One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/01/04/peak-motifs.2025-01-04.134936_2025-01-04.134936_03J25g/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/2025/01/04/peak-motifs.2025-01-04.134936_2025-01-04.134936_03J25g/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift5 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=24; shift=5; ncol=29; -----skgGrCATGyCYrGRCATGyCysg ; Alignment reference a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34

oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.989085; -----sbrGrCATGYCyrGrCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30

oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.987844; -----sbrGrCATGYCyrGRCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27

oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=4/10; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.980473; -----bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=5/10; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.899211; ----yssrGRCATGYCYrGrCATGyCyv- ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 2 6 20 45 0 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 49 137 82 47 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 10 5 11 49 0 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4 105 18 53 25 0

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=6/10; ncol2=19; w=0; offset=0; strand=D; shift=5; score=0.725395; -----csrGACATGCCCrGrcawG----- ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 0 0 0 0 0 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 0 0 0 0 0 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 0 0 0 0 0 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12 0 0 0 0 0

oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=7/10; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.664924; ------srrACATGCCCAGrcawg----- ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 0 0 0 0 0 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 0 0 0 0 0 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 0 0 0 0 0 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15 0 0 0 0 0

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=8/10; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.598495; cwtgyCtGGRCATGYCCaGrcawg----- ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 0 0 0 0 0 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 0 0 0 0 0 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 0 0 0 0 0 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9 0 0 0 0 0

oligos_6nt_mkv2_m2_rc_shift15 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=9/10; ncol2=14; w=0; offset=10; strand=R; shift=15; score=0.53467; ---------------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30

oligos_7nt_mkv2_m3_shift15 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=10/10; ncol2=14; w=0; offset=10; strand=D; shift=15; score=0.522377; ---------------cygGRCATGYCcrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift5 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=24; shift=5; ncol=29; -----bbrGRCATGYCYrGrCATGyCyrr ; Alignment reference a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19

oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19

oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.995969; -----sbrGrCATGYCyrGRCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27

oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.995775; -----sbrGrCATGYCyrGrCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=4/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.980473; -----skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=5/11; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.917401; ----yssrGRCATGYCYrGrCATGyCyv- ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 2 6 20 45 0 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 49 137 82 47 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 10 5 11 49 0 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4 105 18 53 25 0

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=6/11; ncol2=19; w=0; offset=0; strand=D; shift=5; score=0.754748; -----csrGACATGCCCrGrcawG----- ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 0 0 0 0 0 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 0 0 0 0 0 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 0 0 0 0 0 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12 0 0 0 0 0

oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=7/11; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.704945; ------srrACATGCCCAGrcawg----- ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 0 0 0 0 0 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 0 0 0 0 0 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 0 0 0 0 0 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15 0 0 0 0 0

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=8/11; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.580808; cwtgyCtGGRCATGYCCaGrcawg----- ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 0 0 0 0 0 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 0 0 0 0 0 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 0 0 0 0 0 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9 0 0 0 0 0

oligos_6nt_mkv2_m2_rc_shift15 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=9/11; ncol2=14; w=0; offset=10; strand=R; shift=15; score=0.532537; ---------------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30

oligos_7nt_mkv2_m3_shift15 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=10/11; ncol2=14; w=0; offset=10; strand=D; shift=15; score=0.519435; ---------------cygGRCATGYCcrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_7nt_mkv2_m2 versus positions_6nt_m1; m=11/11; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.401432; --------GrCATGCCyr----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 11 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=24; shift=0; ncol=24; cwtgyCtGGRCATGYCCaGrcawg ; Alignment reference a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; cwtgyCtGGRCATGYCCaGrcawg ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/10; ncol2=19; w=0; offset=5; strand=D; shift=5; score= 0.7282; -----csrGACATGCCCrGrcawG ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12

oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/10; ncol2=18; w=0; offset=6; strand=D; shift=6; score=0.660655; ------srrACATGCCCAGrcawg ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=4/10; ncol2=24; w=0; offset=4; strand=R; shift=4; score=0.628009; ----yssrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=5/10; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.598495; -----skgGrCATGyCYrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1

oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=6/10; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.587354; -----sbrGrCATGYCyrGrCATG ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3

oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.583601; -----sbrGrCATGYCyrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3

oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=8/10; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.580808; -----bbrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3

oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=9/10; ncol2=14; w=0; offset=5; strand=R; shift=5; score=0.509311; -----cyrGRCATGYCyrg----- ; cor=; Ncor= a 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 0 0 0 0 0 c 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 0 0 0 0 0 g 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 0 0 0 0 0 t 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30 0 0 0 0 0

oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=10/10; ncol2=14; w=0; offset=5; strand=R; shift=5; score=0.505167; -----cygGRCATGYCcrg----- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift5 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=14; shift=5; ncol=19; -----cyrGRCATGYCyrg ; Alignment reference a 0 0 0 0 0 30 38 79 14 168 2 231 9 2 0 3 20 65 54 c 0 0 0 0 0 116 103 6 1 0 242 2 4 1 76 228 141 41 45 g 0 0 0 0 0 46 41 141 228 77 1 4 2 241 0 1 5 103 118 t 0 0 0 0 0 54 64 20 3 1 1 9 231 2 170 14 80 37 29

oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/12; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 30 38 79 14 168 2 231 9 2 0 3 20 65 54 c 0 0 0 0 0 116 103 6 1 0 242 2 4 1 76 228 141 41 45 g 0 0 0 0 0 46 41 141 228 77 1 4 2 241 0 1 5 103 118 t 0 0 0 0 0 54 64 20 3 1 1 9 231 2 170 14 80 37 29

oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=2/12; ncol2=14; w=0; offset=0; strand=D; shift=5; score=0.994348; -----cygGRCATGYCcrg ; cor=; Ncor= a 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22

positions_6nt_m2_shift8 (positions_6nt_m2)
; oligos_6nt_mkv2_m2 versus positions_6nt_m2; m=3/12; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.689491; --------GrCATGTCyg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 0 c 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 0 g 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 0 t 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30 0

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=4/12; ncol2=19; w=-5; offset=-5; strand=R; shift=0; score=0.664615; CwtgyCyGGGCATGTCysg ; cor=; Ncor= a 12 100 24 19 24 7 16 35 1 21 0 179 22 0 3 9 28 45 41 c 142 30 19 20 70 143 56 3 2 1 199 6 6 3 39 169 100 50 36 g 19 16 31 131 26 37 4 159 194 177 0 3 6 195 0 2 8 70 101 t 26 53 125 29 79 12 123 2 2 0 0 11 165 1 157 19 63 34 21

positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)
; oligos_6nt_mkv2_m2 versus positions_6nt_m1_rc; m=5/12; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.645045; ------yrGGCATGyC--- ; cor=; Ncor= a 0 0 0 0 0 0 32 74 1 8 1 204 0 1 8 18 0 0 0 c 0 0 0 0 0 0 84 8 4 0 209 1 9 3 59 145 0 0 0 g 0 0 0 0 0 0 17 115 204 202 0 5 0 206 5 17 0 0 0 t 0 0 0 0 0 0 77 13 1 0 0 0 201 0 138 30 0 0 0

oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5_rc; m=6/12; ncol2=18; w=-5; offset=-5; strand=R; shift=0; score=0.578709; cwtgyCTGGGCATGTyys- ; cor=; Ncor= a 15 82 24 19 16 1 19 20 4 14 2 158 21 2 2 13 31 41 0 c 116 27 10 17 55 141 31 1 3 1 169 6 4 2 16 100 62 48 0 g 18 13 24 109 28 22 3 151 161 156 1 2 10 169 1 7 16 63 0 t 24 51 115 28 74 9 120 1 5 2 1 7 138 0 154 53 64 21 0

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=7/12; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.534753; ----yssrGRCATGYCYrG ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1

oligos_7nt_mkv2_m4_rc_shift5 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=8/12; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.53467; -----csrGrCATGYCyRG ; cor=; Ncor= a 0 0 0 0 0 34 32 48 19 118 1 137 9 0 1 5 2 48 15 c 0 0 0 0 0 63 51 5 4 8 170 7 1 0 126 169 67 3 10 g 0 0 0 0 0 44 55 113 156 54 2 3 7 183 0 0 11 130 157 t 0 0 0 0 0 42 45 17 4 3 10 36 166 0 56 9 103 2 1

oligos_6nt_mkv2_m3_rc_shift5 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=9/12; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.53294; -----ybrGrCATGyCyrG ; cor=; Ncor= a 0 0 0 0 0 30 29 55 18 120 3 132 9 2 2 2 5 63 12 c 0 0 0 0 0 63 52 10 6 9 170 8 1 0 123 176 76 2 0 g 0 0 0 0 0 45 56 102 158 54 3 3 7 184 0 0 3 120 174 t 0 0 0 0 0 49 50 20 5 4 11 44 170 1 62 9 103 2 1

oligos_7nt_mkv2_m2_rc_shift5 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=10/12; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.532537; -----yyrGrCATGyCyRG ; cor=; Ncor= a 0 0 0 0 0 19 28 43 18 99 3 119 7 1 1 0 4 45 9 c 0 0 0 0 0 62 46 8 6 10 146 8 2 0 102 153 57 1 0 g 0 0 0 0 0 35 40 99 135 51 3 3 6 161 0 0 3 115 153 t 0 0 0 0 0 47 49 13 4 3 11 33 148 1 60 10 99 2 1

oligos_7nt_mkv2_m1_rc_shift5 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=11/12; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.528289; -----ybrGrCATGYCyrG ; cor=; Ncor= a 0 0 0 0 0 27 26 46 17 106 3 115 8 1 2 1 3 51 6 c 0 0 0 0 0 53 46 7 6 8 148 7 1 0 111 155 65 1 0 g 0 0 0 0 0 37 47 95 138 45 3 3 6 161 0 0 2 110 156 t 0 0 0 0 0 46 44 15 2 4 9 38 148 1 50 7 93 1 1

oligos_6nt_mkv2_m4_rc_shift0 (oligos_6nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=12/12; ncol2=24; w=-5; offset=-5; strand=R; shift=0; score=0.509311; cwtgyCtGGRCATGYCCaG ; cor=; Ncor= a 9 57 14 12 7 11 7 22 6 34 1 112 8 0 2 2 3 82 5 c 85 20 11 18 58 102 27 6 0 1 129 8 3 1 93 122 100 14 13 g 15 14 24 86 21 13 14 100 123 94 1 3 8 129 1 0 6 27 102 t 22 40 82 15 45 5 83 3 2 2 0 8 112 1 35 7 22 8 11

