Database and Motifs High-scoring Motif Occurrences Debugging Information



FIMO - Motif search tool

FIMO version 4.10.1, (Release date: Thu Mar 19 15:50:28 2015 +1000)

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

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 memechip_example_output_files/Klf1.fna
Database contains 904 sequences, 452000 residues

MOTIFS memechip_example_output_files/meme_out/meme.xml (nucleotide)

MOTIF WIDTH BEST POSSIBLE MATCH
1 12 CAGCCACACCCA
2 8 CAGATAAG
3 29 CTGCATCTCTTCAAGACACACCTAACTGC

Random model letter frequencies (from memechip_example_output_files/background):
A 0.256 C 0.244 G 0.244 T 0.256


SECTION I: HIGH-SCORING MOTIF OCCURRENCES

Motif Sequence Name Strand Start End p-value q-value Matched Sequence
2 chr1 77295361 77295368 1.6e-05 0.206 CAGATAAG
2 chr1 92186194 92186201 1.6e-05 0.206 CAGATAAG
2 chr1 + 173211157 173211164 1.6e-05 0.206 CAGATAAG
2 chr2 + 34638700 34638707 1.6e-05 0.206 CAGATAAG
2 chr2 + 37405294 37405301 1.6e-05 0.206 CAGATAAG
2 chr2 93306629 93306636 1.6e-05 0.206 CAGATAAG
2 chr3 + 60623753 60623760 1.6e-05 0.206 CAGATAAG
2 chr3 101355939 101355946 1.6e-05 0.206 CAGATAAG
2 chr4 129141107 129141114 1.6e-05 0.206 CAGATAAG
2 chr5 + 37127459 37127466 1.6e-05 0.206 CAGATAAG
2 chr5 64827033 64827040 1.6e-05 0.206 CAGATAAG
2 chr5 65203463 65203470 1.6e-05 0.206 CAGATAAG
2 chr5 139672881 139672888 1.6e-05 0.206 CAGATAAG
2 chr5 + 140280283 140280290 1.6e-05 0.206 CAGATAAG
2 chr6 + 38874342 38874349 1.6e-05 0.206 CAGATAAG
2 chr7 + 71081624 71081631 1.6e-05 0.206 CAGATAAG
2 chr7 104332701 104332708 1.6e-05 0.206 CAGATAAG
2 chr7 110976645 110976652 1.6e-05 0.206 CAGATAAG
2 chr7 + 111007774 111007781 1.6e-05 0.206 CAGATAAG
2 chr7 128112955 128112962 1.6e-05 0.206 CAGATAAG
2 chr8 122895877 122895884 1.6e-05 0.206 CAGATAAG
2 chr9 + 75406773 75406780 1.6e-05 0.206 CAGATAAG
2 chr9 + 114376116 114376123 1.6e-05 0.206 CAGATAAG
2 chr11 32169132 32169139 1.6e-05 0.206 CAGATAAG
2 chr11 94859085 94859092 1.6e-05 0.206 CAGATAAG
2 chr11 121295705 121295712 1.6e-05 0.206 CAGATAAG
2 chr14 71023831 71023838 1.6e-05 0.206 CAGATAAG
2 chr14 + 79703162 79703169 1.6e-05 0.206 CAGATAAG
2 chr15 + 73573716 73573723 1.6e-05 0.206 CAGATAAG
2 chr16 12052334 12052341 1.6e-05 0.206 CAGATAAG
2 chr16 + 32509275 32509282 1.6e-05 0.206 CAGATAAG
2 chr16 32510146 32510153 1.6e-05 0.206 CAGATAAG
2 chr16 92716218 92716225 1.6e-05 0.206 CAGATAAG
2 chr17 + 12397974 12397981 1.6e-05 0.206 CAGATAAG
