One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.190736_2025-12-18.190736_aiIxB3/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/2025/12/18/peak-motifs.2025-12-18.190736_2025-12-18.190736_aiIxB3/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 5 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=17; shift=0; ncol=17; GAATsGAATGGAATsrA ; Alignment reference a 191 1816 1879 118 122 167 2150 2058 83 70 45 2160 2034 107 154 552 1809 c 92 275 168 125 554 65 13 16 77 56 31 13 84 84 631 86 54 g 1582 36 97 23 1368 1911 7 98 11 2042 2097 5 40 18 1301 1475 19 t 335 73 56 1934 156 57 30 28 2029 32 27 22 42 1991 114 87 318

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; GAATsGAATGGAATsrA ; cor=; Ncor= a 191 1816 1879 118 122 167 2150 2058 83 70 45 2160 2034 107 154 552 1809 c 92 275 168 125 554 65 13 16 77 56 31 13 84 84 631 86 54 g 1582 36 97 23 1368 1911 7 98 11 2042 2097 5 40 18 1301 1475 19 t 335 73 56 1934 156 57 30 28 2029 32 27 22 42 1991 114 87 318

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/4; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.944088; GAATgGAATGGAATsGA ; cor=; Ncor= a 196 1822 1812 107 110 154 2138 2042 73 68 51 2139 2038 97 135 482 1827 c 88 259 183 126 537 57 11 15 71 54 45 12 74 78 601 63 44 g 1577 36 129 22 1385 1924 7 99 15 2016 2063 4 36 14 1346 1577 18 t 324 68 61 1930 153 50 29 29 2026 47 26 30 37 1996 103 63 296

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5; m=3/4; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.540949; --aTGGAmTCGAat--- ; cor=; Ncor= a 0 0 188 29 18 14 250 75 14 3 20 265 186 46 0 0 0 c 0 0 46 23 18 7 7 194 8 257 7 3 23 44 0 0 0 g 0 0 25 34 233 257 5 10 5 13 254 7 47 22 0 0 0 t 0 0 27 200 17 8 24 7 259 13 5 11 30 174 0 0 0

oligos_7nt_mkv4_m3_rc_shift1 (oligos_7nt_mkv4_m3_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m3_rc; m=4/4; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.501282; -awTCkAATGgw----- ; cor=; Ncor= a 0 299 278 27 49 6 572 531 13 38 133 310 0 0 0 0 0 c 0 114 96 11 522 7 4 31 8 5 63 74 0 0 0 0 0 g 0 55 71 8 17 199 6 12 8 535 260 58 0 0 0 0 0 t 0 128 151 550 8 384 14 22 567 18 140 154 0 0 0 0 0

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=18; shift=0; ncol=18; GAATgGAATGGAATsGAA ; Alignment reference a 196 1822 1812 107 110 154 2138 2042 73 68 51 2139 2038 97 135 482 1827 1643 c 88 259 183 126 537 57 11 15 71 54 45 12 74 78 601 63 44 369 g 1577 36 129 22 1385 1924 7 99 15 2016 2063 4 36 14 1346 1577 18 69 t 324 68 61 1930 153 50 29 29 2026 47 26 30 37 1996 103 63 296 104

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/4; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; GAATgGAATGGAATsGAA ; cor=; Ncor= a 196 1822 1812 107 110 154 2138 2042 73 68 51 2139 2038 97 135 482 1827 1643 c 88 259 183 126 537 57 11 15 71 54 45 12 74 78 601 63 44 369 g 1577 36 129 22 1385 1924 7 99 15 2016 2063 4 36 14 1346 1577 18 69 t 324 68 61 1930 153 50 29 29 2026 47 26 30 37 1996 103 63 296 104

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=2/4; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.944088; GAATsGAATGGAATsrA- ; cor=; Ncor= a 191 1816 1879 118 122 167 2150 2058 83 70 45 2160 2034 107 154 552 1809 0 c 92 275 168 125 554 65 13 16 77 56 31 13 84 84 631 86 54 0 g 1582 36 97 23 1368 1911 7 98 11 2042 2097 5 40 18 1301 1475 19 0 t 335 73 56 1934 156 57 30 28 2029 32 27 22 42 1991 114 87 318 0