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift12 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift12 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=10; shift=12; ncol=22; ------------GrCATGTCyg ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 c 0 0 0 0 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 g 0 0 0 0 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 t 0 0 0 0 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30

positions_6nt_m2_shift12 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/7; ncol2=10; w=0; offset=0; strand=D; shift=12; score= 1; ------------GrCATGTCyg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 c 0 0 0 0 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 g 0 0 0 0 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 t 0 0 0 0 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30

positions_6nt_m1_shift12 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=2/7; ncol2=10; w=0; offset=0; strand=D; shift=12; score=0.819197; ------------GrCATGCCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 c 0 0 0 0 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 g 0 0 0 0 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 t 0 0 0 0 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32

oligos_6nt_mkv2_m2_shift9 (oligos_6nt_mkv2_m2)
; positions_6nt_m2 versus oligos_6nt_mkv2_m2; m=3/7; ncol2=14; w=-3; offset=-3; strand=D; shift=9; score=0.689491; ---------cyrGRCATGYCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 30 38 79 14 168 2 231 9 2 0 3 20 65 c 0 0 0 0 0 0 0 0 0 116 103 6 1 0 242 2 4 1 76 228 141 41 g 0 0 0 0 0 0 0 0 0 46 41 141 228 77 1 4 2 241 0 1 5 103 t 0 0 0 0 0 0 0 0 0 54 64 20 3 1 1 9 231 2 170 14 80 37

oligos_7nt_mkv2_m3_shift9 (oligos_7nt_mkv2_m3)
; positions_6nt_m2 versus oligos_7nt_mkv2_m3; m=4/7; ncol2=14; w=-3; offset=-3; strand=D; shift=9; score= 0.6836; ---------cygGRCATGYCcr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 c 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 g 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 t 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20

oligos_6nt_mkv2_m5_rc_shift4 (oligos_6nt_mkv2_m5_rc)
; positions_6nt_m2 versus oligos_6nt_mkv2_m5_rc; m=5/7; ncol2=18; w=-8; offset=-8; strand=R; shift=4; score=0.517197; ----cwtgyCTGGGCATGTyys ; cor=; Ncor= a 0 0 0 0 15 82 24 19 16 1 19 20 4 14 2 158 21 2 2 13 31 41 c 0 0 0 0 116 27 10 17 55 141 31 1 3 1 169 6 4 2 16 100 62 48 g 0 0 0 0 18 13 24 109 28 22 3 151 161 156 1 2 10 169 1 7 16 63 t 0 0 0 0 24 51 115 28 74 9 120 1 5 2 1 7 138 0 154 53 64 21

oligos_6nt_mkv2_m1_rc_shift4 (oligos_6nt_mkv2_m1_rc)
; positions_6nt_m2 versus oligos_6nt_mkv2_m1_rc; m=6/7; ncol2=19; w=-8; offset=-8; strand=R; shift=4; score=0.503065; ----CwtgyCyGGGCATGTCys ; cor=; Ncor= a 0 0 0 0 12 100 24 19 24 7 16 35 1 21 0 179 22 0 3 9 28 45 c 0 0 0 0 142 30 19 20 70 143 56 3 2 1 199 6 6 3 39 169 100 50 g 0 0 0 0 19 16 31 131 26 37 4 159 194 177 0 3 6 195 0 2 8 70 t 0 0 0 0 26 53 125 29 79 12 123 2 2 0 0 11 165 1 157 19 63 34

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; positions_6nt_m2 versus oligos_7nt_mkv2_m5; m=7/7; ncol2=24; w=-12; offset=-12; strand=D; shift=0; score=0.402903; brGrCATGyCyRGRCATGYCys ; cor=; Ncor= a 25 53 18 105 4 123 7 1 1 1 6 49 9 50 1 147 34 1 3 8 25 36 c 49 11 5 10 151 5 3 0 105 152 63 1 0 0 163 6 4 3 42 139 64 44 g 47 82 137 49 3 4 7 162 2 0 3 114 156 114 0 1 6 159 3 3 7 68 t 45 20 6 2 8 34 149 3 58 13 94 2 1 2 2 12 122 3 118 16 70 18

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift5 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=24; shift=5; ncol=29; -----sbrGrCATGYCyrGrCATGyCyvr ; Alignment reference a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30

oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----sbrGrCATGYCyrGrCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30

oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.998926; -----sbrGrCATGYCyrGRCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27

oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=3/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.995775; -----bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=4/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.989085; -----skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5_rc; m=5/11; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.915362; ----yssrGRCATGYCYrGrCATGyCyv- ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 2 6 20 45 0 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 49 137 82 47 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 10 5 11 49 0 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4 105 18 53 25 0

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=6/11; ncol2=19; w=0; offset=0; strand=D; shift=5; score=0.746764; -----csrGACATGCCCrGrcawG----- ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 0 0 0 0 0 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 0 0 0 0 0 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 0 0 0 0 0 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12 0 0 0 0 0

oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=7/11; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.690713; ------srrACATGCCCAGrcawg----- ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 0 0 0 0 0 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 0 0 0 0 0 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 0 0 0 0 0 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15 0 0 0 0 0

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=8/11; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.587354; cwtgyCtGGRCATGYCCaGrcawg----- ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 0 0 0 0 0 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 0 0 0 0 0 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 0 0 0 0 0 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9 0 0 0 0 0

oligos_6nt_mkv2_m2_rc_shift15 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=9/11; ncol2=14; w=0; offset=10; strand=R; shift=15; score=0.53294; ---------------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30

oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3_rc; m=10/11; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.524974; -----cygGRCATGYCcrg---------- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0 0 0 0 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_6nt_mkv2_m3 versus positions_6nt_m1; m=11/11; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.401431; --------GrCATGCCyr----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift10 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift10 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=14; shift=10; ncol=24; ----------cygGRCATGYCcrg ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22

oligos_7nt_mkv2_m3_shift10 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/12; ncol2=14; w=0; offset=0; strand=D; shift=10; score= 1; ----------cygGRCATGYCcrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22

oligos_6nt_mkv2_m2_shift10 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=2/12; ncol2=14; w=0; offset=0; strand=D; shift=10; score=0.994348; ----------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 30 38 79 14 168 2 231 9 2 0 3 20 65 54 c 0 0 0 0 0 0 0 0 0 0 116 103 6 1 0 242 2 4 1 76 228 141 41 45 g 0 0 0 0 0 0 0 0 0 0 46 41 141 228 77 1 4 2 241 0 1 5 103 118 t 0 0 0 0 0 0 0 0 0 0 54 64 20 3 1 1 9 231 2 170 14 80 37 29

positions_6nt_m2_shift13 (positions_6nt_m2)
; oligos_7nt_mkv2_m3 versus positions_6nt_m2; m=3/12; ncol2=10; w=0; offset=3; strand=D; shift=13; score= 0.6836; -------------GrCATGTCyg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30 0

oligos_6nt_mkv2_m1_rc_shift5 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=4/12; ncol2=19; w=-5; offset=-5; strand=R; shift=5; score=0.658143; -----CwtgyCyGGGCATGTCysg ; cor=; Ncor= a 0 0 0 0 0 12 100 24 19 24 7 16 35 1 21 0 179 22 0 3 9 28 45 41 c 0 0 0 0 0 142 30 19 20 70 143 56 3 2 1 199 6 6 3 39 169 100 50 36 g 0 0 0 0 0 19 16 31 131 26 37 4 159 194 177 0 3 6 195 0 2 8 70 101 t 0 0 0 0 0 26 53 125 29 79 12 123 2 2 0 0 11 165 1 157 19 63 34 21

positions_6nt_m1_rc_shift11 (positions_6nt_m1_rc)
; oligos_7nt_mkv2_m3 versus positions_6nt_m1_rc; m=5/12; ncol2=10; w=0; offset=1; strand=R; shift=11; score=0.634151; -----------yrGGCATGyC--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 32 74 1 8 1 204 0 1 8 18 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 84 8 4 0 209 1 9 3 59 145 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 17 115 204 202 0 5 0 206 5 17 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 77 13 1 0 0 0 201 0 138 30 0 0 0

oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=6/12; ncol2=18; w=-5; offset=-5; strand=R; shift=5; score=0.574255; -----cwtgyCTGGGCATGTyys- ; cor=; Ncor= a 0 0 0 0 0 15 82 24 19 16 1 19 20 4 14 2 158 21 2 2 13 31 41 0 c 0 0 0 0 0 116 27 10 17 55 141 31 1 3 1 169 6 4 2 16 100 62 48 0 g 0 0 0 0 0 18 13 24 109 28 22 3 151 161 156 1 2 10 169 1 7 16 63 0 t 0 0 0 0 0 24 51 115 28 74 9 120 1 5 2 1 7 138 0 154 53 64 21 0

oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=7/12; ncol2=24; w=-9; offset=-9; strand=D; shift=1; score=0.525781; -brGrCATGyCyRGRCATGYCyss ; cor=; Ncor= a 0 25 53 18 105 4 123 7 1 1 1 6 49 9 50 1 147 34 1 3 8 25 36 41 c 0 49 11 5 10 151 5 3 0 105 152 63 1 0 0 163 6 4 3 42 139 64 44 43 g 0 47 82 137 49 3 4 7 162 2 0 3 114 156 114 0 1 6 159 3 3 7 68 61 t 0 45 20 6 2 8 34 149 3 58 13 94 2 1 2 2 12 122 3 118 16 70 18 21

oligos_6nt_mkv2_m3_rc_shift0 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=8/12; ncol2=24; w=-10; offset=-10; strand=R; shift=0; score=0.524974; ybrGrCATGyCyrGRCATGyCyvs ; cor=; Ncor= a 30 29 55 18 120 3 132 9 2 2 2 5 63 12 55 0 167 41 8 3 8 29 55 45 c 63 52 10 6 9 170 8 1 0 123 176 76 2 0 0 183 7 4 2 58 157 96 53 49 g 45 56 102 158 54 3 3 7 184 0 0 3 120 174 131 0 1 7 175 9 5 8 55 64 t 49 50 20 5 4 11 44 170 1 62 9 103 2 1 1 4 12 135 2 117 17 54 24 29

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=9/12; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.522377; skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=10/12; ncol2=24; w=-10; offset=-10; strand=R; shift=0; score=0.519504; ybrGrCATGYCyrGRCATGyCyvs ; cor=; Ncor= a 27 26 46 17 106 3 115 8 1 2 1 3 51 6 42 0 144 39 7 2 7 26 41 38 c 53 46 7 6 8 148 7 1 0 111 155 65 1 0 0 162 6 3 2 46 136 87 53 45 g 37 47 95 138 45 3 3 6 161 0 0 2 110 156 120 0 1 7 152 8 4 7 48 53 t 46 44 15 2 4 9 38 148 1 50 7 93 1 1 1 1 12 114 2 107 16 43 21 27

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=11/12; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.519435; bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19

oligos_6nt_mkv2_m4_rc_shift5 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=12/12; ncol2=24; w=-5; offset=-5; strand=R; shift=5; score=0.505167; -----cwtgyCtGGRCATGYCCaG ; cor=; Ncor= a 0 0 0 0 0 9 57 14 12 7 11 7 22 6 34 1 112 8 0 2 2 3 82 5 c 0 0 0 0 0 85 20 11 18 58 102 27 6 0 1 129 8 3 1 93 122 100 14 13 g 0 0 0 0 0 15 14 24 86 21 13 14 100 123 94 1 3 8 129 1 0 6 27 102 t 0 0 0 0 0 22 40 82 15 45 5 83 3 2 2 0 8 112 1 35 7 22 8 11

