One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184256_2025-05-16.184256_DOHBqC/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.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=13; shift=2; ncol=15; --mAGCCAGCCAGCC ; Alignment reference a 0 0 32 59 1 1 1 63 1 0 0 62 1 2 3 c 0 0 33 0 8 62 63 1 8 65 63 0 0 58 58 g 0 0 0 5 56 1 0 0 56 0 1 3 64 4 3 t 0 0 0 1 0 1 1 1 0 0 1 0 0 1 1

oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --mAGCCAGCCAGCC ; cor=; Ncor= a 0 0 32 59 1 1 1 63 1 0 0 62 1 2 3 c 0 0 33 0 8 62 63 1 8 65 63 0 0 58 58 g 0 0 0 5 56 1 0 0 56 0 1 3 64 4 3 t 0 0 0 1 0 1 1 1 0 0 1 0 0 1 1

oligos_6nt_mkv1_m2_rc_shift0 (oligos_6nt_mkv1_m2_rc)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.743816; sCmAGCCAGCCArsC ; cor=; Ncor= a 3 3 55 108 0 0 1 104 2 2 2 106 63 2 7 c 56 97 54 1 2 105 106 2 6 100 102 0 4 42 89 g 47 4 0 0 104 4 1 2 100 4 3 3 41 63 8 t 3 5 0 0 3 0 1 1 1 3 2 0 1 2 5

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=3/3; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.600748; sCmAGCCAGCCAAGC ; cor=; Ncor= a 2 2 33 54 0 0 0 53 2 0 1 55 53 0 3 c 34 49 22 1 0 51 53 1 3 52 52 0 0 2 47 g 18 2 0 0 52 4 1 1 50 2 2 0 2 52 3 t 1 2 0 0 3 0 1 0 0 1 0 0 0 1 2

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=16; shift=1; ncol=17; -kGsyTGGCTGGCTkGs ; Alignment reference a 0 5 5 2 1 0 2 3 1 1 1 0 3 0 0 5 3 c 0 4 8 63 41 3 3 4 100 2 1 4 104 0 0 4 47 g 0 57 89 42 4 0 102 100 6 2 106 105 2 1 54 97 56 t 0 43 7 2 63 106 2 2 2 104 1 0 0 108 55 3 3

oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -kGsyTGGCTGGCTkGs ; cor=; Ncor= a 0 5 5 2 1 0 2 3 1 1 1 0 3 0 0 5 3 c 0 4 8 63 41 3 3 4 100 2 1 4 104 0 0 4 47 g 0 57 89 42 4 0 102 100 6 2 106 105 2 1 54 97 56 t 0 43 7 2 63 106 2 2 2 104 1 0 0 108 55 3 3

oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1_rc; m=2/3; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score= 0.9005; TGGCTTGGCTGGCTkGs ; cor=; Ncor= a 1 2 2 1 0 0 0 1 0 0 1 0 3 0 0 2 1 c 3 1 3 52 2 0 2 2 50 1 1 4 52 0 0 2 18 g 1 48 47 2 0 0 52 52 3 1 53 51 0 1 22 49 34 t 50 4 3 0 53 55 1 0 2 53 0 0 0 54 33 2 2

oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=13; w=0; offset=1; strand=R; shift=2; score=0.743816; --GGCTGGCTGGCTk-- ; cor=; Ncor= a 0 0 1 1 0 0 1 0 0 1 1 1 0 1 0 0 0 c 0 0 3 4 64 3 1 0 56 0 0 1 56 5 0 0 0 g 0 0 58 58 0 0 63 65 8 1 63 62 8 0 33 0 0 t 0 0 3 2 1 62 0 0 1 63 1 1 1 59 32 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; dgCAGAGAgw ; Alignment reference a 4 2 0 10 0 10 0 10 1 4 c 0 2 10 0 0 0 0 0 2 1 g 3 5 0 0 10 0 10 0 6 2 t 3 1 0 0 0 0 0 0 1 3

oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; dgCAGAGAgw ; cor=; Ncor= a 4 2 0 10 0 10 0 10 1 4 c 0 2 10 0 0 0 0 0 2 1 g 3 5 0 0 10 0 10 0 6 2 t 3 1 0 0 0 0 0 0 1 3

