One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184046_2025-05-16.184046_ZEi16E/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/2025/05/16/peak-motifs.2025-05-16.184046_2025-05-16.184046_ZEi16E/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---gsCCCGCChy ; Alignment reference a 0 0 0 6 4 0 0 0 0 0 0 8 3 c 0 0 0 5 12 32 32 32 0 32 31 14 14 g 0 0 0 14 10 0 0 0 32 0 1 2 3 t 0 0 0 7 6 0 0 0 0 0 0 8 12

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---gsCCCGCChy ; cor=; Ncor= a 0 0 0 6 4 0 0 0 0 0 0 8 3 c 0 0 0 5 12 32 32 32 0 32 31 14 14 g 0 0 0 14 10 0 0 0 32 0 1 2 3 t 0 0 0 7 6 0 0 0 0 0 0 8 12

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=2/3; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.610268; cyGGCCCCGCcc- ; cor=; Ncor= a 4 9 2 3 2 0 1 0 0 2 7 3 0 c 19 14 3 1 35 38 35 35 0 32 22 23 0 g 7 6 34 35 2 1 1 4 38 4 7 8 0 t 9 10 0 0 0 0 2 0 1 1 3 5 0

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=3/3; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.548811; -yrGCCCCGmc-- ; cor=; Ncor= a 0 4 8 1 0 0 1 0 0 8 7 0 0 c 0 15 5 0 32 30 31 32 0 16 16 0 0 g 0 5 17 31 0 2 0 0 32 7 6 0 0 t 0 8 2 0 0 0 0 0 0 1 3 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --gkCGGGGCyr ; Alignment reference a 0 0 3 1 0 0 0 0 0 0 2 8 c 0 0 6 7 32 0 0 2 0 31 17 5 g 0 0 16 16 0 32 31 30 32 0 5 15 t 0 0 7 8 0 0 1 0 0 1 8 4

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --gkCGGGGCyr ; cor=; Ncor= a 0 0 3 1 0 0 0 0 0 0 2 8 c 0 0 6 7 32 0 0 2 0 31 17 5 g 0 0 16 16 0 32 31 30 32 0 5 15 t 0 0 7 8 0 0 1 0 0 1 8 4

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.797323; -ggGCGGGGCCr ; cor=; Ncor= a 0 5 3 1 1 0 2 0 0 0 0 10 c 0 8 7 4 38 4 1 1 2 35 34 6 g 0 23 22 32 0 35 35 38 35 1 3 14 t 0 3 7 2 0 0 1 0 2 3 2 9

oligos_6nt_mkv2_m2_rc_shift0 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=3/3; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.548811; rdGGCGGGsc-- ; cor=; Ncor= a 12 8 0 0 0 0 0 0 6 7 0 0 c 3 2 1 0 32 0 0 0 10 14 0 0 g 14 14 31 32 0 32 32 32 12 5 0 0 t 3 8 0 0 0 0 0 0 4 6 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ykCTACTMArwr ; Alignment reference a 2 1 0 0 9 0 0 8 11 7 6 5 c 5 2 11 1 0 10 0 3 0 0 1 1 g 1 3 0 0 1 1 0 0 0 3 1 4 t 3 5 0 10 1 0 11 0 0 1 3 1

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ykCTACTMArwr ; cor=; Ncor= a 2 1 0 0 9 0 0 8 11 7 6 5 c 5 2 11 1 0 10 0 3 0 0 1 1 g 1 3 0 0 1 1 0 0 0 3 1 4 t 3 5 0 10 1 0 11 0 0 1 3 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 2 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=11; shift=0; ncol=11; vwCTTGAACty ; Alignment reference a 6 8 0 1 0 0 21 20 1 5 3 c 7 3 22 1 2 0 0 0 19 4 11 g 9 3 0 0 3 21 0 2 0 3 1 t 0 8 0 20 17 1 1 0 2 10 7

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; vwCTTGAACty ; cor=; Ncor= a 6 8 0 1 0 0 21 20 1 5 3 c 7 3 22 1 2 0 0 0 19 4 11 g 9 3 0 0 3 21 0 2 0 3 1 t 0 8 0 20 17 1 1 0 2 10 7

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; gsGATTACAGgy ; Alignment reference a 2 0 0 11 0 0 11 0 11 1 1 1 c 0 3 0 0 1 1 0 10 0 0 2 6 g 8 8 12 1 0 0 1 0 0 11 8 2 t 2 1 0 0 11 11 0 2 1 0 1 3

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gsGATTACAGgy ; cor=; Ncor= a 2 0 0 11 0 0 11 0 11 1 1 1 c 0 3 0 0 1 1 0 10 0 0 2 6 g 8 8 12 1 0 0 1 0 0 11 8 2 t 2 1 0 0 11 11 0 2 1 0 1 3

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; ykCCTCCCGrs ; Alignment reference a 3 1 1 0 1 0 1 0 0 8 4 c 7 4 19 19 0 21 19 21 0 3 8 g 5 9 1 2 0 0 0 0 21 8 7 t 6 7 0 0 20 0 1 0 0 2 2

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ykCCTCCCGrs ; cor=; Ncor= a 3 1 1 0 1 0 1 0 0 8 4 c 7 4 19 19 0 21 19 21 0 3 8 g 5 9 1 2 0 0 0 0 21 8 7 t 6 7 0 0 20 0 1 0 0 2 2

