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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4)
; oligos_6-8nt_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; rgaGAGcGAGAgr ; Alignment reference a 187 100 341 11 483 23 129 13 478 36 377 93 195 c 113 94 71 7 9 11 347 7 14 29 64 87 123 g 141 280 74 497 21 479 30 496 28 423 54 268 145 t 85 52 40 11 13 13 20 10 6 38 31 78 63

Trl_rc_shift0 (Trl_rc)
; oligos_6-8nt_m4 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.746623; agaGaGAGmrmaA ; cor=; Ncor= a 42 17 46 7 50 11 62 0 40 26 30 41 57 c 14 9 6 1 9 8 11 5 27 10 24 13 0 g 3 47 16 56 12 56 0 72 3 41 19 8 10 t 18 4 9 13 6 2 4 0 7 0 4 15 10

One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m1_shift1 (positions_6-8nt_m1)
; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -wyATTTTCww ; Alignment reference a 0 76 51 279 0 11 7 4 0 87 80 c 0 61 76 0 0 0 1 0 279 61 61 g 0 56 57 0 0 0 1 0 0 58 57 t 0 86 95 0 279 268 270 275 0 73 81

dl_shift0 (dl)
; positions_6-8nt_m1 versus dl; m=1/1; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.654598; kkrwTTTyCym ; cor=; Ncor= a 0 2 20 13 2 0 2 0 1 0 12 c 1 3 0 4 0 1 4 21 36 16 17 g 22 21 18 3 2 3 1 0 0 9 8 t 15 12 0 18 34 34 31 17 1 13 1

One-to-n matrix alignment; reference matrix: positions_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)
; positions_6-8nt_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; ggCGGCGChs ; Alignment reference a 54 38 0 0 0 0 0 0 62 43 c 52 41 235 0 0 235 0 235 68 67 g 86 104 0 235 235 0 235 0 42 82 t 43 52 0 0 0 0 0 0 63 43

brk_rc_shift2 (brk_rc)
; positions_6-8nt_m4 versus brk_rc; m=1/1; ncol2=7; w=0; offset=2; strand=R; shift=2; score=0.631842; --yGGCGCy- ; cor=; Ncor= a 0 0 0 0 0 1.1 1.1 0 0 0 c 0 0 5.5 0 0 9.9 0 8.8 6.6 0 g 0 0 0 11 11 0 9.9 0 0 0 t 0 0 5.5 0 0 0 0 2.2 4.4 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; positions_6-8nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; ktAGATTAth ; Alignment reference a 37 37 144 0 146 7 6 154 23 53 c 35 16 4 6 0 7 1 1 37 40 g 39 33 6 112 7 12 0 1 24 23 t 45 70 2 38 3 130 149 0 72 40

bcd_shift1 (bcd)
; positions_6-8nt_m3 versus bcd; m=1/5; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.624778; -vrGMTTAd- ; cor=; Ncor= a 0 13.2708 15.3125 5.10417 33.6875 0 1.02083 36.75 16.3333 0 c 0 18.375 2.04167 0 15.3125 0 2.04167 1.02083 2.04167 0 g 0 12.25 29.6042 42.875 0 0 0 3.0625 18.375 0 t 0 5.10417 2.04167 1.02083 0 49 45.9375 8.16667 12.25 0

Antp_rc_shift4 (Antp_rc)
; positions_6-8nt_m3 versus Antp_rc; m=2/5; ncol2=6; w=0; offset=4; strand=R; shift=4; score=0.505137; ----wTTATk ; cor=; Ncor= a 0 0 0 0 10.5 0 0 18 0 0 c 0 0 0 0 0 0 1.5 0 0 3 g 0 0 0 0 0 0 0 0 0 4.5 t 0 0 0 0 7.5 18 16.5 0 18 10.5

abd-A_rc_shift3 (abd-A_rc)
; positions_6-8nt_m3 versus abd-A_rc; m=3/5; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.454221; ---AWTTAt- ; cor=; Ncor= a 0 0 0 35.122 30.7317 4.39024 0 40.6098 7.68293 0 c 0 0 0 6.58537 0 0 3.29268 1.09756 4.39024 0 g 0 0 0 3.29268 0 0 1.09756 3.29268 5.4878 0 t 0 0 0 0 14.2683 40.6098 40.6098 0 27.439 0

