452 13 452 16 56 101 145 g 145 101 56 16 452 13 452 12 9 297 141 106 t 126 115 58 443 10 13 8 12 18 75 129 109

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; kmcTGCGCAgkm ; cor=; Ncor= a 109 129 75 18 12 8 13 10 443 58 115 126 c 106 141 297 9 12 452 13 452 16 56 101 145 g 145 101 56 16 452 13 452 12 9 297 141 106 t 126 115 58 443 10 13 8 12 18 75 129 109

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.978775; kvCTGCGCAGbm ; cor=; Ncor= a 68 81 19 16 2 7 13 10 283 15 69 82 c 69 91 281 9 10 292 12 302 16 9 83 105 g 105 83 9 16 302 12 292 10 9 281 91 69 t 82 69 15 283 10 13 7 2 16 19 81 68

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_6nt_m1 versus positions_7nt_m2_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.581369; --mtGCGCATGc ; cor=; Ncor= a 0 0 193 166 28 39 48 36 640 26 24 172 c 0 0 221 135 22 649 22 674 46 21 27 249 g 0 0 178 190 695 43 668 41 37 64 695 159 t 0 0 175 276 22 36 29 16 44 656 21 187

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; kwCTAGGAyw ; Alignment reference a 49 87 5 0 187 2 3 160 43 71 c 35 33 186 1 11 13 0 4 53 30 g 54 28 7 33 0 177 167 14 48 38 t 60 50 0 164 0 6 28 20 54 59

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; kwCTAGGAyw ; cor=; Ncor= a 49 87 5 0 187 2 3 160 43 71 c 35 33 186 1 11 13 0 4 53 30 g 54 28 7 33 0 177 167 14 48 38 t 60 50 0 164 0 6 28 20 54 59

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; wwATCGATww ; Alignment reference a 106 111 317 0 1 0 318 0 111 90 c 71 61 3 4 320 0 0 1 38 54 g 54 38 1 0 0 318 3 3 61 73 t 90 111 0 317 0 3 0 317 111 104

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wwATCGATww ; cor=; Ncor= a 106 111 317 0 1 0 318 0 111 90 c 71 61 3 4 320 0 0 1 38 54 g 54 38 1 0 0 318 3 3 61 73 t 90 111 0 317 0 3 0 317 111 104

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; kvCTGCGCAGbm ; Alignment reference a 68 81 19 16 2 7 13 10 283 15 69 82 c 69 91 281 9 10 292 12 302 16 9 83 105 g 105 83 9 16 302 12 292 10 9 281 91 69 t 82 69 15 283 10 13 7 2 16 19 81 68

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; kvCTGCGCAGbm ; cor=; Ncor= a 68 81 19 16 2 7 13 10 283 15 69 82 c 69 91 281 9 10 292 12 302 16 9 83 105 g 105 83 9 16 302 12 292 10 9 281 91 69 t 82 69 15 283 10 13 7 2 16 19 81 68

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.978775; kmcTGCGCAgkm ; cor=; Ncor= a 109 129 75 18 12 8 13 10 443 58 115 126 c 106 141 297 9 12 452 13 452 16 56 101 145 g 145 101 56 16 452 13 452 12 9 297 141 106 t 126 115 58 443 10 13 8 12 18 75 129 109

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; awATATgTATat ; Alignment reference a 476 237 855 41 849 12 228 30 851 31 427 196 c 105 184 10 14 15 20 24 25 12 43 90 122 g 147 100 28 6 17 16 566 18 21 14 178 110 t 191 398 26 858 38 871 101 846 35 831 224 491

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; awATATgTATat ; cor=; Ncor= a 476 237 855 41 849 12 228 30 851 31 427 196 c 105 184 10 14 15 20 24 25 12 43 90 122 g 147 100 28 6 17 16 566 18 21 14 178 110 t 191 398 26 858 38 871 101 846 35 831 224 491

oligos_6nt_mkv3_m1_rc_shift1 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1_rc; m=2/4; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.891244; -taTATrTATat ; cor=; Ncor= a 0 283 626 35 1139 37 340 28 1126 71 600 273 c 0 218 153 16 33 34 51 11 25 79 171 163 g 0 147 249 15 43 35 789 36 59 36 241 156 t 0 583 203 1165 16 1125 51 1156 21 1045 219 639

oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m2_rc; m=3/4; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.684373; wwTTATTTATtw ; cor=; Ncor= a 331 306 140 41 899 34 76 36 879 109 240 271 c 146 132 35 13 16 18 12 22 27 57 89 152 g 135 136 43 28 22 26 26 22 31 29 107 156 t 370 408 764 900 45 904 868 902 45 787 546 403

