One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/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/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; csAGGCTGgs ; Alignment reference a 6 9 37 0 0 0 0 0 8 2 c 20 17 0 2 0 37 0 0 9 10 g 6 10 0 35 37 0 0 36 16 20 t 5 1 0 0 0 0 37 1 4 5

oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; csAGGCTGgs ; cor=; Ncor= a 6 9 37 0 0 0 0 0 8 2 c 20 17 0 2 0 37 0 0 9 10 g 6 10 0 35 37 0 0 36 16 20 t 5 1 0 0 0 0 37 1 4 5

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; yskCCCCGCCCsss ; Alignment reference a 8 8 3 0 0 0 0 1 3 1 1 4 10 8 c 20 14 11 42 46 44 44 0 42 43 43 14 18 23 g 7 20 21 3 0 2 2 45 2 2 3 19 14 13 t 12 5 12 2 1 1 1 1 0 1 0 10 5 3

oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; yskCCCCGCCCsss ; cor=; Ncor= a 8 8 3 0 0 0 0 1 3 1 1 4 10 8 c 20 14 11 42 46 44 44 0 42 43 43 14 18 23 g 7 20 21 3 0 2 2 45 2 2 3 19 14 13 t 12 5 12 2 1 1 1 1 0 1 0 10 5 3

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.900487; csGCCCCGCCCyv- ; cor=; Ncor= a 10 7 1 2 0 1 2 3 2 1 0 5 15 0 c 28 18 5 50 56 53 53 1 51 55 50 26 20 0 g 8 27 47 3 0 1 0 50 3 1 3 10 18 0 t 11 5 4 2 1 2 2 3 1 0 4 16 4 0

oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.531599; --ssCCCGGCsc-- ; cor=; Ncor= a 0 0 7 5 1 0 0 0 3 0 7 5 0 0 c 0 0 10 13 33 34 34 0 0 34 13 14 0 0 g 0 0 10 12 0 0 0 34 31 0 11 8 0 0 t 0 0 7 4 0 0 0 0 0 0 3 7 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m3_shift3 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---ssCACACGCmss ; Alignment reference a 0 0 0 1 2 0 12 0 14 0 0 0 9 3 2 c 0 0 0 8 8 15 1 14 2 16 0 16 4 4 7 g 0 0 0 5 5 1 3 1 0 0 16 0 2 7 6 t 0 0 0 2 1 0 0 1 0 0 0 0 1 2 1

oligos_7nt_mkv1_m3_shift3 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCACACGCmss ; cor=; Ncor= a 0 0 0 1 2 0 12 0 14 0 0 0 9 3 2 c 0 0 0 8 8 15 1 14 2 16 0 16 4 4 7 g 0 0 0 5 5 1 3 1 0 0 16 0 2 7 6 t 0 0 0 2 1 0 0 1 0 0 0 0 1 2 1

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/2; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.424031; msAGACACACaC--- ; cor=; Ncor= a 10 4 20 1 21 0 21 0 22 1 10 2 0 0 0 c 6 7 1 3 0 18 0 22 0 19 4 15 0 0 0 g 3 8 1 17 1 3 1 0 0 2 4 5 0 0 0 t 3 3 0 1 0 1 0 0 0 0 4 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ycCCCAGCAcv ; Alignment reference a 3 4 0 0 0 20 0 0 22 3 6 c 8 8 22 21 22 1 1 21 0 13 9 g 5 5 0 1 0 1 21 1 0 3 6 t 6 5 0 0 0 0 0 0 0 3 1

oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ycCCCAGCAcv ; cor=; Ncor= a 3 4 0 0 0 20 0 0 22 3 6 c 8 8 22 21 22 1 1 21 0 13 9 g 5 5 0 1 0 1 21 1 0 3 6 t 6 5 0 0 0 0 0 0 0 3 1

oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5)
; oligos_7nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.646404; ssCCCGGCsc- ; cor=; Ncor= a 7 5 1 0 0 0 3 0 7 5 0 c 10 13 33 34 34 0 0 34 13 14 0 g 10 12 0 0 0 34 31 0 11 8 0 t 7 4 0 0 0 0 0 0 3 7 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; sbAAATATkw ; Alignment reference a 4 5 21 19 22 1 18 1 4 6 c 9 6 1 1 1 1 2 0 2 3 g 6 6 1 1 0 2 3 1 7 2 t 4 6 0 2 0 19 0 21 10 12

oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; sbAAATATkw ; cor=; Ncor= a 4 5 21 19 22 1 18 1 4 6 c 9 6 1 1 1 1 2 0 2 3 g 6 6 1 1 0 2 3 1 7 2 t 4 6 0 2 0 19 0 21 10 12

