One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.123202_2025-04-03.123202_wcmL4R/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.2025-04-03.123202_2025-04-03.123202_wcmL4R/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=15; shift=3; ncol=18; ---rhTkAGTAAGCArdy ; Alignment reference a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 14 12 11 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 6 9 14 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 20 15 7 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8 8 12 16

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/7; ncol2=15; w=0; offset=0; strand=D; shift=3; score= 1; ---rhTkAGTAAGCArdy ; cor=; Ncor= a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 14 12 11 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 6 9 14 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 20 15 7 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8 8 12 16

oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=2/7; ncol2=13; w=0; offset=1; strand=R; shift=4; score=0.852625; ----mtkAGTMAGCArr- ; cor=; Ncor= a 0 0 0 0 15 6 5 50 2 0 39 53 0 3 43 17 15 0 c 0 0 0 0 22 8 9 5 4 2 15 2 0 50 2 7 12 0 g 0 0 0 0 5 4 21 0 48 1 1 0 54 1 2 19 16 0 t 0 0 0 0 13 37 20 0 1 52 0 0 1 1 8 12 12 0

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=3/7; ncol2=17; w=-3; offset=-3; strand=R; shift=0; score=0.670136; vttGCTGAsTCAGCaay- ; cor=; Ncor= a 21 19 12 2 19 0 0 82 0 0 11 82 0 0 50 29 18 0 c 23 18 11 0 63 0 2 0 33 0 70 0 0 81 13 17 24 0 g 21 18 14 77 0 0 66 0 49 0 1 0 63 0 10 20 19 0 t 17 27 45 3 0 82 14 0 0 82 0 0 19 1 9 16 21 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.667681; sttGCTGAsTCAGCaac- ; cor=; Ncor= a 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 0 c 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 0 g 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 0 t 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20 0

oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5_rc; m=5/7; ncol2=17; w=-3; offset=-3; strand=R; shift=0; score=0.653799; rttGmTGAsTCAGCaas- ; cor=; Ncor= a 26 20 12 4 28 0 0 81 0 0 16 81 0 2 43 32 15 0 c 17 17 6 1 52 0 1 0 49 0 64 0 0 78 14 15 22 0 g 24 16 12 75 0 0 73 0 32 1 1 0 66 0 14 20 27 0 t 14 28 51 1 1 81 7 0 0 80 0 0 15 1 10 14 17 0

oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=6/7; ncol2=12; w=0; offset=2; strand=D; shift=5; score=0.640673; -----TkAGTCAkCAwk- ; cor=; Ncor= a 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 0 c 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 0 g 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 0 t 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20 0

oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=7/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.638248; ---GmTGACTmAgcr--- ; cor=; Ncor= a 0 0 0 6 23 2 0 86 3 2 53 83 7 9 36 0 0 0 c 0 0 0 12 44 0 1 0 78 1 31 2 11 59 13 0 0 0 g 0 0 0 63 10 1 76 0 6 2 3 2 51 3 23 0 0 0 t 0 0 0 7 11 85 11 2 1 83 1 1 19 17 16 0 0 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; sttGCTGAsTCAGCaac ; Alignment reference a 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 c 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 g 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 t 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20

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; sttGCTGAsTCAGCaac ; cor=; Ncor= a 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 c 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 g 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 t 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1_rc; m=2/7; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.999713; vttGCTGAsTCAGCaay ; cor=; Ncor= a 21 19 12 2 19 0 0 82 0 0 11 82 0 0 50 29 18 c 23 18 11 0 63 0 2 0 33 0 70 0 0 81 13 17 24 g 21 18 14 77 0 0 66 0 49 0 1 0 63 0 10 20 19 t 17 27 45 3 0 82 14 0 0 82 0 0 19 1 9 16 21

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=3/7; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.994903; sttGCTGAsTCAkCaay ; cor=; Ncor= a 17 14 10 1 15 0 0 80 0 0 7 81 1 1 51 28 14 c 27 20 14 0 66 0 1 1 32 0 73 0 0 75 12 16 24 g 22 15 14 78 0 0 64 0 49 0 1 0 52 1 6 17 17 t 15 32 43 2 0 81 16 0 0 81 0 0 28 4 12 20 26

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=4/7; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.667681; ---rhTkAGTAAGCArd ; cor=; Ncor= a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 14 12 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 6 9 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 20 15 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8 8 12

oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4_rc; m=5/7; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.64884; --ygcTkAGTCAkC--- ; cor=; Ncor= a 0 0 16 17 19 1 1 83 1 2 11 85 11 7 0 0 0 c 0 0 23 3 51 2 3 2 6 0 76 1 10 63 0 0 0 g 0 0 13 59 11 2 31 1 78 0 1 0 44 12 0 0 0 t 0 0 36 9 7 83 53 2 3 86 0 2 23 6 0 0 0

oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=6/7; ncol2=13; w=0; offset=4; strand=R; shift=4; score=0.647245; ----mtkAGTMAGCArr ; cor=; Ncor= a 0 0 0 0 15 6 5 50 2 0 39 53 0 3 43 17 15 c 0 0 0 0 22 8 9 5 4 2 15 2 0 50 2 7 12 g 0 0 0 0 5 4 21 0 48 1 1 0 54 1 2 19 16 t 0 0 0 0 13 37 20 0 1 52 0 0 1 1 8 12 12

oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=7/7; ncol2=12; w=0; offset=5; strand=D; shift=5; score=0.64288; -----TkAGTCAkCAwk ; cor=; Ncor= a 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 c 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 g 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 t 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 8 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=17; shift=1; ncol=18; -sttGCTGAsTCAkCaay ; Alignment reference a 0 17 14 10 1 15 0 0 80 0 0 7 81 1 1 51 28 14 c 0 27 20 14 0 66 0 1 1 32 0 73 0 0 75 12 16 24 g 0 22 15 14 78 0 0 64 0 49 0 1 0 52 1 6 17 17 t 0 15 32 43 2 0 81 16 0 0 81 0 0 28 4 12 20 26

