One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/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/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift3 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wkyCGATAsTATCGATaswwtygw ; Alignment reference a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8

oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8

dyads_m3_shift3 (dyads_m3)
; oligos_6nt_mkv2_m4 versus dyads_m3; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.999187; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.985095; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5

oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.960259; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6

dyads_m1_shift3 (dyads_m1)
; oligos_6nt_mkv2_m4 versus dyads_m1; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.956768; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9

oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.865453; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.862574; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.819057; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.787886; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_6nt_mkv2_m4 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.724759; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.709251; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; oligos_6nt_mkv2_m4 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.600008; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0

positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)
; oligos_6nt_mkv2_m4 versus positions_6nt_m2_rc; m=13/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.532834; ---------wasTATCGATAGtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0

positions_6nt_m1_shift9 (positions_6nt_m1)
; oligos_6nt_mkv2_m4 versus positions_6nt_m1; m=14/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.517272; ---------wacTATCGATAgyw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0

positions_7nt_m2_shift8 (positions_7nt_m2)
; oligos_6nt_mkv2_m4 versus positions_7nt_m2; m=15/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.515321; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 4 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; -rwAAAATAwh ; Alignment reference a 0 19 24 59 59 59 59 0 59 18 17 c 0 11 11 0 0 0 0 0 0 11 15 g 0 15 7 0 0 0 0 0 0 5 11 t 0 14 17 0 0 0 0 59 0 25 16

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -rwAAAATAwh ; cor=; Ncor= a 0 19 24 59 59 59 59 0 59 18 17 c 0 11 11 0 0 0 0 0 0 11 15 g 0 15 7 0 0 0 0 0 0 5 11 t 0 14 17 0 0 0 0 59 0 25 16

dyads_m4_shift0 (dyads_m4)
; oligos_6nt_mkv2_m5 versus dyads_m4; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.829458; wdwAAAATAtw ; cor=; Ncor= a 27 21 23 63 66 63 67 0 66 16 21 c 15 12 11 1 0 0 0 0 0 12 15 g 2 17 6 2 0 0 0 1 1 5 13 t 23 17 27 1 1 4 0 66 0 34 18

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.673752; hrATAAATAwh ; cor=; Ncor= a 19 19 52 1 51 44 48 0 53 17 17 c 14 8 2 1 2 2 1 2 1 10 14 g 6 16 1 4 0 4 6 0 1 9 8 t 16 12 0 49 2 5 0 53 0 19 16

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wdwAAAATAtwd ; Alignment reference a 27 21 23 63 66 63 67 0 66 16 21 17 c 15 12 11 1 0 0 0 0 0 12 15 7 g 2 17 6 2 0 0 0 1 1 5 13 20 t 23 17 27 1 1 4 0 66 0 34 18 23

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wdwAAAATAtwd ; cor=; Ncor= a 27 21 23 63 66 63 67 0 66 16 21 17 c 15 12 11 1 0 0 0 0 0 12 15 7 g 2 17 6 2 0 0 0 1 1 5 13 20 t 23 17 27 1 1 4 0 66 0 34 18 23

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; dyads_m4 versus oligos_6nt_mkv2_m5; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.829458; -rwAAAATAwh- ; cor=; Ncor= a 0 19 24 59 59 59 59 0 59 18 17 0 c 0 11 11 0 0 0 0 0 0 11 15 0 g 0 15 7 0 0 0 0 0 0 5 11 0 t 0 14 17 0 0 0 0 59 0 25 16 0

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; dyads_m4 versus oligos_7nt_mkv2_m5; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.673977; hrATAAATAwh- ; cor=; Ncor= a 19 19 52 1 51 44 48 0 53 17 17 0 c 14 8 2 1 2 2 1 2 1 10 14 0 g 6 16 1 4 0 4 6 0 1 9 8 0 t 16 12 0 49 2 5 0 53 0 19 16 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift9 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift9 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=14; shift=9; ncol=23; ---------awacTATCGATrgt ; Alignment reference a 0 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 c 0 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 g 0 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 t 0 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43

positions_7nt_m2_shift9 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/15; ncol2=14; w=0; offset=0; strand=D; shift=9; score= 1; ---------awacTATCGATrgt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 c 0 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 g 0 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 t 0 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43

positions_7nt_m1_shift9 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=2/15; ncol2=16; w=0; offset=0; strand=D; shift=9; score=0.831139; ---------awacTATCGATAgt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 c 0 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 g 0 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 t 0 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51

positions_6nt_m1_shift10 (positions_6nt_m1)
; positions_7nt_m2 versus positions_6nt_m1; m=3/15; ncol2=14; w=0; offset=1; strand=D; shift=10; score=0.822423; ----------wacTATCGATAgy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 c 0 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 g 0 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 t 0 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39

positions_6nt_m2_shift10 (positions_6nt_m2)
; positions_7nt_m2 versus positions_6nt_m2; m=4/15; ncol2=14; w=0; offset=1; strand=D; shift=10; score=0.813542; ----------waCTATCGATAst ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 c 0 0 0 0 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 g 0 0 0 0 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 t 0 0 0 0 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39

oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)
; positions_7nt_m2 versus oligos_6nt_mkv2_m2_rc; m=5/15; ncol2=20; w=-5; offset=-5; strand=R; shift=4; score=0.615595; ----yrtCGATAsTATCGatrkh ; cor=; Ncor= a 0 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 c 0 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 g 0 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 t 0 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19

oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; positions_7nt_m2 versus oligos_7nt_mkv2_m4; m=6/15; ncol2=22; w=-6; offset=-6; strand=D; shift=3; score=0.556698; ---yhryCGATAsTATCGAtagh ; cor=; Ncor= a 0 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 c 0 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 g 0 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 t 0 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13

dyads_m1_shift4 (dyads_m1)
; positions_7nt_m2 versus dyads_m1; m=7/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.544202; ----mvkCGaTACTATCGATAgt ; cor=; Ncor= a 0 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 c 0 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 g 0 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 t 0 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27

oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)
; positions_7nt_m2 versus oligos_7nt_mkv2_m3; m=8/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.53522; ----mdkCGaTASTATCGATAst ; cor=; Ncor= a 0 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 c 0 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 g 0 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 t 0 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; positions_7nt_m2 versus oligos_6nt_mkv2_m1; m=9/15; ncol2=24; w=-4; offset=-4; strand=D; shift=5; score=0.533663; -----ktCGatACTATCGATAGT ; cor=; Ncor= a 0 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 c 0 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 g 0 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 t 0 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34

oligos_7nt_mkv2_m1_rc_shift5 (oligos_7nt_mkv2_m1_rc)
; positions_7nt_m2 versus oligos_7nt_mkv2_m1_rc; m=10/15; ncol2=24; w=-4; offset=-4; strand=R; shift=5; score=0.529333; -----ktCGaTACTATCGATAgT ; cor=; Ncor= a 0 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 c 0 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 g 0 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 t 0 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26

oligos_6nt_mkv2_m3_shift4 (oligos_6nt_mkv2_m3)
; positions_7nt_m2 versus oligos_6nt_mkv2_m3; m=11/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.519322; ----wkkCGATAsTATCGATAsw ; cor=; Ncor= a 0 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 c 0 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 g 0 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 t 0 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14

dyads_m3_shift4 (dyads_m3)
; positions_7nt_m2 versus dyads_m3; m=12/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.516029; ----wkyCGATAsTATCGATasw ; cor=; Ncor= a 0 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 c 0 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 g 0 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 t 0 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14

oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)
; positions_7nt_m2 versus oligos_6nt_mkv2_m4; m=13/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.515321; ----wkyCGATAsTATCGATasw ; cor=; Ncor= a 0 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 c 0 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 g 0 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 t 0 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14

dyads_m2_rc_shift1 (dyads_m2_rc)
; positions_7nt_m2 versus dyads_m2_rc; m=14/15; ncol2=24; w=-8; offset=-8; strand=R; shift=1; score=0.511813; -hdmyatCGATAsTATCGatrkw ; cor=; Ncor= a 0 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 c 0 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 g 0 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 t 0 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; positions_7nt_m2 versus oligos_7nt_mkv2_m2; m=15/15; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.510286; smwmyatCGATAsTATCGatrkw ; cor=; Ncor= a 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 13 8 13 c 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 5 7 8 g 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 20 16 8 t 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22 5 12 14

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ssGGCAGCAAwa ; Alignment reference a 9 7 5 3 1 38 0 2 34 31 13 15 c 10 10 1 5 37 0 0 37 3 3 9 8 g 11 14 30 30 1 1 37 0 2 4 7 8 t 9 8 3 1 0 0 2 0 0 1 10 8

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssGGCAGCAAwa ; cor=; Ncor= a 9 7 5 3 1 38 0 2 34 31 13 15 c 10 10 1 5 37 0 0 37 3 3 9 8 g 11 14 30 30 1 1 37 0 2 4 7 8 t 9 8 3 1 0 0 2 0 0 1 10 8

One-to-n matrix alignment; reference matrix: dyads_m2_shift4 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift4 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=24; shift=4; ncol=28; ----vmwmyatCGATAsTATCGatrkhd ; Alignment reference a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 14 10 14 13 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 7 8 13 5 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 20 20 10 17 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22 11 14 15 17

dyads_m2_shift4 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----vmwmyatCGATAsTATCGatrkhd ; cor=; Ncor= a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 14 10 14 13 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 7 8 13 5 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 20 20 10 17 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22 11 14 15 17

oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)
; dyads_m2 versus oligos_7nt_mkv2_m2; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.984009; ----smwmyatCGATAsTATCGatrkwk ; cor=; Ncor= a 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 13 8 13 10 c 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 5 7 8 5 g 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 20 16 8 12 t 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22 5 12 14 16

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4_rc)
; dyads_m2 versus oligos_7nt_mkv2_m4_rc; m=3/15; ncol2=22; w=0; offset=0; strand=R; shift=4; score=0.878897; ----wwdctaTCGATAsTATCGrydr-- ; cor=; Ncor= a 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 4 0 2 24 10 16 13 0 0 c 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 0 50 2 9 20 7 10 0 0 g 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 5 0 46 13 6 15 17 0 0 t 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4 42 1 1 5 15 13 11 0 0

oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)
; dyads_m2 versus oligos_6nt_mkv2_m2; m=4/15; ncol2=20; w=0; offset=1; strand=D; shift=5; score=0.828499; -----hdmyatCGATAsTATCGayr--- ; cor=; Ncor= a 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 22 0 0 0 c 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 9 0 0 0 g 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 18 0 0 0 t 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22 15 0 0 0

dyads_m3_rc_shift1 (dyads_m3_rc)
; dyads_m2 versus dyads_m3_rc; m=5/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.727411; -wcrawwstATCGATAsTATCGrmw--- ; cor=; Ncor= a 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 9 0 0 0 c 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 4 0 0 0 g 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 7 0 0 0 t 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4 11 0 0 0

oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)
; dyads_m2 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.724759; -wcrawwstATCGATAsTATCGrmw--- ; cor=; Ncor= a 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 9 0 0 0 c 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 4 0 0 0 g 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 6 0 0 0 t 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4 11 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; dyads_m2 versus oligos_6nt_mkv2_m3_rc; m=7/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.718717; -kcGatwsTATCGATAsTATCGmmw--- ; cor=; Ncor= a 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 8 0 0 0 c 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 4 0 0 0 g 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 6 0 0 0 t 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3 8 0 0 0

dyads_m1_rc_shift1 (dyads_m1_rc)
; dyads_m2 versus dyads_m1_rc; m=8/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.718107; -tcratacTATCGATAGTAtCGmbk--- ; cor=; Ncor= a 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 4 4 3 19 10 11 0 0 0 c 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 4 37 5 14 12 9 0 0 0 g 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 8 3 37 6 12 13 0 0 0 t 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6 30 2 1 7 12 13 0 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; dyads_m2 versus oligos_7nt_mkv2_m3_rc; m=9/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.705209; -tsgatasTATCGATASTAtCGmhk--- ; cor=; Ncor= a 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 7 0 0 0 c 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 5 0 0 0 g 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 9 0 0 0 t 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8 11 0 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; dyads_m2 versus oligos_7nt_mkv2_m1; m=10/15; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.622676; ktCGatAcTATCGATAGTAtCGam---- ; cor=; Ncor= a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 0 0 0 0 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 0 0 0 0 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 0 0 0 0 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7 0 0 0 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; dyads_m2 versus oligos_6nt_mkv2_m1; m=11/15; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.615371; ktCGatACTATCGATAGTatCGam---- ; cor=; Ncor= a 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 0 0 0 0 c 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 0 0 0 0 g 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 0 0 0 0 t 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10 0 0 0 0

positions_7nt_m1_shift4 (positions_7nt_m1)
; dyads_m2 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.549637; ----awacTATCGATAgtwt-------- ; cor=; Ncor= a 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 0 0 0 0 c 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 0 0 0 0 g 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 0 0 0 0 t 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0 0 0 0 0

positions_7nt_m2_rc_shift6 (positions_7nt_m2_rc)
; dyads_m2 versus positions_7nt_m2_rc; m=13/15; ncol2=14; w=0; offset=2; strand=R; shift=6; score=0.511813; ------acyATCGATAgtwt-------- ; cor=; Ncor= a 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42 0 0 0 0 0 0 0 0

positions_6nt_m1_shift5 (positions_6nt_m1)
; dyads_m2 versus positions_6nt_m1; m=14/15; ncol2=14; w=0; offset=1; strand=D; shift=5; score=0.480487; -----wacTATCGATAgyw--------- ; cor=; Ncor= a 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0 0 0 0 0 0

positions_6nt_m2_shift5 (positions_6nt_m2)
; dyads_m2 versus positions_6nt_m2; m=15/15; ncol2=14; w=0; offset=1; strand=D; shift=5; score=0.476785; -----waCTATCGATAstw--------- ; cor=; Ncor= a 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 16 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=24; shift=0; ncol=24; ktCGatAcTATCGATAGTAtCGam ; Alignment reference a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ktCGatAcTATCGATAGTAtCGam ; cor=; Ncor= a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.993057; ktCGatACTATCGATAGTatCGam ; cor=; Ncor= a 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 c 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 g 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 t 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=3/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.909054; -tsgatasTATCGATASTAtCGmh ; cor=; Ncor= a 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 c 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 g 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 t 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8

dyads_m1_rc_shift1 (dyads_m1_rc)
; oligos_7nt_mkv2_m1 versus dyads_m1_rc; m=4/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.899073; -tcratacTATCGATAGTAtCGmb ; cor=; Ncor= a 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 4 4 3 19 10 c 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 4 37 5 14 12 g 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 8 3 37 6 12 t 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6 30 2 1 7 12

