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.2026-01-25.180941_2026-01-25.180941_K9UVGH/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.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m7_shift0 (oligos_6-8nt_m7)
; oligos_6-8nt_m7; m=0 (reference); ncol1=16; shift=0; ncol=16; gaGAGAGAGmGAGaga ; Alignment reference a 221 629 103 976 66 983 52 998 58 517 58 956 71 823 166 594 c 166 228 76 97 43 124 27 83 26 508 58 103 53 199 164 248 g 738 225 1005 83 1096 54 1123 65 1119 117 1086 119 1072 115 776 261 t 112 155 53 81 32 76 35 91 34 95 35 59 41 100 131 134

Trl_rc_shift1 (Trl_rc)
; oligos_6-8nt_m7 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.67147; -agaGaGAGmrmaA-- ; cor=; Ncor= a 0 42 17 46 7 50 11 62 0 40 26 30 41 57 0 0 c 0 14 9 6 1 9 8 11 5 27 10 24 13 0 0 0 g 0 3 47 16 56 12 56 0 72 3 41 19 8 10 0 0 t 0 18 4 9 13 6 2 4 0 7 0 4 15 10 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)
; oligos_6-8nt_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waAATGAAaw ; Alignment reference a 145 194 429 429 0 0 429 429 202 160 c 76 70 0 0 0 0 0 0 64 68 g 93 92 0 0 0 429 0 0 62 75 t 115 73 0 0 429 0 0 0 101 126

en_rc_shift1 (en_rc)
; oligos_6-8nt_m9 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.607235; -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_6-8nt_m9 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.534902; -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_6-8nt_m9 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484903; --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_6-8nt_m9 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.422116; --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: positions_6-8nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m1_shift0 (positions_6-8nt_m1)
; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; kyCGCCGCyg ; Alignment reference a 107 85 0 1 0 0 0 0 88 108 c 88 148 448 4 448 448 1 448 166 110 g 137 102 0 434 0 0 443 0 68 137 t 116 113 0 9 0 0 4 0 126 93

brk_shift0 (brk)
; positions_6-8nt_m1 versus brk; m=1/2; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.580827; rGCGCCr--- ; cor=; Ncor= a 4.4 2.2 0 0 0 0 5.5 0 0 0 c 0 0 9.9 0 11 11 0 0 0 0 g 6.6 8.8 0 9.9 0 0 5.5 0 0 0 t 0 0 1.1 1.1 0 0 0 0 0 0

Mad_shift2 (Mad)
; positions_6-8nt_m1 versus Mad; m=2/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.472012; --CGmsrCgm ; cor=; Ncor= a 0 0 3 1 7 1 6 2 3 6 c 0 0 15 0 11 7 3 14 1 8 g 0 0 1 17 1 8 10 0 12 2 t 0 0 0 1 0 3 0 3 3 3

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=20; shift=0; ncol=20; tctCTCTCTCTCTCTCTCtc ; Alignment reference a 147 126 110 69 83 58 83 52 77 38 89 43 95 40 102 40 111 49 172 114 c 288 819 185 1046 137 1080 140 1116 114 1144 91 1135 101 1130 88 1123 108 1068 219 817 g 259 146 212 84 186 81 180 60 137 47 135 40 163 44 149 48 137 76 208 164 t 614 217 801 109 902 89 905 80 980 79 993 90 949 94 969 97 952 115 709 213

Trl_shift0 (Trl)
; dyads_m2 versus Trl; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.553802; TtkykCTCtCtct------- ; cor=; Ncor= a 10 15 4 0 7 0 4 2 6 13 9 4 18 0 0 0 0 0 0 0 c 10 8 19 41 3 72 0 56 12 56 16 47 3 0 0 0 0 0 0 0 g 0 13 24 10 27 5 11 8 9 1 6 9 14 0 0 0 0 0 0 0 t 57 41 30 26 40 0 62 11 50 7 46 17 42 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift0 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; wwTTATTTAAww ; Alignment reference a 372 298 90 45 858 52 36 56 864 819 335 277 c 118 138 29 23 18 22 14 23 37 34 157 146 g 166 145 27 35 52 15 25 27 25 25 143 144 t 329 404 839 882 57 896 910 879 59 107 350 418

