One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/26/peak-motifs.2025-04-26.160500_2025-04-26.160500_72i0jt/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/2025/04/26/peak-motifs.2025-04-26.160500_2025-04-26.160500_72i0jt/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift2 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --ytCyCCtCyy ; Alignment reference a 0 0 8 9 1 1 0 0 6 0 5 3 c 0 0 17 10 36 26 37 39 4 40 14 21 g 0 0 2 2 2 0 1 0 10 0 1 4 t 0 0 14 20 2 14 3 2 21 1 21 13

oligos_6nt_mkv1_m4_shift2 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ytCyCCtCyy ; cor=; Ncor= a 0 0 8 9 1 1 0 0 6 0 5 3 c 0 0 17 10 36 26 37 39 4 40 14 21 g 0 0 2 2 2 0 1 0 10 0 1 4 t 0 0 14 20 2 14 3 2 21 1 21 13

oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m1_rc; m=2/6; ncol2=12; w=0; offset=0; strand=R; shift=2; score= 0.7526; --mwCCCCTCTb ; cor=; Ncor= a 0 0 5 6 1 0 0 1 0 0 0 2 c 0 0 6 2 14 12 13 14 0 15 1 5 g 0 0 2 0 0 0 1 0 0 0 0 4 t 0 0 2 7 0 3 1 0 15 0 14 4

oligos_6nt_mkv1_m3_rc_shift2 (oligos_6nt_mkv1_m3_rc)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m3_rc; m=3/6; ncol2=11; w=0; offset=0; strand=R; shift=2; score=0.732918; --hTMTCCTCYh ; cor=; Ncor= a 0 0 3 1 3 0 0 0 0 0 0 3 c 0 0 5 2 9 0 12 11 0 12 9 4 g 0 0 1 0 0 0 0 0 0 0 0 0 t 0 0 3 9 0 12 0 1 12 0 3 5

oligos_7nt_mkv1_m1_rc_shift2 (oligos_7nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m1_rc; m=4/6; ncol2=13; w=0; offset=0; strand=R; shift=2; score=0.693086; --mwCCCCTCTb ; cor=; Ncor= a 0 0 4 4 1 0 0 0 0 0 0 0 c 0 0 4 1 10 9 9 11 0 11 0 5 g 0 0 1 0 0 0 1 0 0 0 0 3 t 0 0 2 6 0 2 1 0 11 0 11 3

oligos_7nt_mkv1_m2_rc_shift0 (oligos_7nt_mkv1_m2_rc)
; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m2_rc; m=5/6; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.620806; yyyTCTCCTCCy ; cor=; Ncor= a 1 1 0 0 1 0 0 0 0 0 1 1 c 6 4 7 0 9 0 11 10 1 11 8 5 g 0 1 1 0 0 0 0 0 0 0 0 1 t 4 5 3 11 1 11 0 1 10 0 2 4

oligos_6nt_mkv1_m2_rc_shift0 (oligos_6nt_mkv1_m2_rc)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m2_rc; m=6/6; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.537452; mmCTCTCCtC-- ; cor=; Ncor= a 3 3 0 1 0 0 0 0 1 0 0 0 c 5 3 10 0 10 0 10 10 2 8 0 0 g 1 2 0 0 0 0 0 0 1 0 0 0 t 1 2 0 9 0 10 0 0 6 2 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----rrvAGAGGGGwk ; Alignment reference a 0 0 0 0 9 7 4 14 0 15 0 1 3 0 7 2 c 0 0 0 0 0 1 4 0 0 0 0 1 0 0 0 2 g 0 0 0 0 4 4 5 1 15 0 14 13 12 14 2 6 t 0 0 0 0 2 3 2 0 0 0 1 0 0 1 6 5

oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----rrvAGAGGGGwk ; cor=; Ncor= a 0 0 0 0 9 7 4 14 0 15 0 1 3 0 7 2 c 0 0 0 0 0 1 4 0 0 0 0 1 0 0 0 2 g 0 0 0 0 4 4 5 1 15 0 14 13 12 14 2 6 t 0 0 0 0 2 3 2 0 0 0 1 0 0 1 6 5

oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/6; ncol2=13; w=-1; offset=-1; strand=D; shift=3; score=0.911122; ---GrrvAGAGGGGwk ; cor=; Ncor= a 0 0 0 1 7 7 3 11 0 11 0 1 2 0 6 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 0 0 1 g 0 0 0 8 4 3 5 0 11 0 11 9 9 10 1 4 t 0 0 0 1 0 1 0 0 0 0 0 0 0 1 4 4

oligos_6nt_mkv1_m4_rc_shift6 (oligos_6nt_mkv1_m4_rc)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m4_rc; m=3/6; ncol2=10; w=0; offset=2; strand=R; shift=6; score= 0.7526; ------rrGaGGrGar ; cor=; Ncor= a 0 0 0 0 0 0 13 21 1 21 2 3 14 2 20 14 c 0 0 0 0 0 0 4 1 0 10 0 1 0 2 2 2 g 0 0 0 0 0 0 21 14 40 4 39 37 26 36 10 17 t 0 0 0 0 0 0 3 5 0 6 0 0 1 1 9 8

oligos_6nt_mkv1_m3_shift5 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m3; m=4/6; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.650494; -----kdRGAGGAKAd ; cor=; Ncor= a 0 0 0 0 0 2 5 3 0 12 1 0 12 0 9 3 c 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 g 0 0 0 0 0 4 4 9 12 0 11 12 0 9 2 5 t 0 0 0 0 0 5 3 0 0 0 0 0 0 3 1 3

oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=5/6; ncol2=10; w=-1; offset=-1; strand=D; shift=3; score=0.524329; ---GaGGAGAGkk--- ; cor=; Ncor= a 0 0 0 2 6 0 0 10 0 9 0 2 1 0 0 0 c 0 0 0 0 1 0 0 0 0 0 0 2 1 0 0 0 g 0 0 0 8 2 10 10 0 10 0 10 3 5 0 0 0 t 0 0 0 0 1 0 0 0 0 1 0 3 3 0 0 0

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2; m=6/6; ncol2=13; w=-4; offset=-4; strand=D; shift=0; score=0.42249; trGGAGGAGArrr--- ; cor=; Ncor= a 2 4 2 0 10 1 0 11 1 11 3 5 4 0 0 0 c 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 0 0 0 t 6 1 1 0 0 0 0 0 1 0 0 1 1 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; whMGWGMAGKdd ; Alignment reference a 2 2 1 0 3 0 1 4 0 0 2 2 c 0 1 3 0 0 0 3 0 0 0 0 0 g 0 0 0 4 0 4 0 0 4 3 1 1 t 2 1 0 0 1 0 0 0 0 1 1 1

oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; whMGWGMAGKdd ; cor=; Ncor= a 2 2 1 0 3 0 1 4 0 0 2 2 c 0 1 3 0 0 0 3 0 0 0 0 0 g 0 0 0 4 0 4 0 0 4 3 1 1 t 2 1 0 0 1 0 0 0 0 1 1 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=13; shift=3; ncol=16; ---GrrvAGAGGGGwk ; Alignment reference a 0 0 0 1 7 7 3 11 0 11 0 1 2 0 6 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 0 0 1 g 0 0 0 8 4 3 5 0 11 0 11 9 9 10 1 4 t 0 0 0 1 0 1 0 0 0 0 0 0 0 1 4 4

oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---GrrvAGAGGGGwk ; cor=; Ncor= a 0 0 0 1 7 7 3 11 0 11 0 1 2 0 6 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 0 0 1 g 0 0 0 8 4 3 5 0 11 0 11 9 9 10 1 4 t 0 0 0 1 0 1 0 0 0 0 0 0 0 1 4 4

oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=4; score=0.911122; ----rrvAGAGGGGwk ; cor=; Ncor= a 0 0 0 0 9 7 4 14 0 15 0 1 3 0 7 2 c 0 0 0 0 0 1 4 0 0 0 0 1 0 0 0 2 g 0 0 0 0 4 4 5 1 15 0 14 13 12 14 2 6 t 0 0 0 0 2 3 2 0 0 0 1 0 0 1 6 5

oligos_6nt_mkv1_m4_rc_shift6 (oligos_6nt_mkv1_m4_rc)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m4_rc; m=3/5; ncol2=10; w=0; offset=3; strand=R; shift=6; score=0.693086; ------rrGaGGrGar ; cor=; Ncor= a 0 0 0 0 0 0 13 21 1 21 2 3 14 2 20 14 c 0 0 0 0 0 0 4 1 0 10 0 1 0 2 2 2 g 0 0 0 0 0 0 21 14 40 4 39 37 26 36 10 17 t 0 0 0 0 0 0 3 5 0 6 0 0 1 1 9 8

oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=4/5; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.607106; ---GaGGAGAGkk--- ; cor=; Ncor= a 0 0 0 2 6 0 0 10 0 9 0 2 1 0 0 0 c 0 0 0 0 1 0 0 0 0 0 0 2 1 0 0 0 g 0 0 0 8 2 10 10 0 10 0 10 3 5 0 0 0 t 0 0 0 0 1 0 0 0 0 1 0 3 3 0 0 0

