One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/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/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; mwwGCTKACTAAwyr ; Alignment reference a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; mwwGCTKACTAAwyr ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3_rc; m=2/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.932358; mtwGCTTACTaAwyr ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.884796; aaTGmTGACTAAkCr ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=4/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.830504; rhTGMTGASTmAkCa ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=5/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.769996; rhtGmTGASTmAkCa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=6/9; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.742899; amTGmTGACTmAKCa ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=7/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.730899; -atGmTGACTmAGCr ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=8/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.702419; -atGmTGACTMAGCr ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=9/9; ncol2=12; w=0; offset=5; strand=D; shift=5; score=0.414149; -----wwwCTAAATA ; cor=; Ncor= a 0 0 0 0 0 17 24 26 3 6 57 54 54 0 47 c 0 0 0 0 0 6 9 11 53 0 0 0 1 4 1 g 0 0 0 0 0 5 5 3 0 1 0 1 1 0 8 t 0 0 0 0 0 29 19 17 1 50 0 2 1 53 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=16; shift=1; ncol=17; -tyrwTtAGTAAGCwak ; Alignment reference a 0 16 10 21 34 1 1 62 0 0 50 64 2 1 30 32 12 c 0 8 18 2 12 1 6 3 9 0 15 0 1 62 3 5 8 g 0 12 8 34 1 2 16 0 56 1 0 0 55 0 10 12 24 t 0 29 29 8 18 61 42 0 0 64 0 1 7 2 22 16 21

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -tyrwTtAGTAAGCwak ; cor=; Ncor= a 0 16 10 21 34 1 1 62 0 0 50 64 2 1 30 32 12 c 0 8 18 2 12 1 6 3 9 0 15 0 1 62 3 5 8 g 0 12 8 34 1 2 16 0 56 1 0 0 55 0 10 12 24 t 0 29 29 8 18 61 42 0 0 64 0 1 7 2 22 16 21

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=2/8; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.932358; --yrwTTAGTMAGCwwk ; cor=; Ncor= a 0 0 9 18 26 0 0 50 0 0 37 50 1 1 29 24 9 c 0 0 15 2 10 1 3 1 4 0 14 0 1 49 1 2 6 g 0 0 5 23 0 0 10 0 47 1 0 0 42 0 3 10 18 t 0 0 22 8 15 50 38 0 0 50 0 1 7 1 18 15 18

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=1; score=0.823857; -ttGmTkASTCAkCady ; cor=; Ncor= a 0 14 10 3 23 1 0 71 0 0 7 73 0 0 45 19 12 c 0 16 18 0 49 0 5 1 22 0 66 0 1 71 9 10 20 g 0 14 15 64 1 0 44 0 51 1 0 0 47 0 11 21 16 t 0 29 30 6 0 72 24 1 0 72 0 0 25 2 8 23 25

oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=4/8; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.813308; --yGmTTAGTCAkCAtt ; cor=; Ncor= a 0 0 9 6 35 0 0 52 1 1 6 54 0 1 42 12 8 c 0 0 21 2 18 0 3 0 8 1 48 0 0 46 1 3 12 g 0 0 7 37 1 0 13 1 45 0 0 0 36 1 6 13 10 t 0 0 17 9 0 54 38 1 0 52 0 0 18 6 5 26 24

oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=5/8; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.783139; cytGMTkAGTCAkCAkt ; cor=; Ncor= a 17 11 6 2 18 0 0 68 0 0 10 70 2 0 49 14 14 c 25 21 17 0 52 0 2 1 17 0 59 0 0 64 4 9 16 g 12 11 9 62 0 0 28 0 52 0 1 0 41 1 7 19 9 t 16 27 38 6 0 70 40 1 1 70 0 0 27 5 10 28 31

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=6/8; ncol2=15; w=0; offset=1; strand=D; shift=2; score=0.77851; --tGmTkASTCAKCAdy ; cor=; Ncor= a 0 0 10 3 22 1 0 67 1 0 7 67 0 0 47 18 11 c 0 0 16 2 44 1 5 1 18 0 61 0 0 66 9 8 17 g 0 0 15 56 1 0 42 0 49 2 0 0 48 1 7 17 16 t 0 0 27 7 1 66 21 0 0 66 0 1 20 1 5 25 24

