One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084418_2026-01-22.084418_6mH0tk/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.2026-01-22.084418_2026-01-22.084418_6mH0tk/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift1 ; 7 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=14; shift=1; ncol=15; -sgGCGAGTTGcgss ; Alignment reference a 0 39 34 22 4 4 244 3 7 4 5 23 14 17 44 c 0 110 67 51 220 26 9 6 18 1 37 182 56 108 84 g 0 101 138 184 37 238 17 260 25 3 225 53 157 125 116 t 0 20 31 13 9 2 0 1 220 262 3 12 43 20 26

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=1/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -sgGCGAGTTGcgss ; cor=; Ncor= a 0 39 34 22 4 4 244 3 7 4 5 23 14 17 44 c 0 110 67 51 220 26 9 6 18 1 37 182 56 108 84 g 0 101 138 184 37 238 17 260 25 3 225 53 157 125 116 t 0 20 31 13 9 2 0 1 220 262 3 12 43 20 26

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=2/6; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.874591; -sggCGAGTTGGCss ; cor=; Ncor= a 0 47 50 27 5 5 287 3 5 4 1 18 21 23 40 c 0 151 72 63 257 33 17 13 16 7 69 22 218 126 104 g 0 102 177 202 48 272 9 300 24 11 243 267 50 140 135 t 0 16 17 24 6 6 3 0 271 294 3 9 27 27 37

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=3/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.867785; -ssgGGAGTTGcsss ; cor=; Ncor= a 0 57 75 68 8 26 397 0 9 8 6 46 54 24 72 c 0 178 146 84 50 47 25 14 15 9 55 287 190 156 137 g 0 181 175 242 374 345 7 424 23 9 374 83 113 231 172 t 0 24 44 46 8 22 11 2 393 414 5 24 83 29 59

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=4/6; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.812013; -sgsCGAGTTGGmss ; cor=; Ncor= a 0 60 69 83 3 8 424 2 13 3 0 17 177 35 68 c 0 212 109 163 369 37 15 10 47 12 101 38 116 258 138 g 0 152 247 162 72 401 11 441 41 14 347 380 96 145 199 t 0 29 28 45 9 7 3 0 352 424 5 18 64 15 48

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=5/6; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.723009; -ssgGGAGTTGGass ; cor=; Ncor= a 0 54 57 59 3 10 356 3 11 8 1 26 191 28 63 c 0 180 154 66 45 32 24 16 35 12 78 35 81 206 115 g 0 146 165 245 350 347 10 386 23 18 324 333 88 152 176 t 0 27 31 37 9 18 17 2 338 369 4 13 47 21 53

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=6/6; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.702873; cssGGGAGTTGGcss ; cor=; Ncor= a 62 57 37 24 2 10 278 4 6 10 4 16 31 22 50 c 107 123 187 32 30 39 23 14 27 14 51 28 207 128 93 g 76 122 80 244 280 249 8 298 21 14 261 259 51 147 133 t 74 17 15 19 7 21 10 3 265 281 3 16 30 22 43

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift1 ; 11 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; -ssgCCAACTCCCssg ; Alignment reference a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 74 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 76 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 107 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57 62

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=1/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 74 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 76 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 107 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57 62

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.912579; -ssGCCAACTGCCsss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 66 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 70 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 96 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44 47

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=3/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.839118; -sssgCAACTCCcss- ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 0 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 0 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 0 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57 0

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=4/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.830775; ssstCCAACTCCcss- ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 0 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 0 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 0 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 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=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.807872; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 0 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 0 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 0 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47 0

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=6/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.760268; ssstCCAACTGCcss- ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 0 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 0 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 0 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57 0

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=7/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.755706; ssGCCGAACTCCCssv ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 93 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 93 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 107 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40 72

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=8/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.709528; ssscCGAACTCCcss- ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 0 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 0 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 0 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59 0

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=9/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.708278; ssskCCAACTCGscs- ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 0 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 0 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 0 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60 0

oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.702873; -sscgCAACTCGCcs- ; cor=; Ncor= a 0 26 20 43 12 3 262 220 1 0 2 9 13 31 20 0 c 0 116 125 157 53 225 3 25 260 17 238 37 184 138 101 0 g 0 84 108 56 182 37 1 18 6 9 26 220 51 67 110 0 t 0 44 17 14 23 5 4 7 3 244 4 4 22 34 39 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; ssstCCAACTGCcss ; Alignment reference a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssstCCAACTGCcss ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=2/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.893456; ssstCCAACTCCcss ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=3/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.824594; -ssGCCAACTGCCss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=4/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.77759; ssskCCAACTCGscs ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60

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=5/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.76927; ssscCGAACTCCcss ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59

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=6/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.760268; -ssgCCAACTCCCss ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57

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=7/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.747205; -sssgCAACTCCcss ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57

