One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.150933_2026-01-05.150933_rtRXPK/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/2026/01/05/peak-motifs.2026-01-05.150933_2026-01-05.150933_rtRXPK/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; rsAGACCAGvm ; Alignment reference a 16 10 51 1 54 1 0 43 2 17 17 c 13 16 2 3 1 48 52 4 4 18 17 g 15 20 1 51 0 4 2 2 49 15 12 t 12 10 2 1 1 3 2 7 1 6 10

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; rsAGACCAGvm ; cor=; Ncor= a 16 10 51 1 54 1 0 43 2 17 17 c 13 16 2 3 1 48 52 4 4 18 17 g 15 20 1 51 0 4 2 2 49 15 12 t 12 10 2 1 1 3 2 7 1 6 10

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; syyCCTGAAATaa ; Alignment reference a 5 5 6 4 0 1 1 26 28 23 3 10 10 c 9 9 11 21 29 1 0 0 1 2 1 6 6 g 12 7 4 2 0 2 28 2 0 2 4 7 7 t 3 8 8 2 0 25 0 1 0 2 21 6 6

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; syyCCTGAAATaa ; cor=; Ncor= a 5 5 6 4 0 1 1 26 28 23 3 10 10 c 9 9 11 21 29 1 0 0 1 2 1 6 6 g 12 7 4 2 0 2 28 2 0 2 4 7 7 t 3 8 8 2 0 25 0 1 0 2 21 6 6

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; hyCTTTCAAAwa ; Alignment reference a 13 10 1 4 2 4 1 42 41 42 16 15 c 13 11 32 1 0 1 36 1 0 1 8 10 g 6 7 6 0 3 4 4 0 1 0 9 10 t 12 16 5 39 39 35 3 1 2 1 11 9

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; hyCTTTCAAAwa ; cor=; Ncor= a 13 10 1 4 2 4 1 42 41 42 16 15 c 13 11 32 1 0 1 36 1 0 1 8 10 g 6 7 6 0 3 4 4 0 1 0 9 10 t 12 16 5 39 39 35 3 1 2 1 11 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; vbGACTGGCgs ; Alignment reference a 15 4 1 50 1 1 1 4 2 12 10 c 19 18 6 2 53 5 2 0 47 13 23 g 16 19 49 3 2 2 52 47 5 20 16 t 6 15 0 1 0 48 1 5 2 11 7

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; vbGACTGGCgs ; cor=; Ncor= a 15 4 1 50 1 1 1 4 2 12 10 c 19 18 6 2 53 5 2 0 47 13 23 g 16 19 49 3 2 2 52 47 5 20 16 t 6 15 0 1 0 48 1 5 2 11 7

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; dhcAAAACTTagyy ; Alignment reference a 10 8 5 25 26 25 29 3 0 3 20 2 7 5 c 2 11 16 3 0 4 1 28 1 2 2 2 8 8 g 9 4 4 2 2 1 1 0 0 3 6 21 6 7 t 10 8 6 1 3 1 0 0 30 23 3 6 10 11

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; dhcAAAACTTagyy ; cor=; Ncor= a 10 8 5 25 26 25 29 3 0 3 20 2 7 5 c 2 11 16 3 0 4 1 28 1 2 2 2 8 8 g 9 4 4 2 2 1 1 0 0 3 6 21 6 7 t 10 8 6 1 3 1 0 0 30 23 3 6 10 11

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.769646; ywyAAAACTTTtd- ; cor=; Ncor= a 9 14 7 37 36 34 37 2 0 3 3 10 11 0 c 14 9 13 1 1 0 4 33 0 2 2 10 5 0 g 7 7 9 2 0 2 0 3 3 3 3 10 11 0 t 11 11 12 1 4 5 0 3 38 33 33 11 14 0

oligos_7nt_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.574228; --gsAAACTCAvy- ; cor=; Ncor= a 0 0 21 17 77 77 76 5 5 2 75 23 20 0 c 0 0 17 25 2 6 3 72 5 72 1 28 27 0 g 0 0 27 26 3 2 3 6 3 4 6 24 15 0 t 0 0 20 17 3 0 3 2 72 7 3 10 23 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=2; ncol=13; --gsAAACTCAvy ; Alignment reference a 0 0 21 17 77 77 76 5 5 2 75 23 20 c 0 0 17 25 2 6 3 72 5 72 1 28 27 g 0 0 27 26 3 2 3 6 3 4 6 24 15 t 0 0 20 17 3 0 3 2 72 7 3 10 23

oligos_7nt_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --gsAAACTCAvy ; cor=; Ncor= a 0 0 21 17 77 77 76 5 5 2 75 23 20 c 0 0 17 25 2 6 3 72 5 72 1 28 27 g 0 0 27 26 3 2 3 6 3 4 6 24 15 t 0 0 20 17 3 0 3 2 72 7 3 10 23

