One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.111011_2025-04-03.111011_OYKgLb/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.2025-04-03.111011_2025-04-03.111011_OYKgLb/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -twGCTTACta ; Alignment reference a 0 4 11 1 0 0 0 26 0 3 10 c 0 6 6 0 25 0 0 0 26 2 5 g 0 2 2 25 1 0 0 0 0 4 6 t 0 14 7 0 0 26 26 0 0 17 5

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -twGCTTACta ; cor=; Ncor= a 0 4 11 1 0 0 0 26 0 3 10 c 0 6 6 0 25 0 0 0 26 2 5 g 0 2 2 25 1 0 0 0 0 4 6 t 0 14 7 0 0 26 26 0 0 17 5

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5_rc; m=2/4; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.854562; -twGCTkACTm ; cor=; Ncor= a 0 16 30 2 2 2 1 84 1 3 26 c 0 24 17 1 96 0 2 12 84 2 43 g 0 20 14 97 1 1 31 3 12 2 23 t 0 40 39 0 1 97 66 1 3 93 8

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=3/4; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.518977; mwTGCTGACTm ; cor=; Ncor= a 27 23 10 1 15 0 0 71 0 1 35 c 18 17 4 2 54 0 1 0 60 0 28 g 15 7 5 67 2 0 57 0 11 0 6 t 11 24 52 1 0 71 13 0 0 70 2

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=4/4; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.413927; rwtGCTGAsTC ; cor=; Ncor= a 22 18 5 2 15 0 0 66 0 0 16 c 15 14 4 0 50 0 1 0 42 0 48 g 19 12 13 64 1 0 57 0 24 0 2 t 10 22 44 0 0 66 8 0 0 66 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -rgrAAAGGAGgs ; Alignment reference a 0 12 10 26 32 43 45 0 0 38 3 9 10 c 0 11 5 2 4 1 0 0 0 1 1 9 14 g 0 14 22 12 1 1 0 43 45 6 41 22 13 t 0 8 8 5 8 0 0 2 0 0 0 5 8

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rgrAAAGGAGgs ; cor=; Ncor= a 0 12 10 26 32 43 45 0 0 38 3 9 10 c 0 11 5 2 4 1 0 0 0 1 1 9 14 g 0 14 22 12 1 1 0 43 45 6 41 22 13 t 0 8 8 5 8 0 0 2 0 0 0 5 8

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=2/2; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.826121; yrGrAAAGGAGGs ; cor=; Ncor= a 7 9 5 19 25 31 31 1 0 26 1 4 7 c 9 6 2 1 1 1 0 0 1 2 1 1 8 g 7 12 25 9 1 0 1 27 31 3 30 27 13 t 9 5 0 3 5 0 0 4 0 1 0 0 4

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=13; shift=4; ncol=17; ----GmTGACTmAGCva ; Alignment reference a 0 0 0 0 6 20 0 0 64 0 2 41 65 2 10 17 30 c 0 0 0 0 8 31 1 1 0 60 2 19 0 4 45 17 9 g 0 0 0 0 48 8 0 59 0 4 1 4 0 51 3 20 12 t 0 0 0 0 3 6 64 5 1 1 60 1 0 8 7 11 14

oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=4; score= 1; ----GmTGACTmAGCva ; cor=; Ncor= a 0 0 0 0 6 20 0 0 64 0 2 41 65 2 10 17 30 c 0 0 0 0 8 31 1 1 0 60 2 19 0 4 45 17 9 g 0 0 0 0 48 8 0 59 0 4 1 4 0 51 3 20 12 t 0 0 0 0 3 6 64 5 1 1 60 1 0 8 7 11 14

oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=2/6; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.764735; -rwtGMTGAsTMAGCaa ; cor=; Ncor= a 0 26 21 5 1 19 0 0 74 0 0 19 73 1 6 33 28 c 0 18 18 10 1 53 0 1 0 50 0 51 0 1 63 17 15 g 0 20 15 14 72 2 0 68 0 24 0 4 0 55 1 16 15 t 0 10 20 45 0 0 74 5 0 0 74 0 1 17 4 8 16

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=3/6; ncol2=15; w=-3; offset=-3; strand=D; shift=1; score=0.728089; -mwTGCTGACTmAgcr- ; cor=; Ncor= a 0 27 23 10 1 15 0 0 71 0 1 35 66 7 9 27 0 c 0 18 17 4 2 54 0 1 0 60 0 28 2 2 48 13 0 g 0 15 7 5 67 2 0 57 0 11 0 6 2 45 2 21 0 t 0 11 24 52 1 0 71 13 0 0 70 2 1 17 12 10 0

