One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184201_2025-05-16.184201_aBOVlS/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.2025-05-16.184201_2025-05-16.184201_aBOVlS/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 2 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=11; shift=0; ncol=11; aaAAAGCCGcg ; Alignment reference a 45 40 73 78 74 2 3 5 3 17 12 c 10 15 0 2 1 4 76 75 1 33 12 g 14 15 7 1 6 72 1 2 75 14 49 t 13 12 2 1 1 4 2 0 3 18 9

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; aaAAAGCCGcg ; cor=; Ncor= a 45 40 73 78 74 2 3 5 3 17 12 c 10 15 0 2 1 4 76 75 1 33 12 g 14 15 7 1 6 72 1 2 75 14 49 t 13 12 2 1 1 4 2 0 3 18 9

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 5 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=11; shift=0; ncol=11; cccCCCACCsc ; Alignment reference a 36 25 13 10 2 5 126 1 0 36 29 c 48 58 95 124 140 132 1 142 136 38 57 g 33 32 17 10 3 6 17 3 8 43 29 t 29 31 21 2 1 3 2 0 2 29 31

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; cccCCCACCsc ; cor=; Ncor= a 36 25 13 10 2 5 126 1 0 36 29 c 48 58 95 124 140 132 1 142 136 38 57 g 33 32 17 10 3 6 17 3 8 43 29 t 29 31 21 2 1 3 2 0 2 29 31

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.869008; ccCCCCACCCc ; cor=; Ncor= a 26 31 0 9 5 4 108 4 2 11 35 c 55 43 133 127 133 133 8 132 131 102 57 g 34 35 7 6 3 3 16 7 6 21 21 t 30 36 5 3 4 5 13 2 6 11 32

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score= 0.6578; -mkCCCAGChy ; cor=; Ncor= a 0 35 32 2 3 0 121 1 0 34 29 c 0 42 23 128 126 119 7 4 130 35 39 g 0 26 37 0 3 5 4 125 0 26 27 t 0 29 40 2 0 8 0 2 2 37 37

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.489143; cyCsCCGCCGC ; cor=; Ncor= a 23 19 13 14 3 4 15 3 4 6 2 c 55 52 84 68 110 108 12 113 99 11 116 g 19 21 19 34 5 7 90 2 18 99 1 t 26 31 7 7 5 4 6 5 2 7 4

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=11; shift=1; ncol=12; -wsCCTCCCAmy ; Alignment reference a 0 47 37 6 6 10 5 7 5 119 48 41 c 0 39 43 162 158 0 160 158 158 14 50 56 g 0 31 50 1 4 6 0 3 4 7 41 31 t 0 54 41 2 3 155 6 3 4 31 32 43

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wsCCTCCCAmy ; cor=; Ncor= a 0 47 37 6 6 10 5 7 5 119 48 41 c 0 39 43 162 158 0 160 158 158 14 50 56 g 0 31 50 1 4 6 0 3 4 7 41 31 t 0 54 41 2 3 155 6 3 4 31 32 43

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.878797; cwGCCTCCCArv ; cor=; Ncor= a 21 31 8 5 2 3 3 3 1 83 34 32 c 45 25 10 93 101 2 101 103 101 7 24 32 g 22 20 83 6 4 2 2 1 5 7 27 27 t 20 32 7 4 1 101 2 1 1 11 23 17

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=17; shift=3; ncol=20; ---rmmGCsGCGGCGGsGrg ; Alignment reference a 0 0 0 48 46 52 6 2 5 4 7 2 5 6 4 5 7 7 31 26 c 0 0 0 29 48 40 10 111 81 1 99 18 2 90 7 5 34 19 21 19 g 0 0 0 42 21 26 103 9 33 116 11 99 113 12 108 110 68 84 52 55 t 0 0 0 4 8 5 4 1 4 2 6 4 3 15 4 3 14 13 19 23

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---rmmGCsGCGGCGGsGrg ; cor=; Ncor= a 0 0 0 48 46 52 6 2 5 4 7 2 5 6 4 5 7 7 31 26 c 0 0 0 29 48 40 10 111 81 1 99 18 2 90 7 5 34 19 21 19 g 0 0 0 42 21 26 103 9 33 116 11 99 113 12 108 110 68 84 52 55 t 0 0 0 4 8 5 4 1 4 2 6 4 3 15 4 3 14 13 19 23

