One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 2 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=10; shift=0; ncol=10; rtATATATat ; Alignment reference a 14 7 30 0 32 0 33 0 18 5 c 8 8 3 1 1 2 1 2 3 8 g 9 3 2 0 2 1 1 3 8 8 t 4 17 0 34 0 32 0 30 6 14

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; rtATATATat ; cor=; Ncor= a 14 7 30 0 32 0 33 0 18 5 c 8 8 3 1 1 2 1 2 3 8 g 9 3 2 0 2 1 1 3 8 8 t 4 17 0 34 0 32 0 30 6 14

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; syCGTCGTCsb ; Alignment reference a 6 8 0 0 2 0 0 1 1 6 6 c 15 15 44 7 5 44 4 2 44 12 14 g 21 11 2 38 4 1 41 4 1 23 13 t 4 12 0 1 35 1 1 39 0 5 13

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; syCGTCGTCsb ; cor=; Ncor= a 6 8 0 0 2 0 0 1 1 6 6 c 15 15 44 7 5 44 4 2 44 12 14 g 21 11 2 38 4 1 41 4 1 23 13 t 4 12 0 1 35 1 1 39 0 5 13

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift1 ; 3 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=10; shift=1; ncol=11; -ysCTCCTCkk ; Alignment reference a 0 2 3 0 0 0 0 0 0 1 4 c 0 8 9 18 0 18 18 0 18 4 3 g 0 3 5 0 0 0 0 0 0 6 5 t 0 5 1 0 18 0 0 18 0 7 6

oligos_6nt_mkv1_m1_shift1 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ysCTCCTCkk ; cor=; Ncor= a 0 2 3 0 0 0 0 0 0 1 4 c 0 8 9 18 0 18 18 0 18 4 3 g 0 3 5 0 0 0 0 0 0 6 5 t 0 5 1 0 18 0 0 18 0 7 6

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m3; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.808137; yyCCTCCTCkk ; cor=; Ncor= a 1 5 2 0 0 0 0 0 0 4 5 c 12 7 19 25 0 24 20 1 23 2 4 g 4 5 3 0 0 0 5 1 1 7 8 t 8 8 1 0 25 1 0 23 1 12 8

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; sgAGGTAGwm ; Alignment reference a 3 3 16 0 0 0 18 0 6 5 c 7 4 0 0 2 0 0 1 3 5 g 5 7 0 17 16 0 0 16 4 4 t 3 4 2 1 0 18 0 1 5 4

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; sgAGGTAGwm ; cor=; Ncor= a 3 3 16 0 0 0 18 0 6 5 c 7 4 0 0 2 0 0 1 3 5 g 5 7 0 17 16 0 0 16 4 4 t 3 4 2 1 0 18 0 1 5 4

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 2 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; raAAAAAAAww ; Alignment reference a 32 29 69 70 73 71 70 71 74 33 33 c 15 16 3 4 5 3 3 1 0 9 8 g 22 19 7 5 2 5 4 4 4 18 19 t 12 17 2 2 1 2 4 5 3 21 21

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; raAAAAAAAww ; cor=; Ncor= a 32 29 69 70 73 71 70 71 74 33 33 c 15 16 3 4 5 3 3 1 0 9 8 g 22 19 7 5 2 5 4 4 4 18 19 t 12 17 2 2 1 2 4 5 3 21 21

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=12; shift=0; ncol=12; yyCCTCCTCkkc ; Alignment reference a 1 5 2 0 0 0 0 0 0 4 5 3 c 12 7 19 25 0 24 20 1 23 2 4 13 g 4 5 3 0 0 0 5 1 1 7 8 3 t 8 8 1 0 25 1 0 23 1 12 8 6

oligos_7nt_mkv1_m3_shift0 (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=0; score= 1; yyCCTCCTCkkc ; cor=; Ncor= a 1 5 2 0 0 0 0 0 0 4 5 3 c 12 7 19 25 0 24 20 1 23 2 4 13 g 4 5 3 0 0 0 5 1 1 7 8 3 t 8 8 1 0 25 1 0 23 1 12 8 6

