One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/12/19/peak-motifs.2025-12-19.083021_2025-12-19.083021_rq17AB/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/2025/12/19/peak-motifs.2025-12-19.083021_2025-12-19.083021_rq17AB/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=13; shift=3; ncol=16; ---sssGCGGCGGCss ; Alignment reference a 0 0 0 18 33 26 5 9 10 2 10 6 7 3 34 14 c 0 0 0 68 79 52 22 174 19 19 160 20 10 172 57 61 g 0 0 0 100 65 108 170 15 172 176 24 167 179 25 84 99 t 0 0 0 17 26 17 6 5 2 6 9 10 7 3 28 29

oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---sssGCGGCGGCss ; cor=; Ncor= a 0 0 0 18 33 26 5 9 10 2 10 6 7 3 34 14 c 0 0 0 68 79 52 22 174 19 19 160 20 10 172 57 61 g 0 0 0 100 65 108 170 15 172 176 24 167 179 25 84 99 t 0 0 0 17 26 17 6 5 2 6 9 10 7 3 28 29

oligos_6nt_mkv2_m3_rc_shift4 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3_rc; m=2/3; ncol2=17; w=0; offset=1; strand=R; shift=4; score=0.540196; ----ssGsGGCGGGGc ; cor=; Ncor= a 0 0 0 0 25 32 11 12 6 10 10 8 13 7 15 17 c 0 0 0 0 64 66 20 100 20 14 153 19 21 31 24 118 g 0 0 0 0 73 69 140 55 148 150 12 144 137 138 135 27 t 0 0 0 0 17 12 8 12 5 5 4 8 8 3 5 17

oligos_6nt_mkv2_m4_rc_shift0 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4_rc; m=3/3; ncol2=21; w=-3; offset=-3; strand=R; shift=0; score=0.466794; sssGGCGgGGCGGsGc ; cor=; Ncor= a 21 20 10 3 8 8 8 11 8 9 9 6 12 7 7 8 c 56 40 82 21 23 101 16 29 20 22 102 26 19 79 29 94 g 50 69 42 111 107 29 117 95 109 104 25 102 104 49 99 32 t 15 13 8 7 4 4 1 7 5 7 6 8 7 7 7 8

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=21; shift=0; ncol=21; ssccCgCsCCGCCcCGCCsss ; Alignment reference a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 7 8 13 15 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 111 42 69 50 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 21 82 40 56 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8 3 10 20 21

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/5; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; ssccCgCsCCGCCcCGCCsss ; cor=; Ncor= a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 7 8 13 15 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 111 42 69 50 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 21 82 40 56 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8 3 10 20 21

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=2/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.708657; sssCcgCCCCGCCsCss---- ; cor=; Ncor= a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 0 0 0 0 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 0 0 0 0 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 0 0 0 0 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25 0 0 0 0

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=3/5; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.620269; ---ssGCCCCGCCCCgss--- ; cor=; Ncor= a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 0 0 0 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 0 0 0 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 0 0 0 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21 0 0 0

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=4/5; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.568818; ----ssCCCCGCCCCgss--- ; cor=; Ncor= a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 29 0 0 0 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 115 0 0 0 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 72 0 0 0 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36 28 0 0 0

oligos_7nt_mkv2_m4_rc_shift5 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4_rc; m=5/5; ncol2=13; w=0; offset=5; strand=R; shift=5; score=0.466794; -----ssGCCGCCGCsss--- ; cor=; Ncor= a 0 0 0 0 0 29 28 3 7 10 9 6 2 5 6 17 26 17 0 0 0 c 0 0 0 0 0 99 84 25 179 167 24 176 172 15 170 108 65 100 0 0 0 g 0 0 0 0 0 61 57 172 10 20 160 19 19 174 22 52 79 68 0 0 0 t 0 0 0 0 0 14 34 3 7 6 10 2 10 9 5 26 33 18 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=15; shift=3; ncol=18; ---ssGCCCCGCCCCgss ; Alignment reference a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=3; score= 1; ---ssGCCCCGCCCCgss ; cor=; Ncor= a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=2/5; ncol2=14; w=0; offset=1; strand=D; shift=4; score=0.915863; ----ssCCCCGCCCCgss ; cor=; Ncor= a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 29 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 115 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 72 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36 28

