Database and Motifs | High-scoring Motif Occurrences | Debugging Information

FIMO - Motif search tool

FIMO version 4.10.0, (Release date: Wed May 21 10:35:36 2014 +1000)

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 memechip_example_output_files/sample-dna-Klf1.fa
Database contains 904 sequences, 452000 residues

MOTIFS JASPAR_CORE_2009.meme (nucleotide)

MOTIF | WIDTH | BEST POSSIBLE MATCH
--- | --- | ---
MA0001.1 | 10 | CCATAAATAG
MA0002.1 | 11 | TATTGTGGTTA
MA0002.2 | 11 | GTCTGTGGTTT
MA0003.1 | 9 | GCCCGGGGG
MA0004.1 | 6 | CACGTG
MA0005.1 | 11 | CCAAATTTGGT
MA0006.1 | 6 | TGCGTG
MA0007.1 | 22 | ATAAGAACATCGTGTACCCGCC
MA0008.1 | 8 | CAATTATT
MA0009.1 | 11 | CTAGGTGTGAA
MA0010.1 | 14 | GTAATAAACAAATC
MA0011.1 | 8 | TACTATTT
MA0012.1 | 11 | TAAACTAAAAG
MA0013.1 | 11 | TAGTAAACAAA
MA0014.1 | 20 | AGAGCACTGAAGCGTAACGG
MA0015.1 | 10 | GTATATATAC
MA0016.1 | 10 | GGGGTCACGG
MA0017.1 | 14 | TGACCTTTGAACCT
MA0018.1 | 12 | CCTGGTGACGTC
MA0018.2 | 8 | TGACGTCA
MA0019.1 | 12 | AGATGCAATCCC
MA0020.1 | 6 | AAAGCA
MA0021.1 | 6 | AAAGCG
MA0022.1 | 12 | GGGGTTTTTCCG
MA0023.1 | 10 | GGGGTTTTCC
MA0024.1 | 8 | TTTGGCGC
MA0025.1 | 11 | TTATGTAACAT
MA0026.1 | 7 | CCGGAAG
MA0027.1 | 11 | AAGTAGTGTTC
MA0028.1 | 10 | GAGCCGGAAG
MA0029.1 | 14 | AAGATAAGATAATA
MA0030.1 | 14 | CAAACGTAAACAAT
MA0031.1 | 8 | GTAAACAT
MA0032.1 | 8 | GGTAAGTA
MA0033.1 | 8 | TATACATA
MA0034.1 | 10 | GACAACCGCC
MA0035.1 | 6 | GGATGG
MA0035.2 | 11 | ACAGATAAGAA
MA0036.1 | 5 | GGATA
MA0037.1 | 6 | AGATAG
MA0038.1 | 10 | CAAATCACTG
MA0039.1 | 10 | TAAAGGAAGG
MA0039.2 | 10 | TGGGTGGGGC
MA0040.1 | 11 | TATTGTTTATT
MA0041.1 | 12 | GAATGTTTGTTT
MA0042.1 | 12 | GGATGTTTGTTT
MA0043.1 | 12 | GGTTACGTAATT
MA0044.1 | 9 | GTTGTATTC
MA00445.1 | 11 | TCCATTGTTCT
MA0045.1 | 16 | CAACAAATGGAAAAAC
MA0046.1 | 14 | GGTTAATAATTAAC
MA0047.1 | 12 | CAATATTTACTT
MA0047.2 | 12 | TGTTTACTTAGG
MA0048.1 | 12 | GCGCAGCTGCGT
MA0049.1 | 10 | GCATAAAAAA
MA0050.1 | 12 | GAAAGTGAAACC
MA0051.1 | 18 | GGAAAGTGAAAGCAAAAC
MA0052.1 | 10 | CTATTTATAG
MA0053.1 | 5 | AAAGC
MA0054.1 | 9 | TAACCGTTT
MA0055.1 | 12 | CAGCAGCTGCTG
MA0056.1 | 6 | TGGGGA
MA0057.1 | 10 | GTAGGGGGAA
MA0058.1 | 10 | AACCACGTGA
MA0059.1 | 11 | GAGCACGTGGT
MA0060.1 | 16 | CTCAGCCAATCAGCGC
