One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084309_2026-01-22.084309_ujjUO0/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.2026-01-22.084309_2026-01-22.084309_ujjUO0/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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=14; shift=1; ncol=15; -ssgGGAGTTCGGss ; Alignment reference a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35

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=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTCGGss ; cor=; Ncor= a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35

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=0.860185; cssGGGAGTTCGGCs ; cor=; Ncor= a 60 34 18 26 4 9 229 2 7 14 1 7 21 13 32 c 74 121 150 25 45 36 15 20 7 13 230 14 29 180 84 g 64 87 81 184 203 209 7 234 17 7 25 231 190 47 119 t 59 15 8 22 5 3 6 1 226 223 1 5 17 17 22

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=3/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.839079; -ssgCCAGTTCGgss ; cor=; Ncor= a 0 49 33 64 8 7 382 2 4 20 1 4 41 28 42 c 0 215 129 67 342 343 23 15 22 16 406 39 75 222 146 g 0 133 252 243 70 85 12 418 30 8 31 390 281 130 210 t 0 42 25 65 19 4 22 4 383 395 1 6 42 59 41

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=4/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.825543; -ssgGGAGTTGGcss ; cor=; Ncor= a 0 50 49 46 3 10 293 2 4 7 1 22 41 25 61 c 0 125 115 77 43 27 24 16 23 16 41 24 186 135 90 g 0 136 143 172 281 278 5 312 13 12 290 270 69 144 136 t 0 22 26 38 6 18 11 3 293 298 1 17 37 29 46

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=5/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.813803; sssGGGAGTTGGgss ; cor=; Ncor= a 46 41 15 17 0 8 184 2 4 3 1 21 21 11 34 c 57 82 127 15 17 15 14 9 19 5 38 20 34 85 59 g 57 70 54 164 183 171 4 192 13 7 163 156 132 88 86 t 45 12 9 9 5 11 3 2 169 190 3 8 18 21 26

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=6/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.765054; -ssGCCAGTTCGGCs ; cor=; Ncor= a 0 46 27 34 6 4 293 5 7 18 0 4 21 7 39 c 0 189 111 36 280 277 27 19 34 24 339 26 28 298 111 g 0 94 199 248 50 70 14 330 29 13 15 319 277 33 173 t 0 27 19 38 20 5 22 2 286 301 2 7 30 18 33

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=7/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.732477; csGcCGAGTTSGgss ; cor=; Ncor= a 60 35 22 35 4 4 231 4 3 5 0 9 23 25 32 c 75 110 37 143 203 20 4 5 34 4 64 18 38 120 73 g 51 74 170 43 31 211 4 231 22 2 175 208 156 72 118 t 55 22 12 20 3 6 2 1 182 230 2 6 24 24 18

oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=8/9; ncol2=13; w=0; offset=1; strand=R; shift=2; score=0.713379; --gsCGAGTTGGcss ; cor=; Ncor= a 0 0 43 61 7 6 300 1 2 4 1 13 42 29 48 c 0 0 70 110 252 35 13 11 23 11 60 32 160 134 96 g 0 0 191 113 57 274 9 309 19 6 261 272 80 127 146 t 0 0 18 38 6 7 0 1 278 301 0 5 40 32 32

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=9/9; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.703615; cscGGGAGTTGGcss ; cor=; Ncor= a 51 35 21 19 2 9 204 5 5 6 1 14 20 13 46 c 76 88 151 26 21 26 26 13 17 13 38 14 161 83 63 g 59 106 57 184 214 190 5 223 18 10 202 200 44 130 93 t 56 13 13 13 5 17 7 1 202 213 1 14 17 16 40

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=13; shift=1; ncol=14; -ssgCCAACTCGsc ; Alignment reference a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43

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=13; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTCGsc ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=2/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.834576; -ssgCCAACTGGcs ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.82937; -ssgCCAACTCCcs ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=4/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.827232; -sscCSAACTCGgC ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22

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=5/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.713379; -ssCCGAACTCCcs ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41

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=6/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.701056; -sscCCAACTCCCs ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15

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=0; strand=R; shift=1; score=0.700236; -sscCGAACTGGcs ; cor=; Ncor= a 0 41 59 42 6 1 395 383 4 22 4 19 65 25 c 0 210 130 281 390 31 8 30 418 12 85 70 243 252 g 0 146 222 75 39 406 16 22 15 23 343 342 67 129 t 0 42 28 41 4 1 20 4 2 382 7 8 64 33

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.674343; sssgCCAACTCCCg ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21

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=-1; offset=-1; strand=D; shift=0; score=0.592661; ssGCCGAACTCCCs ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18

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=15; shift=1; ncol=16; -ssGCCAGTTCGGCsv ; Alignment reference a 0 46 27 34 6 4 293 5 7 18 0 4 21 7 39 97 c 0 189 111 36 280 277 27 19 34 24 339 26 28 298 111 90 g 0 94 199 248 50 70 14 330 29 13 15 319 277 33 173 103 t 0 27 19 38 20 5 22 2 286 301 2 7 30 18 33 66

