One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/07/28/peak-motifs.2026-07-28.110936_2026-07-28.110936_IaTuP0/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/2026/07/28/peak-motifs.2026-07-28.110936_2026-07-28.110936_IaTuP0/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --ssgGCCCGGCss ; Alignment reference a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 c 0 0 90 104 35 7 218 201 225 15 4 223 77 87 g 0 0 88 84 157 209 9 23 7 216 224 6 88 92 t 0 0 26 18 16 7 3 4 1 1 3 1 39 25

oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ssgGCCCGGCss ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 c 0 0 90 104 35 7 218 201 225 15 4 223 77 87 g 0 0 88 84 157 209 9 23 7 216 224 6 88 92 t 0 0 26 18 16 7 3 4 1 1 3 1 39 25

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.659071; --smGGCCmCGCCc ; cor=; Ncor= a 0 0 30 66 17 5 6 1 117 1 4 3 3 14 c 0 0 103 60 6 4 209 213 84 210 5 212 191 138 g 0 0 57 41 191 208 3 4 7 8 207 0 19 34 t 0 0 29 52 5 2 1 1 11 0 3 4 6 33

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=3/4; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.560825; --cmgGCCCCGCCC ; cor=; Ncor= a 0 0 47 122 72 23 5 7 31 5 13 4 4 7 c 0 0 230 130 79 39 412 400 390 415 3 415 415 379 g 0 0 91 97 273 357 10 8 14 19 415 12 12 24 t 0 0 74 93 18 23 15 27 7 3 11 11 11 32

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5; m=4/4; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.450461; ssCAGGCCCcg--- ; cor=; Ncor= a 11 27 0 141 0 2 0 3 1 22 21 0 0 0 c 74 50 139 0 17 1 141 122 135 61 27 0 0 0 g 38 44 0 0 124 138 0 16 5 32 72 0 0 0 t 18 20 2 0 0 0 0 0 0 26 21 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=5; ncol=15; -----ssCGAGGCss ; Alignment reference a 0 0 0 0 0 16 12 0 0 167 0 0 0 17 22 c 0 0 0 0 0 58 68 167 0 0 4 0 167 63 62 g 0 0 0 0 0 73 64 0 167 0 163 167 0 56 64 t 0 0 0 0 0 20 23 0 0 0 0 0 0 31 19

oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCGAGGCss ; cor=; Ncor= a 0 0 0 0 0 16 12 0 0 167 0 0 0 17 22 c 0 0 0 0 0 58 68 167 0 0 4 0 167 63 62 g 0 0 0 0 0 73 64 0 167 0 163 167 0 56 64 t 0 0 0 0 0 20 23 0 0 0 0 0 0 31 19

oligos_7nt_mkv4_m2_rc_shift3 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=13; w=-2; offset=-2; strand=R; shift=3; score=0.569779; ---ggGGCGkGGCCk ; cor=; Ncor= a 0 0 0 39 33 6 4 3 0 11 1 1 2 5 52 c 0 0 0 21 34 19 0 207 8 7 4 3 208 191 41 g 0 0 0 126 138 191 212 5 210 84 213 209 4 6 60 t 0 0 0 33 14 3 3 4 1 117 1 6 5 17 66

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=3/3; ncol2=16; w=-5; offset=-5; strand=R; shift=0; score=0.441491; ssGGGGGCGGGGCck ; cor=; Ncor= a 57 103 52 29 32 11 11 11 3 7 27 15 23 18 93 c 158 113 58 15 24 12 12 415 19 14 8 10 357 273 97 g 164 149 309 362 379 415 415 3 415 390 400 412 39 79 130 t 63 77 23 36 7 4 4 13 5 31 7 5 23 72 122

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=12; shift=0; ncol=12; srGCCAATCass ; Alignment reference a 23 42 20 4 6 152 147 4 6 79 30 30 c 58 36 14 153 153 7 9 10 138 25 48 57 g 42 61 118 4 1 2 4 3 14 37 59 48 t 40 24 11 2 3 2 3 146 5 22 26 28