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=8/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.713693; -ssGCCAACTCGccs ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=9/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.713102; ssGCCGAACTCCCss ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 10 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; ssGCCGAACTCCCssv ; Alignment reference a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 93 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 93 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 107 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40 72

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=1/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; ssGCCGAACTCCCssv ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 93 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 93 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 107 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40 72

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=2/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.925822; ssscCGAACTCCcss- ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 0 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 0 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 0 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59 0

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=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.784431; ssstCCAACTCCcss- ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 0 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 0 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 0 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54 0

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=4/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.755706; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 74 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 76 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 107 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57 62

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=5/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.713102; ssstCCAACTGCcss- ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 0 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 0 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 0 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57 0

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=6/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.691837; ssskCCAACTCGscs- ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 0 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 0 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 0 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60 0

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=7/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.681195; -ssGCCAACTGCCsss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 66 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 70 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 96 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44 47

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=8/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.631343; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 0 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 0 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 0 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47 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=9/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.626608; -sssgCAACTCCcss- ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 0 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 0 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 0 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57 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 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 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 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=2/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.88822; ssskCCAACTCGscs ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60

oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5_rc; m=3/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.874591; -sscgCAACTCGCcs ; cor=; Ncor= a 0 26 20 43 12 3 262 220 1 0 2 9 13 31 20 c 0 116 125 157 53 225 3 25 260 17 238 37 184 138 101 g 0 84 108 56 182 37 1 18 6 9 26 220 51 67 110 t 0 44 17 14 23 5 4 7 3 244 4 4 22 34 39

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=4/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.807872; -ssgCCAACTCCCss ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57

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=5/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.798563; -sssgCAACTCCcss ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57

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=6/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.790946; ssstCCAACTCCcss ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=7/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.713693; ssstCCAACTGCcss ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.712872; -ssGCCAACTGCCss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44

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=0.703991; ssscCGAACTCCcss ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59

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=10/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.631343; ssGCCGAACTCCCss ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssGCCAACTGCCsss ; Alignment reference a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 66 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 70 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 96 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44 47

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTGCCsss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 66 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 70 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 96 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44 47

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=2/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.912579; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 74 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 76 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 107 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57 62

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=3/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.824594; ssstCCAACTGCcss- ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 0 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 0 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 0 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57 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=4/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.749019; -sssgCAACTCCcss- ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 0 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 0 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 0 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57 0

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.729035; ssstCCAACTCCcss- ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 0 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 0 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 0 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54 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=6/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.712872; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 0 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 0 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 0 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47 0

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=7/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.681195; ssGCCGAACTCCCssv ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 93 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 93 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 107 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40 72

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=8/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.635531; ssscCGAACTCCcss- ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 0 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 0 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 0 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 11 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; ssstCCAACTCCcss ; Alignment reference a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54

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=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssstCCAACTCCcss ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.893456; ssstCCAACTGCcss ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.876049; ssskCCAACTCGscs ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60

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=4/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.851606; ssscCGAACTCCcss ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59

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=5/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.833654; -sssgCAACTCCcss ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57

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=6/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.830775; -ssgCCAACTCCCss ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57

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=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.790946; -ssGCCAACTCGccs ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47

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=8/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.784431; ssGCCGAACTCCCss ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=9/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.729035; -ssGCCAACTGCCss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44

oligos_7nt_test_vs_ctrl_m5_rc_shift1 (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=14; w=0; offset=1; strand=R; shift=1; score=0.723009; -sscgCAACTCGCcs ; cor=; Ncor= a 0 26 20 43 12 3 262 220 1 0 2 9 13 31 20 c 0 116 125 157 53 225 3 25 260 17 238 37 184 138 101 g 0 84 108 56 182 37 1 18 6 9 26 220 51 67 110 t 0 44 17 14 23 5 4 7 3 244 4 4 22 34 39

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 59 60 86 8 19 462 1 15 26 3 14 50 35 80 128 c 0 250 193 73 88 81 29 33 11 12 479 38 70 296 176 156 g 0 177 231 311 413 415 16 485 24 17 41 466 350 148 214 138 t 0 39 41 55 16 10 18 6 475 470 2 7 55 46 55 103

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 59 60 86 8 19 462 1 15 26 3 14 50 35 80 128 c 0 250 193 73 88 81 29 33 11 12 479 38 70 296 176 156 g 0 177 231 311 413 415 16 485 24 17 41 466 350 148 214 138 t 0 39 41 55 16 10 18 6 475 470 2 7 55 46 55 103

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=2/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.925822; bssGGGAGTTCGGCss ; cor=; Ncor= a 72 40 32 44 6 11 316 2 13 21 3 7 29 14 54 80 c 107 169 198 35 55 59 23 24 15 17 331 25 43 277 121 116 g 93 128 121 258 297 291 15 334 23 14 29 329 267 54 154 104 t 93 28 14 28 7 4 11 5 314 313 2 4 26 20 36 65

