One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; GhGAAGTGCAw ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 c 0 1 0 0 0 0 0 0 3 0 0 g 3 0 3 0 0 3 0 3 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; GhGAAGTGCAw ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 c 0 1 0 0 0 0 0 0 3 0 0 g 3 0 3 0 0 3 0 3 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1

oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)
; oligos_7nt_mkv1_m3 versus oligos_8nt_mkv1_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.916667; GhGAAGTGCAw ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 c 0 1 0 0 0 0 0 0 3 0 0 g 3 0 3 0 0 3 0 3 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1

oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.678706; --swAGTGmAr ; cor=; Ncor= a 0 0 1 3 6 0 0 0 2 6 3 c 0 0 2 0 0 0 0 0 4 0 0 g 0 0 3 1 0 6 0 6 0 0 2 t 0 0 0 2 0 0 6 0 0 0 1

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --swAGTGmArw ; Alignment reference a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2

oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --swAGTGmArw ; cor=; Ncor= a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2

oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)
; oligos_6nt_mkv1_m1 versus oligos_8nt_mkv1_m2; m=2/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.754655; GhGAAGTGCAww ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m3; m=3/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.678706; GhGAAGTGCAw- ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 0 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 3 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=11; shift=0; ncol=11; ctCTGTGGAwt ; Alignment reference a 0 1 0 0 1 0 0 0 5 3 1 c 3 1 5 0 0 0 0 0 0 0 0 g 1 1 0 0 4 0 4 5 0 0 1 t 1 2 0 5 0 5 1 0 0 2 3

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ctCTGTGGAwt ; cor=; Ncor= a 0 1 0 0 1 0 0 0 5 3 1 c 3 1 5 0 0 0 0 0 0 0 0 g 1 1 0 0 4 0 4 5 0 0 1 t 1 2 0 5 0 5 1 0 0 2 3

oligos_8nt_mkv1_m1_shift0 (oligos_8nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_8nt_mkv1_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.870312; ybCTGTGGAAk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 3 3 0 c 2 1 3 0 0 0 0 0 0 0 0 g 0 1 0 0 3 0 3 3 0 0 1 t 1 1 0 3 0 3 0 0 0 0 2

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m4_shift0 (oligos_8nt_mkv1_m4)
; oligos_8nt_mkv1_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; wAAAAGCTCCTry ; Alignment reference a 1 2 2 2 2 0 0 0 0 0 0 1 0 c 0 0 0 0 0 0 2 0 2 2 0 0 1 g 0 0 0 0 0 2 0 0 0 0 0 1 0 t 1 0 0 0 0 0 0 2 0 0 2 0 1

oligos_8nt_mkv1_m4_shift0 (oligos_8nt_mkv1_m4)
; oligos_8nt_mkv1_m4 versus oligos_8nt_mkv1_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wAAAAGCTCCTry ; cor=; Ncor= a 1 2 2 2 2 0 0 0 0 0 0 1 0 c 0 0 0 0 0 0 2 0 2 2 0 0 1 g 0 0 0 0 0 2 0 0 0 0 0 1 0 t 1 0 0 0 0 0 0 2 0 0 2 0 1

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m5_shift0 (oligos_8nt_mkv1_m5)
; oligos_8nt_mkv1_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; vMCAATWTTARh ; Alignment reference a 2 1 0 4 4 0 3 0 0 4 3 1 c 1 3 4 0 0 0 0 0 0 0 0 1 g 1 0 0 0 0 0 0 0 0 0 1 0 t 0 0 0 0 0 4 1 4 4 0 0 2

oligos_8nt_mkv1_m5_shift0 (oligos_8nt_mkv1_m5)
; oligos_8nt_mkv1_m5 versus oligos_8nt_mkv1_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; vMCAATWTTARh ; cor=; Ncor= a 2 1 0 4 4 0 3 0 0 4 3 1 c 1 3 4 0 0 0 0 0 0 0 0 1 g 1 0 0 0 0 0 0 0 0 0 1 0 t 0 0 0 0 0 4 1 4 4 0 0 2