2 chr17 + 36139154 36139161 1.6e-05 0.206 CAGATAAG
2 chr17 37006354 37006361 1.6e-05 0.206 CAGATAAG
2 chr18 62325951 62325958 1.6e-05 0.206 CAGATAAG
2 chr18 + 78548258 78548265 1.6e-05 0.206 CAGATAAG
2 chr19 24354257 24354264 1.6e-05 0.206 CAGATAAG
2 chr19 + 55940488 55940495 1.6e-05 0.206 CAGATAAG
2 chr1 36977332 36977339 3.19e-05 0.206 GAGATAAG
2 chr1 + 59011056 59011063 3.19e-05 0.206 GAGATAAG
2 chr1 + 134264551 134264558 3.19e-05 0.206 GAGATAAG
2 chr1 + 135847023 135847030 3.19e-05 0.206 GAGATAAG
2 chr1 + 169314584 169314591 3.19e-05 0.206 GAGATAAG
2 chr2 28463356 28463363 3.19e-05 0.206 GAGATAAG
2 chr2 103324507 103324514 3.19e-05 0.206 GAGATAAG
2 chr2 121964007 121964014 3.19e-05 0.206 GAGATAAG
2 chr3 39901756 39901763 3.19e-05 0.206 GAGATAAG
2 chr3 121365904 121365911 3.19e-05 0.206 GAGATAAG
2 chr3 + 138480135 138480142 3.19e-05 0.206 GAGATAAG
2 chr4 + 8631930 8631937 3.19e-05 0.206 GAGATAAG
2 chr4 9588295 9588302 3.19e-05 0.206 GAGATAAG
2 chr4 42890742 42890749 3.19e-05 0.206 GAGATAAG
2 chr4 + 118241534 118241541 3.19e-05 0.206 GAGATAAG
2 chr4 134537975 134537982 3.19e-05 0.206 GAGATAAG
2 chr5 + 89056795 89056802 3.19e-05 0.206 GAGATAAG
2 chr5 + 105995025 105995032 3.19e-05 0.206 GAGATAAG
2 chr5 137731018 137731025 3.19e-05 0.206 GAGATAAG
2 chr6 117858738 117858745 3.19e-05 0.206 GAGATAAG
2 chr7 + 16685470 16685477 3.19e-05 0.206 GAGATAAG
2 chr7 53194022 53194029 3.19e-05 0.206 GAGATAAG
2 chr7 + 106743016 106743023 3.19e-05 0.206 GAGATAAG
2 chr7 + 139969710 139969717 3.19e-05 0.206 GAGATAAG
2 chr8 + 83025439 83025446 3.19e-05 0.206 GAGATAAG
2 chr8 97964245 97964252 3.19e-05 0.206 GAGATAAG
2 chr8 108345053 108345060 3.19e-05 0.206 GAGATAAG
2 chr9 + 21069620 21069627 3.19e-05 0.206 GAGATAAG
2 chr9 44096716 44096723 3.19e-05 0.206 GAGATAAG
2 chr9 + 70774809 70774816 3.19e-05 0.206 GAGATAAG
2 chr9 121335783 121335790 3.19e-05 0.206 GAGATAAG
2 chr10 40924919 40924926 3.19e-05 0.206 GAGATAAG
2 chr10 60612430 60612437 3.19e-05 0.206 GAGATAAG
2 chr10 + 110604526 110604533 3.19e-05 0.206 GAGATAAG
2 chr10 127624600 127624607 3.19e-05 0.206 GAGATAAG
2 chr11 31712398 31712405 3.19e-05 0.206 GAGATAAG
2 chr11 32145858 32145865 3.19e-05 0.206 GAGATAAG
2 chr11 + 53840219 53840226 3.19e-05 0.206 GAGATAAG
2 chr11 69186917 69186924 3.19e-05 0.206 GAGATAAG
2 chr11 + 90524587 90524594 3.19e-05 0.206 GAGATAAG
2 chr11 + 97307712 97307719 3.19e-05 0.206 GAGATAAG
2 chr11 104890501 104890508 3.19e-05 0.206 GAGATAAG