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=4/6; ncol2=17; w=-3; offset=-3; strand=R; shift=1; score=0.707083; -rwtGCTGAsTCAGCaw ; cor=; Ncor= a 0 22 18 5 2 15 0 0 66 0 0 16 66 0 5 38 23 c 0 15 14 4 0 50 0 1 0 42 0 48 0 1 58 12 14 g 0 19 12 13 64 1 0 57 0 24 0 2 0 53 0 10 12 t 0 10 22 44 0 0 66 8 0 0 66 0 0 12 3 6 17

oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=5/6; ncol2=11; w=0; offset=2; strand=D; shift=6; score=0.661146; ------tkAGTmAGCwa ; cor=; Ncor= a 0 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 c 0 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 g 0 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 t 0 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=6/6; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.510721; raaTGmTGACTmA---- ; cor=; Ncor= a 18 26 26 3 1 31 0 0 53 1 0 22 42 0 0 0 0 c 11 7 11 0 0 21 0 1 0 44 0 21 5 0 0 0 0 g 18 13 8 5 52 1 1 51 0 5 0 6 2 0 0 0 0 t 6 7 8 45 0 0 52 1 0 3 53 4 4 0 0 0 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; yrGrAAAGGAGGsd ; Alignment reference a 7 9 5 19 25 31 31 1 0 26 1 4 7 10 c 9 6 2 1 1 1 0 0 1 2 1 1 8 4 g 7 12 25 9 1 0 1 27 31 3 30 27 13 8 t 9 5 0 3 5 0 0 4 0 1 0 0 4 10

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; yrGrAAAGGAGGsd ; cor=; Ncor= a 7 9 5 19 25 31 31 1 0 26 1 4 7 10 c 9 6 2 1 1 1 0 0 1 2 1 1 8 4 g 7 12 25 9 1 0 1 27 31 3 30 27 13 8 t 9 5 0 3 5 0 0 4 0 1 0 0 4 10

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.826121; -rgrAAAGGAGgs- ; cor=; Ncor= a 0 12 10 26 32 43 45 0 0 38 3 9 10 0 c 0 11 5 2 4 1 0 0 0 1 1 9 14 0 g 0 14 22 12 1 1 0 43 45 6 41 22 13 0 t 0 8 8 5 8 0 0 2 0 0 0 5 8 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; mwtGCTGAsTCAGCawy ; Alignment reference a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 10 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 19 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 15 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18 22

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; mwtGCTGAsTCAGCawy ; cor=; Ncor= a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 10 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 19 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 15 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18 22

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/7; ncol2=16; w=0; offset=1; strand=D; shift=1; score=0.936684; -ttGCTKAsTCAKCawy ; cor=; Ncor= a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 10 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 20 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 18 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21 26

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=3/7; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.849234; --ygcTkAGTCAGCAwk ; cor=; Ncor= a 0 0 10 12 17 1 2 70 0 0 13 71 0 1 52 24 11 c 0 0 21 2 45 2 6 0 11 0 57 0 2 67 5 7 15 g 0 0 13 48 2 2 28 0 60 0 1 0 54 2 4 17 18 t 0 0 27 9 7 66 35 1 0 71 0 0 15 1 10 23 27

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/7; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.707083; -tbGCTkAGTCAkC--- ; cor=; Ncor= a 0 14 11 7 8 0 1 60 1 1 5 64 6 3 0 0 0 c 0 12 20 3 51 0 4 1 4 0 59 0 8 48 0 0 0 g 0 9 17 45 4 0 19 2 60 0 1 1 31 8 0 0 0 t 0 30 17 10 2 65 41 2 0 64 0 0 20 6 0 0 0

oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=5/7; ncol2=13; w=0; offset=5; strand=D; shift=5; score=0.619675; -----TkAGTCAkCAtt ; cor=; Ncor= a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 7 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 13 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 7 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26 26

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=6/7; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.561931; -----tkAGTmAGCwa- ; cor=; Ncor= a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 0 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 0 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 0 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16 0

oligos_6nt_mkv2_m5_rc_shift6 (oligos_6nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=7/7; ncol2=10; w=0; offset=6; strand=R; shift=6; score=0.413927; ------taGTAAGCwa- ; cor=; Ncor= a 0 0 0 0 0 0 5 17 0 0 26 26 0 0 7 14 0 c 0 0 0 0 0 0 6 4 0 0 0 0 1 25 2 2 0 g 0 0 0 0 0 0 5 2 26 0 0 0 25 0 6 6 0 t 0 0 0 0 0 0 10 3 0 26 0 0 0 1 11 4 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift5 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=13; shift=5; ncol=18; -----TkAGTCAkCAtty ; Alignment reference a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 7 6 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 13 18 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 7 11 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26 26 18

oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=5; score= 1; -----TkAGTCAkCAtty ; cor=; Ncor= a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 7 6 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 13 18 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 7 11 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26 26 18

