One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/18/peak-motifs.2026-03-18.173738_2026-03-18.173738_ZkH2jH/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/2026/03/18/peak-motifs.2026-03-18.173738_2026-03-18.173738_ZkH2jH/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 4 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=15; shift=0; ncol=15; tdgAAGATAGAArww ; Alignment reference a 2 4 2 10 11 0 8 0 11 0 10 10 7 5 4 c 1 0 1 1 0 0 1 1 0 0 0 0 0 1 0 g 2 3 7 0 0 11 0 0 0 11 1 1 4 2 1 t 6 4 1 0 0 0 2 10 0 0 0 0 0 3 6

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; tdgAAGATAGAArww ; cor=; Ncor= a 2 4 2 10 11 0 8 0 11 0 10 10 7 5 4 c 1 0 1 1 0 0 1 1 0 0 0 0 0 1 0 g 2 3 7 0 0 11 0 0 0 11 1 1 4 2 1 t 6 4 1 0 0 0 2 10 0 0 0 0 0 3 6

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m3 versus oligos_6-8nt_m2; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.70915; rtsAAGCTAGGAar- ; cor=; Ncor= a 4 2 0 9 9 0 1 0 9 1 1 8 6 4 0 c 0 1 3 0 0 0 8 0 0 0 0 1 2 0 0 g 4 1 6 0 0 8 0 0 0 8 8 0 1 4 0 t 1 5 0 0 0 1 0 9 0 0 0 0 0 1 0

dyads_m1_shift1 (dyads_m1)
; oligos_6-8nt_m3 versus dyads_m1; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.593479; -tvAAGCTAGdA--- ; cor=; Ncor= a 0 3 4 16 15 0 1 0 16 0 4 13 0 0 0 c 0 2 5 0 0 0 14 0 0 2 1 2 0 0 0 g 0 3 5 0 0 15 0 2 0 12 6 1 0 0 0 t 0 8 2 0 1 1 1 14 0 2 5 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=26; shift=0; ncol=26; awTTAaAahrrawdyhwbmrrAAGgw ; Alignment reference a 8 4 1 0 15 10 12 7 4 8 7 8 6 4 3 4 7 3 4 7 5 15 15 2 3 4 c 2 1 0 0 0 1 0 2 4 1 0 3 2 1 4 4 0 4 6 1 1 0 0 1 2 2 g 3 2 0 0 0 2 1 3 3 4 5 2 3 5 3 3 2 4 2 4 6 0 0 11 7 2 t 2 8 14 15 0 2 2 3 4 2 3 2 4 5 5 4 6 4 3 3 3 0 0 1 3 7

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/1; ncol2=26; w=0; offset=0; strand=D; shift=0; score= 1; awTTAaAahrrawdyhwbmrrAAGgw ; cor=; Ncor= a 8 4 1 0 15 10 12 7 4 8 7 8 6 4 3 4 7 3 4 7 5 15 15 2 3 4 c 2 1 0 0 0 1 0 2 4 1 0 3 2 1 4 4 0 4 6 1 1 0 0 1 2 2 g 3 2 0 0 0 2 1 3 3 4 5 2 3 5 3 3 2 4 2 4 6 0 0 11 7 2 t 2 8 14 15 0 2 2 3 4 2 3 2 4 5 5 4 6 4 3 3 3 0 0 1 3 7

One-to-n matrix alignment; reference matrix: dyads_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift1 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -tvAAGCTAGdA ; Alignment reference a 0 3 4 16 15 0 1 0 16 0 4 13 c 0 2 5 0 0 0 14 0 0 2 1 2 g 0 3 5 0 0 15 0 2 0 12 6 1 t 0 8 2 0 1 1 1 14 0 2 5 0

dyads_m1_shift1 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -tvAAGCTAGdA ; cor=; Ncor= a 0 3 4 16 15 0 1 0 16 0 4 13 c 0 2 5 0 0 0 14 0 0 2 1 2 g 0 3 5 0 0 15 0 2 0 12 6 1 t 0 8 2 0 1 1 1 14 0 2 5 0

