One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.012313_2025-05-16.012313_WYQ09F/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/2025/05/16/peak-motifs.2025-05-16.012313_2025-05-16.012313_WYQ09F/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 6 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=16; shift=0; ncol=16; wysArCCAATCAgawh ; Alignment reference a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 18 19 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 13 19 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 12 12 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9 26 19

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; wysArCCAATCAgawh ; cor=; Ncor= a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 18 19 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 13 19 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 12 12 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9 26 19

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.897049; hykGACCAATCAgawy ; cor=; Ncor= a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 20 13 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 18 27 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 11 12 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10 31 28

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=3/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.794181; -yyrgCCAATCAga-- ; cor=; Ncor= a 0 15 9 36 17 2 1 78 76 1 3 77 17 44 0 0 c 0 25 24 5 6 74 74 0 0 1 62 0 15 17 0 0 g 0 8 17 23 48 1 2 1 2 1 9 2 30 5 0 0 t 0 31 29 15 8 2 2 0 1 76 5 0 17 13 0 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=4/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.771781; hykGACCAATcAga-- ; cor=; Ncor= a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 0 0 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 0 0 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 0 0 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=5/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.75502; wykGACCAATgAgaw- ; cor=; Ncor= a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 21 0 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 8 0 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 13 0 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11 21 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; agCtCATCGCwwm ; Alignment reference a 38 17 9 4 2 68 1 2 4 3 25 23 19 c 12 14 57 11 67 2 0 72 3 67 12 16 23 g 8 29 7 11 2 2 4 0 61 3 9 15 17 t 16 14 1 48 3 2 69 0 6 1 28 20 15

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; agCtCATCGCwwm ; cor=; Ncor= a 38 17 9 4 2 68 1 2 4 3 25 23 19 c 12 14 57 11 67 2 0 72 3 67 12 16 23 g 8 29 7 11 2 2 4 0 61 3 9 15 17 t 16 14 1 48 3 2 69 0 6 1 28 20 15

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 6 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; hykGACCAATCAgawy ; Alignment reference a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 20 13 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 18 27 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 11 12 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10 31 28

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; hykGACCAATCAgawy ; cor=; Ncor= a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 20 13 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 18 27 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 11 12 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10 31 28

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=2/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.897049; wysArCCAATCAgawh ; cor=; Ncor= a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 18 19 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 13 19 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 12 12 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9 26 19

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.884006; wykGACCAATgAgaw- ; cor=; Ncor= a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 21 0 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 8 0 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 13 0 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11 21 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=4/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.86307; hykGACCAATcAga-- ; cor=; Ncor= a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 0 0 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 0 0 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 0 0 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10 0 0

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=5/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.743174; -yyrgCCAATCAga-- ; cor=; Ncor= a 0 15 9 36 17 2 1 78 76 1 3 77 17 44 0 0 c 0 25 24 5 6 74 74 0 0 1 62 0 15 17 0 0 g 0 8 17 23 48 1 2 1 2 1 9 2 30 5 0 0 t 0 31 29 15 8 2 2 0 1 76 5 0 17 13 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 6 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=15; shift=0; ncol=15; wykGACCAATgAgaw ; Alignment reference a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 21 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 8 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 13 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11 21

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wykGACCAATgAgaw ; cor=; Ncor= a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 21 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 8 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 13 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11 21

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.884006; hykGACCAATCAgaw ; cor=; Ncor= a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 20 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 18 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 11 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10 31

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=3/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.881912; hykGACCAATcAga- ; cor=; Ncor= a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 0 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 0 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 0 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10 0

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=4/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.75502; wysArCCAATCAgaw ; cor=; Ncor= a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 18 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 13 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 12 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9 26

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=5/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.704913; -yyrgCCAATCAga- ; cor=; Ncor= a 0 15 9 36 17 2 1 78 76 1 3 77 17 44 0 c 0 25 24 5 6 74 74 0 0 1 62 0 15 17 0 g 0 8 17 23 48 1 2 1 2 1 9 2 30 5 0 t 0 31 29 15 8 2 2 0 1 76 5 0 17 13 0