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=2/6; ncol2=15; w=-3; offset=-3; strand=R; shift=2; score=0.715759; --ygcTkAGTCAGCAwk- ; cor=; Ncor= a 0 0 10 12 17 1 2 70 0 0 13 71 0 1 52 24 11 0 c 0 0 21 2 45 2 6 0 11 0 57 0 2 67 5 7 15 0 g 0 0 13 48 2 2 28 0 60 0 1 0 54 2 4 17 18 0 t 0 0 27 9 7 66 35 1 0 71 0 0 15 1 10 23 27 0

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=5; score=0.664877; -----tkAGTmAGCwa-- ; cor=; Ncor= a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 0 0 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 0 0 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 0 0 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16 0 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=4/6; ncol2=16; w=-4; offset=-4; strand=D; shift=1; score=0.663849; -ttGCTKAsTCAKCawy- ; cor=; Ncor= a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 10 0 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 20 0 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 18 0 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21 26 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=5/6; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.619675; mwtGCTGAsTCAGCawy- ; cor=; Ncor= a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 10 0 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 19 0 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 15 0 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18 22 0

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=6/6; ncol2=13; w=-4; offset=-4; strand=R; shift=1; score=0.510721; -tbGCTkAGTCAkC---- ; cor=; Ncor= a 0 14 11 7 8 0 1 60 1 1 5 64 6 3 0 0 0 0 c 0 12 20 3 51 0 4 1 4 0 59 0 8 48 0 0 0 0 g 0 9 17 45 4 0 19 2 60 0 1 1 31 8 0 0 0 0 t 0 30 17 10 2 65 41 2 0 64 0 0 20 6 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift5 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=5; ncol=16; -----tkAGTmAGCwa ; Alignment reference a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----tkAGTmAGCwa ; cor=; Ncor= a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16

oligos_6nt_mkv2_m5_rc_shift6 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5_rc; m=2/7; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.854562; ------taGTAAGCwa ; cor=; Ncor= a 0 0 0 0 0 0 5 17 0 0 26 26 0 0 7 14 c 0 0 0 0 0 0 6 4 0 0 0 0 1 25 2 2 g 0 0 0 0 0 0 5 2 26 0 0 0 25 0 6 6 t 0 0 0 0 0 0 10 3 0 26 0 0 0 1 11 4

oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=3/7; ncol2=13; w=0; offset=0; strand=D; shift=5; score=0.664877; -----TkAGTCAkCAt ; cor=; Ncor= a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=4/7; ncol2=13; w=-2; offset=-2; strand=D; shift=3; score=0.661146; ---GmTGACTmAGCva ; cor=; Ncor= a 0 0 0 6 20 0 0 64 0 2 41 65 2 10 17 30 c 0 0 0 8 31 1 1 0 60 2 19 0 4 45 17 9 g 0 0 0 48 8 0 59 0 4 1 4 0 51 3 20 12 t 0 0 0 3 6 64 5 1 1 60 1 0 8 7 11 14

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4_rc; m=5/7; ncol2=15; w=-3; offset=-3; strand=R; shift=2; score=0.65826; --ygcTkAGTCAGCAw ; cor=; Ncor= a 0 0 10 12 17 1 2 70 0 0 13 71 0 1 52 24 c 0 0 21 2 45 2 6 0 11 0 57 0 2 67 5 7 g 0 0 13 48 2 2 28 0 60 0 1 0 54 2 4 17 t 0 0 27 9 7 66 35 1 0 71 0 0 15 1 10 23

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=6/7; ncol2=16; w=-4; offset=-4; strand=D; shift=1; score=0.591553; -ttGCTKAsTCAKCaw ; cor=; Ncor= a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=7/7; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.561931; mwtGCTGAsTCAGCaw ; cor=; Ncor= a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift1 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=15; shift=1; ncol=16; -mwTGCTGACTmAgcr ; Alignment reference a 0 27 23 10 1 15 0 0 71 0 1 35 66 7 9 27 c 0 18 17 4 2 54 0 1 0 60 0 28 2 2 48 13 g 0 15 7 5 67 2 0 57 0 11 0 6 2 45 2 21 t 0 11 24 52 1 0 71 13 0 0 70 2 1 17 12 10