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=7/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.763914; -atGmTGACTMAGCra- ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 0 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 0 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 0 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9 0

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=8/8; ncol2=14; w=0; offset=1; strand=R; shift=2; score=0.682749; --yGCTkAGTCAkCat- ; cor=; Ncor= a 0 0 9 2 13 0 0 63 0 1 3 65 1 0 33 13 0 c 0 0 21 0 50 0 2 2 14 0 62 0 3 60 11 14 0 g 0 0 10 56 2 1 40 0 51 0 1 1 26 1 9 15 0 t 0 0 26 8 1 65 24 1 1 65 0 0 36 5 13 24 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=5; ncol=17; -----wwwCTAAATAAy ; Alignment reference a 0 0 0 0 0 17 24 26 3 6 57 54 54 0 47 39 5 c 0 0 0 0 0 6 9 11 53 0 0 0 1 4 1 11 22 g 0 0 0 0 0 5 5 3 0 1 0 1 1 0 8 3 7 t 0 0 0 0 0 29 19 17 1 50 0 2 1 53 1 4 23

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----wwwCTAAATAAy ; cor=; Ncor= a 0 0 0 0 0 17 24 26 3 6 57 54 54 0 47 39 5 c 0 0 0 0 0 6 9 11 53 0 0 0 1 4 1 11 22 g 0 0 0 0 0 5 5 3 0 1 0 1 1 0 8 3 7 t 0 0 0 0 0 29 19 17 1 50 0 2 1 53 1 4 23

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=2/3; ncol2=15; w=-5; offset=-5; strand=D; shift=0; score=0.414149; mwwGCTKACTAAwyr-- ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 0 0 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 0 0 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 0 0 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9 0 0

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=11; w=-3; offset=-3; strand=D; shift=2; score=0.401616; --rmCTATCTAwa---- ; cor=; Ncor= a 0 0 24 17 4 1 57 1 2 0 58 23 40 0 0 0 0 c 0 0 7 27 55 7 4 4 55 1 0 9 7 0 0 0 0 g 0 0 20 4 0 0 1 0 4 2 0 11 10 0 0 0 0 t 0 0 11 14 3 54 0 57 1 59 4 19 5 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -atGmTGACTmAGCr ; Alignment reference a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -atGmTGACTmAGCr ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1_rc; m=2/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.909839; rhTGMTGASTmAkCa ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=3/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.906898; -atGmTGACTMAGCr ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=4/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.860067; rhtGmTGASTmAkCa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.856824; aaTGmTGACTAAkCr ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=6/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.804897; amTGmTGACTmAKCa ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=7/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.730899; mwwGCTKACTAAwyr ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=8/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.682749; mtwGCTTACTaAwyr ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; aaTGmTGACTAAkCr ; Alignment reference a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; aaTGmTGACTAAkCr ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.944094; rhTGMTGASTmAkCa ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.884796; mwwGCTKACTAAwyr ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=4/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.880313; rhtGmTGASTmAkCa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=5/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.856824; -atGmTGACTmAGCr ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=6/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.841817; amTGmTGACTmAKCa ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=7/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.824185; -atGmTGACTMAGCr ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=8/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.813308; mtwGCTTACTaAwyr ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 9 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=15; shift=2; ncol=17; --tGmTkASTCAKCAdy ; Alignment reference a 0 0 10 3 22 1 0 67 1 0 7 67 0 0 47 18 11 c 0 0 16 2 44 1 5 1 18 0 61 0 0 66 9 8 17 g 0 0 15 56 1 0 42 0 49 2 0 0 48 1 7 17 16 t 0 0 27 7 1 66 21 0 0 66 0 1 20 1 5 25 24