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; oligos_7nt_mkv4_m1 versus positions_6nt_m2_rc; m=4/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.63269; wwATATTTww-- ; cor=; Ncor= a 344 292 825 0 825 0 0 0 259 245 0 0 c 110 139 0 0 0 0 0 0 114 149 0 0 g 129 110 0 0 0 0 0 0 127 132 0 0 t 242 284 0 825 0 825 825 825 325 299 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCATTATAtw ; Alignment reference a 249 252 45 600 71 48 650 13 634 172 221 c 127 119 525 17 27 20 26 17 23 126 103 g 104 99 35 17 30 22 18 18 13 107 123 t 218 228 93 64 570 608 4 650 28 293 251

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCATTATAtw ; cor=; Ncor= a 249 252 45 600 71 48 650 13 634 172 221 c 127 119 525 17 27 20 26 17 23 126 103 g 104 99 35 17 30 22 18 18 13 107 123 t 218 228 93 64 570 608 4 650 28 293 251

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; akACCGGGwa ; Alignment reference a 87 61 275 8 18 24 49 19 133 90 c 73 52 8 287 273 7 6 2 30 79 g 79 99 7 2 13 268 245 289 49 73 t 79 106 28 21 14 19 18 8 106 76

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; akACCGGGwa ; cor=; Ncor= a 87 61 275 8 18 24 49 19 133 90 c 73 52 8 287 273 7 6 2 30 79 g 79 99 7 2 13 268 245 289 49 73 t 79 106 28 21 14 19 18 8 106 76

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwGTAAACAww ; Alignment reference a 213 225 32 25 583 573 593 6 574 205 241 c 132 103 32 1 37 42 25 574 28 128 116 g 144 125 599 21 17 25 19 13 23 158 125 t 181 217 7 623 33 30 33 77 45 179 188

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwGTAAACAww ; cor=; Ncor= a 213 225 32 25 583 573 593 6 574 205 241 c 132 103 32 1 37 42 25 574 28 128 116 g 144 125 599 21 17 25 19 13 23 158 125 t 181 217 7 623 33 30 33 77 45 179 188

oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3; m=2/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.519196; --awAAACAAA ; cor=; Ncor= a 0 0 210 179 507 531 587 0 540 520 579 c 0 0 125 104 9 9 2 594 4 17 6 g 0 0 131 89 26 14 0 0 15 20 5 t 0 0 128 222 52 40 5 0 35 37 4

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; ytCTCTTTCTyt ; Alignment reference a 105 72 10 10 16 9 9 6 13 15 83 87 c 188 80 461 5 450 18 104 14 447 21 184 106 g 67 100 9 8 26 12 12 17 13 28 121 83 t 159 267 39 496 27 480 394 482 46 455 131 243

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ytCTCTTTCTyt ; cor=; Ncor= a 105 72 10 10 16 9 9 6 13 15 83 87 c 188 80 461 5 450 18 104 14 447 21 184 106 g 67 100 9 8 26 12 12 17 13 28 121 83 t 159 267 39 496 27 480 394 482 46 455 131 243

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; cgCATGCGCak ; Alignment reference a 172 187 21 656 44 16 29 36 22 276 175 c 235 159 695 64 37 41 668 43 695 190 178 g 173 249 27 21 46 674 22 649 22 135 221 t 187 172 24 26 640 36 48 39 28 166 193

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; cgCATGCGCak ; cor=; Ncor= a 172 187 21 656 44 16 29 36 22 276 175 c 235 159 695 64 37 41 668 43 695 190 178 g 173 249 27 21 46 674 22 649 22 135 221 t 187 172 24 26 640 36 48 39 28 166 193

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m2 versus positions_6nt_m1; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.581369; -kmcTGCGCAg ; cor=; Ncor= a 0 109 129 75 18 12 8 13 10 443 58 c 0 106 141 297 9 12 452 13 452 16 56 g 0 145 101 56 16 452 13 452 12 9 297 t 0 126 115 58 443 10 13 8 12 18 75

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; wwaATAAATAAww ; Alignment reference a 327 403 546 787 45 902 868 904 45 900 764 408 370 c 159 156 107 29 31 22 26 26 22 28 43 136 135 g 144 152 89 57 27 22 12 18 16 13 35 132 146 t 352 271 240 109 879 36 76 34 899 41 140 306 331

