One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.201729_2026-01-25.201729_P12xBT/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/2026/01/25/peak-motifs.2026-01-25.201729_2026-01-25.201729_P12xBT/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift11 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift11 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=11; ncol=22; -----------gaGAGCGAGag ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 c 0 0 0 0 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 g 0 0 0 0 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 t 0 0 0 0 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67

oligos_6nt_mkv3_m3_shift11 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=11; score= 1; -----------gaGAGCGAGag ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 c 0 0 0 0 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 g 0 0 0 0 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 t 0 0 0 0 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67

oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3; m=2/6; ncol2=12; w=0; offset=0; strand=D; shift=11; score=0.890023; -----------gaGAGCGAGAg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 c 0 0 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 g 0 0 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 t 0 0 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32

dyads_m2_rc_shift10 (dyads_m2_rc)
; oligos_6nt_mkv3_m3 versus dyads_m2_rc; m=3/6; ncol2=18; w=-1; offset=-1; strand=R; shift=10; score=0.532369; ----------agaGAGAGAGAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 194 56 188 30 289 20 291 23 288 19 290 15 c 0 0 0 0 0 0 0 0 0 0 58 45 84 19 39 18 52 14 42 18 48 13 g 0 0 0 0 0 0 0 0 0 0 76 254 68 321 35 331 19 337 32 340 23 346 t 0 0 0 0 0 0 0 0 0 0 56 29 44 14 21 15 22 10 22 7 23 10

dyads_m8_shift4 (dyads_m8)
; oligos_6nt_mkv3_m3 versus dyads_m8; m=4/6; ncol2=22; w=-7; offset=-7; strand=D; shift=4; score=0.447313; ----agrGAGAGAGAGmGAGAG ; cor=; Ncor= a 0 0 0 0 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 c 0 0 0 0 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 g 0 0 0 0 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 t 0 0 0 0 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12

dyads_m6_shift8 (dyads_m6)
; oligos_6nt_mkv3_m3 versus dyads_m6; m=5/6; ncol2=22; w=-3; offset=-3; strand=D; shift=8; score=0.430098; --------agrGAGAGrGAGAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 125 36 113 18 195 22 190 19 129 8 189 9 192 9 c 0 0 0 0 0 0 0 0 39 40 32 12 17 8 22 10 34 17 25 14 24 10 g 0 0 0 0 0 0 0 0 59 149 83 209 25 212 20 213 68 217 19 220 20 223 t 0 0 0 0 0 0 0 0 27 25 22 11 13 8 18 8 19 8 17 7 14 8

dyads_m10_shift0 (dyads_m10)
; oligos_6nt_mkv3_m3 versus dyads_m10; m=6/6; ncol2=23; w=-11; offset=-11; strand=D; shift=0; score=0.411883; agrGAGaGrGAGAGAGAGAGag ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13

One-to-n matrix alignment; reference matrix: dyads_m2_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift4 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=18; shift=4; ncol=22; ----ctCTCTCTCTCTCTCtct ; Alignment reference a 0 0 0 0 43 38 14 16 17 17 10 23 7 22 10 22 15 21 14 44 29 56 c 0 0 0 0 240 58 322 30 330 28 346 23 340 32 337 19 331 35 321 68 254 76 g 0 0 0 0 44 89 23 65 17 47 13 48 18 42 14 52 18 39 19 84 45 58 t 0 0 0 0 57 199 25 273 20 292 15 290 19 288 23 291 20 289 30 188 56 194

dyads_m2_shift4 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/6; ncol2=18; w=0; offset=0; strand=D; shift=4; score= 1; ----ctCTCTCTCTCTCTCtct ; cor=; Ncor= a 0 0 0 0 43 38 14 16 17 17 10 23 7 22 10 22 15 21 14 44 29 56 c 0 0 0 0 240 58 322 30 330 28 346 23 340 32 337 19 331 35 321 68 254 76 g 0 0 0 0 44 89 23 65 17 47 13 48 18 42 14 52 18 39 19 84 45 58 t 0 0 0 0 57 199 25 273 20 292 15 290 19 288 23 291 20 289 30 188 56 194

dyads_m8_rc_shift2 (dyads_m8_rc)
; dyads_m2 versus dyads_m8_rc; m=2/6; ncol2=22; w=-2; offset=-2; strand=R; shift=2; score=0.803559; --ctCtCTCTCkCTCTCTCTCy ; cor=; Ncor= a 0 0 27 29 16 16 12 12 6 15 5 26 6 18 5 19 10 16 13 23 14 26 c 0 0 183 53 216 33 241 12 250 25 254 28 255 21 255 25 248 25 235 36 219 85 g 0 0 35 63 21 52 18 39 13 29 11 85 12 25 13 30 10 33 12 28 23 32 t 0 0 40 140 32 184 14 222 16 216 15 146 12 221 12 211 17 211 25 198 29 142

dyads_m6_rc_shift0 (dyads_m6_rc)
; dyads_m2 versus dyads_m6_rc; m=3/6; ncol2=22; w=-4; offset=-4; strand=R; shift=0; score=0.79832; ctCTCTCTCTCTCyCTCTCyct ; cor=; Ncor= a 24 18 15 17 6 16 7 15 8 14 7 17 8 19 8 18 8 13 11 22 25 27 c 154 59 191 18 217 14 213 25 223 20 220 19 217 68 213 20 212 25 209 83 149 59 g 32 46 17 42 13 31 14 24 10 24 14 25 17 34 10 22 8 17 12 32 40 39 t 40 127 27 173 14 189 16 186 9 192 9 189 8 129 19 190 22 195 18 113 36 125

dyads_m10_rc_shift3 (dyads_m10_rc)
; dyads_m2 versus dyads_m10_rc; m=4/6; ncol2=23; w=-1; offset=-1; strand=R; shift=3; score=0.76558; ---tctCTCTCTCTCTCyCtCT ; cor=; Ncor= a 0 0 0 22 13 9 8 11 5 13 4 11 6 12 7 8 8 17 7 39 7 15 c 0 0 0 45 133 26 166 17 180 9 180 15 179 14 179 16 173 54 172 24 177 22 g 0 0 0 35 22 31 10 23 8 23 8 17 8 20 11 22 13 24 8 26 5 11 t 0 0 0 99 33 135 17 150 8 156 9 158 8 155 4 155 7 106 14 112 12 153

oligos_7nt_mkv4_m3_rc_shift9 (oligos_7nt_mkv4_m3_rc)
; dyads_m2 versus oligos_7nt_mkv4_m3_rc; m=5/6; ncol2=12; w=0; offset=5; strand=R; shift=9; score=0.593529; ---------ycTCTCGCTCtc- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 29 32 3 0 3 3 8 5 6 3 39 21 0 c 0 0 0 0 0 0 0 0 0 62 139 6 224 8 227 8 226 8 226 40 137 0 g 0 0 0 0 0 0 0 0 0 50 36 18 4 5 7 170 1 10 4 55 44 0 t 0 0 0 0 0 0 0 0 0 102 36 216 15 227 6 57 11 219 10 109 41 0

oligos_6nt_mkv3_m3_rc_shift10 (oligos_6nt_mkv3_m3_rc)
; dyads_m2 versus oligos_6nt_mkv3_m3_rc; m=6/6; ncol2=11; w=0; offset=6; strand=R; shift=10; score=0.532369; ----------ctCTCGCTCtc- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 67 75 14 14 5 22 11 27 8 76 50 0 c 0 0 0 0 0 0 0 0 0 0 241 76 391 18 434 21 422 20 437 99 232 0 g 0 0 0 0 0 0 0 0 0 0 74 107 20 6 15 320 6 10 9 102 90 0 t 0 0 0 0 0 0 0 0 0 0 80 204 37 424 8 99 23 405 8 185 90 0

One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m8_shift0 (dyads_m8)
; dyads_m8; m=0 (reference); ncol1=22; shift=0; ncol=22; agrGAGAGAGAGmGAGAGaGag ; Alignment reference a 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 32 140 40 c 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 21 63 35 g 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 216 53 183 t 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16 16 29 27

dyads_m8_shift0 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; agrGAGAGAGAGmGAGAGaGag ; cor=; Ncor= a 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 32 140 40 c 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 21 63 35 g 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 216 53 183 t 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16 16 29 27

dyads_m6_shift0 (dyads_m6)
; dyads_m8 versus dyads_m6; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.984238; agrGAGAGrGAGAGAGAGAGag ; cor=; Ncor= a 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 40 c 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 32 g 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 154 t 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18 24

dyads_m10_shift0 (dyads_m10)
; dyads_m8 versus dyads_m10; m=3/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.935356; agrGAGaGrGAGAGAGAGAGag ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13

dyads_m2_rc_shift2 (dyads_m2_rc)
; dyads_m8 versus dyads_m2_rc; m=4/6; ncol2=18; w=0; offset=2; strand=R; shift=2; score=0.803559; --agaGAGAGAGAGAGAGag-- ; cor=; Ncor= a 0 0 194 56 188 30 289 20 291 23 288 19 290 15 292 20 273 25 199 57 0 0 c 0 0 58 45 84 19 39 18 52 14 42 18 48 13 47 17 65 23 89 44 0 0 g 0 0 76 254 68 321 35 331 19 337 32 340 23 346 28 330 30 322 58 240 0 0 t 0 0 56 29 44 14 21 15 22 10 22 7 23 10 17 17 16 14 38 43 0 0

oligos_7nt_mkv4_m3_shift7 (oligos_7nt_mkv4_m3)
; dyads_m8 versus oligos_7nt_mkv4_m3; m=5/6; ncol2=12; w=0; offset=7; strand=D; shift=7; score=0.503326; -------gaGAGCGAGAgr--- ; cor=; Ncor= a 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 0 0 0 c 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 0 0 0 g 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 0 0 0 t 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29 0 0 0

oligos_6nt_mkv3_m3_shift7 (oligos_6nt_mkv3_m3)
; dyads_m8 versus oligos_6nt_mkv3_m3; m=6/6; ncol2=11; w=0; offset=7; strand=D; shift=7; score=0.447313; -------gaGAGCGAGag---- ; cor=; Ncor= a 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 0 0 0 0 c 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 0 0 0 0 g 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 0 0 0 0 t 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m6_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m6_shift2 (oligos_7nt_mkv4_m6)
; oligos_7nt_mkv4_m6; m=0 (reference); ncol1=11; shift=2; ncol=13; --yrAACTGAAww ; Alignment reference a 0 0 59 74 240 243 12 13 18 238 226 77 83 c 0 0 74 65 15 4 246 10 7 4 9 62 42 g 0 0 57 79 7 7 9 15 230 11 19 54 67 t 0 0 80 52 8 16 3 232 15 17 16 77 78

oligos_7nt_mkv4_m6_shift2 (oligos_7nt_mkv4_m6)
; oligos_7nt_mkv4_m6 versus oligos_7nt_mkv4_m6; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --yrAACTGAAww ; cor=; Ncor= a 0 0 59 74 240 243 12 13 18 238 226 77 83 c 0 0 74 65 15 4 246 10 7 4 9 62 42 g 0 0 57 79 7 7 9 15 230 11 19 54 67 t 0 0 80 52 8 16 3 232 15 17 16 77 78

oligos_6nt_mkv3_m8_shift2 (oligos_6nt_mkv3_m8)
; oligos_7nt_mkv4_m6 versus oligos_6nt_mkv3_m8; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.861834; --smAACTGArw- ; cor=; Ncor= a 0 0 21 31 87 89 0 0 0 94 35 37 0 c 0 0 26 28 0 0 94 0 0 0 11 18 0 g 0 0 29 20 0 0 0 0 94 0 25 13 0 t 0 0 18 15 7 5 0 94 0 0 23 26 0

oligos_6nt_mkv3_m6_shift3 (oligos_6nt_mkv3_m6)
; oligos_7nt_mkv4_m6 versus oligos_6nt_mkv3_m6; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.672378; ---aaAATGAAar ; cor=; Ncor= a 0 0 0 50 50 111 111 0 0 110 111 50 37 c 0 0 0 15 21 0 0 0 0 0 0 21 17 g 0 0 0 24 22 0 0 0 111 0 0 19 31 t 0 0 0 22 18 0 0 111 0 1 0 21 26

oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m6 versus oligos_7nt_mkv4_m4_rc; m=4/4; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.486931; brCCAACTGkw-- ; cor=; Ncor= a 50 79 10 6 222 211 6 14 7 63 73 0 0 c 82 47 246 245 29 23 239 8 7 63 60 0 0 g 69 85 8 11 16 29 13 9 252 69 64 0 0 t 69 59 6 8 3 7 12 239 4 75 73 0 0

