One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084332_2026-01-22.084332_TmUoVo/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.2026-01-22.084332_2026-01-22.084332_TmUoVo/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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; -ssgGGAGTTGcmss ; Alignment reference a 0 58 66 56 10 17 389 4 10 5 10 57 125 36 61 c 0 168 150 61 45 50 18 8 21 13 57 245 117 154 131 g 0 172 167 270 352 338 7 407 17 16 351 93 103 201 163 t 0 24 39 35 15 17 8 3 374 388 4 27 77 31 67

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; -ssgGGAGTTGcmss ; cor=; Ncor= a 0 58 66 56 10 17 389 4 10 5 10 57 125 36 61 c 0 168 150 61 45 50 18 8 21 13 57 245 117 154 131 g 0 172 167 270 352 338 7 407 17 16 351 93 103 201 163 t 0 24 39 35 15 17 8 3 374 388 4 27 77 31 67

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=2/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.85884; -ssgGGAGTTGGgss ; cor=; Ncor= a 0 58 49 51 6 11 309 1 6 4 2 30 40 31 59 c 0 135 123 51 44 29 18 11 30 10 69 32 65 143 99 g 0 140 146 216 287 290 10 331 15 5 274 269 198 135 137 t 0 12 27 27 8 15 8 2 294 326 0 14 42 36 50

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=3/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.840615; yscGGGAGTTGGgss ; cor=; Ncor= a 45 50 18 17 1 7 215 1 7 5 3 25 22 26 35 c 78 84 163 9 23 26 12 10 29 8 44 26 41 97 79 g 54 99 56 208 217 204 11 233 13 12 196 185 156 99 96 t 68 12 8 11 4 8 7 1 196 220 2 9 26 23 35

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.829327; ssCGGGAGTTGGCss ; cor=; Ncor= a 45 42 11 19 0 8 207 3 4 4 2 13 18 20 29 c 78 84 179 25 16 29 20 12 26 16 35 23 165 96 77 g 68 101 42 186 222 194 7 226 20 10 203 194 39 108 95 t 51 15 10 12 4 11 8 1 192 212 2 12 20 18 41

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.808081; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 49 54 69 8 11 405 1 6 19 2 23 57 39 55 c 0 205 176 71 64 48 24 26 8 8 387 49 79 208 154 g 0 176 195 269 366 382 10 422 12 14 57 372 258 164 195 t 0 22 27 43 14 11 13 3 426 411 6 8 58 41 48

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.768594; -ssgGCAGTTGGgss ; cor=; Ncor= a 0 54 37 45 13 16 320 1 10 5 3 19 34 33 52 c 0 136 141 73 64 257 17 14 22 12 57 33 72 143 124 g 0 138 160 220 265 67 8 343 19 4 292 300 217 141 142 t 0 31 21 21 17 19 14 1 308 338 7 7 36 42 41

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=7/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.702583; ssCGGCAGTTGGCss ; cor=; Ncor= a 42 33 10 9 3 7 175 5 4 5 1 10 12 13 22 c 63 70 177 14 21 177 13 12 24 17 36 17 173 94 66 g 65 97 27 194 192 27 18 201 35 10 181 185 23 88 97 t 50 20 6 3 4 9 14 2 157 188 2 8 12 25 35

oligos_6nt_test_vs_ctrl_m4_rc_shift2 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=8/10; ncol2=14; w=0; offset=1; strand=R; shift=2; score=0.701412; --gsCGAGTTGGgss ; cor=; Ncor= a 0 0 43 91 6 6 373 3 6 5 1 25 43 39 62 c 0 0 94 109 287 34 8 13 32 13 86 32 93 183 125 g 0 0 221 145 87 349 10 376 24 5 303 325 208 141 159 t 0 0 34 47 12 3 1 0 330 369 2 10 48 29 46

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=9/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.690664; csgaCGAGTTGGCss ; cor=; Ncor= a 79 39 36 202 6 5 327 8 12 6 3 15 34 26 55 c 108 163 71 62 290 33 22 20 46 18 59 23 244 154 109 g 87 138 222 61 55 317 7 329 35 13 294 316 47 159 149 t 85 19 30 34 8 4 3 2 266 322 3 5 34 20 46

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=10/10; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.685658; kscGGGAGTTCGgss ; cor=; Ncor= a 72 44 19 27 3 9 292 9 9 22 2 15 36 27 42 c 84 139 228 35 42 40 21 17 10 14 291 31 53 175 120 g 89 139 78 254 289 285 15 311 17 11 42 287 214 105 144 t 94 17 14 23 5 5 11 2 303 292 4 6 36 32 33

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; gsscCCAACTGCcss ; Alignment reference a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gsscCCAACTGCcss ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.907031; ssscCCAACTCCcss ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58

oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=3/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.779531; -sscCCAACTCCCgs ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50

oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=4/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.778922; -ssGCCAACTGCCGs ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=5/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.768594; -sskgCAACTCCcss ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=6/10; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.768356; gsscCCAACTCGsc- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 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=7/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.756578; -sscCGAACTCCcss ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=8/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.74965; ssscCGAACTCCCgs ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=9/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.742775; -ssGCCAACTCCCGs ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=10/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.636895; -ssGCCAACTCGtcs ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 10 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; ssscCGAACTCCCgsm ; Alignment reference a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 94 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 89 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 84 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44 72

