One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/10/28/peak-motifs.2025-10-28.145428_2025-10-28.145428_er30Hd/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/2025/10/28/peak-motifs.2025-10-28.145428_2025-10-28.145428_er30Hd/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift1 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=24; shift=1; ncol=25; -krrrCATGYCCrGrCATGTcyrmv ; Alignment reference a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 46 9 2 3 6 7 19 17 18 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 1 0 1 12 38 30 13 18 15 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 2 3 56 1 4 6 16 13 16 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0 10 47 0 43 11 16 11 11 10

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -krrrCATGYCCrGrCATGTcyrmv ; cor=; Ncor= a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 46 9 2 3 6 7 19 17 18 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 1 0 1 12 38 30 13 18 15 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 2 3 56 1 4 6 16 13 16 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0 10 47 0 43 11 16 11 11 10

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=2/7; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.908159; gkgGrCATGYCYrGrCATGyCyac- ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 16 0 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 24 0 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 14 0 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14 11 0

oligos_6nt_mkv2_m4_shift8 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=3/7; ncol2=15; w=0; offset=7; strand=D; shift=8; score=0.576049; --------syccrGGCATGTCyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 0 0 c 0 0 0 0 0 0 0 0 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 0 0 g 0 0 0 0 0 0 0 0 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 0 0 t 0 0 0 0 0 0 0 0 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18 0 0

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.557843; -yrGACATGCCCasrs--------- ; cor=; Ncor= a 0 18 32 20 94 1 107 11 0 2 4 2 79 12 52 21 0 0 0 0 0 0 0 0 0 c 0 32 12 8 3 119 7 3 0 106 117 109 12 34 19 58 0 0 0 0 0 0 0 0 0 g 0 28 61 89 26 2 2 2 123 1 1 2 19 66 41 36 0 0 0 0 0 0 0 0 0 t 0 47 20 8 2 3 9 109 2 16 3 12 15 13 13 10 0 0 0 0 0 0 0 0 0

oligos_6nt_mkv2_m5_shift11 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=5/7; ncol2=12; w=0; offset=10; strand=D; shift=11; score=0.462233; -----------yrGACATGTCyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 0 0 c 0 0 0 0 0 0 0 0 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 0 0 g 0 0 0 0 0 0 0 0 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 0 0 t 0 0 0 0 0 0 0 0 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27 0 0

oligos_7nt_mkv2_m3_rc_shift10 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=6/7; ncol2=13; w=0; offset=9; strand=R; shift=10; score=0.425875; ----------cyrGACTTGTcyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 12 14 37 3 54 0 10 0 0 0 6 10 16 0 0 c 0 0 0 0 0 0 0 0 0 0 29 25 3 6 0 64 3 0 2 5 41 18 7 0 0 g 0 0 0 0 0 0 0 0 0 0 8 9 16 54 6 0 2 3 62 2 10 13 26 0 0 t 0 0 0 0 0 0 0 0 0 0 15 16 8 1 4 0 49 61 0 57 7 23 15 0 0

oligos_6nt_mkv2_m2_rc_shift11 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=7/7; ncol2=12; w=0; offset=10; strand=R; shift=11; score=0.413608; -----------yrGACTTGTCyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 11 24 3 48 0 9 0 0 0 2 7 19 0 0 c 0 0 0 0 0 0 0 0 0 0 0 22 3 1 1 62 2 0 0 10 52 20 6 0 0 g 0 0 0 0 0 0 0 0 0 0 0 13 24 58 10 0 2 2 62 2 3 6 23 0 0 t 0 0 0 0 0 0 0 0 0 0 0 16 11 0 3 0 49 60 0 50 5 29 14 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift11 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift11 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------yrGACAAGTCyr ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 14 29 5 50 0 60 49 0 3 0 11 16 c 0 0 0 0 0 0 0 0 0 0 0 23 6 3 2 62 2 2 0 10 58 24 13 g 0 0 0 0 0 0 0 0 0 0 0 6 20 52 10 0 0 2 62 1 1 3 22 t 0 0 0 0 0 0 0 0 0 0 0 19 7 2 0 0 0 9 0 48 3 24 11

oligos_6nt_mkv2_m2_shift11 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------yrGACAAGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 14 29 5 50 0 60 49 0 3 0 11 16 c 0 0 0 0 0 0 0 0 0 0 0 23 6 3 2 62 2 2 0 10 58 24 13 g 0 0 0 0 0 0 0 0 0 0 0 6 20 52 10 0 0 2 62 1 1 3 22 t 0 0 0 0 0 0 0 0 0 0 0 19 7 2 0 0 0 9 0 48 3 24 11

oligos_7nt_mkv2_m3_shift11 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=2/7; ncol2=13; w=0; offset=0; strand=D; shift=11; score=0.903904; -----------yrgACAAGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 15 23 7 57 0 61 49 0 4 1 8 16 c 0 0 0 0 0 0 0 0 0 0 0 26 13 10 2 62 3 2 0 6 54 16 9 g 0 0 0 0 0 0 0 0 0 0 0 7 18 41 5 2 0 3 64 0 6 3 25 t 0 0 0 0 0 0 0 0 0 0 0 16 10 6 0 0 0 10 0 54 3 37 14

oligos_6nt_mkv2_m5_shift11 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=3/7; ncol2=12; w=0; offset=0; strand=D; shift=11; score=0.871965; -----------yrGACATGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 c 0 0 0 0 0 0 0 0 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 g 0 0 0 0 0 0 0 0 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 t 0 0 0 0 0 0 0 0 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27

oligos_6nt_mkv2_m4_rc_shift11 (oligos_6nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=4/7; ncol2=15; w=0; offset=0; strand=R; shift=11; score=0.61905; -----------yrGACATGCCyg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 18 31 17 85 0 88 8 1 1 0 3 18 c 0 0 0 0 0 0 0 0 0 0 0 26 11 5 1 91 1 2 2 82 91 36 14 g 0 0 0 0 0 0 0 0 0 0 0 23 41 68 9 4 1 2 94 1 1 2 53 t 0 0 0 0 0 0 0 0 0 0 0 30 14 7 2 2 7 85 0 13 5 56 12

oligos_6nt_mkv2_m1_shift11 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=5/7; ncol2=15; w=0; offset=0; strand=D; shift=11; score=0.583808; -----------yrGACATGCCCa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 18 32 20 94 1 107 11 0 2 4 2 79 c 0 0 0 0 0 0 0 0 0 0 0 32 12 8 3 119 7 3 0 106 117 109 12 g 0 0 0 0 0 0 0 0 0 0 0 28 61 89 26 2 2 2 123 1 1 2 19 t 0 0 0 0 0 0 0 0 0 0 0 47 20 8 2 3 9 109 2 16 3 12 15

