One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124532_2025-04-03.124532_W6xMnm/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.2025-04-03.124532_2025-04-03.124532_W6xMnm/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 9 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=19; shift=0; ncol=19; rrmtGCTGAsTCAGCaryy ; Alignment reference a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 14 16 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 22 25 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 19 15 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18 22 21

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/8; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; rrmtGCTGAsTCAGCaryy ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 14 16 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 22 25 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 19 15 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18 22 21

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/8; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.893468; -rhtGCTGAsTMAGCarb- ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 13 0 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 21 0 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 18 0 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15 20 0

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=3/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.887333; rrmtGMTGAsTMAkCar-- ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 0 0 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 0 0 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 0 0 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19 0 0

oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=4/8; ncol2=16; w=0; offset=2; strand=R; shift=2; score=0.830819; --mtGmTGAsTCAGCarc- ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 17 0 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 24 0 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 17 0 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14 15 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=5/8; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.818884; -rmTGMTGACTmAkCar-- ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 0 0 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 0 0 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 0 0 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12 0 0

oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=6/8; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.745915; --atGmTGACTmAKCrr-- ; cor=; Ncor= a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 0 0 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 0 0 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 0 0 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.619686; -mywGCTKACTmAdy---- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=8/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.512421; --ywGCTTACTmad----- ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 0 0 0 0 0 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 0 0 0 0 0 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 0 0 0 0 0 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; rrTCACGTGAyy ; Alignment reference a 10 13 1 1 25 0 3 0 0 20 2 4 c 5 3 3 25 0 21 2 1 0 2 8 7 g 7 8 2 0 1 2 21 0 25 3 3 5 t 4 2 20 0 0 3 0 25 1 1 13 10

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; rrTCACGTGAyy ; cor=; Ncor= a 10 13 1 1 25 0 3 0 0 20 2 4 c 5 3 3 25 0 21 2 1 0 2 8 7 g 7 8 2 0 1 2 21 0 25 3 3 5 t 4 2 20 0 0 3 0 25 1 1 13 10

oligos_6nt_mkv2_m4_rc_shift0 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4_rc; m=2/2; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.830744; argCACGTGcyt ; cor=; Ncor= a 23 11 3 0 31 0 0 0 2 9 9 2 c 9 6 6 34 6 37 0 0 2 18 12 3 g 3 12 19 1 0 0 37 6 33 7 6 9 t 2 8 9 2 0 0 0 31 0 3 10 23

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; argCACGTGcyt ; Alignment reference a 23 10 3 0 31 0 0 0 2 9 8 2 c 9 6 7 33 6 37 0 0 1 19 12 3 g 3 12 18 2 0 0 37 6 34 6 6 9 t 2 9 9 2 0 0 0 31 0 3 11 23

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; argCACGTGcyt ; cor=; Ncor= a 23 10 3 0 31 0 0 0 2 9 8 2 c 9 6 7 33 6 37 0 0 1 19 12 3 g 3 12 18 2 0 0 37 6 34 6 6 9 t 2 9 9 2 0 0 0 31 0 3 11 23

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.830744; rrTCACGTGAyy ; cor=; Ncor= a 10 13 1 1 25 0 3 0 0 20 2 4 c 5 3 3 25 0 21 2 1 0 2 8 7 g 7 8 2 0 1 2 21 0 25 3 3 5 t 4 2 20 0 0 3 0 25 1 1 13 10

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --ywGCTTACTmad ; Alignment reference a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ywGCTTACTmad ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=2/8; ncol2=14; w=-1; offset=-1; strand=R; shift=1; score=0.840531; -mywGCTKACTmAd ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=3/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.637693; --yyGMTkAGTCAk ; cor=; Ncor= a 0 0 12 9 1 17 0 0 59 0 0 5 62 2 c 0 0 18 20 1 45 0 1 0 12 0 57 0 0 g 0 0 6 10 55 0 0 23 1 50 0 0 0 23 t 0 0 26 23 5 0 62 38 2 0 62 0 0 37

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=4/8; ncol2=16; w=-1; offset=-1; strand=R; shift=1; score=0.621978; -rmTGMTGACTmAk ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=5/8; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.583956; -gytGCTGAsTCAk ; cor=; Ncor= a 0 15 14 6 3 11 0 0 69 0 0 9 73 1 c 0 17 25 14 1 62 1 0 3 23 1 64 0 2 g 0 24 12 12 68 0 0 60 0 49 0 0 0 40 t 0 17 22 41 1 0 72 13 1 1 72 0 0 30

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=6/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.575068; rrmtGMTGAsTMAk ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=7/8; ncol2=17; w=-1; offset=-1; strand=D; shift=1; score=0.573561; -rhtGCTGAsTMAG ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=8/8; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.512421; rrmtGCTGAsTCAG ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=16; shift=2; ncol=18; --ytGmTkAGTCAKCAky ; Alignment reference a 0 0 12 14 7 22 1 1 69 0 0 9 70 1 0 55 15 11 c 0 0 18 17 0 47 1 3 0 15 0 60 0 1 66 5 7 18 g 0 0 12 10 56 1 1 30 0 54 0 1 0 50 1 7 24 11 t 0 0 28 29 7 0 67 36 1 1 70 0 0 18 3 3 24 30

