One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/08/17/peak-motifs.2025-08-17.121501_2025-08-17.121501_7wfl8K/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/2025/08/17/peak-motifs.2025-08-17.121501_2025-08-17.121501_7wfl8K/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 3 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=12; shift=0; ncol=12; sdCCACGAGGvy ; Alignment reference a 4 13 2 1 29 0 0 24 0 0 10 4 c 9 1 24 29 1 30 2 1 2 4 8 12 g 11 8 4 0 0 0 28 3 27 24 8 5 t 6 8 0 0 0 0 0 2 1 2 4 9

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; sdCCACGAGGvy ; cor=; Ncor= a 4 13 2 1 29 0 0 24 0 0 10 4 c 9 1 24 29 1 30 2 1 2 4 8 12 g 11 8 4 0 0 0 28 3 27 24 8 5 t 6 8 0 0 0 0 0 2 1 2 4 9

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.891003; -rsCACGAGGrc ; cor=; Ncor= a 0 19 9 1 52 0 0 45 1 2 18 11 c 0 7 24 51 4 55 3 3 3 7 13 22 g 0 21 16 3 1 1 53 4 52 45 17 13 t 0 10 8 2 0 1 1 5 1 3 9 11

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -rsCACGAGGrc ; Alignment reference a 0 19 9 1 52 0 0 45 1 2 18 11 c 0 7 24 51 4 55 3 3 3 7 13 22 g 0 21 16 3 1 1 53 4 52 45 17 13 t 0 10 8 2 0 1 1 5 1 3 9 11

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -rsCACGAGGrc ; cor=; Ncor= a 0 19 9 1 52 0 0 45 1 2 18 11 c 0 7 24 51 4 55 3 3 3 7 13 22 g 0 21 16 3 1 1 53 4 52 45 17 13 t 0 10 8 2 0 1 1 5 1 3 9 11

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=2/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.891003; sdCCACGAGGvy ; cor=; Ncor= a 4 13 2 1 29 0 0 24 0 0 10 4 c 9 1 24 29 1 30 2 1 2 4 8 12 g 11 8 4 0 0 0 28 3 27 24 8 5 t 6 8 0 0 0 0 0 2 1 2 4 9

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.672273; csgCACGTGcsg ; cor=; Ncor= a 11 11 7 0 58 0 1 2 0 6 13 15 c 21 18 11 62 2 58 3 0 0 38 20 15 g 15 20 38 0 0 3 58 2 62 11 18 21 t 15 13 6 0 2 1 0 58 0 7 11 11

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=4/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.642027; csGCACGTGCsg ; cor=; Ncor= a 10 9 5 0 46 0 1 2 0 0 10 11 c 19 16 7 50 2 46 3 0 0 38 15 10 g 10 15 38 0 0 3 46 2 50 7 16 19 t 11 10 0 0 2 1 0 46 0 5 9 10

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -thGCTTACtv ; Alignment reference a 0 3 7 0 1 0 0 21 0 2 7 c 0 5 7 0 19 1 0 0 21 2 6 g 0 3 0 21 1 0 0 0 0 5 7 t 0 10 7 0 0 20 21 0 0 12 1

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -thGCTTACtv ; cor=; Ncor= a 0 3 7 0 1 0 0 21 0 2 7 c 0 5 7 0 19 1 0 0 21 2 6 g 0 3 0 21 1 0 0 0 0 5 7 t 0 10 7 0 0 20 21 0 0 12 1

oligos_7nt_mkv2_m4_rc_shift1 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=2/4; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.878954; -yhGCTTACTm ; cor=; Ncor= a 0 9 13 0 2 1 2 45 0 2 17 c 0 13 14 0 44 1 2 2 42 2 17 g 0 10 8 49 1 1 8 0 5 4 12 t 0 17 14 0 2 46 37 2 2 41 3