Ubx_shift2 (Ubx)
; positions_6-8nt_m3 versus Ubx; m=4/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.446863; --mmATTA-- ; cor=; Ncor= a 0 0 21 42 67.6667 3.5 1.16667 58.3333 0 0 c 0 0 36.1667 17.5 2.33333 0 4.66667 2.33333 0 0 g 0 0 3.5 3.5 0 0 0 0 0 0 t 0 0 9.33333 7 0 66.5 64.1667 9.33333 0 0

prd_rc_shift4 (prd_rc)
; positions_6-8nt_m3 versus prd_rc; m=5/5; ncol2=8; w=0; offset=4; strand=R; shift=4; score= 0.401; ----wTTrtC ; cor=; Ncor= a 0 0 0 0 6 0 0 7 2 1 c 0 0 0 0 0 0 0 0 1 9 g 0 0 0 0 2 0 1 3 2 1 t 0 0 0 0 3 11 10 1 6 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=17; shift=0; ncol=17; tcyCTCTCyCTCTCccy ; Alignment reference a 41 24 9 6 14 7 12 4 12 11 14 6 16 6 27 28 28 c 61 138 144 215 16 225 8 220 137 212 17 220 4 206 144 138 66 g 58 45 32 16 24 8 13 14 31 10 23 8 19 25 19 44 47 t 92 45 67 15 198 12 219 14 72 19 198 18 213 15 62 42 111

Trl_shift0 (Trl)
; dyads_m2 versus Trl; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.615738; TtkykCTCtCtct---- ; cor=; Ncor= a 10 15 4 0 7 0 4 2 6 13 9 4 18 0 0 0 0 c 10 8 19 41 3 72 0 56 12 56 16 47 3 0 0 0 0 g 0 13 24 10 27 5 11 8 9 1 6 9 14 0 0 0 0 t 57 41 30 26 40 0 62 11 50 7 46 17 42 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m6_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m6_shift0 (positions_6-8nt_m6)
; positions_6-8nt_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; arTAAACAAAaa ; Alignment reference a 142 141 61 384 385 389 34 390 386 376 168 172 c 90 78 38 17 16 9 345 12 17 15 81 72 g 86 113 17 5 5 11 8 7 6 12 66 84 t 99 85 301 11 11 8 30 8 8 14 102 89

hb_shift0 (hb)
; positions_6-8nt_m6 versus hb; m=1/3; ncol2=9; w=0; offset=0; strand=D; shift=0; score=0.584528; mayAAAAAa--- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0

zen_shift0 (zen)
; positions_6-8nt_m6 versus zen; m=2/3; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.414317; AATwAA------ ; cor=; Ncor= a 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 0 c 0.541667 0 1.08333 0 0 0 0 0 0 0 0 0 g 0 0 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 0 0

pan_shift4 (pan)
; positions_6-8nt_m6 versus pan; m=3/3; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.412932; ----WtCAAA-- ; cor=; Ncor= a 0 0 0 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 c 0 0 0 0 0 4.16 20.8 0 1.04 0 0 0 g 0 0 0 0 0 0 1.04 0 0 0 0 0 t 0 0 0 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m8_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATAAATAwww ; Alignment reference a 232 183 433 17 573 471 548 10 575 267 221 205 c 94 108 38 12 15 47 23 22 16 105 105 119 g 123 109 76 24 10 28 29 17 16 81 117 93 t 176 225 78 572 27 79 25 576 18 172 182 208

br-Z4_rc_shift3 (br-Z4_rc)
; oligos_6-8nt_m8 versus br-Z4_rc; m=1/5; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.540736; ---TAAhYAdT- ; cor=; Ncor= a 0 0 0 1 7 8 2 0 8 3 1 0 c 0 0 0 0 0 0 3 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2 0 0 t 0 0 0 7 1 0 3 6 0 3 7 0