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=15; w=0; offset=0; strand=R; shift=1; score=0.851606; -ssgGGAGTTGGasss ; cor=; Ncor= a 0 54 57 59 3 10 356 3 11 8 1 26 191 28 63 94 c 0 180 154 66 45 32 24 16 35 12 78 35 81 206 115 117 g 0 146 165 245 350 347 10 386 23 18 324 333 88 152 176 111 t 0 27 31 37 9 18 17 2 338 369 4 13 47 21 53 85

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=4/9; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.76927; -ssgGCAGTTGGasss ; cor=; Ncor= a 0 57 38 49 13 13 350 1 11 7 2 19 184 27 62 93 c 0 155 163 58 61 297 20 12 28 14 76 39 86 203 130 111 g 0 151 158 261 309 59 11 380 29 10 310 321 78 136 150 107 t 0 31 35 26 11 25 13 1 326 363 6 15 46 28 52 83

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=5/9; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.767352; -sgsCGAGTTGGmsss ; cor=; Ncor= a 0 60 69 83 3 8 424 2 13 3 0 17 177 35 68 83 c 0 212 109 163 369 37 15 10 47 12 101 38 116 258 138 133 g 0 152 247 162 72 401 11 441 41 14 347 380 96 145 199 130 t 0 29 28 45 9 7 3 0 352 424 5 18 64 15 48 107

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=6/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.709528; cssGGGAGTTGGcss- ; cor=; Ncor= a 62 57 37 24 2 10 278 4 6 10 4 16 31 22 50 0 c 107 123 187 32 30 39 23 14 27 14 51 28 207 128 93 0 g 76 122 80 244 280 249 8 298 21 14 261 259 51 147 133 0 t 74 17 15 19 7 21 10 3 265 281 3 16 30 22 43 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=7/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.703991; -sggCGAGTTGGCss- ; cor=; Ncor= a 0 47 50 27 5 5 287 3 5 4 1 18 21 23 40 0 c 0 151 72 63 257 33 17 13 16 7 69 22 218 126 104 0 g 0 102 177 202 48 272 9 300 24 11 243 267 50 140 135 0 t 0 16 17 24 6 6 3 0 271 294 3 9 27 27 37 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=8/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.694345; -ssgGGAGTTGcsss- ; cor=; Ncor= a 0 57 75 68 8 26 397 0 9 8 6 46 54 24 72 0 c 0 178 146 84 50 47 25 14 15 9 55 287 190 156 137 0 g 0 181 175 242 374 345 7 424 23 9 374 83 113 231 172 0 t 0 24 44 46 8 22 11 2 393 414 5 24 83 29 59 0

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=9/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.635531; sssGGCAGTTGGCss- ; cor=; Ncor= a 47 44 21 12 3 9 238 4 4 4 3 16 24 16 38 0 c 96 100 169 19 28 212 16 14 23 12 57 31 194 105 84 0 g 70 108 70 241 245 37 13 259 29 9 216 218 38 130 113 0 t 66 27 19 7 3 21 12 2 223 254 3 14 23 28 44 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ssskCCAACTCGscs ; Alignment reference a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssskCCAACTCGscs ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60

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=1; strand=D; shift=1; score=0.88822; -ssGCCAACTCGccs ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47

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=0; offset=0; strand=D; shift=0; score=0.876049; ssstCCAACTCCcss ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54

oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=4/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.812013; -sscgCAACTCGCcs ; cor=; Ncor= a 0 26 20 43 12 3 262 220 1 0 2 9 13 31 20 c 0 116 125 157 53 225 3 25 260 17 238 37 184 138 101 g 0 84 108 56 182 37 1 18 6 9 26 220 51 67 110 t 0 44 17 14 23 5 4 7 3 244 4 4 22 34 39

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=5/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.77759; ssstCCAACTGCcss ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 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=6/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.767352; ssscCGAACTCCcss ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59

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=7/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.72436; -sssgCAACTCCcss ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=8/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.708278; -ssgCCAACTCCCss ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57

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=9/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.691837; ssGCCGAACTCCCss ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift1 ; 11 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; -ssgGGAGTTGcsss ; Alignment reference a 0 57 75 68 8 26 397 0 9 8 6 46 54 24 72 c 0 178 146 84 50 47 25 14 15 9 55 287 190 156 137 g 0 181 175 242 374 345 7 424 23 9 374 83 113 231 172 t 0 24 44 46 8 22 11 2 393 414 5 24 83 29 59

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=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTGcsss ; cor=; Ncor= a 0 57 75 68 8 26 397 0 9 8 6 46 54 24 72 c 0 178 146 84 50 47 25 14 15 9 55 287 190 156 137 g 0 181 175 242 374 345 7 424 23 9 374 83 113 231 172 t 0 24 44 46 8 22 11 2 393 414 5 24 83 29 59