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -ggGCGGGGCCrg ; Alignment reference a 0 5 3 1 1 0 2 0 0 0 0 10 9 c 0 8 7 4 38 4 1 1 2 35 34 6 7 g 0 23 22 32 0 35 35 38 35 1 3 14 19 t 0 3 7 2 0 0 1 0 2 3 2 9 4

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ggGCGGGGCCrg ; cor=; Ncor= a 0 5 3 1 1 0 2 0 0 0 0 10 9 c 0 8 7 4 38 4 1 1 2 35 34 6 7 g 0 23 22 32 0 35 35 38 35 1 3 14 19 t 0 3 7 2 0 0 1 0 2 3 2 9 4

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.797323; --gkCGGGGCyr- ; cor=; Ncor= a 0 0 3 1 0 0 0 0 0 0 2 8 0 c 0 0 6 7 32 0 0 2 0 31 17 5 0 g 0 0 16 16 0 32 31 30 32 0 5 15 0 t 0 0 7 8 0 0 1 0 0 1 8 4 0

oligos_6nt_mkv2_m2_rc_shift0 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=3/3; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.610268; rdGGCGGGsc--- ; cor=; Ncor= a 12 8 0 0 0 0 0 0 6 7 0 0 0 c 3 2 1 0 32 0 0 0 10 14 0 0 0 g 14 14 31 32 0 32 32 32 12 5 0 0 0 t 3 8 0 0 0 0 0 0 4 6 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---gsCCCGCChy ; Alignment reference a 0 0 0 6 4 0 0 0 0 0 0 8 3 c 0 0 0 5 12 32 32 32 0 32 31 14 14 g 0 0 0 14 10 0 0 0 32 0 1 2 3 t 0 0 0 7 6 0 0 0 0 0 0 8 12
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---gsCCCGCChy ; cor=; Ncor= a 0 0 0 6 4 0 0 0 0 0 0 8 3 c 0 0 0 5 12 32 32 32 0 32 31 14 14 g 0 0 0 14 10 0 0 0 32 0 1 2 3 t 0 0 0 7 6 0 0 0 0 0 0 8 12
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=2/3; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.610268; cyGGCCCCGCcc- ; cor=; Ncor= a 4 9 2 3 2 0 1 0 0 2 7 3 0 c 19 14 3 1 35 38 35 35 0 32 22 23 0 g 7 6 34 35 2 1 1 4 38 4 7 8 0 t 9 10 0 0 0 0 2 0 1 1 3 5 0
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=3/3; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.548811; -yrGCCCCGmc-- ; cor=; Ncor= a 0 4 8 1 0 0 1 0 0 8 7 0 0 c 0 15 5 0 32 30 31 32 0 16 16 0 0 g 0 5 17 31 0 2 0 0 32 7 6 0 0 t 0 8 2 0 0 0 0 0 0 1 3 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --gkCGGGGCyr ; Alignment reference a 0 0 3 1 0 0 0 0 0 0 2 8 c 0 0 6 7 32 0 0 2 0 31 17 5 g 0 0 16 16 0 32 31 30 32 0 5 15 t 0 0 7 8 0 0 1 0 0 1 8 4
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --gkCGGGGCyr ; cor=; Ncor= a 0 0 3 1 0 0 0 0 0 0 2 8 c 0 0 6 7 32 0 0 2 0 31 17 5 g 0 0 16 16 0 32 31 30 32 0 5 15 t 0 0 7 8 0 0 1 0 0 1 8 4
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.797323; -ggGCGGGGCCr ; cor=; Ncor= a 0 5 3 1 1 0 2 0 0 0 0 10 c 0 8 7 4 38 4 1 1 2 35 34 6 g 0 23 22 32 0 35 35 38 35 1 3 14 t 0 3 7 2 0 0 1 0 2 3 2 9
oligos_6nt_mkv2_m2_rc_shift0 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=3/3; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.548811; rdGGCGGGsc-- ; cor=; Ncor= a 12 8 0 0 0 0 0 0 6 7 0 0 c 3 2 1 0 32 0 0 0 10 14 0 0 g 14 14 31 32 0 32 32 32 12 5 0 0 t 3 8 0 0 0 0 0 0 4 6 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -ggGCGGGGCCrg ; Alignment reference a 0 5 3 1 1 0 2 0 0 0 0 10 9 c 0 8 7 4 38 4 1 1 2 35 34 6 7 g 0 23 22 32 0 35 35 38 35 1 3 14 19 t 0 3 7 2 0 0 1 0 2 3 2 9 4
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ggGCGGGGCCrg ; cor=; Ncor= a 0 5 3 1 1 0 2 0 0 0 0 10 9 c 0 8 7 4 38 4 1 1 2 35 34 6 7 g 0 23 22 32 0 35 35 38 35 1 3 14 19 t 0 3 7 2 0 0 1 0 2 3 2 9 4
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.797323; --gkCGGGGCyr- ; cor=; Ncor= a 0 0 3 1 0 0 0 0 0 0 2 8 0 c 0 0 6 7 32 0 0 2 0 31 17 5 0 g 0 0 16 16 0 32 31 30 32 0 5 15 0 t 0 0 7 8 0 0 1 0 0 1 8 4 0
oligos_6nt_mkv2_m2_rc_shift0 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=3/3; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.610268; rdGGCGGGsc--- ; cor=; Ncor= a 12 8 0 0 0 0 0 0 6 7 0 0 0 c 3 2 1 0 32 0 0 0 10 14 0 0 0 g 14 14 31 32 0 32 32 32 12 5 0 0 0 t 3 8 0 0 0 0 0 0 4 6 0 0 0