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; srGCCAATCass ; cor=; Ncor= a 23 42 20 4 6 152 147 4 6 79 30 30 c 58 36 14 153 153 7 9 10 138 25 48 57 g 42 61 118 4 1 2 4 3 14 37 59 48 t 40 24 11 2 3 2 3 146 5 22 26 28

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=14; shift=3; ncol=17; ---scCCCGCCCCGCsc ; Alignment reference a 0 0 0 29 14 1 5 15 5 3 4 1 3 8 12 24 27 c 0 0 0 88 148 230 220 215 2 234 229 241 235 10 218 122 133 g 0 0 0 102 46 12 17 13 230 7 14 5 5 200 11 70 55 t 0 0 0 30 41 6 7 6 12 5 2 2 6 31 8 33 34

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---scCCCGCCCCGCsc ; cor=; Ncor= a 0 0 0 29 14 1 5 15 5 3 4 1 3 8 12 24 27 c 0 0 0 88 148 230 220 215 2 234 229 241 235 10 218 122 133 g 0 0 0 102 46 12 17 13 230 7 14 5 5 200 11 70 55 t 0 0 0 30 41 6 7 6 12 5 2 2 6 31 8 33 34

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/4; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.653224; cmgGCCCCGCCCCCss- ; cor=; Ncor= a 47 122 72 23 5 7 31 5 13 4 4 7 36 23 77 63 0 c 230 130 79 39 412 400 390 415 3 415 415 379 362 309 149 164 0 g 91 97 273 357 10 8 14 19 415 12 12 24 15 58 113 158 0 t 74 93 18 23 15 27 7 3 11 11 11 32 29 52 103 57 0

oligos_7nt_mkv4_m2_shift5 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/4; ncol2=13; w=0; offset=2; strand=D; shift=5; score=0.587444; -----smGGCCmCGCCc ; cor=; Ncor= a 0 0 0 0 0 30 66 17 5 6 1 117 1 4 3 3 14 c 0 0 0 0 0 103 60 6 4 209 213 84 210 5 212 191 138 g 0 0 0 0 0 57 41 191 208 3 4 7 8 207 0 19 34 t 0 0 0 0 0 29 52 5 2 1 1 11 0 3 4 6 33

oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=10; w=0; offset=4; strand=D; shift=7; score=0.551722; -------ssCCCCTCcs ; cor=; Ncor= a 0 0 0 0 0 0 0 38 34 0 0 0 0 0 0 42 34 c 0 0 0 0 0 0 0 139 99 320 320 320 320 0 320 171 158 g 0 0 0 0 0 0 0 100 117 0 0 0 0 0 0 46 85 t 0 0 0 0 0 0 0 43 70 0 0 0 0 320 0 61 43

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 4 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; ssCAGGCCCcg ; Alignment reference a 11 27 0 141 0 2 0 3 1 22 21 c 74 50 139 0 17 1 141 122 135 61 27 g 38 44 0 0 124 138 0 16 5 32 72 t 18 20 2 0 0 0 0 0 0 26 21

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCAGGCCCcg ; cor=; Ncor= a 11 27 0 141 0 2 0 3 1 22 21 c 74 50 139 0 17 1 141 122 135 61 27 g 38 44 0 0 124 138 0 16 5 32 72 t 18 20 2 0 0 0 0 0 0 26 21

oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.450461; --ssgGCCCGG ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 c 0 0 90 104 35 7 218 201 225 15 4 g 0 0 88 84 157 209 9 23 7 216 224 t 0 0 26 18 16 7 3 4 1 1 3

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.446646; --smGGCCmCG ; cor=; Ncor= a 0 0 30 66 17 5 6 1 117 1 4 c 0 0 103 60 6 4 209 213 84 210 5 g 0 0 57 41 191 208 3 4 7 8 207 t 0 0 29 52 5 2 1 1 11 0 3

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 2 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=10; shift=0; ncol=10; ybACGkCAbs ; Alignment reference a 12 9 60 0 0 3 0 59 8 11 c 21 15 0 60 3 1 51 0 21 18 g 11 21 0 0 56 38 2 1 15 20 t 16 15 0 0 1 18 7 0 16 11

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ybACGkCAbs ; cor=; Ncor= a 12 9 60 0 0 3 0 59 8 11 c 21 15 0 60 3 1 51 0 21 18 g 11 21 0 0 56 38 2 1 15 20 t 16 15 0 0 1 18 7 0 16 11