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift5 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=24; shift=5; ncol=29; -----sbrGrCATGYCyrGRCATGyCyvr ; Alignment reference a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27

oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----sbrGrCATGYCyrGRCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27

oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.998926; -----sbrGrCATGYCyrGrCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30

oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.995969; -----bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=4/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.987844; -----skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=5/11; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.914295; ----yssrGRCATGYCYrGrCATGyCyv- ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 2 6 20 45 0 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 49 137 82 47 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 10 5 11 49 0 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4 105 18 53 25 0

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=6/11; ncol2=19; w=0; offset=0; strand=D; shift=5; score=0.74873; -----csrGACATGCCCrGrcawG----- ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 0 0 0 0 0 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 0 0 0 0 0 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 0 0 0 0 0 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12 0 0 0 0 0

oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=7/11; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.694553; ------srrACATGCCCAGrcawg----- ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 0 0 0 0 0 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 0 0 0 0 0 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 0 0 0 0 0 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15 0 0 0 0 0

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=8/11; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.583601; cwtgyCtGGRCATGYCCaGrcawg----- ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 0 0 0 0 0 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 0 0 0 0 0 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 0 0 0 0 0 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9 0 0 0 0 0

oligos_6nt_mkv2_m2_rc_shift15 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=9/11; ncol2=14; w=0; offset=10; strand=R; shift=15; score=0.528289; ---------------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30

oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=10/11; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.519504; -----cygGRCATGYCcrg---------- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0 0 0 0 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_7nt_mkv2_m1 versus positions_6nt_m1; m=11/11; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.401283; --------GrCATGCCyr----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift5 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=19; shift=5; ncol=24; -----csrGACATGCCCrGrcawG ; Alignment reference a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/12; ncol2=19; w=0; offset=0; strand=D; shift=5; score= 1; -----csrGACATGCCCrGrcawG ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12

oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=2/12; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.930576; ------srrACATGCCCAGrcawg ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15

oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/12; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.754748; -----bbrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=4/12; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.751957; ----yssrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4

oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=5/12; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.74873; -----sbrGrCATGYCyrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3

oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=6/12; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.746764; -----sbrGrCATGYCyrGrCATG ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=7/12; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score= 0.7282; cwtgyCtGGRCATGYCCaGrcawg ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=8/12; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.725395; -----skgGrCATGyCYrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1

oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=9/12; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.664615; -----cyrGRCATGYCyrg----- ; cor=; Ncor= a 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 0 0 0 0 0 c 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 0 0 0 0 0 g 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 0 0 0 0 0 t 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30 0 0 0 0 0

oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=10/12; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.658143; -----cygGRCATGYCcrg----- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_6nt_mkv2_m1 versus positions_6nt_m1; m=11/12; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.511487; --------GrCATGCCyr------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0

positions_6nt_m2_rc_shift6 (positions_6nt_m2_rc)
; oligos_6nt_mkv2_m1 versus positions_6nt_m2_rc; m=12/12; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.503065; ------crGACATGyC-------- ; cor=; Ncor= a 0 0 0 0 0 0 30 75 2 179 0 183 1 0 7 13 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 97 4 1 0 194 0 6 0 105 143 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 35 90 191 15 0 11 2 194 4 7 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 32 25 0 0 0 0 185 0 78 31 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift6 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=18; shift=6; ncol=24; ------srrACATGCCCAGrcawg ; Alignment reference a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15

oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/12; ncol2=18; w=0; offset=0; strand=D; shift=6; score= 1; ------srrACATGCCCAGrcawg ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=2/12; ncol2=19; w=-1; offset=-1; strand=D; shift=5; score=0.930576; -----csrGACATGCCCrGrcawG ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12

oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=3/12; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.704945; -----bbrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5_rc; m=4/12; ncol2=24; w=-2; offset=-2; strand=R; shift=4; score=0.700279; ----yssrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4

oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=5/12; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.694553; -----sbrGrCATGYCyrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3

oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=6/12; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.690713; -----sbrGrCATGYCyrGrCATG ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=7/12; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.664924; -----skgGrCATGyCYrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=8/12; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.660655; cwtgyCtGGRCATGYCCaGrcawg ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9

oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=9/12; ncol2=14; w=-1; offset=-1; strand=R; shift=5; score=0.578709; -----cyrGRCATGYCyrg----- ; cor=; Ncor= a 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 0 0 0 0 0 c 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 0 0 0 0 0 g 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 0 0 0 0 0 t 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30 0 0 0 0 0

oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=10/12; ncol2=14; w=-1; offset=-1; strand=R; shift=5; score=0.574255; -----cygGRCATGYCcrg----- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_6nt_mkv2_m5 versus positions_6nt_m1; m=11/12; ncol2=10; w=0; offset=2; strand=D; shift=8; score=0.52709; --------GrCATGCCyr------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0

positions_6nt_m2_rc_shift6 (positions_6nt_m2_rc)
; oligos_6nt_mkv2_m5 versus positions_6nt_m2_rc; m=12/12; ncol2=10; w=0; offset=0; strand=R; shift=6; score=0.517197; ------crGACATGyC-------- ; cor=; Ncor= a 0 0 0 0 0 0 30 75 2 179 0 183 1 0 7 13 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 97 4 1 0 194 0 6 0 105 143 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 35 90 191 15 0 11 2 194 4 7 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 32 25 0 0 0 0 185 0 78 31 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift4 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift4 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=10; shift=4; ncol=14; ----GrCATGCCyr ; Alignment reference a 0 0 0 0 30 138 0 201 0 0 0 1 13 77 c 0 0 0 0 17 5 206 0 5 0 202 204 115 17 g 0 0 0 0 145 59 3 9 1 209 0 4 8 84 t 0 0 0 0 18 8 1 0 204 1 8 1 74 32

positions_6nt_m1_shift4 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/10; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----GrCATGCCyr ; cor=; Ncor= a 0 0 0 0 30 138 0 201 0 0 0 1 13 77 c 0 0 0 0 17 5 206 0 5 0 202 204 115 17 g 0 0 0 0 145 59 3 9 1 209 0 4 8 84 t 0 0 0 0 18 8 1 0 204 1 8 1 74 32

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=2/10; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.819197; ----GrCATGTCyg ; cor=; Ncor= a 0 0 0 0 31 78 0 185 0 0 0 0 25 32 c 0 0 0 0 7 4 194 2 11 0 15 191 90 35 g 0 0 0 0 143 105 0 6 0 194 0 1 4 97 t 0 0 0 0 13 7 0 1 183 0 179 2 75 30

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; positions_6nt_m1 versus oligos_6nt_mkv2_m2_rc; m=3/10; ncol2=14; w=-3; offset=-3; strand=R; shift=1; score=0.645045; -cyrGRCATGYCyr ; cor=; Ncor= a 0 29 37 80 14 170 2 231 9 1 1 3 20 64 c 0 118 103 5 1 0 241 2 4 1 77 228 141 41 g 0 45 41 141 228 76 1 4 2 242 0 1 6 103 t 0 54 65 20 3 0 2 9 231 2 168 14 79 38

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)
; positions_6nt_m1 versus oligos_7nt_mkv2_m3_rc; m=4/10; ncol2=14; w=-3; offset=-3; strand=R; shift=1; score=0.634151; -cygGRCATGYCcr ; cor=; Ncor= a 0 22 20 34 8 104 3 133 5 2 2 3 10 40 c 0 62 56 2 2 1 138 2 3 0 37 131 97 26 g 0 24 26 97 130 37 0 3 2 138 1 2 2 56 t 0 35 41 10 3 1 2 5 133 3 103 7 34 21

oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)
; positions_6nt_m1 versus oligos_6nt_mkv2_m5; m=5/10; ncol2=18; w=-2; offset=-2; strand=D; shift=2; score=0.52709; --srrACATGCCCA ; cor=; Ncor= a 0 0 21 64 53 154 0 138 7 1 2 5 1 120 c 0 0 63 16 7 1 169 10 2 1 156 161 151 3 g 0 0 48 62 100 16 2 4 6 169 1 3 1 31 t 0 0 41 31 13 2 2 21 158 2 14 4 20 19

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; positions_6nt_m1 versus oligos_6nt_mkv2_m1; m=6/10; ncol2=19; w=-3; offset=-3; strand=D; shift=1; score=0.511487; -csrGACATGCCCr ; cor=; Ncor= a 0 21 34 63 19 157 1 165 11 0 0 2 2 123 c 0 101 70 8 2 0 195 6 3 0 177 194 159 4 g 0 36 50 100 169 39 3 6 6 199 1 2 3 56 t 0 41 45 28 9 3 0 22 179 0 21 1 35 16

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; positions_6nt_m1 versus oligos_7nt_mkv2_m2; m=7/10; ncol2=24; w=-3; offset=-3; strand=D; shift=1; score=0.401432; -bbrGRCATGYCYr ; cor=; Ncor= a 0 21 20 61 16 115 2 118 11 2 1 1 2 99 c 0 58 53 8 5 4 156 6 1 0 121 153 115 3 g 0 41 47 67 133 41 2 3 6 161 0 0 1 57 t 0 43 43 27 9 3 3 36 145 0 41 9 45 4

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; positions_6nt_m1 versus oligos_6nt_mkv2_m3; m=8/10; ncol2=24; w=-3; offset=-3; strand=D; shift=1; score=0.401431; -sbrGrCATGYCyr ; cor=; Ncor= a 0 29 24 54 17 117 2 135 12 4 1 1 2 103 c 0 64 55 8 5 9 175 7 1 0 131 174 120 3 g 0 49 53 96 157 58 2 4 7 183 0 0 2 76 t 0 45 55 29 8 3 8 41 167 0 55 12 63 5

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; positions_6nt_m1 versus oligos_7nt_mkv2_m1; m=9/10; ncol2=24; w=-3; offset=-3; strand=D; shift=1; score=0.401283; -sbrGrCATGYCyr ; cor=; Ncor= a 0 27 21 43 16 107 2 114 12 1 1 1 1 93 c 0 53 48 7 4 8 152 7 1 0 120 156 110 2 g 0 45 53 87 136 46 2 3 6 162 0 0 1 65 t 0 38 41 26 7 2 7 39 144 0 42 6 51 3

oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)
; positions_6nt_m1 versus oligos_7nt_mkv2_m5_rc; m=10/10; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.400673; yssrGRCATGYCYr ; cor=; Ncor= a 30 21 18 70 16 118 3 122 12 2 2 1 2 94 c 57 61 68 7 3 3 159 6 1 0 114 156 114 3 g 29 43 44 64 139 42 3 4 6 163 0 0 1 63 t 50 41 36 25 8 3 1 34 147 1 50 9 49 6

