One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.012409_2025-05-16.012409_IdvjkC/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.2025-05-16.012409_2025-05-16.012409_IdvjkC/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; kwGAATCGAwa ; Alignment reference a 14 19 2 54 53 4 7 3 51 18 19 c 9 8 1 0 1 0 44 2 3 8 14 g 16 11 51 2 1 3 2 48 2 10 13 t 19 20 4 2 3 51 5 5 2 22 12

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; kwGAATCGAwa ; cor=; Ncor= a 14 19 2 54 53 4 7 3 51 18 19 c 9 8 1 0 1 0 44 2 3 8 14 g 16 11 51 2 1 3 2 48 2 10 13 t 19 20 4 2 3 51 5 5 2 22 12

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; waAAATAATAAwww ; Alignment reference a 39 37 66 77 76 7 78 77 7 73 78 32 42 34 c 10 19 2 1 3 0 1 1 1 4 3 10 7 14 g 9 12 4 3 1 2 3 3 3 3 1 15 11 8 t 25 15 11 2 3 74 1 2 72 3 1 26 23 27

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; waAAATAATAAwww ; cor=; Ncor= a 39 37 66 77 76 7 78 77 7 73 78 32 42 34 c 10 19 2 1 3 0 1 1 1 4 3 10 7 14 g 9 12 4 3 1 2 3 3 3 3 1 15 11 8 t 25 15 11 2 3 74 1 2 72 3 1 26 23 27

oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.776658; --waATAATAATaw ; cor=; Ncor= a 0 0 61 65 131 10 139 132 8 139 130 15 81 57 c 0 0 15 21 10 0 0 3 3 3 9 8 14 25 g 0 0 19 27 1 8 8 6 7 1 2 3 29 16 t 0 0 54 36 7 131 2 8 131 6 8 123 25 51

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.72635; amAAATAATrw--- ; cor=; Ncor= a 15 10 33 33 33 0 33 33 0 12 17 0 0 0 c 6 10 0 0 0 0 0 0 0 4 5 0 0 0 g 4 6 0 0 0 0 0 0 0 10 2 0 0 0 t 8 7 0 0 0 33 0 0 33 7 9 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=11; shift=1; ncol=12; -amAAATAATrw ; Alignment reference a 0 15 10 33 33 33 0 33 33 0 12 17 c 0 6 10 0 0 0 0 0 0 0 4 5 g 0 4 6 0 0 0 0 0 0 0 10 2 t 0 8 7 0 0 0 33 0 0 33 7 9

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -amAAATAATrw ; cor=; Ncor= a 0 15 10 33 33 33 0 33 33 0 12 17 c 0 6 10 0 0 0 0 0 0 0 4 5 g 0 4 6 0 0 0 0 0 0 0 10 2 t 0 8 7 0 0 0 33 0 0 33 7 9

oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.72635; -waAAATAATAA ; cor=; Ncor= a 0 39 37 66 77 76 7 78 77 7 73 78 c 0 10 19 2 1 3 0 1 1 1 4 3 g 0 9 12 4 3 1 2 3 3 3 3 1 t 0 25 15 11 2 3 74 1 2 72 3 1

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.710646; waATAATAATaw ; cor=; Ncor= a 61 65 131 10 139 132 8 139 130 15 81 57 c 15 21 10 0 0 3 3 3 9 8 14 25 g 19 27 1 8 8 6 7 1 2 3 29 16 t 54 36 7 131 2 8 131 6 8 123 25 51

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --waATAATAATaw ; Alignment reference a 0 0 61 65 131 10 139 132 8 139 130 15 81 57 c 0 0 15 21 10 0 0 3 3 3 9 8 14 25 g 0 0 19 27 1 8 8 6 7 1 2 3 29 16 t 0 0 54 36 7 131 2 8 131 6 8 123 25 51

oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --waATAATAATaw ; cor=; Ncor= a 0 0 61 65 131 10 139 132 8 139 130 15 81 57 c 0 0 15 21 10 0 0 3 3 3 9 8 14 25 g 0 0 19 27 1 8 8 6 7 1 2 3 29 16 t 0 0 54 36 7 131 2 8 131 6 8 123 25 51

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.776658; waAAATAATAAwww ; cor=; Ncor= a 39 37 66 77 76 7 78 77 7 73 78 32 42 34 c 10 19 2 1 3 0 1 1 1 4 3 10 7 14 g 9 12 4 3 1 2 3 3 3 3 1 15 11 8 t 25 15 11 2 3 74 1 2 72 3 1 26 23 27

oligos_7nt_test_vs_ctrl_m4_shift3 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.710646; ---amAAATAATrw ; cor=; Ncor= a 0 0 0 15 10 33 33 33 0 33 33 0 12 17 c 0 0 0 6 10 0 0 0 0 0 0 0 4 5 g 0 0 0 4 6 0 0 0 0 0 0 0 10 2 t 0 0 0 8 7 0 0 0 33 0 0 33 7 9

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wrCACCTGAww ; Alignment reference a 22 20 2 55 2 2 2 3 42 15 20 c 11 8 45 0 52 49 2 1 6 5 10 g 7 16 3 0 0 4 0 54 4 11 9 t 18 14 8 3 4 3 54 0 6 27 19

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wrCACCTGAww ; cor=; Ncor= a 22 20 2 55 2 2 2 3 42 15 20 c 11 8 45 0 52 49 2 1 6 5 10 g 7 16 3 0 0 4 0 54 4 11 9 t 18 14 8 3 4 3 54 0 6 27 19