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=3/4; ncol2=13; w=0; offset=0; strand=R; shift=1; score=0.588497; -btGCTGACTC ; cor=; Ncor= a 0 3 10 0 3 0 1 54 0 0 8 c 0 19 11 0 51 1 0 1 44 1 39 g 0 18 12 53 0 1 46 0 11 3 5 t 0 15 22 2 1 53 8 0 0 51 3

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=4/4; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.437656; rstGCTGAsTC ; cor=; Ncor= a 13 5 5 0 5 0 0 40 0 0 5 c 10 17 10 0 36 1 0 1 28 0 36 g 15 12 7 40 0 0 38 1 14 2 1 t 4 8 20 2 1 41 4 0 0 40 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --gcTGAGTCAGCav ; Alignment reference a 0 0 11 11 6 3 51 0 0 8 53 1 2 22 15 c 0 0 5 24 7 5 3 11 0 46 1 0 53 12 18 g 0 0 35 10 4 39 1 44 1 0 1 51 0 11 19 t 0 0 4 10 38 8 0 0 54 1 0 3 0 10 3

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --gcTGAGTCAGCav ; cor=; Ncor= a 0 0 11 11 6 3 51 0 0 8 53 1 2 22 15 c 0 0 5 24 7 5 3 11 0 46 1 0 53 12 18 g 0 0 35 10 4 39 1 44 1 0 1 51 0 11 19 t 0 0 4 10 38 8 0 0 54 1 0 3 0 10 3

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.789004; ytGCTGAsTCAGCas ; cor=; Ncor= a 7 8 3 7 1 0 40 0 0 4 41 1 2 20 8 c 12 10 0 29 2 1 2 14 1 38 0 0 40 7 12 g 10 9 38 4 1 36 0 28 1 0 1 36 0 10 17 t 13 15 1 2 38 5 0 0 40 0 0 5 0 5 5

oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=3/4; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.728442; ----tkAGTAAGCdr ; cor=; Ncor= a 0 0 0 0 8 3 41 2 2 37 46 2 0 14 17 c 0 0 0 0 12 12 4 5 0 8 1 1 49 8 10 g 0 0 0 0 10 17 2 42 2 2 1 44 0 14 13 t 0 0 0 0 19 17 2 0 45 2 1 2 0 13 9

oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5_rc; m=4/4; ncol2=10; w=0; offset=3; strand=R; shift=5; score=0.588497; -----baGTAAGCda ; cor=; Ncor= a 0 0 0 0 0 1 12 0 0 21 20 0 0 7 10 c 0 0 0 0 0 7 5 0 0 0 0 1 21 0 3 g 0 0 0 0 0 6 2 21 0 0 1 19 0 7 5 t 0 0 0 0 0 7 2 0 21 0 0 1 0 7 3

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; csgCACGTGcsg ; Alignment reference a 11 11 7 0 58 0 1 2 0 6 13 15 c 21 18 11 62 2 58 3 0 0 38 20 15 g 15 20 38 0 0 3 58 2 62 11 18 21 t 15 13 6 0 2 1 0 58 0 7 11 11

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; csgCACGTGcsg ; cor=; Ncor= a 11 11 7 0 58 0 1 2 0 6 13 15 c 21 18 11 62 2 58 3 0 0 38 20 15 g 15 20 38 0 0 3 58 2 62 11 18 21 t 15 13 6 0 2 1 0 58 0 7 11 11

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.991808; csGCACGTGCsg ; cor=; Ncor= a 10 9 5 0 46 0 1 2 0 0 10 11 c 19 16 7 50 2 46 3 0 0 38 15 10 g 10 15 38 0 0 3 46 2 50 7 16 19 t 11 10 0 0 2 1 0 46 0 5 9 10

oligos_6nt_mkv2_m3_rc_shift0 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=3/3; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.672273; gyCCTCGTGsy- ; cor=; Ncor= a 11 9 3 1 5 1 1 0 2 8 10 0 c 13 17 45 52 4 53 1 1 3 16 21 0 g 22 13 7 3 3 3 55 4 51 24 7 0 t 11 18 2 1 45 0 0 52 1 9 19 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; vsCTGTCArw ; Alignment reference a 8 7 0 0 0 0 0 30 9 9 c 10 10 30 0 0 0 30 0 6 5 g 8 13 0 0 30 0 0 0 11 6 t 4 0 0 30 0 30 0 0 4 10

