One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/12/19/peak-motifs.2025-12-19.115413_2025-12-19.115413_FZ7H1y/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/2025/12/19/peak-motifs.2025-12-19.115413_2025-12-19.115413_FZ7H1y/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=14; shift=3; ncol=17; ---yywkAGGCCTmwrr ; Alignment reference a 0 0 0 1 0 2 1 8 0 0 0 0 0 3 4 4 4 c 0 0 0 3 4 1 0 0 0 0 8 8 0 4 1 0 0 g 0 0 0 0 0 1 4 0 8 8 0 0 0 0 1 4 3 t 0 0 0 4 4 4 3 0 0 0 0 0 8 1 2 0 1

oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---yywkAGGCCTmwrr ; cor=; Ncor= a 0 0 0 1 0 2 1 8 0 0 0 0 0 3 4 4 4 c 0 0 0 3 4 1 0 0 0 0 8 8 0 4 1 0 0 g 0 0 0 0 0 1 4 0 8 8 0 0 0 0 1 4 3 t 0 0 0 4 4 4 3 0 0 0 0 0 8 1 2 0 1

oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=2/2; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score= 0.6833; ysryywkAGGCCTmwrr ; cor=; Ncor= a 0 0 1 0 0 1 0 2 0 0 0 0 0 1 1 1 1 c 1 1 0 1 1 0 0 0 0 0 2 2 0 1 0 0 0 g 0 1 1 0 0 0 1 0 2 2 0 0 0 0 0 1 1 t 1 0 0 1 1 1 1 0 0 0 0 0 2 0 1 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 3 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; TAAAATATCAA ; Alignment reference a 3 35 41 37 41 0 41 0 2 32 36 c 1 2 0 0 0 0 0 1 39 2 1 g 3 4 0 0 0 0 0 0 0 3 1 t 34 0 0 4 0 41 0 40 0 4 3

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; TAAAATATCAA ; cor=; Ncor= a 3 35 41 37 41 0 41 0 2 32 36 c 1 2 0 0 0 0 0 1 39 2 1 g 3 4 0 0 0 0 0 0 0 3 1 t 34 0 0 4 0 41 0 40 0 4 3

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; TAAAATATCAA ; cor=; Ncor= a 3 35 41 37 41 0 41 0 2 32 36 c 1 2 0 0 0 0 0 1 39 2 1 g 3 4 0 0 0 0 0 0 0 3 1 t 34 0 0 4 0 41 0 40 0 4 3

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 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=14; shift=0; ncol=14; aswGAGTTGAAyvy ; Alignment reference a 7 1 4 0 11 0 1 1 0 11 10 1 3 1 c 2 4 0 0 0 0 0 0 0 0 1 5 4 5 g 0 4 1 11 0 11 0 0 10 0 0 1 3 1 t 2 2 6 0 0 0 10 10 1 0 0 4 1 4

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; aswGAGTTGAAyvy ; cor=; Ncor= a 7 1 4 0 11 0 1 1 0 11 10 1 3 1 c 2 4 0 0 0 0 0 0 0 0 1 5 4 5 g 0 4 1 11 0 11 0 0 10 0 0 1 3 1 t 2 2 6 0 0 0 10 10 1 0 0 4 1 4

oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m2_rc; m=2/2; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.834905; -bdGAGTTGAAys- ; cor=; Ncor= a 0 2 5 0 16 3 1 1 0 16 15 1 3 0 c 0 6 0 0 0 0 0 0 0 0 1 5 4 0 g 0 4 4 16 0 13 0 2 15 0 0 1 8 0 t 0 4 7 0 0 0 15 13 1 0 0 9 1 0

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; TCCATTCCATTCCA ; Alignment reference a 0 3 3 44 2 0 2 3 46 2 0 3 7 40 c 0 35 36 0 0 0 43 42 0 3 0 42 35 1 g 2 2 5 2 0 0 1 0 1 0 1 1 2 5 t 46 8 4 2 46 48 2 3 1 43 47 2 4 2