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAGCAACArh ; Alignment reference a 33 23 83 6 4 77 64 0 80 27 29 c 12 14 1 1 79 1 10 78 5 19 26 g 20 19 1 71 1 2 8 4 2 22 10 t 23 32 3 10 4 8 6 6 1 20 23

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAGCAACArh ; cor=; Ncor= a 33 23 83 6 4 77 64 0 80 27 29 c 12 14 1 1 79 1 10 78 5 19 26 g 20 19 1 71 1 2 8 4 2 22 10 t 23 32 3 10 4 8 6 6 1 20 23

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; rtCATCGATGay ; Alignment reference a 7 4 2 20 0 0 1 19 2 1 9 4 c 4 4 18 0 2 20 1 1 0 1 5 7 g 7 5 1 0 1 1 20 2 0 18 4 4 t 4 9 1 2 19 1 0 0 20 2 4 7

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; rtCATCGATGay ; cor=; Ncor= a 7 4 2 20 0 0 1 19 2 1 9 4 c 4 4 18 0 2 20 1 1 0 1 5 7 g 7 5 1 0 1 1 20 2 0 18 4 4 t 4 9 1 2 19 1 0 0 20 2 4 7

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; waAAATAATAAwww ; Alignment reference a 39 37 66 77 76 7 78 77 7 73 78 32 42 34 c 10 19 2 1 3 0 1 1 1 4 3 10 7 14 g 9 12 4 3 1 2 3 3 3 3 1 15 11 8 t 25 15 11 2 3 74 1 2 72 3 1 26 23 27
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; waAAATAATAAwww ; cor=; Ncor= a 39 37 66 77 76 7 78 77 7 73 78 32 42 34 c 10 19 2 1 3 0 1 1 1 4 3 10 7 14 g 9 12 4 3 1 2 3 3 3 3 1 15 11 8 t 25 15 11 2 3 74 1 2 72 3 1 26 23 27
oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.776658; --waATAATAATaw ; cor=; Ncor= a 0 0 61 65 131 10 139 132 8 139 130 15 81 57 c 0 0 15 21 10 0 0 3 3 3 9 8 14 25 g 0 0 19 27 1 8 8 6 7 1 2 3 29 16 t 0 0 54 36 7 131 2 8 131 6 8 123 25 51
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.72635; amAAATAATrw--- ; cor=; Ncor= a 15 10 33 33 33 0 33 33 0 12 17 0 0 0 c 6 10 0 0 0 0 0 0 0 4 5 0 0 0 g 4 6 0 0 0 0 0 0 0 10 2 0 0 0 t 8 7 0 0 0 33 0 0 33 7 9 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=11; shift=1; ncol=12; -amAAATAATrw ; Alignment reference a 0 15 10 33 33 33 0 33 33 0 12 17 c 0 6 10 0 0 0 0 0 0 0 4 5 g 0 4 6 0 0 0 0 0 0 0 10 2 t 0 8 7 0 0 0 33 0 0 33 7 9
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -amAAATAATrw ; cor=; Ncor= a 0 15 10 33 33 33 0 33 33 0 12 17 c 0 6 10 0 0 0 0 0 0 0 4 5 g 0 4 6 0 0 0 0 0 0 0 10 2 t 0 8 7 0 0 0 33 0 0 33 7 9
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.72635; -waAAATAATAA ; cor=; Ncor= a 0 39 37 66 77 76 7 78 77 7 73 78 c 0 10 19 2 1 3 0 1 1 1 4 3 g 0 9 12 4 3 1 2 3 3 3 3 1 t 0 25 15 11 2 3 74 1 2 72 3 1
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.710646; waATAATAATaw ; cor=; Ncor= a 61 65 131 10 139 132 8 139 130 15 81 57 c 15 21 10 0 0 3 3 3 9 8 14 25 g 19 27 1 8 8 6 7 1 2 3 29 16 t 54 36 7 131 2 8 131 6 8 123 25 51

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --waATAATAATaw ; Alignment reference a 0 0 61 65 131 10 139 132 8 139 130 15 81 57 c 0 0 15 21 10 0 0 3 3 3 9 8 14 25 g 0 0 19 27 1 8 8 6 7 1 2 3 29 16 t 0 0 54 36 7 131 2 8 131 6 8 123 25 51
oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --waATAATAATaw ; cor=; Ncor= a 0 0 61 65 131 10 139 132 8 139 130 15 81 57 c 0 0 15 21 10 0 0 3 3 3 9 8 14 25 g 0 0 19 27 1 8 8 6 7 1 2 3 29 16 t 0 0 54 36 7 131 2 8 131 6 8 123 25 51
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.776658; waAAATAATAAwww ; cor=; Ncor= a 39 37 66 77 76 7 78 77 7 73 78 32 42 34 c 10 19 2 1 3 0 1 1 1 4 3 10 7 14 g 9 12 4 3 1 2 3 3 3 3 1 15 11 8 t 25 15 11 2 3 74 1 2 72 3 1 26 23 27
oligos_7nt_test_vs_ctrl_m4_shift3 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.710646; ---amAAATAATrw ; cor=; Ncor= a 0 0 0 15 10 33 33 33 0 33 33 0 12 17 c 0 0 0 6 10 0 0 0 0 0 0 0 4 5 g 0 0 0 4 6 0 0 0 0 0 0 0 10 2 t 0 0 0 8 7 0 0 0 33 0 0 33 7 9