One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.083823_2026-01-22.083823_ivLZA5/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/2026/01/22/peak-motifs.2026-01-22.083823_2026-01-22.083823_ivLZA5/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=1; ncol=16; -sgcCCAGTTGAGCss ; Alignment reference a 0 19 23 23 4 9 110 2 2 1 1 99 3 3 28 28 c 0 44 31 79 102 106 11 7 6 7 14 19 8 96 42 37 g 0 48 59 25 29 19 9 128 7 6 120 15 115 30 48 48 t 0 26 24 10 2 3 7 0 122 123 2 4 11 8 19 24

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -sgcCCAGTTGAGCss ; cor=; Ncor= a 0 19 23 23 4 9 110 2 2 1 1 99 3 3 28 28 c 0 44 31 79 102 106 11 7 6 7 14 19 8 96 42 37 g 0 48 59 25 29 19 9 128 7 6 120 15 115 30 48 48 t 0 26 24 10 2 3 7 0 122 123 2 4 11 8 19 24

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/4; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.753545; -ssGGCAGTTGGgssc ; cor=; Ncor= a 0 51 27 34 7 9 254 1 5 2 2 19 29 19 44 64 c 0 112 127 38 49 211 15 10 13 8 58 29 56 130 95 86 g 0 93 113 199 218 50 6 274 15 5 222 231 177 111 106 69 t 0 30 19 15 12 16 11 1 253 271 4 7 24 26 41 67

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5_rc; m=3/4; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.744811; -sgrSGAGTTGGgssm ; cor=; Ncor= a 0 47 32 117 6 9 272 2 5 9 1 11 28 24 56 73 c 0 128 69 57 201 31 5 5 22 7 65 30 52 150 79 84 g 0 93 164 85 75 244 10 281 17 2 222 239 179 92 122 70 t 0 21 24 30 7 5 2 1 245 271 1 9 30 23 32 62

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2_rc; m=4/4; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.664811; bsCGGCAGTTSGGsss ; cor=; Ncor= a 33 44 11 14 2 10 174 2 3 4 2 16 15 10 36 44 c 55 71 146 14 19 149 14 7 17 5 51 24 31 114 64 64 g 64 63 38 167 178 37 9 193 12 5 147 156 148 64 79 57 t 51 25 8 8 4 7 6 1 171 189 3 7 9 15 24 38

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; yssGGGAGTTGGCGss ; Alignment reference a 46 44 40 26 1 9 203 6 8 6 4 8 20 10 47 45 c 84 82 120 29 17 28 21 11 15 11 29 21 166 58 66 74 g 51 100 62 175 220 185 7 225 23 15 208 202 41 168 90 71 t 61 16 20 12 4 20 11 0 196 210 1 11 15 6 39 52

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; yssGGGAGTTGGCGss ; cor=; Ncor= a 46 44 40 26 1 9 203 6 8 6 4 8 20 10 47 45 c 84 82 120 29 17 28 21 11 15 11 29 21 166 58 66 74 g 51 100 62 175 220 185 7 225 23 15 208 202 41 168 90 71 t 61 16 20 12 4 20 11 0 196 210 1 11 15 6 39 52

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.90242; sssGGGAGTTGGGsss ; cor=; Ncor= a 47 45 31 27 3 10 209 2 8 5 1 18 21 13 44 51 c 74 96 112 16 18 30 13 9 26 5 49 25 32 145 67 70 g 66 79 79 185 211 187 7 223 7 9 185 183 168 67 96 68 t 50 17 15 9 5 10 8 3 196 218 2 11 16 12 30 48

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.86561; -ssGGGAGTTGGgsss ; cor=; Ncor= a 0 53 43 33 5 8 240 1 6 5 1 23 29 20 58 62 c 0 101 95 32 19 33 13 10 21 8 55 24 42 124 73 81 g 0 92 106 189 240 218 4 256 10 6 214 209 176 105 105 74 t 0 24 26 16 6 11 13 3 233 251 0 14 23 21 34 53

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=4/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.826919; bsCGGCAGTTSGGsss ; cor=; Ncor= a 33 44 11 14 2 10 174 2 3 4 2 16 15 10 36 44 c 55 71 146 14 19 149 14 7 17 5 51 24 31 114 64 64 g 64 63 38 167 178 37 9 193 12 5 147 156 148 64 79 57 t 51 25 8 8 4 7 6 1 171 189 3 7 9 15 24 38

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=5/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.805773; -ssgGGAGTTGCtsss ; cor=; Ncor= a 0 40 53 41 4 9 267 2 17 4 2 21 31 12 55 73 c 0 129 102 61 25 30 16 11 24 4 35 212 61 83 83 93 g 0 107 115 170 263 241 7 285 22 10 259 48 70 195 114 87 t 0 23 29 27 7 19 9 1 236 281 3 18 137 9 47 46

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.797594; -ssGGCAGTTGGgssc ; cor=; Ncor= a 0 51 27 34 7 9 254 1 5 2 2 19 29 19 44 64 c 0 112 127 38 49 211 15 10 13 8 58 29 56 130 95 86 g 0 93 113 199 218 50 6 274 15 5 222 231 177 111 106 69 t 0 30 19 15 12 16 11 1 253 271 4 7 24 26 41 67

