One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.234316_2026-02-26.234316_5Dj251/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/2026/02/26/peak-motifs.2026-02-26.234316_2026-02-26.234316_5Dj251/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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=15; shift=0; ncol=15; TCTCCATAACACAAG ; Alignment reference a 0 0 0 0 0 1 0 1 1 0 1 0 1 1 0 c 0 1 0 1 1 0 0 0 0 1 0 1 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 t 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0

oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/1; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; TCTCCATAACACAAG ; cor=; Ncor= a 0 0 0 0 0 1 0 1 1 0 1 0 1 1 0 c 0 1 0 1 1 0 0 0 0 1 0 1 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 t 1 0 1 0 0 0 1 0 0 0 0 0 0 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; ttCCCTGCCyw ; Alignment reference a 1 1 0 0 0 0 0 0 0 0 3 c 1 1 5 5 5 1 0 5 4 3 0 g 1 1 0 0 0 0 5 0 0 0 0 t 2 2 0 0 0 4 0 0 1 2 2

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ttCCCTGCCyw ; cor=; Ncor= a 1 1 0 0 0 0 0 0 0 0 3 c 1 1 5 5 5 1 0 5 4 3 0 g 1 1 0 0 0 0 5 0 0 0 0 t 2 2 0 0 0 4 0 0 1 2 2

oligos_7nt_mkv1_m2_rc_shift2 (oligos_7nt_mkv1_m2_rc)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m2_rc; m=2/2; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.422322; --CCCCGCTTA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1 c 0 0 1 1 1 1 0 1 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 t 0 0 0 0 0 0 0 0 1 1 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift5 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=5; ncol=15; -----CCCGCTTATC ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 0 1 1 1 0 1 0 0 0 0 1 g 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0

oligos_6nt_mkv1_m1_shift5 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----CCCGCTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 0 1 1 1 0 1 0 0 0 0 1 g 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0

oligos_7nt_mkv1_m2_rc_shift4 (oligos_7nt_mkv1_m2_rc)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2_rc; m=2/3; ncol2=13; w=-1; offset=-1; strand=R; shift=4; score=0.769231; ----CCCCGCTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 1 1 1 1 0 1 0 0 0 0 1 g 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0

oligos_7nt_mkv1_m5_rc_shift0 (oligos_7nt_mkv1_m5_rc)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m5_rc; m=3/3; ncol2=11; w=-5; offset=-5; strand=R; shift=0; score= 0.4; CCTACCCCGCT---- ; cor=; Ncor= a 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 c 1 1 0 0 1 1 1 1 0 1 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 t 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 5 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=13; shift=0; ncol=13; GTGATAAGCGGGG ; Alignment reference a 0 0 0 1 0 1 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 g 1 0 1 0 0 0 0 1 0 1 1 1 1 t 0 1 0 0 1 0 0 0 0 0 0 0 0

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; GTGATAAGCGGGG ; cor=; Ncor= a 0 0 0 1 0 1 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 g 1 0 1 0 0 0 0 1 0 1 1 1 1 t 0 1 0 0 1 0 0 0 0 0 0 0 0

oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1_rc; m=2/4; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.769231; --GATAAGCGGG- ; cor=; Ncor= a 0 0 0 1 0 1 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 g 0 0 1 0 0 0 0 1 0 1 1 1 0 t 0 0 0 0 1 0 0 0 0 0 0 0 0

oligos_7nt_mkv1_m3_rc_shift4 (oligos_7nt_mkv1_m3_rc)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m3_rc; m=3/4; ncol2=11; w=0; offset=4; strand=R; shift=4; score=0.422322; ----wrGGCAGGG ; cor=; Ncor= a 0 0 0 0 2 2 1 0 0 4 0 0 0 c 0 0 0 0 0 0 0 0 5 0 0 0 0 g 0 0 0 0 0 3 4 5 0 1 5 5 5 t 0 0 0 0 3 0 0 0 0 0 0 0 0

oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m5; m=4/4; ncol2=11; w=0; offset=6; strand=D; shift=6; score=0.411765; ------AGCGGGG ; cor=; Ncor= a 0 0 0 0 0 0 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 g 0 0 0 0 0 0 0 1 0 1 1 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift2 ; 3 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=10; shift=2; ncol=12; --AGAGTCAAmw ; Alignment reference a 0 0 2 0 2 0 0 0 2 2 1 1 c 0 0 0 0 0 0 0 2 0 0 1 0 g 0 0 0 2 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 2 0 0 0 0 1

oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --AGAGTCAAmw ; cor=; Ncor= a 0 0 2 0 2 0 0 0 2 2 1 1 c 0 0 0 0 0 0 0 2 0 0 1 0 g 0 0 0 2 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 2 0 0 0 0 1

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=2/2; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.833333; srAGAGTCAAmw ; cor=; Ncor= a 0 1 2 0 2 0 0 0 2 2 1 1 c 1 0 0 0 0 0 0 2 0 0 1 0 g 1 1 0 2 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 2 0 0 0 0 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 3 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=12; shift=0; ncol=12; srAGAGTCAAmw ; Alignment reference a 0 1 2 0 2 0 0 0 2 2 1 1 c 1 0 0 0 0 0 0 2 0 0 1 0 g 1 1 0 2 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 2 0 0 0 0 1