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; dyads_m1 versus oligos_6-8nt_m2; m=2/3; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.74037; rtsAAGCTAGGA ; cor=; Ncor= a 4 2 0 9 9 0 1 0 9 1 1 8 c 0 1 3 0 0 0 8 0 0 0 0 1 g 4 1 6 0 0 8 0 0 0 8 8 0 t 1 5 0 0 0 1 0 9 0 0 0 0

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; dyads_m1 versus oligos_6-8nt_m3; m=3/3; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.593479; tdgAAGATAGAA ; cor=; Ncor= a 2 4 2 10 11 0 8 0 11 0 10 10 c 1 0 1 1 0 0 1 1 0 0 0 0 g 2 3 7 0 0 11 0 0 0 11 1 1 t 6 4 1 0 0 0 2 10 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift0 ; 2 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=11; shift=0; ncol=11; gdGCCTGTGkk ; Alignment reference a 3 5 1 1 0 2 1 0 0 2 0 c 3 2 0 13 16 0 0 1 1 2 3 g 9 4 15 0 0 0 14 0 15 4 9 t 1 5 0 2 0 14 1 15 0 8 4

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; gdGCCTGTGkk ; cor=; Ncor= a 3 5 1 1 0 2 1 0 0 2 0 c 3 2 0 13 16 0 0 1 1 2 3 g 9 4 15 0 0 0 14 0 15 4 9 t 1 5 0 2 0 14 1 15 0 8 4

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; rtsAAGCTAGGAar ; Alignment reference a 4 2 0 9 9 0 1 0 9 1 1 8 6 4 c 0 1 3 0 0 0 8 0 0 0 0 1 2 0 g 4 1 6 0 0 8 0 0 0 8 8 0 1 4 t 1 5 0 0 0 1 0 9 0 0 0 0 0 1

oligos_6-8nt_m2_shift0 (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=0; score= 1; rtsAAGCTAGGAar ; cor=; Ncor= a 4 2 0 9 9 0 1 0 9 1 1 8 6 4 c 0 1 3 0 0 0 8 0 0 0 0 1 2 0 g 4 1 6 0 0 8 0 0 0 8 8 0 1 4 t 1 5 0 0 0 1 0 9 0 0 0 0 0 1

dyads_m1_shift1 (dyads_m1)
; oligos_6-8nt_m2 versus dyads_m1; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.74037; -tvAAGCTAGdA-- ; cor=; Ncor= a 0 3 4 16 15 0 1 0 16 0 4 13 0 0 c 0 2 5 0 0 0 14 0 0 2 1 2 0 0 g 0 3 5 0 0 15 0 2 0 12 6 1 0 0 t 0 8 2 0 1 1 1 14 0 2 5 0 0 0

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m2 versus oligos_6-8nt_m3; m=3/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.70915; tdgAAGATAGAArw ; cor=; Ncor= a 2 4 2 10 11 0 8 0 11 0 10 10 7 5 c 1 0 1 1 0 0 1 1 0 0 0 0 0 1 g 2 3 7 0 0 11 0 0 0 11 1 1 4 2 t 6 4 1 0 0 0 2 10 0 0 0 0 0 3

One-to-n matrix alignment; reference matrix: dyads_m4_shift4 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift4 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=10; shift=4; ncol=14; ----gGCGGCGGyg ; Alignment reference a 0 0 0 0 2 2 0 0 1 1 0 0 1 1 c 0 0 0 0 1 1 13 0 0 11 0 1 7 1 g 0 0 0 0 8 10 1 13 13 2 13 13 1 9 t 0 0 0 0 3 1 0 1 0 0 1 0 5 3

dyads_m4_shift4 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----gGCGGCGGyg ; cor=; Ncor= a 0 0 0 0 2 2 0 0 1 1 0 0 1 1 c 0 0 0 0 1 1 13 0 0 11 0 1 7 1 g 0 0 0 0 8 10 1 13 13 2 13 13 1 9 t 0 0 0 0 3 1 0 1 0 0 1 0 5 3

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; dyads_m4 versus oligos_6-8nt_m1; m=2/2; ncol2=14; w=-4; offset=-4; strand=D; shift=0; score=0.662229; csGCsGCSGCSScg ; cor=; Ncor= a 1 1 0 1 0 0 0 0 1 0 0 0 1 1 c 10 5 0 12 4 1 14 4 1 14 4 4 10 3 g 2 6 15 1 10 14 1 11 13 0 11 11 1 10 t 2 3 0 1 1 0 0 0 0 1 0 0 3 1

