One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124233_2025-04-03.124233_lUir6h/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.2025-04-03.124233_2025-04-03.124233_lUir6h/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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=12; shift=0; ncol=12; gmkCGTACGmkc ; Alignment reference a 4 5 0 0 1 0 20 1 0 12 4 4 c 4 9 3 20 0 0 0 18 0 5 2 8 g 8 2 5 0 18 0 0 0 20 3 9 4 t 4 4 12 0 1 20 0 1 0 0 5 4

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gmkCGTACGmkc ; cor=; Ncor= a 4 5 0 0 1 0 20 1 0 12 4 4 c 4 9 3 20 0 0 0 18 0 5 2 8 g 8 2 5 0 18 0 0 0 20 3 9 4 t 4 4 12 0 1 20 0 1 0 0 5 4

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.756588; -ywCGTACGwr- ; cor=; Ncor= a 0 5 22 0 0 1 57 0 10 19 25 0 c 0 19 13 50 0 2 0 60 0 7 11 0 g 0 11 7 0 59 1 2 0 50 13 19 0 t 0 25 18 10 1 56 1 0 0 21 5 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----tkAGTAAGCda ; Alignment reference a 0 0 0 0 11 13 51 0 3 49 54 1 4 17 25 c 0 0 0 0 7 7 1 9 0 7 0 1 51 9 13 g 0 0 0 0 3 18 1 45 4 0 0 54 0 15 11 t 0 0 0 0 35 18 3 2 49 0 2 0 1 15 7

oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----tkAGTAAGCda ; cor=; Ncor= a 0 0 0 0 11 13 51 0 3 49 54 1 4 17 25 c 0 0 0 0 7 7 1 9 0 7 0 1 51 9 13 g 0 0 0 0 3 18 1 45 4 0 0 54 0 15 11 t 0 0 0 0 35 18 3 2 49 0 2 0 1 15 7

oligos_6nt_mkv2_m3_rc_shift4 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=2/6; ncol2=11; w=0; offset=0; strand=R; shift=4; score=0.994687; ----tkAGTAAGCra ; cor=; Ncor= a 0 0 0 0 11 15 65 0 6 54 67 1 5 24 28 c 0 0 0 0 11 11 1 9 0 16 0 1 64 13 17 g 0 0 0 0 5 26 1 59 4 0 0 68 0 18 16 t 0 0 0 0 43 18 3 2 60 0 3 0 1 15 9

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=3/6; ncol2=14; w=-3; offset=-3; strand=R; shift=1; score=0.630218; -tGCTGASTCAKCaw ; cor=; Ncor= a 0 5 1 10 0 0 42 0 0 6 42 1 0 21 14 c 0 9 0 31 0 0 0 13 0 36 0 0 39 10 8 g 0 10 37 0 0 35 0 29 0 0 0 30 1 7 9 t 0 18 4 1 42 7 0 0 42 0 0 11 2 4 11

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=4/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.570417; kkGmTGASTCAGCar ; cor=; Ncor= a 9 4 0 19 0 0 42 0 0 10 42 0 0 22 17 c 8 9 0 25 0 0 0 14 0 34 0 0 44 9 5 g 11 11 42 0 0 37 0 30 0 0 0 34 0 8 12 t 16 20 2 0 44 7 2 0 44 0 2 10 0 5 10

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=5/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.535735; tkGCTGAsTCAkCaa ; cor=; Ncor= a 8 4 0 12 0 0 53 0 0 6 53 0 0 32 21 c 11 12 0 41 7 0 0 18 0 47 0 7 45 9 9 g 9 17 51 0 0 42 0 35 0 0 0 32 0 9 11 t 25 20 2 0 46 11 0 0 53 0 0 14 8 3 12

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=6/6; ncol2=10; w=-2; offset=-2; strand=R; shift=2; score=0.470707; --rwTTAGTAwr--- ; cor=; Ncor= a 0 0 14 9 0 0 22 0 0 22 10 10 0 0 0 c 0 0 2 4 0 0 0 0 0 0 4 0 0 0 0 g 0 0 6 2 0 0 0 22 0 0 0 7 0 0 0 t 0 0 0 7 22 22 0 0 22 0 8 5 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift1 ; 8 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=11; shift=1; ncol=12; -tyGCTTACTma ; Alignment reference a 0 9 15 1 0 3 0 60 2 3 18 43 c 0 16 18 0 68 0 0 4 59 1 26 5 g 0 17 13 64 1 0 16 0 9 1 11 11 t 0 28 24 5 1 67 54 6 0 65 15 11