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=7/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.741817; sssGGGAGTTCGGCss ; cor=; Ncor= a 50 35 26 30 8 8 226 2 9 16 2 8 22 7 49 58 c 86 127 120 22 42 41 19 15 9 10 239 18 21 218 80 87 g 69 88 108 193 210 217 13 251 18 12 28 241 213 33 117 80 t 65 20 16 25 10 4 12 2 234 232 1 3 14 12 24 45

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=8/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.740259; -sgrSGAGTTGGgssm ; cor=; Ncor= a 0 47 32 117 6 9 272 2 5 9 1 11 28 24 56 73 c 0 128 69 57 201 31 5 5 22 7 65 30 52 150 79 84 g 0 93 164 85 75 244 10 281 17 2 222 239 179 92 122 70 t 0 21 24 30 7 5 2 1 245 271 1 9 30 23 32 62

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=9/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.70255; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 50 37 57 8 11 328 2 10 17 1 9 35 33 60 0 c 0 171 148 48 54 50 21 23 7 7 315 35 45 173 116 0 g 0 121 157 226 301 304 8 343 14 14 53 318 258 132 156 0 t 0 29 29 40 8 6 14 3 340 333 2 9 33 33 39 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; sssCCCAACTCCCsss ; Alignment reference a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 50 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 66 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 74 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45 47

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; sssCCCAACTCCCsss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 50 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 66 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 74 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45 47

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.930299; ssscCCAACTCCCss- ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 0 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 0 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 0 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53 0

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=3/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.915277; sssCCSAACTGCCGsv ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 51 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 64 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 55 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44 33

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.90242; ssCGCCAACTCCCssr ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 61 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 51 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 84 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44 46

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3_rc; m=5/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.896862; ssGCCGAACTCCCsss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 65 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 69 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 86 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35 50

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=6/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.854355; gsscCCAACTGCCss- ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 0 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 0 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 0 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51 0

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=7/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.814157; ksscCCAACTCSycs- ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 0 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 0 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 0 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47 0

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.793157; sssaGCAACTCCcss- ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 0 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 0 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 0 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40 0

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=9/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.791319; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 0 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 0 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 0 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssgGGAGTTGCtsss ; Alignment reference a 0 40 53 41 4 9 267 2 17 4 2 21 31 12 55 73 c 0 129 102 61 25 30 16 11 24 4 35 212 61 83 83 93 g 0 107 115 170 263 241 7 285 22 10 259 48 70 195 114 87 t 0 23 29 27 7 19 9 1 236 281 3 18 137 9 47 46

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTGCtsss ; cor=; Ncor= a 0 40 53 41 4 9 267 2 17 4 2 21 31 12 55 73 c 0 129 102 61 25 30 16 11 24 4 35 212 61 83 83 93 g 0 107 115 170 263 241 7 285 22 10 259 48 70 195 114 87 t 0 23 29 27 7 19 9 1 236 281 3 18 137 9 47 46

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.868789; -ssGGGAGTTGGgsss ; cor=; Ncor= a 0 53 43 33 5 8 240 1 6 5 1 23 29 20 58 62 c 0 101 95 32 19 33 13 10 21 8 55 24 42 124 73 81 g 0 92 106 189 240 218 4 256 10 6 214 209 176 105 105 74 t 0 24 26 16 6 11 13 3 233 251 0 14 23 21 34 53

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=3/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.805773; yssGGGAGTTGGCGss ; cor=; Ncor= a 46 44 40 26 1 9 203 6 8 6 4 8 20 10 47 45 c 84 82 120 29 17 28 21 11 15 11 29 21 166 58 66 74 g 51 100 62 175 220 185 7 225 23 15 208 202 41 168 90 71 t 61 16 20 12 4 20 11 0 196 210 1 11 15 6 39 52

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.793157; sssGGGAGTTGGGsss ; cor=; Ncor= a 47 45 31 27 3 10 209 2 8 5 1 18 21 13 44 51 c 74 96 112 16 18 30 13 9 26 5 49 25 32 145 67 70 g 66 79 79 185 211 187 7 223 7 9 185 183 168 67 96 68 t 50 17 15 9 5 10 8 3 196 218 2 11 16 12 30 48

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.775028; -ssGGCAGTTGGgssc ; cor=; Ncor= a 0 51 27 34 7 9 254 1 5 2 2 19 29 19 44 64 c 0 112 127 38 49 211 15 10 13 8 58 29 56 130 95 86 g 0 93 113 199 218 50 6 274 15 5 222 231 177 111 106 69 t 0 30 19 15 12 16 11 1 253 271 4 7 24 26 41 67

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=6/8; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.757738; -sgrSGAGTTGGgssm ; cor=; Ncor= a 0 47 32 117 6 9 272 2 5 9 1 11 28 24 56 73 c 0 128 69 57 201 31 5 5 22 7 65 30 52 150 79 84 g 0 93 164 85 75 244 10 281 17 2 222 239 179 92 122 70 t 0 21 24 30 7 5 2 1 245 271 1 9 30 23 32 62