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5; m=3/4; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.511893; --aTGGAmTCGAat---- ; cor=; Ncor= a 0 0 188 29 18 14 250 75 14 3 20 265 186 46 0 0 0 0 c 0 0 46 23 18 7 7 194 8 257 7 3 23 44 0 0 0 0 g 0 0 25 34 233 257 5 10 5 13 254 7 47 22 0 0 0 0 t 0 0 27 200 17 8 24 7 259 13 5 11 30 174 0 0 0 0

oligos_7nt_mkv4_m3_rc_shift1 (oligos_7nt_mkv4_m3_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3_rc; m=4/4; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.472864; -awTCkAATGgw------ ; cor=; Ncor= a 0 299 278 27 49 6 572 531 13 38 133 310 0 0 0 0 0 0 c 0 114 96 11 522 7 4 31 8 5 63 74 0 0 0 0 0 0 g 0 55 71 8 17 199 6 12 8 535 260 58 0 0 0 0 0 0 t 0 128 151 550 8 384 14 22 567 18 140 154 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --aTGGAmTCGAat ; Alignment reference a 0 0 188 29 18 14 250 75 14 3 20 265 186 46 c 0 0 46 23 18 7 7 194 8 257 7 3 23 44 g 0 0 25 34 233 257 5 10 5 13 254 7 47 22 t 0 0 27 200 17 8 24 7 259 13 5 11 30 174

oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --aTGGAmTCGAat ; cor=; Ncor= a 0 0 188 29 18 14 250 75 14 3 20 265 186 46 c 0 0 46 23 18 7 7 194 8 257 7 3 23 44 g 0 0 25 34 233 257 5 10 5 13 254 7 47 22 t 0 0 27 200 17 8 24 7 259 13 5 11 30 174

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1; m=2/4; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.540949; GAATsGAATGGAAT ; cor=; Ncor= a 191 1816 1879 118 122 167 2150 2058 83 70 45 2160 2034 107 c 92 275 168 125 554 65 13 16 77 56 31 13 84 84 g 1582 36 97 23 1368 1911 7 98 11 2042 2097 5 40 18 t 335 73 56 1934 156 57 30 28 2029 32 27 22 42 1991

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m1; m=3/4; ncol2=18; w=-2; offset=-2; strand=D; shift=0; score=0.511893; GAATgGAATGGAAT ; cor=; Ncor= a 196 1822 1812 107 110 154 2138 2042 73 68 51 2139 2038 97 c 88 259 183 126 537 57 11 15 71 54 45 12 74 78 g 1577 36 129 22 1385 1924 7 99 15 2016 2063 4 36 14 t 324 68 61 1930 153 50 29 29 2026 47 26 30 37 1996

oligos_7nt_mkv4_m3_rc_shift6 (oligos_7nt_mkv4_m3_rc)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m3_rc; m=4/4; ncol2=11; w=0; offset=4; strand=R; shift=6; score=0.416756; ------awTCkAAT ; cor=; Ncor= a 0 0 0 0 0 0 299 278 27 49 6 572 531 13 c 0 0 0 0 0 0 114 96 11 522 7 4 31 8 g 0 0 0 0 0 0 55 71 8 17 199 6 12 8 t 0 0 0 0 0 0 128 151 550 8 384 14 22 567

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=13; shift=0; ncol=13; rkmATCATCrAat ; Alignment reference a 111 42 203 301 6 5 297 10 17 80 226 198 35 c 17 14 79 2 4 300 2 7 267 9 11 62 13 g 165 153 8 5 4 5 3 4 4 208 10 33 74 t 19 103 22 4 298 2 10 291 24 15 65 19 190