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -mwTGCTGACTmAgcr ; cor=; Ncor= a 0 27 23 10 1 15 0 0 71 0 1 35 66 7 9 27 c 0 18 17 4 2 54 0 1 0 60 0 28 2 2 48 13 g 0 15 7 5 67 2 0 57 0 11 0 6 2 45 2 21 t 0 11 24 52 1 0 71 13 0 0 70 2 1 17 12 10

oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1_rc; m=2/7; ncol2=16; w=0; offset=0; strand=R; shift=1; score=0.908741; -rwtGMTGAsTMAGCa ; cor=; Ncor= a 0 26 21 5 1 19 0 0 74 0 0 19 73 1 6 33 c 0 18 18 10 1 53 0 1 0 50 0 51 0 1 63 17 g 0 20 15 14 72 2 0 68 0 24 0 4 0 55 1 16 t 0 10 20 45 0 0 74 5 0 0 74 0 1 17 4 8

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1_rc; m=3/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.849234; -rwtGCTGAsTCAGCa ; cor=; Ncor= a 0 22 18 5 2 15 0 0 66 0 0 16 66 0 5 38 c 0 15 14 4 0 50 0 1 0 42 0 48 0 1 58 12 g 0 19 12 13 64 1 0 57 0 24 0 2 0 53 0 10 t 0 10 22 44 0 0 66 8 0 0 66 0 0 12 3 6

oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=4/7; ncol2=13; w=0; offset=3; strand=D; shift=4; score=0.728089; ----GmTGACTmAGCv ; cor=; Ncor= a 0 0 0 0 6 20 0 0 64 0 2 41 65 2 10 17 c 0 0 0 0 8 31 1 1 0 60 2 19 0 4 45 17 g 0 0 0 0 48 8 0 59 0 4 1 4 0 51 3 20 t 0 0 0 0 3 6 64 5 1 1 60 1 0 8 7 11

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=5/7; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.715759; raaTGmTGACTmA--- ; cor=; Ncor= a 18 26 26 3 1 31 0 0 53 1 0 22 42 0 0 0 c 11 7 11 0 0 21 0 1 0 44 0 21 5 0 0 0 g 18 13 8 5 52 1 1 51 0 5 0 6 2 0 0 0 t 6 7 8 45 0 0 52 1 0 3 53 4 4 0 0 0

oligos_7nt_mkv2_m5_rc_shift2 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=6/7; ncol2=11; w=0; offset=1; strand=R; shift=2; score=0.65826; --twGCTkACTma--- ; cor=; Ncor= a 0 0 16 30 2 2 2 1 84 1 3 26 61 0 0 0 c 0 0 24 17 1 96 0 2 12 84 2 43 10 0 0 0 g 0 0 20 14 97 1 1 31 3 12 2 23 22 0 0 0 t 0 0 40 39 0 1 97 66 1 3 93 8 7 0 0 0

oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=7/7; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.518977; --twGCTTACta---- ; cor=; Ncor= a 0 0 4 11 1 0 0 0 26 0 3 10 0 0 0 0 c 0 0 6 6 0 25 0 0 0 26 2 5 0 0 0 0 g 0 0 2 2 25 1 0 0 0 0 4 6 0 0 0 0 t 0 0 14 7 0 0 26 26 0 0 17 5 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=16; shift=1; ncol=17; -ttGCTKAsTCAKCawy ; Alignment reference a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 10 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 20 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 18 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21 26

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/6; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -ttGCTKAsTCAKCawy ; cor=; Ncor= a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 10 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 20 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 18 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21 26

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/6; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.936684; mwtGCTGAsTCAGCawy ; cor=; Ncor= a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 10 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 19 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 15 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18 22

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=3/6; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.908741; --ygcTkAGTCAGCAwk ; cor=; Ncor= a 0 0 10 12 17 1 2 70 0 0 13 71 0 1 52 24 11 c 0 0 21 2 45 2 6 0 11 0 57 0 2 67 5 7 15 g 0 0 13 48 2 2 28 0 60 0 1 0 54 2 4 17 18 t 0 0 27 9 7 66 35 1 0 71 0 0 15 1 10 23 27

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/6; ncol2=13; w=0; offset=0; strand=R; shift=1; score=0.764735; -tbGCTkAGTCAkC--- ; cor=; Ncor= a 0 14 11 7 8 0 1 60 1 1 5 64 6 3 0 0 0 c 0 12 20 3 51 0 4 1 4 0 59 0 8 48 0 0 0 g 0 9 17 45 4 0 19 2 60 0 1 1 31 8 0 0 0 t 0 30 17 10 2 65 41 2 0 64 0 0 20 6 0 0 0

oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=5/6; ncol2=13; w=0; offset=4; strand=D; shift=5; score=0.663849; -----TkAGTCAkCAtt ; cor=; Ncor= a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 7 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 13 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 7 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26 26