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=2/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.867785; -sgGCGAGTTGcgss ; cor=; Ncor= a 0 39 34 22 4 4 244 3 7 4 5 23 14 17 44 c 0 110 67 51 220 26 9 6 18 1 37 182 56 108 84 g 0 101 138 184 37 238 17 260 25 3 225 53 157 125 116 t 0 20 31 13 9 2 0 1 220 262 3 12 43 20 26

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=3/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.839118; cssGGGAGTTGGcss ; cor=; Ncor= a 62 57 37 24 2 10 278 4 6 10 4 16 31 22 50 c 107 123 187 32 30 39 23 14 27 14 51 28 207 128 93 g 76 122 80 244 280 249 8 298 21 14 261 259 51 147 133 t 74 17 15 19 7 21 10 3 265 281 3 16 30 22 43

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=4/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.833654; -ssgGGAGTTGGass ; cor=; Ncor= a 0 54 57 59 3 10 356 3 11 8 1 26 191 28 63 c 0 180 154 66 45 32 24 16 35 12 78 35 81 206 115 g 0 146 165 245 350 347 10 386 23 18 324 333 88 152 176 t 0 27 31 37 9 18 17 2 338 369 4 13 47 21 53

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=5/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.798563; -sggCGAGTTGGCss ; cor=; Ncor= a 0 47 50 27 5 5 287 3 5 4 1 18 21 23 40 c 0 151 72 63 257 33 17 13 16 7 69 22 218 126 104 g 0 102 177 202 48 272 9 300 24 11 243 267 50 140 135 t 0 16 17 24 6 6 3 0 271 294 3 9 27 27 37

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=6/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.749019; sssGGCAGTTGGCss ; cor=; Ncor= a 47 44 21 12 3 9 238 4 4 4 3 16 24 16 38 c 96 100 169 19 28 212 16 14 23 12 57 31 194 105 84 g 70 108 70 241 245 37 13 259 29 9 216 218 38 130 113 t 66 27 19 7 3 21 12 2 223 254 3 14 23 28 44

oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=7/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.747205; -ssgGCAGTTGGass ; cor=; Ncor= a 0 57 38 49 13 13 350 1 11 7 2 19 184 27 62 c 0 155 163 58 61 297 20 12 28 14 76 39 86 203 130 g 0 151 158 261 309 59 11 380 29 10 310 321 78 136 150 t 0 31 35 26 11 25 13 1 326 363 6 15 46 28 52

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=8/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.72436; -sgsCGAGTTGGmss ; cor=; Ncor= a 0 60 69 83 3 8 424 2 13 3 0 17 177 35 68 c 0 212 109 163 369 37 15 10 47 12 101 38 116 258 138 g 0 152 247 162 72 401 11 441 41 14 347 380 96 145 199 t 0 29 28 45 9 7 3 0 352 424 5 18 64 15 48

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=9/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.694345; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 59 60 86 8 19 462 1 15 26 3 14 50 35 80 c 0 250 193 73 88 81 29 33 11 12 479 38 70 296 176 g 0 177 231 311 413 415 16 485 24 17 41 466 350 148 214 t 0 39 41 55 16 10 18 6 475 470 2 7 55 46 55

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=10/10; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.626608; bssGGGAGTTCGGCs ; cor=; Ncor= a 72 40 32 44 6 11 316 2 13 21 3 7 29 14 54 c 107 169 198 35 55 59 23 24 15 17 331 25 43 277 121 g 93 128 121 258 297 291 15 334 23 14 29 329 267 54 154 t 93 28 14 28 7 4 11 5 314 313 2 4 26 20 36

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=14; shift=1; ncol=15; -sgGCGAGTTGcgss ; Alignment reference a 0 39 34 22 4 4 244 3 7 4 5 23 14 17 44 c 0 110 67 51 220 26 9 6 18 1 37 182 56 108 84 g 0 101 138 184 37 238 17 260 25 3 225 53 157 125 116 t 0 20 31 13 9 2 0 1 220 262 3 12 43 20 26
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=1/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -sgGCGAGTTGcgss ; cor=; Ncor= a 0 39 34 22 4 4 244 3 7 4 5 23 14 17 44 c 0 110 67 51 220 26 9 6 18 1 37 182 56 108 84 g 0 101 138 184 37 238 17 260 25 3 225 53 157 125 116 t 0 20 31 13 9 2 0 1 220 262 3 12 43 20 26
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=2/6; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.874591; -sggCGAGTTGGCss ; cor=; Ncor= a 0 47 50 27 5 5 287 3 5 4 1 18 21 23 40 c 0 151 72 63 257 33 17 13 16 7 69 22 218 126 104 g 0 102 177 202 48 272 9 300 24 11 243 267 50 140 135 t 0 16 17 24 6 6 3 0 271 294 3 9 27 27 37
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=3/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.867785; -ssgGGAGTTGcsss ; cor=; Ncor= a 0 57 75 68 8 26 397 0 9 8 6 46 54 24 72 c 0 178 146 84 50 47 25 14 15 9 55 287 190 156 137 g 0 181 175 242 374 345 7 424 23 9 374 83 113 231 172 t 0 24 44 46 8 22 11 2 393 414 5 24 83 29 59
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=4/6; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.812013; -sgsCGAGTTGGmss ; cor=; Ncor= a 0 60 69 83 3 8 424 2 13 3 0 17 177 35 68 c 0 212 109 163 369 37 15 10 47 12 101 38 116 258 138 g 0 152 247 162 72 401 11 441 41 14 347 380 96 145 199 t 0 29 28 45 9 7 3 0 352 424 5 18 64 15 48
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=5/6; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.723009; -ssgGGAGTTGGass ; cor=; Ncor= a 0 54 57 59 3 10 356 3 11 8 1 26 191 28 63 c 0 180 154 66 45 32 24 16 35 12 78 35 81 206 115 g 0 146 165 245 350 347 10 386 23 18 324 333 88 152 176 t 0 27 31 37 9 18 17 2 338 369 4 13 47 21 53
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=6/6; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.702873; cssGGGAGTTGGcss ; cor=; Ncor= a 62 57 37 24 2 10 278 4 6 10 4 16 31 22 50 c 107 123 187 32 30 39 23 14 27 14 51 28 207 128 93 g 76 122 80 244 280 249 8 298 21 14 261 259 51 147 133 t 74 17 15 19 7 21 10 3 265 281 3 16 30 22 43

