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.2026-01-25.180905_2026-01-25.180905_kvVFaU/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.2026-01-25.180905_2026-01-25.180905_kvVFaU/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab

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=14; shift=0; ncol=14; agAGAGAGmGAGag ; Alignment reference a 994 451 1769 160 1792 102 1845 112 705 108 1804 142 986 408 c 454 356 160 92 213 70 140 46 1215 80 176 86 498 337 g 461 1198 165 1923 83 1997 89 1996 156 1989 146 1907 385 1205 t 308 212 123 42 129 48 143 63 141 40 91 82 348 267

Trl_rc_shift0 (Trl_rc)
; oligos_6-8nt_m8 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.732476; agaGaGAGmrmaA- ; cor=; Ncor= a 42 17 46 7 50 11 62 0 40 26 30 41 57 0 c 14 9 6 1 9 8 11 5 27 10 24 13 0 0 g 3 47 16 56 12 56 0 72 3 41 19 8 10 0 t 18 4 9 13 6 2 4 0 7 0 4 15 10 0

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift0 ; 2 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=12; shift=0; ncol=12; vmaATCGATtkb ; Alignment reference a 458 571 1111 1593 40 41 81 1641 90 308 349 402 c 446 480 201 48 36 1597 41 44 32 139 360 455 g 454 362 141 30 44 41 1598 36 48 201 481 447 t 403 348 308 90 1641 82 41 40 1591 1113 571 457

Dref_rc_shift1 (Dref_rc)
; oligos_6-8nt_m6 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.631936; -yTATCGwTAt- ; cor=; Ncor= a 0 0 0 10 0 0 0 6.66667 1.11111 7.77778 2.22222 0 c 0 6.66667 1.11111 0 0 8.88889 0 0 0 1.11111 0 0 g 0 0 1.11111 0 0 0 10 0 1.11111 0 1.11111 0 t 0 3.33333 7.77778 0 10 1.11111 0 3.33333 7.77778 1.11111 6.66667 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; tccCTCTCyCTCTCyct ; Alignment reference a 133 107 47 51 65 16 31 24 54 61 57 14 41 26 73 152 156 c 248 507 595 798 81 909 52 848 568 780 87 891 39 824 589 474 245 g 189 177 111 65 83 27 48 51 105 59 78 34 73 83 74 170 199 t 431 210 248 87 772 49 870 78 274 101 779 62 848 68 265 205 401

Trl_shift0 (Trl)
; dyads_m2 versus Trl; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.622227; 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: oligos_6-8nt_m3_shift0 ; 7 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=13; shift=0; ncol=13; wwaATAAATAAww ; Alignment reference a 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 c 423 379 194 186 84 59 90 76 107 49 150 395 415 g 386 352 185 227 50 42 62 55 61 55 132 371 357 t 772 694 453 339 2110 127 186 121 2142 112 291 702 790

hb_shift2 (hb)
; oligos_6-8nt_m3 versus hb; m=1/6; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.503858; --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_m3 versus br-Z4_rc; m=2/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.492269; ----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_m3 versus zen; m=3/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.440206; --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_m3 versus Dfd_rc; m=4/6; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.436383; ---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_m3 versus Antp; m=5/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.433461; ------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_m3 versus ap; m=6/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.403627; ------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: 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; -rtATAGGAww ; Alignment reference a 0 170 118 470 0 527 4 9 441 146 185 c 0 110 78 26 1 3 18 0 4 98 104 g 0 138 114 34 14 4 489 429 35 128 95 t 0 116 224 4 519 0 23 96 54 162 150

br-Z2_rc_shift0 (br-Z2_rc)
; positions_6-8nt_m1 versus br-Z2_rc; m=1/1; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.498118; twaaTAG---- ; cor=; Ncor= a 5 9 12 11 0 21 1 0 0 0 0 c 4 1 3 3 0 0 0 0 0 0 0 g 0 3 1 3 0 0 20 0 0 0 0 t 12 8 5 4 21 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; gyCGCCGCCGcc ; Alignment reference a 394 275 67 76 73 57 54 68 61 101 418 352 c 311 600 1501 24 1551 1549 27 1519 1558 83 634 660 g 617 420 65 1583 54 19 1622 84 26 1483 360 307 t 423 450 112 62 67 120 42 74 100 78 333 426

brk_shift0 (brk)
; dyads_m6 versus brk; m=1/2; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.483643; 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_m6 versus Med; m=2/2; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.460441; ---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: dyads_m7_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift1 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=19; shift=1; ncol=20; -yyCTCyyyctcyyyCTCyy ; Alignment reference a 0 423 426 86 69 71 289 396 357 312 460 340 339 370 446 82 87 73 327 428 c 0 885 617 2072 75 2103 638 923 700 1137 411 1132 664 925 592 2073 77 2116 646 869 g 0 320 424 71 36 48 457 372 343 423 351 372 477 325 372 68 38 31 478 363 t 0 628 789 27 2076 34 872 565 856 384 1034 412 776 636 846 33 2054 36 805 596

Trl_shift0 (Trl)
; dyads_m7 versus Trl; m=1/1; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.427559; 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: 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=14; shift=0; ncol=14; acgCACTCACctay ; Alignment reference a 336 229 199 113 1001 22 76 27 984 29 222 165 328 216 c 276 407 193 832 26 1046 54 1004 36 1030 616 238 274 376 g 243 206 572 77 45 26 33 31 43 36 106 132 242 243 t 264 277 155 97 47 25 956 57 56 24 175 584 275 284

z_rc_shift3 (z_rc)
; oligos_6-8nt_m4 versus z_rc; m=1/1; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.410393; ---CaCTCA----- ; cor=; Ncor= a 0 0 0 5.12195 24.5854 0 0 0 29.7073 0 0 0 0 0 c 0 0 0 30.7317 0 42 0 42 3.07317 0 0 0 0 0 g 0 0 0 5.12195 10.2439 0 0 0 7.17073 0 0 0 0 0 t 0 0 0 1.02439 7.17073 0 42 0 2.04878 0 0 0 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; -ykGCCACCrv ; Alignment reference a 0 176 193 19 7 0 866 0 0 272 236 c 0 246 210 15 856 862 0 867 867 169 251 g 0 192 222 822 2 1 0 0 0 223 218 t 0 253 242 11 2 4 1 0 0 203 162

brk_shift0 (brk)
; dyads_m8 versus brk; m=1/1; ncol2=7; w=-1; offset=-1; strand=D; shift=0; score=0.406384; 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_m3_shift0 (oligos_6-8nt_m3)				; oligos_6-8nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; wwaATAAATAAww ; Alignment reference a 808 964 1557 1637 145 2161 2051 2137 79 2173 1816 921 827 c 423 379 194 186 84 59 90 76 107 49 150 395 415 g 386 352 185 227 50 42 62 55 61 55 132 371 357 t 772 694 453 339 2110 127 186 121 2142 112 291 702 790
hb_shift2 (hb)				; oligos_6-8nt_m3 versus hb; m=1/6; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.503858; --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_m3 versus br-Z4_rc; m=2/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.492269; ----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_m3 versus zen; m=3/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.440206; --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_m3 versus Dfd_rc; m=4/6; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.436383; ---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_m3 versus Antp; m=5/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.433461; ------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_m3 versus ap; m=6/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.403627; ------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