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=19; shift=0; ncol=19; acrCACACACACACACrca ; Alignment reference a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 49 179 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 200 38 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 44 86 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40 56 46

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/5; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; acrCACACACACACACrca ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 49 179 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 200 38 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 44 86 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40 56 46

dyads_m7_shift0 (dyads_m7)
; dyads_m1 versus dyads_m7; m=2/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.654976; mmrCAcmCACAmmmACAmm ; cor=; Ncor= a 31 34 42 4 80 16 64 19 91 3 91 45 34 28 92 2 89 49 27 c 35 44 9 92 6 68 28 71 2 97 4 40 45 66 3 92 4 32 59 g 19 7 43 2 5 12 6 5 6 0 4 10 11 3 4 3 2 10 11 t 16 16 7 3 10 5 3 6 2 1 2 6 11 4 2 4 6 10 4

oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)
; dyads_m1 versus oligos_6nt_mkv3_m2; m=3/5; ncol2=13; w=0; offset=5; strand=D; shift=5; score= 0.6035; -----caCACrCACasac- ; cor=; Ncor= a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 125 63 0 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 70 149 0 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 65 74 0 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41 85 59 0

oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)
; dyads_m1 versus oligos_6nt_mkv3_m7; m=4/5; ncol2=11; w=0; offset=6; strand=D; shift=6; score=0.548469; ------acACACACAca-- ; cor=; Ncor= a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 287 0 0 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 90 0 0 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 123 0 0 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110 106 0 0

oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)
; dyads_m1 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.511484; -----caCACrCACac--- ; cor=; Ncor= a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 0 0 0 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 0 0 0 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 0 0 0 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=19; shift=0; ncol=19; wagAAAAATATAAATAaww ; Alignment reference a 34 43 19 72 73 80 82 80 14 87 15 81 78 86 9 85 56 42 42 c 21 12 15 8 3 4 3 4 8 0 7 4 5 5 8 1 11 13 14 g 12 19 43 8 6 7 1 7 4 6 7 5 2 3 3 2 7 14 13 t 31 24 21 10 16 7 12 7 72 5 69 8 13 4 78 10 24 29 29

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; wagAAAAATATAAATAaww ; cor=; Ncor= a 34 43 19 72 73 80 82 80 14 87 15 81 78 86 9 85 56 42 42 c 21 12 15 8 3 4 3 4 8 0 7 4 5 5 8 1 11 13 14 g 12 19 43 8 6 7 1 7 4 6 7 5 2 3 3 2 7 14 13 t 31 24 21 10 16 7 12 7 72 5 69 8 13 4 78 10 24 29 29

oligos_6nt_mkv3_m9_shift8 (oligos_6nt_mkv3_m9)
; dyads_m3 versus oligos_6nt_mkv3_m9; m=2/3; ncol2=10; w=0; offset=8; strand=D; shift=8; score=0.471137; --------waTAwATAtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 74 122 0 245 151 236 0 248 51 106 0 c 0 0 0 0 0 0 0 0 30 27 0 0 15 8 0 0 51 39 0 g 0 0 0 0 0 0 0 0 33 44 0 2 15 4 0 0 34 29 0 t 0 0 0 0 0 0 0 0 111 55 248 1 67 0 248 0 112 74 0

oligos_6nt_mkv3_m4_shift8 (oligos_6nt_mkv3_m4)
; dyads_m3 versus oligos_6nt_mkv3_m4; m=3/3; ncol2=10; w=0; offset=8; strand=D; shift=8; score=0.404313; --------taTAkATAtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 36 104 3 182 2 185 0 197 23 98 0 c 0 0 0 0 0 0 0 0 27 25 5 17 15 0 2 1 49 21 0 g 0 0 0 0 0 0 0 0 40 44 9 3 118 10 12 2 39 31 0 t 0 0 0 0 0 0 0 0 99 29 185 0 67 7 188 2 91 52 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m7_shift6 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=11; shift=6; ncol=17; ------acACACACAca ; Alignment reference a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 287 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 90 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 123 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110 106

oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=6; score= 1; ------acACACACAca ; cor=; Ncor= a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 287 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 90 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 123 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110 106

oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m2; m=2/5; ncol2=13; w=-1; offset=-1; strand=D; shift=5; score=0.737517; -----caCACrCACasa ; cor=; Ncor= a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 125 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 70 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 65 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41 85

oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m5; m=3/5; ncol2=11; w=-1; offset=-1; strand=D; shift=5; score=0.714736; -----caCACrCACac- ; cor=; Ncor= a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 0 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 0 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 0 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72 0

dyads_m1_shift0 (dyads_m1)
; oligos_6nt_mkv3_m7 versus dyads_m1; m=4/5; ncol2=19; w=-6; offset=-6; strand=D; shift=0; score=0.548469; acrCACACACACACACr ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40

dyads_m7_shift4 (dyads_m7)
; oligos_6nt_mkv3_m7 versus dyads_m7; m=5/5; ncol2=24; w=-2; offset=-2; strand=D; shift=4; score=0.413638; ----mmrCAcmCACAmm ; cor=; Ncor= a 0 0 0 0 31 34 42 4 80 16 64 19 91 3 91 45 34 c 0 0 0 0 35 44 9 92 6 68 28 71 2 97 4 40 45 g 0 0 0 0 19 7 43 2 5 12 6 5 6 0 4 10 11 t 0 0 0 0 16 16 7 3 10 5 3 6 2 1 2 6 11

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --wmCAGTTGGyv ; Alignment reference a 0 0 73 75 4 239 12 7 3 8 6 59 69 c 0 0 64 69 252 9 13 29 16 11 8 85 69 g 0 0 60 63 7 8 239 23 29 245 246 47 82 t 0 0 73 63 7 14 6 211 222 6 10 79 50

oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wmCAGTTGGyv ; cor=; Ncor= a 0 0 73 75 4 239 12 7 3 8 6 59 69 c 0 0 64 69 252 9 13 29 16 11 8 85 69 g 0 0 60 63 7 8 239 23 29 245 246 47 82 t 0 0 73 63 7 14 6 211 222 6 10 79 50

oligos_6nt_mkv3_m8_rc_shift1 (oligos_6nt_mkv3_m8_rc)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m8_rc; m=2/3; ncol2=10; w=-1; offset=-1; strand=R; shift=1; score=0.566034; -wyTCAGTTks-- ; cor=; Ncor= a 0 26 23 0 0 94 0 5 7 15 18 0 0 c 0 13 25 0 94 0 0 0 0 20 29 0 0 g 0 18 11 0 0 0 94 0 0 28 26 0 0 t 0 37 35 94 0 0 0 89 87 31 21 0 0

oligos_7nt_mkv4_m6_rc_shift0 (oligos_7nt_mkv4_m6_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m6_rc; m=3/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.486931; wwTTCAGTTyr-- ; cor=; Ncor= a 78 77 16 17 15 232 3 16 8 52 80 0 0 c 67 54 19 11 230 15 9 7 7 79 57 0 0 g 42 62 9 4 7 10 246 4 15 65 74 0 0 t 83 77 226 238 18 13 12 243 240 74 59 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; ssgCACAGTGGsg ; Alignment reference a 33 30 20 12 128 10 126 2 5 0 7 29 32 c 40 41 23 97 5 120 3 10 2 6 2 39 34 g 45 42 86 11 5 5 4 125 0 131 127 49 41 t 22 27 11 20 2 5 7 3 133 3 4 23 33

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ssgCACAGTGGsg ; cor=; Ncor= a 33 30 20 12 128 10 126 2 5 0 7 29 32 c 40 41 23 97 5 120 3 10 2 6 2 39 34 g 45 42 86 11 5 5 4 125 0 131 127 49 41 t 22 27 11 20 2 5 7 3 133 3 4 23 33

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; acGACGACgr ; Alignment reference a 49 23 0 127 0 0 127 0 29 57 c 31 56 1 0 119 1 0 119 22 15 g 24 30 118 0 9 122 0 5 54 33 t 25 20 10 2 1 6 2 5 24 24

dyads_m9_shift0 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; acGACGACgr ; cor=; Ncor= a 49 23 0 127 0 0 127 0 29 57 c 31 56 1 0 119 1 0 119 22 15 g 24 30 118 0 9 122 0 5 54 33 t 25 20 10 2 1 6 2 5 24 24

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -asAGGCACAsa ; Alignment reference a 0 91 39 188 4 18 4 208 7 204 34 80 c 0 45 89 11 27 14 208 7 200 4 84 45 g 0 51 58 14 188 189 5 5 15 6 68 47 t 0 38 39 12 6 4 8 5 3 11 39 53

oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -asAGGCACAsa ; cor=; Ncor= a 0 91 39 188 4 18 4 208 7 204 34 80 c 0 45 89 11 27 14 208 7 200 4 84 45 g 0 51 58 14 188 189 5 5 15 6 68 47 t 0 38 39 12 6 4 8 5 3 11 39 53

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.654638; caCACrCACasa ; cor=; Ncor= a 53 158 13 315 4 93 12 319 4 222 47 125 c 183 62 302 5 319 18 322 12 333 37 164 70 g 44 80 13 7 13 208 5 4 5 39 93 65 t 65 45 17 18 9 26 6 10 3 47 41 85

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.617634; caCACrCACac- ; cor=; Ncor= a 65 200 13 396 8 128 18 409 0 211 68 0 c 237 83 399 10 408 26 409 16 428 66 219 0 g 64 96 14 7 18 258 9 4 8 78 84 0 t 77 64 17 30 9 31 7 14 7 88 72 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift5 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=5; ncol=16; -----caCACrCACac ; Alignment reference a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72

oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----caCACrCACac ; cor=; Ncor= a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72

oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2; m=2/6; ncol2=13; w=0; offset=0; strand=D; shift=5; score=0.841232; -----caCACrCACas ; cor=; Ncor= a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41

oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m7; m=3/6; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.714736; ------acACACACAc ; cor=; Ncor= a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110

oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m5; m=4/6; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.646014; ------hyACTCAChm ; cor=; Ncor= a 0 0 0 0 0 0 29 22 103 1 3 1 99 1 31 29 c 0 0 0 0 0 0 34 43 3 111 3 109 3 110 37 45 g 0 0 0 0 0 0 22 16 0 2 0 1 0 3 12 16 t 0 0 0 0 0 0 30 34 9 1 109 4 13 1 35 25

oligos_7nt_mkv4_m2_shift6 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=5/6; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.617634; ------asAGGCACAs ; cor=; Ncor= a 0 0 0 0 0 0 91 39 188 4 18 4 208 7 204 34 c 0 0 0 0 0 0 45 89 11 27 14 208 7 200 4 84 g 0 0 0 0 0 0 51 58 14 188 189 5 5 15 6 68 t 0 0 0 0 0 0 38 39 12 6 4 8 5 3 11 39

dyads_m1_shift0 (dyads_m1)
; oligos_7nt_mkv4_m5 versus dyads_m1; m=6/6; ncol2=19; w=-5; offset=-5; strand=D; shift=0; score=0.511484; acrCACACACACACAC ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift8 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift8 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=8; ncol=18; --------waTAwATAtw ; Alignment reference a 0 0 0 0 0 0 0 0 74 122 0 245 151 236 0 248 51 106 c 0 0 0 0 0 0 0 0 30 27 0 0 15 8 0 0 51 39 g 0 0 0 0 0 0 0 0 33 44 0 2 15 4 0 0 34 29 t 0 0 0 0 0 0 0 0 111 55 248 1 67 0 248 0 112 74

oligos_6nt_mkv3_m9_shift8 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=8; score= 1; --------waTAwATAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 74 122 0 245 151 236 0 248 51 106 c 0 0 0 0 0 0 0 0 30 27 0 0 15 8 0 0 51 39 g 0 0 0 0 0 0 0 0 33 44 0 2 15 4 0 0 34 29 t 0 0 0 0 0 0 0 0 111 55 248 1 67 0 248 0 112 74

oligos_6nt_mkv3_m4_shift8 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m4; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=8; score=0.907713; --------taTAkATAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 36 104 3 182 2 185 0 197 23 98 c 0 0 0 0 0 0 0 0 27 25 5 17 15 0 2 1 49 21 g 0 0 0 0 0 0 0 0 40 44 9 3 118 10 12 2 39 31 t 0 0 0 0 0 0 0 0 99 29 185 0 67 7 188 2 91 52

oligos_6nt_mkv3_m1_shift8 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=8; score=0.739621; --------haTACATACa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 86 125 7 248 20 251 5 256 17 116 c 0 0 0 0 0 0 0 0 80 33 18 9 218 7 25 4 214 40 g 0 0 0 0 0 0 0 0 27 51 4 9 13 8 4 7 12 65 t 0 0 0 0 0 0 0 0 81 65 245 8 23 8 240 7 31 53

