One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/27/peak-motifs.2025-06-27.165408_2025-06-27.165408_kPhdjj/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/2025/06/27/peak-motifs.2025-06-27.165408_2025-06-27.165408_kPhdjj/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -ssCCCGCCssc ; Alignment reference a 0 38 35 0 0 0 0 5 0 47 37 38 c 0 75 62 204 206 202 1 199 204 70 71 87 g 0 55 63 0 0 4 202 0 2 58 60 49 t 0 38 46 2 0 0 3 2 0 31 38 32

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -ssCCCGCCssc ; cor=; Ncor= a 0 38 35 0 0 0 0 5 0 47 37 38 c 0 75 62 204 206 202 1 199 204 70 71 87 g 0 55 63 0 0 4 202 0 2 58 60 49 t 0 38 46 2 0 0 3 2 0 31 38 32

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.958152; -cyCCCGCCCbc ; cor=; Ncor= a 0 25 22 2 0 0 0 9 0 0 20 27 c 0 60 61 140 138 147 5 136 145 118 46 64 g 0 29 24 0 1 1 134 1 0 17 44 35 t 0 34 41 6 9 0 9 2 3 13 38 22

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.830005; scTCCCGCCCcc ; cor=; Ncor= a 33 34 10 4 5 5 5 1 6 7 43 32 c 74 73 25 177 177 176 8 184 175 174 72 86 g 58 42 17 10 4 5 171 8 5 8 39 44 t 29 45 142 3 8 8 10 1 8 5 40 32

oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=4/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.612697; --csCCGCCGCC ; cor=; Ncor= a 0 0 46 45 8 4 11 9 5 6 5 15 c 0 0 123 93 257 264 12 258 260 30 260 245 g 0 0 65 112 15 8 251 14 10 239 14 15 t 0 0 51 35 5 9 11 4 10 10 6 10

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.507813; ---cyCGCCCCC ; cor=; Ncor= a 0 0 0 20 28 0 0 14 0 0 0 0 c 0 0 0 54 49 123 6 101 118 123 114 119 g 0 0 0 28 15 1 113 2 2 0 2 3 t 0 0 0 22 32 0 5 7 4 1 8 2

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---cyCGCCCCCbs ; Alignment reference a 0 0 0 20 28 0 0 14 0 0 0 0 20 30 c 0 0 0 54 49 123 6 101 118 123 114 119 31 42 g 0 0 0 28 15 1 113 2 2 0 2 3 40 34 t 0 0 0 22 32 0 5 7 4 1 8 2 33 18

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---cyCGCCCCCbs ; cor=; Ncor= a 0 0 0 20 28 0 0 14 0 0 0 0 20 30 c 0 0 0 54 49 123 6 101 118 123 114 119 31 42 g 0 0 0 28 15 1 113 2 2 0 2 3 40 34 t 0 0 0 22 32 0 5 7 4 1 8 2 33 18

oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=2/5; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.717414; --csCCGCCGCCsc ; cor=; Ncor= a 0 0 46 45 8 4 11 9 5 6 5 15 54 44 c 0 0 123 93 257 264 12 258 260 30 260 245 89 125 g 0 0 65 112 15 8 251 14 10 239 14 15 94 69 t 0 0 51 35 5 9 11 4 10 10 6 10 48 47

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=3/5; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.559771; -cyCCCGCCCbc-- ; cor=; Ncor= a 0 25 22 2 0 0 0 9 0 0 20 27 0 0 c 0 60 61 140 138 147 5 136 145 118 46 64 0 0 g 0 29 24 0 1 1 134 1 0 17 44 35 0 0 t 0 34 41 6 9 0 9 2 3 13 38 22 0 0

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=4/5; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.532303; scTCCCGCCCcc-- ; cor=; Ncor= a 33 34 10 4 5 5 5 1 6 7 43 32 0 0 c 74 73 25 177 177 176 8 184 175 174 72 86 0 0 g 58 42 17 10 4 5 171 8 5 8 39 44 0 0 t 29 45 142 3 8 8 10 1 8 5 40 32 0 0

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=5/5; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.507813; -ssCCCGCCssc-- ; cor=; Ncor= a 0 38 35 0 0 0 0 5 0 47 37 38 0 0 c 0 75 62 204 206 202 1 199 204 70 71 87 0 0 g 0 55 63 0 0 4 202 0 2 58 60 49 0 0 t 0 38 46 2 0 0 3 2 0 31 38 32 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -cyCCCGCCCbc ; Alignment reference a 0 25 22 2 0 0 0 9 0 0 20 27 c 0 60 61 140 138 147 5 136 145 118 46 64 g 0 29 24 0 1 1 134 1 0 17 44 35 t 0 34 41 6 9 0 9 2 3 13 38 22