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=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAGTTCGGCsv ; cor=; Ncor= a 0 46 27 34 6 4 293 5 7 18 0 4 21 7 39 97 c 0 189 111 36 280 277 27 19 34 24 339 26 28 298 111 90 g 0 94 199 248 50 70 14 330 29 13 15 319 277 33 173 103 t 0 27 19 38 20 5 22 2 286 301 2 7 30 18 33 66

oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=2/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.912657; -ssgCCAGTTCGgss- ; cor=; Ncor= a 0 49 33 64 8 7 382 2 4 20 1 4 41 28 42 0 c 0 215 129 67 342 343 23 15 22 16 406 39 75 222 146 0 g 0 133 252 243 70 85 12 418 30 8 31 390 281 130 210 0 t 0 42 25 65 19 4 22 4 383 395 1 6 42 59 41 0

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/6; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.782931; cssGGGAGTTCGGCss ; cor=; Ncor= a 60 34 18 26 4 9 229 2 7 14 1 7 21 13 32 62 c 74 121 150 25 45 36 15 20 7 13 230 14 29 180 84 81 g 64 87 81 184 203 209 7 234 17 7 25 231 190 47 119 74 t 59 15 8 22 5 3 6 1 226 223 1 5 17 17 22 40

oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=4/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.765054; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 0 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 0 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 0 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35 0

oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=5/6; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.741014; -ssgCCAGTTGGcss- ; cor=; Ncor= a 0 33 27 40 5 12 279 2 5 6 2 12 37 18 34 0 c 0 138 88 73 237 225 9 14 12 11 57 28 155 123 93 0 g 0 111 155 164 58 54 10 286 22 4 240 258 60 132 136 0 t 0 21 33 26 3 12 5 1 264 282 4 5 51 30 40 0

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=6/6; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.652106; csGcCGAGTTSGgss- ; cor=; Ncor= a 60 35 22 35 4 4 231 4 3 5 0 9 23 25 32 0 c 75 110 37 143 203 20 4 5 34 4 64 18 38 120 73 0 g 51 74 170 43 31 211 4 231 22 2 175 208 156 72 118 0 t 55 22 12 20 3 6 2 1 182 230 2 6 24 24 18 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; cscGGGAGTTGGcsss ; Alignment reference a 51 35 21 19 2 9 204 5 5 6 1 14 20 13 46 52 c 76 88 151 26 21 26 26 13 17 13 38 14 161 83 63 75 g 59 106 57 184 214 190 5 223 18 10 202 200 44 130 93 71 t 56 13 13 13 5 17 7 1 202 213 1 14 17 16 40 44

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cscGGGAGTTGGcsss ; cor=; Ncor= a 51 35 21 19 2 9 204 5 5 6 1 14 20 13 46 52 c 76 88 151 26 21 26 26 13 17 13 38 14 161 83 63 75 g 59 106 57 184 214 190 5 223 18 10 202 200 44 130 93 71 t 56 13 13 13 5 17 7 1 202 213 1 14 17 16 40 44

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.888246; sssGGGAGTTGGgss- ; cor=; Ncor= a 46 41 15 17 0 8 184 2 4 3 1 21 21 11 34 0 c 57 82 127 15 17 15 14 9 19 5 38 20 34 85 59 0 g 57 70 54 164 183 171 4 192 13 7 163 156 132 88 86 0 t 45 12 9 9 5 11 3 2 169 190 3 8 18 21 26 0

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.852605; -ssgGGAGTTGGcss- ; cor=; Ncor= a 0 50 49 46 3 10 293 2 4 7 1 22 41 25 61 0 c 0 125 115 77 43 27 24 16 23 16 41 24 186 135 90 0 g 0 136 143 172 281 278 5 312 13 12 290 270 69 144 136 0 t 0 22 26 38 6 18 11 3 293 298 1 17 37 29 46 0

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=4/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.803722; cssGGGAGTTCGGCss ; cor=; Ncor= a 60 34 18 26 4 9 229 2 7 14 1 7 21 13 32 62 c 74 121 150 25 45 36 15 20 7 13 230 14 29 180 84 81 g 64 87 81 184 203 209 7 234 17 7 25 231 190 47 119 74 t 59 15 8 22 5 3 6 1 226 223 1 5 17 17 22 40

oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=5/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.703615; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 0 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 0 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 0 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35 0

oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.684506; -ssgCCAGTTGGcss- ; cor=; Ncor= a 0 33 27 40 5 12 279 2 5 6 2 12 37 18 34 0 c 0 138 88 73 237 225 9 14 12 11 57 28 155 123 93 0 g 0 111 155 164 58 54 10 286 22 4 240 258 60 132 136 0 t 0 21 33 26 3 12 5 1 264 282 4 5 51 30 40 0

oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=7/8; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.674343; --gsCGAGTTGGcss- ; cor=; Ncor= a 0 0 43 61 7 6 300 1 2 4 1 13 42 29 48 0 c 0 0 70 110 252 35 13 11 23 11 60 32 160 134 96 0 g 0 0 191 113 57 274 9 309 19 6 261 272 80 127 146 0 t 0 0 18 38 6 7 0 1 278 301 0 5 40 32 32 0

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3_rc; m=8/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.673326; csGcCGAGTTSGgss- ; cor=; Ncor= a 60 35 22 35 4 4 231 4 3 5 0 9 23 25 32 0 c 75 110 37 143 203 20 4 5 34 4 64 18 38 120 73 0 g 51 74 170 43 31 211 4 231 22 2 175 208 156 72 118 0 t 55 22 12 20 3 6 2 1 182 230 2 6 24 24 18 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssgCCAACTGGcss ; Alignment reference a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTGGcss ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33

