One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/08/17/peak-motifs.2025-08-17.121447_2025-08-17.121447_Kvls6d/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/2025/08/17/peak-motifs.2025-08-17.121447_2025-08-17.121447_Kvls6d/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; dmkGCACGTGCmkh ; Alignment reference a 13 15 10 3 0 47 0 2 3 0 3 15 9 14 c 11 16 12 10 52 2 49 1 0 0 36 15 12 14 g 14 12 15 36 0 0 1 49 2 52 10 12 16 11 t 14 9 15 3 0 3 2 0 47 0 3 10 15 13

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; dmkGCACGTGCmkh ; cor=; Ncor= a 13 15 10 3 0 47 0 2 3 0 3 15 9 14 c 11 16 12 10 52 2 49 1 0 0 36 15 12 14 g 14 12 15 36 0 0 1 49 2 52 10 12 16 11 t 14 9 15 3 0 3 2 0 47 0 3 10 15 13

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.901108; rssGCACGTGGkvc ; cor=; Ncor= a 13 11 11 0 3 44 0 1 4 1 3 9 13 11 c 11 14 13 4 46 2 48 0 3 0 4 12 14 16 g 15 14 16 42 0 0 1 48 1 45 39 15 15 10 t 10 10 9 3 0 3 0 0 41 3 3 13 7 12

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.856722; -mkGCACGTGCmk- ; cor=; Ncor= a 0 15 10 4 0 49 0 2 3 0 3 15 9 0 c 0 18 12 10 54 2 51 1 0 0 37 17 12 0 g 0 12 17 37 0 0 1 51 2 54 10 12 18 0 t 0 9 15 3 0 3 2 0 49 0 4 10 15 0

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=4/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.772112; -srGCACGTGGsv- ; cor=; Ncor= a 0 11 14 0 3 49 0 1 4 1 3 10 15 0 c 0 18 13 4 52 2 53 1 3 0 4 17 14 0 g 0 15 17 48 0 0 1 53 1 49 44 15 16 0 t 0 11 11 3 0 4 1 0 47 5 4 13 10 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift3 ; 4 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=13; shift=3; ncol=16; ---mTGAGTmAGCaar ; Alignment reference a 0 0 0 10 2 0 31 0 1 21 32 0 0 14 15 9 c 0 0 0 14 7 0 0 3 0 10 0 0 32 6 7 6 g 0 0 0 4 1 27 1 29 3 0 0 32 0 6 7 10 t 0 0 0 4 22 5 0 0 28 1 0 0 0 6 3 7

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---mTGAGTmAGCaar ; cor=; Ncor= a 0 0 0 10 2 0 31 0 1 21 32 0 0 14 15 9 c 0 0 0 14 7 0 0 3 0 10 0 0 32 6 7 6 g 0 0 0 4 1 27 1 29 3 0 0 32 0 6 7 10 t 0 0 0 4 22 5 0 0 28 1 0 0 0 6 3 7

oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.702621; --gmTGAGTCAGcm-- ; cor=; Ncor= a 0 0 6 15 3 0 50 0 0 6 51 2 9 17 0 0 c 0 0 6 26 3 1 0 11 1 47 0 4 32 14 0 0 g 0 0 35 7 2 52 1 42 1 1 1 43 7 10 0 0 t 0 0 7 6 46 1 3 1 52 0 2 5 6 13 0 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=3/3; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.663391; ykGCTGAsTCAGCms- ; cor=; Ncor= a 8 5 0 5 1 0 38 0 1 6 36 1 1 15 9 0 c 13 7 0 33 0 0 0 14 0 32 0 0 34 10 10 0 g 6 10 38 0 1 32 0 24 0 0 1 30 2 8 12 0 t 11 16 0 0 36 6 0 0 37 0 1 7 1 5 7 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 4 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=13; shift=0; ncol=13; swCCTGTCAgacc ; Alignment reference a 3 7 0 0 0 0 0 1 22 1 9 3 5 c 7 4 20 21 0 1 0 20 0 5 3 10 8 g 8 5 2 1 1 21 0 1 0 13 5 4 5 t 4 6 0 0 21 0 22 0 0 3 5 5 4