br-Z4_shift1 (br-Z4)
; dyads_m10 versus br-Z4; m=1/7; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.527905; -AhTRdTTA--- ; cor=; Ncor= a 0 7 3 0 6 3 0 1 7 0 0 0 c 0 0 2 0 0 0 0 0 0 0 0 0 g 0 0 0 0 2 3 0 0 0 0 0 0 t 0 1 3 8 0 2 8 7 1 0 0 0

hb_rc_shift2 (hb_rc)
; dyads_m10 versus hb_rc; m=2/7; ncol2=9; w=0; offset=2; strand=R; shift=2; score=0.526578; --tTTTTTrtk- ; cor=; Ncor= a 0 0 15.1456 0 1.00971 0 1.00971 2.01942 62.6019 23.2233 3.02913 0 c 0 0 12.1165 0 4.03883 0 0 4.03883 11.1068 17.165 21.2039 0 g 0 0 8.07767 1.00971 1.00971 0 1.00971 1.00971 29.2816 16.1553 49.4757 0 t 0 0 68.6602 102.99 97.9417 104 101.981 96.932 1.00971 47.4563 30.2913 0

Antp_rc_shift1 (Antp_rc)
; dyads_m10 versus Antp_rc; m=3/7; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.469918; -wTTATk----- ; cor=; Ncor= a 0 10.5 0 0 18 0 0 0 0 0 0 0 c 0 0 0 1.5 0 0 3 0 0 0 0 0 g 0 0 0 0 0 0 4.5 0 0 0 0 0 t 0 7.5 18 16.5 0 18 10.5 0 0 0 0 0

zen_rc_shift1 (zen_rc)
; dyads_m10 versus zen_rc; m=4/7; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.452011; -TTwATT----- ; cor=; Ncor= a 0 0 0 4.33333 11.9167 1.08333 0.541667 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 1.08333 0 0.541667 0 0 0 0 0 t 0 13 13 8.66667 0 11.9167 11.9167 0 0 0 0 0

ap_rc_shift1 (ap_rc)
; dyads_m10 versus ap_rc; m=5/7; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.445503; -aTdATT----- ; cor=; Ncor= a 0 8 0 4 12 0 0 0 0 0 0 0 c 0 3 1 1 1 0 0 0 0 0 0 0 g 0 1 0 4 1 0 0 0 0 0 0 0 t 0 2 13 5 0 14 14 0 0 0 0 0

abd-A_rc_shift0 (abd-A_rc)
; dyads_m10 versus abd-A_rc; m=6/7; ncol2=6; w=0; offset=0; strand=R; shift=0; score=0.437727; AWTTAt------ ; cor=; Ncor= a 35.122 30.7317 4.39024 0 40.6098 7.68293 0 0 0 0 0 0 c 6.58537 0 0 3.29268 1.09756 4.39024 0 0 0 0 0 0 g 3.29268 0 0 1.09756 3.29268 5.4878 0 0 0 0 0 0 t 0 14.2683 40.6098 40.6098 0 27.439 0 0 0 0 0 0

ftz_rc_shift5 (ftz_rc)
; dyads_m10 versus ftz_rc; m=7/7; ncol2=8; w=0; offset=5; strand=R; shift=5; score=0.407677; -----kyTaATk ; cor=; Ncor= a 0 0 0 0 0 7 6 0 44 64 2 7 c 0 0 0 0 0 14 18 1 3 1 0 0 g 0 0 0 0 0 17 7 3 4 1 1 29 t 0 0 0 0 0 28 35 62 15 0 63 30

One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift0 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=21; shift=0; ncol=21; agrGAGAGaGAGAGAGAGAga ; Alignment reference a 437 175 436 80 707 66 713 59 476 62 715 49 717 49 692 47 686 59 637 141 448 c 154 129 110 57 89 27 87 29 142 48 94 34 84 39 91 39 120 62 130 107 196 g 206 540 293 761 75 807 57 819 227 797 73 824 72 820 100 821 70 783 108 616 207 t 137 90 95 36 63 34 77 27 89 27 52 27 61 26 51 27 58 30 59 70 83