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift5 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift5 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=5; ncol=16; -----ssCGGAGCCss ; Alignment reference a 0 0 0 0 0 17 24 0 0 1 151 5 10 3 16 29 c 0 0 0 0 0 47 41 153 4 7 2 5 133 131 48 40 g 0 0 0 0 0 61 72 0 149 136 0 140 2 19 67 62 t 0 0 0 0 0 28 16 0 0 9 0 3 8 0 22 22

oligos_7nt_mkv4_m4_shift5 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCGGAGCCss ; cor=; Ncor= a 0 0 0 0 0 17 24 0 0 1 151 5 10 3 16 29 c 0 0 0 0 0 47 41 153 4 7 2 5 133 131 48 40 g 0 0 0 0 0 61 72 0 149 136 0 140 2 19 67 62 t 0 0 0 0 0 28 16 0 0 9 0 3 8 0 22 22

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=2/2; ncol2=16; w=-5; offset=-5; strand=R; shift=0; score=0.502753; ssGGGGGCGGGGCckg ; cor=; Ncor= a 57 103 52 29 32 11 11 11 3 7 27 15 23 18 93 74 c 158 113 58 15 24 12 12 415 19 14 8 10 357 273 97 91 g 164 149 309 362 379 415 415 3 415 390 400 412 39 79 130 230 t 63 77 23 36 7 4 4 13 5 31 7 5 23 72 122 47

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; vsCGAGCGass ; Alignment reference a 47 25 5 2 160 4 3 1 97 23 31 c 58 60 155 6 11 5 171 4 38 57 63 g 53 75 13 169 6 168 3 174 33 74 57 t 21 19 6 2 2 2 2 0 11 25 28

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; vsCGAGCGass ; cor=; Ncor= a 47 25 5 2 160 4 3 1 97 23 31 c 58 60 155 6 11 5 171 4 38 57 63 g 53 75 13 169 6 168 3 174 33 74 57 t 21 19 6 2 2 2 2 0 11 25 28

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 8 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=16; shift=0; ncol=16; cmgGCCCCGCCCCCss ; Alignment reference a 47 122 72 23 5 7 31 5 13 4 4 7 36 23 77 63 c 230 130 79 39 412 400 390 415 3 415 415 379 362 309 149 164 g 91 97 273 357 10 8 14 19 415 12 12 24 15 58 113 158 t 74 93 18 23 15 27 7 3 11 11 11 32 29 52 103 57

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cmgGCCCCGCCCCCss ; cor=; Ncor= a 47 122 72 23 5 7 31 5 13 4 4 7 36 23 77 63 c 230 130 79 39 412 400 390 415 3 415 415 379 362 309 149 164 g 91 97 273 357 10 8 14 19 415 12 12 24 15 58 113 158 t 74 93 18 23 15 27 7 3 11 11 11 32 29 52 103 57

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=2/7; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.758555; smGGCCmCGCCcc--- ; cor=; Ncor= a 30 66 17 5 6 1 117 1 4 3 3 14 33 0 0 0 c 103 60 6 4 209 213 84 210 5 212 191 138 126 0 0 0 g 57 41 191 208 3 4 7 8 207 0 19 34 21 0 0 0 t 29 52 5 2 1 1 11 0 3 4 6 33 39 0 0 0

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/7; ncol2=14; w=0; offset=3; strand=D; shift=3; score=0.653224; ---scCCCGCCCCGCs ; cor=; Ncor= a 0 0 0 29 14 1 5 15 5 3 4 1 3 8 12 24 c 0 0 0 88 148 230 220 215 2 234 229 241 235 10 218 122 g 0 0 0 102 46 12 17 13 230 7 14 5 5 200 11 70 t 0 0 0 30 41 6 7 6 12 5 2 2 6 31 8 33