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; -ssgCCAACTCCCssg ; Alignment reference a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 74 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 76 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 107 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57 62
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=1/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 74 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 76 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 107 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57 62
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.912579; -ssGCCAACTGCCsss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 66 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 70 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 96 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44 47
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=3/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.839118; -sssgCAACTCCcss- ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 0 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 0 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 0 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57 0
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=4/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.830775; ssstCCAACTCCcss- ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 0 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 0 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 0 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 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=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.807872; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 0 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 0 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 0 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47 0
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=6/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.760268; ssstCCAACTGCcss- ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 0 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 0 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 0 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57 0
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=7/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.755706; ssGCCGAACTCCCssv ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 93 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 93 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 107 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40 72
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=8/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.709528; ssscCGAACTCCcss- ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 0 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 0 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 0 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59 0
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=9/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.708278; ssskCCAACTCGscs- ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 0 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 0 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 0 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60 0
oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.702873; -sscgCAACTCGCcs- ; cor=; Ncor= a 0 26 20 43 12 3 262 220 1 0 2 9 13 31 20 0 c 0 116 125 157 53 225 3 25 260 17 238 37 184 138 101 0 g 0 84 108 56 182 37 1 18 6 9 26 220 51 67 110 0 t 0 44 17 14 23 5 4 7 3 244 4 4 22 34 39 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; ssstCCAACTGCcss ; Alignment reference a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssstCCAACTGCcss ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=2/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.893456; ssstCCAACTCCcss ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=3/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.824594; -ssGCCAACTGCCss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=4/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.77759; ssskCCAACTCGscs ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60
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=5/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.76927; ssscCGAACTCCcss ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59
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=6/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.760268; -ssgCCAACTCCCss ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57
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=7/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.747205; -sssgCAACTCCcss ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57
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=8/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.713693; -ssGCCAACTCGccs ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=9/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.713102; ssGCCGAACTCCCss ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40

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; ssGCCGAACTCCCssv ; Alignment reference a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 93 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 93 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 107 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40 72
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=1/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; ssGCCGAACTCCCssv ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 93 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 93 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 107 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40 72
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=2/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.925822; ssscCGAACTCCcss- ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 0 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 0 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 0 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59 0
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=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.784431; ssstCCAACTCCcss- ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 0 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 0 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 0 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54 0
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=4/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.755706; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 74 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 76 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 107 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57 62
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=5/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.713102; ssstCCAACTGCcss- ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 0 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 0 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 0 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57 0
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=6/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.691837; ssskCCAACTCGscs- ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 0 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 0 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 0 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60 0
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=7/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.681195; -ssGCCAACTGCCsss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 66 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 70 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 96 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44 47
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=8/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.631343; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 0 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 0 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 0 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47 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=9/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.626608; -sssgCAACTCCcss- ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 0 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 0 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 0 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57 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 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 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 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=2/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.88822; ssskCCAACTCGscs ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60
oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5_rc; m=3/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.874591; -sscgCAACTCGCcs ; cor=; Ncor= a 0 26 20 43 12 3 262 220 1 0 2 9 13 31 20 c 0 116 125 157 53 225 3 25 260 17 238 37 184 138 101 g 0 84 108 56 182 37 1 18 6 9 26 220 51 67 110 t 0 44 17 14 23 5 4 7 3 244 4 4 22 34 39
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=4/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.807872; -ssgCCAACTCCCss ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57
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=5/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.798563; -sssgCAACTCCcss ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57
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=6/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.790946; ssstCCAACTCCcss ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=7/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.713693; ssstCCAACTGCcss ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.712872; -ssGCCAACTGCCss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44
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=0.703991; ssscCGAACTCCcss ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59
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=10/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.631343; ssGCCGAACTCCCss ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssGCCAACTGCCsss ; Alignment reference a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 66 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 70 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 96 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44 47
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTGCCsss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 66 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 70 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 96 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44 47
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=2/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.912579; -ssgCCAACTCCCssg ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 74 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 76 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 107 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57 62
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=3/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.824594; ssstCCAACTGCcss- ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 0 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 0 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 0 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57 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=4/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.749019; -sssgCAACTCCcss- ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 0 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 0 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 0 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57 0
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.729035; ssstCCAACTCCcss- ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 0 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 0 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 0 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54 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=6/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.712872; -ssGCCAACTCGccs- ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 0 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 0 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 0 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47 0
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=7/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.681195; ssGCCGAACTCCCssv ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 93 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 93 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 107 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40 72
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=8/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.635531; ssscCGAACTCCcss- ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 0 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 0 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 0 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59 0