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=5/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.878954; -kcGatwsTATCGATAsTATCGmm ; cor=; Ncor= a 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 c 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 g 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 t 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3

oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.865453; -wcrawwstATCGATAsTATCGrm ; cor=; Ncor= a 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 c 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 g 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 t 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4

dyads_m3_rc_shift1 (dyads_m3_rc)
; oligos_7nt_mkv2_m1 versus dyads_m3_rc; m=7/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.861835; -wcrawwstATCGATAsTATCGrm ; cor=; Ncor= a 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 c 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 g 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 t 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4_rc; m=8/15; ncol2=22; w=0; offset=4; strand=R; shift=4; score=0.689944; ----wwdctaTCGATAsTATCGry ; cor=; Ncor= a 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 4 0 2 24 10 c 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 0 50 2 9 20 g 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 5 0 46 13 6 t 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4 42 1 1 5 15

oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=9/15; ncol2=20; w=0; offset=5; strand=D; shift=5; score=0.667303; -----hdmyatCGATAsTATCGay ; cor=; Ncor= a 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 c 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 g 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 t 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22

positions_7nt_m1_shift4 (positions_7nt_m1)
; oligos_7nt_mkv2_m1 versus positions_7nt_m1; m=10/15; ncol2=16; w=0; offset=4; strand=D; shift=4; score=0.635788; ----awacTATCGATAgtwt---- ; cor=; Ncor= a 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 c 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 g 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 t 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0

dyads_m2_shift4 (dyads_m2)
; oligos_7nt_mkv2_m1 versus dyads_m2; m=11/15; ncol2=24; w=0; offset=4; strand=D; shift=4; score=0.622676; ----vmwmyatCGATAsTATCGat ; cor=; Ncor= a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22

oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=12/15; ncol2=24; w=0; offset=4; strand=D; shift=4; score=0.590402; ----smwmyatCGATAsTATCGat ; cor=; Ncor= a 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 c 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 g 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 t 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22

positions_6nt_m1_shift5 (positions_6nt_m1)
; oligos_7nt_mkv2_m1 versus positions_6nt_m1; m=13/15; ncol2=14; w=0; offset=5; strand=D; shift=5; score=0.541209; -----wacTATCGATAgyw----- ; cor=; Ncor= a 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 0 c 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 0 g 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 0 t 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0 0

positions_6nt_m2_rc_shift5 (positions_6nt_m2_rc)
; oligos_7nt_mkv2_m1 versus positions_6nt_m2_rc; m=14/15; ncol2=14; w=0; offset=5; strand=R; shift=5; score=0.531232; -----wasTATCGATAGtw----- ; cor=; Ncor= a 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 0 c 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 0 g 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 0 t 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0 0

positions_7nt_m2_rc_shift6 (positions_7nt_m2_rc)
; oligos_7nt_mkv2_m1 versus positions_7nt_m2_rc; m=15/15; ncol2=14; w=0; offset=6; strand=R; shift=6; score=0.529333; ------acyATCGATAgtwt---- ; cor=; Ncor= a 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 0 0 0 0 c 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 0 0 0 0 g 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 0 0 0 0 t 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift3 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---mdkCGaTASTATCGATAstatcsa ; Alignment reference a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6

oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6

dyads_m1_shift3 (dyads_m1)
; oligos_7nt_mkv2_m3 versus dyads_m1; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.991469; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.967715; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5

oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.960259; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8

dyads_m3_shift3 (dyads_m3)
; oligos_7nt_mkv2_m3 versus dyads_m3; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.958158; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8

oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.909054; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.905315; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.779619; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.760224; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv2_m3 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.705209; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.669953; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; oligos_7nt_mkv2_m3 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.634156; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0

positions_6nt_m1_shift9 (positions_6nt_m1)
; oligos_7nt_mkv2_m3 versus positions_6nt_m1; m=13/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.542644; ---------wacTATCGATAgyw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0

positions_7nt_m2_shift8 (positions_7nt_m2)
; oligos_7nt_mkv2_m3 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.53522; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0

positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)
; oligos_7nt_mkv2_m3 versus positions_6nt_m2_rc; m=15/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.53301; ---------wasTATCGATAGtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift6 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift6 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=14; shift=6; ncol=20; ------waCTATCGATAstw ; Alignment reference a 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 c 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 g 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 t 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32

positions_6nt_m2_shift6 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/15; ncol2=14; w=0; offset=0; strand=D; shift=6; score= 1; ------waCTATCGATAstw ; cor=; Ncor= a 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 c 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 g 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 t 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32

positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)
; positions_6nt_m2 versus positions_6nt_m1_rc; m=2/15; ncol2=14; w=0; offset=0; strand=R; shift=6; score=0.974699; ------wrcTATCGATAgtw ; cor=; Ncor= a 0 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 c 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 g 0 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 t 0 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34

positions_7nt_m1_shift5 (positions_7nt_m1)
; positions_6nt_m2 versus positions_7nt_m1; m=3/15; ncol2=16; w=-1; offset=-1; strand=D; shift=5; score=0.849716; -----awacTATCGATAgtw ; cor=; Ncor= a 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 c 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 g 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 t 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29

positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_6nt_m2 versus positions_7nt_m2; m=4/15; ncol2=14; w=-1; offset=-1; strand=D; shift=5; score=0.813542; -----awacTATCGATrgt- ; cor=; Ncor= a 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 c 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 g 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 t 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0

oligos_6nt_mkv2_m2_shift6 (oligos_6nt_mkv2_m2)
; positions_6nt_m2 versus oligos_6nt_mkv2_m2; m=5/15; ncol2=20; w=0; offset=0; strand=D; shift=6; score=0.577258; ------hdmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 c 0 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 g 0 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 t 0 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2

oligos_7nt_mkv2_m4_rc_shift5 (oligos_7nt_mkv2_m4_rc)
; positions_6nt_m2 versus oligos_7nt_mkv2_m4_rc; m=6/15; ncol2=22; w=-1; offset=-1; strand=R; shift=5; score=0.572853; -----wwdctaTCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 c 0 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 g 0 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 t 0 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; positions_6nt_m2 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.539556; -ktCGatACTATCGATAGTa ; cor=; Ncor= a 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 c 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 g 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 t 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10

dyads_m1_shift0 (dyads_m1)
; positions_6nt_m2 versus dyads_m1; m=8/15; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.538402; mvkCGaTACTATCGATAgta ; cor=; Ncor= a 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 c 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 g 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 t 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11

oligos_7nt_mkv2_m3_rc_shift2 (oligos_7nt_mkv2_m3_rc)
; positions_6nt_m2 versus oligos_7nt_mkv2_m3_rc; m=9/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.53301; --tsgatasTATCGATASTA ; cor=; Ncor= a 0 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 c 0 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 g 0 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 t 0 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; positions_6nt_m2 versus oligos_6nt_mkv2_m4_rc; m=10/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.532834; --wcrawwstATCGATAsTA ; cor=; Ncor= a 0 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 c 0 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 g 0 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 t 0 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3

oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)
; positions_6nt_m2 versus oligos_7nt_mkv2_m1_rc; m=11/15; ncol2=24; w=-5; offset=-5; strand=R; shift=1; score=0.531232; -ktCGaTACTATCGATAgTa ; cor=; Ncor= a 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 c 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 g 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 t 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6

dyads_m3_rc_shift2 (dyads_m3_rc)
; positions_6nt_m2 versus dyads_m3_rc; m=12/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.531079; --wcrawwstATCGATAsTA ; cor=; Ncor= a 0 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 c 0 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 g 0 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 t 0 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3_rc)
; positions_6nt_m2 versus oligos_6nt_mkv2_m3_rc; m=13/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.52871; --kcGatwsTATCGATAsTA ; cor=; Ncor= a 0 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 c 0 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 g 0 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 t 0 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3

dyads_m2_shift5 (dyads_m2)
; positions_6nt_m2 versus dyads_m2; m=14/15; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.476785; -----vmwmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 c 0 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 g 0 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 t 0 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1

oligos_7nt_mkv2_m2_rc_shift6 (oligos_7nt_mkv2_m2_rc)
; positions_6nt_m2 versus oligos_7nt_mkv2_m2_rc; m=15/15; ncol2=24; w=0; offset=0; strand=R; shift=6; score=0.473315; ------mwmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 0 16 14 12 5 22 4 0 0 41 2 42 1 0 42 c 0 0 0 0 0 0 12 8 16 20 8 5 42 0 0 0 0 16 1 1 g 0 0 0 0 0 0 5 8 7 5 8 5 0 40 1 2 0 25 0 0 t 0 0 0 0 0 0 10 13 8 13 5 29 1 3 1 39 1 1 42 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift4 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=24; shift=4; ncol=28; ----smwmyatCGATAsTATCGatrkwk ; Alignment reference a 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 13 8 13 10 c 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 5 7 8 5 g 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 20 16 8 12 t 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22 5 12 14 16

oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----smwmyatCGATAsTATCGatrkwk ; cor=; Ncor= a 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 13 8 13 10 c 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 5 7 8 5 g 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 20 16 8 12 t 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22 5 12 14 16

dyads_m2_shift4 (dyads_m2)
; oligos_7nt_mkv2_m2 versus dyads_m2; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.984009; ----vmwmyatCGATAsTATCGatrkhd ; cor=; Ncor= a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 14 10 14 13 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 7 8 13 5 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 20 20 10 17 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22 11 14 15 17

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=3/15; ncol2=22; w=0; offset=0; strand=R; shift=4; score=0.874021; ----wwdctaTCGATAsTATCGrydr-- ; cor=; Ncor= a 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 4 0 2 24 10 16 13 0 0 c 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 0 50 2 9 20 7 10 0 0 g 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 5 0 46 13 6 15 17 0 0 t 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4 42 1 1 5 15 13 11 0 0

oligos_6nt_mkv2_m2_rc_shift8 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=4/15; ncol2=20; w=0; offset=4; strand=R; shift=8; score=0.82733; --------yrtCGATAsTATCGatrkhd ; cor=; Ncor= a 0 0 0 0 0 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 c 0 0 0 0 0 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 g 0 0 0 0 0 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 t 0 0 0 0 0 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22

dyads_m3_rc_shift1 (dyads_m3_rc)
; oligos_7nt_mkv2_m2 versus dyads_m3_rc; m=5/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.713031; -wcrawwstATCGATAsTATCGrmw--- ; cor=; Ncor= a 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 9 0 0 0 c 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 4 0 0 0 g 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 7 0 0 0 t 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4 11 0 0 0

oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.709251; -wcrawwstATCGATAsTATCGrmw--- ; cor=; Ncor= a 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 9 0 0 0 c 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 4 0 0 0 g 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 6 0 0 0 t 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4 11 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=7/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.697768; -kcGatwsTATCGATAsTATCGmmw--- ; cor=; Ncor= a 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 8 0 0 0 c 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 4 0 0 0 g 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 6 0 0 0 t 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3 8 0 0 0

dyads_m1_rc_shift1 (dyads_m1_rc)
; oligos_7nt_mkv2_m2 versus dyads_m1_rc; m=8/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.681951; -tcratacTATCGATAGTAtCGmbk--- ; cor=; Ncor= a 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 4 4 3 19 10 11 0 0 0 c 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 4 37 5 14 12 9 0 0 0 g 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 8 3 37 6 12 13 0 0 0 t 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6 30 2 1 7 12 13 0 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=9/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.669953; -tsgatasTATCGATASTAtCGmhk--- ; cor=; Ncor= a 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 7 0 0 0 c 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 5 0 0 0 g 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 9 0 0 0 t 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8 11 0 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=10/15; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.590402; ktCGatAcTATCGATAGTAtCGam---- ; cor=; Ncor= a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 0 0 0 0 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 0 0 0 0 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 0 0 0 0 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7 0 0 0 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=11/15; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.580869; ktCGatACTATCGATAGTatCGam---- ; cor=; Ncor= a 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 0 0 0 0 c 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 0 0 0 0 g 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 0 0 0 0 t 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10 0 0 0 0

positions_7nt_m1_shift4 (positions_7nt_m1)
; oligos_7nt_mkv2_m2 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.522256; ----awacTATCGATAgtwt-------- ; cor=; Ncor= a 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 0 0 0 0 c 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 0 0 0 0 g 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 0 0 0 0 t 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0 0 0 0 0

positions_7nt_m2_shift13 (positions_7nt_m2)
; oligos_7nt_mkv2_m2 versus positions_7nt_m2; m=13/15; ncol2=14; w=0; offset=9; strand=D; shift=13; score=0.510286; -------------awacTATCGATrgt- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0

positions_6nt_m1_rc_shift14 (positions_6nt_m1_rc)
; oligos_7nt_mkv2_m2 versus positions_6nt_m1_rc; m=14/15; ncol2=14; w=0; offset=10; strand=R; shift=14; score=0.475669; --------------wrcTATCGATAgtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34

positions_6nt_m2_rc_shift14 (positions_6nt_m2_rc)
; oligos_7nt_mkv2_m2 versus positions_6nt_m2_rc; m=15/15; ncol2=14; w=0; offset=10; strand=R; shift=14; score=0.473315; --------------wasTATCGATAGtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37

One-to-n matrix alignment; reference matrix: dyads_m3_shift3 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift3 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wkyCGATAsTATCGATaswwtygw ; Alignment reference a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8

dyads_m3_shift3 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8

oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; dyads_m3 versus oligos_6nt_mkv2_m4; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.999187; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; dyads_m3 versus oligos_6nt_mkv2_m3; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.98515; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5

oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; dyads_m3 versus oligos_7nt_mkv2_m3; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.958158; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6

dyads_m1_shift3 (dyads_m1)
; dyads_m3 versus dyads_m1; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.955336; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9

oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)
; dyads_m3 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.861835; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; dyads_m3 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score= 0.8588; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; dyads_m3 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.820891; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)
; dyads_m3 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.790569; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; dyads_m3 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.727411; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; dyads_m3 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.713031; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; dyads_m3 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.596937; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0

positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)
; dyads_m3 versus positions_6nt_m2_rc; m=13/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.531079; ---------wasTATCGATAGtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0

positions_7nt_m2_shift8 (positions_7nt_m2)
; dyads_m3 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.516029; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0

positions_6nt_m1_shift9 (positions_6nt_m1)
; dyads_m3 versus positions_6nt_m1; m=15/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.51515; ---------wacTATCGATAgyw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift5 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=20; shift=5; ncol=25; -----hdmyatCGATAsTATCGayr ; Alignment reference a 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 22 c 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 9 g 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 18 t 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22 15

oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/15; ncol2=20; w=0; offset=0; strand=D; shift=5; score= 1; -----hdmyatCGATAsTATCGayr ; cor=; Ncor= a 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 22 c 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 9 g 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 18 t 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22 15