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=2/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.850348; -sscCGAACTGGcss ; cor=; Ncor= a 0 41 59 42 6 1 395 383 4 22 4 19 65 25 42 c 0 210 130 281 390 31 8 30 418 12 85 70 243 252 133 g 0 146 222 75 39 406 16 22 15 23 343 342 67 129 215 t 0 42 28 41 4 1 20 4 2 382 7 8 64 33 49

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=3/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.834576; -ssgCCAACTCGsc- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=4/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.808905; -ssgCCAACTCCcss ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50

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=5/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.776572; -sscCSAACTCGgCs ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=6/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.741014; bsGCCGAACTGGCss ; cor=; Ncor= a 66 33 18 30 7 2 301 286 2 22 5 20 38 19 27 c 103 173 33 277 319 15 13 29 330 14 70 50 248 199 94 g 90 111 298 28 26 339 24 34 19 27 277 280 36 111 189 t 97 39 7 21 4 0 18 7 5 293 4 6 34 27 46

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=7/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.694814; -sscCCAACTCCCss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4_rc; m=8/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.684506; sssgCCAACTCCCgs ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift1 ; 11 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; -sscCSAACTCGgCsg ; Alignment reference a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 55 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 51 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 75 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35 60

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=1/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -sscCSAACTCGgCsg ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 55 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 51 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 75 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35 60

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=2/10; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.827232; -ssgCCAACTCGsc-- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0 0

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=3/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.776572; -ssgCCAACTGGcss- ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 0 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 0 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 0 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33 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=4/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.772351; -sscCCAACTCCCsss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 45 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 57 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 57 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41 46

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.755198; -ssgCCAACTCCcss- ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 0 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 0 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 0 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50 0

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.732477; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 25 0 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 132 0 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 179 0 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41 45 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=7/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.727237; -sscCGAACTGGcss- ; cor=; Ncor= a 0 41 59 42 6 1 395 383 4 22 4 19 65 25 42 0 c 0 210 130 281 390 31 8 30 418 12 85 70 243 252 133 0 g 0 146 222 75 39 406 16 22 15 23 343 342 67 129 215 0 t 0 42 28 41 4 1 20 4 2 382 7 8 64 33 49 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=8/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.699649; ssGCCGAACTCCCssg ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 59 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 64 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 74 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34 60

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=9/10; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.673326; sssgCCAACTCCCgsg ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 56 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 59 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 76 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35 51

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.652106; bsGCCGAACTGGCss- ; cor=; Ncor= a 66 33 18 30 7 2 301 286 2 22 5 20 38 19 27 0 c 103 173 33 277 319 15 13 29 330 14 70 50 248 199 94 0 g 90 111 298 28 26 339 24 34 19 27 277 280 36 111 189 0 t 97 39 7 21 4 0 18 7 5 293 4 6 34 27 46 0

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; ssGCCGAACTCCCssg ; Alignment reference a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 59 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 64 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 74 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34 60

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; ssGCCGAACTCCCssg ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 59 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 64 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 74 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34 60

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (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=14; w=0; offset=1; strand=R; shift=1; score=0.860185; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 25 0 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 132 0 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 179 0 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41 45 0

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=3/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.826733; -sscCCAACTCCCsss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 45 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 57 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 57 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41 46

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.803722; sssgCCAACTCCCgsg ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 56 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 59 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 76 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35 51

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=5/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.782931; bsGCCGAACTGGCss- ; cor=; Ncor= a 66 33 18 30 7 2 301 286 2 22 5 20 38 19 27 0 c 103 173 33 277 319 15 13 29 330 14 70 50 248 199 94 0 g 90 111 298 28 26 339 24 34 19 27 277 280 36 111 189 0 t 97 39 7 21 4 0 18 7 5 293 4 6 34 27 46 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=6/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.722195; -sscCGAACTGGcss- ; cor=; Ncor= a 0 41 59 42 6 1 395 383 4 22 4 19 65 25 42 0 c 0 210 130 281 390 31 8 30 418 12 85 70 243 252 133 0 g 0 146 222 75 39 406 16 22 15 23 343 342 67 129 215 0 t 0 42 28 41 4 1 20 4 2 382 7 8 64 33 49 0

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=7/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.701685; -ssgCCAACTCCcss- ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 0 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 0 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 0 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50 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=8/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.699649; -sscCSAACTCGgCsg ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 55 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 51 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 75 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35 60

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=9/9; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.592661; -ssgCCAACTCGsc-- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift1 ; 8 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; -ssgCCAGTTCGgss ; Alignment reference a 0 49 33 64 8 7 382 2 4 20 1 4 41 28 42 c 0 215 129 67 342 343 23 15 22 16 406 39 75 222 146 g 0 133 252 243 70 85 12 418 30 8 31 390 281 130 210 t 0 42 25 65 19 4 22 4 383 395 1 6 42 59 41

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=1/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAGTTCGgss ; cor=; Ncor= a 0 49 33 64 8 7 382 2 4 20 1 4 41 28 42 c 0 215 129 67 342 343 23 15 22 16 406 39 75 222 146 g 0 133 252 243 70 85 12 418 30 8 31 390 281 130 210 t 0 42 25 65 19 4 22 4 383 395 1 6 42 59 41