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/5; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.703729; sssCcgCCCCGCCsCss- ; cor=; Ncor= a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 0 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 0 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 0 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25 0

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=4/5; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.620269; ssccCgCsCCGCCcCGCC ; cor=; Ncor= a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 7 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 111 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 21 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8 3

oligos_7nt_mkv2_m5_shift7 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.513897; -------ssCGCCCGCss ; cor=; Ncor= a 0 0 0 0 0 0 0 30 29 4 4 3 6 8 17 1 34 31 c 0 0 0 0 0 0 0 92 91 201 18 199 198 192 21 209 83 94 g 0 0 0 0 0 0 0 61 76 9 190 15 16 12 176 11 67 70 t 0 0 0 0 0 0 0 41 28 10 12 7 4 12 10 3 40 29

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift4 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=14; shift=4; ncol=18; ----ssCCCCGCCCCgss ; Alignment reference a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 29 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 115 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 72 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36 28

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCCCCGCCCCgss ; cor=; Ncor= a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 29 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 115 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 72 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36 28

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/5; ncol2=15; w=-1; offset=-1; strand=D; shift=3; score=0.915863; ---ssGCCCCGCCCCgss ; cor=; Ncor= a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/5; ncol2=17; w=-4; offset=-4; strand=D; shift=0; score=0.65133; sssCcgCCCCGCCsCss- ; cor=; Ncor= a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 0 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 0 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 0 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25 0

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=4/5; ncol2=21; w=-4; offset=-4; strand=D; shift=0; score=0.568818; ssccCgCsCCGCCcCGCC ; cor=; Ncor= a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 7 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 111 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 21 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8 3

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.494809; ---ssCGCCCGCss---- ; cor=; Ncor= a 0 0 0 30 29 4 4 3 6 8 17 1 34 31 0 0 0 0 c 0 0 0 92 91 201 18 199 198 192 21 209 83 94 0 0 0 0 g 0 0 0 61 76 9 190 15 16 12 176 11 67 70 0 0 0 0 t 0 0 0 41 28 10 12 7 4 12 10 3 40 29 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; sssCcgCCCCGCCsCss ; Alignment reference a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; sssCcgCCCCGCCsCss ; cor=; Ncor= a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=2/5; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.708657; ssccCgCsCCGCCcCGC ; cor=; Ncor= a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=3/5; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.703729; ---ssGCCCCGCCCCgs ; cor=; Ncor= a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=4/5; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.65133; ----ssCCCCGCCCCgs ; cor=; Ncor= a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36

oligos_7nt_mkv2_m4_rc_shift5 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=5/5; ncol2=13; w=0; offset=5; strand=R; shift=5; score=0.540196; -----ssGCCGCCGCss ; cor=; Ncor= a 0 0 0 0 0 29 28 3 7 10 9 6 2 5 6 17 26 c 0 0 0 0 0 99 84 25 179 167 24 176 172 15 170 108 65 g 0 0 0 0 0 61 57 172 10 20 160 19 19 174 22 52 79 t 0 0 0 0 0 14 34 3 7 6 10 2 10 9 5 26 33

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; twttATTATTAww ; Alignment reference a 30 62 23 27 142 11 5 133 10 10 132 42 51 c 34 26 20 22 4 9 6 7 5 7 4 33 32 g 31 28 11 14 6 1 4 6 9 3 14 23 22 t 67 46 108 99 10 141 147 16 138 142 12 64 57