oligos_6nt_mkv1_m1_shift1 (oligos_6nt_mkv1_m1)
; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.808137; -ysCTCCTCkk- ; cor=; Ncor= a 0 2 3 0 0 0 0 0 0 1 4 0 c 0 8 9 18 0 18 18 0 18 4 3 0 g 0 3 5 0 0 0 0 0 0 6 5 0 t 0 5 1 0 18 0 0 18 0 7 6 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift2 ; 4 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; --scCGCCGCsg ; Alignment reference a 0 0 2 2 0 0 0 0 0 0 5 3 c 0 0 8 10 21 0 21 21 0 21 6 5 g 0 0 9 5 0 21 0 0 21 0 6 11 t 0 0 2 4 0 0 0 0 0 0 4 2

oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --scCGCCGCsg ; cor=; Ncor= a 0 0 2 2 0 0 0 0 0 0 5 3 c 0 0 8 10 21 0 21 21 0 21 6 5 g 0 0 9 5 0 21 0 0 21 0 6 11 t 0 0 2 4 0 0 0 0 0 0 4 2

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.648406; shCCCGCCGhs- ; cor=; Ncor= a 4 6 0 2 0 0 2 0 0 6 1 0 c 8 6 21 18 21 0 20 23 0 8 10 0 g 10 5 2 2 2 23 0 0 23 3 7 0 t 1 6 0 1 0 0 1 0 0 6 5 0

oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m2; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.543838; vcCCCGCCsc-- ; cor=; Ncor= a 6 3 0 0 0 0 0 0 4 3 0 0 c 8 9 22 22 22 0 22 22 6 10 0 0 g 7 5 0 0 0 22 0 0 11 4 0 0 t 1 5 0 0 0 0 0 0 1 5 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift0 ; 4 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; vcCCCGCCsc ; Alignment reference a 6 3 0 0 0 0 0 0 4 3 c 8 9 22 22 22 0 22 22 6 10 g 7 5 0 0 0 22 0 0 11 4 t 1 5 0 0 0 0 0 0 1 5

oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; vcCCCGCCsc ; cor=; Ncor= a 6 3 0 0 0 0 0 0 4 3 c 8 9 22 22 22 0 22 22 6 10 g 7 5 0 0 0 22 0 0 11 4 t 1 5 0 0 0 0 0 0 1 5

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.853035; shCCCGCCGh ; cor=; Ncor= a 4 6 0 2 0 0 2 0 0 6 c 8 6 21 18 21 0 20 23 0 8 g 10 5 2 2 2 23 0 0 23 3 t 1 6 0 1 0 0 1 0 0 6

oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.543838; --scCGCCGC ; cor=; Ncor= a 0 0 2 2 0 0 0 0 0 0 c 0 0 8 10 21 0 21 21 0 21 g 0 0 9 5 0 21 0 0 21 0 t 0 0 2 4 0 0 0 0 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=11; shift=0; ncol=11; shCCCGCCGhs ; Alignment reference a 4 6 0 2 0 0 2 0 0 6 1 c 8 6 21 18 21 0 20 23 0 8 10 g 10 5 2 2 2 23 0 0 23 3 7 t 1 6 0 1 0 0 1 0 0 6 5

oligos_7nt_mkv1_m2_shift0 (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=0; score= 1; shCCCGCCGhs ; cor=; Ncor= a 4 6 0 2 0 0 2 0 0 6 1 c 8 6 21 18 21 0 20 23 0 8 10 g 10 5 2 2 2 23 0 0 23 3 7 t 1 6 0 1 0 0 1 0 0 6 5

oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.853035; vcCCCGCCsc- ; cor=; Ncor= a 6 3 0 0 0 0 0 0 4 3 0 c 8 9 22 22 22 0 22 22 6 10 0 g 7 5 0 0 0 22 0 0 11 4 0 t 1 5 0 0 0 0 0 0 1 5 0

oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.648406; --scCGCCGCs ; cor=; Ncor= a 0 0 2 2 0 0 0 0 0 0 5 c 0 0 8 10 21 0 21 21 0 21 6 g 0 0 9 5 0 21 0 0 21 0 6 t 0 0 2 4 0 0 0 0 0 0 4

