One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084248_2026-01-22.084248_6xcnbh/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.2026-01-22.084248_2026-01-22.084248_6xcnbh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift1 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssgGGAGTTGctss ; Alignment reference a 0 54 71 58 4 15 381 1 15 8 6 38 50 22 74 c 0 174 148 75 47 50 21 11 31 8 46 274 101 161 123 g 0 169 163 244 357 335 7 405 23 14 365 82 95 212 166 t 0 23 38 43 12 20 11 3 351 390 3 26 174 25 57

oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTGctss ; cor=; Ncor= a 0 54 71 58 4 15 381 1 15 8 6 38 50 22 74 c 0 174 148 75 47 50 21 11 31 8 46 274 101 161 123 g 0 169 163 244 357 335 7 405 23 14 365 82 95 212 166 t 0 23 38 43 12 20 11 3 351 390 3 26 174 25 57

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1_rc; m=2/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.903208; -ssgGGAGTTGGgss ; cor=; Ncor= a 0 58 50 51 4 9 320 0 6 6 2 25 43 30 62 c 0 136 127 56 36 38 16 15 26 9 73 34 74 151 105 g 0 145 148 220 308 289 7 335 13 5 278 281 194 141 143 t 0 15 29 27 6 18 11 4 309 334 1 14 43 32 44

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.828191; cssGGGAGTTGGcss ; cor=; Ncor= a 59 57 35 22 3 7 266 4 5 8 3 19 29 19 48 c 106 113 174 37 31 35 20 13 23 14 49 27 193 131 95 g 71 119 82 228 265 243 8 287 20 11 252 244 54 136 120 t 69 16 14 18 6 20 11 1 257 272 1 15 29 19 42

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=4/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.814431; -ssgCGAGTTGCtss ; cor=; Ncor= a 0 32 47 42 2 6 319 5 15 5 3 19 22 11 41 c 0 168 90 72 292 33 13 9 39 8 56 264 63 123 124 g 0 137 180 207 47 305 14 332 47 13 287 55 48 199 148 t 0 11 31 27 7 4 2 2 247 322 2 10 215 15 35

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=5/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.774336; -sgsCGAGTTGGsss ; cor=; Ncor= a 0 58 51 76 3 4 372 2 4 6 3 17 53 38 59 c 0 175 90 130 334 31 14 12 37 12 81 33 128 170 118 g 0 135 221 144 54 355 10 379 32 8 309 338 162 158 173 t 0 28 34 46 5 6 0 3 323 370 3 8 53 30 46

oligos_7nt_test_vs_ctrl_m1_rc_shift1 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=6/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.770908; -sggCGAGTTGGCss ; cor=; Ncor= a 0 47 46 28 5 4 273 3 6 4 1 18 20 22 43 c 0 143 67 64 244 31 20 14 18 9 63 18 217 121 95 g 0 99 171 185 47 263 8 286 20 10 238 259 44 134 126 t 0 14 19 26 7 5 2 0 259 280 1 8 22 26 39

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=7/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.737449; cssGGCAGTTGGCss ; cor=; Ncor= a 49 42 18 11 3 8 213 4 6 5 3 11 22 14 31 c 84 87 152 22 24 187 14 15 18 11 39 30 180 102 76 g 60 102 66 217 224 40 17 234 26 7 210 200 34 115 105 t 62 24 19 5 4 20 11 2 205 232 3 14 19 24 43

oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=8/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.699874; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 51 54 81 8 14 427 3 12 19 2 14 44 40 70 c 0 227 179 70 75 62 23 31 5 7 432 35 73 235 157 g 0 171 216 278 382 397 14 443 25 20 47 423 313 159 207 t 0 32 32 52 16 8 17 4 439 435 0 9 51 47 47

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=9/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.629623; sssGGGAGTTCGGCs ; cor=; Ncor= a 67 38 29 40 5 6 289 2 9 21 1 6 23 13 47 c 99 151 182 32 52 49 21 24 10 14 301 24 44 249 113 g 86 122 111 235 270 275 14 304 22 13 31 299 242 53 144 t 82 23 12 27 7 4 10 4 293 286 1 5 25 19 30

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssGCCAACTGCCssg ; Alignment reference a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 62 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 60 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 84 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42 49

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTGCCssg ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 62 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 60 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 84 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42 49

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=2/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.91521; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 69 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 71 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 106 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57 59

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.794016; -sscCCAACTCCcss- ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 0 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 0 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 0 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58 0

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=4/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.754628; -sssCCAACTGGsss- ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 0 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 0 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 0 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50 0