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=7/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.699065; bsCGGCAGTTSGGsss ; cor=; Ncor= a 33 44 11 14 2 10 174 2 3 4 2 16 15 10 36 44 c 55 71 146 14 19 149 14 7 17 5 51 24 31 114 64 64 g 64 63 38 167 178 37 9 193 12 5 147 156 148 64 79 57 t 51 25 8 8 4 7 6 1 171 189 3 7 9 15 24 38

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=8/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.692523; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 50 37 57 8 11 328 2 10 17 1 9 35 33 60 0 c 0 171 148 48 54 50 21 23 7 7 315 35 45 173 116 0 g 0 121 157 226 301 304 8 343 14 14 53 318 258 132 156 0 t 0 29 29 40 8 6 14 3 340 333 2 9 33 33 39 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift1 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssCCGAACTCCcss ; Alignment reference a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssCCGAACTCCcss ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.856592; ssGCCGAACTCCCss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.846323; ssscCCAACTCCCss ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=4/9; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.791319; sssCCCAACTCCCss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=5/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.775068; ksscCCAACTCSycs ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=6/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.773548; gsscCCAACTGCCss ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=7/9; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.722145; sssCCSAACTGCCGs ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.70255; ssCGCCAACTCCCss ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=9/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.692523; sssaGCAACTCCcss ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ssscCCAACTCCCss ; Alignment reference a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssscCCAACTCCCss ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=2/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.930299; sssCCCAACTCCCss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.911965; gsscCCAACTGCCss ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=4/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.882446; ksscCCAACTCSycs ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4_rc; m=5/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.868789; sssaGCAACTCCcss ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=6/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.86561; ssCGCCAACTCCCss ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=7/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.846323; -ssCCGAACTCCcss ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=8/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.841363; sssCCSAACTGCCGs ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3_rc; m=9/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.823406; ssGCCGAACTCCCss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; gsscCCAACTGCCss ; Alignment reference a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gsscCCAACTGCCss ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=2/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.917168; sssCCSAACTGCCGs ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.911965; ssscCCAACTCCCss ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=4/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.854355; sssCCCAACTCCCss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=5/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.815857; ksscCCAACTCSycs ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=6/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.797594; ssCGCCAACTCCCss ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=7/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.775028; sssaGCAACTCCcss ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=8/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.773548; -ssCCGAACTCCcss ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=9/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.756681; ssGCCGAACTCCCss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.753545; ssGCTCAACTGGgcs ; cor=; Ncor= a 24 19 8 11 4 2 123 122 0 7 3 2 10 24 26 c 48 48 30 115 15 120 6 7 128 9 19 29 25 59 48 g 37 42 96 8 19 14 7 6 7 11 106 102 79 31 44 t 28 28 3 3 99 1 1 2 2 110 9 4 23 23 19

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=16; shift=0; ncol=16; sssGGGAGTTCGGCss ; Alignment reference a 50 35 26 30 8 8 226 2 9 16 2 8 22 7 49 58 c 86 127 120 22 42 41 19 15 9 10 239 18 21 218 80 87 g 69 88 108 193 210 217 13 251 18 12 28 241 213 33 117 80 t 65 20 16 25 10 4 12 2 234 232 1 3 14 12 24 45

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; sssGGGAGTTCGGCss ; cor=; Ncor= a 50 35 26 30 8 8 226 2 9 16 2 8 22 7 49 58 c 86 127 120 22 42 41 19 15 9 10 239 18 21 218 80 87 g 69 88 108 193 210 217 13 251 18 12 28 241 213 33 117 80 t 65 20 16 25 10 4 12 2 234 232 1 3 14 12 24 45

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.896862; sssGGGAGTTGGGsss ; cor=; Ncor= a 47 45 31 27 3 10 209 2 8 5 1 18 21 13 44 51 c 74 96 112 16 18 30 13 9 26 5 49 25 32 145 67 70 g 66 79 79 185 211 187 7 223 7 9 185 183 168 67 96 68 t 50 17 15 9 5 10 8 3 196 218 2 11 16 12 30 48

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.856592; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 50 37 57 8 11 328 2 10 17 1 9 35 33 60 0 c 0 171 148 48 54 50 21 23 7 7 315 35 45 173 116 0 g 0 121 157 226 301 304 8 343 14 14 53 318 258 132 156 0 t 0 29 29 40 8 6 14 3 340 333 2 9 33 33 39 0

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=4/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.824766; bsCGGCAGTTSGGsss ; cor=; Ncor= a 33 44 11 14 2 10 174 2 3 4 2 16 15 10 36 44 c 55 71 146 14 19 149 14 7 17 5 51 24 31 114 64 64 g 64 63 38 167 178 37 9 193 12 5 147 156 148 64 79 57 t 51 25 8 8 4 7 6 1 171 189 3 7 9 15 24 38

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/8; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.823406; -ssGGGAGTTGGgsss ; cor=; Ncor= a 0 53 43 33 5 8 240 1 6 5 1 23 29 20 58 62 c 0 101 95 32 19 33 13 10 21 8 55 24 42 124 73 81 g 0 92 106 189 240 218 4 256 10 6 214 209 176 105 105 74 t 0 24 26 16 6 11 13 3 233 251 0 14 23 21 34 53