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; twttATTATTAww ; cor=; Ncor= a 30 62 23 27 142 11 5 133 10 10 132 42 51 c 34 26 20 22 4 9 6 7 5 7 4 33 32 g 31 28 11 14 6 1 4 6 9 3 14 23 22 t 67 46 108 99 10 141 147 16 138 142 12 64 57

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift4 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----ssCGCCCGCss ; Alignment reference a 0 0 0 0 30 29 4 4 3 6 8 17 1 34 31 c 0 0 0 0 92 91 201 18 199 198 192 21 209 83 94 g 0 0 0 0 61 76 9 190 15 16 12 176 11 67 70 t 0 0 0 0 41 28 10 12 7 4 12 10 3 40 29

oligos_7nt_mkv2_m5_shift4 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCGCCCGCss ; cor=; Ncor= a 0 0 0 0 30 29 4 4 3 6 8 17 1 34 31 c 0 0 0 0 92 91 201 18 199 198 192 21 209 83 94 g 0 0 0 0 61 76 9 190 15 16 12 176 11 67 70 t 0 0 0 0 41 28 10 12 7 4 12 10 3 40 29

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.513897; ssGCCCCGCCCCgss ; cor=; Ncor= a 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 c 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 g 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 t 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21

oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=14; w=0; offset=1; strand=D; shift=5; score=0.494809; -----ssCCCCGCCC ; cor=; Ncor= a 0 0 0 0 0 41 33 7 11 8 14 11 7 4 12 c 0 0 0 0 0 82 81 179 211 205 192 11 211 214 188 g 0 0 0 0 0 88 93 40 15 21 24 208 18 21 25 t 0 0 0 0 0 33 37 18 7 10 14 14 8 5 19

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ysCCTTCCtbs ; Alignment reference a 43 35 4 7 2 4 4 2 42 29 44 c 50 52 179 179 0 1 187 182 34 48 50 g 40 58 3 5 15 3 0 7 6 65 62 t 59 47 6 1 175 184 1 1 110 50 36

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ysCCTTCCtbs ; cor=; Ncor= a 43 35 4 7 2 4 4 2 42 29 44 c 50 52 179 179 0 1 187 182 34 48 50 g 40 58 3 5 15 3 0 7 6 65 62 t 59 47 6 1 175 184 1 1 110 50 36

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=18; shift=0; ncol=18; msctkcCAGGACCTGgsr ; Alignment reference a 59 30 23 31 17 18 9 181 4 4 136 5 3 3 7 45 35 70 c 59 56 112 34 24 129 173 2 3 2 10 181 179 17 6 26 70 39 g 47 62 39 22 106 21 6 9 189 184 14 3 3 6 142 109 55 49 t 31 48 22 109 49 28 8 4 0 6 36 7 11 170 41 16 36 38

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/2; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; msctkcCAGGACCTGgsr ; cor=; Ncor= a 59 30 23 31 17 18 9 181 4 4 136 5 3 3 7 45 35 70 c 59 56 112 34 24 129 173 2 3 2 10 181 179 17 6 26 70 39 g 47 62 39 22 106 21 6 9 189 184 14 3 3 6 142 109 55 49 t 31 48 22 109 49 28 8 4 0 6 36 7 11 170 41 16 36 38

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/2; ncol2=17; w=0; offset=2; strand=D; shift=2; score=0.818496; --syscCAGGACCTGggr ; cor=; Ncor= a 0 0 19 21 14 13 6 126 0 2 115 3 2 5 3 21 12 48 c 0 0 60 38 50 91 129 4 5 2 6 132 129 13 10 17 35 26 g 0 0 38 25 47 11 5 5 136 134 5 5 3 8 104 90 77 43 t 0 0 25 58 31 27 2 7 1 4 16 2 8 116 25 14 18 25