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=6/7; ncol2=24; w=-11; offset=-11; strand=D; shift=0; score=0.415971; gkgGrCATGYCYrGrCATGyCya ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14

oligos_7nt_mkv2_m4_rc_shift9 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=7/7; ncol2=24; w=-2; offset=-2; strand=R; shift=9; score=0.413608; ---------bkyrgACATGyCyG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 10 11 11 16 11 43 0 47 10 0 0 0 4 13 c 0 0 0 0 0 0 0 0 0 16 13 16 6 4 1 56 3 2 0 36 57 28 3 g 0 0 0 0 0 0 0 0 0 15 18 13 30 38 12 1 0 1 59 0 0 2 42 t 0 0 0 0 0 0 0 0 0 18 17 19 7 6 3 2 9 46 0 23 2 25 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --yrgACAAGTCyrg ; Alignment reference a 0 0 15 23 7 57 0 61 49 0 4 1 8 16 15 c 0 0 26 13 10 2 62 3 2 0 6 54 16 9 8 g 0 0 7 18 41 5 2 0 3 64 0 6 3 25 29 t 0 0 16 10 6 0 0 0 10 0 54 3 37 14 12

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --yrgACAAGTCyrg ; cor=; Ncor= a 0 0 15 23 7 57 0 61 49 0 4 1 8 16 15 c 0 0 26 13 10 2 62 3 2 0 6 54 16 9 8 g 0 0 7 18 41 5 2 0 3 64 0 6 3 25 29 t 0 0 16 10 6 0 0 0 10 0 54 3 37 14 12

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=2/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.903904; --yrGACAAGTCyr- ; cor=; Ncor= a 0 0 14 29 5 50 0 60 49 0 3 0 11 16 0 c 0 0 23 6 3 2 62 2 2 0 10 58 24 13 0 g 0 0 6 20 52 10 0 0 2 62 1 1 3 22 0 t 0 0 19 7 2 0 0 0 9 0 48 3 24 11 0

oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.776473; --yrGACATGTCyr- ; cor=; Ncor= a 0 0 27 34 4 84 1 100 9 0 1 4 20 33 0 c 0 0 35 3 2 0 110 2 1 1 27 102 55 17 0 g 0 0 17 55 102 27 1 1 2 110 0 2 3 35 0 t 0 0 33 20 4 1 0 9 100 1 84 4 34 27 0

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=4/6; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.656943; --yrGACATGCCygg ; cor=; Ncor= a 0 0 18 31 17 85 0 88 8 1 1 0 3 18 10 c 0 0 26 11 5 1 91 1 2 2 82 91 36 14 17 g 0 0 23 41 68 9 4 1 2 94 1 1 2 53 60 t 0 0 30 14 7 2 2 7 85 0 13 5 56 12 10

oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=5/6; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.425875; bkyrgACATGyCyGG ; cor=; Ncor= a 10 11 11 16 11 43 0 47 10 0 0 0 4 13 2 c 16 13 16 6 4 1 56 3 2 0 36 57 28 3 0 g 15 18 13 30 38 12 1 0 1 59 0 0 2 42 56 t 18 17 19 7 6 3 2 9 46 0 23 2 25 1 1

oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=6/6; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.414756; -gtrGrCATGyCyRG ; cor=; Ncor= a 0 11 14 18 10 40 0 46 11 0 0 0 3 17 4 c 0 14 16 7 2 1 62 4 2 0 42 61 26 2 0 g 0 24 16 34 46 21 3 0 1 65 0 1 2 45 59 t 0 16 19 6 7 3 0 15 51 0 23 3 34 1 2

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift3 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=12; shift=3; ncol=15; ---yrGACATGTCyr ; Alignment reference a 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 c 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 g 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 t 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27

oligos_6nt_mkv2_m5_shift3 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---yrGACATGTCyr ; cor=; Ncor= a 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 c 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 g 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 t 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=2/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.871965; ---yrGACAAGTCyr ; cor=; Ncor= a 0 0 0 14 29 5 50 0 60 49 0 3 0 11 16 c 0 0 0 23 6 3 2 62 2 2 0 10 58 24 13 g 0 0 0 6 20 52 10 0 0 2 62 1 1 3 22 t 0 0 0 19 7 2 0 0 0 9 0 48 3 24 11

oligos_7nt_mkv2_m3_rc_shift2 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=3/7; ncol2=13; w=-1; offset=-1; strand=R; shift=2; score=0.776473; --cyrGACTTGTcyr ; cor=; Ncor= a 0 0 12 14 37 3 54 0 10 0 0 0 6 10 16 c 0 0 29 25 3 6 0 64 3 0 2 5 41 18 7 g 0 0 8 9 16 54 6 0 2 3 62 2 10 13 26 t 0 0 15 16 8 1 4 0 49 61 0 57 7 23 15