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=2/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.912657; -ssGCCAGTTCGGCs ; cor=; Ncor= a 0 46 27 34 6 4 293 5 7 18 0 4 21 7 39 c 0 189 111 36 280 277 27 19 34 24 339 26 28 298 111 g 0 94 199 248 50 70 14 330 29 13 15 319 277 33 173 t 0 27 19 38 20 5 22 2 286 301 2 7 30 18 33

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=3/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.850348; -ssgCCAGTTGGcss ; cor=; Ncor= a 0 33 27 40 5 12 279 2 5 6 2 12 37 18 34 c 0 138 88 73 237 225 9 14 12 11 57 28 155 123 93 g 0 111 155 164 58 54 10 286 22 4 240 258 60 132 136 t 0 21 33 26 3 12 5 1 264 282 4 5 51 30 40

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=4/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.839079; -ssgGGAGTTCGGss ; cor=; Ncor= a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35

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=5/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.727237; csGcCGAGTTSGgss ; cor=; Ncor= a 60 35 22 35 4 4 231 4 3 5 0 9 23 25 32 c 75 110 37 143 203 20 4 5 34 4 64 18 38 120 73 g 51 74 170 43 31 211 4 231 22 2 175 208 156 72 118 t 55 22 12 20 3 6 2 1 182 230 2 6 24 24 18

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=6/7; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.722195; cssGGGAGTTCGGCs ; cor=; Ncor= a 60 34 18 26 4 9 229 2 7 14 1 7 21 13 32 c 74 121 150 25 45 36 15 20 7 13 230 14 29 180 84 g 64 87 81 184 203 209 7 234 17 7 25 231 190 47 119 t 59 15 8 22 5 3 6 1 226 223 1 5 17 17 22

oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=7/7; ncol2=13; w=0; offset=1; strand=R; shift=2; score=0.700236; --gsCGAGTTGGcss ; cor=; Ncor= a 0 0 43 61 7 6 300 1 2 4 1 13 42 29 48 c 0 0 70 110 252 35 13 11 23 11 60 32 160 134 96 g 0 0 191 113 57 274 9 309 19 6 261 272 80 127 146 t 0 0 18 38 6 7 0 1 278 301 0 5 40 32 32

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssgCCAACTCCcss ; Alignment reference a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTCCcss ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50

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=2/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.87643; -sscCCAACTCCCss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.852605; sssgCCAACTCCCgs ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.82937; -ssgCCAACTCGsc- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.825543; -ssCCGAACTCCcss ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 25 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 132 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 179 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41 45

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=6/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.808905; -ssgCCAACTGGcss ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33

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=7/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.755198; -sscCSAACTCGgCs ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35

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=8/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.701685; ssGCCGAACTCCCss ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift1 ; 9 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; -sscCCAACTCCCsss ; Alignment reference a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 45 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 57 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 57 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41 46

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=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -sscCCAACTCCCsss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 45 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 57 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 57 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41 46

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=2/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.888246; sssgCCAACTCCCgsg ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 56 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 59 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 76 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35 51

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=3/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.87643; -ssgCCAACTCCcss- ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 0 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 0 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 0 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50 0

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=4/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.826733; ssGCCGAACTCCCssg ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 59 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 64 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 74 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34 60

oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.813803; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 25 0 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 132 0 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 179 0 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41 45 0

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=6/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.772351; -sscCSAACTCGgCsg ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 55 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 51 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 75 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35 60

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=7/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.701056; -ssgCCAACTCGsc-- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0 0

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=8/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.694814; -ssgCCAACTGGcss- ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 0 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 0 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 0 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33 0