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m2; m=5/5; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.491427; trGGAGGAGArrr--- ; cor=; Ncor= a 2 4 2 0 10 1 0 11 1 11 3 5 4 0 0 0 c 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 0 0 0 t 6 1 1 0 0 0 0 0 1 0 0 1 1 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wdGCATAGTww ; Alignment reference a 5 3 0 0 9 0 8 0 1 4 3 c 1 0 0 8 0 1 1 1 0 0 0 g 0 3 9 1 0 0 0 8 0 2 2 t 3 3 0 0 0 8 0 0 8 3 4

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wdGCATAGTww ; cor=; Ncor= a 5 3 0 0 9 0 8 0 1 4 3 c 1 0 0 8 0 1 1 1 0 0 0 g 0 3 9 1 0 0 0 8 0 2 2 t 3 3 0 0 0 8 0 0 8 3 4

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -kdRGAGGAKAd ; Alignment reference a 0 2 5 3 0 12 1 0 12 0 9 3 c 0 1 0 0 0 0 0 0 0 0 0 1 g 0 4 4 9 12 0 11 12 0 9 2 5 t 0 5 3 0 0 0 0 0 0 3 1 3

oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -kdRGAGGAKAd ; cor=; Ncor= a 0 2 5 3 0 12 1 0 12 0 9 3 c 0 1 0 0 0 0 0 0 0 0 0 1 g 0 4 4 9 12 0 11 12 0 9 2 5 t 0 5 3 0 0 0 0 0 0 3 1 3

oligos_7nt_mkv1_m2_shift1 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/5; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.816826; -trGGAGGAGAr ; cor=; Ncor= a 0 2 4 2 0 10 1 0 11 1 11 3 c 0 1 1 0 0 0 0 0 0 0 0 1 g 0 2 5 8 11 1 10 11 0 9 0 7 t 0 6 1 1 0 0 0 0 0 1 0 0

oligos_6nt_mkv1_m4_rc_shift2 (oligos_6nt_mkv1_m4_rc)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m4_rc; m=3/5; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.732918; --rrGaGGrGar ; cor=; Ncor= a 0 0 13 21 1 21 2 3 14 2 20 14 c 0 0 4 1 0 10 0 1 0 2 2 2 g 0 0 21 14 40 4 39 37 26 36 10 17 t 0 0 3 5 0 6 0 0 1 1 9 8

oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=4/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.650494; rrvAGAGGGGwk ; cor=; Ncor= a 9 7 4 14 0 15 0 1 3 0 7 2 c 0 1 4 0 0 0 0 1 0 0 0 2 g 4 4 5 1 15 0 14 13 12 14 2 6 t 2 3 2 0 0 0 1 0 0 1 6 5

oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m2; m=5/5; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.552667; ----GaGGAGAG ; cor=; Ncor= a 0 0 0 0 2 6 0 0 10 0 9 0 c 0 0 0 0 0 1 0 0 0 0 0 0 g 0 0 0 0 8 2 10 10 0 10 0 10 t 0 0 0 0 0 1 0 0 0 0 1 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; wTTTGTAAAw ; Alignment reference a 17 5 0 0 0 0 37 37 31 14 c 2 2 0 0 0 0 0 0 0 1 g 0 1 0 0 37 0 0 0 0 2 t 18 29 37 37 0 37 0 0 6 20

oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wTTTGTAAAw ; cor=; Ncor= a 17 5 0 0 0 0 37 37 31 14 c 2 2 0 0 0 0 0 0 0 1 g 0 1 0 0 37 0 0 0 0 2 t 18 29 37 37 0 37 0 0 6 20