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; wvtAGTACTAct ; Alignment reference a 10 5 2 17 0 0 18 0 0 13 3 4 c 0 5 2 0 4 0 0 14 0 2 7 3 g 3 5 2 0 14 0 0 3 0 1 4 1 t 5 3 12 1 0 18 0 1 18 2 4 10

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; wvtAGTACTAct ; cor=; Ncor= a 10 5 2 17 0 0 18 0 0 13 3 4 c 0 5 2 0 4 0 0 14 0 2 7 3 g 3 5 2 0 14 0 0 3 0 1 4 1 t 5 3 12 1 0 18 0 1 18 2 4 10

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; --scCGCCGCsg ; Alignment reference a 0 0 2 2 0 0 0 0 0 0 5 3 c 0 0 8 10 21 0 21 21 0 21 6 5 g 0 0 9 5 0 21 0 0 21 0 6 11 t 0 0 2 4 0 0 0 0 0 0 4 2
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)				; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --scCGCCGCsg ; cor=; Ncor= a 0 0 2 2 0 0 0 0 0 0 5 3 c 0 0 8 10 21 0 21 21 0 21 6 5 g 0 0 9 5 0 21 0 0 21 0 6 11 t 0 0 2 4 0 0 0 0 0 0 4 2
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.648406; shCCCGCCGhs- ; cor=; Ncor= a 4 6 0 2 0 0 2 0 0 6 1 0 c 8 6 21 18 21 0 20 23 0 8 10 0 g 10 5 2 2 2 23 0 0 23 3 7 0 t 1 6 0 1 0 0 1 0 0 6 5 0
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m2; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.543838; vcCCCGCCsc-- ; cor=; Ncor= a 6 3 0 0 0 0 0 0 4 3 0 0 c 8 9 22 22 22 0 22 22 6 10 0 0 g 7 5 0 0 0 22 0 0 11 4 0 0 t 1 5 0 0 0 0 0 0 1 5 0 0

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; vcCCCGCCsc ; Alignment reference a 6 3 0 0 0 0 0 0 4 3 c 8 9 22 22 22 0 22 22 6 10 g 7 5 0 0 0 22 0 0 11 4 t 1 5 0 0 0 0 0 0 1 5
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; vcCCCGCCsc ; cor=; Ncor= a 6 3 0 0 0 0 0 0 4 3 c 8 9 22 22 22 0 22 22 6 10 g 7 5 0 0 0 22 0 0 11 4 t 1 5 0 0 0 0 0 0 1 5
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.853035; shCCCGCCGh ; cor=; Ncor= a 4 6 0 2 0 0 2 0 0 6 c 8 6 21 18 21 0 20 23 0 8 g 10 5 2 2 2 23 0 0 23 3 t 1 6 0 1 0 0 1 0 0 6
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.543838; --scCGCCGC ; cor=; Ncor= a 0 0 2 2 0 0 0 0 0 0 c 0 0 8 10 21 0 21 21 0 21 g 0 0 9 5 0 21 0 0 21 0 t 0 0 2 4 0 0 0 0 0 0

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=11; shift=0; ncol=11; shCCCGCCGhs ; Alignment reference a 4 6 0 2 0 0 2 0 0 6 1 c 8 6 21 18 21 0 20 23 0 8 10 g 10 5 2 2 2 23 0 0 23 3 7 t 1 6 0 1 0 0 1 0 0 6 5
oligos_7nt_mkv1_m2_shift0 (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=0; score= 1; shCCCGCCGhs ; cor=; Ncor= a 4 6 0 2 0 0 2 0 0 6 1 c 8 6 21 18 21 0 20 23 0 8 10 g 10 5 2 2 2 23 0 0 23 3 7 t 1 6 0 1 0 0 1 0 0 6 5
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.853035; vcCCCGCCsc- ; cor=; Ncor= a 6 3 0 0 0 0 0 0 4 3 0 c 8 9 22 22 22 0 22 22 6 10 0 g 7 5 0 0 0 22 0 0 11 4 0 t 1 5 0 0 0 0 0 0 1 5 0
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.648406; --scCGCCGCs ; cor=; Ncor= a 0 0 2 2 0 0 0 0 0 0 5 c 0 0 8 10 21 0 21 21 0 21 6 g 0 0 9 5 0 21 0 0 21 0 6 t 0 0 2 4 0 0 0 0 0 0 4