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; swCCTGTCAgacc ; cor=; Ncor= a 3 7 0 0 0 0 0 1 22 1 9 3 5 c 7 4 20 21 0 1 0 20 0 5 3 10 8 g 8 5 2 1 1 21 0 1 0 13 5 4 5 t 4 6 0 0 21 0 22 0 0 3 5 5 4

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.859851; srvCTGTCAgwb- ; cor=; Ncor= a 15 21 19 1 2 2 3 1 62 9 18 14 0 c 20 11 22 64 2 2 4 66 1 9 14 18 0 g 22 23 20 1 2 64 1 0 0 46 14 18 0 t 11 13 7 2 62 0 60 1 5 4 22 18 0

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=3/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.833587; mrsCTGTCArdb- ; cor=; Ncor= a 17 17 10 1 1 0 2 3 59 35 17 13 0 c 23 13 25 57 1 2 0 59 2 9 13 16 0 g 12 20 22 3 1 60 0 1 2 16 17 17 0 t 12 14 7 3 61 2 62 1 1 4 17 18 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=15; shift=1; ncol=16; -skGCTGAsTCAGCmr ; Alignment reference a 0 7 5 1 7 1 0 37 0 0 6 36 0 0 16 11 c 0 12 8 2 30 1 0 0 24 0 32 1 0 38 10 6 g 0 10 10 34 0 0 32 0 14 0 0 0 33 0 7 13 t 0 9 15 1 1 36 6 1 0 38 0 1 5 0 5 8

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -skGCTGAsTCAGCmr ; cor=; Ncor= a 0 7 5 1 7 1 0 37 0 0 6 36 0 0 16 11 c 0 12 8 2 30 1 0 0 24 0 32 1 0 38 10 6 g 0 10 10 34 0 0 32 0 14 0 0 0 33 0 7 13 t 0 9 15 1 1 36 6 1 0 38 0 1 5 0 5 8

oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=2/3; ncol2=12; w=0; offset=1; strand=R; shift=2; score=0.760537; --kgCTGACTCAkc-- ; cor=; Ncor= a 0 0 13 6 5 2 0 52 1 3 1 46 6 7 0 0 c 0 0 10 7 43 1 1 1 42 1 52 2 7 35 0 0 g 0 0 14 32 4 0 47 1 11 0 1 3 26 6 0 0 t 0 0 17 9 2 51 6 0 0 50 0 3 15 6 0 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=3/3; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.663391; yttGCTkACTCAk--- ; cor=; Ncor= a 7 3 6 0 0 0 1 28 0 0 5 22 4 0 0 0 c 10 7 6 0 32 0 0 3 29 1 27 1 4 0 0 0 g 6 7 6 32 0 0 10 0 3 0 0 7 14 0 0 0 t 9 15 14 0 0 32 21 1 0 31 0 2 10 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --gmTGAGTCAGcm ; Alignment reference a 0 0 6 15 3 0 50 0 0 6 51 2 9 17 c 0 0 6 26 3 1 0 11 1 47 0 4 32 14 g 0 0 35 7 2 52 1 42 1 1 1 43 7 10 t 0 0 7 6 46 1 3 1 52 0 2 5 6 13

oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --gmTGAGTCAGcm ; cor=; Ncor= a 0 0 6 15 3 0 50 0 0 6 51 2 9 17 c 0 0 6 26 3 1 0 11 1 47 0 4 32 14 g 0 0 35 7 2 52 1 42 1 1 1 43 7 10 t 0 0 7 6 46 1 3 1 52 0 2 5 6 13

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=2/3; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.760537; ykGCTGAsTCAGCm ; cor=; Ncor= a 8 5 0 5 1 0 38 0 1 6 36 1 1 15 c 13 7 0 33 0 0 0 14 0 32 0 0 34 10 g 6 10 38 0 1 32 0 24 0 0 1 30 2 8 t 11 16 0 0 36 6 0 0 37 0 1 7 1 5