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; yrCAAGrATww ; Alignment reference a 1 6 0 9 10 1 3 10 0 4 4 c 3 0 10 0 0 1 0 0 0 0 0 g 1 3 0 1 0 8 6 0 0 1 2 t 5 1 0 0 0 0 1 0 10 5 4

oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; yrCAAGrATww ; cor=; Ncor= a 1 6 0 9 10 1 3 10 0 4 4 c 3 0 10 0 0 1 0 0 0 0 0 g 1 3 0 1 0 8 6 0 0 1 2 t 5 1 0 0 0 0 1 0 10 5 4

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift3 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---GaGGAGAGkk ; Alignment reference a 0 0 0 2 6 0 0 10 0 9 0 2 1 c 0 0 0 0 1 0 0 0 0 0 0 2 1 g 0 0 0 8 2 10 10 0 10 0 10 3 5 t 0 0 0 0 1 0 0 0 0 1 0 3 3

oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---GaGGAGAGkk ; cor=; Ncor= a 0 0 0 2 6 0 0 10 0 9 0 2 1 c 0 0 0 0 1 0 0 0 0 0 0 2 1 g 0 0 0 8 2 10 10 0 10 0 10 3 5 t 0 0 0 0 1 0 0 0 0 1 0 3 3

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=2/6; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.711952; trGGAGGAGArrr ; cor=; Ncor= a 2 4 2 0 10 1 0 11 1 11 3 5 4 c 1 1 0 0 0 0 0 0 0 0 1 1 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 t 6 1 1 0 0 0 0 0 1 0 0 1 1

oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=3/6; ncol2=13; w=0; offset=0; strand=D; shift=3; score=0.607106; ---GrrvAGAGGG ; cor=; Ncor= a 0 0 0 1 7 7 3 11 0 11 0 1 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 g 0 0 0 8 4 3 5 0 11 0 11 9 9 t 0 0 0 1 0 1 0 0 0 0 0 0 0

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=4/6; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.552667; kdRGAGGAKAd-- ; cor=; Ncor= a 2 5 3 0 12 1 0 12 0 9 3 0 0 c 1 0 0 0 0 0 0 0 0 0 1 0 0 g 4 4 9 12 0 11 12 0 9 2 5 0 0 t 5 3 0 0 0 0 0 0 3 1 3 0 0

oligos_6nt_mkv1_m4_rc_shift1 (oligos_6nt_mkv1_m4_rc)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m4_rc; m=5/6; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.537452; -rrGaGGrGar-- ; cor=; Ncor= a 0 13 21 1 21 2 3 14 2 20 14 0 0 c 0 4 1 0 10 0 1 0 2 2 2 0 0 g 0 21 14 40 4 39 37 26 36 10 17 0 0 t 0 3 5 0 6 0 0 1 1 9 8 0 0

oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=6/6; ncol2=12; w=0; offset=1; strand=D; shift=4; score=0.524329; ----rrvAGAGGG ; cor=; Ncor= a 0 0 0 0 9 7 4 14 0 15 0 1 3 c 0 0 0 0 0 1 4 0 0 0 0 1 0 g 0 0 0 0 4 4 5 1 15 0 14 13 12 t 0 0 0 0 2 3 2 0 0 0 1 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 7 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=13; shift=0; ncol=13; trGGAGGAGArrr ; Alignment reference a 2 4 2 0 10 1 0 11 1 11 3 5 4 c 1 1 0 0 0 0 0 0 0 0 1 1 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 t 6 1 1 0 0 0 0 0 1 0 0 1 1

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; trGGAGGAGArrr ; cor=; Ncor= a 2 4 2 0 10 1 0 11 1 11 3 5 4 c 1 1 0 0 0 0 0 0 0 0 1 1 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 t 6 1 1 0 0 0 0 0 1 0 0 1 1

oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.816826; kdRGAGGAKAd-- ; cor=; Ncor= a 2 5 3 0 12 1 0 12 0 9 3 0 0 c 1 0 0 0 0 0 0 0 0 0 1 0 0 g 4 4 9 12 0 11 12 0 9 2 5 0 0 t 5 3 0 0 0 0 0 0 3 1 3 0 0

oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=3/6; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.711952; ---GaGGAGAGkk ; cor=; Ncor= a 0 0 0 2 6 0 0 10 0 9 0 2 1 c 0 0 0 0 1 0 0 0 0 0 0 2 1 g 0 0 0 8 2 10 10 0 10 0 10 3 5 t 0 0 0 0 1 0 0 0 0 1 0 3 3