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=1/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; ssscCGAACTCCCgsm ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 94 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 89 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 84 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44 72

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.859299; -sscCGAACTCCcss- ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 0 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 0 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 0 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49 0

oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=3/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.844648; -sscCCAACTCCCgsr ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 68 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 54 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 78 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50 45

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=4/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.833212; ssscCCAACTCCcss- ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 0 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 0 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 0 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 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=5/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.790293; -ssGCCAACTCCCGss ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=6/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.74965; gsscCCAACTGCcss- ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 0 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 0 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 0 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54 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=7/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.685965; -ssGCCAACTGCCGss ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 50 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 65 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 63 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33 42

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=8/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.685658; -sskgCAACTCCcss- ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 0 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 0 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 0 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58 0

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=9/9; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.681087; gsscCCAACTCGsc-- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 0 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; -ssgGGAGTTCGgss ; Alignment reference a 0 49 54 69 8 11 405 1 6 19 2 23 57 39 55 c 0 205 176 71 64 48 24 26 8 8 387 49 79 208 154 g 0 176 195 269 366 382 10 422 12 14 57 372 258 164 195 t 0 22 27 43 14 11 13 3 426 411 6 8 58 41 48

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; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 49 54 69 8 11 405 1 6 19 2 23 57 39 55 c 0 205 176 71 64 48 24 26 8 8 387 49 79 208 154 g 0 176 195 269 366 382 10 422 12 14 57 372 258 164 195 t 0 22 27 43 14 11 13 3 426 411 6 8 58 41 48

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.859299; kscGGGAGTTCGgss ; cor=; Ncor= a 72 44 19 27 3 9 292 9 9 22 2 15 36 27 42 c 84 139 228 35 42 40 21 17 10 14 291 31 53 175 120 g 89 139 78 254 289 285 15 311 17 11 42 287 214 105 144 t 94 17 14 23 5 5 11 2 303 292 4 6 36 32 33

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/9; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.844696; -ssgGGAGTTGGgss ; cor=; Ncor= a 0 58 49 51 6 11 309 1 6 4 2 30 40 31 59 c 0 135 123 51 44 29 18 11 30 10 69 32 65 143 99 g 0 140 146 216 287 290 10 331 15 5 274 269 198 135 137 t 0 12 27 27 8 15 8 2 294 326 0 14 42 36 50

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=4/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.820823; yscGGGAGTTGGgss ; cor=; Ncor= a 45 50 18 17 1 7 215 1 7 5 3 25 22 26 35 c 78 84 163 9 23 26 12 10 29 8 44 26 41 97 79 g 54 99 56 208 217 204 11 233 13 12 196 185 156 99 96 t 68 12 8 11 4 8 7 1 196 220 2 9 26 23 35

oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=5/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.808081; -ssgGGAGTTGcmss ; cor=; Ncor= a 0 58 66 56 10 17 389 4 10 5 10 57 125 36 61 c 0 168 150 61 45 50 18 8 21 13 57 245 117 154 131 g 0 172 167 270 352 338 7 407 17 16 351 93 103 201 163 t 0 24 39 35 15 17 8 3 374 388 4 27 77 31 67

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=6/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.768924; ssCGGGAGTTGGCss ; cor=; Ncor= a 45 42 11 19 0 8 207 3 4 4 2 13 18 20 29 c 78 84 179 25 16 29 20 12 26 16 35 23 165 96 77 g 68 101 42 186 222 194 7 226 20 10 203 194 39 108 95 t 51 15 10 12 4 11 8 1 192 212 2 12 20 18 41

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=7/9; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.756578; -ssgGCAGTTGGgss ; cor=; Ncor= a 0 54 37 45 13 16 320 1 10 5 3 19 34 33 52 c 0 136 141 73 64 257 17 14 22 12 57 33 72 143 124 g 0 138 160 220 265 67 8 343 19 4 292 300 217 141 142 t 0 31 21 21 17 19 14 1 308 338 7 7 36 42 41

oligos_6nt_test_vs_ctrl_m4_rc_shift2 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=14; w=0; offset=1; strand=R; shift=2; score=0.714111; --gsCGAGTTGGgss ; cor=; Ncor= a 0 0 43 91 6 6 373 3 6 5 1 25 43 39 62 c 0 0 94 109 287 34 8 13 32 13 86 32 93 183 125 g 0 0 221 145 87 349 10 376 24 5 303 325 208 141 159 t 0 0 34 47 12 3 1 0 330 369 2 10 48 29 46

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=9/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.669235; csgaCGAGTTGGCss ; cor=; Ncor= a 79 39 36 202 6 5 327 8 12 6 3 15 34 26 55 c 108 163 71 62 290 33 22 20 46 18 59 23 244 154 109 g 87 138 222 61 55 317 7 329 35 13 294 316 47 159 149 t 85 19 30 34 8 4 3 2 266 322 3 5 34 20 46