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=3/3; ncol2=13; w=0; offset=1; strand=D; shift=3; score=0.702621; ---mTGAGTmAGCa ; cor=; Ncor= a 0 0 0 10 2 0 31 0 1 21 32 0 0 14 c 0 0 0 14 7 0 0 3 0 10 0 0 32 6 g 0 0 0 4 1 27 1 29 3 0 0 32 0 6 t 0 0 0 4 22 5 0 0 28 1 0 0 0 6

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; mrsCTGTCArdb ; Alignment reference a 17 17 10 1 1 0 2 3 59 35 17 13 c 23 13 25 57 1 2 0 59 2 9 13 16 g 12 20 22 3 1 60 0 1 2 16 17 17 t 12 14 7 3 61 2 62 1 1 4 17 18

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; mrsCTGTCArdb ; cor=; Ncor= a 17 17 10 1 1 0 2 3 59 35 17 13 c 23 13 25 57 1 2 0 59 2 9 13 16 g 12 20 22 3 1 60 0 1 2 16 17 17 t 12 14 7 3 61 2 62 1 1 4 17 18

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.944519; srvCTGTCAgwb ; cor=; Ncor= a 15 21 19 1 2 2 3 1 62 9 18 14 c 20 11 22 64 2 2 4 66 1 9 14 18 g 22 23 20 1 2 64 1 0 0 46 14 18 t 11 13 7 2 62 0 60 1 5 4 22 18

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.833587; swCCTGTCAgac ; cor=; Ncor= a 3 7 0 0 0 0 0 1 22 1 9 3 c 7 4 20 21 0 1 0 20 0 5 3 10 g 8 5 2 1 1 21 0 1 0 13 5 4 t 4 6 0 0 21 0 22 0 0 3 5 5

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift1 ; 5 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; -srGCACGTGGsv ; Alignment reference a 0 11 14 0 3 49 0 1 4 1 3 10 15 c 0 18 13 4 52 2 53 1 3 0 4 17 14 g 0 15 17 48 0 0 1 53 1 49 44 15 16 t 0 11 11 3 0 4 1 0 47 5 4 13 10

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -srGCACGTGGsv ; cor=; Ncor= a 0 11 14 0 3 49 0 1 4 1 3 10 15 c 0 18 13 4 52 2 53 1 3 0 4 17 14 g 0 15 17 48 0 0 1 53 1 49 44 15 16 t 0 11 11 3 0 4 1 0 47 5 4 13 10

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.90082; -mkGCACGTGCmk ; cor=; Ncor= a 0 15 10 4 0 49 0 2 3 0 3 15 9 c 0 18 12 10 54 2 51 1 0 0 37 17 12 g 0 12 17 37 0 0 1 51 2 54 10 12 18 t 0 9 15 3 0 3 2 0 49 0 4 10 15

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=3/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.855486; rssGCACGTGGkv ; cor=; Ncor= a 13 11 11 0 3 44 0 1 4 1 3 9 13 c 11 14 13 4 46 2 48 0 3 0 4 12 14 g 15 14 16 42 0 0 1 48 1 45 39 15 15 t 10 10 9 3 0 3 0 0 41 3 3 13 7

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=4/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.772112; dmkGCACGTGCmk ; cor=; Ncor= a 13 15 10 3 0 47 0 2 3 0 3 15 9 c 11 16 12 10 52 2 49 1 0 0 36 15 12 g 14 12 15 36 0 0 1 49 2 52 10 12 16 t 14 9 15 3 0 3 2 0 47 0 3 10 15

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 4 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=12; shift=0; ncol=12; srvCTGTCAgwb ; Alignment reference a 15 21 19 1 2 2 3 1 62 9 18 14 c 20 11 22 64 2 2 4 66 1 9 14 18 g 22 23 20 1 2 64 1 0 0 46 14 18 t 11 13 7 2 62 0 60 1 5 4 22 18

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; srvCTGTCAgwb ; cor=; Ncor= a 15 21 19 1 2 2 3 1 62 9 18 14 c 20 11 22 64 2 2 4 66 1 9 14 18 g 22 23 20 1 2 64 1 0 0 46 14 18 t 11 13 7 2 62 0 60 1 5 4 22 18