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=5/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.737449; -ssagCAACTCCcss- ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 0 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 0 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 0 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54 0

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1; m=6/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.716658; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 0 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 0 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 0 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47 0

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=7/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.676017; ssGCCGAACTCCCsss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 82 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 86 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 99 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38 67

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.631703; ssscCGAACTCCcss- ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 0 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 0 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 0 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift1 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssgCCAACTCCCssg ; Alignment reference a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 69 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 71 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 106 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57 59

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 69 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 71 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 106 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57 59

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.91521; -ssGCCAACTGCCssg ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 62 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 60 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 84 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42 49

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.892199; -sscCCAACTCCcss- ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 0 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 0 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 0 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58 0

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=4/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.828191; -ssagCAACTCCcss- ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 0 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 0 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 0 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54 0

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.812459; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 0 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 0 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 0 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47 0

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=6/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.76983; -sssCCAACTCGscs- ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 0 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 0 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 0 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58 0

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=7/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.766752; ssGCCGAACTCCCsss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 82 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 86 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 99 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38 67

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.723888; ssscCGAACTCCcss- ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 0 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 0 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 0 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51 0

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=9/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.687863; -sssCCAACTGGsss- ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 0 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 0 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 0 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50 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=-1; offset=-1; strand=R; shift=0; score=0.632408; sssaGCAACTCGcss- ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 0 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 0 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 0 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32 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; -sssCCAACTCGscs ; Alignment reference a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58

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; -sssCCAACTCGscs ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=2/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.966178; -ssGCCAACTCGccs ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=3/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.87216; -sssCCAACTGGsss ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=4/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.864864; -sscCCAACTCCcss ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=5/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.795267; sssaGCAACTCGcss ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=6/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.774336; -ssagCAACTCCcss ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=7/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.76983; -ssgCCAACTCCCss ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.733248; ssscCGAACTCCcss ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=9/9; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.655098; ssGCCGAACTCCCss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift1 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssgGGAGTTCGgsss ; Alignment reference a 0 51 54 81 8 14 427 3 12 19 2 14 44 40 70 118 c 0 227 179 70 75 62 23 31 5 7 432 35 73 235 157 151 g 0 171 216 278 382 397 14 443 25 20 47 423 313 159 207 128 t 0 32 32 52 16 8 17 4 439 435 0 9 51 47 47 84

oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTCGgsss ; cor=; Ncor= a 0 51 54 81 8 14 427 3 12 19 2 14 44 40 70 118 c 0 227 179 70 75 62 23 31 5 7 432 35 73 235 157 151 g 0 171 216 278 382 397 14 443 25 20 47 423 313 159 207 128 t 0 32 32 52 16 8 17 4 439 435 0 9 51 47 47 84

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=2/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.921632; sssGGGAGTTCGGCss ; cor=; Ncor= a 67 38 29 40 5 6 289 2 9 21 1 6 23 13 47 75 c 99 151 182 32 52 49 21 24 10 14 301 24 44 249 113 111 g 86 122 111 235 270 275 14 304 22 13 31 299 242 53 144 90 t 82 23 12 27 7 4 10 4 293 286 1 5 25 19 30 58

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.835504; -ssgGGAGTTGGgss- ; cor=; Ncor= a 0 58 50 51 4 9 320 0 6 6 2 25 43 30 62 0 c 0 136 127 56 36 38 16 15 26 9 73 34 74 151 105 0 g 0 145 148 220 308 289 7 335 13 5 278 281 194 141 143 0 t 0 15 29 27 6 18 11 4 309 334 1 14 43 32 44 0

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=4/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.733248; -sgsCGAGTTGGsss- ; cor=; Ncor= a 0 58 51 76 3 4 372 2 4 6 3 17 53 38 59 0 c 0 175 90 130 334 31 14 12 37 12 81 33 128 170 118 0 g 0 135 221 144 54 355 10 379 32 8 309 338 162 158 173 0 t 0 28 34 46 5 6 0 3 323 370 3 8 53 30 46 0

