One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/05/29/peak-motifs.2026-05-29.111109_2026-05-29.111109_G9ggFA/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/2026/05/29/peak-motifs.2026-05-29.111109_2026-05-29.111109_G9ggFA/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; hykrACCAATCAga ; Alignment reference a 28 10 15 29 74 2 5 92 91 3 8 82 21 53 c 25 32 12 7 4 92 92 0 2 1 69 6 15 18 g 10 21 38 55 11 1 0 3 1 0 18 7 43 13 t 34 34 32 6 8 2 0 2 3 93 2 2 18 13

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; hykrACCAATCAga ; cor=; Ncor= a 28 10 15 29 74 2 5 92 91 3 8 82 21 53 c 25 32 12 7 4 92 92 0 2 1 69 6 15 18 g 10 21 38 55 11 1 0 3 1 0 18 7 43 13 t 34 34 32 6 8 2 0 2 3 93 2 2 18 13

oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=2/5; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.793407; --yrgCCAATCAga ; cor=; Ncor= a 0 0 13 35 19 2 1 85 80 2 3 80 20 50 c 0 0 23 7 7 80 81 0 0 1 66 2 16 16 g 0 0 20 27 51 1 1 0 3 0 10 1 32 7 t 0 0 29 16 8 2 2 0 2 82 6 2 17 12

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=3/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score= 0.7575; ---raCCAATCAra ; cor=; Ncor= a 0 0 0 56 62 1 10 140 122 6 9 137 37 61 c 0 0 0 16 17 133 125 0 6 2 116 4 29 34 g 0 0 0 47 33 4 3 1 7 2 9 1 46 17 t 0 0 0 24 31 5 5 2 8 133 9 1 31 31

oligos_7nt_mkv4_m4_rc_shift1 (oligos_7nt_mkv4_m4_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4_rc; m=4/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.738787; -ykGACCAATca-- ; cor=; Ncor= a 0 21 23 4 92 1 7 102 100 3 20 60 0 0 c 0 39 13 0 4 94 100 0 2 2 42 13 0 0 g 0 13 34 102 8 8 1 4 5 2 26 22 0 0 t 0 37 40 4 6 7 2 4 3 103 22 15 0 0

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.702895; ---raCCAATGAda ; cor=; Ncor= a 0 0 0 53 63 4 12 139 132 4 9 134 38 66 c 0 0 0 9 33 137 127 1 4 5 19 7 19 30 g 0 0 0 51 26 3 1 4 4 2 110 3 53 20 t 0 0 0 34 25 3 7 3 7 136 9 3 37 31

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m6_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=1; ncol=11; -wwCACGTGww ; Alignment reference a 0 19 16 1 49 0 0 1 0 30 19 c 0 7 6 56 2 59 0 5 1 5 14 g 0 14 5 1 5 0 59 2 57 8 8 t 0 19 32 1 3 0 0 51 1 16 18

oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wwCACGTGww ; cor=; Ncor= a 0 19 16 1 49 0 0 1 0 30 19 c 0 7 6 56 2 59 0 5 1 5 14 g 0 14 5 1 5 0 59 2 57 8 8 t 0 19 32 1 3 0 0 51 1 16 18

oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m5; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.753393; -rtCACATGwy ; cor=; Ncor= a 0 20 10 1 45 0 48 0 0 19 11 c 0 4 4 44 0 48 0 0 0 11 17 g 0 14 2 3 2 0 0 0 48 2 5 t 0 10 32 0 1 0 0 48 0 16 15

oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m6 versus oligos_7nt_mkv4_m2_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.71708; wrTCACATGwh ; cor=; Ncor= a 63 58 7 3 138 2 120 2 6 69 51 c 24 19 2 135 7 120 2 4 2 26 40 g 19 44 1 4 4 7 23 5 139 15 17 t 44 29 140 8 1 21 5 139 3 40 42

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; vyCTTATCtd ; Alignment reference a 13 8 0 0 2 51 7 0 11 14 c 13 15 51 2 0 0 1 51 12 6 g 15 6 0 0 0 0 1 0 10 14 t 10 22 0 49 49 0 42 0 18 17

oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; vyCTTATCtd ; cor=; Ncor= a 13 8 0 0 2 51 7 0 11 14 c 13 15 51 2 0 0 1 51 12 6 g 15 6 0 0 0 0 1 0 10 14 t 10 22 0 49 49 0 42 0 18 17

oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m7; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.78739; rkCTCATCkc ; cor=; Ncor= a 29 12 0 0 2 63 1 1 7 16 c 7 15 66 0 56 0 0 66 14 28 g 17 22 1 2 0 4 3 0 27 9 t 14 18 0 65 9 0 63 0 19 14