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score= 1; --tGmTkASTCAKCAdy ; cor=; Ncor= a 0 0 10 3 22 1 0 67 1 0 7 67 0 0 47 18 11 c 0 0 16 2 44 1 5 1 18 0 61 0 0 66 9 8 17 g 0 0 15 56 1 0 42 0 49 2 0 0 48 1 7 17 16 t 0 0 27 7 1 66 21 0 0 66 0 1 20 1 5 25 24

oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.944094; --yGmTTAGTCAkCAtt ; cor=; Ncor= a 0 0 9 6 35 0 0 52 1 1 6 54 0 1 42 12 8 c 0 0 21 2 18 0 3 0 8 1 48 0 0 46 1 3 12 g 0 0 7 37 1 0 13 1 45 0 0 0 36 1 6 13 10 t 0 0 17 9 0 54 38 1 0 52 0 0 18 6 5 26 24

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=3/8; ncol2=16; w=-1; offset=-1; strand=R; shift=1; score=0.935054; -ttGmTkASTCAkCady ; cor=; Ncor= a 0 14 10 3 23 1 0 71 0 0 7 73 0 0 45 19 12 c 0 16 18 0 49 0 5 1 22 0 66 0 1 71 9 10 20 g 0 14 15 64 1 0 44 0 51 1 0 0 47 0 11 21 16 t 0 29 30 6 0 72 24 1 0 72 0 0 25 2 8 23 25

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=4/8; ncol2=14; w=0; offset=0; strand=R; shift=2; score=0.909839; --yGCTkAGTCAkCat- ; cor=; Ncor= a 0 0 9 2 13 0 0 63 0 1 3 65 1 0 33 13 0 c 0 0 21 0 50 0 2 2 14 0 62 0 3 60 11 14 0 g 0 0 10 56 2 1 40 0 51 0 1 1 26 1 9 15 0 t 0 0 26 8 1 65 24 1 1 65 0 0 36 5 13 24 0

oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=5/8; ncol2=17; w=-2; offset=-2; strand=R; shift=0; score=0.864645; cytGMTkAGTCAkCAkt ; cor=; Ncor= a 17 11 6 2 18 0 0 68 0 0 10 70 2 0 49 14 14 c 25 21 17 0 52 0 2 1 17 0 59 0 0 64 4 9 16 g 12 11 9 62 0 0 28 0 52 0 1 0 41 1 7 19 9 t 16 27 38 6 0 70 40 1 1 70 0 0 27 5 10 28 31

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=6/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.830504; --yrwTTAGTMAGCwwk ; cor=; Ncor= a 0 0 9 18 26 0 0 50 0 0 37 50 1 1 29 24 9 c 0 0 15 2 10 1 3 1 4 0 14 0 1 49 1 2 6 g 0 0 5 23 0 0 10 0 47 1 0 0 42 0 3 10 18 t 0 0 22 8 15 50 38 0 0 50 0 1 7 1 18 15 18

oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1_rc; m=7/8; ncol2=15; w=-1; offset=-1; strand=R; shift=1; score=0.820629; -tyGCTKAGTCAkCat- ; cor=; Ncor= a 0 9 7 3 15 0 0 60 0 0 5 60 2 0 39 11 0 c 0 12 22 0 46 0 0 0 12 0 56 0 0 49 4 9 0 g 0 8 8 53 0 0 17 0 49 0 0 0 18 0 6 13 0 t 0 32 24 5 0 61 44 1 0 61 0 1 41 12 12 28 0

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=8/8; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.77851; -tyrwTtAGTAAGCwak ; cor=; Ncor= a 0 16 10 21 34 1 1 62 0 0 50 64 2 1 30 32 12 c 0 8 18 2 12 1 6 3 9 0 15 0 1 62 3 5 8 g 0 12 8 34 1 2 16 0 56 1 0 0 55 0 10 12 24 t 0 29 29 8 18 61 42 0 0 64 0 1 7 2 22 16 21

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; rmCTATCTAwa ; Alignment reference a 24 17 4 1 57 1 2 0 58 23 40 c 7 27 55 7 4 4 55 1 0 9 7 g 20 4 0 0 1 0 4 2 0 11 10 t 11 14 3 54 0 57 1 59 4 19 5

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; rmCTATCTAwa ; cor=; Ncor= a 24 17 4 1 57 1 2 0 58 23 40 c 7 27 55 7 4 4 55 1 0 9 7 g 20 4 0 0 1 0 4 2 0 11 10 t 11 14 3 54 0 57 1 59 4 19 5