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=6/6; ncol2=11; w=0; offset=4; strand=D; shift=5; score=0.591553; -----tkAGTmAGCwa- ; cor=; Ncor= a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 0 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 0 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 0 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; ryCAGGGGykr ; Alignment reference a 12 9 0 44 0 0 0 1 7 10 13 c 11 12 44 0 0 2 1 0 13 11 7 g 12 9 0 1 45 43 43 44 8 12 21 t 10 15 1 0 0 0 1 0 17 12 4

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ryCAGGGGykr ; cor=; Ncor= a 12 9 0 44 0 0 0 1 7 10 13 c 11 12 44 0 0 2 1 0 13 11 7 g 12 9 0 1 45 43 43 44 8 12 21 t 10 15 1 0 0 0 1 0 17 12 4

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -twGCTTACta ; Alignment reference a 0 4 11 1 0 0 0 26 0 3 10 c 0 6 6 0 25 0 0 0 26 2 5 g 0 2 2 25 1 0 0 0 0 4 6 t 0 14 7 0 0 26 26 0 0 17 5
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -twGCTTACta ; cor=; Ncor= a 0 4 11 1 0 0 0 26 0 3 10 c 0 6 6 0 25 0 0 0 26 2 5 g 0 2 2 25 1 0 0 0 0 4 6 t 0 14 7 0 0 26 26 0 0 17 5
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5_rc; m=2/4; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.854562; -twGCTkACTm ; cor=; Ncor= a 0 16 30 2 2 2 1 84 1 3 26 c 0 24 17 1 96 0 2 12 84 2 43 g 0 20 14 97 1 1 31 3 12 2 23 t 0 40 39 0 1 97 66 1 3 93 8
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=3/4; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.518977; mwTGCTGACTm ; cor=; Ncor= a 27 23 10 1 15 0 0 71 0 1 35 c 18 17 4 2 54 0 1 0 60 0 28 g 15 7 5 67 2 0 57 0 11 0 6 t 11 24 52 1 0 71 13 0 0 70 2
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=4/4; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.413927; rwtGCTGAsTC ; cor=; Ncor= a 22 18 5 2 15 0 0 66 0 0 16 c 15 14 4 0 50 0 1 0 42 0 48 g 19 12 13 64 1 0 57 0 24 0 2 t 10 22 44 0 0 66 8 0 0 66 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=13; shift=4; ncol=17; ----GmTGACTmAGCva ; Alignment reference a 0 0 0 0 6 20 0 0 64 0 2 41 65 2 10 17 30 c 0 0 0 0 8 31 1 1 0 60 2 19 0 4 45 17 9 g 0 0 0 0 48 8 0 59 0 4 1 4 0 51 3 20 12 t 0 0 0 0 3 6 64 5 1 1 60 1 0 8 7 11 14
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=4; score= 1; ----GmTGACTmAGCva ; cor=; Ncor= a 0 0 0 0 6 20 0 0 64 0 2 41 65 2 10 17 30 c 0 0 0 0 8 31 1 1 0 60 2 19 0 4 45 17 9 g 0 0 0 0 48 8 0 59 0 4 1 4 0 51 3 20 12 t 0 0 0 0 3 6 64 5 1 1 60 1 0 8 7 11 14
oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=2/6; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.764735; -rwtGMTGAsTMAGCaa ; cor=; Ncor= a 0 26 21 5 1 19 0 0 74 0 0 19 73 1 6 33 28 c 0 18 18 10 1 53 0 1 0 50 0 51 0 1 63 17 15 g 0 20 15 14 72 2 0 68 0 24 0 4 0 55 1 16 15 t 0 10 20 45 0 0 74 5 0 0 74 0 1 17 4 8 16
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=3/6; ncol2=15; w=-3; offset=-3; strand=D; shift=1; score=0.728089; -mwTGCTGACTmAgcr- ; cor=; Ncor= a 0 27 23 10 1 15 0 0 71 0 1 35 66 7 9 27 0 c 0 18 17 4 2 54 0 1 0 60 0 28 2 2 48 13 0 g 0 15 7 5 67 2 0 57 0 11 0 6 2 45 2 21 0 t 0 11 24 52 1 0 71 13 0 0 70 2 1 17 12 10 0
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=4/6; ncol2=17; w=-3; offset=-3; strand=R; shift=1; score=0.707083; -rwtGCTGAsTCAGCaw ; cor=; Ncor= a 0 22 18 5 2 15 0 0 66 0 0 16 66 0 5 38 23 c 0 15 14 4 0 50 0 1 0 42 0 48 0 1 58 12 14 g 0 19 12 13 64 1 0 57 0 24 0 2 0 53 0 10 12 t 0 10 22 44 0 0 66 8 0 0 66 0 0 12 3 6 17
oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=5/6; ncol2=11; w=0; offset=2; strand=D; shift=6; score=0.661146; ------tkAGTmAGCwa ; cor=; Ncor= a 0 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 c 0 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 g 0 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 t 0 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=6/6; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.510721; raaTGmTGACTmA---- ; cor=; Ncor= a 18 26 26 3 1 31 0 0 53 1 0 22 42 0 0 0 0 c 11 7 11 0 0 21 0 1 0 44 0 21 5 0 0 0 0 g 18 13 8 5 52 1 1 51 0 5 0 6 2 0 0 0 0 t 6 7 8 45 0 0 52 1 0 3 53 4 4 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; mwtGCTGAsTCAGCawy ; Alignment reference a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 10 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 19 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 15 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18 22