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=2/15; ncol2=22; w=-1; offset=-1; strand=R; shift=4; score=0.882628; ----wwdctaTCGATAsTATCGryd ; cor=; Ncor= a 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 4 0 2 24 10 16 c 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 0 50 2 9 20 7 g 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 5 0 46 13 6 15 t 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4 42 1 1 5 15 13

dyads_m2_shift4 (dyads_m2)
; oligos_6nt_mkv2_m2 versus dyads_m2; m=3/15; ncol2=24; w=-1; offset=-1; strand=D; shift=4; score=0.828499; ----vmwmyatCGATAsTATCGatr ; cor=; Ncor= a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 14 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 7 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 20 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22 11

oligos_7nt_mkv2_m2_rc_shift5 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=4/15; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.82733; -----mwmyatCGATAsTATCGatr ; cor=; Ncor= a 0 0 0 0 0 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 c 0 0 0 0 0 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 g 0 0 0 0 0 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 t 0 0 0 0 0 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6

dyads_m3_rc_shift1 (dyads_m3_rc)
; oligos_6nt_mkv2_m2 versus dyads_m3_rc; m=5/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.790569; -wcrawwstATCGATAsTATCGrmw ; cor=; Ncor= a 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 9 c 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 4 g 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 7 t 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4 11

oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.787886; -wcrawwstATCGATAsTATCGrmw ; cor=; Ncor= a 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 9 c 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 4 g 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 6 t 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4 11

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=7/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.775462; -kcGatwsTATCGATAsTATCGmmw ; cor=; Ncor= a 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 8 c 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 4 g 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 6 t 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3 8

dyads_m1_rc_shift1 (dyads_m1_rc)
; oligos_6nt_mkv2_m2 versus dyads_m1_rc; m=8/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.771777; -tcratacTATCGATAGTAtCGmbk ; cor=; Ncor= a 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 4 4 3 19 10 11 c 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 4 37 5 14 12 9 g 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 8 3 37 6 12 13 t 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6 30 2 1 7 12 13

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=9/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.760224; -tsgatasTATCGATASTAtCGmhk ; cor=; Ncor= a 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 7 c 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 5 g 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 9 t 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8 11

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=10/15; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.667303; ktCGatAcTATCGATAGTAtCGam- ; cor=; Ncor= a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 0 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 0 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 0 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=11/15; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.664392; ktCGatACTATCGATAGTatCGam- ; cor=; Ncor= a 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 0 c 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 0 g 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 0 t 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10 0

positions_7nt_m2_rc_shift6 (positions_7nt_m2_rc)
; oligos_6nt_mkv2_m2 versus positions_7nt_m2_rc; m=12/15; ncol2=14; w=0; offset=1; strand=R; shift=6; score=0.615595; ------acyATCGATAgtwt----- ; cor=; Ncor= a 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 0 0 0 0 0 c 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 0 0 0 0 0 g 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 0 0 0 0 0 t 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42 0 0 0 0 0

positions_7nt_m1_shift4 (positions_7nt_m1)
; oligos_6nt_mkv2_m2 versus positions_7nt_m1; m=13/15; ncol2=16; w=-1; offset=-1; strand=D; shift=4; score=0.589551; ----awacTATCGATAgtwt----- ; cor=; Ncor= a 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 0 c 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 0 g 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 0 t 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0 0

positions_6nt_m1_rc_shift5 (positions_6nt_m1_rc)
; oligos_6nt_mkv2_m2 versus positions_6nt_m1_rc; m=14/15; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.578118; -----wrcTATCGATAgtw------ ; cor=; Ncor= a 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 0 0 0 0 0 0 c 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 0 0 0 0 0 0 g 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 0 0 t 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34 0 0 0 0 0 0

positions_6nt_m2_shift5 (positions_6nt_m2)
; oligos_6nt_mkv2_m2 versus positions_6nt_m2; m=15/15; ncol2=14; w=0; offset=0; strand=D; shift=5; score=0.577258; -----waCTATCGATAstw------ ; cor=; Ncor= a 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 0 0 0 0 0 0 c 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 0 0 0 0 0 0 g 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 0 0 0 0 0 0 t 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift7 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift7 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=14; shift=7; ncol=21; -------wacTATCGATAgyw ; Alignment reference a 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 c 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 g 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 t 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34

positions_6nt_m1_shift7 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/15; ncol2=14; w=0; offset=0; strand=D; shift=7; score= 1; -------wacTATCGATAgyw ; cor=; Ncor= a 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 c 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 g 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 t 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34

positions_6nt_m2_rc_shift7 (positions_6nt_m2_rc)
; positions_6nt_m1 versus positions_6nt_m2_rc; m=2/15; ncol2=14; w=0; offset=0; strand=R; shift=7; score=0.974699; -------wasTATCGATAGtw ; cor=; Ncor= a 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 c 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 g 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 t 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37

positions_7nt_m1_shift6 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=3/15; ncol2=16; w=-1; offset=-1; strand=D; shift=6; score=0.866118; ------awacTATCGATAgtw ; cor=; Ncor= a 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 c 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 g 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 t 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29

positions_7nt_m2_shift6 (positions_7nt_m2)
; positions_6nt_m1 versus positions_7nt_m2; m=4/15; ncol2=14; w=-1; offset=-1; strand=D; shift=6; score=0.822423; ------awacTATCGATrgt- ; cor=; Ncor= a 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 c 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 g 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 t 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; positions_6nt_m1 versus oligos_6nt_mkv2_m2_rc; m=5/15; ncol2=20; w=-6; offset=-6; strand=R; shift=1; score=0.578118; -yrtCGATAsTATCGatrkhd ; cor=; Ncor= a 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 c 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 g 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 t 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; positions_6nt_m1 versus oligos_7nt_mkv2_m4; m=6/15; ncol2=22; w=-7; offset=-7; strand=D; shift=0; score=0.554481; yhryCGATAsTATCGAtaghw ; cor=; Ncor= a 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 c 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 g 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 t 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; positions_6nt_m1 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=-5; offset=-5; strand=D; shift=2; score=0.552426; --ktCGatACTATCGATAGTa ; cor=; Ncor= a 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 c 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 g 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 t 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10

dyads_m1_rc_shift3 (dyads_m1_rc)
; positions_6nt_m1 versus dyads_m1_rc; m=8/15; ncol2=24; w=-4; offset=-4; strand=R; shift=3; score=0.547498; ---tcratacTATCGATAGTA ; cor=; Ncor= a 0 0 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 c 0 0 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 g 0 0 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 t 0 0 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; positions_6nt_m1 versus oligos_7nt_mkv2_m3; m=9/15; ncol2=24; w=-6; offset=-6; strand=D; shift=1; score=0.542644; -mdkCGaTASTATCGATAsta ; cor=; Ncor= a 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 c 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 g 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 t 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7

oligos_7nt_mkv2_m1_rc_shift2 (oligos_7nt_mkv2_m1_rc)
; positions_6nt_m1 versus oligos_7nt_mkv2_m1_rc; m=10/15; ncol2=24; w=-5; offset=-5; strand=R; shift=2; score=0.541209; --ktCGaTACTATCGATAgTa ; cor=; Ncor= a 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 c 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 g 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 t 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; positions_6nt_m1 versus oligos_6nt_mkv2_m3; m=11/15; ncol2=24; w=-6; offset=-6; strand=D; shift=1; score=0.518788; -wkkCGATAsTATCGATAswa ; cor=; Ncor= a 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 c 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 g 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 t 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; positions_6nt_m1 versus oligos_6nt_mkv2_m4; m=12/15; ncol2=24; w=-6; offset=-6; strand=D; shift=1; score=0.517272; -wkyCGATAsTATCGATasww ; cor=; Ncor= a 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 c 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 g 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 t 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8

dyads_m3_shift1 (dyads_m3)
; positions_6nt_m1 versus dyads_m3; m=13/15; ncol2=24; w=-6; offset=-6; strand=D; shift=1; score=0.51515; -wkyCGATAsTATCGATasww ; cor=; Ncor= a 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 c 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 g 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 t 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8

dyads_m2_shift6 (dyads_m2)
; positions_6nt_m1 versus dyads_m2; m=14/15; ncol2=24; w=-1; offset=-1; strand=D; shift=6; score=0.480487; ------vmwmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 c 0 0 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 g 0 0 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 t 0 0 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1

oligos_7nt_mkv2_m2_rc_shift7 (oligos_7nt_mkv2_m2_rc)
; positions_6nt_m1 versus oligos_7nt_mkv2_m2_rc; m=15/15; ncol2=24; w=0; offset=0; strand=R; shift=7; score=0.475669; -------mwmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 0 0 16 14 12 5 22 4 0 0 41 2 42 1 0 42 c 0 0 0 0 0 0 0 12 8 16 20 8 5 42 0 0 0 0 16 1 1 g 0 0 0 0 0 0 0 5 8 7 5 8 5 0 40 1 2 0 25 0 0 t 0 0 0 0 0 0 0 10 13 8 13 5 29 1 3 1 39 1 1 42 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift3 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wkkCGATAsTATCGATAswatCgm ; Alignment reference a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5

dyads_m3_shift3 (dyads_m3)
; oligos_6nt_mkv2_m3 versus dyads_m3; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.98515; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8

oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.985095; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8

oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.967715; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6

dyads_m1_shift3 (dyads_m1)
; oligos_6nt_mkv2_m3 versus dyads_m1; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.961179; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9

oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.878954; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.874783; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.801146; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.775462; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_6nt_mkv2_m3 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.718717; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.697768; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; oligos_6nt_mkv2_m3 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.605621; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0

positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)
; oligos_6nt_mkv2_m3 versus positions_6nt_m2_rc; m=13/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.52871; ---------wasTATCGATAGtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0

positions_7nt_m2_shift8 (positions_7nt_m2)
; oligos_6nt_mkv2_m3 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.519322; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0

positions_6nt_m1_shift9 (positions_6nt_m1)
; oligos_6nt_mkv2_m3 versus positions_6nt_m1; m=15/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.518788; ---------wacTATCGATAgyw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=24; shift=2; ncol=26; --ktCGatACTATCGATAGTatCGam ; Alignment reference a 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 c 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 g 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 t 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ktCGatACTATCGATAGTatCGam ; cor=; Ncor= a 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 c 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 g 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 t 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10

oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.993057; --ktCGatAcTATCGATAGTAtCGam ; cor=; Ncor= a 0 0 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 c 0 0 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 g 0 0 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 t 0 0 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7

oligos_7nt_mkv2_m3_rc_shift3 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=3/15; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.905315; ---tsgatasTATCGATASTAtCGmh ; cor=; Ncor= a 0 0 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 c 0 0 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 g 0 0 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 t 0 0 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8

dyads_m1_shift1 (dyads_m1)
; oligos_6nt_mkv2_m1 versus dyads_m1; m=4/15; ncol2=24; w=-1; offset=-1; strand=D; shift=1; score=0.896607; -mvkCGaTACTATCGATAgtatyga- ; cor=; Ncor= a 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 0 c 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 0 g 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 0 t 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9 0

oligos_6nt_mkv2_m3_rc_shift3 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=5/15; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.874783; ---kcGatwsTATCGATAsTATCGmm ; cor=; Ncor= a 0 0 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 c 0 0 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 g 0 0 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 t 0 0 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3

oligos_6nt_mkv2_m4_rc_shift3 (oligos_6nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.862574; ---wcrawwstATCGATAsTATCGrm ; cor=; Ncor= a 0 0 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 c 0 0 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 g 0 0 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 t 0 0 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4

dyads_m3_rc_shift3 (dyads_m3_rc)
; oligos_6nt_mkv2_m1 versus dyads_m3_rc; m=7/15; ncol2=24; w=0; offset=1; strand=R; shift=3; score= 0.8588; ---wcrawwstATCGATAsTATCGrm ; cor=; Ncor= a 0 0 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 c 0 0 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 g 0 0 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 t 0 0 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.686897; yhryCGATAsTATCGAtaghww---- ; cor=; Ncor= a 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 0 c 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 0 g 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 0 t 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0 0

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=-1; offset=-1; strand=R; shift=1; score=0.664392; -yrtCGATAsTATCGatrkhd----- ; cor=; Ncor= a 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 0 c 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 0 g 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 0 t 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0 0

positions_7nt_m1_shift6 (positions_7nt_m1)
; oligos_6nt_mkv2_m1 versus positions_7nt_m1; m=10/15; ncol2=16; w=0; offset=4; strand=D; shift=6; score=0.638604; ------awacTATCGATAgtwt---- ; cor=; Ncor= a 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 c 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 g 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 t 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0

dyads_m2_shift6 (dyads_m2)
; oligos_6nt_mkv2_m1 versus dyads_m2; m=11/15; ncol2=24; w=0; offset=4; strand=D; shift=6; score=0.615371; ------vmwmyatCGATAsTATCGat ; cor=; Ncor= a 0 0 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 c 0 0 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 g 0 0 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 t 0 0 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22

oligos_7nt_mkv2_m2_shift6 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=12/15; ncol2=24; w=0; offset=4; strand=D; shift=6; score=0.580869; ------smwmyatCGATAsTATCGat ; cor=; Ncor= a 0 0 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 c 0 0 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 g 0 0 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 t 0 0 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22

positions_6nt_m1_shift7 (positions_6nt_m1)
; oligos_6nt_mkv2_m1 versus positions_6nt_m1; m=13/15; ncol2=14; w=0; offset=5; strand=D; shift=7; score=0.552426; -------wacTATCGATAgyw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 0 c 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 0 g 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 0 t 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0 0

positions_6nt_m2_rc_shift7 (positions_6nt_m2_rc)
; oligos_6nt_mkv2_m1 versus positions_6nt_m2_rc; m=14/15; ncol2=14; w=0; offset=5; strand=R; shift=7; score=0.539556; -------wasTATCGATAGtw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 0 c 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 0 g 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 0 t 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0 0

positions_7nt_m2_rc_shift8 (positions_7nt_m2_rc)
; oligos_6nt_mkv2_m1 versus positions_7nt_m2_rc; m=15/15; ncol2=14; w=0; offset=6; strand=R; shift=8; score=0.533663; --------acyATCGATAgtwt---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 0 0 0 0 c 0 0 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 0 0 0 0 g 0 0 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 0 0 0 0 t 0 0 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift2 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=22; shift=2; ncol=24; --yhryCGATAsTATCGAtaghww ; Alignment reference a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/15; ncol2=22; w=0; offset=0; strand=D; shift=2; score= 1; --yhryCGATAsTATCGAtaghww ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=2/15; ncol2=20; w=0; offset=1; strand=R; shift=3; score=0.882628; ---yrtCGATAsTATCGatrkhd- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv2_m4 versus dyads_m2_rc; m=3/15; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.878897; hdmyatCGATAsTATCGatrkwkb ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2_rc; m=4/15; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.874021; mwmyatCGATAsTATCGatrkwks ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10

dyads_m3_shift3 (dyads_m3)
; oligos_7nt_mkv2_m4 versus dyads_m3; m=5/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.820891; ---wkyCGATAsTATCGATaswwt ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15

oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=6/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.819057; ---wkyCGATAsTATCGATaswwt ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.801146; ---wkkCGATAsTATCGATAswat ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12

dyads_m1_shift3 (dyads_m1)
; oligos_7nt_mkv2_m4 versus dyads_m1; m=8/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.781949; ---mvkCGaTACTATCGATAgtat ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24

oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=9/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.779619; ---mdkCGaTASTATCGATAstat ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18

oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1_rc; m=10/15; ncol2=24; w=0; offset=2; strand=R; shift=4; score=0.689944; ----ktCGaTACTATCGATAgTat ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=11/15; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.686897; ----ktCGatACTATCGATAGTat ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32

positions_7nt_m1_shift8 (positions_7nt_m1)
; oligos_7nt_mkv2_m4 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=6; strand=D; shift=8; score=0.633015; --------awacTATCGATAgtwt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35

positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)
; oligos_7nt_mkv2_m4 versus positions_6nt_m2_rc; m=13/15; ncol2=14; w=0; offset=7; strand=R; shift=9; score=0.572853; ---------wasTATCGATAGtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0

positions_7nt_m2_shift8 (positions_7nt_m2)
; oligos_7nt_mkv2_m4 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=6; strand=D; shift=8; score=0.556698; --------awacTATCGATrgt-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0

positions_6nt_m1_shift9 (positions_6nt_m1)
; oligos_7nt_mkv2_m4 versus positions_6nt_m1; m=15/15; ncol2=14; w=0; offset=7; strand=D; shift=9; score=0.554481; ---------wacTATCGATAgyw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 4 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; hrATAAATAwh ; Alignment reference a 19 19 52 1 51 44 48 0 53 17 17 c 14 8 2 1 2 2 1 2 1 10 14 g 6 16 1 4 0 4 6 0 1 9 8 t 16 12 0 49 2 5 0 53 0 19 16