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -sttGCTGAsTCAkCaay ; cor=; Ncor= a 0 17 14 10 1 15 0 0 80 0 0 7 81 1 1 51 28 14 c 0 27 20 14 0 66 0 1 1 32 0 73 0 0 75 12 16 24 g 0 22 15 14 78 0 0 64 0 49 0 1 0 52 1 6 17 17 t 0 15 32 43 2 0 81 16 0 0 81 0 0 28 4 12 20 26

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=2/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.994903; -sttGCTGAsTCAGCaac ; cor=; Ncor= a 0 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 c 0 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 g 0 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 t 0 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20

oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=3/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.994081; -vttGCTGAsTCAGCaay ; cor=; Ncor= a 0 21 19 12 2 19 0 0 82 0 0 11 82 0 0 50 29 18 c 0 23 18 11 0 63 0 2 0 33 0 70 0 0 81 13 17 24 g 0 21 18 14 77 0 0 66 0 49 0 1 0 63 0 10 20 19 t 0 17 27 45 3 0 82 14 0 0 82 0 0 19 1 9 16 21

oligos_7nt_mkv2_m3_shift6 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=4/7; ncol2=12; w=0; offset=5; strand=D; shift=6; score=0.659041; ------TkAGTCAkCAwk ; cor=; Ncor= a 0 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 c 0 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 g 0 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 t 0 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20

oligos_7nt_mkv2_m4_rc_shift3 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=5/7; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.655112; ---ygcTkAGTCAkC--- ; cor=; Ncor= a 0 0 0 16 17 19 1 1 83 1 2 11 85 11 7 0 0 0 c 0 0 0 23 3 51 2 3 2 6 0 76 1 10 63 0 0 0 g 0 0 0 13 59 11 2 31 1 78 0 1 0 44 12 0 0 0 t 0 0 0 36 9 7 83 53 2 3 86 0 2 23 6 0 0 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc; m=6/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.653799; rhyTGCTTACTmAdy--- ; cor=; Ncor= a 16 12 8 8 1 4 2 0 46 0 0 26 43 12 3 0 0 0 c 7 15 20 3 1 43 0 1 0 39 0 18 1 2 30 0 0 0 g 14 9 6 2 45 0 0 11 2 7 4 3 3 22 3 0 0 0 t 11 12 14 35 1 1 46 36 0 2 44 1 1 12 12 0 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=7/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.629988; -yyTGCTKACTmak---- ; cor=; Ncor= a 0 12 12 8 1 1 0 0 52 1 0 20 37 13 0 0 0 0 c 0 16 19 2 1 54 0 1 1 48 0 21 4 5 0 0 0 0 g 0 12 7 2 50 0 2 15 2 4 5 9 8 22 0 0 0 0 t 0 15 17 43 3 0 53 39 0 2 50 5 6 15 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---GmTGACTmAgcr ; Alignment reference a 0 0 0 6 23 2 0 86 3 2 53 83 7 9 36 c 0 0 0 12 44 0 1 0 78 1 31 2 11 59 13 g 0 0 0 63 10 1 76 0 6 2 3 2 51 3 23 t 0 0 0 7 11 85 11 2 1 83 1 1 19 17 16

oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---GmTGACTmAgcr ; cor=; Ncor= a 0 0 0 6 23 2 0 86 3 2 53 83 7 9 36 c 0 0 0 12 44 0 1 0 78 1 31 2 11 59 13 g 0 0 0 63 10 1 76 0 6 2 3 2 51 3 23 t 0 0 0 7 11 85 11 2 1 83 1 1 19 17 16

oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5_rc; m=2/7; ncol2=17; w=-3; offset=-3; strand=R; shift=0; score=0.655112; rttGmTGAsTCAGCa ; cor=; Ncor= a 26 20 12 4 28 0 0 81 0 0 16 81 0 2 43 c 17 17 6 1 52 0 1 0 49 0 64 0 0 78 14 g 24 16 12 75 0 0 73 0 32 1 1 0 66 0 14 t 14 28 51 1 1 81 7 0 0 80 0 0 15 1 10

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=3/7; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.650058; rttGCTGAsTCAGCa ; cor=; Ncor= a 21 16 9 1 19 0 0 82 0 0 14 82 0 3 45 c 19 20 10 0 63 0 1 0 49 0 66 0 0 77 14 g 24 17 13 81 0 0 70 0 33 0 2 0 63 0 11 t 18 29 50 0 0 82 11 0 0 82 0 0 19 2 12

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1_rc; m=4/7; ncol2=17; w=-3; offset=-3; strand=R; shift=0; score=0.64884; gttGCTGAsTCAGCa ; cor=; Ncor= a 20 17 9 1 19 0 0 81 0 0 14 81 0 3 46 c 20 19 8 0 62 0 1 0 47 0 65 0 0 76 13 g 24 17 13 80 0 0 70 0 34 0 2 0 63 0 11 t 17 28 51 0 0 81 10 0 0 81 0 0 18 2 11

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=5/7; ncol2=15; w=0; offset=0; strand=D; shift=3; score=0.638248; ---rhTkAGTAAGCA ; cor=; Ncor= a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8

oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=6/7; ncol2=13; w=0; offset=1; strand=R; shift=4; score=0.58966; ----mtkAGTMAGCA ; cor=; Ncor= a 0 0 0 0 15 6 5 50 2 0 39 53 0 3 43 c 0 0 0 0 22 8 9 5 4 2 15 2 0 50 2 g 0 0 0 0 5 4 21 0 48 1 1 0 54 1 2 t 0 0 0 0 13 37 20 0 1 52 0 0 1 1 8