MA0061.1 | 10 | GGGAATTTCC
MA0062.1 | 10 | ACCGGAAGAG
MA0062.2 | 11 | CCGGAAGTGGC
MA0063.1 | 7 | TTAATTG
MA0064.1 | 5 | AAAGC
MA0065.1 | 20 | TTAGGGGTCAAAGGTCATCT
MA0065.2 | 15 | GTAGGGCAAAGGTCA
MA0066.1 | 20 | GTAGGTCACGGTGACCTACT
MA0067.1 | 8 | AGTCACGG
MA0068.1 | 30 | GAAAAATTTCCAATACTCCACTCCCCCCCC
MA0069.1 | 14 | TTCACGCATGAGTT
MA0070.1 | 12 | CCATCAATCAAA
MA0071.1 | 10 | ATCAAGGTCA
MA0072.1 | 14 | TATAAGTAGGTCAA
MA0073.1 | 20 | CCCCAAACCACCCCCCCCCA
MA0074.1 | 15 | GGGTCATCGAGTTCA
MA0075.1 | 5 | AATTA
MA0076.1 | 9 | ACCGGAAGT
MA0077.1 | 9 | GAACAATGG
MA0078.1 | 9 | TTCATTGTC
MA0079.1 | 10 | GGGGCGGGGT
MA0079.2 | 10 | CCCCGCCCCC
MA0080.1 | 6 | CGGAAG
MA0080.2 | 7 | AGGAAGT
MA0081.1 | 7 | AGAGGAA
MA0082.1 | 14 | CCAAAAATGGAAAT
MA0083.1 | 12 | GCCCATATATGG
MA0084.1 | 9 | GTAAACAAT
MA0085.1 | 16 | TTGTGGGAAACGAGAT
MA0086.1 | 6 | CAGGTG
MA0087.1 | 7 | TAACAAT
MA0088.1 | 20 | GATTTCCCATAATGCCTTGC
MA0089.1 | 6 | CATGAC
MA0090.1 | 12 | CACATTCCTCCG
MA0091.1 | 12 | CGACCATCTGTT
MA0092.1 | 10 | GGTCTGGCAT
MA0093.1 | 7 | CACGTGG
MA0094.1 | 4 | TAAT
MA0094.2 | 8 | TTTAATTA
MA0095.1 | 6 | GCCATC
MA0096.1 | 7 | ATGACGT
MA0097.1 | 12 | GATGACGTGGCC
MA0098.1 | 6 | TTTCCG
MA0099.1 | 8 | GTGAGTCA
MA0099.2 | 7 | TGACTCA
MA0100.1 | 8 | GGCCGTTG
MA0101.1 | 10 | GGGGATTTCC
MA0102.1 | 12 | TTTCGCAATCTT
MA0102.2 | 9 | TTTCGCAAT
MA0103.1 | 6 | CACCTG
MA0104.1 | 6 | CACGTG
MA0104.2 | 10 | CGCACGTGGC
MA0105.1 | 11 | GGGGATTCCCC
MA0106.1 | 20 | CCGGACATGCCCGGGCATGT
MA0107.1 | 10 | GGGAATTTCC
MA0108.1 | 15 | GTATAAAAGGCGGGG
MA0108.2 | 15 | GTATAAAAGGCGGGG
MA0109.1 | 10 | AACCTTATAT
MA0110.1 | 9 | CCAATTATT
MA0111.1 | 11 | AGGGTAACAGC
MA0112.1 | 18 | CCAGGTCACCGTGACCCC
MA0112.2 | 20 | GGCCCAGGTCACCCTGACCT
MA0113.1 | 18 | GGGAACATTATGTCCTAT
MA0114.1 | 13 | AGGCCAAAGGTCA
MA0115.1 | 17 | AAAGGTCAAAGGTCAAC
MA0116.1 | 15 | GGCACCCAGGGGTGC
MA0117.1 | 8 | GCTGACGG
MA0118.1 | 9 | TGGGGGTTC
MA0119.1 | 14 | TGGCACCATGCCAA
MA0120.1 | 12 | TTTTCCTTTTCG
MA0121.1 | 8 | AGATCCGC
MA0122.1 | 9 | TTAAGTGGA
MA0123.1 | 10 | CGGTGCCCCC
MA0124.1 | 7 | ATACTTA
MA0125.1 | 8 | TAATTGGT
MA0126.1 | 9 | AGTAACAGT
MA0127.1 | 10 | ACTTCTTATT
MA0128.1 | 8 | ACACGTGG
MA0129.1 | 7 | TACGTCA
MA0130.1 | 6 | ATCCAC
