One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.094218_2025-06-19.094218_4xfDGW/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.2025-06-19.094218_2025-06-19.094218_4xfDGW/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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=23; shift=0; ncol=23; CgCCsCCryCsCCGCCGCCGCCv ; Alignment reference a 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 12 c 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 11 g 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 18 t 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0 2

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/3; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; CgCCsCCryCsCCGCCGCCGCCv ; cor=; Ncor= a 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 12 c 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 11 g 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 18 t 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0 2

oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)
; oligos_6-8nt_m2 versus oligos_6-8nt_m4; m=2/3; ncol2=17; w=0; offset=6; strand=D; shift=6; score=0.725454; ------CsCCsCCGCCGCCGCCs ; cor=; Ncor= a 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 21 c 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 33 g 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 63 t 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15 7

oligos_6-8nt_m1_shift7 (oligos_6-8nt_m1)
; oligos_6-8nt_m2 versus oligos_6-8nt_m1; m=3/3; ncol2=15; w=0; offset=7; strand=D; shift=7; score=0.620308; -------scCGCCGCCGCCscC- ; cor=; Ncor= a 0 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5 0 c 0 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83 0 g 0 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18 0 t 0 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift6 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)
; oligos_6-8nt_m4; m=0 (reference); ncol1=17; shift=6; ncol=23; ------CsCCsCCGCCGCCGCCs ; Alignment reference a 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 21 c 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 33 g 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 63 t 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15 7

oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)
; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=6; score= 1; ------CsCCsCCGCCGCCGCCs ; cor=; Ncor= a 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 21 c 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 33 g 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 63 t 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15 7

oligos_6-8nt_m1_shift7 (oligos_6-8nt_m1)
; oligos_6-8nt_m4 versus oligos_6-8nt_m1; m=2/3; ncol2=15; w=0; offset=1; strand=D; shift=7; score=0.843748; -------scCGCCGCCGCCscC- ; cor=; Ncor= a 0 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5 0 c 0 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83 0 g 0 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18 0 t 0 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9 0

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m4 versus oligos_6-8nt_m2; m=3/3; ncol2=23; w=-6; offset=-6; strand=D; shift=0; score=0.725454; CgCCsCCryCsCCGCCGCCGCCv ; cor=; Ncor= a 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 12 c 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 11 g 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 18 t 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0 2

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=13; shift=0; ncol=13; ssaCTGAGCCCym ; Alignment reference a 2 3 16 1 0 0 27 0 2 0 0 6 7 c 17 9 5 23 2 0 0 2 23 27 23 10 12 g 8 13 3 3 1 26 0 25 2 0 4 3 4 t 0 2 3 0 24 1 0 0 0 0 0 8 4

oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ssaCTGAGCCCym ; cor=; Ncor= a 2 3 16 1 0 0 27 0 2 0 0 6 7 c 17 9 5 23 2 0 0 2 23 27 23 10 12 g 8 13 3 3 1 26 0 25 2 0 4 3 4 t 0 2 3 0 24 1 0 0 0 0 0 8 4

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=12; shift=0; ncol=12; yyACCCAGCCms ; Alignment reference a 10 6 42 1 1 0 53 1 1 3 19 10 c 22 23 7 53 56 56 3 6 57 53 24 22 g 9 14 7 4 0 2 1 49 0 2 11 16 t 17 15 2 0 1 0 1 2 0 0 4 10

oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; yyACCCAGCCms ; cor=; Ncor= a 10 6 42 1 1 0 53 1 1 3 19 10 c 22 23 7 53 56 56 3 6 57 53 24 22 g 9 14 7 4 0 2 1 49 0 2 11 16 t 17 15 2 0 1 0 1 2 0 0 4 10