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.944519; mrsCTGTCArdb ; cor=; Ncor= a 17 17 10 1 1 0 2 3 59 35 17 13 c 23 13 25 57 1 2 0 59 2 9 13 16 g 12 20 22 3 1 60 0 1 2 16 17 17 t 12 14 7 3 61 2 62 1 1 4 17 18

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.859851; swCCTGTCAgac ; cor=; Ncor= a 3 7 0 0 0 0 0 1 22 1 9 3 c 7 4 20 21 0 1 0 20 0 5 3 10 g 8 5 2 1 1 21 0 1 0 13 5 4 t 4 6 0 0 21 0 22 0 0 3 5 5

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -mkGCACGTGCmk ; Alignment reference a 0 15 10 4 0 49 0 2 3 0 3 15 9 c 0 18 12 10 54 2 51 1 0 0 37 17 12 g 0 12 17 37 0 0 1 51 2 54 10 12 18 t 0 9 15 3 0 3 2 0 49 0 4 10 15

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -mkGCACGTGCmk ; cor=; Ncor= a 0 15 10 4 0 49 0 2 3 0 3 15 9 c 0 18 12 10 54 2 51 1 0 0 37 17 12 g 0 12 17 37 0 0 1 51 2 54 10 12 18 t 0 9 15 3 0 3 2 0 49 0 4 10 15

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=2/4; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.90082; -bsCCACGTGCys ; cor=; Ncor= a 0 10 13 4 5 47 0 1 4 0 3 11 11 c 0 16 15 44 49 1 53 1 0 0 48 17 15 g 0 14 17 4 0 3 1 53 2 52 4 13 18 t 0 15 10 3 1 4 1 0 49 3 0 14 11

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.856722; dmkGCACGTGCmk ; cor=; Ncor= a 13 15 10 3 0 47 0 2 3 0 3 15 9 c 11 16 12 10 52 2 49 1 0 0 36 15 12 g 14 12 15 36 0 0 1 49 2 52 10 12 16 t 14 9 15 3 0 3 2 0 47 0 3 10 15

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=4/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.772777; rssGCACGTGGkv ; cor=; Ncor= a 13 11 11 0 3 44 0 1 4 1 3 9 13 c 11 14 13 4 46 2 48 0 3 0 4 12 14 g 15 14 16 42 0 0 1 48 1 45 39 15 15 t 10 10 9 3 0 3 0 0 41 3 3 13 7

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 5 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=14; shift=0; ncol=14; rssGCACGTGGkvc ; Alignment reference a 13 11 11 0 3 44 0 1 4 1 3 9 13 11 c 11 14 13 4 46 2 48 0 3 0 4 12 14 16 g 15 14 16 42 0 0 1 48 1 45 39 15 15 10 t 10 10 9 3 0 3 0 0 41 3 3 13 7 12

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rssGCACGTGGkvc ; cor=; Ncor= a 13 11 11 0 3 44 0 1 4 1 3 9 13 11 c 11 14 13 4 46 2 48 0 3 0 4 12 14 16 g 15 14 16 42 0 0 1 48 1 45 39 15 15 10 t 10 10 9 3 0 3 0 0 41 3 3 13 7 12

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.901108; dmkGCACGTGCmkh ; cor=; Ncor= a 13 15 10 3 0 47 0 2 3 0 3 15 9 14 c 11 16 12 10 52 2 49 1 0 0 36 15 12 14 g 14 12 15 36 0 0 1 49 2 52 10 12 16 11 t 14 9 15 3 0 3 2 0 47 0 3 10 15 13

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.855486; -srGCACGTGGsv- ; cor=; Ncor= a 0 11 14 0 3 49 0 1 4 1 3 10 15 0 c 0 18 13 4 52 2 53 1 3 0 4 17 14 0 g 0 15 17 48 0 0 1 53 1 49 44 15 16 0 t 0 11 11 3 0 4 1 0 47 5 4 13 10 0