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; yscGGGAGTTGGgss ; Alignment reference a 45 50 18 17 1 7 215 1 7 5 3 25 22 26 35 c 78 84 163 9 23 26 12 10 29 8 44 26 41 97 79 g 54 99 56 208 217 204 11 233 13 12 196 185 156 99 96 t 68 12 8 11 4 8 7 1 196 220 2 9 26 23 35

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; yscGGGAGTTGGgss ; cor=; Ncor= a 45 50 18 17 1 7 215 1 7 5 3 25 22 26 35 c 78 84 163 9 23 26 12 10 29 8 44 26 41 97 79 g 54 99 56 208 217 204 11 233 13 12 196 185 156 99 96 t 68 12 8 11 4 8 7 1 196 220 2 9 26 23 35

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.946938; ssCGGGAGTTGGCss ; cor=; Ncor= a 45 42 11 19 0 8 207 3 4 4 2 13 18 20 29 c 78 84 179 25 16 29 20 12 26 16 35 23 165 96 77 g 68 101 42 186 222 194 7 226 20 10 203 194 39 108 95 t 51 15 10 12 4 11 8 1 192 212 2 12 20 18 41

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=3/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.854389; -ssgGGAGTTGGgss ; cor=; Ncor= a 0 58 49 51 6 11 309 1 6 4 2 30 40 31 59 c 0 135 123 51 44 29 18 11 30 10 69 32 65 143 99 g 0 140 146 216 287 290 10 331 15 5 274 269 198 135 137 t 0 12 27 27 8 15 8 2 294 326 0 14 42 36 50

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3_rc; m=4/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.844648; kscGGGAGTTCGgss ; cor=; Ncor= a 72 44 19 27 3 9 292 9 9 22 2 15 36 27 42 c 84 139 228 35 42 40 21 17 10 14 291 31 53 175 120 g 89 139 78 254 289 285 15 311 17 11 42 287 214 105 144 t 94 17 14 23 5 5 11 2 303 292 4 6 36 32 33

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=5/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.840615; -ssgGGAGTTGcmss ; cor=; Ncor= a 0 58 66 56 10 17 389 4 10 5 10 57 125 36 61 c 0 168 150 61 45 50 18 8 21 13 57 245 117 154 131 g 0 172 167 270 352 338 7 407 17 16 351 93 103 201 163 t 0 24 39 35 15 17 8 3 374 388 4 27 77 31 67

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=6/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.828339; ssCGGCAGTTGGCss ; cor=; Ncor= a 42 33 10 9 3 7 175 5 4 5 1 10 12 13 22 c 63 70 177 14 21 177 13 12 24 17 36 17 173 94 66 g 65 97 27 194 192 27 18 201 35 10 181 185 23 88 97 t 50 20 6 3 4 9 14 2 157 188 2 8 12 25 35

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.820823; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 49 54 69 8 11 405 1 6 19 2 23 57 39 55 c 0 205 176 71 64 48 24 26 8 8 387 49 79 208 154 g 0 176 195 269 366 382 10 422 12 14 57 372 258 164 195 t 0 22 27 43 14 11 13 3 426 411 6 8 58 41 48

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.779531; -ssgGCAGTTGGgss ; cor=; Ncor= a 0 54 37 45 13 16 320 1 10 5 3 19 34 33 52 c 0 136 141 73 64 257 17 14 22 12 57 33 72 143 124 g 0 138 160 220 265 67 8 343 19 4 292 300 217 141 142 t 0 31 21 21 17 19 14 1 308 338 7 7 36 42 41

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=9/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.725905; csgaCGAGTTGGCss ; cor=; Ncor= a 79 39 36 202 6 5 327 8 12 6 3 15 34 26 55 c 108 163 71 62 290 33 22 20 46 18 59 23 244 154 109 g 87 138 222 61 55 317 7 329 35 13 294 316 47 159 149 t 85 19 30 34 8 4 3 2 266 322 3 5 34 20 46

oligos_6nt_test_vs_ctrl_m4_rc_shift2 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=10/10; ncol2=14; w=0; offset=2; strand=R; shift=2; score=0.684513; --gsCGAGTTGGgss ; cor=; Ncor= a 0 0 43 91 6 6 373 3 6 5 1 25 43 39 62 c 0 0 94 109 287 34 8 13 32 13 86 32 93 183 125 g 0 0 221 145 87 349 10 376 24 5 303 325 208 141 159 t 0 0 34 47 12 3 1 0 330 369 2 10 48 29 46

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=14; shift=0; ncol=14; gsscCCAACTCGsc ; Alignment reference a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43

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=14; w=0; offset=0; strand=D; shift=0; score= 1; gsscCCAACTCGsc ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43

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=0.843775; ssscCCAACTCCcs ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.768356; gsscCCAACTGCcs ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37

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=4/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.762916; -ssGCCAACTCGtc ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=5/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.714111; -sscCGAACTCCcs ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=6/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.701412; -sskgCAACTCCcs ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66

oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=7/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.684513; -sscCCAACTCCCg ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=8/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.681087; ssscCGAACTCCCg ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19