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=4/7; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.560825; ssgGCCCGGCss---- ; cor=; Ncor= a 29 27 25 10 3 5 0 1 2 3 29 29 0 0 0 0 c 90 104 35 7 218 201 225 15 4 223 77 87 0 0 0 0 g 88 84 157 209 9 23 7 216 224 6 88 92 0 0 0 0 t 26 18 16 7 3 4 1 1 3 1 39 25 0 0 0 0

oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=5/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.502753; ssGGCTCCGss----- ; cor=; Ncor= a 22 22 0 8 3 0 9 0 0 16 28 0 0 0 0 0 c 62 67 19 2 140 0 136 149 0 72 61 0 0 0 0 0 g 40 48 131 133 5 2 7 4 153 41 47 0 0 0 0 0 t 29 16 3 10 5 151 1 0 0 24 17 0 0 0 0 0

oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m5; m=6/7; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.457525; --ssCCCCTCcs---- ; cor=; Ncor= a 0 0 38 34 0 0 0 0 0 0 42 34 0 0 0 0 c 0 0 139 99 320 320 320 320 0 320 171 158 0 0 0 0 g 0 0 100 117 0 0 0 0 0 0 46 85 0 0 0 0 t 0 0 43 70 0 0 0 0 320 0 61 43 0 0 0 0

oligos_6nt_mkv3_m4_rc_shift1 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=7/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.441491; -ssGCCTCGss----- ; cor=; Ncor= a 0 19 31 0 0 0 0 0 0 23 20 0 0 0 0 0 c 0 64 56 0 167 163 0 167 0 64 73 0 0 0 0 0 g 0 62 63 167 0 4 0 0 167 68 58 0 0 0 0 0 t 0 22 17 0 0 0 167 0 0 12 16 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --smGGCCmCGCCcc ; Alignment reference a 0 0 30 66 17 5 6 1 117 1 4 3 3 14 33 c 0 0 103 60 6 4 209 213 84 210 5 212 191 138 126 g 0 0 57 41 191 208 3 4 7 8 207 0 19 34 21 t 0 0 29 52 5 2 1 1 11 0 3 4 6 33 39

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --smGGCCmCGCCcc ; cor=; Ncor= a 0 0 30 66 17 5 6 1 117 1 4 3 3 14 33 c 0 0 103 60 6 4 209 213 84 210 5 212 191 138 126 g 0 0 57 41 191 208 3 4 7 8 207 0 19 34 21 t 0 0 29 52 5 2 1 1 11 0 3 4 6 33 39

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.758555; --cmgGCCCCGCCCC ; cor=; Ncor= a 0 0 47 122 72 23 5 7 31 5 13 4 4 7 36 c 0 0 230 130 79 39 412 400 390 415 3 415 415 379 362 g 0 0 91 97 273 357 10 8 14 19 415 12 12 24 15 t 0 0 74 93 18 23 15 27 7 3 11 11 11 32 29

oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.659071; --ssgGCCCGGCss- ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 0 c 0 0 90 104 35 7 218 201 225 15 4 223 77 87 0 g 0 0 88 84 157 209 9 23 7 216 224 6 88 92 0 t 0 0 26 18 16 7 3 4 1 1 3 1 39 25 0

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=4/6; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.587444; scCCCGCCCCGCsc- ; cor=; Ncor= a 29 14 1 5 15 5 3 4 1 3 8 12 24 27 0 c 88 148 230 220 215 2 234 229 241 235 10 218 122 133 0 g 102 46 12 17 13 230 7 14 5 5 200 11 70 55 0 t 30 41 6 7 6 12 5 2 2 6 31 8 33 34 0

oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4_rc; m=5/6; ncol2=10; w=0; offset=1; strand=R; shift=3; score=0.569779; ---ssGCCTCGss-- ; cor=; Ncor= a 0 0 0 19 31 0 0 0 0 0 0 23 20 0 0 c 0 0 0 64 56 0 167 163 0 167 0 64 73 0 0 g 0 0 0 62 63 167 0 4 0 0 167 68 58 0 0 t 0 0 0 22 17 0 0 0 167 0 0 12 16 0 0