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift4 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----bhATGGCYCww ; Alignment reference a 0 0 0 0 1 2 8 0 0 0 1 0 0 3 2 c 0 0 0 0 2 2 0 0 1 0 7 2 7 1 1 g 0 0 0 0 3 1 0 0 7 7 0 0 1 1 0 t 0 0 0 0 2 3 0 8 0 1 0 6 0 3 5

oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----bhATGGCYCww ; cor=; Ncor= a 0 0 0 0 1 2 8 0 0 0 1 0 0 3 2 c 0 0 0 0 2 2 0 0 1 0 7 2 7 1 1 g 0 0 0 0 3 1 0 0 7 7 0 0 1 1 0 t 0 0 0 0 2 3 0 8 0 1 0 6 0 3 5

oligos_8nt_mkv1_m3_shift0 (oligos_8nt_mkv1_m3)
; oligos_7nt_mkv1_m2 versus oligos_8nt_mkv1_m3; m=2/2; ncol2=12; w=-4; offset=-4; strand=D; shift=0; score=0.406473; rvCmCTATrGhT--- ; cor=; Ncor= a 2 1 0 2 0 0 3 0 1 0 1 0 0 0 0 c 0 1 3 1 3 0 0 0 0 0 1 0 0 0 0 g 1 1 0 0 0 0 0 0 2 3 0 0 0 0 0 t 0 0 0 0 0 3 0 3 0 0 1 3 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)
; oligos_8nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; GhGAAGTGCAww ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1

oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)
; oligos_8nt_mkv1_m2 versus oligos_8nt_mkv1_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; GhGAAGTGCAww ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_8nt_mkv1_m2 versus oligos_7nt_mkv1_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.916667; GhGAAGTGCAw- ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 0 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 0

oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_8nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.754655; --swAGTGmArw ; cor=; Ncor= a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=29; shift=0; ncol=29; rvAgGrwwytdaywhwdwwhdwwdAGAdk ; Alignment reference a 5 4 11 0 0 6 5 5 2 2 3 7 2 7 3 6 4 5 4 4 3 6 4 4 9 0 12 3 1 c 2 3 0 2 0 1 1 0 3 1 0 1 5 0 4 0 2 2 0 4 1 1 1 0 1 0 0 1 1 g 3 3 1 8 12 3 2 2 2 1 3 2 1 1 0 1 3 2 2 0 4 0 2 5 1 12 0 4 5 t 2 2 0 2 0 2 4 5 5 8 6 2 4 4 5 5 3 3 6 4 4 5 5 3 1 0 0 4 5

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/1; ncol2=29; w=0; offset=0; strand=D; shift=0; score= 1; rvAgGrwwytdaywhwdwwhdwwdAGAdk ; cor=; Ncor= a 5 4 11 0 0 6 5 5 2 2 3 7 2 7 3 6 4 5 4 4 3 6 4 4 9 0 12 3 1 c 2 3 0 2 0 1 1 0 3 1 0 1 5 0 4 0 2 2 0 4 1 1 1 0 1 0 0 1 1 g 3 3 1 8 12 3 2 2 2 1 3 2 1 1 0 1 3 2 2 0 4 0 2 5 1 12 0 4 5 t 2 2 0 2 0 2 4 5 5 8 6 2 4 4 5 5 3 3 6 4 4 5 5 3 1 0 0 4 5

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=11; shift=0; ncol=11; hdAAAAGAGsr ; Alignment reference a 1 1 4 4 4 4 0 4 0 0 2 c 1 0 0 0 0 0 0 0 0 2 0 g 0 2 0 0 0 0 4 0 4 2 2 t 2 1 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; hdAAAAGAGsr ; cor=; Ncor= a 1 1 4 4 4 4 0 4 0 0 2 c 1 0 0 0 0 0 0 0 0 2 0 g 0 2 0 0 0 0 4 0 4 2 2 t 2 1 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m3_shift0 (oligos_8nt_mkv1_m3)
; oligos_8nt_mkv1_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; rvCmCTATrGhT ; Alignment reference a 2 1 0 2 0 0 3 0 1 0 1 0 c 0 1 3 1 3 0 0 0 0 0 1 0 g 1 1 0 0 0 0 0 0 2 3 0 0 t 0 0 0 0 0 3 0 3 0 0 1 3