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m5; m=2/2; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.401616; ---wwwCTAAA ; cor=; Ncor= a 0 0 0 17 24 26 3 6 57 54 54 c 0 0 0 6 9 11 53 0 0 0 1 g 0 0 0 5 5 3 0 1 0 1 1 t 0 0 0 29 19 17 1 50 0 2 1

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; amTGmTGACTmAKCarg ; Alignment reference a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 27 16 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 11 12 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 21 25 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6 11 17

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; amTGmTGACTmAKCarg ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 27 16 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 11 12 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 21 25 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6 11 17

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=2/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.924785; rhtGmTGASTmAkCaa- ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 29 0 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 14 0 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 16 0 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10 14 0

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=3/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.864645; rhTGMTGASTmAkCa-- ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 0 0 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 0 0 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 0 0 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10 0 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=4/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.859171; -atGmTGACTMAGCra- ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 0 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 0 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 0 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9 0

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=5/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.841817; aaTGmTGACTAAkCr-- ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 0 0 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 0 0 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 0 0 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9 0 0

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=6/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.804897; -atGmTGACTmAGCr-- ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 0 0 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 0 0 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 0 0 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9 0 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.783139; mtwGCTTACTaAwyra- ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 29 0 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 12 0 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 8 0 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10 16 0

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=8/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.742899; mwwGCTKACTAAwyr-- ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 0 0 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 0 0 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 0 0 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -atGmTGACTMAGCra ; Alignment reference a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -atGmTGACTMAGCra ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.906898; -atGmTGACTmAGCr- ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 0 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 0 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 0 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.886811; rhtGmTGASTmAkCaa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 29 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 14 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 16 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10 14

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=4/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.859171; amTGmTGACTmAKCar ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 27 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 11 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 21 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6 11

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.824185; aaTGmTGACTAAkCr- ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 0 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 0 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 0 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9 0

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1_rc; m=6/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.820629; rhTGMTGASTmAkCa- ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 0 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 0 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 0 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10 0

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=7/8; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.763914; -tyrwTtAGTAAGCwa ; cor=; Ncor= a 0 16 10 21 34 1 1 62 0 0 50 64 2 1 30 32 c 0 8 18 2 12 1 6 3 9 0 15 0 1 62 3 5 g 0 12 8 34 1 2 16 0 56 1 0 0 55 0 10 12 t 0 29 29 8 18 61 42 0 0 64 0 1 7 2 22 16

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=8/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.702419; mwwGCTKACTAAwyr- ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 0 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 0 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 0 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; rhtGmTGASTmAkCaa ; Alignment reference a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 29 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 14 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 16 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10 14

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; rhtGmTGASTmAkCaa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 29 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 14 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 16 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10 14

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.935054; rhTGMTGASTmAkCa- ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 0 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 0 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 0 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10 0

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=3/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.924785; amTGmTGACTmAKCar ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 27 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 11 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 21 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6 11

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=4/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.886811; -atGmTGACTMAGCra ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=5/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.880313; aaTGmTGACTAAkCr- ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 0 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 0 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 0 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9 0

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=6/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.860067; -atGmTGACTmAGCr- ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 0 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 0 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 0 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.823857; mtwGCTTACTaAwyra ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 29 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 12 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 8 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10 16