Antp_shift5 (Antp)
; oligos_6-8nt_m8 versus Antp; m=2/5; ncol2=6; w=0; offset=5; strand=D; shift=5; score=0.443294; -----mATAAw- ; cor=; Ncor= a 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 18 0 0 10.5 0

zen_shift1 (zen)
; oligos_6-8nt_m8 versus zen; m=3/5; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.436814; -AATwAA----- ; cor=; Ncor= a 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 c 0 0.541667 0 1.08333 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0 0

abd-A_shift2 (abd-A)
; oligos_6-8nt_m8 versus abd-A; m=4/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.426345; --aTAAWT---- ; cor=; Ncor= a 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 0 c 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 0 g 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 0 t 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0 0

br-Z2_rc_shift3 (br-Z2_rc)
; oligos_6-8nt_m8 versus br-Z2_rc; m=5/5; ncol2=7; w=0; offset=3; strand=R; shift=3; score=0.417786; ---twaaTAG-- ; cor=; Ncor= a 0 0 0 5 9 12 11 0 21 1 0 0 c 0 0 0 4 1 3 3 0 0 0 0 0 g 0 0 0 0 3 1 3 0 0 20 0 0 t 0 0 0 12 8 5 4 21 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m7_shift1 (oligos_6-8nt_m7)
; oligos_6-8nt_m7; m=0 (reference); ncol1=11; shift=1; ncol=12; -rwAAACAAAha ; Alignment reference a 0 249 233 703 665 716 5 682 645 688 215 280 c 0 144 158 9 31 24 640 27 42 25 199 146 g 0 198 142 18 24 9 33 21 32 26 144 176 t 0 173 231 34 44 15 86 34 45 25 206 162

br-Z1_shift2 (br-Z1)
; oligos_6-8nt_m7 versus br-Z1; m=1/4; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.513627; --raTaCwAA-- ; cor=; Ncor= a 0 0 10.5882 11.6471 2.11765 11.6471 3.17647 9.52941 15.8824 18 0 0 c 0 0 0 0 0 3.17647 12.7059 1.05882 2.11765 0 0 0 g 0 0 7.41176 3.17647 1.05882 3.17647 2.11765 0 0 0 0 0 t 0 0 0 3.17647 14.8235 0 0 7.41176 0 0 0 0

hb_shift0 (hb)
; oligos_6-8nt_m7 versus hb; m=2/4; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.495667; mayAAAAAa--- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0

pan_shift4 (pan)
; oligos_6-8nt_m7 versus pan; m=3/4; ncol2=6; w=0; offset=3; strand=D; shift=4; score=0.445629; ----WtCAAA-- ; cor=; Ncor= a 0 0 0 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 c 0 0 0 0 0 4.16 20.8 0 1.04 0 0 0 g 0 0 0 0 0 0 1.04 0 0 0 0 0 t 0 0 0 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0

zen_shift4 (zen)
; oligos_6-8nt_m7 versus zen; m=4/4; ncol2=6; w=0; offset=3; strand=D; shift=4; score=0.433024; ----AATwAA-- ; cor=; Ncor= a 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 c 0 0 0 0 0.541667 0 1.08333 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0

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; gsCGCCGCCGcy ; Alignment reference a 132 86 24 27 23 16 19 30 18 39 140 126 c 108 202 523 8 531 544 12 527 548 36 223 218 g 230 173 18 553 20 8 564 22 7 509 128 108 t 137 146 42 19 33 39 12 28 34 23 116 155

brk_shift0 (brk)
; dyads_m4 versus brk; m=1/2; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.49084; 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=0.457286; ---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_6-8nt_m9_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m9_shift1 (oligos_6-8nt_m9)
; oligos_6-8nt_m9; m=0 (reference); ncol1=14; shift=1; ncol=15; -awAAACAACAAAma ; Alignment reference a 0 150 129 275 318 329 26 327 321 38 323 323 275 130 125 c 0 58 64 53 18 16 286 15 14 282 14 19 37 93 66 g 0 84 70 25 14 9 20 12 17 13 19 16 19 65 88 t 0 79 108 18 21 17 39 17 19 38 15 13 40 83 92