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2_rc; m=5/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.723888; cssGGGAGTTGGcss- ; cor=; Ncor= a 59 57 35 22 3 7 266 4 5 8 3 19 29 19 48 0 c 106 113 174 37 31 35 20 13 23 14 49 27 193 131 95 0 g 71 119 82 228 265 243 8 287 20 11 252 244 54 136 120 0 t 69 16 14 18 6 20 11 1 257 272 1 15 29 19 42 0

oligos_7nt_test_vs_ctrl_m1_rc_shift1 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=6/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.706718; -sggCGAGTTGGCss- ; cor=; Ncor= a 0 47 46 28 5 4 273 3 6 4 1 18 20 22 43 0 c 0 143 67 64 244 31 20 14 18 9 63 18 217 121 95 0 g 0 99 171 185 47 263 8 286 20 10 238 259 44 134 126 0 t 0 14 19 26 7 5 2 0 259 280 1 8 22 26 39 0

oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=7/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.699874; -ssgGGAGTTGctss- ; cor=; Ncor= a 0 54 71 58 4 15 381 1 15 8 6 38 50 22 74 0 c 0 174 148 75 47 50 21 11 31 8 46 274 101 161 123 0 g 0 169 163 244 357 335 7 405 23 14 365 82 95 212 166 0 t 0 23 38 43 12 20 11 3 351 390 3 26 174 25 57 0

oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.659673; -sssCCAGTTGGsss- ; cor=; Ncor= a 0 50 30 70 7 4 374 0 9 10 1 20 55 21 55 0 c 0 179 117 144 308 338 12 11 31 10 90 31 101 186 134 0 g 0 138 211 138 79 53 11 391 31 2 307 341 172 160 170 0 t 0 36 45 51 9 8 6 1 332 381 5 11 75 36 44 0

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=9/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.631703; cssGGCAGTTGGCss- ; cor=; Ncor= a 49 42 18 11 3 8 213 4 6 5 3 11 22 14 31 0 c 84 87 152 22 24 187 14 15 18 11 39 30 180 102 76 0 g 60 102 66 217 224 40 17 234 26 7 210 200 34 115 105 0 t 62 24 19 5 4 20 11 2 205 232 3 14 19 24 43 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift1 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssGCCAACTCGccs ; Alignment reference a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTCGccs ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47

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=2/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.966178; -sssCCAACTCGscs ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.846526; -sscCCAACTCCcss ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=4/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.841494; -sssCCAACTGGsss ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=5/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.812459; -ssgCCAACTCCCss ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5_rc; m=6/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.779385; sssaGCAACTCGcss ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=7/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.770908; -ssagCAACTCCcss ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.716658; -ssGCCAACTGCCss ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=9/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.706718; ssscCGAACTCCcss ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=10/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.631618; ssGCCGAACTCCCss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift1 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -sscCCAACTCCcss ; Alignment reference a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -sscCCAACTCCcss ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.903208; -ssagCAACTCCcss ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.892199; -ssgCCAACTCCCss ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57

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=4/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.864864; -sssCCAACTCGscs ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.846526; -ssGCCAACTCGccs ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.835504; ssscCGAACTCCcss ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=7/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.794016; -ssGCCAACTGCCss ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=8/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.777021; -sssCCAACTGGsss ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=9/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.765782; ssGCCGAACTCCCss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.692658; sssaGCAACTCGcss ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32

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=14; shift=1; ncol=15; -sssCCAACTGGsss ; Alignment reference a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50

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=14; w=0; offset=0; strand=D; shift=1; score= 1; -sssCCAACTGGsss ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.87216; -sssCCAACTCGscs ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1; m=3/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.841494; -ssGCCAACTCGccs ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=4/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.777021; -sscCCAACTCCcss ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=5/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.754628; -ssGCCAACTGCCss ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=6/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.687863; -ssgCCAACTCCCss ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=7/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.685264; sssaGCAACTCGcss ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.659673; ssscCGAACTCCcss ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51

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; ssGCCGAACTCCCsss ; Alignment reference a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 82 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 86 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 99 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38 67

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; ssGCCGAACTCCCsss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 82 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 86 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 99 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38 67

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.921632; ssscCGAACTCCcss- ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 0 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 0 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 0 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51 0

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=3/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.766752; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 69 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 71 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 106 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57 59

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=4/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.765782; -sscCCAACTCCcss- ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 0 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 0 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 0 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58 0

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=5/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.676017; -ssGCCAACTGCCssg ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 62 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 60 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 84 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42 49

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=6/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.655098; -sssCCAACTCGscs- ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 0 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 0 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 0 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58 0

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=7/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.631618; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 0 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 0 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 0 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47 0

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=8/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.629623; -ssagCAACTCCcss- ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 0 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 0 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 0 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift1 ; 8 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; -ssgCGAGTTGCtsss ; Alignment reference a 0 32 47 42 2 6 319 5 15 5 3 19 22 11 41 76 c 0 168 90 72 292 33 13 9 39 8 56 264 63 123 124 98 g 0 137 180 207 47 305 14 332 47 13 287 55 48 199 148 99 t 0 11 31 27 7 4 2 2 247 322 2 10 215 15 35 75