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m9 versus dyads_m3; m=4/4; ncol2=19; w=-8; offset=-8; strand=D; shift=0; score=0.471137; wagAAAAATATAAATAaw ; cor=; Ncor= a 34 43 19 72 73 80 82 80 14 87 15 81 78 86 9 85 56 42 c 21 12 15 8 3 4 3 4 8 0 7 4 5 5 8 1 11 13 g 12 19 43 8 6 7 1 7 4 6 7 5 2 3 3 2 7 14 t 31 24 21 10 16 7 12 7 72 5 69 8 13 4 78 10 24 29

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift0 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=24; shift=0; ncol=24; mmrCAcmCACAmmmACAmmmACam ; Alignment reference a 31 34 42 4 80 16 64 19 91 3 91 45 34 28 92 2 89 49 27 46 78 8 53 27 c 35 44 9 92 6 68 28 71 2 97 4 40 45 66 3 92 4 32 59 33 8 79 15 34 g 19 7 43 2 5 12 6 5 6 0 4 10 11 3 4 3 2 10 11 13 8 9 20 25 t 16 16 7 3 10 5 3 6 2 1 2 6 11 4 2 4 6 10 4 9 7 5 13 15

dyads_m7_shift0 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; mmrCAcmCACAmmmACAmmmACam ; cor=; Ncor= a 31 34 42 4 80 16 64 19 91 3 91 45 34 28 92 2 89 49 27 46 78 8 53 27 c 35 44 9 92 6 68 28 71 2 97 4 40 45 66 3 92 4 32 59 33 8 79 15 34 g 19 7 43 2 5 12 6 5 6 0 4 10 11 3 4 3 2 10 11 13 8 9 20 25 t 16 16 7 3 10 5 3 6 2 1 2 6 11 4 2 4 6 10 4 9 7 5 13 15

dyads_m1_shift0 (dyads_m1)
; dyads_m7 versus dyads_m1; m=2/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.654976; acrCACACACACACACrca----- ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 49 179 0 0 0 0 0 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 200 38 0 0 0 0 0 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 44 86 0 0 0 0 0 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40 56 46 0 0 0 0 0

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; dyads_m7 versus oligos_6nt_mkv3_m2; m=3/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.466054; -caCACrCACasac---------- ; cor=; Ncor= a 0 53 158 13 315 4 93 12 319 4 222 47 125 63 0 0 0 0 0 0 0 0 0 0 c 0 183 62 302 5 319 18 322 12 333 37 164 70 149 0 0 0 0 0 0 0 0 0 0 g 0 44 80 13 7 13 208 5 4 5 39 93 65 74 0 0 0 0 0 0 0 0 0 0 t 0 65 45 17 18 9 26 6 10 3 47 41 85 59 0 0 0 0 0 0 0 0 0 0

oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)
; dyads_m7 versus oligos_6nt_mkv3_m7; m=4/4; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.413638; --acACACACAca----------- ; cor=; Ncor= a 0 0 299 90 489 9 555 8 552 7 535 110 287 0 0 0 0 0 0 0 0 0 0 0 c 0 0 87 321 25 548 12 537 15 542 16 296 90 0 0 0 0 0 0 0 0 0 0 0 g 0 0 129 77 61 17 16 23 16 24 24 90 123 0 0 0 0 0 0 0 0 0 0 0 t 0 0 91 118 31 32 23 38 23 33 31 110 106 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -hyACTCAChmy ; Alignment reference a 0 29 22 103 1 3 1 99 1 31 29 28 c 0 34 43 3 111 3 109 3 110 37 45 29 g 0 22 16 0 2 0 1 0 3 12 16 21 t 0 30 34 9 1 109 4 13 1 35 25 37

oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -hyACTCAChmy ; cor=; Ncor= a 0 29 22 103 1 3 1 99 1 31 29 28 c 0 34 43 3 111 3 109 3 110 37 45 29 g 0 22 16 0 2 0 1 0 3 12 16 21 t 0 30 34 9 1 109 4 13 1 35 25 37

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m5; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.646014; caCACrCACac- ; cor=; Ncor= a 65 200 13 396 8 128 18 409 0 211 68 0 c 237 83 399 10 408 26 409 16 428 66 219 0 g 64 96 14 7 18 258 9 4 8 78 84 0 t 77 64 17 30 9 31 7 14 7 88 72 0

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.645663; caCACrCACasa ; cor=; Ncor= a 53 158 13 315 4 93 12 319 4 222 47 125 c 183 62 302 5 319 18 322 12 333 37 164 70 g 44 80 13 7 13 208 5 4 5 39 93 65 t 65 45 17 18 9 26 6 10 3 47 41 85

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift5 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=13; shift=5; ncol=18; -----caCACrCACasac ; Alignment reference a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 125 63 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 70 149 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 65 74 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41 85 59

oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=5; score= 1; -----caCACrCACasac ; cor=; Ncor= a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 125 63 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 70 149 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 65 74 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41 85 59

oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=5; score=0.841232; -----caCACrCACac-- ; cor=; Ncor= a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 0 0 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 0 0 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 0 0 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72 0 0

oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m7; m=3/7; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.737517; ------acACACACAca- ; cor=; Ncor= a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 287 0 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 90 0 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 123 0 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110 106 0

oligos_7nt_mkv4_m2_shift6 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2; m=4/7; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.654638; ------asAGGCACAsa- ; cor=; Ncor= a 0 0 0 0 0 0 91 39 188 4 18 4 208 7 204 34 80 0 c 0 0 0 0 0 0 45 89 11 27 14 208 7 200 4 84 45 0 g 0 0 0 0 0 0 51 58 14 188 189 5 5 15 6 68 47 0 t 0 0 0 0 0 0 38 39 12 6 4 8 5 3 11 39 53 0

oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m5; m=5/7; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.645663; ------hyACTCAChmy- ; cor=; Ncor= a 0 0 0 0 0 0 29 22 103 1 3 1 99 1 31 29 28 0 c 0 0 0 0 0 0 34 43 3 111 3 109 3 110 37 45 29 0 g 0 0 0 0 0 0 22 16 0 2 0 1 0 3 12 16 21 0 t 0 0 0 0 0 0 30 34 9 1 109 4 13 1 35 25 37 0

dyads_m1_shift0 (dyads_m1)
; oligos_6nt_mkv3_m2 versus dyads_m1; m=6/7; ncol2=19; w=-5; offset=-5; strand=D; shift=0; score= 0.6035; acrCACACACACACACrc ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 49 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 200 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 44 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40 56

dyads_m7_shift4 (dyads_m7)
; oligos_6nt_mkv3_m2 versus dyads_m7; m=7/7; ncol2=24; w=-1; offset=-1; strand=D; shift=4; score=0.466054; ----mmrCAcmCACAmmm ; cor=; Ncor= a 0 0 0 0 31 34 42 4 80 16 64 19 91 3 91 45 34 28 c 0 0 0 0 35 44 9 92 6 68 28 71 2 97 4 40 45 66 g 0 0 0 0 19 7 43 2 5 12 6 5 6 0 4 10 11 3 t 0 0 0 0 16 16 7 3 10 5 3 6 2 1 2 6 11 4

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; tacGTATAya ; Alignment reference a 22 50 14 11 2 112 0 108 14 52 c 20 22 73 3 0 5 2 3 30 18 g 22 20 11 98 3 0 4 5 11 18 t 53 25 19 5 112 0 111 1 62 29

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; tacGTATAya ; cor=; Ncor= a 22 50 14 11 2 112 0 108 14 52 c 20 22 73 3 0 5 2 3 30 18 g 22 20 11 98 3 0 4 5 11 18 t 53 25 19 5 112 0 111 1 62 29

oligos_6nt_mkv3_m1_rc_shift1 (oligos_6nt_mkv3_m1_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m1_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.537931; -dtGTATGTA ; cor=; Ncor= a 0 90 53 31 7 240 8 23 8 245 c 0 37 65 12 7 4 8 13 9 4 g 0 70 40 214 4 25 7 218 9 18 t 0 77 116 17 256 5 251 20 248 7

oligos_6nt_mkv3_m4_rc_shift2 (oligos_6nt_mkv3_m4_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m4_rc; m=3/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.467736; --waTATmTA ; cor=; Ncor= a 0 0 52 91 2 188 7 67 0 185 c 0 0 31 39 2 12 10 118 3 9 g 0 0 21 49 1 2 0 15 17 5 t 0 0 98 23 197 0 185 2 182 3

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; haTACATACah ; Alignment reference a 86 125 7 248 20 251 5 256 17 116 77 c 80 33 18 9 218 7 25 4 214 40 70 g 27 51 4 9 13 8 4 7 12 65 37 t 81 65 245 8 23 8 240 7 31 53 90

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; haTACATACah ; cor=; Ncor= a 86 125 7 248 20 251 5 256 17 116 77 c 80 33 18 9 218 7 25 4 214 40 70 g 27 51 4 9 13 8 4 7 12 65 37 t 81 65 245 8 23 8 240 7 31 53 90

oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m9; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.739621; waTAwATAtw- ; cor=; Ncor= a 74 122 0 245 151 236 0 248 51 106 0 c 30 27 0 0 15 8 0 0 51 39 0 g 33 44 0 2 15 4 0 0 34 29 0 t 111 55 248 1 67 0 248 0 112 74 0

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.731445; taTAkATAtw- ; cor=; Ncor= a 36 104 3 182 2 185 0 197 23 98 0 c 27 25 5 17 15 0 2 1 49 21 0 g 40 44 9 3 118 10 12 2 39 31 0 t 99 29 185 0 67 7 188 2 91 52 0

positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=4/4; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.537931; --trTATACgt ; cor=; Ncor= a 0 0 29 62 1 111 0 112 5 19 25 c 0 0 18 11 5 4 0 3 98 11 20 g 0 0 18 30 3 2 5 0 3 73 22 t 0 0 52 14 108 0 112 2 11 14 50

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift8 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift8 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=8; ncol=18; --------taTAkATAtw ; Alignment reference a 0 0 0 0 0 0 0 0 36 104 3 182 2 185 0 197 23 98 c 0 0 0 0 0 0 0 0 27 25 5 17 15 0 2 1 49 21 g 0 0 0 0 0 0 0 0 40 44 9 3 118 10 12 2 39 31 t 0 0 0 0 0 0 0 0 99 29 185 0 67 7 188 2 91 52

oligos_6nt_mkv3_m4_shift8 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/5; ncol2=10; w=0; offset=0; strand=D; shift=8; score= 1; --------taTAkATAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 36 104 3 182 2 185 0 197 23 98 c 0 0 0 0 0 0 0 0 27 25 5 17 15 0 2 1 49 21 g 0 0 0 0 0 0 0 0 40 44 9 3 118 10 12 2 39 31 t 0 0 0 0 0 0 0 0 99 29 185 0 67 7 188 2 91 52

oligos_6nt_mkv3_m9_shift8 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m9; m=2/5; ncol2=10; w=0; offset=0; strand=D; shift=8; score=0.907713; --------waTAwATAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 74 122 0 245 151 236 0 248 51 106 c 0 0 0 0 0 0 0 0 30 27 0 0 15 8 0 0 51 39 g 0 0 0 0 0 0 0 0 33 44 0 2 15 4 0 0 34 29 t 0 0 0 0 0 0 0 0 111 55 248 1 67 0 248 0 112 74

oligos_6nt_mkv3_m1_shift8 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m1; m=3/5; ncol2=11; w=0; offset=0; strand=D; shift=8; score=0.731445; --------haTACATACa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 86 125 7 248 20 251 5 256 17 116 c 0 0 0 0 0 0 0 0 80 33 18 9 218 7 25 4 214 40 g 0 0 0 0 0 0 0 0 27 51 4 9 13 8 4 7 12 65 t 0 0 0 0 0 0 0 0 81 65 245 8 23 8 240 7 31 53

positions_6nt_m1_rc_shift10 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m4 versus positions_6nt_m1_rc; m=4/5; ncol2=10; w=0; offset=2; strand=R; shift=10; score=0.467736; ----------trTATACg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 29 62 1 111 0 112 5 19 c 0 0 0 0 0 0 0 0 0 0 18 11 5 4 0 3 98 11 g 0 0 0 0 0 0 0 0 0 0 18 30 3 2 5 0 3 73 t 0 0 0 0 0 0 0 0 0 0 52 14 108 0 112 2 11 14

dyads_m3_shift0 (dyads_m3)
; oligos_6nt_mkv3_m4 versus dyads_m3; m=5/5; ncol2=19; w=-8; offset=-8; strand=D; shift=0; score=0.404313; wagAAAAATATAAATAaw ; cor=; Ncor= a 34 43 19 72 73 80 82 80 14 87 15 81 78 86 9 85 56 42 c 21 12 15 8 3 4 3 4 8 0 7 4 5 5 8 1 11 13 g 12 19 43 8 6 7 1 7 4 6 7 5 2 3 3 2 7 14 t 31 24 21 10 16 7 12 7 72 5 69 8 13 4 78 10 24 29