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=9/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.648695; -ssGCCAACTCCCG ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11

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=15; shift=1; ncol=16; -ssGCCAACTCCCGss ; Alignment reference a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45

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=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTCCCGss ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45

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=2/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.946938; -sscCCAACTCCCgsr ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 68 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 54 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 78 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50 45

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=3/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.902543; -ssGCCAACTGCCGss ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 50 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 65 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 63 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33 42

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=4/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.829327; -sskgCAACTCCcss- ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 0 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 0 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 0 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58 0

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=5/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.812235; ssscCCAACTCCcss- ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 0 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 0 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 0 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58 0

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=6/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.790293; ssscCGAACTCCCgsm ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 94 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 89 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 84 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44 72

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=7/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.772145; -ssGCCAACTCGtcsg ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 85 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 87 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 108 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39 79

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=8/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.768924; -sscCGAACTCCcss- ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 0 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 0 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 0 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49 0

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=9/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.742775; gsscCCAACTGCcss- ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 0 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 0 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 0 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54 0

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=10/10; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.648695; gsscCCAACTCGsc-- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift1 ; 8 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; -ssGCCAACTGCCGss ; Alignment reference a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 50 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 65 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 63 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33 42

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=1/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTGCCGss ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 50 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 65 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 63 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33 42

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=2/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.902543; -ssGCCAACTCCCGss ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45

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=3/7; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.828339; -sscCCAACTCCCgsr ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 68 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 54 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 78 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50 45

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=4/7; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.778922; gsscCCAACTGCcss- ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 0 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 0 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 0 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54 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=5/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.702583; -sskgCAACTCCcss- ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 0 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 0 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 0 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58 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=6/7; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.690801; ssscCCAACTCCcss- ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 0 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 0 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 0 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58 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=7/7; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.685965; ssscCGAACTCCCgsm ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 94 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 89 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 84 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44 72

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift1 ; 9 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; -ssGCCAACTCGtcsg ; Alignment reference a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 85 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 87 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 108 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39 79

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=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTCGtcsg ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 85 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 87 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 108 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39 79

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=2/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.772145; -ssGCCAACTCCCGss ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45

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=3/8; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.762916; gsscCCAACTCGsc-- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 0 0

oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=4/8; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.725905; -sscCCAACTCCCgsr ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 68 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 54 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 78 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50 45

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=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.705297; ssscCCAACTCCcss- ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 0 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 0 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 0 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 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=6/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.690664; -sskgCAACTCCcss- ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 0 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 0 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 0 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58 0

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=7/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.669235; -sscCGAACTCCcss- ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 0 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 0 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 0 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49 0

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=8/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.636895; gsscCCAACTGCcss- ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 0 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 0 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 0 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54 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; ssscCCAACTCCcss ; Alignment reference a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58

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; ssscCCAACTCCcss ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.907031; gsscCCAACTGCcss ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54

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=3/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.85884; -sskgCAACTCCcss ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58

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=4/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.854389; -sscCCAACTCCCgs ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=5/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.844696; -sscCGAACTCCcss ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49

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=6/10; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.843775; gsscCCAACTCGsc- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 0

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=7/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.833212; ssscCGAACTCCCgs ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44

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=8/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.812235; -ssGCCAACTCCCGs ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42

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=9/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.705297; -ssGCCAACTCGtcs ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39

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=10/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.690801; -ssGCCAACTGCCGs ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33