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m7_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; rkCTCATCkc ; Alignment reference a 29 12 0 0 2 63 1 1 7 16 c 7 15 66 0 56 0 0 66 14 28 g 17 22 1 2 0 4 3 0 27 9 t 14 18 0 65 9 0 63 0 19 14

oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; rkCTCATCkc ; cor=; Ncor= a 29 12 0 0 2 63 1 1 7 16 c 7 15 66 0 56 0 0 66 14 28 g 17 22 1 2 0 4 3 0 27 9 t 14 18 0 65 9 0 63 0 19 14

oligos_7nt_mkv4_m3_rc_shift0 (oligos_7nt_mkv4_m3_rc)
; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m3_rc; m=2/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.870961; wkCTCATCGc ; cor=; Ncor= a 38 24 6 3 2 92 3 5 4 15 c 17 20 92 6 91 3 0 81 7 42 g 19 28 0 2 1 1 1 1 79 24 t 26 28 2 89 6 4 96 13 10 19

oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m8; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.78739; vyCTTATCtd ; cor=; Ncor= a 13 8 0 0 2 51 7 0 11 14 c 13 15 51 2 0 0 1 51 12 6 g 15 6 0 0 0 0 1 0 10 14 t 10 22 0 49 49 0 42 0 18 17

oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m4; m=4/4; ncol2=10; w=0; offset=2; strand=D; shift=2; score= 0.5196; --ctCATCGC ; cor=; Ncor= a 0 0 16 12 1 68 6 0 0 0 c 0 0 33 13 66 2 4 78 0 72 g 0 0 18 18 6 3 5 0 78 4 t 0 0 11 35 5 5 63 0 0 2

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; tyCCCTCCChh ; Alignment reference a 29 28 2 4 8 4 2 2 8 35 33 c 25 32 112 115 109 0 107 116 111 39 37 g 28 21 4 1 2 6 4 1 2 20 22 t 44 45 8 6 7 116 13 7 5 32 34

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; tyCCCTCCChh ; cor=; Ncor= a 29 28 2 4 8 4 2 2 8 35 33 c 25 32 112 115 109 0 107 116 111 39 37 g 28 21 4 1 2 6 4 1 2 20 22 t 44 45 8 6 7 116 13 7 5 32 34

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---raCCAATGAda ; Alignment reference a 0 0 0 53 63 4 12 139 132 4 9 134 38 66 c 0 0 0 9 33 137 127 1 4 5 19 7 19 30 g 0 0 0 51 26 3 1 4 4 2 110 3 53 20 t 0 0 0 34 25 3 7 3 7 136 9 3 37 31

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---raCCAATGAda ; cor=; Ncor= a 0 0 0 53 63 4 12 139 132 4 9 134 38 66 c 0 0 0 9 33 137 127 1 4 5 19 7 19 30 g 0 0 0 51 26 3 1 4 4 2 110 3 53 20 t 0 0 0 34 25 3 7 3 7 136 9 3 37 31

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m1; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.881474; ---raCCAATCAra ; cor=; Ncor= a 0 0 0 56 62 1 10 140 122 6 9 137 37 61 c 0 0 0 16 17 133 125 0 6 2 116 4 29 34 g 0 0 0 47 33 4 3 1 7 2 9 1 46 17 t 0 0 0 24 31 5 5 2 8 133 9 1 31 31

oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m3_rc; m=3/5; ncol2=12; w=-1; offset=-1; strand=R; shift=2; score=0.802417; --yrgCCAATCAga ; cor=; Ncor= a 0 0 13 35 19 2 1 85 80 2 3 80 20 50 c 0 0 23 7 7 80 81 0 0 1 66 2 16 16 g 0 0 20 27 51 1 1 0 3 0 10 1 32 7 t 0 0 29 16 8 2 2 0 2 82 6 2 17 12

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.702895; hykrACCAATCAga ; cor=; Ncor= a 28 10 15 29 74 2 5 92 91 3 8 82 21 53 c 25 32 12 7 4 92 92 0 2 1 69 6 15 18 g 10 21 38 55 11 1 0 3 1 0 18 7 43 13 t 34 34 32 6 8 2 0 2 3 93 2 2 18 13

oligos_7nt_mkv4_m4_rc_shift1 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m4_rc; m=5/5; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.583394; -ykGACCAATca-- ; cor=; Ncor= a 0 21 23 4 92 1 7 102 100 3 20 60 0 0 c 0 39 13 0 4 94 100 0 2 2 42 13 0 0 g 0 13 34 102 8 8 1 4 5 2 26 22 0 0 t 0 37 40 4 6 7 2 4 3 103 22 15 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --tgATTGGTCmr ; Alignment reference a 0 0 15 22 103 3 4 2 7 6 4 40 37 c 0 0 22 26 2 5 4 1 8 8 102 34 13 g 0 0 13 42 2 2 0 100 94 4 0 13 39 t 0 0 60 20 3 100 102 7 1 92 4 23 21

oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --tgATTGGTCmr ; cor=; Ncor= a 0 0 15 22 103 3 4 2 7 6 4 40 37 c 0 0 22 26 2 5 4 1 8 8 102 34 13 g 0 0 13 42 2 2 0 100 94 4 0 13 39 t 0 0 60 20 3 100 102 7 1 92 4 23 21

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m1_rc; m=2/5; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.738787; tcTGATTGGTymr ; cor=; Ncor= a 13 18 2 2 93 3 2 0 2 8 6 32 34 c 13 43 7 18 0 1 3 0 1 11 55 38 21 g 18 15 6 69 1 2 0 92 92 4 7 12 32 t 53 21 82 8 3 91 92 5 2 74 29 15 10