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=2; score= 1; --ytGmTkAGTCAKCAky ; cor=; Ncor= a 0 0 12 14 7 22 1 1 69 0 0 9 70 1 0 55 15 11 c 0 0 18 17 0 47 1 3 0 15 0 60 0 1 66 5 7 18 g 0 0 12 10 56 1 1 30 0 54 0 1 0 50 1 7 24 11 t 0 0 28 29 7 0 67 36 1 1 70 0 0 18 3 3 24 30

oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.919638; --ytGmTKAsTCAKCaky ; cor=; Ncor= a 0 0 19 15 5 34 1 0 87 1 0 10 89 0 3 51 21 19 c 0 0 24 22 0 55 1 1 0 29 0 80 0 0 83 16 12 26 g 0 0 19 16 80 1 0 64 0 60 1 0 1 65 1 13 27 15 t 0 0 28 37 5 0 88 25 3 0 89 0 0 25 3 10 30 30

oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.914071; --mtGmTGAsTCAGCarc ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 17 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 24 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 17 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14 15

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=4/8; ncol2=17; w=-1; offset=-1; strand=R; shift=1; score=0.91395; -vytGCTKAsTCAGCady ; cor=; Ncor= a 0 20 15 8 3 13 0 0 70 0 0 11 72 0 1 46 19 13 c 0 18 21 11 0 59 0 1 1 25 0 61 0 0 67 11 12 22 g 0 21 15 11 64 0 0 52 0 47 0 0 0 56 1 8 21 15 t 0 13 21 42 5 0 72 19 1 0 72 0 0 16 3 7 20 22

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=5/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.90864; --yyGMTkAGTCAkCat- ; cor=; Ncor= a 0 0 12 9 1 17 0 0 59 0 0 5 62 2 0 38 12 0 c 0 0 18 20 1 45 0 1 0 12 0 57 0 0 55 9 14 0 g 0 0 6 10 55 0 0 23 1 50 0 0 0 23 2 6 14 0 t 0 0 26 23 5 0 62 38 2 0 62 0 0 37 5 9 22 0

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=6/8; ncol2=19; w=-2; offset=-2; strand=R; shift=0; score=0.818884; rrytGCTGAsTCAGCaky ; cor=; Ncor= a 21 22 18 11 5 16 0 0 75 0 0 10 77 0 1 45 18 14 c 15 19 21 13 0 61 0 2 1 25 0 67 0 0 72 13 13 25 g 25 22 15 12 66 0 0 56 0 52 0 0 0 58 1 11 25 15 t 16 14 23 41 6 0 77 19 1 0 77 0 0 19 3 8 21 23

oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=7/8; ncol2=14; w=0; offset=2; strand=D; shift=4; score=0.765372; ----rhTkAGTMAGCwrk ; cor=; Ncor= a 0 0 0 0 19 18 1 3 57 4 0 46 63 1 2 38 26 15 c 0 0 0 0 6 23 5 6 4 6 1 16 0 0 59 3 7 9 g 0 0 0 0 32 3 2 18 1 53 0 0 0 59 1 6 21 22 t 0 0 0 0 6 19 55 36 1 0 62 1 0 3 1 16 9 17

oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=8/8; ncol2=12; w=0; offset=3; strand=R; shift=5; score=0.621978; -----htkAGTAAGCwr- ; cor=; Ncor= a 0 0 0 0 0 25 9 6 69 4 1 58 76 2 2 26 30 0 c 0 0 0 0 0 21 12 10 3 7 0 16 0 1 73 9 15 0 g 0 0 0 0 0 3 4 25 2 65 4 0 0 73 1 18 25 0 t 0 0 0 0 0 28 52 36 3 1 72 3 1 1 1 24 7 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=17; shift=1; ncol=18; -rhtGCTGAsTMAGCarb ; Alignment reference a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 13 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 21 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 18 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15 20

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -rhtGCTGAsTMAGCarb ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 13 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 21 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 18 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15 20

oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=2/8; ncol2=16; w=0; offset=1; strand=R; shift=2; score=0.926779; --mtGmTGAsTCAGCarc ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 17 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 24 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 17 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14 15

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=1; score=0.91395; -rmTGMTGACTmAkCar- ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 0 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 0 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 0 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=4/8; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.893468; rrmtGCTGAsTCAGCary ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 14 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 22 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 19 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18 22

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=5/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.878471; rrmtGMTGAsTMAkCar- ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 0 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 0 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 0 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19 0

oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=6/8; ncol2=15; w=0; offset=1; strand=D; shift=2; score=0.82959; --atGmTGACTmAKCrr- ; cor=; Ncor= a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 0 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 0 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 0 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.695834; -mywGCTKACTmAdy--- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=8/8; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.573561; --ywGCTTACTmad---- ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 0 0 0 0 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 0 0 0 0 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 0 0 0 0 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 9 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=16; shift=1; ncol=17; -gytGCTGAsTCAkCak ; Alignment reference a 0 15 14 6 3 11 0 0 69 0 0 9 73 1 2 33 18 c 0 17 25 14 1 62 1 0 3 23 1 64 0 2 62 13 14 g 0 24 12 12 68 0 0 60 0 49 0 0 0 40 3 12 21 t 0 17 22 41 1 0 72 13 1 1 72 0 0 30 6 15 20