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=4/7; ncol2=15; w=-3; offset=-3; strand=D; shift=0; score=0.709311; syccrGGCATGTCyr ; cor=; Ncor= a 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 c 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 g 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 t 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=5/7; ncol2=15; w=0; offset=0; strand=D; shift=3; score=0.699131; ---yrGACATGCCCa ; cor=; Ncor= a 0 0 0 18 32 20 94 1 107 11 0 2 4 2 79 c 0 0 0 32 12 8 3 119 7 3 0 106 117 109 12 g 0 0 0 28 61 89 26 2 2 2 123 1 1 2 19 t 0 0 0 47 20 8 2 3 9 109 2 16 3 12 15

oligos_7nt_mkv2_m4_rc_shift1 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=6/7; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.462233; -bkyrgACATGyCyG ; cor=; Ncor= a 0 10 11 11 16 11 43 0 47 10 0 0 0 4 13 c 0 16 13 16 6 4 1 56 3 2 0 36 57 28 3 g 0 15 18 13 30 38 12 1 0 1 59 0 0 2 42 t 0 18 17 19 7 6 3 2 9 46 0 23 2 25 1

oligos_7nt_mkv2_m1_rc_shift2 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=7/7; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.455401; --gtrGrCATGyCyR ; cor=; Ncor= a 0 0 11 14 18 10 40 0 46 11 0 0 0 3 17 c 0 0 14 16 7 2 1 62 4 2 0 42 61 26 2 g 0 0 24 16 34 46 21 3 0 1 65 0 1 2 45 t 0 0 16 19 6 7 3 0 15 51 0 23 3 34 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 8 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=24; shift=0; ncol=24; gkgGrCATGYCYrGrCATGyCyac ; Alignment reference a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 16 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 24 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 14 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14 11

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; gkgGrCATGYCYrGrCATGyCyac ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 16 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 24 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 14 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14 11

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=2/7; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.908159; -krrrCATGYCCrGrCATGTcyrm ; cor=; Ncor= a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 46 9 2 3 6 7 19 17 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 1 0 1 12 38 30 13 18 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 2 3 56 1 4 6 16 13 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0 10 47 0 43 11 16 11 11

oligos_6nt_mkv2_m4_shift8 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=3/7; ncol2=15; w=0; offset=8; strand=D; shift=8; score=0.570608; --------syccrGGCATGTCyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 0 c 0 0 0 0 0 0 0 0 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 0 g 0 0 0 0 0 0 0 0 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 0 t 0 0 0 0 0 0 0 0 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18 0

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.565137; -yrGACATGCCCasrs-------- ; cor=; Ncor= a 0 18 32 20 94 1 107 11 0 2 4 2 79 12 52 21 0 0 0 0 0 0 0 0 c 0 32 12 8 3 119 7 3 0 106 117 109 12 34 19 58 0 0 0 0 0 0 0 0 g 0 28 61 89 26 2 2 2 123 1 1 2 19 66 41 36 0 0 0 0 0 0 0 0 t 0 47 20 8 2 3 9 109 2 16 3 12 15 13 13 10 0 0 0 0 0 0 0 0

oligos_6nt_mkv2_m5_shift11 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=5/7; ncol2=12; w=0; offset=11; strand=D; shift=11; score=0.455401; -----------yrGACATGTCyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 0 c 0 0 0 0 0 0 0 0 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 0 g 0 0 0 0 0 0 0 0 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 0 t 0 0 0 0 0 0 0 0 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27 0

oligos_6nt_mkv2_m2_shift11 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=6/7; ncol2=12; w=0; offset=11; strand=D; shift=11; score=0.415971; -----------yrGACAAGTCyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 14 29 5 50 0 60 49 0 3 0 11 16 0 c 0 0 0 0 0 0 0 0 0 0 0 23 6 3 2 62 2 2 0 10 58 24 13 0 g 0 0 0 0 0 0 0 0 0 0 0 6 20 52 10 0 0 2 62 1 1 3 22 0 t 0 0 0 0 0 0 0 0 0 0 0 19 7 2 0 0 0 9 0 48 3 24 11 0

oligos_7nt_mkv2_m3_rc_shift10 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=7/7; ncol2=13; w=0; offset=10; strand=R; shift=10; score=0.414756; ----------cyrGACTTGTcyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 12 14 37 3 54 0 10 0 0 0 6 10 16 0 c 0 0 0 0 0 0 0 0 0 0 29 25 3 6 0 64 3 0 2 5 41 18 7 0 g 0 0 0 0 0 0 0 0 0 0 8 9 16 54 6 0 2 3 62 2 10 13 26 0 t 0 0 0 0 0 0 0 0 0 0 15 16 8 1 4 0 49 61 0 57 7 23 15 0

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=15; shift=1; ncol=16; -yrGACATGCCCasrs ; Alignment reference a 0 18 32 20 94 1 107 11 0 2 4 2 79 12 52 21 c 0 32 12 8 3 119 7 3 0 106 117 109 12 34 19 58 g 0 28 61 89 26 2 2 2 123 1 1 2 19 66 41 36 t 0 47 20 8 2 3 9 109 2 16 3 12 15 13 13 10

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -yrGACATGCCCasrs ; cor=; Ncor= a 0 18 32 20 94 1 107 11 0 2 4 2 79 12 52 21 c 0 32 12 8 3 119 7 3 0 106 117 109 12 34 19 58 g 0 28 61 89 26 2 2 2 123 1 1 2 19 66 41 36 t 0 47 20 8 2 3 9 109 2 16 3 12 15 13 13 10

oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=2/6; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.909388; -yrGACATGCCyggrs ; cor=; Ncor= a 0 18 31 17 85 0 88 8 1 1 0 3 18 10 29 18 c 0 26 11 5 1 91 1 2 2 82 91 36 14 17 15 47 g 0 23 41 68 9 4 1 2 94 1 1 2 53 60 43 25 t 0 30 14 7 2 2 7 85 0 13 5 56 12 10 10 7