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.772777; -mkGCACGTGCmk- ; cor=; Ncor= a 0 15 10 4 0 49 0 2 3 0 3 15 9 0 c 0 18 12 10 54 2 51 1 0 0 37 17 12 0 g 0 12 17 37 0 0 1 51 2 54 10 12 18 0 t 0 9 15 3 0 3 2 0 49 0 4 10 15 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; dmkGCACGTGCmkh ; Alignment reference a 13 15 10 3 0 47 0 2 3 0 3 15 9 14 c 11 16 12 10 52 2 49 1 0 0 36 15 12 14 g 14 12 15 36 0 0 1 49 2 52 10 12 16 11 t 14 9 15 3 0 3 2 0 47 0 3 10 15 13
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; dmkGCACGTGCmkh ; cor=; Ncor= a 13 15 10 3 0 47 0 2 3 0 3 15 9 14 c 11 16 12 10 52 2 49 1 0 0 36 15 12 14 g 14 12 15 36 0 0 1 49 2 52 10 12 16 11 t 14 9 15 3 0 3 2 0 47 0 3 10 15 13
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.901108; rssGCACGTGGkvc ; cor=; Ncor= a 13 11 11 0 3 44 0 1 4 1 3 9 13 11 c 11 14 13 4 46 2 48 0 3 0 4 12 14 16 g 15 14 16 42 0 0 1 48 1 45 39 15 15 10 t 10 10 9 3 0 3 0 0 41 3 3 13 7 12
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.856722; -mkGCACGTGCmk- ; cor=; Ncor= a 0 15 10 4 0 49 0 2 3 0 3 15 9 0 c 0 18 12 10 54 2 51 1 0 0 37 17 12 0 g 0 12 17 37 0 0 1 51 2 54 10 12 18 0 t 0 9 15 3 0 3 2 0 49 0 4 10 15 0
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=4/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.772112; -srGCACGTGGsv- ; cor=; Ncor= a 0 11 14 0 3 49 0 1 4 1 3 10 15 0 c 0 18 13 4 52 2 53 1 3 0 4 17 14 0 g 0 15 17 48 0 0 1 53 1 49 44 15 16 0 t 0 11 11 3 0 4 1 0 47 5 4 13 10 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=13; shift=3; ncol=16; ---mTGAGTmAGCaar ; Alignment reference a 0 0 0 10 2 0 31 0 1 21 32 0 0 14 15 9 c 0 0 0 14 7 0 0 3 0 10 0 0 32 6 7 6 g 0 0 0 4 1 27 1 29 3 0 0 32 0 6 7 10 t 0 0 0 4 22 5 0 0 28 1 0 0 0 6 3 7
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---mTGAGTmAGCaar ; cor=; Ncor= a 0 0 0 10 2 0 31 0 1 21 32 0 0 14 15 9 c 0 0 0 14 7 0 0 3 0 10 0 0 32 6 7 6 g 0 0 0 4 1 27 1 29 3 0 0 32 0 6 7 10 t 0 0 0 4 22 5 0 0 28 1 0 0 0 6 3 7
oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.702621; --gmTGAGTCAGcm-- ; cor=; Ncor= a 0 0 6 15 3 0 50 0 0 6 51 2 9 17 0 0 c 0 0 6 26 3 1 0 11 1 47 0 4 32 14 0 0 g 0 0 35 7 2 52 1 42 1 1 1 43 7 10 0 0 t 0 0 7 6 46 1 3 1 52 0 2 5 6 13 0 0
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=3/3; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.663391; ykGCTGAsTCAGCms- ; cor=; Ncor= a 8 5 0 5 1 0 38 0 1 6 36 1 1 15 9 0 c 13 7 0 33 0 0 0 14 0 32 0 0 34 10 10 0 g 6 10 38 0 1 32 0 24 0 0 1 30 2 8 12 0 t 11 16 0 0 36 6 0 0 37 0 1 7 1 5 7 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; swCCTGTCAgacc ; Alignment reference a 3 7 0 0 0 0 0 1 22 1 9 3 5 c 7 4 20 21 0 1 0 20 0 5 3 10 8 g 8 5 2 1 1 21 0 1 0 13 5 4 5 t 4 6 0 0 21 0 22 0 0 3 5 5 4
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; swCCTGTCAgacc ; cor=; Ncor= a 3 7 0 0 0 0 0 1 22 1 9 3 5 c 7 4 20 21 0 1 0 20 0 5 3 10 8 g 8 5 2 1 1 21 0 1 0 13 5 4 5 t 4 6 0 0 21 0 22 0 0 3 5 5 4
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.859851; srvCTGTCAgwb- ; cor=; Ncor= a 15 21 19 1 2 2 3 1 62 9 18 14 0 c 20 11 22 64 2 2 4 66 1 9 14 18 0 g 22 23 20 1 2 64 1 0 0 46 14 18 0 t 11 13 7 2 62 0 60 1 5 4 22 18 0
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=3/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.833587; mrsCTGTCArdb- ; cor=; Ncor= a 17 17 10 1 1 0 2 3 59 35 17 13 0 c 23 13 25 57 1 2 0 59 2 9 13 16 0 g 12 20 22 3 1 60 0 1 2 16 17 17 0 t 12 14 7 3 61 2 62 1 1 4 17 18 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=15; shift=1; ncol=16; -skGCTGAsTCAGCmr ; Alignment reference a 0 7 5 1 7 1 0 37 0 0 6 36 0 0 16 11 c 0 12 8 2 30 1 0 0 24 0 32 1 0 38 10 6 g 0 10 10 34 0 0 32 0 14 0 0 0 33 0 7 13 t 0 9 15 1 1 36 6 1 0 38 0 1 5 0 5 8
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -skGCTGAsTCAGCmr ; cor=; Ncor= a 0 7 5 1 7 1 0 37 0 0 6 36 0 0 16 11 c 0 12 8 2 30 1 0 0 24 0 32 1 0 38 10 6 g 0 10 10 34 0 0 32 0 14 0 0 0 33 0 7 13 t 0 9 15 1 1 36 6 1 0 38 0 1 5 0 5 8
oligos_6nt_mkv2_m5_rc_shift2 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=2/3; ncol2=12; w=0; offset=1; strand=R; shift=2; score=0.760537; --kgCTGACTCAkc-- ; cor=; Ncor= a 0 0 13 6 5 2 0 52 1 3 1 46 6 7 0 0 c 0 0 10 7 43 1 1 1 42 1 52 2 7 35 0 0 g 0 0 14 32 4 0 47 1 11 0 1 3 26 6 0 0 t 0 0 17 9 2 51 6 0 0 50 0 3 15 6 0 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=3/3; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.663391; yttGCTkACTCAk--- ; cor=; Ncor= a 7 3 6 0 0 0 1 28 0 0 5 22 4 0 0 0 c 10 7 6 0 32 0 0 3 29 1 27 1 4 0 0 0 g 6 7 6 32 0 0 10 0 3 0 0 7 14 0 0 0 t 9 15 14 0 0 32 21 1 0 31 0 2 10 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --gmTGAGTCAGcm ; Alignment reference a 0 0 6 15 3 0 50 0 0 6 51 2 9 17 c 0 0 6 26 3 1 0 11 1 47 0 4 32 14 g 0 0 35 7 2 52 1 42 1 1 1 43 7 10 t 0 0 7 6 46 1 3 1 52 0 2 5 6 13
oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --gmTGAGTCAGcm ; cor=; Ncor= a 0 0 6 15 3 0 50 0 0 6 51 2 9 17 c 0 0 6 26 3 1 0 11 1 47 0 4 32 14 g 0 0 35 7 2 52 1 42 1 1 1 43 7 10 t 0 0 7 6 46 1 3 1 52 0 2 5 6 13
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=2/3; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.760537; ykGCTGAsTCAGCm ; cor=; Ncor= a 8 5 0 5 1 0 38 0 1 6 36 1 1 15 c 13 7 0 33 0 0 0 14 0 32 0 0 34 10 g 6 10 38 0 1 32 0 24 0 0 1 30 2 8 t 11 16 0 0 36 6 0 0 37 0 1 7 1 5
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=3/3; ncol2=13; w=0; offset=1; strand=D; shift=3; score=0.702621; ---mTGAGTmAGCa ; cor=; Ncor= a 0 0 0 10 2 0 31 0 1 21 32 0 0 14 c 0 0 0 14 7 0 0 3 0 10 0 0 32 6 g 0 0 0 4 1 27 1 29 3 0 0 32 0 6 t 0 0 0 4 22 5 0 0 28 1 0 0 0 6