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.787097; cmmsCCGCsGCSGCGGskkk ; cor=; Ncor= a 22 33 25 16 11 12 8 2 2 4 1 1 2 2 3 4 1 2 10 10 c 40 35 54 41 69 66 7 83 61 2 83 26 5 74 8 7 32 10 14 18 g 19 13 10 34 7 10 74 5 27 84 2 63 82 9 68 69 42 53 35 40 t 10 10 2 0 4 3 2 1 1 1 5 1 2 6 12 11 16 26 32 23

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=3/5; ncol2=18; w=-2; offset=-2; strand=D; shift=1; score=0.782542; -mmsCCGCSGCSGCGGskk- ; cor=; Ncor= a 0 37 37 22 20 18 5 2 2 6 4 0 3 1 3 4 3 5 15 0 c 0 34 40 40 69 69 4 87 71 1 88 25 6 88 8 4 32 15 12 0 g 0 13 16 33 6 8 88 6 25 90 1 71 87 4 72 74 44 43 35 0 t 0 14 5 3 3 3 1 3 0 1 5 2 2 5 15 16 19 35 36 0

oligos_7nt_mkv2_m3_rc_shift8 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=4/5; ncol2=12; w=0; offset=5; strand=R; shift=8; score=0.498561; --------sgGGGTGGGGgg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 28 32 11 6 2 13 5 4 3 5 36 30 c 0 0 0 0 0 0 0 0 46 21 21 6 7 16 3 3 6 7 35 34 g 0 0 0 0 0 0 0 0 52 57 102 131 132 8 133 133 127 133 43 55 t 0 0 0 0 0 0 0 0 19 35 11 2 4 108 4 5 9 0 31 26

oligos_6nt_mkv2_m4_rc_shift9 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=5/5; ncol2=11; w=0; offset=6; strand=R; shift=9; score=0.489143; ---------gsGGTGGGggg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 31 29 2 0 2 3 1 2 21 31 29 c 0 0 0 0 0 0 0 0 0 29 43 8 3 17 6 3 10 17 32 33 g 0 0 0 0 0 0 0 0 0 57 38 136 142 1 132 140 124 95 58 48 t 0 0 0 0 0 0 0 0 0 29 36 0 1 126 5 2 10 13 25 36

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=10; shift=1; ncol=11; -mkCCCAGChy ; Alignment reference a 0 35 32 2 3 0 121 1 0 34 29 c 0 42 23 128 126 119 7 4 130 35 39 g 0 26 37 0 3 5 4 125 0 26 27 t 0 29 40 2 0 8 0 2 2 37 37

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -mkCCCAGChy ; cor=; Ncor= a 0 35 32 2 3 0 121 1 0 34 29 c 0 42 23 128 126 119 7 4 130 35 39 g 0 26 37 0 3 5 4 125 0 26 27 t 0 29 40 2 0 8 0 2 2 37 37

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score= 0.6578; cccCCCACCsc ; cor=; Ncor= a 36 25 13 10 2 5 126 1 0 36 29 c 48 58 95 124 140 132 1 142 136 38 57 g 33 32 17 10 3 6 17 3 8 43 29 t 29 31 21 2 1 3 2 0 2 29 31

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 4 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; ccCCCCACCCcs ; Alignment reference a 26 31 0 9 5 4 108 4 2 11 35 19 c 55 43 133 127 133 133 8 132 131 102 57 52 g 34 35 7 6 3 3 16 7 6 21 21 46 t 30 36 5 3 4 5 13 2 6 11 32 28

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ccCCCCACCCcs ; cor=; Ncor= a 26 31 0 9 5 4 108 4 2 11 35 19 c 55 43 133 127 133 133 8 132 131 102 57 52 g 34 35 7 6 3 3 16 7 6 21 21 46 t 30 36 5 3 4 5 13 2 6 11 32 28