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -cyCCCGCCCbc ; cor=; Ncor= a 0 25 22 2 0 0 0 9 0 0 20 27 c 0 60 61 140 138 147 5 136 145 118 46 64 g 0 29 24 0 1 1 134 1 0 17 44 35 t 0 34 41 6 9 0 9 2 3 13 38 22

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.958152; -ssCCCGCCssc ; cor=; Ncor= a 0 38 35 0 0 0 0 5 0 47 37 38 c 0 75 62 204 206 202 1 199 204 70 71 87 g 0 55 63 0 0 4 202 0 2 58 60 49 t 0 38 46 2 0 0 3 2 0 31 38 32

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.877693; scTCCCGCCCcc ; cor=; Ncor= a 33 34 10 4 5 5 5 1 6 7 43 32 c 74 73 25 177 177 176 8 184 175 174 72 86 g 58 42 17 10 4 5 171 8 5 8 39 44 t 29 45 142 3 8 8 10 1 8 5 40 32

oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=4/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.566681; --csCCGCCGCC ; cor=; Ncor= a 0 0 46 45 8 4 11 9 5 6 5 15 c 0 0 123 93 257 264 12 258 260 30 260 245 g 0 0 65 112 15 8 251 14 10 239 14 15 t 0 0 51 35 5 9 11 4 10 10 6 10

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.559771; ---cyCGCCCCC ; cor=; Ncor= a 0 0 0 20 28 0 0 14 0 0 0 0 c 0 0 0 54 49 123 6 101 118 123 114 119 g 0 0 0 28 15 1 113 2 2 0 2 3 t 0 0 0 22 32 0 5 7 4 1 8 2

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 2 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=11; shift=0; ncol=11; srTACCGTAyb ; Alignment reference a 33 50 3 130 5 12 6 3 141 29 20 c 48 30 8 8 142 107 7 5 4 46 46 g 50 50 5 10 3 21 134 1 5 30 48 t 21 22 136 4 2 12 5 143 2 47 38

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; srTACCGTAyb ; cor=; Ncor= a 33 50 3 130 5 12 6 3 141 29 20 c 48 30 8 8 142 107 7 5 4 46 46 g 50 50 5 10 3 21 134 1 5 30 48 t 21 22 136 4 2 12 5 143 2 47 38

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 2 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=10; shift=0; ncol=10; ssAGTCAGgm ; Alignment reference a 18 11 73 0 0 3 70 0 16 20 c 25 27 0 2 0 70 2 1 17 19 g 20 26 0 71 0 0 1 72 22 18 t 10 9 0 0 73 0 0 0 18 16

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssAGTCAGgm ; cor=; Ncor= a 18 11 73 0 0 3 70 0 16 20 c 25 27 0 2 0 70 2 1 17 19 g 20 26 0 71 0 0 1 72 22 18 t 10 9 0 0 73 0 0 0 18 16

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; CACACACACACACA ; Alignment reference a 32 415 6 524 3 496 2 524 3 396 9 464 35 409 c 442 29 526 2 531 1 533 5 526 7 506 29 449 40 g 43 71 3 10 2 39 3 7 6 126 14 31 32 73 t 22 24 4 3 3 3 1 3 4 10 10 15 23 17

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; CACACACACACACA ; cor=; Ncor= a 32 415 6 524 3 496 2 524 3 396 9 464 35 409 c 442 29 526 2 531 1 533 5 526 7 506 29 449 40 g 43 71 3 10 2 39 3 7 6 126 14 31 32 73 t 22 24 4 3 3 3 1 3 4 10 10 15 23 17

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 2 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=10; shift=0; ncol=10; asGCACGCmc ; Alignment reference a 80 33 0 0 203 0 0 0 72 34 c 49 74 0 203 0 203 0 203 53 83 g 47 52 203 0 0 0 203 0 48 45 t 27 44 0 0 0 0 0 0 30 41

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; asGCACGCmc ; cor=; Ncor= a 80 33 0 0 203 0 0 0 72 34 c 49 74 0 203 0 203 0 203 53 83 g 47 52 203 0 0 0 203 0 48 45 t 27 44 0 0 0 0 0 0 30 41