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; mrsCTGTCArdb ; Alignment reference a 17 17 10 1 1 0 2 3 59 35 17 13 c 23 13 25 57 1 2 0 59 2 9 13 16 g 12 20 22 3 1 60 0 1 2 16 17 17 t 12 14 7 3 61 2 62 1 1 4 17 18
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; mrsCTGTCArdb ; cor=; Ncor= a 17 17 10 1 1 0 2 3 59 35 17 13 c 23 13 25 57 1 2 0 59 2 9 13 16 g 12 20 22 3 1 60 0 1 2 16 17 17 t 12 14 7 3 61 2 62 1 1 4 17 18
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.944519; srvCTGTCAgwb ; cor=; Ncor= a 15 21 19 1 2 2 3 1 62 9 18 14 c 20 11 22 64 2 2 4 66 1 9 14 18 g 22 23 20 1 2 64 1 0 0 46 14 18 t 11 13 7 2 62 0 60 1 5 4 22 18
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.833587; swCCTGTCAgac ; cor=; Ncor= a 3 7 0 0 0 0 0 1 22 1 9 3 c 7 4 20 21 0 1 0 20 0 5 3 10 g 8 5 2 1 1 21 0 1 0 13 5 4 t 4 6 0 0 21 0 22 0 0 3 5 5