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -tyGCTTACTma ; cor=; Ncor= a 0 9 15 1 0 3 0 60 2 3 18 43 c 0 16 18 0 68 0 0 4 59 1 26 5 g 0 17 13 64 1 0 16 0 9 1 11 11 t 0 28 24 5 1 67 54 6 0 65 15 11

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3_rc; m=2/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.994687; -thGCTTACTma ; cor=; Ncor= a 0 7 15 1 0 2 0 49 2 3 18 35 c 0 11 15 0 54 0 0 4 45 1 18 3 g 0 13 9 51 1 0 7 0 9 1 7 7 t 0 25 17 4 1 54 49 3 0 51 13 11

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5_rc; m=3/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.731642; -wtGATGACTma ; cor=; Ncor= a 0 14 8 2 30 0 0 40 0 1 13 26 c 0 5 6 0 9 0 6 1 33 0 16 8 g 0 8 6 39 1 1 35 0 8 1 8 2 t 0 14 21 0 1 40 0 0 0 39 4 5

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.658734; -wtGMTGASTCA ; cor=; Ncor= a 0 11 4 2 11 0 0 42 0 0 7 42 c 0 9 7 1 30 0 0 0 29 0 35 0 g 0 8 10 39 0 0 36 0 13 0 0 0 t 0 14 21 0 1 42 6 0 0 42 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=5/7; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.592703; gytGCTGASTCA ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 c 8 12 8 0 34 0 0 0 30 0 37 0 g 21 5 9 44 0 0 34 0 14 0 0 0 t 8 17 22 0 0 42 10 0 0 42 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=6/7; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.561843; gttGmTGAsTCA ; cor=; Ncor= a 11 12 3 8 14 0 0 53 0 0 11 46 c 13 11 9 0 32 0 0 0 35 0 42 0 g 21 9 9 45 7 0 47 0 18 0 0 7 t 8 21 32 0 0 53 6 0 0 53 0 0

oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=7/7; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.455895; ----ywTACTAA ; cor=; Ncor= a 0 0 0 0 5 8 0 22 0 0 22 22 c 0 0 0 0 7 0 0 0 22 0 0 0 g 0 0 0 0 0 4 0 0 0 0 0 0 t 0 0 0 0 10 10 22 0 0 22 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---ywTACTAAwy ; Alignment reference a 0 0 0 5 8 0 22 0 0 22 22 7 0 c 0 0 0 7 0 0 0 22 0 0 0 2 6 g 0 0 0 0 4 0 0 0 0 0 0 4 2 t 0 0 0 10 10 22 0 0 22 0 0 9 14

oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---ywTACTAAwy ; cor=; Ncor= a 0 0 0 5 8 0 22 0 0 22 22 7 0 c 0 0 0 7 0 0 0 22 0 0 0 2 6 g 0 0 0 0 4 0 0 0 0 0 0 4 2 t 0 0 0 10 10 22 0 0 22 0 0 9 14

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=2/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.470707; thGCTTACTma-- ; cor=; Ncor= a 7 15 1 0 2 0 49 2 3 18 35 0 0 c 11 15 0 54 0 0 4 45 1 18 3 0 0 g 13 9 51 1 0 7 0 9 1 7 7 0 0 t 25 17 4 1 54 49 3 0 51 13 11 0 0

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.455895; tyGCTTACTma-- ; cor=; Ncor= a 9 15 1 0 3 0 60 2 3 18 43 0 0 c 16 18 0 68 0 0 4 59 1 26 5 0 0 g 17 13 64 1 0 16 0 9 1 11 11 0 0 t 28 24 5 1 67 54 6 0 65 15 11 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; gytGCTGASTCAkCmm ; Alignment reference a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 16 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 8 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4 9

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; gytGCTGASTCAkCmm ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 16 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 8 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4 9

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.974454; gttGmTGAsTCAGCma ; cor=; Ncor= a 11 12 3 8 14 0 0 53 0 0 11 46 0 2 20 25 c 13 11 9 0 32 0 0 0 35 0 42 0 0 51 17 9 g 21 9 9 45 7 0 47 0 18 0 0 7 41 0 12 11 t 8 21 32 0 0 53 6 0 0 53 0 0 12 0 4 8

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=3/6; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.866092; -wtGMTGASTCAGCa- ; cor=; Ncor= a 0 11 4 2 11 0 0 42 0 0 7 42 1 4 18 0 c 0 9 7 1 30 0 0 0 29 0 35 0 0 37 10 0 g 0 8 10 39 0 0 36 0 13 0 0 0 31 0 9 0 t 0 14 21 0 1 42 6 0 0 42 0 0 10 1 5 0