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; mwtGCTGAsTCAGCawy ; cor=; Ncor= a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 10 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 19 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 15 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18 22
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/7; ncol2=16; w=0; offset=1; strand=D; shift=1; score=0.936684; -ttGCTKAsTCAKCawy ; cor=; Ncor= a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 10 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 20 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 18 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21 26
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=3/7; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.849234; --ygcTkAGTCAGCAwk ; cor=; Ncor= a 0 0 10 12 17 1 2 70 0 0 13 71 0 1 52 24 11 c 0 0 21 2 45 2 6 0 11 0 57 0 2 67 5 7 15 g 0 0 13 48 2 2 28 0 60 0 1 0 54 2 4 17 18 t 0 0 27 9 7 66 35 1 0 71 0 0 15 1 10 23 27
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/7; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.707083; -tbGCTkAGTCAkC--- ; cor=; Ncor= a 0 14 11 7 8 0 1 60 1 1 5 64 6 3 0 0 0 c 0 12 20 3 51 0 4 1 4 0 59 0 8 48 0 0 0 g 0 9 17 45 4 0 19 2 60 0 1 1 31 8 0 0 0 t 0 30 17 10 2 65 41 2 0 64 0 0 20 6 0 0 0
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=5/7; ncol2=13; w=0; offset=5; strand=D; shift=5; score=0.619675; -----TkAGTCAkCAtt ; cor=; Ncor= a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 7 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 13 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 7 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26 26
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=6/7; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.561931; -----tkAGTmAGCwa- ; cor=; Ncor= a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 0 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 0 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 0 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16 0
oligos_6nt_mkv2_m5_rc_shift6 (oligos_6nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=7/7; ncol2=10; w=0; offset=6; strand=R; shift=6; score=0.413927; ------taGTAAGCwa- ; cor=; Ncor= a 0 0 0 0 0 0 5 17 0 0 26 26 0 0 7 14 0 c 0 0 0 0 0 0 6 4 0 0 0 0 1 25 2 2 0 g 0 0 0 0 0 0 5 2 26 0 0 0 25 0 6 6 0 t 0 0 0 0 0 0 10 3 0 26 0 0 0 1 11 4 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=13; shift=5; ncol=18; -----TkAGTCAkCAtty ; Alignment reference a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 7 6 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 13 18 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 7 11 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26 26 18
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=5; score= 1; -----TkAGTCAkCAtty ; cor=; Ncor= a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 7 6 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 13 18 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 7 11 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26 26 18
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=2/6; ncol2=15; w=-3; offset=-3; strand=R; shift=2; score=0.715759; --ygcTkAGTCAGCAwk- ; cor=; Ncor= a 0 0 10 12 17 1 2 70 0 0 13 71 0 1 52 24 11 0 c 0 0 21 2 45 2 6 0 11 0 57 0 2 67 5 7 15 0 g 0 0 13 48 2 2 28 0 60 0 1 0 54 2 4 17 18 0 t 0 0 27 9 7 66 35 1 0 71 0 0 15 1 10 23 27 0