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=14; shift=0; ncol=14; yyyCCCyCCCCCcc ; Alignment reference a 42 30 17 5 3 3 9 4 4 6 18 13 40 33 c 79 85 65 163 180 172 58 169 183 178 154 155 103 97 g 21 27 18 8 1 2 6 3 1 2 9 10 21 25 t 55 55 97 21 13 20 124 21 9 11 16 19 33 42

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; yyyCCCyCCCCCcc ; cor=; Ncor= a 42 30 17 5 3 3 9 4 4 6 18 13 40 33 c 79 85 65 163 180 172 58 169 183 178 154 155 103 97 g 21 27 18 8 1 2 6 3 1 2 9 10 21 25 t 55 55 97 21 13 20 124 21 9 11 16 19 33 42

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=2/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.805663; yyyCCCyCCCCCCC ; cor=; Ncor= a 32 17 13 8 3 4 3 2 3 3 7 3 15 16 c 69 59 59 124 138 135 58 136 145 144 136 134 130 111 g 15 26 16 7 5 1 6 2 1 0 4 7 3 11 t 41 55 69 18 11 17 90 17 8 10 10 13 9 19

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.792432; yytCCCTTCCCmc- ; cor=; Ncor= a 25 20 10 4 4 3 5 2 0 3 7 29 20 0 c 40 32 26 101 103 105 8 21 107 102 86 47 47 0 g 16 19 21 2 3 1 2 2 4 2 10 10 19 0 t 33 43 57 7 4 5 99 89 3 7 11 28 28 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 4 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=13; shift=0; ncol=13; yytCCCTTCCCmc ; Alignment reference a 25 20 10 4 4 3 5 2 0 3 7 29 20 c 40 32 26 101 103 105 8 21 107 102 86 47 47 g 16 19 21 2 3 1 2 2 4 2 10 10 19 t 33 43 57 7 4 5 99 89 3 7 11 28 28

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; yytCCCTTCCCmc ; cor=; Ncor= a 25 20 10 4 4 3 5 2 0 3 7 29 20 c 40 32 26 101 103 105 8 21 107 102 86 47 47 g 16 19 21 2 3 1 2 2 4 2 10 10 19 t 33 43 57 7 4 5 99 89 3 7 11 28 28

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.792432; yyyCCCyCCCCCc ; cor=; Ncor= a 42 30 17 5 3 3 9 4 4 6 18 13 40 c 79 85 65 163 180 172 58 169 183 178 154 155 103 g 21 27 18 8 1 2 6 3 1 2 9 10 21 t 55 55 97 21 13 20 124 21 9 11 16 19 33

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.626865; yyyCCCyCCCCCC ; cor=; Ncor= a 32 17 13 8 3 4 3 2 3 3 7 3 15 c 69 59 59 124 138 135 58 136 145 144 136 134 130 g 15 26 16 7 5 1 6 2 1 0 4 7 3 t 41 55 69 18 11 17 90 17 8 10 10 13 9

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=17; shift=0; ncol=17; yyyCCCyCCCCCCCmcc ; Alignment reference a 32 17 13 8 3 4 3 2 3 3 7 3 15 16 44 34 36 c 69 59 59 124 138 135 58 136 145 144 136 134 130 111 78 71 67 g 15 26 16 7 5 1 6 2 1 0 4 7 3 11 9 20 21 t 41 55 69 18 11 17 90 17 8 10 10 13 9 19 26 32 33

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; yyyCCCyCCCCCCCmcc ; cor=; Ncor= a 32 17 13 8 3 4 3 2 3 3 7 3 15 16 44 34 36 c 69 59 59 124 138 135 58 136 145 144 136 134 130 111 78 71 67 g 15 26 16 7 5 1 6 2 1 0 4 7 3 11 9 20 21 t 41 55 69 18 11 17 90 17 8 10 10 13 9 19 26 32 33

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.805663; yyyCCCyCCCCCcc--- ; cor=; Ncor= a 42 30 17 5 3 3 9 4 4 6 18 13 40 33 0 0 0 c 79 85 65 163 180 172 58 169 183 178 154 155 103 97 0 0 0 g 21 27 18 8 1 2 6 3 1 2 9 10 21 25 0 0 0 t 55 55 97 21 13 20 124 21 9 11 16 19 33 42 0 0 0