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -gytGCTGAsTCAkCak ; cor=; Ncor= a 0 15 14 6 3 11 0 0 69 0 0 9 73 1 2 33 18 c 0 17 25 14 1 62 1 0 3 23 1 64 0 2 62 13 14 g 0 24 12 12 68 0 0 60 0 49 0 0 0 40 3 12 21 t 0 17 22 41 1 0 72 13 1 1 72 0 0 30 6 15 20

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.926779; -vytGCTKAsTCAGCad ; cor=; Ncor= a 0 20 15 8 3 13 0 0 70 0 0 11 72 0 1 46 19 c 0 18 21 11 0 59 0 1 1 25 0 61 0 0 67 11 12 g 0 21 15 11 64 0 0 52 0 47 0 0 0 56 1 8 21 t 0 13 21 42 5 0 72 19 1 0 72 0 0 16 3 7 20

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m3_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=1; score=0.914071; -rmTGMTGACTmAkCar ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=4/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.908331; rrmtGMTGAsTMAkCar ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc; m=5/8; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.886818; --yyGMTkAGTCAkCat ; cor=; Ncor= a 0 0 12 9 1 17 0 0 59 0 0 5 62 2 0 38 12 c 0 0 18 20 1 45 0 1 0 12 0 57 0 0 55 9 14 g 0 0 6 10 55 0 0 23 1 50 0 0 0 23 2 6 14 t 0 0 26 23 5 0 62 38 2 0 62 0 0 37 5 9 22

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=6/8; ncol2=19; w=-1; offset=-1; strand=R; shift=0; score=0.830819; rrytGCTGAsTCAGCak ; cor=; Ncor= a 21 22 18 11 5 16 0 0 75 0 0 10 77 0 1 45 18 c 15 19 21 13 0 61 0 2 1 25 0 67 0 0 72 13 13 g 25 22 15 12 66 0 0 56 0 52 0 0 0 58 1 11 25 t 16 14 23 41 6 0 77 19 1 0 77 0 0 19 3 8 21

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.701011; -mywGCTKACTmAdy-- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=8/8; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.583956; --ywGCTTACTmad--- ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 0 0 0 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 0 0 0 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 0 0 0 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 9 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=17; shift=0; ncol=17; rrmtGMTGAsTMAkCar ; Alignment reference a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; rrmtGMTGAsTMAkCar ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3_rc; m=2/8; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.919638; -rmTGMTGACTmAkCar ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/8; ncol2=16; w=0; offset=1; strand=D; shift=1; score=0.908331; -gytGCTGAsTCAkCak ; cor=; Ncor= a 0 15 14 6 3 11 0 0 69 0 0 9 73 1 2 33 18 c 0 17 25 14 1 62 1 0 3 23 1 64 0 2 62 13 14 g 0 24 12 12 68 0 0 60 0 49 0 0 0 40 3 12 21 t 0 17 22 41 1 0 72 13 1 1 72 0 0 30 6 15 20

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=4/8; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.887333; rrmtGCTGAsTCAGCar ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=5/8; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.878471; -rhtGCTGAsTMAGCar ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15

oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=6/8; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.840275; --atGmTGACTmAKCrr ; cor=; Ncor= a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.691364; -mywGCTKACTmAdy-- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=8/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.575068; --ywGCTTACTmad--- ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 0 0 0 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 0 0 0 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 0 0 0 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift4 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=14; shift=4; ncol=18; ----rhTkAGTMAGCwrk ; Alignment reference a 0 0 0 0 19 18 1 3 57 4 0 46 63 1 2 38 26 15 c 0 0 0 0 6 23 5 6 4 6 1 16 0 0 59 3 7 9 g 0 0 0 0 32 3 2 18 1 53 0 0 0 59 1 6 21 22 t 0 0 0 0 6 19 55 36 1 0 62 1 0 3 1 16 9 17

oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=4; score= 1; ----rhTkAGTMAGCwrk ; cor=; Ncor= a 0 0 0 0 19 18 1 3 57 4 0 46 63 1 2 38 26 15 c 0 0 0 0 6 23 5 6 4 6 1 16 0 0 59 3 7 9 g 0 0 0 0 32 3 2 18 1 53 0 0 0 59 1 6 21 22 t 0 0 0 0 6 19 55 36 1 0 62 1 0 3 1 16 9 17

oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=2/8; ncol2=12; w=0; offset=1; strand=R; shift=5; score=0.840531; -----htkAGTAAGCwr- ; cor=; Ncor= a 0 0 0 0 0 25 9 6 69 4 1 58 76 2 2 26 30 0 c 0 0 0 0 0 21 12 10 3 7 0 16 0 1 73 9 15 0 g 0 0 0 0 0 3 4 25 2 65 4 0 0 73 1 18 25 0 t 0 0 0 0 0 28 52 36 3 1 72 3 1 1 1 24 7 0