2 chr12 41693278 41693285 3.19e-05 0.206 GAGATAAG
2 chr12 + 41693521 41693528 3.19e-05 0.206 GAGATAAG
2 chr12 + 90222861 90222868 3.19e-05 0.206 GAGATAAG
2 chr12 90222893 90222900 3.19e-05 0.206 GAGATAAG
2 chr13 + 3866626 3866633 3.19e-05 0.206 GAGATAAG
2 chr13 + 73580946 73580953 3.19e-05 0.206 GAGATAAG
2 chr13 76003447 76003454 3.19e-05 0.206 GAGATAAG
2 chr13 + 104819778 104819785 3.19e-05 0.206 GAGATAAG
2 chr14 + 61272960 61272967 3.19e-05 0.206 GAGATAAG
2 chr14 70506950 70506957 3.19e-05 0.206 GAGATAAG
2 chr16 + 10384462 10384469 3.19e-05 0.206 GAGATAAG
2 chr16 34031799 34031806 3.19e-05 0.206 GAGATAAG
2 chr17 24340090 24340097 3.19e-05 0.206 GAGATAAG
2 chr18 80417136 80417143 3.19e-05 0.206 GAGATAAG
2 chr19 + 10736602 10736609 3.19e-05 0.206 GAGATAAG
2 chr19 17398038 17398045 3.19e-05 0.206 GAGATAAG
2 chr19 + 24609412 24609419 3.19e-05 0.206 GAGATAAG
2 chr19 53260174 53260181 3.19e-05 0.206 GAGATAAG
2 chr19 + 56466261 56466268 3.19e-05 0.206 GAGATAAG
2 chr1 + 59011096 59011103 4.79e-05 0.208 CTGATAAG
2 chr1 77295522 77295529 4.79e-05 0.208 CTGATAAG
2 chr1 157198903 157198910 4.79e-05 0.208 CTGATAAG
2 chr2 84652227 84652234 4.79e-05 0.208 CTGATAAG
2 chr2 132521550 132521557 4.79e-05 0.208 CTGATAAG
2 chr2 150491916 150491923 4.79e-05 0.208 CTGATAAG
2 chr2 + 172173994 172174001 4.79e-05 0.208 CTGATAAG
2 chr2 + 172174042 172174049 4.79e-05 0.208 CTGATAAG
2 chr2 180447334 180447341 4.79e-05 0.208 CTGATAAG
2 chr3 60589218 60589225 4.79e-05 0.208 CTGATAAG
2 chr3 + 68858868 68858875 4.79e-05 0.208 CTGATAAG
2 chr3 144333316 144333323 4.79e-05 0.208 CTGATAAG
2 chr4 111174210 111174217 4.79e-05 0.208 CTGATAAG
2 chr4 + 135734047 135734054 4.79e-05 0.208 CTGATAAG
2 chr4 + 154285938 154285945 4.79e-05 0.208 CTGATAAG
2 chr5 27985294 27985301 4.79e-05 0.208 CTGATAAG
2 chr5 38900915 38900922 4.79e-05 0.208 CTGATAAG
2 chr5 96888685 96888692 4.79e-05 0.208 CTGATAAG
2 chr5 140280335 140280342 4.79e-05 0.208 CTGATAAG
2 chr6 41654336 41654343 4.79e-05 0.208 CTGATAAG
2 chr6 + 135115924 135115931 4.79e-05 0.208 CTGATAAG
2 chr7 19832423 19832430 4.79e-05 0.208 CTGATAAG
2 chr7 28267081 28267088 4.79e-05 0.208 CTGATAAG
2 chr7 56247766 56247773 4.79e-05 0.208 CTGATAAG
2 chr7 + 103854192 103854199 4.79e-05 0.208 CTGATAAG
2 chr7 + 139930480 139930487 4.79e-05 0.208 CTGATAAG
2 chr8 + 125244431 125244438 4.79e-05 0.208 CTGATAAG
2 chrX + 39372754 39372761 4.79e-05 0.208 CTGATAAG
2 chrX 39372850 39372857 4.79e-05 0.208 CTGATAAG