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=8/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.769996; mwwGCTKACTAAwyr- ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 0 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 0 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 0 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; mwwGCTKACTAAwyr ; Alignment reference a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; mwwGCTKACTAAwyr ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3_rc; m=2/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.932358; mtwGCTTACTaAwyr ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.884796; aaTGmTGACTAAkCr ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=4/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.830504; rhTGMTGASTmAkCa ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=5/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.769996; rhtGmTGASTmAkCa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=6/9; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.742899; amTGmTGACTmAKCa ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=7/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.730899; -atGmTGACTmAGCr ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=8/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.702419; -atGmTGACTMAGCr ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=9/9; ncol2=12; w=0; offset=5; strand=D; shift=5; score=0.414149; -----wwwCTAAATA ; cor=; Ncor= a 0 0 0 0 0 17 24 26 3 6 57 54 54 0 47 c 0 0 0 0 0 6 9 11 53 0 0 0 1 4 1 g 0 0 0 0 0 5 5 3 0 1 0 1 1 0 8 t 0 0 0 0 0 29 19 17 1 50 0 2 1 53 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=16; shift=1; ncol=17; -tyrwTtAGTAAGCwak ; Alignment reference a 0 16 10 21 34 1 1 62 0 0 50 64 2 1 30 32 12 c 0 8 18 2 12 1 6 3 9 0 15 0 1 62 3 5 8 g 0 12 8 34 1 2 16 0 56 1 0 0 55 0 10 12 24 t 0 29 29 8 18 61 42 0 0 64 0 1 7 2 22 16 21
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -tyrwTtAGTAAGCwak ; cor=; Ncor= a 0 16 10 21 34 1 1 62 0 0 50 64 2 1 30 32 12 c 0 8 18 2 12 1 6 3 9 0 15 0 1 62 3 5 8 g 0 12 8 34 1 2 16 0 56 1 0 0 55 0 10 12 24 t 0 29 29 8 18 61 42 0 0 64 0 1 7 2 22 16 21
oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=2/8; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.932358; --yrwTTAGTMAGCwwk ; cor=; Ncor= a 0 0 9 18 26 0 0 50 0 0 37 50 1 1 29 24 9 c 0 0 15 2 10 1 3 1 4 0 14 0 1 49 1 2 6 g 0 0 5 23 0 0 10 0 47 1 0 0 42 0 3 10 18 t 0 0 22 8 15 50 38 0 0 50 0 1 7 1 18 15 18
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=1; score=0.823857; -ttGmTkASTCAkCady ; cor=; Ncor= a 0 14 10 3 23 1 0 71 0 0 7 73 0 0 45 19 12 c 0 16 18 0 49 0 5 1 22 0 66 0 1 71 9 10 20 g 0 14 15 64 1 0 44 0 51 1 0 0 47 0 11 21 16 t 0 29 30 6 0 72 24 1 0 72 0 0 25 2 8 23 25
oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=4/8; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.813308; --yGmTTAGTCAkCAtt ; cor=; Ncor= a 0 0 9 6 35 0 0 52 1 1 6 54 0 1 42 12 8 c 0 0 21 2 18 0 3 0 8 1 48 0 0 46 1 3 12 g 0 0 7 37 1 0 13 1 45 0 0 0 36 1 6 13 10 t 0 0 17 9 0 54 38 1 0 52 0 0 18 6 5 26 24
oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=5/8; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.783139; cytGMTkAGTCAkCAkt ; cor=; Ncor= a 17 11 6 2 18 0 0 68 0 0 10 70 2 0 49 14 14 c 25 21 17 0 52 0 2 1 17 0 59 0 0 64 4 9 16 g 12 11 9 62 0 0 28 0 52 0 1 0 41 1 7 19 9 t 16 27 38 6 0 70 40 1 1 70 0 0 27 5 10 28 31
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=6/8; ncol2=15; w=0; offset=1; strand=D; shift=2; score=0.77851; --tGmTkASTCAKCAdy ; cor=; Ncor= a 0 0 10 3 22 1 0 67 1 0 7 67 0 0 47 18 11 c 0 0 16 2 44 1 5 1 18 0 61 0 0 66 9 8 17 g 0 0 15 56 1 0 42 0 49 2 0 0 48 1 7 17 16 t 0 0 27 7 1 66 21 0 0 66 0 1 20 1 5 25 24