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.626865; yytCCCTTCCCmc---- ; cor=; Ncor= a 25 20 10 4 4 3 5 2 0 3 7 29 20 0 0 0 0 c 40 32 26 101 103 105 8 21 107 102 86 47 47 0 0 0 0 g 16 19 21 2 3 1 2 2 4 2 10 10 19 0 0 0 0 t 33 43 57 7 4 5 99 89 3 7 11 28 28 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --tcTGATTGGcyrr ; Alignment reference a 0 0 13 17 0 5 76 1 0 2 2 8 15 29 31 c 0 0 5 30 2 9 1 2 1 2 1 48 23 17 8 g 0 0 17 15 0 62 1 0 0 74 74 6 5 24 25 t 0 0 44 17 77 3 1 76 78 1 2 17 36 9 15

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --tcTGATTGGcyrr ; cor=; Ncor= a 0 0 13 17 0 5 76 1 0 2 2 8 15 29 31 c 0 0 5 30 2 9 1 2 1 2 1 48 23 17 8 g 0 0 17 15 0 62 1 0 0 74 74 6 5 24 25 t 0 0 44 17 77 3 1 76 78 1 2 17 36 9 15

oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=2/5; ncol2=14; w=0; offset=0; strand=R; shift=2; score=0.829881; --tcTgATTGGTCmr ; cor=; Ncor= a 0 0 10 15 0 3 77 2 3 1 2 4 3 20 30 c 0 0 11 38 5 19 1 0 3 0 0 11 57 44 16 g 0 0 13 12 2 49 0 0 0 76 75 3 3 8 23 t 0 0 46 15 73 9 2 78 74 3 3 62 17 8 11

oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=3/5; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.794181; dwtcTGATTGGyTsr ; cor=; Ncor= a 19 26 9 6 0 2 65 1 0 1 1 6 5 15 23 c 12 12 5 41 1 11 1 2 2 2 0 38 14 19 8 g 19 13 13 10 1 51 2 1 0 62 68 6 2 31 25 t 19 18 42 12 67 5 1 65 67 4 0 19 48 4 13

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=4/5; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.743174; rwtcTGATTGGTCmr ; cor=; Ncor= a 28 31 10 12 2 2 76 3 2 1 1 8 4 32 32 c 12 11 9 49 4 15 1 0 1 0 2 12 55 25 15 g 27 18 16 9 0 55 0 1 0 76 76 4 6 10 24 t 13 20 45 10 74 8 3 76 77 3 1 56 15 13 9

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=5/5; ncol2=15; w=-1; offset=-1; strand=R; shift=1; score=0.704913; -wtcTcATTGGTCmr ; cor=; Ncor= a 0 21 11 9 1 1 60 2 0 0 1 1 2 27 26 c 0 13 8 41 6 42 2 2 3 3 1 8 54 18 13 g 0 8 8 3 0 12 0 0 0 57 58 4 1 9 17 t 0 21 36 10 56 8 1 59 60 3 3 50 6 9 7

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; wdTCATGTGAyw ; Alignment reference a 36 36 20 1 97 1 18 2 2 97 18 35 c 12 7 3 100 2 22 2 3 1 1 32 12 g 23 30 9 1 4 2 83 0 100 2 11 11 t 33 31 72 2 1 79 1 99 1 4 43 46

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wdTCATGTGAyw ; cor=; Ncor= a 36 36 20 1 97 1 18 2 2 97 18 35 c 12 7 3 100 2 22 2 3 1 1 32 12 g 23 30 9 1 4 2 83 0 100 2 11 11 t 33 31 72 2 1 79 1 99 1 4 43 46

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; hykGACCAATcAga ; Alignment reference a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; hykGACCAATcAga ; cor=; Ncor= a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.881912; wykGACCAATgAga ; cor=; Ncor= a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.86307; hykGACCAATCAga ; cor=; Ncor= a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=4/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.829881; -yyrgCCAATCAga ; cor=; Ncor= a 0 15 9 36 17 2 1 78 76 1 3 77 17 44 c 0 25 24 5 6 74 74 0 0 1 62 0 15 17 g 0 8 17 23 48 1 2 1 2 1 9 2 30 5 t 0 31 29 15 8 2 2 0 1 76 5 0 17 13