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=7/7; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.566546; mwTGmTGACTmA--- ; cor=; Ncor= a 20 18 1 1 33 0 0 45 1 0 16 38 0 0 0 c 13 9 0 0 15 0 1 3 43 0 26 5 0 0 0 g 9 8 4 48 1 2 47 1 5 0 4 4 0 0 0 t 7 14 44 0 0 47 1 0 0 49 3 2 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; khyCGTACGrkm ; Alignment reference a 9 14 5 1 1 0 44 0 2 17 11 16 c 10 13 23 44 1 2 3 46 2 7 9 12 g 12 8 7 1 45 4 1 1 41 19 14 9 t 17 13 13 2 1 42 0 1 3 5 14 11

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; khyCGTACGrkm ; cor=; Ncor= a 9 14 5 1 1 0 44 0 2 17 11 16 c 10 13 23 44 1 2 3 46 2 7 9 12 g 12 8 7 1 45 4 1 1 41 19 14 9 t 17 13 13 2 1 42 0 1 3 5 14 11

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift1 ; 3 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=10; shift=1; ncol=11; -gwAAGGAGrg ; Alignment reference a 0 5 11 26 26 0 0 26 0 8 6 c 0 2 1 0 0 0 0 0 0 3 4 g 0 14 5 0 0 26 26 0 26 13 11 t 0 5 9 0 0 0 0 0 0 2 5

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -gwAAGGAGrg ; cor=; Ncor= a 0 5 11 26 26 0 0 26 0 8 6 c 0 2 1 0 0 0 0 0 0 3 4 g 0 14 5 0 0 26 26 0 26 13 11 t 0 5 9 0 0 0 0 0 0 2 5

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.795305; grAAAGGAGGr ; cor=; Ncor= a 7 11 24 32 29 1 0 30 0 3 11 c 1 1 2 1 2 1 0 1 0 1 4 g 20 17 1 1 3 29 34 2 34 29 12 t 6 5 7 0 0 3 0 1 0 1 7

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; grAAAGGAGGra ; Alignment reference a 7 11 24 32 29 1 0 30 0 3 11 10 c 1 1 2 1 2 1 0 1 0 1 4 8 g 20 17 1 1 3 29 34 2 34 29 12 8 t 6 5 7 0 0 3 0 1 0 1 7 8

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; grAAAGGAGGra ; cor=; Ncor= a 7 11 24 32 29 1 0 30 0 3 11 10 c 1 1 2 1 2 1 0 1 0 1 4 8 g 20 17 1 1 3 29 34 2 34 29 12 8 t 6 5 7 0 0 3 0 1 0 1 7 8

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.795305; -gwAAGGAGrg- ; cor=; Ncor= a 0 5 11 26 26 0 0 26 0 8 6 0 c 0 2 1 0 0 0 0 0 0 3 4 0 g 0 14 5 0 0 26 26 0 26 13 11 0 t 0 5 9 0 0 0 0 0 0 2 5 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift5 ; 8 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=12; shift=5; ncol=17; -----TkAGTCAkCAwk ; Alignment reference a 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 c 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 g 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 t 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20

oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----TkAGTCAkCAwk ; cor=; Ncor= a 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 c 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 g 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 t 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20

oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=2/7; ncol2=13; w=-1; offset=-1; strand=R; shift=4; score=0.737931; ----mtkAGTMAGCArr ; cor=; Ncor= a 0 0 0 0 15 6 5 50 2 0 39 53 0 3 43 17 15 c 0 0 0 0 22 8 9 5 4 2 15 2 0 50 2 7 12 g 0 0 0 0 5 4 21 0 48 1 1 0 54 1 2 19 16 t 0 0 0 0 13 37 20 0 1 52 0 0 1 1 8 12 12

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=3/7; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.659041; sttGCTGAsTCAkCaay ; cor=; Ncor= a 17 14 10 1 15 0 0 80 0 0 7 81 1 1 51 28 14 c 27 20 14 0 66 0 1 1 32 0 73 0 0 75 12 16 24 g 22 15 14 78 0 0 64 0 49 0 1 0 52 1 6 17 17 t 15 32 43 2 0 81 16 0 0 81 0 0 28 4 12 20 26

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.64288; sttGCTGAsTCAGCaac ; cor=; Ncor= a 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 c 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 g 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 t 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=5/7; ncol2=17; w=-5; offset=-5; strand=R; shift=0; score=0.641984; vttGCTGAsTCAGCaay ; cor=; Ncor= a 21 19 12 2 19 0 0 82 0 0 11 82 0 0 50 29 18 c 23 18 11 0 63 0 2 0 33 0 70 0 0 81 13 17 24 g 21 18 14 77 0 0 66 0 49 0 1 0 63 0 10 20 19 t 17 27 45 3 0 82 14 0 0 82 0 0 19 1 9 16 21

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=6/7; ncol2=15; w=-2; offset=-2; strand=D; shift=3; score=0.640673; ---rhTkAGTAAGCArd ; cor=; Ncor= a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 14 12 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 6 9 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 20 15 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8 8 12

oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=7/7; ncol2=12; w=-3; offset=-3; strand=R; shift=2; score=0.566546; --ygcTkAGTCAkC--- ; cor=; Ncor= a 0 0 16 17 19 1 1 83 1 2 11 85 11 7 0 0 0 c 0 0 23 3 51 2 3 2 6 0 76 1 10 63 0 0 0 g 0 0 13 59 11 2 31 1 78 0 1 0 44 12 0 0 0 t 0 0 36 9 7 83 53 2 3 86 0 2 23 6 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift1 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -yyTGCTKACTmak ; Alignment reference a 0 12 12 8 1 1 0 0 52 1 0 20 37 13 c 0 16 19 2 1 54 0 1 1 48 0 21 4 5 g 0 12 7 2 50 0 2 15 2 4 5 9 8 22 t 0 15 17 43 3 0 53 39 0 2 50 5 6 15