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; -srGCACGTGGsv ; Alignment reference a 0 11 14 0 3 49 0 1 4 1 3 10 15 c 0 18 13 4 52 2 53 1 3 0 4 17 14 g 0 15 17 48 0 0 1 53 1 49 44 15 16 t 0 11 11 3 0 4 1 0 47 5 4 13 10
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -srGCACGTGGsv ; cor=; Ncor= a 0 11 14 0 3 49 0 1 4 1 3 10 15 c 0 18 13 4 52 2 53 1 3 0 4 17 14 g 0 15 17 48 0 0 1 53 1 49 44 15 16 t 0 11 11 3 0 4 1 0 47 5 4 13 10
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.90082; -mkGCACGTGCmk ; cor=; Ncor= a 0 15 10 4 0 49 0 2 3 0 3 15 9 c 0 18 12 10 54 2 51 1 0 0 37 17 12 g 0 12 17 37 0 0 1 51 2 54 10 12 18 t 0 9 15 3 0 3 2 0 49 0 4 10 15
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=3/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.855486; rssGCACGTGGkv ; cor=; Ncor= a 13 11 11 0 3 44 0 1 4 1 3 9 13 c 11 14 13 4 46 2 48 0 3 0 4 12 14 g 15 14 16 42 0 0 1 48 1 45 39 15 15 t 10 10 9 3 0 3 0 0 41 3 3 13 7
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=4/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.772112; dmkGCACGTGCmk ; cor=; Ncor= a 13 15 10 3 0 47 0 2 3 0 3 15 9 c 11 16 12 10 52 2 49 1 0 0 36 15 12 g 14 12 15 36 0 0 1 49 2 52 10 12 16 t 14 9 15 3 0 3 2 0 47 0 3 10 15

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=12; shift=0; ncol=12; srvCTGTCAgwb ; Alignment reference a 15 21 19 1 2 2 3 1 62 9 18 14 c 20 11 22 64 2 2 4 66 1 9 14 18 g 22 23 20 1 2 64 1 0 0 46 14 18 t 11 13 7 2 62 0 60 1 5 4 22 18
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; srvCTGTCAgwb ; cor=; Ncor= a 15 21 19 1 2 2 3 1 62 9 18 14 c 20 11 22 64 2 2 4 66 1 9 14 18 g 22 23 20 1 2 64 1 0 0 46 14 18 t 11 13 7 2 62 0 60 1 5 4 22 18
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.944519; mrsCTGTCArdb ; cor=; Ncor= a 17 17 10 1 1 0 2 3 59 35 17 13 c 23 13 25 57 1 2 0 59 2 9 13 16 g 12 20 22 3 1 60 0 1 2 16 17 17 t 12 14 7 3 61 2 62 1 1 4 17 18
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.859851; swCCTGTCAgac ; cor=; Ncor= a 3 7 0 0 0 0 0 1 22 1 9 3 c 7 4 20 21 0 1 0 20 0 5 3 10 g 8 5 2 1 1 21 0 1 0 13 5 4 t 4 6 0 0 21 0 22 0 0 3 5 5