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.771781; wysArCCAATCAga ; cor=; Ncor= a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9

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=16; shift=0; ncol=16; wysArCCAATCAgawh ; Alignment reference a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 18 19 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 13 19 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 12 12 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9 26 19
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; wysArCCAATCAgawh ; cor=; Ncor= a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 18 19 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 13 19 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 12 12 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9 26 19
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.897049; hykGACCAATCAgawy ; cor=; Ncor= a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 20 13 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 18 27 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 11 12 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10 31 28
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=3/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.794181; -yyrgCCAATCAga-- ; cor=; Ncor= a 0 15 9 36 17 2 1 78 76 1 3 77 17 44 0 0 c 0 25 24 5 6 74 74 0 0 1 62 0 15 17 0 0 g 0 8 17 23 48 1 2 1 2 1 9 2 30 5 0 0 t 0 31 29 15 8 2 2 0 1 76 5 0 17 13 0 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=4/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.771781; hykGACCAATcAga-- ; cor=; Ncor= a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 0 0 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 0 0 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 0 0 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10 0 0
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=5/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.75502; wykGACCAATgAgaw- ; cor=; Ncor= a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 21 0 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 8 0 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 13 0 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11 21 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=16; shift=0; ncol=16; hykGACCAATCAgawy ; Alignment reference a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 20 13 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 18 27 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 11 12 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10 31 28
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; hykGACCAATCAgawy ; cor=; Ncor= a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 20 13 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 18 27 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 11 12 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10 31 28
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=2/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.897049; wysArCCAATCAgawh ; cor=; Ncor= a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 18 19 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 13 19 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 12 12 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9 26 19
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.884006; wykGACCAATgAgaw- ; cor=; Ncor= a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 21 0 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 8 0 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 13 0 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11 21 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=4/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.86307; hykGACCAATcAga-- ; cor=; Ncor= a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 0 0 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 0 0 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 0 0 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10 0 0
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=5/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.743174; -yyrgCCAATCAga-- ; cor=; Ncor= a 0 15 9 36 17 2 1 78 76 1 3 77 17 44 0 0 c 0 25 24 5 6 74 74 0 0 1 62 0 15 17 0 0 g 0 8 17 23 48 1 2 1 2 1 9 2 30 5 0 0 t 0 31 29 15 8 2 2 0 1 76 5 0 17 13 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=15; shift=0; ncol=15; wykGACCAATgAgaw ; Alignment reference a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 21 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 8 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 13 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11 21
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wykGACCAATgAgaw ; cor=; Ncor= a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 21 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 8 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 13 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11 21
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.884006; hykGACCAATCAgaw ; cor=; Ncor= a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 20 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 18 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 11 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10 31
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=3/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.881912; hykGACCAATcAga- ; cor=; Ncor= a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 0 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 0 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 0 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10 0
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=4/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.75502; wysArCCAATCAgaw ; cor=; Ncor= a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 18 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 13 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 12 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9 26
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=5/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.704913; -yyrgCCAATCAga- ; cor=; Ncor= a 0 15 9 36 17 2 1 78 76 1 3 77 17 44 0 c 0 25 24 5 6 74 74 0 0 1 62 0 15 17 0 g 0 8 17 23 48 1 2 1 2 1 9 2 30 5 0 t 0 31 29 15 8 2 2 0 1 76 5 0 17 13 0

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=14; shift=0; ncol=14; yyyCCCyCCCCCcc ; Alignment reference a 42 30 17 5 3 3 9 4 4 6 18 13 40 33 c 79 85 65 163 180 172 58 169 183 178 154 155 103 97 g 21 27 18 8 1 2 6 3 1 2 9 10 21 25 t 55 55 97 21 13 20 124 21 9 11 16 19 33 42
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; yyyCCCyCCCCCcc ; cor=; Ncor= a 42 30 17 5 3 3 9 4 4 6 18 13 40 33 c 79 85 65 163 180 172 58 169 183 178 154 155 103 97 g 21 27 18 8 1 2 6 3 1 2 9 10 21 25 t 55 55 97 21 13 20 124 21 9 11 16 19 33 42
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=2/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.805663; yyyCCCyCCCCCCC ; cor=; Ncor= a 32 17 13 8 3 4 3 2 3 3 7 3 15 16 c 69 59 59 124 138 135 58 136 145 144 136 134 130 111 g 15 26 16 7 5 1 6 2 1 0 4 7 3 11 t 41 55 69 18 11 17 90 17 8 10 10 13 9 19
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.792432; yytCCCTTCCCmc- ; cor=; Ncor= a 25 20 10 4 4 3 5 2 0 3 7 29 20 0 c 40 32 26 101 103 105 8 21 107 102 86 47 47 0 g 16 19 21 2 3 1 2 2 4 2 10 10 19 0 t 33 43 57 7 4 5 99 89 3 7 11 28 28 0