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=4/6; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.604925; -----tkAGTCATCaw ; cor=; Ncor= a 0 0 0 0 0 5 4 39 0 0 0 40 1 0 21 14 c 0 0 0 0 0 2 8 1 8 0 35 1 1 39 6 8 g 0 0 0 0 0 8 16 0 33 1 6 0 9 0 6 5 t 0 0 0 0 0 26 13 1 0 40 0 0 30 2 8 14

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=5/6; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.592703; -tyGCTTACTma---- ; cor=; Ncor= a 0 9 15 1 0 3 0 60 2 3 18 43 0 0 0 0 c 0 16 18 0 68 0 0 4 59 1 26 5 0 0 0 0 g 0 17 13 64 1 0 16 0 9 1 11 11 0 0 0 0 t 0 28 24 5 1 67 54 6 0 65 15 11 0 0 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=6/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.570417; -thGCTTACTma---- ; cor=; Ncor= a 0 7 15 1 0 2 0 49 2 3 18 35 0 0 0 0 c 0 11 15 0 54 0 0 4 45 1 18 3 0 0 0 0 g 0 13 9 51 1 0 7 0 9 1 7 7 0 0 0 0 t 0 25 17 4 1 54 49 3 0 51 13 11 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; mkGCACGTGCmk ; Alignment reference a 7 3 1 0 16 0 0 0 0 2 8 3 c 7 2 0 16 2 18 0 0 2 15 5 1 g 1 5 15 2 0 0 18 2 16 0 2 7 t 3 8 2 0 0 0 0 16 0 1 3 7

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; mkGCACGTGCmk ; cor=; Ncor= a 7 3 1 0 16 0 0 0 0 2 8 3 c 7 2 0 16 2 18 0 0 2 15 5 1 g 1 5 15 2 0 0 18 2 16 0 2 7 t 3 8 2 0 0 0 0 16 0 1 3 7

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 7 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=14; shift=1; ncol=15; -wtGMTGASTCAGCa ; Alignment reference a 0 11 4 2 11 0 0 42 0 0 7 42 1 4 18 c 0 9 7 1 30 0 0 0 29 0 35 0 0 37 10 g 0 8 10 39 0 0 36 0 13 0 0 0 31 0 9 t 0 14 21 0 1 42 6 0 0 42 0 0 10 1 5

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wtGMTGASTCAGCa ; cor=; Ncor= a 0 11 4 2 11 0 0 42 0 0 7 42 1 4 18 c 0 9 7 1 30 0 0 0 29 0 35 0 0 37 10 g 0 8 10 39 0 0 36 0 13 0 0 0 31 0 9 t 0 14 21 0 1 42 6 0 0 42 0 0 10 1 5

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/6; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.866092; gytGCTGASTCAkCm ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/6; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.865492; gttGmTGAsTCAGCm ; cor=; Ncor= a 11 12 3 8 14 0 0 53 0 0 11 46 0 2 20 c 13 11 9 0 32 0 0 0 35 0 42 0 0 51 17 g 21 9 9 45 7 0 47 0 18 0 0 7 41 0 12 t 8 21 32 0 0 53 6 0 0 53 0 0 12 0 4

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=4/6; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.70599; -wtGATGACTma--- ; cor=; Ncor= a 0 14 8 2 30 0 0 40 0 1 13 26 0 0 0 c 0 5 6 0 9 0 6 1 33 0 16 8 0 0 0 g 0 8 6 39 1 1 35 0 8 1 8 2 0 0 0 t 0 14 21 0 1 40 0 0 0 39 4 5 0 0 0

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=5/6; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.658734; -tyGCTTACTma--- ; cor=; Ncor= a 0 9 15 1 0 3 0 60 2 3 18 43 0 0 0 c 0 16 18 0 68 0 0 4 59 1 26 5 0 0 0 g 0 17 13 64 1 0 16 0 9 1 11 11 0 0 0 t 0 28 24 5 1 67 54 6 0 65 15 11 0 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=6/6; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.630218; -thGCTTACTma--- ; cor=; Ncor= a 0 7 15 1 0 2 0 49 2 3 18 35 0 0 0 c 0 11 15 0 54 0 0 4 45 1 18 3 0 0 0 g 0 13 9 51 1 0 7 0 9 1 7 7 0 0 0 t 0 25 17 4 1 54 49 3 0 51 13 11 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift5 ; 6 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; -----tkAGTCATCaw ; Alignment reference a 0 0 0 0 0 5 4 39 0 0 0 40 1 0 21 14 c 0 0 0 0 0 2 8 1 8 0 35 1 1 39 6 8 g 0 0 0 0 0 8 16 0 33 1 6 0 9 0 6 5 t 0 0 0 0 0 26 13 1 0 40 0 0 30 2 8 14