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; vsCTGTCArw ; cor=; Ncor= a 8 7 0 0 0 0 0 30 9 9 c 10 10 30 0 0 0 30 0 6 5 g 8 13 0 0 30 0 0 0 11 6 t 4 0 0 30 0 30 0 0 4 10

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=2/2; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.643641; -ssTGTCAGA ; cor=; Ncor= a 0 10 10 6 1 0 0 50 9 40 c 0 17 18 1 2 0 49 0 0 5 g 0 18 16 1 47 1 1 1 42 3 t 0 7 8 44 2 51 2 1 1 4

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----tkAGTAAGCdr ; Alignment reference a 0 0 0 0 8 3 41 2 2 37 46 2 0 14 17 c 0 0 0 0 12 12 4 5 0 8 1 1 49 8 10 g 0 0 0 0 10 17 2 42 2 2 1 44 0 14 13 t 0 0 0 0 19 17 2 0 45 2 1 2 0 13 9

oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----tkAGTAAGCdr ; cor=; Ncor= a 0 0 0 0 8 3 41 2 2 37 46 2 0 14 17 c 0 0 0 0 12 12 4 5 0 8 1 1 49 8 10 g 0 0 0 0 10 17 2 42 2 2 1 44 0 14 13 t 0 0 0 0 19 17 2 0 45 2 1 2 0 13 9

oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5_rc; m=2/4; ncol2=10; w=0; offset=1; strand=R; shift=5; score=0.878954; -----baGTAAGCda ; cor=; Ncor= a 0 0 0 0 0 1 12 0 0 21 20 0 0 7 10 c 0 0 0 0 0 7 5 0 0 0 0 1 21 0 3 g 0 0 0 0 0 6 2 21 0 0 1 19 0 7 5 t 0 0 0 0 0 7 2 0 21 0 0 1 0 7 3

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=3/4; ncol2=13; w=-2; offset=-2; strand=D; shift=2; score=0.728442; --gcTGAGTCAGCav ; cor=; Ncor= a 0 0 11 11 6 3 51 0 0 8 53 1 2 22 15 c 0 0 5 24 7 5 3 11 0 46 1 0 53 12 18 g 0 0 35 10 4 39 1 44 1 0 1 51 0 11 19 t 0 0 4 10 38 8 0 0 54 1 0 3 0 10 3

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=4/4; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.547095; ytGCTGAsTCAGCas ; cor=; Ncor= a 7 8 3 7 1 0 40 0 0 4 41 1 2 20 8 c 12 10 0 29 2 1 2 14 1 38 0 0 40 7 12 g 10 9 38 4 1 36 0 28 1 0 1 36 0 10 17 t 13 15 1 2 38 5 0 0 40 0 0 5 0 5 5

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; ytGCTGAsTCAGCasy ; Alignment reference a 7 8 3 7 1 0 40 0 0 4 41 1 2 20 8 4 c 12 10 0 29 2 1 2 14 1 38 0 0 40 7 12 15 g 10 9 38 4 1 36 0 28 1 0 1 36 0 10 17 10 t 13 15 1 2 38 5 0 0 40 0 0 5 0 5 5 13

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; ytGCTGAsTCAGCasy ; cor=; Ncor= a 7 8 3 7 1 0 40 0 0 4 41 1 2 20 8 4 c 12 10 0 29 2 1 2 14 1 38 0 0 40 7 12 15 g 10 9 38 4 1 36 0 28 1 0 1 36 0 10 17 10 t 13 15 1 2 38 5 0 0 40 0 0 5 0 5 5 13