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.869008; cccCCCACCsc- ; cor=; Ncor= a 36 25 13 10 2 5 126 1 0 36 29 0 c 48 58 95 124 140 132 1 142 136 38 57 0 g 33 32 17 10 3 6 17 3 8 43 29 0 t 29 31 21 2 1 3 2 0 2 29 31 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=3/3; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.498561; cyCsCCGCCGCs ; cor=; Ncor= a 23 19 13 14 3 4 15 3 4 6 2 4 c 55 52 84 68 110 108 12 113 99 11 116 33 g 19 21 19 34 5 7 90 2 18 99 1 81 t 26 31 7 7 5 4 6 5 2 7 4 5

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 4 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=20; shift=0; ncol=20; cmmsCCGCsGCSGCGGskkk ; Alignment reference a 22 33 25 16 11 12 8 2 2 4 1 1 2 2 3 4 1 2 10 10 c 40 35 54 41 69 66 7 83 61 2 83 26 5 74 8 7 32 10 14 18 g 19 13 10 34 7 10 74 5 27 84 2 63 82 9 68 69 42 53 35 40 t 10 10 2 0 4 3 2 1 1 1 5 1 2 6 12 11 16 26 32 23

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; cmmsCCGCsGCSGCGGskkk ; cor=; Ncor= a 22 33 25 16 11 12 8 2 2 4 1 1 2 2 3 4 1 2 10 10 c 40 35 54 41 69 66 7 83 61 2 83 26 5 74 8 7 32 10 14 18 g 19 13 10 34 7 10 74 5 27 84 2 63 82 9 68 69 42 53 35 40 t 10 10 2 0 4 3 2 1 1 1 5 1 2 6 12 11 16 26 32 23

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=18; w=0; offset=1; strand=D; shift=1; score=0.88915; -mmsCCGCSGCSGCGGskk- ; cor=; Ncor= a 0 37 37 22 20 18 5 2 2 6 4 0 3 1 3 4 3 5 15 0 c 0 34 40 40 69 69 4 87 71 1 88 25 6 88 8 4 32 15 12 0 g 0 13 16 33 6 8 88 6 25 90 1 71 87 4 72 74 44 43 35 0 t 0 14 5 3 3 3 1 3 0 1 5 2 2 5 15 16 19 35 36 0

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/3; ncol2=17; w=0; offset=3; strand=D; shift=3; score=0.787097; ---rmmGCsGCGGCGGsGrg ; cor=; Ncor= a 0 0 0 48 46 52 6 2 5 4 7 2 5 6 4 5 7 7 31 26 c 0 0 0 29 48 40 10 111 81 1 99 18 2 90 7 5 34 19 21 19 g 0 0 0 42 21 26 103 9 33 116 11 99 113 12 108 110 68 84 52 55 t 0 0 0 4 8 5 4 1 4 2 6 4 3 15 4 3 14 13 19 23

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 4 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=18; shift=1; ncol=19; -mmsCCGCSGCSGCGGskk ; Alignment reference a 0 37 37 22 20 18 5 2 2 6 4 0 3 1 3 4 3 5 15 c 0 34 40 40 69 69 4 87 71 1 88 25 6 88 8 4 32 15 12 g 0 13 16 33 6 8 88 6 25 90 1 71 87 4 72 74 44 43 35 t 0 14 5 3 3 3 1 3 0 1 5 2 2 5 15 16 19 35 36

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=1; score= 1; -mmsCCGCSGCSGCGGskk ; cor=; Ncor= a 0 37 37 22 20 18 5 2 2 6 4 0 3 1 3 4 3 5 15 c 0 34 40 40 69 69 4 87 71 1 88 25 6 88 8 4 32 15 12 g 0 13 16 33 6 8 88 6 25 90 1 71 87 4 72 74 44 43 35 t 0 14 5 3 3 3 1 3 0 1 5 2 2 5 15 16 19 35 36

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/3; ncol2=20; w=-1; offset=-1; strand=D; shift=0; score=0.88915; cmmsCCGCsGCSGCGGskk ; cor=; Ncor= a 22 33 25 16 11 12 8 2 2 4 1 1 2 2 3 4 1 2 10 c 40 35 54 41 69 66 7 83 61 2 83 26 5 74 8 7 32 10 14 g 19 13 10 34 7 10 74 5 27 84 2 63 82 9 68 69 42 53 35 t 10 10 2 0 4 3 2 1 1 1 5 1 2 6 12 11 16 26 32