2 chr11 95195402 95195409 4.79e-05 0.208 CTGATAAG
2 chr11 96809404 96809411 4.79e-05 0.208 CTGATAAG
2 chr11 96809460 96809467 4.79e-05 0.208 CTGATAAG
2 chr11 + 115368094 115368101 4.79e-05 0.208 CTGATAAG
2 chr12 + 41846460 41846467 4.79e-05 0.208 CTGATAAG
2 chr13 + 59915840 59915847 4.79e-05 0.208 CTGATAAG
2 chr13 + 96735288 96735295 4.79e-05 0.208 CTGATAAG
2 chr14 + 61273048 61273055 4.79e-05 0.208 CTGATAAG
2 chr14 + 69923064 69923071 4.79e-05 0.208 CTGATAAG
2 chr15 + 38999432 38999439 4.79e-05 0.208 CTGATAAG
2 chr15 66969382 66969389 4.79e-05 0.208 CTGATAAG
2 chr15 91082700 91082707 4.79e-05 0.208 CTGATAAG
2 chr17 + 87913345 87913352 4.79e-05 0.208 CTGATAAG
2 chr18 + 32702254 32702261 4.79e-05 0.208 CTGATAAG
2 chr18 32702283 32702290 4.79e-05 0.208 CTGATAAG
2 chr18 32716545 32716552 4.79e-05 0.208 CTGATAAG
2 chr18 61379975 61379982 4.79e-05 0.208 CTGATAAG
2 chr18 62325910 62325917 4.79e-05 0.208 CTGATAAG
2 chr18 + 62326283 62326290 4.79e-05 0.208 CTGATAAG
2 chr18 85054516 85054523 4.79e-05 0.208 CTGATAAG
2 chr2 + 130961728 130961735 6.39e-05 0.233 GTGATAAG
2 chr2 130961816 130961823 6.39e-05 0.233 GTGATAAG
2 chr3 100351583 100351590 6.39e-05 0.233 GTGATAAG
2 chr3 104477762 104477769 6.39e-05 0.233 GTGATAAG
2 chr4 + 46420052 46420059 6.39e-05 0.233 GTGATAAG
2 chr5 + 33616512 33616519 6.39e-05 0.233 GTGATAAG
2 chr5 + 97380870 97380877 6.39e-05 0.233 GTGATAAG
2 chr5 + 129513384 129513391 6.39e-05 0.233 GTGATAAG
2 chr5 + 144580013 144580020 6.39e-05 0.233 GTGATAAG
2 chr6 + 57695593 57695600 6.39e-05 0.233 GTGATAAG
2 chr6 + 86027950 86027957 6.39e-05 0.233 GTGATAAG
2 chr6 + 146179217 146179224 6.39e-05 0.233 GTGATAAG
2 chr7 + 106743090 106743097 6.39e-05 0.233 GTGATAAG
2 chr7 134369324 134369331 6.39e-05 0.233 GTGATAAG
2 chr7 139930666 139930673 6.39e-05 0.233 GTGATAAG
2 chr8 3522487 3522494 6.39e-05 0.233 GTGATAAG
2 chr8 + 83024311 83024318 6.39e-05 0.233 GTGATAAG
2 chr8 87495103 87495110 6.39e-05 0.233 GTGATAAG
2 chr8 122895830 122895837 6.39e-05 0.233 GTGATAAG
2 chr9 + 40980714 40980721 6.39e-05 0.233 GTGATAAG
2 chrX + 146984377 146984384 6.39e-05 0.233 GTGATAAG
2 chr10 + 93585738 93585745 6.39e-05 0.233 GTGATAAG
2 chr11 + 68709971 68709978 6.39e-05 0.233 GTGATAAG
2 chr13 94151422 94151429 6.39e-05 0.233 GTGATAAG
2 chr14 + 71023921 71023928 6.39e-05 0.233 GTGATAAG
2 chr15 36250892 36250899 6.39e-05 0.233 GTGATAAG
2 chr16 8687079 8687086 6.39e-05 0.233 GTGATAAG
2 chr17 + 5112287 5112294 6.39e-05 0.233 GTGATAAG