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -yyTGCTKACTmak ; cor=; Ncor= a 0 12 12 8 1 1 0 0 52 1 0 20 37 13 c 0 16 19 2 1 54 0 1 1 48 0 21 4 5 g 0 12 7 2 50 0 2 15 2 4 5 9 8 22 t 0 15 17 43 3 0 53 39 0 2 50 5 6 15

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=2/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.852625; rhyTGCTTACTmAd ; cor=; Ncor= a 16 12 8 8 1 4 2 0 46 0 0 26 43 12 c 7 15 20 3 1 43 0 1 0 39 0 18 1 2 g 14 9 6 2 45 0 0 11 2 7 4 3 3 22 t 11 12 14 35 1 1 46 36 0 2 44 1 1 12

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=3/7; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.737931; -mwTGmTGACTmA- ; cor=; Ncor= a 0 20 18 1 1 33 0 0 45 1 0 16 38 0 c 0 13 9 0 0 15 0 1 3 43 0 26 5 0 g 0 9 8 4 48 1 2 47 1 5 0 4 4 0 t 0 7 14 44 0 0 47 1 0 0 49 3 2 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=4/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.649948; -rttGCTGAsTCAG ; cor=; Ncor= a 0 21 16 9 1 19 0 0 82 0 0 14 82 0 c 0 19 20 10 0 63 0 1 0 49 0 66 0 0 g 0 24 17 13 81 0 0 70 0 33 0 2 0 63 t 0 18 29 50 0 0 82 11 0 0 82 0 0 19

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=5/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.647245; -gttGCTGAsTCAG ; cor=; Ncor= a 0 20 17 9 1 19 0 0 81 0 0 14 81 0 c 0 20 19 8 0 62 0 1 0 47 0 65 0 0 g 0 24 17 13 80 0 0 70 0 34 0 2 0 63 t 0 17 28 51 0 0 81 10 0 0 81 0 0 18

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=6/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.629988; -sttGCTGAsTCAk ; cor=; Ncor= a 0 17 14 10 1 15 0 0 80 0 0 7 81 1 c 0 27 20 14 0 66 0 1 1 32 0 73 0 0 g 0 22 15 14 78 0 0 64 0 49 0 1 0 52 t 0 15 32 43 2 0 81 16 0 0 81 0 0 28

oligos_7nt_mkv2_m4_rc_shift3 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=7/7; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.58966; ---ygcTkAGTCAk ; cor=; Ncor= a 0 0 0 16 17 19 1 1 83 1 2 11 85 11 c 0 0 0 23 3 51 2 3 2 6 0 76 1 10 g 0 0 0 13 59 11 2 31 1 78 0 1 0 44 t 0 0 0 36 9 7 83 53 2 3 86 0 2 23

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 8 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=17; shift=1; ncol=18; -rttGCTGAsTCAGCaab ; Alignment reference a 0 21 16 9 1 19 0 0 82 0 0 14 82 0 3 45 27 17 c 0 19 20 10 0 63 0 1 0 49 0 66 0 0 77 14 18 21 g 0 24 17 13 81 0 0 70 0 33 0 2 0 63 0 11 18 23 t 0 18 29 50 0 0 82 11 0 0 82 0 0 19 2 12 19 21

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -rttGCTGAsTCAGCaab ; cor=; Ncor= a 0 21 16 9 1 19 0 0 82 0 0 14 82 0 3 45 27 17 c 0 19 20 10 0 63 0 1 0 49 0 66 0 0 77 14 18 21 g 0 24 17 13 81 0 0 70 0 33 0 2 0 63 0 11 18 23 t 0 18 29 50 0 0 82 11 0 0 82 0 0 19 2 12 19 21

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1_rc; m=2/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.999713; -gttGCTGAsTCAGCaas ; cor=; Ncor= a 0 20 17 9 1 19 0 0 81 0 0 14 81 0 3 46 28 17 c 0 20 19 8 0 62 0 1 0 47 0 65 0 0 76 13 17 21 g 0 24 17 13 80 0 0 70 0 34 0 2 0 63 0 11 18 23 t 0 17 28 51 0 0 81 10 0 0 81 0 0 18 2 11 18 20

oligos_6nt_mkv2_m5_rc_shift1 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=3/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.994081; -rttGmTGAsTCAGCaas ; cor=; Ncor= a 0 26 20 12 4 28 0 0 81 0 0 16 81 0 2 43 32 15 c 0 17 17 6 1 52 0 1 0 49 0 64 0 0 78 14 15 22 g 0 24 16 12 75 0 0 73 0 32 1 1 0 66 0 14 20 27 t 0 14 28 51 1 1 81 7 0 0 80 0 0 15 1 10 14 17

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.670136; rhyTGCTTACTmAdy--- ; cor=; Ncor= a 16 12 8 8 1 4 2 0 46 0 0 26 43 12 3 0 0 0 c 7 15 20 3 1 43 0 1 0 39 0 18 1 2 30 0 0 0 g 14 9 6 2 45 0 0 11 2 7 4 3 3 22 3 0 0 0 t 11 12 14 35 1 1 46 36 0 2 44 1 1 12 12 0 0 0

oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=5/7; ncol2=12; w=0; offset=3; strand=D; shift=4; score=0.650058; ----GmTGACTmAgcr-- ; cor=; Ncor= a 0 0 0 0 6 23 2 0 86 3 2 53 83 7 9 36 0 0 c 0 0 0 0 12 44 0 1 0 78 1 31 2 11 59 13 0 0 g 0 0 0 0 63 10 1 76 0 6 2 3 2 51 3 23 0 0 t 0 0 0 0 7 11 85 11 2 1 83 1 1 19 17 16 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=6/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.649948; -yyTGCTKACTmak---- ; cor=; Ncor= a 0 12 12 8 1 1 0 0 52 1 0 20 37 13 0 0 0 0 c 0 16 19 2 1 54 0 1 1 48 0 21 4 5 0 0 0 0 g 0 12 7 2 50 0 2 15 2 4 5 9 8 22 0 0 0 0 t 0 15 17 43 3 0 53 39 0 2 50 5 6 15 0 0 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=7/7; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.641984; -mwTGmTGACTmA----- ; cor=; Ncor= a 0 20 18 1 1 33 0 0 45 1 0 16 38 0 0 0 0 0 c 0 13 9 0 0 15 0 1 3 43 0 26 5 0 0 0 0 0 g 0 9 8 4 48 1 2 47 1 5 0 4 4 0 0 0 0 0 t 0 7 14 44 0 0 47 1 0 0 49 3 2 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=15; shift=3; ncol=18; ---rhTkAGTAAGCArdy ; Alignment reference a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 14 12 11 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 6 9 14 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 20 15 7 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8 8 12 16
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/7; ncol2=15; w=0; offset=0; strand=D; shift=3; score= 1; ---rhTkAGTAAGCArdy ; cor=; Ncor= a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 14 12 11 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 6 9 14 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 20 15 7 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8 8 12 16
oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=2/7; ncol2=13; w=0; offset=1; strand=R; shift=4; score=0.852625; ----mtkAGTMAGCArr- ; cor=; Ncor= a 0 0 0 0 15 6 5 50 2 0 39 53 0 3 43 17 15 0 c 0 0 0 0 22 8 9 5 4 2 15 2 0 50 2 7 12 0 g 0 0 0 0 5 4 21 0 48 1 1 0 54 1 2 19 16 0 t 0 0 0 0 13 37 20 0 1 52 0 0 1 1 8 12 12 0
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=3/7; ncol2=17; w=-3; offset=-3; strand=R; shift=0; score=0.670136; vttGCTGAsTCAGCaay- ; cor=; Ncor= a 21 19 12 2 19 0 0 82 0 0 11 82 0 0 50 29 18 0 c 23 18 11 0 63 0 2 0 33 0 70 0 0 81 13 17 24 0 g 21 18 14 77 0 0 66 0 49 0 1 0 63 0 10 20 19 0 t 17 27 45 3 0 82 14 0 0 82 0 0 19 1 9 16 21 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.667681; sttGCTGAsTCAGCaac- ; cor=; Ncor= a 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 0 c 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 0 g 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 0 t 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20 0
oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5_rc; m=5/7; ncol2=17; w=-3; offset=-3; strand=R; shift=0; score=0.653799; rttGmTGAsTCAGCaas- ; cor=; Ncor= a 26 20 12 4 28 0 0 81 0 0 16 81 0 2 43 32 15 0 c 17 17 6 1 52 0 1 0 49 0 64 0 0 78 14 15 22 0 g 24 16 12 75 0 0 73 0 32 1 1 0 66 0 14 20 27 0 t 14 28 51 1 1 81 7 0 0 80 0 0 15 1 10 14 17 0
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=6/7; ncol2=12; w=0; offset=2; strand=D; shift=5; score=0.640673; -----TkAGTCAkCAwk- ; cor=; Ncor= a 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 0 c 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 0 g 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 0 t 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20 0
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=7/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.638248; ---GmTGACTmAgcr--- ; cor=; Ncor= a 0 0 0 6 23 2 0 86 3 2 53 83 7 9 36 0 0 0 c 0 0 0 12 44 0 1 0 78 1 31 2 11 59 13 0 0 0 g 0 0 0 63 10 1 76 0 6 2 3 2 51 3 23 0 0 0 t 0 0 0 7 11 85 11 2 1 83 1 1 19 17 16 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; sttGCTGAsTCAGCaac ; Alignment reference a 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 c 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 g 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 t 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20
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; sttGCTGAsTCAGCaac ; cor=; Ncor= a 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 c 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 g 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 t 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1_rc; m=2/7; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.999713; vttGCTGAsTCAGCaay ; cor=; Ncor= a 21 19 12 2 19 0 0 82 0 0 11 82 0 0 50 29 18 c 23 18 11 0 63 0 2 0 33 0 70 0 0 81 13 17 24 g 21 18 14 77 0 0 66 0 49 0 1 0 63 0 10 20 19 t 17 27 45 3 0 82 14 0 0 82 0 0 19 1 9 16 21
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=3/7; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.994903; sttGCTGAsTCAkCaay ; cor=; Ncor= a 17 14 10 1 15 0 0 80 0 0 7 81 1 1 51 28 14 c 27 20 14 0 66 0 1 1 32 0 73 0 0 75 12 16 24 g 22 15 14 78 0 0 64 0 49 0 1 0 52 1 6 17 17 t 15 32 43 2 0 81 16 0 0 81 0 0 28 4 12 20 26
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=4/7; ncol2=15; w=0; offset=3; strand=D; shift=3; score=0.667681; ---rhTkAGTAAGCArd ; cor=; Ncor= a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 14 12 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 6 9 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 20 15 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8 8 12
oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4_rc; m=5/7; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.64884; --ygcTkAGTCAkC--- ; cor=; Ncor= a 0 0 16 17 19 1 1 83 1 2 11 85 11 7 0 0 0 c 0 0 23 3 51 2 3 2 6 0 76 1 10 63 0 0 0 g 0 0 13 59 11 2 31 1 78 0 1 0 44 12 0 0 0 t 0 0 36 9 7 83 53 2 3 86 0 2 23 6 0 0 0
oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=6/7; ncol2=13; w=0; offset=4; strand=R; shift=4; score=0.647245; ----mtkAGTMAGCArr ; cor=; Ncor= a 0 0 0 0 15 6 5 50 2 0 39 53 0 3 43 17 15 c 0 0 0 0 22 8 9 5 4 2 15 2 0 50 2 7 12 g 0 0 0 0 5 4 21 0 48 1 1 0 54 1 2 19 16 t 0 0 0 0 13 37 20 0 1 52 0 0 1 1 8 12 12
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=7/7; ncol2=12; w=0; offset=5; strand=D; shift=5; score=0.64288; -----TkAGTCAkCAwk ; cor=; Ncor= a 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 c 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 g 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 t 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20