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift1 ; 13 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=24; shift=1; ncol=25; -brGrCATGyCyRGRCATGYCyssr ; Alignment reference a 0 25 53 18 105 4 123 7 1 1 1 6 49 9 50 1 147 34 1 3 8 25 36 41 50 c 0 49 11 5 10 151 5 3 0 105 152 63 1 0 0 163 6 4 3 42 139 64 44 43 29 g 0 47 82 137 49 3 4 7 162 2 0 3 114 156 114 0 1 6 159 3 3 7 68 61 57 t 0 45 20 6 2 8 34 149 3 58 13 94 2 1 2 2 12 122 3 118 16 70 18 21 30

oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/12; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -brGrCATGyCyRGRCATGYCyssr ; cor=; Ncor= a 0 25 53 18 105 4 123 7 1 1 1 6 49 9 50 1 147 34 1 3 8 25 36 41 50 c 0 49 11 5 10 151 5 3 0 105 152 63 1 0 0 163 6 4 3 42 139 64 44 43 29 g 0 47 82 137 49 3 4 7 162 2 0 3 114 156 114 0 1 6 159 3 3 7 68 61 57 t 0 45 20 6 2 8 34 149 3 58 13 94 2 1 2 2 12 122 3 118 16 70 18 21 30

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc; m=2/12; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.917401; yyrGrCATGyCyRGRCATGYCyvv- ; cor=; Ncor= a 19 28 43 18 99 3 119 7 1 1 0 4 45 9 41 0 145 36 3 3 9 27 43 43 0 c 62 46 8 6 10 146 8 2 0 102 153 57 1 0 0 161 6 3 2 41 133 67 47 41 0 g 35 40 99 135 51 3 3 6 161 0 0 3 115 153 121 0 1 6 156 4 5 8 53 58 0 t 47 49 13 4 3 11 33 148 1 60 10 99 2 1 1 2 11 118 2 115 16 61 20 21 0

oligos_6nt_mkv2_m3_rc_shift0 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3_rc; m=3/12; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.915362; ybrGrCATGyCyrGRCATGyCyvs- ; cor=; Ncor= a 30 29 55 18 120 3 132 9 2 2 2 5 63 12 55 0 167 41 8 3 8 29 55 45 0 c 63 52 10 6 9 170 8 1 0 123 176 76 2 0 0 183 7 4 2 58 157 96 53 49 0 g 45 56 102 158 54 3 3 7 184 0 0 3 120 174 131 0 1 7 175 9 5 8 55 64 0 t 49 50 20 5 4 11 44 170 1 62 9 103 2 1 1 4 12 135 2 117 17 54 24 29 0

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=4/12; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.914295; ybrGrCATGYCyrGRCATGyCyvs- ; cor=; Ncor= a 27 26 46 17 106 3 115 8 1 2 1 3 51 6 42 0 144 39 7 2 7 26 41 38 0 c 53 46 7 6 8 148 7 1 0 111 155 65 1 0 0 162 6 3 2 46 136 87 53 45 0 g 37 47 95 138 45 3 3 6 161 0 0 2 110 156 120 0 1 7 152 8 4 7 48 53 0 t 46 44 15 2 4 9 38 148 1 50 7 93 1 1 1 1 12 114 2 107 16 43 21 27 0

oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=5/12; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.899211; csrGrCATGYCyRGrCATGyCcms- ; cor=; Ncor= a 34 32 48 19 118 1 137 9 0 1 5 2 48 15 59 0 152 41 6 2 5 21 58 30 0 c 63 51 5 4 8 170 7 1 0 126 169 67 3 10 0 181 5 3 2 92 154 108 59 58 0 g 44 55 113 156 54 2 3 7 183 0 0 11 130 157 114 0 12 11 174 17 3 17 42 68 0 t 42 45 17 4 3 10 36 166 0 56 9 103 2 1 10 2 14 128 1 72 21 37 24 27 0

oligos_6nt_mkv2_m1_rc_shift5 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=6/12; ncol2=19; w=0; offset=4; strand=R; shift=5; score=0.751957; -----CwtgyCyGGGCATGTCysg- ; cor=; Ncor= a 0 0 0 0 0 12 100 24 19 24 7 16 35 1 21 0 179 22 0 3 9 28 45 41 0 c 0 0 0 0 0 142 30 19 20 70 143 56 3 2 1 199 6 6 3 39 169 100 50 36 0 g 0 0 0 0 0 19 16 31 131 26 37 4 159 194 177 0 3 6 195 0 2 8 70 101 0 t 0 0 0 0 0 26 53 125 29 79 12 123 2 2 0 0 11 165 1 157 19 63 34 21 0

oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5_rc; m=7/12; ncol2=18; w=0; offset=4; strand=R; shift=5; score=0.700279; -----cwtgyCTGGGCATGTyys-- ; cor=; Ncor= a 0 0 0 0 0 15 82 24 19 16 1 19 20 4 14 2 158 21 2 2 13 31 41 0 0 c 0 0 0 0 0 116 27 10 17 55 141 31 1 3 1 169 6 4 2 16 100 62 48 0 0 g 0 0 0 0 0 18 13 24 109 28 22 3 151 161 156 1 2 10 169 1 7 16 63 0 0 t 0 0 0 0 0 24 51 115 28 74 9 120 1 5 2 1 7 138 0 154 53 64 21 0 0

oligos_6nt_mkv2_m4_rc_shift5 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4_rc; m=8/12; ncol2=24; w=0; offset=4; strand=R; shift=5; score=0.628009; -----cwtgyCtGGRCATGYCCaGr ; cor=; Ncor= a 0 0 0 0 0 9 57 14 12 7 11 7 22 6 34 1 112 8 0 2 2 3 82 5 46 c 0 0 0 0 0 85 20 11 18 58 102 27 6 0 1 129 8 3 1 93 122 100 14 13 21 g 0 0 0 0 0 15 14 24 86 21 13 14 100 123 94 1 3 8 129 1 0 6 27 102 57 t 0 0 0 0 0 22 40 82 15 45 5 83 3 2 2 0 8 112 1 35 7 22 8 11 7

oligos_6nt_mkv2_m2_rc_shift10 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=9/12; ncol2=14; w=0; offset=9; strand=R; shift=10; score=0.534753; ----------cyrGRCATGYCyrg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 0 c 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 0 g 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 0 t 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30 0

oligos_7nt_mkv2_m3_shift10 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=10/12; ncol2=14; w=0; offset=9; strand=D; shift=10; score=0.525781; ----------cygGRCATGYCcrg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 0 c 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 0 g 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 0 t 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22 0

positions_6nt_m2_shift13 (positions_6nt_m2)
; oligos_7nt_mkv2_m5 versus positions_6nt_m2; m=11/12; ncol2=10; w=0; offset=12; strand=D; shift=13; score=0.402903; -------------GrCATGTCyg-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30 0 0