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=14; shift=1; ncol=15; -ssgGGAGTTCGGss ; Alignment reference a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35
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=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgGGAGTTCGGss ; cor=; Ncor= a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35
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=0.860185; cssGGGAGTTCGGCs ; cor=; Ncor= a 60 34 18 26 4 9 229 2 7 14 1 7 21 13 32 c 74 121 150 25 45 36 15 20 7 13 230 14 29 180 84 g 64 87 81 184 203 209 7 234 17 7 25 231 190 47 119 t 59 15 8 22 5 3 6 1 226 223 1 5 17 17 22
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=3/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.839079; -ssgCCAGTTCGgss ; cor=; Ncor= a 0 49 33 64 8 7 382 2 4 20 1 4 41 28 42 c 0 215 129 67 342 343 23 15 22 16 406 39 75 222 146 g 0 133 252 243 70 85 12 418 30 8 31 390 281 130 210 t 0 42 25 65 19 4 22 4 383 395 1 6 42 59 41
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=4/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.825543; -ssgGGAGTTGGcss ; cor=; Ncor= a 0 50 49 46 3 10 293 2 4 7 1 22 41 25 61 c 0 125 115 77 43 27 24 16 23 16 41 24 186 135 90 g 0 136 143 172 281 278 5 312 13 12 290 270 69 144 136 t 0 22 26 38 6 18 11 3 293 298 1 17 37 29 46
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=5/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.813803; sssGGGAGTTGGgss ; cor=; Ncor= a 46 41 15 17 0 8 184 2 4 3 1 21 21 11 34 c 57 82 127 15 17 15 14 9 19 5 38 20 34 85 59 g 57 70 54 164 183 171 4 192 13 7 163 156 132 88 86 t 45 12 9 9 5 11 3 2 169 190 3 8 18 21 26
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=6/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.765054; -ssGCCAGTTCGGCs ; cor=; Ncor= a 0 46 27 34 6 4 293 5 7 18 0 4 21 7 39 c 0 189 111 36 280 277 27 19 34 24 339 26 28 298 111 g 0 94 199 248 50 70 14 330 29 13 15 319 277 33 173 t 0 27 19 38 20 5 22 2 286 301 2 7 30 18 33
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=7/9; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.732477; csGcCGAGTTSGgss ; cor=; Ncor= a 60 35 22 35 4 4 231 4 3 5 0 9 23 25 32 c 75 110 37 143 203 20 4 5 34 4 64 18 38 120 73 g 51 74 170 43 31 211 4 231 22 2 175 208 156 72 118 t 55 22 12 20 3 6 2 1 182 230 2 6 24 24 18
oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=8/9; ncol2=13; w=0; offset=1; strand=R; shift=2; score=0.713379; --gsCGAGTTGGcss ; cor=; Ncor= a 0 0 43 61 7 6 300 1 2 4 1 13 42 29 48 c 0 0 70 110 252 35 13 11 23 11 60 32 160 134 96 g 0 0 191 113 57 274 9 309 19 6 261 272 80 127 146 t 0 0 18 38 6 7 0 1 278 301 0 5 40 32 32
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=9/9; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.703615; cscGGGAGTTGGcss ; cor=; Ncor= a 51 35 21 19 2 9 204 5 5 6 1 14 20 13 46 c 76 88 151 26 21 26 26 13 17 13 38 14 161 83 63 g 59 106 57 184 214 190 5 223 18 10 202 200 44 130 93 t 56 13 13 13 5 17 7 1 202 213 1 14 17 16 40