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.699131; -yrGACATGTCyr--- ; cor=; Ncor= a 0 27 34 4 84 1 100 9 0 1 4 20 33 0 0 0 c 0 35 3 2 0 110 2 1 1 27 102 55 17 0 0 0 g 0 17 55 102 27 1 1 2 110 0 2 3 35 0 0 0 t 0 33 20 4 1 0 9 100 1 84 4 34 27 0 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=4/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.583808; -yrGACAAGTCyr--- ; cor=; Ncor= a 0 14 29 5 50 0 60 49 0 3 0 11 16 0 0 0 c 0 23 6 3 2 62 2 2 0 10 58 24 13 0 0 0 g 0 6 20 52 10 0 0 2 62 1 1 3 22 0 0 0 t 0 19 7 2 0 0 0 9 0 48 3 24 11 0 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=5/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.565137; gkgGrCATGYCYrGrC ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=6/6; ncol2=24; w=0; offset=0; strand=D; shift=1; score=0.557843; -krrrCATGYCCrGrC ; cor=; Ncor= a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift8 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift8 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=15; shift=8; ncol=23; --------syccrGGCATGTCyr ; Alignment reference a 0 0 0 0 0 0 0 0 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 c 0 0 0 0 0 0 0 0 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 g 0 0 0 0 0 0 0 0 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 t 0 0 0 0 0 0 0 0 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18

oligos_6nt_mkv2_m4_shift8 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/7; ncol2=15; w=0; offset=0; strand=D; shift=8; score= 1; --------syccrGGCATGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 c 0 0 0 0 0 0 0 0 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 g 0 0 0 0 0 0 0 0 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 t 0 0 0 0 0 0 0 0 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18

oligos_6nt_mkv2_m1_rc_shift8 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1_rc; m=2/7; ncol2=15; w=0; offset=0; strand=R; shift=8; score=0.909388; --------systGGGCATGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 10 13 13 15 12 3 16 2 109 9 3 2 8 20 47 c 0 0 0 0 0 0 0 0 36 41 66 19 2 1 1 123 2 2 2 26 89 61 28 g 0 0 0 0 0 0 0 0 58 19 34 12 109 117 106 0 3 7 119 3 8 12 32 t 0 0 0 0 0 0 0 0 21 52 12 79 2 4 2 0 11 107 1 94 20 32 18

oligos_6nt_mkv2_m5_shift11 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/7; ncol2=12; w=0; offset=3; strand=D; shift=11; score=0.709311; -----------yrGACATGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 c 0 0 0 0 0 0 0 0 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 g 0 0 0 0 0 0 0 0 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 t 0 0 0 0 0 0 0 0 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27

oligos_7nt_mkv2_m3_rc_shift10 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=4/7; ncol2=13; w=0; offset=2; strand=R; shift=10; score=0.656943; ----------cyrGACTTGTcyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 12 14 37 3 54 0 10 0 0 0 6 10 16 c 0 0 0 0 0 0 0 0 0 0 29 25 3 6 0 64 3 0 2 5 41 18 7 g 0 0 0 0 0 0 0 0 0 0 8 9 16 54 6 0 2 3 62 2 10 13 26 t 0 0 0 0 0 0 0 0 0 0 15 16 8 1 4 0 49 61 0 57 7 23 15

oligos_6nt_mkv2_m2_rc_shift11 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=5/7; ncol2=12; w=0; offset=3; strand=R; shift=11; score=0.61905; -----------yrGACTTGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 11 24 3 48 0 9 0 0 0 2 7 19 c 0 0 0 0 0 0 0 0 0 0 0 22 3 1 1 62 2 0 0 10 52 20 6 g 0 0 0 0 0 0 0 0 0 0 0 13 24 58 10 0 2 2 62 2 3 6 23 t 0 0 0 0 0 0 0 0 0 0 0 16 11 0 3 0 49 60 0 50 5 29 14

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=6/7; ncol2=24; w=-7; offset=-7; strand=D; shift=1; score=0.576049; -krrrCATGYCCrGrCATGTcyr ; cor=; Ncor= a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 46 9 2 3 6 7 19 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 1 0 1 12 38 30 13 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 2 3 56 1 4 6 16 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0 10 47 0 43 11 16 11

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=7/7; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.570608; gkgGrCATGYCYrGrCATGyCya ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 3 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=14; shift=0; ncol=14; ssGtCCCCGCCgss ; Alignment reference a 13 9 4 6 1 1 2 2 0 2 4 3 7 6 c 34 30 14 17 66 63 61 65 1 67 60 13 31 26 g 20 19 51 14 4 9 9 4 71 5 8 49 22 32 t 7 16 5 37 3 1 2 3 2 0 2 9 14 10

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; ssGtCCCCGCCgss ; cor=; Ncor= a 13 9 4 6 1 1 2 2 0 2 4 3 7 6 c 34 30 14 17 66 63 61 65 1 67 60 13 31 26 g 20 19 51 14 4 9 9 4 71 5 8 49 22 32 t 7 16 5 37 3 1 2 3 2 0 2 9 14 10

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.818353; -sstCCCCGCCss- ; cor=; Ncor= a 0 16 9 7 3 2 1 4 2 3 2 13 12 0 c 0 42 40 22 82 87 87 91 0 92 86 36 47 0 g 0 26 32 22 9 9 7 3 93 3 10 33 28 0 t 0 15 18 48 5 1 4 1 4 1 1 17 12 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 2 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=11; shift=0; ncol=11; svTGAcTCAbm ; Alignment reference a 17 20 1 0 77 6 3 3 73 11 20 c 21 25 2 4 0 52 2 67 1 23 22 g 20 23 3 68 0 13 3 5 1 23 19 t 19 9 71 5 0 6 69 2 2 20 16

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; svTGAcTCAbm ; cor=; Ncor= a 17 20 1 0 77 6 3 3 73 11 20 c 21 25 2 4 0 52 2 67 1 23 22 g 20 23 3 68 0 13 3 5 1 23 19 t 19 9 71 5 0 6 69 2 2 20 16

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -sstCCCCGCCss ; Alignment reference a 0 16 9 7 3 2 1 4 2 3 2 13 12 c 0 42 40 22 82 87 87 91 0 92 86 36 47 g 0 26 32 22 9 9 7 3 93 3 10 33 28 t 0 15 18 48 5 1 4 1 4 1 1 17 12