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/8; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.756681; -ssGGCAGTTGGgssc ; cor=; Ncor= a 0 51 27 34 7 9 254 1 5 2 2 19 29 19 44 64 c 0 112 127 38 49 211 15 10 13 8 58 29 56 130 95 86 g 0 93 113 199 218 50 6 274 15 5 222 231 177 111 106 69 t 0 30 19 15 12 16 11 1 253 271 4 7 24 26 41 67

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=7/8; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.752899; -sgrSGAGTTGGgssm ; cor=; Ncor= a 0 47 32 117 6 9 272 2 5 9 1 11 28 24 56 73 c 0 128 69 57 201 31 5 5 22 7 65 30 52 150 79 84 g 0 93 164 85 75 244 10 281 17 2 222 239 179 92 122 70 t 0 21 24 30 7 5 2 1 245 271 1 9 30 23 32 62

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=8/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.741817; yssGGGAGTTGGCGss ; cor=; Ncor= a 46 44 40 26 1 9 203 6 8 6 4 8 20 10 47 45 c 84 82 120 29 17 28 21 11 15 11 29 21 166 58 66 74 g 51 100 62 175 220 185 7 225 23 15 208 202 41 168 90 71 t 61 16 20 12 4 20 11 0 196 210 1 11 15 6 39 52

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; sssCCSAACTGCCGsv ; Alignment reference a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 51 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 64 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 55 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44 33

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; sssCCSAACTGCCGsv ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 51 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 64 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 55 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44 33

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.917168; gsscCCAACTGCCss- ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 0 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 0 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 0 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51 0

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=3/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.915277; sssCCCAACTCCCsss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 50 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 66 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 74 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45 47

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=4/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.841363; ssscCCAACTCCCss- ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 0 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 0 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 0 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53 0

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=5/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.826919; ssCGCCAACTCCCssr ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 61 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 51 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 84 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44 46

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=6/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.824766; ssGCCGAACTCCCsss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 65 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 69 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 86 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35 50

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.722145; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 0 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 0 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 0 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50 0

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.706099; ksscCCAACTCSycs- ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 0 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 0 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 0 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47 0

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=9/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.699065; sssaGCAACTCCcss- ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 0 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 0 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 0 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40 0

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.664811; ssGCTCAACTGGgcs- ; cor=; Ncor= a 24 19 8 11 4 2 123 122 0 7 3 2 10 24 26 0 c 48 48 30 115 15 120 6 7 128 9 19 29 25 59 48 0 g 37 42 96 8 19 14 7 6 7 11 106 102 79 31 44 0 t 28 28 3 3 99 1 1 2 2 110 9 4 23 23 19 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; ksscCCAACTCSycs ; Alignment reference a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ksscCCAACTCSycs ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.882446; ssscCCAACTCCCss ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.815857; gsscCCAACTGCCss ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=4/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.814157; sssCCCAACTCCCss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=5/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.775068; -ssCCGAACTCCcss ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.757738; sssaGCAACTCCcss ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3_rc; m=7/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.752899; ssGCCGAACTCCCss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5_rc; m=8/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.744811; ssGCTCAACTGGgcs ; cor=; Ncor= a 24 19 8 11 4 2 123 122 0 7 3 2 10 24 26 c 48 48 30 115 15 120 6 7 128 9 19 29 25 59 48 g 37 42 96 8 19 14 7 6 7 11 106 102 79 31 44 t 28 28 3 3 99 1 1 2 2 110 9 4 23 23 19

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=9/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.740259; ssCGCCAACTCCCss ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=10/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.706099; sssCCSAACTGCCGs ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=1; ncol=16; -sgcCCAGTTGAGCss ; Alignment reference a 0 19 23 23 4 9 110 2 2 1 1 99 3 3 28 28 c 0 44 31 79 102 106 11 7 6 7 14 19 8 96 42 37 g 0 48 59 25 29 19 9 128 7 6 120 15 115 30 48 48 t 0 26 24 10 2 3 7 0 122 123 2 4 11 8 19 24
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -sgcCCAGTTGAGCss ; cor=; Ncor= a 0 19 23 23 4 9 110 2 2 1 1 99 3 3 28 28 c 0 44 31 79 102 106 11 7 6 7 14 19 8 96 42 37 g 0 48 59 25 29 19 9 128 7 6 120 15 115 30 48 48 t 0 26 24 10 2 3 7 0 122 123 2 4 11 8 19 24
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/4; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.753545; -ssGGCAGTTGGgssc ; cor=; Ncor= a 0 51 27 34 7 9 254 1 5 2 2 19 29 19 44 64 c 0 112 127 38 49 211 15 10 13 8 58 29 56 130 95 86 g 0 93 113 199 218 50 6 274 15 5 222 231 177 111 106 69 t 0 30 19 15 12 16 11 1 253 271 4 7 24 26 41 67
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5_rc; m=3/4; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.744811; -sgrSGAGTTGGgssm ; cor=; Ncor= a 0 47 32 117 6 9 272 2 5 9 1 11 28 24 56 73 c 0 128 69 57 201 31 5 5 22 7 65 30 52 150 79 84 g 0 93 164 85 75 244 10 281 17 2 222 239 179 92 122 70 t 0 21 24 30 7 5 2 1 245 271 1 9 30 23 32 62
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2_rc; m=4/4; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.664811; bsCGGCAGTTSGGsss ; cor=; Ncor= a 33 44 11 14 2 10 174 2 3 4 2 16 15 10 36 44 c 55 71 146 14 19 149 14 7 17 5 51 24 31 114 64 64 g 64 63 38 167 178 37 9 193 12 5 147 156 148 64 79 57 t 51 25 8 8 4 7 6 1 171 189 3 7 9 15 24 38