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=17; shift=1; ncol=18; -sttGCTGAsTCAkCaay ; Alignment reference a 0 17 14 10 1 15 0 0 80 0 0 7 81 1 1 51 28 14 c 0 27 20 14 0 66 0 1 1 32 0 73 0 0 75 12 16 24 g 0 22 15 14 78 0 0 64 0 49 0 1 0 52 1 6 17 17 t 0 15 32 43 2 0 81 16 0 0 81 0 0 28 4 12 20 26
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -sttGCTGAsTCAkCaay ; cor=; Ncor= a 0 17 14 10 1 15 0 0 80 0 0 7 81 1 1 51 28 14 c 0 27 20 14 0 66 0 1 1 32 0 73 0 0 75 12 16 24 g 0 22 15 14 78 0 0 64 0 49 0 1 0 52 1 6 17 17 t 0 15 32 43 2 0 81 16 0 0 81 0 0 28 4 12 20 26
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=2/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.994903; -sttGCTGAsTCAGCaac ; cor=; Ncor= a 0 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 c 0 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 g 0 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 t 0 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20
oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=3/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.994081; -vttGCTGAsTCAGCaay ; cor=; Ncor= a 0 21 19 12 2 19 0 0 82 0 0 11 82 0 0 50 29 18 c 0 23 18 11 0 63 0 2 0 33 0 70 0 0 81 13 17 24 g 0 21 18 14 77 0 0 66 0 49 0 1 0 63 0 10 20 19 t 0 17 27 45 3 0 82 14 0 0 82 0 0 19 1 9 16 21
oligos_7nt_mkv2_m3_shift6 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=4/7; ncol2=12; w=0; offset=5; strand=D; shift=6; score=0.659041; ------TkAGTCAkCAwk ; cor=; Ncor= a 0 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 c 0 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 g 0 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 t 0 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20
oligos_7nt_mkv2_m4_rc_shift3 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=5/7; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.655112; ---ygcTkAGTCAkC--- ; cor=; Ncor= a 0 0 0 16 17 19 1 1 83 1 2 11 85 11 7 0 0 0 c 0 0 0 23 3 51 2 3 2 6 0 76 1 10 63 0 0 0 g 0 0 0 13 59 11 2 31 1 78 0 1 0 44 12 0 0 0 t 0 0 0 36 9 7 83 53 2 3 86 0 2 23 6 0 0 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc; m=6/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.653799; rhyTGCTTACTmAdy--- ; cor=; Ncor= a 16 12 8 8 1 4 2 0 46 0 0 26 43 12 3 0 0 0 c 7 15 20 3 1 43 0 1 0 39 0 18 1 2 30 0 0 0 g 14 9 6 2 45 0 0 11 2 7 4 3 3 22 3 0 0 0 t 11 12 14 35 1 1 46 36 0 2 44 1 1 12 12 0 0 0
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=7/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.629988; -yyTGCTKACTmak---- ; cor=; Ncor= a 0 12 12 8 1 1 0 0 52 1 0 20 37 13 0 0 0 0 c 0 16 19 2 1 54 0 1 1 48 0 21 4 5 0 0 0 0 g 0 12 7 2 50 0 2 15 2 4 5 9 8 22 0 0 0 0 t 0 15 17 43 3 0 53 39 0 2 50 5 6 15 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---GmTGACTmAgcr ; Alignment reference a 0 0 0 6 23 2 0 86 3 2 53 83 7 9 36 c 0 0 0 12 44 0 1 0 78 1 31 2 11 59 13 g 0 0 0 63 10 1 76 0 6 2 3 2 51 3 23 t 0 0 0 7 11 85 11 2 1 83 1 1 19 17 16
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---GmTGACTmAgcr ; cor=; Ncor= a 0 0 0 6 23 2 0 86 3 2 53 83 7 9 36 c 0 0 0 12 44 0 1 0 78 1 31 2 11 59 13 g 0 0 0 63 10 1 76 0 6 2 3 2 51 3 23 t 0 0 0 7 11 85 11 2 1 83 1 1 19 17 16
oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5_rc; m=2/7; ncol2=17; w=-3; offset=-3; strand=R; shift=0; score=0.655112; rttGmTGAsTCAGCa ; cor=; Ncor= a 26 20 12 4 28 0 0 81 0 0 16 81 0 2 43 c 17 17 6 1 52 0 1 0 49 0 64 0 0 78 14 g 24 16 12 75 0 0 73 0 32 1 1 0 66 0 14 t 14 28 51 1 1 81 7 0 0 80 0 0 15 1 10
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=3/7; ncol2=17; w=-3; offset=-3; strand=D; shift=0; score=0.650058; rttGCTGAsTCAGCa ; cor=; Ncor= a 21 16 9 1 19 0 0 82 0 0 14 82 0 3 45 c 19 20 10 0 63 0 1 0 49 0 66 0 0 77 14 g 24 17 13 81 0 0 70 0 33 0 2 0 63 0 11 t 18 29 50 0 0 82 11 0 0 82 0 0 19 2 12
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1_rc; m=4/7; ncol2=17; w=-3; offset=-3; strand=R; shift=0; score=0.64884; gttGCTGAsTCAGCa ; cor=; Ncor= a 20 17 9 1 19 0 0 81 0 0 14 81 0 3 46 c 20 19 8 0 62 0 1 0 47 0 65 0 0 76 13 g 24 17 13 80 0 0 70 0 34 0 2 0 63 0 11 t 17 28 51 0 0 81 10 0 0 81 0 0 18 2 11
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=5/7; ncol2=15; w=0; offset=0; strand=D; shift=3; score=0.638248; ---rhTkAGTAAGCA ; cor=; Ncor= a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8
oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=6/7; ncol2=13; w=0; offset=1; strand=R; shift=4; score=0.58966; ----mtkAGTMAGCA ; cor=; Ncor= a 0 0 0 0 15 6 5 50 2 0 39 53 0 3 43 c 0 0 0 0 22 8 9 5 4 2 15 2 0 50 2 g 0 0 0 0 5 4 21 0 48 1 1 0 54 1 2 t 0 0 0 0 13 37 20 0 1 52 0 0 1 1 8