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=6/6; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.446646; ssCAGGCCCcg---- ; cor=; Ncor= a 11 27 0 141 0 2 0 3 1 22 21 0 0 0 0 c 74 50 139 0 17 1 141 122 135 61 27 0 0 0 0 g 38 44 0 0 124 138 0 16 5 32 72 0 0 0 0 t 18 20 2 0 0 0 0 0 0 26 21 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ssCCCCTCcs ; Alignment reference a 0 0 0 0 38 34 0 0 0 0 0 0 42 34 c 0 0 0 0 139 99 320 320 320 320 0 320 171 158 g 0 0 0 0 100 117 0 0 0 0 0 0 46 85 t 0 0 0 0 43 70 0 0 0 0 320 0 61 43

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCCCCTCcs ; cor=; Ncor= a 0 0 0 0 38 34 0 0 0 0 0 0 42 34 c 0 0 0 0 139 99 320 320 320 320 0 320 171 158 g 0 0 0 0 100 117 0 0 0 0 0 0 46 85 t 0 0 0 0 43 70 0 0 0 0 320 0 61 43

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m1; m=2/3; ncol2=14; w=-4; offset=-4; strand=D; shift=0; score=0.551722; scCCCGCCCCGCsc ; cor=; Ncor= a 29 14 1 5 15 5 3 4 1 3 8 12 24 27 c 88 148 230 220 215 2 234 229 241 235 10 218 122 133 g 102 46 12 17 13 230 7 14 5 5 200 11 70 55 t 30 41 6 7 6 12 5 2 2 6 31 8 33 34

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m1; m=3/3; ncol2=16; w=-2; offset=-2; strand=D; shift=2; score=0.457525; --cmgGCCCCGCCC ; cor=; Ncor= a 0 0 47 122 72 23 5 7 31 5 13 4 4 7 c 0 0 230 130 79 39 412 400 390 415 3 415 415 379 g 0 0 91 97 273 357 10 8 14 19 415 12 12 24 t 0 0 74 93 18 23 15 27 7 3 11 11 11 32

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --ssgGCCCGGCss ; Alignment reference a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 c 0 0 90 104 35 7 218 201 225 15 4 223 77 87 g 0 0 88 84 157 209 9 23 7 216 224 6 88 92 t 0 0 26 18 16 7 3 4 1 1 3 1 39 25
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ssgGCCCGGCss ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 c 0 0 90 104 35 7 218 201 225 15 4 223 77 87 g 0 0 88 84 157 209 9 23 7 216 224 6 88 92 t 0 0 26 18 16 7 3 4 1 1 3 1 39 25
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.659071; --smGGCCmCGCCc ; cor=; Ncor= a 0 0 30 66 17 5 6 1 117 1 4 3 3 14 c 0 0 103 60 6 4 209 213 84 210 5 212 191 138 g 0 0 57 41 191 208 3 4 7 8 207 0 19 34 t 0 0 29 52 5 2 1 1 11 0 3 4 6 33
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=3/4; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.560825; --cmgGCCCCGCCC ; cor=; Ncor= a 0 0 47 122 72 23 5 7 31 5 13 4 4 7 c 0 0 230 130 79 39 412 400 390 415 3 415 415 379 g 0 0 91 97 273 357 10 8 14 19 415 12 12 24 t 0 0 74 93 18 23 15 27 7 3 11 11 11 32
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5; m=4/4; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.450461; ssCAGGCCCcg--- ; cor=; Ncor= a 11 27 0 141 0 2 0 3 1 22 21 0 0 0 c 74 50 139 0 17 1 141 122 135 61 27 0 0 0 g 38 44 0 0 124 138 0 16 5 32 72 0 0 0 t 18 20 2 0 0 0 0 0 0 26 21 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=5; ncol=15; -----ssCGAGGCss ; Alignment reference a 0 0 0 0 0 16 12 0 0 167 0 0 0 17 22 c 0 0 0 0 0 58 68 167 0 0 4 0 167 63 62 g 0 0 0 0 0 73 64 0 167 0 163 167 0 56 64 t 0 0 0 0 0 20 23 0 0 0 0 0 0 31 19
oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCGAGGCss ; cor=; Ncor= a 0 0 0 0 0 16 12 0 0 167 0 0 0 17 22 c 0 0 0 0 0 58 68 167 0 0 4 0 167 63 62 g 0 0 0 0 0 73 64 0 167 0 163 167 0 56 64 t 0 0 0 0 0 20 23 0 0 0 0 0 0 31 19
oligos_7nt_mkv4_m2_rc_shift3 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=13; w=-2; offset=-2; strand=R; shift=3; score=0.569779; ---ggGGCGkGGCCk ; cor=; Ncor= a 0 0 0 39 33 6 4 3 0 11 1 1 2 5 52 c 0 0 0 21 34 19 0 207 8 7 4 3 208 191 41 g 0 0 0 126 138 191 212 5 210 84 213 209 4 6 60 t 0 0 0 33 14 3 3 4 1 117 1 6 5 17 66
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=3/3; ncol2=16; w=-5; offset=-5; strand=R; shift=0; score=0.441491; ssGGGGGCGGGGCck ; cor=; Ncor= a 57 103 52 29 32 11 11 11 3 7 27 15 23 18 93 c 158 113 58 15 24 12 12 415 19 14 8 10 357 273 97 g 164 149 309 362 379 415 415 3 415 390 400 412 39 79 130 t 63 77 23 36 7 4 4 13 5 31 7 5 23 72 122