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rkmATCATCrAat ; cor=; Ncor= a 111 42 203 301 6 5 297 10 17 80 226 198 35 c 17 14 79 2 4 300 2 7 267 9 11 62 13 g 165 153 8 5 4 5 3 4 4 208 10 33 74 t 19 103 22 4 298 2 10 291 24 15 65 19 190

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; caCACATGCay ; Alignment reference a 145 282 24 547 3 544 22 60 37 321 119 c 219 77 539 10 568 20 18 19 509 91 229 g 93 114 10 21 10 26 40 500 7 58 54 t 148 132 32 27 24 15 525 26 52 135 203

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; caCACATGCay ; cor=; Ncor= a 145 282 24 547 3 544 22 60 37 321 119 c 219 77 539 10 568 20 18 19 509 91 229 g 93 114 10 21 10 26 40 500 7 58 54 t 148 132 32 27 24 15 525 26 52 135 203

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 2 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=11; shift=0; ncol=11; wwTACATACaw ; Alignment reference a 250 319 29 644 42 706 22 652 44 350 205 c 138 88 60 49 633 14 74 10 607 144 172 g 110 129 10 36 24 6 24 32 19 72 98 t 249 211 648 18 48 21 627 53 77 181 272

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwTACATACaw ; cor=; Ncor= a 250 319 29 644 42 706 22 652 44 350 205 c 138 88 60 49 633 14 74 10 607 144 172 g 110 129 10 36 24 6 24 32 19 72 98 t 249 211 648 18 48 21 627 53 77 181 272

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift6 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=6; ncol=17; ------wcCATTmGAwt ; Alignment reference a 0 0 0 0 0 0 154 140 18 567 22 14 384 8 550 151 128 c 0 0 0 0 0 0 58 260 535 8 12 6 199 17 8 71 55 g 0 0 0 0 0 0 74 63 5 8 31 4 7 522 11 96 114 t 0 0 0 0 0 0 310 133 38 13 531 572 6 49 27 278 299

oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=6; score= 1; ------wcCATTmGAwt ; cor=; Ncor= a 0 0 0 0 0 0 154 140 18 567 22 14 384 8 550 151 128 c 0 0 0 0 0 0 58 260 535 8 12 6 199 17 8 71 55 g 0 0 0 0 0 0 74 63 5 8 31 4 7 522 11 96 114 t 0 0 0 0 0 0 310 133 38 13 531 572 6 49 27 278 299

oligos_6nt_mkv3_m1_rc_shift1 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m1_rc; m=2/4; ncol2=17; w=-5; offset=-5; strand=R; shift=1; score=0.501282; -TysATTCCATTCsATT ; cor=; Ncor= a 0 318 87 114 1991 42 22 27 32 2029 28 30 57 156 1934 56 73 c 0 19 1475 1301 18 40 5 2097 2042 11 98 7 1911 1368 23 97 36 g 0 54 86 631 84 84 13 31 56 77 16 13 65 554 125 168 275 t 0 1809 552 154 107 2034 2160 45 70 83 2058 2150 167 122 118 1879 1816

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1_rc; m=3/4; ncol2=18; w=-6; offset=-6; strand=R; shift=0; score=0.472864; TTCsATTCCATTCcATT ; cor=; Ncor= a 104 296 63 103 1996 37 30 26 47 2026 29 29 50 153 1930 61 68 c 69 18 1577 1346 14 36 4 2063 2016 15 99 7 1924 1385 22 129 36 g 369 44 63 601 78 74 12 45 54 71 15 11 57 537 126 183 259 t 1643 1827 482 135 97 2038 2139 51 68 73 2042 2138 154 110 107 1812 1822

oligos_7nt_mkv4_m5_rc_shift9 (oligos_7nt_mkv4_m5_rc)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5_rc; m=4/4; ncol2=12; w=0; offset=3; strand=R; shift=9; score=0.416756; ---------atTCGAkT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 174 30 11 5 13 259 7 24 c 0 0 0 0 0 0 0 0 0 22 47 7 254 13 5 10 5 g 0 0 0 0 0 0 0 0 0 44 23 3 7 257 8 194 7 t 0 0 0 0 0 0 0 0 0 46 186 265 20 3 14 75 250