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift7 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m1_shift7 (oligos_6-8nt_m1)
; oligos_6-8nt_m1; m=0 (reference); ncol1=15; shift=7; ncol=22; -------scCGCCGCCGCCscC ; Alignment reference a 0 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5 c 0 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83 g 0 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18 t 0 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9

oligos_6-8nt_m1_shift7 (oligos_6-8nt_m1)
; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=7; score= 1; -------scCGCCGCCGCCscC ; cor=; Ncor= a 0 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5 c 0 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83 g 0 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18 t 0 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9

oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)
; oligos_6-8nt_m1 versus oligos_6-8nt_m4; m=2/3; ncol2=17; w=-1; offset=-1; strand=D; shift=6; score=0.843748; ------CsCCsCCGCCGCCGCC ; cor=; Ncor= a 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 c 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 g 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 t 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15

oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)
; oligos_6-8nt_m1 versus oligos_6-8nt_m2; m=3/3; ncol2=23; w=-7; offset=-7; strand=D; shift=0; score=0.620308; CgCCsCCryCsCCGCCGCCGCC ; cor=; Ncor= a 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 c 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 g 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 t 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 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=23; shift=0; ncol=23; CgCCsCCryCsCCGCCGCCGCCv ; Alignment reference a 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 12 c 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 11 g 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 18 t 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0 2
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/3; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; CgCCsCCryCsCCGCCGCCGCCv ; cor=; Ncor= a 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 12 c 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 11 g 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 18 t 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0 2
oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)				; oligos_6-8nt_m2 versus oligos_6-8nt_m4; m=2/3; ncol2=17; w=0; offset=6; strand=D; shift=6; score=0.725454; ------CsCCsCCGCCGCCGCCs ; cor=; Ncor= a 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 21 c 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 33 g 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 63 t 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15 7
oligos_6-8nt_m1_shift7 (oligos_6-8nt_m1)				; oligos_6-8nt_m2 versus oligos_6-8nt_m1; m=3/3; ncol2=15; w=0; offset=7; strand=D; shift=7; score=0.620308; -------scCGCCGCCGCCscC- ; cor=; Ncor= a 0 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5 0 c 0 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83 0 g 0 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18 0 t 0 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)				; oligos_6-8nt_m4; m=0 (reference); ncol1=17; shift=6; ncol=23; ------CsCCsCCGCCGCCGCCs ; Alignment reference a 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 21 c 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 33 g 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 63 t 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15 7
oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)				; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=6; score= 1; ------CsCCsCCGCCGCCGCCs ; cor=; Ncor= a 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 21 c 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 33 g 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 63 t 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15 7
oligos_6-8nt_m1_shift7 (oligos_6-8nt_m1)				; oligos_6-8nt_m4 versus oligos_6-8nt_m1; m=2/3; ncol2=15; w=0; offset=1; strand=D; shift=7; score=0.843748; -------scCGCCGCCGCCscC- ; cor=; Ncor= a 0 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5 0 c 0 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83 0 g 0 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18 0 t 0 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9 0
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; oligos_6-8nt_m4 versus oligos_6-8nt_m2; m=3/3; ncol2=23; w=-6; offset=-6; strand=D; shift=0; score=0.725454; CgCCsCCryCsCCGCCGCCGCCv ; cor=; Ncor= a 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 12 c 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 11 g 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 18 t 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m1_shift7 (oligos_6-8nt_m1)				; oligos_6-8nt_m1; m=0 (reference); ncol1=15; shift=7; ncol=22; -------scCGCCGCCGCCscC ; Alignment reference a 0 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5 c 0 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83 g 0 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18 t 0 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9
oligos_6-8nt_m1_shift7 (oligos_6-8nt_m1)				; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=7; score= 1; -------scCGCCGCCGCCscC ; cor=; Ncor= a 0 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5 c 0 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83 g 0 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18 t 0 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9
oligos_6-8nt_m4_shift6 (oligos_6-8nt_m4)				; oligos_6-8nt_m1 versus oligos_6-8nt_m4; m=2/3; ncol2=17; w=-1; offset=-1; strand=D; shift=6; score=0.843748; ------CsCCsCCGCCGCCGCC ; cor=; Ncor= a 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 c 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 g 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 t 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2)				; oligos_6-8nt_m1 versus oligos_6-8nt_m2; m=3/3; ncol2=23; w=-7; offset=-7; strand=D; shift=0; score=0.620308; CgCCsCCryCsCCGCCGCCGCC ; cor=; Ncor= a 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 c 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 g 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 t 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0