Database and Motifs High-scoring Motif Occurences Debugging Information


FIMO - Motif search tool

FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

If you use FIMO in your research, please cite the following paper:
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics, 27(7):1017-1018, 2011. [full text]

DATABASE AND MOTIFS

DATABASE /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Database contains 814 sequences, 863675 residues

MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
GGWTCGA 7 GGTTCGA
AARAAAAW 8 AAAAAAAA
TACCACYA 8 TACCACTA
GCCTTAMC 8 GCCTTAAC
CTBGGCCA 8 CTCGGCCA
RGAAGA 6 AGAAGA
GMTACCGA 8 GCTACCGA
AGATCGKG 8 AGATCGGG
CTGGGGW 7 CTGGGGT

Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background):
A 0.317 C 0.183 G 0.183 T 0.317

SECTION I: HIGH-SCORING MOTIF OCCURENCES
Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
TACCACYA DREME-3 chrV + 61940 61947 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrI + 72819 72826 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIV - 83559 83566 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVI - 84036 84043 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXV + 87893 87900 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXII - 92559 92566 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVI - 101387 101394 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrV - 102425 102432 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrI - 139163 139170 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIII + 142751 142758 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrI - 151655 151662 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrX + 157121 157128 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVI - 162239 162246 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVI + 167477 167484 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIII + 168835 168842 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVI + 181024 181031 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrI + 181400 181407 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIII + 183948 183955 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII + 185995 186002 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIII + 196150 196157 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrII + 197679 197686 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIX + 197709 197716 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVI - 210658 210665 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIV + 217273 217280 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXV + 226661 226668 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXI + 229840 229847 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrV + 241988 241995 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXV - 282175 282182 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIX - 300041 300048 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXV - 301108 301115 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIV + 308661 308668 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXI - 326418 326425 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrX + 354284 354291 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVIII + 388975 388982 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrX + 396776 396783 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIV + 417001 417008 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIX + 427202 427209 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXV - 438830 438837 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXV - 464461 464468 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVIII - 467001 467008 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrII + 477732 477739 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXI + 520783 520790 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrX - 531839 531846 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIV - 547105 547112 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIV - 568126 568133 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXVI - 572280 572287 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIII + 652033 652040 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII - 661760 661767 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII + 662051 662058 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXII - 674997 675004 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXVI + 700655 700662 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXVI - 744295 744302 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXII + 806648 806655 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIII + 837968 837975 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII - 844784 844791 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII - 845241 845248 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII - 845660 845667 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXII - 857329 857336 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXVI - 860390 860397 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII - 876937 876944 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIII + 913208 913215 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXIII - 915201 915208 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIV - 929079 929086 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIV - 929408 929415 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII + 931003 931010 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIV - 992843 992850 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrVII - 1004227 1004234 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrIV + 1402674 1402681 1.96e-05 0.361 TACCACTA
TACCACYA DREME-3 chrXI + 819 826 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXV + 859 866 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIV - 24550 24557 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIV + 25873 25880 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrVIII + 35316 35323 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV + 68062 68069 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrI + 72063 72070 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrX - 74325 74332 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrX - 74454 74461 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV - 78426 78433 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXI + 101625 101632 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV + 102247 102254 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXI - 103189 103196 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrVIII + 120629 120636 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIII - 138449 138456 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXI - 159163 159170 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIII + 177777 177784 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIX + 231758 231765 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrII - 234654 234661 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV + 235419 235426 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV - 236284 236291 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrII + 239177 239184 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII + 241642 241649 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV + 241740 241747 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrII - 256365 256372 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXV - 259088 259095 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXI + 259383 259390 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV + 267476 267483 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrVII + 277765 277772 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrVIII + 291868 291875 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrVIII + 292234 292241 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIII + 294071 294078 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIV + 301653 301660 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV - 306982 306989 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV - 307076 307083 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIX - 317679 317686 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIX - 317802 317809 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV + 331841 331848 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV - 331889 331896 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV + 355080 355087 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrII + 374780 374787 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIV + 443531 443538 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrII - 477762 477769 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrVII - 481633 481640 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV - 491919 491926 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII - 499170 499177 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXV - 506349 506356 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXV - 506625 506632 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV - 508826 508833 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrII + 530972 530979 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrVII + 534397 534404 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrII - 548622 548629 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrV - 569578 569585 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIV + 576007 576014 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV + 580399 580406 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV + 601917 601924 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXI - 618067 618074 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXV - 623096 623103 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIII - 650571 650578 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII + 669490 669497 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXVI - 700685 700692 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII - 708962 708969 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII + 709292 709299 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXV + 728542 728549 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII - 794404 794411 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII + 795838 795845 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII - 812932 812939 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXII - 813556 813563 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXV + 877827 877834 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrVII - 883353 883360 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIII - 887868 887875 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIII + 888083 888090 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIII - 888315 888322 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV - 892407 892414 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXV + 961897 961904 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV - 1013592 1013599 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV - 1016769 1016776 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV + 1164119 1164126 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrIV + 1164278 1164285 3.1e-05 0.361 TACCACCA
TACCACYA DREME-3 chrXIII - 24124 24131 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrVII - 25124 25131 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrIV + 46296 46303 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrVI - 65265 65272 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrI + 71959 71966 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrV - 78101 78108 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrVIII + 80928 80935 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXII - 88262 88269 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXI + 102496 102503 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXV + 113910 113917 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrIII - 162290 162297 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXIII + 162513 162520 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXIII + 162732 162739 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXI + 163462 163469 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrVI + 167399 167406 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXI + 203255 203262 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrIII - 228141 228148 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrV + 242006 242013 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrV + 283241 283248 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXIII - 296701 296708 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrIV + 306180 306187 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXI + 309714 309721 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrV + 322431 322438 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrV - 363995 364002 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXI + 365051 365058 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrVIII + 375679 375686 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXIII + 389310 389317 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrIX - 395093 395100 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrVII - 398983 398990 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrX - 414020 414027 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrVII + 441498 441505 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrVIII + 451896 451903 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrVIII - 475492 475499 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXIV + 494296 494303 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXIV - 494388 494395 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXIII + 499209 499216 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrII - 504683 504690 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrV + 505000 505007 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXIII - 553265 553272 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXV + 622137 622144 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXIII + 634795 634802 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXII - 638176 638183 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrII - 643396 643403 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXV - 663660 663667 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrX - 701790 701797 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrVII - 706891 706898 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrXII + 838616 838623 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXII + 856637 856644 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXV + 867484 867491 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrVII + 878492 878499 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXII + 898131 898138 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXII + 951532 951539 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrXV + 963103 963110 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrIV - 1150382 1150389 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrIV - 1236640 1236647 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrIV - 1237458 1237465 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrIV - 1257104 1257111 6.2e-05 0.516 TACCACAA
TACCACYA DREME-3 chrIV - 1355537 1355544 6.2e-05 0.516 TACCACGA
TACCACYA DREME-3 chrIV - 1360722 1360729 6.2e-05 0.516 TACCACGA
DEBUGGING INFORMATION

Command line: 

/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif TACCACYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa

Settings: 


  

    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_4
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
  
  

    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background
    alphabet = DNA
    max stored scores = 100000
  
  

    allow clobber = true
    compute q-values = true
    parse genomic coord. = true
  

  

    text only = false
    scan both strands = true
    max strand = false
  

  

    threshold type = p-value
    output theshold = 0.0001
    pseudocount = 0.1
  

  

    alpha = 1
    verbosity = 1

This information can be useful in the event you wish to report a problem with the FIMO software.

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