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=7/7; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.566546; mwTGmTGACTmA--- ; cor=; Ncor= a 20 18 1 1 33 0 0 45 1 0 16 38 0 0 0 c 13 9 0 0 15 0 1 3 43 0 26 5 0 0 0 g 9 8 4 48 1 2 47 1 5 0 4 4 0 0 0 t 7 14 44 0 0 47 1 0 0 49 3 2 0 0 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=12; shift=5; ncol=17; -----TkAGTCAkCAwk ; Alignment reference a 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 c 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 g 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 t 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=5; score= 1; -----TkAGTCAkCAwk ; cor=; Ncor= a 0 0 0 0 0 2 3 49 0 0 1 47 0 0 44 14 7 c 0 0 0 0 0 4 4 0 5 1 47 2 1 48 4 8 9 g 0 0 0 0 0 5 26 0 43 3 1 0 15 0 0 9 13 t 0 0 0 0 0 38 16 0 1 45 0 0 33 1 1 18 20
oligos_6nt_mkv2_m2_rc_shift4 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=2/7; ncol2=13; w=-1; offset=-1; strand=R; shift=4; score=0.737931; ----mtkAGTMAGCArr ; cor=; Ncor= a 0 0 0 0 15 6 5 50 2 0 39 53 0 3 43 17 15 c 0 0 0 0 22 8 9 5 4 2 15 2 0 50 2 7 12 g 0 0 0 0 5 4 21 0 48 1 1 0 54 1 2 19 16 t 0 0 0 0 13 37 20 0 1 52 0 0 1 1 8 12 12
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=3/7; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.659041; sttGCTGAsTCAkCaay ; cor=; Ncor= a 17 14 10 1 15 0 0 80 0 0 7 81 1 1 51 28 14 c 27 20 14 0 66 0 1 1 32 0 73 0 0 75 12 16 24 g 22 15 14 78 0 0 64 0 49 0 1 0 52 1 6 17 17 t 15 32 43 2 0 81 16 0 0 81 0 0 28 4 12 20 26
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score=0.64288; sttGCTGAsTCAGCaac ; cor=; Ncor= a 20 18 11 2 18 0 0 81 0 0 10 81 0 0 51 28 17 c 23 18 11 0 63 0 2 0 34 0 70 0 0 80 13 17 24 g 21 17 13 76 0 0 65 0 47 0 1 0 62 0 8 19 20 t 17 28 46 3 0 81 14 0 0 81 0 0 19 1 9 17 20
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=5/7; ncol2=17; w=-5; offset=-5; strand=R; shift=0; score=0.641984; vttGCTGAsTCAGCaay ; cor=; Ncor= a 21 19 12 2 19 0 0 82 0 0 11 82 0 0 50 29 18 c 23 18 11 0 63 0 2 0 33 0 70 0 0 81 13 17 24 g 21 18 14 77 0 0 66 0 49 0 1 0 63 0 10 20 19 t 17 27 45 3 0 82 14 0 0 82 0 0 19 1 9 16 21
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=6/7; ncol2=15; w=-2; offset=-2; strand=D; shift=3; score=0.640673; ---rhTkAGTAAGCArd ; cor=; Ncor= a 0 0 0 12 12 1 1 44 2 0 36 46 1 1 35 14 12 c 0 0 0 3 22 3 3 4 7 2 11 0 0 45 2 6 9 g 0 0 0 30 2 1 18 0 39 0 1 0 43 1 3 20 15 t 0 0 0 3 12 43 26 0 0 46 0 2 4 1 8 8 12
oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=7/7; ncol2=12; w=-3; offset=-3; strand=R; shift=2; score=0.566546; --ygcTkAGTCAkC--- ; cor=; Ncor= a 0 0 16 17 19 1 1 83 1 2 11 85 11 7 0 0 0 c 0 0 23 3 51 2 3 2 6 0 76 1 10 63 0 0 0 g 0 0 13 59 11 2 31 1 78 0 1 0 44 12 0 0 0 t 0 0 36 9 7 83 53 2 3 86 0 2 23 6 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -yyTGCTKACTmak ; Alignment reference a 0 12 12 8 1 1 0 0 52 1 0 20 37 13 c 0 16 19 2 1 54 0 1 1 48 0 21 4 5 g 0 12 7 2 50 0 2 15 2 4 5 9 8 22 t 0 15 17 43 3 0 53 39 0 2 50 5 6 15
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -yyTGCTKACTmak ; cor=; Ncor= a 0 12 12 8 1 1 0 0 52 1 0 20 37 13 c 0 16 19 2 1 54 0 1 1 48 0 21 4 5 g 0 12 7 2 50 0 2 15 2 4 5 9 8 22 t 0 15 17 43 3 0 53 39 0 2 50 5 6 15
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=2/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.852625; rhyTGCTTACTmAd ; cor=; Ncor= a 16 12 8 8 1 4 2 0 46 0 0 26 43 12 c 7 15 20 3 1 43 0 1 0 39 0 18 1 2 g 14 9 6 2 45 0 0 11 2 7 4 3 3 22 t 11 12 14 35 1 1 46 36 0 2 44 1 1 12
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=3/7; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.737931; -mwTGmTGACTmA- ; cor=; Ncor= a 0 20 18 1 1 33 0 0 45 1 0 16 38 0 c 0 13 9 0 0 15 0 1 3 43 0 26 5 0 g 0 9 8 4 48 1 2 47 1 5 0 4 4 0 t 0 7 14 44 0 0 47 1 0 0 49 3 2 0
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=4/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.649948; -rttGCTGAsTCAG ; cor=; Ncor= a 0 21 16 9 1 19 0 0 82 0 0 14 82 0 c 0 19 20 10 0 63 0 1 0 49 0 66 0 0 g 0 24 17 13 81 0 0 70 0 33 0 2 0 63 t 0 18 29 50 0 0 82 11 0 0 82 0 0 19
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=5/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.647245; -gttGCTGAsTCAG ; cor=; Ncor= a 0 20 17 9 1 19 0 0 81 0 0 14 81 0 c 0 20 19 8 0 62 0 1 0 47 0 65 0 0 g 0 24 17 13 80 0 0 70 0 34 0 2 0 63 t 0 17 28 51 0 0 81 10 0 0 81 0 0 18
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=6/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.629988; -sttGCTGAsTCAk ; cor=; Ncor= a 0 17 14 10 1 15 0 0 80 0 0 7 81 1 c 0 27 20 14 0 66 0 1 1 32 0 73 0 0 g 0 22 15 14 78 0 0 64 0 49 0 1 0 52 t 0 15 32 43 2 0 81 16 0 0 81 0 0 28
oligos_7nt_mkv2_m4_rc_shift3 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=7/7; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.58966; ---ygcTkAGTCAk ; cor=; Ncor= a 0 0 0 16 17 19 1 1 83 1 2 11 85 11 c 0 0 0 23 3 51 2 3 2 6 0 76 1 10 g 0 0 0 13 59 11 2 31 1 78 0 1 0 44 t 0 0 0 36 9 7 83 53 2 3 86 0 2 23