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; -ssgGGAGTTGcmss ; Alignment reference a 0 58 66 56 10 17 389 4 10 5 10 57 125 36 61 c 0 168 150 61 45 50 18 8 21 13 57 245 117 154 131 g 0 172 167 270 352 338 7 407 17 16 351 93 103 201 163 t 0 24 39 35 15 17 8 3 374 388 4 27 77 31 67
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; -ssgGGAGTTGcmss ; cor=; Ncor= a 0 58 66 56 10 17 389 4 10 5 10 57 125 36 61 c 0 168 150 61 45 50 18 8 21 13 57 245 117 154 131 g 0 172 167 270 352 338 7 407 17 16 351 93 103 201 163 t 0 24 39 35 15 17 8 3 374 388 4 27 77 31 67
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=2/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.85884; -ssgGGAGTTGGgss ; cor=; Ncor= a 0 58 49 51 6 11 309 1 6 4 2 30 40 31 59 c 0 135 123 51 44 29 18 11 30 10 69 32 65 143 99 g 0 140 146 216 287 290 10 331 15 5 274 269 198 135 137 t 0 12 27 27 8 15 8 2 294 326 0 14 42 36 50
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=3/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.840615; yscGGGAGTTGGgss ; cor=; Ncor= a 45 50 18 17 1 7 215 1 7 5 3 25 22 26 35 c 78 84 163 9 23 26 12 10 29 8 44 26 41 97 79 g 54 99 56 208 217 204 11 233 13 12 196 185 156 99 96 t 68 12 8 11 4 8 7 1 196 220 2 9 26 23 35
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.829327; ssCGGGAGTTGGCss ; cor=; Ncor= a 45 42 11 19 0 8 207 3 4 4 2 13 18 20 29 c 78 84 179 25 16 29 20 12 26 16 35 23 165 96 77 g 68 101 42 186 222 194 7 226 20 10 203 194 39 108 95 t 51 15 10 12 4 11 8 1 192 212 2 12 20 18 41
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.808081; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 49 54 69 8 11 405 1 6 19 2 23 57 39 55 c 0 205 176 71 64 48 24 26 8 8 387 49 79 208 154 g 0 176 195 269 366 382 10 422 12 14 57 372 258 164 195 t 0 22 27 43 14 11 13 3 426 411 6 8 58 41 48
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.768594; -ssgGCAGTTGGgss ; cor=; Ncor= a 0 54 37 45 13 16 320 1 10 5 3 19 34 33 52 c 0 136 141 73 64 257 17 14 22 12 57 33 72 143 124 g 0 138 160 220 265 67 8 343 19 4 292 300 217 141 142 t 0 31 21 21 17 19 14 1 308 338 7 7 36 42 41
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=7/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.702583; ssCGGCAGTTGGCss ; cor=; Ncor= a 42 33 10 9 3 7 175 5 4 5 1 10 12 13 22 c 63 70 177 14 21 177 13 12 24 17 36 17 173 94 66 g 65 97 27 194 192 27 18 201 35 10 181 185 23 88 97 t 50 20 6 3 4 9 14 2 157 188 2 8 12 25 35
oligos_6nt_test_vs_ctrl_m4_rc_shift2 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=8/10; ncol2=14; w=0; offset=1; strand=R; shift=2; score=0.701412; --gsCGAGTTGGgss ; cor=; Ncor= a 0 0 43 91 6 6 373 3 6 5 1 25 43 39 62 c 0 0 94 109 287 34 8 13 32 13 86 32 93 183 125 g 0 0 221 145 87 349 10 376 24 5 303 325 208 141 159 t 0 0 34 47 12 3 1 0 330 369 2 10 48 29 46
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=9/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.690664; csgaCGAGTTGGCss ; cor=; Ncor= a 79 39 36 202 6 5 327 8 12 6 3 15 34 26 55 c 108 163 71 62 290 33 22 20 46 18 59 23 244 154 109 g 87 138 222 61 55 317 7 329 35 13 294 316 47 159 149 t 85 19 30 34 8 4 3 2 266 322 3 5 34 20 46
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=10/10; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.685658; kscGGGAGTTCGgss ; cor=; Ncor= a 72 44 19 27 3 9 292 9 9 22 2 15 36 27 42 c 84 139 228 35 42 40 21 17 10 14 291 31 53 175 120 g 89 139 78 254 289 285 15 311 17 11 42 287 214 105 144 t 94 17 14 23 5 5 11 2 303 292 4 6 36 32 33

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; gsscCCAACTGCcss ; Alignment reference a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gsscCCAACTGCcss ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.907031; ssscCCAACTCCcss ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58
oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=3/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.779531; -sscCCAACTCCCgs ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=4/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.778922; -ssGCCAACTGCCGs ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=5/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.768594; -sskgCAACTCCcss ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=6/10; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.768356; gsscCCAACTCGsc- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 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=7/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.756578; -sscCGAACTCCcss ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=8/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.74965; ssscCGAACTCCCgs ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=9/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.742775; -ssGCCAACTCCCGs ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=10/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.636895; -ssGCCAACTCGtcs ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39