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=3/8; ncol2=16; w=-2; offset=-2; strand=D; shift=2; score=0.765372; --ytGmTkAGTCAKCAky ; cor=; Ncor= a 0 0 12 14 7 22 1 1 69 0 0 9 70 1 0 55 15 11 c 0 0 18 17 0 47 1 3 0 15 0 60 0 1 66 5 7 18 g 0 0 12 10 56 1 1 30 0 54 0 1 0 50 1 7 24 11 t 0 0 28 29 7 0 67 36 1 1 70 0 0 18 3 3 24 30

oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=4/8; ncol2=16; w=-2; offset=-2; strand=R; shift=2; score=0.701011; --mtGmTGAsTCAGCarc ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 17 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 24 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 17 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14 15

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=5/8; ncol2=17; w=-3; offset=-3; strand=R; shift=1; score=0.695834; -vytGCTKAsTCAGCady ; cor=; Ncor= a 0 20 15 8 3 13 0 0 70 0 0 11 72 0 1 46 19 13 c 0 18 21 11 0 59 0 1 1 25 0 61 0 0 67 11 12 22 g 0 21 15 11 64 0 0 52 0 47 0 0 0 56 1 8 21 15 t 0 13 21 42 5 0 72 19 1 0 72 0 0 16 3 7 20 22

oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=6/8; ncol2=17; w=-2; offset=-2; strand=R; shift=2; score=0.691364; --ytGmTKAsTCAKCaky ; cor=; Ncor= a 0 0 19 15 5 34 1 0 87 1 0 10 89 0 3 51 21 19 c 0 0 24 22 0 55 1 1 0 29 0 80 0 0 83 16 12 26 g 0 0 19 16 80 1 0 64 0 60 1 0 1 65 1 13 27 15 t 0 0 28 37 5 0 88 25 3 0 89 0 0 25 3 10 30 30

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=7/8; ncol2=15; w=-2; offset=-2; strand=R; shift=2; score=0.659976; --yyGMTkAGTCAkCat- ; cor=; Ncor= a 0 0 12 9 1 17 0 0 59 0 0 5 62 2 0 38 12 0 c 0 0 18 20 1 45 0 1 0 12 0 57 0 0 55 9 14 0 g 0 0 6 10 55 0 0 23 1 50 0 0 0 23 2 6 14 0 t 0 0 26 23 5 0 62 38 2 0 62 0 0 37 5 9 22 0

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=8/8; ncol2=19; w=-4; offset=-4; strand=R; shift=0; score=0.619686; rrytGCTGAsTCAGCaky ; cor=; Ncor= a 21 22 18 11 5 16 0 0 75 0 0 10 77 0 1 45 18 14 c 15 19 21 13 0 61 0 2 1 25 0 67 0 0 72 13 13 25 g 25 22 15 12 66 0 0 56 0 52 0 0 0 58 1 11 25 15 t 16 14 23 41 6 0 77 19 1 0 77 0 0 19 3 8 21 23

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=15; shift=2; ncol=17; --atGmTGACTmAKCrr ; Alignment reference a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12

oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score= 1; --atGmTGACTmAKCrr ; cor=; Ncor= a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=2/8; ncol2=16; w=-1; offset=-1; strand=R; shift=1; score=0.90864; -rmTGMTGACTmAkCar ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12

oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.886818; --mtGmTGAsTCAGCar ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=4/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.840275; rrmtGMTGAsTMAkCar ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=5/8; ncol2=17; w=-1; offset=-1; strand=D; shift=1; score=0.82959; -rhtGCTGAsTMAGCar ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=6/8; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.745915; rrmtGCTGAsTCAGCar ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=-1; offset=-1; strand=R; shift=1; score=0.659976; -mywGCTKACTmAdy-- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0

oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=8/8; ncol2=12; w=0; offset=3; strand=R; shift=5; score=0.637693; -----htkAGTAAGCwr ; cor=; Ncor= a 0 0 0 0 0 25 9 6 69 4 1 58 76 2 2 26 30 c 0 0 0 0 0 21 12 10 3 7 0 16 0 1 73 9 15 g 0 0 0 0 0 3 4 25 2 65 4 0 0 73 1 18 25 t 0 0 0 0 0 28 52 36 3 1 72 3 1 1 1 24 7