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; hrATAAATAwh ; cor=; Ncor= a 19 19 52 1 51 44 48 0 53 17 17 c 14 8 2 1 2 2 1 2 1 10 14 g 6 16 1 4 0 4 6 0 1 9 8 t 16 12 0 49 2 5 0 53 0 19 16

dyads_m4_shift0 (dyads_m4)
; oligos_7nt_mkv2_m5 versus dyads_m4; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.673977; wdwAAAATAtw ; cor=; Ncor= a 27 21 23 63 66 63 67 0 66 16 21 c 15 12 11 1 0 0 0 0 0 12 15 g 2 17 6 2 0 0 0 1 1 5 13 t 23 17 27 1 1 4 0 66 0 34 18

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.673752; -rwAAAATAwh ; cor=; Ncor= a 0 19 24 59 59 59 59 0 59 18 17 c 0 11 11 0 0 0 0 0 0 11 15 g 0 15 7 0 0 0 0 0 0 5 11 t 0 14 17 0 0 0 0 59 0 25 16

One-to-n matrix alignment; reference matrix: dyads_m1_shift3 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift3 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---mvkCGaTACTATCGATAgtatyga ; Alignment reference a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9

dyads_m1_shift3 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9

oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; dyads_m1 versus oligos_7nt_mkv2_m3; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.991469; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; dyads_m1 versus oligos_6nt_mkv2_m3; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.961179; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5

oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; dyads_m1 versus oligos_6nt_mkv2_m4; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.956768; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8

dyads_m3_shift3 (dyads_m3)
; dyads_m1 versus dyads_m3; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.955336; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8

oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)
; dyads_m1 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.899073; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; dyads_m1 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.896607; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; dyads_m1 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.781949; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)
; dyads_m1 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.771777; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; dyads_m1 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.718107; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; dyads_m1 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.681951; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; dyads_m1 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.637309; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0

positions_6nt_m1_rc_shift9 (positions_6nt_m1_rc)
; dyads_m1 versus positions_6nt_m1_rc; m=13/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.547498; ---------wrcTATCGATAgtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34 0 0 0 0

positions_7nt_m2_shift8 (positions_7nt_m2)
; dyads_m1 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.544202; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0

positions_6nt_m2_shift9 (positions_6nt_m2)
; dyads_m1 versus positions_6nt_m2; m=15/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.538402; ---------waCTATCGATAstw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 0 0 0 0 c 0 0 0 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift6 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift6 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=16; shift=6; ncol=22; ------awacTATCGATAgtwt ; Alignment reference a 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 c 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 g 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 t 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35

positions_7nt_m1_shift6 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/15; ncol2=16; w=0; offset=0; strand=D; shift=6; score= 1; ------awacTATCGATAgtwt ; cor=; Ncor= a 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 c 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 g 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 t 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35

positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)
; positions_7nt_m1 versus positions_6nt_m1_rc; m=2/15; ncol2=14; w=0; offset=1; strand=R; shift=7; score=0.866118; -------wrcTATCGATAgtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 0 c 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 0 g 0 0 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 0 t 0 0 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34 0

positions_6nt_m2_shift7 (positions_6nt_m2)
; positions_7nt_m1 versus positions_6nt_m2; m=3/15; ncol2=14; w=0; offset=1; strand=D; shift=7; score=0.849716; -------waCTATCGATAstw- ; cor=; Ncor= a 0 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 0 c 0 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 0 g 0 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 0 t 0 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32 0

positions_7nt_m2_rc_shift8 (positions_7nt_m2_rc)
; positions_7nt_m1 versus positions_7nt_m2_rc; m=4/15; ncol2=14; w=0; offset=2; strand=R; shift=8; score=0.831139; --------acyATCGATAgtwt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 c 0 0 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 g 0 0 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 t 0 0 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; positions_7nt_m1 versus oligos_6nt_mkv2_m1; m=5/15; ncol2=24; w=-4; offset=-4; strand=D; shift=2; score=0.638604; --ktCGatACTATCGATAGTat ; cor=; Ncor= a 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 c 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 g 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 t 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32

dyads_m1_shift1 (dyads_m1)
; positions_7nt_m1 versus dyads_m1; m=6/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.637309; -mvkCGaTACTATCGATAgtat ; cor=; Ncor= a 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 c 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 g 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 t 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24

oligos_7nt_mkv2_m1_rc_shift2 (oligos_7nt_mkv2_m1_rc)
; positions_7nt_m1 versus oligos_7nt_mkv2_m1_rc; m=7/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.635788; --ktCGaTACTATCGATAgTat ; cor=; Ncor= a 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 c 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 g 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 t 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; positions_7nt_m1 versus oligos_7nt_mkv2_m3; m=8/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.634156; -mdkCGaTASTATCGATAstat ; cor=; Ncor= a 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 c 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 g 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 t 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; positions_7nt_m1 versus oligos_7nt_mkv2_m4; m=9/15; ncol2=22; w=-6; offset=-6; strand=D; shift=0; score=0.633015; yhryCGATAsTATCGAtaghww ; cor=; Ncor= a 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 c 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 g 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 t 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; positions_7nt_m1 versus oligos_6nt_mkv2_m3; m=10/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.605621; -wkkCGATAsTATCGATAswat ; cor=; Ncor= a 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 c 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 g 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 t 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; positions_7nt_m1 versus oligos_6nt_mkv2_m4; m=11/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.600008; -wkyCGATAsTATCGATaswwt ; cor=; Ncor= a 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 c 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 g 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 t 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15

dyads_m3_rc_shift3 (dyads_m3_rc)
; positions_7nt_m1 versus dyads_m3_rc; m=12/15; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.596937; ---wcrawwstATCGATAsTAT ; cor=; Ncor= a 0 0 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 c 0 0 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 g 0 0 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 t 0 0 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26

oligos_6nt_mkv2_m2_shift7 (oligos_6nt_mkv2_m2)
; positions_7nt_m1 versus oligos_6nt_mkv2_m2; m=13/15; ncol2=20; w=0; offset=1; strand=D; shift=7; score=0.589551; -------hdmyatCGATAsTAT ; cor=; Ncor= a 0 0 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 c 0 0 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 g 0 0 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 t 0 0 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58

dyads_m2_shift6 (dyads_m2)
; positions_7nt_m1 versus dyads_m2; m=14/15; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.549637; ------vmwmyatCGATAsTAT ; cor=; Ncor= a 0 0 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 c 0 0 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 g 0 0 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 t 0 0 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49

oligos_7nt_mkv2_m2_shift6 (oligos_7nt_mkv2_m2)
; positions_7nt_m1 versus oligos_7nt_mkv2_m2; m=15/15; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.522256; ------smwmyatCGATAsTAT ; cor=; Ncor= a 0 0 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 c 0 0 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 g 0 0 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 t 0 0 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wkyCGATAsTATCGATaswwtygw ; Alignment reference a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8
dyads_m3_shift3 (dyads_m3)				; oligos_6nt_mkv2_m4 versus dyads_m3; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.999187; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.985095; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.960259; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6
dyads_m1_shift3 (dyads_m1)				; oligos_6nt_mkv2_m4 versus dyads_m1; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.956768; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9
oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.865453; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.862574; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.819057; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.787886; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_6nt_mkv2_m4 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.724759; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.709251; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; oligos_6nt_mkv2_m4 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.600008; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0
positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)				; oligos_6nt_mkv2_m4 versus positions_6nt_m2_rc; m=13/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.532834; ---------wasTATCGATAGtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0
positions_6nt_m1_shift9 (positions_6nt_m1)				; oligos_6nt_mkv2_m4 versus positions_6nt_m1; m=14/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.517272; ---------wacTATCGATAgyw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0
positions_7nt_m2_shift8 (positions_7nt_m2)				; oligos_6nt_mkv2_m4 versus positions_7nt_m2; m=15/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.515321; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0

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; -rwAAAATAwh ; Alignment reference a 0 19 24 59 59 59 59 0 59 18 17 c 0 11 11 0 0 0 0 0 0 11 15 g 0 15 7 0 0 0 0 0 0 5 11 t 0 14 17 0 0 0 0 59 0 25 16
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -rwAAAATAwh ; cor=; Ncor= a 0 19 24 59 59 59 59 0 59 18 17 c 0 11 11 0 0 0 0 0 0 11 15 g 0 15 7 0 0 0 0 0 0 5 11 t 0 14 17 0 0 0 0 59 0 25 16
dyads_m4_shift0 (dyads_m4)				; oligos_6nt_mkv2_m5 versus dyads_m4; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.829458; wdwAAAATAtw ; cor=; Ncor= a 27 21 23 63 66 63 67 0 66 16 21 c 15 12 11 1 0 0 0 0 0 12 15 g 2 17 6 2 0 0 0 1 1 5 13 t 23 17 27 1 1 4 0 66 0 34 18
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.673752; hrATAAATAwh ; cor=; Ncor= a 19 19 52 1 51 44 48 0 53 17 17 c 14 8 2 1 2 2 1 2 1 10 14 g 6 16 1 4 0 4 6 0 1 9 8 t 16 12 0 49 2 5 0 53 0 19 16