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -sstCCCCGCCss ; cor=; Ncor= a 0 16 9 7 3 2 1 4 2 3 2 13 12 c 0 42 40 22 82 87 87 91 0 92 86 36 47 g 0 26 32 22 9 9 7 3 93 3 10 33 28 t 0 15 18 48 5 1 4 1 4 1 1 17 12

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=2/2; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.818353; ssGtCCCCGCCgs ; cor=; Ncor= a 13 9 4 6 1 1 2 2 0 2 4 3 7 c 34 30 14 17 66 63 61 65 1 67 60 13 31 g 20 19 51 14 4 9 9 4 71 5 8 49 22 t 7 16 5 37 3 1 2 3 2 0 2 9 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=24; shift=1; ncol=25; -krrrCATGYCCrGrCATGTcyrmv ; Alignment reference a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 46 9 2 3 6 7 19 17 18 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 1 0 1 12 38 30 13 18 15 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 2 3 56 1 4 6 16 13 16 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0 10 47 0 43 11 16 11 11 10
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -krrrCATGYCCrGrCATGTcyrmv ; cor=; Ncor= a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 46 9 2 3 6 7 19 17 18 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 1 0 1 12 38 30 13 18 15 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 2 3 56 1 4 6 16 13 16 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0 10 47 0 43 11 16 11 11 10
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=2/7; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.908159; gkgGrCATGYCYrGrCATGyCyac- ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 16 0 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 24 0 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 14 0 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14 11 0
oligos_6nt_mkv2_m4_shift8 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=3/7; ncol2=15; w=0; offset=7; strand=D; shift=8; score=0.576049; --------syccrGGCATGTCyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 0 0 c 0 0 0 0 0 0 0 0 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 0 0 g 0 0 0 0 0 0 0 0 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 0 0 t 0 0 0 0 0 0 0 0 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18 0 0
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.557843; -yrGACATGCCCasrs--------- ; cor=; Ncor= a 0 18 32 20 94 1 107 11 0 2 4 2 79 12 52 21 0 0 0 0 0 0 0 0 0 c 0 32 12 8 3 119 7 3 0 106 117 109 12 34 19 58 0 0 0 0 0 0 0 0 0 g 0 28 61 89 26 2 2 2 123 1 1 2 19 66 41 36 0 0 0 0 0 0 0 0 0 t 0 47 20 8 2 3 9 109 2 16 3 12 15 13 13 10 0 0 0 0 0 0 0 0 0
oligos_6nt_mkv2_m5_shift11 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=5/7; ncol2=12; w=0; offset=10; strand=D; shift=11; score=0.462233; -----------yrGACATGTCyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 0 0 c 0 0 0 0 0 0 0 0 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 0 0 g 0 0 0 0 0 0 0 0 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 0 0 t 0 0 0 0 0 0 0 0 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27 0 0
oligos_7nt_mkv2_m3_rc_shift10 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=6/7; ncol2=13; w=0; offset=9; strand=R; shift=10; score=0.425875; ----------cyrGACTTGTcyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 12 14 37 3 54 0 10 0 0 0 6 10 16 0 0 c 0 0 0 0 0 0 0 0 0 0 29 25 3 6 0 64 3 0 2 5 41 18 7 0 0 g 0 0 0 0 0 0 0 0 0 0 8 9 16 54 6 0 2 3 62 2 10 13 26 0 0 t 0 0 0 0 0 0 0 0 0 0 15 16 8 1 4 0 49 61 0 57 7 23 15 0 0
oligos_6nt_mkv2_m2_rc_shift11 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=7/7; ncol2=12; w=0; offset=10; strand=R; shift=11; score=0.413608; -----------yrGACTTGTCyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 11 24 3 48 0 9 0 0 0 2 7 19 0 0 c 0 0 0 0 0 0 0 0 0 0 0 22 3 1 1 62 2 0 0 10 52 20 6 0 0 g 0 0 0 0 0 0 0 0 0 0 0 13 24 58 10 0 2 2 62 2 3 6 23 0 0 t 0 0 0 0 0 0 0 0 0 0 0 16 11 0 3 0 49 60 0 50 5 29 14 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift11 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------yrGACAAGTCyr ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 14 29 5 50 0 60 49 0 3 0 11 16 c 0 0 0 0 0 0 0 0 0 0 0 23 6 3 2 62 2 2 0 10 58 24 13 g 0 0 0 0 0 0 0 0 0 0 0 6 20 52 10 0 0 2 62 1 1 3 22 t 0 0 0 0 0 0 0 0 0 0 0 19 7 2 0 0 0 9 0 48 3 24 11
oligos_6nt_mkv2_m2_shift11 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------yrGACAAGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 14 29 5 50 0 60 49 0 3 0 11 16 c 0 0 0 0 0 0 0 0 0 0 0 23 6 3 2 62 2 2 0 10 58 24 13 g 0 0 0 0 0 0 0 0 0 0 0 6 20 52 10 0 0 2 62 1 1 3 22 t 0 0 0 0 0 0 0 0 0 0 0 19 7 2 0 0 0 9 0 48 3 24 11
oligos_7nt_mkv2_m3_shift11 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=2/7; ncol2=13; w=0; offset=0; strand=D; shift=11; score=0.903904; -----------yrgACAAGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 15 23 7 57 0 61 49 0 4 1 8 16 c 0 0 0 0 0 0 0 0 0 0 0 26 13 10 2 62 3 2 0 6 54 16 9 g 0 0 0 0 0 0 0 0 0 0 0 7 18 41 5 2 0 3 64 0 6 3 25 t 0 0 0 0 0 0 0 0 0 0 0 16 10 6 0 0 0 10 0 54 3 37 14
oligos_6nt_mkv2_m5_shift11 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=3/7; ncol2=12; w=0; offset=0; strand=D; shift=11; score=0.871965; -----------yrGACATGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 c 0 0 0 0 0 0 0 0 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 g 0 0 0 0 0 0 0 0 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 t 0 0 0 0 0 0 0 0 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27
oligos_6nt_mkv2_m4_rc_shift11 (oligos_6nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=4/7; ncol2=15; w=0; offset=0; strand=R; shift=11; score=0.61905; -----------yrGACATGCCyg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 18 31 17 85 0 88 8 1 1 0 3 18 c 0 0 0 0 0 0 0 0 0 0 0 26 11 5 1 91 1 2 2 82 91 36 14 g 0 0 0 0 0 0 0 0 0 0 0 23 41 68 9 4 1 2 94 1 1 2 53 t 0 0 0 0 0 0 0 0 0 0 0 30 14 7 2 2 7 85 0 13 5 56 12