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m3; m=3/5; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.622733; tcTGATTGGcyr- ; cor=; Ncor= a 12 17 2 6 82 2 0 2 2 8 16 29 0 c 7 32 1 10 0 3 0 1 1 51 27 20 0 g 16 16 2 66 1 0 0 81 80 7 7 23 0 t 50 20 80 3 2 80 85 1 2 19 35 13 0

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=4/5; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.588793; tyTGATTGGty-- ; cor=; Ncor= a 31 31 1 9 133 8 2 5 5 31 24 0 0 c 17 46 1 9 2 7 1 3 4 33 47 0 0 g 34 29 4 116 2 6 0 125 133 17 16 0 0 t 61 37 137 9 6 122 140 10 1 62 56 0 0

oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m5_rc; m=5/5; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.583394; thTCATTGGty-- ; cor=; Ncor= a 31 37 3 9 136 7 3 7 3 25 34 0 0 c 20 53 3 110 2 4 4 1 3 26 51 0 0 g 30 19 7 19 5 4 1 127 137 33 9 0 0 t 66 38 134 9 4 132 139 12 4 63 53 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; tcTGATTGGcyr ; Alignment reference a 12 17 2 6 82 2 0 2 2 8 16 29 c 7 32 1 10 0 3 0 1 1 51 27 20 g 16 16 2 66 1 0 0 81 80 7 7 23 t 50 20 80 3 2 80 85 1 2 19 35 13

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; tcTGATTGGcyr ; cor=; Ncor= a 12 17 2 6 82 2 0 2 2 8 16 29 c 7 32 1 10 0 3 0 1 1 51 27 20 g 16 16 2 66 1 0 0 81 80 7 7 23 t 50 20 80 3 2 80 85 1 2 19 35 13

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m1_rc; m=2/5; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.891326; tyTGATTGGty- ; cor=; Ncor= a 31 31 1 9 133 8 2 5 5 31 24 0 c 17 46 1 9 2 7 1 3 4 33 47 0 g 34 29 4 116 2 6 0 125 133 17 16 0 t 61 37 137 9 6 122 140 10 1 62 56 0

oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m5_rc; m=3/5; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.802417; thTCATTGGty- ; cor=; Ncor= a 31 37 3 9 136 7 3 7 3 25 34 0 c 20 53 3 110 2 4 4 1 3 26 51 0 g 30 19 7 19 5 4 1 127 137 33 9 0 t 66 38 134 9 4 132 139 12 4 63 53 0

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1_rc; m=4/5; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.793407; tcTGATTGGTym ; cor=; Ncor= a 13 18 2 2 93 3 2 0 2 8 6 32 c 13 43 7 18 0 1 3 0 1 11 55 38 g 18 15 6 69 1 2 0 92 92 4 7 12 t 53 21 82 8 3 91 92 5 2 74 29 15

oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m4; m=5/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.622733; --tgATTGGTCm ; cor=; Ncor= a 0 0 15 22 103 3 4 2 7 6 4 40 c 0 0 22 26 2 5 4 1 8 8 102 34 g 0 0 13 42 2 2 0 100 94 4 0 13 t 0 0 60 20 3 100 102 7 1 92 4 23

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -rtCACATGwy ; Alignment reference a 0 20 10 1 45 0 48 0 0 19 11 c 0 4 4 44 0 48 0 0 0 11 17 g 0 14 2 3 2 0 0 0 48 2 5 t 0 10 32 0 1 0 0 48 0 16 15

oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -rtCACATGwy ; cor=; Ncor= a 0 20 10 1 45 0 48 0 0 19 11 c 0 4 4 44 0 48 0 0 0 11 17 g 0 14 2 3 2 0 0 0 48 2 5 t 0 10 32 0 1 0 0 48 0 16 15

oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.880952; wrTCACATGwh ; cor=; Ncor= a 63 58 7 3 138 2 120 2 6 69 51 c 24 19 2 135 7 120 2 4 2 26 40 g 19 44 1 4 4 7 23 5 139 15 17 t 44 29 140 8 1 21 5 139 3 40 42

oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m6; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.753393; -wwCACGTGww ; cor=; Ncor= a 0 19 16 1 49 0 0 1 0 30 19 c 0 7 6 56 2 59 0 5 1 5 14 g 0 14 5 1 5 0 59 2 57 8 8 t 0 19 32 1 3 0 0 51 1 16 18

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; dwCATGTGAyw ; Alignment reference a 42 40 3 139 5 21 1 8 140 29 44 c 17 15 139 5 23 7 4 4 1 44 19 g 40 26 2 4 2 120 7 135 2 19 24 t 51 69 6 2 120 2 138 3 7 58 63