MA0131.1 | 10 | TAACGTCCGC
MA0132.1 | 6 | CTAATT
MA0133.1 | 7 | ACAACAC
MA0135.1 | 13 | AAATTAATTAATC
MA0136.1 | 9 | TACTTCCTT
MA0137.1 | 14 | GGAAAATGAAACTG
MA0137.2 | 15 | CATTTCCCGGAAACC
MA0138.1 | 19 | GCGCTGTCCATGGTGCTGA
MA0138.2 | 21 | TTCAGCACCATGGACAGCGCC
MA0139.1 | 19 | TGGCCACCAGGGGGCGCTA
MA0140.1 | 18 | CTGGTGGGGACAGATAAG
MA0141.1 | 12 | AGCTCAAGGTCA
MA0142.1 | 15 | CTTTGTTATGCAAAT
MA0143.1 | 15 | CCTTTGTTATGCAAA
MA0144.1 | 10 | TTCCAGGAAG
MA0145.1 | 14 | CCAGTTCAAACCAG
MA0146.1 | 14 | GGGGCCGAGGCCTG
MA0147.1 | 10 | CGCACGTGGC
MA0148.1 | 11 | TGTTTACTTTG
MA0149.1 | 18 | GGAAGGAAGGAAGGAAGG
MA0150.1 | 11 | ATGACTCAGCA
MA0151.1 | 6 | ATTAAA
MA0152.1 | 7 | TTTTCCA
MA0153.1 | 12 | TTAATATTTAAC
MA0154.1 | 10 | ACCCAAGGGA
MA0155.1 | 12 | TGTCAGGGGGCG
MA0156.1 | 8 | CAGGAAAT
MA0157.1 | 8 | TGTAAACA
MA0158.1 | 8 | CACTAATT
MA0159.1 | 17 | AGGTCATGGAGAGGTCA
MA0160.1 | 8 | AAGGTCAC
MA0161.1 | 6 | TTGGCA
MA0162.1 | 11 | TGCGTGGGCGT
MA0163.1 | 14 | GGGGCCCAAGGGGG
MA0164.1 | 7 | CAAGCTT
MA0165.1 | 7 | TTTATGA
MA0166.1 | 7 | TTAATGA
MA0167.1 | 7 | TTAATTA
MA0168.1 | 7 | TTAATTG
MA0169.1 | 7 | TTAATTG
MA0170.1 | 7 | TTAATTA
MA0171.1 | 7 | TTAATTG
MA0172.1 | 7 | TTAATTA
MA0173.1 | 7 | TTAACAT
MA0174.1 | 7 | TTTATTA
MA0175.1 | 7 | TTAATTG
MA0176.1 | 7 | TTAATTA
MA0177.1 | 7 | TTAATTA
MA0178.1 | 7 | TTAATTA
MA0179.1 | 7 | TTAATTA
MA0180.1 | 9 | TTTAATTAG
MA0181.1 | 7 | TTAATTA
MA0182.1 | 7 | TTTATTA
MA0183.1 | 8 | TTTAATTA
MA0184.1 | 7 | CTAATTA
MA0185.1 | 6 | TTCGTG
MA0186.1 | 7 | TTAATGA
MA0187.1 | 7 | TAATTAC
MA0188.1 | 7 | CCAATTA
MA0189.1 | 7 | TTAATTA
MA0190.1 | 6 | TAATCC
MA0191.1 | 7 | TTAATTA
MA0192.1 | 7 | TTAATTG
MA0193.1 | 7 | CTACCAA
MA0194.1 | 7 | TTAATTA
MA0195.1 | 7 | TTAATTA
MA0196.1 | 7 | TTAATTG
MA0197.1 | 8 | TTTAATTA
MA0198.1 | 7 | CTAATTA
MA0199.1 | 5 | TGATA
MA0200.1 | 7 | CTAATTA
MA0201.1 | 7 | TTAATCC
MA0202.1 | 7 | CTAATTA
MA0203.1 | 7 | TTAATGA
MA0204.1 | 6 | TGATAC
MA0205.1 | 10 | TTGCTCTCTC
MA0206.1 | 7 | TTAATTA
MA0207.1 | 6 | TGACAG
MA0208.1 | 7 | TAATTAA
MA0209.1 | 7 | CTAATTA
MA0210.1 | 5 | TAACA
MA0211.1 | 7 | TTAAGTG
MA0212.1 | 6 | TAATCC
MA0213.1 | 8 | CTGGCGCC
MA0214.1 | 7 | TTAATTG
MA0215.1 | 7 | TTAATGA
MA0216.1 | 7 | TTTATTG
MA0217.1 | 5 | TAACA
MA0218.1 | 6 | TTGAAC