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; srAGAGTCAAmw ; cor=; Ncor= a 0 1 2 0 2 0 0 0 2 2 1 1 c 1 0 0 0 0 0 0 2 0 0 1 0 g 1 1 0 2 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 2 0 0 0 0 1

oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=2/2; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.833333; --AGAGTCAAmw ; cor=; Ncor= a 0 0 2 0 2 0 0 0 2 2 1 1 c 0 0 0 0 0 0 0 2 0 0 1 0 g 0 0 0 2 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 2 0 0 0 0 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift6 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=6; ncol=17; ------AGCGGGGTAGG ; Alignment reference a 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1 0 1 1 1 1 0 0 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0

oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=6; score= 1; ------AGCGGGGTAGG ; cor=; Ncor= a 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1 0 1 1 1 1 0 0 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=13; w=-6; offset=-6; strand=D; shift=0; score=0.411765; GTGATAAGCGGGG---- ; cor=; Ncor= a 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 g 1 0 1 0 0 0 0 1 0 1 1 1 1 0 0 0 0 t 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0

oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc)
; oligos_7nt_mkv1_m5 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=10; w=-4; offset=-4; strand=R; shift=2; score= 0.4; --GATAAGCGGG----- ; cor=; Ncor= a 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 g 0 0 1 0 0 0 0 1 0 1 1 1 0 0 0 0 0 t 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift5 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=5; ncol=15; -----CCCGCTTATC ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 0 1 1 1 0 1 0 0 0 0 1 g 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0
oligos_6nt_mkv1_m1_shift5 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----CCCGCTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 0 1 1 1 0 1 0 0 0 0 1 g 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0
oligos_7nt_mkv1_m2_rc_shift4 (oligos_7nt_mkv1_m2_rc)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2_rc; m=2/3; ncol2=13; w=-1; offset=-1; strand=R; shift=4; score=0.769231; ----CCCCGCTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 1 1 1 1 0 1 0 0 0 0 1 g 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0
oligos_7nt_mkv1_m5_rc_shift0 (oligos_7nt_mkv1_m5_rc)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m5_rc; m=3/3; ncol2=11; w=-5; offset=-5; strand=R; shift=0; score= 0.4; CCTACCCCGCT---- ; cor=; Ncor= a 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 c 1 1 0 0 1 1 1 1 0 1 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 t 0 0 1 0 0 0 0 0 0 0 1 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=13; shift=0; ncol=13; GTGATAAGCGGGG ; Alignment reference a 0 0 0 1 0 1 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 g 1 0 1 0 0 0 0 1 0 1 1 1 1 t 0 1 0 0 1 0 0 0 0 0 0 0 0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; GTGATAAGCGGGG ; cor=; Ncor= a 0 0 0 1 0 1 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 g 1 0 1 0 0 0 0 1 0 1 1 1 1 t 0 1 0 0 1 0 0 0 0 0 0 0 0
oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1_rc; m=2/4; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.769231; --GATAAGCGGG- ; cor=; Ncor= a 0 0 0 1 0 1 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 g 0 0 1 0 0 0 0 1 0 1 1 1 0 t 0 0 0 0 1 0 0 0 0 0 0 0 0
oligos_7nt_mkv1_m3_rc_shift4 (oligos_7nt_mkv1_m3_rc)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m3_rc; m=3/4; ncol2=11; w=0; offset=4; strand=R; shift=4; score=0.422322; ----wrGGCAGGG ; cor=; Ncor= a 0 0 0 0 2 2 1 0 0 4 0 0 0 c 0 0 0 0 0 0 0 0 5 0 0 0 0 g 0 0 0 0 0 3 4 5 0 1 5 5 5 t 0 0 0 0 3 0 0 0 0 0 0 0 0
oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m5; m=4/4; ncol2=11; w=0; offset=6; strand=D; shift=6; score=0.411765; ------AGCGGGG ; cor=; Ncor= a 0 0 0 0 0 0 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 g 0 0 0 0 0 0 0 1 0 1 1 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=6; ncol=17; ------AGCGGGGTAGG ; Alignment reference a 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1 0 1 1 1 1 0 0 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=6; score= 1; ------AGCGGGGTAGG ; cor=; Ncor= a 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1 0 1 1 1 1 0 0 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=13; w=-6; offset=-6; strand=D; shift=0; score=0.411765; GTGATAAGCGGGG---- ; cor=; Ncor= a 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 g 1 0 1 0 0 0 0 1 0 1 1 1 1 0 0 0 0 t 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc)				; oligos_7nt_mkv1_m5 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=10; w=-4; offset=-4; strand=R; shift=2; score= 0.4; --GATAAGCGGG----- ; cor=; Ncor= a 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 g 0 0 1 0 0 0 0 1 0 1 1 1 0 0 0 0 0 t 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0