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=13; shift=1; ncol=14; -ssgCCAACTCGsc ; Alignment reference a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43
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=13; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTCGsc ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=2/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.834576; -ssgCCAACTGGcs ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/9; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.82937; -ssgCCAACTCCcs ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=4/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.827232; -sscCSAACTCGgC ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22
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=5/9; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.713379; -ssCCGAACTCCcs ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41
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=6/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.701056; -sscCCAACTCCCs ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15
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=0; strand=R; shift=1; score=0.700236; -sscCGAACTGGcs ; cor=; Ncor= a 0 41 59 42 6 1 395 383 4 22 4 19 65 25 c 0 210 130 281 390 31 8 30 418 12 85 70 243 252 g 0 146 222 75 39 406 16 22 15 23 343 342 67 129 t 0 42 28 41 4 1 20 4 2 382 7 8 64 33
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=8/9; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.674343; sssgCCAACTCCCg ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21
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=-1; offset=-1; strand=D; shift=0; score=0.592661; ssGCCGAACTCCCs ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssGCCAGTTCGGCsv ; Alignment reference a 0 46 27 34 6 4 293 5 7 18 0 4 21 7 39 97 c 0 189 111 36 280 277 27 19 34 24 339 26 28 298 111 90 g 0 94 199 248 50 70 14 330 29 13 15 319 277 33 173 103 t 0 27 19 38 20 5 22 2 286 301 2 7 30 18 33 66
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=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCAGTTCGGCsv ; cor=; Ncor= a 0 46 27 34 6 4 293 5 7 18 0 4 21 7 39 97 c 0 189 111 36 280 277 27 19 34 24 339 26 28 298 111 90 g 0 94 199 248 50 70 14 330 29 13 15 319 277 33 173 103 t 0 27 19 38 20 5 22 2 286 301 2 7 30 18 33 66
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=2/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.912657; -ssgCCAGTTCGgss- ; cor=; Ncor= a 0 49 33 64 8 7 382 2 4 20 1 4 41 28 42 0 c 0 215 129 67 342 343 23 15 22 16 406 39 75 222 146 0 g 0 133 252 243 70 85 12 418 30 8 31 390 281 130 210 0 t 0 42 25 65 19 4 22 4 383 395 1 6 42 59 41 0
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/6; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.782931; cssGGGAGTTCGGCss ; cor=; Ncor= a 60 34 18 26 4 9 229 2 7 14 1 7 21 13 32 62 c 74 121 150 25 45 36 15 20 7 13 230 14 29 180 84 81 g 64 87 81 184 203 209 7 234 17 7 25 231 190 47 119 74 t 59 15 8 22 5 3 6 1 226 223 1 5 17 17 22 40
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=4/6; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.765054; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 0 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 0 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 0 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35 0
oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=5/6; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.741014; -ssgCCAGTTGGcss- ; cor=; Ncor= a 0 33 27 40 5 12 279 2 5 6 2 12 37 18 34 0 c 0 138 88 73 237 225 9 14 12 11 57 28 155 123 93 0 g 0 111 155 164 58 54 10 286 22 4 240 258 60 132 136 0 t 0 21 33 26 3 12 5 1 264 282 4 5 51 30 40 0
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=6/6; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.652106; csGcCGAGTTSGgss- ; cor=; Ncor= a 60 35 22 35 4 4 231 4 3 5 0 9 23 25 32 0 c 75 110 37 143 203 20 4 5 34 4 64 18 38 120 73 0 g 51 74 170 43 31 211 4 231 22 2 175 208 156 72 118 0 t 55 22 12 20 3 6 2 1 182 230 2 6 24 24 18 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; cscGGGAGTTGGcsss ; Alignment reference a 51 35 21 19 2 9 204 5 5 6 1 14 20 13 46 52 c 76 88 151 26 21 26 26 13 17 13 38 14 161 83 63 75 g 59 106 57 184 214 190 5 223 18 10 202 200 44 130 93 71 t 56 13 13 13 5 17 7 1 202 213 1 14 17 16 40 44
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cscGGGAGTTGGcsss ; cor=; Ncor= a 51 35 21 19 2 9 204 5 5 6 1 14 20 13 46 52 c 76 88 151 26 21 26 26 13 17 13 38 14 161 83 63 75 g 59 106 57 184 214 190 5 223 18 10 202 200 44 130 93 71 t 56 13 13 13 5 17 7 1 202 213 1 14 17 16 40 44
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.888246; sssGGGAGTTGGgss- ; cor=; Ncor= a 46 41 15 17 0 8 184 2 4 3 1 21 21 11 34 0 c 57 82 127 15 17 15 14 9 19 5 38 20 34 85 59 0 g 57 70 54 164 183 171 4 192 13 7 163 156 132 88 86 0 t 45 12 9 9 5 11 3 2 169 190 3 8 18 21 26 0
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.852605; -ssgGGAGTTGGcss- ; cor=; Ncor= a 0 50 49 46 3 10 293 2 4 7 1 22 41 25 61 0 c 0 125 115 77 43 27 24 16 23 16 41 24 186 135 90 0 g 0 136 143 172 281 278 5 312 13 12 290 270 69 144 136 0 t 0 22 26 38 6 18 11 3 293 298 1 17 37 29 46 0
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=4/8; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.803722; cssGGGAGTTCGGCss ; cor=; Ncor= a 60 34 18 26 4 9 229 2 7 14 1 7 21 13 32 62 c 74 121 150 25 45 36 15 20 7 13 230 14 29 180 84 81 g 64 87 81 184 203 209 7 234 17 7 25 231 190 47 119 74 t 59 15 8 22 5 3 6 1 226 223 1 5 17 17 22 40
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=5/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.703615; -ssgGGAGTTCGGss- ; cor=; Ncor= a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 0 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 0 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 0 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35 0
oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.684506; -ssgCCAGTTGGcss- ; cor=; Ncor= a 0 33 27 40 5 12 279 2 5 6 2 12 37 18 34 0 c 0 138 88 73 237 225 9 14 12 11 57 28 155 123 93 0 g 0 111 155 164 58 54 10 286 22 4 240 258 60 132 136 0 t 0 21 33 26 3 12 5 1 264 282 4 5 51 30 40 0
oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=7/8; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.674343; --gsCGAGTTGGcss- ; cor=; Ncor= a 0 0 43 61 7 6 300 1 2 4 1 13 42 29 48 0 c 0 0 70 110 252 35 13 11 23 11 60 32 160 134 96 0 g 0 0 191 113 57 274 9 309 19 6 261 272 80 127 146 0 t 0 0 18 38 6 7 0 1 278 301 0 5 40 32 32 0
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3_rc; m=8/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.673326; csGcCGAGTTSGgss- ; cor=; Ncor= a 60 35 22 35 4 4 231 4 3 5 0 9 23 25 32 0 c 75 110 37 143 203 20 4 5 34 4 64 18 38 120 73 0 g 51 74 170 43 31 211 4 231 22 2 175 208 156 72 118 0 t 55 22 12 20 3 6 2 1 182 230 2 6 24 24 18 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssgCCAACTGGcss ; Alignment reference a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTGGcss ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33
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=2/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.850348; -sscCGAACTGGcss ; cor=; Ncor= a 0 41 59 42 6 1 395 383 4 22 4 19 65 25 42 c 0 210 130 281 390 31 8 30 418 12 85 70 243 252 133 g 0 146 222 75 39 406 16 22 15 23 343 342 67 129 215 t 0 42 28 41 4 1 20 4 2 382 7 8 64 33 49
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=3/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.834576; -ssgCCAACTCGsc- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=4/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.808905; -ssgCCAACTCCcss ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50
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=5/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.776572; -sscCSAACTCGgCs ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=6/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.741014; bsGCCGAACTGGCss ; cor=; Ncor= a 66 33 18 30 7 2 301 286 2 22 5 20 38 19 27 c 103 173 33 277 319 15 13 29 330 14 70 50 248 199 94 g 90 111 298 28 26 339 24 34 19 27 277 280 36 111 189 t 97 39 7 21 4 0 18 7 5 293 4 6 34 27 46
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=7/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.694814; -sscCCAACTCCCss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4_rc; m=8/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.684506; sssgCCAACTCCCgs ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35

