One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/26/peak-motifs.2025-04-26.155957_2025-04-26.155957_kQZNmB/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/2025/04/26/peak-motifs.2025-04-26.155957_2025-04-26.155957_kQZNmB/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=15; shift=0; ncol=15; AAwTCCTCGyCTwww ; Alignment reference a 3 3 2 0 0 0 0 0 0 0 0 0 1 1 1 c 0 0 0 0 3 3 0 3 0 2 3 0 0 0 0 g 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 t 0 0 1 3 0 0 3 0 0 1 0 3 2 2 2

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; AAwTCCTCGyCTwww ; cor=; Ncor= a 3 3 2 0 0 0 0 0 0 0 0 0 1 1 1 c 0 0 0 0 3 3 0 3 0 2 3 0 0 0 0 g 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 t 0 0 1 3 0 0 3 0 0 1 0 3 2 2 2

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.593217; wwCTCCTCsym---- ; cor=; Ncor= a 6 4 2 0 0 0 0 0 0 1 3 0 0 0 0 c 0 2 7 0 10 10 0 10 4 5 5 0 0 0 0 g 1 0 0 0 0 0 0 0 4 0 1 0 0 0 0 t 3 4 1 10 0 0 10 0 2 4 1 0 0 0 0

oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m2; m=3/3; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.52739; ----ysTCGTCThw- ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 0 1 0 2 3 0 c 0 0 0 0 3 3 0 7 0 0 5 0 2 0 0 g 0 0 0 0 0 3 0 0 7 0 0 0 1 0 0 t 0 0 0 0 3 1 7 0 0 7 1 7 2 4 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 4 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=11; shift=0; ncol=11; wwCTCCTCsym ; Alignment reference a 6 4 2 0 0 0 0 0 0 1 3 c 0 2 7 0 10 10 0 10 4 5 5 g 1 0 0 0 0 0 0 0 4 0 1 t 3 4 1 10 0 0 10 0 2 4 1

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCTCCTCsym ; cor=; Ncor= a 6 4 2 0 0 0 0 0 0 1 3 c 0 2 7 0 10 10 0 10 4 5 5 g 1 0 0 0 0 0 0 0 4 0 1 t 3 4 1 10 0 0 10 0 2 4 1

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.950227; whCTYCTCCym ; cor=; Ncor= a 6 5 1 0 0 0 0 0 0 1 3 c 2 3 11 0 9 12 0 12 9 6 6 g 1 0 0 0 0 0 0 0 1 0 1 t 3 4 0 12 3 0 12 0 2 5 2

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=3/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.593217; AAwTCCTCGyC ; cor=; Ncor= a 3 3 2 0 0 0 0 0 0 0 0 c 0 0 0 0 3 3 0 3 0 2 3 g 0 0 0 0 0 0 0 0 3 0 0 t 0 0 1 3 0 0 3 0 0 1 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift4 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ysTCGTCThw ; Alignment reference a 0 0 0 0 1 0 0 0 0 0 1 0 2 3 c 0 0 0 0 3 3 0 7 0 0 5 0 2 0 g 0 0 0 0 0 3 0 0 7 0 0 0 1 0 t 0 0 0 0 3 1 7 0 0 7 1 7 2 4

oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----ysTCGTCThw ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 0 1 0 2 3 c 0 0 0 0 3 3 0 7 0 0 5 0 2 0 g 0 0 0 0 0 3 0 0 7 0 0 0 1 0 t 0 0 0 0 3 1 7 0 0 7 1 7 2 4

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m3; m=2/2; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.52739; AAwTCCTCGyCTww ; cor=; Ncor= a 3 3 2 0 0 0 0 0 0 0 0 0 1 1 c 0 0 0 0 3 3 0 3 0 2 3 0 0 0 g 0 0 0 0 0 0 0 0 3 0 0 0 0 0 t 0 0 1 3 0 0 3 0 0 1 0 3 2 2

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift1 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -whCTYCTCCym ; Alignment reference a 0 6 5 1 0 0 0 0 0 0 1 3 c 0 2 3 11 0 9 12 0 12 9 6 6 g 0 1 0 0 0 0 0 0 0 1 0 1 t 0 3 4 0 12 3 0 12 0 2 5 2

oligos_7nt_mkv1_m2_shift1 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -whCTYCTCCym ; cor=; Ncor= a 0 6 5 1 0 0 0 0 0 0 1 3 c 0 2 3 11 0 9 12 0 12 9 6 6 g 0 1 0 0 0 0 0 0 0 1 0 1 t 0 3 4 0 12 3 0 12 0 2 5 2

oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.950227; -wwCTCCTCsym ; cor=; Ncor= a 0 6 4 2 0 0 0 0 0 0 1 3 c 0 0 2 7 0 10 10 0 10 4 5 5 g 0 1 0 0 0 0 0 0 0 4 0 1 t 0 3 4 1 10 0 0 10 0 2 4 1

oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.568466; mmcCyTCTCCCC ; cor=; Ncor= a 5 4 2 0 1 0 0 0 0 0 0 1 c 3 5 5 7 5 0 9 0 9 8 9 8 g 0 0 0 1 0 0 0 0 0 0 0 0 t 1 0 2 1 3 9 0 9 0 1 0 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=16; shift=0; ncol=16; mMMCCYTCTCCCCAwm ; Alignment reference a 3 2 2 0 0 0 0 0 0 0 0 0 1 5 3 2 c 2 5 5 6 6 5 1 7 0 7 6 7 6 1 1 4 g 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 t 1 0 0 1 1 2 6 0 7 0 1 0 0 1 3 0

