One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124321_2025-04-03.124321_p2X2cO/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/2025/04/03/peak-motifs.2025-04-03.124321_2025-04-03.124321_p2X2cO/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 5 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=14; shift=0; ncol=14; rsmyCGTACGrksy ; Alignment reference a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=3/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.826135; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.825624; wkcTCGTACGGtr- ; cor=; Ncor= a 10 4 6 3 0 0 0 28 0 3 5 7 14 0 c 5 3 23 1 29 0 0 6 31 1 1 6 6 0 g 8 14 0 0 1 34 1 0 3 30 26 6 10 0 t 11 13 5 30 4 0 33 0 0 0 2 15 4 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -yaGATATCtr ; Alignment reference a 0 10 20 1 41 0 39 0 0 4 12 c 0 12 10 0 0 3 0 0 40 8 7 g 0 7 8 40 0 0 2 0 0 9 13 t 0 12 3 0 0 38 0 41 1 20 9

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -yaGATATCtr ; cor=; Ncor= a 0 10 20 1 41 0 39 0 0 4 12 c 0 12 10 0 0 3 0 0 40 8 7 g 0 7 8 40 0 0 2 0 0 9 13 t 0 12 3 0 0 38 0 41 1 20 9

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.819988; khAGATATCTd ; cor=; Ncor= a 5 10 22 0 31 0 32 0 1 1 8 c 4 8 6 0 1 0 0 0 31 3 6 g 14 6 3 31 0 0 0 1 0 6 8 t 9 8 1 1 0 32 0 31 0 22 10

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 3 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; khAGATATCTdm ; Alignment reference a 5 10 22 0 31 0 32 0 1 1 8 9 c 4 8 6 0 1 0 0 0 31 3 6 14 g 14 6 3 31 0 0 0 1 0 6 8 4 t 9 8 1 1 0 32 0 31 0 22 10 5

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; khAGATATCTdm ; cor=; Ncor= a 5 10 22 0 31 0 32 0 1 1 8 9 c 4 8 6 0 1 0 0 0 31 3 6 14 g 14 6 3 31 0 0 0 1 0 6 8 4 t 9 8 1 1 0 32 0 31 0 22 10 5

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=2/2; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.819988; -yaGATATCtr- ; cor=; Ncor= a 0 9 20 1 41 0 38 0 0 3 12 0 c 0 13 9 0 0 2 0 0 40 8 7 0 g 0 7 8 40 0 0 3 0 0 10 12 0 t 0 12 4 0 0 39 0 41 1 20 10 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; rsmyCGTACGrksy ; Alignment reference a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=3/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.826135; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.825624; wkcTCGTACGGtr- ; cor=; Ncor= a 10 4 6 3 0 0 0 28 0 3 5 7 14 0 c 5 3 23 1 29 0 0 6 31 1 1 6 6 0 g 8 14 0 0 1 34 1 0 3 30 26 6 10 0 t 11 13 5 30 4 0 33 0 0 0 2 15 4 0

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; mcAAAGGCmm ; Alignment reference a 10 1 24 24 23 0 0 0 8 6 c 10 15 0 0 1 0 0 24 8 11 g 2 5 0 0 0 24 24 0 4 3 t 2 3 0 0 0 0 0 0 4 4

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; mcAAAGGCmm ; cor=; Ncor= a 10 1 24 24 23 0 0 0 8 6 c 10 15 0 0 1 0 0 24 8 11 g 2 5 0 0 0 24 24 0 4 3 t 2 3 0 0 0 0 0 0 4 4

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=13; shift=1; ncol=14; -yaCCGTACGAgmw ; Alignment reference a 0 4 15 2 0 0 0 33 0 4 30 5 13 11 c 0 10 6 26 30 3 0 1 34 1 0 0 14 8 g 0 6 6 1 1 31 6 0 0 29 1 23 3 5 t 0 14 7 5 3 0 28 0 0 0 3 6 4 10

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 30 5 13 11 c 0 10 6 26 30 3 0 1 34 1 0 0 14 8 g 0 6 6 1 1 31 6 0 0 29 1 23 3 5 t 0 14 7 5 3 0 28 0 0 0 3 6 4 10

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.99933; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=3/4; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.825624; rsmyCGTACGrksy ; cor=; Ncor= a 12 5 9 0 1 0 0 33 0 3 20 5 6 6 c 5 10 19 12 29 0 0 0 32 0 1 0 11 11 g 11 11 0 1 0 33 0 0 1 30 12 19 10 5 t 5 7 5 20 3 0 33 0 0 0 0 9 6 11

