One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $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 -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -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_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; gaGAGCGAGAgr ; Alignment reference a 41 109 10 219 11 57 6 227 15 216 36 102 c 44 55 4 10 1 170 7 5 4 18 36 50 g 137 40 226 8 226 8 227 8 224 6 139 62 t 21 39 3 6 5 8 3 3 0 3 32 29

Trl_rc_shift1 (Trl_rc)
; oligos_7nt_mkv4_m3 versus Trl_rc; m=1/2; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.673254; -agaGaGAGmrm ; cor=; Ncor= a 0 42 17 46 7 50 11 62 0 40 26 30 c 0 14 9 6 1 9 8 11 5 27 10 24 g 0 3 47 16 56 12 56 0 72 3 41 19 t 0 18 4 9 13 6 2 4 0 7 0 4

z_shift1 (z)
; oligos_7nt_mkv4_m3 versus z; m=2/2; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.407681; -TGAGtG----- ; cor=; Ncor= a 0 2.04878 0 42 0 7.17073 1.02439 0 0 0 0 0 c 0 7.17073 0 0 0 10.2439 5.12195 0 0 0 0 0 g 0 3.07317 42 0 42 0 30.7317 0 0 0 0 0 t 0 29.7073 0 0 0 24.5854 5.12195 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -gaGAGCGAGag ; Alignment reference a 0 90 185 8 405 23 99 8 424 37 204 80 c 0 90 102 9 10 6 320 15 6 20 107 74 g 0 232 99 437 20 422 21 434 18 391 76 241 t 0 50 76 8 27 11 22 5 14 14 75 67

Trl_rc_shift0 (Trl_rc)
; oligos_6nt_mkv3_m3 versus Trl_rc; m=1/2; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.641769; agaGaGAGmrma ; cor=; Ncor= a 42 17 46 7 50 11 62 0 40 26 30 41 c 14 9 6 1 9 8 11 5 27 10 24 13 g 3 47 16 56 12 56 0 72 3 41 19 8 t 18 4 9 13 6 2 4 0 7 0 4 15

z_shift2 (z)
; oligos_6nt_mkv3_m3 versus z; m=2/2; ncol2=6; w=0; offset=1; strand=D; shift=2; score=0.447867; --TGAGtG---- ; cor=; Ncor= a 0 0 2.04878 0 42 0 7.17073 1.02439 0 0 0 0 c 0 0 7.17073 0 0 0 10.2439 5.12195 0 0 0 0 g 0 0 3.07317 42 0 42 0 30.7317 0 0 0 0 t 0 0 29.7073 0 0 0 24.5854 5.12195 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waTAwATAtw ; Alignment reference a 74 122 0 245 151 236 0 248 51 106 c 30 27 0 0 15 8 0 0 51 39 g 33 44 0 2 15 4 0 0 34 29 t 111 55 248 1 67 0 248 0 112 74

br-Z4_rc_shift2 (br-Z4_rc)
; oligos_6nt_mkv3_m9 versus br-Z4_rc; m=1/6; ncol2=8; w=0; offset=2; strand=R; shift=2; score=0.619645; --TAAhYAdT ; cor=; Ncor= a 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 2 0 t 0 0 7 1 0 3 6 0 3 7

br-Z2_rc_shift2 (br-Z2_rc)
; oligos_6nt_mkv3_m9 versus br-Z2_rc; m=2/6; ncol2=7; w=0; offset=2; strand=R; shift=2; score=0.501528; --twaaTAG- ; cor=; Ncor= a 0 0 5 9 12 11 0 21 1 0 c 0 0 4 1 3 3 0 0 0 0 g 0 0 0 3 1 3 0 0 20 0 t 0 0 12 8 5 4 21 0 0 0

abd-A_shift1 (abd-A)
; oligos_6nt_mkv3_m9 versus abd-A; m=3/6; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.48587; -aTAAWT--- ; cor=; Ncor= a 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0