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=1/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCGAGTTGCtsss ; cor=; Ncor= a 0 32 47 42 2 6 319 5 15 5 3 19 22 11 41 76 c 0 168 90 72 292 33 13 9 39 8 56 264 63 123 124 98 g 0 137 180 207 47 305 14 332 47 13 287 55 48 199 148 99 t 0 11 31 27 7 4 2 2 247 322 2 10 215 15 35 75

oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=2/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.814431; -ssgGGAGTTGctss- ; cor=; Ncor= a 0 54 71 58 4 15 381 1 15 8 6 38 50 22 74 0 c 0 174 148 75 47 50 21 11 31 8 46 274 101 161 123 0 g 0 169 163 244 357 335 7 405 23 14 365 82 95 212 166 0 t 0 23 38 43 12 20 11 3 351 390 3 26 174 25 57 0

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.795267; -sgsCGAGTTGGsss- ; cor=; Ncor= a 0 58 51 76 3 4 372 2 4 6 3 17 53 38 59 0 c 0 175 90 130 334 31 14 12 37 12 81 33 128 170 118 0 g 0 135 221 144 54 355 10 379 32 8 309 338 162 158 173 0 t 0 28 34 46 5 6 0 3 323 370 3 8 53 30 46 0

oligos_7nt_test_vs_ctrl_m1_rc_shift1 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.779385; -sggCGAGTTGGCss- ; cor=; Ncor= a 0 47 46 28 5 4 273 3 6 4 1 18 20 22 43 0 c 0 143 67 64 244 31 20 14 18 9 63 18 217 121 95 0 g 0 99 171 185 47 263 8 286 20 10 238 259 44 134 126 0 t 0 14 19 26 7 5 2 0 259 280 1 8 22 26 39 0

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.692658; -ssgGGAGTTGGgss- ; cor=; Ncor= a 0 58 50 51 4 9 320 0 6 6 2 25 43 30 62 0 c 0 136 127 56 36 38 16 15 26 9 73 34 74 151 105 0 g 0 145 148 220 308 289 7 335 13 5 278 281 194 141 143 0 t 0 15 29 27 6 18 11 4 309 334 1 14 43 32 44 0

oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.685264; -sssCCAGTTGGsss- ; cor=; Ncor= a 0 50 30 70 7 4 374 0 9 10 1 20 55 21 55 0 c 0 179 117 144 308 338 12 11 31 10 90 31 101 186 134 0 g 0 138 211 138 79 53 11 391 31 2 307 341 172 160 170 0 t 0 36 45 51 9 8 6 1 332 381 5 11 75 36 44 0