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=4/4; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.825624; rsmyCGTACGrksy ; cor=; Ncor= a 12 5 9 0 1 0 0 33 0 3 20 5 6 6 c 5 10 19 12 29 0 0 0 32 0 1 0 11 11 g 11 11 0 1 0 33 0 0 1 30 12 19 10 5 t 5 7 5 20 3 0 33 0 0 0 0 9 6 11

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -yaCCGTACGAgmw ; Alignment reference a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.99933; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 30 5 13 11 c 0 10 6 26 30 3 0 1 34 1 0 0 14 8 g 0 6 6 1 1 31 6 0 0 29 1 23 3 5 t 0 14 7 5 3 0 28 0 0 0 3 6 4 10

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.826135; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.826135; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; ycAGTCACst ; Alignment reference a 2 1 9 0 0 0 9 0 1 1 c 3 5 0 0 0 9 0 9 4 0 g 0 1 0 9 0 0 0 0 3 2 t 4 2 0 0 9 0 0 0 1 6

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ycAGTCACst ; cor=; Ncor= a 2 1 9 0 0 0 9 0 1 1 c 3 5 0 0 0 9 0 9 4 0 g 0 1 0 9 0 0 0 0 3 2 t 4 2 0 0 9 0 0 0 1 6

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=14; shift=0; ncol=14; rsmyCGTACGrksy ; Alignment reference a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=3/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.826135; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.825624; wkcTCGTACGGtr- ; cor=; Ncor= a 10 4 6 3 0 0 0 28 0 3 5 7 14 0 c 5 3 23 1 29 0 0 6 31 1 1 6 6 0 g 8 14 0 0 1 34 1 0 3 30 26 6 10 0 t 11 13 5 30 4 0 33 0 0 0 2 15 4 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; rsmyCGTACGrksy ; Alignment reference a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=3/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.826135; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.825624; wkcTCGTACGGtr- ; cor=; Ncor= a 10 4 6 3 0 0 0 28 0 3 5 7 14 0 c 5 3 23 1 29 0 0 6 31 1 1 6 6 0 g 8 14 0 0 1 34 1 0 3 30 26 6 10 0 t 11 13 5 30 4 0 33 0 0 0 2 15 4 0

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=13; shift=1; ncol=14; -yaCCGTACGAgmw ; Alignment reference a 0 4 15 2 0 0 0 33 0 4 30 5 13 11 c 0 10 6 26 30 3 0 1 34 1 0 0 14 8 g 0 6 6 1 1 31 6 0 0 29 1 23 3 5 t 0 14 7 5 3 0 28 0 0 0 3 6 4 10
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 30 5 13 11 c 0 10 6 26 30 3 0 1 34 1 0 0 14 8 g 0 6 6 1 1 31 6 0 0 29 1 23 3 5 t 0 14 7 5 3 0 28 0 0 0 3 6 4 10
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.99933; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=3/4; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.825624; rsmyCGTACGrksy ; cor=; Ncor= a 12 5 9 0 1 0 0 33 0 3 20 5 6 6 c 5 10 19 12 29 0 0 0 32 0 1 0 11 11 g 11 11 0 1 0 33 0 0 1 30 12 19 10 5 t 5 7 5 20 3 0 33 0 0 0 0 9 6 11
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=4/4; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.825624; rsmyCGTACGrksy ; cor=; Ncor= a 12 5 9 0 1 0 0 33 0 3 20 5 6 6 c 5 10 19 12 29 0 0 0 32 0 1 0 11 11 g 11 11 0 1 0 33 0 0 1 30 12 19 10 5 t 5 7 5 20 3 0 33 0 0 0 0 9 6 11

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -yaCCGTACGAgmw ; Alignment reference a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 29 5 13 10 c 0 10 6 25 30 3 0 0 33 1 0 0 14 8 g 0 5 5 1 0 30 6 0 0 28 1 22 2 5 t 0 14 7 5 3 0 27 0 0 0 3 6 4 10
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.99933; -yaCCGTACGAgmw ; cor=; Ncor= a 0 4 15 2 0 0 0 33 0 4 30 5 13 11 c 0 10 6 26 30 3 0 1 34 1 0 0 14 8 g 0 6 6 1 1 31 6 0 0 29 1 23 3 5 t 0 14 7 5 3 0 28 0 0 0 3 6 4 10
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.826135; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.826135; rsmyCGTACGrksy ; cor=; Ncor= a 11 6 9 0 0 0 0 33 0 3 20 5 7 5 c 5 10 19 12 30 1 0 0 33 0 1 0 11 11 g 11 11 0 1 0 32 0 0 0 29 12 19 10 5 t 6 6 5 20 3 0 33 0 0 1 0 9 5 12