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=13; shift=0; ncol=13; yytCCCTTCCCmc ; Alignment reference a 25 20 10 4 4 3 5 2 0 3 7 29 20 c 40 32 26 101 103 105 8 21 107 102 86 47 47 g 16 19 21 2 3 1 2 2 4 2 10 10 19 t 33 43 57 7 4 5 99 89 3 7 11 28 28
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; yytCCCTTCCCmc ; cor=; Ncor= a 25 20 10 4 4 3 5 2 0 3 7 29 20 c 40 32 26 101 103 105 8 21 107 102 86 47 47 g 16 19 21 2 3 1 2 2 4 2 10 10 19 t 33 43 57 7 4 5 99 89 3 7 11 28 28
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.792432; yyyCCCyCCCCCc ; cor=; Ncor= a 42 30 17 5 3 3 9 4 4 6 18 13 40 c 79 85 65 163 180 172 58 169 183 178 154 155 103 g 21 27 18 8 1 2 6 3 1 2 9 10 21 t 55 55 97 21 13 20 124 21 9 11 16 19 33
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=0.626865; yyyCCCyCCCCCC ; cor=; Ncor= a 32 17 13 8 3 4 3 2 3 3 7 3 15 c 69 59 59 124 138 135 58 136 145 144 136 134 130 g 15 26 16 7 5 1 6 2 1 0 4 7 3 t 41 55 69 18 11 17 90 17 8 10 10 13 9