2 chr17 43466888 43466895 6.39e-05 0.233 GTGATAAG
2 chr1 + 169323195 169323202 8.06e-05 0.233 AAGATAAG
2 chr2 25742927 25742934 8.06e-05 0.233 AAGATAAG
2 chr2 + 25869441 25869448 8.06e-05 0.233 AAGATAAG
2 chr2 + 103798093 103798100 8.06e-05 0.233 AAGATAAG
2 chr2 + 131039972 131039979 8.06e-05 0.233 AAGATAAG
2 chr2 180447126 180447133 8.06e-05 0.233 AAGATAAG
2 chr3 + 107899731 107899738 8.06e-05 0.233 AAGATAAG
2 chr4 76585121 76585128 8.06e-05 0.233 AAGATAAG
2 chr5 28369364 28369371 8.06e-05 0.233 AAGATAAG
2 chr5 + 33375033 33375040 8.06e-05 0.233 AAGATAAG
2 chr5 77087406 77087413 8.06e-05 0.233 AAGATAAG
2 chr5 + 121049840 121049847 8.06e-05 0.233 AAGATAAG
2 chr6 + 38861079 38861086 8.06e-05 0.233 AAGATAAG
2 chr6 + 38874311 38874318 8.06e-05 0.233 AAGATAAG
2 chr6 + 120124683 120124690 8.06e-05 0.233 AAGATAAG
2 chr7 + 16987564 16987571 8.06e-05 0.233 AAGATAAG
2 chr7 + 28266986 28266993 8.06e-05 0.233 AAGATAAG
2 chr7 28320568 28320575 8.06e-05 0.233 AAGATAAG
2 chr7 + 36133146 36133153 8.06e-05 0.233 AAGATAAG
2 chr7 + 87847657 87847664 8.06e-05 0.233 AAGATAAG
2 chr7 + 135432720 135432727 8.06e-05 0.233 AAGATAAG
2 chr7 + 138568665 138568672 8.06e-05 0.233 AAGATAAG
2 chr8 126512744 126512751 8.06e-05 0.233 AAGATAAG
2 chr9 42910168 42910175 8.06e-05 0.233 AAGATAAG
2 chr9 98390191 98390198 8.06e-05 0.233 AAGATAAG
2 chr9 + 118957709 118957716 8.06e-05 0.233 AAGATAAG
2 chrX + 68727678 68727685 8.06e-05 0.233 AAGATAAG
2 chrX 68727825 68727832 8.06e-05 0.233 AAGATAAG
2 chr10 + 60586067 60586074 8.06e-05 0.233 AAGATAAG
2 chr10 + 126642619 126642626 8.06e-05 0.233 AAGATAAG
2 chr11 87539831 87539838 8.06e-05 0.233 AAGATAAG
2 chr11 87563780 87563787 8.06e-05 0.233 AAGATAAG
2 chr11 + 95661880 95661887 8.06e-05 0.233 AAGATAAG
2 chr11 97307503 97307510 8.06e-05 0.233 AAGATAAG
2 chr12 70884783 70884790 8.06e-05 0.233 AAGATAAG
2 chr13 + 54346113 54346120 8.06e-05 0.233 AAGATAAG
2 chr13 + 112447259 112447266 8.06e-05 0.233 AAGATAAG
2 chr15 + 34829948 34829955 8.06e-05 0.233 AAGATAAG
2 chr15 + 56455244 56455251 8.06e-05 0.233 AAGATAAG
2 chr15 62052574 62052581 8.06e-05 0.233 AAGATAAG
2 chr16 12052260 12052267 8.06e-05 0.233 AAGATAAG
2 chr16 91353149 91353156 8.06e-05 0.233 AAGATAAG
2 chr17 26651606 26651613 8.06e-05 0.233 AAGATAAG
2 chr17 29584356 29584363 8.06e-05 0.233 AAGATAAG
2 chr17 43466930 43466937 8.06e-05 0.233 AAGATAAG
2 chr18 + 62326110 62326117 8.06e-05 0.233 AAGATAAG
2 chr18 65888375 65888382 8.06e-05 0.233 AAGATAAG