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wwaATAAATAAww ; cor=; Ncor= a 327 403 546 787 45 902 868 904 45 900 764 408 370 c 159 156 107 29 31 22 26 26 22 28 43 136 135 g 144 152 89 57 27 22 12 18 16 13 35 132 146 t 352 271 240 109 879 36 76 34 899 41 140 306 331

oligos_7nt_mkv4_m1_rc_shift1 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m1_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.684373; -atATAcATATwt ; cor=; Ncor= a 0 491 224 831 35 846 101 871 38 858 26 398 191 c 0 110 178 14 21 18 566 16 17 6 28 100 147 g 0 122 90 43 12 25 24 20 15 14 10 184 105 t 0 196 427 31 851 30 228 12 849 41 855 237 476

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.658356; -atATAyATAta- ; cor=; Ncor= a 0 639 219 1045 21 1156 51 1125 16 1165 203 583 0 c 0 156 241 36 59 36 789 35 43 15 249 147 0 g 0 163 171 79 25 11 51 34 33 16 153 218 0 t 0 273 600 71 1126 28 340 37 1139 35 626 283 0

positions_6nt_m2_shift3 (positions_6nt_m2)
; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=4/4; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.584816; ---wwAAATATww ; cor=; Ncor= a 0 0 0 299 325 825 825 825 0 825 0 284 242 c 0 0 0 132 127 0 0 0 0 0 0 110 129 g 0 0 0 149 114 0 0 0 0 0 0 139 110 t 0 0 0 245 259 0 0 0 825 0 825 292 344

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=2; ncol=13; --awAAACAAAww ; Alignment reference a 0 0 210 179 507 531 587 0 540 520 579 168 219 c 0 0 125 104 9 9 2 594 4 17 6 133 85 g 0 0 131 89 26 14 0 0 15 20 5 114 108 t 0 0 128 222 52 40 5 0 35 37 4 179 182

oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --awAAACAAAww ; cor=; Ncor= a 0 0 210 179 507 531 587 0 540 520 579 168 219 c 0 0 125 104 9 9 2 594 4 17 6 133 85 g 0 0 131 89 26 14 0 0 15 20 5 114 108 t 0 0 128 222 52 40 5 0 35 37 4 179 182

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m5; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.758592; --wwAACCAAAww ; cor=; Ncor= a 0 0 196 175 513 549 0 0 506 500 512 170 180 c 0 0 114 104 26 15 588 531 18 32 30 132 140 g 0 0 129 120 21 6 0 11 34 33 28 108 99 t 0 0 154 194 33 23 5 51 35 28 23 183 174

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3; m=3/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.519196; wwGTAAACAww-- ; cor=; Ncor= a 213 225 32 25 583 573 593 6 574 205 241 0 0 c 132 103 32 1 37 42 25 574 28 128 116 0 0 g 144 125 599 21 17 25 19 13 23 158 125 0 0 t 181 217 7 623 33 30 33 77 45 179 188 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -atATAyATAta ; Alignment reference a 0 639 219 1045 21 1156 51 1125 16 1165 203 583 c 0 156 241 36 59 36 789 35 43 15 249 147 g 0 163 171 79 25 11 51 34 33 16 153 218 t 0 273 600 71 1126 28 340 37 1139 35 626 283

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -atATAyATAta ; cor=; Ncor= a 0 639 219 1045 21 1156 51 1125 16 1165 203 583 c 0 156 241 36 59 36 789 35 43 15 249 147 g 0 163 171 79 25 11 51 34 33 16 153 218 t 0 273 600 71 1126 28 340 37 1139 35 626 283

oligos_7nt_mkv4_m1_rc_shift1 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1_rc; m=2/3; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.891244; -atATAcATATw ; cor=; Ncor= a 0 491 224 831 35 846 101 871 38 858 26 398 c 0 110 178 14 21 18 566 16 17 6 28 100 g 0 122 90 43 12 25 24 20 15 14 10 184 t 0 196 427 31 851 30 228 12 849 41 855 237

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.658356; wwaATAAATAAw ; cor=; Ncor= a 327 403 546 787 45 902 868 904 45 900 764 408 c 159 156 107 29 31 22 26 26 22 28 43 136 g 144 152 89 57 27 22 12 18 16 13 35 132 t 352 271 240 109 879 36 76 34 899 41 140 306