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; TCCATTCCATTCCA ; cor=; Ncor= a 0 3 3 44 2 0 2 3 46 2 0 3 7 40 c 0 35 36 0 0 0 43 42 0 3 0 42 35 1 g 2 2 5 2 0 0 1 0 1 0 1 1 2 5 t 46 8 4 2 46 48 2 3 1 43 47 2 4 2

oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1_rc; m=2/3; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.932269; TCCATTCCATTCCA ; cor=; Ncor= a 1 4 3 43 2 0 2 3 44 2 0 2 6 41 c 0 33 37 0 0 0 43 41 1 2 0 41 37 1 g 1 2 5 2 0 1 1 0 1 0 1 1 0 3 t 45 8 2 2 45 46 1 3 1 43 46 3 4 2

oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.621589; --srTTCAACTChv ; cor=; Ncor= a 0 0 1 9 0 0 1 13 15 0 0 0 7 4 c 0 0 8 1 0 0 15 2 0 13 0 16 4 4 g 0 0 4 5 1 0 0 0 0 0 0 0 0 6 t 0 0 3 1 15 16 0 1 1 3 16 0 5 2

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --srTTCAACTChv ; Alignment reference a 0 0 1 9 0 0 1 13 15 0 0 0 7 4 c 0 0 8 1 0 0 15 2 0 13 0 16 4 4 g 0 0 4 5 1 0 0 0 0 0 0 0 0 6 t 0 0 3 1 15 16 0 1 1 3 16 0 5 2

oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --srTTCAACTChv ; cor=; Ncor= a 0 0 1 9 0 0 1 13 15 0 0 0 7 4 c 0 0 8 1 0 0 15 2 0 13 0 16 4 4 g 0 0 4 5 1 0 0 0 0 0 0 0 0 6 t 0 0 3 1 15 16 0 1 1 3 16 0 5 2

oligos_7nt_mkv1_m2_rc_shift1 (oligos_7nt_mkv1_m2_rc)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2_rc; m=2/4; ncol2=14; w=-1; offset=-1; strand=R; shift=1; score=0.834905; -rbrTTCAACTCws ; cor=; Ncor= a 0 4 1 4 0 0 1 10 10 0 0 0 6 2 c 0 1 3 1 0 0 10 0 0 11 0 11 1 4 g 0 5 4 5 1 0 0 0 0 0 0 0 0 4 t 0 1 3 1 10 11 0 1 1 0 11 0 4 1

oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=3/4; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.621589; TCCATTCCATTCCA ; cor=; Ncor= a 0 3 3 44 2 0 2 3 46 2 0 3 7 40 c 0 35 36 0 0 0 43 42 0 3 0 42 35 1 g 2 2 5 2 0 0 1 0 1 0 1 1 2 5 t 46 8 4 2 46 48 2 3 1 43 47 2 4 2

oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1_rc; m=4/4; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.569648; TCCATTCCATTCCA ; cor=; Ncor= a 1 4 3 43 2 0 2 3 44 2 0 2 6 41 c 0 33 37 0 0 0 43 41 1 2 0 41 37 1 g 1 2 5 2 0 1 1 0 1 0 1 1 0 3 t 45 8 2 2 45 46 1 3 1 43 46 3 4 2

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=15; shift=0; ncol=15; ATGGAATGGAATGGA ; Alignment reference a 40 2 4 3 46 43 1 3 1 46 45 2 2 8 45 c 1 3 0 1 1 0 1 0 1 1 0 2 5 2 1 g 4 1 37 41 0 2 1 41 43 0 0 0 37 33 0 t 2 41 6 2 0 2 44 3 2 0 2 43 3 4 1

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ATGGAATGGAATGGA ; cor=; Ncor= a 40 2 4 3 46 43 1 3 1 46 45 2 2 8 45 c 1 3 0 1 1 0 1 0 1 1 0 2 5 2 1 g 4 1 37 41 0 2 1 41 43 0 0 0 37 33 0 t 2 41 6 2 0 2 44 3 2 0 2 43 3 4 1

oligos_6nt_mkv1_m1_rc_shift1 (oligos_6nt_mkv1_m1_rc)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1_rc; m=2/3; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.932269; -TGGAATGGAATGGA ; cor=; Ncor= a 0 2 4 2 47 43 1 3 2 48 46 2 4 8 46 c 0 5 2 1 1 0 1 0 1 0 0 2 5 2 2 g 0 1 35 42 0 3 0 42 43 0 0 0 36 35 0 t 0 40 7 3 0 2 46 3 2 0 2 44 3 3 0

oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=3/3; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.569648; -bdGAGTTGAAys-- ; cor=; Ncor= a 0 2 5 0 16 3 1 1 0 16 15 1 3 0 0 c 0 6 0 0 0 0 0 0 0 0 1 5 4 0 0 g 0 4 4 16 0 13 0 2 15 0 0 1 8 0 0 t 0 4 7 0 0 0 15 13 1 0 0 9 1 0 0