oligos_6nt_mkv1_m4_rc_shift1 (oligos_6nt_mkv1_m4_rc)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m4_rc; m=4/6; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.620806; -rrGaGGrGar-- ; cor=; Ncor= a 0 13 21 1 21 2 3 14 2 20 14 0 0 c 0 4 1 0 10 0 1 0 2 2 2 0 0 g 0 21 14 40 4 39 37 26 36 10 17 0 0 t 0 3 5 0 6 0 0 1 1 9 8 0 0

oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=5/6; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.491427; ---GrrvAGAGGG ; cor=; Ncor= a 0 0 0 1 7 7 3 11 0 11 0 1 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 g 0 0 0 8 4 3 5 0 11 0 11 9 9 t 0 0 0 1 0 1 0 0 0 0 0 0 0

oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=6/6; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.42249; ----rrvAGAGGG ; cor=; Ncor= a 0 0 0 0 9 7 4 14 0 15 0 1 3 c 0 0 0 0 0 1 4 0 0 0 0 1 0 g 0 0 0 0 4 4 5 1 15 0 14 13 12 t 0 0 0 0 2 3 2 0 0 0 1 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m4_shift2 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --ytCyCCtCyy ; Alignment reference a 0 0 8 9 1 1 0 0 6 0 5 3 c 0 0 17 10 36 26 37 39 4 40 14 21 g 0 0 2 2 2 0 1 0 10 0 1 4 t 0 0 14 20 2 14 3 2 21 1 21 13
oligos_6nt_mkv1_m4_shift2 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ytCyCCtCyy ; cor=; Ncor= a 0 0 8 9 1 1 0 0 6 0 5 3 c 0 0 17 10 36 26 37 39 4 40 14 21 g 0 0 2 2 2 0 1 0 10 0 1 4 t 0 0 14 20 2 14 3 2 21 1 21 13
oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m1_rc; m=2/6; ncol2=12; w=0; offset=0; strand=R; shift=2; score= 0.7526; --mwCCCCTCTb ; cor=; Ncor= a 0 0 5 6 1 0 0 1 0 0 0 2 c 0 0 6 2 14 12 13 14 0 15 1 5 g 0 0 2 0 0 0 1 0 0 0 0 4 t 0 0 2 7 0 3 1 0 15 0 14 4
oligos_6nt_mkv1_m3_rc_shift2 (oligos_6nt_mkv1_m3_rc)				; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m3_rc; m=3/6; ncol2=11; w=0; offset=0; strand=R; shift=2; score=0.732918; --hTMTCCTCYh ; cor=; Ncor= a 0 0 3 1 3 0 0 0 0 0 0 3 c 0 0 5 2 9 0 12 11 0 12 9 4 g 0 0 1 0 0 0 0 0 0 0 0 0 t 0 0 3 9 0 12 0 1 12 0 3 5
oligos_7nt_mkv1_m1_rc_shift2 (oligos_7nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m1_rc; m=4/6; ncol2=13; w=0; offset=0; strand=R; shift=2; score=0.693086; --mwCCCCTCTb ; cor=; Ncor= a 0 0 4 4 1 0 0 0 0 0 0 0 c 0 0 4 1 10 9 9 11 0 11 0 5 g 0 0 1 0 0 0 1 0 0 0 0 3 t 0 0 2 6 0 2 1 0 11 0 11 3
oligos_7nt_mkv1_m2_rc_shift0 (oligos_7nt_mkv1_m2_rc)				; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m2_rc; m=5/6; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.620806; yyyTCTCCTCCy ; cor=; Ncor= a 1 1 0 0 1 0 0 0 0 0 1 1 c 6 4 7 0 9 0 11 10 1 11 8 5 g 0 1 1 0 0 0 0 0 0 0 0 1 t 4 5 3 11 1 11 0 1 10 0 2 4
oligos_6nt_mkv1_m2_rc_shift0 (oligos_6nt_mkv1_m2_rc)				; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m2_rc; m=6/6; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.537452; mmCTCTCCtC-- ; cor=; Ncor= a 3 3 0 1 0 0 0 0 1 0 0 0 c 5 3 10 0 10 0 10 10 2 8 0 0 g 1 2 0 0 0 0 0 0 1 0 0 0 t 1 2 0 9 0 10 0 0 6 2 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----rrvAGAGGGGwk ; Alignment reference a 0 0 0 0 9 7 4 14 0 15 0 1 3 0 7 2 c 0 0 0 0 0 1 4 0 0 0 0 1 0 0 0 2 g 0 0 0 0 4 4 5 1 15 0 14 13 12 14 2 6 t 0 0 0 0 2 3 2 0 0 0 1 0 0 1 6 5
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----rrvAGAGGGGwk ; cor=; Ncor= a 0 0 0 0 9 7 4 14 0 15 0 1 3 0 7 2 c 0 0 0 0 0 1 4 0 0 0 0 1 0 0 0 2 g 0 0 0 0 4 4 5 1 15 0 14 13 12 14 2 6 t 0 0 0 0 2 3 2 0 0 0 1 0 0 1 6 5