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; bgCAGCTGcv ; Alignment reference a 38 31 0 180 0 0 0 0 31 47 c 45 43 180 0 0 180 0 0 75 50 g 50 75 0 0 180 0 0 180 43 45 t 47 31 0 0 0 0 180 0 31 38

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; bgCAGCTGcv ; cor=; Ncor= a 38 31 0 180 0 0 0 0 31 47 c 45 43 180 0 0 180 0 0 75 50 g 50 75 0 0 180 0 0 180 43 45 t 47 31 0 0 0 0 180 0 31 38

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 5 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=12; shift=0; ncol=12; scTCCCGCCCcc ; Alignment reference a 33 34 10 4 5 5 5 1 6 7 43 32 c 74 73 25 177 177 176 8 184 175 174 72 86 g 58 42 17 10 4 5 171 8 5 8 39 44 t 29 45 142 3 8 8 10 1 8 5 40 32

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; scTCCCGCCCcc ; cor=; Ncor= a 33 34 10 4 5 5 5 1 6 7 43 32 c 74 73 25 177 177 176 8 184 175 174 72 86 g 58 42 17 10 4 5 171 8 5 8 39 44 t 29 45 142 3 8 8 10 1 8 5 40 32

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.877693; -cyCCCGCCCbc ; cor=; Ncor= a 0 25 22 2 0 0 0 9 0 0 20 27 c 0 60 61 140 138 147 5 136 145 118 46 64 g 0 29 24 0 1 1 134 1 0 17 44 35 t 0 34 41 6 9 0 9 2 3 13 38 22

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=3/4; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.830005; -ssCCCGCCssc ; cor=; Ncor= a 0 38 35 0 0 0 0 5 0 47 37 38 c 0 75 62 204 206 202 1 199 204 70 71 87 g 0 55 63 0 0 4 202 0 2 58 60 49 t 0 38 46 2 0 0 3 2 0 31 38 32

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=4/4; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.532303; ---cyCGCCCCC ; cor=; Ncor= a 0 0 0 20 28 0 0 14 0 0 0 0 c 0 0 0 54 49 123 6 101 118 123 114 119 g 0 0 0 28 15 1 113 2 2 0 2 3 t 0 0 0 22 32 0 5 7 4 1 8 2

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -csCCGCCGCCsc ; Alignment reference a 0 46 45 8 4 11 9 5 6 5 15 54 44 c 0 123 93 257 264 12 258 260 30 260 245 89 125 g 0 65 112 15 8 251 14 10 239 14 15 94 69 t 0 51 35 5 9 11 4 10 10 6 10 48 47

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -csCCGCCGCCsc ; cor=; Ncor= a 0 46 45 8 4 11 9 5 6 5 15 54 44 c 0 123 93 257 264 12 258 260 30 260 245 89 125 g 0 65 112 15 8 251 14 10 239 14 15 94 69 t 0 51 35 5 9 11 4 10 10 6 10 48 47

oligos_7nt_mkv2_m5_shift2 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.717414; --cyCGCCCCCbs ; cor=; Ncor= a 0 0 20 28 0 0 14 0 0 0 0 20 30 c 0 0 54 49 123 6 101 118 123 114 119 31 42 g 0 0 28 15 1 113 2 2 0 2 3 40 34 t 0 0 22 32 0 5 7 4 1 8 2 33 18