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; yssGGGAGTTGGCGss ; Alignment reference a 46 44 40 26 1 9 203 6 8 6 4 8 20 10 47 45 c 84 82 120 29 17 28 21 11 15 11 29 21 166 58 66 74 g 51 100 62 175 220 185 7 225 23 15 208 202 41 168 90 71 t 61 16 20 12 4 20 11 0 196 210 1 11 15 6 39 52
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; yssGGGAGTTGGCGss ; cor=; Ncor= a 46 44 40 26 1 9 203 6 8 6 4 8 20 10 47 45 c 84 82 120 29 17 28 21 11 15 11 29 21 166 58 66 74 g 51 100 62 175 220 185 7 225 23 15 208 202 41 168 90 71 t 61 16 20 12 4 20 11 0 196 210 1 11 15 6 39 52
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.90242; sssGGGAGTTGGGsss ; cor=; Ncor= a 47 45 31 27 3 10 209 2 8 5 1 18 21 13 44 51 c 74 96 112 16 18 30 13 9 26 5 49 25 32 145 67 70 g 66 79 79 185 211 187 7 223 7 9 185 183 168 67 96 68 t 50 17 15 9 5 10 8 3 196 218 2 11 16 12 30 48
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.86561; -ssGGGAGTTGGgsss ; cor=; Ncor= a 0 53 43 33 5 8 240 1 6 5 1 23 29 20 58 62 c 0 101 95 32 19 33 13 10 21 8 55 24 42 124 73 81 g 0 92 106 189 240 218 4 256 10 6 214 209 176 105 105 74 t 0 24 26 16 6 11 13 3 233 251 0 14 23 21 34 53
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=4/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.826919; bsCGGCAGTTSGGsss ; cor=; Ncor= a 33 44 11 14 2 10 174 2 3 4 2 16 15 10 36 44 c 55 71 146 14 19 149 14 7 17 5 51 24 31 114 64 64 g 64 63 38 167 178 37 9 193 12 5 147 156 148 64 79 57 t 51 25 8 8 4 7 6 1 171 189 3 7 9 15 24 38
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=5/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.805773; -ssgGGAGTTGCtsss ; cor=; Ncor= a 0 40 53 41 4 9 267 2 17 4 2 21 31 12 55 73 c 0 129 102 61 25 30 16 11 24 4 35 212 61 83 83 93 g 0 107 115 170 263 241 7 285 22 10 259 48 70 195 114 87 t 0 23 29 27 7 19 9 1 236 281 3 18 137 9 47 46
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.797594; -ssGGCAGTTGGgssc ; cor=; Ncor= a 0 51 27 34 7 9 254 1 5 2 2 19 29 19 44 64 c 0 112 127 38 49 211 15 10 13 8 58 29 56 130 95 86 g 0 93 113 199 218 50 6 274 15 5 222 231 177 111 106 69 t 0 30 19 15 12 16 11 1 253 271 4 7 24 26 41 67
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=7/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.741817; sssGGGAGTTCGGCss ; cor=; Ncor= a 50 35 26 30 8 8 226 2 9 16 2 8 22 7 49 58 c 86 127 120 22 42 41 19 15 9 10 239 18 21 218 80 87 g 69 88 108 193 210 217 13 251 18 12 28 241 213 33 117 80 t 65 20 16 25 10 4 12 2 234 232 1 3 14 12 24 45
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=8/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.740259; -sgrSGAGTTGGgssm ; cor=; Ncor= a 0 47 32 117 6 9 272 2 5 9 1 11 28 24 56 73 c 0 128 69 57 201 31 5 5 22 7 65 30 52 150 79 84 g 0 93 164 85 75 244 10 281 17 2 222 239 179 92 122 70 t 0 21 24 30 7 5 2 1 245 271 1 9 30 23 32 62
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=9/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.70255; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 50 37 57 8 11 328 2 10 17 1 9 35 33 60 0 c 0 171 148 48 54 50 21 23 7 7 315 35 45 173 116 0 g 0 121 157 226 301 304 8 343 14 14 53 318 258 132 156 0 t 0 29 29 40 8 6 14 3 340 333 2 9 33 33 39 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; sssCCCAACTCCCsss ; Alignment reference a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 50 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 66 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 74 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45 47
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; sssCCCAACTCCCsss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 50 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 66 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 74 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45 47
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.930299; ssscCCAACTCCCss- ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 0 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 0 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 0 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53 0
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=3/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.915277; sssCCSAACTGCCGsv ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 51 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 64 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 55 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44 33
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.90242; ssCGCCAACTCCCssr ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 61 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 51 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 84 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44 46
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3_rc; m=5/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.896862; ssGCCGAACTCCCsss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 65 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 69 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 86 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35 50
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=6/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.854355; gsscCCAACTGCCss- ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 0 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 0 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 0 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51 0
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=7/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.814157; ksscCCAACTCSycs- ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 0 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 0 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 0 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47 0
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.793157; sssaGCAACTCCcss- ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 0 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 0 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 0 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40 0
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=9/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.791319; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 0 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 0 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 0 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssgGGAGTTGCtsss ; Alignment reference a 0 40 53 41 4 9 267 2 17 4 2 21 31 12 55 73 c 0 129 102 61 25 30 16 11 24 4 35 212 61 83 83 93 g 0 107 115 170 263 241 7 285 22 10 259 48 70 195 114 87 t 0 23 29 27 7 19 9 1 236 281 3 18 137 9 47 46