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----tkAGTCATCaw ; cor=; Ncor= a 0 0 0 0 0 5 4 39 0 0 0 40 1 0 21 14 c 0 0 0 0 0 2 8 1 8 0 35 1 1 39 6 8 g 0 0 0 0 0 8 16 0 33 1 6 0 9 0 6 5 t 0 0 0 0 0 26 13 1 0 40 0 0 30 2 8 14

oligos_6nt_mkv2_m3_rc_shift5 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3_rc; m=2/5; ncol2=11; w=0; offset=0; strand=R; shift=5; score=0.731642; -----tkAGTAAGCra ; cor=; Ncor= a 0 0 0 0 0 11 15 65 0 6 54 67 1 5 24 28 c 0 0 0 0 0 11 11 1 9 0 16 0 1 64 13 17 g 0 0 0 0 0 5 26 1 59 4 0 0 68 0 18 16 t 0 0 0 0 0 43 18 3 2 60 0 3 0 1 15 9

oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=3/5; ncol2=14; w=-3; offset=-3; strand=R; shift=2; score=0.70599; --tGCTGASTCAKCaw ; cor=; Ncor= a 0 0 5 1 10 0 0 42 0 0 6 42 1 0 21 14 c 0 0 9 0 31 0 0 0 13 0 36 0 0 39 10 8 g 0 0 10 37 0 0 35 0 29 0 0 0 30 1 7 9 t 0 0 18 4 1 42 7 0 0 42 0 0 11 2 4 11

oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=4/5; ncol2=16; w=-4; offset=-4; strand=R; shift=1; score=0.624395; -tkGCTGAsTCAkCaa ; cor=; Ncor= a 0 8 4 0 12 0 0 53 0 0 6 53 0 0 32 21 c 0 11 12 0 41 7 0 0 18 0 47 0 7 45 9 9 g 0 9 17 51 0 0 42 0 35 0 0 0 32 0 9 11 t 0 25 20 2 0 46 11 0 0 53 0 0 14 8 3 12

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=5/5; ncol2=16; w=-5; offset=-5; strand=D; shift=0; score=0.604925; gytGCTGASTCAkCmm ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 16 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 8 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4 9

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift1 ; 3 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=10; shift=1; ncol=11; -ywCGTACGwr ; Alignment reference a 0 5 22 0 0 1 57 0 10 19 25 c 0 19 13 50 0 2 0 60 0 7 11 g 0 11 7 0 59 1 2 0 50 13 19 t 0 25 18 10 1 56 1 0 0 21 5

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ywCGTACGwr ; cor=; Ncor= a 0 5 22 0 0 1 57 0 10 19 25 c 0 19 13 50 0 2 0 60 0 7 11 g 0 11 7 0 59 1 2 0 50 13 19 t 0 25 18 10 1 56 1 0 0 21 5

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.756588; gmkCGTACGmk ; cor=; Ncor= a 4 5 0 0 1 0 20 1 0 12 4 c 4 9 3 20 0 0 0 18 0 5 2 g 8 2 5 0 18 0 0 0 20 3 9 t 4 4 12 0 1 20 0 1 0 0 5

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 7 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=16; shift=0; ncol=16; gttGmTGAsTCAGCma ; Alignment reference a 11 12 3 8 14 0 0 53 0 0 11 46 0 2 20 25 c 13 11 9 0 32 0 0 0 35 0 42 0 0 51 17 9 g 21 9 9 45 7 0 47 0 18 0 0 7 41 0 12 11 t 8 21 32 0 0 53 6 0 0 53 0 0 12 0 4 8

oligos_7nt_mkv2_m1_shift0 (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=0; score= 1; gttGmTGAsTCAGCma ; cor=; Ncor= a 11 12 3 8 14 0 0 53 0 0 11 46 0 2 20 25 c 13 11 9 0 32 0 0 0 35 0 42 0 0 51 17 9 g 21 9 9 45 7 0 47 0 18 0 0 7 41 0 12 11 t 8 21 32 0 0 53 6 0 0 53 0 0 12 0 4 8

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.974454; gytGCTGASTCAkCmm ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 16 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 8 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4 9

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/6; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.865492; -wtGMTGASTCAGCa- ; cor=; Ncor= a 0 11 4 2 11 0 0 42 0 0 7 42 1 4 18 0 c 0 9 7 1 30 0 0 0 29 0 35 0 0 37 10 0 g 0 8 10 39 0 0 36 0 13 0 0 0 31 0 9 0 t 0 14 21 0 1 42 6 0 0 42 0 0 10 1 5 0