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=22; shift=0; ncol=22; agrGAGAGrGAGAGAGAGAGag ; Alignment reference a 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 40 c 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 32 g 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 154 t 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18 24

dyads_m6_shift0 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; agrGAGAGrGAGAGAGAGAGag ; cor=; Ncor= a 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 40 c 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 32 g 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 154 t 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18 24

dyads_m8_shift0 (dyads_m8)
; dyads_m6 versus dyads_m8; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.984238; agrGAGAGAGAGmGAGAGaGag ; cor=; Ncor= a 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 32 140 40 c 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 21 63 35 g 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 216 53 183 t 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16 16 29 27

dyads_m10_shift0 (dyads_m10)
; dyads_m6 versus dyads_m10; m=3/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.94845; agrGAGaGrGAGAGAGAGAGag ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13

dyads_m2_rc_shift0 (dyads_m2_rc)
; dyads_m6 versus dyads_m2_rc; m=4/6; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.79832; agaGAGAGAGAGAGAGag---- ; cor=; Ncor= a 194 56 188 30 289 20 291 23 288 19 290 15 292 20 273 25 199 57 0 0 0 0 c 58 45 84 19 39 18 52 14 42 18 48 13 47 17 65 23 89 44 0 0 0 0 g 76 254 68 321 35 331 19 337 32 340 23 346 28 330 30 322 58 240 0 0 0 0 t 56 29 44 14 21 15 22 10 22 7 23 10 17 17 16 14 38 43 0 0 0 0

oligos_7nt_mkv4_m3_shift9 (oligos_7nt_mkv4_m3)
; dyads_m6 versus oligos_7nt_mkv4_m3; m=5/6; ncol2=12; w=0; offset=9; strand=D; shift=9; score=0.483439; ---------gaGAGCGAGAgr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 0 c 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 0 g 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 0 t 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29 0

oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; dyads_m6 versus oligos_6nt_mkv3_m3; m=6/6; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.430098; ---gaGAGCGAGag-------- ; cor=; Ncor= a 0 0 0 90 185 8 405 23 99 8 424 37 204 80 0 0 0 0 0 0 0 0 c 0 0 0 90 102 9 10 6 320 15 6 20 107 74 0 0 0 0 0 0 0 0 g 0 0 0 232 99 437 20 422 21 434 18 391 76 241 0 0 0 0 0 0 0 0 t 0 0 0 50 76 8 27 11 22 5 14 14 75 67 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; vrACGAACGAav ; Alignment reference a 47 51 128 3 5 137 136 7 16 114 53 43 c 48 32 5 143 4 4 7 141 5 14 36 44 g 39 40 13 4 140 7 5 1 112 17 34 38 t 18 29 6 2 3 4 4 3 19 7 29 27

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; vrACGAACGAav ; cor=; Ncor= a 47 51 128 3 5 137 136 7 16 114 53 43 c 48 32 5 143 4 4 7 141 5 14 36 44 g 39 40 13 4 140 7 5 1 112 17 34 38 t 18 29 6 2 3 4 4 3 19 7 29 27

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; gyCGCCGCCGmc ; Alignment reference a 53 36 8 6 8 10 2 12 6 16 59 47 c 43 80 198 4 208 204 2 198 208 7 98 80 g 83 57 10 222 10 2 228 8 4 201 32 52 t 56 62 19 3 9 19 3 17 17 11 46 56

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gyCGCCGCCGmc ; cor=; Ncor= a 53 36 8 6 8 10 2 12 6 16 59 47 c 43 80 198 4 208 204 2 198 208 7 98 80 g 83 57 10 222 10 2 228 8 4 201 32 52 t 56 62 19 3 9 19 3 17 17 11 46 56

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift11 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------gaGAGCGAGAgr ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 c 0 0 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 g 0 0 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 t 0 0 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29

oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------gaGAGCGAGAgr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 c 0 0 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 g 0 0 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 t 0 0 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29

oligos_6nt_mkv3_m3_shift11 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=11; score=0.890023; -----------gaGAGCGAGag- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 0 c 0 0 0 0 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 0 g 0 0 0 0 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 0 t 0 0 0 0 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67 0

dyads_m2_rc_shift10 (dyads_m2_rc)
; oligos_7nt_mkv4_m3 versus dyads_m2_rc; m=3/6; ncol2=18; w=-1; offset=-1; strand=R; shift=10; score=0.593529; ----------agaGAGAGAGAGA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 194 56 188 30 289 20 291 23 288 19 290 15 292 c 0 0 0 0 0 0 0 0 0 0 58 45 84 19 39 18 52 14 42 18 48 13 47 g 0 0 0 0 0 0 0 0 0 0 76 254 68 321 35 331 19 337 32 340 23 346 28 t 0 0 0 0 0 0 0 0 0 0 56 29 44 14 21 15 22 10 22 7 23 10 17

dyads_m8_shift4 (dyads_m8)
; oligos_7nt_mkv4_m3 versus dyads_m8; m=4/6; ncol2=22; w=-7; offset=-7; strand=D; shift=4; score=0.503326; ----agrGAGAGAGAGmGAGAGa ; cor=; Ncor= a 0 0 0 0 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 c 0 0 0 0 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 g 0 0 0 0 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 t 0 0 0 0 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16

dyads_m6_shift2 (dyads_m6)
; oligos_7nt_mkv4_m3 versus dyads_m6; m=5/6; ncol2=22; w=-9; offset=-9; strand=D; shift=2; score=0.483439; --agrGAGAGrGAGAGAGAGAGa ; cor=; Ncor= a 0 0 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 c 0 0 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 g 0 0 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 t 0 0 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18

dyads_m10_shift0 (dyads_m10)
; oligos_7nt_mkv4_m3 versus dyads_m10; m=6/6; ncol2=23; w=-11; offset=-11; strand=D; shift=0; score=0.461828; agrGAGaGrGAGAGAGAGAGaga ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 99 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 35 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 45 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13 22

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m8_shift2 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=2; ncol=12; --smAACTGArw ; Alignment reference a 0 0 21 31 87 89 0 0 0 94 35 37 c 0 0 26 28 0 0 94 0 0 0 11 18 g 0 0 29 20 0 0 0 0 94 0 25 13 t 0 0 18 15 7 5 0 94 0 0 23 26

oligos_6nt_mkv3_m8_shift2 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --smAACTGArw ; cor=; Ncor= a 0 0 21 31 87 89 0 0 0 94 35 37 c 0 0 26 28 0 0 94 0 0 0 11 18 g 0 0 29 20 0 0 0 0 94 0 25 13 t 0 0 18 15 7 5 0 94 0 0 23 26

oligos_7nt_mkv4_m6_shift2 (oligos_7nt_mkv4_m6)
; oligos_6nt_mkv3_m8 versus oligos_7nt_mkv4_m6; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.861834; --yrAACTGAAw ; cor=; Ncor= a 0 0 59 74 240 243 12 13 18 238 226 77 c 0 0 74 65 15 4 246 10 7 4 9 62 g 0 0 57 79 7 7 9 15 230 11 19 54 t 0 0 80 52 8 16 3 232 15 17 16 77

oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)
; oligos_6nt_mkv3_m8 versus oligos_7nt_mkv4_m4_rc; m=3/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.566034; brCCAACTGkw- ; cor=; Ncor= a 50 79 10 6 222 211 6 14 7 63 73 0 c 82 47 246 245 29 23 239 8 7 63 60 0 g 69 85 8 11 16 29 13 9 252 69 64 0 t 69 59 6 8 3 7 12 239 4 75 73 0

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; rgCrGCAGCAGCAgc ; Alignment reference a 75 33 8 67 16 4 159 9 7 149 19 5 152 42 29 c 33 36 147 11 8 172 3 6 164 5 3 159 7 25 109 g 49 86 11 89 148 2 12 160 3 17 157 6 17 95 22 t 23 25 14 13 8 2 6 5 6 9 1 10 4 18 20

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/1; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; rgCrGCAGCAGCAgc ; cor=; Ncor= a 75 33 8 67 16 4 159 9 7 149 19 5 152 42 29 c 33 36 147 11 8 172 3 6 164 5 3 159 7 25 109 g 49 86 11 89 148 2 12 160 3 17 157 6 17 95 22 t 23 25 14 13 8 2 6 5 6 9 1 10 4 18 20

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m6_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=1; ncol=11; -aaAATGAAar ; Alignment reference a 0 50 50 111 111 0 0 110 111 50 37 c 0 15 21 0 0 0 0 0 0 21 17 g 0 24 22 0 0 0 111 0 0 19 31 t 0 22 18 0 0 111 0 1 0 21 26

oligos_6nt_mkv3_m6_shift1 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -aaAATGAAar ; cor=; Ncor= a 0 50 50 111 111 0 0 110 111 50 37 c 0 15 21 0 0 0 0 0 0 21 17 g 0 24 22 0 0 0 111 0 0 19 31 t 0 22 18 0 0 111 0 1 0 21 26

oligos_7nt_mkv4_m6_shift0 (oligos_7nt_mkv4_m6)
; oligos_6nt_mkv3_m6 versus oligos_7nt_mkv4_m6; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.672378; yrAACTGAAww ; cor=; Ncor= a 59 74 240 243 12 13 18 238 226 77 83 c 74 65 15 4 246 10 7 4 9 62 42 g 57 79 7 7 9 15 230 11 19 54 67 t 80 52 8 16 3 232 15 17 16 77 78

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift0 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=23; shift=0; ncol=23; agrGAGaGrGAGAGAGAGAGaga ; Alignment reference a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 99 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 35 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 45 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13 22

dyads_m10_shift0 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; agrGAGaGrGAGAGAGAGAGaga ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 99 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 35 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 45 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13 22

dyads_m6_shift0 (dyads_m6)
; dyads_m10 versus dyads_m6; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.94845; agrGAGAGrGAGAGAGAGAGag- ; cor=; Ncor= a 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 40 0 c 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 32 0 g 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 154 0 t 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18 24 0

dyads_m8_shift0 (dyads_m8)
; dyads_m10 versus dyads_m8; m=3/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.935356; agrGAGAGAGAGmGAGAGaGag- ; cor=; Ncor= a 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 32 140 40 0 c 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 21 63 35 0 g 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 216 53 183 0 t 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16 16 29 27 0

dyads_m2_rc_shift4 (dyads_m2_rc)
; dyads_m10 versus dyads_m2_rc; m=4/6; ncol2=18; w=0; offset=4; strand=R; shift=4; score=0.76558; ----agaGAGAGAGAGAGAGag- ; cor=; Ncor= a 0 0 0 0 194 56 188 30 289 20 291 23 288 19 290 15 292 20 273 25 199 57 0 c 0 0 0 0 58 45 84 19 39 18 52 14 42 18 48 13 47 17 65 23 89 44 0 g 0 0 0 0 76 254 68 321 35 331 19 337 32 340 23 346 28 330 30 322 58 240 0 t 0 0 0 0 56 29 44 14 21 15 22 10 22 7 23 10 17 17 16 14 38 43 0

oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)
; dyads_m10 versus oligos_7nt_mkv4_m3; m=5/6; ncol2=12; w=0; offset=11; strand=D; shift=11; score=0.461828; -----------gaGAGCGAGAgr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 c 0 0 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 g 0 0 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 t 0 0 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29