Trl_rc_shift8 (Trl_rc)
; dyads_m7 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=8; strand=R; shift=8; score=0.521186; --------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 c 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 3 47 16 56 12 56 0 72 3 41 19 8 10 t 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: oligos_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3)
; oligos_6-8nt_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; wygaATCGATtcgw ; Alignment reference a 150 135 100 346 500 15 17 13 517 41 114 79 141 169 c 131 157 107 66 18 18 525 10 18 7 42 283 129 120 g 119 130 283 42 7 18 12 527 18 15 67 107 160 129 t 167 145 77 113 42 516 13 17 14 504 344 98 137 149

Dref_shift2 (Dref)
; oligos_6-8nt_m3 versus Dref; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.508009; --aTAwCGATAr-- ; cor=; Ncor= a 0 0 6.66667 1.11111 7.77778 3.33333 0 1.11111 10 0 7.77778 3.33333 0 0 c 0 0 1.11111 0 1.11111 0 10 0 0 0 1.11111 0 0 0 g 0 0 0 1.11111 0 0 0 8.88889 0 0 1.11111 6.66667 0 0 t 0 0 2.22222 7.77778 1.11111 6.66667 0 0 0 10 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m6; m=0 (reference); ncol1=13; shift=0; ncol=13; wwaATAAATAAww ; Alignment reference a 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 205 174 85 76 46 25 47 38 47 22 66 185 183 g 191 175 100 91 18 20 34 22 30 25 55 181 171 t 373 317 200 160 1021 64 90 60 1037 47 156 322 394

hb_shift2 (hb)
; oligos_6-8nt_m6 versus hb; m=1/6; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.502525; --mayAAAAAa-- ; cor=; Ncor= a 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 c 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 g 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 t 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0

br-Z4_rc_shift4 (br-Z4_rc)
; oligos_6-8nt_m6 versus br-Z4_rc; m=2/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.490747; ----TAAhYAdT- ; cor=; Ncor= a 0 0 0 0 1 7 8 2 0 8 3 1 0 c 0 0 0 0 0 0 0 3 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 0 0 t 0 0 0 0 7 1 0 3 6 0 3 7 0

zen_shift2 (zen)
; oligos_6-8nt_m6 versus zen; m=3/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.441955; --AATwAA----- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 c 0 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 0 t 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0 0

Dfd_rc_shift3 (Dfd_rc)
; oligos_6-8nt_m6 versus Dfd_rc; m=4/6; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.436099; ---rymATTAA-- ; cor=; Ncor= a 0 0 0 9 2 10 16 0 0 15 11 0 0 c 0 0 0 2 6 5 0 0 0 0 2 0 0 g 0 0 0 5 0 0 0 1 1 0 2 0 0 t 0 0 0 0 8 1 0 15 15 1 1 0 0

Antp_shift6 (Antp)
; oligos_6-8nt_m6 versus Antp; m=5/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.43327; ------mATAAw- ; cor=; Ncor= a 0 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 0 18 0 0 10.5 0

ap_shift6 (ap)
; oligos_6-8nt_m6 versus ap; m=6/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.400727; ------AAThAt- ; cor=; Ncor= a 0 0 0 0 0 0 14 14 0 5 13 2 0 c 0 0 0 0 0 0 0 0 1 4 0 1 0 g 0 0 0 0 0 0 0 0 1 1 1 3 0 t 0 0 0 0 0 0 0 0 12 4 0 8 0

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=12; shift=0; ncol=12; cvCACTCACccw ; Alignment reference a 116 153 37 516 8 44 7 512 11 93 146 166 c 270 157 494 19 574 31 550 11 554 345 226 145 g 74 151 29 20 4 15 7 22 13 38 103 116 t 134 133 34 39 8 504 30 49 16 118 119 167