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=7/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.632408; cssGGGAGTTGGcss- ; cor=; Ncor= a 59 57 35 22 3 7 266 4 5 8 3 19 29 19 48 0 c 106 113 174 37 31 35 20 13 23 14 49 27 193 131 95 0 g 71 119 82 228 265 243 8 287 20 11 252 244 54 136 120 0 t 69 16 14 18 6 20 11 1 257 272 1 15 29 19 42 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssgGGAGTTGctss ; Alignment reference a 0 54 71 58 4 15 381 1 15 8 6 38 50 22 74 c 0 174 148 75 47 50 21 11 31 8 46 274 101 161 123 g 0 169 163 244 357 335 7 405 23 14 365 82 95 212 166 t 0 23 38 43 12 20 11 3 351 390 3 26 174 25 57
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTGctss ; cor=; Ncor= a 0 54 71 58 4 15 381 1 15 8 6 38 50 22 74 c 0 174 148 75 47 50 21 11 31 8 46 274 101 161 123 g 0 169 163 244 357 335 7 405 23 14 365 82 95 212 166 t 0 23 38 43 12 20 11 3 351 390 3 26 174 25 57
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1_rc; m=2/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.903208; -ssgGGAGTTGGgss ; cor=; Ncor= a 0 58 50 51 4 9 320 0 6 6 2 25 43 30 62 c 0 136 127 56 36 38 16 15 26 9 73 34 74 151 105 g 0 145 148 220 308 289 7 335 13 5 278 281 194 141 143 t 0 15 29 27 6 18 11 4 309 334 1 14 43 32 44
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.828191; cssGGGAGTTGGcss ; cor=; Ncor= a 59 57 35 22 3 7 266 4 5 8 3 19 29 19 48 c 106 113 174 37 31 35 20 13 23 14 49 27 193 131 95 g 71 119 82 228 265 243 8 287 20 11 252 244 54 136 120 t 69 16 14 18 6 20 11 1 257 272 1 15 29 19 42
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=4/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.814431; -ssgCGAGTTGCtss ; cor=; Ncor= a 0 32 47 42 2 6 319 5 15 5 3 19 22 11 41 c 0 168 90 72 292 33 13 9 39 8 56 264 63 123 124 g 0 137 180 207 47 305 14 332 47 13 287 55 48 199 148 t 0 11 31 27 7 4 2 2 247 322 2 10 215 15 35
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=5/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.774336; -sgsCGAGTTGGsss ; cor=; Ncor= a 0 58 51 76 3 4 372 2 4 6 3 17 53 38 59 c 0 175 90 130 334 31 14 12 37 12 81 33 128 170 118 g 0 135 221 144 54 355 10 379 32 8 309 338 162 158 173 t 0 28 34 46 5 6 0 3 323 370 3 8 53 30 46
oligos_7nt_test_vs_ctrl_m1_rc_shift1 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=6/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.770908; -sggCGAGTTGGCss ; cor=; Ncor= a 0 47 46 28 5 4 273 3 6 4 1 18 20 22 43 c 0 143 67 64 244 31 20 14 18 9 63 18 217 121 95 g 0 99 171 185 47 263 8 286 20 10 238 259 44 134 126 t 0 14 19 26 7 5 2 0 259 280 1 8 22 26 39
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=7/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.737449; cssGGCAGTTGGCss ; cor=; Ncor= a 49 42 18 11 3 8 213 4 6 5 3 11 22 14 31 c 84 87 152 22 24 187 14 15 18 11 39 30 180 102 76 g 60 102 66 217 224 40 17 234 26 7 210 200 34 115 105 t 62 24 19 5 4 20 11 2 205 232 3 14 19 24 43
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=8/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.699874; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 51 54 81 8 14 427 3 12 19 2 14 44 40 70 c 0 227 179 70 75 62 23 31 5 7 432 35 73 235 157 g 0 171 216 278 382 397 14 443 25 20 47 423 313 159 207 t 0 32 32 52 16 8 17 4 439 435 0 9 51 47 47
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=9/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.629623; sssGGGAGTTCGGCs ; cor=; Ncor= a 67 38 29 40 5 6 289 2 9 21 1 6 23 13 47 c 99 151 182 32 52 49 21 24 10 14 301 24 44 249 113 g 86 122 111 235 270 275 14 304 22 13 31 299 242 53 144 t 82 23 12 27 7 4 10 4 293 286 1 5 25 19 30