MA0219.1 | 7 | TTAATGA
MA0220.1 | 7 | TTAATTA
MA0221.1 | 7 | CTAATGA
MA0222.1 | 8 | TTTTGACA
MA0223.1 | 7 | GTAATTA
MA0224.1 | 7 | GTAATTA
MA0225.1 | 7 | TTAATTA
MA0226.1 | 7 | TTAATTA
MA0227.1 | 6 | TGACAG
MA0228.1 | 7 | CTAATTA
MA0229.1 | 8 | TCTAATTA
MA0230.1 | 7 | TTAATTA
MA0231.1 | 6 | TAACTA
MA0232.1 | 6 | TAATTA
MA0233.1 | 5 | AAACA
MA0234.1 | 6 | TAATCC
MA0235.1 | 7 | TTGATTT
MA0236.1 | 7 | TTAATTA
MA0237.1 | 8 | CTTTGATC
MA0238.1 | 7 | TTAATTA
MA0239.1 | 9 | AGTAACAGT
MA0240.1 | 7 | TTAATTA
MA0241.1 | 7 | CTAATTA
MA0242.1 | 9 | TAACCGCAA
MA0243.1 | 12 | GACATTCCTCGA
MA0244.1 | 8 | ATTGCAAA
MA0245.1 | 7 | TTAATTA
MA0246.1 | 6 | TGATAC
MA0247.1 | 8 | CTCAAGTG
MA0248.1 | 7 | TTAATTG
MA0249.1 | 12 | TCGCATATGTTG
MA0250.1 | 7 | TTAATTG
MA0251.1 | 7 | TTAATTA
MA0252.1 | 6 | TGACAG
MA0253.1 | 9 | TTTCAAGTG
MA0254.1 | 6 | TATGCA
MA0255.1 | 10 | TTGAGTGATT
MA0256.1 | 7 | CTAATGA
MA0257.1 | 7 | TTAATTA
MA0258.1 | 18 | CAAGGTCACGGTGACCTG
MA0259.1 | 8 | GGACGTGC
MA0260.1 | 6 | GAAACC
MA0261.1 | 6 | GAACAC
MA0262.1 | 13 | AATGTTGCGAATT
MA0263.1 | 14 | ATTGGCTTCGTTAA
MA0264.1 | 11 | ACCACTTGAAA
MA0265.1 | 16 | TCGTATAAAGTGATAT
MA0266.1 | 7 | CTCTAGA
MA0267.1 | 7 | ACCAGCA
MA0268.1 | 7 | ACCCCAC
MA0269.1 | 21 | TTACATATTGCACCCGATTGG
MA0270.1 | 8 | CACACCCC
MA0271.1 | 6 | AGACGC
MA0272.1 | 8 | GTGACTCT
MA0273.1 | 21 | GATAATTCTCGGCAAGTATGT
MA0274.1 | 8 | ACTTGAAT
MA0275.1 | 6 | CCGGAA
MA0276.1 | 10 | CCGGATCGGG
MA0277.1 | 9 | AAAAAGAAA
MA0278.1 | 21 | GCACAGCCAGAGTCAAGTCAA
MA0279.1 | 10 | ATTAGTAAGC
MA0280.1 | 6 | CCGGAA
MA0281.1 | 8 | GCACGTGA
MA0282.1 | 8 | CTCGGAAA
MA0283.1 | 8 | GGCGGAGA
MA0284.1 | 10 | TTACGTAATC
MA0285.1 | 9 | CTAAGCCAC
MA0286.1 | 9 | ATGACGTAA
MA0287.1 | 11 | CAGCAAAAATG
MA0288.1 | 9 | TGACACATT
MA0289.1 | 7 | CGATAAG
MA0290.1 | 19 | AAAAGCCGCGGGCGGGATT
MA0291.1 | 9 | AATGTGCGC
MA0292.1 | 7 | CTCCGGA
MA0293.1 | 11 | AAAGATCTAAA
MA0294.1 | 9 | CGGAAAAAT
MA0295.1 | 8 | GACGCAAA
MA0296.1 | 20 | TGAATTGTAAACAAAGAGGA
MA0297.1 | 7 | GTAAACA
MA0298.1 | 6 | CTATCA
MA0299.1 | 15 | CGGGGAACAGTACTC
MA0300.1 | 8 | CCGATAAG
MA0301.1 | 9 | AGATCTACA
MA0302.1 | 11 | AAAGATCTAAA
MA0303.1 | 21 | CAAGGGATGAGTCATACTTCA
MA0304.1 | 8 | TGGAAGCC
MA0305.1 | 7 | GCTTCCT