positions_6nt_m1_rc_shift11 (positions_6nt_m1_rc)
; oligos_7nt_mkv2_m5 versus positions_6nt_m1_rc; m=12/12; ncol2=10; w=0; offset=10; strand=R; shift=11; score=0.400673; -----------yrGGCATGyC---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 32 74 1 8 1 204 0 1 8 18 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 84 8 4 0 209 1 9 3 59 145 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 17 115 204 202 0 5 0 206 5 17 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 77 13 1 0 0 0 201 0 138 30 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=24; shift=5; ncol=29; -----skgGrCATGyCYrGRCATGyCysg ; Alignment reference a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.989085; -----sbrGrCATGYCyrGrCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.987844; -----sbrGrCATGYCyrGRCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=4/10; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.980473; -----bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=5/10; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.899211; ----yssrGRCATGYCYrGrCATGyCyv- ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 2 6 20 45 0 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 49 137 82 47 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 10 5 11 49 0 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4 105 18 53 25 0
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=6/10; ncol2=19; w=0; offset=0; strand=D; shift=5; score=0.725395; -----csrGACATGCCCrGrcawG----- ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 0 0 0 0 0 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 0 0 0 0 0 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 0 0 0 0 0 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12 0 0 0 0 0
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=7/10; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.664924; ------srrACATGCCCAGrcawg----- ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 0 0 0 0 0 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 0 0 0 0 0 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 0 0 0 0 0 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15 0 0 0 0 0
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=8/10; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.598495; cwtgyCtGGRCATGYCCaGrcawg----- ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 0 0 0 0 0 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 0 0 0 0 0 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 0 0 0 0 0 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9 0 0 0 0 0
oligos_6nt_mkv2_m2_rc_shift15 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=9/10; ncol2=14; w=0; offset=10; strand=R; shift=15; score=0.53467; ---------------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30
oligos_7nt_mkv2_m3_shift15 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=10/10; ncol2=14; w=0; offset=10; strand=D; shift=15; score=0.522377; ---------------cygGRCATGYCcrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=24; shift=5; ncol=29; -----bbrGRCATGYCYrGrCATGyCyrr ; Alignment reference a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.995969; -----sbrGrCATGYCyrGRCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.995775; -----sbrGrCATGYCyrGrCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=4/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.980473; -----skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=5/11; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.917401; ----yssrGRCATGYCYrGrCATGyCyv- ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 2 6 20 45 0 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 49 137 82 47 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 10 5 11 49 0 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4 105 18 53 25 0
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=6/11; ncol2=19; w=0; offset=0; strand=D; shift=5; score=0.754748; -----csrGACATGCCCrGrcawG----- ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 0 0 0 0 0 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 0 0 0 0 0 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 0 0 0 0 0 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12 0 0 0 0 0
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m5; m=7/11; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.704945; ------srrACATGCCCAGrcawg----- ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 0 0 0 0 0 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 0 0 0 0 0 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 0 0 0 0 0 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15 0 0 0 0 0
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4; m=8/11; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.580808; cwtgyCtGGRCATGYCCaGrcawg----- ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 0 0 0 0 0 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 0 0 0 0 0 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 0 0 0 0 0 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9 0 0 0 0 0
oligos_6nt_mkv2_m2_rc_shift15 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=9/11; ncol2=14; w=0; offset=10; strand=R; shift=15; score=0.532537; ---------------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30
oligos_7nt_mkv2_m3_shift15 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=10/11; ncol2=14; w=0; offset=10; strand=D; shift=15; score=0.519435; ---------------cygGRCATGYCcrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_7nt_mkv2_m2 versus positions_6nt_m1; m=11/11; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.401432; --------GrCATGCCyr----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0 0 0 0 0 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=24; shift=0; ncol=24; cwtgyCtGGRCATGYCCaGrcawg ; Alignment reference a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; cwtgyCtGGRCATGYCCaGrcawg ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/10; ncol2=19; w=0; offset=5; strand=D; shift=5; score= 0.7282; -----csrGACATGCCCrGrcawG ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m5; m=3/10; ncol2=18; w=0; offset=6; strand=D; shift=6; score=0.660655; ------srrACATGCCCAGrcawg ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=4/10; ncol2=24; w=0; offset=4; strand=R; shift=4; score=0.628009; ----yssrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=5/10; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.598495; -----skgGrCATGyCYrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=6/10; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.587354; -----sbrGrCATGYCyrGrCATG ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.583601; -----sbrGrCATGYCyrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=8/10; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.580808; -----bbrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3
oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=9/10; ncol2=14; w=0; offset=5; strand=R; shift=5; score=0.509311; -----cyrGRCATGYCyrg----- ; cor=; Ncor= a 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 0 0 0 0 0 c 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 0 0 0 0 0 g 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 0 0 0 0 0 t 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30 0 0 0 0 0
oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=10/10; ncol2=14; w=0; offset=5; strand=R; shift=5; score=0.505167; -----cygGRCATGYCcrg----- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=14; shift=5; ncol=19; -----cyrGRCATGYCyrg ; Alignment reference a 0 0 0 0 0 30 38 79 14 168 2 231 9 2 0 3 20 65 54 c 0 0 0 0 0 116 103 6 1 0 242 2 4 1 76 228 141 41 45 g 0 0 0 0 0 46 41 141 228 77 1 4 2 241 0 1 5 103 118 t 0 0 0 0 0 54 64 20 3 1 1 9 231 2 170 14 80 37 29
oligos_6nt_mkv2_m2_shift5 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/12; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 30 38 79 14 168 2 231 9 2 0 3 20 65 54 c 0 0 0 0 0 116 103 6 1 0 242 2 4 1 76 228 141 41 45 g 0 0 0 0 0 46 41 141 228 77 1 4 2 241 0 1 5 103 118 t 0 0 0 0 0 54 64 20 3 1 1 9 231 2 170 14 80 37 29
oligos_7nt_mkv2_m3_shift5 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=2/12; ncol2=14; w=0; offset=0; strand=D; shift=5; score=0.994348; -----cygGRCATGYCcrg ; cor=; Ncor= a 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22
positions_6nt_m2_shift8 (positions_6nt_m2)				; oligos_6nt_mkv2_m2 versus positions_6nt_m2; m=3/12; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.689491; --------GrCATGTCyg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 0 c 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 0 g 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 0 t 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30 0
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=4/12; ncol2=19; w=-5; offset=-5; strand=R; shift=0; score=0.664615; CwtgyCyGGGCATGTCysg ; cor=; Ncor= a 12 100 24 19 24 7 16 35 1 21 0 179 22 0 3 9 28 45 41 c 142 30 19 20 70 143 56 3 2 1 199 6 6 3 39 169 100 50 36 g 19 16 31 131 26 37 4 159 194 177 0 3 6 195 0 2 8 70 101 t 26 53 125 29 79 12 123 2 2 0 0 11 165 1 157 19 63 34 21
positions_6nt_m1_rc_shift6 (positions_6nt_m1_rc)				; oligos_6nt_mkv2_m2 versus positions_6nt_m1_rc; m=5/12; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.645045; ------yrGGCATGyC--- ; cor=; Ncor= a 0 0 0 0 0 0 32 74 1 8 1 204 0 1 8 18 0 0 0 c 0 0 0 0 0 0 84 8 4 0 209 1 9 3 59 145 0 0 0 g 0 0 0 0 0 0 17 115 204 202 0 5 0 206 5 17 0 0 0 t 0 0 0 0 0 0 77 13 1 0 0 0 201 0 138 30 0 0 0
oligos_6nt_mkv2_m5_rc_shift0 (oligos_6nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m5_rc; m=6/12; ncol2=18; w=-5; offset=-5; strand=R; shift=0; score=0.578709; cwtgyCTGGGCATGTyys- ; cor=; Ncor= a 15 82 24 19 16 1 19 20 4 14 2 158 21 2 2 13 31 41 0 c 116 27 10 17 55 141 31 1 3 1 169 6 4 2 16 100 62 48 0 g 18 13 24 109 28 22 3 151 161 156 1 2 10 169 1 7 16 63 0 t 24 51 115 28 74 9 120 1 5 2 1 7 138 0 154 53 64 21 0
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=7/12; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.534753; ----yssrGRCATGYCYrG ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1
oligos_7nt_mkv2_m4_rc_shift5 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=8/12; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.53467; -----csrGrCATGYCyRG ; cor=; Ncor= a 0 0 0 0 0 34 32 48 19 118 1 137 9 0 1 5 2 48 15 c 0 0 0 0 0 63 51 5 4 8 170 7 1 0 126 169 67 3 10 g 0 0 0 0 0 44 55 113 156 54 2 3 7 183 0 0 11 130 157 t 0 0 0 0 0 42 45 17 4 3 10 36 166 0 56 9 103 2 1
oligos_6nt_mkv2_m3_rc_shift5 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=9/12; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.53294; -----ybrGrCATGyCyrG ; cor=; Ncor= a 0 0 0 0 0 30 29 55 18 120 3 132 9 2 2 2 5 63 12 c 0 0 0 0 0 63 52 10 6 9 170 8 1 0 123 176 76 2 0 g 0 0 0 0 0 45 56 102 158 54 3 3 7 184 0 0 3 120 174 t 0 0 0 0 0 49 50 20 5 4 11 44 170 1 62 9 103 2 1
oligos_7nt_mkv2_m2_rc_shift5 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=10/12; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.532537; -----yyrGrCATGyCyRG ; cor=; Ncor= a 0 0 0 0 0 19 28 43 18 99 3 119 7 1 1 0 4 45 9 c 0 0 0 0 0 62 46 8 6 10 146 8 2 0 102 153 57 1 0 g 0 0 0 0 0 35 40 99 135 51 3 3 6 161 0 0 3 115 153 t 0 0 0 0 0 47 49 13 4 3 11 33 148 1 60 10 99 2 1
oligos_7nt_mkv2_m1_rc_shift5 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=11/12; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.528289; -----ybrGrCATGYCyrG ; cor=; Ncor= a 0 0 0 0 0 27 26 46 17 106 3 115 8 1 2 1 3 51 6 c 0 0 0 0 0 53 46 7 6 8 148 7 1 0 111 155 65 1 0 g 0 0 0 0 0 37 47 95 138 45 3 3 6 161 0 0 2 110 156 t 0 0 0 0 0 46 44 15 2 4 9 38 148 1 50 7 93 1 1
oligos_6nt_mkv2_m4_rc_shift0 (oligos_6nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=12/12; ncol2=24; w=-5; offset=-5; strand=R; shift=0; score=0.509311; cwtgyCtGGRCATGYCCaG ; cor=; Ncor= a 9 57 14 12 7 11 7 22 6 34 1 112 8 0 2 2 3 82 5 c 85 20 11 18 58 102 27 6 0 1 129 8 3 1 93 122 100 14 13 g 15 14 24 86 21 13 14 100 123 94 1 3 8 129 1 0 6 27 102 t 22 40 82 15 45 5 83 3 2 2 0 8 112 1 35 7 22 8 11

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift12 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=10; shift=12; ncol=22; ------------GrCATGTCyg ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 c 0 0 0 0 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 g 0 0 0 0 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 t 0 0 0 0 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30
positions_6nt_m2_shift12 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/7; ncol2=10; w=0; offset=0; strand=D; shift=12; score= 1; ------------GrCATGTCyg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 c 0 0 0 0 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 g 0 0 0 0 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 t 0 0 0 0 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30
positions_6nt_m1_shift12 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=2/7; ncol2=10; w=0; offset=0; strand=D; shift=12; score=0.819197; ------------GrCATGCCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 c 0 0 0 0 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 g 0 0 0 0 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 t 0 0 0 0 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32
oligos_6nt_mkv2_m2_shift9 (oligos_6nt_mkv2_m2)				; positions_6nt_m2 versus oligos_6nt_mkv2_m2; m=3/7; ncol2=14; w=-3; offset=-3; strand=D; shift=9; score=0.689491; ---------cyrGRCATGYCyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 30 38 79 14 168 2 231 9 2 0 3 20 65 c 0 0 0 0 0 0 0 0 0 116 103 6 1 0 242 2 4 1 76 228 141 41 g 0 0 0 0 0 0 0 0 0 46 41 141 228 77 1 4 2 241 0 1 5 103 t 0 0 0 0 0 0 0 0 0 54 64 20 3 1 1 9 231 2 170 14 80 37
oligos_7nt_mkv2_m3_shift9 (oligos_7nt_mkv2_m3)				; positions_6nt_m2 versus oligos_7nt_mkv2_m3; m=4/7; ncol2=14; w=-3; offset=-3; strand=D; shift=9; score= 0.6836; ---------cygGRCATGYCcr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 c 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 g 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 t 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20
oligos_6nt_mkv2_m5_rc_shift4 (oligos_6nt_mkv2_m5_rc)				; positions_6nt_m2 versus oligos_6nt_mkv2_m5_rc; m=5/7; ncol2=18; w=-8; offset=-8; strand=R; shift=4; score=0.517197; ----cwtgyCTGGGCATGTyys ; cor=; Ncor= a 0 0 0 0 15 82 24 19 16 1 19 20 4 14 2 158 21 2 2 13 31 41 c 0 0 0 0 116 27 10 17 55 141 31 1 3 1 169 6 4 2 16 100 62 48 g 0 0 0 0 18 13 24 109 28 22 3 151 161 156 1 2 10 169 1 7 16 63 t 0 0 0 0 24 51 115 28 74 9 120 1 5 2 1 7 138 0 154 53 64 21
oligos_6nt_mkv2_m1_rc_shift4 (oligos_6nt_mkv2_m1_rc)				; positions_6nt_m2 versus oligos_6nt_mkv2_m1_rc; m=6/7; ncol2=19; w=-8; offset=-8; strand=R; shift=4; score=0.503065; ----CwtgyCyGGGCATGTCys ; cor=; Ncor= a 0 0 0 0 12 100 24 19 24 7 16 35 1 21 0 179 22 0 3 9 28 45 c 0 0 0 0 142 30 19 20 70 143 56 3 2 1 199 6 6 3 39 169 100 50 g 0 0 0 0 19 16 31 131 26 37 4 159 194 177 0 3 6 195 0 2 8 70 t 0 0 0 0 26 53 125 29 79 12 123 2 2 0 0 11 165 1 157 19 63 34
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; positions_6nt_m2 versus oligos_7nt_mkv2_m5; m=7/7; ncol2=24; w=-12; offset=-12; strand=D; shift=0; score=0.402903; brGrCATGyCyRGRCATGYCys ; cor=; Ncor= a 25 53 18 105 4 123 7 1 1 1 6 49 9 50 1 147 34 1 3 8 25 36 c 49 11 5 10 151 5 3 0 105 152 63 1 0 0 163 6 4 3 42 139 64 44 g 47 82 137 49 3 4 7 162 2 0 3 114 156 114 0 1 6 159 3 3 7 68 t 45 20 6 2 8 34 149 3 58 13 94 2 1 2 2 12 122 3 118 16 70 18