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; ssstCCAACTCCcss ; Alignment reference a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54
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=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssstCCAACTCCcss ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.893456; ssstCCAACTGCcss ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 57
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.876049; ssskCCAACTCGscs ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60
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=4/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.851606; ssscCGAACTCCcss ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59
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=5/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.833654; -sssgCAACTCCcss ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57
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=6/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.830775; -ssgCCAACTCCCss ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57
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=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.790946; -ssGCCAACTCGccs ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47
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=8/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.784431; ssGCCGAACTCCCss ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=9/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.729035; -ssGCCAACTGCCss ; cor=; Ncor= a 0 44 28 23 14 3 254 223 2 12 21 3 7 19 27 c 0 113 130 38 218 216 9 29 259 13 37 245 241 70 108 g 0 84 105 194 31 57 12 23 14 16 212 28 19 169 100 t 0 38 16 24 16 3 4 4 4 238 9 3 12 21 44
oligos_7nt_test_vs_ctrl_m5_rc_shift1 (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=14; w=0; offset=1; strand=R; shift=1; score=0.723009; -sscgCAACTCGCcs ; cor=; Ncor= a 0 26 20 43 12 3 262 220 1 0 2 9 13 31 20 c 0 116 125 157 53 225 3 25 260 17 238 37 184 138 101 g 0 84 108 56 182 37 1 18 6 9 26 220 51 67 110 t 0 44 17 14 23 5 4 7 3 244 4 4 22 34 39