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=11; shift=0; ncol=11; cwcCCTCCCas ; Alignment reference a 122 212 60 15 14 35 22 30 13 252 166 c 267 167 387 615 634 13 627 615 631 145 199 g 148 115 153 18 14 42 21 10 17 124 183 t 141 184 78 30 16 588 8 23 17 157 130

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; cwcCCTCCCas ; cor=; Ncor= a 122 212 60 15 14 35 22 30 13 252 166 c 267 167 387 615 634 13 627 615 631 145 199 g 148 115 153 18 14 42 21 10 17 124 183 t 141 184 78 30 16 588 8 23 17 157 130

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=12; shift=0; ncol=12; wwTAAAATAAww ; Alignment reference a 230 199 107 518 534 569 557 18 543 527 236 236 c 88 90 35 23 12 9 11 12 10 29 86 96 g 91 95 48 27 17 8 10 14 19 18 95 94 t 194 219 413 35 40 17 25 559 31 29 186 177

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwTAAAATAAww ; cor=; Ncor= a 230 199 107 518 534 569 557 18 543 527 236 236 c 88 90 35 23 12 9 11 12 10 29 86 96 g 91 95 48 27 17 8 10 14 19 18 95 94 t 194 219 413 35 40 17 25 559 31 29 186 177

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=13; shift=0; ncol=13; ysACCCCAGGChk ; Alignment reference a 40 54 202 13 12 24 7 201 12 6 6 82 55 c 93 68 18 196 187 199 217 16 9 19 220 63 35 g 49 91 14 23 23 10 12 15 223 209 5 34 79 t 63 32 11 13 23 12 9 13 1 11 14 66 76

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ysACCCCAGGChk ; cor=; Ncor= a 40 54 202 13 12 24 7 201 12 6 6 82 55 c 93 68 18 196 187 199 217 16 9 19 220 63 35 g 49 91 14 23 23 10 12 15 223 209 5 34 79 t 63 32 11 13 23 12 9 13 1 11 14 66 76

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=17; shift=0; ncol=17; GAATsGAATGGAATsrA ; Alignment reference a 191 1816 1879 118 122 167 2150 2058 83 70 45 2160 2034 107 154 552 1809 c 92 275 168 125 554 65 13 16 77 56 31 13 84 84 631 86 54 g 1582 36 97 23 1368 1911 7 98 11 2042 2097 5 40 18 1301 1475 19 t 335 73 56 1934 156 57 30 28 2029 32 27 22 42 1991 114 87 318
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; GAATsGAATGGAATsrA ; cor=; Ncor= a 191 1816 1879 118 122 167 2150 2058 83 70 45 2160 2034 107 154 552 1809 c 92 275 168 125 554 65 13 16 77 56 31 13 84 84 631 86 54 g 1582 36 97 23 1368 1911 7 98 11 2042 2097 5 40 18 1301 1475 19 t 335 73 56 1934 156 57 30 28 2029 32 27 22 42 1991 114 87 318
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/4; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.944088; GAATgGAATGGAATsGA ; cor=; Ncor= a 196 1822 1812 107 110 154 2138 2042 73 68 51 2139 2038 97 135 482 1827 c 88 259 183 126 537 57 11 15 71 54 45 12 74 78 601 63 44 g 1577 36 129 22 1385 1924 7 99 15 2016 2063 4 36 14 1346 1577 18 t 324 68 61 1930 153 50 29 29 2026 47 26 30 37 1996 103 63 296
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5; m=3/4; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.540949; --aTGGAmTCGAat--- ; cor=; Ncor= a 0 0 188 29 18 14 250 75 14 3 20 265 186 46 0 0 0 c 0 0 46 23 18 7 7 194 8 257 7 3 23 44 0 0 0 g 0 0 25 34 233 257 5 10 5 13 254 7 47 22 0 0 0 t 0 0 27 200 17 8 24 7 259 13 5 11 30 174 0 0 0
oligos_7nt_mkv4_m3_rc_shift1 (oligos_7nt_mkv4_m3_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m3_rc; m=4/4; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.501282; -awTCkAATGgw----- ; cor=; Ncor= a 0 299 278 27 49 6 572 531 13 38 133 310 0 0 0 0 0 c 0 114 96 11 522 7 4 31 8 5 63 74 0 0 0 0 0 g 0 55 71 8 17 199 6 12 8 535 260 58 0 0 0 0 0 t 0 128 151 550 8 384 14 22 567 18 140 154 0 0 0 0 0