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/2; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; mMMCCYTCTCCCCAwm ; cor=; Ncor= a 3 2 2 0 0 0 0 0 0 0 0 0 1 5 3 2 c 2 5 5 6 6 5 1 7 0 7 6 7 6 1 1 4 g 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 t 1 0 0 1 1 2 6 0 7 0 1 0 0 1 3 0

oligos_6nt_mkv1_m1_shift1 (oligos_6nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=2/2; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.825737; -mmcCyTCTCCCChw- ; cor=; Ncor= a 0 5 4 2 0 1 0 0 0 0 0 0 1 3 3 0 c 0 3 5 5 7 5 0 9 0 9 8 9 8 3 2 0 g 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 t 0 1 0 2 1 3 9 0 9 0 1 0 0 3 4 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift1 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -mmcCyTCTCCCChw ; Alignment reference a 0 5 4 2 0 1 0 0 0 0 0 0 1 3 3 c 0 3 5 5 7 5 0 9 0 9 8 9 8 3 2 g 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 t 0 1 0 2 1 3 9 0 9 0 1 0 0 3 4

oligos_6nt_mkv1_m1_shift1 (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=1; score= 1; -mmcCyTCTCCCChw ; cor=; Ncor= a 0 5 4 2 0 1 0 0 0 0 0 0 1 3 3 c 0 3 5 5 7 5 0 9 0 9 8 9 8 3 2 g 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 t 0 1 0 2 1 3 9 0 9 0 1 0 0 3 4

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/3; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.825737; mMMCCYTCTCCCCAw ; cor=; Ncor= a 3 2 2 0 0 0 0 0 0 0 0 0 1 5 3 c 2 5 5 6 6 5 1 7 0 7 6 7 6 1 1 g 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 1 0 0 1 1 2 6 0 7 0 1 0 0 1 3

oligos_7nt_mkv1_m2_shift2 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.568466; --whCTYCTCCym-- ; cor=; Ncor= a 0 0 6 5 1 0 0 0 0 0 0 1 3 0 0 c 0 0 2 3 11 0 9 12 0 12 9 6 6 0 0 g 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 t 0 0 3 4 0 12 3 0 12 0 2 5 2 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift0 ; 2 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=12; shift=0; ncol=12; twTATTAATAww ; Alignment reference a 3 9 0 15 0 0 13 13 0 14 7 8 c 1 2 1 0 1 0 0 0 0 0 2 2 g 2 0 0 0 0 0 1 0 0 1 0 1 t 9 4 14 0 14 15 1 2 15 0 6 4

oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; twTATTAATAww ; cor=; Ncor= a 3 9 0 15 0 0 13 13 0 14 7 8 c 1 2 1 0 1 0 0 0 0 0 2 2 g 2 0 0 0 0 0 1 0 0 1 0 1 t 9 4 14 0 14 15 1 2 15 0 6 4

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; whCACATAArm ; Alignment reference a 3 2 0 7 0 6 0 6 7 3 4 c 1 2 7 0 7 0 1 0 0 0 2 g 0 1 0 0 0 0 0 0 0 4 0 t 3 2 0 0 0 1 6 1 0 0 1

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; whCACATAArm ; cor=; Ncor= a 3 2 0 7 0 6 0 6 7 3 4 c 1 2 7 0 7 0 1 0 0 0 2 g 0 1 0 0 0 0 0 0 0 4 0 t 3 2 0 0 0 1 6 1 0 0 1

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; raGACAGAgr ; Alignment reference a 2 3 0 5 0 5 0 4 1 2 c 0 1 0 0 5 0 0 0 1 0 g 2 1 5 0 0 0 5 0 2 2 t 1 0 0 0 0 0 0 1 1 1

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; raGACAGAgr ; cor=; Ncor= a 2 3 0 5 0 5 0 4 1 2 c 0 1 0 0 5 0 0 0 1 0 g 2 1 5 0 0 0 5 0 2 2 t 1 0 0 0 0 0 0 1 1 1