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=7/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.763914; -atGmTGACTMAGCra- ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 0 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 0 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 0 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9 0
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=8/8; ncol2=14; w=0; offset=1; strand=R; shift=2; score=0.682749; --yGCTkAGTCAkCat- ; cor=; Ncor= a 0 0 9 2 13 0 0 63 0 1 3 65 1 0 33 13 0 c 0 0 21 0 50 0 2 2 14 0 62 0 3 60 11 14 0 g 0 0 10 56 2 1 40 0 51 0 1 1 26 1 9 15 0 t 0 0 26 8 1 65 24 1 1 65 0 0 36 5 13 24 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=5; ncol=17; -----wwwCTAAATAAy ; Alignment reference a 0 0 0 0 0 17 24 26 3 6 57 54 54 0 47 39 5 c 0 0 0 0 0 6 9 11 53 0 0 0 1 4 1 11 22 g 0 0 0 0 0 5 5 3 0 1 0 1 1 0 8 3 7 t 0 0 0 0 0 29 19 17 1 50 0 2 1 53 1 4 23
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----wwwCTAAATAAy ; cor=; Ncor= a 0 0 0 0 0 17 24 26 3 6 57 54 54 0 47 39 5 c 0 0 0 0 0 6 9 11 53 0 0 0 1 4 1 11 22 g 0 0 0 0 0 5 5 3 0 1 0 1 1 0 8 3 7 t 0 0 0 0 0 29 19 17 1 50 0 2 1 53 1 4 23
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=2/3; ncol2=15; w=-5; offset=-5; strand=D; shift=0; score=0.414149; mwwGCTKACTAAwyr-- ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 0 0 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 0 0 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 0 0 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9 0 0
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=11; w=-3; offset=-3; strand=D; shift=2; score=0.401616; --rmCTATCTAwa---- ; cor=; Ncor= a 0 0 24 17 4 1 57 1 2 0 58 23 40 0 0 0 0 c 0 0 7 27 55 7 4 4 55 1 0 9 7 0 0 0 0 g 0 0 20 4 0 0 1 0 4 2 0 11 10 0 0 0 0 t 0 0 11 14 3 54 0 57 1 59 4 19 5 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -atGmTGACTmAGCr ; Alignment reference a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -atGmTGACTmAGCr ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1_rc; m=2/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.909839; rhTGMTGASTmAkCa ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=3/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.906898; -atGmTGACTMAGCr ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=4/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.860067; rhtGmTGASTmAkCa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.856824; aaTGmTGACTAAkCr ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=6/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.804897; amTGmTGACTmAKCa ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=7/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.730899; mwwGCTKACTAAwyr ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=8/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.682749; mtwGCTTACTaAwyr ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; aaTGmTGACTAAkCr ; Alignment reference a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; aaTGmTGACTAAkCr ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.944094; rhTGMTGASTmAkCa ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.884796; mwwGCTKACTAAwyr ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=4/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.880313; rhtGmTGASTmAkCa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=5/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.856824; -atGmTGACTmAGCr ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=6/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.841817; amTGmTGACTmAKCa ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=7/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.824185; -atGmTGACTMAGCr ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=8/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.813308; mtwGCTTACTaAwyr ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10