oligos_6nt_mkv2_m1_shift11 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=5/7; ncol2=15; w=0; offset=0; strand=D; shift=11; score=0.583808; -----------yrGACATGCCCa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 18 32 20 94 1 107 11 0 2 4 2 79 c 0 0 0 0 0 0 0 0 0 0 0 32 12 8 3 119 7 3 0 106 117 109 12 g 0 0 0 0 0 0 0 0 0 0 0 28 61 89 26 2 2 2 123 1 1 2 19 t 0 0 0 0 0 0 0 0 0 0 0 47 20 8 2 3 9 109 2 16 3 12 15
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=6/7; ncol2=24; w=-11; offset=-11; strand=D; shift=0; score=0.415971; gkgGrCATGYCYrGrCATGyCya ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14
oligos_7nt_mkv2_m4_rc_shift9 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=7/7; ncol2=24; w=-2; offset=-2; strand=R; shift=9; score=0.413608; ---------bkyrgACATGyCyG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 10 11 11 16 11 43 0 47 10 0 0 0 4 13 c 0 0 0 0 0 0 0 0 0 16 13 16 6 4 1 56 3 2 0 36 57 28 3 g 0 0 0 0 0 0 0 0 0 15 18 13 30 38 12 1 0 1 59 0 0 2 42 t 0 0 0 0 0 0 0 0 0 18 17 19 7 6 3 2 9 46 0 23 2 25 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --yrgACAAGTCyrg ; Alignment reference a 0 0 15 23 7 57 0 61 49 0 4 1 8 16 15 c 0 0 26 13 10 2 62 3 2 0 6 54 16 9 8 g 0 0 7 18 41 5 2 0 3 64 0 6 3 25 29 t 0 0 16 10 6 0 0 0 10 0 54 3 37 14 12
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --yrgACAAGTCyrg ; cor=; Ncor= a 0 0 15 23 7 57 0 61 49 0 4 1 8 16 15 c 0 0 26 13 10 2 62 3 2 0 6 54 16 9 8 g 0 0 7 18 41 5 2 0 3 64 0 6 3 25 29 t 0 0 16 10 6 0 0 0 10 0 54 3 37 14 12
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=2/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.903904; --yrGACAAGTCyr- ; cor=; Ncor= a 0 0 14 29 5 50 0 60 49 0 3 0 11 16 0 c 0 0 23 6 3 2 62 2 2 0 10 58 24 13 0 g 0 0 6 20 52 10 0 0 2 62 1 1 3 22 0 t 0 0 19 7 2 0 0 0 9 0 48 3 24 11 0
oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.776473; --yrGACATGTCyr- ; cor=; Ncor= a 0 0 27 34 4 84 1 100 9 0 1 4 20 33 0 c 0 0 35 3 2 0 110 2 1 1 27 102 55 17 0 g 0 0 17 55 102 27 1 1 2 110 0 2 3 35 0 t 0 0 33 20 4 1 0 9 100 1 84 4 34 27 0
oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=4/6; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.656943; --yrGACATGCCygg ; cor=; Ncor= a 0 0 18 31 17 85 0 88 8 1 1 0 3 18 10 c 0 0 26 11 5 1 91 1 2 2 82 91 36 14 17 g 0 0 23 41 68 9 4 1 2 94 1 1 2 53 60 t 0 0 30 14 7 2 2 7 85 0 13 5 56 12 10
oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=5/6; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.425875; bkyrgACATGyCyGG ; cor=; Ncor= a 10 11 11 16 11 43 0 47 10 0 0 0 4 13 2 c 16 13 16 6 4 1 56 3 2 0 36 57 28 3 0 g 15 18 13 30 38 12 1 0 1 59 0 0 2 42 56 t 18 17 19 7 6 3 2 9 46 0 23 2 25 1 1
oligos_7nt_mkv2_m1_rc_shift1 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=6/6; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.414756; -gtrGrCATGyCyRG ; cor=; Ncor= a 0 11 14 18 10 40 0 46 11 0 0 0 3 17 4 c 0 14 16 7 2 1 62 4 2 0 42 61 26 2 0 g 0 24 16 34 46 21 3 0 1 65 0 1 2 45 59 t 0 16 19 6 7 3 0 15 51 0 23 3 34 1 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m5_shift3 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=12; shift=3; ncol=15; ---yrGACATGTCyr ; Alignment reference a 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 c 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 g 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 t 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27
oligos_6nt_mkv2_m5_shift3 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---yrGACATGTCyr ; cor=; Ncor= a 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 c 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 g 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 t 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=2/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.871965; ---yrGACAAGTCyr ; cor=; Ncor= a 0 0 0 14 29 5 50 0 60 49 0 3 0 11 16 c 0 0 0 23 6 3 2 62 2 2 0 10 58 24 13 g 0 0 0 6 20 52 10 0 0 2 62 1 1 3 22 t 0 0 0 19 7 2 0 0 0 9 0 48 3 24 11
oligos_7nt_mkv2_m3_rc_shift2 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=3/7; ncol2=13; w=-1; offset=-1; strand=R; shift=2; score=0.776473; --cyrGACTTGTcyr ; cor=; Ncor= a 0 0 12 14 37 3 54 0 10 0 0 0 6 10 16 c 0 0 29 25 3 6 0 64 3 0 2 5 41 18 7 g 0 0 8 9 16 54 6 0 2 3 62 2 10 13 26 t 0 0 15 16 8 1 4 0 49 61 0 57 7 23 15
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=4/7; ncol2=15; w=-3; offset=-3; strand=D; shift=0; score=0.709311; syccrGGCATGTCyr ; cor=; Ncor= a 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 c 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 g 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 t 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=5/7; ncol2=15; w=0; offset=0; strand=D; shift=3; score=0.699131; ---yrGACATGCCCa ; cor=; Ncor= a 0 0 0 18 32 20 94 1 107 11 0 2 4 2 79 c 0 0 0 32 12 8 3 119 7 3 0 106 117 109 12 g 0 0 0 28 61 89 26 2 2 2 123 1 1 2 19 t 0 0 0 47 20 8 2 3 9 109 2 16 3 12 15
oligos_7nt_mkv2_m4_rc_shift1 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=6/7; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.462233; -bkyrgACATGyCyG ; cor=; Ncor= a 0 10 11 11 16 11 43 0 47 10 0 0 0 4 13 c 0 16 13 16 6 4 1 56 3 2 0 36 57 28 3 g 0 15 18 13 30 38 12 1 0 1 59 0 0 2 42 t 0 18 17 19 7 6 3 2 9 46 0 23 2 25 1
oligos_7nt_mkv2_m1_rc_shift2 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=7/7; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.455401; --gtrGrCATGyCyR ; cor=; Ncor= a 0 0 11 14 18 10 40 0 46 11 0 0 0 3 17 c 0 0 14 16 7 2 1 62 4 2 0 42 61 26 2 g 0 0 24 16 34 46 21 3 0 1 65 0 1 2 45 t 0 0 16 19 6 7 3 0 15 51 0 23 3 34 1