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m2; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.891545; drCAGAGAGr ; cor=; Ncor= a 2 2 0 7 0 7 0 7 0 3 c 0 1 7 0 0 0 0 0 0 1 g 3 3 0 0 7 0 7 0 6 2 t 2 1 0 0 0 0 0 0 1 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 4 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=17; shift=0; ncol=17; sCmAGCCAGCCAAGCCA ; Alignment reference a 2 2 33 54 0 0 0 53 2 0 1 55 53 0 3 4 50 c 34 49 22 1 0 51 53 1 3 52 52 0 0 2 47 48 1 g 18 2 0 0 52 4 1 1 50 2 2 0 2 52 3 1 3 t 1 2 0 0 3 0 1 0 0 1 0 0 0 1 2 2 1

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; sCmAGCCAGCCAAGCCA ; cor=; Ncor= a 2 2 33 54 0 0 0 53 2 0 1 55 53 0 3 4 50 c 34 49 22 1 0 51 53 1 3 52 52 0 0 2 47 48 1 g 18 2 0 0 52 4 1 1 50 2 2 0 2 52 3 1 3 t 1 2 0 0 3 0 1 0 0 1 0 0 0 1 2 2 1

oligos_6nt_mkv1_m2_rc_shift0 (oligos_6nt_mkv1_m2_rc)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=16; w=0; offset=0; strand=R; shift=0; score= 0.9005; sCmAGCCAGCCArsCm- ; cor=; Ncor= a 3 3 55 108 0 0 1 104 2 2 2 106 63 2 7 43 0 c 56 97 54 1 2 105 106 2 6 100 102 0 4 42 89 57 0 g 47 4 0 0 104 4 1 2 100 4 3 3 41 63 8 4 0 t 3 5 0 0 3 0 1 1 1 3 2 0 1 2 5 5 0

oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.600748; --mAGCCAGCCAGCC-- ; cor=; Ncor= a 0 0 32 59 1 1 1 63 1 0 0 62 1 2 3 0 0 c 0 0 33 0 8 62 63 1 8 65 63 0 0 58 58 0 0 g 0 0 0 5 56 1 0 0 56 0 1 3 64 4 3 0 0 t 0 0 0 1 0 1 1 1 0 0 1 0 0 1 1 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; ycATTGTGhg ; Alignment reference a 2 2 9 0 0 0 0 0 3 2 c 3 3 0 0 0 0 0 0 3 1 g 1 2 0 0 0 9 0 9 0 5 t 3 2 0 9 9 0 9 0 3 1

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ycATTGTGhg ; cor=; Ncor= a 2 2 9 0 0 0 0 0 3 2 c 3 3 0 0 0 0 0 0 3 1 g 1 2 0 0 0 9 0 9 0 5 t 3 2 0 9 9 0 9 0 3 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 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=11; shift=0; ncol=11; drCAGAGAGrv ; Alignment reference a 2 2 0 7 0 7 0 7 0 3 2 c 0 1 7 0 0 0 0 0 0 1 2 g 3 3 0 0 7 0 7 0 6 2 2 t 2 1 0 0 0 0 0 0 1 1 1

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; drCAGAGAGrv ; cor=; Ncor= a 2 2 0 7 0 7 0 7 0 3 2 c 0 1 7 0 0 0 0 0 0 1 2 g 3 3 0 0 7 0 7 0 6 2 2 t 2 1 0 0 0 0 0 0 1 1 1

oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m4; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.891545; dgCAGAGAgw- ; cor=; Ncor= a 4 2 0 10 0 10 0 10 1 4 0 c 0 2 10 0 0 0 0 0 2 1 0 g 3 5 0 0 10 0 10 0 6 2 0 t 3 1 0 0 0 0 0 0 1 3 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=13; shift=2; ncol=15; --mAGCCAGCCAGCC ; Alignment reference a 0 0 32 59 1 1 1 63 1 0 0 62 1 2 3 c 0 0 33 0 8 62 63 1 8 65 63 0 0 58 58 g 0 0 0 5 56 1 0 0 56 0 1 3 64 4 3 t 0 0 0 1 0 1 1 1 0 0 1 0 0 1 1
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --mAGCCAGCCAGCC ; cor=; Ncor= a 0 0 32 59 1 1 1 63 1 0 0 62 1 2 3 c 0 0 33 0 8 62 63 1 8 65 63 0 0 58 58 g 0 0 0 5 56 1 0 0 56 0 1 3 64 4 3 t 0 0 0 1 0 1 1 1 0 0 1 0 0 1 1
oligos_6nt_mkv1_m2_rc_shift0 (oligos_6nt_mkv1_m2_rc)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.743816; sCmAGCCAGCCArsC ; cor=; Ncor= a 3 3 55 108 0 0 1 104 2 2 2 106 63 2 7 c 56 97 54 1 2 105 106 2 6 100 102 0 4 42 89 g 47 4 0 0 104 4 1 2 100 4 3 3 41 63 8 t 3 5 0 0 3 0 1 1 1 3 2 0 1 2 5
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=3/3; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.600748; sCmAGCCAGCCAAGC ; cor=; Ncor= a 2 2 33 54 0 0 0 53 2 0 1 55 53 0 3 c 34 49 22 1 0 51 53 1 3 52 52 0 0 2 47 g 18 2 0 0 52 4 1 1 50 2 2 0 2 52 3 t 1 2 0 0 3 0 1 0 0 1 0 0 0 1 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=16; shift=1; ncol=17; -kGsyTGGCTGGCTkGs ; Alignment reference a 0 5 5 2 1 0 2 3 1 1 1 0 3 0 0 5 3 c 0 4 8 63 41 3 3 4 100 2 1 4 104 0 0 4 47 g 0 57 89 42 4 0 102 100 6 2 106 105 2 1 54 97 56 t 0 43 7 2 63 106 2 2 2 104 1 0 0 108 55 3 3
oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -kGsyTGGCTGGCTkGs ; cor=; Ncor= a 0 5 5 2 1 0 2 3 1 1 1 0 3 0 0 5 3 c 0 4 8 63 41 3 3 4 100 2 1 4 104 0 0 4 47 g 0 57 89 42 4 0 102 100 6 2 106 105 2 1 54 97 56 t 0 43 7 2 63 106 2 2 2 104 1 0 0 108 55 3 3
oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1_rc; m=2/3; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score= 0.9005; TGGCTTGGCTGGCTkGs ; cor=; Ncor= a 1 2 2 1 0 0 0 1 0 0 1 0 3 0 0 2 1 c 3 1 3 52 2 0 2 2 50 1 1 4 52 0 0 2 18 g 1 48 47 2 0 0 52 52 3 1 53 51 0 1 22 49 34 t 50 4 3 0 53 55 1 0 2 53 0 0 0 54 33 2 2
oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=13; w=0; offset=1; strand=R; shift=2; score=0.743816; --GGCTGGCTGGCTk-- ; cor=; Ncor= a 0 0 1 1 0 0 1 0 0 1 1 1 0 1 0 0 0 c 0 0 3 4 64 3 1 0 56 0 0 1 56 5 0 0 0 g 0 0 58 58 0 0 63 65 8 1 63 62 8 0 33 0 0 t 0 0 3 2 1 62 0 0 1 63 1 1 1 59 32 0 0

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=17; shift=0; ncol=17; sCmAGCCAGCCAAGCCA ; Alignment reference a 2 2 33 54 0 0 0 53 2 0 1 55 53 0 3 4 50 c 34 49 22 1 0 51 53 1 3 52 52 0 0 2 47 48 1 g 18 2 0 0 52 4 1 1 50 2 2 0 2 52 3 1 3 t 1 2 0 0 3 0 1 0 0 1 0 0 0 1 2 2 1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; sCmAGCCAGCCAAGCCA ; cor=; Ncor= a 2 2 33 54 0 0 0 53 2 0 1 55 53 0 3 4 50 c 34 49 22 1 0 51 53 1 3 52 52 0 0 2 47 48 1 g 18 2 0 0 52 4 1 1 50 2 2 0 2 52 3 1 3 t 1 2 0 0 3 0 1 0 0 1 0 0 0 1 2 2 1
oligos_6nt_mkv1_m2_rc_shift0 (oligos_6nt_mkv1_m2_rc)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=16; w=0; offset=0; strand=R; shift=0; score= 0.9005; sCmAGCCAGCCArsCm- ; cor=; Ncor= a 3 3 55 108 0 0 1 104 2 2 2 106 63 2 7 43 0 c 56 97 54 1 2 105 106 2 6 100 102 0 4 42 89 57 0 g 47 4 0 0 104 4 1 2 100 4 3 3 41 63 8 4 0 t 3 5 0 0 3 0 1 1 1 3 2 0 1 2 5 5 0
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.600748; --mAGCCAGCCAGCC-- ; cor=; Ncor= a 0 0 32 59 1 1 1 63 1 0 0 62 1 2 3 0 0 c 0 0 33 0 8 62 63 1 8 65 63 0 0 58 58 0 0 g 0 0 0 5 56 1 0 0 56 0 1 3 64 4 3 0 0 t 0 0 0 1 0 1 1 1 0 0 1 0 0 1 1 0 0