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; -sscCSAACTCGgCsg ; Alignment reference a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 55 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 51 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 75 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35 60
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=1/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -sscCSAACTCGgCsg ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 55 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 51 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 75 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35 60
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=2/10; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.827232; -ssgCCAACTCGsc-- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0 0
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=3/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.776572; -ssgCCAACTGGcss- ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 0 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 0 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 0 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33 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=4/10; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.772351; -sscCCAACTCCCsss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 45 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 57 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 57 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41 46
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.755198; -ssgCCAACTCCcss- ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 0 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 0 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 0 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50 0
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.732477; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 25 0 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 132 0 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 179 0 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41 45 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=7/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.727237; -sscCGAACTGGcss- ; cor=; Ncor= a 0 41 59 42 6 1 395 383 4 22 4 19 65 25 42 0 c 0 210 130 281 390 31 8 30 418 12 85 70 243 252 133 0 g 0 146 222 75 39 406 16 22 15 23 343 342 67 129 215 0 t 0 42 28 41 4 1 20 4 2 382 7 8 64 33 49 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=8/10; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.699649; ssGCCGAACTCCCssg ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 59 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 64 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 74 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34 60
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=9/10; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.673326; sssgCCAACTCCCgsg ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 56 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 59 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 76 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35 51
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=10/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.652106; bsGCCGAACTGGCss- ; cor=; Ncor= a 66 33 18 30 7 2 301 286 2 22 5 20 38 19 27 0 c 103 173 33 277 319 15 13 29 330 14 70 50 248 199 94 0 g 90 111 298 28 26 339 24 34 19 27 277 280 36 111 189 0 t 97 39 7 21 4 0 18 7 5 293 4 6 34 27 46 0

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; ssGCCGAACTCCCssg ; Alignment reference a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 59 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 64 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 74 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34 60
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; ssGCCGAACTCCCssg ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 59 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 64 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 74 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34 60
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (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=14; w=0; offset=1; strand=R; shift=1; score=0.860185; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 25 0 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 132 0 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 179 0 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41 45 0
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=3/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.826733; -sscCCAACTCCCsss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 45 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 57 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 57 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41 46
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/9; ncol2=16; w=0; offset=0; strand=R; shift=0; score=0.803722; sssgCCAACTCCCgsg ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 56 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 59 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 76 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35 51
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=5/9; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.782931; bsGCCGAACTGGCss- ; cor=; Ncor= a 66 33 18 30 7 2 301 286 2 22 5 20 38 19 27 0 c 103 173 33 277 319 15 13 29 330 14 70 50 248 199 94 0 g 90 111 298 28 26 339 24 34 19 27 277 280 36 111 189 0 t 97 39 7 21 4 0 18 7 5 293 4 6 34 27 46 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=6/9; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.722195; -sscCGAACTGGcss- ; cor=; Ncor= a 0 41 59 42 6 1 395 383 4 22 4 19 65 25 42 0 c 0 210 130 281 390 31 8 30 418 12 85 70 243 252 133 0 g 0 146 222 75 39 406 16 22 15 23 343 342 67 129 215 0 t 0 42 28 41 4 1 20 4 2 382 7 8 64 33 49 0
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=7/9; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.701685; -ssgCCAACTCCcss- ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 0 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 0 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 0 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50 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=8/9; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.699649; -sscCSAACTCGgCsg ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 55 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 51 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 75 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35 60
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=9/9; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.592661; -ssgCCAACTCGsc-- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssgCCAGTTCGgss ; Alignment reference a 0 49 33 64 8 7 382 2 4 20 1 4 41 28 42 c 0 215 129 67 342 343 23 15 22 16 406 39 75 222 146 g 0 133 252 243 70 85 12 418 30 8 31 390 281 130 210 t 0 42 25 65 19 4 22 4 383 395 1 6 42 59 41
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=1/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAGTTCGgss ; cor=; Ncor= a 0 49 33 64 8 7 382 2 4 20 1 4 41 28 42 c 0 215 129 67 342 343 23 15 22 16 406 39 75 222 146 g 0 133 252 243 70 85 12 418 30 8 31 390 281 130 210 t 0 42 25 65 19 4 22 4 383 395 1 6 42 59 41
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=2/7; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.912657; -ssGCCAGTTCGGCs ; cor=; Ncor= a 0 46 27 34 6 4 293 5 7 18 0 4 21 7 39 c 0 189 111 36 280 277 27 19 34 24 339 26 28 298 111 g 0 94 199 248 50 70 14 330 29 13 15 319 277 33 173 t 0 27 19 38 20 5 22 2 286 301 2 7 30 18 33
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=3/7; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.850348; -ssgCCAGTTGGcss ; cor=; Ncor= a 0 33 27 40 5 12 279 2 5 6 2 12 37 18 34 c 0 138 88 73 237 225 9 14 12 11 57 28 155 123 93 g 0 111 155 164 58 54 10 286 22 4 240 258 60 132 136 t 0 21 33 26 3 12 5 1 264 282 4 5 51 30 40
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=4/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.839079; -ssgGGAGTTCGGss ; cor=; Ncor= a 0 45 41 65 9 12 340 4 10 19 1 9 36 32 52 c 0 179 143 60 66 48 19 30 4 5 344 19 51 183 120 g 0 132 179 214 297 314 13 345 19 14 35 346 259 122 174 t 0 25 18 42 9 7 9 2 348 343 1 7 35 44 35
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=5/7; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.727237; csGcCGAGTTSGgss ; cor=; Ncor= a 60 35 22 35 4 4 231 4 3 5 0 9 23 25 32 c 75 110 37 143 203 20 4 5 34 4 64 18 38 120 73 g 51 74 170 43 31 211 4 231 22 2 175 208 156 72 118 t 55 22 12 20 3 6 2 1 182 230 2 6 24 24 18
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=6/7; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.722195; cssGGGAGTTCGGCs ; cor=; Ncor= a 60 34 18 26 4 9 229 2 7 14 1 7 21 13 32 c 74 121 150 25 45 36 15 20 7 13 230 14 29 180 84 g 64 87 81 184 203 209 7 234 17 7 25 231 190 47 119 t 59 15 8 22 5 3 6 1 226 223 1 5 17 17 22
oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=7/7; ncol2=13; w=0; offset=1; strand=R; shift=2; score=0.700236; --gsCGAGTTGGcss ; cor=; Ncor= a 0 0 43 61 7 6 300 1 2 4 1 13 42 29 48 c 0 0 70 110 252 35 13 11 23 11 60 32 160 134 96 g 0 0 191 113 57 274 9 309 19 6 261 272 80 127 146 t 0 0 18 38 6 7 0 1 278 301 0 5 40 32 32

