One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/04/peak-motifs.2026-03-04.105925_2026-03-04.105925_GBNx32/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/2026/03/04/peak-motifs.2026-03-04.105925_2026-03-04.105925_GBNx32/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 4 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=1/3; 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

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=2/3; 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=3/3; 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_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=14; shift=0; ncol=14; amaAAACAAAGcma ; Alignment reference a 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 155 126 106 82 26 9 29 11 16 28 39 84 128 141

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; amaAAACAAAGcma ; cor=; Ncor= a 265 218 421 586 628 671 13 688 646 649 124 171 263 273 c 119 225 95 25 34 9 643 10 30 16 62 335 187 152 g 178 148 95 24 29 28 32 8 25 24 492 127 139 151 t 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_shift0 ; 2 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; ccCCCCACCCCcc ; Alignment reference a 238 226 62 65 35 22 821 29 28 29 113 220 281 c 512 445 912 984 1089 1100 109 1080 1067 1076 895 515 438 g 228 269 95 80 43 44 171 55 65 49 94 241 255 t 217 255 126 66 28 29 94 31 35 41 93 219 221

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ccCCCCACCCCcc ; cor=; Ncor= a 238 226 62 65 35 22 821 29 28 29 113 220 281 c 512 445 912 984 1089 1100 109 1080 1067 1076 895 515 438 g 228 269 95 80 43 44 171 55 65 49 94 241 255 t 217 255 126 66 28 29 94 31 35 41 93 219 221

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 3 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=1/2; 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

oligos_6nt_mkv3_m3_rc_shift1 (oligos_6nt_mkv3_m3_rc)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=2/2; 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

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

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=1/3; 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
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=2/3; 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=3/3; 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