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=24; shift=5; ncol=29; -----sbrGrCATGYCyrGrCATGyCyvr ; Alignment reference a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----sbrGrCATGYCyrGrCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.998926; -----sbrGrCATGYCyrGRCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=3/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.995775; -----bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=4/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.989085; -----skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5_rc; m=5/11; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.915362; ----yssrGRCATGYCYrGrCATGyCyv- ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 2 6 20 45 0 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 49 137 82 47 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 10 5 11 49 0 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4 105 18 53 25 0
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=6/11; ncol2=19; w=0; offset=0; strand=D; shift=5; score=0.746764; -----csrGACATGCCCrGrcawG----- ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 0 0 0 0 0 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 0 0 0 0 0 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 0 0 0 0 0 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12 0 0 0 0 0
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=7/11; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.690713; ------srrACATGCCCAGrcawg----- ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 0 0 0 0 0 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 0 0 0 0 0 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 0 0 0 0 0 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15 0 0 0 0 0
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=8/11; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.587354; cwtgyCtGGRCATGYCCaGrcawg----- ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 0 0 0 0 0 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 0 0 0 0 0 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 0 0 0 0 0 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9 0 0 0 0 0
oligos_6nt_mkv2_m2_rc_shift15 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc; m=9/11; ncol2=14; w=0; offset=10; strand=R; shift=15; score=0.53294; ---------------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30
oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3_rc; m=10/11; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.524974; -----cygGRCATGYCcrg---------- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0 0 0 0 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_6nt_mkv2_m3 versus positions_6nt_m1; m=11/11; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.401431; --------GrCATGCCyr----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift10 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=14; shift=10; ncol=24; ----------cygGRCATGYCcrg ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22
oligos_7nt_mkv2_m3_shift10 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/12; ncol2=14; w=0; offset=0; strand=D; shift=10; score= 1; ----------cygGRCATGYCcrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 c 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 g 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 t 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22
oligos_6nt_mkv2_m2_shift10 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=2/12; ncol2=14; w=0; offset=0; strand=D; shift=10; score=0.994348; ----------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 30 38 79 14 168 2 231 9 2 0 3 20 65 54 c 0 0 0 0 0 0 0 0 0 0 116 103 6 1 0 242 2 4 1 76 228 141 41 45 g 0 0 0 0 0 0 0 0 0 0 46 41 141 228 77 1 4 2 241 0 1 5 103 118 t 0 0 0 0 0 0 0 0 0 0 54 64 20 3 1 1 9 231 2 170 14 80 37 29
positions_6nt_m2_shift13 (positions_6nt_m2)				; oligos_7nt_mkv2_m3 versus positions_6nt_m2; m=3/12; ncol2=10; w=0; offset=3; strand=D; shift=13; score= 0.6836; -------------GrCATGTCyg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30 0
oligos_6nt_mkv2_m1_rc_shift5 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=4/12; ncol2=19; w=-5; offset=-5; strand=R; shift=5; score=0.658143; -----CwtgyCyGGGCATGTCysg ; cor=; Ncor= a 0 0 0 0 0 12 100 24 19 24 7 16 35 1 21 0 179 22 0 3 9 28 45 41 c 0 0 0 0 0 142 30 19 20 70 143 56 3 2 1 199 6 6 3 39 169 100 50 36 g 0 0 0 0 0 19 16 31 131 26 37 4 159 194 177 0 3 6 195 0 2 8 70 101 t 0 0 0 0 0 26 53 125 29 79 12 123 2 2 0 0 11 165 1 157 19 63 34 21
positions_6nt_m1_rc_shift11 (positions_6nt_m1_rc)				; oligos_7nt_mkv2_m3 versus positions_6nt_m1_rc; m=5/12; ncol2=10; w=0; offset=1; strand=R; shift=11; score=0.634151; -----------yrGGCATGyC--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 32 74 1 8 1 204 0 1 8 18 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 84 8 4 0 209 1 9 3 59 145 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 17 115 204 202 0 5 0 206 5 17 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 77 13 1 0 0 0 201 0 138 30 0 0 0
oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m5_rc; m=6/12; ncol2=18; w=-5; offset=-5; strand=R; shift=5; score=0.574255; -----cwtgyCTGGGCATGTyys- ; cor=; Ncor= a 0 0 0 0 0 15 82 24 19 16 1 19 20 4 14 2 158 21 2 2 13 31 41 0 c 0 0 0 0 0 116 27 10 17 55 141 31 1 3 1 169 6 4 2 16 100 62 48 0 g 0 0 0 0 0 18 13 24 109 28 22 3 151 161 156 1 2 10 169 1 7 16 63 0 t 0 0 0 0 0 24 51 115 28 74 9 120 1 5 2 1 7 138 0 154 53 64 21 0
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=7/12; ncol2=24; w=-9; offset=-9; strand=D; shift=1; score=0.525781; -brGrCATGyCyRGRCATGYCyss ; cor=; Ncor= a 0 25 53 18 105 4 123 7 1 1 1 6 49 9 50 1 147 34 1 3 8 25 36 41 c 0 49 11 5 10 151 5 3 0 105 152 63 1 0 0 163 6 4 3 42 139 64 44 43 g 0 47 82 137 49 3 4 7 162 2 0 3 114 156 114 0 1 6 159 3 3 7 68 61 t 0 45 20 6 2 8 34 149 3 58 13 94 2 1 2 2 12 122 3 118 16 70 18 21
oligos_6nt_mkv2_m3_rc_shift0 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=8/12; ncol2=24; w=-10; offset=-10; strand=R; shift=0; score=0.524974; ybrGrCATGyCyrGRCATGyCyvs ; cor=; Ncor= a 30 29 55 18 120 3 132 9 2 2 2 5 63 12 55 0 167 41 8 3 8 29 55 45 c 63 52 10 6 9 170 8 1 0 123 176 76 2 0 0 183 7 4 2 58 157 96 53 49 g 45 56 102 158 54 3 3 7 184 0 0 3 120 174 131 0 1 7 175 9 5 8 55 64 t 49 50 20 5 4 11 44 170 1 62 9 103 2 1 1 4 12 135 2 117 17 54 24 29
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=9/12; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.522377; skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=10/12; ncol2=24; w=-10; offset=-10; strand=R; shift=0; score=0.519504; ybrGrCATGYCyrGRCATGyCyvs ; cor=; Ncor= a 27 26 46 17 106 3 115 8 1 2 1 3 51 6 42 0 144 39 7 2 7 26 41 38 c 53 46 7 6 8 148 7 1 0 111 155 65 1 0 0 162 6 3 2 46 136 87 53 45 g 37 47 95 138 45 3 3 6 161 0 0 2 110 156 120 0 1 7 152 8 4 7 48 53 t 46 44 15 2 4 9 38 148 1 50 7 93 1 1 1 1 12 114 2 107 16 43 21 27
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2; m=11/12; ncol2=24; w=-10; offset=-10; strand=D; shift=0; score=0.519435; bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19
oligos_6nt_mkv2_m4_rc_shift5 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m4_rc; m=12/12; ncol2=24; w=-5; offset=-5; strand=R; shift=5; score=0.505167; -----cwtgyCtGGRCATGYCCaG ; cor=; Ncor= a 0 0 0 0 0 9 57 14 12 7 11 7 22 6 34 1 112 8 0 2 2 3 82 5 c 0 0 0 0 0 85 20 11 18 58 102 27 6 0 1 129 8 3 1 93 122 100 14 13 g 0 0 0 0 0 15 14 24 86 21 13 14 100 123 94 1 3 8 129 1 0 6 27 102 t 0 0 0 0 0 22 40 82 15 45 5 83 3 2 2 0 8 112 1 35 7 22 8 11