hb_shift0 (hb)
; oligos_6-8nt_m9 versus hb; m=1/1; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.400658; mayAAAAAa------ ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 0 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 0 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 0 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)				; positions_6-8nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; ktAGATTAth ; Alignment reference a 37 37 144 0 146 7 6 154 23 53 c 35 16 4 6 0 7 1 1 37 40 g 39 33 6 112 7 12 0 1 24 23 t 45 70 2 38 3 130 149 0 72 40
bcd_shift1 (bcd)				; positions_6-8nt_m3 versus bcd; m=1/5; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.624778; -vrGMTTAd- ; cor=; Ncor= a 0 13.2708 15.3125 5.10417 33.6875 0 1.02083 36.75 16.3333 0 c 0 18.375 2.04167 0 15.3125 0 2.04167 1.02083 2.04167 0 g 0 12.25 29.6042 42.875 0 0 0 3.0625 18.375 0 t 0 5.10417 2.04167 1.02083 0 49 45.9375 8.16667 12.25 0
Antp_rc_shift4 (Antp_rc)				; positions_6-8nt_m3 versus Antp_rc; m=2/5; ncol2=6; w=0; offset=4; strand=R; shift=4; score=0.505137; ----wTTATk ; cor=; Ncor= a 0 0 0 0 10.5 0 0 18 0 0 c 0 0 0 0 0 0 1.5 0 0 3 g 0 0 0 0 0 0 0 0 0 4.5 t 0 0 0 0 7.5 18 16.5 0 18 10.5
abd-A_rc_shift3 (abd-A_rc)				; positions_6-8nt_m3 versus abd-A_rc; m=3/5; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.454221; ---AWTTAt- ; cor=; Ncor= a 0 0 0 35.122 30.7317 4.39024 0 40.6098 7.68293 0 c 0 0 0 6.58537 0 0 3.29268 1.09756 4.39024 0 g 0 0 0 3.29268 0 0 1.09756 3.29268 5.4878 0 t 0 0 0 0 14.2683 40.6098 40.6098 0 27.439 0
Ubx_shift2 (Ubx)				; positions_6-8nt_m3 versus Ubx; m=4/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.446863; --mmATTA-- ; cor=; Ncor= a 0 0 21 42 67.6667 3.5 1.16667 58.3333 0 0 c 0 0 36.1667 17.5 2.33333 0 4.66667 2.33333 0 0 g 0 0 3.5 3.5 0 0 0 0 0 0 t 0 0 9.33333 7 0 66.5 64.1667 9.33333 0 0
prd_rc_shift4 (prd_rc)				; positions_6-8nt_m3 versus prd_rc; m=5/5; ncol2=8; w=0; offset=4; strand=R; shift=4; score= 0.401; ----wTTrtC ; cor=; Ncor= a 0 0 0 0 6 0 0 7 2 1 c 0 0 0 0 0 0 0 0 1 9 g 0 0 0 0 2 0 1 3 2 1 t 0 0 0 0 3 11 10 1 6 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m6_shift0 (positions_6-8nt_m6)				; positions_6-8nt_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; arTAAACAAAaa ; Alignment reference a 142 141 61 384 385 389 34 390 386 376 168 172 c 90 78 38 17 16 9 345 12 17 15 81 72 g 86 113 17 5 5 11 8 7 6 12 66 84 t 99 85 301 11 11 8 30 8 8 14 102 89
hb_shift0 (hb)				; positions_6-8nt_m6 versus hb; m=1/3; ncol2=9; w=0; offset=0; strand=D; shift=0; score=0.584528; mayAAAAAa--- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0
zen_shift0 (zen)				; positions_6-8nt_m6 versus zen; m=2/3; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.414317; AATwAA------ ; cor=; Ncor= a 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 0 c 0.541667 0 1.08333 0 0 0 0 0 0 0 0 0 g 0 0 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 0 0