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=12; shift=0; ncol=12; ksATTCCAGGra ; Alignment reference a 3 2 14 2 0 0 0 13 0 0 6 5 c 3 5 0 0 1 11 14 1 0 0 2 3 g 4 6 0 2 1 1 0 0 14 14 5 3 t 4 1 0 10 12 2 0 0 0 0 1 3

oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4)
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ksATTCCAGGra ; cor=; Ncor= a 3 2 14 2 0 0 0 13 0 0 6 5 c 3 5 0 0 1 11 14 1 0 0 2 3 g 4 6 0 2 1 1 0 0 14 14 5 3 t 4 1 0 10 12 2 0 0 0 0 1 3

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; csGCsGCSGCSScg ; Alignment reference a 1 1 0 1 0 0 0 0 1 0 0 0 1 1 c 10 5 0 12 4 1 14 4 1 14 4 4 10 3 g 2 6 15 1 10 14 1 11 13 0 11 11 1 10 t 2 3 0 1 1 0 0 0 0 1 0 0 3 1

oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1)
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; csGCsGCSGCSScg ; cor=; Ncor= a 1 1 0 1 0 0 0 0 1 0 0 0 1 1 c 10 5 0 12 4 1 14 4 1 14 4 4 10 3 g 2 6 15 1 10 14 1 11 13 0 11 11 1 10 t 2 3 0 1 1 0 0 0 0 1 0 0 3 1

dyads_m4_shift4 (dyads_m4)
; oligos_6-8nt_m1 versus dyads_m4; m=2/2; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.662229; ----gGCGGCGGyg ; cor=; Ncor= a 0 0 0 0 2 2 0 0 1 1 0 0 1 1 c 0 0 0 0 1 1 13 0 0 11 0 1 7 1 g 0 0 0 0 8 10 1 13 13 2 13 13 1 9 t 0 0 0 0 3 1 0 1 0 0 1 0 5 3

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=28; shift=0; ncol=28; bkTAArdmrrbkwwkdddddhwwATAkr ; Alignment reference a 1 2 0 12 11 5 4 4 3 6 1 2 3 7 2 4 4 4 4 4 4 4 3 11 1 11 2 5 c 3 2 0 0 1 1 1 4 1 1 3 1 2 1 1 1 0 2 2 2 3 2 1 0 0 1 1 1 g 4 5 1 0 0 4 3 2 6 3 3 5 1 1 3 4 4 3 3 3 2 2 1 1 0 0 4 4 t 4 3 11 0 0 2 4 2 2 2 5 4 6 3 6 3 4 3 3 3 3 4 7 0 11 0 5 2

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/1; ncol2=28; w=0; offset=0; strand=D; shift=0; score= 1; bkTAArdmrrbkwwkdddddhwwATAkr ; cor=; Ncor= a 1 2 0 12 11 5 4 4 3 6 1 2 3 7 2 4 4 4 4 4 4 4 3 11 1 11 2 5 c 3 2 0 0 1 1 1 4 1 1 3 1 2 1 1 1 0 2 2 2 3 2 1 0 0 1 1 1 g 4 5 1 0 0 4 3 2 6 3 3 5 1 1 3 4 4 3 3 3 2 2 1 1 0 0 4 4 t 4 3 11 0 0 2 4 2 2 2 5 4 6 3 6 3 4 3 3 3 3 4 7 0 11 0 5 2