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=19; shift=0; ncol=19; rrmtGCTGAsTCAGCaryy ; Alignment reference a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 14 16 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 22 25 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 19 15 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18 22 21
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/8; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; rrmtGCTGAsTCAGCaryy ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 14 16 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 22 25 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 19 15 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18 22 21
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/8; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.893468; -rhtGCTGAsTMAGCarb- ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 13 0 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 21 0 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 18 0 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15 20 0
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=3/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.887333; rrmtGMTGAsTMAkCar-- ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 0 0 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 0 0 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 0 0 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19 0 0
oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=4/8; ncol2=16; w=0; offset=2; strand=R; shift=2; score=0.830819; --mtGmTGAsTCAGCarc- ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 17 0 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 24 0 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 17 0 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14 15 0
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=5/8; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.818884; -rmTGMTGACTmAkCar-- ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 0 0 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 0 0 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 0 0 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12 0 0
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=6/8; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.745915; --atGmTGACTmAKCrr-- ; cor=; Ncor= a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 0 0 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 0 0 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 0 0 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.619686; -mywGCTKACTmAdy---- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0 0 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=8/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.512421; --ywGCTTACTmad----- ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 0 0 0 0 0 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 0 0 0 0 0 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 0 0 0 0 0 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --ywGCTTACTmad ; Alignment reference a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/8; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ywGCTTACTmad ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=2/8; ncol2=14; w=-1; offset=-1; strand=R; shift=1; score=0.840531; -mywGCTKACTmAd ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18
oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=3/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.637693; --yyGMTkAGTCAk ; cor=; Ncor= a 0 0 12 9 1 17 0 0 59 0 0 5 62 2 c 0 0 18 20 1 45 0 1 0 12 0 57 0 0 g 0 0 6 10 55 0 0 23 1 50 0 0 0 23 t 0 0 26 23 5 0 62 38 2 0 62 0 0 37
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=4/8; ncol2=16; w=-1; offset=-1; strand=R; shift=1; score=0.621978; -rmTGMTGACTmAk ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=5/8; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.583956; -gytGCTGAsTCAk ; cor=; Ncor= a 0 15 14 6 3 11 0 0 69 0 0 9 73 1 c 0 17 25 14 1 62 1 0 3 23 1 64 0 2 g 0 24 12 12 68 0 0 60 0 49 0 0 0 40 t 0 17 22 41 1 0 72 13 1 1 72 0 0 30
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=6/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.575068; rrmtGMTGAsTMAk ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=7/8; ncol2=17; w=-1; offset=-1; strand=D; shift=1; score=0.573561; -rhtGCTGAsTMAG ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=8/8; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.512421; rrmtGCTGAsTCAG ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=16; shift=2; ncol=18; --ytGmTkAGTCAKCAky ; Alignment reference a 0 0 12 14 7 22 1 1 69 0 0 9 70 1 0 55 15 11 c 0 0 18 17 0 47 1 3 0 15 0 60 0 1 66 5 7 18 g 0 0 12 10 56 1 1 30 0 54 0 1 0 50 1 7 24 11 t 0 0 28 29 7 0 67 36 1 1 70 0 0 18 3 3 24 30
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=2; score= 1; --ytGmTkAGTCAKCAky ; cor=; Ncor= a 0 0 12 14 7 22 1 1 69 0 0 9 70 1 0 55 15 11 c 0 0 18 17 0 47 1 3 0 15 0 60 0 1 66 5 7 18 g 0 0 12 10 56 1 1 30 0 54 0 1 0 50 1 7 24 11 t 0 0 28 29 7 0 67 36 1 1 70 0 0 18 3 3 24 30
oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.919638; --ytGmTKAsTCAKCaky ; cor=; Ncor= a 0 0 19 15 5 34 1 0 87 1 0 10 89 0 3 51 21 19 c 0 0 24 22 0 55 1 1 0 29 0 80 0 0 83 16 12 26 g 0 0 19 16 80 1 0 64 0 60 1 0 1 65 1 13 27 15 t 0 0 28 37 5 0 88 25 3 0 89 0 0 25 3 10 30 30
oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.914071; --mtGmTGAsTCAGCarc ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 17 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 24 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 17 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14 15
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=4/8; ncol2=17; w=-1; offset=-1; strand=R; shift=1; score=0.91395; -vytGCTKAsTCAGCady ; cor=; Ncor= a 0 20 15 8 3 13 0 0 70 0 0 11 72 0 1 46 19 13 c 0 18 21 11 0 59 0 1 1 25 0 61 0 0 67 11 12 22 g 0 21 15 11 64 0 0 52 0 47 0 0 0 56 1 8 21 15 t 0 13 21 42 5 0 72 19 1 0 72 0 0 16 3 7 20 22
oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=5/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.90864; --yyGMTkAGTCAkCat- ; cor=; Ncor= a 0 0 12 9 1 17 0 0 59 0 0 5 62 2 0 38 12 0 c 0 0 18 20 1 45 0 1 0 12 0 57 0 0 55 9 14 0 g 0 0 6 10 55 0 0 23 1 50 0 0 0 23 2 6 14 0 t 0 0 26 23 5 0 62 38 2 0 62 0 0 37 5 9 22 0