pan_shift4 (pan)				; positions_6-8nt_m6 versus pan; m=3/3; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.412932; ----WtCAAA-- ; cor=; Ncor= a 0 0 0 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 c 0 0 0 0 0 4.16 20.8 0 1.04 0 0 0 g 0 0 0 0 0 0 1.04 0 0 0 0 0 t 0 0 0 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)				; oligos_6-8nt_m8; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATAAATAwww ; Alignment reference a 232 183 433 17 573 471 548 10 575 267 221 205 c 94 108 38 12 15 47 23 22 16 105 105 119 g 123 109 76 24 10 28 29 17 16 81 117 93 t 176 225 78 572 27 79 25 576 18 172 182 208
br-Z4_rc_shift3 (br-Z4_rc)				; oligos_6-8nt_m8 versus br-Z4_rc; m=1/5; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.540736; ---TAAhYAdT- ; cor=; Ncor= a 0 0 0 1 7 8 2 0 8 3 1 0 c 0 0 0 0 0 0 3 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2 0 0 t 0 0 0 7 1 0 3 6 0 3 7 0
Antp_shift5 (Antp)				; oligos_6-8nt_m8 versus Antp; m=2/5; ncol2=6; w=0; offset=5; strand=D; shift=5; score=0.443294; -----mATAAw- ; cor=; Ncor= a 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 18 0 0 10.5 0
zen_shift1 (zen)				; oligos_6-8nt_m8 versus zen; m=3/5; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.436814; -AATwAA----- ; cor=; Ncor= a 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 c 0 0.541667 0 1.08333 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0 0
abd-A_shift2 (abd-A)				; oligos_6-8nt_m8 versus abd-A; m=4/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.426345; --aTAAWT---- ; cor=; Ncor= a 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 0 c 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 0 g 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 0 t 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0 0
br-Z2_rc_shift3 (br-Z2_rc)				; oligos_6-8nt_m8 versus br-Z2_rc; m=5/5; ncol2=7; w=0; offset=3; strand=R; shift=3; score=0.417786; ---twaaTAG-- ; cor=; Ncor= a 0 0 0 5 9 12 11 0 21 1 0 0 c 0 0 0 4 1 3 3 0 0 0 0 0 g 0 0 0 0 3 1 3 0 0 20 0 0 t 0 0 0 12 8 5 4 21 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m7_shift1 (oligos_6-8nt_m7)				; oligos_6-8nt_m7; m=0 (reference); ncol1=11; shift=1; ncol=12; -rwAAACAAAha ; Alignment reference a 0 249 233 703 665 716 5 682 645 688 215 280 c 0 144 158 9 31 24 640 27 42 25 199 146 g 0 198 142 18 24 9 33 21 32 26 144 176 t 0 173 231 34 44 15 86 34 45 25 206 162
br-Z1_shift2 (br-Z1)				; oligos_6-8nt_m7 versus br-Z1; m=1/4; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.513627; --raTaCwAA-- ; cor=; Ncor= a 0 0 10.5882 11.6471 2.11765 11.6471 3.17647 9.52941 15.8824 18 0 0 c 0 0 0 0 0 3.17647 12.7059 1.05882 2.11765 0 0 0 g 0 0 7.41176 3.17647 1.05882 3.17647 2.11765 0 0 0 0 0 t 0 0 0 3.17647 14.8235 0 0 7.41176 0 0 0 0
hb_shift0 (hb)				; oligos_6-8nt_m7 versus hb; m=2/4; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.495667; mayAAAAAa--- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0
pan_shift4 (pan)				; oligos_6-8nt_m7 versus pan; m=3/4; ncol2=6; w=0; offset=3; strand=D; shift=4; score=0.445629; ----WtCAAA-- ; cor=; Ncor= a 0 0 0 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 c 0 0 0 0 0 4.16 20.8 0 1.04 0 0 0 g 0 0 0 0 0 0 1.04 0 0 0 0 0 t 0 0 0 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0
zen_shift4 (zen)				; oligos_6-8nt_m7 versus zen; m=4/4; ncol2=6; w=0; offset=3; strand=D; shift=4; score=0.433024; ----AATwAA-- ; cor=; Ncor= a 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 c 0 0 0 0 0.541667 0 1.08333 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0