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.2026-01-25.180830_2026-01-25.180830_qbHDLg/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.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift0 ; 5 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=10; shift=0; ncol=10; waAATGAAaw ; Alignment reference a 747 1105 2596 2596 0 0 2579 2596 1120 908 c 538 506 0 0 0 0 0 0 401 416 g 598 535 0 0 0 2596 0 0 437 491 t 713 450 0 0 2596 0 17 0 638 781

en_rc_shift1 (en_rc)
; oligos_6-8nt_m7 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.610809; -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_m7 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.533446; -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_m7 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484627; --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_m7 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.421699; --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: oligos_6-8nt_m8_shift0 ; 2 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=11; shift=0; ncol=11; arTAGGAAGwr ; Alignment reference a 1613 1509 422 4272 283 274 4456 4610 261 1534 1315 c 1026 1014 477 210 173 174 206 74 142 1092 1105 g 1163 1321 558 234 4248 4331 130 124 4291 972 1399 t 1120 1078 3465 206 218 143 130 114 228 1324 1103

Eip74EF_shift2 (Eip74EF)
; oligos_6-8nt_m8 versus Eip74EF; m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.589285; --mMGGAAkT- ; cor=; Ncor= a 0 0 3 6 1 0 8 8 1 1 0 c 0 0 5 2 0 1 0 0 0 1 0 g 0 0 0 0 7 7 0 0 5 0 0 t 0 0 0 0 0 0 0 0 2 6 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=10; shift=0; ncol=10; ryACTCAChc ; Alignment reference a 697 469 2269 0 10 104 2121 0 680 544 c 513 822 12 2285 25 2062 75 2253 605 793 g 595 268 0 4 2 5 9 7 347 405 t 484 730 8 0 2252 118 84 29 657 547

z_rc_shift1 (z_rc)
; oligos_6-8nt_m5 versus z_rc; m=1/1; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.547185; -CaCTCA--- ; cor=; Ncor= a 0 5.12195 24.5854 0 0 0 29.7073 0 0 0 c 0 30.7317 0 42 0 42 3.07317 0 0 0 g 0 5.12195 10.2439 0 0 0 7.17073 0 0 0 t 0 1.02439 7.17073 0 42 0 2.04878 0 0 0

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=10; shift=0; ncol=10; ygCCGCCGmc ; Alignment reference a 516 670 7 1 41 29 3 4 730 692 c 903 398 2819 2827 22 2775 2826 0 961 1043 g 624 1071 0 2 2713 1 2 2816 573 474 t 789 693 6 2 56 27 1 12 568 623

brk_shift1 (brk)
; dyads_m7 versus brk; m=1/1; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.496144; -rGCGCCr-- ; cor=; Ncor= a 0 4.4 2.2 0 0 0 0 5.5 0 0 c 0 0 0 9.9 0 11 11 0 0 0 g 0 6.6 8.8 0 9.9 0 0 5.5 0 0 t 0 0 0 1.1 1.1 0 0 0 0 0

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=10; shift=0; ncol=10; atAGATACww ; Alignment reference a 1239 519 3086 11 2979 0 3234 30 1203 884 c 563 739 96 127 61 1 19 2879 573 801 g 810 569 62 2371 119 42 0 96 585 661 t 647 1432 15 750 100 3216 6 254 898 913

br-Z1_shift3 (br-Z1)
; oligos_6-8nt_m3 versus br-Z1; m=1/1; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.455515; ---raTaCwA ; cor=; Ncor= a 0 0 0 10.5882 11.6471 2.11765 11.6471 3.17647 9.52941 15.8824 c 0 0 0 0 0 0 3.17647 12.7059 1.05882 2.11765 g 0 0 0 7.41176 3.17647 1.05882 3.17647 2.11765 0 0 t 0 0 0 0 3.17647 14.8235 0 0 7.41176 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m10_shift0 (positions_6-8nt_m10)
; positions_6-8nt_m10; m=0 (reference); ncol1=15; shift=0; ncol=15; waaAAATAAAAcmaa ; Alignment reference a 1966 2098 3639 5182 5164 5108 553 5165 5002 5022 4826 1350 1570 2199 2346 c 1099 1015 593 145 159 187 395 152 196 188 258 2773 2264 1095 982 g 1069 1166 563 109 104 150 247 162 185 124 201 591 748 1114 1037 t 1550 1405 889 248 257 239 4489 205 301 350 399 970 1102 1276 1319

hb_shift4 (hb)
; positions_6-8nt_m10 versus hb; m=1/1; ncol2=9; w=0; offset=4; strand=D; shift=4; score=0.438683; ----mayAAAAAa-- ; cor=; Ncor= a 0 0 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 c 0 0 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 g 0 0 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 t 0 0 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m2_shift0 (positions_6-8nt_m2)
; positions_6-8nt_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; wwaAAATAAAAcAtww ; Alignment reference a 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905 c 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884 g 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865 t 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445

hb_shift4 (hb)
; positions_6-8nt_m2 versus hb; m=1/1; ncol2=9; w=0; offset=4; strand=D; shift=4; score=0.434193; ----mayAAAAAa--- ; cor=; Ncor= a 0 0 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 0 0 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 0 0 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 0 0 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0