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 59 60 86 8 19 462 1 15 26 3 14 50 35 80 128 c 0 250 193 73 88 81 29 33 11 12 479 38 70 296 176 156 g 0 177 231 311 413 415 16 485 24 17 41 466 350 148 214 138 t 0 39 41 55 16 10 18 6 475 470 2 7 55 46 55 103
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 59 60 86 8 19 462 1 15 26 3 14 50 35 80 128 c 0 250 193 73 88 81 29 33 11 12 479 38 70 296 176 156 g 0 177 231 311 413 415 16 485 24 17 41 466 350 148 214 138 t 0 39 41 55 16 10 18 6 475 470 2 7 55 46 55 103
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=2/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.925822; bssGGGAGTTCGGCss ; cor=; Ncor= a 72 40 32 44 6 11 316 2 13 21 3 7 29 14 54 80 c 107 169 198 35 55 59 23 24 15 17 331 25 43 277 121 116 g 93 128 121 258 297 291 15 334 23 14 29 329 267 54 154 104 t 93 28 14 28 7 4 11 5 314 313 2 4 26 20 36 65
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=15; w=0; offset=0; strand=R; shift=1; score=0.851606; -ssgGGAGTTGGasss ; cor=; Ncor= a 0 54 57 59 3 10 356 3 11 8 1 26 191 28 63 94 c 0 180 154 66 45 32 24 16 35 12 78 35 81 206 115 117 g 0 146 165 245 350 347 10 386 23 18 324 333 88 152 176 111 t 0 27 31 37 9 18 17 2 338 369 4 13 47 21 53 85
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=4/9; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.76927; -ssgGCAGTTGGasss ; cor=; Ncor= a 0 57 38 49 13 13 350 1 11 7 2 19 184 27 62 93 c 0 155 163 58 61 297 20 12 28 14 76 39 86 203 130 111 g 0 151 158 261 309 59 11 380 29 10 310 321 78 136 150 107 t 0 31 35 26 11 25 13 1 326 363 6 15 46 28 52 83
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=5/9; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.767352; -sgsCGAGTTGGmsss ; cor=; Ncor= a 0 60 69 83 3 8 424 2 13 3 0 17 177 35 68 83 c 0 212 109 163 369 37 15 10 47 12 101 38 116 258 138 133 g 0 152 247 162 72 401 11 441 41 14 347 380 96 145 199 130 t 0 29 28 45 9 7 3 0 352 424 5 18 64 15 48 107
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=6/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.709528; cssGGGAGTTGGcss- ; cor=; Ncor= a 62 57 37 24 2 10 278 4 6 10 4 16 31 22 50 0 c 107 123 187 32 30 39 23 14 27 14 51 28 207 128 93 0 g 76 122 80 244 280 249 8 298 21 14 261 259 51 147 133 0 t 74 17 15 19 7 21 10 3 265 281 3 16 30 22 43 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=7/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.703991; -sggCGAGTTGGCss- ; cor=; Ncor= a 0 47 50 27 5 5 287 3 5 4 1 18 21 23 40 0 c 0 151 72 63 257 33 17 13 16 7 69 22 218 126 104 0 g 0 102 177 202 48 272 9 300 24 11 243 267 50 140 135 0 t 0 16 17 24 6 6 3 0 271 294 3 9 27 27 37 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=8/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.694345; -ssgGGAGTTGcsss- ; cor=; Ncor= a 0 57 75 68 8 26 397 0 9 8 6 46 54 24 72 0 c 0 178 146 84 50 47 25 14 15 9 55 287 190 156 137 0 g 0 181 175 242 374 345 7 424 23 9 374 83 113 231 172 0 t 0 24 44 46 8 22 11 2 393 414 5 24 83 29 59 0
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=9/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.635531; sssGGCAGTTGGCss- ; cor=; Ncor= a 47 44 21 12 3 9 238 4 4 4 3 16 24 16 38 0 c 96 100 169 19 28 212 16 14 23 12 57 31 194 105 84 0 g 70 108 70 241 245 37 13 259 29 9 216 218 38 130 113 0 t 66 27 19 7 3 21 12 2 223 254 3 14 23 28 44 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ssskCCAACTCGscs ; Alignment reference a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssskCCAACTCGscs ; cor=; Ncor= a 107 48 15 64 18 5 424 352 0 3 7 9 45 28 29 c 130 199 145 96 380 347 14 41 441 11 401 72 162 247 152 g 133 138 258 116 38 101 12 47 10 15 37 369 163 109 212 t 83 68 35 177 17 0 3 13 2 424 8 3 83 69 60
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=1; strand=D; shift=1; score=0.88822; -ssGCCAACTCGccs ; cor=; Ncor= a 0 37 27 27 9 3 294 271 0 3 6 6 24 17 16 c 0 135 140 50 267 243 11 24 300 9 272 48 202 177 102 g 0 104 126 218 22 69 7 16 13 17 33 257 63 72 151 t 0 40 23 21 18 1 4 5 3 287 5 5 27 50 47
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=0; offset=0; strand=D; shift=0; score=0.876049; ssstCCAACTCCcss ; cor=; Ncor= a 85 53 21 47 13 4 369 338 2 17 18 9 37 31 27 c 111 176 152 88 333 324 18 23 386 10 347 350 245 165 146 g 117 115 206 81 35 78 12 35 16 24 32 45 66 154 180 t 94 63 28 191 26 1 8 11 3 356 10 3 59 57 54
oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=4/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.812013; -sscgCAACTCGCcs ; cor=; Ncor= a 0 26 20 43 12 3 262 220 1 0 2 9 13 31 20 c 0 116 125 157 53 225 3 25 260 17 238 37 184 138 101 g 0 84 108 56 182 37 1 18 6 9 26 220 51 67 110 t 0 44 17 14 23 5 4 7 3 244 4 4 22 34 39
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=5/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.77759; ssstCCAACTGCcss ; cor=; Ncor= a 83 52 28 46 15 6 363 326 1 13 25 11 26 35 31 c 107 150 136 78 321 310 10 29 380 11 59 309 261 158 151 g 111 130 203 86 39 76 14 28 12 20 297 61 58 163 155 t 93 62 27 184 19 2 7 11 1 350 13 13 49 38 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=6/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.767352; ssscCGAACTCCcss ; cor=; Ncor= a 103 55 46 55 7 2 470 475 6 18 10 16 55 41 39 c 138 214 148 350 466 41 17 24 485 16 415 413 311 231 177 g 156 176 296 70 38 479 12 11 33 29 81 88 73 193 250 t 128 80 35 50 14 3 26 15 1 462 19 8 86 60 59
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=7/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.72436; -sssgCAACTCCcss ; cor=; Ncor= a 0 59 29 83 24 5 414 393 2 11 22 8 46 44 24 c 0 172 231 113 83 374 9 23 424 7 345 374 242 175 181 g 0 137 156 190 287 55 9 15 14 25 47 50 84 146 178 t 0 72 24 54 46 6 8 9 0 397 26 8 68 75 57
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=8/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.708278; -ssgCCAACTCCCss ; cor=; Ncor= a 0 43 22 30 16 3 281 265 3 10 21 7 19 15 17 c 0 133 147 51 259 261 14 21 298 8 249 280 244 80 122 g 0 93 128 207 28 51 14 27 14 23 39 30 32 187 123 t 0 50 22 31 16 4 10 6 4 278 10 2 24 37 57
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=9/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.691837; ssGCCGAACTCCCss ; cor=; Ncor= a 65 36 20 26 4 2 313 314 5 11 4 7 28 14 28 c 104 154 54 267 329 29 14 23 334 15 291 297 258 121 128 g 116 121 277 43 25 331 17 15 24 23 59 55 35 198 169 t 80 54 14 29 7 3 21 13 2 316 11 6 44 32 40