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=17; shift=1; ncol=18; -rttGCTGAsTCAGCaab ; Alignment reference a 0 21 16 9 1 19 0 0 82 0 0 14 82 0 3 45 27 17 c 0 19 20 10 0 63 0 1 0 49 0 66 0 0 77 14 18 21 g 0 24 17 13 81 0 0 70 0 33 0 2 0 63 0 11 18 23 t 0 18 29 50 0 0 82 11 0 0 82 0 0 19 2 12 19 21
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -rttGCTGAsTCAGCaab ; cor=; Ncor= a 0 21 16 9 1 19 0 0 82 0 0 14 82 0 3 45 27 17 c 0 19 20 10 0 63 0 1 0 49 0 66 0 0 77 14 18 21 g 0 24 17 13 81 0 0 70 0 33 0 2 0 63 0 11 18 23 t 0 18 29 50 0 0 82 11 0 0 82 0 0 19 2 12 19 21
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1_rc; m=2/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.999713; -gttGCTGAsTCAGCaas ; cor=; Ncor= a 0 20 17 9 1 19 0 0 81 0 0 14 81 0 3 46 28 17 c 0 20 19 8 0 62 0 1 0 47 0 65 0 0 76 13 17 21 g 0 24 17 13 80 0 0 70 0 34 0 2 0 63 0 11 18 23 t 0 17 28 51 0 0 81 10 0 0 81 0 0 18 2 11 18 20
oligos_6nt_mkv2_m5_rc_shift1 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5_rc; m=3/7; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.994081; -rttGmTGAsTCAGCaas ; cor=; Ncor= a 0 26 20 12 4 28 0 0 81 0 0 16 81 0 2 43 32 15 c 0 17 17 6 1 52 0 1 0 49 0 64 0 0 78 14 15 22 g 0 24 16 12 75 0 0 73 0 32 1 1 0 66 0 14 20 27 t 0 14 28 51 1 1 81 7 0 0 80 0 0 15 1 10 14 17
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.670136; rhyTGCTTACTmAdy--- ; cor=; Ncor= a 16 12 8 8 1 4 2 0 46 0 0 26 43 12 3 0 0 0 c 7 15 20 3 1 43 0 1 0 39 0 18 1 2 30 0 0 0 g 14 9 6 2 45 0 0 11 2 7 4 3 3 22 3 0 0 0 t 11 12 14 35 1 1 46 36 0 2 44 1 1 12 12 0 0 0
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=5/7; ncol2=12; w=0; offset=3; strand=D; shift=4; score=0.650058; ----GmTGACTmAgcr-- ; cor=; Ncor= a 0 0 0 0 6 23 2 0 86 3 2 53 83 7 9 36 0 0 c 0 0 0 0 12 44 0 1 0 78 1 31 2 11 59 13 0 0 g 0 0 0 0 63 10 1 76 0 6 2 3 2 51 3 23 0 0 t 0 0 0 0 7 11 85 11 2 1 83 1 1 19 17 16 0 0
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=6/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.649948; -yyTGCTKACTmak---- ; cor=; Ncor= a 0 12 12 8 1 1 0 0 52 1 0 20 37 13 0 0 0 0 c 0 16 19 2 1 54 0 1 1 48 0 21 4 5 0 0 0 0 g 0 12 7 2 50 0 2 15 2 4 5 9 8 22 0 0 0 0 t 0 15 17 43 3 0 53 39 0 2 50 5 6 15 0 0 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=7/7; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.641984; -mwTGmTGACTmA----- ; cor=; Ncor= a 0 20 18 1 1 33 0 0 45 1 0 16 38 0 0 0 0 0 c 0 13 9 0 0 15 0 1 3 43 0 26 5 0 0 0 0 0 g 0 9 8 4 48 1 2 47 1 5 0 4 4 0 0 0 0 0 t 0 7 14 44 0 0 47 1 0 0 49 3 2 0 0 0 0 0