MA0306.1 | 9 | ACCCCTAAA
MA0307.1 | 5 | GATAA
MA0308.1 | 21 | ATTAAAAAACTCCGGAGTATA
MA0309.1 | 8 | TGATAAGA
MA0310.1 | 8 | GACACGTG
MA0311.1 | 5 | CGGAA
MA0312.1 | 8 | CGGAGATA
MA0313.1 | 5 | TTGGT
MA0314.1 | 15 | TCTGATTGGTTCAGA
MA0315.1 | 15 | ACCAATCAGAGGCGA
MA0316.1 | 15 | TGGGATCTGATTGGT
MA0317.1 | 8 | ATAAACAA
MA0318.1 | 8 | CATGTAAT
MA0319.1 | 8 | ATGGAACA
MA0320.1 | 8 | CCGCCGAG
MA0321.1 | 9 | GCATGTGAA
MA0322.1 | 9 | GCATGTGAA
MA0323.1 | 15 | AAGCCGGAAGCGGGG
MA0324.1 | 10 | CCGTTACCGG
MA0325.1 | 8 | CCGGAATT
MA0326.1 | 8 | TTTGCTCA
MA0327.1 | 7 | ACACAAT
MA0328.1 | 9 | CATGTAATT
MA0329.1 | 7 | ACGCGTA
MA0330.1 | 7 | ACGCGTT
MA0331.1 | 12 | CCCAATTAGGAA
MA0332.1 | 6 | CTGTGG
MA0333.1 | 9 | AGTGTGGCG
MA0334.1 | 7 | CGCCACA
MA0335.1 | 8 | AACTGTGG
MA0336.1 | 21 | AGGACTATAGAACACTCTAAA
MA0337.1 | 7 | CCCCCGC
MA0338.1 | 7 | CCCCGCA
MA0339.1 | 7 | CCCCGCA
MA0340.1 | 6 | TAGGTA
MA0341.1 | 5 | AGGGG
MA0342.1 | 5 | AGGGG
MA0343.1 | 21 | TTTCCGGCCACAAAAACGCAA
MA0344.1 | 8 | GCCGGGGA
MA0345.1 | 21 | ATGACCTATATATAAAAATGA
MA0346.1 | 20 | TTTATTTATATATAATATGA
MA0347.1 | 20 | CTAGATCAGGGTCCATCGCA
MA0348.1 | 9 | TCGGAGATA
MA0349.1 | 7 | CGAACCG
MA0350.1 | 21 | AGGCACAGCTCATCGCGTTTT
MA0351.1 | 21 | TTCTGCACCTCATCGCATCCT
MA0352.1 | 8 | TCCGCGGA
MA0353.1 | 8 | TCCGCGGA
MA0354.1 | 8 | ACGGAGAT
MA0355.1 | 10 | ACCTGCAGCA
MA0356.1 | 6 | ATAATA
MA0357.1 | 8 | GCACGTGC
MA0358.1 | 8 | CCCGGGAA
MA0359.1 | 10 | CACCCATACA
MA0360.1 | 8 | TGCGGAAC
MA0361.1 | 7 | CGGCCGA
MA0362.1 | 7 | CTCGGGG
MA0363.1 | 9 | GTTACCCGG
MA0364.1 | 7 | CCCCTGA
MA0365.1 | 8 | GGTTGCTA
MA0366.1 | 5 | AGGGG
MA0367.1 | 11 | AATTTTTCCGG
MA0368.1 | 7 | CGCCAAG
MA0369.1 | 18 | AGTTCTATAAATAGATTC
MA0370.1 | 10 | TCCAAAGGAA
MA0371.1 | 12 | TCCATTGTTCTC
MA0372.1 | 8 | ACCCCTAA
MA0373.1 | 7 | GGTGGCG
MA0374.1 | 7 | CGCGCGG
MA0375.1 | 8 | CGCGCGCG
MA0376.1 | 20 | ATATTAGCACGTGCTTAGTC
MA0377.1 | 21 | TAGAGAATAGAAGAAATAAAA
MA0378.1 | 21 | ATTGAAAAAAATTTTCTACGG
MA0379.1 | 5 | ATATA
MA0380.1 | 7 | CTCCGGA
MA0381.1 | 6 | GGCCAT
MA0382.1 | 8 | ACGTAATG
MA0383.1 | 21 | TTACCTATAATTAAATTAGCA
MA0384.1 | 11 | TGGTAGCGCCG
MA0385.1 | 11 | ACCTGCAGGCA
MA0386.1 | 21 | GACTAGATATATATATTCGAT
MA0387.1 | 10 | AATTAAAGAA
MA0388.1 | 8 | GAAATCAA