oligos_6nt_mkv3_m3_shift11 (oligos_6nt_mkv3_m3)
; dyads_m10 versus oligos_6nt_mkv3_m3; m=6/6; ncol2=11; w=0; offset=11; strand=D; shift=11; score=0.411883; -----------gaGAGCGAGag- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 0 c 0 0 0 0 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 0 g 0 0 0 0 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 0 t 0 0 0 0 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift11 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=11; ncol=22; -----------gaGAGCGAGag ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 c 0 0 0 0 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 g 0 0 0 0 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 t 0 0 0 0 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67
oligos_6nt_mkv3_m3_shift11 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=11; score= 1; -----------gaGAGCGAGag ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 c 0 0 0 0 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 g 0 0 0 0 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 t 0 0 0 0 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67
oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3; m=2/6; ncol2=12; w=0; offset=0; strand=D; shift=11; score=0.890023; -----------gaGAGCGAGAg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 c 0 0 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 g 0 0 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 t 0 0 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32
dyads_m2_rc_shift10 (dyads_m2_rc)				; oligos_6nt_mkv3_m3 versus dyads_m2_rc; m=3/6; ncol2=18; w=-1; offset=-1; strand=R; shift=10; score=0.532369; ----------agaGAGAGAGAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 194 56 188 30 289 20 291 23 288 19 290 15 c 0 0 0 0 0 0 0 0 0 0 58 45 84 19 39 18 52 14 42 18 48 13 g 0 0 0 0 0 0 0 0 0 0 76 254 68 321 35 331 19 337 32 340 23 346 t 0 0 0 0 0 0 0 0 0 0 56 29 44 14 21 15 22 10 22 7 23 10
dyads_m8_shift4 (dyads_m8)				; oligos_6nt_mkv3_m3 versus dyads_m8; m=4/6; ncol2=22; w=-7; offset=-7; strand=D; shift=4; score=0.447313; ----agrGAGAGAGAGmGAGAG ; cor=; Ncor= a 0 0 0 0 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 c 0 0 0 0 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 g 0 0 0 0 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 t 0 0 0 0 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12
dyads_m6_shift8 (dyads_m6)				; oligos_6nt_mkv3_m3 versus dyads_m6; m=5/6; ncol2=22; w=-3; offset=-3; strand=D; shift=8; score=0.430098; --------agrGAGAGrGAGAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 125 36 113 18 195 22 190 19 129 8 189 9 192 9 c 0 0 0 0 0 0 0 0 39 40 32 12 17 8 22 10 34 17 25 14 24 10 g 0 0 0 0 0 0 0 0 59 149 83 209 25 212 20 213 68 217 19 220 20 223 t 0 0 0 0 0 0 0 0 27 25 22 11 13 8 18 8 19 8 17 7 14 8
dyads_m10_shift0 (dyads_m10)				; oligos_6nt_mkv3_m3 versus dyads_m10; m=6/6; ncol2=23; w=-11; offset=-11; strand=D; shift=0; score=0.411883; agrGAGaGrGAGAGAGAGAGag ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift4 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=18; shift=4; ncol=22; ----ctCTCTCTCTCTCTCtct ; Alignment reference a 0 0 0 0 43 38 14 16 17 17 10 23 7 22 10 22 15 21 14 44 29 56 c 0 0 0 0 240 58 322 30 330 28 346 23 340 32 337 19 331 35 321 68 254 76 g 0 0 0 0 44 89 23 65 17 47 13 48 18 42 14 52 18 39 19 84 45 58 t 0 0 0 0 57 199 25 273 20 292 15 290 19 288 23 291 20 289 30 188 56 194
dyads_m2_shift4 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/6; ncol2=18; w=0; offset=0; strand=D; shift=4; score= 1; ----ctCTCTCTCTCTCTCtct ; cor=; Ncor= a 0 0 0 0 43 38 14 16 17 17 10 23 7 22 10 22 15 21 14 44 29 56 c 0 0 0 0 240 58 322 30 330 28 346 23 340 32 337 19 331 35 321 68 254 76 g 0 0 0 0 44 89 23 65 17 47 13 48 18 42 14 52 18 39 19 84 45 58 t 0 0 0 0 57 199 25 273 20 292 15 290 19 288 23 291 20 289 30 188 56 194
dyads_m8_rc_shift2 (dyads_m8_rc)				; dyads_m2 versus dyads_m8_rc; m=2/6; ncol2=22; w=-2; offset=-2; strand=R; shift=2; score=0.803559; --ctCtCTCTCkCTCTCTCTCy ; cor=; Ncor= a 0 0 27 29 16 16 12 12 6 15 5 26 6 18 5 19 10 16 13 23 14 26 c 0 0 183 53 216 33 241 12 250 25 254 28 255 21 255 25 248 25 235 36 219 85 g 0 0 35 63 21 52 18 39 13 29 11 85 12 25 13 30 10 33 12 28 23 32 t 0 0 40 140 32 184 14 222 16 216 15 146 12 221 12 211 17 211 25 198 29 142
dyads_m6_rc_shift0 (dyads_m6_rc)				; dyads_m2 versus dyads_m6_rc; m=3/6; ncol2=22; w=-4; offset=-4; strand=R; shift=0; score=0.79832; ctCTCTCTCTCTCyCTCTCyct ; cor=; Ncor= a 24 18 15 17 6 16 7 15 8 14 7 17 8 19 8 18 8 13 11 22 25 27 c 154 59 191 18 217 14 213 25 223 20 220 19 217 68 213 20 212 25 209 83 149 59 g 32 46 17 42 13 31 14 24 10 24 14 25 17 34 10 22 8 17 12 32 40 39 t 40 127 27 173 14 189 16 186 9 192 9 189 8 129 19 190 22 195 18 113 36 125
dyads_m10_rc_shift3 (dyads_m10_rc)				; dyads_m2 versus dyads_m10_rc; m=4/6; ncol2=23; w=-1; offset=-1; strand=R; shift=3; score=0.76558; ---tctCTCTCTCTCTCyCtCT ; cor=; Ncor= a 0 0 0 22 13 9 8 11 5 13 4 11 6 12 7 8 8 17 7 39 7 15 c 0 0 0 45 133 26 166 17 180 9 180 15 179 14 179 16 173 54 172 24 177 22 g 0 0 0 35 22 31 10 23 8 23 8 17 8 20 11 22 13 24 8 26 5 11 t 0 0 0 99 33 135 17 150 8 156 9 158 8 155 4 155 7 106 14 112 12 153
oligos_7nt_mkv4_m3_rc_shift9 (oligos_7nt_mkv4_m3_rc)				; dyads_m2 versus oligos_7nt_mkv4_m3_rc; m=5/6; ncol2=12; w=0; offset=5; strand=R; shift=9; score=0.593529; ---------ycTCTCGCTCtc- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 29 32 3 0 3 3 8 5 6 3 39 21 0 c 0 0 0 0 0 0 0 0 0 62 139 6 224 8 227 8 226 8 226 40 137 0 g 0 0 0 0 0 0 0 0 0 50 36 18 4 5 7 170 1 10 4 55 44 0 t 0 0 0 0 0 0 0 0 0 102 36 216 15 227 6 57 11 219 10 109 41 0
oligos_6nt_mkv3_m3_rc_shift10 (oligos_6nt_mkv3_m3_rc)				; dyads_m2 versus oligos_6nt_mkv3_m3_rc; m=6/6; ncol2=11; w=0; offset=6; strand=R; shift=10; score=0.532369; ----------ctCTCGCTCtc- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 67 75 14 14 5 22 11 27 8 76 50 0 c 0 0 0 0 0 0 0 0 0 0 241 76 391 18 434 21 422 20 437 99 232 0 g 0 0 0 0 0 0 0 0 0 0 74 107 20 6 15 320 6 10 9 102 90 0 t 0 0 0 0 0 0 0 0 0 0 80 204 37 424 8 99 23 405 8 185 90 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m8_shift0 (dyads_m8)				; dyads_m8; m=0 (reference); ncol1=22; shift=0; ncol=22; agrGAGAGAGAGmGAGAGaGag ; Alignment reference a 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 32 140 40 c 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 21 63 35 g 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 216 53 183 t 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16 16 29 27
dyads_m8_shift0 (dyads_m8)				; dyads_m8 versus dyads_m8; m=1/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; agrGAGAGAGAGmGAGAGaGag ; cor=; Ncor= a 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 32 140 40 c 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 21 63 35 g 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 216 53 183 t 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16 16 29 27
dyads_m6_shift0 (dyads_m6)				; dyads_m8 versus dyads_m6; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.984238; agrGAGAGrGAGAGAGAGAGag ; cor=; Ncor= a 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 40 c 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 32 g 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 154 t 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18 24
dyads_m10_shift0 (dyads_m10)				; dyads_m8 versus dyads_m10; m=3/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.935356; agrGAGaGrGAGAGAGAGAGag ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13
dyads_m2_rc_shift2 (dyads_m2_rc)				; dyads_m8 versus dyads_m2_rc; m=4/6; ncol2=18; w=0; offset=2; strand=R; shift=2; score=0.803559; --agaGAGAGAGAGAGAGag-- ; cor=; Ncor= a 0 0 194 56 188 30 289 20 291 23 288 19 290 15 292 20 273 25 199 57 0 0 c 0 0 58 45 84 19 39 18 52 14 42 18 48 13 47 17 65 23 89 44 0 0 g 0 0 76 254 68 321 35 331 19 337 32 340 23 346 28 330 30 322 58 240 0 0 t 0 0 56 29 44 14 21 15 22 10 22 7 23 10 17 17 16 14 38 43 0 0
oligos_7nt_mkv4_m3_shift7 (oligos_7nt_mkv4_m3)				; dyads_m8 versus oligos_7nt_mkv4_m3; m=5/6; ncol2=12; w=0; offset=7; strand=D; shift=7; score=0.503326; -------gaGAGCGAGAgr--- ; cor=; Ncor= a 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 0 0 0 c 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 0 0 0 g 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 0 0 0 t 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29 0 0 0
oligos_6nt_mkv3_m3_shift7 (oligos_6nt_mkv3_m3)				; dyads_m8 versus oligos_6nt_mkv3_m3; m=6/6; ncol2=11; w=0; offset=7; strand=D; shift=7; score=0.447313; -------gaGAGCGAGag---- ; cor=; Ncor= a 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 0 0 0 0 c 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 0 0 0 0 g 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 0 0 0 0 t 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m6_shift2 (oligos_7nt_mkv4_m6)				; oligos_7nt_mkv4_m6; m=0 (reference); ncol1=11; shift=2; ncol=13; --yrAACTGAAww ; Alignment reference a 0 0 59 74 240 243 12 13 18 238 226 77 83 c 0 0 74 65 15 4 246 10 7 4 9 62 42 g 0 0 57 79 7 7 9 15 230 11 19 54 67 t 0 0 80 52 8 16 3 232 15 17 16 77 78
oligos_7nt_mkv4_m6_shift2 (oligos_7nt_mkv4_m6)				; oligos_7nt_mkv4_m6 versus oligos_7nt_mkv4_m6; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --yrAACTGAAww ; cor=; Ncor= a 0 0 59 74 240 243 12 13 18 238 226 77 83 c 0 0 74 65 15 4 246 10 7 4 9 62 42 g 0 0 57 79 7 7 9 15 230 11 19 54 67 t 0 0 80 52 8 16 3 232 15 17 16 77 78
oligos_6nt_mkv3_m8_shift2 (oligos_6nt_mkv3_m8)				; oligos_7nt_mkv4_m6 versus oligos_6nt_mkv3_m8; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.861834; --smAACTGArw- ; cor=; Ncor= a 0 0 21 31 87 89 0 0 0 94 35 37 0 c 0 0 26 28 0 0 94 0 0 0 11 18 0 g 0 0 29 20 0 0 0 0 94 0 25 13 0 t 0 0 18 15 7 5 0 94 0 0 23 26 0
oligos_6nt_mkv3_m6_shift3 (oligos_6nt_mkv3_m6)				; oligos_7nt_mkv4_m6 versus oligos_6nt_mkv3_m6; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.672378; ---aaAATGAAar ; cor=; Ncor= a 0 0 0 50 50 111 111 0 0 110 111 50 37 c 0 0 0 15 21 0 0 0 0 0 0 21 17 g 0 0 0 24 22 0 0 0 111 0 0 19 31 t 0 0 0 22 18 0 0 111 0 1 0 21 26
oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m6 versus oligos_7nt_mkv4_m4_rc; m=4/4; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.486931; brCCAACTGkw-- ; cor=; Ncor= a 50 79 10 6 222 211 6 14 7 63 73 0 0 c 82 47 246 245 29 23 239 8 7 63 60 0 0 g 69 85 8 11 16 29 13 9 252 69 64 0 0 t 69 59 6 8 3 7 12 239 4 75 73 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift0 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=19; shift=0; ncol=19; acrCACACACACACACrca ; Alignment reference a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 49 179 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 200 38 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 44 86 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40 56 46
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/5; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; acrCACACACACACACrca ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 49 179 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 200 38 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 44 86 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40 56 46
dyads_m7_shift0 (dyads_m7)				; dyads_m1 versus dyads_m7; m=2/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.654976; mmrCAcmCACAmmmACAmm ; cor=; Ncor= a 31 34 42 4 80 16 64 19 91 3 91 45 34 28 92 2 89 49 27 c 35 44 9 92 6 68 28 71 2 97 4 40 45 66 3 92 4 32 59 g 19 7 43 2 5 12 6 5 6 0 4 10 11 3 4 3 2 10 11 t 16 16 7 3 10 5 3 6 2 1 2 6 11 4 2 4 6 10 4
oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)				; dyads_m1 versus oligos_6nt_mkv3_m2; m=3/5; ncol2=13; w=0; offset=5; strand=D; shift=5; score= 0.6035; -----caCACrCACasac- ; cor=; Ncor= a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 125 63 0 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 70 149 0 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 65 74 0 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41 85 59 0
oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)				; dyads_m1 versus oligos_6nt_mkv3_m7; m=4/5; ncol2=11; w=0; offset=6; strand=D; shift=6; score=0.548469; ------acACACACAca-- ; cor=; Ncor= a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 287 0 0 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 90 0 0 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 123 0 0 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110 106 0 0
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)				; dyads_m1 versus oligos_7nt_mkv4_m5; m=5/5; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.511484; -----caCACrCACac--- ; cor=; Ncor= a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 0 0 0 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 0 0 0 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 0 0 0 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift0 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=19; shift=0; ncol=19; wagAAAAATATAAATAaww ; Alignment reference a 34 43 19 72 73 80 82 80 14 87 15 81 78 86 9 85 56 42 42 c 21 12 15 8 3 4 3 4 8 0 7 4 5 5 8 1 11 13 14 g 12 19 43 8 6 7 1 7 4 6 7 5 2 3 3 2 7 14 13 t 31 24 21 10 16 7 12 7 72 5 69 8 13 4 78 10 24 29 29
dyads_m3_shift0 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; wagAAAAATATAAATAaww ; cor=; Ncor= a 34 43 19 72 73 80 82 80 14 87 15 81 78 86 9 85 56 42 42 c 21 12 15 8 3 4 3 4 8 0 7 4 5 5 8 1 11 13 14 g 12 19 43 8 6 7 1 7 4 6 7 5 2 3 3 2 7 14 13 t 31 24 21 10 16 7 12 7 72 5 69 8 13 4 78 10 24 29 29
oligos_6nt_mkv3_m9_shift8 (oligos_6nt_mkv3_m9)				; dyads_m3 versus oligos_6nt_mkv3_m9; m=2/3; ncol2=10; w=0; offset=8; strand=D; shift=8; score=0.471137; --------waTAwATAtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 74 122 0 245 151 236 0 248 51 106 0 c 0 0 0 0 0 0 0 0 30 27 0 0 15 8 0 0 51 39 0 g 0 0 0 0 0 0 0 0 33 44 0 2 15 4 0 0 34 29 0 t 0 0 0 0 0 0 0 0 111 55 248 1 67 0 248 0 112 74 0
oligos_6nt_mkv3_m4_shift8 (oligos_6nt_mkv3_m4)				; dyads_m3 versus oligos_6nt_mkv3_m4; m=3/3; ncol2=10; w=0; offset=8; strand=D; shift=8; score=0.404313; --------taTAkATAtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 36 104 3 182 2 185 0 197 23 98 0 c 0 0 0 0 0 0 0 0 27 25 5 17 15 0 2 1 49 21 0 g 0 0 0 0 0 0 0 0 40 44 9 3 118 10 12 2 39 31 0 t 0 0 0 0 0 0 0 0 99 29 185 0 67 7 188 2 91 52 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=11; shift=6; ncol=17; ------acACACACAca ; Alignment reference a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 287 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 90 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 123 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110 106
oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=6; score= 1; ------acACACACAca ; cor=; Ncor= a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 287 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 90 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 123 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110 106
oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m2; m=2/5; ncol2=13; w=-1; offset=-1; strand=D; shift=5; score=0.737517; -----caCACrCACasa ; cor=; Ncor= a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 125 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 70 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 65 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41 85
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m7 versus oligos_7nt_mkv4_m5; m=3/5; ncol2=11; w=-1; offset=-1; strand=D; shift=5; score=0.714736; -----caCACrCACac- ; cor=; Ncor= a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 0 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 0 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 0 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72 0
dyads_m1_shift0 (dyads_m1)				; oligos_6nt_mkv3_m7 versus dyads_m1; m=4/5; ncol2=19; w=-6; offset=-6; strand=D; shift=0; score=0.548469; acrCACACACACACACr ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40
dyads_m7_shift4 (dyads_m7)				; oligos_6nt_mkv3_m7 versus dyads_m7; m=5/5; ncol2=24; w=-2; offset=-2; strand=D; shift=4; score=0.413638; ----mmrCAcmCACAmm ; cor=; Ncor= a 0 0 0 0 31 34 42 4 80 16 64 19 91 3 91 45 34 c 0 0 0 0 35 44 9 92 6 68 28 71 2 97 4 40 45 g 0 0 0 0 19 7 43 2 5 12 6 5 6 0 4 10 11 t 0 0 0 0 16 16 7 3 10 5 3 6 2 1 2 6 11