One-to-n matrix alignment; reference matrix: positions_6-8nt_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m8_shift0 (positions_6-8nt_m8)
; positions_6-8nt_m8; m=0 (reference); ncol1=16; shift=0; ncol=16; wwwAAATAAAAcAtww ; Alignment reference a 1701 1831 1285 4250 4176 4182 427 4168 4114 4024 3938 1117 3360 1055 1903 1705 c 792 757 586 114 157 154 310 151 197 190 245 2186 378 512 756 819 g 832 925 545 129 87 138 193 123 110 140 165 415 370 511 776 790 t 1386 1198 2295 218 291 237 3781 269 290 357 363 993 603 2633 1276 1397

hb_shift4 (hb)
; positions_6-8nt_m8 versus hb; m=1/1; ncol2=9; w=0; offset=4; strand=D; shift=4; score=0.432321; ----mayAAAAAa--- ; cor=; Ncor= a 0 0 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 0 0 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 0 0 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 0 0 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; wwgAAAATAAAATwa ; Alignment reference a 1375 1173 631 3213 3485 3462 3232 529 3099 3390 3399 3218 583 1306 1421 c 686 751 288 192 94 75 113 307 206 125 117 123 266 688 687 g 714 767 2477 174 78 69 124 275 228 103 98 139 213 752 732 t 999 1083 378 195 117 168 305 2663 241 156 160 294 2712 1028 934

hb_shift0 (hb)
; dyads_m3 versus hb; m=1/1; ncol2=9; w=0; offset=0; strand=D; shift=0; score=0.42808; 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: 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=14; shift=0; ncol=14; yaTACATATGTAtr ; Alignment reference a 996 1897 264 3886 456 3858 281 3905 190 822 186 3770 919 1731 c 1142 659 321 142 3081 98 195 129 368 155 304 159 1040 645 g 646 1040 159 304 155 368 129 195 98 3081 142 321 659 1142 t 1730 918 3770 182 822 190 3909 285 3858 456 3882 264 1896 996

twi_rc_shift4 (twi_rc)
; positions_6-8nt_m4 versus twi_rc; m=1/1; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.413866; ----CAtrTGTk-- ; cor=; Ncor= a 0 0 0 0 1.06667 11.7333 0 6.4 0 0 0 0 0 0 c 0 0 0 0 13.8667 1.06667 2.13333 1.06667 0 0 0 0 0 0 g 0 0 0 0 0 3.2 3.2 7.46667 0 16 3.2 5.33333 0 0 t 0 0 0 0 1.06667 0 10.6667 1.06667 16 0 12.8 10.6667 0 0

One-to-n matrix alignment; reference matrix: dyads_m8_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m8_shift1 (dyads_m8)
; dyads_m8; m=0 (reference); ncol1=10; shift=1; ncol=11; -ykGCCACCrm ; Alignment reference a 0 536 670 67 33 0 2893 0 0 886 857 c 0 837 665 49 2834 2835 0 2896 2885 527 828 g 0 619 804 2757 3 1 0 0 1 782 661 t 0 904 757 23 26 60 3 0 10 701 550

brk_shift0 (brk)
; dyads_m8 versus brk; m=1/1; ncol2=7; w=-1; offset=-1; strand=D; shift=0; score=0.401047; rGCGCCr---- ; cor=; Ncor= a 4.4 2.2 0 0 0 0 5.5 0 0 0 0 c 0 0 9.9 0 11 11 0 0 0 0 0 g 6.6 8.8 0 9.9 0 0 5.5 0 0 0 0 t 0 0 1.1 1.1 0 0 0 0 0 0 0

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=10; shift=0; ncol=10; waAATGAAaw ; Alignment reference a 747 1105 2596 2596 0 0 2579 2596 1120 908 c 538 506 0 0 0 0 0 0 401 416 g 598 535 0 0 0 2596 0 0 437 491 t 713 450 0 0 2596 0 17 0 638 781
en_rc_shift1 (en_rc)				; oligos_6-8nt_m7 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.610809; -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_m7 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.533446; -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_m7 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484627; --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_m7 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.421699; --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