One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093641_2025-06-19.093641_ZnDYv6/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/2025/06/19/peak-motifs.2025-06-19.093641_2025-06-19.093641_ZnDYv6/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; tsCATAATAgg ; Alignment reference a 11 7 0 41 1 42 38 3 43 11 10 c 8 12 42 1 1 2 4 5 1 9 11 g 9 16 3 3 2 0 2 1 1 18 17 t 18 11 1 1 42 2 2 37 1 8 8

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; tsCATAATAgg ; cor=; Ncor= a 11 7 0 41 1 42 38 3 43 11 10 c 8 12 42 1 1 2 4 5 1 9 11 g 9 16 3 3 2 0 2 1 1 18 17 t 18 11 1 1 42 2 2 37 1 8 8

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; svCaCACACGCccr ; Alignment reference a 7 13 2 27 1 40 1 43 0 7 1 8 4 18 c 21 13 37 8 37 3 44 3 47 2 44 29 23 6 g 14 12 5 7 4 4 1 0 0 38 0 6 10 13 t 5 9 3 5 5 0 1 1 0 0 2 4 10 10

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; svCaCACACGCccr ; cor=; Ncor= a 7 13 2 27 1 40 1 43 0 7 1 8 4 18 c 21 13 37 8 37 3 44 3 47 2 44 29 23 6 g 14 12 5 7 4 4 1 0 0 38 0 6 10 13 t 5 9 3 5 5 0 1 1 0 0 2 4 10 10

oligos_6-8nt_m1_shift2 (oligos_6-8nt_m1)
; oligos_6-8nt_m5 versus oligos_6-8nt_m1; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.827833; --cvCACACGCCcr ; cor=; Ncor= a 0 0 8 14 2 40 1 46 0 7 0 9 8 17 c 0 0 24 15 42 6 49 3 49 0 50 37 24 5 g 0 0 9 14 3 3 0 1 0 43 0 4 11 18 t 0 0 9 7 3 1 0 0 1 0 0 0 7 10

oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; oligos_6-8nt_m5 versus oligos_6-8nt_m2; m=3/3; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.635303; --cmCACACGCACG ; cor=; Ncor= a 0 0 6 14 2 29 0 37 0 4 2 31 0 3 c 0 0 26 14 32 4 39 1 39 5 38 2 37 3 g 0 0 5 8 5 6 2 2 1 32 1 5 3 34 t 0 0 4 5 2 2 0 1 1 0 0 3 1 1

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; oligos_6-8nt_m2; m=0 (reference); ncol1=14; shift=2; ncol=16; --cmCACACGCACGcw ; Alignment reference a 0 0 6 14 2 29 0 37 0 4 2 31 0 3 4 14 c 0 0 26 14 32 4 39 1 39 5 38 2 37 3 20 9 g 0 0 5 8 5 6 2 2 1 32 1 5 3 34 8 6 t 0 0 4 5 2 2 0 1 1 0 0 3 1 1 9 12

oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --cmCACACGCACGcw ; cor=; Ncor= a 0 0 6 14 2 29 0 37 0 4 2 31 0 3 4 14 c 0 0 26 14 32 4 39 1 39 5 38 2 37 3 20 9 g 0 0 5 8 5 6 2 2 1 32 1 5 3 34 8 6 t 0 0 4 5 2 2 0 1 1 0 0 3 1 1 9 12

oligos_6-8nt_m1_shift2 (oligos_6-8nt_m1)
; oligos_6-8nt_m2 versus oligos_6-8nt_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.727979; --cvCACACGCCcr-- ; cor=; Ncor= a 0 0 8 14 2 40 1 46 0 7 0 9 8 17 0 0 c 0 0 24 15 42 6 49 3 49 0 50 37 24 5 0 0 g 0 0 9 14 3 3 0 1 0 43 0 4 11 18 0 0 t 0 0 9 7 3 1 0 0 1 0 0 0 7 10 0 0