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=4/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.624395; -wtGATGACTma---- ; cor=; Ncor= a 0 14 8 2 30 0 0 40 0 1 13 26 0 0 0 0 c 0 5 6 0 9 0 6 1 33 0 16 8 0 0 0 0 g 0 8 6 39 1 1 35 0 8 1 8 2 0 0 0 0 t 0 14 21 0 1 40 0 0 0 39 4 5 0 0 0 0

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=5/6; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.561843; -tyGCTTACTma---- ; cor=; Ncor= a 0 9 15 1 0 3 0 60 2 3 18 43 0 0 0 0 c 0 16 18 0 68 0 0 4 59 1 26 5 0 0 0 0 g 0 17 13 64 1 0 16 0 9 1 11 11 0 0 0 0 t 0 28 24 5 1 67 54 6 0 65 15 11 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=6/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.535735; -thGCTTACTma---- ; cor=; Ncor= a 0 7 15 1 0 2 0 49 2 3 18 35 0 0 0 0 c 0 11 15 0 54 0 0 4 45 1 18 3 0 0 0 0 g 0 13 9 51 1 0 7 0 9 1 7 7 0 0 0 0 t 0 25 17 4 1 54 49 3 0 51 13 11 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----tkAGTAAGCda ; Alignment reference a 0 0 0 0 11 13 51 0 3 49 54 1 4 17 25 c 0 0 0 0 7 7 1 9 0 7 0 1 51 9 13 g 0 0 0 0 3 18 1 45 4 0 0 54 0 15 11 t 0 0 0 0 35 18 3 2 49 0 2 0 1 15 7
oligos_7nt_mkv2_m3_shift4 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----tkAGTAAGCda ; cor=; Ncor= a 0 0 0 0 11 13 51 0 3 49 54 1 4 17 25 c 0 0 0 0 7 7 1 9 0 7 0 1 51 9 13 g 0 0 0 0 3 18 1 45 4 0 0 54 0 15 11 t 0 0 0 0 35 18 3 2 49 0 2 0 1 15 7
oligos_6nt_mkv2_m3_rc_shift4 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=2/6; ncol2=11; w=0; offset=0; strand=R; shift=4; score=0.994687; ----tkAGTAAGCra ; cor=; Ncor= a 0 0 0 0 11 15 65 0 6 54 67 1 5 24 28 c 0 0 0 0 11 11 1 9 0 16 0 1 64 13 17 g 0 0 0 0 5 26 1 59 4 0 0 68 0 18 16 t 0 0 0 0 43 18 3 2 60 0 3 0 1 15 9
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=3/6; ncol2=14; w=-3; offset=-3; strand=R; shift=1; score=0.630218; -tGCTGASTCAKCaw ; cor=; Ncor= a 0 5 1 10 0 0 42 0 0 6 42 1 0 21 14 c 0 9 0 31 0 0 0 13 0 36 0 0 39 10 8 g 0 10 37 0 0 35 0 29 0 0 0 30 1 7 9 t 0 18 4 1 42 7 0 0 42 0 0 11 2 4 11
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=4/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.570417; kkGmTGASTCAGCar ; cor=; Ncor= a 9 4 0 19 0 0 42 0 0 10 42 0 0 22 17 c 8 9 0 25 0 0 0 14 0 34 0 0 44 9 5 g 11 11 42 0 0 37 0 30 0 0 0 34 0 8 12 t 16 20 2 0 44 7 2 0 44 0 2 10 0 5 10
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=5/6; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.535735; tkGCTGAsTCAkCaa ; cor=; Ncor= a 8 4 0 12 0 0 53 0 0 6 53 0 0 32 21 c 11 12 0 41 7 0 0 18 0 47 0 7 45 9 9 g 9 17 51 0 0 42 0 35 0 0 0 32 0 9 11 t 25 20 2 0 46 11 0 0 53 0 0 14 8 3 12
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=6/6; ncol2=10; w=-2; offset=-2; strand=R; shift=2; score=0.470707; --rwTTAGTAwr--- ; cor=; Ncor= a 0 0 14 9 0 0 22 0 0 22 10 10 0 0 0 c 0 0 2 4 0 0 0 0 0 0 4 0 0 0 0 g 0 0 6 2 0 0 0 22 0 0 0 7 0 0 0 t 0 0 0 7 22 22 0 0 22 0 8 5 0 0 0