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; -ssgGGAGTTGcsss ; Alignment reference a 0 57 75 68 8 26 397 0 9 8 6 46 54 24 72 c 0 178 146 84 50 47 25 14 15 9 55 287 190 156 137 g 0 181 175 242 374 345 7 424 23 9 374 83 113 231 172 t 0 24 44 46 8 22 11 2 393 414 5 24 83 29 59
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=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTGcsss ; cor=; Ncor= a 0 57 75 68 8 26 397 0 9 8 6 46 54 24 72 c 0 178 146 84 50 47 25 14 15 9 55 287 190 156 137 g 0 181 175 242 374 345 7 424 23 9 374 83 113 231 172 t 0 24 44 46 8 22 11 2 393 414 5 24 83 29 59
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=2/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.867785; -sgGCGAGTTGcgss ; cor=; Ncor= a 0 39 34 22 4 4 244 3 7 4 5 23 14 17 44 c 0 110 67 51 220 26 9 6 18 1 37 182 56 108 84 g 0 101 138 184 37 238 17 260 25 3 225 53 157 125 116 t 0 20 31 13 9 2 0 1 220 262 3 12 43 20 26
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=3/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.839118; cssGGGAGTTGGcss ; cor=; Ncor= a 62 57 37 24 2 10 278 4 6 10 4 16 31 22 50 c 107 123 187 32 30 39 23 14 27 14 51 28 207 128 93 g 76 122 80 244 280 249 8 298 21 14 261 259 51 147 133 t 74 17 15 19 7 21 10 3 265 281 3 16 30 22 43
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=4/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.833654; -ssgGGAGTTGGass ; cor=; Ncor= a 0 54 57 59 3 10 356 3 11 8 1 26 191 28 63 c 0 180 154 66 45 32 24 16 35 12 78 35 81 206 115 g 0 146 165 245 350 347 10 386 23 18 324 333 88 152 176 t 0 27 31 37 9 18 17 2 338 369 4 13 47 21 53
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=5/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.798563; -sggCGAGTTGGCss ; cor=; Ncor= a 0 47 50 27 5 5 287 3 5 4 1 18 21 23 40 c 0 151 72 63 257 33 17 13 16 7 69 22 218 126 104 g 0 102 177 202 48 272 9 300 24 11 243 267 50 140 135 t 0 16 17 24 6 6 3 0 271 294 3 9 27 27 37
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=6/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.749019; sssGGCAGTTGGCss ; cor=; Ncor= a 47 44 21 12 3 9 238 4 4 4 3 16 24 16 38 c 96 100 169 19 28 212 16 14 23 12 57 31 194 105 84 g 70 108 70 241 245 37 13 259 29 9 216 218 38 130 113 t 66 27 19 7 3 21 12 2 223 254 3 14 23 28 44
oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=7/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.747205; -ssgGCAGTTGGass ; cor=; Ncor= a 0 57 38 49 13 13 350 1 11 7 2 19 184 27 62 c 0 155 163 58 61 297 20 12 28 14 76 39 86 203 130 g 0 151 158 261 309 59 11 380 29 10 310 321 78 136 150 t 0 31 35 26 11 25 13 1 326 363 6 15 46 28 52
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=8/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.72436; -sgsCGAGTTGGmss ; cor=; Ncor= a 0 60 69 83 3 8 424 2 13 3 0 17 177 35 68 c 0 212 109 163 369 37 15 10 47 12 101 38 116 258 138 g 0 152 247 162 72 401 11 441 41 14 347 380 96 145 199 t 0 29 28 45 9 7 3 0 352 424 5 18 64 15 48
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=9/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.694345; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 59 60 86 8 19 462 1 15 26 3 14 50 35 80 c 0 250 193 73 88 81 29 33 11 12 479 38 70 296 176 g 0 177 231 311 413 415 16 485 24 17 41 466 350 148 214 t 0 39 41 55 16 10 18 6 475 470 2 7 55 46 55
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=10/10; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.626608; bssGGGAGTTCGGCs ; cor=; Ncor= a 72 40 32 44 6 11 316 2 13 21 3 7 29 14 54 c 107 169 198 35 55 59 23 24 15 17 331 25 43 277 121 g 93 128 121 258 297 291 15 334 23 14 29 329 267 54 154 t 93 28 14 28 7 4 11 5 314 313 2 4 26 20 36