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; ssscCGAACTCCCgsm ; Alignment reference a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 94 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 89 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 84 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44 72
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=1/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; ssscCGAACTCCCgsm ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 94 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 89 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 84 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44 72
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.859299; -sscCGAACTCCcss- ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 0 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 0 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 0 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49 0
oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=3/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.844648; -sscCCAACTCCCgsr ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 68 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 54 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 78 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50 45
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=4/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.833212; ssscCCAACTCCcss- ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 0 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 0 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 0 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 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=5/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.790293; -ssGCCAACTCCCGss ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=6/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.74965; gsscCCAACTGCcss- ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 0 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 0 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 0 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54 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=7/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.685965; -ssGCCAACTGCCGss ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 50 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 65 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 63 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33 42
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=8/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.685658; -sskgCAACTCCcss- ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 0 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 0 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 0 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58 0
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=9/9; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.681087; gsscCCAACTCGsc-- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 0 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; -ssgGGAGTTCGgss ; Alignment reference a 0 49 54 69 8 11 405 1 6 19 2 23 57 39 55 c 0 205 176 71 64 48 24 26 8 8 387 49 79 208 154 g 0 176 195 269 366 382 10 422 12 14 57 372 258 164 195 t 0 22 27 43 14 11 13 3 426 411 6 8 58 41 48
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; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 49 54 69 8 11 405 1 6 19 2 23 57 39 55 c 0 205 176 71 64 48 24 26 8 8 387 49 79 208 154 g 0 176 195 269 366 382 10 422 12 14 57 372 258 164 195 t 0 22 27 43 14 11 13 3 426 411 6 8 58 41 48
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.859299; kscGGGAGTTCGgss ; cor=; Ncor= a 72 44 19 27 3 9 292 9 9 22 2 15 36 27 42 c 84 139 228 35 42 40 21 17 10 14 291 31 53 175 120 g 89 139 78 254 289 285 15 311 17 11 42 287 214 105 144 t 94 17 14 23 5 5 11 2 303 292 4 6 36 32 33
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/9; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.844696; -ssgGGAGTTGGgss ; cor=; Ncor= a 0 58 49 51 6 11 309 1 6 4 2 30 40 31 59 c 0 135 123 51 44 29 18 11 30 10 69 32 65 143 99 g 0 140 146 216 287 290 10 331 15 5 274 269 198 135 137 t 0 12 27 27 8 15 8 2 294 326 0 14 42 36 50
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=4/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.820823; yscGGGAGTTGGgss ; cor=; Ncor= a 45 50 18 17 1 7 215 1 7 5 3 25 22 26 35 c 78 84 163 9 23 26 12 10 29 8 44 26 41 97 79 g 54 99 56 208 217 204 11 233 13 12 196 185 156 99 96 t 68 12 8 11 4 8 7 1 196 220 2 9 26 23 35
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=5/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.808081; -ssgGGAGTTGcmss ; cor=; Ncor= a 0 58 66 56 10 17 389 4 10 5 10 57 125 36 61 c 0 168 150 61 45 50 18 8 21 13 57 245 117 154 131 g 0 172 167 270 352 338 7 407 17 16 351 93 103 201 163 t 0 24 39 35 15 17 8 3 374 388 4 27 77 31 67
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=6/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.768924; ssCGGGAGTTGGCss ; cor=; Ncor= a 45 42 11 19 0 8 207 3 4 4 2 13 18 20 29 c 78 84 179 25 16 29 20 12 26 16 35 23 165 96 77 g 68 101 42 186 222 194 7 226 20 10 203 194 39 108 95 t 51 15 10 12 4 11 8 1 192 212 2 12 20 18 41
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=7/9; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.756578; -ssgGCAGTTGGgss ; cor=; Ncor= a 0 54 37 45 13 16 320 1 10 5 3 19 34 33 52 c 0 136 141 73 64 257 17 14 22 12 57 33 72 143 124 g 0 138 160 220 265 67 8 343 19 4 292 300 217 141 142 t 0 31 21 21 17 19 14 1 308 338 7 7 36 42 41
oligos_6nt_test_vs_ctrl_m4_rc_shift2 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=14; w=0; offset=1; strand=R; shift=2; score=0.714111; --gsCGAGTTGGgss ; cor=; Ncor= a 0 0 43 91 6 6 373 3 6 5 1 25 43 39 62 c 0 0 94 109 287 34 8 13 32 13 86 32 93 183 125 g 0 0 221 145 87 349 10 376 24 5 303 325 208 141 159 t 0 0 34 47 12 3 1 0 330 369 2 10 48 29 46
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=9/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.669235; csgaCGAGTTGGCss ; cor=; Ncor= a 79 39 36 202 6 5 327 8 12 6 3 15 34 26 55 c 108 163 71 62 290 33 22 20 46 18 59 23 244 154 109 g 87 138 222 61 55 317 7 329 35 13 294 316 47 159 149 t 85 19 30 34 8 4 3 2 266 322 3 5 34 20 46