Antp_shift4 (Antp)
; oligos_6nt_mkv3_m9 versus Antp; m=4/6; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.484807; ----mATAAw ; cor=; Ncor= a 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 18 0 0 10.5

zen_shift0 (zen)
; oligos_6nt_mkv3_m9 versus zen; m=5/6; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.482115; AATwAA---- ; cor=; Ncor= a 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0.541667 0 1.08333 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 t 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0

vvl_rc_shift2 (vvl_rc)
; oligos_6nt_mkv3_m9 versus vvl_rc; m=6/6; ncol2=6; w=0; offset=2; strand=R; shift=2; score=0.443719; --TgmwTA-- ; cor=; Ncor= a 0 0 0 2.36364 8.27273 5.90909 0 13 0 0 c 0 0 0 1.18182 4.72727 0 0 0 0 0 g 0 0 0 8.27273 0 0 1.18182 0 0 0 t 0 0 13 1.18182 0 7.09091 11.8182 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m6_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; aaAATGAAar ; Alignment reference a 50 50 111 111 0 0 110 111 50 37 c 15 21 0 0 0 0 0 0 21 17 g 24 22 0 0 0 111 0 0 19 31 t 22 18 0 0 111 0 1 0 21 26

en_rc_shift1 (en_rc)
; oligos_6nt_mkv3_m6 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.60802; -yAATtAah- ; cor=; Ncor= a 0 10.125 58.5 57.375 1.125 5.625 51.75 31.5 18 0 c 0 31.5 3.375 2.25 0 14.625 4.5 11.25 21.375 0 g 0 1.125 0 1.125 1.125 6.75 6.75 12.375 0 0 t 0 20.25 1.125 2.25 60.75 36 0 7.875 23.625 0

sd_rc_shift1 (sd_rc)
; oligos_6nt_mkv3_m6 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.526432; -mAAwGdAAT ; cor=; Ncor= a 0 8 16 14 7 0 9 13 15 1 c 0 7 0 0 0 4 0 3 0 1 g 0 4 0 1 2 14 5 0 3 1 t 0 0 3 4 10 1 5 3 1 16

zen_shift2 (zen)
; oligos_6nt_mkv3_m6 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484521; --AATwAA-- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 c 0 0 0.541667 0 1.08333 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 t 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0

ap_shift2 (ap)
; oligos_6nt_mkv3_m6 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.421541; --AAThAt-- ; cor=; Ncor= a 0 0 14 14 0 5 13 2 0 0 c 0 0 0 0 1 4 0 1 0 0 g 0 0 0 0 1 1 1 3 0 0 t 0 0 0 0 12 4 0 8 0 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; ctCTCTCTCTCTCTCtct ; Alignment reference a 43 38 14 16 17 17 10 23 7 22 10 22 15 21 14 44 29 56 c 240 58 322 30 330 28 346 23 340 32 337 19 331 35 321 68 254 76 g 44 89 23 65 17 47 13 48 18 42 14 52 18 39 19 84 45 58 t 57 199 25 273 20 292 15 290 19 288 23 291 20 289 30 188 56 194

Trl_shift3 (Trl)
; dyads_m2 versus Trl; m=1/1; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.592713; ---TtkykCTCtCtct-- ; cor=; Ncor= a 0 0 0 10 15 4 0 7 0 4 2 6 13 9 4 18 0 0 c 0 0 0 10 8 19 41 3 72 0 56 12 56 16 47 3 0 0 g 0 0 0 0 13 24 10 27 5 11 8 9 1 6 9 14 0 0 t 0 0 0 57 41 30 26 40 0 62 11 50 7 46 17 42 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; hyACTCAChmy ; Alignment reference a 29 22 103 1 3 1 99 1 31 29 28 c 34 43 3 111 3 109 3 110 37 45 29 g 22 16 0 2 0 1 0 3 12 16 21 t 30 34 9 1 109 4 13 1 35 25 37

z_rc_shift1 (z_rc)
; oligos_6nt_mkv3_m5 versus z_rc; m=1/1; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.50615; -CaCTCA---- ; cor=; Ncor= a 0 5.12195 24.5854 0 0 0 29.7073 0 0 0 0 c 0 30.7317 0 42 0 42 3.07317 0 0 0 0 g 0 5.12195 10.2439 0 0 0 7.17073 0 0 0 0 t 0 1.02439 7.17073 0 42 0 2.04878 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 2 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