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/3; ncol2=17; w=0; offset=2; strand=D; shift=3; score=0.782542; ---rmmGCsGCGGCGGsGr ; cor=; Ncor= a 0 0 0 48 46 52 6 2 5 4 7 2 5 6 4 5 7 7 31 c 0 0 0 29 48 40 10 111 81 1 99 18 2 90 7 5 34 19 21 g 0 0 0 42 21 26 103 9 33 116 11 99 113 12 108 110 68 84 52 t 0 0 0 4 8 5 4 1 4 2 6 4 3 15 4 3 14 13 19

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; cwGCCTCCCArv ; Alignment reference a 21 31 8 5 2 3 3 3 1 83 34 32 c 45 25 10 93 101 2 101 103 101 7 24 32 g 22 20 83 6 4 2 2 1 5 7 27 27 t 20 32 7 4 1 101 2 1 1 11 23 17

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; cwGCCTCCCArv ; cor=; Ncor= a 21 31 8 5 2 3 3 3 1 83 34 32 c 45 25 10 93 101 2 101 103 101 7 24 32 g 22 20 83 6 4 2 2 1 5 7 27 27 t 20 32 7 4 1 101 2 1 1 11 23 17

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.878797; -wsCCTCCCAmy ; cor=; Ncor= a 0 47 37 6 6 10 5 7 5 119 48 41 c 0 39 43 162 158 0 160 158 158 14 50 56 g 0 31 50 1 4 6 0 3 4 7 41 31 t 0 54 41 2 3 155 6 3 4 31 32 43

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=13; shift=0; ncol=13; mrdTCACTGCAvy ; Alignment reference a 37 29 28 6 1 99 5 2 2 3 90 29 23 c 27 26 23 12 100 2 97 1 3 94 9 30 29 g 20 31 27 8 3 2 3 1 98 6 3 27 18 t 24 22 30 82 4 5 3 104 5 5 6 22 38

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; mrdTCACTGCAvy ; cor=; Ncor= a 37 29 28 6 1 99 5 2 2 3 90 29 23 c 27 26 23 12 100 2 97 1 3 94 9 30 29 g 20 31 27 8 3 2 3 1 98 6 3 27 18 t 24 22 30 82 4 5 3 104 5 5 6 22 38

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=11; shift=0; ncol=11; cccCCCACCsc ; Alignment reference a 36 25 13 10 2 5 126 1 0 36 29 c 48 58 95 124 140 132 1 142 136 38 57 g 33 32 17 10 3 6 17 3 8 43 29 t 29 31 21 2 1 3 2 0 2 29 31
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; cccCCCACCsc ; cor=; Ncor= a 36 25 13 10 2 5 126 1 0 36 29 c 48 58 95 124 140 132 1 142 136 38 57 g 33 32 17 10 3 6 17 3 8 43 29 t 29 31 21 2 1 3 2 0 2 29 31
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.869008; ccCCCCACCCc ; cor=; Ncor= a 26 31 0 9 5 4 108 4 2 11 35 c 55 43 133 127 133 133 8 132 131 102 57 g 34 35 7 6 3 3 16 7 6 21 21 t 30 36 5 3 4 5 13 2 6 11 32
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score= 0.6578; -mkCCCAGChy ; cor=; Ncor= a 0 35 32 2 3 0 121 1 0 34 29 c 0 42 23 128 126 119 7 4 130 35 39 g 0 26 37 0 3 5 4 125 0 26 27 t 0 29 40 2 0 8 0 2 2 37 37
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.489143; cyCsCCGCCGC ; cor=; Ncor= a 23 19 13 14 3 4 15 3 4 6 2 c 55 52 84 68 110 108 12 113 99 11 116 g 19 21 19 34 5 7 90 2 18 99 1 t 26 31 7 7 5 4 6 5 2 7 4