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=24; shift=5; ncol=29; -----sbrGrCATGYCyrGRCATGyCyvr ; Alignment reference a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----sbrGrCATGYCyrGRCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 4 2 15 44 46 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 45 138 95 47 37 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 8 6 7 46 53 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3 106 17 46 26 27
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=2/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.998926; -----sbrGrCATGYCyrGrCATGyCyvr ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 4 5 20 50 49 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 54 158 102 56 45 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 9 6 10 52 63 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3 120 18 55 29 30
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.995969; -----bbrGRCATGYCYrGrCATGyCyrr ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 3 4 13 49 47 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 51 135 99 40 35 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 10 6 8 46 62 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3 99 18 43 28 19
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=4/11; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.987844; -----skgGrCATGyCYrGRCATGyCysg ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 3 4 17 45 42 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 54 156 113 55 44 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 8 4 5 51 63 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1 118 19 48 32 34
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=5/11; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.914295; ----yssrGRCATGYCYrGrCATGyCyv- ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 2 6 20 45 0 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 49 137 82 47 0 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 10 5 11 49 0 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4 105 18 53 25 0
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=6/11; ncol2=19; w=0; offset=0; strand=D; shift=5; score=0.74873; -----csrGACATGCCCrGrcawG----- ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 0 0 0 0 0 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 0 0 0 0 0 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 0 0 0 0 0 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12 0 0 0 0 0
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=7/11; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.694553; ------srrACATGCCCAGrcawg----- ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 0 0 0 0 0 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 0 0 0 0 0 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 0 0 0 0 0 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15 0 0 0 0 0
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=8/11; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.583601; cwtgyCtGGRCATGYCCaGrcawg----- ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 0 0 0 0 0 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 0 0 0 0 0 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 0 0 0 0 0 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9 0 0 0 0 0
oligos_6nt_mkv2_m2_rc_shift15 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=9/11; ncol2=14; w=0; offset=10; strand=R; shift=15; score=0.528289; ---------------cyrGRCATGYCyrg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30
oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=10/11; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.519504; -----cygGRCATGYCcrg---------- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0 0 0 0 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_7nt_mkv2_m1 versus positions_6nt_m1; m=11/11; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.401283; --------GrCATGCCyr----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=19; shift=5; ncol=24; -----csrGACATGCCCrGrcawG ; Alignment reference a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/12; ncol2=19; w=0; offset=0; strand=D; shift=5; score= 1; -----csrGACATGCCCrGrcawG ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m5; m=2/12; ncol2=18; w=0; offset=1; strand=D; shift=6; score=0.930576; ------srrACATGCCCAGrcawg ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=3/12; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.754748; -----bbrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=4/12; ncol2=24; w=-1; offset=-1; strand=R; shift=4; score=0.751957; ----yssrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=5/12; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.74873; -----sbrGrCATGYCyrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=6/12; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.746764; -----sbrGrCATGYCyrGrCATG ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=7/12; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score= 0.7282; cwtgyCtGGRCATGYCCaGrcawg ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=8/12; ncol2=24; w=0; offset=0; strand=D; shift=5; score=0.725395; -----skgGrCATGyCYrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1
oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=9/12; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.664615; -----cyrGRCATGYCyrg----- ; cor=; Ncor= a 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 0 0 0 0 0 c 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 0 0 0 0 0 g 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 0 0 0 0 0 t 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30 0 0 0 0 0
oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=10/12; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.658143; -----cygGRCATGYCcrg----- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_6nt_mkv2_m1 versus positions_6nt_m1; m=11/12; ncol2=10; w=0; offset=3; strand=D; shift=8; score=0.511487; --------GrCATGCCyr------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0
positions_6nt_m2_rc_shift6 (positions_6nt_m2_rc)				; oligos_6nt_mkv2_m1 versus positions_6nt_m2_rc; m=12/12; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.503065; ------crGACATGyC-------- ; cor=; Ncor= a 0 0 0 0 0 0 30 75 2 179 0 183 1 0 7 13 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 97 4 1 0 194 0 6 0 105 143 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 35 90 191 15 0 11 2 194 4 7 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 32 25 0 0 0 0 185 0 78 31 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=18; shift=6; ncol=24; ------srrACATGCCCAGrcawg ; Alignment reference a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/12; ncol2=18; w=0; offset=0; strand=D; shift=6; score= 1; ------srrACATGCCCAGrcawg ; cor=; Ncor= a 0 0 0 0 0 0 21 64 53 154 0 138 7 1 2 5 1 120 9 74 28 115 51 24 c 0 0 0 0 0 0 63 16 7 1 169 10 2 1 156 161 151 3 22 28 109 24 13 18 g 0 0 0 0 0 0 48 62 100 16 2 4 6 169 1 3 1 31 141 55 17 10 27 116 t 0 0 0 0 0 0 41 31 13 2 2 21 158 2 14 4 20 19 1 16 19 24 82 15
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=2/12; ncol2=19; w=-1; offset=-1; strand=D; shift=5; score=0.930576; -----csrGACATGCCCrGrcawG ; cor=; Ncor= a 0 0 0 0 0 21 34 63 19 157 1 165 11 0 0 2 2 123 12 79 29 125 53 26 c 0 0 0 0 0 101 70 8 2 0 195 6 3 0 177 194 159 4 37 26 131 31 16 19 g 0 0 0 0 0 36 50 100 169 39 3 6 6 199 1 2 3 56 143 70 20 19 30 142 t 0 0 0 0 0 41 45 28 9 3 0 22 179 0 21 1 35 16 7 24 19 24 100 12
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m2; m=3/12; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.704945; -----bbrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 0 21 20 61 16 115 2 118 11 2 1 1 2 99 10 60 1 148 33 11 c 0 0 0 0 0 58 53 8 5 4 156 6 1 0 121 153 115 3 0 0 161 6 3 3 g 0 0 0 0 0 41 47 67 133 41 2 3 6 161 0 0 1 57 153 102 0 2 8 146 t 0 0 0 0 0 43 43 27 9 3 3 36 145 0 41 9 45 4 0 1 1 7 119 3
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5_rc; m=4/12; ncol2=24; w=-2; offset=-2; strand=R; shift=4; score=0.700279; ----yssrGRCATGYCYrGrCATG ; cor=; Ncor= a 0 0 0 0 30 21 18 70 16 118 3 122 12 2 2 1 2 94 13 58 3 149 34 8 c 0 0 0 0 57 61 68 7 3 3 159 6 1 0 114 156 114 3 0 2 162 7 4 3 g 0 0 0 0 29 43 44 64 139 42 3 4 6 163 0 0 1 63 152 105 0 3 5 151 t 0 0 0 0 50 41 36 25 8 3 1 34 147 1 50 9 49 6 1 1 1 7 123 4
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=5/12; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.694553; -----sbrGrCATGYCyrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 21 43 16 107 2 114 12 1 1 1 1 93 7 50 1 148 38 9 c 0 0 0 0 0 53 48 7 4 8 152 7 1 0 120 156 110 2 0 0 161 6 3 3 g 0 0 0 0 0 45 53 87 136 46 2 3 6 162 0 0 1 65 155 111 0 1 7 148 t 0 0 0 0 0 38 41 26 7 2 7 39 144 0 42 6 51 3 1 2 1 8 115 3
oligos_6nt_mkv2_m3_shift5 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=6/12; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.690713; -----sbrGrCATGYCyrGrCATG ; cor=; Ncor= a 0 0 0 0 0 29 24 54 17 117 2 135 12 4 1 1 2 103 9 62 1 170 44 11 c 0 0 0 0 0 64 55 8 5 9 175 7 1 0 131 174 120 3 0 0 184 7 3 3 g 0 0 0 0 0 49 53 96 157 58 2 4 7 183 0 0 2 76 176 123 0 1 8 170 t 0 0 0 0 0 45 55 29 8 3 8 41 167 0 55 12 63 5 2 2 2 9 132 3
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=7/12; ncol2=24; w=-1; offset=-1; strand=D; shift=5; score=0.664924; -----skgGrCATGyCYrGRCATG ; cor=; Ncor= a 0 0 0 0 0 27 24 37 21 72 1 128 14 2 10 1 2 103 9 56 0 166 36 10 c 0 0 0 0 0 68 42 17 3 17 174 11 12 0 114 157 130 11 0 0 183 7 3 2 g 0 0 0 0 0 58 59 108 154 92 2 3 5 181 0 10 3 67 169 126 0 1 7 170 t 0 0 0 0 0 30 58 21 5 2 6 41 152 0 59 15 48 2 5 1 0 9 137 1
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=8/12; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.660655; cwtgyCtGGRCATGYCCaGrcawg ; cor=; Ncor= a 9 56 15 12 7 11 8 22 7 35 1 112 8 0 2 2 3 83 5 45 15 82 40 22 c 84 20 11 18 57 102 27 6 0 1 129 8 3 1 94 123 100 14 13 21 86 24 14 15 g 16 15 24 85 21 13 14 100 122 93 1 3 8 129 1 0 6 27 102 58 18 11 20 85 t 22 40 81 16 46 5 82 3 2 2 0 8 112 1 34 6 22 7 11 7 12 14 57 9
oligos_6nt_mkv2_m2_rc_shift5 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=9/12; ncol2=14; w=-1; offset=-1; strand=R; shift=5; score=0.578709; -----cyrGRCATGYCyrg----- ; cor=; Ncor= a 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 0 0 0 0 0 c 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 0 0 0 0 0 g 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 0 0 0 0 0 t 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30 0 0 0 0 0
oligos_7nt_mkv2_m3_rc_shift5 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=10/12; ncol2=14; w=-1; offset=-1; strand=R; shift=5; score=0.574255; -----cygGRCATGYCcrg----- ; cor=; Ncor= a 0 0 0 0 0 22 20 34 8 104 3 133 5 2 2 3 10 40 35 0 0 0 0 0 c 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 131 97 26 24 0 0 0 0 0 g 0 0 0 0 0 24 26 97 130 37 0 3 2 138 1 2 2 56 62 0 0 0 0 0 t 0 0 0 0 0 35 41 10 3 1 2 5 133 3 103 7 34 21 22 0 0 0 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_6nt_mkv2_m5 versus positions_6nt_m1; m=11/12; ncol2=10; w=0; offset=2; strand=D; shift=8; score=0.52709; --------GrCATGCCyr------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 30 138 0 201 0 0 0 1 13 77 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 17 5 206 0 5 0 202 204 115 17 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 145 59 3 9 1 209 0 4 8 84 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 18 8 1 0 204 1 8 1 74 32 0 0 0 0 0 0
positions_6nt_m2_rc_shift6 (positions_6nt_m2_rc)				; oligos_6nt_mkv2_m5 versus positions_6nt_m2_rc; m=12/12; ncol2=10; w=0; offset=0; strand=R; shift=6; score=0.517197; ------crGACATGyC-------- ; cor=; Ncor= a 0 0 0 0 0 0 30 75 2 179 0 183 1 0 7 13 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 97 4 1 0 194 0 6 0 105 143 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 35 90 191 15 0 11 2 194 4 7 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 32 25 0 0 0 0 185 0 78 31 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift4 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=10; shift=4; ncol=14; ----GrCATGCCyr ; Alignment reference a 0 0 0 0 30 138 0 201 0 0 0 1 13 77 c 0 0 0 0 17 5 206 0 5 0 202 204 115 17 g 0 0 0 0 145 59 3 9 1 209 0 4 8 84 t 0 0 0 0 18 8 1 0 204 1 8 1 74 32
positions_6nt_m1_shift4 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/10; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----GrCATGCCyr ; cor=; Ncor= a 0 0 0 0 30 138 0 201 0 0 0 1 13 77 c 0 0 0 0 17 5 206 0 5 0 202 204 115 17 g 0 0 0 0 145 59 3 9 1 209 0 4 8 84 t 0 0 0 0 18 8 1 0 204 1 8 1 74 32
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=2/10; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.819197; ----GrCATGTCyg ; cor=; Ncor= a 0 0 0 0 31 78 0 185 0 0 0 0 25 32 c 0 0 0 0 7 4 194 2 11 0 15 191 90 35 g 0 0 0 0 143 105 0 6 0 194 0 1 4 97 t 0 0 0 0 13 7 0 1 183 0 179 2 75 30
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; positions_6nt_m1 versus oligos_6nt_mkv2_m2_rc; m=3/10; ncol2=14; w=-3; offset=-3; strand=R; shift=1; score=0.645045; -cyrGRCATGYCyr ; cor=; Ncor= a 0 29 37 80 14 170 2 231 9 1 1 3 20 64 c 0 118 103 5 1 0 241 2 4 1 77 228 141 41 g 0 45 41 141 228 76 1 4 2 242 0 1 6 103 t 0 54 65 20 3 0 2 9 231 2 168 14 79 38
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3_rc)				; positions_6nt_m1 versus oligos_7nt_mkv2_m3_rc; m=4/10; ncol2=14; w=-3; offset=-3; strand=R; shift=1; score=0.634151; -cygGRCATGYCcr ; cor=; Ncor= a 0 22 20 34 8 104 3 133 5 2 2 3 10 40 c 0 62 56 2 2 1 138 2 3 0 37 131 97 26 g 0 24 26 97 130 37 0 3 2 138 1 2 2 56 t 0 35 41 10 3 1 2 5 133 3 103 7 34 21
oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5)				; positions_6nt_m1 versus oligos_6nt_mkv2_m5; m=5/10; ncol2=18; w=-2; offset=-2; strand=D; shift=2; score=0.52709; --srrACATGCCCA ; cor=; Ncor= a 0 0 21 64 53 154 0 138 7 1 2 5 1 120 c 0 0 63 16 7 1 169 10 2 1 156 161 151 3 g 0 0 48 62 100 16 2 4 6 169 1 3 1 31 t 0 0 41 31 13 2 2 21 158 2 14 4 20 19
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; positions_6nt_m1 versus oligos_6nt_mkv2_m1; m=6/10; ncol2=19; w=-3; offset=-3; strand=D; shift=1; score=0.511487; -csrGACATGCCCr ; cor=; Ncor= a 0 21 34 63 19 157 1 165 11 0 0 2 2 123 c 0 101 70 8 2 0 195 6 3 0 177 194 159 4 g 0 36 50 100 169 39 3 6 6 199 1 2 3 56 t 0 41 45 28 9 3 0 22 179 0 21 1 35 16
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; positions_6nt_m1 versus oligos_7nt_mkv2_m2; m=7/10; ncol2=24; w=-3; offset=-3; strand=D; shift=1; score=0.401432; -bbrGRCATGYCYr ; cor=; Ncor= a 0 21 20 61 16 115 2 118 11 2 1 1 2 99 c 0 58 53 8 5 4 156 6 1 0 121 153 115 3 g 0 41 47 67 133 41 2 3 6 161 0 0 1 57 t 0 43 43 27 9 3 3 36 145 0 41 9 45 4
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; positions_6nt_m1 versus oligos_6nt_mkv2_m3; m=8/10; ncol2=24; w=-3; offset=-3; strand=D; shift=1; score=0.401431; -sbrGrCATGYCyr ; cor=; Ncor= a 0 29 24 54 17 117 2 135 12 4 1 1 2 103 c 0 64 55 8 5 9 175 7 1 0 131 174 120 3 g 0 49 53 96 157 58 2 4 7 183 0 0 2 76 t 0 45 55 29 8 3 8 41 167 0 55 12 63 5
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; positions_6nt_m1 versus oligos_7nt_mkv2_m1; m=9/10; ncol2=24; w=-3; offset=-3; strand=D; shift=1; score=0.401283; -sbrGrCATGYCyr ; cor=; Ncor= a 0 27 21 43 16 107 2 114 12 1 1 1 1 93 c 0 53 48 7 4 8 152 7 1 0 120 156 110 2 g 0 45 53 87 136 46 2 3 6 162 0 0 1 65 t 0 38 41 26 7 2 7 39 144 0 42 6 51 3
oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)				; positions_6nt_m1 versus oligos_7nt_mkv2_m5_rc; m=10/10; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.400673; yssrGRCATGYCYr ; cor=; Ncor= a 30 21 18 70 16 118 3 122 12 2 2 1 2 94 c 57 61 68 7 3 3 159 6 1 0 114 156 114 3 g 29 43 44 64 139 42 3 4 6 163 0 0 1 63 t 50 41 36 25 8 3 1 34 147 1 50 9 49 6

