One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.175823_2025-05-16.175823_YJjJog/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.2025-05-16.175823_2025-05-16.175823_YJjJog/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 3 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=11; shift=0; ncol=11; csgCCTCCCcs ; Alignment reference a 29 27 13 2 2 3 2 5 1 40 39 c 60 53 34 160 155 1 160 155 161 59 51 g 37 44 85 1 4 6 1 5 2 25 50 t 39 41 33 2 4 155 2 0 1 41 25

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; csgCCTCCCcs ; cor=; Ncor= a 29 27 13 2 2 3 2 5 1 40 39 c 60 53 34 160 155 1 160 155 161 59 51 g 37 44 85 1 4 6 1 5 2 25 50 t 39 41 33 2 4 155 2 0 1 41 25

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.876049; syGCCTCCCCm ; cor=; Ncor= a 21 28 4 6 7 7 0 5 3 20 38 c 61 38 10 124 124 2 132 124 124 100 51 g 35 34 112 4 5 7 2 6 7 10 25 t 21 38 12 4 2 122 4 3 4 8 24

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; sscCGCCGCGss ; Alignment reference a 17 9 16 4 11 4 5 6 4 5 17 11 c 49 37 60 97 8 97 88 3 101 14 37 49 g 34 56 20 9 91 8 16 100 6 87 46 40 t 14 12 18 4 4 5 5 5 3 8 14 14

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; sscCGCCGCGss ; cor=; Ncor= a 17 9 16 4 11 4 5 6 4 5 17 11 c 49 37 60 97 8 97 88 3 101 14 37 49 g 34 56 20 9 91 8 16 100 6 87 46 40 t 14 12 18 4 4 5 5 5 3 8 14 14

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---raATGAATGah ; Alignment reference a 0 0 0 33 41 100 2 2 94 100 0 10 41 31 c 0 0 0 17 16 1 1 5 4 5 1 10 19 29 g 0 0 0 35 25 3 1 99 8 3 6 79 27 20 t 0 0 0 24 27 5 105 3 3 1 102 10 22 29

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---raATGAATGah ; cor=; Ncor= a 0 0 0 33 41 100 2 2 94 100 0 10 41 31 c 0 0 0 17 16 1 1 5 4 5 1 10 19 29 g 0 0 0 35 25 3 1 99 8 3 6 79 27 20 t 0 0 0 24 27 5 105 3 3 1 102 10 22 29

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=2/2; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.747309; rwtgAATGAATGra ; cor=; Ncor= a 25 28 13 14 62 68 3 4 68 64 1 4 32 25 c 11 12 6 9 3 3 3 2 3 2 1 1 11 18 g 27 15 15 43 3 4 2 68 4 8 4 70 21 15 t 13 21 42 10 8 1 68 2 1 2 70 1 12 18

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=15; shift=0; ncol=15; aaaAtAAATAAAAwa ; Alignment reference a 53 57 78 93 25 100 105 105 3 101 102 100 82 39 47 c 17 16 9 4 6 5 3 5 12 3 3 5 7 20 22 g 19 19 11 5 11 6 6 2 4 5 7 6 8 23 19 t 28 25 19 15 75 6 3 5 98 8 5 6 20 35 29

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; aaaAtAAATAAAAwa ; cor=; Ncor= a 53 57 78 93 25 100 105 105 3 101 102 100 82 39 47 c 17 16 9 4 6 5 3 5 12 3 3 5 7 20 22 g 19 19 11 5 11 6 6 2 4 5 7 6 8 23 19 t 28 25 19 15 75 6 3 5 98 8 5 6 20 35 29

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=2/3; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.915709; -wwatAAATAAAawa ; cor=; Ncor= a 0 57 58 77 28 111 117 114 4 113 111 100 72 47 61 c 0 15 14 10 4 3 2 3 2 2 2 8 8 19 19 g 0 17 16 11 17 5 4 4 2 3 7 8 18 21 18 t 0 36 37 27 76 6 2 4 117 7 5 9 27 38 27

oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=3/3; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.868301; -wwaaAAATAAAAaa ; cor=; Ncor= a 0 73 78 93 115 161 162 161 22 152 153 158 117 78 81 c 0 29 26 19 9 2 3 2 15 7 7 4 9 27 33 g 0 19 22 24 18 2 4 2 5 6 9 4 21 32 23 t 0 50 45 35 29 6 2 6 129 6 2 5 24 34 34