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; yscGGGAGTTGGgss ; Alignment reference a 45 50 18 17 1 7 215 1 7 5 3 25 22 26 35 c 78 84 163 9 23 26 12 10 29 8 44 26 41 97 79 g 54 99 56 208 217 204 11 233 13 12 196 185 156 99 96 t 68 12 8 11 4 8 7 1 196 220 2 9 26 23 35
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; yscGGGAGTTGGgss ; cor=; Ncor= a 45 50 18 17 1 7 215 1 7 5 3 25 22 26 35 c 78 84 163 9 23 26 12 10 29 8 44 26 41 97 79 g 54 99 56 208 217 204 11 233 13 12 196 185 156 99 96 t 68 12 8 11 4 8 7 1 196 220 2 9 26 23 35
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.946938; ssCGGGAGTTGGCss ; cor=; Ncor= a 45 42 11 19 0 8 207 3 4 4 2 13 18 20 29 c 78 84 179 25 16 29 20 12 26 16 35 23 165 96 77 g 68 101 42 186 222 194 7 226 20 10 203 194 39 108 95 t 51 15 10 12 4 11 8 1 192 212 2 12 20 18 41
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=3/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.854389; -ssgGGAGTTGGgss ; cor=; Ncor= a 0 58 49 51 6 11 309 1 6 4 2 30 40 31 59 c 0 135 123 51 44 29 18 11 30 10 69 32 65 143 99 g 0 140 146 216 287 290 10 331 15 5 274 269 198 135 137 t 0 12 27 27 8 15 8 2 294 326 0 14 42 36 50
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3_rc; m=4/10; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.844648; kscGGGAGTTCGgss ; cor=; Ncor= a 72 44 19 27 3 9 292 9 9 22 2 15 36 27 42 c 84 139 228 35 42 40 21 17 10 14 291 31 53 175 120 g 89 139 78 254 289 285 15 311 17 11 42 287 214 105 144 t 94 17 14 23 5 5 11 2 303 292 4 6 36 32 33
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=5/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.840615; -ssgGGAGTTGcmss ; cor=; Ncor= a 0 58 66 56 10 17 389 4 10 5 10 57 125 36 61 c 0 168 150 61 45 50 18 8 21 13 57 245 117 154 131 g 0 172 167 270 352 338 7 407 17 16 351 93 103 201 163 t 0 24 39 35 15 17 8 3 374 388 4 27 77 31 67
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=6/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.828339; ssCGGCAGTTGGCss ; cor=; Ncor= a 42 33 10 9 3 7 175 5 4 5 1 10 12 13 22 c 63 70 177 14 21 177 13 12 24 17 36 17 173 94 66 g 65 97 27 194 192 27 18 201 35 10 181 185 23 88 97 t 50 20 6 3 4 9 14 2 157 188 2 8 12 25 35
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.820823; -ssgGGAGTTCGgss ; cor=; Ncor= a 0 49 54 69 8 11 405 1 6 19 2 23 57 39 55 c 0 205 176 71 64 48 24 26 8 8 387 49 79 208 154 g 0 176 195 269 366 382 10 422 12 14 57 372 258 164 195 t 0 22 27 43 14 11 13 3 426 411 6 8 58 41 48
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.779531; -ssgGCAGTTGGgss ; cor=; Ncor= a 0 54 37 45 13 16 320 1 10 5 3 19 34 33 52 c 0 136 141 73 64 257 17 14 22 12 57 33 72 143 124 g 0 138 160 220 265 67 8 343 19 4 292 300 217 141 142 t 0 31 21 21 17 19 14 1 308 338 7 7 36 42 41
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=9/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.725905; csgaCGAGTTGGCss ; cor=; Ncor= a 79 39 36 202 6 5 327 8 12 6 3 15 34 26 55 c 108 163 71 62 290 33 22 20 46 18 59 23 244 154 109 g 87 138 222 61 55 317 7 329 35 13 294 316 47 159 149 t 85 19 30 34 8 4 3 2 266 322 3 5 34 20 46
oligos_6nt_test_vs_ctrl_m4_rc_shift2 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=10/10; ncol2=14; w=0; offset=2; strand=R; shift=2; score=0.684513; --gsCGAGTTGGgss ; cor=; Ncor= a 0 0 43 91 6 6 373 3 6 5 1 25 43 39 62 c 0 0 94 109 287 34 8 13 32 13 86 32 93 183 125 g 0 0 221 145 87 349 10 376 24 5 303 325 208 141 159 t 0 0 34 47 12 3 1 0 330 369 2 10 48 29 46

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=14; shift=0; ncol=14; gsscCCAACTCGsc ; Alignment reference a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43
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=14; w=0; offset=0; strand=D; shift=0; score= 1; gsscCCAACTCGsc ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43
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=0.843775; ssscCCAACTCCcs ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.768356; gsscCCAACTGCcs ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37
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=4/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.762916; -ssGCCAACTCGtc ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=5/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.714111; -sscCGAACTCCcs ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54
oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=6/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.701412; -sskgCAACTCCcs ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66
oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=7/9; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.684513; -sscCCAACTCCCg ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=8/9; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.681087; ssscCGAACTCCCg ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19
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=9/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.648695; -ssGCCAACTCCCG ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11

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=15; shift=1; ncol=16; -ssGCCAACTCCCGss ; Alignment reference a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45
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=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTCCCGss ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45
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=2/10; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.946938; -sscCCAACTCCCgsr ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 68 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 54 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 78 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50 45
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=3/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.902543; -ssGCCAACTGCCGss ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 50 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 65 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 63 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33 42
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=4/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.829327; -sskgCAACTCCcss- ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 0 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 0 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 0 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58 0
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=5/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.812235; ssscCCAACTCCcss- ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 0 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 0 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 0 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58 0
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=6/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.790293; ssscCGAACTCCCgsm ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 94 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 89 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 84 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44 72
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=7/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.772145; -ssGCCAACTCGtcsg ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 85 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 87 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 108 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39 79
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=8/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.768924; -sscCGAACTCCcss- ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 0 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 0 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 0 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49 0
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=9/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.742775; gsscCCAACTGCcss- ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 0 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 0 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 0 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54 0
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=10/10; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.648695; gsscCCAACTCGsc-- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 0 0

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; -ssGCCAACTGCCGss ; Alignment reference a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 50 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 65 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 63 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33 42
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=1/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTGCCGss ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 50 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 65 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 63 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33 42
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=2/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.902543; -ssGCCAACTCCCGss ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45
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=3/7; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.828339; -sscCCAACTCCCgsr ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 68 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 54 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 78 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50 45
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=4/7; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.778922; gsscCCAACTGCcss- ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 0 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 0 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 0 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54 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=5/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.702583; -sskgCAACTCCcss- ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 0 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 0 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 0 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58 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=6/7; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.690801; ssscCCAACTCCcss- ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 0 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 0 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 0 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58 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=7/7; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.685965; ssscCGAACTCCCgsm ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 94 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 89 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 84 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44 72