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=24; shift=0; ncol=24; gkgGrCATGYCYrGrCATGyCyac ; Alignment reference a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 16 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 24 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 14 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14 11
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; gkgGrCATGYCYrGrCATGyCyac ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 16 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 24 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 14 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14 11
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=2/7; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.908159; -krrrCATGYCCrGrCATGTcyrm ; cor=; Ncor= a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 46 9 2 3 6 7 19 17 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 1 0 1 12 38 30 13 18 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 2 3 56 1 4 6 16 13 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0 10 47 0 43 11 16 11 11
oligos_6nt_mkv2_m4_shift8 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=3/7; ncol2=15; w=0; offset=8; strand=D; shift=8; score=0.570608; --------syccrGGCATGTCyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 0 c 0 0 0 0 0 0 0 0 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 0 g 0 0 0 0 0 0 0 0 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 0 t 0 0 0 0 0 0 0 0 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18 0
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=4/7; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.565137; -yrGACATGCCCasrs-------- ; cor=; Ncor= a 0 18 32 20 94 1 107 11 0 2 4 2 79 12 52 21 0 0 0 0 0 0 0 0 c 0 32 12 8 3 119 7 3 0 106 117 109 12 34 19 58 0 0 0 0 0 0 0 0 g 0 28 61 89 26 2 2 2 123 1 1 2 19 66 41 36 0 0 0 0 0 0 0 0 t 0 47 20 8 2 3 9 109 2 16 3 12 15 13 13 10 0 0 0 0 0 0 0 0
oligos_6nt_mkv2_m5_shift11 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=5/7; ncol2=12; w=0; offset=11; strand=D; shift=11; score=0.455401; -----------yrGACATGTCyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 0 c 0 0 0 0 0 0 0 0 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 0 g 0 0 0 0 0 0 0 0 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 0 t 0 0 0 0 0 0 0 0 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27 0
oligos_6nt_mkv2_m2_shift11 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=6/7; ncol2=12; w=0; offset=11; strand=D; shift=11; score=0.415971; -----------yrGACAAGTCyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 14 29 5 50 0 60 49 0 3 0 11 16 0 c 0 0 0 0 0 0 0 0 0 0 0 23 6 3 2 62 2 2 0 10 58 24 13 0 g 0 0 0 0 0 0 0 0 0 0 0 6 20 52 10 0 0 2 62 1 1 3 22 0 t 0 0 0 0 0 0 0 0 0 0 0 19 7 2 0 0 0 9 0 48 3 24 11 0
oligos_7nt_mkv2_m3_rc_shift10 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=7/7; ncol2=13; w=0; offset=10; strand=R; shift=10; score=0.414756; ----------cyrGACTTGTcyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 12 14 37 3 54 0 10 0 0 0 6 10 16 0 c 0 0 0 0 0 0 0 0 0 0 29 25 3 6 0 64 3 0 2 5 41 18 7 0 g 0 0 0 0 0 0 0 0 0 0 8 9 16 54 6 0 2 3 62 2 10 13 26 0 t 0 0 0 0 0 0 0 0 0 0 15 16 8 1 4 0 49 61 0 57 7 23 15 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=15; shift=1; ncol=16; -yrGACATGCCCasrs ; Alignment reference a 0 18 32 20 94 1 107 11 0 2 4 2 79 12 52 21 c 0 32 12 8 3 119 7 3 0 106 117 109 12 34 19 58 g 0 28 61 89 26 2 2 2 123 1 1 2 19 66 41 36 t 0 47 20 8 2 3 9 109 2 16 3 12 15 13 13 10
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -yrGACATGCCCasrs ; cor=; Ncor= a 0 18 32 20 94 1 107 11 0 2 4 2 79 12 52 21 c 0 32 12 8 3 119 7 3 0 106 117 109 12 34 19 58 g 0 28 61 89 26 2 2 2 123 1 1 2 19 66 41 36 t 0 47 20 8 2 3 9 109 2 16 3 12 15 13 13 10
oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=2/6; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.909388; -yrGACATGCCyggrs ; cor=; Ncor= a 0 18 31 17 85 0 88 8 1 1 0 3 18 10 29 18 c 0 26 11 5 1 91 1 2 2 82 91 36 14 17 15 47 g 0 23 41 68 9 4 1 2 94 1 1 2 53 60 43 25 t 0 30 14 7 2 2 7 85 0 13 5 56 12 10 10 7