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=4; ncol=16; ----syGCCTCCCCmv ; Alignment reference a 0 0 0 0 21 28 4 6 7 7 0 5 3 20 38 38 c 0 0 0 0 61 38 10 124 124 2 132 124 124 100 51 40 g 0 0 0 0 35 34 112 4 5 7 2 6 7 10 25 35 t 0 0 0 0 21 38 12 4 2 122 4 3 4 8 24 25

oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----syGCCTCCCCmv ; cor=; Ncor= a 0 0 0 0 21 28 4 6 7 7 0 5 3 20 38 38 c 0 0 0 0 61 38 10 124 124 2 132 124 124 100 51 40 g 0 0 0 0 35 34 112 4 5 7 2 6 7 10 25 35 t 0 0 0 0 21 38 12 4 2 122 4 3 4 8 24 25

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.876049; ----csgCCTCCCcs- ; cor=; Ncor= a 0 0 0 0 29 27 13 2 2 3 2 5 1 40 39 0 c 0 0 0 0 60 53 34 160 155 1 160 155 161 59 51 0 g 0 0 0 0 37 44 85 1 4 6 1 5 2 25 50 0 t 0 0 0 0 39 41 33 2 4 155 2 0 1 41 25 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=3/3; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.415986; vccCCAGCCTsss--- ; cor=; Ncor= a 38 15 18 2 1 106 2 2 5 4 8 25 24 0 0 0 c 34 53 67 109 119 7 4 122 114 4 75 42 41 0 0 0 g 36 27 12 4 3 5 115 1 5 8 32 39 42 0 0 0 t 18 31 29 11 3 8 5 1 2 110 11 20 19 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=13; shift=3; ncol=16; ---sssAGGCTGGggb ; Alignment reference a 0 0 0 19 20 11 110 2 1 5 8 3 11 29 31 18 c 0 0 0 42 39 32 8 5 1 115 5 3 4 12 27 36 g 0 0 0 41 42 75 4 114 122 4 7 119 109 67 53 34 t 0 0 0 24 25 8 4 5 2 2 106 1 2 18 15 38

oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---sssAGGCTGGggb ; cor=; Ncor= a 0 0 0 19 20 11 110 2 1 5 8 3 11 29 31 18 c 0 0 0 42 39 32 8 5 1 115 5 3 4 12 27 36 g 0 0 0 41 42 75 4 114 122 4 7 119 109 67 53 34 t 0 0 0 24 25 8 4 5 2 2 106 1 2 18 15 38

oligos_6nt_mkv2_m5_shift4 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=2/3; ncol2=13; w=0; offset=1; strand=D; shift=4; score=0.799682; ----ssAGGCTGGGcm ; cor=; Ncor= a 0 0 0 0 15 17 76 1 1 2 3 3 1 2 10 25 c 0 0 0 0 33 40 7 7 10 84 3 1 4 6 56 25 g 0 0 0 0 31 25 6 84 79 4 5 87 83 78 16 21 t 0 0 0 0 14 11 4 1 3 3 82 2 5 7 11 22

oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=3/3; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.415986; bkGGGGAGGCrs---- ; cor=; Ncor= a 25 24 8 4 3 4 122 2 4 12 38 21 0 0 0 0 c 35 25 10 7 6 2 7 5 4 112 34 35 0 0 0 0 g 40 51 100 124 124 132 2 124 124 10 38 61 0 0 0 0 t 38 38 20 3 5 0 7 7 6 4 28 21 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=13; shift=1; ncol=14; -ssAGGCTGGGcmg ; Alignment reference a 0 15 17 76 1 1 2 3 3 1 2 10 25 23 c 0 33 40 7 7 10 84 3 1 4 6 56 25 22 g 0 31 25 6 84 79 4 5 87 83 78 16 21 26 t 0 14 11 4 1 3 3 82 2 5 7 11 22 22

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -ssAGGCTGGGcmg ; cor=; Ncor= a 0 15 17 76 1 1 2 3 3 1 2 10 25 23 c 0 33 40 7 7 10 84 3 1 4 6 56 25 22 g 0 31 25 6 84 79 4 5 87 83 78 16 21 26 t 0 14 11 4 1 3 3 82 2 5 7 11 22 22