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -mkGCACGTGCmk ; Alignment reference a 0 15 10 4 0 49 0 2 3 0 3 15 9 c 0 18 12 10 54 2 51 1 0 0 37 17 12 g 0 12 17 37 0 0 1 51 2 54 10 12 18 t 0 9 15 3 0 3 2 0 49 0 4 10 15
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -mkGCACGTGCmk ; cor=; Ncor= a 0 15 10 4 0 49 0 2 3 0 3 15 9 c 0 18 12 10 54 2 51 1 0 0 37 17 12 g 0 12 17 37 0 0 1 51 2 54 10 12 18 t 0 9 15 3 0 3 2 0 49 0 4 10 15
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=2/4; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.90082; -bsCCACGTGCys ; cor=; Ncor= a 0 10 13 4 5 47 0 1 4 0 3 11 11 c 0 16 15 44 49 1 53 1 0 0 48 17 15 g 0 14 17 4 0 3 1 53 2 52 4 13 18 t 0 15 10 3 1 4 1 0 49 3 0 14 11
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.856722; dmkGCACGTGCmk ; cor=; Ncor= a 13 15 10 3 0 47 0 2 3 0 3 15 9 c 11 16 12 10 52 2 49 1 0 0 36 15 12 g 14 12 15 36 0 0 1 49 2 52 10 12 16 t 14 9 15 3 0 3 2 0 47 0 3 10 15
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=4/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.772777; rssGCACGTGGkv ; cor=; Ncor= a 13 11 11 0 3 44 0 1 4 1 3 9 13 c 11 14 13 4 46 2 48 0 3 0 4 12 14 g 15 14 16 42 0 0 1 48 1 45 39 15 15 t 10 10 9 3 0 3 0 0 41 3 3 13 7

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=14; shift=0; ncol=14; rssGCACGTGGkvc ; Alignment reference a 13 11 11 0 3 44 0 1 4 1 3 9 13 11 c 11 14 13 4 46 2 48 0 3 0 4 12 14 16 g 15 14 16 42 0 0 1 48 1 45 39 15 15 10 t 10 10 9 3 0 3 0 0 41 3 3 13 7 12
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rssGCACGTGGkvc ; cor=; Ncor= a 13 11 11 0 3 44 0 1 4 1 3 9 13 11 c 11 14 13 4 46 2 48 0 3 0 4 12 14 16 g 15 14 16 42 0 0 1 48 1 45 39 15 15 10 t 10 10 9 3 0 3 0 0 41 3 3 13 7 12
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.901108; dmkGCACGTGCmkh ; cor=; Ncor= a 13 15 10 3 0 47 0 2 3 0 3 15 9 14 c 11 16 12 10 52 2 49 1 0 0 36 15 12 14 g 14 12 15 36 0 0 1 49 2 52 10 12 16 11 t 14 9 15 3 0 3 2 0 47 0 3 10 15 13
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=3/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.855486; -srGCACGTGGsv- ; cor=; Ncor= a 0 11 14 0 3 49 0 1 4 1 3 10 15 0 c 0 18 13 4 52 2 53 1 3 0 4 17 14 0 g 0 15 17 48 0 0 1 53 1 49 44 15 16 0 t 0 11 11 3 0 4 1 0 47 5 4 13 10 0
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.772777; -mkGCACGTGCmk- ; cor=; Ncor= a 0 15 10 4 0 49 0 2 3 0 3 15 9 0 c 0 18 12 10 54 2 51 1 0 0 37 17 12 0 g 0 12 17 37 0 0 1 51 2 54 10 12 18 0 t 0 9 15 3 0 3 2 0 49 0 4 10 15 0