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=15; shift=0; ncol=15; AAwTCCTCGyCTwww ; Alignment reference a 3 3 2 0 0 0 0 0 0 0 0 0 1 1 1 c 0 0 0 0 3 3 0 3 0 2 3 0 0 0 0 g 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 t 0 0 1 3 0 0 3 0 0 1 0 3 2 2 2
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)				; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; AAwTCCTCGyCTwww ; cor=; Ncor= a 3 3 2 0 0 0 0 0 0 0 0 0 1 1 1 c 0 0 0 0 3 3 0 3 0 2 3 0 0 0 0 g 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 t 0 0 1 3 0 0 3 0 0 1 0 3 2 2 2
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)				; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.593217; wwCTCCTCsym---- ; cor=; Ncor= a 6 4 2 0 0 0 0 0 0 1 3 0 0 0 0 c 0 2 7 0 10 10 0 10 4 5 5 0 0 0 0 g 1 0 0 0 0 0 0 0 4 0 1 0 0 0 0 t 3 4 1 10 0 0 10 0 2 4 1 0 0 0 0
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)				; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m2; m=3/3; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.52739; ----ysTCGTCThw- ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 0 1 0 2 3 0 c 0 0 0 0 3 3 0 7 0 0 5 0 2 0 0 g 0 0 0 0 0 3 0 0 7 0 0 0 1 0 0 t 0 0 0 0 3 1 7 0 0 7 1 7 2 4 0

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=11; shift=0; ncol=11; wwCTCCTCsym ; Alignment reference a 6 4 2 0 0 0 0 0 0 1 3 c 0 2 7 0 10 10 0 10 4 5 5 g 1 0 0 0 0 0 0 0 4 0 1 t 3 4 1 10 0 0 10 0 2 4 1
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCTCCTCsym ; cor=; Ncor= a 6 4 2 0 0 0 0 0 0 1 3 c 0 2 7 0 10 10 0 10 4 5 5 g 1 0 0 0 0 0 0 0 4 0 1 t 3 4 1 10 0 0 10 0 2 4 1
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.950227; whCTYCTCCym ; cor=; Ncor= a 6 5 1 0 0 0 0 0 0 1 3 c 2 3 11 0 9 12 0 12 9 6 6 g 1 0 0 0 0 0 0 0 1 0 1 t 3 4 0 12 3 0 12 0 2 5 2
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)				; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=3/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.593217; AAwTCCTCGyC ; cor=; Ncor= a 3 3 2 0 0 0 0 0 0 0 0 c 0 0 0 0 3 3 0 3 0 2 3 g 0 0 0 0 0 0 0 0 3 0 0 t 0 0 1 3 0 0 3 0 0 1 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m2_shift1 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -whCTYCTCCym ; Alignment reference a 0 6 5 1 0 0 0 0 0 0 1 3 c 0 2 3 11 0 9 12 0 12 9 6 6 g 0 1 0 0 0 0 0 0 0 1 0 1 t 0 3 4 0 12 3 0 12 0 2 5 2
oligos_7nt_mkv1_m2_shift1 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -whCTYCTCCym ; cor=; Ncor= a 0 6 5 1 0 0 0 0 0 0 1 3 c 0 2 3 11 0 9 12 0 12 9 6 6 g 0 1 0 0 0 0 0 0 0 1 0 1 t 0 3 4 0 12 3 0 12 0 2 5 2
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.950227; -wwCTCCTCsym ; cor=; Ncor= a 0 6 4 2 0 0 0 0 0 0 1 3 c 0 0 2 7 0 10 10 0 10 4 5 5 g 0 1 0 0 0 0 0 0 0 4 0 1 t 0 3 4 1 10 0 0 10 0 2 4 1
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.568466; mmcCyTCTCCCC ; cor=; Ncor= a 5 4 2 0 1 0 0 0 0 0 0 1 c 3 5 5 7 5 0 9 0 9 8 9 8 g 0 0 0 1 0 0 0 0 0 0 0 0 t 1 0 2 1 3 9 0 9 0 1 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift1 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -mmcCyTCTCCCChw ; Alignment reference a 0 5 4 2 0 1 0 0 0 0 0 0 1 3 3 c 0 3 5 5 7 5 0 9 0 9 8 9 8 3 2 g 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 t 0 1 0 2 1 3 9 0 9 0 1 0 0 3 4
oligos_6nt_mkv1_m1_shift1 (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=1; score= 1; -mmcCyTCTCCCChw ; cor=; Ncor= a 0 5 4 2 0 1 0 0 0 0 0 0 1 3 3 c 0 3 5 5 7 5 0 9 0 9 8 9 8 3 2 g 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 t 0 1 0 2 1 3 9 0 9 0 1 0 0 3 4
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/3; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.825737; mMMCCYTCTCCCCAw ; cor=; Ncor= a 3 2 2 0 0 0 0 0 0 0 0 0 1 5 3 c 2 5 5 6 6 5 1 7 0 7 6 7 6 1 1 g 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 1 0 0 1 1 2 6 0 7 0 1 0 0 1 3
oligos_7nt_mkv1_m2_shift2 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.568466; --whCTYCTCCym-- ; cor=; Ncor= a 0 0 6 5 1 0 0 0 0 0 0 1 3 0 0 c 0 0 2 3 11 0 9 12 0 12 9 6 6 0 0 g 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 t 0 0 3 4 0 12 3 0 12 0 2 5 2 0 0