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=3/6; ncol2=11; w=0; offset=0; strand=D; shift=5; score=0.664877; -----tkAGTmAGCwa-- ; cor=; Ncor= a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 0 0 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 0 0 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 0 0 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16 0 0
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=4/6; ncol2=16; w=-4; offset=-4; strand=D; shift=1; score=0.663849; -ttGCTKAsTCAKCawy- ; cor=; Ncor= a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 10 0 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 20 0 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 18 0 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21 26 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=5/6; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.619675; mwtGCTGAsTCAGCawy- ; cor=; Ncor= a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 10 0 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 19 0 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 15 0 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18 22 0
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=6/6; ncol2=13; w=-4; offset=-4; strand=R; shift=1; score=0.510721; -tbGCTkAGTCAkC---- ; cor=; Ncor= a 0 14 11 7 8 0 1 60 1 1 5 64 6 3 0 0 0 0 c 0 12 20 3 51 0 4 1 4 0 59 0 8 48 0 0 0 0 g 0 9 17 45 4 0 19 2 60 0 1 1 31 8 0 0 0 0 t 0 30 17 10 2 65 41 2 0 64 0 0 20 6 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=5; ncol=16; -----tkAGTmAGCwa ; Alignment reference a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----tkAGTmAGCwa ; cor=; Ncor= a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16
oligos_6nt_mkv2_m5_rc_shift6 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5_rc; m=2/7; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.854562; ------taGTAAGCwa ; cor=; Ncor= a 0 0 0 0 0 0 5 17 0 0 26 26 0 0 7 14 c 0 0 0 0 0 0 6 4 0 0 0 0 1 25 2 2 g 0 0 0 0 0 0 5 2 26 0 0 0 25 0 6 6 t 0 0 0 0 0 0 10 3 0 26 0 0 0 1 11 4
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=3/7; ncol2=13; w=0; offset=0; strand=D; shift=5; score=0.664877; -----TkAGTCAkCAt ; cor=; Ncor= a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=4/7; ncol2=13; w=-2; offset=-2; strand=D; shift=3; score=0.661146; ---GmTGACTmAGCva ; cor=; Ncor= a 0 0 0 6 20 0 0 64 0 2 41 65 2 10 17 30 c 0 0 0 8 31 1 1 0 60 2 19 0 4 45 17 9 g 0 0 0 48 8 0 59 0 4 1 4 0 51 3 20 12 t 0 0 0 3 6 64 5 1 1 60 1 0 8 7 11 14
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4_rc; m=5/7; ncol2=15; w=-3; offset=-3; strand=R; shift=2; score=0.65826; --ygcTkAGTCAGCAw ; cor=; Ncor= a 0 0 10 12 17 1 2 70 0 0 13 71 0 1 52 24 c 0 0 21 2 45 2 6 0 11 0 57 0 2 67 5 7 g 0 0 13 48 2 2 28 0 60 0 1 0 54 2 4 17 t 0 0 27 9 7 66 35 1 0 71 0 0 15 1 10 23
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=6/7; ncol2=16; w=-4; offset=-4; strand=D; shift=1; score=0.591553; -ttGCTKAsTCAKCaw ; cor=; Ncor= a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=7/7; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.561931; mwtGCTGAsTCAGCaw ; cor=; Ncor= a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=15; shift=1; ncol=16; -mwTGCTGACTmAgcr ; Alignment reference a 0 27 23 10 1 15 0 0 71 0 1 35 66 7 9 27 c 0 18 17 4 2 54 0 1 0 60 0 28 2 2 48 13 g 0 15 7 5 67 2 0 57 0 11 0 6 2 45 2 21 t 0 11 24 52 1 0 71 13 0 0 70 2 1 17 12 10
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -mwTGCTGACTmAgcr ; cor=; Ncor= a 0 27 23 10 1 15 0 0 71 0 1 35 66 7 9 27 c 0 18 17 4 2 54 0 1 0 60 0 28 2 2 48 13 g 0 15 7 5 67 2 0 57 0 11 0 6 2 45 2 21 t 0 11 24 52 1 0 71 13 0 0 70 2 1 17 12 10
oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1_rc; m=2/7; ncol2=16; w=0; offset=0; strand=R; shift=1; score=0.908741; -rwtGMTGAsTMAGCa ; cor=; Ncor= a 0 26 21 5 1 19 0 0 74 0 0 19 73 1 6 33 c 0 18 18 10 1 53 0 1 0 50 0 51 0 1 63 17 g 0 20 15 14 72 2 0 68 0 24 0 4 0 55 1 16 t 0 10 20 45 0 0 74 5 0 0 74 0 1 17 4 8