z_rc_shift2 (z_rc)
; oligos_6-8nt_m4 versus z_rc; m=1/1; ncol2=6; w=0; offset=2; strand=R; shift=2; score=0.480791; --CaCTCA---- ; cor=; Ncor= a 0 0 5.12195 24.5854 0 0 0 29.7073 0 0 0 0 c 0 0 30.7317 0 42 0 42 3.07317 0 0 0 0 g 0 0 5.12195 10.2439 0 0 0 7.17073 0 0 0 0 t 0 0 1.02439 7.17073 0 42 0 2.04878 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5)
; oligos_6-8nt_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; aacAAACAACAAAaa ; Alignment reference a 188 200 106 394 423 436 54 451 441 49 452 444 399 196 229 c 121 98 287 61 31 24 388 17 15 410 17 23 56 107 85 g 90 123 50 26 18 23 19 10 28 19 15 17 20 82 83 t 101 79 57 19 28 17 39 22 16 22 16 16 25 115 103

hb_shift0 (hb)
; oligos_6-8nt_m5 versus hb; m=1/1; ncol2=9; w=0; offset=0; strand=D; shift=0; score=0.442201; 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

One-to-n matrix alignment; reference matrix: dyads_m9_shift3 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift3 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=10; shift=3; ncol=13; ---ykCTTTTCyy ; Alignment reference a 0 0 0 92 123 0 0 0 9 1 0 102 117 c 0 0 0 168 84 511 0 0 0 0 511 145 140 g 0 0 0 83 166 0 0 0 0 0 0 123 116 t 0 0 0 168 138 0 511 511 502 510 0 141 138

Kr_rc_shift0 (Kr_rc)
; dyads_m9 versus Kr_rc; m=1/1; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.40095; taACCCtTTt--- ; cor=; Ncor= a 5 30 40 1 1 2 5 2 1 5 0 0 0 c 7 4 2 34 39 41 7 2 3 9 0 0 0 g 6 5 0 4 0 0 10 8 3 7 0 0 0 t 27 6 3 6 5 2 23 33 38 24 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)				; oligos_6-8nt_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waAATGAAaw ; Alignment reference a 145 194 429 429 0 0 429 429 202 160 c 76 70 0 0 0 0 0 0 64 68 g 93 92 0 0 0 429 0 0 62 75 t 115 73 0 0 429 0 0 0 101 126
en_rc_shift1 (en_rc)				; oligos_6-8nt_m9 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.607235; -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_6-8nt_m9 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.534902; -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_6-8nt_m9 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484903; --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_6-8nt_m9 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.422116; --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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m10_shift0 (dyads_m10)				; dyads_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; wwTTATTTAAww ; Alignment reference a 372 298 90 45 858 52 36 56 864 819 335 277 c 118 138 29 23 18 22 14 23 37 34 157 146 g 166 145 27 35 52 15 25 27 25 25 143 144 t 329 404 839 882 57 896 910 879 59 107 350 418
br-Z4_shift1 (br-Z4)				; dyads_m10 versus br-Z4; m=1/7; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.527905; -AhTRdTTA--- ; cor=; Ncor= a 0 7 3 0 6 3 0 1 7 0 0 0 c 0 0 2 0 0 0 0 0 0 0 0 0 g 0 0 0 0 2 3 0 0 0 0 0 0 t 0 1 3 8 0 2 8 7 1 0 0 0
hb_rc_shift2 (hb_rc)				; dyads_m10 versus hb_rc; m=2/7; ncol2=9; w=0; offset=2; strand=R; shift=2; score=0.526578; --tTTTTTrtk- ; cor=; Ncor= a 0 0 15.1456 0 1.00971 0 1.00971 2.01942 62.6019 23.2233 3.02913 0 c 0 0 12.1165 0 4.03883 0 0 4.03883 11.1068 17.165 21.2039 0 g 0 0 8.07767 1.00971 1.00971 0 1.00971 1.00971 29.2816 16.1553 49.4757 0 t 0 0 68.6602 102.99 97.9417 104 101.981 96.932 1.00971 47.4563 30.2913 0
Antp_rc_shift1 (Antp_rc)				; dyads_m10 versus Antp_rc; m=3/7; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.469918; -wTTATk----- ; cor=; Ncor= a 0 10.5 0 0 18 0 0 0 0 0 0 0 c 0 0 0 1.5 0 0 3 0 0 0 0 0 g 0 0 0 0 0 0 4.5 0 0 0 0 0 t 0 7.5 18 16.5 0 18 10.5 0 0 0 0 0
zen_rc_shift1 (zen_rc)				; dyads_m10 versus zen_rc; m=4/7; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.452011; -TTwATT----- ; cor=; Ncor= a 0 0 0 4.33333 11.9167 1.08333 0.541667 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 1.08333 0 0.541667 0 0 0 0 0 t 0 13 13 8.66667 0 11.9167 11.9167 0 0 0 0 0
ap_rc_shift1 (ap_rc)				; dyads_m10 versus ap_rc; m=5/7; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.445503; -aTdATT----- ; cor=; Ncor= a 0 8 0 4 12 0 0 0 0 0 0 0 c 0 3 1 1 1 0 0 0 0 0 0 0 g 0 1 0 4 1 0 0 0 0 0 0 0 t 0 2 13 5 0 14 14 0 0 0 0 0
abd-A_rc_shift0 (abd-A_rc)				; dyads_m10 versus abd-A_rc; m=6/7; ncol2=6; w=0; offset=0; strand=R; shift=0; score=0.437727; AWTTAt------ ; cor=; Ncor= a 35.122 30.7317 4.39024 0 40.6098 7.68293 0 0 0 0 0 0 c 6.58537 0 0 3.29268 1.09756 4.39024 0 0 0 0 0 0 g 3.29268 0 0 1.09756 3.29268 5.4878 0 0 0 0 0 0 t 0 14.2683 40.6098 40.6098 0 27.439 0 0 0 0 0 0
ftz_rc_shift5 (ftz_rc)				; dyads_m10 versus ftz_rc; m=7/7; ncol2=8; w=0; offset=5; strand=R; shift=5; score=0.407677; -----kyTaATk ; cor=; Ncor= a 0 0 0 0 0 7 6 0 44 64 2 7 c 0 0 0 0 0 14 18 1 3 1 0 0 g 0 0 0 0 0 17 7 3 4 1 1 29 t 0 0 0 0 0 28 35 62 15 0 63 30