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=14; shift=3; ncol=17; ---scCCCGCCCCGCsc ; Alignment reference a 0 0 0 29 14 1 5 15 5 3 4 1 3 8 12 24 27 c 0 0 0 88 148 230 220 215 2 234 229 241 235 10 218 122 133 g 0 0 0 102 46 12 17 13 230 7 14 5 5 200 11 70 55 t 0 0 0 30 41 6 7 6 12 5 2 2 6 31 8 33 34
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---scCCCGCCCCGCsc ; cor=; Ncor= a 0 0 0 29 14 1 5 15 5 3 4 1 3 8 12 24 27 c 0 0 0 88 148 230 220 215 2 234 229 241 235 10 218 122 133 g 0 0 0 102 46 12 17 13 230 7 14 5 5 200 11 70 55 t 0 0 0 30 41 6 7 6 12 5 2 2 6 31 8 33 34
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/4; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.653224; cmgGCCCCGCCCCCss- ; cor=; Ncor= a 47 122 72 23 5 7 31 5 13 4 4 7 36 23 77 63 0 c 230 130 79 39 412 400 390 415 3 415 415 379 362 309 149 164 0 g 91 97 273 357 10 8 14 19 415 12 12 24 15 58 113 158 0 t 74 93 18 23 15 27 7 3 11 11 11 32 29 52 103 57 0
oligos_7nt_mkv4_m2_shift5 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/4; ncol2=13; w=0; offset=2; strand=D; shift=5; score=0.587444; -----smGGCCmCGCCc ; cor=; Ncor= a 0 0 0 0 0 30 66 17 5 6 1 117 1 4 3 3 14 c 0 0 0 0 0 103 60 6 4 209 213 84 210 5 212 191 138 g 0 0 0 0 0 57 41 191 208 3 4 7 8 207 0 19 34 t 0 0 0 0 0 29 52 5 2 1 1 11 0 3 4 6 33
oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=10; w=0; offset=4; strand=D; shift=7; score=0.551722; -------ssCCCCTCcs ; cor=; Ncor= a 0 0 0 0 0 0 0 38 34 0 0 0 0 0 0 42 34 c 0 0 0 0 0 0 0 139 99 320 320 320 320 0 320 171 158 g 0 0 0 0 0 0 0 100 117 0 0 0 0 0 0 46 85 t 0 0 0 0 0 0 0 43 70 0 0 0 0 320 0 61 43

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; ssCAGGCCCcg ; Alignment reference a 11 27 0 141 0 2 0 3 1 22 21 c 74 50 139 0 17 1 141 122 135 61 27 g 38 44 0 0 124 138 0 16 5 32 72 t 18 20 2 0 0 0 0 0 0 26 21
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCAGGCCCcg ; cor=; Ncor= a 11 27 0 141 0 2 0 3 1 22 21 c 74 50 139 0 17 1 141 122 135 61 27 g 38 44 0 0 124 138 0 16 5 32 72 t 18 20 2 0 0 0 0 0 0 26 21
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.450461; --ssgGCCCGG ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 c 0 0 90 104 35 7 218 201 225 15 4 g 0 0 88 84 157 209 9 23 7 216 224 t 0 0 26 18 16 7 3 4 1 1 3
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.446646; --smGGCCmCG ; cor=; Ncor= a 0 0 30 66 17 5 6 1 117 1 4 c 0 0 103 60 6 4 209 213 84 210 5 g 0 0 57 41 191 208 3 4 7 8 207 t 0 0 29 52 5 2 1 1 11 0 3