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m2 versus oligos_6-8nt_m5; m=3/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.635303; svCaCACACGCccr-- ; cor=; Ncor= a 7 13 2 27 1 40 1 43 0 7 1 8 4 18 0 0 c 21 13 37 8 37 3 44 3 47 2 44 29 23 6 0 0 g 14 12 5 7 4 4 1 0 0 38 0 6 10 13 0 0 t 5 9 3 5 5 0 1 1 0 0 2 4 10 10 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4)
; oligos_6-8nt_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; sbCCTGGCmy ; Alignment reference a 5 6 0 0 0 0 0 0 13 7 c 14 13 42 42 0 0 0 42 13 14 g 17 12 0 0 0 42 42 0 10 10 t 6 11 0 0 42 0 0 0 6 11

oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4)
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; sbCCTGGCmy ; cor=; Ncor= a 5 6 0 0 0 0 0 0 13 7 c 14 13 42 42 0 0 0 42 13 14 g 17 12 0 0 0 42 42 0 10 10 t 6 11 0 0 42 0 0 0 6 11

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m1_shift2 (oligos_6-8nt_m1)
; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --cvCACACGCCcr ; Alignment reference a 0 0 8 14 2 40 1 46 0 7 0 9 8 17 c 0 0 24 15 42 6 49 3 49 0 50 37 24 5 g 0 0 9 14 3 3 0 1 0 43 0 4 11 18 t 0 0 9 7 3 1 0 0 1 0 0 0 7 10

oligos_6-8nt_m1_shift2 (oligos_6-8nt_m1)
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --cvCACACGCCcr ; cor=; Ncor= a 0 0 8 14 2 40 1 46 0 7 0 9 8 17 c 0 0 24 15 42 6 49 3 49 0 50 37 24 5 g 0 0 9 14 3 3 0 1 0 43 0 4 11 18 t 0 0 9 7 3 1 0 0 1 0 0 0 7 10

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m1 versus oligos_6-8nt_m5; m=2/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.827833; svCaCACACGCccr ; cor=; Ncor= a 7 13 2 27 1 40 1 43 0 7 1 8 4 18 c 21 13 37 8 37 3 44 3 47 2 44 29 23 6 g 14 12 5 7 4 4 1 0 0 38 0 6 10 13 t 5 9 3 5 5 0 1 1 0 0 2 4 10 10

oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)
; oligos_6-8nt_m1 versus oligos_6-8nt_m2; m=3/3; ncol2=14; w=0; offset=0; strand=D; shift=2; score=0.727979; --cmCACACGCACG ; cor=; Ncor= a 0 0 6 14 2 29 0 37 0 4 2 31 0 3 c 0 0 26 14 32 4 39 1 39 5 38 2 37 3 g 0 0 5 8 5 6 2 2 1 32 1 5 3 34 t 0 0 4 5 2 2 0 1 1 0 0 3 1 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)				; oligos_6-8nt_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; svCaCACACGCccr ; Alignment reference a 7 13 2 27 1 40 1 43 0 7 1 8 4 18 c 21 13 37 8 37 3 44 3 47 2 44 29 23 6 g 14 12 5 7 4 4 1 0 0 38 0 6 10 13 t 5 9 3 5 5 0 1 1 0 0 2 4 10 10
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)				; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; svCaCACACGCccr ; cor=; Ncor= a 7 13 2 27 1 40 1 43 0 7 1 8 4 18 c 21 13 37 8 37 3 44 3 47 2 44 29 23 6 g 14 12 5 7 4 4 1 0 0 38 0 6 10 13 t 5 9 3 5 5 0 1 1 0 0 2 4 10 10
oligos_6-8nt_m1_shift2 (oligos_6-8nt_m1)				; oligos_6-8nt_m5 versus oligos_6-8nt_m1; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.827833; --cvCACACGCCcr ; cor=; Ncor= a 0 0 8 14 2 40 1 46 0 7 0 9 8 17 c 0 0 24 15 42 6 49 3 49 0 50 37 24 5 g 0 0 9 14 3 3 0 1 0 43 0 4 11 18 t 0 0 9 7 3 1 0 0 1 0 0 0 7 10
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; oligos_6-8nt_m5 versus oligos_6-8nt_m2; m=3/3; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.635303; --cmCACACGCACG ; cor=; Ncor= a 0 0 6 14 2 29 0 37 0 4 2 31 0 3 c 0 0 26 14 32 4 39 1 39 5 38 2 37 3 g 0 0 5 8 5 6 2 2 1 32 1 5 3 34 t 0 0 4 5 2 2 0 1 1 0 0 3 1 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; oligos_6-8nt_m2; m=0 (reference); ncol1=14; shift=2; ncol=16; --cmCACACGCACGcw ; Alignment reference a 0 0 6 14 2 29 0 37 0 4 2 31 0 3 4 14 c 0 0 26 14 32 4 39 1 39 5 38 2 37 3 20 9 g 0 0 5 8 5 6 2 2 1 32 1 5 3 34 8 6 t 0 0 4 5 2 2 0 1 1 0 0 3 1 1 9 12
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --cmCACACGCACGcw ; cor=; Ncor= a 0 0 6 14 2 29 0 37 0 4 2 31 0 3 4 14 c 0 0 26 14 32 4 39 1 39 5 38 2 37 3 20 9 g 0 0 5 8 5 6 2 2 1 32 1 5 3 34 8 6 t 0 0 4 5 2 2 0 1 1 0 0 3 1 1 9 12
oligos_6-8nt_m1_shift2 (oligos_6-8nt_m1)				; oligos_6-8nt_m2 versus oligos_6-8nt_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.727979; --cvCACACGCCcr-- ; cor=; Ncor= a 0 0 8 14 2 40 1 46 0 7 0 9 8 17 0 0 c 0 0 24 15 42 6 49 3 49 0 50 37 24 5 0 0 g 0 0 9 14 3 3 0 1 0 43 0 4 11 18 0 0 t 0 0 9 7 3 1 0 0 1 0 0 0 7 10 0 0
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)				; oligos_6-8nt_m2 versus oligos_6-8nt_m5; m=3/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.635303; svCaCACACGCccr-- ; cor=; Ncor= a 7 13 2 27 1 40 1 43 0 7 1 8 4 18 0 0 c 21 13 37 8 37 3 44 3 47 2 44 29 23 6 0 0 g 14 12 5 7 4 4 1 0 0 38 0 6 10 13 0 0 t 5 9 3 5 5 0 1 1 0 0 2 4 10 10 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m1_shift2 (oligos_6-8nt_m1)				; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --cvCACACGCCcr ; Alignment reference a 0 0 8 14 2 40 1 46 0 7 0 9 8 17 c 0 0 24 15 42 6 49 3 49 0 50 37 24 5 g 0 0 9 14 3 3 0 1 0 43 0 4 11 18 t 0 0 9 7 3 1 0 0 1 0 0 0 7 10
oligos_6-8nt_m1_shift2 (oligos_6-8nt_m1)				; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --cvCACACGCCcr ; cor=; Ncor= a 0 0 8 14 2 40 1 46 0 7 0 9 8 17 c 0 0 24 15 42 6 49 3 49 0 50 37 24 5 g 0 0 9 14 3 3 0 1 0 43 0 4 11 18 t 0 0 9 7 3 1 0 0 1 0 0 0 7 10
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)				; oligos_6-8nt_m1 versus oligos_6-8nt_m5; m=2/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.827833; svCaCACACGCccr ; cor=; Ncor= a 7 13 2 27 1 40 1 43 0 7 1 8 4 18 c 21 13 37 8 37 3 44 3 47 2 44 29 23 6 g 14 12 5 7 4 4 1 0 0 38 0 6 10 13 t 5 9 3 5 5 0 1 1 0 0 2 4 10 10
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2)				; oligos_6-8nt_m1 versus oligos_6-8nt_m2; m=3/3; ncol2=14; w=0; offset=0; strand=D; shift=2; score=0.727979; --cmCACACGCACG ; cor=; Ncor= a 0 0 6 14 2 29 0 37 0 4 2 31 0 3 c 0 0 26 14 32 4 39 1 39 5 38 2 37 3 g 0 0 5 8 5 6 2 2 1 32 1 5 3 34 t 0 0 4 5 2 2 0 1 1 0 0 3 1 1