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift0 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wdwAAAATAtwd ; Alignment reference a 27 21 23 63 66 63 67 0 66 16 21 17 c 15 12 11 1 0 0 0 0 0 12 15 7 g 2 17 6 2 0 0 0 1 1 5 13 20 t 23 17 27 1 1 4 0 66 0 34 18 23
dyads_m4_shift0 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wdwAAAATAtwd ; cor=; Ncor= a 27 21 23 63 66 63 67 0 66 16 21 17 c 15 12 11 1 0 0 0 0 0 12 15 7 g 2 17 6 2 0 0 0 1 1 5 13 20 t 23 17 27 1 1 4 0 66 0 34 18 23
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; dyads_m4 versus oligos_6nt_mkv2_m5; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.829458; -rwAAAATAwh- ; cor=; Ncor= a 0 19 24 59 59 59 59 0 59 18 17 0 c 0 11 11 0 0 0 0 0 0 11 15 0 g 0 15 7 0 0 0 0 0 0 5 11 0 t 0 14 17 0 0 0 0 59 0 25 16 0
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; dyads_m4 versus oligos_7nt_mkv2_m5; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.673977; hrATAAATAwh- ; cor=; Ncor= a 19 19 52 1 51 44 48 0 53 17 17 0 c 14 8 2 1 2 2 1 2 1 10 14 0 g 6 16 1 4 0 4 6 0 1 9 8 0 t 16 12 0 49 2 5 0 53 0 19 16 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift9 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=14; shift=9; ncol=23; ---------awacTATCGATrgt ; Alignment reference a 0 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 c 0 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 g 0 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 t 0 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43
positions_7nt_m2_shift9 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/15; ncol2=14; w=0; offset=0; strand=D; shift=9; score= 1; ---------awacTATCGATrgt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 c 0 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 g 0 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 t 0 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43
positions_7nt_m1_shift9 (positions_7nt_m1)				; positions_7nt_m2 versus positions_7nt_m1; m=2/15; ncol2=16; w=0; offset=0; strand=D; shift=9; score=0.831139; ---------awacTATCGATAgt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 c 0 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 g 0 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 t 0 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51
positions_6nt_m1_shift10 (positions_6nt_m1)				; positions_7nt_m2 versus positions_6nt_m1; m=3/15; ncol2=14; w=0; offset=1; strand=D; shift=10; score=0.822423; ----------wacTATCGATAgy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 c 0 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 g 0 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 t 0 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39
positions_6nt_m2_shift10 (positions_6nt_m2)				; positions_7nt_m2 versus positions_6nt_m2; m=4/15; ncol2=14; w=0; offset=1; strand=D; shift=10; score=0.813542; ----------waCTATCGATAst ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 c 0 0 0 0 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 g 0 0 0 0 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 t 0 0 0 0 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39
oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)				; positions_7nt_m2 versus oligos_6nt_mkv2_m2_rc; m=5/15; ncol2=20; w=-5; offset=-5; strand=R; shift=4; score=0.615595; ----yrtCGATAsTATCGatrkh ; cor=; Ncor= a 0 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 c 0 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 g 0 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 t 0 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; positions_7nt_m2 versus oligos_7nt_mkv2_m4; m=6/15; ncol2=22; w=-6; offset=-6; strand=D; shift=3; score=0.556698; ---yhryCGATAsTATCGAtagh ; cor=; Ncor= a 0 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 c 0 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 g 0 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 t 0 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13
dyads_m1_shift4 (dyads_m1)				; positions_7nt_m2 versus dyads_m1; m=7/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.544202; ----mvkCGaTACTATCGATAgt ; cor=; Ncor= a 0 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 c 0 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 g 0 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 t 0 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27
oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)				; positions_7nt_m2 versus oligos_7nt_mkv2_m3; m=8/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.53522; ----mdkCGaTASTATCGATAst ; cor=; Ncor= a 0 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 c 0 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 g 0 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 t 0 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; positions_7nt_m2 versus oligos_6nt_mkv2_m1; m=9/15; ncol2=24; w=-4; offset=-4; strand=D; shift=5; score=0.533663; -----ktCGatACTATCGATAGT ; cor=; Ncor= a 0 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 c 0 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 g 0 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 t 0 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34
oligos_7nt_mkv2_m1_rc_shift5 (oligos_7nt_mkv2_m1_rc)				; positions_7nt_m2 versus oligos_7nt_mkv2_m1_rc; m=10/15; ncol2=24; w=-4; offset=-4; strand=R; shift=5; score=0.529333; -----ktCGaTACTATCGATAgT ; cor=; Ncor= a 0 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 c 0 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 g 0 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 t 0 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26
oligos_6nt_mkv2_m3_shift4 (oligos_6nt_mkv2_m3)				; positions_7nt_m2 versus oligos_6nt_mkv2_m3; m=11/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.519322; ----wkkCGATAsTATCGATAsw ; cor=; Ncor= a 0 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 c 0 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 g 0 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 t 0 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14
dyads_m3_shift4 (dyads_m3)				; positions_7nt_m2 versus dyads_m3; m=12/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.516029; ----wkyCGATAsTATCGATasw ; cor=; Ncor= a 0 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 c 0 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 g 0 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 t 0 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14
oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)				; positions_7nt_m2 versus oligos_6nt_mkv2_m4; m=13/15; ncol2=24; w=-5; offset=-5; strand=D; shift=4; score=0.515321; ----wkyCGATAsTATCGATasw ; cor=; Ncor= a 0 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 c 0 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 g 0 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 t 0 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14
dyads_m2_rc_shift1 (dyads_m2_rc)				; positions_7nt_m2 versus dyads_m2_rc; m=14/15; ncol2=24; w=-8; offset=-8; strand=R; shift=1; score=0.511813; -hdmyatCGATAsTATCGatrkw ; cor=; Ncor= a 0 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 c 0 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 g 0 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 t 0 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; positions_7nt_m2 versus oligos_7nt_mkv2_m2; m=15/15; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.510286; smwmyatCGATAsTATCGatrkw ; cor=; Ncor= a 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 13 8 13 c 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 5 7 8 g 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 20 16 8 t 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22 5 12 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift4 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=24; shift=4; ncol=28; ----vmwmyatCGATAsTATCGatrkhd ; Alignment reference a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 14 10 14 13 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 7 8 13 5 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 20 20 10 17 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22 11 14 15 17
dyads_m2_shift4 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----vmwmyatCGATAsTATCGatrkhd ; cor=; Ncor= a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 14 10 14 13 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 7 8 13 5 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 20 20 10 17 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22 11 14 15 17
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)				; dyads_m2 versus oligos_7nt_mkv2_m2; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.984009; ----smwmyatCGATAsTATCGatrkwk ; cor=; Ncor= a 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 13 8 13 10 c 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 5 7 8 5 g 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 20 16 8 12 t 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22 5 12 14 16
oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4_rc)				; dyads_m2 versus oligos_7nt_mkv2_m4_rc; m=3/15; ncol2=22; w=0; offset=0; strand=R; shift=4; score=0.878897; ----wwdctaTCGATAsTATCGrydr-- ; cor=; Ncor= a 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 4 0 2 24 10 16 13 0 0 c 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 0 50 2 9 20 7 10 0 0 g 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 5 0 46 13 6 15 17 0 0 t 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4 42 1 1 5 15 13 11 0 0
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)				; dyads_m2 versus oligos_6nt_mkv2_m2; m=4/15; ncol2=20; w=0; offset=1; strand=D; shift=5; score=0.828499; -----hdmyatCGATAsTATCGayr--- ; cor=; Ncor= a 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 22 0 0 0 c 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 9 0 0 0 g 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 18 0 0 0 t 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22 15 0 0 0
dyads_m3_rc_shift1 (dyads_m3_rc)				; dyads_m2 versus dyads_m3_rc; m=5/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.727411; -wcrawwstATCGATAsTATCGrmw--- ; cor=; Ncor= a 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 9 0 0 0 c 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 4 0 0 0 g 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 7 0 0 0 t 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4 11 0 0 0
oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)				; dyads_m2 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.724759; -wcrawwstATCGATAsTATCGrmw--- ; cor=; Ncor= a 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 9 0 0 0 c 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 4 0 0 0 g 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 6 0 0 0 t 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4 11 0 0 0
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; dyads_m2 versus oligos_6nt_mkv2_m3_rc; m=7/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.718717; -kcGatwsTATCGATAsTATCGmmw--- ; cor=; Ncor= a 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 8 0 0 0 c 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 4 0 0 0 g 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 6 0 0 0 t 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3 8 0 0 0
dyads_m1_rc_shift1 (dyads_m1_rc)				; dyads_m2 versus dyads_m1_rc; m=8/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.718107; -tcratacTATCGATAGTAtCGmbk--- ; cor=; Ncor= a 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 4 4 3 19 10 11 0 0 0 c 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 4 37 5 14 12 9 0 0 0 g 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 8 3 37 6 12 13 0 0 0 t 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6 30 2 1 7 12 13 0 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; dyads_m2 versus oligos_7nt_mkv2_m3_rc; m=9/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.705209; -tsgatasTATCGATASTAtCGmhk--- ; cor=; Ncor= a 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 7 0 0 0 c 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 5 0 0 0 g 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 9 0 0 0 t 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8 11 0 0 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; dyads_m2 versus oligos_7nt_mkv2_m1; m=10/15; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.622676; ktCGatAcTATCGATAGTAtCGam---- ; cor=; Ncor= a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 0 0 0 0 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 0 0 0 0 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 0 0 0 0 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7 0 0 0 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; dyads_m2 versus oligos_6nt_mkv2_m1; m=11/15; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.615371; ktCGatACTATCGATAGTatCGam---- ; cor=; Ncor= a 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 0 0 0 0 c 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 0 0 0 0 g 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 0 0 0 0 t 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10 0 0 0 0
positions_7nt_m1_shift4 (positions_7nt_m1)				; dyads_m2 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.549637; ----awacTATCGATAgtwt-------- ; cor=; Ncor= a 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 0 0 0 0 c 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 0 0 0 0 g 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 0 0 0 0 t 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0 0 0 0 0
positions_7nt_m2_rc_shift6 (positions_7nt_m2_rc)				; dyads_m2 versus positions_7nt_m2_rc; m=13/15; ncol2=14; w=0; offset=2; strand=R; shift=6; score=0.511813; ------acyATCGATAgtwt-------- ; cor=; Ncor= a 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42 0 0 0 0 0 0 0 0
positions_6nt_m1_shift5 (positions_6nt_m1)				; dyads_m2 versus positions_6nt_m1; m=14/15; ncol2=14; w=0; offset=1; strand=D; shift=5; score=0.480487; -----wacTATCGATAgyw--------- ; cor=; Ncor= a 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0 0 0 0 0 0
positions_6nt_m2_shift5 (positions_6nt_m2)				; dyads_m2 versus positions_6nt_m2; m=15/15; ncol2=14; w=0; offset=1; strand=D; shift=5; score=0.476785; -----waCTATCGATAstw--------- ; cor=; Ncor= a 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32 0 0 0 0 0 0 0 0 0