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)				; oligos_6-8nt_m6; m=0 (reference); ncol1=13; shift=0; ncol=13; wwaATAAATAAww ; Alignment reference a 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 205 174 85 76 46 25 47 38 47 22 66 185 183 g 191 175 100 91 18 20 34 22 30 25 55 181 171 t 373 317 200 160 1021 64 90 60 1037 47 156 322 394
hb_shift2 (hb)				; oligos_6-8nt_m6 versus hb; m=1/6; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.502525; --mayAAAAAa-- ; cor=; Ncor= a 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 c 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 g 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 t 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0
br-Z4_rc_shift4 (br-Z4_rc)				; oligos_6-8nt_m6 versus br-Z4_rc; m=2/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.490747; ----TAAhYAdT- ; cor=; Ncor= a 0 0 0 0 1 7 8 2 0 8 3 1 0 c 0 0 0 0 0 0 0 3 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 0 0 t 0 0 0 0 7 1 0 3 6 0 3 7 0
zen_shift2 (zen)				; oligos_6-8nt_m6 versus zen; m=3/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.441955; --AATwAA----- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 c 0 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 0 t 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0 0
Dfd_rc_shift3 (Dfd_rc)				; oligos_6-8nt_m6 versus Dfd_rc; m=4/6; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.436099; ---rymATTAA-- ; cor=; Ncor= a 0 0 0 9 2 10 16 0 0 15 11 0 0 c 0 0 0 2 6 5 0 0 0 0 2 0 0 g 0 0 0 5 0 0 0 1 1 0 2 0 0 t 0 0 0 0 8 1 0 15 15 1 1 0 0
Antp_shift6 (Antp)				; oligos_6-8nt_m6 versus Antp; m=5/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.43327; ------mATAAw- ; cor=; Ncor= a 0 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 0 18 0 0 10.5 0
ap_shift6 (ap)				; oligos_6-8nt_m6 versus ap; m=6/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.400727; ------AAThAt- ; cor=; Ncor= a 0 0 0 0 0 0 14 14 0 5 13 2 0 c 0 0 0 0 0 0 0 0 1 4 0 1 0 g 0 0 0 0 0 0 0 0 1 1 1 3 0 t 0 0 0 0 0 0 0 0 12 4 0 8 0