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=16; shift=0; ncol=16; cmgGCCCCGCCCCCss ; Alignment reference a 47 122 72 23 5 7 31 5 13 4 4 7 36 23 77 63 c 230 130 79 39 412 400 390 415 3 415 415 379 362 309 149 164 g 91 97 273 357 10 8 14 19 415 12 12 24 15 58 113 158 t 74 93 18 23 15 27 7 3 11 11 11 32 29 52 103 57
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cmgGCCCCGCCCCCss ; cor=; Ncor= a 47 122 72 23 5 7 31 5 13 4 4 7 36 23 77 63 c 230 130 79 39 412 400 390 415 3 415 415 379 362 309 149 164 g 91 97 273 357 10 8 14 19 415 12 12 24 15 58 113 158 t 74 93 18 23 15 27 7 3 11 11 11 32 29 52 103 57
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=2/7; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.758555; smGGCCmCGCCcc--- ; cor=; Ncor= a 30 66 17 5 6 1 117 1 4 3 3 14 33 0 0 0 c 103 60 6 4 209 213 84 210 5 212 191 138 126 0 0 0 g 57 41 191 208 3 4 7 8 207 0 19 34 21 0 0 0 t 29 52 5 2 1 1 11 0 3 4 6 33 39 0 0 0
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/7; ncol2=14; w=0; offset=3; strand=D; shift=3; score=0.653224; ---scCCCGCCCCGCs ; cor=; Ncor= a 0 0 0 29 14 1 5 15 5 3 4 1 3 8 12 24 c 0 0 0 88 148 230 220 215 2 234 229 241 235 10 218 122 g 0 0 0 102 46 12 17 13 230 7 14 5 5 200 11 70 t 0 0 0 30 41 6 7 6 12 5 2 2 6 31 8 33
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=4/7; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.560825; ssgGCCCGGCss---- ; cor=; Ncor= a 29 27 25 10 3 5 0 1 2 3 29 29 0 0 0 0 c 90 104 35 7 218 201 225 15 4 223 77 87 0 0 0 0 g 88 84 157 209 9 23 7 216 224 6 88 92 0 0 0 0 t 26 18 16 7 3 4 1 1 3 1 39 25 0 0 0 0
oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=5/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.502753; ssGGCTCCGss----- ; cor=; Ncor= a 22 22 0 8 3 0 9 0 0 16 28 0 0 0 0 0 c 62 67 19 2 140 0 136 149 0 72 61 0 0 0 0 0 g 40 48 131 133 5 2 7 4 153 41 47 0 0 0 0 0 t 29 16 3 10 5 151 1 0 0 24 17 0 0 0 0 0
oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m5; m=6/7; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.457525; --ssCCCCTCcs---- ; cor=; Ncor= a 0 0 38 34 0 0 0 0 0 0 42 34 0 0 0 0 c 0 0 139 99 320 320 320 320 0 320 171 158 0 0 0 0 g 0 0 100 117 0 0 0 0 0 0 46 85 0 0 0 0 t 0 0 43 70 0 0 0 0 320 0 61 43 0 0 0 0
oligos_6nt_mkv3_m4_rc_shift1 (oligos_6nt_mkv3_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=7/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.441491; -ssGCCTCGss----- ; cor=; Ncor= a 0 19 31 0 0 0 0 0 0 23 20 0 0 0 0 0 c 0 64 56 0 167 163 0 167 0 64 73 0 0 0 0 0 g 0 62 63 167 0 4 0 0 167 68 58 0 0 0 0 0 t 0 22 17 0 0 0 167 0 0 12 16 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --smGGCCmCGCCcc ; Alignment reference a 0 0 30 66 17 5 6 1 117 1 4 3 3 14 33 c 0 0 103 60 6 4 209 213 84 210 5 212 191 138 126 g 0 0 57 41 191 208 3 4 7 8 207 0 19 34 21 t 0 0 29 52 5 2 1 1 11 0 3 4 6 33 39