Trl_rc_shift4 (Trl_rc)
; dyads_m8 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=4; strand=R; shift=4; score=0.492951; ----agaGaGAGmrmaA----- ; cor=; Ncor= a 0 0 0 0 42 17 46 7 50 11 62 0 40 26 30 41 57 0 0 0 0 0 c 0 0 0 0 14 9 6 1 9 8 11 5 27 10 24 13 0 0 0 0 0 0 g 0 0 0 0 3 47 16 56 12 56 0 72 3 41 19 8 10 0 0 0 0 0 t 0 0 0 0 18 4 9 13 6 2 4 0 7 0 4 15 10 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 2 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

Trl_rc_shift8 (Trl_rc)
; dyads_m6 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=8; strand=R; shift=8; score=0.484677; --------agaGaGAGmrmaA- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 42 17 46 7 50 11 62 0 40 26 30 41 57 0 c 0 0 0 0 0 0 0 0 14 9 6 1 9 8 11 5 27 10 24 13 0 0 g 0 0 0 0 0 0 0 0 3 47 16 56 12 56 0 72 3 41 19 8 10 0 t 0 0 0 0 0 0 0 0 18 4 9 13 6 2 4 0 7 0 4 15 10 0

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 2 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

Trl_rc_shift10 (Trl_rc)
; dyads_m10 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=10; strand=R; shift=10; score=0.484208; ----------agaGaGAGmrmaA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 42 17 46 7 50 11 62 0 40 26 30 41 57 c 0 0 0 0 0 0 0 0 0 0 14 9 6 1 9 8 11 5 27 10 24 13 0 g 0 0 0 0 0 0 0 0 0 0 3 47 16 56 12 56 0 72 3 41 19 8 10 t 0 0 0 0 0 0 0 0 0 0 18 4 9 13 6 2 4 0 7 0 4 15 10

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 3 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

brk_shift0 (brk)
; dyads_m4 versus brk; m=1/2; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.477766; rGCGCCr----- ; cor=; Ncor= a 4.4 2.2 0 0 0 0 5.5 0 0 0 0 0 c 0 0 9.9 0 11 11 0 0 0 0 0 0 g 6.6 8.8 0 9.9 0 0 5.5 0 0 0 0 0 t 0 0 1.1 1.1 0 0 0 0 0 0 0 0

Med_shift3 (Med)
; dyads_m4 versus Med; m=2/2; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.460207; ---sCmssCsmm ; cor=; Ncor= a 0 0 0 1 0 5 0 0 0 0 3 4 c 0 0 0 2 8 3 3 4 7 3 5 4 g 0 0 0 5 0 0 4 4 1 5 0 0 t 0 0 0 0 0 0 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; smAACTGArw ; Alignment reference a 21 31 87 89 0 0 0 94 35 37 c 26 28 0 0 94 0 0 0 11 18 g 29 20 0 0 0 0 94 0 25 13 t 18 15 7 5 0 94 0 0 23 26

ovo_rc_shift1 (ovo_rc)
; oligos_6nt_mkv3_m8 versus ovo_rc; m=1/1; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.444501; -TAACrG--- ; cor=; Ncor= a 0 0 13 11.9167 0 4.33333 0 0 0 0 c 0 1.08333 0 0 13 0 0 0 0 0 g 0 0 0 0.541667 0 6.5 13 0 0 0 t 0 11.9167 0 0.541667 0 2.16667 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m6_shift0 (oligos_7nt_mkv4_m6)
; oligos_7nt_mkv4_m6; m=0 (reference); ncol1=11; shift=0; ncol=11; yrAACTGAAww ; Alignment reference 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

ovo_rc_shift1 (ovo_rc)
; oligos_7nt_mkv4_m6 versus ovo_rc; m=1/1; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.416522; -TAACrG---- ; cor=; Ncor= a 0 0 13 11.9167 0 4.33333 0 0 0 0 0 c 0 1.08333 0 0 13 0 0 0 0 0 0 g 0 0 0 0.541667 0 6.5 13 0 0 0 0 t 0 11.9167 0 0.541667 0 2.16667 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; caCACrCACac ; Alignment reference a 65 200 13 396 8 128 18 409 0 211 68 c 237 83 399 10 408 26 409 16 428 66 219 g 64 96 14 7 18 258 9 4 8 78 84 t 77 64 17 30 9 31 7 14 7 88 72