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=17; shift=3; ncol=20; ---rmmGCsGCGGCGGsGrg ; Alignment reference a 0 0 0 48 46 52 6 2 5 4 7 2 5 6 4 5 7 7 31 26 c 0 0 0 29 48 40 10 111 81 1 99 18 2 90 7 5 34 19 21 19 g 0 0 0 42 21 26 103 9 33 116 11 99 113 12 108 110 68 84 52 55 t 0 0 0 4 8 5 4 1 4 2 6 4 3 15 4 3 14 13 19 23
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---rmmGCsGCGGCGGsGrg ; cor=; Ncor= a 0 0 0 48 46 52 6 2 5 4 7 2 5 6 4 5 7 7 31 26 c 0 0 0 29 48 40 10 111 81 1 99 18 2 90 7 5 34 19 21 19 g 0 0 0 42 21 26 103 9 33 116 11 99 113 12 108 110 68 84 52 55 t 0 0 0 4 8 5 4 1 4 2 6 4 3 15 4 3 14 13 19 23
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.787097; cmmsCCGCsGCSGCGGskkk ; cor=; Ncor= a 22 33 25 16 11 12 8 2 2 4 1 1 2 2 3 4 1 2 10 10 c 40 35 54 41 69 66 7 83 61 2 83 26 5 74 8 7 32 10 14 18 g 19 13 10 34 7 10 74 5 27 84 2 63 82 9 68 69 42 53 35 40 t 10 10 2 0 4 3 2 1 1 1 5 1 2 6 12 11 16 26 32 23
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=3/5; ncol2=18; w=-2; offset=-2; strand=D; shift=1; score=0.782542; -mmsCCGCSGCSGCGGskk- ; cor=; Ncor= a 0 37 37 22 20 18 5 2 2 6 4 0 3 1 3 4 3 5 15 0 c 0 34 40 40 69 69 4 87 71 1 88 25 6 88 8 4 32 15 12 0 g 0 13 16 33 6 8 88 6 25 90 1 71 87 4 72 74 44 43 35 0 t 0 14 5 3 3 3 1 3 0 1 5 2 2 5 15 16 19 35 36 0
oligos_7nt_mkv2_m3_rc_shift8 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc; m=4/5; ncol2=12; w=0; offset=5; strand=R; shift=8; score=0.498561; --------sgGGGTGGGGgg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 28 32 11 6 2 13 5 4 3 5 36 30 c 0 0 0 0 0 0 0 0 46 21 21 6 7 16 3 3 6 7 35 34 g 0 0 0 0 0 0 0 0 52 57 102 131 132 8 133 133 127 133 43 55 t 0 0 0 0 0 0 0 0 19 35 11 2 4 108 4 5 9 0 31 26
oligos_6nt_mkv2_m4_rc_shift9 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=5/5; ncol2=11; w=0; offset=6; strand=R; shift=9; score=0.489143; ---------gsGGTGGGggg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 31 29 2 0 2 3 1 2 21 31 29 c 0 0 0 0 0 0 0 0 0 29 43 8 3 17 6 3 10 17 32 33 g 0 0 0 0 0 0 0 0 0 57 38 136 142 1 132 140 124 95 58 48 t 0 0 0 0 0 0 0 0 0 29 36 0 1 126 5 2 10 13 25 36

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; ccCCCCACCCcs ; Alignment reference a 26 31 0 9 5 4 108 4 2 11 35 19 c 55 43 133 127 133 133 8 132 131 102 57 52 g 34 35 7 6 3 3 16 7 6 21 21 46 t 30 36 5 3 4 5 13 2 6 11 32 28
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ccCCCCACCCcs ; cor=; Ncor= a 26 31 0 9 5 4 108 4 2 11 35 19 c 55 43 133 127 133 133 8 132 131 102 57 52 g 34 35 7 6 3 3 16 7 6 21 21 46 t 30 36 5 3 4 5 13 2 6 11 32 28
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.869008; cccCCCACCsc- ; cor=; Ncor= a 36 25 13 10 2 5 126 1 0 36 29 0 c 48 58 95 124 140 132 1 142 136 38 57 0 g 33 32 17 10 3 6 17 3 8 43 29 0 t 29 31 21 2 1 3 2 0 2 29 31 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=3/3; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.498561; cyCsCCGCCGCs ; cor=; Ncor= a 23 19 13 14 3 4 15 3 4 6 2 4 c 55 52 84 68 110 108 12 113 99 11 116 33 g 19 21 19 34 5 7 90 2 18 99 1 81 t 26 31 7 7 5 4 6 5 2 7 4 5