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=2/4; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.789004; --gcTGAGTCAGCav- ; cor=; Ncor= a 0 0 11 11 6 3 51 0 0 8 53 1 2 22 15 0 c 0 0 5 24 7 5 3 11 0 46 1 0 53 12 18 0 g 0 0 35 10 4 39 1 44 1 0 1 51 0 11 19 0 t 0 0 4 10 38 8 0 0 54 1 0 3 0 10 3 0

oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=3/4; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.547095; ----tkAGTAAGCdr- ; cor=; Ncor= a 0 0 0 0 8 3 41 2 2 37 46 2 0 14 17 0 c 0 0 0 0 12 12 4 5 0 8 1 1 49 8 10 0 g 0 0 0 0 10 17 2 42 2 2 1 44 0 14 13 0 t 0 0 0 0 19 17 2 0 45 2 1 2 0 13 9 0

oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=4/4; ncol2=10; w=0; offset=5; strand=R; shift=5; score=0.437656; -----baGTAAGCda- ; cor=; Ncor= a 0 0 0 0 0 1 12 0 0 21 20 0 0 7 10 0 c 0 0 0 0 0 7 5 0 0 0 0 1 21 0 3 0 g 0 0 0 0 0 6 2 21 0 0 1 19 0 7 5 0 t 0 0 0 0 0 7 2 0 21 0 0 1 0 7 3 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 4 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=12; shift=0; ncol=12; csGCACGTGCsg ; Alignment reference a 10 9 5 0 46 0 1 2 0 0 10 11 c 19 16 7 50 2 46 3 0 0 38 15 10 g 10 15 38 0 0 3 46 2 50 7 16 19 t 11 10 0 0 2 1 0 46 0 5 9 10

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; csGCACGTGCsg ; cor=; Ncor= a 10 9 5 0 46 0 1 2 0 0 10 11 c 19 16 7 50 2 46 3 0 0 38 15 10 g 10 15 38 0 0 3 46 2 50 7 16 19 t 11 10 0 0 2 1 0 46 0 5 9 10

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.991808; csgCACGTGcsg ; cor=; Ncor= a 11 11 7 0 58 0 1 2 0 6 13 15 c 21 18 11 62 2 58 3 0 0 38 20 15 g 15 20 38 0 0 3 58 2 62 11 18 21 t 15 13 6 0 2 1 0 58 0 7 11 11

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.642027; -rsCACGAGGrc ; cor=; Ncor= a 0 19 9 1 52 0 0 45 1 2 18 11 c 0 7 24 51 4 55 3 3 3 7 13 22 g 0 21 16 3 1 1 53 4 52 45 17 13 t 0 10 8 2 0 1 1 5 1 3 9 11

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 3 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=11; shift=0; ncol=11; rrTCTGACAss ; Alignment reference a 18 18 4 1 1 2 51 2 44 8 7 c 6 10 3 42 1 1 1 47 1 16 18 g 16 15 5 0 0 49 0 2 1 18 17 t 12 9 40 9 50 0 0 1 6 10 10

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; rrTCTGACAss ; cor=; Ncor= a 18 18 4 1 1 2 51 2 44 8 7 c 6 10 3 42 1 1 1 47 1 16 18 g 16 15 5 0 0 49 0 2 1 18 17 t 12 9 40 9 50 0 0 1 6 10 10

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4_rc; m=2/2; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.643641; --wyTGACAGs ; cor=; Ncor= a 0 0 10 4 0 0 30 0 30 0 0 c 0 0 6 11 0 0 0 30 0 0 13 g 0 0 5 6 0 30 0 0 0 30 10 t 0 0 9 9 30 0 0 0 0 0 7