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=2/2; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.799682; sssAGGCTGGggb- ; cor=; Ncor= a 19 20 11 110 2 1 5 8 3 11 29 31 18 0 c 42 39 32 8 5 1 115 5 3 4 12 27 36 0 g 41 42 75 4 114 122 4 7 119 109 67 53 34 0 t 24 25 8 4 5 2 2 106 1 2 18 15 38 0

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; rwtgAATGAATGra ; Alignment reference a 25 28 13 14 62 68 3 4 68 64 1 4 32 25 c 11 12 6 9 3 3 3 2 3 2 1 1 11 18 g 27 15 15 43 3 4 2 68 4 8 4 70 21 15 t 13 21 42 10 8 1 68 2 1 2 70 1 12 18

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; rwtgAATGAATGra ; cor=; Ncor= a 25 28 13 14 62 68 3 4 68 64 1 4 32 25 c 11 12 6 9 3 3 3 2 3 2 1 1 11 18 g 27 15 15 43 3 4 2 68 4 8 4 70 21 15 t 13 21 42 10 8 1 68 2 1 2 70 1 12 18

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=2/2; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.747309; ---raATGAATGah ; cor=; Ncor= a 0 0 0 33 41 100 2 2 94 100 0 10 41 31 c 0 0 0 17 16 1 1 5 4 5 1 10 19 29 g 0 0 0 35 25 3 1 99 8 3 6 79 27 20 t 0 0 0 24 27 5 105 3 3 1 102 10 22 29

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -wwaaAAATAAAAaa ; Alignment reference a 0 73 78 93 115 161 162 161 22 152 153 158 117 78 81 c 0 29 26 19 9 2 3 2 15 7 7 4 9 27 33 g 0 19 22 24 18 2 4 2 5 6 9 4 21 32 23 t 0 50 45 35 29 6 2 6 129 6 2 5 24 34 34

oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wwaaAAATAAAAaa ; cor=; Ncor= a 0 73 78 93 115 161 162 161 22 152 153 158 117 78 81 c 0 29 26 19 9 2 3 2 15 7 7 4 9 27 33 g 0 19 22 24 18 2 4 2 5 6 9 4 21 32 23 t 0 50 45 35 29 6 2 6 129 6 2 5 24 34 34

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.945098; -wwatAAATAAAawa ; cor=; Ncor= a 0 57 58 77 28 111 117 114 4 113 111 100 72 47 61 c 0 15 14 10 4 3 2 3 2 2 2 8 8 19 19 g 0 17 16 11 17 5 4 4 2 3 7 8 18 21 18 t 0 36 37 27 76 6 2 4 117 7 5 9 27 38 27

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=3/3; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.868301; aaaAtAAATAAAAwa ; cor=; Ncor= a 53 57 78 93 25 100 105 105 3 101 102 100 82 39 47 c 17 16 9 4 6 5 3 5 12 3 3 5 7 20 22 g 19 19 11 5 11 6 6 2 4 5 7 6 8 23 19 t 28 25 19 15 75 6 3 5 98 8 5 6 20 35 29

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift1 ; 4 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=14; shift=1; ncol=15; -wwatAAATAAAawa ; Alignment reference a 0 57 58 77 28 111 117 114 4 113 111 100 72 47 61 c 0 15 14 10 4 3 2 3 2 2 2 8 8 19 19 g 0 17 16 11 17 5 4 4 2 3 7 8 18 21 18 t 0 36 37 27 76 6 2 4 117 7 5 9 27 38 27

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wwatAAATAAAawa ; cor=; Ncor= a 0 57 58 77 28 111 117 114 4 113 111 100 72 47 61 c 0 15 14 10 4 3 2 3 2 2 2 8 8 19 19 g 0 17 16 11 17 5 4 4 2 3 7 8 18 21 18 t 0 36 37 27 76 6 2 4 117 7 5 9 27 38 27

oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.945098; -wwaaAAATAAAAaa ; cor=; Ncor= a 0 73 78 93 115 161 162 161 22 152 153 158 117 78 81 c 0 29 26 19 9 2 3 2 15 7 7 4 9 27 33 g 0 19 22 24 18 2 4 2 5 6 9 4 21 32 23 t 0 50 45 35 29 6 2 6 129 6 2 5 24 34 34