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=10; shift=2; ncol=12; --ssCCCGGCsc ; Alignment reference a 0 0 7 5 1 0 0 0 3 0 7 5 c 0 0 10 13 33 34 34 0 0 34 13 14 g 0 0 10 12 0 0 0 34 31 0 11 8 t 0 0 7 4 0 0 0 0 0 0 3 7

oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ssCCCGGCsc ; cor=; Ncor= a 0 0 7 5 1 0 0 0 3 0 7 5 c 0 0 10 13 33 34 34 0 0 34 13 14 g 0 0 10 12 0 0 0 34 31 0 11 8 t 0 0 7 4 0 0 0 0 0 0 3 7

oligos_7nt_mkv1_m5_shift2 (oligos_7nt_mkv1_m5)
; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.646404; --ycCCCAGCAc ; cor=; Ncor= a 0 0 3 4 0 0 0 20 0 0 22 3 c 0 0 8 8 22 21 22 1 1 21 0 13 g 0 0 5 5 0 1 0 1 21 1 0 3 t 0 0 6 5 0 0 0 0 0 0 0 3

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m1; m=3/4; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.558556; csGCCCCGCCCy ; cor=; Ncor= a 10 7 1 2 0 1 2 3 2 1 0 5 c 28 18 5 50 56 53 53 1 51 55 50 26 g 8 27 47 3 0 1 0 50 3 1 3 10 t 11 5 4 2 1 2 2 3 1 0 4 16

oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m1; m=4/4; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.531599; yskCCCCGCCCs ; cor=; Ncor= a 8 8 3 0 0 0 0 1 3 1 1 4 c 20 14 11 42 46 44 44 0 42 43 43 14 g 7 20 21 3 0 2 2 45 2 2 3 19 t 12 5 12 2 1 1 1 1 0 1 0 10

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; msAGACACACacm ; Alignment reference a 8 3 16 0 18 0 17 0 18 1 7 2 5 c 5 6 1 2 0 14 0 18 0 16 3 12 5 g 2 6 1 15 0 3 1 0 0 1 4 4 4 t 3 3 0 1 0 1 0 0 0 0 4 0 4

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; msAGACACACacm ; cor=; Ncor= a 8 3 16 0 18 0 17 0 18 1 7 2 5 c 5 6 1 2 0 14 0 18 0 16 3 12 5 g 2 6 1 15 0 3 1 0 0 1 4 4 4 t 3 3 0 1 0 1 0 0 0 0 4 0 4

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.92055; msAGACACACaC- ; cor=; Ncor= a 10 4 20 1 21 0 21 0 22 1 10 2 0 c 6 7 1 3 0 18 0 22 0 19 4 15 0 g 3 8 1 17 1 3 1 0 0 2 4 5 0 t 3 3 0 1 0 1 0 0 0 0 4 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; msAGACACACaC ; Alignment reference a 10 4 20 1 21 0 21 0 22 1 10 2 c 6 7 1 3 0 18 0 22 0 19 4 15 g 3 8 1 17 1 3 1 0 0 2 4 5 t 3 3 0 1 0 1 0 0 0 0 4 0

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; msAGACACACaC ; cor=; Ncor= a 10 4 20 1 21 0 21 0 22 1 10 2 c 6 7 1 3 0 18 0 22 0 19 4 15 g 3 8 1 17 1 3 1 0 0 2 4 5 t 3 3 0 1 0 1 0 0 0 0 4 0