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -rsCACGAGGrc ; Alignment reference a 0 19 9 1 52 0 0 45 1 2 18 11 c 0 7 24 51 4 55 3 3 3 7 13 22 g 0 21 16 3 1 1 53 4 52 45 17 13 t 0 10 8 2 0 1 1 5 1 3 9 11
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -rsCACGAGGrc ; cor=; Ncor= a 0 19 9 1 52 0 0 45 1 2 18 11 c 0 7 24 51 4 55 3 3 3 7 13 22 g 0 21 16 3 1 1 53 4 52 45 17 13 t 0 10 8 2 0 1 1 5 1 3 9 11
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=2/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.891003; sdCCACGAGGvy ; cor=; Ncor= a 4 13 2 1 29 0 0 24 0 0 10 4 c 9 1 24 29 1 30 2 1 2 4 8 12 g 11 8 4 0 0 0 28 3 27 24 8 5 t 6 8 0 0 0 0 0 2 1 2 4 9
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.672273; csgCACGTGcsg ; cor=; Ncor= a 11 11 7 0 58 0 1 2 0 6 13 15 c 21 18 11 62 2 58 3 0 0 38 20 15 g 15 20 38 0 0 3 58 2 62 11 18 21 t 15 13 6 0 2 1 0 58 0 7 11 11
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=4/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.642027; csGCACGTGCsg ; cor=; Ncor= a 10 9 5 0 46 0 1 2 0 0 10 11 c 19 16 7 50 2 46 3 0 0 38 15 10 g 10 15 38 0 0 3 46 2 50 7 16 19 t 11 10 0 0 2 1 0 46 0 5 9 10

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -thGCTTACtv ; Alignment reference a 0 3 7 0 1 0 0 21 0 2 7 c 0 5 7 0 19 1 0 0 21 2 6 g 0 3 0 21 1 0 0 0 0 5 7 t 0 10 7 0 0 20 21 0 0 12 1
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -thGCTTACtv ; cor=; Ncor= a 0 3 7 0 1 0 0 21 0 2 7 c 0 5 7 0 19 1 0 0 21 2 6 g 0 3 0 21 1 0 0 0 0 5 7 t 0 10 7 0 0 20 21 0 0 12 1
oligos_7nt_mkv2_m4_rc_shift1 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=2/4; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.878954; -yhGCTTACTm ; cor=; Ncor= a 0 9 13 0 2 1 2 45 0 2 17 c 0 13 14 0 44 1 2 2 42 2 17 g 0 10 8 49 1 1 8 0 5 4 12 t 0 17 14 0 2 46 37 2 2 41 3
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=3/4; ncol2=13; w=0; offset=0; strand=R; shift=1; score=0.588497; -btGCTGACTC ; cor=; Ncor= a 0 3 10 0 3 0 1 54 0 0 8 c 0 19 11 0 51 1 0 1 44 1 39 g 0 18 12 53 0 1 46 0 11 3 5 t 0 15 22 2 1 53 8 0 0 51 3
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=4/4; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.437656; rstGCTGAsTC ; cor=; Ncor= a 13 5 5 0 5 0 0 40 0 0 5 c 10 17 10 0 36 1 0 1 28 0 36 g 15 12 7 40 0 0 38 1 14 2 1 t 4 8 20 2 1 41 4 0 0 40 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --gcTGAGTCAGCav ; Alignment reference a 0 0 11 11 6 3 51 0 0 8 53 1 2 22 15 c 0 0 5 24 7 5 3 11 0 46 1 0 53 12 18 g 0 0 35 10 4 39 1 44 1 0 1 51 0 11 19 t 0 0 4 10 38 8 0 0 54 1 0 3 0 10 3
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --gcTGAGTCAGCav ; cor=; Ncor= a 0 0 11 11 6 3 51 0 0 8 53 1 2 22 15 c 0 0 5 24 7 5 3 11 0 46 1 0 53 12 18 g 0 0 35 10 4 39 1 44 1 0 1 51 0 11 19 t 0 0 4 10 38 8 0 0 54 1 0 3 0 10 3
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.789004; ytGCTGAsTCAGCas ; cor=; Ncor= a 7 8 3 7 1 0 40 0 0 4 41 1 2 20 8 c 12 10 0 29 2 1 2 14 1 38 0 0 40 7 12 g 10 9 38 4 1 36 0 28 1 0 1 36 0 10 17 t 13 15 1 2 38 5 0 0 40 0 0 5 0 5 5
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=3/4; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.728442; ----tkAGTAAGCdr ; cor=; Ncor= a 0 0 0 0 8 3 41 2 2 37 46 2 0 14 17 c 0 0 0 0 12 12 4 5 0 8 1 1 49 8 10 g 0 0 0 0 10 17 2 42 2 2 1 44 0 14 13 t 0 0 0 0 19 17 2 0 45 2 1 2 0 13 9
oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5_rc; m=4/4; ncol2=10; w=0; offset=3; strand=R; shift=5; score=0.588497; -----baGTAAGCda ; cor=; Ncor= a 0 0 0 0 0 1 12 0 0 21 20 0 0 7 10 c 0 0 0 0 0 7 5 0 0 0 0 1 21 0 3 g 0 0 0 0 0 6 2 21 0 0 1 19 0 7 5 t 0 0 0 0 0 7 2 0 21 0 0 1 0 7 3