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; -ssGCCAACTCGtcsg ; Alignment reference a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 85 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 87 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 108 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39 79
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=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAACTCGtcsg ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 85 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 87 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 108 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39 79
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=2/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.772145; -ssGCCAACTCCCGss ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 51 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 68 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 78 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42 45
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=3/8; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.762916; gsscCCAACTCGsc-- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 0 0
oligos_7nt_test_vs_ctrl_m5_rc_shift1 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=4/8; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.725905; -sscCCAACTCCCgsr ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 68 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 54 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 78 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50 45
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=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.705297; ssscCCAACTCCcss- ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 0 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 0 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 0 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 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=6/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.690664; -sskgCAACTCCcss- ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 0 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 0 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 0 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58 0
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=7/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.669235; -sscCGAACTCCcss- ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 0 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 0 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 0 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49 0
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=8/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.636895; gsscCCAACTGCcss- ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 0 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 0 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 0 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54 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; ssscCCAACTCCcss ; Alignment reference a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58
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; ssscCCAACTCCcss ; cor=; Ncor= a 64 50 36 42 14 0 326 294 2 8 15 8 27 27 12 c 87 137 135 198 269 274 5 15 331 10 290 287 216 146 140 g 112 99 143 65 32 69 10 30 11 18 29 44 51 123 135 t 82 59 31 40 30 2 4 6 1 309 11 6 51 49 58
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.907031; gsscCCAACTGCcss ; cor=; Ncor= a 71 41 42 36 7 7 338 308 1 14 19 17 21 21 31 c 85 142 141 217 300 292 4 19 343 8 67 265 220 160 138 g 121 124 143 72 33 57 12 22 14 17 257 64 73 141 136 t 82 52 33 34 19 3 5 10 1 320 16 13 45 37 54
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=3/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.85884; -sskgCAACTCCcss ; cor=; Ncor= a 0 67 31 77 27 4 388 374 3 8 17 15 35 39 24 c 0 163 201 103 93 351 16 17 407 7 338 352 270 167 172 g 0 131 154 117 245 57 13 21 8 18 50 45 61 150 168 t 0 61 36 125 57 10 5 10 4 389 17 10 56 66 58
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=4/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.854389; -sscCCAACTCCCgs ; cor=; Ncor= a 0 35 23 26 9 2 220 196 1 7 8 4 11 8 12 c 0 96 99 156 185 196 12 13 233 11 204 217 208 56 99 g 0 79 97 41 26 44 8 29 10 12 26 23 9 163 84 t 0 35 26 22 25 3 5 7 1 215 7 1 17 18 50
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=5/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.844696; -sscCGAACTCCcss ; cor=; Ncor= a 0 48 41 58 8 6 411 426 3 13 11 14 43 27 22 c 0 195 164 258 372 57 14 12 422 10 382 366 269 195 176 g 0 154 208 79 49 387 8 8 26 24 48 64 71 176 205 t 0 55 39 57 23 2 19 6 1 405 11 8 69 54 49
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=6/10; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.843775; gsscCCAACTCGsc- ; cor=; Ncor= a 86 46 29 48 10 2 369 330 0 1 3 12 47 34 0 c 92 159 141 208 325 303 5 24 376 10 349 87 145 221 0 g 121 125 183 93 32 86 13 32 13 8 34 287 109 94 0 t 93 62 39 43 25 1 5 6 3 373 6 6 91 43 0
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=7/10; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.833212; ssscCGAACTCCCgs ; cor=; Ncor= a 66 33 32 36 6 4 292 303 2 11 5 5 23 14 17 c 95 144 105 214 287 42 11 17 311 15 285 289 254 78 139 g 108 120 175 53 31 291 14 10 17 21 40 42 35 228 139 t 70 42 27 36 15 2 22 9 9 292 9 3 27 19 44
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=8/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.812235; -ssGCCAACTCCCGs ; cor=; Ncor= a 0 41 18 20 12 2 212 192 1 8 11 4 12 10 15 c 0 95 108 39 194 203 10 20 226 7 194 222 186 42 101 g 0 77 96 165 23 35 16 26 12 20 29 16 25 179 84 t 0 29 20 18 13 2 4 4 3 207 8 0 19 11 42
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=9/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.705297; -ssGCCAACTCGtcs ; cor=; Ncor= a 0 46 20 34 5 3 322 266 2 3 4 8 34 30 19 c 0 149 159 47 316 294 13 35 329 7 317 55 61 222 138 g 0 109 154 244 23 59 18 46 20 22 33 290 62 71 163 t 0 55 26 34 15 3 6 12 8 327 5 6 202 36 39
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=10/10; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.690801; -ssGCCAACTGCCGs ; cor=; Ncor= a 0 35 25 12 8 2 188 157 2 14 9 4 3 6 20 c 0 97 88 23 185 181 10 35 201 18 27 192 194 27 97 g 0 66 94 173 17 36 17 24 12 13 177 21 14 177 70 t 0 22 13 12 10 1 5 4 5 175 7 3 9 10 33