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=2/2; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.574228; dhcAAAACTTagy ; cor=; Ncor= a 10 8 5 25 26 25 29 3 0 3 20 2 7 c 2 11 16 3 0 4 1 28 1 2 2 2 8 g 9 4 4 2 2 1 1 0 0 3 6 21 6 t 10 8 6 1 3 1 0 0 30 23 3 6 10

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=13; shift=0; ncol=13; wwtTAAAAAAAhm ; Alignment reference a 26 27 12 6 73 70 71 73 72 76 72 22 27 c 17 18 9 3 2 10 5 5 3 2 4 24 28 g 16 14 9 8 3 4 3 3 6 6 4 16 13 t 27 27 56 69 8 2 7 5 5 2 6 24 18

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=13; w=0; offset=0; strand=D; shift=0; score= 1; wwtTAAAAAAAhm ; cor=; Ncor= a 26 27 12 6 73 70 71 73 72 76 72 22 27 c 17 18 9 3 2 10 5 5 3 2 4 24 28 g 16 14 9 8 3 4 3 3 6 6 4 16 13 t 27 27 56 69 8 2 7 5 5 2 6 24 18

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; mvATGACAAmr ; Alignment reference a 13 16 41 1 2 44 3 46 46 16 17 c 17 15 5 1 0 5 46 3 0 15 10 g 12 15 2 4 48 1 2 2 4 11 16 t 10 6 4 46 2 2 1 1 2 10 9

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; mvATGACAAmr ; cor=; Ncor= a 13 16 41 1 2 44 3 46 46 16 17 c 17 15 5 1 0 5 46 3 0 15 10 g 12 15 2 4 48 1 2 2 4 11 16 t 10 6 4 46 2 2 1 1 2 10 9

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; masTTTACAAad ; Alignment reference a 14 17 6 6 1 3 45 3 43 33 16 15 c 14 9 14 1 1 0 0 34 1 6 10 3 g 8 9 19 3 1 4 0 3 1 2 8 15 t 9 10 6 35 42 38 0 5 0 4 11 12

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; masTTTACAAad ; cor=; Ncor= a 14 17 6 6 1 3 45 3 43 33 16 15 c 14 9 14 1 1 0 0 34 1 6 10 3 g 8 9 19 3 1 4 0 3 1 2 8 15 t 9 10 6 35 42 38 0 5 0 4 11 12

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -haAAAGTTTTrwr ; Alignment reference a 0 14 11 33 33 38 3 0 5 4 1 12 11 11 c 0 11 10 3 3 3 3 0 2 0 2 9 7 7 g 0 5 10 2 2 0 33 4 0 1 1 13 9 14 t 0 11 10 3 3 0 2 37 34 36 37 7 14 9

oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -haAAAGTTTTrwr ; cor=; Ncor= a 0 14 11 33 33 38 3 0 5 4 1 12 11 11 c 0 11 10 3 3 3 3 0 2 0 2 9 7 7 g 0 5 10 2 2 0 33 4 0 1 1 13 9 14 t 0 11 10 3 3 0 2 37 34 36 37 7 14 9

oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/2; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.769646; rrctAAGTTTTgdh ; cor=; Ncor= a 11 10 6 3 23 30 0 0 1 3 1 6 8 10 c 7 6 21 6 3 0 0 1 1 2 2 4 4 9 g 8 8 2 2 2 1 28 1 4 0 3 16 11 2 t 5 7 2 20 3 0 3 29 25 26 25 5 8 10

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; dhcAAAACTTagyy ; Alignment reference a 10 8 5 25 26 25 29 3 0 3 20 2 7 5 c 2 11 16 3 0 4 1 28 1 2 2 2 8 8 g 9 4 4 2 2 1 1 0 0 3 6 21 6 7 t 10 8 6 1 3 1 0 0 30 23 3 6 10 11
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; dhcAAAACTTagyy ; cor=; Ncor= a 10 8 5 25 26 25 29 3 0 3 20 2 7 5 c 2 11 16 3 0 4 1 28 1 2 2 2 8 8 g 9 4 4 2 2 1 1 0 0 3 6 21 6 7 t 10 8 6 1 3 1 0 0 30 23 3 6 10 11
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.769646; ywyAAAACTTTtd- ; cor=; Ncor= a 9 14 7 37 36 34 37 2 0 3 3 10 11 0 c 14 9 13 1 1 0 4 33 0 2 2 10 5 0 g 7 7 9 2 0 2 0 3 3 3 3 10 11 0 t 11 11 12 1 4 5 0 3 38 33 33 11 14 0
oligos_7nt_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.574228; --gsAAACTCAvy- ; cor=; Ncor= a 0 0 21 17 77 77 76 5 5 2 75 23 20 0 c 0 0 17 25 2 6 3 72 5 72 1 28 27 0 g 0 0 27 26 3 2 3 6 3 4 6 24 15 0 t 0 0 20 17 3 0 3 2 72 7 3 10 23 0