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=17; shift=0; ncol=17; yyyCCCyCCCCCCCmcc ; Alignment reference a 32 17 13 8 3 4 3 2 3 3 7 3 15 16 44 34 36 c 69 59 59 124 138 135 58 136 145 144 136 134 130 111 78 71 67 g 15 26 16 7 5 1 6 2 1 0 4 7 3 11 9 20 21 t 41 55 69 18 11 17 90 17 8 10 10 13 9 19 26 32 33
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; yyyCCCyCCCCCCCmcc ; cor=; Ncor= a 32 17 13 8 3 4 3 2 3 3 7 3 15 16 44 34 36 c 69 59 59 124 138 135 58 136 145 144 136 134 130 111 78 71 67 g 15 26 16 7 5 1 6 2 1 0 4 7 3 11 9 20 21 t 41 55 69 18 11 17 90 17 8 10 10 13 9 19 26 32 33
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.805663; yyyCCCyCCCCCcc--- ; cor=; Ncor= a 42 30 17 5 3 3 9 4 4 6 18 13 40 33 0 0 0 c 79 85 65 163 180 172 58 169 183 178 154 155 103 97 0 0 0 g 21 27 18 8 1 2 6 3 1 2 9 10 21 25 0 0 0 t 55 55 97 21 13 20 124 21 9 11 16 19 33 42 0 0 0
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.626865; yytCCCTTCCCmc---- ; cor=; Ncor= a 25 20 10 4 4 3 5 2 0 3 7 29 20 0 0 0 0 c 40 32 26 101 103 105 8 21 107 102 86 47 47 0 0 0 0 g 16 19 21 2 3 1 2 2 4 2 10 10 19 0 0 0 0 t 33 43 57 7 4 5 99 89 3 7 11 28 28 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --tcTGATTGGcyrr ; Alignment reference a 0 0 13 17 0 5 76 1 0 2 2 8 15 29 31 c 0 0 5 30 2 9 1 2 1 2 1 48 23 17 8 g 0 0 17 15 0 62 1 0 0 74 74 6 5 24 25 t 0 0 44 17 77 3 1 76 78 1 2 17 36 9 15
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --tcTGATTGGcyrr ; cor=; Ncor= a 0 0 13 17 0 5 76 1 0 2 2 8 15 29 31 c 0 0 5 30 2 9 1 2 1 2 1 48 23 17 8 g 0 0 17 15 0 62 1 0 0 74 74 6 5 24 25 t 0 0 44 17 77 3 1 76 78 1 2 17 36 9 15
oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=2/5; ncol2=14; w=0; offset=0; strand=R; shift=2; score=0.829881; --tcTgATTGGTCmr ; cor=; Ncor= a 0 0 10 15 0 3 77 2 3 1 2 4 3 20 30 c 0 0 11 38 5 19 1 0 3 0 0 11 57 44 16 g 0 0 13 12 2 49 0 0 0 76 75 3 3 8 23 t 0 0 46 15 73 9 2 78 74 3 3 62 17 8 11
oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=3/5; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.794181; dwtcTGATTGGyTsr ; cor=; Ncor= a 19 26 9 6 0 2 65 1 0 1 1 6 5 15 23 c 12 12 5 41 1 11 1 2 2 2 0 38 14 19 8 g 19 13 13 10 1 51 2 1 0 62 68 6 2 31 25 t 19 18 42 12 67 5 1 65 67 4 0 19 48 4 13
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=4/5; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.743174; rwtcTGATTGGTCmr ; cor=; Ncor= a 28 31 10 12 2 2 76 3 2 1 1 8 4 32 32 c 12 11 9 49 4 15 1 0 1 0 2 12 55 25 15 g 27 18 16 9 0 55 0 1 0 76 76 4 6 10 24 t 13 20 45 10 74 8 3 76 77 3 1 56 15 13 9
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=5/5; ncol2=15; w=-1; offset=-1; strand=R; shift=1; score=0.704913; -wtcTcATTGGTCmr ; cor=; Ncor= a 0 21 11 9 1 1 60 2 0 0 1 1 2 27 26 c 0 13 8 41 6 42 2 2 3 3 1 8 54 18 13 g 0 8 8 3 0 12 0 0 0 57 58 4 1 9 17 t 0 21 36 10 56 8 1 59 60 3 3 50 6 9 7

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; hykGACCAATcAga ; Alignment reference a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; hykGACCAATcAga ; cor=; Ncor= a 22 11 8 17 62 3 3 74 78 2 9 73 15 46 c 20 23 8 3 3 75 76 0 0 0 49 2 12 13 g 10 16 44 57 11 0 0 3 0 1 19 5 38 11 t 28 30 20 3 4 2 1 3 2 77 3 0 15 10
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.881912; wykGACCAATgAga ; cor=; Ncor= a 22 7 9 6 50 3 3 60 59 1 8 56 10 36 c 13 17 9 1 4 58 57 0 0 0 12 0 3 8 g 6 13 18 54 8 1 3 3 2 2 42 6 41 8 t 22 26 27 2 1 1 0 0 2 60 1 1 9 11
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.86307; hykGACCAATCAga ; cor=; Ncor= a 22 9 13 15 56 1 3 77 76 3 8 74 10 45 c 22 24 10 6 4 76 76 0 1 0 55 0 9 16 g 8 15 25 55 12 2 0 1 0 1 15 4 49 9 t 28 32 32 4 8 1 1 2 3 76 2 2 12 10
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=4/5; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.829881; -yyrgCCAATCAga ; cor=; Ncor= a 0 15 9 36 17 2 1 78 76 1 3 77 17 44 c 0 25 24 5 6 74 74 0 0 1 62 0 15 17 g 0 8 17 23 48 1 2 1 2 1 9 2 30 5 t 0 31 29 15 8 2 2 0 1 76 5 0 17 13
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=5/5; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.771781; wysArCCAATCAga ; cor=; Ncor= a 20 13 4 48 19 0 4 67 65 1 5 67 12 42 c 16 25 31 2 6 68 62 0 1 2 51 1 10 13 g 12 8 19 14 38 0 2 2 2 1 11 1 41 5 t 21 23 15 5 6 1 1 0 1 65 2 0 6 9