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=18; shift=0; ncol=18; GAATgGAATGGAATsGAA ; Alignment reference a 196 1822 1812 107 110 154 2138 2042 73 68 51 2139 2038 97 135 482 1827 1643 c 88 259 183 126 537 57 11 15 71 54 45 12 74 78 601 63 44 369 g 1577 36 129 22 1385 1924 7 99 15 2016 2063 4 36 14 1346 1577 18 69 t 324 68 61 1930 153 50 29 29 2026 47 26 30 37 1996 103 63 296 104
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/4; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; GAATgGAATGGAATsGAA ; cor=; Ncor= a 196 1822 1812 107 110 154 2138 2042 73 68 51 2139 2038 97 135 482 1827 1643 c 88 259 183 126 537 57 11 15 71 54 45 12 74 78 601 63 44 369 g 1577 36 129 22 1385 1924 7 99 15 2016 2063 4 36 14 1346 1577 18 69 t 324 68 61 1930 153 50 29 29 2026 47 26 30 37 1996 103 63 296 104
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=2/4; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.944088; GAATsGAATGGAATsrA- ; cor=; Ncor= a 191 1816 1879 118 122 167 2150 2058 83 70 45 2160 2034 107 154 552 1809 0 c 92 275 168 125 554 65 13 16 77 56 31 13 84 84 631 86 54 0 g 1582 36 97 23 1368 1911 7 98 11 2042 2097 5 40 18 1301 1475 19 0 t 335 73 56 1934 156 57 30 28 2029 32 27 22 42 1991 114 87 318 0
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5; m=3/4; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.511893; --aTGGAmTCGAat---- ; cor=; Ncor= a 0 0 188 29 18 14 250 75 14 3 20 265 186 46 0 0 0 0 c 0 0 46 23 18 7 7 194 8 257 7 3 23 44 0 0 0 0 g 0 0 25 34 233 257 5 10 5 13 254 7 47 22 0 0 0 0 t 0 0 27 200 17 8 24 7 259 13 5 11 30 174 0 0 0 0
oligos_7nt_mkv4_m3_rc_shift1 (oligos_7nt_mkv4_m3_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3_rc; m=4/4; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.472864; -awTCkAATGgw------ ; cor=; Ncor= a 0 299 278 27 49 6 572 531 13 38 133 310 0 0 0 0 0 0 c 0 114 96 11 522 7 4 31 8 5 63 74 0 0 0 0 0 0 g 0 55 71 8 17 199 6 12 8 535 260 58 0 0 0 0 0 0 t 0 128 151 550 8 384 14 22 567 18 140 154 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --aTGGAmTCGAat ; Alignment reference a 0 0 188 29 18 14 250 75 14 3 20 265 186 46 c 0 0 46 23 18 7 7 194 8 257 7 3 23 44 g 0 0 25 34 233 257 5 10 5 13 254 7 47 22 t 0 0 27 200 17 8 24 7 259 13 5 11 30 174
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --aTGGAmTCGAat ; cor=; Ncor= a 0 0 188 29 18 14 250 75 14 3 20 265 186 46 c 0 0 46 23 18 7 7 194 8 257 7 3 23 44 g 0 0 25 34 233 257 5 10 5 13 254 7 47 22 t 0 0 27 200 17 8 24 7 259 13 5 11 30 174
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1; m=2/4; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.540949; GAATsGAATGGAAT ; cor=; Ncor= a 191 1816 1879 118 122 167 2150 2058 83 70 45 2160 2034 107 c 92 275 168 125 554 65 13 16 77 56 31 13 84 84 g 1582 36 97 23 1368 1911 7 98 11 2042 2097 5 40 18 t 335 73 56 1934 156 57 30 28 2029 32 27 22 42 1991
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m1; m=3/4; ncol2=18; w=-2; offset=-2; strand=D; shift=0; score=0.511893; GAATgGAATGGAAT ; cor=; Ncor= a 196 1822 1812 107 110 154 2138 2042 73 68 51 2139 2038 97 c 88 259 183 126 537 57 11 15 71 54 45 12 74 78 g 1577 36 129 22 1385 1924 7 99 15 2016 2063 4 36 14 t 324 68 61 1930 153 50 29 29 2026 47 26 30 37 1996
oligos_7nt_mkv4_m3_rc_shift6 (oligos_7nt_mkv4_m3_rc)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m3_rc; m=4/4; ncol2=11; w=0; offset=4; strand=R; shift=6; score=0.416756; ------awTCkAAT ; cor=; Ncor= a 0 0 0 0 0 0 299 278 27 49 6 572 531 13 c 0 0 0 0 0 0 114 96 11 522 7 4 31 8 g 0 0 0 0 0 0 55 71 8 17 199 6 12 8 t 0 0 0 0 0 0 128 151 550 8 384 14 22 567