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/6; ncol2=13; w=-1; offset=-1; strand=D; shift=3; score=0.911122; ---GrrvAGAGGGGwk ; cor=; Ncor= a 0 0 0 1 7 7 3 11 0 11 0 1 2 0 6 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 0 0 1 g 0 0 0 8 4 3 5 0 11 0 11 9 9 10 1 4 t 0 0 0 1 0 1 0 0 0 0 0 0 0 1 4 4
oligos_6nt_mkv1_m4_rc_shift6 (oligos_6nt_mkv1_m4_rc)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m4_rc; m=3/6; ncol2=10; w=0; offset=2; strand=R; shift=6; score= 0.7526; ------rrGaGGrGar ; cor=; Ncor= a 0 0 0 0 0 0 13 21 1 21 2 3 14 2 20 14 c 0 0 0 0 0 0 4 1 0 10 0 1 0 2 2 2 g 0 0 0 0 0 0 21 14 40 4 39 37 26 36 10 17 t 0 0 0 0 0 0 3 5 0 6 0 0 1 1 9 8
oligos_6nt_mkv1_m3_shift5 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m3; m=4/6; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.650494; -----kdRGAGGAKAd ; cor=; Ncor= a 0 0 0 0 0 2 5 3 0 12 1 0 12 0 9 3 c 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 g 0 0 0 0 0 4 4 9 12 0 11 12 0 9 2 5 t 0 0 0 0 0 5 3 0 0 0 0 0 0 3 1 3
oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=5/6; ncol2=10; w=-1; offset=-1; strand=D; shift=3; score=0.524329; ---GaGGAGAGkk--- ; cor=; Ncor= a 0 0 0 2 6 0 0 10 0 9 0 2 1 0 0 0 c 0 0 0 0 1 0 0 0 0 0 0 2 1 0 0 0 g 0 0 0 8 2 10 10 0 10 0 10 3 5 0 0 0 t 0 0 0 0 1 0 0 0 0 1 0 3 3 0 0 0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2; m=6/6; ncol2=13; w=-4; offset=-4; strand=D; shift=0; score=0.42249; trGGAGGAGArrr--- ; cor=; Ncor= a 2 4 2 0 10 1 0 11 1 11 3 5 4 0 0 0 c 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 0 0 0 t 6 1 1 0 0 0 0 0 1 0 0 1 1 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=13; shift=3; ncol=16; ---GrrvAGAGGGGwk ; Alignment reference a 0 0 0 1 7 7 3 11 0 11 0 1 2 0 6 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 0 0 1 g 0 0 0 8 4 3 5 0 11 0 11 9 9 10 1 4 t 0 0 0 1 0 1 0 0 0 0 0 0 0 1 4 4
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---GrrvAGAGGGGwk ; cor=; Ncor= a 0 0 0 1 7 7 3 11 0 11 0 1 2 0 6 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 0 0 1 g 0 0 0 8 4 3 5 0 11 0 11 9 9 10 1 4 t 0 0 0 1 0 1 0 0 0 0 0 0 0 1 4 4
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=4; score=0.911122; ----rrvAGAGGGGwk ; cor=; Ncor= a 0 0 0 0 9 7 4 14 0 15 0 1 3 0 7 2 c 0 0 0 0 0 1 4 0 0 0 0 1 0 0 0 2 g 0 0 0 0 4 4 5 1 15 0 14 13 12 14 2 6 t 0 0 0 0 2 3 2 0 0 0 1 0 0 1 6 5
oligos_6nt_mkv1_m4_rc_shift6 (oligos_6nt_mkv1_m4_rc)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m4_rc; m=3/5; ncol2=10; w=0; offset=3; strand=R; shift=6; score=0.693086; ------rrGaGGrGar ; cor=; Ncor= a 0 0 0 0 0 0 13 21 1 21 2 3 14 2 20 14 c 0 0 0 0 0 0 4 1 0 10 0 1 0 2 2 2 g 0 0 0 0 0 0 21 14 40 4 39 37 26 36 10 17 t 0 0 0 0 0 0 3 5 0 6 0 0 1 1 9 8
oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=4/5; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.607106; ---GaGGAGAGkk--- ; cor=; Ncor= a 0 0 0 2 6 0 0 10 0 9 0 2 1 0 0 0 c 0 0 0 0 1 0 0 0 0 0 0 2 1 0 0 0 g 0 0 0 8 2 10 10 0 10 0 10 3 5 0 0 0 t 0 0 0 0 1 0 0 0 0 1 0 3 3 0 0 0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m2; m=5/5; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.491427; trGGAGGAGArrr--- ; cor=; Ncor= a 2 4 2 0 10 1 0 11 1 11 3 5 4 0 0 0 c 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 0 0 0 t 6 1 1 0 0 0 0 0 1 0 0 1 1 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -kdRGAGGAKAd ; Alignment reference a 0 2 5 3 0 12 1 0 12 0 9 3 c 0 1 0 0 0 0 0 0 0 0 0 1 g 0 4 4 9 12 0 11 12 0 9 2 5 t 0 5 3 0 0 0 0 0 0 3 1 3