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.92055; msAGACACACac ; cor=; Ncor= a 8 3 16 0 18 0 17 0 18 1 7 2 c 5 6 1 2 0 14 0 18 0 16 3 12 g 2 6 1 15 0 3 1 0 0 1 4 4 t 3 3 0 1 0 1 0 0 0 0 4 0

oligos_7nt_mkv1_m3_shift3 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m3; m=3/3; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.424031; ---ssCACACGC ; cor=; Ncor= a 0 0 0 1 2 0 12 0 14 0 0 0 c 0 0 0 8 8 15 1 14 2 16 0 16 g 0 0 0 5 5 1 3 1 0 0 16 0 t 0 0 0 2 1 0 0 1 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCCGCCGCGss ; Alignment reference a 3 2 3 1 0 0 3 0 0 0 1 6 c 12 15 29 33 2 32 26 3 31 6 15 13 g 12 16 2 0 31 2 5 31 2 27 12 10 t 7 1 0 0 1 0 0 0 1 1 6 5

oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCCGCCGCGss ; cor=; Ncor= a 3 2 3 1 0 0 3 0 0 0 1 6 c 12 15 29 33 2 32 26 3 31 6 15 13 g 12 16 2 0 31 2 5 31 2 27 12 10 t 7 1 0 0 1 0 0 0 1 1 6 5

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; csGCCCCGCCCyv ; Alignment reference a 10 7 1 2 0 1 2 3 2 1 0 5 15 c 28 18 5 50 56 53 53 1 51 55 50 26 20 g 8 27 47 3 0 1 0 50 3 1 3 10 18 t 11 5 4 2 1 2 2 3 1 0 4 16 4

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; csGCCCCGCCCyv ; cor=; Ncor= a 10 7 1 2 0 1 2 3 2 1 0 5 15 c 28 18 5 50 56 53 53 1 51 55 50 26 20 g 8 27 47 3 0 1 0 50 3 1 3 10 18 t 11 5 4 2 1 2 2 3 1 0 4 16 4

oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.900487; yskCCCCGCCCss ; cor=; Ncor= a 8 8 3 0 0 0 0 1 3 1 1 4 10 c 20 14 11 42 46 44 44 0 42 43 43 14 18 g 7 20 21 3 0 2 2 45 2 2 3 19 14 t 12 5 12 2 1 1 1 1 0 1 0 10 5

oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.558556; --ssCCCGGCsc- ; cor=; Ncor= a 0 0 7 5 1 0 0 0 3 0 7 5 0 c 0 0 10 13 33 34 34 0 0 34 13 14 0 g 0 0 10 12 0 0 0 34 31 0 11 8 0 t 0 0 7 4 0 0 0 0 0 0 3 7 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; yskCCCCGCCCsss ; Alignment reference a 8 8 3 0 0 0 0 1 3 1 1 4 10 8 c 20 14 11 42 46 44 44 0 42 43 43 14 18 23 g 7 20 21 3 0 2 2 45 2 2 3 19 14 13 t 12 5 12 2 1 1 1 1 0 1 0 10 5 3
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; yskCCCCGCCCsss ; cor=; Ncor= a 8 8 3 0 0 0 0 1 3 1 1 4 10 8 c 20 14 11 42 46 44 44 0 42 43 43 14 18 23 g 7 20 21 3 0 2 2 45 2 2 3 19 14 13 t 12 5 12 2 1 1 1 1 0 1 0 10 5 3
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.900487; csGCCCCGCCCyv- ; cor=; Ncor= a 10 7 1 2 0 1 2 3 2 1 0 5 15 0 c 28 18 5 50 56 53 53 1 51 55 50 26 20 0 g 8 27 47 3 0 1 0 50 3 1 3 10 18 0 t 11 5 4 2 1 2 2 3 1 0 4 16 4 0
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.531599; --ssCCCGGCsc-- ; cor=; Ncor= a 0 0 7 5 1 0 0 0 3 0 7 5 0 0 c 0 0 10 13 33 34 34 0 0 34 13 14 0 0 g 0 0 10 12 0 0 0 34 31 0 11 8 0 0 t 0 0 7 4 0 0 0 0 0 0 3 7 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)				; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=10; shift=2; ncol=12; --ssCCCGGCsc ; Alignment reference a 0 0 7 5 1 0 0 0 3 0 7 5 c 0 0 10 13 33 34 34 0 0 34 13 14 g 0 0 10 12 0 0 0 34 31 0 11 8 t 0 0 7 4 0 0 0 0 0 0 3 7
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)				; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ssCCCGGCsc ; cor=; Ncor= a 0 0 7 5 1 0 0 0 3 0 7 5 c 0 0 10 13 33 34 34 0 0 34 13 14 g 0 0 10 12 0 0 0 34 31 0 11 8 t 0 0 7 4 0 0 0 0 0 0 3 7
oligos_7nt_mkv1_m5_shift2 (oligos_7nt_mkv1_m5)				; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.646404; --ycCCCAGCAc ; cor=; Ncor= a 0 0 3 4 0 0 0 20 0 0 22 3 c 0 0 8 8 22 21 22 1 1 21 0 13 g 0 0 5 5 0 1 0 1 21 1 0 3 t 0 0 6 5 0 0 0 0 0 0 0 3
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m1; m=3/4; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.558556; csGCCCCGCCCy ; cor=; Ncor= a 10 7 1 2 0 1 2 3 2 1 0 5 c 28 18 5 50 56 53 53 1 51 55 50 26 g 8 27 47 3 0 1 0 50 3 1 3 10 t 11 5 4 2 1 2 2 3 1 0 4 16
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m1; m=4/4; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.531599; yskCCCCGCCCs ; cor=; Ncor= a 8 8 3 0 0 0 0 1 3 1 1 4 c 20 14 11 42 46 44 44 0 42 43 43 14 g 7 20 21 3 0 2 2 45 2 2 3 19 t 12 5 12 2 1 1 1 1 0 1 0 10