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.612697; ssCCCGCCssc-- ; cor=; Ncor= a 38 35 0 0 0 0 5 0 47 37 38 0 0 c 75 62 204 206 202 1 199 204 70 71 87 0 0 g 55 63 0 0 4 202 0 2 58 60 49 0 0 t 38 46 2 0 0 3 2 0 31 38 32 0 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.566681; cyCCCGCCCbc-- ; cor=; Ncor= a 25 22 2 0 0 0 9 0 0 20 27 0 0 c 60 61 140 138 147 5 136 145 118 46 64 0 0 g 29 24 0 1 1 134 1 0 17 44 35 0 0 t 34 41 6 9 0 9 2 3 13 38 22 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -ssCCCGCCssc ; Alignment reference a 0 38 35 0 0 0 0 5 0 47 37 38 c 0 75 62 204 206 202 1 199 204 70 71 87 g 0 55 63 0 0 4 202 0 2 58 60 49 t 0 38 46 2 0 0 3 2 0 31 38 32
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -ssCCCGCCssc ; cor=; Ncor= a 0 38 35 0 0 0 0 5 0 47 37 38 c 0 75 62 204 206 202 1 199 204 70 71 87 g 0 55 63 0 0 4 202 0 2 58 60 49 t 0 38 46 2 0 0 3 2 0 31 38 32
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.958152; -cyCCCGCCCbc ; cor=; Ncor= a 0 25 22 2 0 0 0 9 0 0 20 27 c 0 60 61 140 138 147 5 136 145 118 46 64 g 0 29 24 0 1 1 134 1 0 17 44 35 t 0 34 41 6 9 0 9 2 3 13 38 22
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.830005; scTCCCGCCCcc ; cor=; Ncor= a 33 34 10 4 5 5 5 1 6 7 43 32 c 74 73 25 177 177 176 8 184 175 174 72 86 g 58 42 17 10 4 5 171 8 5 8 39 44 t 29 45 142 3 8 8 10 1 8 5 40 32
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=4/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.612697; --csCCGCCGCC ; cor=; Ncor= a 0 0 46 45 8 4 11 9 5 6 5 15 c 0 0 123 93 257 264 12 258 260 30 260 245 g 0 0 65 112 15 8 251 14 10 239 14 15 t 0 0 51 35 5 9 11 4 10 10 6 10
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.507813; ---cyCGCCCCC ; cor=; Ncor= a 0 0 0 20 28 0 0 14 0 0 0 0 c 0 0 0 54 49 123 6 101 118 123 114 119 g 0 0 0 28 15 1 113 2 2 0 2 3 t 0 0 0 22 32 0 5 7 4 1 8 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---cyCGCCCCCbs ; Alignment reference a 0 0 0 20 28 0 0 14 0 0 0 0 20 30 c 0 0 0 54 49 123 6 101 118 123 114 119 31 42 g 0 0 0 28 15 1 113 2 2 0 2 3 40 34 t 0 0 0 22 32 0 5 7 4 1 8 2 33 18
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---cyCGCCCCCbs ; cor=; Ncor= a 0 0 0 20 28 0 0 14 0 0 0 0 20 30 c 0 0 0 54 49 123 6 101 118 123 114 119 31 42 g 0 0 0 28 15 1 113 2 2 0 2 3 40 34 t 0 0 0 22 32 0 5 7 4 1 8 2 33 18
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=2/5; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.717414; --csCCGCCGCCsc ; cor=; Ncor= a 0 0 46 45 8 4 11 9 5 6 5 15 54 44 c 0 0 123 93 257 264 12 258 260 30 260 245 89 125 g 0 0 65 112 15 8 251 14 10 239 14 15 94 69 t 0 0 51 35 5 9 11 4 10 10 6 10 48 47
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=3/5; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.559771; -cyCCCGCCCbc-- ; cor=; Ncor= a 0 25 22 2 0 0 0 9 0 0 20 27 0 0 c 0 60 61 140 138 147 5 136 145 118 46 64 0 0 g 0 29 24 0 1 1 134 1 0 17 44 35 0 0 t 0 34 41 6 9 0 9 2 3 13 38 22 0 0
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=4/5; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.532303; scTCCCGCCCcc-- ; cor=; Ncor= a 33 34 10 4 5 5 5 1 6 7 43 32 0 0 c 74 73 25 177 177 176 8 184 175 174 72 86 0 0 g 58 42 17 10 4 5 171 8 5 8 39 44 0 0 t 29 45 142 3 8 8 10 1 8 5 40 32 0 0
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=5/5; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.507813; -ssCCCGCCssc-- ; cor=; Ncor= a 0 38 35 0 0 0 0 5 0 47 37 38 0 0 c 0 75 62 204 206 202 1 199 204 70 71 87 0 0 g 0 55 63 0 0 4 202 0 2 58 60 49 0 0 t 0 38 46 2 0 0 3 2 0 31 38 32 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -cyCCCGCCCbc ; Alignment reference a 0 25 22 2 0 0 0 9 0 0 20 27 c 0 60 61 140 138 147 5 136 145 118 46 64 g 0 29 24 0 1 1 134 1 0 17 44 35 t 0 34 41 6 9 0 9 2 3 13 38 22
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -cyCCCGCCCbc ; cor=; Ncor= a 0 25 22 2 0 0 0 9 0 0 20 27 c 0 60 61 140 138 147 5 136 145 118 46 64 g 0 29 24 0 1 1 134 1 0 17 44 35 t 0 34 41 6 9 0 9 2 3 13 38 22
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.958152; -ssCCCGCCssc ; cor=; Ncor= a 0 38 35 0 0 0 0 5 0 47 37 38 c 0 75 62 204 206 202 1 199 204 70 71 87 g 0 55 63 0 0 4 202 0 2 58 60 49 t 0 38 46 2 0 0 3 2 0 31 38 32
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.877693; scTCCCGCCCcc ; cor=; Ncor= a 33 34 10 4 5 5 5 1 6 7 43 32 c 74 73 25 177 177 176 8 184 175 174 72 86 g 58 42 17 10 4 5 171 8 5 8 39 44 t 29 45 142 3 8 8 10 1 8 5 40 32
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=4/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.566681; --csCCGCCGCC ; cor=; Ncor= a 0 0 46 45 8 4 11 9 5 6 5 15 c 0 0 123 93 257 264 12 258 260 30 260 245 g 0 0 65 112 15 8 251 14 10 239 14 15 t 0 0 51 35 5 9 11 4 10 10 6 10
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.559771; ---cyCGCCCCC ; cor=; Ncor= a 0 0 0 20 28 0 0 14 0 0 0 0 c 0 0 0 54 49 123 6 101 118 123 114 119 g 0 0 0 28 15 1 113 2 2 0 2 3 t 0 0 0 22 32 0 5 7 4 1 8 2