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=15; shift=0; ncol=15; tdgAAGATAGAArww ; Alignment reference a 2 4 2 10 11 0 8 0 11 0 10 10 7 5 4 c 1 0 1 1 0 0 1 1 0 0 0 0 0 1 0 g 2 3 7 0 0 11 0 0 0 11 1 1 4 2 1 t 6 4 1 0 0 0 2 10 0 0 0 0 0 3 6
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)				; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; tdgAAGATAGAArww ; cor=; Ncor= a 2 4 2 10 11 0 8 0 11 0 10 10 7 5 4 c 1 0 1 1 0 0 1 1 0 0 0 0 0 1 0 g 2 3 7 0 0 11 0 0 0 11 1 1 4 2 1 t 6 4 1 0 0 0 2 10 0 0 0 0 0 3 6
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; oligos_6-8nt_m3 versus oligos_6-8nt_m2; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.70915; rtsAAGCTAGGAar- ; cor=; Ncor= a 4 2 0 9 9 0 1 0 9 1 1 8 6 4 0 c 0 1 3 0 0 0 8 0 0 0 0 1 2 0 0 g 4 1 6 0 0 8 0 0 0 8 8 0 1 4 0 t 1 5 0 0 0 1 0 9 0 0 0 0 0 1 0
dyads_m1_shift1 (dyads_m1)				; oligos_6-8nt_m3 versus dyads_m1; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.593479; -tvAAGCTAGdA--- ; cor=; Ncor= a 0 3 4 16 15 0 1 0 16 0 4 13 0 0 0 c 0 2 5 0 0 0 14 0 0 2 1 2 0 0 0 g 0 3 5 0 0 15 0 2 0 12 6 1 0 0 0 t 0 8 2 0 1 1 1 14 0 2 5 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift1 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -tvAAGCTAGdA ; Alignment reference a 0 3 4 16 15 0 1 0 16 0 4 13 c 0 2 5 0 0 0 14 0 0 2 1 2 g 0 3 5 0 0 15 0 2 0 12 6 1 t 0 8 2 0 1 1 1 14 0 2 5 0
dyads_m1_shift1 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -tvAAGCTAGdA ; cor=; Ncor= a 0 3 4 16 15 0 1 0 16 0 4 13 c 0 2 5 0 0 0 14 0 0 2 1 2 g 0 3 5 0 0 15 0 2 0 12 6 1 t 0 8 2 0 1 1 1 14 0 2 5 0
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; dyads_m1 versus oligos_6-8nt_m2; m=2/3; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.74037; rtsAAGCTAGGA ; cor=; Ncor= a 4 2 0 9 9 0 1 0 9 1 1 8 c 0 1 3 0 0 0 8 0 0 0 0 1 g 4 1 6 0 0 8 0 0 0 8 8 0 t 1 5 0 0 0 1 0 9 0 0 0 0
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)				; dyads_m1 versus oligos_6-8nt_m3; m=3/3; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.593479; tdgAAGATAGAA ; cor=; Ncor= a 2 4 2 10 11 0 8 0 11 0 10 10 c 1 0 1 1 0 0 1 1 0 0 0 0 g 2 3 7 0 0 11 0 0 0 11 1 1 t 6 4 1 0 0 0 2 10 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; oligos_6-8nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; rtsAAGCTAGGAar ; Alignment reference a 4 2 0 9 9 0 1 0 9 1 1 8 6 4 c 0 1 3 0 0 0 8 0 0 0 0 1 2 0 g 4 1 6 0 0 8 0 0 0 8 8 0 1 4 t 1 5 0 0 0 1 0 9 0 0 0 0 0 1
oligos_6-8nt_m2_shift0 (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=0; score= 1; rtsAAGCTAGGAar ; cor=; Ncor= a 4 2 0 9 9 0 1 0 9 1 1 8 6 4 c 0 1 3 0 0 0 8 0 0 0 0 1 2 0 g 4 1 6 0 0 8 0 0 0 8 8 0 1 4 t 1 5 0 0 0 1 0 9 0 0 0 0 0 1
dyads_m1_shift1 (dyads_m1)				; oligos_6-8nt_m2 versus dyads_m1; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.74037; -tvAAGCTAGdA-- ; cor=; Ncor= a 0 3 4 16 15 0 1 0 16 0 4 13 0 0 c 0 2 5 0 0 0 14 0 0 2 1 2 0 0 g 0 3 5 0 0 15 0 2 0 12 6 1 0 0 t 0 8 2 0 1 1 1 14 0 2 5 0 0 0
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)				; oligos_6-8nt_m2 versus oligos_6-8nt_m3; m=3/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.70915; tdgAAGATAGAArw ; cor=; Ncor= a 2 4 2 10 11 0 8 0 11 0 10 10 7 5 c 1 0 1 1 0 0 1 1 0 0 0 0 0 1 g 2 3 7 0 0 11 0 0 0 11 1 1 4 2 t 6 4 1 0 0 0 2 10 0 0 0 0 0 3