2 chr1 + 36111463 36111470 9.74e-05 0.247 CAGATAAA
2 chr1 + 36976658 36976665 9.74e-05 0.247 CAGATAAA
2 chr1 88057085 88057092 9.74e-05 0.247 CAGATAAA
2 chr1 + 157198976 157198983 9.74e-05 0.247 CAGATAAA
2 chr1 183078941 183078948 9.74e-05 0.247 CAGATAAA
2 chr2 52304718 52304725 9.74e-05 0.247 CAGATAAA
2 chr3 + 51034554 51034561 9.74e-05 0.247 CAGATAAA
2 chr3 154291677 154291684 9.74e-05 0.247 CAGATAAA
2 chr4 43977292 43977299 9.74e-05 0.247 CAGATAAA
2 chr4 + 46610203 46610210 9.74e-05 0.247 CAGATAAA
2 chr4 124283654 124283661 9.74e-05 0.247 CAGATAAA
2 chr4 134538017 134538024 9.74e-05 0.247 CAGATAAA
2 chr5 45951789 45951796 9.74e-05 0.247 CAGATAAA
2 chr5 + 97380737 97380744 9.74e-05 0.247 CAGATAAA
2 chr5 140488385 140488392 9.74e-05 0.247 CAGATAAA
2 chr6 86027977 86027984 9.74e-05 0.247 CAGATAAA
2 chr7 + 28233942 28233949 9.74e-05 0.247 CAGATAAA
2 chr7 + 106951943 106951950 9.74e-05 0.247 CAGATAAA
2 chr7 111007646 111007653 9.74e-05 0.247 CAGATAAA
2 chr8 87494985 87494992 9.74e-05 0.247 CAGATAAA
2 chr8 + 122895787 122895794 9.74e-05 0.247 CAGATAAA
2 chr10 25440471 25440478 9.74e-05 0.247 CAGATAAA
2 chr10 + 57527851 57527858 9.74e-05 0.247 CAGATAAA
2 chr10 59256089 59256096 9.74e-05 0.247 CAGATAAA
2 chr11 + 116481689 116481696 9.74e-05 0.247 CAGATAAA
2 chr12 + 27136183 27136190 9.74e-05 0.247 CAGATAAA
2 chr13 + 74873453 74873460 9.74e-05 0.247 CAGATAAA
2 chr15 56455284 56455291 9.74e-05 0.247 CAGATAAA
2 chr17 5112243 5112250 9.74e-05 0.247 CAGATAAA
2 chr17 + 84179851 84179858 9.74e-05 0.247 CAGATAAA
2 chr19 4047026 4047033 9.74e-05 0.247 CAGATAAA

DEBUGGING INFORMATION

Command line:

/home/james/dist/BUILD/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_2 --bgfile memechip_example_output_files/background --motif 2 memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/Klf1.fna

Settings:

output directory = memechip_example_output_files/fimo_out_2 MEME file name = memechip_example_output_files/meme_out/meme.xml sequence file name = memechip_example_output_files/Klf1.fna
background file name = memechip_example_output_files/background allow clobber = true compute q-values = true
parse genomic coord. = true text only = false scan both strands = true
output threshold = 0.0001 threshold type = p-value max stored scores = 100000
pseudocount = 0.1 verbosity = 1 selected motif = 2

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


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