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=11; shift=0; ncol=11; TAAAATATCAA ; Alignment reference a 3 35 41 37 41 0 41 0 2 32 36 c 1 2 0 0 0 0 0 1 39 2 1 g 3 4 0 0 0 0 0 0 0 3 1 t 34 0 0 4 0 41 0 40 0 4 3

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; TAAAATATCAA ; cor=; Ncor= a 3 35 41 37 41 0 41 0 2 32 36 c 1 2 0 0 0 0 0 1 39 2 1 g 3 4 0 0 0 0 0 0 0 3 1 t 34 0 0 4 0 41 0 40 0 4 3

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; TAAAATATCAA ; cor=; Ncor= a 3 35 41 37 41 0 41 0 2 32 36 c 1 2 0 0 0 0 0 1 39 2 1 g 3 4 0 0 0 0 0 0 0 3 1 t 34 0 0 4 0 41 0 40 0 4 3

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift0 ; 3 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=20; shift=0; ncol=20; ysryywkAGGCCTmwrrysr ; Alignment reference a 0 0 1 0 0 1 0 2 0 0 0 0 0 1 1 1 1 0 0 1 c 1 1 0 1 1 0 0 0 0 0 2 2 0 1 0 0 0 1 1 0 g 0 1 1 0 0 0 1 0 2 2 0 0 0 0 0 1 1 0 1 1 t 1 0 0 1 1 1 1 0 0 0 0 0 2 0 1 0 0 1 0 0

oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/2; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; ysryywkAGGCCTmwrrysr ; cor=; Ncor= a 0 0 1 0 0 1 0 2 0 0 0 0 0 1 1 1 1 0 0 1 c 1 1 0 1 1 0 0 0 0 0 2 2 0 1 0 0 0 1 1 0 g 0 1 1 0 0 0 1 0 2 2 0 0 0 0 0 1 1 0 1 1 t 1 0 0 1 1 1 1 0 0 0 0 0 2 0 1 0 0 1 0 0

oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=2/2; ncol2=14; w=0; offset=3; strand=D; shift=3; score= 0.6833; ---yywkAGGCCTmwrr--- ; cor=; Ncor= a 0 0 0 1 0 2 1 8 0 0 0 0 0 3 4 4 4 0 0 0 c 0 0 0 3 4 1 0 0 0 0 8 8 0 4 1 0 0 0 0 0 g 0 0 0 0 0 1 4 0 8 8 0 0 0 0 1 4 3 0 0 0 t 0 0 0 4 4 4 3 0 0 0 0 0 8 1 2 0 1 0 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; myCAAAGTAysy ; Alignment reference a 41 2 2 61 63 61 0 1 62 0 1 2 c 21 19 57 0 0 1 0 0 0 42 35 36 g 0 2 2 2 0 0 61 0 1 1 21 1 t 1 40 2 0 0 1 2 62 0 20 6 24

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; myCAAAGTAysy ; cor=; Ncor= a 41 2 2 61 63 61 0 1 62 0 1 2 c 21 19 57 0 0 1 0 0 0 42 35 36 g 0 2 2 2 0 0 61 0 1 1 21 1 t 1 40 2 0 0 1 2 62 0 20 6 24

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; GTACATAAAAT ; Alignment reference a 2 1 40 0 39 0 40 40 34 36 4 c 0 3 0 40 1 0 0 0 0 1 1 g 33 3 0 0 0 0 0 0 0 1 0 t 5 33 0 0 0 40 0 0 6 2 35

oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; GTACATAAAAT ; cor=; Ncor= a 2 1 40 0 39 0 40 40 34 36 4 c 0 3 0 40 1 0 0 0 0 1 1 g 33 3 0 0 0 0 0 0 0 1 0 t 5 33 0 0 0 40 0 0 6 2 35