oligos_8nt_mkv1_m3_shift0 (oligos_8nt_mkv1_m3)
; oligos_8nt_mkv1_m3 versus oligos_8nt_mkv1_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; rvCmCTATrGhT ; cor=; Ncor= a 2 1 0 2 0 0 3 0 1 0 1 0 c 0 1 3 1 3 0 0 0 0 0 1 0 g 1 1 0 0 0 0 0 0 2 3 0 0 t 0 0 0 0 0 3 0 3 0 0 1 3

oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)
; oligos_8nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/2; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.406473; ----bhATGGCY ; cor=; Ncor= a 0 0 0 0 1 2 8 0 0 0 1 0 c 0 0 0 0 2 2 0 0 1 0 7 2 g 0 0 0 0 3 1 0 0 7 7 0 0 t 0 0 0 0 2 3 0 8 0 1 0 6

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m1_shift0 (oligos_8nt_mkv1_m1)
; oligos_8nt_mkv1_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; ybCTGTGGAAkh ; Alignment reference a 0 0 0 0 0 0 0 0 3 3 0 1 c 2 1 3 0 0 0 0 0 0 0 0 1 g 0 1 0 0 3 0 3 3 0 0 1 0 t 1 1 0 3 0 3 0 0 0 0 2 1

oligos_8nt_mkv1_m1_shift0 (oligos_8nt_mkv1_m1)
; oligos_8nt_mkv1_m1 versus oligos_8nt_mkv1_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ybCTGTGGAAkh ; cor=; Ncor= a 0 0 0 0 0 0 0 0 3 3 0 1 c 2 1 3 0 0 0 0 0 0 0 0 1 g 0 1 0 0 3 0 3 3 0 0 1 0 t 1 1 0 3 0 3 0 0 0 0 2 1

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_8nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.870312; ctCTGTGGAwt- ; cor=; Ncor= a 0 1 0 0 1 0 0 0 5 3 1 0 c 3 1 5 0 0 0 0 0 0 0 0 0 g 1 1 0 0 4 0 4 5 0 0 1 0 t 1 2 0 5 0 5 1 0 0 2 3 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)				; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; GhGAAGTGCAw ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 c 0 1 0 0 0 0 0 0 3 0 0 g 3 0 3 0 0 3 0 3 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)				; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; GhGAAGTGCAw ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 c 0 1 0 0 0 0 0 0 3 0 0 g 3 0 3 0 0 3 0 3 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)				; oligos_7nt_mkv1_m3 versus oligos_8nt_mkv1_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.916667; GhGAAGTGCAw ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 c 0 1 0 0 0 0 0 0 3 0 0 g 3 0 3 0 0 3 0 3 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.678706; --swAGTGmAr ; cor=; Ncor= a 0 0 1 3 6 0 0 0 2 6 3 c 0 0 2 0 0 0 0 0 4 0 0 g 0 0 3 1 0 6 0 6 0 0 2 t 0 0 0 2 0 0 6 0 0 0 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --swAGTGmArw ; Alignment reference a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --swAGTGmArw ; cor=; Ncor= a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)				; oligos_6nt_mkv1_m1 versus oligos_8nt_mkv1_m2; m=2/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.754655; GhGAAGTGCAww ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m3; m=3/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.678706; GhGAAGTGCAw- ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 0 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)				; oligos_8nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; GhGAAGTGCAww ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)				; oligos_8nt_mkv1_m2 versus oligos_8nt_mkv1_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; GhGAAGTGCAww ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)				; oligos_8nt_mkv1_m2 versus oligos_7nt_mkv1_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.916667; GhGAAGTGCAw- ; cor=; Ncor= a 0 1 0 3 3 0 0 0 0 3 2 0 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 0
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_8nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.754655; --swAGTGmArw ; cor=; Ncor= a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2