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=17; shift=2; ncol=19; --syscCAGGACCTGggrs ; Alignment reference a 0 0 19 21 14 13 6 126 0 2 115 3 2 5 3 21 12 48 23 c 0 0 60 38 50 91 129 4 5 2 6 132 129 13 10 17 35 26 45 g 0 0 38 25 47 11 5 5 136 134 5 5 3 8 104 90 77 43 50 t 0 0 25 58 31 27 2 7 1 4 16 2 8 116 25 14 18 25 24

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/2; ncol2=17; w=0; offset=0; strand=D; shift=2; score= 1; --syscCAGGACCTGggrs ; cor=; Ncor= a 0 0 19 21 14 13 6 126 0 2 115 3 2 5 3 21 12 48 23 c 0 0 60 38 50 91 129 4 5 2 6 132 129 13 10 17 35 26 45 g 0 0 38 25 47 11 5 5 136 134 5 5 3 8 104 90 77 43 50 t 0 0 25 58 31 27 2 7 1 4 16 2 8 116 25 14 18 25 24

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/2; ncol2=18; w=-2; offset=-2; strand=D; shift=0; score=0.818496; msctkcCAGGACCTGgsr- ; cor=; Ncor= a 59 30 23 31 17 18 9 181 4 4 136 5 3 3 7 45 35 70 0 c 59 56 112 34 24 129 173 2 3 2 10 181 179 17 6 26 70 39 0 g 47 62 39 22 106 21 6 9 189 184 14 3 3 6 142 109 55 49 0 t 31 48 22 109 49 28 8 4 0 6 36 7 11 170 41 16 36 38 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=13; shift=3; ncol=16; ---sssGCGGCGGCss ; Alignment reference a 0 0 0 18 33 26 5 9 10 2 10 6 7 3 34 14 c 0 0 0 68 79 52 22 174 19 19 160 20 10 172 57 61 g 0 0 0 100 65 108 170 15 172 176 24 167 179 25 84 99 t 0 0 0 17 26 17 6 5 2 6 9 10 7 3 28 29
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---sssGCGGCGGCss ; cor=; Ncor= a 0 0 0 18 33 26 5 9 10 2 10 6 7 3 34 14 c 0 0 0 68 79 52 22 174 19 19 160 20 10 172 57 61 g 0 0 0 100 65 108 170 15 172 176 24 167 179 25 84 99 t 0 0 0 17 26 17 6 5 2 6 9 10 7 3 28 29
oligos_6nt_mkv2_m3_rc_shift4 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3_rc; m=2/3; ncol2=17; w=0; offset=1; strand=R; shift=4; score=0.540196; ----ssGsGGCGGGGc ; cor=; Ncor= a 0 0 0 0 25 32 11 12 6 10 10 8 13 7 15 17 c 0 0 0 0 64 66 20 100 20 14 153 19 21 31 24 118 g 0 0 0 0 73 69 140 55 148 150 12 144 137 138 135 27 t 0 0 0 0 17 12 8 12 5 5 4 8 8 3 5 17
oligos_6nt_mkv2_m4_rc_shift0 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4_rc; m=3/3; ncol2=21; w=-3; offset=-3; strand=R; shift=0; score=0.466794; sssGGCGgGGCGGsGc ; cor=; Ncor= a 21 20 10 3 8 8 8 11 8 9 9 6 12 7 7 8 c 56 40 82 21 23 101 16 29 20 22 102 26 19 79 29 94 g 50 69 42 111 107 29 117 95 109 104 25 102 104 49 99 32 t 15 13 8 7 4 4 1 7 5 7 6 8 7 7 7 8