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssgCCAACTCCcss ; Alignment reference a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssgCCAACTCCcss ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50
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=2/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.87643; -sscCCAACTCCCss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.852605; sssgCCAACTCCCgs ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.82937; -ssgCCAACTCGsc- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.825543; -ssCCGAACTCCcss ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 25 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 132 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 179 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41 45
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=6/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.808905; -ssgCCAACTGGcss ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33
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=7/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.755198; -sscCSAACTCGgCs ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35
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=8/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.701685; ssGCCGAACTCCCss ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34

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; -sscCCAACTCCCsss ; Alignment reference a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 45 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 57 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 57 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41 46
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=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -sscCCAACTCCCsss ; cor=; Ncor= a 0 26 21 18 8 3 190 169 2 3 11 5 9 9 12 45 c 0 86 88 132 156 163 7 13 192 4 171 183 164 54 70 57 g 0 59 85 34 20 38 5 19 9 14 15 17 15 127 82 57 t 0 34 11 21 21 1 3 4 2 184 8 0 17 15 41 46
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=2/8; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.888246; sssgCCAACTCCCgsg ; cor=; Ncor= a 44 40 16 17 14 1 213 202 1 7 17 5 13 13 13 56 c 71 93 130 44 200 202 10 18 223 5 190 214 184 57 106 59 g 75 63 83 161 14 38 13 17 13 26 26 21 26 151 88 76 t 52 46 13 20 14 1 6 5 5 204 9 2 19 21 35 51
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=3/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.87643; -ssgCCAACTCCcss- ; cor=; Ncor= a 0 46 29 37 17 1 298 293 3 11 18 6 38 26 22 0 c 0 136 144 69 270 290 12 13 312 5 278 281 172 143 136 0 g 0 90 135 186 24 41 16 23 16 24 27 43 77 115 125 0 t 0 61 25 41 22 1 7 4 2 293 10 3 46 49 50 0
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=4/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.826733; ssGCCGAACTCCCssg ; cor=; Ncor= a 40 22 17 17 5 1 223 226 1 6 3 5 22 8 15 59 c 74 119 47 190 231 25 7 17 234 7 209 203 184 81 87 64 g 81 84 180 29 14 230 13 7 20 15 36 45 25 150 121 74 t 62 32 13 21 7 1 14 7 2 229 9 4 26 18 34 60
oligos_6nt_test_vs_ctrl_m2_rc_shift1 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.813803; -ssCCGAACTCCcss- ; cor=; Ncor= a 0 35 44 35 7 1 343 348 2 9 7 9 42 18 25 0 c 0 174 122 259 346 35 14 19 345 13 314 297 214 179 132 0 g 0 120 183 51 19 344 5 4 30 19 48 66 60 143 179 0 t 0 52 32 36 9 1 19 10 4 340 12 9 65 41 45 0
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=6/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.772351; -sscCSAACTCGgCsg ; cor=; Ncor= a 0 18 24 24 6 2 230 182 1 2 6 3 20 12 22 55 c 0 118 72 156 208 175 2 22 231 4 211 31 43 170 74 51 g 0 73 120 38 18 64 4 34 5 4 20 203 143 37 110 75 t 0 32 25 23 9 0 5 3 4 231 4 4 35 22 35 60
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=7/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.701056; -ssgCCAACTCGsc-- ; cor=; Ncor= a 0 32 32 40 5 0 301 278 1 0 7 6 38 18 0 0 c 0 146 127 80 272 261 6 19 309 9 274 57 113 191 0 0 g 0 96 134 160 32 60 11 23 11 13 35 252 110 70 0 0 t 0 48 29 42 13 1 4 2 1 300 6 7 61 43 0 0
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=8/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.694814; -ssgCCAACTGGcss- ; cor=; Ncor= a 0 40 30 51 5 4 282 264 1 5 12 3 26 33 21 0 c 0 136 132 60 258 240 4 22 286 10 54 58 164 155 111 0 g 0 93 123 155 28 57 11 12 14 9 225 237 73 88 138 0 t 0 34 18 37 12 2 6 5 2 279 12 5 40 27 33 0