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -kdRGAGGAKAd ; cor=; Ncor= a 0 2 5 3 0 12 1 0 12 0 9 3 c 0 1 0 0 0 0 0 0 0 0 0 1 g 0 4 4 9 12 0 11 12 0 9 2 5 t 0 5 3 0 0 0 0 0 0 3 1 3
oligos_7nt_mkv1_m2_shift1 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/5; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.816826; -trGGAGGAGAr ; cor=; Ncor= a 0 2 4 2 0 10 1 0 11 1 11 3 c 0 1 1 0 0 0 0 0 0 0 0 1 g 0 2 5 8 11 1 10 11 0 9 0 7 t 0 6 1 1 0 0 0 0 0 1 0 0
oligos_6nt_mkv1_m4_rc_shift2 (oligos_6nt_mkv1_m4_rc)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m4_rc; m=3/5; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.732918; --rrGaGGrGar ; cor=; Ncor= a 0 0 13 21 1 21 2 3 14 2 20 14 c 0 0 4 1 0 10 0 1 0 2 2 2 g 0 0 21 14 40 4 39 37 26 36 10 17 t 0 0 3 5 0 6 0 0 1 1 9 8
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=4/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.650494; rrvAGAGGGGwk ; cor=; Ncor= a 9 7 4 14 0 15 0 1 3 0 7 2 c 0 1 4 0 0 0 0 1 0 0 0 2 g 4 4 5 1 15 0 14 13 12 14 2 6 t 2 3 2 0 0 0 1 0 0 1 6 5
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m2; m=5/5; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.552667; ----GaGGAGAG ; cor=; Ncor= a 0 0 0 0 2 6 0 0 10 0 9 0 c 0 0 0 0 0 1 0 0 0 0 0 0 g 0 0 0 0 8 2 10 10 0 10 0 10 t 0 0 0 0 0 1 0 0 0 0 1 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---GaGGAGAGkk ; Alignment reference a 0 0 0 2 6 0 0 10 0 9 0 2 1 c 0 0 0 0 1 0 0 0 0 0 0 2 1 g 0 0 0 8 2 10 10 0 10 0 10 3 5 t 0 0 0 0 1 0 0 0 0 1 0 3 3
oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---GaGGAGAGkk ; cor=; Ncor= a 0 0 0 2 6 0 0 10 0 9 0 2 1 c 0 0 0 0 1 0 0 0 0 0 0 2 1 g 0 0 0 8 2 10 10 0 10 0 10 3 5 t 0 0 0 0 1 0 0 0 0 1 0 3 3
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=2/6; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.711952; trGGAGGAGArrr ; cor=; Ncor= a 2 4 2 0 10 1 0 11 1 11 3 5 4 c 1 1 0 0 0 0 0 0 0 0 1 1 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 t 6 1 1 0 0 0 0 0 1 0 0 1 1
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=3/6; ncol2=13; w=0; offset=0; strand=D; shift=3; score=0.607106; ---GrrvAGAGGG ; cor=; Ncor= a 0 0 0 1 7 7 3 11 0 11 0 1 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 g 0 0 0 8 4 3 5 0 11 0 11 9 9 t 0 0 0 1 0 1 0 0 0 0 0 0 0
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=4/6; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.552667; kdRGAGGAKAd-- ; cor=; Ncor= a 2 5 3 0 12 1 0 12 0 9 3 0 0 c 1 0 0 0 0 0 0 0 0 0 1 0 0 g 4 4 9 12 0 11 12 0 9 2 5 0 0 t 5 3 0 0 0 0 0 0 3 1 3 0 0
oligos_6nt_mkv1_m4_rc_shift1 (oligos_6nt_mkv1_m4_rc)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m4_rc; m=5/6; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.537452; -rrGaGGrGar-- ; cor=; Ncor= a 0 13 21 1 21 2 3 14 2 20 14 0 0 c 0 4 1 0 10 0 1 0 2 2 2 0 0 g 0 21 14 40 4 39 37 26 36 10 17 0 0 t 0 3 5 0 6 0 0 1 1 9 8 0 0
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=6/6; ncol2=12; w=0; offset=1; strand=D; shift=4; score=0.524329; ----rrvAGAGGG ; cor=; Ncor= a 0 0 0 0 9 7 4 14 0 15 0 1 3 c 0 0 0 0 0 1 4 0 0 0 0 1 0 g 0 0 0 0 4 4 5 1 15 0 14 13 12 t 0 0 0 0 2 3 2 0 0 0 1 0 0