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --wmCAGTTGGyv ; Alignment reference a 0 0 73 75 4 239 12 7 3 8 6 59 69 c 0 0 64 69 252 9 13 29 16 11 8 85 69 g 0 0 60 63 7 8 239 23 29 245 246 47 82 t 0 0 73 63 7 14 6 211 222 6 10 79 50
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wmCAGTTGGyv ; cor=; Ncor= a 0 0 73 75 4 239 12 7 3 8 6 59 69 c 0 0 64 69 252 9 13 29 16 11 8 85 69 g 0 0 60 63 7 8 239 23 29 245 246 47 82 t 0 0 73 63 7 14 6 211 222 6 10 79 50
oligos_6nt_mkv3_m8_rc_shift1 (oligos_6nt_mkv3_m8_rc)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m8_rc; m=2/3; ncol2=10; w=-1; offset=-1; strand=R; shift=1; score=0.566034; -wyTCAGTTks-- ; cor=; Ncor= a 0 26 23 0 0 94 0 5 7 15 18 0 0 c 0 13 25 0 94 0 0 0 0 20 29 0 0 g 0 18 11 0 0 0 94 0 0 28 26 0 0 t 0 37 35 94 0 0 0 89 87 31 21 0 0
oligos_7nt_mkv4_m6_rc_shift0 (oligos_7nt_mkv4_m6_rc)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m6_rc; m=3/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.486931; wwTTCAGTTyr-- ; cor=; Ncor= a 78 77 16 17 15 232 3 16 8 52 80 0 0 c 67 54 19 11 230 15 9 7 7 79 57 0 0 g 42 62 9 4 7 10 246 4 15 65 74 0 0 t 83 77 226 238 18 13 12 243 240 74 59 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -asAGGCACAsa ; Alignment reference a 0 91 39 188 4 18 4 208 7 204 34 80 c 0 45 89 11 27 14 208 7 200 4 84 45 g 0 51 58 14 188 189 5 5 15 6 68 47 t 0 38 39 12 6 4 8 5 3 11 39 53
oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -asAGGCACAsa ; cor=; Ncor= a 0 91 39 188 4 18 4 208 7 204 34 80 c 0 45 89 11 27 14 208 7 200 4 84 45 g 0 51 58 14 188 189 5 5 15 6 68 47 t 0 38 39 12 6 4 8 5 3 11 39 53
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.654638; caCACrCACasa ; cor=; Ncor= a 53 158 13 315 4 93 12 319 4 222 47 125 c 183 62 302 5 319 18 322 12 333 37 164 70 g 44 80 13 7 13 208 5 4 5 39 93 65 t 65 45 17 18 9 26 6 10 3 47 41 85
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.617634; caCACrCACac- ; cor=; Ncor= a 65 200 13 396 8 128 18 409 0 211 68 0 c 237 83 399 10 408 26 409 16 428 66 219 0 g 64 96 14 7 18 258 9 4 8 78 84 0 t 77 64 17 30 9 31 7 14 7 88 72 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=5; ncol=16; -----caCACrCACac ; Alignment reference a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----caCACrCACac ; cor=; Ncor= a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72
oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2; m=2/6; ncol2=13; w=0; offset=0; strand=D; shift=5; score=0.841232; -----caCACrCACas ; cor=; Ncor= a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41
oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m7; m=3/6; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.714736; ------acACACACAc ; cor=; Ncor= a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m5; m=4/6; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.646014; ------hyACTCAChm ; cor=; Ncor= a 0 0 0 0 0 0 29 22 103 1 3 1 99 1 31 29 c 0 0 0 0 0 0 34 43 3 111 3 109 3 110 37 45 g 0 0 0 0 0 0 22 16 0 2 0 1 0 3 12 16 t 0 0 0 0 0 0 30 34 9 1 109 4 13 1 35 25
oligos_7nt_mkv4_m2_shift6 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=5/6; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.617634; ------asAGGCACAs ; cor=; Ncor= a 0 0 0 0 0 0 91 39 188 4 18 4 208 7 204 34 c 0 0 0 0 0 0 45 89 11 27 14 208 7 200 4 84 g 0 0 0 0 0 0 51 58 14 188 189 5 5 15 6 68 t 0 0 0 0 0 0 38 39 12 6 4 8 5 3 11 39
dyads_m1_shift0 (dyads_m1)				; oligos_7nt_mkv4_m5 versus dyads_m1; m=6/6; ncol2=19; w=-5; offset=-5; strand=D; shift=0; score=0.511484; acrCACACACACACAC ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m9_shift8 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=8; ncol=18; --------waTAwATAtw ; Alignment reference a 0 0 0 0 0 0 0 0 74 122 0 245 151 236 0 248 51 106 c 0 0 0 0 0 0 0 0 30 27 0 0 15 8 0 0 51 39 g 0 0 0 0 0 0 0 0 33 44 0 2 15 4 0 0 34 29 t 0 0 0 0 0 0 0 0 111 55 248 1 67 0 248 0 112 74
oligos_6nt_mkv3_m9_shift8 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=8; score= 1; --------waTAwATAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 74 122 0 245 151 236 0 248 51 106 c 0 0 0 0 0 0 0 0 30 27 0 0 15 8 0 0 51 39 g 0 0 0 0 0 0 0 0 33 44 0 2 15 4 0 0 34 29 t 0 0 0 0 0 0 0 0 111 55 248 1 67 0 248 0 112 74
oligos_6nt_mkv3_m4_shift8 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m4; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=8; score=0.907713; --------taTAkATAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 36 104 3 182 2 185 0 197 23 98 c 0 0 0 0 0 0 0 0 27 25 5 17 15 0 2 1 49 21 g 0 0 0 0 0 0 0 0 40 44 9 3 118 10 12 2 39 31 t 0 0 0 0 0 0 0 0 99 29 185 0 67 7 188 2 91 52
oligos_6nt_mkv3_m1_shift8 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=8; score=0.739621; --------haTACATACa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 86 125 7 248 20 251 5 256 17 116 c 0 0 0 0 0 0 0 0 80 33 18 9 218 7 25 4 214 40 g 0 0 0 0 0 0 0 0 27 51 4 9 13 8 4 7 12 65 t 0 0 0 0 0 0 0 0 81 65 245 8 23 8 240 7 31 53
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m9 versus dyads_m3; m=4/4; ncol2=19; w=-8; offset=-8; strand=D; shift=0; score=0.471137; wagAAAAATATAAATAaw ; cor=; Ncor= a 34 43 19 72 73 80 82 80 14 87 15 81 78 86 9 85 56 42 c 21 12 15 8 3 4 3 4 8 0 7 4 5 5 8 1 11 13 g 12 19 43 8 6 7 1 7 4 6 7 5 2 3 3 2 7 14 t 31 24 21 10 16 7 12 7 72 5 69 8 13 4 78 10 24 29