z_rc_shift2 (z_rc)
; oligos_7nt_mkv4_m5 versus z_rc; m=1/1; ncol2=6; w=0; offset=2; strand=R; shift=2; score=0.404675; --CaCTCA--- ; cor=; Ncor= a 0 0 5.12195 24.5854 0 0 0 29.7073 0 0 0 c 0 0 30.7317 0 42 0 42 3.07317 0 0 0 g 0 0 5.12195 10.2439 0 0 0 7.17073 0 0 0 t 0 0 1.02439 7.17073 0 42 0 2.04878 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waTAwATAtw ; Alignment reference a 74 122 0 245 151 236 0 248 51 106 c 30 27 0 0 15 8 0 0 51 39 g 33 44 0 2 15 4 0 0 34 29 t 111 55 248 1 67 0 248 0 112 74
br-Z4_rc_shift2 (br-Z4_rc)				; oligos_6nt_mkv3_m9 versus br-Z4_rc; m=1/6; ncol2=8; w=0; offset=2; strand=R; shift=2; score=0.619645; --TAAhYAdT ; cor=; Ncor= a 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 2 0 t 0 0 7 1 0 3 6 0 3 7
br-Z2_rc_shift2 (br-Z2_rc)				; oligos_6nt_mkv3_m9 versus br-Z2_rc; m=2/6; ncol2=7; w=0; offset=2; strand=R; shift=2; score=0.501528; --twaaTAG- ; cor=; Ncor= a 0 0 5 9 12 11 0 21 1 0 c 0 0 4 1 3 3 0 0 0 0 g 0 0 0 3 1 3 0 0 20 0 t 0 0 12 8 5 4 21 0 0 0
abd-A_shift1 (abd-A)				; oligos_6nt_mkv3_m9 versus abd-A; m=3/6; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.48587; -aTAAWT--- ; cor=; Ncor= a 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0
Antp_shift4 (Antp)				; oligos_6nt_mkv3_m9 versus Antp; m=4/6; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.484807; ----mATAAw ; cor=; Ncor= a 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 18 0 0 10.5
zen_shift0 (zen)				; oligos_6nt_mkv3_m9 versus zen; m=5/6; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.482115; AATwAA---- ; cor=; Ncor= a 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0.541667 0 1.08333 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 t 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0
vvl_rc_shift2 (vvl_rc)				; oligos_6nt_mkv3_m9 versus vvl_rc; m=6/6; ncol2=6; w=0; offset=2; strand=R; shift=2; score=0.443719; --TgmwTA-- ; cor=; Ncor= a 0 0 0 2.36364 8.27273 5.90909 0 13 0 0 c 0 0 0 1.18182 4.72727 0 0 0 0 0 g 0 0 0 8.27273 0 0 1.18182 0 0 0 t 0 0 13 1.18182 0 7.09091 11.8182 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; aaAATGAAar ; Alignment reference a 50 50 111 111 0 0 110 111 50 37 c 15 21 0 0 0 0 0 0 21 17 g 24 22 0 0 0 111 0 0 19 31 t 22 18 0 0 111 0 1 0 21 26
en_rc_shift1 (en_rc)				; oligos_6nt_mkv3_m6 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.60802; -yAATtAah- ; cor=; Ncor= a 0 10.125 58.5 57.375 1.125 5.625 51.75 31.5 18 0 c 0 31.5 3.375 2.25 0 14.625 4.5 11.25 21.375 0 g 0 1.125 0 1.125 1.125 6.75 6.75 12.375 0 0 t 0 20.25 1.125 2.25 60.75 36 0 7.875 23.625 0
sd_rc_shift1 (sd_rc)				; oligos_6nt_mkv3_m6 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.526432; -mAAwGdAAT ; cor=; Ncor= a 0 8 16 14 7 0 9 13 15 1 c 0 7 0 0 0 4 0 3 0 1 g 0 4 0 1 2 14 5 0 3 1 t 0 0 3 4 10 1 5 3 1 16
zen_shift2 (zen)				; oligos_6nt_mkv3_m6 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484521; --AATwAA-- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 c 0 0 0.541667 0 1.08333 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 t 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0
ap_shift2 (ap)				; oligos_6nt_mkv3_m6 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.421541; --AAThAt-- ; cor=; Ncor= a 0 0 14 14 0 5 13 2 0 0 c 0 0 0 0 1 4 0 1 0 0 g 0 0 0 0 1 1 1 3 0 0 t 0 0 0 0 12 4 0 8 0 0