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; dwCATGTGAyw ; cor=; Ncor= a 42 40 3 139 5 21 1 8 140 29 44 c 17 15 139 5 23 7 4 4 1 44 19 g 40 26 2 4 2 120 7 135 2 19 24 t 51 69 6 2 120 2 138 3 7 58 63

oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m5_rc; m=2/3; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.880952; rwCATGTGay- ; cor=; Ncor= a 15 16 0 48 0 0 1 0 32 10 0 c 5 2 48 0 0 0 2 3 2 14 0 g 17 11 0 0 0 48 0 44 4 4 0 t 11 19 0 0 48 0 45 1 10 20 0

oligos_6nt_mkv3_m6_rc_shift0 (oligos_6nt_mkv3_m6_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m6_rc; m=3/3; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.71708; wwCACGTGww- ; cor=; Ncor= a 18 16 1 51 0 0 3 1 32 19 0 c 8 8 57 2 59 0 5 1 5 14 0 g 14 5 1 5 0 59 2 56 6 7 0 t 19 30 0 1 0 0 49 1 16 19 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wgCGATGAGmw ; Alignment reference a 0 35 19 10 13 96 4 6 89 2 28 26 c 0 10 24 79 1 1 1 1 2 0 28 19 g 0 23 42 7 81 0 3 91 6 92 20 17 t 0 32 15 4 5 3 92 2 3 6 24 38

oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wgCGATGAGmw ; cor=; Ncor= a 0 35 19 10 13 96 4 6 89 2 28 26 c 0 10 24 79 1 1 1 1 2 0 28 19 g 0 23 42 7 81 0 3 91 6 92 20 17 t 0 32 15 4 5 3 92 2 3 6 24 38

oligos_6nt_mkv3_m7_rc_shift2 (oligos_6nt_mkv3_m7_rc)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m7_rc; m=2/3; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.870961; --gmGATGAGmy ; cor=; Ncor= a 0 0 14 19 0 63 0 9 65 0 18 14 c 0 0 9 27 0 3 4 0 2 1 22 17 g 0 0 28 14 66 0 0 56 0 66 15 7 t 0 0 16 7 1 1 63 2 0 0 12 29

oligos_6nt_mkv3_m4_rc_shift0 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m4_rc; m=3/3; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.640537; wdGCGATGag-- ; cor=; Ncor= a 27 30 2 0 0 63 5 5 35 11 0 0 c 15 8 4 78 0 5 3 6 18 18 0 0 g 13 20 72 0 78 4 2 66 13 33 0 0 t 23 20 0 0 0 6 68 1 12 16 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --ctCATCGChw ; Alignment reference a 0 0 16 12 1 68 6 0 0 0 20 23 c 0 0 33 13 66 2 4 78 0 72 20 13 g 0 0 18 18 6 3 5 0 78 4 8 15 t 0 0 11 35 5 5 63 0 0 2 30 27

oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ctCATCGChw ; cor=; Ncor= a 0 0 16 12 1 68 6 0 0 0 20 23 c 0 0 33 13 66 2 4 78 0 72 20 13 g 0 0 18 18 6 3 5 0 78 4 8 15 t 0 0 11 35 5 5 63 0 0 2 30 27

oligos_7nt_mkv4_m3_rc_shift0 (oligos_7nt_mkv4_m3_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m3_rc; m=2/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.640537; wkCTCATCGcw- ; cor=; Ncor= a 38 24 6 3 2 92 3 5 4 15 32 0 c 17 20 92 6 91 3 0 81 7 42 23 0 g 19 28 0 2 1 1 1 1 79 24 10 0 t 26 28 2 89 6 4 96 13 10 19 35 0

oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m7; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score= 0.5196; rkCTCATCkc-- ; cor=; Ncor= a 29 12 0 0 2 63 1 1 7 16 0 0 c 7 15 66 0 56 0 0 66 14 28 0 0 g 17 22 1 2 0 4 3 0 27 9 0 0 t 14 18 0 65 9 0 63 0 19 14 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=11; shift=3; ncol=14; ---raCCAATCAra ; Alignment reference a 0 0 0 56 62 1 10 140 122 6 9 137 37 61 c 0 0 0 16 17 133 125 0 6 2 116 4 29 34 g 0 0 0 47 33 4 3 1 7 2 9 1 46 17 t 0 0 0 24 31 5 5 2 8 133 9 1 31 31

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---raCCAATCAra ; cor=; Ncor= a 0 0 0 56 62 1 10 140 122 6 9 137 37 61 c 0 0 0 16 17 133 125 0 6 2 116 4 29 34 g 0 0 0 47 33 4 3 1 7 2 9 1 46 17 t 0 0 0 24 31 5 5 2 8 133 9 1 31 31

oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m3_rc; m=2/5; ncol2=12; w=-1; offset=-1; strand=R; shift=2; score=0.891326; --yrgCCAATCAga ; cor=; Ncor= a 0 0 13 35 19 2 1 85 80 2 3 80 20 50 c 0 0 23 7 7 80 81 0 0 1 66 2 16 16 g 0 0 20 27 51 1 1 0 3 0 10 1 32 7 t 0 0 29 16 8 2 2 0 2 82 6 2 17 12

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5; m=3/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.881474; ---raCCAATGAda ; cor=; Ncor= a 0 0 0 53 63 4 12 139 132 4 9 134 38 66 c 0 0 0 9 33 137 127 1 4 5 19 7 19 30 g 0 0 0 51 26 3 1 4 4 2 110 3 53 20 t 0 0 0 34 25 3 7 3 7 136 9 3 37 31