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTGCtsss ; cor=; Ncor= a 0 40 53 41 4 9 267 2 17 4 2 21 31 12 55 73 c 0 129 102 61 25 30 16 11 24 4 35 212 61 83 83 93 g 0 107 115 170 263 241 7 285 22 10 259 48 70 195 114 87 t 0 23 29 27 7 19 9 1 236 281 3 18 137 9 47 46
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.868789; -ssGGGAGTTGGgsss ; cor=; Ncor= a 0 53 43 33 5 8 240 1 6 5 1 23 29 20 58 62 c 0 101 95 32 19 33 13 10 21 8 55 24 42 124 73 81 g 0 92 106 189 240 218 4 256 10 6 214 209 176 105 105 74 t 0 24 26 16 6 11 13 3 233 251 0 14 23 21 34 53
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=3/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.805773; yssGGGAGTTGGCGss ; cor=; Ncor= a 46 44 40 26 1 9 203 6 8 6 4 8 20 10 47 45 c 84 82 120 29 17 28 21 11 15 11 29 21 166 58 66 74 g 51 100 62 175 220 185 7 225 23 15 208 202 41 168 90 71 t 61 16 20 12 4 20 11 0 196 210 1 11 15 6 39 52
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.793157; sssGGGAGTTGGGsss ; cor=; Ncor= a 47 45 31 27 3 10 209 2 8 5 1 18 21 13 44 51 c 74 96 112 16 18 30 13 9 26 5 49 25 32 145 67 70 g 66 79 79 185 211 187 7 223 7 9 185 183 168 67 96 68 t 50 17 15 9 5 10 8 3 196 218 2 11 16 12 30 48
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.775028; -ssGGCAGTTGGgssc ; cor=; Ncor= a 0 51 27 34 7 9 254 1 5 2 2 19 29 19 44 64 c 0 112 127 38 49 211 15 10 13 8 58 29 56 130 95 86 g 0 93 113 199 218 50 6 274 15 5 222 231 177 111 106 69 t 0 30 19 15 12 16 11 1 253 271 4 7 24 26 41 67
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=6/8; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.757738; -sgrSGAGTTGGgssm ; cor=; Ncor= a 0 47 32 117 6 9 272 2 5 9 1 11 28 24 56 73 c 0 128 69 57 201 31 5 5 22 7 65 30 52 150 79 84 g 0 93 164 85 75 244 10 281 17 2 222 239 179 92 122 70 t 0 21 24 30 7 5 2 1 245 271 1 9 30 23 32 62
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=7/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.699065; bsCGGCAGTTSGGsss ; cor=; Ncor= a 33 44 11 14 2 10 174 2 3 4 2 16 15 10 36 44 c 55 71 146 14 19 149 14 7 17 5 51 24 31 114 64 64 g 64 63 38 167 178 37 9 193 12 5 147 156 148 64 79 57 t 51 25 8 8 4 7 6 1 171 189 3 7 9 15 24 38
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=8/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.692523; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 50 37 57 8 11 328 2 10 17 1 9 35 33 60 0 c 0 171 148 48 54 50 21 23 7 7 315 35 45 173 116 0 g 0 121 157 226 301 304 8 343 14 14 53 318 258 132 156 0 t 0 29 29 40 8 6 14 3 340 333 2 9 33 33 39 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssCCGAACTCCcss ; Alignment reference a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssCCGAACTCCcss ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.856592; ssGCCGAACTCCCss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.846323; ssscCCAACTCCCss ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=4/9; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.791319; sssCCCAACTCCCss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=5/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.775068; ksscCCAACTCSycs ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=6/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.773548; gsscCCAACTGCCss ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=7/9; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.722145; sssCCSAACTGCCGs ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.70255; ssCGCCAACTCCCss ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=9/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.692523; sssaGCAACTCCcss ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ssscCCAACTCCCss ; Alignment reference a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssscCCAACTCCCss ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=2/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.930299; sssCCCAACTCCCss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.911965; gsscCCAACTGCCss ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=4/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.882446; ksscCCAACTCSycs ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4_rc; m=5/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.868789; sssaGCAACTCCcss ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=6/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.86561; ssCGCCAACTCCCss ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=7/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.846323; -ssCCGAACTCCcss ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=8/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.841363; sssCCSAACTGCCGs ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3_rc; m=9/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.823406; ssGCCGAACTCCCss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; gsscCCAACTGCCss ; Alignment reference a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gsscCCAACTGCCss ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=2/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.917168; sssCCSAACTGCCGs ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.911965; ssscCCAACTCCCss ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=4/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.854355; sssCCCAACTCCCss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=5/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.815857; ksscCCAACTCSycs ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=6/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.797594; ssCGCCAACTCCCss ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=7/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.775028; sssaGCAACTCCcss ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=8/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.773548; -ssCCGAACTCCcss ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=9/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.756681; ssGCCGAACTCCCss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.753545; ssGCTCAACTGGgcs ; cor=; Ncor= a 24 19 8 11 4 2 123 122 0 7 3 2 10 24 26 c 48 48 30 115 15 120 6 7 128 9 19 29 25 59 48 g 37 42 96 8 19 14 7 6 7 11 106 102 79 31 44 t 28 28 3 3 99 1 1 2 2 110 9 4 23 23 19