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=21; shift=0; ncol=21; ssccCgCsCCGCCcCGCCsss ; Alignment reference a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 7 8 13 15 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 111 42 69 50 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 21 82 40 56 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8 3 10 20 21
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/5; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; ssccCgCsCCGCCcCGCCsss ; cor=; Ncor= a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 7 8 13 15 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 111 42 69 50 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 21 82 40 56 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8 3 10 20 21
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=2/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.708657; sssCcgCCCCGCCsCss---- ; cor=; Ncor= a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 0 0 0 0 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 0 0 0 0 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 0 0 0 0 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25 0 0 0 0
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=3/5; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.620269; ---ssGCCCCGCCCCgss--- ; cor=; Ncor= a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 0 0 0 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 0 0 0 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 0 0 0 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21 0 0 0
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=4/5; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.568818; ----ssCCCCGCCCCgss--- ; cor=; Ncor= a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 29 0 0 0 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 115 0 0 0 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 72 0 0 0 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36 28 0 0 0
oligos_7nt_mkv2_m4_rc_shift5 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4_rc; m=5/5; ncol2=13; w=0; offset=5; strand=R; shift=5; score=0.466794; -----ssGCCGCCGCsss--- ; cor=; Ncor= a 0 0 0 0 0 29 28 3 7 10 9 6 2 5 6 17 26 17 0 0 0 c 0 0 0 0 0 99 84 25 179 167 24 176 172 15 170 108 65 100 0 0 0 g 0 0 0 0 0 61 57 172 10 20 160 19 19 174 22 52 79 68 0 0 0 t 0 0 0 0 0 14 34 3 7 6 10 2 10 9 5 26 33 18 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=15; shift=3; ncol=18; ---ssGCCCCGCCCCgss ; Alignment reference a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=3; score= 1; ---ssGCCCCGCCCCgss ; cor=; Ncor= a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=2/5; ncol2=14; w=0; offset=1; strand=D; shift=4; score=0.915863; ----ssCCCCGCCCCgss ; cor=; Ncor= a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 29 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 115 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 72 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36 28
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/5; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.703729; sssCcgCCCCGCCsCss- ; cor=; Ncor= a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 0 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 0 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 0 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25 0
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=4/5; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.620269; ssccCgCsCCGCCcCGCC ; cor=; Ncor= a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 7 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 111 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 21 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8 3
oligos_7nt_mkv2_m5_shift7 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=11; w=0; offset=4; strand=D; shift=7; score=0.513897; -------ssCGCCCGCss ; cor=; Ncor= a 0 0 0 0 0 0 0 30 29 4 4 3 6 8 17 1 34 31 c 0 0 0 0 0 0 0 92 91 201 18 199 198 192 21 209 83 94 g 0 0 0 0 0 0 0 61 76 9 190 15 16 12 176 11 67 70 t 0 0 0 0 0 0 0 41 28 10 12 7 4 12 10 3 40 29