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=15; shift=2; ncol=17; --tGmTkASTCAKCAdy ; Alignment reference a 0 0 10 3 22 1 0 67 1 0 7 67 0 0 47 18 11 c 0 0 16 2 44 1 5 1 18 0 61 0 0 66 9 8 17 g 0 0 15 56 1 0 42 0 49 2 0 0 48 1 7 17 16 t 0 0 27 7 1 66 21 0 0 66 0 1 20 1 5 25 24
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score= 1; --tGmTkASTCAKCAdy ; cor=; Ncor= a 0 0 10 3 22 1 0 67 1 0 7 67 0 0 47 18 11 c 0 0 16 2 44 1 5 1 18 0 61 0 0 66 9 8 17 g 0 0 15 56 1 0 42 0 49 2 0 0 48 1 7 17 16 t 0 0 27 7 1 66 21 0 0 66 0 1 20 1 5 25 24
oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.944094; --yGmTTAGTCAkCAtt ; cor=; Ncor= a 0 0 9 6 35 0 0 52 1 1 6 54 0 1 42 12 8 c 0 0 21 2 18 0 3 0 8 1 48 0 0 46 1 3 12 g 0 0 7 37 1 0 13 1 45 0 0 0 36 1 6 13 10 t 0 0 17 9 0 54 38 1 0 52 0 0 18 6 5 26 24
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=3/8; ncol2=16; w=-1; offset=-1; strand=R; shift=1; score=0.935054; -ttGmTkASTCAkCady ; cor=; Ncor= a 0 14 10 3 23 1 0 71 0 0 7 73 0 0 45 19 12 c 0 16 18 0 49 0 5 1 22 0 66 0 1 71 9 10 20 g 0 14 15 64 1 0 44 0 51 1 0 0 47 0 11 21 16 t 0 29 30 6 0 72 24 1 0 72 0 0 25 2 8 23 25
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=4/8; ncol2=14; w=0; offset=0; strand=R; shift=2; score=0.909839; --yGCTkAGTCAkCat- ; cor=; Ncor= a 0 0 9 2 13 0 0 63 0 1 3 65 1 0 33 13 0 c 0 0 21 0 50 0 2 2 14 0 62 0 3 60 11 14 0 g 0 0 10 56 2 1 40 0 51 0 1 1 26 1 9 15 0 t 0 0 26 8 1 65 24 1 1 65 0 0 36 5 13 24 0
oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=5/8; ncol2=17; w=-2; offset=-2; strand=R; shift=0; score=0.864645; cytGMTkAGTCAkCAkt ; cor=; Ncor= a 17 11 6 2 18 0 0 68 0 0 10 70 2 0 49 14 14 c 25 21 17 0 52 0 2 1 17 0 59 0 0 64 4 9 16 g 12 11 9 62 0 0 28 0 52 0 1 0 41 1 7 19 9 t 16 27 38 6 0 70 40 1 1 70 0 0 27 5 10 28 31
oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=6/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.830504; --yrwTTAGTMAGCwwk ; cor=; Ncor= a 0 0 9 18 26 0 0 50 0 0 37 50 1 1 29 24 9 c 0 0 15 2 10 1 3 1 4 0 14 0 1 49 1 2 6 g 0 0 5 23 0 0 10 0 47 1 0 0 42 0 3 10 18 t 0 0 22 8 15 50 38 0 0 50 0 1 7 1 18 15 18
oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1_rc; m=7/8; ncol2=15; w=-1; offset=-1; strand=R; shift=1; score=0.820629; -tyGCTKAGTCAkCat- ; cor=; Ncor= a 0 9 7 3 15 0 0 60 0 0 5 60 2 0 39 11 0 c 0 12 22 0 46 0 0 0 12 0 56 0 0 49 4 9 0 g 0 8 8 53 0 0 17 0 49 0 0 0 18 0 6 13 0 t 0 32 24 5 0 61 44 1 0 61 0 1 41 12 12 28 0
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=8/8; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.77851; -tyrwTtAGTAAGCwak ; cor=; Ncor= a 0 16 10 21 34 1 1 62 0 0 50 64 2 1 30 32 12 c 0 8 18 2 12 1 6 3 9 0 15 0 1 62 3 5 8 g 0 12 8 34 1 2 16 0 56 1 0 0 55 0 10 12 24 t 0 29 29 8 18 61 42 0 0 64 0 1 7 2 22 16 21