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=13; shift=0; ncol=13; trGGAGGAGArrr ; Alignment reference a 2 4 2 0 10 1 0 11 1 11 3 5 4 c 1 1 0 0 0 0 0 0 0 0 1 1 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 t 6 1 1 0 0 0 0 0 1 0 0 1 1
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; trGGAGGAGArrr ; cor=; Ncor= a 2 4 2 0 10 1 0 11 1 11 3 5 4 c 1 1 0 0 0 0 0 0 0 0 1 1 0 g 2 5 8 11 1 10 11 0 9 0 7 4 6 t 6 1 1 0 0 0 0 0 1 0 0 1 1
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.816826; kdRGAGGAKAd-- ; cor=; Ncor= a 2 5 3 0 12 1 0 12 0 9 3 0 0 c 1 0 0 0 0 0 0 0 0 0 1 0 0 g 4 4 9 12 0 11 12 0 9 2 5 0 0 t 5 3 0 0 0 0 0 0 3 1 3 0 0
oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=3/6; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.711952; ---GaGGAGAGkk ; cor=; Ncor= a 0 0 0 2 6 0 0 10 0 9 0 2 1 c 0 0 0 0 1 0 0 0 0 0 0 2 1 g 0 0 0 8 2 10 10 0 10 0 10 3 5 t 0 0 0 0 1 0 0 0 0 1 0 3 3
oligos_6nt_mkv1_m4_rc_shift1 (oligos_6nt_mkv1_m4_rc)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m4_rc; m=4/6; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.620806; -rrGaGGrGar-- ; cor=; Ncor= a 0 13 21 1 21 2 3 14 2 20 14 0 0 c 0 4 1 0 10 0 1 0 2 2 2 0 0 g 0 21 14 40 4 39 37 26 36 10 17 0 0 t 0 3 5 0 6 0 0 1 1 9 8 0 0
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=5/6; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.491427; ---GrrvAGAGGG ; cor=; Ncor= a 0 0 0 1 7 7 3 11 0 11 0 1 2 c 0 0 0 1 0 0 3 0 0 0 0 1 0 g 0 0 0 8 4 3 5 0 11 0 11 9 9 t 0 0 0 1 0 1 0 0 0 0 0 0 0
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=6/6; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.42249; ----rrvAGAGGG ; cor=; Ncor= a 0 0 0 0 9 7 4 14 0 15 0 1 3 c 0 0 0 0 0 1 4 0 0 0 0 1 0 g 0 0 0 0 4 4 5 1 15 0 14 13 12 t 0 0 0 0 2 3 2 0 0 0 1 0 0