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --smGGCCmCGCCcc ; cor=; Ncor= a 0 0 30 66 17 5 6 1 117 1 4 3 3 14 33 c 0 0 103 60 6 4 209 213 84 210 5 212 191 138 126 g 0 0 57 41 191 208 3 4 7 8 207 0 19 34 21 t 0 0 29 52 5 2 1 1 11 0 3 4 6 33 39
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.758555; --cmgGCCCCGCCCC ; cor=; Ncor= a 0 0 47 122 72 23 5 7 31 5 13 4 4 7 36 c 0 0 230 130 79 39 412 400 390 415 3 415 415 379 362 g 0 0 91 97 273 357 10 8 14 19 415 12 12 24 15 t 0 0 74 93 18 23 15 27 7 3 11 11 11 32 29
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.659071; --ssgGCCCGGCss- ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 0 c 0 0 90 104 35 7 218 201 225 15 4 223 77 87 0 g 0 0 88 84 157 209 9 23 7 216 224 6 88 92 0 t 0 0 26 18 16 7 3 4 1 1 3 1 39 25 0
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=4/6; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.587444; scCCCGCCCCGCsc- ; cor=; Ncor= a 29 14 1 5 15 5 3 4 1 3 8 12 24 27 0 c 88 148 230 220 215 2 234 229 241 235 10 218 122 133 0 g 102 46 12 17 13 230 7 14 5 5 200 11 70 55 0 t 30 41 6 7 6 12 5 2 2 6 31 8 33 34 0
oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4_rc; m=5/6; ncol2=10; w=0; offset=1; strand=R; shift=3; score=0.569779; ---ssGCCTCGss-- ; cor=; Ncor= a 0 0 0 19 31 0 0 0 0 0 0 23 20 0 0 c 0 0 0 64 56 0 167 163 0 167 0 64 73 0 0 g 0 0 0 62 63 167 0 4 0 0 167 68 58 0 0 t 0 0 0 22 17 0 0 0 167 0 0 12 16 0 0
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=6/6; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.446646; ssCAGGCCCcg---- ; cor=; Ncor= a 11 27 0 141 0 2 0 3 1 22 21 0 0 0 0 c 74 50 139 0 17 1 141 122 135 61 27 0 0 0 0 g 38 44 0 0 124 138 0 16 5 32 72 0 0 0 0 t 18 20 2 0 0 0 0 0 0 26 21 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ssCCCCTCcs ; Alignment reference a 0 0 0 0 38 34 0 0 0 0 0 0 42 34 c 0 0 0 0 139 99 320 320 320 320 0 320 171 158 g 0 0 0 0 100 117 0 0 0 0 0 0 46 85 t 0 0 0 0 43 70 0 0 0 0 320 0 61 43
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCCCCTCcs ; cor=; Ncor= a 0 0 0 0 38 34 0 0 0 0 0 0 42 34 c 0 0 0 0 139 99 320 320 320 320 0 320 171 158 g 0 0 0 0 100 117 0 0 0 0 0 0 46 85 t 0 0 0 0 43 70 0 0 0 0 320 0 61 43
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m1; m=2/3; ncol2=14; w=-4; offset=-4; strand=D; shift=0; score=0.551722; scCCCGCCCCGCsc ; cor=; Ncor= a 29 14 1 5 15 5 3 4 1 3 8 12 24 27 c 88 148 230 220 215 2 234 229 241 235 10 218 122 133 g 102 46 12 17 13 230 7 14 5 5 200 11 70 55 t 30 41 6 7 6 12 5 2 2 6 31 8 33 34
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m1; m=3/3; ncol2=16; w=-2; offset=-2; strand=D; shift=2; score=0.457525; --cmgGCCCCGCCC ; cor=; Ncor= a 0 0 47 122 72 23 5 7 31 5 13 4 4 7 c 0 0 230 130 79 39 412 400 390 415 3 415 415 379 g 0 0 91 97 273 357 10 8 14 19 415 12 12 24 t 0 0 74 93 18 23 15 27 7 3 11 11 11 32