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score= 0.7575; hykrACCAATCAga ; cor=; Ncor= a 28 10 15 29 74 2 5 92 91 3 8 82 21 53 c 25 32 12 7 4 92 92 0 2 1 69 6 15 18 g 10 21 38 55 11 1 0 3 1 0 18 7 43 13 t 34 34 32 6 8 2 0 2 3 93 2 2 18 13

oligos_7nt_mkv4_m4_rc_shift1 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=5/5; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.588793; -ykGACCAATca-- ; cor=; Ncor= a 0 21 23 4 92 1 7 102 100 3 20 60 0 0 c 0 39 13 0 4 94 100 0 2 2 42 13 0 0 g 0 13 34 102 8 8 1 4 5 2 26 22 0 0 t 0 37 40 4 6 7 2 4 3 103 22 15 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; amCTTGCCkw ; Alignment reference a 26 24 0 8 4 8 4 0 17 19 c 14 19 70 5 5 0 67 73 15 17 g 17 16 3 2 2 66 1 1 20 17 t 17 15 1 59 63 0 2 0 22 21

oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; amCTTGCCkw ; cor=; Ncor= a 26 24 0 8 4 8 4 0 17 19 c 14 19 70 5 5 0 67 73 15 17 g 17 16 3 2 2 66 1 1 20 17 t 17 15 1 59 63 0 2 0 22 21

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; hykrACCAATCAga ; Alignment reference a 28 10 15 29 74 2 5 92 91 3 8 82 21 53 c 25 32 12 7 4 92 92 0 2 1 69 6 15 18 g 10 21 38 55 11 1 0 3 1 0 18 7 43 13 t 34 34 32 6 8 2 0 2 3 93 2 2 18 13
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; hykrACCAATCAga ; cor=; Ncor= a 28 10 15 29 74 2 5 92 91 3 8 82 21 53 c 25 32 12 7 4 92 92 0 2 1 69 6 15 18 g 10 21 38 55 11 1 0 3 1 0 18 7 43 13 t 34 34 32 6 8 2 0 2 3 93 2 2 18 13
oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=2/5; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.793407; --yrgCCAATCAga ; cor=; Ncor= a 0 0 13 35 19 2 1 85 80 2 3 80 20 50 c 0 0 23 7 7 80 81 0 0 1 66 2 16 16 g 0 0 20 27 51 1 1 0 3 0 10 1 32 7 t 0 0 29 16 8 2 2 0 2 82 6 2 17 12
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=3/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score= 0.7575; ---raCCAATCAra ; cor=; Ncor= a 0 0 0 56 62 1 10 140 122 6 9 137 37 61 c 0 0 0 16 17 133 125 0 6 2 116 4 29 34 g 0 0 0 47 33 4 3 1 7 2 9 1 46 17 t 0 0 0 24 31 5 5 2 8 133 9 1 31 31
oligos_7nt_mkv4_m4_rc_shift1 (oligos_7nt_mkv4_m4_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4_rc; m=4/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.738787; -ykGACCAATca-- ; cor=; Ncor= a 0 21 23 4 92 1 7 102 100 3 20 60 0 0 c 0 39 13 0 4 94 100 0 2 2 42 13 0 0 g 0 13 34 102 8 8 1 4 5 2 26 22 0 0 t 0 37 40 4 6 7 2 4 3 103 22 15 0 0
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.702895; ---raCCAATGAda ; cor=; Ncor= a 0 0 0 53 63 4 12 139 132 4 9 134 38 66 c 0 0 0 9 33 137 127 1 4 5 19 7 19 30 g 0 0 0 51 26 3 1 4 4 2 110 3 53 20 t 0 0 0 34 25 3 7 3 7 136 9 3 37 31

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=1; ncol=11; -wwCACGTGww ; Alignment reference a 0 19 16 1 49 0 0 1 0 30 19 c 0 7 6 56 2 59 0 5 1 5 14 g 0 14 5 1 5 0 59 2 57 8 8 t 0 19 32 1 3 0 0 51 1 16 18
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wwCACGTGww ; cor=; Ncor= a 0 19 16 1 49 0 0 1 0 30 19 c 0 7 6 56 2 59 0 5 1 5 14 g 0 14 5 1 5 0 59 2 57 8 8 t 0 19 32 1 3 0 0 51 1 16 18
oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m5; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.753393; -rtCACATGwy ; cor=; Ncor= a 0 20 10 1 45 0 48 0 0 19 11 c 0 4 4 44 0 48 0 0 0 11 17 g 0 14 2 3 2 0 0 0 48 2 5 t 0 10 32 0 1 0 0 48 0 16 15
oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m6 versus oligos_7nt_mkv4_m2_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.71708; wrTCACATGwh ; cor=; Ncor= a 63 58 7 3 138 2 120 2 6 69 51 c 24 19 2 135 7 120 2 4 2 26 40 g 19 44 1 4 4 7 23 5 139 15 17 t 44 29 140 8 1 21 5 139 3 40 42