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAACCAAAww ; Alignment reference a 196 175 513 549 0 0 506 500 512 170 180 c 114 104 26 15 588 531 18 32 30 132 140 g 129 120 21 6 0 11 34 33 28 108 99 t 154 194 33 23 5 51 35 28 23 183 174

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAACCAAAww ; cor=; Ncor= a 196 175 513 549 0 0 506 500 512 170 180 c 114 104 26 15 588 531 18 32 30 132 140 g 129 120 21 6 0 11 34 33 28 108 99 t 154 194 33 23 5 51 35 28 23 183 174

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m3; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.758592; awAAACAAAww ; cor=; Ncor= a 210 179 507 531 587 0 540 520 579 168 219 c 125 104 9 9 2 594 4 17 6 133 85 g 131 89 26 14 0 0 15 20 5 114 108 t 128 222 52 40 5 0 35 37 4 179 182

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift3 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---wwAAATATww ; Alignment reference a 0 0 0 299 325 825 825 825 0 825 0 284 242 c 0 0 0 132 127 0 0 0 0 0 0 110 129 g 0 0 0 149 114 0 0 0 0 0 0 139 110 t 0 0 0 245 259 0 0 0 825 0 825 292 344

positions_6nt_m2_shift3 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wwAAATATww ; cor=; Ncor= a 0 0 0 299 325 825 825 825 0 825 0 284 242 c 0 0 0 132 127 0 0 0 0 0 0 110 129 g 0 0 0 149 114 0 0 0 0 0 0 139 110 t 0 0 0 245 259 0 0 0 825 0 825 292 344

oligos_7nt_mkv4_m1_rc_shift1 (oligos_7nt_mkv4_m1_rc)
; positions_6nt_m2 versus oligos_7nt_mkv4_m1_rc; m=2/3; ncol2=12; w=-2; offset=-2; strand=R; shift=1; score=0.63269; -atATAcATATwt ; cor=; Ncor= a 0 491 224 831 35 846 101 871 38 858 26 398 191 c 0 110 178 14 21 18 566 16 17 6 28 100 147 g 0 122 90 43 12 25 24 20 15 14 10 184 105 t 0 196 427 31 851 30 228 12 849 41 855 237 476

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.584816; wwaATAAATAAww ; cor=; Ncor= a 327 403 546 787 45 902 868 904 45 900 764 408 370 c 159 156 107 29 31 22 26 26 22 28 43 136 135 g 144 152 89 57 27 22 12 18 16 13 35 132 146 t 352 271 240 109 879 36 76 34 899 41 140 306 331

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; ywGCTGCCdv ; Alignment reference a 40 80 4 1 2 19 6 0 86 77 c 101 73 0 298 2 5 283 299 58 77 g 66 66 294 0 0 275 0 0 76 77 t 92 80 1 0 295 0 10 0 79 68

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ywGCTGCCdv ; cor=; Ncor= a 40 80 4 1 2 19 6 0 86 77 c 101 73 0 298 2 5 283 299 58 77 g 66 66 294 0 0 275 0 0 76 77 t 92 80 1 0 295 0 10 0 79 68

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; wrCAGCTGyw ; Alignment reference a 147 138 0 476 0 3 1 1 106 134 c 85 102 480 2 0 479 3 1 136 116 g 116 136 1 3 479 0 2 480 102 85 t 134 106 1 1 3 0 476 0 138 147

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wrCAGCTGyw ; cor=; Ncor= a 147 138 0 476 0 3 1 1 106 134 c 85 102 480 2 0 479 3 1 136 116 g 116 136 1 3 479 0 2 480 102 85 t 134 106 1 1 3 0 476 0 138 147

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; kmcTGCGCAgkm ; Alignment reference a 109 129 75 18 12 8 13 10 443 58 115 126 c 106 141 297 9 12 452 13 452 16 56 101 145 g 145 101 56 16 452 13 452 12 9 297 141 106 t 126 115 58 443 10 13 8 12 18 75 129 109
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; kmcTGCGCAgkm ; cor=; Ncor= a 109 129 75 18 12 8 13 10 443 58 115 126 c 106 141 297 9 12 452 13 452 16 56 101 145 g 145 101 56 16 452 13 452 12 9 297 141 106 t 126 115 58 443 10 13 8 12 18 75 129 109
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.978775; kvCTGCGCAGbm ; cor=; Ncor= a 68 81 19 16 2 7 13 10 283 15 69 82 c 69 91 281 9 10 292 12 302 16 9 83 105 g 105 83 9 16 302 12 292 10 9 281 91 69 t 82 69 15 283 10 13 7 2 16 19 81 68
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_6nt_m1 versus positions_7nt_m2_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.581369; --mtGCGCATGc ; cor=; Ncor= a 0 0 193 166 28 39 48 36 640 26 24 172 c 0 0 221 135 22 649 22 674 46 21 27 249 g 0 0 178 190 695 43 668 41 37 64 695 159 t 0 0 175 276 22 36 29 16 44 656 21 187