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=24; shift=0; ncol=24; ktCGatAcTATCGATAGTAtCGam ; Alignment reference a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ktCGatAcTATCGATAGTAtCGam ; cor=; Ncor= a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.993057; ktCGatACTATCGATAGTatCGam ; cor=; Ncor= a 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 c 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 g 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 t 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=3/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.909054; -tsgatasTATCGATASTAtCGmh ; cor=; Ncor= a 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 c 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 g 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 t 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8
dyads_m1_rc_shift1 (dyads_m1_rc)				; oligos_7nt_mkv2_m1 versus dyads_m1_rc; m=4/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.899073; -tcratacTATCGATAGTAtCGmb ; cor=; Ncor= a 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 4 4 3 19 10 c 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 4 37 5 14 12 g 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 8 3 37 6 12 t 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6 30 2 1 7 12
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=5/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.878954; -kcGatwsTATCGATAsTATCGmm ; cor=; Ncor= a 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 c 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 g 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 t 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3
oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.865453; -wcrawwstATCGATAsTATCGrm ; cor=; Ncor= a 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 c 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 g 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 t 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4
dyads_m3_rc_shift1 (dyads_m3_rc)				; oligos_7nt_mkv2_m1 versus dyads_m3_rc; m=7/15; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.861835; -wcrawwstATCGATAsTATCGrm ; cor=; Ncor= a 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 c 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 g 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 t 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4
oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4_rc; m=8/15; ncol2=22; w=0; offset=4; strand=R; shift=4; score=0.689944; ----wwdctaTCGATAsTATCGry ; cor=; Ncor= a 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 4 0 2 24 10 c 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 0 50 2 9 20 g 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 5 0 46 13 6 t 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4 42 1 1 5 15
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=9/15; ncol2=20; w=0; offset=5; strand=D; shift=5; score=0.667303; -----hdmyatCGATAsTATCGay ; cor=; Ncor= a 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 c 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 g 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 t 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22
positions_7nt_m1_shift4 (positions_7nt_m1)				; oligos_7nt_mkv2_m1 versus positions_7nt_m1; m=10/15; ncol2=16; w=0; offset=4; strand=D; shift=4; score=0.635788; ----awacTATCGATAgtwt---- ; cor=; Ncor= a 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 c 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 g 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 t 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0
dyads_m2_shift4 (dyads_m2)				; oligos_7nt_mkv2_m1 versus dyads_m2; m=11/15; ncol2=24; w=0; offset=4; strand=D; shift=4; score=0.622676; ----vmwmyatCGATAsTATCGat ; cor=; Ncor= a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=12/15; ncol2=24; w=0; offset=4; strand=D; shift=4; score=0.590402; ----smwmyatCGATAsTATCGat ; cor=; Ncor= a 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 c 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 g 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 t 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22
positions_6nt_m1_shift5 (positions_6nt_m1)				; oligos_7nt_mkv2_m1 versus positions_6nt_m1; m=13/15; ncol2=14; w=0; offset=5; strand=D; shift=5; score=0.541209; -----wacTATCGATAgyw----- ; cor=; Ncor= a 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 0 c 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 0 g 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 0 t 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0 0
positions_6nt_m2_rc_shift5 (positions_6nt_m2_rc)				; oligos_7nt_mkv2_m1 versus positions_6nt_m2_rc; m=14/15; ncol2=14; w=0; offset=5; strand=R; shift=5; score=0.531232; -----wasTATCGATAGtw----- ; cor=; Ncor= a 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 0 c 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 0 g 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 0 t 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0 0
positions_7nt_m2_rc_shift6 (positions_7nt_m2_rc)				; oligos_7nt_mkv2_m1 versus positions_7nt_m2_rc; m=15/15; ncol2=14; w=0; offset=6; strand=R; shift=6; score=0.529333; ------acyATCGATAgtwt---- ; cor=; Ncor= a 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 0 0 0 0 c 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 0 0 0 0 g 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 0 0 0 0 t 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---mdkCGaTASTATCGATAstatcsa ; Alignment reference a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6
dyads_m1_shift3 (dyads_m1)				; oligos_7nt_mkv2_m3 versus dyads_m1; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.991469; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.967715; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.960259; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8
dyads_m3_shift3 (dyads_m3)				; oligos_7nt_mkv2_m3 versus dyads_m3; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.958158; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8
oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.909054; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.905315; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.779619; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.760224; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv2_m3 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.705209; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.669953; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; oligos_7nt_mkv2_m3 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.634156; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0
positions_6nt_m1_shift9 (positions_6nt_m1)				; oligos_7nt_mkv2_m3 versus positions_6nt_m1; m=13/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.542644; ---------wacTATCGATAgyw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0
positions_7nt_m2_shift8 (positions_7nt_m2)				; oligos_7nt_mkv2_m3 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.53522; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0
positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)				; oligos_7nt_mkv2_m3 versus positions_6nt_m2_rc; m=15/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.53301; ---------wasTATCGATAGtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift6 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=14; shift=6; ncol=20; ------waCTATCGATAstw ; Alignment reference a 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 c 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 g 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 t 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32
positions_6nt_m2_shift6 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/15; ncol2=14; w=0; offset=0; strand=D; shift=6; score= 1; ------waCTATCGATAstw ; cor=; Ncor= a 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 c 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 g 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 t 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32
positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)				; positions_6nt_m2 versus positions_6nt_m1_rc; m=2/15; ncol2=14; w=0; offset=0; strand=R; shift=6; score=0.974699; ------wrcTATCGATAgtw ; cor=; Ncor= a 0 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 c 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 g 0 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 t 0 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34
positions_7nt_m1_shift5 (positions_7nt_m1)				; positions_6nt_m2 versus positions_7nt_m1; m=3/15; ncol2=16; w=-1; offset=-1; strand=D; shift=5; score=0.849716; -----awacTATCGATAgtw ; cor=; Ncor= a 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 c 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 g 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 t 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_6nt_m2 versus positions_7nt_m2; m=4/15; ncol2=14; w=-1; offset=-1; strand=D; shift=5; score=0.813542; -----awacTATCGATrgt- ; cor=; Ncor= a 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 c 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 g 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 t 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0
oligos_6nt_mkv2_m2_shift6 (oligos_6nt_mkv2_m2)				; positions_6nt_m2 versus oligos_6nt_mkv2_m2; m=5/15; ncol2=20; w=0; offset=0; strand=D; shift=6; score=0.577258; ------hdmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 c 0 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 g 0 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 t 0 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2
oligos_7nt_mkv2_m4_rc_shift5 (oligos_7nt_mkv2_m4_rc)				; positions_6nt_m2 versus oligos_7nt_mkv2_m4_rc; m=6/15; ncol2=22; w=-1; offset=-1; strand=R; shift=5; score=0.572853; -----wwdctaTCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 c 0 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 g 0 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 t 0 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; positions_6nt_m2 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.539556; -ktCGatACTATCGATAGTa ; cor=; Ncor= a 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 c 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 g 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 t 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10
dyads_m1_shift0 (dyads_m1)				; positions_6nt_m2 versus dyads_m1; m=8/15; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.538402; mvkCGaTACTATCGATAgta ; cor=; Ncor= a 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 c 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 g 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 t 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11
oligos_7nt_mkv2_m3_rc_shift2 (oligos_7nt_mkv2_m3_rc)				; positions_6nt_m2 versus oligos_7nt_mkv2_m3_rc; m=9/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.53301; --tsgatasTATCGATASTA ; cor=; Ncor= a 0 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 c 0 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 g 0 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 t 0 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; positions_6nt_m2 versus oligos_6nt_mkv2_m4_rc; m=10/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.532834; --wcrawwstATCGATAsTA ; cor=; Ncor= a 0 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 c 0 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 g 0 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 t 0 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3
oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)				; positions_6nt_m2 versus oligos_7nt_mkv2_m1_rc; m=11/15; ncol2=24; w=-5; offset=-5; strand=R; shift=1; score=0.531232; -ktCGaTACTATCGATAgTa ; cor=; Ncor= a 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 c 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 g 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 t 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6
dyads_m3_rc_shift2 (dyads_m3_rc)				; positions_6nt_m2 versus dyads_m3_rc; m=12/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.531079; --wcrawwstATCGATAsTA ; cor=; Ncor= a 0 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 c 0 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 g 0 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 t 0 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3
oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3_rc)				; positions_6nt_m2 versus oligos_6nt_mkv2_m3_rc; m=13/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.52871; --kcGatwsTATCGATAsTA ; cor=; Ncor= a 0 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 c 0 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 g 0 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 t 0 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3
dyads_m2_shift5 (dyads_m2)				; positions_6nt_m2 versus dyads_m2; m=14/15; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.476785; -----vmwmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 c 0 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 g 0 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 t 0 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1
oligos_7nt_mkv2_m2_rc_shift6 (oligos_7nt_mkv2_m2_rc)				; positions_6nt_m2 versus oligos_7nt_mkv2_m2_rc; m=15/15; ncol2=24; w=0; offset=0; strand=R; shift=6; score=0.473315; ------mwmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 0 16 14 12 5 22 4 0 0 41 2 42 1 0 42 c 0 0 0 0 0 0 12 8 16 20 8 5 42 0 0 0 0 16 1 1 g 0 0 0 0 0 0 5 8 7 5 8 5 0 40 1 2 0 25 0 0 t 0 0 0 0 0 0 10 13 8 13 5 29 1 3 1 39 1 1 42 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=24; shift=4; ncol=28; ----smwmyatCGATAsTATCGatrkwk ; Alignment reference a 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 13 8 13 10 c 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 5 7 8 5 g 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 20 16 8 12 t 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22 5 12 14 16
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----smwmyatCGATAsTATCGatrkwk ; cor=; Ncor= a 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 13 8 13 10 c 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 5 7 8 5 g 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 20 16 8 12 t 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22 5 12 14 16
dyads_m2_shift4 (dyads_m2)				; oligos_7nt_mkv2_m2 versus dyads_m2; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.984009; ----vmwmyatCGATAsTATCGatrkhd ; cor=; Ncor= a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 14 10 14 13 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 7 8 13 5 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 20 20 10 17 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22 11 14 15 17
oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=3/15; ncol2=22; w=0; offset=0; strand=R; shift=4; score=0.874021; ----wwdctaTCGATAsTATCGrydr-- ; cor=; Ncor= a 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 4 0 2 24 10 16 13 0 0 c 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 0 50 2 9 20 7 10 0 0 g 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 5 0 46 13 6 15 17 0 0 t 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4 42 1 1 5 15 13 11 0 0
oligos_6nt_mkv2_m2_rc_shift8 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=4/15; ncol2=20; w=0; offset=4; strand=R; shift=8; score=0.82733; --------yrtCGATAsTATCGatrkhd ; cor=; Ncor= a 0 0 0 0 0 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 c 0 0 0 0 0 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 g 0 0 0 0 0 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 t 0 0 0 0 0 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22
dyads_m3_rc_shift1 (dyads_m3_rc)				; oligos_7nt_mkv2_m2 versus dyads_m3_rc; m=5/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.713031; -wcrawwstATCGATAsTATCGrmw--- ; cor=; Ncor= a 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 9 0 0 0 c 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 4 0 0 0 g 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 7 0 0 0 t 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4 11 0 0 0
oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.709251; -wcrawwstATCGATAsTATCGrmw--- ; cor=; Ncor= a 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 9 0 0 0 c 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 4 0 0 0 g 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 6 0 0 0 t 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4 11 0 0 0
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=7/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.697768; -kcGatwsTATCGATAsTATCGmmw--- ; cor=; Ncor= a 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 8 0 0 0 c 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 4 0 0 0 g 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 6 0 0 0 t 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3 8 0 0 0
dyads_m1_rc_shift1 (dyads_m1_rc)				; oligos_7nt_mkv2_m2 versus dyads_m1_rc; m=8/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.681951; -tcratacTATCGATAGTAtCGmbk--- ; cor=; Ncor= a 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 4 4 3 19 10 11 0 0 0 c 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 4 37 5 14 12 9 0 0 0 g 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 8 3 37 6 12 13 0 0 0 t 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6 30 2 1 7 12 13 0 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=9/15; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.669953; -tsgatasTATCGATASTAtCGmhk--- ; cor=; Ncor= a 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 7 0 0 0 c 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 5 0 0 0 g 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 9 0 0 0 t 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8 11 0 0 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=10/15; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.590402; ktCGatAcTATCGATAGTAtCGam---- ; cor=; Ncor= a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 0 0 0 0 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 0 0 0 0 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 0 0 0 0 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7 0 0 0 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=11/15; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.580869; ktCGatACTATCGATAGTatCGam---- ; cor=; Ncor= a 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 0 0 0 0 c 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 0 0 0 0 g 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 0 0 0 0 t 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10 0 0 0 0
positions_7nt_m1_shift4 (positions_7nt_m1)				; oligos_7nt_mkv2_m2 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.522256; ----awacTATCGATAgtwt-------- ; cor=; Ncor= a 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 0 0 0 0 c 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 0 0 0 0 g 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 0 0 0 0 t 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0 0 0 0 0
positions_7nt_m2_shift13 (positions_7nt_m2)				; oligos_7nt_mkv2_m2 versus positions_7nt_m2; m=13/15; ncol2=14; w=0; offset=9; strand=D; shift=13; score=0.510286; -------------awacTATCGATrgt- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0
positions_6nt_m1_rc_shift14 (positions_6nt_m1_rc)				; oligos_7nt_mkv2_m2 versus positions_6nt_m1_rc; m=14/15; ncol2=14; w=0; offset=10; strand=R; shift=14; score=0.475669; --------------wrcTATCGATAgtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34
positions_6nt_m2_rc_shift14 (positions_6nt_m2_rc)				; oligos_7nt_mkv2_m2 versus positions_6nt_m2_rc; m=15/15; ncol2=14; w=0; offset=10; strand=R; shift=14; score=0.473315; --------------wasTATCGATAGtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift3 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wkyCGATAsTATCGATaswwtygw ; Alignment reference a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8
dyads_m3_shift3 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; dyads_m3 versus oligos_6nt_mkv2_m4; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.999187; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)				; dyads_m3 versus oligos_6nt_mkv2_m3; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.98515; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; dyads_m3 versus oligos_7nt_mkv2_m3; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.958158; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6
dyads_m1_shift3 (dyads_m1)				; dyads_m3 versus dyads_m1; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.955336; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9
oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)				; dyads_m3 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.861835; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; dyads_m3 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score= 0.8588; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; dyads_m3 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.820891; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)				; dyads_m3 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.790569; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; dyads_m3 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.727411; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; dyads_m3 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.713031; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; dyads_m3 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.596937; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0
positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)				; dyads_m3 versus positions_6nt_m2_rc; m=13/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.531079; ---------wasTATCGATAGtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0
positions_7nt_m2_shift8 (positions_7nt_m2)				; dyads_m3 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.516029; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0
positions_6nt_m1_shift9 (positions_6nt_m1)				; dyads_m3 versus positions_6nt_m1; m=15/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.51515; ---------wacTATCGATAgyw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=20; shift=5; ncol=25; -----hdmyatCGATAsTATCGayr ; Alignment reference a 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 22 c 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 9 g 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 18 t 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22 15
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/15; ncol2=20; w=0; offset=0; strand=D; shift=5; score= 1; -----hdmyatCGATAsTATCGayr ; cor=; Ncor= a 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 22 c 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 9 g 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 18 t 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22 15
oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=2/15; ncol2=22; w=-1; offset=-1; strand=R; shift=4; score=0.882628; ----wwdctaTCGATAsTATCGryd ; cor=; Ncor= a 0 0 0 0 14 18 13 4 11 31 3 0 0 48 3 48 1 2 46 4 0 2 24 10 16 c 0 0 0 0 12 11 8 31 7 2 5 51 0 0 2 0 30 1 1 0 50 2 9 20 7 g 0 0 0 0 12 6 16 8 6 11 5 0 51 2 1 1 19 3 0 5 0 46 13 6 15 t 0 0 0 0 13 16 14 8 27 7 38 0 0 1 45 2 1 45 4 42 1 1 5 15 13
dyads_m2_shift4 (dyads_m2)				; oligos_6nt_mkv2_m2 versus dyads_m2; m=3/15; ncol2=24; w=-1; offset=-1; strand=D; shift=4; score=0.828499; ----vmwmyatCGATAsTATCGatr ; cor=; Ncor= a 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 14 c 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 7 g 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 20 t 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22 11
oligos_7nt_mkv2_m2_rc_shift5 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=4/15; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.82733; -----mwmyatCGATAsTATCGatr ; cor=; Ncor= a 0 0 0 0 0 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 c 0 0 0 0 0 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 g 0 0 0 0 0 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 t 0 0 0 0 0 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6
dyads_m3_rc_shift1 (dyads_m3_rc)				; oligos_6nt_mkv2_m2 versus dyads_m3_rc; m=5/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.790569; -wcrawwstATCGATAsTATCGrmw ; cor=; Ncor= a 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 9 c 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 4 g 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 7 t 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4 11
oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.787886; -wcrawwstATCGATAsTATCGrmw ; cor=; Ncor= a 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 9 c 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 4 g 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 6 t 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4 11
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=7/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.775462; -kcGatwsTATCGATAsTATCGmmw ; cor=; Ncor= a 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 8 c 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 4 g 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 6 t 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3 8
dyads_m1_rc_shift1 (dyads_m1_rc)				; oligos_6nt_mkv2_m2 versus dyads_m1_rc; m=8/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.771777; -tcratacTATCGATAGTAtCGmbk ; cor=; Ncor= a 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 4 4 3 19 10 11 c 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 4 37 5 14 12 9 g 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 8 3 37 6 12 13 t 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6 30 2 1 7 12 13
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=9/15; ncol2=24; w=-4; offset=-4; strand=R; shift=1; score=0.760224; -tsgatasTATCGATASTAtCGmhk ; cor=; Ncor= a 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 7 c 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 5 g 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 9 t 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8 11
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=10/15; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.667303; ktCGatAcTATCGATAGTAtCGam- ; cor=; Ncor= a 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 0 c 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 0 g 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 0 t 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=11/15; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.664392; ktCGatACTATCGATAGTatCGam- ; cor=; Ncor= a 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 0 c 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 0 g 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 0 t 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10 0
positions_7nt_m2_rc_shift6 (positions_7nt_m2_rc)				; oligos_6nt_mkv2_m2 versus positions_7nt_m2_rc; m=12/15; ncol2=14; w=0; offset=1; strand=R; shift=6; score=0.615595; ------acyATCGATAgtwt----- ; cor=; Ncor= a 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 0 0 0 0 0 c 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 0 0 0 0 0 g 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 0 0 0 0 0 t 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42 0 0 0 0 0
positions_7nt_m1_shift4 (positions_7nt_m1)				; oligos_6nt_mkv2_m2 versus positions_7nt_m1; m=13/15; ncol2=16; w=-1; offset=-1; strand=D; shift=4; score=0.589551; ----awacTATCGATAgtwt----- ; cor=; Ncor= a 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 0 c 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 0 g 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 0 t 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0 0
positions_6nt_m1_rc_shift5 (positions_6nt_m1_rc)				; oligos_6nt_mkv2_m2 versus positions_6nt_m1_rc; m=14/15; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.578118; -----wrcTATCGATAgtw------ ; cor=; Ncor= a 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 0 0 0 0 0 0 c 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 0 0 0 0 0 0 g 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 0 0 t 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34 0 0 0 0 0 0
positions_6nt_m2_shift5 (positions_6nt_m2)				; oligos_6nt_mkv2_m2 versus positions_6nt_m2; m=15/15; ncol2=14; w=0; offset=0; strand=D; shift=5; score=0.577258; -----waCTATCGATAstw------ ; cor=; Ncor= a 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 0 0 0 0 0 0 c 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 0 0 0 0 0 0 g 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 0 0 0 0 0 0 t 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift7 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=14; shift=7; ncol=21; -------wacTATCGATAgyw ; Alignment reference a 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 c 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 g 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 t 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34
positions_6nt_m1_shift7 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/15; ncol2=14; w=0; offset=0; strand=D; shift=7; score= 1; -------wacTATCGATAgyw ; cor=; Ncor= a 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 c 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 g 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 t 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34
positions_6nt_m2_rc_shift7 (positions_6nt_m2_rc)				; positions_6nt_m1 versus positions_6nt_m2_rc; m=2/15; ncol2=14; w=0; offset=0; strand=R; shift=7; score=0.974699; -------wasTATCGATAGtw ; cor=; Ncor= a 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 c 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 g 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 t 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37
positions_7nt_m1_shift6 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=3/15; ncol2=16; w=-1; offset=-1; strand=D; shift=6; score=0.866118; ------awacTATCGATAgtw ; cor=; Ncor= a 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 c 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 g 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 t 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29
positions_7nt_m2_shift6 (positions_7nt_m2)				; positions_6nt_m1 versus positions_7nt_m2; m=4/15; ncol2=14; w=-1; offset=-1; strand=D; shift=6; score=0.822423; ------awacTATCGATrgt- ; cor=; Ncor= a 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 c 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 g 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 t 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; positions_6nt_m1 versus oligos_6nt_mkv2_m2_rc; m=5/15; ncol2=20; w=-6; offset=-6; strand=R; shift=1; score=0.578118; -yrtCGATAsTATCGatrkhd ; cor=; Ncor= a 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 c 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 g 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 t 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; positions_6nt_m1 versus oligos_7nt_mkv2_m4; m=6/15; ncol2=22; w=-7; offset=-7; strand=D; shift=0; score=0.554481; yhryCGATAsTATCGAtaghw ; cor=; Ncor= a 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 c 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 g 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 t 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; positions_6nt_m1 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=-5; offset=-5; strand=D; shift=2; score=0.552426; --ktCGatACTATCGATAGTa ; cor=; Ncor= a 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 c 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 g 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 t 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10
dyads_m1_rc_shift3 (dyads_m1_rc)				; positions_6nt_m1 versus dyads_m1_rc; m=8/15; ncol2=24; w=-4; offset=-4; strand=R; shift=3; score=0.547498; ---tcratacTATCGATAGTA ; cor=; Ncor= a 0 0 0 9 2 13 24 11 27 7 3 35 2 0 0 42 1 41 0 5 34 c 0 0 0 6 24 5 7 10 4 26 8 4 4 45 0 1 4 1 9 4 2 g 0 0 0 9 11 25 8 2 5 9 3 6 1 0 46 2 2 2 35 1 4 t 0 0 0 22 9 3 7 23 10 4 32 1 39 1 0 1 39 2 2 36 6
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; positions_6nt_m1 versus oligos_7nt_mkv2_m3; m=9/15; ncol2=24; w=-6; offset=-6; strand=D; shift=1; score=0.542644; -mdkCGaTASTATCGATAsta ; cor=; Ncor= a 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 c 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 g 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 t 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7
oligos_7nt_mkv2_m1_rc_shift2 (oligos_7nt_mkv2_m1_rc)				; positions_6nt_m1 versus oligos_7nt_mkv2_m1_rc; m=10/15; ncol2=24; w=-5; offset=-5; strand=R; shift=2; score=0.541209; --ktCGaTACTATCGATAgTa ; cor=; Ncor= a 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 c 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 g 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 t 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; positions_6nt_m1 versus oligos_6nt_mkv2_m3; m=11/15; ncol2=24; w=-6; offset=-6; strand=D; shift=1; score=0.518788; -wkkCGATAsTATCGATAswa ; cor=; Ncor= a 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 c 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 g 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 t 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; positions_6nt_m1 versus oligos_6nt_mkv2_m4; m=12/15; ncol2=24; w=-6; offset=-6; strand=D; shift=1; score=0.517272; -wkyCGATAsTATCGATasww ; cor=; Ncor= a 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 c 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 g 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 t 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8
dyads_m3_shift1 (dyads_m3)				; positions_6nt_m1 versus dyads_m3; m=13/15; ncol2=24; w=-6; offset=-6; strand=D; shift=1; score=0.51515; -wkyCGATAsTATCGATasww ; cor=; Ncor= a 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 c 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 g 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 t 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8
dyads_m2_shift6 (dyads_m2)				; positions_6nt_m1 versus dyads_m2; m=14/15; ncol2=24; w=-1; offset=-1; strand=D; shift=6; score=0.480487; ------vmwmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 c 0 0 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 g 0 0 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 t 0 0 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1
oligos_7nt_mkv2_m2_rc_shift7 (oligos_7nt_mkv2_m2_rc)				; positions_6nt_m1 versus oligos_7nt_mkv2_m2_rc; m=15/15; ncol2=24; w=0; offset=0; strand=R; shift=7; score=0.475669; -------mwmyatCGATAsTA ; cor=; Ncor= a 0 0 0 0 0 0 0 16 14 12 5 22 4 0 0 41 2 42 1 0 42 c 0 0 0 0 0 0 0 12 8 16 20 8 5 42 0 0 0 0 16 1 1 g 0 0 0 0 0 0 0 5 8 7 5 8 5 0 40 1 2 0 25 0 0 t 0 0 0 0 0 0 0 10 13 8 13 5 29 1 3 1 39 1 1 42 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wkkCGATAsTATCGATAswatCgm ; Alignment reference a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5
dyads_m3_shift3 (dyads_m3)				; oligos_6nt_mkv2_m3 versus dyads_m3; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.98515; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.985095; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.967715; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6
dyads_m1_shift3 (dyads_m1)				; oligos_6nt_mkv2_m3 versus dyads_m1; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.961179; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9
oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.878954; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.874783; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.801146; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.775462; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_6nt_mkv2_m3 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.718717; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.697768; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; oligos_6nt_mkv2_m3 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.605621; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0
positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)				; oligos_6nt_mkv2_m3 versus positions_6nt_m2_rc; m=13/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.52871; ---------wasTATCGATAGtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0
positions_7nt_m2_shift8 (positions_7nt_m2)				; oligos_6nt_mkv2_m3 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.519322; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0
positions_6nt_m1_shift9 (positions_6nt_m1)				; oligos_6nt_mkv2_m3 versus positions_6nt_m1; m=15/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.518788; ---------wacTATCGATAgyw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=24; shift=2; ncol=26; --ktCGatACTATCGATAGTatCGam ; Alignment reference a 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 c 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 g 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 t 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ktCGatACTATCGATAGTatCGam ; cor=; Ncor= a 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 15 c 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 15 g 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 10 t 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9 10
oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.993057; --ktCGatAcTATCGATAGTAtCGam ; cor=; Ncor= a 0 0 7 8 0 4 21 6 26 3 2 27 1 0 1 31 0 29 1 5 24 4 2 3 17 12 c 0 0 6 4 25 3 6 5 1 23 4 3 2 34 0 1 5 1 8 2 1 4 27 6 6 10 g 0 0 10 6 6 26 4 1 2 8 1 5 1 0 34 2 3 3 24 1 5 6 3 26 5 6 t 0 0 12 17 4 2 4 23 6 1 28 0 31 1 0 1 27 2 2 27 5 21 3 0 7 7
oligos_7nt_mkv2_m3_rc_shift3 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=3/15; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.905315; ---tsgatasTATCGATASTAtCGmh ; cor=; Ncor= a 0 0 0 6 2 5 18 7 21 3 3 26 1 0 0 28 0 29 0 3 24 3 1 2 15 8 c 0 0 0 4 17 4 7 4 2 21 4 1 2 31 0 1 3 0 8 1 1 2 28 4 8 9 g 0 0 0 6 8 21 4 2 3 8 2 4 1 0 32 2 2 1 23 1 3 6 1 26 4 7 t 0 0 0 16 5 2 3 19 6 0 23 1 28 1 0 1 27 2 1 27 4 21 2 0 5 8
dyads_m1_shift1 (dyads_m1)				; oligos_6nt_mkv2_m1 versus dyads_m1; m=4/15; ncol2=24; w=-1; offset=-1; strand=D; shift=1; score=0.896607; -mvkCGaTACTATCGATAgtatyga- ; cor=; Ncor= a 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 0 c 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 0 g 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 0 t 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9 0
oligos_6nt_mkv2_m3_rc_shift3 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=5/15; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.874783; ---kcGatwsTATCGATAsTATCGmm ; cor=; Ncor= a 0 0 0 5 3 4 12 6 14 3 2 21 1 0 0 23 0 23 0 3 23 2 0 2 13 8 c 0 0 0 5 16 2 4 4 2 11 4 0 2 25 0 0 2 0 14 0 0 0 24 1 7 9 g 0 0 0 7 2 18 6 0 2 10 1 4 1 0 26 2 1 1 11 1 0 3 0 23 2 6 t 0 0 0 9 5 2 4 16 8 2 19 1 22 1 0 1 23 2 1 22 3 21 2 0 4 3
oligos_6nt_mkv2_m4_rc_shift3 (oligos_6nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=3; score=0.862574; ---wcrawwstATCGATAsTATCGrm ; cor=; Ncor= a 0 0 0 8 3 8 15 8 14 2 5 22 2 0 0 27 1 29 0 3 27 2 0 2 13 8 c 0 0 0 4 16 3 6 7 2 15 3 1 2 30 0 0 2 0 18 0 0 0 27 1 4 13 g 0 0 0 6 4 18 5 1 5 10 2 5 1 0 30 2 0 0 12 1 0 3 0 27 8 5 t 0 0 0 12 7 1 4 14 9 3 20 2 25 0 0 1 27 1 0 26 3 25 3 0 5 4
dyads_m3_rc_shift3 (dyads_m3_rc)				; oligos_6nt_mkv2_m1 versus dyads_m3_rc; m=7/15; ncol2=24; w=0; offset=1; strand=R; shift=3; score= 0.8588; ---wcrawwstATCGATAsTATCGrm ; cor=; Ncor= a 0 0 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 0 2 13 9 c 0 0 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 28 1 5 13 g 0 0 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 0 28 8 5 t 0 0 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26 3 0 5 4
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-2; offset=-2; strand=D; shift=0; score=0.686897; yhryCGATAsTATCGAtaghww---- ; cor=; Ncor= a 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 0 c 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 0 g 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 0 t 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0 0
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=-1; offset=-1; strand=R; shift=1; score=0.664392; -yrtCGATAsTATCGatrkhd----- ; cor=; Ncor= a 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 0 c 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 0 g 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 0 t 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0 0
positions_7nt_m1_shift6 (positions_7nt_m1)				; oligos_6nt_mkv2_m1 versus positions_7nt_m1; m=10/15; ncol2=16; w=0; offset=4; strand=D; shift=6; score=0.638604; ------awacTATCGATAgtwt---- ; cor=; Ncor= a 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 0 c 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 0 g 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 0 t 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0 0
dyads_m2_shift6 (dyads_m2)				; oligos_6nt_mkv2_m1 versus dyads_m2; m=11/15; ncol2=24; w=0; offset=4; strand=D; shift=6; score=0.615371; ------vmwmyatCGATAsTATCGat ; cor=; Ncor= a 0 0 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 3 2 30 10 c 0 0 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 47 1 12 12 g 0 0 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 0 48 5 8 t 0 0 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49 2 1 5 22
oligos_7nt_mkv2_m2_shift6 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=12/15; ncol2=24; w=0; offset=4; strand=D; shift=6; score=0.580869; ------smwmyatCGATAsTATCGat ; cor=; Ncor= a 0 0 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 3 1 29 5 c 0 0 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 40 0 5 8 g 0 0 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 0 42 5 8 t 0 0 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41 0 0 4 22
positions_6nt_m1_shift7 (positions_6nt_m1)				; oligos_6nt_mkv2_m1 versus positions_6nt_m1; m=13/15; ncol2=14; w=0; offset=5; strand=D; shift=7; score=0.552426; -------wacTATCGATAgyw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 0 0 0 0 c 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 0 0 0 0 g 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 0 t 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0 0 0 0 0
positions_6nt_m2_rc_shift7 (positions_6nt_m2_rc)				; oligos_6nt_mkv2_m1 versus positions_6nt_m2_rc; m=14/15; ncol2=14; w=0; offset=5; strand=R; shift=7; score=0.539556; -------wasTATCGATAGtw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 0 0 0 0 c 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 0 0 0 0 g 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 0 0 0 0 t 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0 0 0 0 0
positions_7nt_m2_rc_shift8 (positions_7nt_m2_rc)				; oligos_6nt_mkv2_m1 versus positions_7nt_m2_rc; m=15/15; ncol2=14; w=0; offset=6; strand=R; shift=8; score=0.533663; --------acyATCGATAgtwt---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 0 0 0 0 c 0 0 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 0 0 0 0 g 0 0 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 0 0 0 0 t 0 0 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=22; shift=2; ncol=24; --yhryCGATAsTATCGAtaghww ; Alignment reference a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/15; ncol2=22; w=0; offset=0; strand=D; shift=2; score= 1; --yhryCGATAsTATCGAtaghww ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=2/15; ncol2=20; w=0; offset=1; strand=R; shift=3; score=0.882628; ---yrtCGATAsTATCGatrkhd- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv2_m4 versus dyads_m2_rc; m=3/15; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.878897; hdmyatCGATAsTATCGatrkwkb ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2_rc; m=4/15; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.874021; mwmyatCGATAsTATCGatrkwks ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10
dyads_m3_shift3 (dyads_m3)				; oligos_7nt_mkv2_m4 versus dyads_m3; m=5/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.820891; ---wkyCGATAsTATCGATaswwt ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=6/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.819057; ---wkyCGATAsTATCGATaswwt ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.801146; ---wkkCGATAsTATCGATAswat ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12
dyads_m1_shift3 (dyads_m1)				; oligos_7nt_mkv2_m4 versus dyads_m1; m=8/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.781949; ---mvkCGaTACTATCGATAgtat ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=9/15; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.779619; ---mdkCGaTASTATCGATAstat ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18
oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1_rc; m=10/15; ncol2=24; w=0; offset=2; strand=R; shift=4; score=0.689944; ----ktCGaTACTATCGATAgTat ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=11/15; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.686897; ----ktCGatACTATCGATAGTat ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32
positions_7nt_m1_shift8 (positions_7nt_m1)				; oligos_7nt_mkv2_m4 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=6; strand=D; shift=8; score=0.633015; --------awacTATCGATAgtwt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35
positions_6nt_m2_rc_shift9 (positions_6nt_m2_rc)				; oligos_7nt_mkv2_m4 versus positions_6nt_m2_rc; m=13/15; ncol2=14; w=0; offset=7; strand=R; shift=9; score=0.572853; ---------wasTATCGATAGtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 32 39 7 6 86 2 1 0 87 2 68 6 20 28 0 c 0 0 0 0 0 0 0 0 0 13 17 31 12 0 4 91 0 2 5 3 17 22 14 0 g 0 0 0 0 0 0 0 0 0 16 16 47 2 5 2 0 90 2 3 10 67 14 14 0 t 0 0 0 0 0 0 0 0 0 32 21 8 73 2 85 1 3 2 83 12 3 37 37 0
positions_7nt_m2_shift8 (positions_7nt_m2)				; oligos_7nt_mkv2_m4 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=6; strand=D; shift=8; score=0.556698; --------awacTATCGATrgt-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0
positions_6nt_m1_shift9 (positions_6nt_m1)				; oligos_7nt_mkv2_m4 versus positions_6nt_m1; m=15/15; ncol2=14; w=0; offset=7; strand=D; shift=9; score=0.554481; ---------wacTATCGATAgyw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 40 7 11 88 2 0 0 92 2 69 8 19 34 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 25 16 0 g 0 0 0 0 0 0 0 0 0 17 24 17 2 4 2 0 97 1 3 15 65 14 13 0 t 0 0 0 0 0 0 0 0 0 33 19 8 69 2 92 0 0 2 88 11 7 39 34 0