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; rkCTCATCkc ; Alignment reference a 29 12 0 0 2 63 1 1 7 16 c 7 15 66 0 56 0 0 66 14 28 g 17 22 1 2 0 4 3 0 27 9 t 14 18 0 65 9 0 63 0 19 14
oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; rkCTCATCkc ; cor=; Ncor= a 29 12 0 0 2 63 1 1 7 16 c 7 15 66 0 56 0 0 66 14 28 g 17 22 1 2 0 4 3 0 27 9 t 14 18 0 65 9 0 63 0 19 14
oligos_7nt_mkv4_m3_rc_shift0 (oligos_7nt_mkv4_m3_rc)				; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m3_rc; m=2/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.870961; wkCTCATCGc ; cor=; Ncor= a 38 24 6 3 2 92 3 5 4 15 c 17 20 92 6 91 3 0 81 7 42 g 19 28 0 2 1 1 1 1 79 24 t 26 28 2 89 6 4 96 13 10 19
oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m8; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.78739; vyCTTATCtd ; cor=; Ncor= a 13 8 0 0 2 51 7 0 11 14 c 13 15 51 2 0 0 1 51 12 6 g 15 6 0 0 0 0 1 0 10 14 t 10 22 0 49 49 0 42 0 18 17
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m4; m=4/4; ncol2=10; w=0; offset=2; strand=D; shift=2; score= 0.5196; --ctCATCGC ; cor=; Ncor= a 0 0 16 12 1 68 6 0 0 0 c 0 0 33 13 66 2 4 78 0 72 g 0 0 18 18 6 3 5 0 78 4 t 0 0 11 35 5 5 63 0 0 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---raCCAATGAda ; Alignment reference a 0 0 0 53 63 4 12 139 132 4 9 134 38 66 c 0 0 0 9 33 137 127 1 4 5 19 7 19 30 g 0 0 0 51 26 3 1 4 4 2 110 3 53 20 t 0 0 0 34 25 3 7 3 7 136 9 3 37 31
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---raCCAATGAda ; cor=; Ncor= a 0 0 0 53 63 4 12 139 132 4 9 134 38 66 c 0 0 0 9 33 137 127 1 4 5 19 7 19 30 g 0 0 0 51 26 3 1 4 4 2 110 3 53 20 t 0 0 0 34 25 3 7 3 7 136 9 3 37 31
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m1; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.881474; ---raCCAATCAra ; cor=; Ncor= a 0 0 0 56 62 1 10 140 122 6 9 137 37 61 c 0 0 0 16 17 133 125 0 6 2 116 4 29 34 g 0 0 0 47 33 4 3 1 7 2 9 1 46 17 t 0 0 0 24 31 5 5 2 8 133 9 1 31 31
oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m3_rc; m=3/5; ncol2=12; w=-1; offset=-1; strand=R; shift=2; score=0.802417; --yrgCCAATCAga ; cor=; Ncor= a 0 0 13 35 19 2 1 85 80 2 3 80 20 50 c 0 0 23 7 7 80 81 0 0 1 66 2 16 16 g 0 0 20 27 51 1 1 0 3 0 10 1 32 7 t 0 0 29 16 8 2 2 0 2 82 6 2 17 12
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.702895; hykrACCAATCAga ; cor=; Ncor= a 28 10 15 29 74 2 5 92 91 3 8 82 21 53 c 25 32 12 7 4 92 92 0 2 1 69 6 15 18 g 10 21 38 55 11 1 0 3 1 0 18 7 43 13 t 34 34 32 6 8 2 0 2 3 93 2 2 18 13
oligos_7nt_mkv4_m4_rc_shift1 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m4_rc; m=5/5; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.583394; -ykGACCAATca-- ; cor=; Ncor= a 0 21 23 4 92 1 7 102 100 3 20 60 0 0 c 0 39 13 0 4 94 100 0 2 2 42 13 0 0 g 0 13 34 102 8 8 1 4 5 2 26 22 0 0 t 0 37 40 4 6 7 2 4 3 103 22 15 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --tgATTGGTCmr ; Alignment reference a 0 0 15 22 103 3 4 2 7 6 4 40 37 c 0 0 22 26 2 5 4 1 8 8 102 34 13 g 0 0 13 42 2 2 0 100 94 4 0 13 39 t 0 0 60 20 3 100 102 7 1 92 4 23 21