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; awATATgTATat ; Alignment reference a 476 237 855 41 849 12 228 30 851 31 427 196 c 105 184 10 14 15 20 24 25 12 43 90 122 g 147 100 28 6 17 16 566 18 21 14 178 110 t 191 398 26 858 38 871 101 846 35 831 224 491
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; awATATgTATat ; cor=; Ncor= a 476 237 855 41 849 12 228 30 851 31 427 196 c 105 184 10 14 15 20 24 25 12 43 90 122 g 147 100 28 6 17 16 566 18 21 14 178 110 t 191 398 26 858 38 871 101 846 35 831 224 491
oligos_6nt_mkv3_m1_rc_shift1 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1_rc; m=2/4; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.891244; -taTATrTATat ; cor=; Ncor= a 0 283 626 35 1139 37 340 28 1126 71 600 273 c 0 218 153 16 33 34 51 11 25 79 171 163 g 0 147 249 15 43 35 789 36 59 36 241 156 t 0 583 203 1165 16 1125 51 1156 21 1045 219 639
oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m2_rc; m=3/4; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.684373; wwTTATTTATtw ; cor=; Ncor= a 331 306 140 41 899 34 76 36 879 109 240 271 c 146 132 35 13 16 18 12 22 27 57 89 152 g 135 136 43 28 22 26 26 22 31 29 107 156 t 370 408 764 900 45 904 868 902 45 787 546 403
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; oligos_7nt_mkv4_m1 versus positions_6nt_m2_rc; m=4/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.63269; wwATATTTww-- ; cor=; Ncor= a 344 292 825 0 825 0 0 0 259 245 0 0 c 110 139 0 0 0 0 0 0 114 149 0 0 g 129 110 0 0 0 0 0 0 127 132 0 0 t 242 284 0 825 0 825 825 825 325 299 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; wwaATAAATAAww ; Alignment reference a 327 403 546 787 45 902 868 904 45 900 764 408 370 c 159 156 107 29 31 22 26 26 22 28 43 136 135 g 144 152 89 57 27 22 12 18 16 13 35 132 146 t 352 271 240 109 879 36 76 34 899 41 140 306 331
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wwaATAAATAAww ; cor=; Ncor= a 327 403 546 787 45 902 868 904 45 900 764 408 370 c 159 156 107 29 31 22 26 26 22 28 43 136 135 g 144 152 89 57 27 22 12 18 16 13 35 132 146 t 352 271 240 109 879 36 76 34 899 41 140 306 331
oligos_7nt_mkv4_m1_rc_shift1 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m1_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.684373; -atATAcATATwt ; cor=; Ncor= a 0 491 224 831 35 846 101 871 38 858 26 398 191 c 0 110 178 14 21 18 566 16 17 6 28 100 147 g 0 122 90 43 12 25 24 20 15 14 10 184 105 t 0 196 427 31 851 30 228 12 849 41 855 237 476
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.658356; -atATAyATAta- ; cor=; Ncor= a 0 639 219 1045 21 1156 51 1125 16 1165 203 583 0 c 0 156 241 36 59 36 789 35 43 15 249 147 0 g 0 163 171 79 25 11 51 34 33 16 153 218 0 t 0 273 600 71 1126 28 340 37 1139 35 626 283 0
positions_6nt_m2_shift3 (positions_6nt_m2)				; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=4/4; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.584816; ---wwAAATATww ; cor=; Ncor= a 0 0 0 299 325 825 825 825 0 825 0 284 242 c 0 0 0 132 127 0 0 0 0 0 0 110 129 g 0 0 0 149 114 0 0 0 0 0 0 139 110 t 0 0 0 245 259 0 0 0 825 0 825 292 344