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=11; shift=1; ncol=12; -tyGCTTACTma ; Alignment reference a 0 9 15 1 0 3 0 60 2 3 18 43 c 0 16 18 0 68 0 0 4 59 1 26 5 g 0 17 13 64 1 0 16 0 9 1 11 11 t 0 28 24 5 1 67 54 6 0 65 15 11
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -tyGCTTACTma ; cor=; Ncor= a 0 9 15 1 0 3 0 60 2 3 18 43 c 0 16 18 0 68 0 0 4 59 1 26 5 g 0 17 13 64 1 0 16 0 9 1 11 11 t 0 28 24 5 1 67 54 6 0 65 15 11
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3_rc; m=2/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.994687; -thGCTTACTma ; cor=; Ncor= a 0 7 15 1 0 2 0 49 2 3 18 35 c 0 11 15 0 54 0 0 4 45 1 18 3 g 0 13 9 51 1 0 7 0 9 1 7 7 t 0 25 17 4 1 54 49 3 0 51 13 11
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5_rc; m=3/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.731642; -wtGATGACTma ; cor=; Ncor= a 0 14 8 2 30 0 0 40 0 1 13 26 c 0 5 6 0 9 0 6 1 33 0 16 8 g 0 8 6 39 1 1 35 0 8 1 8 2 t 0 14 21 0 1 40 0 0 0 39 4 5
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.658734; -wtGMTGASTCA ; cor=; Ncor= a 0 11 4 2 11 0 0 42 0 0 7 42 c 0 9 7 1 30 0 0 0 29 0 35 0 g 0 8 10 39 0 0 36 0 13 0 0 0 t 0 14 21 0 1 42 6 0 0 42 0 0
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=5/7; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.592703; gytGCTGASTCA ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 c 8 12 8 0 34 0 0 0 30 0 37 0 g 21 5 9 44 0 0 34 0 14 0 0 0 t 8 17 22 0 0 42 10 0 0 42 0 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=6/7; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.561843; gttGmTGAsTCA ; cor=; Ncor= a 11 12 3 8 14 0 0 53 0 0 11 46 c 13 11 9 0 32 0 0 0 35 0 42 0 g 21 9 9 45 7 0 47 0 18 0 0 7 t 8 21 32 0 0 53 6 0 0 53 0 0
oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=7/7; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.455895; ----ywTACTAA ; cor=; Ncor= a 0 0 0 0 5 8 0 22 0 0 22 22 c 0 0 0 0 7 0 0 0 22 0 0 0 g 0 0 0 0 0 4 0 0 0 0 0 0 t 0 0 0 0 10 10 22 0 0 22 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---ywTACTAAwy ; Alignment reference a 0 0 0 5 8 0 22 0 0 22 22 7 0 c 0 0 0 7 0 0 0 22 0 0 0 2 6 g 0 0 0 0 4 0 0 0 0 0 0 4 2 t 0 0 0 10 10 22 0 0 22 0 0 9 14
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---ywTACTAAwy ; cor=; Ncor= a 0 0 0 5 8 0 22 0 0 22 22 7 0 c 0 0 0 7 0 0 0 22 0 0 0 2 6 g 0 0 0 0 4 0 0 0 0 0 0 4 2 t 0 0 0 10 10 22 0 0 22 0 0 9 14
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=2/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.470707; thGCTTACTma-- ; cor=; Ncor= a 7 15 1 0 2 0 49 2 3 18 35 0 0 c 11 15 0 54 0 0 4 45 1 18 3 0 0 g 13 9 51 1 0 7 0 9 1 7 7 0 0 t 25 17 4 1 54 49 3 0 51 13 11 0 0
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.455895; tyGCTTACTma-- ; cor=; Ncor= a 9 15 1 0 3 0 60 2 3 18 43 0 0 c 16 18 0 68 0 0 4 59 1 26 5 0 0 g 17 13 64 1 0 16 0 9 1 11 11 0 0 t 28 24 5 1 67 54 6 0 65 15 11 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; gytGCTGASTCAkCmm ; Alignment reference a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 16 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 8 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4 9
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; gytGCTGASTCAkCmm ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 16 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 8 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4 9
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.974454; gttGmTGAsTCAGCma ; cor=; Ncor= a 11 12 3 8 14 0 0 53 0 0 11 46 0 2 20 25 c 13 11 9 0 32 0 0 0 35 0 42 0 0 51 17 9 g 21 9 9 45 7 0 47 0 18 0 0 7 41 0 12 11 t 8 21 32 0 0 53 6 0 0 53 0 0 12 0 4 8
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=3/6; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.866092; -wtGMTGASTCAGCa- ; cor=; Ncor= a 0 11 4 2 11 0 0 42 0 0 7 42 1 4 18 0 c 0 9 7 1 30 0 0 0 29 0 35 0 0 37 10 0 g 0 8 10 39 0 0 36 0 13 0 0 0 31 0 9 0 t 0 14 21 0 1 42 6 0 0 42 0 0 10 1 5 0
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=4/6; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.604925; -----tkAGTCATCaw ; cor=; Ncor= a 0 0 0 0 0 5 4 39 0 0 0 40 1 0 21 14 c 0 0 0 0 0 2 8 1 8 0 35 1 1 39 6 8 g 0 0 0 0 0 8 16 0 33 1 6 0 9 0 6 5 t 0 0 0 0 0 26 13 1 0 40 0 0 30 2 8 14