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=3/3; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.915709; aaaAtAAATAAAAwa ; cor=; Ncor= a 53 57 78 93 25 100 105 105 3 101 102 100 82 39 47 c 17 16 9 4 6 5 3 5 12 3 3 5 7 20 22 g 19 19 11 5 11 6 6 2 4 5 7 6 8 23 19 t 28 25 19 15 75 6 3 5 98 8 5 6 20 35 29

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=15; shift=0; ncol=15; aaaAtAAATAAAAwa ; Alignment reference a 53 57 78 93 25 100 105 105 3 101 102 100 82 39 47 c 17 16 9 4 6 5 3 5 12 3 3 5 7 20 22 g 19 19 11 5 11 6 6 2 4 5 7 6 8 23 19 t 28 25 19 15 75 6 3 5 98 8 5 6 20 35 29
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; aaaAtAAATAAAAwa ; cor=; Ncor= a 53 57 78 93 25 100 105 105 3 101 102 100 82 39 47 c 17 16 9 4 6 5 3 5 12 3 3 5 7 20 22 g 19 19 11 5 11 6 6 2 4 5 7 6 8 23 19 t 28 25 19 15 75 6 3 5 98 8 5 6 20 35 29
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=2/3; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.915709; -wwatAAATAAAawa ; cor=; Ncor= a 0 57 58 77 28 111 117 114 4 113 111 100 72 47 61 c 0 15 14 10 4 3 2 3 2 2 2 8 8 19 19 g 0 17 16 11 17 5 4 4 2 3 7 8 18 21 18 t 0 36 37 27 76 6 2 4 117 7 5 9 27 38 27
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=3/3; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.868301; -wwaaAAATAAAAaa ; cor=; Ncor= a 0 73 78 93 115 161 162 161 22 152 153 158 117 78 81 c 0 29 26 19 9 2 3 2 15 7 7 4 9 27 33 g 0 19 22 24 18 2 4 2 5 6 9 4 21 32 23 t 0 50 45 35 29 6 2 6 129 6 2 5 24 34 34