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.699131; -yrGACATGTCyr--- ; cor=; Ncor= a 0 27 34 4 84 1 100 9 0 1 4 20 33 0 0 0 c 0 35 3 2 0 110 2 1 1 27 102 55 17 0 0 0 g 0 17 55 102 27 1 1 2 110 0 2 3 35 0 0 0 t 0 33 20 4 1 0 9 100 1 84 4 34 27 0 0 0
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=4/6; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.583808; -yrGACAAGTCyr--- ; cor=; Ncor= a 0 14 29 5 50 0 60 49 0 3 0 11 16 0 0 0 c 0 23 6 3 2 62 2 2 0 10 58 24 13 0 0 0 g 0 6 20 52 10 0 0 2 62 1 1 3 22 0 0 0 t 0 19 7 2 0 0 0 9 0 48 3 24 11 0 0 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=5/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.565137; gkgGrCATGYCYrGrC ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=6/6; ncol2=24; w=0; offset=0; strand=D; shift=1; score=0.557843; -krrrCATGYCCrGrC ; cor=; Ncor= a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift8 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=15; shift=8; ncol=23; --------syccrGGCATGTCyr ; Alignment reference a 0 0 0 0 0 0 0 0 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 c 0 0 0 0 0 0 0 0 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 g 0 0 0 0 0 0 0 0 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 t 0 0 0 0 0 0 0 0 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18
oligos_6nt_mkv2_m4_shift8 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/7; ncol2=15; w=0; offset=0; strand=D; shift=8; score= 1; --------syccrGGCATGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 7 10 10 12 56 5 13 0 85 7 2 2 7 14 30 c 0 0 0 0 0 0 0 0 25 43 60 53 2 1 1 94 2 1 4 9 68 41 23 g 0 0 0 0 0 0 0 0 47 15 17 14 36 91 82 2 2 1 91 1 5 11 26 t 0 0 0 0 0 0 0 0 18 29 10 18 3 0 1 1 8 88 0 85 17 31 18
oligos_6nt_mkv2_m1_rc_shift8 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1_rc; m=2/7; ncol2=15; w=0; offset=0; strand=R; shift=8; score=0.909388; --------systGGGCATGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 10 13 13 15 12 3 16 2 109 9 3 2 8 20 47 c 0 0 0 0 0 0 0 0 36 41 66 19 2 1 1 123 2 2 2 26 89 61 28 g 0 0 0 0 0 0 0 0 58 19 34 12 109 117 106 0 3 7 119 3 8 12 32 t 0 0 0 0 0 0 0 0 21 52 12 79 2 4 2 0 11 107 1 94 20 32 18
oligos_6nt_mkv2_m5_shift11 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/7; ncol2=12; w=0; offset=3; strand=D; shift=11; score=0.709311; -----------yrGACATGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 27 34 4 84 1 100 9 0 1 4 20 33 c 0 0 0 0 0 0 0 0 0 0 0 35 3 2 0 110 2 1 1 27 102 55 17 g 0 0 0 0 0 0 0 0 0 0 0 17 55 102 27 1 1 2 110 0 2 3 35 t 0 0 0 0 0 0 0 0 0 0 0 33 20 4 1 0 9 100 1 84 4 34 27
oligos_7nt_mkv2_m3_rc_shift10 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=4/7; ncol2=13; w=0; offset=2; strand=R; shift=10; score=0.656943; ----------cyrGACTTGTcyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 12 14 37 3 54 0 10 0 0 0 6 10 16 c 0 0 0 0 0 0 0 0 0 0 29 25 3 6 0 64 3 0 2 5 41 18 7 g 0 0 0 0 0 0 0 0 0 0 8 9 16 54 6 0 2 3 62 2 10 13 26 t 0 0 0 0 0 0 0 0 0 0 15 16 8 1 4 0 49 61 0 57 7 23 15
oligos_6nt_mkv2_m2_rc_shift11 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=5/7; ncol2=12; w=0; offset=3; strand=R; shift=11; score=0.61905; -----------yrGACTTGTCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 11 24 3 48 0 9 0 0 0 2 7 19 c 0 0 0 0 0 0 0 0 0 0 0 22 3 1 1 62 2 0 0 10 52 20 6 g 0 0 0 0 0 0 0 0 0 0 0 13 24 58 10 0 2 2 62 2 3 6 23 t 0 0 0 0 0 0 0 0 0 0 0 16 11 0 3 0 49 60 0 50 5 29 14
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=6/7; ncol2=24; w=-7; offset=-7; strand=D; shift=1; score=0.576049; -krrrCATGYCCrGrCATGTcyr ; cor=; Ncor= a 0 12 17 16 37 0 47 12 0 0 1 1 25 2 23 0 46 9 2 3 6 7 19 c 0 13 6 4 1 56 2 2 1 42 56 42 2 0 0 59 1 0 1 12 38 30 13 g 0 18 25 32 19 2 1 2 58 0 0 3 28 57 36 0 2 3 56 1 4 6 16 t 0 16 11 7 2 1 9 43 0 17 2 13 4 0 0 0 10 47 0 43 11 16 11
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=7/7; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.570608; gkgGrCATGYCYrGrCATGyCya ; cor=; Ncor= a 11 13 14 7 37 0 51 12 0 0 2 1 34 3 23 0 51 15 0 3 7 6 19 c 10 13 4 3 1 63 1 2 0 47 59 45 2 1 0 65 1 0 3 21 46 34 16 g 31 17 37 49 24 2 0 1 65 0 0 2 26 61 42 0 2 4 62 1 2 7 16 t 13 22 10 6 3 0 13 50 0 18 4 17 3 0 0 0 11 46 0 40 10 18 14