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; csgCACGTGcsg ; Alignment reference a 11 11 7 0 58 0 1 2 0 6 13 15 c 21 18 11 62 2 58 3 0 0 38 20 15 g 15 20 38 0 0 3 58 2 62 11 18 21 t 15 13 6 0 2 1 0 58 0 7 11 11
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; csgCACGTGcsg ; cor=; Ncor= a 11 11 7 0 58 0 1 2 0 6 13 15 c 21 18 11 62 2 58 3 0 0 38 20 15 g 15 20 38 0 0 3 58 2 62 11 18 21 t 15 13 6 0 2 1 0 58 0 7 11 11
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.991808; csGCACGTGCsg ; cor=; Ncor= a 10 9 5 0 46 0 1 2 0 0 10 11 c 19 16 7 50 2 46 3 0 0 38 15 10 g 10 15 38 0 0 3 46 2 50 7 16 19 t 11 10 0 0 2 1 0 46 0 5 9 10
oligos_6nt_mkv2_m3_rc_shift0 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=3/3; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.672273; gyCCTCGTGsy- ; cor=; Ncor= a 11 9 3 1 5 1 1 0 2 8 10 0 c 13 17 45 52 4 53 1 1 3 16 21 0 g 22 13 7 3 3 3 55 4 51 24 7 0 t 11 18 2 1 45 0 0 52 1 9 19 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----tkAGTAAGCdr ; Alignment reference a 0 0 0 0 8 3 41 2 2 37 46 2 0 14 17 c 0 0 0 0 12 12 4 5 0 8 1 1 49 8 10 g 0 0 0 0 10 17 2 42 2 2 1 44 0 14 13 t 0 0 0 0 19 17 2 0 45 2 1 2 0 13 9
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----tkAGTAAGCdr ; cor=; Ncor= a 0 0 0 0 8 3 41 2 2 37 46 2 0 14 17 c 0 0 0 0 12 12 4 5 0 8 1 1 49 8 10 g 0 0 0 0 10 17 2 42 2 2 1 44 0 14 13 t 0 0 0 0 19 17 2 0 45 2 1 2 0 13 9
oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5_rc; m=2/4; ncol2=10; w=0; offset=1; strand=R; shift=5; score=0.878954; -----baGTAAGCda ; cor=; Ncor= a 0 0 0 0 0 1 12 0 0 21 20 0 0 7 10 c 0 0 0 0 0 7 5 0 0 0 0 1 21 0 3 g 0 0 0 0 0 6 2 21 0 0 1 19 0 7 5 t 0 0 0 0 0 7 2 0 21 0 0 1 0 7 3
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=3/4; ncol2=13; w=-2; offset=-2; strand=D; shift=2; score=0.728442; --gcTGAGTCAGCav ; cor=; Ncor= a 0 0 11 11 6 3 51 0 0 8 53 1 2 22 15 c 0 0 5 24 7 5 3 11 0 46 1 0 53 12 18 g 0 0 35 10 4 39 1 44 1 0 1 51 0 11 19 t 0 0 4 10 38 8 0 0 54 1 0 3 0 10 3
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=4/4; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.547095; ytGCTGAsTCAGCas ; cor=; Ncor= a 7 8 3 7 1 0 40 0 0 4 41 1 2 20 8 c 12 10 0 29 2 1 2 14 1 38 0 0 40 7 12 g 10 9 38 4 1 36 0 28 1 0 1 36 0 10 17 t 13 15 1 2 38 5 0 0 40 0 0 5 0 5 5