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssGCCAACTGCCssg ; Alignment reference a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 62 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 60 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 84 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42 49
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTGCCssg ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 62 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 60 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 84 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42 49
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=2/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.91521; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 69 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 71 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 106 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57 59
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.794016; -sscCCAACTCCcss- ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 0 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 0 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 0 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58 0
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=4/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.754628; -sssCCAACTGGsss- ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 0 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 0 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 0 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50 0
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=5/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.737449; -ssagCAACTCCcss- ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 0 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 0 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 0 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54 0
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1; m=6/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.716658; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 0 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 0 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 0 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47 0
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=7/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.676017; ssGCCGAACTCCCsss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 82 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 86 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 99 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38 67
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.631703; ssscCGAACTCCcss- ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 0 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 0 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 0 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssgCCAACTCCCssg ; Alignment reference a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 69 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 71 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 106 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57 59
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 69 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 71 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 106 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57 59
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.91521; -ssGCCAACTGCCssg ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 62 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 60 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 84 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42 49
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.892199; -sscCCAACTCCcss- ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 0 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 0 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 0 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58 0
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=4/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.828191; -ssagCAACTCCcss- ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 0 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 0 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 0 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54 0
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.812459; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 0 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 0 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 0 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47 0
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=6/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.76983; -sssCCAACTCGscs- ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 0 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 0 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 0 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58 0
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=7/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.766752; ssGCCGAACTCCCsss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 82 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 86 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 99 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38 67
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.723888; ssscCGAACTCCcss- ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 0 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 0 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 0 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51 0
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=9/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.687863; -sssCCAACTGGsss- ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 0 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 0 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 0 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50 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=-1; offset=-1; strand=R; shift=0; score=0.632408; sssaGCAACTCGcss- ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 0 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 0 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 0 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32 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; -sssCCAACTCGscs ; Alignment reference a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58
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; -sssCCAACTCGscs ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=2/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.966178; -ssGCCAACTCGccs ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=3/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.87216; -sssCCAACTGGsss ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=4/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.864864; -sscCCAACTCCcss ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=5/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.795267; sssaGCAACTCGcss ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=6/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.774336; -ssagCAACTCCcss ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=7/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.76983; -ssgCCAACTCCCss ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.733248; ssscCGAACTCCcss ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=9/9; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.655098; ssGCCGAACTCCCss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssgGGAGTTCGgsss ; Alignment reference a 0 51 54 81 8 14 427 3 12 19 2 14 44 40 70 118 c 0 227 179 70 75 62 23 31 5 7 432 35 73 235 157 151 g 0 171 216 278 382 397 14 443 25 20 47 423 313 159 207 128 t 0 32 32 52 16 8 17 4 439 435 0 9 51 47 47 84
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTCGgsss ; cor=; Ncor= a 0 51 54 81 8 14 427 3 12 19 2 14 44 40 70 118 c 0 227 179 70 75 62 23 31 5 7 432 35 73 235 157 151 g 0 171 216 278 382 397 14 443 25 20 47 423 313 159 207 128 t 0 32 32 52 16 8 17 4 439 435 0 9 51 47 47 84
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=2/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.921632; sssGGGAGTTCGGCss ; cor=; Ncor= a 67 38 29 40 5 6 289 2 9 21 1 6 23 13 47 75 c 99 151 182 32 52 49 21 24 10 14 301 24 44 249 113 111 g 86 122 111 235 270 275 14 304 22 13 31 299 242 53 144 90 t 82 23 12 27 7 4 10 4 293 286 1 5 25 19 30 58
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.835504; -ssgGGAGTTGGgss- ; cor=; Ncor= a 0 58 50 51 4 9 320 0 6 6 2 25 43 30 62 0 c 0 136 127 56 36 38 16 15 26 9 73 34 74 151 105 0 g 0 145 148 220 308 289 7 335 13 5 278 281 194 141 143 0 t 0 15 29 27 6 18 11 4 309 334 1 14 43 32 44 0
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=4/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.733248; -sgsCGAGTTGGsss- ; cor=; Ncor= a 0 58 51 76 3 4 372 2 4 6 3 17 53 38 59 0 c 0 175 90 130 334 31 14 12 37 12 81 33 128 170 118 0 g 0 135 221 144 54 355 10 379 32 8 309 338 162 158 173 0 t 0 28 34 46 5 6 0 3 323 370 3 8 53 30 46 0
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2_rc; m=5/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.723888; cssGGGAGTTGGcss- ; cor=; Ncor= a 59 57 35 22 3 7 266 4 5 8 3 19 29 19 48 0 c 106 113 174 37 31 35 20 13 23 14 49 27 193 131 95 0 g 71 119 82 228 265 243 8 287 20 11 252 244 54 136 120 0 t 69 16 14 18 6 20 11 1 257 272 1 15 29 19 42 0
oligos_7nt_test_vs_ctrl_m1_rc_shift1 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=6/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.706718; -sggCGAGTTGGCss- ; cor=; Ncor= a 0 47 46 28 5 4 273 3 6 4 1 18 20 22 43 0 c 0 143 67 64 244 31 20 14 18 9 63 18 217 121 95 0 g 0 99 171 185 47 263 8 286 20 10 238 259 44 134 126 0 t 0 14 19 26 7 5 2 0 259 280 1 8 22 26 39 0
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=7/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.699874; -ssgGGAGTTGctss- ; cor=; Ncor= a 0 54 71 58 4 15 381 1 15 8 6 38 50 22 74 0 c 0 174 148 75 47 50 21 11 31 8 46 274 101 161 123 0 g 0 169 163 244 357 335 7 405 23 14 365 82 95 212 166 0 t 0 23 38 43 12 20 11 3 351 390 3 26 174 25 57 0
oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.659673; -sssCCAGTTGGsss- ; cor=; Ncor= a 0 50 30 70 7 4 374 0 9 10 1 20 55 21 55 0 c 0 179 117 144 308 338 12 11 31 10 90 31 101 186 134 0 g 0 138 211 138 79 53 11 391 31 2 307 341 172 160 170 0 t 0 36 45 51 9 8 6 1 332 381 5 11 75 36 44 0
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=9/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.631703; cssGGCAGTTGGCss- ; cor=; Ncor= a 49 42 18 11 3 8 213 4 6 5 3 11 22 14 31 0 c 84 87 152 22 24 187 14 15 18 11 39 30 180 102 76 0 g 60 102 66 217 224 40 17 234 26 7 210 200 34 115 105 0 t 62 24 19 5 4 20 11 2 205 232 3 14 19 24 43 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssGCCAACTCGccs ; Alignment reference a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTCGccs ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47
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=2/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.966178; -sssCCAACTCGscs ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.846526; -sscCCAACTCCcss ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=4/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.841494; -sssCCAACTGGsss ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=5/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.812459; -ssgCCAACTCCCss ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5_rc; m=6/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.779385; sssaGCAACTCGcss ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=7/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.770908; -ssagCAACTCCcss ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.716658; -ssGCCAACTGCCss ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=9/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.706718; ssscCGAACTCCcss ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=10/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.631618; ssGCCGAACTCCCss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -sscCCAACTCCcss ; Alignment reference a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -sscCCAACTCCcss ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.903208; -ssagCAACTCCcss ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.892199; -ssgCCAACTCCCss ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57
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=4/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.864864; -sssCCAACTCGscs ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.846526; -ssGCCAACTCGccs ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.835504; ssscCGAACTCCcss ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=7/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.794016; -ssGCCAACTGCCss ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=8/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.777021; -sssCCAACTGGsss ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=9/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.765782; ssGCCGAACTCCCss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.692658; sssaGCAACTCGcss ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32