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=6/8; ncol2=19; w=-2; offset=-2; strand=R; shift=0; score=0.818884; rrytGCTGAsTCAGCaky ; cor=; Ncor= a 21 22 18 11 5 16 0 0 75 0 0 10 77 0 1 45 18 14 c 15 19 21 13 0 61 0 2 1 25 0 67 0 0 72 13 13 25 g 25 22 15 12 66 0 0 56 0 52 0 0 0 58 1 11 25 15 t 16 14 23 41 6 0 77 19 1 0 77 0 0 19 3 8 21 23
oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=7/8; ncol2=14; w=0; offset=2; strand=D; shift=4; score=0.765372; ----rhTkAGTMAGCwrk ; cor=; Ncor= a 0 0 0 0 19 18 1 3 57 4 0 46 63 1 2 38 26 15 c 0 0 0 0 6 23 5 6 4 6 1 16 0 0 59 3 7 9 g 0 0 0 0 32 3 2 18 1 53 0 0 0 59 1 6 21 22 t 0 0 0 0 6 19 55 36 1 0 62 1 0 3 1 16 9 17
oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=8/8; ncol2=12; w=0; offset=3; strand=R; shift=5; score=0.621978; -----htkAGTAAGCwr- ; cor=; Ncor= a 0 0 0 0 0 25 9 6 69 4 1 58 76 2 2 26 30 0 c 0 0 0 0 0 21 12 10 3 7 0 16 0 1 73 9 15 0 g 0 0 0 0 0 3 4 25 2 65 4 0 0 73 1 18 25 0 t 0 0 0 0 0 28 52 36 3 1 72 3 1 1 1 24 7 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=17; shift=1; ncol=18; -rhtGCTGAsTMAGCarb ; Alignment reference a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 13 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 21 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 18 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15 20
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -rhtGCTGAsTMAGCarb ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 13 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 21 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 18 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15 20
oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=2/8; ncol2=16; w=0; offset=1; strand=R; shift=2; score=0.926779; --mtGmTGAsTCAGCarc ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 17 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 24 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 17 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14 15
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=1; score=0.91395; -rmTGMTGACTmAkCar- ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 0 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 0 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 0 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=4/8; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.893468; rrmtGCTGAsTCAGCary ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 14 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 22 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 19 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18 22
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=5/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.878471; rrmtGMTGAsTMAkCar- ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 0 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 0 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 0 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19 0
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=6/8; ncol2=15; w=0; offset=1; strand=D; shift=2; score=0.82959; --atGmTGACTmAKCrr- ; cor=; Ncor= a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 0 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 0 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 0 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.695834; -mywGCTKACTmAdy--- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=8/8; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.573561; --ywGCTTACTmad---- ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 0 0 0 0 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 0 0 0 0 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 0 0 0 0 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25 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=16; shift=1; ncol=17; -gytGCTGAsTCAkCak ; Alignment reference a 0 15 14 6 3 11 0 0 69 0 0 9 73 1 2 33 18 c 0 17 25 14 1 62 1 0 3 23 1 64 0 2 62 13 14 g 0 24 12 12 68 0 0 60 0 49 0 0 0 40 3 12 21 t 0 17 22 41 1 0 72 13 1 1 72 0 0 30 6 15 20
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -gytGCTGAsTCAkCak ; cor=; Ncor= a 0 15 14 6 3 11 0 0 69 0 0 9 73 1 2 33 18 c 0 17 25 14 1 62 1 0 3 23 1 64 0 2 62 13 14 g 0 24 12 12 68 0 0 60 0 49 0 0 0 40 3 12 21 t 0 17 22 41 1 0 72 13 1 1 72 0 0 30 6 15 20
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.926779; -vytGCTKAsTCAGCad ; cor=; Ncor= a 0 20 15 8 3 13 0 0 70 0 0 11 72 0 1 46 19 c 0 18 21 11 0 59 0 1 1 25 0 61 0 0 67 11 12 g 0 21 15 11 64 0 0 52 0 47 0 0 0 56 1 8 21 t 0 13 21 42 5 0 72 19 1 0 72 0 0 16 3 7 20
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m3_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=1; score=0.914071; -rmTGMTGACTmAkCar ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=4/8; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.908331; rrmtGMTGAsTMAkCar ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19
oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc; m=5/8; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.886818; --yyGMTkAGTCAkCat ; cor=; Ncor= a 0 0 12 9 1 17 0 0 59 0 0 5 62 2 0 38 12 c 0 0 18 20 1 45 0 1 0 12 0 57 0 0 55 9 14 g 0 0 6 10 55 0 0 23 1 50 0 0 0 23 2 6 14 t 0 0 26 23 5 0 62 38 2 0 62 0 0 37 5 9 22
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=6/8; ncol2=19; w=-1; offset=-1; strand=R; shift=0; score=0.830819; rrytGCTGAsTCAGCak ; cor=; Ncor= a 21 22 18 11 5 16 0 0 75 0 0 10 77 0 1 45 18 c 15 19 21 13 0 61 0 2 1 25 0 67 0 0 72 13 13 g 25 22 15 12 66 0 0 56 0 52 0 0 0 58 1 11 25 t 16 14 23 41 6 0 77 19 1 0 77 0 0 19 3 8 21
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.701011; -mywGCTKACTmAdy-- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=8/8; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.583956; --ywGCTTACTmad--- ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 0 0 0 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 0 0 0 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 0 0 0 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25 0 0 0