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift0 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=24; shift=0; ncol=24; mmrCAcmCACAmmmACAmmmACam ; Alignment reference a 31 34 42 4 80 16 64 19 91 3 91 45 34 28 92 2 89 49 27 46 78 8 53 27 c 35 44 9 92 6 68 28 71 2 97 4 40 45 66 3 92 4 32 59 33 8 79 15 34 g 19 7 43 2 5 12 6 5 6 0 4 10 11 3 4 3 2 10 11 13 8 9 20 25 t 16 16 7 3 10 5 3 6 2 1 2 6 11 4 2 4 6 10 4 9 7 5 13 15
dyads_m7_shift0 (dyads_m7)				; dyads_m7 versus dyads_m7; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; mmrCAcmCACAmmmACAmmmACam ; cor=; Ncor= a 31 34 42 4 80 16 64 19 91 3 91 45 34 28 92 2 89 49 27 46 78 8 53 27 c 35 44 9 92 6 68 28 71 2 97 4 40 45 66 3 92 4 32 59 33 8 79 15 34 g 19 7 43 2 5 12 6 5 6 0 4 10 11 3 4 3 2 10 11 13 8 9 20 25 t 16 16 7 3 10 5 3 6 2 1 2 6 11 4 2 4 6 10 4 9 7 5 13 15
dyads_m1_shift0 (dyads_m1)				; dyads_m7 versus dyads_m1; m=2/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score=0.654976; acrCACACACACACACrca----- ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 49 179 0 0 0 0 0 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 200 38 0 0 0 0 0 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 44 86 0 0 0 0 0 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40 56 46 0 0 0 0 0
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; dyads_m7 versus oligos_6nt_mkv3_m2; m=3/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.466054; -caCACrCACasac---------- ; cor=; Ncor= a 0 53 158 13 315 4 93 12 319 4 222 47 125 63 0 0 0 0 0 0 0 0 0 0 c 0 183 62 302 5 319 18 322 12 333 37 164 70 149 0 0 0 0 0 0 0 0 0 0 g 0 44 80 13 7 13 208 5 4 5 39 93 65 74 0 0 0 0 0 0 0 0 0 0 t 0 65 45 17 18 9 26 6 10 3 47 41 85 59 0 0 0 0 0 0 0 0 0 0
oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)				; dyads_m7 versus oligos_6nt_mkv3_m7; m=4/4; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.413638; --acACACACAca----------- ; cor=; Ncor= a 0 0 299 90 489 9 555 8 552 7 535 110 287 0 0 0 0 0 0 0 0 0 0 0 c 0 0 87 321 25 548 12 537 15 542 16 296 90 0 0 0 0 0 0 0 0 0 0 0 g 0 0 129 77 61 17 16 23 16 24 24 90 123 0 0 0 0 0 0 0 0 0 0 0 t 0 0 91 118 31 32 23 38 23 33 31 110 106 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -hyACTCAChmy ; Alignment reference a 0 29 22 103 1 3 1 99 1 31 29 28 c 0 34 43 3 111 3 109 3 110 37 45 29 g 0 22 16 0 2 0 1 0 3 12 16 21 t 0 30 34 9 1 109 4 13 1 35 25 37
oligos_6nt_mkv3_m5_shift1 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -hyACTCAChmy ; cor=; Ncor= a 0 29 22 103 1 3 1 99 1 31 29 28 c 0 34 43 3 111 3 109 3 110 37 45 29 g 0 22 16 0 2 0 1 0 3 12 16 21 t 0 30 34 9 1 109 4 13 1 35 25 37
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m5; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.646014; caCACrCACac- ; cor=; Ncor= a 65 200 13 396 8 128 18 409 0 211 68 0 c 237 83 399 10 408 26 409 16 428 66 219 0 g 64 96 14 7 18 258 9 4 8 78 84 0 t 77 64 17 30 9 31 7 14 7 88 72 0
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.645663; caCACrCACasa ; cor=; Ncor= a 53 158 13 315 4 93 12 319 4 222 47 125 c 183 62 302 5 319 18 322 12 333 37 164 70 g 44 80 13 7 13 208 5 4 5 39 93 65 t 65 45 17 18 9 26 6 10 3 47 41 85

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=13; shift=5; ncol=18; -----caCACrCACasac ; Alignment reference a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 125 63 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 70 149 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 65 74 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41 85 59
oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=5; score= 1; -----caCACrCACasac ; cor=; Ncor= a 0 0 0 0 0 53 158 13 315 4 93 12 319 4 222 47 125 63 c 0 0 0 0 0 183 62 302 5 319 18 322 12 333 37 164 70 149 g 0 0 0 0 0 44 80 13 7 13 208 5 4 5 39 93 65 74 t 0 0 0 0 0 65 45 17 18 9 26 6 10 3 47 41 85 59
oligos_7nt_mkv4_m5_shift5 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=5; score=0.841232; -----caCACrCACac-- ; cor=; Ncor= a 0 0 0 0 0 65 200 13 396 8 128 18 409 0 211 68 0 0 c 0 0 0 0 0 237 83 399 10 408 26 409 16 428 66 219 0 0 g 0 0 0 0 0 64 96 14 7 18 258 9 4 8 78 84 0 0 t 0 0 0 0 0 77 64 17 30 9 31 7 14 7 88 72 0 0
oligos_6nt_mkv3_m7_shift6 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m7; m=3/7; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.737517; ------acACACACAca- ; cor=; Ncor= a 0 0 0 0 0 0 299 90 489 9 555 8 552 7 535 110 287 0 c 0 0 0 0 0 0 87 321 25 548 12 537 15 542 16 296 90 0 g 0 0 0 0 0 0 129 77 61 17 16 23 16 24 24 90 123 0 t 0 0 0 0 0 0 91 118 31 32 23 38 23 33 31 110 106 0
oligos_7nt_mkv4_m2_shift6 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2; m=4/7; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.654638; ------asAGGCACAsa- ; cor=; Ncor= a 0 0 0 0 0 0 91 39 188 4 18 4 208 7 204 34 80 0 c 0 0 0 0 0 0 45 89 11 27 14 208 7 200 4 84 45 0 g 0 0 0 0 0 0 51 58 14 188 189 5 5 15 6 68 47 0 t 0 0 0 0 0 0 38 39 12 6 4 8 5 3 11 39 53 0
oligos_6nt_mkv3_m5_shift6 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m5; m=5/7; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.645663; ------hyACTCAChmy- ; cor=; Ncor= a 0 0 0 0 0 0 29 22 103 1 3 1 99 1 31 29 28 0 c 0 0 0 0 0 0 34 43 3 111 3 109 3 110 37 45 29 0 g 0 0 0 0 0 0 22 16 0 2 0 1 0 3 12 16 21 0 t 0 0 0 0 0 0 30 34 9 1 109 4 13 1 35 25 37 0
dyads_m1_shift0 (dyads_m1)				; oligos_6nt_mkv3_m2 versus dyads_m1; m=6/7; ncol2=19; w=-5; offset=-5; strand=D; shift=0; score= 0.6035; acrCACACACACACACrc ; cor=; Ncor= a 162 56 153 28 266 18 289 13 297 17 286 11 292 14 268 28 167 49 c 54 205 27 290 18 305 9 311 5 292 12 311 5 303 12 253 31 200 g 66 30 122 11 40 7 33 12 33 18 29 6 36 14 38 30 111 44 t 67 58 47 20 25 19 18 13 14 22 22 21 16 18 31 38 40 56
dyads_m7_shift4 (dyads_m7)				; oligos_6nt_mkv3_m2 versus dyads_m7; m=7/7; ncol2=24; w=-1; offset=-1; strand=D; shift=4; score=0.466054; ----mmrCAcmCACAmmm ; cor=; Ncor= a 0 0 0 0 31 34 42 4 80 16 64 19 91 3 91 45 34 28 c 0 0 0 0 35 44 9 92 6 68 28 71 2 97 4 40 45 66 g 0 0 0 0 19 7 43 2 5 12 6 5 6 0 4 10 11 3 t 0 0 0 0 16 16 7 3 10 5 3 6 2 1 2 6 11 4

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; tacGTATAya ; Alignment reference a 22 50 14 11 2 112 0 108 14 52 c 20 22 73 3 0 5 2 3 30 18 g 22 20 11 98 3 0 4 5 11 18 t 53 25 19 5 112 0 111 1 62 29
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; tacGTATAya ; cor=; Ncor= a 22 50 14 11 2 112 0 108 14 52 c 20 22 73 3 0 5 2 3 30 18 g 22 20 11 98 3 0 4 5 11 18 t 53 25 19 5 112 0 111 1 62 29
oligos_6nt_mkv3_m1_rc_shift1 (oligos_6nt_mkv3_m1_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m1_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.537931; -dtGTATGTA ; cor=; Ncor= a 0 90 53 31 7 240 8 23 8 245 c 0 37 65 12 7 4 8 13 9 4 g 0 70 40 214 4 25 7 218 9 18 t 0 77 116 17 256 5 251 20 248 7
oligos_6nt_mkv3_m4_rc_shift2 (oligos_6nt_mkv3_m4_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m4_rc; m=3/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.467736; --waTATmTA ; cor=; Ncor= a 0 0 52 91 2 188 7 67 0 185 c 0 0 31 39 2 12 10 118 3 9 g 0 0 21 49 1 2 0 15 17 5 t 0 0 98 23 197 0 185 2 182 3

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; haTACATACah ; Alignment reference a 86 125 7 248 20 251 5 256 17 116 77 c 80 33 18 9 218 7 25 4 214 40 70 g 27 51 4 9 13 8 4 7 12 65 37 t 81 65 245 8 23 8 240 7 31 53 90
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; haTACATACah ; cor=; Ncor= a 86 125 7 248 20 251 5 256 17 116 77 c 80 33 18 9 218 7 25 4 214 40 70 g 27 51 4 9 13 8 4 7 12 65 37 t 81 65 245 8 23 8 240 7 31 53 90
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m9; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.739621; waTAwATAtw- ; cor=; Ncor= a 74 122 0 245 151 236 0 248 51 106 0 c 30 27 0 0 15 8 0 0 51 39 0 g 33 44 0 2 15 4 0 0 34 29 0 t 111 55 248 1 67 0 248 0 112 74 0
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.731445; taTAkATAtw- ; cor=; Ncor= a 36 104 3 182 2 185 0 197 23 98 0 c 27 25 5 17 15 0 2 1 49 21 0 g 40 44 9 3 118 10 12 2 39 31 0 t 99 29 185 0 67 7 188 2 91 52 0
positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=4/4; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.537931; --trTATACgt ; cor=; Ncor= a 0 0 29 62 1 111 0 112 5 19 25 c 0 0 18 11 5 4 0 3 98 11 20 g 0 0 18 30 3 2 5 0 3 73 22 t 0 0 52 14 108 0 112 2 11 14 50