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; hrATAAATAwh ; Alignment reference a 19 19 52 1 51 44 48 0 53 17 17 c 14 8 2 1 2 2 1 2 1 10 14 g 6 16 1 4 0 4 6 0 1 9 8 t 16 12 0 49 2 5 0 53 0 19 16
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; hrATAAATAwh ; cor=; Ncor= a 19 19 52 1 51 44 48 0 53 17 17 c 14 8 2 1 2 2 1 2 1 10 14 g 6 16 1 4 0 4 6 0 1 9 8 t 16 12 0 49 2 5 0 53 0 19 16
dyads_m4_shift0 (dyads_m4)				; oligos_7nt_mkv2_m5 versus dyads_m4; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.673977; wdwAAAATAtw ; cor=; Ncor= a 27 21 23 63 66 63 67 0 66 16 21 c 15 12 11 1 0 0 0 0 0 12 15 g 2 17 6 2 0 0 0 1 1 5 13 t 23 17 27 1 1 4 0 66 0 34 18
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.673752; -rwAAAATAwh ; cor=; Ncor= a 0 19 24 59 59 59 59 0 59 18 17 c 0 11 11 0 0 0 0 0 0 11 15 g 0 15 7 0 0 0 0 0 0 5 11 t 0 14 17 0 0 0 0 59 0 25 16