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=17; shift=0; ncol=17; rrmtGMTGAsTMAkCar ; Alignment reference a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; rrmtGMTGAsTMAkCar ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3_rc; m=2/8; ncol2=16; w=0; offset=1; strand=R; shift=1; score=0.919638; -rmTGMTGACTmAkCar ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/8; ncol2=16; w=0; offset=1; strand=D; shift=1; score=0.908331; -gytGCTGAsTCAkCak ; cor=; Ncor= a 0 15 14 6 3 11 0 0 69 0 0 9 73 1 2 33 18 c 0 17 25 14 1 62 1 0 3 23 1 64 0 2 62 13 14 g 0 24 12 12 68 0 0 60 0 49 0 0 0 40 3 12 21 t 0 17 22 41 1 0 72 13 1 1 72 0 0 30 6 15 20
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=4/8; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.887333; rrmtGCTGAsTCAGCar ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=5/8; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.878471; -rhtGCTGAsTMAGCar ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=6/8; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.840275; --atGmTGACTmAKCrr ; cor=; Ncor= a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.691364; -mywGCTKACTmAdy-- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=8/8; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.575068; --ywGCTTACTmad--- ; cor=; Ncor= a 0 0 7 24 1 1 1 3 72 1 3 36 52 28 0 0 0 c 0 0 25 18 1 73 0 0 4 65 2 25 4 3 0 0 0 g 0 0 15 9 73 1 0 16 0 7 3 10 12 21 0 0 0 t 0 0 30 26 2 2 76 58 1 4 69 6 9 25 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=14; shift=4; ncol=18; ----rhTkAGTMAGCwrk ; Alignment reference a 0 0 0 0 19 18 1 3 57 4 0 46 63 1 2 38 26 15 c 0 0 0 0 6 23 5 6 4 6 1 16 0 0 59 3 7 9 g 0 0 0 0 32 3 2 18 1 53 0 0 0 59 1 6 21 22 t 0 0 0 0 6 19 55 36 1 0 62 1 0 3 1 16 9 17
oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=4; score= 1; ----rhTkAGTMAGCwrk ; cor=; Ncor= a 0 0 0 0 19 18 1 3 57 4 0 46 63 1 2 38 26 15 c 0 0 0 0 6 23 5 6 4 6 1 16 0 0 59 3 7 9 g 0 0 0 0 32 3 2 18 1 53 0 0 0 59 1 6 21 22 t 0 0 0 0 6 19 55 36 1 0 62 1 0 3 1 16 9 17
oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=2/8; ncol2=12; w=0; offset=1; strand=R; shift=5; score=0.840531; -----htkAGTAAGCwr- ; cor=; Ncor= a 0 0 0 0 0 25 9 6 69 4 1 58 76 2 2 26 30 0 c 0 0 0 0 0 21 12 10 3 7 0 16 0 1 73 9 15 0 g 0 0 0 0 0 3 4 25 2 65 4 0 0 73 1 18 25 0 t 0 0 0 0 0 28 52 36 3 1 72 3 1 1 1 24 7 0
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=3/8; ncol2=16; w=-2; offset=-2; strand=D; shift=2; score=0.765372; --ytGmTkAGTCAKCAky ; cor=; Ncor= a 0 0 12 14 7 22 1 1 69 0 0 9 70 1 0 55 15 11 c 0 0 18 17 0 47 1 3 0 15 0 60 0 1 66 5 7 18 g 0 0 12 10 56 1 1 30 0 54 0 1 0 50 1 7 24 11 t 0 0 28 29 7 0 67 36 1 1 70 0 0 18 3 3 24 30
oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=4/8; ncol2=16; w=-2; offset=-2; strand=R; shift=2; score=0.701011; --mtGmTGAsTCAGCarc ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 17 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 24 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 17 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14 15
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=5/8; ncol2=17; w=-3; offset=-3; strand=R; shift=1; score=0.695834; -vytGCTKAsTCAGCady ; cor=; Ncor= a 0 20 15 8 3 13 0 0 70 0 0 11 72 0 1 46 19 13 c 0 18 21 11 0 59 0 1 1 25 0 61 0 0 67 11 12 22 g 0 21 15 11 64 0 0 52 0 47 0 0 0 56 1 8 21 15 t 0 13 21 42 5 0 72 19 1 0 72 0 0 16 3 7 20 22
oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=6/8; ncol2=17; w=-2; offset=-2; strand=R; shift=2; score=0.691364; --ytGmTKAsTCAKCaky ; cor=; Ncor= a 0 0 19 15 5 34 1 0 87 1 0 10 89 0 3 51 21 19 c 0 0 24 22 0 55 1 1 0 29 0 80 0 0 83 16 12 26 g 0 0 19 16 80 1 0 64 0 60 1 0 1 65 1 13 27 15 t 0 0 28 37 5 0 88 25 3 0 89 0 0 25 3 10 30 30
oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=7/8; ncol2=15; w=-2; offset=-2; strand=R; shift=2; score=0.659976; --yyGMTkAGTCAkCat- ; cor=; Ncor= a 0 0 12 9 1 17 0 0 59 0 0 5 62 2 0 38 12 0 c 0 0 18 20 1 45 0 1 0 12 0 57 0 0 55 9 14 0 g 0 0 6 10 55 0 0 23 1 50 0 0 0 23 2 6 14 0 t 0 0 26 23 5 0 62 38 2 0 62 0 0 37 5 9 22 0
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=8/8; ncol2=19; w=-4; offset=-4; strand=R; shift=0; score=0.619686; rrytGCTGAsTCAGCaky ; cor=; Ncor= a 21 22 18 11 5 16 0 0 75 0 0 10 77 0 1 45 18 14 c 15 19 21 13 0 61 0 2 1 25 0 67 0 0 72 13 13 25 g 25 22 15 12 66 0 0 56 0 52 0 0 0 58 1 11 25 15 t 16 14 23 41 6 0 77 19 1 0 77 0 0 19 3 8 21 23