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=5/6; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.592703; -tyGCTTACTma---- ; cor=; Ncor= a 0 9 15 1 0 3 0 60 2 3 18 43 0 0 0 0 c 0 16 18 0 68 0 0 4 59 1 26 5 0 0 0 0 g 0 17 13 64 1 0 16 0 9 1 11 11 0 0 0 0 t 0 28 24 5 1 67 54 6 0 65 15 11 0 0 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=6/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.570417; -thGCTTACTma---- ; cor=; Ncor= a 0 7 15 1 0 2 0 49 2 3 18 35 0 0 0 0 c 0 11 15 0 54 0 0 4 45 1 18 3 0 0 0 0 g 0 13 9 51 1 0 7 0 9 1 7 7 0 0 0 0 t 0 25 17 4 1 54 49 3 0 51 13 11 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -wtGMTGASTCAGCa ; Alignment reference a 0 11 4 2 11 0 0 42 0 0 7 42 1 4 18 c 0 9 7 1 30 0 0 0 29 0 35 0 0 37 10 g 0 8 10 39 0 0 36 0 13 0 0 0 31 0 9 t 0 14 21 0 1 42 6 0 0 42 0 0 10 1 5
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wtGMTGASTCAGCa ; cor=; Ncor= a 0 11 4 2 11 0 0 42 0 0 7 42 1 4 18 c 0 9 7 1 30 0 0 0 29 0 35 0 0 37 10 g 0 8 10 39 0 0 36 0 13 0 0 0 31 0 9 t 0 14 21 0 1 42 6 0 0 42 0 0 10 1 5
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/6; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.866092; gytGCTGASTCAkCm ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/6; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.865492; gttGmTGAsTCAGCm ; cor=; Ncor= a 11 12 3 8 14 0 0 53 0 0 11 46 0 2 20 c 13 11 9 0 32 0 0 0 35 0 42 0 0 51 17 g 21 9 9 45 7 0 47 0 18 0 0 7 41 0 12 t 8 21 32 0 0 53 6 0 0 53 0 0 12 0 4
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=4/6; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.70599; -wtGATGACTma--- ; cor=; Ncor= a 0 14 8 2 30 0 0 40 0 1 13 26 0 0 0 c 0 5 6 0 9 0 6 1 33 0 16 8 0 0 0 g 0 8 6 39 1 1 35 0 8 1 8 2 0 0 0 t 0 14 21 0 1 40 0 0 0 39 4 5 0 0 0
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=5/6; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.658734; -tyGCTTACTma--- ; cor=; Ncor= a 0 9 15 1 0 3 0 60 2 3 18 43 0 0 0 c 0 16 18 0 68 0 0 4 59 1 26 5 0 0 0 g 0 17 13 64 1 0 16 0 9 1 11 11 0 0 0 t 0 28 24 5 1 67 54 6 0 65 15 11 0 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=6/6; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.630218; -thGCTTACTma--- ; cor=; Ncor= a 0 7 15 1 0 2 0 49 2 3 18 35 0 0 0 c 0 11 15 0 54 0 0 4 45 1 18 3 0 0 0 g 0 13 9 51 1 0 7 0 9 1 7 7 0 0 0 t 0 25 17 4 1 54 49 3 0 51 13 11 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; -----tkAGTCATCaw ; Alignment reference a 0 0 0 0 0 5 4 39 0 0 0 40 1 0 21 14 c 0 0 0 0 0 2 8 1 8 0 35 1 1 39 6 8 g 0 0 0 0 0 8 16 0 33 1 6 0 9 0 6 5 t 0 0 0 0 0 26 13 1 0 40 0 0 30 2 8 14
oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----tkAGTCATCaw ; cor=; Ncor= a 0 0 0 0 0 5 4 39 0 0 0 40 1 0 21 14 c 0 0 0 0 0 2 8 1 8 0 35 1 1 39 6 8 g 0 0 0 0 0 8 16 0 33 1 6 0 9 0 6 5 t 0 0 0 0 0 26 13 1 0 40 0 0 30 2 8 14
oligos_6nt_mkv2_m3_rc_shift5 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3_rc; m=2/5; ncol2=11; w=0; offset=0; strand=R; shift=5; score=0.731642; -----tkAGTAAGCra ; cor=; Ncor= a 0 0 0 0 0 11 15 65 0 6 54 67 1 5 24 28 c 0 0 0 0 0 11 11 1 9 0 16 0 1 64 13 17 g 0 0 0 0 0 5 26 1 59 4 0 0 68 0 18 16 t 0 0 0 0 0 43 18 3 2 60 0 3 0 1 15 9
oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=3/5; ncol2=14; w=-3; offset=-3; strand=R; shift=2; score=0.70599; --tGCTGASTCAKCaw ; cor=; Ncor= a 0 0 5 1 10 0 0 42 0 0 6 42 1 0 21 14 c 0 0 9 0 31 0 0 0 13 0 36 0 0 39 10 8 g 0 0 10 37 0 0 35 0 29 0 0 0 30 1 7 9 t 0 0 18 4 1 42 7 0 0 42 0 0 11 2 4 11
oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=4/5; ncol2=16; w=-4; offset=-4; strand=R; shift=1; score=0.624395; -tkGCTGAsTCAkCaa ; cor=; Ncor= a 0 8 4 0 12 0 0 53 0 0 6 53 0 0 32 21 c 0 11 12 0 41 7 0 0 18 0 47 0 7 45 9 9 g 0 9 17 51 0 0 42 0 35 0 0 0 32 0 9 11 t 0 25 20 2 0 46 11 0 0 53 0 0 14 8 3 12
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=5/5; ncol2=16; w=-5; offset=-5; strand=D; shift=0; score=0.604925; gytGCTGASTCAkCmm ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 16 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 8 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4 9