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=6; ncol=17; ------wcCATTmGAwt ; Alignment reference a 0 0 0 0 0 0 154 140 18 567 22 14 384 8 550 151 128 c 0 0 0 0 0 0 58 260 535 8 12 6 199 17 8 71 55 g 0 0 0 0 0 0 74 63 5 8 31 4 7 522 11 96 114 t 0 0 0 0 0 0 310 133 38 13 531 572 6 49 27 278 299
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=6; score= 1; ------wcCATTmGAwt ; cor=; Ncor= a 0 0 0 0 0 0 154 140 18 567 22 14 384 8 550 151 128 c 0 0 0 0 0 0 58 260 535 8 12 6 199 17 8 71 55 g 0 0 0 0 0 0 74 63 5 8 31 4 7 522 11 96 114 t 0 0 0 0 0 0 310 133 38 13 531 572 6 49 27 278 299
oligos_6nt_mkv3_m1_rc_shift1 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m1_rc; m=2/4; ncol2=17; w=-5; offset=-5; strand=R; shift=1; score=0.501282; -TysATTCCATTCsATT ; cor=; Ncor= a 0 318 87 114 1991 42 22 27 32 2029 28 30 57 156 1934 56 73 c 0 19 1475 1301 18 40 5 2097 2042 11 98 7 1911 1368 23 97 36 g 0 54 86 631 84 84 13 31 56 77 16 13 65 554 125 168 275 t 0 1809 552 154 107 2034 2160 45 70 83 2058 2150 167 122 118 1879 1816
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1_rc; m=3/4; ncol2=18; w=-6; offset=-6; strand=R; shift=0; score=0.472864; TTCsATTCCATTCcATT ; cor=; Ncor= a 104 296 63 103 1996 37 30 26 47 2026 29 29 50 153 1930 61 68 c 69 18 1577 1346 14 36 4 2063 2016 15 99 7 1924 1385 22 129 36 g 369 44 63 601 78 74 12 45 54 71 15 11 57 537 126 183 259 t 1643 1827 482 135 97 2038 2139 51 68 73 2042 2138 154 110 107 1812 1822
oligos_7nt_mkv4_m5_rc_shift9 (oligos_7nt_mkv4_m5_rc)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5_rc; m=4/4; ncol2=12; w=0; offset=3; strand=R; shift=9; score=0.416756; ---------atTCGAkT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 174 30 11 5 13 259 7 24 c 0 0 0 0 0 0 0 0 0 22 47 7 254 13 5 10 5 g 0 0 0 0 0 0 0 0 0 44 23 3 7 257 8 194 7 t 0 0 0 0 0 0 0 0 0 46 186 265 20 3 14 75 250