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=2; ncol=13; --awAAACAAAww ; Alignment reference a 0 0 210 179 507 531 587 0 540 520 579 168 219 c 0 0 125 104 9 9 2 594 4 17 6 133 85 g 0 0 131 89 26 14 0 0 15 20 5 114 108 t 0 0 128 222 52 40 5 0 35 37 4 179 182
oligos_6nt_mkv3_m3_shift2 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --awAAACAAAww ; cor=; Ncor= a 0 0 210 179 507 531 587 0 540 520 579 168 219 c 0 0 125 104 9 9 2 594 4 17 6 133 85 g 0 0 131 89 26 14 0 0 15 20 5 114 108 t 0 0 128 222 52 40 5 0 35 37 4 179 182
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m5; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.758592; --wwAACCAAAww ; cor=; Ncor= a 0 0 196 175 513 549 0 0 506 500 512 170 180 c 0 0 114 104 26 15 588 531 18 32 30 132 140 g 0 0 129 120 21 6 0 11 34 33 28 108 99 t 0 0 154 194 33 23 5 51 35 28 23 183 174
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3; m=3/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.519196; wwGTAAACAww-- ; cor=; Ncor= a 213 225 32 25 583 573 593 6 574 205 241 0 0 c 132 103 32 1 37 42 25 574 28 128 116 0 0 g 144 125 599 21 17 25 19 13 23 158 125 0 0 t 181 217 7 623 33 30 33 77 45 179 188 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -atATAyATAta ; Alignment reference a 0 639 219 1045 21 1156 51 1125 16 1165 203 583 c 0 156 241 36 59 36 789 35 43 15 249 147 g 0 163 171 79 25 11 51 34 33 16 153 218 t 0 273 600 71 1126 28 340 37 1139 35 626 283
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -atATAyATAta ; cor=; Ncor= a 0 639 219 1045 21 1156 51 1125 16 1165 203 583 c 0 156 241 36 59 36 789 35 43 15 249 147 g 0 163 171 79 25 11 51 34 33 16 153 218 t 0 273 600 71 1126 28 340 37 1139 35 626 283
oligos_7nt_mkv4_m1_rc_shift1 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1_rc; m=2/3; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.891244; -atATAcATATw ; cor=; Ncor= a 0 491 224 831 35 846 101 871 38 858 26 398 c 0 110 178 14 21 18 566 16 17 6 28 100 g 0 122 90 43 12 25 24 20 15 14 10 184 t 0 196 427 31 851 30 228 12 849 41 855 237
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.658356; wwaATAAATAAw ; cor=; Ncor= a 327 403 546 787 45 902 868 904 45 900 764 408 c 159 156 107 29 31 22 26 26 22 28 43 136 g 144 152 89 57 27 22 12 18 16 13 35 132 t 352 271 240 109 879 36 76 34 899 41 140 306

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift3 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---wwAAATATww ; Alignment reference a 0 0 0 299 325 825 825 825 0 825 0 284 242 c 0 0 0 132 127 0 0 0 0 0 0 110 129 g 0 0 0 149 114 0 0 0 0 0 0 139 110 t 0 0 0 245 259 0 0 0 825 0 825 292 344
positions_6nt_m2_shift3 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wwAAATATww ; cor=; Ncor= a 0 0 0 299 325 825 825 825 0 825 0 284 242 c 0 0 0 132 127 0 0 0 0 0 0 110 129 g 0 0 0 149 114 0 0 0 0 0 0 139 110 t 0 0 0 245 259 0 0 0 825 0 825 292 344
oligos_7nt_mkv4_m1_rc_shift1 (oligos_7nt_mkv4_m1_rc)				; positions_6nt_m2 versus oligos_7nt_mkv4_m1_rc; m=2/3; ncol2=12; w=-2; offset=-2; strand=R; shift=1; score=0.63269; -atATAcATATwt ; cor=; Ncor= a 0 491 224 831 35 846 101 871 38 858 26 398 191 c 0 110 178 14 21 18 566 16 17 6 28 100 147 g 0 122 90 43 12 25 24 20 15 14 10 184 105 t 0 196 427 31 851 30 228 12 849 41 855 237 476
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.584816; wwaATAAATAAww ; cor=; Ncor= a 327 403 546 787 45 902 868 904 45 900 764 408 370 c 159 156 107 29 31 22 26 26 22 28 43 136 135 g 144 152 89 57 27 22 12 18 16 13 35 132 146 t 352 271 240 109 879 36 76 34 899 41 140 306 331