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; msAGACACACaC ; Alignment reference a 10 4 20 1 21 0 21 0 22 1 10 2 c 6 7 1 3 0 18 0 22 0 19 4 15 g 3 8 1 17 1 3 1 0 0 2 4 5 t 3 3 0 1 0 1 0 0 0 0 4 0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; msAGACACACaC ; cor=; Ncor= a 10 4 20 1 21 0 21 0 22 1 10 2 c 6 7 1 3 0 18 0 22 0 19 4 15 g 3 8 1 17 1 3 1 0 0 2 4 5 t 3 3 0 1 0 1 0 0 0 0 4 0
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.92055; msAGACACACac ; cor=; Ncor= a 8 3 16 0 18 0 17 0 18 1 7 2 c 5 6 1 2 0 14 0 18 0 16 3 12 g 2 6 1 15 0 3 1 0 0 1 4 4 t 3 3 0 1 0 1 0 0 0 0 4 0
oligos_7nt_mkv1_m3_shift3 (oligos_7nt_mkv1_m3)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m3; m=3/3; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.424031; ---ssCACACGC ; cor=; Ncor= a 0 0 0 1 2 0 12 0 14 0 0 0 c 0 0 0 8 8 15 1 14 2 16 0 16 g 0 0 0 5 5 1 3 1 0 0 16 0 t 0 0 0 2 1 0 0 1 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; csGCCCCGCCCyv ; Alignment reference a 10 7 1 2 0 1 2 3 2 1 0 5 15 c 28 18 5 50 56 53 53 1 51 55 50 26 20 g 8 27 47 3 0 1 0 50 3 1 3 10 18 t 11 5 4 2 1 2 2 3 1 0 4 16 4
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; csGCCCCGCCCyv ; cor=; Ncor= a 10 7 1 2 0 1 2 3 2 1 0 5 15 c 28 18 5 50 56 53 53 1 51 55 50 26 20 g 8 27 47 3 0 1 0 50 3 1 3 10 18 t 11 5 4 2 1 2 2 3 1 0 4 16 4
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.900487; yskCCCCGCCCss ; cor=; Ncor= a 8 8 3 0 0 0 0 1 3 1 1 4 10 c 20 14 11 42 46 44 44 0 42 43 43 14 18 g 7 20 21 3 0 2 2 45 2 2 3 19 14 t 12 5 12 2 1 1 1 1 0 1 0 10 5
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.558556; --ssCCCGGCsc- ; cor=; Ncor= a 0 0 7 5 1 0 0 0 3 0 7 5 0 c 0 0 10 13 33 34 34 0 0 34 13 14 0 g 0 0 10 12 0 0 0 34 31 0 11 8 0 t 0 0 7 4 0 0 0 0 0 0 3 7 0