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=12; shift=0; ncol=12; scTCCCGCCCcc ; Alignment reference a 33 34 10 4 5 5 5 1 6 7 43 32 c 74 73 25 177 177 176 8 184 175 174 72 86 g 58 42 17 10 4 5 171 8 5 8 39 44 t 29 45 142 3 8 8 10 1 8 5 40 32
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; scTCCCGCCCcc ; cor=; Ncor= a 33 34 10 4 5 5 5 1 6 7 43 32 c 74 73 25 177 177 176 8 184 175 174 72 86 g 58 42 17 10 4 5 171 8 5 8 39 44 t 29 45 142 3 8 8 10 1 8 5 40 32
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.877693; -cyCCCGCCCbc ; cor=; Ncor= a 0 25 22 2 0 0 0 9 0 0 20 27 c 0 60 61 140 138 147 5 136 145 118 46 64 g 0 29 24 0 1 1 134 1 0 17 44 35 t 0 34 41 6 9 0 9 2 3 13 38 22
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=3/4; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.830005; -ssCCCGCCssc ; cor=; Ncor= a 0 38 35 0 0 0 0 5 0 47 37 38 c 0 75 62 204 206 202 1 199 204 70 71 87 g 0 55 63 0 0 4 202 0 2 58 60 49 t 0 38 46 2 0 0 3 2 0 31 38 32
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=4/4; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.532303; ---cyCGCCCCC ; cor=; Ncor= a 0 0 0 20 28 0 0 14 0 0 0 0 c 0 0 0 54 49 123 6 101 118 123 114 119 g 0 0 0 28 15 1 113 2 2 0 2 3 t 0 0 0 22 32 0 5 7 4 1 8 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -csCCGCCGCCsc ; Alignment reference a 0 46 45 8 4 11 9 5 6 5 15 54 44 c 0 123 93 257 264 12 258 260 30 260 245 89 125 g 0 65 112 15 8 251 14 10 239 14 15 94 69 t 0 51 35 5 9 11 4 10 10 6 10 48 47
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -csCCGCCGCCsc ; cor=; Ncor= a 0 46 45 8 4 11 9 5 6 5 15 54 44 c 0 123 93 257 264 12 258 260 30 260 245 89 125 g 0 65 112 15 8 251 14 10 239 14 15 94 69 t 0 51 35 5 9 11 4 10 10 6 10 48 47
oligos_7nt_mkv2_m5_shift2 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.717414; --cyCGCCCCCbs ; cor=; Ncor= a 0 0 20 28 0 0 14 0 0 0 0 20 30 c 0 0 54 49 123 6 101 118 123 114 119 31 42 g 0 0 28 15 1 113 2 2 0 2 3 40 34 t 0 0 22 32 0 5 7 4 1 8 2 33 18
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.612697; ssCCCGCCssc-- ; cor=; Ncor= a 38 35 0 0 0 0 5 0 47 37 38 0 0 c 75 62 204 206 202 1 199 204 70 71 87 0 0 g 55 63 0 0 4 202 0 2 58 60 49 0 0 t 38 46 2 0 0 3 2 0 31 38 32 0 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.566681; cyCCCGCCCbc-- ; cor=; Ncor= a 25 22 2 0 0 0 9 0 0 20 27 0 0 c 60 61 140 138 147 5 136 145 118 46 64 0 0 g 29 24 0 1 1 134 1 0 17 44 35 0 0 t 34 41 6 9 0 9 2 3 13 38 22 0 0