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift3 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---mvkCGaTACTATCGATAgtatyga ; Alignment reference a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9
dyads_m1_shift3 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---mvkCGaTACTATCGATAgtatyga ; cor=; Ncor= a 0 0 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 3 9 22 c 0 0 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 25 11 9 g 0 0 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 5 24 6 t 0 0 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24 13 2 9
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; dyads_m1 versus oligos_7nt_mkv2_m3; m=2/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.991469; ---mdkCGaTASTATCGATAstatcsa ; cor=; Ncor= a 0 0 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 2 5 16 c 0 0 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 21 8 6 g 0 0 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 4 17 4 t 0 0 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18 5 2 6
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)				; dyads_m1 versus oligos_6nt_mkv2_m3; m=3/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.961179; ---wkkCGATAsTATCGATAswatCgm ; cor=; Ncor= a 0 0 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 2 5 9 c 0 0 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 18 2 7 g 0 0 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 2 16 5 t 0 0 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12 4 3 5
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; dyads_m1 versus oligos_6nt_mkv2_m4; m=4/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.956768; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 1 7 12 c 0 0 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 18 4 6 g 0 0 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 3 16 4 t 0 0 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15 8 3 8
dyads_m3_shift3 (dyads_m3)				; dyads_m1 versus dyads_m3; m=5/15; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.955336; ---wkyCGATAsTATCGATaswwtygw ; cor=; Ncor= a 0 0 0 11 4 5 0 3 26 3 27 0 1 28 1 0 0 25 2 20 4 9 15 5 2 7 13 c 0 0 0 7 5 8 28 0 3 0 1 12 0 0 2 31 0 2 5 2 10 6 1 5 18 4 6 g 0 0 0 4 13 5 1 28 0 0 0 19 0 2 0 0 31 2 1 4 15 2 7 6 3 16 4 t 0 0 0 9 9 13 2 0 2 28 3 0 30 1 28 0 0 2 23 5 2 14 8 15 8 4 8
oligos_7nt_mkv2_m1_rc_shift4 (oligos_7nt_mkv2_m1_rc)				; dyads_m1 versus oligos_7nt_mkv2_m1_rc; m=6/15; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.899073; ----ktCGaTACTATCGATAgTatCGa ; cor=; Ncor= a 0 0 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 2 4 17 c 0 0 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 26 6 6 g 0 0 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 3 25 4 t 0 0 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21 4 0 8
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; dyads_m1 versus oligos_6nt_mkv2_m1; m=7/15; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.896607; ----ktCGatACTATCGATAGTatCGa ; cor=; Ncor= a 0 0 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 4 5 22 c 0 0 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 34 8 10 g 0 0 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 4 36 9 t 0 0 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32 8 1 9
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; dyads_m1 versus oligos_7nt_mkv2_m4; m=8/15; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.781949; --yhryCGATAsTATCGAtaghww--- ; cor=; Ncor= a 0 0 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 0 0 0 c 0 0 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 0 0 0 g 0 0 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 0 0 0 t 0 0 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14 0 0 0
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)				; dyads_m1 versus oligos_6nt_mkv2_m2_rc; m=9/15; ncol2=20; w=0; offset=0; strand=R; shift=3; score=0.771777; ---yrtCGATAsTATCGatrkhd---- ; cor=; Ncor= a 0 0 0 15 22 6 1 3 58 2 60 3 2 60 1 2 1 40 10 19 11 17 18 0 0 0 0 c 0 0 0 18 12 10 59 0 1 1 0 35 1 3 1 60 0 7 12 9 10 18 6 0 0 0 0 g 0 0 0 9 16 13 1 59 3 2 3 25 0 1 0 0 63 11 10 22 24 10 18 0 0 0 0 t 0 0 0 22 14 35 3 2 2 59 1 1 61 0 62 2 0 6 32 14 19 19 22 0 0 0 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; dyads_m1 versus dyads_m2_rc; m=10/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.718107; hdmyatCGATAsTATCGatrkwkb--- ; cor=; Ncor= a 17 15 14 11 22 5 1 2 49 1 50 2 2 49 1 2 1 33 6 18 9 14 12 9 0 0 0 c 17 10 20 20 8 5 48 0 1 0 0 31 1 2 1 48 0 7 11 6 9 9 5 15 0 0 0 g 5 13 8 7 12 12 1 47 0 1 1 18 0 0 0 0 51 8 9 21 19 9 16 14 0 0 0 t 13 14 10 14 10 30 2 3 2 50 1 1 49 1 50 2 0 4 26 7 15 20 19 14 0 0 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; dyads_m1 versus oligos_7nt_mkv2_m2_rc; m=11/15; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.681951; mwmyatCGATAsTATCGatrkwks--- ; cor=; Ncor= a 16 14 12 5 22 4 0 0 41 2 42 1 0 42 1 2 1 25 9 13 10 13 9 9 0 0 0 c 12 8 16 20 8 5 42 0 0 0 0 16 1 1 0 40 0 9 10 6 6 9 3 13 0 0 0 g 5 8 7 5 8 5 0 40 1 2 0 25 0 0 1 0 41 5 6 18 16 7 16 11 0 0 0 t 10 13 8 13 5 29 1 3 1 39 1 1 42 0 41 1 1 4 18 6 11 14 15 10 0 0 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; dyads_m1 versus positions_7nt_m1; m=12/15; ncol2=16; w=0; offset=5; strand=D; shift=8; score=0.637309; --------awacTATCGATAgtwt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 0 0 0 c 0 0 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 0 0 0 g 0 0 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 0 0 0 t 0 0 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35 0 0 0
positions_6nt_m1_rc_shift9 (positions_6nt_m1_rc)				; dyads_m1 versus positions_6nt_m1_rc; m=13/15; ncol2=14; w=0; offset=6; strand=R; shift=9; score=0.547498; ---------wrcTATCGATAgtw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 0 0 0 0 c 0 0 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 0 0 0 0 g 0 0 0 0 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34 0 0 0 0
positions_7nt_m2_shift8 (positions_7nt_m2)				; dyads_m1 versus positions_7nt_m2; m=14/15; ncol2=14; w=0; offset=5; strand=D; shift=8; score=0.544202; --------awacTATCGATrgt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 38 68 15 4 103 0 0 0 93 6 37 19 25 0 0 0 0 0 c 0 0 0 0 0 0 0 0 22 15 11 69 9 3 0 109 0 6 8 5 25 24 0 0 0 0 0 g 0 0 0 0 0 0 0 0 19 16 18 21 1 2 4 0 110 7 4 56 42 18 0 0 0 0 0 t 0 0 0 0 0 0 0 0 27 41 13 5 96 2 106 1 0 4 92 12 24 43 0 0 0 0 0
positions_6nt_m2_shift9 (positions_6nt_m2)				; dyads_m1 versus positions_6nt_m2; m=15/15; ncol2=14; w=0; offset=6; strand=D; shift=9; score=0.538402; ---------waCTATCGATAstw---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 0 0 0 0 c 0 0 0 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift6 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=16; shift=6; ncol=22; ------awacTATCGATAgtwt ; Alignment reference a 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 c 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 g 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 t 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35
positions_7nt_m1_shift6 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/15; ncol2=16; w=0; offset=0; strand=D; shift=6; score= 1; ------awacTATCGATAgtwt ; cor=; Ncor= a 0 0 0 0 0 0 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 c 0 0 0 0 0 0 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 g 0 0 0 0 0 0 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 t 0 0 0 0 0 0 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35
positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)				; positions_7nt_m1 versus positions_6nt_m1_rc; m=2/15; ncol2=14; w=0; offset=1; strand=R; shift=7; score=0.866118; -------wrcTATCGATAgtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 34 39 7 11 88 2 0 0 92 2 69 8 19 33 0 c 0 0 0 0 0 0 0 13 14 65 15 3 1 97 0 2 4 2 17 24 17 0 g 0 0 0 0 0 0 0 16 25 17 2 4 2 0 97 1 3 15 65 14 13 0 t 0 0 0 0 0 0 0 34 19 8 69 2 92 0 0 2 88 11 7 40 34 0
positions_6nt_m2_shift7 (positions_6nt_m2)				; positions_7nt_m1 versus positions_6nt_m2; m=3/15; ncol2=14; w=0; offset=1; strand=D; shift=7; score=0.849716; -------waCTATCGATAstw- ; cor=; Ncor= a 0 0 0 0 0 0 0 37 37 3 12 83 2 3 1 85 2 73 8 21 32 0 c 0 0 0 0 0 0 0 14 14 67 10 3 2 90 0 2 5 2 47 16 16 0 g 0 0 0 0 0 0 0 14 22 17 3 5 2 0 91 4 0 12 31 17 13 0 t 0 0 0 0 0 0 0 28 20 6 68 2 87 0 1 2 86 6 7 39 32 0
positions_7nt_m2_rc_shift8 (positions_7nt_m2_rc)				; positions_7nt_m1 versus positions_7nt_m2_rc; m=4/15; ncol2=14; w=0; offset=2; strand=R; shift=8; score=0.831139; --------acyATCGATAgtwt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 43 24 12 92 4 0 1 106 2 96 5 13 41 27 c 0 0 0 0 0 0 0 0 18 42 56 4 7 110 0 4 2 1 21 18 16 19 g 0 0 0 0 0 0 0 0 24 25 5 8 6 0 109 0 3 9 69 11 15 22 t 0 0 0 0 0 0 0 0 25 19 37 6 93 0 0 0 103 4 15 68 38 42
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; positions_7nt_m1 versus oligos_6nt_mkv2_m1; m=5/15; ncol2=24; w=-4; offset=-4; strand=D; shift=2; score=0.638604; --ktCGatACTATCGATAGTat ; cor=; Ncor= a 0 0 10 9 1 8 32 10 34 4 6 40 1 0 1 44 2 37 1 7 33 4 c 0 0 10 9 36 4 9 5 3 34 5 3 4 48 1 1 5 2 11 6 2 5 g 0 0 15 10 8 34 5 2 6 11 2 5 1 1 48 4 3 5 34 3 5 9 t 0 0 15 22 5 4 4 33 7 1 37 2 44 1 0 1 40 6 4 34 10 32
dyads_m1_shift1 (dyads_m1)				; positions_7nt_m1 versus dyads_m1; m=6/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.637309; -mvkCGaTACTATCGATAgtat ; cor=; Ncor= a 0 13 12 7 1 2 30 6 36 2 2 39 1 0 1 39 1 32 4 10 23 7 c 0 13 12 6 37 3 8 4 1 35 2 2 2 46 0 1 6 3 9 5 2 8 g 0 9 12 14 5 37 4 2 4 9 1 4 1 0 45 4 4 8 26 4 10 7 t 0 11 10 19 3 4 4 34 5 0 41 1 42 0 0 2 35 3 7 27 11 24
oligos_7nt_mkv2_m1_rc_shift2 (oligos_7nt_mkv2_m1_rc)				; positions_7nt_m1 versus oligos_7nt_mkv2_m1_rc; m=7/15; ncol2=24; w=-4; offset=-4; strand=R; shift=2; score=0.635788; --ktCGaTACTATCGATAgTat ; cor=; Ncor= a 0 0 7 7 0 3 21 5 27 2 2 27 1 0 1 31 0 28 1 6 23 4 c 0 0 6 5 26 3 6 5 1 24 3 3 2 34 0 1 5 1 8 2 1 4 g 0 0 10 6 6 27 4 1 2 8 1 5 1 0 34 2 3 4 23 1 5 6 t 0 0 12 17 3 2 4 24 5 1 29 0 31 1 0 1 27 2 3 26 6 21
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; positions_7nt_m1 versus oligos_7nt_mkv2_m3; m=8/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.634156; -mdkCGaTASTATCGATAstat ; cor=; Ncor= a 0 11 8 5 0 2 21 4 27 1 2 27 1 0 1 28 1 23 0 6 19 3 c 0 9 7 4 26 1 6 3 1 23 1 2 2 32 0 1 4 2 8 3 2 4 g 0 5 9 8 4 28 2 1 1 8 0 3 1 0 31 2 1 4 21 2 4 7 t 0 7 8 15 2 1 3 24 3 0 29 0 28 0 0 1 26 3 3 21 7 18
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; positions_7nt_m1 versus oligos_7nt_mkv2_m4; m=9/15; ncol2=22; w=-6; offset=-6; strand=D; shift=0; score=0.633015; yhryCGATAsTATCGAtaghww ; cor=; Ncor= a 11 13 15 5 1 1 42 4 45 1 2 45 1 0 0 38 7 27 8 14 16 13 c 17 15 6 13 46 0 5 0 3 19 1 1 2 51 0 5 11 6 8 16 6 12 g 10 7 20 9 2 50 0 1 1 30 0 2 0 0 51 5 2 7 31 8 11 12 t 13 16 10 24 2 0 4 46 2 1 48 3 48 0 0 3 31 11 4 13 18 14
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; positions_7nt_m1 versus oligos_6nt_mkv2_m3; m=10/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.605621; -wkkCGATAsTATCGATAswat ; cor=; Ncor= a 0 8 3 4 0 2 21 3 22 1 2 23 1 0 1 22 1 19 2 8 16 4 c 0 6 6 2 23 0 3 0 1 11 1 1 2 26 0 1 4 1 10 2 0 6 g 0 4 9 7 1 24 0 0 0 14 0 2 0 0 25 2 0 4 11 2 4 4 t 0 8 8 13 2 0 2 23 3 0 23 0 23 0 0 1 21 2 3 14 6 12
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; positions_7nt_m1 versus oligos_6nt_mkv2_m4; m=11/15; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.600008; -wkyCGATAsTATCGATaswwt ; cor=; Ncor= a 0 11 4 5 0 3 25 3 26 0 1 27 1 0 0 25 2 20 3 9 14 4 c 0 6 5 8 27 0 3 0 1 12 0 0 2 30 0 1 5 2 10 5 1 5 g 0 4 13 4 1 27 0 0 0 18 0 2 0 0 30 2 1 3 15 2 7 6 t 0 9 8 13 2 0 2 27 3 0 29 1 27 0 0 2 22 5 2 14 8 15
dyads_m3_rc_shift3 (dyads_m3_rc)				; positions_7nt_m1 versus dyads_m3_rc; m=12/15; ncol2=24; w=-3; offset=-3; strand=R; shift=3; score=0.596937; ---wcrawwstATCGATAsTAT ; cor=; Ncor= a 0 0 0 8 4 8 15 8 14 2 5 23 2 0 0 28 1 30 0 3 28 2 c 0 0 0 4 16 3 6 7 2 15 4 1 2 31 0 0 2 0 19 0 0 0 g 0 0 0 6 4 18 5 1 6 10 2 5 2 0 31 2 0 0 12 1 0 3 t 0 0 0 13 7 2 5 15 9 4 20 2 25 0 0 1 28 1 0 27 3 26
oligos_6nt_mkv2_m2_shift7 (oligos_6nt_mkv2_m2)				; positions_7nt_m1 versus oligos_6nt_mkv2_m2; m=13/15; ncol2=20; w=0; offset=1; strand=D; shift=7; score=0.589551; -------hdmyatCGATAsTAT ; cor=; Ncor= a 0 0 0 0 0 0 0 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 c 0 0 0 0 0 0 0 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 g 0 0 0 0 0 0 0 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 t 0 0 0 0 0 0 0 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58
dyads_m2_shift6 (dyads_m2)				; positions_7nt_m1 versus dyads_m2; m=14/15; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.549637; ------vmwmyatCGATAsTAT ; cor=; Ncor= a 0 0 0 0 0 0 14 19 20 15 7 26 4 0 2 50 1 49 1 1 50 2 c 0 0 0 0 0 0 14 16 9 19 21 9 8 51 0 0 0 0 18 1 1 0 g 0 0 0 0 0 0 15 5 9 9 6 11 7 0 48 1 2 1 31 0 0 1 t 0 0 0 0 0 0 9 12 14 9 18 6 33 1 2 1 49 2 2 50 1 49
oligos_7nt_mkv2_m2_shift6 (oligos_7nt_mkv2_m2)				; positions_7nt_m1 versus oligos_7nt_mkv2_m2; m=15/15; ncol2=24; w=0; offset=0; strand=D; shift=6; score=0.522256; ------smwmyatCGATAsTAT ; cor=; Ncor= a 0 0 0 0 0 0 10 15 14 11 6 18 4 1 1 41 0 42 1 1 39 1 c 0 0 0 0 0 0 11 16 7 16 18 6 5 41 0 1 0 0 25 0 2 1 g 0 0 0 0 0 0 13 3 9 6 6 10 9 0 40 0 1 1 16 0 0 0 t 0 0 0 0 0 0 9 9 13 10 13 9 25 1 2 1 42 0 1 42 2 41