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=16; shift=0; ncol=16; sssGGGAGTTCGGCss ; Alignment reference a 50 35 26 30 8 8 226 2 9 16 2 8 22 7 49 58 c 86 127 120 22 42 41 19 15 9 10 239 18 21 218 80 87 g 69 88 108 193 210 217 13 251 18 12 28 241 213 33 117 80 t 65 20 16 25 10 4 12 2 234 232 1 3 14 12 24 45
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; sssGGGAGTTCGGCss ; cor=; Ncor= a 50 35 26 30 8 8 226 2 9 16 2 8 22 7 49 58 c 86 127 120 22 42 41 19 15 9 10 239 18 21 218 80 87 g 69 88 108 193 210 217 13 251 18 12 28 241 213 33 117 80 t 65 20 16 25 10 4 12 2 234 232 1 3 14 12 24 45
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.896862; sssGGGAGTTGGGsss ; cor=; Ncor= a 47 45 31 27 3 10 209 2 8 5 1 18 21 13 44 51 c 74 96 112 16 18 30 13 9 26 5 49 25 32 145 67 70 g 66 79 79 185 211 187 7 223 7 9 185 183 168 67 96 68 t 50 17 15 9 5 10 8 3 196 218 2 11 16 12 30 48
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.856592; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 50 37 57 8 11 328 2 10 17 1 9 35 33 60 0 c 0 171 148 48 54 50 21 23 7 7 315 35 45 173 116 0 g 0 121 157 226 301 304 8 343 14 14 53 318 258 132 156 0 t 0 29 29 40 8 6 14 3 340 333 2 9 33 33 39 0
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=4/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.824766; bsCGGCAGTTSGGsss ; cor=; Ncor= a 33 44 11 14 2 10 174 2 3 4 2 16 15 10 36 44 c 55 71 146 14 19 149 14 7 17 5 51 24 31 114 64 64 g 64 63 38 167 178 37 9 193 12 5 147 156 148 64 79 57 t 51 25 8 8 4 7 6 1 171 189 3 7 9 15 24 38
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/8; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.823406; -ssGGGAGTTGGgsss ; cor=; Ncor= a 0 53 43 33 5 8 240 1 6 5 1 23 29 20 58 62 c 0 101 95 32 19 33 13 10 21 8 55 24 42 124 73 81 g 0 92 106 189 240 218 4 256 10 6 214 209 176 105 105 74 t 0 24 26 16 6 11 13 3 233 251 0 14 23 21 34 53
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/8; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.756681; -ssGGCAGTTGGgssc ; cor=; Ncor= a 0 51 27 34 7 9 254 1 5 2 2 19 29 19 44 64 c 0 112 127 38 49 211 15 10 13 8 58 29 56 130 95 86 g 0 93 113 199 218 50 6 274 15 5 222 231 177 111 106 69 t 0 30 19 15 12 16 11 1 253 271 4 7 24 26 41 67
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=7/8; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.752899; -sgrSGAGTTGGgssm ; cor=; Ncor= a 0 47 32 117 6 9 272 2 5 9 1 11 28 24 56 73 c 0 128 69 57 201 31 5 5 22 7 65 30 52 150 79 84 g 0 93 164 85 75 244 10 281 17 2 222 239 179 92 122 70 t 0 21 24 30 7 5 2 1 245 271 1 9 30 23 32 62
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=8/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.741817; yssGGGAGTTGGCGss ; cor=; Ncor= a 46 44 40 26 1 9 203 6 8 6 4 8 20 10 47 45 c 84 82 120 29 17 28 21 11 15 11 29 21 166 58 66 74 g 51 100 62 175 220 185 7 225 23 15 208 202 41 168 90 71 t 61 16 20 12 4 20 11 0 196 210 1 11 15 6 39 52