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1_rc; m=3/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.849234; -rwtGCTGAsTCAGCa ; cor=; Ncor= a 0 22 18 5 2 15 0 0 66 0 0 16 66 0 5 38 c 0 15 14 4 0 50 0 1 0 42 0 48 0 1 58 12 g 0 19 12 13 64 1 0 57 0 24 0 2 0 53 0 10 t 0 10 22 44 0 0 66 8 0 0 66 0 0 12 3 6
oligos_7nt_mkv2_m2_shift4 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=4/7; ncol2=13; w=0; offset=3; strand=D; shift=4; score=0.728089; ----GmTGACTmAGCv ; cor=; Ncor= a 0 0 0 0 6 20 0 0 64 0 2 41 65 2 10 17 c 0 0 0 0 8 31 1 1 0 60 2 19 0 4 45 17 g 0 0 0 0 48 8 0 59 0 4 1 4 0 51 3 20 t 0 0 0 0 3 6 64 5 1 1 60 1 0 8 7 11
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=5/7; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.715759; raaTGmTGACTmA--- ; cor=; Ncor= a 18 26 26 3 1 31 0 0 53 1 0 22 42 0 0 0 c 11 7 11 0 0 21 0 1 0 44 0 21 5 0 0 0 g 18 13 8 5 52 1 1 51 0 5 0 6 2 0 0 0 t 6 7 8 45 0 0 52 1 0 3 53 4 4 0 0 0
oligos_7nt_mkv2_m5_rc_shift2 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=6/7; ncol2=11; w=0; offset=1; strand=R; shift=2; score=0.65826; --twGCTkACTma--- ; cor=; Ncor= a 0 0 16 30 2 2 2 1 84 1 3 26 61 0 0 0 c 0 0 24 17 1 96 0 2 12 84 2 43 10 0 0 0 g 0 0 20 14 97 1 1 31 3 12 2 23 22 0 0 0 t 0 0 40 39 0 1 97 66 1 3 93 8 7 0 0 0
oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=7/7; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.518977; --twGCTTACta---- ; cor=; Ncor= a 0 0 4 11 1 0 0 0 26 0 3 10 0 0 0 0 c 0 0 6 6 0 25 0 0 0 26 2 5 0 0 0 0 g 0 0 2 2 25 1 0 0 0 0 4 6 0 0 0 0 t 0 0 14 7 0 0 26 26 0 0 17 5 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=16; shift=1; ncol=17; -ttGCTKAsTCAKCawy ; Alignment reference a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 10 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 20 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 18 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21 26
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/6; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -ttGCTKAsTCAKCawy ; cor=; Ncor= a 0 16 8 4 17 1 0 74 0 0 5 74 0 0 45 20 10 c 0 15 16 1 55 0 4 0 24 0 68 0 2 72 14 15 20 g 0 15 17 63 1 0 51 0 50 0 1 0 53 1 10 18 18 t 0 28 33 6 1 73 19 0 0 74 0 0 19 1 5 21 26
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/6; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.936684; mwtGCTGAsTCAGCawy ; cor=; Ncor= a 20 17 6 3 12 0 0 66 0 0 8 66 0 0 44 22 10 c 21 12 10 0 53 0 2 0 24 0 57 0 1 64 13 12 19 g 14 14 12 58 1 0 48 0 42 0 1 0 50 0 4 14 15 t 11 23 38 5 0 66 16 0 0 66 0 0 15 2 5 18 22
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=3/6; ncol2=15; w=0; offset=1; strand=R; shift=2; score=0.908741; --ygcTkAGTCAGCAwk ; cor=; Ncor= a 0 0 10 12 17 1 2 70 0 0 13 71 0 1 52 24 11 c 0 0 21 2 45 2 6 0 11 0 57 0 2 67 5 7 15 g 0 0 13 48 2 2 28 0 60 0 1 0 54 2 4 17 18 t 0 0 27 9 7 66 35 1 0 71 0 0 15 1 10 23 27
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/6; ncol2=13; w=0; offset=0; strand=R; shift=1; score=0.764735; -tbGCTkAGTCAkC--- ; cor=; Ncor= a 0 14 11 7 8 0 1 60 1 1 5 64 6 3 0 0 0 c 0 12 20 3 51 0 4 1 4 0 59 0 8 48 0 0 0 g 0 9 17 45 4 0 19 2 60 0 1 1 31 8 0 0 0 t 0 30 17 10 2 65 41 2 0 64 0 0 20 6 0 0 0
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=5/6; ncol2=13; w=0; offset=4; strand=D; shift=5; score=0.663849; -----TkAGTCAkCAtt ; cor=; Ncor= a 0 0 0 0 0 4 4 53 3 0 1 52 0 0 45 8 7 c 0 0 0 0 0 2 6 0 5 0 51 1 1 52 5 8 13 g 0 0 0 0 0 5 21 0 44 0 1 0 21 0 0 11 7 t 0 0 0 0 0 42 22 0 1 53 0 0 31 1 3 26 26
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=6/6; ncol2=11; w=0; offset=4; strand=D; shift=5; score=0.591553; -----tkAGTmAGCwa- ; cor=; Ncor= a 0 0 0 0 0 7 8 93 3 1 66 97 1 0 39 40 0 c 0 0 0 0 0 22 23 2 12 3 31 1 1 97 14 20 0 g 0 0 0 0 0 10 43 2 84 12 2 0 96 1 17 24 0 t 0 0 0 0 0 61 26 3 1 84 1 2 2 2 30 16 0