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=14; shift=1; ncol=15; -sssCCAACTGGsss ; Alignment reference a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50
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=14; w=0; offset=0; strand=D; shift=1; score= 1; -sssCCAACTGGsss ; cor=; Ncor= a 0 44 36 75 11 5 381 332 1 6 8 9 51 45 36 c 0 170 160 172 341 307 2 31 391 11 53 79 138 211 138 g 0 134 186 101 31 90 10 31 11 12 338 308 144 117 179 t 0 55 21 55 20 1 10 9 0 374 4 7 70 30 50
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.87216; -sssCCAACTCGscs ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1; m=3/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.841494; -ssGCCAACTCGccs ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=4/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.777021; -sscCCAACTCCcss ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=5/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.754628; -ssGCCAACTGCCss ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=6/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.687863; -ssgCCAACTCCCss ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=7/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.685264; sssaGCAACTCGcss ; cor=; Ncor= a 75 35 15 215 10 2 322 247 2 2 4 7 27 31 11 c 99 148 199 48 55 287 13 47 332 14 305 47 207 180 137 g 98 124 123 63 264 56 8 39 9 13 33 292 72 90 168 t 76 41 11 22 19 3 5 15 5 319 6 2 42 47 32
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.659673; ssscCGAACTCCcss ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51

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; ssGCCGAACTCCCsss ; Alignment reference a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 82 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 86 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 99 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38 67
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; ssGCCGAACTCCCsss ; cor=; Ncor= a 58 30 19 25 5 1 286 293 4 10 4 7 27 12 23 82 c 90 144 53 242 299 31 13 22 304 14 275 270 235 111 122 86 g 111 113 249 44 24 301 14 10 24 21 49 52 32 182 151 99 t 75 47 13 23 6 1 21 9 2 289 6 5 40 29 38 67
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.921632; ssscCGAACTCCcss- ; cor=; Ncor= a 84 47 47 51 9 0 435 439 4 17 8 16 52 32 32 0 c 128 207 159 313 423 47 20 25 443 14 397 382 278 216 171 0 g 151 157 235 73 35 432 7 5 31 23 62 75 70 179 227 0 t 118 70 40 44 14 2 19 12 3 427 14 8 81 54 51 0
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=3/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.766752; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 42 19 29 15 1 272 257 1 11 20 6 18 14 16 69 c 0 120 136 54 244 252 11 20 287 8 243 265 228 82 119 71 g 0 95 131 193 27 49 14 23 13 20 35 31 37 174 113 106 t 0 48 19 29 19 3 8 5 4 266 7 3 22 35 57 59
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=4/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.765782; -sscCCAACTCCcss- ; cor=; Ncor= a 0 44 32 43 14 1 334 309 4 11 18 6 27 29 15 0 c 0 143 141 194 281 278 5 13 335 7 289 308 220 148 145 0 g 0 105 151 74 34 73 9 26 15 16 38 36 56 127 136 0 t 0 62 30 43 25 2 6 6 0 320 9 4 51 50 58 0
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=5/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.676017; -ssGCCAACTGCCssg ; cor=; Ncor= a 0 43 24 19 14 3 232 205 2 11 20 4 5 19 24 62 c 0 105 115 34 200 210 7 26 234 17 40 224 217 66 102 60 g 0 76 102 180 30 39 11 18 15 14 187 24 22 152 87 84 t 0 31 14 22 11 3 5 6 4 213 8 3 11 18 42 49
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=6/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.655098; -sssCCAACTCGscs- ; cor=; Ncor= a 0 46 30 53 8 3 370 323 3 0 6 5 46 34 28 0 c 0 173 158 162 338 309 8 32 379 10 355 54 144 221 135 0 g 0 118 170 128 33 81 12 37 12 14 31 334 130 90 175 0 t 0 59 38 53 17 3 6 4 2 372 4 3 76 51 58 0
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=7/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.631618; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 39 26 22 8 1 280 259 0 2 5 7 26 19 14 0 c 0 126 134 44 259 238 10 20 286 8 263 47 185 171 99 0 g 0 95 121 217 18 63 9 18 14 20 31 244 64 67 143 0 t 0 43 22 20 18 1 4 6 3 273 4 5 28 46 47 0
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=8/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.629623; -ssagCAACTCCcss- ; cor=; Ncor= a 0 57 25 174 26 3 390 351 3 11 20 12 43 38 23 0 c 0 166 212 95 82 365 14 23 405 7 335 357 244 163 169 0 g 0 123 161 101 274 46 8 31 11 21 50 47 75 148 174 0 t 0 74 22 50 38 6 8 15 1 381 15 4 58 71 54 0