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; sssCCSAACTGCCGsv ; Alignment reference a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 51 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 64 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 55 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44 33
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; sssCCSAACTGCCGsv ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 51 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 64 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 55 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44 33
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.917168; gsscCCAACTGCCss- ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 0 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 0 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 0 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51 0
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=3/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.915277; sssCCCAACTCCCsss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 50 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 66 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 74 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45 47
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=4/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.841363; ssscCCAACTCCCss- ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 0 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 0 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 0 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53 0
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=5/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.826919; ssCGCCAACTCCCssr ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 61 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 51 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 84 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44 46
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=6/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.824766; ssGCCGAACTCCCsss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 65 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 69 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 86 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35 50
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.722145; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 0 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 0 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 0 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50 0
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.706099; ksscCCAACTCSycs- ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 0 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 0 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 0 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47 0
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=9/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.699065; sssaGCAACTCCcss- ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 0 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 0 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 0 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40 0
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.664811; ssGCTCAACTGGgcs- ; cor=; Ncor= a 24 19 8 11 4 2 123 122 0 7 3 2 10 24 26 0 c 48 48 30 115 15 120 6 7 128 9 19 29 25 59 48 0 g 37 42 96 8 19 14 7 6 7 11 106 102 79 31 44 0 t 28 28 3 3 99 1 1 2 2 110 9 4 23 23 19 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; ksscCCAACTCSycs ; Alignment reference a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ksscCCAACTCSycs ; cor=; Ncor= a 62 32 23 30 9 1 271 245 1 2 5 7 30 24 21 c 70 122 92 179 239 222 2 17 281 10 244 75 85 164 93 g 84 79 150 52 30 65 7 22 5 5 31 201 57 69 128 t 73 56 24 28 11 1 9 5 2 272 9 6 117 32 47
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.882446; ssscCCAACTCCCss ; cor=; Ncor= a 53 34 21 23 14 0 251 233 3 13 11 6 16 26 24 c 74 105 105 176 209 214 6 10 256 4 218 240 189 106 92 g 81 73 124 42 24 55 8 21 10 13 33 19 32 95 101 t 62 58 20 29 23 1 5 6 1 240 8 5 33 43 53
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.815857; gsscCCAACTGCCss ; cor=; Ncor= a 67 41 26 24 7 4 271 253 1 11 16 12 15 19 30 c 69 106 111 177 231 222 5 15 274 6 50 218 199 113 93 g 86 95 130 56 29 58 8 13 10 15 211 49 38 127 112 t 64 44 19 29 19 2 2 5 1 254 9 7 34 27 51
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=4/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.814157; sssCCCAACTCCCss ; cor=; Ncor= a 48 30 12 16 11 2 218 196 3 8 10 5 9 15 17 c 68 96 67 168 183 185 9 7 223 7 187 211 185 79 79 g 70 67 145 32 25 49 5 26 9 13 30 18 16 112 96 t 51 44 13 21 18 1 5 8 2 209 10 3 27 31 45
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=5/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.775068; -ssCCGAACTCCcss ; cor=; Ncor= a 0 39 33 33 9 2 333 340 3 14 6 8 40 29 29 c 0 156 132 258 318 53 14 14 343 8 304 301 226 157 121 g 0 116 173 45 35 315 7 7 23 21 50 54 48 148 171 t 0 60 33 35 9 1 17 10 2 328 11 8 57 37 50
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.757738; sssaGCAACTCCcss ; cor=; Ncor= a 46 47 9 137 18 3 281 236 1 9 19 7 27 29 23 c 87 114 195 70 48 259 10 22 285 7 241 263 170 115 107 g 93 83 83 61 212 35 4 24 11 16 30 25 61 102 129 t 73 55 12 31 21 2 4 17 2 267 9 4 41 53 40
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3_rc; m=7/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.752899; ssGCCGAACTCCCss ; cor=; Ncor= a 45 24 12 14 3 1 232 234 2 12 4 10 25 16 20 c 80 117 33 213 241 28 12 18 251 13 217 210 193 108 88 g 87 80 218 21 18 239 10 9 15 19 41 42 22 120 127 t 58 49 7 22 8 2 16 9 2 226 8 8 30 26 35
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5_rc; m=8/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.744811; ssGCTCAACTGGgcs ; cor=; Ncor= a 24 19 8 11 4 2 123 122 0 7 3 2 10 24 26 c 48 48 30 115 15 120 6 7 128 9 19 29 25 59 48 g 37 42 96 8 19 14 7 6 7 11 106 102 79 31 44 t 28 28 3 3 99 1 1 2 2 110 9 4 23 23 19
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=9/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.740259; ssCGCCAACTCCCss ; cor=; Ncor= a 52 39 6 15 11 1 210 196 0 11 20 4 12 20 16 c 71 90 168 41 202 208 15 23 225 7 185 220 175 62 100 g 74 66 58 166 21 29 11 15 11 21 28 17 29 120 82 t 45 47 10 20 8 4 6 8 6 203 9 1 26 40 44
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=10/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.706099; sssCCSAACTGCCGs ; cor=; Ncor= a 38 24 15 9 7 3 189 171 1 6 7 4 8 8 25 c 57 79 64 148 156 147 5 12 193 9 37 178 167 38 63 g 64 64 114 31 24 51 5 17 7 14 149 19 14 146 71 t 44 36 10 15 16 2 4 3 2 174 10 2 14 11 44