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; TCCATTCCATTCCA ; Alignment reference a 0 3 3 44 2 0 2 3 46 2 0 3 7 40 c 0 35 36 0 0 0 43 42 0 3 0 42 35 1 g 2 2 5 2 0 0 1 0 1 0 1 1 2 5 t 46 8 4 2 46 48 2 3 1 43 47 2 4 2
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; TCCATTCCATTCCA ; cor=; Ncor= a 0 3 3 44 2 0 2 3 46 2 0 3 7 40 c 0 35 36 0 0 0 43 42 0 3 0 42 35 1 g 2 2 5 2 0 0 1 0 1 0 1 1 2 5 t 46 8 4 2 46 48 2 3 1 43 47 2 4 2
oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1_rc; m=2/3; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.932269; TCCATTCCATTCCA ; cor=; Ncor= a 1 4 3 43 2 0 2 3 44 2 0 2 6 41 c 0 33 37 0 0 0 43 41 1 2 0 41 37 1 g 1 2 5 2 0 1 1 0 1 0 1 1 0 3 t 45 8 2 2 45 46 1 3 1 43 46 3 4 2
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.621589; --srTTCAACTChv ; cor=; Ncor= a 0 0 1 9 0 0 1 13 15 0 0 0 7 4 c 0 0 8 1 0 0 15 2 0 13 0 16 4 4 g 0 0 4 5 1 0 0 0 0 0 0 0 0 6 t 0 0 3 1 15 16 0 1 1 3 16 0 5 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --srTTCAACTChv ; Alignment reference a 0 0 1 9 0 0 1 13 15 0 0 0 7 4 c 0 0 8 1 0 0 15 2 0 13 0 16 4 4 g 0 0 4 5 1 0 0 0 0 0 0 0 0 6 t 0 0 3 1 15 16 0 1 1 3 16 0 5 2
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --srTTCAACTChv ; cor=; Ncor= a 0 0 1 9 0 0 1 13 15 0 0 0 7 4 c 0 0 8 1 0 0 15 2 0 13 0 16 4 4 g 0 0 4 5 1 0 0 0 0 0 0 0 0 6 t 0 0 3 1 15 16 0 1 1 3 16 0 5 2
oligos_7nt_mkv1_m2_rc_shift1 (oligos_7nt_mkv1_m2_rc)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2_rc; m=2/4; ncol2=14; w=-1; offset=-1; strand=R; shift=1; score=0.834905; -rbrTTCAACTCws ; cor=; Ncor= a 0 4 1 4 0 0 1 10 10 0 0 0 6 2 c 0 1 3 1 0 0 10 0 0 11 0 11 1 4 g 0 5 4 5 1 0 0 0 0 0 0 0 0 4 t 0 1 3 1 10 11 0 1 1 0 11 0 4 1
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=3/4; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.621589; TCCATTCCATTCCA ; cor=; Ncor= a 0 3 3 44 2 0 2 3 46 2 0 3 7 40 c 0 35 36 0 0 0 43 42 0 3 0 42 35 1 g 2 2 5 2 0 0 1 0 1 0 1 1 2 5 t 46 8 4 2 46 48 2 3 1 43 47 2 4 2
oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1_rc; m=4/4; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.569648; TCCATTCCATTCCA ; cor=; Ncor= a 1 4 3 43 2 0 2 3 44 2 0 2 6 41 c 0 33 37 0 0 0 43 41 1 2 0 41 37 1 g 1 2 5 2 0 1 1 0 1 0 1 1 0 3 t 45 8 2 2 45 46 1 3 1 43 46 3 4 2

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=15; shift=0; ncol=15; ATGGAATGGAATGGA ; Alignment reference a 40 2 4 3 46 43 1 3 1 46 45 2 2 8 45 c 1 3 0 1 1 0 1 0 1 1 0 2 5 2 1 g 4 1 37 41 0 2 1 41 43 0 0 0 37 33 0 t 2 41 6 2 0 2 44 3 2 0 2 43 3 4 1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ATGGAATGGAATGGA ; cor=; Ncor= a 40 2 4 3 46 43 1 3 1 46 45 2 2 8 45 c 1 3 0 1 1 0 1 0 1 1 0 2 5 2 1 g 4 1 37 41 0 2 1 41 43 0 0 0 37 33 0 t 2 41 6 2 0 2 44 3 2 0 2 43 3 4 1
oligos_6nt_mkv1_m1_rc_shift1 (oligos_6nt_mkv1_m1_rc)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1_rc; m=2/3; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.932269; -TGGAATGGAATGGA ; cor=; Ncor= a 0 2 4 2 47 43 1 3 2 48 46 2 4 8 46 c 0 5 2 1 1 0 1 0 1 0 0 2 5 2 2 g 0 1 35 42 0 3 0 42 43 0 0 0 36 35 0 t 0 40 7 3 0 2 46 3 2 0 2 44 3 3 0
oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=3/3; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.569648; -bdGAGTTGAAys-- ; cor=; Ncor= a 0 2 5 0 16 3 1 1 0 16 15 1 3 0 0 c 0 6 0 0 0 0 0 0 0 0 1 5 4 0 0 g 0 4 4 16 0 13 0 2 15 0 0 1 8 0 0 t 0 4 7 0 0 0 15 13 1 0 0 9 1 0 0