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=24; shift=1; ncol=25; -brGrCATGyCyRGRCATGYCyssr ; Alignment reference a 0 25 53 18 105 4 123 7 1 1 1 6 49 9 50 1 147 34 1 3 8 25 36 41 50 c 0 49 11 5 10 151 5 3 0 105 152 63 1 0 0 163 6 4 3 42 139 64 44 43 29 g 0 47 82 137 49 3 4 7 162 2 0 3 114 156 114 0 1 6 159 3 3 7 68 61 57 t 0 45 20 6 2 8 34 149 3 58 13 94 2 1 2 2 12 122 3 118 16 70 18 21 30
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/12; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -brGrCATGyCyRGRCATGYCyssr ; cor=; Ncor= a 0 25 53 18 105 4 123 7 1 1 1 6 49 9 50 1 147 34 1 3 8 25 36 41 50 c 0 49 11 5 10 151 5 3 0 105 152 63 1 0 0 163 6 4 3 42 139 64 44 43 29 g 0 47 82 137 49 3 4 7 162 2 0 3 114 156 114 0 1 6 159 3 3 7 68 61 57 t 0 45 20 6 2 8 34 149 3 58 13 94 2 1 2 2 12 122 3 118 16 70 18 21 30
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc; m=2/12; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.917401; yyrGrCATGyCyRGRCATGYCyvv- ; cor=; Ncor= a 19 28 43 18 99 3 119 7 1 1 0 4 45 9 41 0 145 36 3 3 9 27 43 43 0 c 62 46 8 6 10 146 8 2 0 102 153 57 1 0 0 161 6 3 2 41 133 67 47 41 0 g 35 40 99 135 51 3 3 6 161 0 0 3 115 153 121 0 1 6 156 4 5 8 53 58 0 t 47 49 13 4 3 11 33 148 1 60 10 99 2 1 1 2 11 118 2 115 16 61 20 21 0
oligos_6nt_mkv2_m3_rc_shift0 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3_rc; m=3/12; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.915362; ybrGrCATGyCyrGRCATGyCyvs- ; cor=; Ncor= a 30 29 55 18 120 3 132 9 2 2 2 5 63 12 55 0 167 41 8 3 8 29 55 45 0 c 63 52 10 6 9 170 8 1 0 123 176 76 2 0 0 183 7 4 2 58 157 96 53 49 0 g 45 56 102 158 54 3 3 7 184 0 0 3 120 174 131 0 1 7 175 9 5 8 55 64 0 t 49 50 20 5 4 11 44 170 1 62 9 103 2 1 1 4 12 135 2 117 17 54 24 29 0
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=4/12; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.914295; ybrGrCATGYCyrGRCATGyCyvs- ; cor=; Ncor= a 27 26 46 17 106 3 115 8 1 2 1 3 51 6 42 0 144 39 7 2 7 26 41 38 0 c 53 46 7 6 8 148 7 1 0 111 155 65 1 0 0 162 6 3 2 46 136 87 53 45 0 g 37 47 95 138 45 3 3 6 161 0 0 2 110 156 120 0 1 7 152 8 4 7 48 53 0 t 46 44 15 2 4 9 38 148 1 50 7 93 1 1 1 1 12 114 2 107 16 43 21 27 0
oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=5/12; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.899211; csrGrCATGYCyRGrCATGyCcms- ; cor=; Ncor= a 34 32 48 19 118 1 137 9 0 1 5 2 48 15 59 0 152 41 6 2 5 21 58 30 0 c 63 51 5 4 8 170 7 1 0 126 169 67 3 10 0 181 5 3 2 92 154 108 59 58 0 g 44 55 113 156 54 2 3 7 183 0 0 11 130 157 114 0 12 11 174 17 3 17 42 68 0 t 42 45 17 4 3 10 36 166 0 56 9 103 2 1 10 2 14 128 1 72 21 37 24 27 0
oligos_6nt_mkv2_m1_rc_shift5 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=6/12; ncol2=19; w=0; offset=4; strand=R; shift=5; score=0.751957; -----CwtgyCyGGGCATGTCysg- ; cor=; Ncor= a 0 0 0 0 0 12 100 24 19 24 7 16 35 1 21 0 179 22 0 3 9 28 45 41 0 c 0 0 0 0 0 142 30 19 20 70 143 56 3 2 1 199 6 6 3 39 169 100 50 36 0 g 0 0 0 0 0 19 16 31 131 26 37 4 159 194 177 0 3 6 195 0 2 8 70 101 0 t 0 0 0 0 0 26 53 125 29 79 12 123 2 2 0 0 11 165 1 157 19 63 34 21 0
oligos_6nt_mkv2_m5_rc_shift5 (oligos_6nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5_rc; m=7/12; ncol2=18; w=0; offset=4; strand=R; shift=5; score=0.700279; -----cwtgyCTGGGCATGTyys-- ; cor=; Ncor= a 0 0 0 0 0 15 82 24 19 16 1 19 20 4 14 2 158 21 2 2 13 31 41 0 0 c 0 0 0 0 0 116 27 10 17 55 141 31 1 3 1 169 6 4 2 16 100 62 48 0 0 g 0 0 0 0 0 18 13 24 109 28 22 3 151 161 156 1 2 10 169 1 7 16 63 0 0 t 0 0 0 0 0 24 51 115 28 74 9 120 1 5 2 1 7 138 0 154 53 64 21 0 0
oligos_6nt_mkv2_m4_rc_shift5 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4_rc; m=8/12; ncol2=24; w=0; offset=4; strand=R; shift=5; score=0.628009; -----cwtgyCtGGRCATGYCCaGr ; cor=; Ncor= a 0 0 0 0 0 9 57 14 12 7 11 7 22 6 34 1 112 8 0 2 2 3 82 5 46 c 0 0 0 0 0 85 20 11 18 58 102 27 6 0 1 129 8 3 1 93 122 100 14 13 21 g 0 0 0 0 0 15 14 24 86 21 13 14 100 123 94 1 3 8 129 1 0 6 27 102 57 t 0 0 0 0 0 22 40 82 15 45 5 83 3 2 2 0 8 112 1 35 7 22 8 11 7
oligos_6nt_mkv2_m2_rc_shift10 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=9/12; ncol2=14; w=0; offset=9; strand=R; shift=10; score=0.534753; ----------cyrGRCATGYCyrg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 29 37 80 14 170 2 231 9 1 1 3 20 64 54 0 c 0 0 0 0 0 0 0 0 0 0 118 103 5 1 0 241 2 4 1 77 228 141 41 46 0 g 0 0 0 0 0 0 0 0 0 0 45 41 141 228 76 1 4 2 242 0 1 6 103 116 0 t 0 0 0 0 0 0 0 0 0 0 54 65 20 3 0 2 9 231 2 168 14 79 38 30 0
oligos_7nt_mkv2_m3_shift10 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m3; m=10/12; ncol2=14; w=0; offset=9; strand=D; shift=10; score=0.525781; ----------cygGRCATGYCcrg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 22 21 34 7 103 3 133 5 2 1 3 10 41 35 0 c 0 0 0 0 0 0 0 0 0 0 62 56 2 2 1 138 2 3 0 37 130 97 26 24 0 g 0 0 0 0 0 0 0 0 0 0 24 26 97 131 37 0 3 2 138 1 2 2 56 62 0 t 0 0 0 0 0 0 0 0 0 0 35 40 10 3 2 2 5 133 3 104 8 34 20 22 0
positions_6nt_m2_shift13 (positions_6nt_m2)				; oligos_7nt_mkv2_m5 versus positions_6nt_m2; m=11/12; ncol2=10; w=0; offset=12; strand=D; shift=13; score=0.402903; -------------GrCATGTCyg-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 31 78 0 185 0 0 0 0 25 32 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 7 4 194 2 11 0 15 191 90 35 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 143 105 0 6 0 194 0 1 4 97 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 13 7 0 1 183 0 179 2 75 30 0 0
positions_6nt_m1_rc_shift11 (positions_6nt_m1_rc)				; oligos_7nt_mkv2_m5 versus positions_6nt_m1_rc; m=12/12; ncol2=10; w=0; offset=10; strand=R; shift=11; score=0.400673; -----------yrGGCATGyC---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 32 74 1 8 1 204 0 1 8 18 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 84 8 4 0 209 1 9 3 59 145 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 17 115 204 202 0 5 0 206 5 17 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 77 13 1 0 0 0 201 0 138 30 0 0 0 0