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=15; shift=2; ncol=17; --atGmTGACTmAKCrr ; Alignment reference a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=2; score= 1; --atGmTGACTmAKCrr ; cor=; Ncor= a 0 0 22 9 5 37 0 0 62 0 2 38 62 0 5 23 26 c 0 0 14 6 2 23 0 0 0 50 1 23 0 0 55 10 6 g 0 0 14 9 55 0 0 57 0 12 0 1 0 45 1 20 18 t 0 0 12 38 0 2 62 5 0 0 59 0 0 17 1 9 12
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=2/8; ncol2=16; w=-1; offset=-1; strand=R; shift=1; score=0.90864; -rmTGMTGACTmAkCar ; cor=; Ncor= a 0 30 24 3 3 18 0 0 70 1 1 36 67 0 7 29 28 c 0 11 24 7 1 50 0 1 0 54 0 30 1 1 56 10 12 g 0 18 7 5 66 1 0 60 0 15 0 3 1 47 0 17 18 t 0 11 15 55 0 1 70 9 0 0 69 1 1 22 7 14 12
oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.886818; --mtGmTGAsTCAGCar ; cor=; Ncor= a 0 0 20 15 6 30 0 0 72 1 1 13 72 0 1 41 22 c 0 0 21 12 3 40 0 0 0 49 0 60 0 0 68 12 12 g 0 0 14 13 62 2 0 64 1 23 3 0 1 62 1 14 25 t 0 0 18 33 2 1 73 9 0 0 69 0 0 11 3 6 14
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=4/8; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.840275; rrmtGMTGAsTMAkCar ; cor=; Ncor= a 33 30 30 10 3 25 0 0 89 0 3 25 88 0 5 37 28 c 19 15 27 13 1 65 1 0 1 60 0 64 0 1 80 16 19 g 25 26 12 16 83 0 0 80 0 29 0 1 1 55 0 22 24 t 13 19 21 51 3 0 89 10 0 1 87 0 1 34 5 15 19
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=5/8; ncol2=17; w=-1; offset=-1; strand=D; shift=1; score=0.82959; -rhtGCTGAsTMAGCar ; cor=; Ncor= a 0 22 20 7 3 16 0 0 72 0 1 19 72 0 5 42 21 c 0 15 21 8 1 56 0 0 0 47 0 52 0 0 64 11 15 g 0 22 12 11 67 0 0 61 0 25 1 1 0 59 0 11 21 t 0 13 19 46 1 0 72 11 0 0 70 0 0 13 3 8 15
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=6/8; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.745915; rrmtGCTGAsTCAGCar ; cor=; Ncor= a 25 23 21 8 3 19 0 0 77 0 1 19 77 0 6 41 23 c 15 15 25 11 1 58 0 0 0 52 0 56 0 0 66 12 15 g 24 25 13 13 72 0 0 67 0 25 1 2 0 61 0 13 21 t 13 14 18 45 1 0 77 10 0 0 75 0 0 16 5 11 18
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=7/8; ncol2=14; w=-1; offset=-1; strand=R; shift=1; score=0.659976; -mywGCTKACTmAdy-- ; cor=; Ncor= a 0 17 9 16 1 3 0 1 62 0 1 36 55 19 6 0 0 c 0 22 21 6 1 59 0 0 0 53 1 18 2 3 32 0 0 g 0 9 7 3 59 0 0 16 1 6 4 6 5 23 6 0 0 t 0 15 26 38 2 1 63 46 0 4 57 3 1 18 19 0 0
oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=8/8; ncol2=12; w=0; offset=3; strand=R; shift=5; score=0.637693; -----htkAGTAAGCwr ; cor=; Ncor= a 0 0 0 0 0 25 9 6 69 4 1 58 76 2 2 26 30 c 0 0 0 0 0 21 12 10 3 7 0 16 0 1 73 9 15 g 0 0 0 0 0 3 4 25 2 65 4 0 0 73 1 18 25 t 0 0 0 0 0 28 52 36 3 1 72 3 1 1 1 24 7