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=4; ncol=16; ----syGCCTCCCCmv ; Alignment reference a 0 0 0 0 21 28 4 6 7 7 0 5 3 20 38 38 c 0 0 0 0 61 38 10 124 124 2 132 124 124 100 51 40 g 0 0 0 0 35 34 112 4 5 7 2 6 7 10 25 35 t 0 0 0 0 21 38 12 4 2 122 4 3 4 8 24 25
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----syGCCTCCCCmv ; cor=; Ncor= a 0 0 0 0 21 28 4 6 7 7 0 5 3 20 38 38 c 0 0 0 0 61 38 10 124 124 2 132 124 124 100 51 40 g 0 0 0 0 35 34 112 4 5 7 2 6 7 10 25 35 t 0 0 0 0 21 38 12 4 2 122 4 3 4 8 24 25
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.876049; ----csgCCTCCCcs- ; cor=; Ncor= a 0 0 0 0 29 27 13 2 2 3 2 5 1 40 39 0 c 0 0 0 0 60 53 34 160 155 1 160 155 161 59 51 0 g 0 0 0 0 37 44 85 1 4 6 1 5 2 25 50 0 t 0 0 0 0 39 41 33 2 4 155 2 0 1 41 25 0
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=3/3; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.415986; vccCCAGCCTsss--- ; cor=; Ncor= a 38 15 18 2 1 106 2 2 5 4 8 25 24 0 0 0 c 34 53 67 109 119 7 4 122 114 4 75 42 41 0 0 0 g 36 27 12 4 3 5 115 1 5 8 32 39 42 0 0 0 t 18 31 29 11 3 8 5 1 2 110 11 20 19 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=13; shift=3; ncol=16; ---sssAGGCTGGggb ; Alignment reference a 0 0 0 19 20 11 110 2 1 5 8 3 11 29 31 18 c 0 0 0 42 39 32 8 5 1 115 5 3 4 12 27 36 g 0 0 0 41 42 75 4 114 122 4 7 119 109 67 53 34 t 0 0 0 24 25 8 4 5 2 2 106 1 2 18 15 38
oligos_7nt_mkv2_m3_shift3 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---sssAGGCTGGggb ; cor=; Ncor= a 0 0 0 19 20 11 110 2 1 5 8 3 11 29 31 18 c 0 0 0 42 39 32 8 5 1 115 5 3 4 12 27 36 g 0 0 0 41 42 75 4 114 122 4 7 119 109 67 53 34 t 0 0 0 24 25 8 4 5 2 2 106 1 2 18 15 38
oligos_6nt_mkv2_m5_shift4 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=2/3; ncol2=13; w=0; offset=1; strand=D; shift=4; score=0.799682; ----ssAGGCTGGGcm ; cor=; Ncor= a 0 0 0 0 15 17 76 1 1 2 3 3 1 2 10 25 c 0 0 0 0 33 40 7 7 10 84 3 1 4 6 56 25 g 0 0 0 0 31 25 6 84 79 4 5 87 83 78 16 21 t 0 0 0 0 14 11 4 1 3 3 82 2 5 7 11 22
oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=3/3; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.415986; bkGGGGAGGCrs---- ; cor=; Ncor= a 25 24 8 4 3 4 122 2 4 12 38 21 0 0 0 0 c 35 25 10 7 6 2 7 5 4 112 34 35 0 0 0 0 g 40 51 100 124 124 132 2 124 124 10 38 61 0 0 0 0 t 38 38 20 3 5 0 7 7 6 4 28 21 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -wwaaAAATAAAAaa ; Alignment reference a 0 73 78 93 115 161 162 161 22 152 153 158 117 78 81 c 0 29 26 19 9 2 3 2 15 7 7 4 9 27 33 g 0 19 22 24 18 2 4 2 5 6 9 4 21 32 23 t 0 50 45 35 29 6 2 6 129 6 2 5 24 34 34
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wwaaAAATAAAAaa ; cor=; Ncor= a 0 73 78 93 115 161 162 161 22 152 153 158 117 78 81 c 0 29 26 19 9 2 3 2 15 7 7 4 9 27 33 g 0 19 22 24 18 2 4 2 5 6 9 4 21 32 23 t 0 50 45 35 29 6 2 6 129 6 2 5 24 34 34
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.945098; -wwatAAATAAAawa ; cor=; Ncor= a 0 57 58 77 28 111 117 114 4 113 111 100 72 47 61 c 0 15 14 10 4 3 2 3 2 2 2 8 8 19 19 g 0 17 16 11 17 5 4 4 2 3 7 8 18 21 18 t 0 36 37 27 76 6 2 4 117 7 5 9 27 38 27
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=3/3; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.868301; aaaAtAAATAAAAwa ; cor=; Ncor= a 53 57 78 93 25 100 105 105 3 101 102 100 82 39 47 c 17 16 9 4 6 5 3 5 12 3 3 5 7 20 22 g 19 19 11 5 11 6 6 2 4 5 7 6 8 23 19 t 28 25 19 15 75 6 3 5 98 8 5 6 20 35 29

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=14; shift=1; ncol=15; -wwatAAATAAAawa ; Alignment reference a 0 57 58 77 28 111 117 114 4 113 111 100 72 47 61 c 0 15 14 10 4 3 2 3 2 2 2 8 8 19 19 g 0 17 16 11 17 5 4 4 2 3 7 8 18 21 18 t 0 36 37 27 76 6 2 4 117 7 5 9 27 38 27
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wwatAAATAAAawa ; cor=; Ncor= a 0 57 58 77 28 111 117 114 4 113 111 100 72 47 61 c 0 15 14 10 4 3 2 3 2 2 2 8 8 19 19 g 0 17 16 11 17 5 4 4 2 3 7 8 18 21 18 t 0 36 37 27 76 6 2 4 117 7 5 9 27 38 27
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.945098; -wwaaAAATAAAAaa ; cor=; Ncor= a 0 73 78 93 115 161 162 161 22 152 153 158 117 78 81 c 0 29 26 19 9 2 3 2 15 7 7 4 9 27 33 g 0 19 22 24 18 2 4 2 5 6 9 4 21 32 23 t 0 50 45 35 29 6 2 6 129 6 2 5 24 34 34
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=3/3; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.915709; aaaAtAAATAAAAwa ; cor=; Ncor= a 53 57 78 93 25 100 105 105 3 101 102 100 82 39 47 c 17 16 9 4 6 5 3 5 12 3 3 5 7 20 22 g 19 19 11 5 11 6 6 2 4 5 7 6 8 23 19 t 28 25 19 15 75 6 3 5 98 8 5 6 20 35 29