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift8 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=8; ncol=18; --------taTAkATAtw ; Alignment reference a 0 0 0 0 0 0 0 0 36 104 3 182 2 185 0 197 23 98 c 0 0 0 0 0 0 0 0 27 25 5 17 15 0 2 1 49 21 g 0 0 0 0 0 0 0 0 40 44 9 3 118 10 12 2 39 31 t 0 0 0 0 0 0 0 0 99 29 185 0 67 7 188 2 91 52
oligos_6nt_mkv3_m4_shift8 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/5; ncol2=10; w=0; offset=0; strand=D; shift=8; score= 1; --------taTAkATAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 36 104 3 182 2 185 0 197 23 98 c 0 0 0 0 0 0 0 0 27 25 5 17 15 0 2 1 49 21 g 0 0 0 0 0 0 0 0 40 44 9 3 118 10 12 2 39 31 t 0 0 0 0 0 0 0 0 99 29 185 0 67 7 188 2 91 52
oligos_6nt_mkv3_m9_shift8 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m9; m=2/5; ncol2=10; w=0; offset=0; strand=D; shift=8; score=0.907713; --------waTAwATAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 74 122 0 245 151 236 0 248 51 106 c 0 0 0 0 0 0 0 0 30 27 0 0 15 8 0 0 51 39 g 0 0 0 0 0 0 0 0 33 44 0 2 15 4 0 0 34 29 t 0 0 0 0 0 0 0 0 111 55 248 1 67 0 248 0 112 74
oligos_6nt_mkv3_m1_shift8 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m1; m=3/5; ncol2=11; w=0; offset=0; strand=D; shift=8; score=0.731445; --------haTACATACa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 86 125 7 248 20 251 5 256 17 116 c 0 0 0 0 0 0 0 0 80 33 18 9 218 7 25 4 214 40 g 0 0 0 0 0 0 0 0 27 51 4 9 13 8 4 7 12 65 t 0 0 0 0 0 0 0 0 81 65 245 8 23 8 240 7 31 53
positions_6nt_m1_rc_shift10 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m4 versus positions_6nt_m1_rc; m=4/5; ncol2=10; w=0; offset=2; strand=R; shift=10; score=0.467736; ----------trTATACg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 29 62 1 111 0 112 5 19 c 0 0 0 0 0 0 0 0 0 0 18 11 5 4 0 3 98 11 g 0 0 0 0 0 0 0 0 0 0 18 30 3 2 5 0 3 73 t 0 0 0 0 0 0 0 0 0 0 52 14 108 0 112 2 11 14
dyads_m3_shift0 (dyads_m3)				; oligos_6nt_mkv3_m4 versus dyads_m3; m=5/5; ncol2=19; w=-8; offset=-8; strand=D; shift=0; score=0.404313; wagAAAAATATAAATAaw ; cor=; Ncor= a 34 43 19 72 73 80 82 80 14 87 15 81 78 86 9 85 56 42 c 21 12 15 8 3 4 3 4 8 0 7 4 5 5 8 1 11 13 g 12 19 43 8 6 7 1 7 4 6 7 5 2 3 3 2 7 14 t 31 24 21 10 16 7 12 7 72 5 69 8 13 4 78 10 24 29

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m6_shift0 (dyads_m6)				; dyads_m6; m=0 (reference); ncol1=22; shift=0; ncol=22; agrGAGAGrGAGAGAGAGAGag ; Alignment reference a 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 40 c 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 32 g 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 154 t 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18 24
dyads_m6_shift0 (dyads_m6)				; dyads_m6 versus dyads_m6; m=1/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; agrGAGAGrGAGAGAGAGAGag ; cor=; Ncor= a 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 40 c 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 32 g 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 154 t 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18 24
dyads_m8_shift0 (dyads_m8)				; dyads_m6 versus dyads_m8; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.984238; agrGAGAGAGAGmGAGAGaGag ; cor=; Ncor= a 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 32 140 40 c 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 21 63 35 g 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 216 53 183 t 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16 16 29 27
dyads_m10_shift0 (dyads_m10)				; dyads_m6 versus dyads_m10; m=3/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.94845; agrGAGaGrGAGAGAGAGAGag ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13
dyads_m2_rc_shift0 (dyads_m2_rc)				; dyads_m6 versus dyads_m2_rc; m=4/6; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.79832; agaGAGAGAGAGAGAGag---- ; cor=; Ncor= a 194 56 188 30 289 20 291 23 288 19 290 15 292 20 273 25 199 57 0 0 0 0 c 58 45 84 19 39 18 52 14 42 18 48 13 47 17 65 23 89 44 0 0 0 0 g 76 254 68 321 35 331 19 337 32 340 23 346 28 330 30 322 58 240 0 0 0 0 t 56 29 44 14 21 15 22 10 22 7 23 10 17 17 16 14 38 43 0 0 0 0
oligos_7nt_mkv4_m3_shift9 (oligos_7nt_mkv4_m3)				; dyads_m6 versus oligos_7nt_mkv4_m3; m=5/6; ncol2=12; w=0; offset=9; strand=D; shift=9; score=0.483439; ---------gaGAGCGAGAgr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 0 c 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 0 g 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 0 t 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29 0
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; dyads_m6 versus oligos_6nt_mkv3_m3; m=6/6; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.430098; ---gaGAGCGAGag-------- ; cor=; Ncor= a 0 0 0 90 185 8 405 23 99 8 424 37 204 80 0 0 0 0 0 0 0 0 c 0 0 0 90 102 9 10 6 320 15 6 20 107 74 0 0 0 0 0 0 0 0 g 0 0 0 232 99 437 20 422 21 434 18 391 76 241 0 0 0 0 0 0 0 0 t 0 0 0 50 76 8 27 11 22 5 14 14 75 67 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------gaGAGCGAGAgr ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 c 0 0 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 g 0 0 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 t 0 0 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29
oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=11; score= 1; -----------gaGAGCGAGAgr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 c 0 0 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 g 0 0 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 t 0 0 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29
oligos_6nt_mkv3_m3_shift11 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=11; score=0.890023; -----------gaGAGCGAGag- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 0 c 0 0 0 0 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 0 g 0 0 0 0 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 0 t 0 0 0 0 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67 0
dyads_m2_rc_shift10 (dyads_m2_rc)				; oligos_7nt_mkv4_m3 versus dyads_m2_rc; m=3/6; ncol2=18; w=-1; offset=-1; strand=R; shift=10; score=0.593529; ----------agaGAGAGAGAGA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 194 56 188 30 289 20 291 23 288 19 290 15 292 c 0 0 0 0 0 0 0 0 0 0 58 45 84 19 39 18 52 14 42 18 48 13 47 g 0 0 0 0 0 0 0 0 0 0 76 254 68 321 35 331 19 337 32 340 23 346 28 t 0 0 0 0 0 0 0 0 0 0 56 29 44 14 21 15 22 10 22 7 23 10 17
dyads_m8_shift4 (dyads_m8)				; oligos_7nt_mkv4_m3 versus dyads_m8; m=4/6; ncol2=22; w=-7; offset=-7; strand=D; shift=4; score=0.503326; ----agrGAGAGAGAGmGAGAGa ; cor=; Ncor= a 0 0 0 0 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 c 0 0 0 0 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 g 0 0 0 0 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 t 0 0 0 0 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16
dyads_m6_shift2 (dyads_m6)				; oligos_7nt_mkv4_m3 versus dyads_m6; m=5/6; ncol2=22; w=-9; offset=-9; strand=D; shift=2; score=0.483439; --agrGAGAGrGAGAGAGAGAGa ; cor=; Ncor= a 0 0 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 c 0 0 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 g 0 0 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 t 0 0 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18
dyads_m10_shift0 (dyads_m10)				; oligos_7nt_mkv4_m3 versus dyads_m10; m=6/6; ncol2=23; w=-11; offset=-11; strand=D; shift=0; score=0.461828; agrGAGaGrGAGAGAGAGAGaga ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 99 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 35 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 45 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13 22

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m8_shift2 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=2; ncol=12; --smAACTGArw ; Alignment reference a 0 0 21 31 87 89 0 0 0 94 35 37 c 0 0 26 28 0 0 94 0 0 0 11 18 g 0 0 29 20 0 0 0 0 94 0 25 13 t 0 0 18 15 7 5 0 94 0 0 23 26
oligos_6nt_mkv3_m8_shift2 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --smAACTGArw ; cor=; Ncor= a 0 0 21 31 87 89 0 0 0 94 35 37 c 0 0 26 28 0 0 94 0 0 0 11 18 g 0 0 29 20 0 0 0 0 94 0 25 13 t 0 0 18 15 7 5 0 94 0 0 23 26
oligos_7nt_mkv4_m6_shift2 (oligos_7nt_mkv4_m6)				; oligos_6nt_mkv3_m8 versus oligos_7nt_mkv4_m6; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score=0.861834; --yrAACTGAAw ; cor=; Ncor= a 0 0 59 74 240 243 12 13 18 238 226 77 c 0 0 74 65 15 4 246 10 7 4 9 62 g 0 0 57 79 7 7 9 15 230 11 19 54 t 0 0 80 52 8 16 3 232 15 17 16 77
oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)				; oligos_6nt_mkv3_m8 versus oligos_7nt_mkv4_m4_rc; m=3/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.566034; brCCAACTGkw- ; cor=; Ncor= a 50 79 10 6 222 211 6 14 7 63 73 0 c 82 47 246 245 29 23 239 8 7 63 60 0 g 69 85 8 11 16 29 13 9 252 69 64 0 t 69 59 6 8 3 7 12 239 4 75 73 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m10_shift0 (dyads_m10)				; dyads_m10; m=0 (reference); ncol1=23; shift=0; ncol=23; agrGAGaGrGAGAGAGAGAGaga ; Alignment reference a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 99 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 35 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 45 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13 22
dyads_m10_shift0 (dyads_m10)				; dyads_m10 versus dyads_m10; m=1/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; agrGAGaGrGAGAGAGAGAGaga ; cor=; Ncor= a 91 30 91 14 153 12 112 14 106 7 155 4 155 8 158 9 156 8 150 17 135 33 99 c 34 31 30 11 11 5 26 8 24 13 22 11 20 8 17 8 23 8 23 10 31 22 35 g 49 123 58 166 22 177 24 172 54 173 16 179 14 179 15 180 9 180 17 166 26 133 45 t 27 17 22 10 15 7 39 7 17 8 8 7 12 6 11 4 13 5 11 8 9 13 22
dyads_m6_shift0 (dyads_m6)				; dyads_m10 versus dyads_m6; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.94845; agrGAGAGrGAGAGAGAGAGag- ; cor=; Ncor= a 125 36 113 18 195 22 190 19 129 8 189 9 192 9 186 16 189 14 173 27 127 40 0 c 39 40 32 12 17 8 22 10 34 17 25 14 24 10 24 14 31 13 42 17 46 32 0 g 59 149 83 209 25 212 20 213 68 217 19 220 20 223 25 213 14 217 18 191 59 154 0 t 27 25 22 11 13 8 18 8 19 8 17 7 14 8 15 7 16 6 17 15 18 24 0
dyads_m8_shift0 (dyads_m8)				; dyads_m10 versus dyads_m8; m=3/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.935356; agrGAGAGAGAGmGAGAGaGag- ; cor=; Ncor= a 142 38 142 29 198 25 211 17 211 12 221 12 146 15 216 16 222 14 184 32 140 40 0 c 44 47 32 23 28 12 33 10 30 13 25 12 85 11 29 13 39 18 52 21 63 35 0 g 67 170 85 219 36 235 25 248 25 255 21 255 28 254 25 250 12 241 33 216 53 183 0 t 32 30 26 14 23 13 16 10 19 5 18 6 26 5 15 6 12 12 16 16 29 27 0
dyads_m2_rc_shift4 (dyads_m2_rc)				; dyads_m10 versus dyads_m2_rc; m=4/6; ncol2=18; w=0; offset=4; strand=R; shift=4; score=0.76558; ----agaGAGAGAGAGAGAGag- ; cor=; Ncor= a 0 0 0 0 194 56 188 30 289 20 291 23 288 19 290 15 292 20 273 25 199 57 0 c 0 0 0 0 58 45 84 19 39 18 52 14 42 18 48 13 47 17 65 23 89 44 0 g 0 0 0 0 76 254 68 321 35 331 19 337 32 340 23 346 28 330 30 322 58 240 0 t 0 0 0 0 56 29 44 14 21 15 22 10 22 7 23 10 17 17 16 14 38 43 0
oligos_7nt_mkv4_m3_shift11 (oligos_7nt_mkv4_m3)				; dyads_m10 versus oligos_7nt_mkv4_m3; m=5/6; ncol2=12; w=0; offset=11; strand=D; shift=11; score=0.461828; -----------gaGAGCGAGAgr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 41 109 10 219 11 57 6 227 15 216 36 102 c 0 0 0 0 0 0 0 0 0 0 0 44 55 4 10 1 170 7 5 4 18 36 50 g 0 0 0 0 0 0 0 0 0 0 0 137 40 226 8 226 8 227 8 224 6 139 62 t 0 0 0 0 0 0 0 0 0 0 0 21 39 3 6 5 8 3 3 0 3 32 29
oligos_6nt_mkv3_m3_shift11 (oligos_6nt_mkv3_m3)				; dyads_m10 versus oligos_6nt_mkv3_m3; m=6/6; ncol2=11; w=0; offset=11; strand=D; shift=11; score=0.411883; -----------gaGAGCGAGag- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 90 185 8 405 23 99 8 424 37 204 80 0 c 0 0 0 0 0 0 0 0 0 0 0 90 102 9 10 6 320 15 6 20 107 74 0 g 0 0 0 0 0 0 0 0 0 0 0 232 99 437 20 422 21 434 18 391 76 241 0 t 0 0 0 0 0 0 0 0 0 0 0 50 76 8 27 11 22 5 14 14 75 67 0