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; ytGCTGAsTCAGCasy ; Alignment reference a 7 8 3 7 1 0 40 0 0 4 41 1 2 20 8 4 c 12 10 0 29 2 1 2 14 1 38 0 0 40 7 12 15 g 10 9 38 4 1 36 0 28 1 0 1 36 0 10 17 10 t 13 15 1 2 38 5 0 0 40 0 0 5 0 5 5 13
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; ytGCTGAsTCAGCasy ; cor=; Ncor= a 7 8 3 7 1 0 40 0 0 4 41 1 2 20 8 4 c 12 10 0 29 2 1 2 14 1 38 0 0 40 7 12 15 g 10 9 38 4 1 36 0 28 1 0 1 36 0 10 17 10 t 13 15 1 2 38 5 0 0 40 0 0 5 0 5 5 13
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=2/4; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.789004; --gcTGAGTCAGCav- ; cor=; Ncor= a 0 0 11 11 6 3 51 0 0 8 53 1 2 22 15 0 c 0 0 5 24 7 5 3 11 0 46 1 0 53 12 18 0 g 0 0 35 10 4 39 1 44 1 0 1 51 0 11 19 0 t 0 0 4 10 38 8 0 0 54 1 0 3 0 10 3 0
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=3/4; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.547095; ----tkAGTAAGCdr- ; cor=; Ncor= a 0 0 0 0 8 3 41 2 2 37 46 2 0 14 17 0 c 0 0 0 0 12 12 4 5 0 8 1 1 49 8 10 0 g 0 0 0 0 10 17 2 42 2 2 1 44 0 14 13 0 t 0 0 0 0 19 17 2 0 45 2 1 2 0 13 9 0
oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=4/4; ncol2=10; w=0; offset=5; strand=R; shift=5; score=0.437656; -----baGTAAGCda- ; cor=; Ncor= a 0 0 0 0 0 1 12 0 0 21 20 0 0 7 10 0 c 0 0 0 0 0 7 5 0 0 0 0 1 21 0 3 0 g 0 0 0 0 0 6 2 21 0 0 1 19 0 7 5 0 t 0 0 0 0 0 7 2 0 21 0 0 1 0 7 3 0

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=12; shift=0; ncol=12; csGCACGTGCsg ; Alignment reference a 10 9 5 0 46 0 1 2 0 0 10 11 c 19 16 7 50 2 46 3 0 0 38 15 10 g 10 15 38 0 0 3 46 2 50 7 16 19 t 11 10 0 0 2 1 0 46 0 5 9 10
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; csGCACGTGCsg ; cor=; Ncor= a 10 9 5 0 46 0 1 2 0 0 10 11 c 19 16 7 50 2 46 3 0 0 38 15 10 g 10 15 38 0 0 3 46 2 50 7 16 19 t 11 10 0 0 2 1 0 46 0 5 9 10
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.991808; csgCACGTGcsg ; cor=; Ncor= a 11 11 7 0 58 0 1 2 0 6 13 15 c 21 18 11 62 2 58 3 0 0 38 20 15 g 15 20 38 0 0 3 58 2 62 11 18 21 t 15 13 6 0 2 1 0 58 0 7 11 11
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.642027; -rsCACGAGGrc ; cor=; Ncor= a 0 19 9 1 52 0 0 45 1 2 18 11 c 0 7 24 51 4 55 3 3 3 7 13 22 g 0 21 16 3 1 1 53 4 52 45 17 13 t 0 10 8 2 0 1 1 5 1 3 9 11