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --tgATTGGTCmr ; cor=; Ncor= a 0 0 15 22 103 3 4 2 7 6 4 40 37 c 0 0 22 26 2 5 4 1 8 8 102 34 13 g 0 0 13 42 2 2 0 100 94 4 0 13 39 t 0 0 60 20 3 100 102 7 1 92 4 23 21
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m1_rc; m=2/5; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.738787; tcTGATTGGTymr ; cor=; Ncor= a 13 18 2 2 93 3 2 0 2 8 6 32 34 c 13 43 7 18 0 1 3 0 1 11 55 38 21 g 18 15 6 69 1 2 0 92 92 4 7 12 32 t 53 21 82 8 3 91 92 5 2 74 29 15 10
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m3; m=3/5; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.622733; tcTGATTGGcyr- ; cor=; Ncor= a 12 17 2 6 82 2 0 2 2 8 16 29 0 c 7 32 1 10 0 3 0 1 1 51 27 20 0 g 16 16 2 66 1 0 0 81 80 7 7 23 0 t 50 20 80 3 2 80 85 1 2 19 35 13 0
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=4/5; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.588793; tyTGATTGGty-- ; cor=; Ncor= a 31 31 1 9 133 8 2 5 5 31 24 0 0 c 17 46 1 9 2 7 1 3 4 33 47 0 0 g 34 29 4 116 2 6 0 125 133 17 16 0 0 t 61 37 137 9 6 122 140 10 1 62 56 0 0
oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m5_rc; m=5/5; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.583394; thTCATTGGty-- ; cor=; Ncor= a 31 37 3 9 136 7 3 7 3 25 34 0 0 c 20 53 3 110 2 4 4 1 3 26 51 0 0 g 30 19 7 19 5 4 1 127 137 33 9 0 0 t 66 38 134 9 4 132 139 12 4 63 53 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; tcTGATTGGcyr ; Alignment reference a 12 17 2 6 82 2 0 2 2 8 16 29 c 7 32 1 10 0 3 0 1 1 51 27 20 g 16 16 2 66 1 0 0 81 80 7 7 23 t 50 20 80 3 2 80 85 1 2 19 35 13
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; tcTGATTGGcyr ; cor=; Ncor= a 12 17 2 6 82 2 0 2 2 8 16 29 c 7 32 1 10 0 3 0 1 1 51 27 20 g 16 16 2 66 1 0 0 81 80 7 7 23 t 50 20 80 3 2 80 85 1 2 19 35 13
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m1_rc; m=2/5; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.891326; tyTGATTGGty- ; cor=; Ncor= a 31 31 1 9 133 8 2 5 5 31 24 0 c 17 46 1 9 2 7 1 3 4 33 47 0 g 34 29 4 116 2 6 0 125 133 17 16 0 t 61 37 137 9 6 122 140 10 1 62 56 0
oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m5_rc; m=3/5; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.802417; thTCATTGGty- ; cor=; Ncor= a 31 37 3 9 136 7 3 7 3 25 34 0 c 20 53 3 110 2 4 4 1 3 26 51 0 g 30 19 7 19 5 4 1 127 137 33 9 0 t 66 38 134 9 4 132 139 12 4 63 53 0
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1_rc; m=4/5; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.793407; tcTGATTGGTym ; cor=; Ncor= a 13 18 2 2 93 3 2 0 2 8 6 32 c 13 43 7 18 0 1 3 0 1 11 55 38 g 18 15 6 69 1 2 0 92 92 4 7 12 t 53 21 82 8 3 91 92 5 2 74 29 15
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m4; m=5/5; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.622733; --tgATTGGTCm ; cor=; Ncor= a 0 0 15 22 103 3 4 2 7 6 4 40 c 0 0 22 26 2 5 4 1 8 8 102 34 g 0 0 13 42 2 2 0 100 94 4 0 13 t 0 0 60 20 3 100 102 7 1 92 4 23