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=16; shift=0; ncol=16; gttGmTGAsTCAGCma ; Alignment reference a 11 12 3 8 14 0 0 53 0 0 11 46 0 2 20 25 c 13 11 9 0 32 0 0 0 35 0 42 0 0 51 17 9 g 21 9 9 45 7 0 47 0 18 0 0 7 41 0 12 11 t 8 21 32 0 0 53 6 0 0 53 0 0 12 0 4 8
oligos_7nt_mkv2_m1_shift0 (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=0; score= 1; gttGmTGAsTCAGCma ; cor=; Ncor= a 11 12 3 8 14 0 0 53 0 0 11 46 0 2 20 25 c 13 11 9 0 32 0 0 0 35 0 42 0 0 51 17 9 g 21 9 9 45 7 0 47 0 18 0 0 7 41 0 12 11 t 8 21 32 0 0 53 6 0 0 53 0 0 12 0 4 8
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.974454; gytGCTGASTCAkCmm ; cor=; Ncor= a 7 10 5 0 10 2 0 44 0 2 7 44 0 2 20 16 c 8 12 8 0 34 0 0 0 30 0 37 0 0 42 11 11 g 21 5 9 44 0 0 34 0 14 0 0 0 25 0 9 8 t 8 17 22 0 0 42 10 0 0 42 0 0 19 0 4 9
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/6; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.865492; -wtGMTGASTCAGCa- ; cor=; Ncor= a 0 11 4 2 11 0 0 42 0 0 7 42 1 4 18 0 c 0 9 7 1 30 0 0 0 29 0 35 0 0 37 10 0 g 0 8 10 39 0 0 36 0 13 0 0 0 31 0 9 0 t 0 14 21 0 1 42 6 0 0 42 0 0 10 1 5 0
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=4/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.624395; -wtGATGACTma---- ; cor=; Ncor= a 0 14 8 2 30 0 0 40 0 1 13 26 0 0 0 0 c 0 5 6 0 9 0 6 1 33 0 16 8 0 0 0 0 g 0 8 6 39 1 1 35 0 8 1 8 2 0 0 0 0 t 0 14 21 0 1 40 0 0 0 39 4 5 0 0 0 0
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=5/6; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.561843; -tyGCTTACTma---- ; cor=; Ncor= a 0 9 15 1 0 3 0 60 2 3 18 43 0 0 0 0 c 0 16 18 0 68 0 0 4 59 1 26 5 0 0 0 0 g 0 17 13 64 1 0 16 0 9 1 11 11 0 0 0 0 t 0 28 24 5 1 67 54 6 0 65 15 11 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=6/6; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.535735; -thGCTTACTma---- ; cor=; Ncor= a 0 7 15 1 0 2 0 49 2 3 18 35 0 0 0 0 c 0 11 15 0 54 0 0 4 45 1 18 3 0 0 0 0 g 0 13 9 51 1 0 7 0 9 1 7 7 0 0 0 0 t 0 25 17 4 1 54 49 3 0 51 13 11 0 0 0 0