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=20; shift=0; ncol=20; cmmsCCGCsGCSGCGGskkk ; Alignment reference a 22 33 25 16 11 12 8 2 2 4 1 1 2 2 3 4 1 2 10 10 c 40 35 54 41 69 66 7 83 61 2 83 26 5 74 8 7 32 10 14 18 g 19 13 10 34 7 10 74 5 27 84 2 63 82 9 68 69 42 53 35 40 t 10 10 2 0 4 3 2 1 1 1 5 1 2 6 12 11 16 26 32 23
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; cmmsCCGCsGCSGCGGskkk ; cor=; Ncor= a 22 33 25 16 11 12 8 2 2 4 1 1 2 2 3 4 1 2 10 10 c 40 35 54 41 69 66 7 83 61 2 83 26 5 74 8 7 32 10 14 18 g 19 13 10 34 7 10 74 5 27 84 2 63 82 9 68 69 42 53 35 40 t 10 10 2 0 4 3 2 1 1 1 5 1 2 6 12 11 16 26 32 23
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=18; w=0; offset=1; strand=D; shift=1; score=0.88915; -mmsCCGCSGCSGCGGskk- ; cor=; Ncor= a 0 37 37 22 20 18 5 2 2 6 4 0 3 1 3 4 3 5 15 0 c 0 34 40 40 69 69 4 87 71 1 88 25 6 88 8 4 32 15 12 0 g 0 13 16 33 6 8 88 6 25 90 1 71 87 4 72 74 44 43 35 0 t 0 14 5 3 3 3 1 3 0 1 5 2 2 5 15 16 19 35 36 0
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/3; ncol2=17; w=0; offset=3; strand=D; shift=3; score=0.787097; ---rmmGCsGCGGCGGsGrg ; cor=; Ncor= a 0 0 0 48 46 52 6 2 5 4 7 2 5 6 4 5 7 7 31 26 c 0 0 0 29 48 40 10 111 81 1 99 18 2 90 7 5 34 19 21 19 g 0 0 0 42 21 26 103 9 33 116 11 99 113 12 108 110 68 84 52 55 t 0 0 0 4 8 5 4 1 4 2 6 4 3 15 4 3 14 13 19 23

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=18; shift=1; ncol=19; -mmsCCGCSGCSGCGGskk ; Alignment reference a 0 37 37 22 20 18 5 2 2 6 4 0 3 1 3 4 3 5 15 c 0 34 40 40 69 69 4 87 71 1 88 25 6 88 8 4 32 15 12 g 0 13 16 33 6 8 88 6 25 90 1 71 87 4 72 74 44 43 35 t 0 14 5 3 3 3 1 3 0 1 5 2 2 5 15 16 19 35 36
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=1; score= 1; -mmsCCGCSGCSGCGGskk ; cor=; Ncor= a 0 37 37 22 20 18 5 2 2 6 4 0 3 1 3 4 3 5 15 c 0 34 40 40 69 69 4 87 71 1 88 25 6 88 8 4 32 15 12 g 0 13 16 33 6 8 88 6 25 90 1 71 87 4 72 74 44 43 35 t 0 14 5 3 3 3 1 3 0 1 5 2 2 5 15 16 19 35 36
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/3; ncol2=20; w=-1; offset=-1; strand=D; shift=0; score=0.88915; cmmsCCGCsGCSGCGGskk ; cor=; Ncor= a 22 33 25 16 11 12 8 2 2 4 1 1 2 2 3 4 1 2 10 c 40 35 54 41 69 66 7 83 61 2 83 26 5 74 8 7 32 10 14 g 19 13 10 34 7 10 74 5 27 84 2 63 82 9 68 69 42 53 35 t 10 10 2 0 4 3 2 1 1 1 5 1 2 6 12 11 16 26 32
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/3; ncol2=17; w=0; offset=2; strand=D; shift=3; score=0.782542; ---rmmGCsGCGGCGGsGr ; cor=; Ncor= a 0 0 0 48 46 52 6 2 5 4 7 2 5 6 4 5 7 7 31 c 0 0 0 29 48 40 10 111 81 1 99 18 2 90 7 5 34 19 21 g 0 0 0 42 21 26 103 9 33 116 11 99 113 12 108 110 68 84 52 t 0 0 0 4 8 5 4 1 4 2 6 4 3 15 4 3 14 13 19