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -rtCACATGwy ; Alignment reference a 0 20 10 1 45 0 48 0 0 19 11 c 0 4 4 44 0 48 0 0 0 11 17 g 0 14 2 3 2 0 0 0 48 2 5 t 0 10 32 0 1 0 0 48 0 16 15
oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -rtCACATGwy ; cor=; Ncor= a 0 20 10 1 45 0 48 0 0 19 11 c 0 4 4 44 0 48 0 0 0 11 17 g 0 14 2 3 2 0 0 0 48 2 5 t 0 10 32 0 1 0 0 48 0 16 15
oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.880952; wrTCACATGwh ; cor=; Ncor= a 63 58 7 3 138 2 120 2 6 69 51 c 24 19 2 135 7 120 2 4 2 26 40 g 19 44 1 4 4 7 23 5 139 15 17 t 44 29 140 8 1 21 5 139 3 40 42
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m6; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.753393; -wwCACGTGww ; cor=; Ncor= a 0 19 16 1 49 0 0 1 0 30 19 c 0 7 6 56 2 59 0 5 1 5 14 g 0 14 5 1 5 0 59 2 57 8 8 t 0 19 32 1 3 0 0 51 1 16 18

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; dwCATGTGAyw ; Alignment reference a 42 40 3 139 5 21 1 8 140 29 44 c 17 15 139 5 23 7 4 4 1 44 19 g 40 26 2 4 2 120 7 135 2 19 24 t 51 69 6 2 120 2 138 3 7 58 63
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; dwCATGTGAyw ; cor=; Ncor= a 42 40 3 139 5 21 1 8 140 29 44 c 17 15 139 5 23 7 4 4 1 44 19 g 40 26 2 4 2 120 7 135 2 19 24 t 51 69 6 2 120 2 138 3 7 58 63
oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m5_rc; m=2/3; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.880952; rwCATGTGay- ; cor=; Ncor= a 15 16 0 48 0 0 1 0 32 10 0 c 5 2 48 0 0 0 2 3 2 14 0 g 17 11 0 0 0 48 0 44 4 4 0 t 11 19 0 0 48 0 45 1 10 20 0
oligos_6nt_mkv3_m6_rc_shift0 (oligos_6nt_mkv3_m6_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m6_rc; m=3/3; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.71708; wwCACGTGww- ; cor=; Ncor= a 18 16 1 51 0 0 3 1 32 19 0 c 8 8 57 2 59 0 5 1 5 14 0 g 14 5 1 5 0 59 2 56 6 7 0 t 19 30 0 1 0 0 49 1 16 19 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wgCGATGAGmw ; Alignment reference a 0 35 19 10 13 96 4 6 89 2 28 26 c 0 10 24 79 1 1 1 1 2 0 28 19 g 0 23 42 7 81 0 3 91 6 92 20 17 t 0 32 15 4 5 3 92 2 3 6 24 38
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wgCGATGAGmw ; cor=; Ncor= a 0 35 19 10 13 96 4 6 89 2 28 26 c 0 10 24 79 1 1 1 1 2 0 28 19 g 0 23 42 7 81 0 3 91 6 92 20 17 t 0 32 15 4 5 3 92 2 3 6 24 38
oligos_6nt_mkv3_m7_rc_shift2 (oligos_6nt_mkv3_m7_rc)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m7_rc; m=2/3; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.870961; --gmGATGAGmy ; cor=; Ncor= a 0 0 14 19 0 63 0 9 65 0 18 14 c 0 0 9 27 0 3 4 0 2 1 22 17 g 0 0 28 14 66 0 0 56 0 66 15 7 t 0 0 16 7 1 1 63 2 0 0 12 29
oligos_6nt_mkv3_m4_rc_shift0 (oligos_6nt_mkv3_m4_rc)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m4_rc; m=3/3; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.640537; wdGCGATGag-- ; cor=; Ncor= a 27 30 2 0 0 63 5 5 35 11 0 0 c 15 8 4 78 0 5 3 6 18 18 0 0 g 13 20 72 0 78 4 2 66 13 33 0 0 t 23 20 0 0 0 6 68 1 12 16 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --ctCATCGChw ; Alignment reference a 0 0 16 12 1 68 6 0 0 0 20 23 c 0 0 33 13 66 2 4 78 0 72 20 13 g 0 0 18 18 6 3 5 0 78 4 8 15 t 0 0 11 35 5 5 63 0 0 2 30 27
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ctCATCGChw ; cor=; Ncor= a 0 0 16 12 1 68 6 0 0 0 20 23 c 0 0 33 13 66 2 4 78 0 72 20 13 g 0 0 18 18 6 3 5 0 78 4 8 15 t 0 0 11 35 5 5 63 0 0 2 30 27
oligos_7nt_mkv4_m3_rc_shift0 (oligos_7nt_mkv4_m3_rc)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m3_rc; m=2/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.640537; wkCTCATCGcw- ; cor=; Ncor= a 38 24 6 3 2 92 3 5 4 15 32 0 c 17 20 92 6 91 3 0 81 7 42 23 0 g 19 28 0 2 1 1 1 1 79 24 10 0 t 26 28 2 89 6 4 96 13 10 19 35 0
oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m7; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score= 0.5196; rkCTCATCkc-- ; cor=; Ncor= a 29 12 0 0 2 63 1 1 7 16 0 0 c 7 15 66 0 56 0 0 66 14 28 0 0 g 17 22 1 2 0 4 3 0 27 9 0 0 t 14 18 0 65 9 0 63 0 19 14 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=11; shift=3; ncol=14; ---raCCAATCAra ; Alignment reference a 0 0 0 56 62 1 10 140 122 6 9 137 37 61 c 0 0 0 16 17 133 125 0 6 2 116 4 29 34 g 0 0 0 47 33 4 3 1 7 2 9 1 46 17 t 0 0 0 24 31 5 5 2 8 133 9 1 31 31
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---raCCAATCAra ; cor=; Ncor= a 0 0 0 56 62 1 10 140 122 6 9 137 37 61 c 0 0 0 16 17 133 125 0 6 2 116 4 29 34 g 0 0 0 47 33 4 3 1 7 2 9 1 46 17 t 0 0 0 24 31 5 5 2 8 133 9 1 31 31
oligos_6nt_mkv3_m3_rc_shift2 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m3_rc; m=2/5; ncol2=12; w=-1; offset=-1; strand=R; shift=2; score=0.891326; --yrgCCAATCAga ; cor=; Ncor= a 0 0 13 35 19 2 1 85 80 2 3 80 20 50 c 0 0 23 7 7 80 81 0 0 1 66 2 16 16 g 0 0 20 27 51 1 1 0 3 0 10 1 32 7 t 0 0 29 16 8 2 2 0 2 82 6 2 17 12
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5; m=3/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.881474; ---raCCAATGAda ; cor=; Ncor= a 0 0 0 53 63 4 12 139 132 4 9 134 38 66 c 0 0 0 9 33 137 127 1 4 5 19 7 19 30 g 0 0 0 51 26 3 1 4 4 2 110 3 53 20 t 0 0 0 34 25 3 7 3 7 136 9 3 37 31
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=4/5; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score= 0.7575; hykrACCAATCAga ; cor=; Ncor= a 28 10 15 29 74 2 5 92 91 3 8 82 21 53 c 25 32 12 7 4 92 92 0 2 1 69 6 15 18 g 10 21 38 55 11 1 0 3 1 0 18 7 43 13 t 34 34 32 6 8 2 0 2 3 93 2 2 18 13
oligos_7nt_mkv4_m4_rc_shift1 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=5/5; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.588793; -ykGACCAATca-- ; cor=; Ncor= a 0 21 23 4 92 1 7 102 100 3 20 60 0 0 c 0 39 13 0 4 94 100 0 2 2 42 13 0 0 g 0 13 34 102 8 8 1 4 5 2 26 22 0 0 t 0 37 40 4 6 7 2 4 3 103 22 15 0 0