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=14; shift=4; ncol=18; ----ssCCCCGCCCCgss ; Alignment reference a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 29 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 115 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 72 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36 28
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCCCCGCCCCgss ; cor=; Ncor= a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 29 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 115 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 72 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36 28
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/5; ncol2=15; w=-1; offset=-1; strand=D; shift=3; score=0.915863; ---ssGCCCCGCCCCgss ; cor=; Ncor= a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/5; ncol2=17; w=-4; offset=-4; strand=D; shift=0; score=0.65133; sssCcgCCCCGCCsCss- ; cor=; Ncor= a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 0 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 0 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 0 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25 0
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=4/5; ncol2=21; w=-4; offset=-4; strand=D; shift=0; score=0.568818; ssccCgCsCCGCCcCGCC ; cor=; Ncor= a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 7 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 111 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 21 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8 3
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.494809; ---ssCGCCCGCss---- ; cor=; Ncor= a 0 0 0 30 29 4 4 3 6 8 17 1 34 31 0 0 0 0 c 0 0 0 92 91 201 18 199 198 192 21 209 83 94 0 0 0 0 g 0 0 0 61 76 9 190 15 16 12 176 11 67 70 0 0 0 0 t 0 0 0 41 28 10 12 7 4 12 10 3 40 29 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; sssCcgCCCCGCCsCss ; Alignment reference a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; sssCcgCCCCGCCsCss ; cor=; Ncor= a 24 23 19 8 14 17 5 3 8 8 4 5 5 12 8 12 17 c 72 71 71 135 119 27 135 138 137 144 12 150 148 55 140 69 73 g 57 60 79 21 34 118 24 31 21 19 153 14 20 100 20 66 64 t 26 25 10 15 12 17 15 7 13 8 10 10 6 12 11 32 25
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=2/5; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.708657; ssccCgCsCCGCCcCGC ; cor=; Ncor= a 17 8 18 11 9 8 7 7 7 8 6 7 5 7 1 4 4 c 51 65 81 96 105 32 99 49 104 102 25 104 109 95 117 29 107 g 56 53 30 27 16 94 29 79 19 26 102 22 20 29 16 101 23 t 18 16 13 8 12 8 7 7 12 6 9 9 8 11 8 8 8
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=3/5; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.703729; ---ssGCCCCGCCCCgs ; cor=; Ncor= a 0 0 0 36 27 19 5 9 9 9 4 5 5 7 6 15 31 c 0 0 0 92 73 31 169 171 163 165 13 171 173 168 172 51 80 g 0 0 0 56 80 142 25 20 27 21 183 22 26 21 17 125 72 t 0 0 0 23 27 15 8 7 8 12 7 9 3 11 12 16 24
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=4/5; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.65133; ----ssCCCCGCCCCgs ; cor=; Ncor= a 0 0 0 0 41 33 7 11 8 14 11 7 4 12 9 16 32 c 0 0 0 0 82 81 179 211 205 192 11 211 214 188 210 58 99 g 0 0 0 0 88 93 40 15 21 24 208 18 21 25 17 152 77 t 0 0 0 0 33 37 18 7 10 14 14 8 5 19 8 18 36
oligos_7nt_mkv2_m4_rc_shift5 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=5/5; ncol2=13; w=0; offset=5; strand=R; shift=5; score=0.540196; -----ssGCCGCCGCss ; cor=; Ncor= a 0 0 0 0 0 29 28 3 7 10 9 6 2 5 6 17 26 c 0 0 0 0 0 99 84 25 179 167 24 176 172 15 170 108 65 g 0 0 0 0 0 61 57 172 10 20 160 19 19 174 22 52 79 t 0 0 0 0 0 14 34 3 7 6 10 2 10 9 5 26 33

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift4 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----ssCGCCCGCss ; Alignment reference a 0 0 0 0 30 29 4 4 3 6 8 17 1 34 31 c 0 0 0 0 92 91 201 18 199 198 192 21 209 83 94 g 0 0 0 0 61 76 9 190 15 16 12 176 11 67 70 t 0 0 0 0 41 28 10 12 7 4 12 10 3 40 29
oligos_7nt_mkv2_m5_shift4 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCGCCCGCss ; cor=; Ncor= a 0 0 0 0 30 29 4 4 3 6 8 17 1 34 31 c 0 0 0 0 92 91 201 18 199 198 192 21 209 83 94 g 0 0 0 0 61 76 9 190 15 16 12 176 11 67 70 t 0 0 0 0 41 28 10 12 7 4 12 10 3 40 29
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.513897; ssGCCCCGCCCCgss ; cor=; Ncor= a 36 27 19 5 9 9 9 4 5 5 7 6 15 31 20 c 92 73 31 169 171 163 165 13 171 173 168 172 51 80 98 g 56 80 142 25 20 27 21 183 22 26 21 17 125 72 68 t 23 27 15 8 7 8 12 7 9 3 11 12 16 24 21
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=14; w=0; offset=1; strand=D; shift=5; score=0.494809; -----ssCCCCGCCC ; cor=; Ncor= a 0 0 0 0 0 41 33 7 11 8 14 11 7 4 12 c 0 0 0 0 0 82 81 179 211 205 192 11 211 214 188 g 0 0 0 0 0 88 93 40 15 21 24 208 18 21 25 t 0 0 0 0 0 33 37 18 7 10 14 14 8 5 19