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; -ssgCGAGTTGCtsss ; Alignment reference a 0 32 47 42 2 6 319 5 15 5 3 19 22 11 41 76 c 0 168 90 72 292 33 13 9 39 8 56 264 63 123 124 98 g 0 137 180 207 47 305 14 332 47 13 287 55 48 199 148 99 t 0 11 31 27 7 4 2 2 247 322 2 10 215 15 35 75
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=1/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCGAGTTGCtsss ; cor=; Ncor= a 0 32 47 42 2 6 319 5 15 5 3 19 22 11 41 76 c 0 168 90 72 292 33 13 9 39 8 56 264 63 123 124 98 g 0 137 180 207 47 305 14 332 47 13 287 55 48 199 148 99 t 0 11 31 27 7 4 2 2 247 322 2 10 215 15 35 75
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=2/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.814431; -ssgGGAGTTGctss- ; cor=; Ncor= a 0 54 71 58 4 15 381 1 15 8 6 38 50 22 74 0 c 0 174 148 75 47 50 21 11 31 8 46 274 101 161 123 0 g 0 169 163 244 357 335 7 405 23 14 365 82 95 212 166 0 t 0 23 38 43 12 20 11 3 351 390 3 26 174 25 57 0
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.795267; -sgsCGAGTTGGsss- ; cor=; Ncor= a 0 58 51 76 3 4 372 2 4 6 3 17 53 38 59 0 c 0 175 90 130 334 31 14 12 37 12 81 33 128 170 118 0 g 0 135 221 144 54 355 10 379 32 8 309 338 162 158 173 0 t 0 28 34 46 5 6 0 3 323 370 3 8 53 30 46 0
oligos_7nt_test_vs_ctrl_m1_rc_shift1 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.779385; -sggCGAGTTGGCss- ; cor=; Ncor= a 0 47 46 28 5 4 273 3 6 4 1 18 20 22 43 0 c 0 143 67 64 244 31 20 14 18 9 63 18 217 121 95 0 g 0 99 171 185 47 263 8 286 20 10 238 259 44 134 126 0 t 0 14 19 26 7 5 2 0 259 280 1 8 22 26 39 0
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.692658; -ssgGGAGTTGGgss- ; cor=; Ncor= a 0 58 50 51 4 9 320 0 6 6 2 25 43 30 62 0 c 0 136 127 56 36 38 16 15 26 9 73 34 74 151 105 0 g 0 145 148 220 308 289 7 335 13 5 278 281 194 141 143 0 t 0 15 29 27 6 18 11 4 309 334 1 14 43 32 44 0
oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.685264; -sssCCAGTTGGsss- ; cor=; Ncor= a 0 50 30 70 7 4 374 0 9 10 1 20 55 21 55 0 c 0 179 117 144 308 338 12 11 31 10 90 31 101 186 134 0 g 0 138 211 138 79 53 11 391 31 2 307 341 172 160 170 0 t 0 36 45 51 9 8 6 1 332 381 5 11 75 36 44 0
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=7/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.632408; cssGGGAGTTGGcss- ; cor=; Ncor= a 59 57 35 22 3 7 266 4 5 8 3 19 29 19 48 0 c 106 113 174 37 31 35 20 13 23 14 49 27 193 131 95 0 g 71 119 82 228 265 243 8 287 20 11 252 244 54 136 120 0 t 69 16 14 18 6 20 11 1 257 272 1 15 29 19 42 0