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; amTGmTGACTmAKCarg ; Alignment reference a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 27 16 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 11 12 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 21 25 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6 11 17
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; amTGmTGACTmAKCarg ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 27 16 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 11 12 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 21 25 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6 11 17
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=2/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.924785; rhtGmTGASTmAkCaa- ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 29 0 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 14 0 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 16 0 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10 14 0
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=3/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.864645; rhTGMTGASTmAkCa-- ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 0 0 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 0 0 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 0 0 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10 0 0
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=4/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.859171; -atGmTGACTMAGCra- ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 0 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 0 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 0 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9 0
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=5/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.841817; aaTGmTGACTAAkCr-- ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 0 0 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 0 0 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 0 0 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9 0 0
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=6/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.804897; -atGmTGACTmAGCr-- ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 0 0 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 0 0 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 0 0 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9 0 0
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.783139; mtwGCTTACTaAwyra- ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 29 0 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 12 0 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 8 0 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10 16 0
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=8/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.742899; mwwGCTKACTAAwyr-- ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 0 0 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 0 0 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 0 0 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -atGmTGACTMAGCra ; Alignment reference a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -atGmTGACTMAGCra ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.906898; -atGmTGACTmAGCr- ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 0 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 0 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 0 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9 0
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.886811; rhtGmTGASTmAkCaa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 29 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 14 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 16 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10 14
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=4/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.859171; amTGmTGACTmAKCar ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 27 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 11 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 21 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6 11
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.824185; aaTGmTGACTAAkCr- ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 0 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 0 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 0 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9 0
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1_rc; m=6/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.820629; rhTGMTGASTmAkCa- ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 0 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 0 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 0 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10 0
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=7/8; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.763914; -tyrwTtAGTAAGCwa ; cor=; Ncor= a 0 16 10 21 34 1 1 62 0 0 50 64 2 1 30 32 c 0 8 18 2 12 1 6 3 9 0 15 0 1 62 3 5 g 0 12 8 34 1 2 16 0 56 1 0 0 55 0 10 12 t 0 29 29 8 18 61 42 0 0 64 0 1 7 2 22 16
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=8/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.702419; mwwGCTKACTAAwyr- ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 0 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 0 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 0 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; rhtGmTGASTmAkCaa ; Alignment reference a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 29 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 14 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 16 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10 14
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; rhtGmTGASTmAkCaa ; cor=; Ncor= a 25 23 8 2 25 0 0 72 0 1 24 72 0 6 30 29 c 16 21 11 0 47 0 0 1 51 0 44 0 1 64 15 14 g 20 10 9 71 1 0 66 0 22 1 5 0 49 0 18 16 t 12 19 45 0 0 73 7 0 0 71 0 1 23 3 10 14
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.935054; rhTGMTGASTmAkCa- ; cor=; Ncor= a 24 25 5 1 20 1 0 66 0 0 21 66 1 7 27 0 c 16 17 7 1 48 0 0 2 49 0 42 0 1 56 15 0 g 17 8 9 66 0 0 61 0 18 1 5 1 44 2 16 0 t 11 18 47 0 0 67 7 0 1 67 0 1 22 3 10 0
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=3/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.924785; amTGmTGACTmAKCar ; cor=; Ncor= a 31 28 10 5 27 0 0 70 1 1 40 70 0 6 38 27 c 9 19 7 1 41 0 1 0 52 0 28 0 0 62 9 11 g 16 9 4 64 0 0 59 0 17 1 2 0 52 0 17 21 t 14 14 49 0 2 70 10 0 0 68 0 0 18 2 6 11
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=4/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.886811; -atGmTGACTMAGCra ; cor=; Ncor= a 0 28 12 12 41 1 0 61 0 1 44 61 0 5 24 32 c 0 13 6 0 18 0 0 0 49 0 17 0 0 53 8 8 g 0 9 4 49 0 0 56 0 12 0 0 0 46 0 22 12 t 0 11 39 0 2 60 5 0 0 60 0 0 15 3 7 9
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=5/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.880313; aaTGmTGACTAAkCr- ; cor=; Ncor= a 24 26 5 6 18 0 0 52 0 1 38 54 0 9 17 0 c 10 13 6 1 36 0 0 0 45 1 13 0 1 37 7 0 g 12 3 1 46 0 0 48 1 8 0 3 0 18 2 21 0 t 8 12 42 1 0 54 6 1 1 52 0 0 35 6 9 0
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=6/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.860067; -atGmTGACTmAGCr- ; cor=; Ncor= a 0 24 13 5 36 0 0 65 1 1 24 65 1 8 26 0 c 0 15 9 1 26 1 1 0 51 0 40 1 2 56 10 0 g 0 14 11 60 3 0 62 0 14 2 2 0 50 0 21 0 t 0 13 33 0 1 65 3 1 0 63 0 0 13 2 9 0
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.823857; mtwGCTTACTaAwyra ; cor=; Ncor= a 21 16 22 2 7 1 0 64 0 0 42 61 18 8 29 29 c 24 12 10 0 55 0 0 1 56 0 16 2 1 34 8 12 g 8 5 3 62 1 0 15 0 9 3 6 1 12 2 18 8 t 12 32 30 1 2 64 50 0 0 62 1 1 34 21 10 16
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=8/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.769996; mwwGCTKACTAAwyr- ; cor=; Ncor= a 18 15 18 1 7 1 0 50 0 0 38 50 15 8 22 0 c 18 10 3 0 42 0 0 1 47 0 10 0 0 23 5 0 g 6 2 1 49 1 0 14 0 4 1 3 1 10 2 15 0 t 9 24 29 1 1 50 37 0 0 50 0 0 26 18 9 0