MA0389.1 | 8 | AGATCTAC
MA0390.1 | 21 | GTCCAAAATTTTTCACTCTGG
MA0391.1 | 7 | CTCGGAA
MA0392.1 | 8 | CGGTGTTA
MA0393.1 | 7 | TGAAACA
MA0394.1 | 8 | TGCGGCGC
MA0395.1 | 20 | TGATCGGCGCCGCACGACGA
MA0396.1 | 9 | GCTAGCGCA
MA0397.1 | 9 | GATAGCGCA
MA0398.1 | 9 | AAAATTTTT
MA0399.1 | 7 | CGCGGGG
MA0400.1 | 20 | ATGATAAACTCCGAAAATTT
MA0401.1 | 8 | ACGCGAAA
MA0402.1 | 8 | TGCTGGTT
MA0403.1 | 8 | AACCCTAA
MA0404.1 | 8 | CGGATCCG
MA0405.1 | 8 | GCGGACAT
MA0406.1 | 8 | ACATTCCC
MA0407.1 | 15 | GGAAACTCTAAGAAC
MA0408.1 | 8 | CTGTCAAA
MA0409.1 | 7 | CACGTGA
MA0410.1 | 8 | CGGCGGGA
MA0411.1 | 7 | TATACGA
MA0412.1 | 13 | TCGGCGGCTAATT
MA0413.1 | 20 | AAATTCCCCCTGAATTTGTG
MA0414.1 | 7 | CTCGAGA
MA0415.1 | 20 | ATTTGCTTACGTAAGCTCGT
MA0416.1 | 8 | ATTACGTA
MA0417.1 | 6 | AAGCAT
MA0418.1 | 20 | GGTCTGATTACGTAAGCGAC
MA0419.1 | 11 | ATTAGTAAGCA
MA0420.1 | 8 | ACCGGAAC
MA0421.1 | 10 | TTTACCCGGC
MA0422.1 | 10 | CCGGAGATAA
MA0423.1 | 9 | ACCCCTATT
MA0424.1 | 8 | CTCCGGAA
MA0425.1 | 14 | ACCCCACTTTTTTA
MA0426.1 | 6 | TAATTG
MA0427.1 | 11 | AGCTCCGGAGA
MA0428.1 | 9 | AACGGAAAT
MA0429.1 | 7 | CGGCCGA
MA0430.1 | 8 | CCGGAGTT
MA0431.1 | 9 | ACCCCGCAC
MA0432.1 | 8 | TCGGAGAT
MA0433.1 | 8 | TTAATTAA
MA0434.1 | 9 | TGTAGATCA
MA0435.1 | 20 | TGAAGACGTAAATCCTTACA
MA0436.1 | 7 | CCCCACG
MA0437.1 | 9 | ATTTCTCCG
MA0438.1 | 8 | ACGGAAAT
MA0439.1 | 11 | CTTATCTCCGC
MA0440.1 | 15 | ACCTTAAAGGTCATG
MA0441.1 | 9 | TTCCCCGCA
MA0442.1 | 6 | CTTTGT
MA0443.1 | 10 | AGGGGGCGGA
MA0444.1 | 7 | TTAATTG
MA0446.1 | 11 | TGTTTGCTTAA
MA0447.1 | 10 | ATTACGTAAT
MA0448.1 | 7 | TTAATTA
MA0449.1 | 10 | GGCACGTGCC
MA0450.1 | 9 | GGGGCGTGA
MA0451.1 | 12 | AAACTAGAGCAC
MA0452.1 | 11 | CAAAAGGGTTA
MA0453.1 | 12 | TATGCAAATTAG
MA0454.1 | 11 | AACAGTAGCAG
MA0455.1 | 7 | CTAATTA
MA0456.1 | 12 | GACCCCCCGCTG
MA0457.1 | 7 | TTAATTA
MA0458.1 | 11 | TTGTTTACATT
MA0459.1 | 10 | AAAAGTCAAA
MA0460.1 | 9 | AAGGATAAT

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

- There were 0 motif occurrences with a p-value less than 0.0001.
- The p-value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.
- The score for the match of a position in a sequence to a motif is computed by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
- The table is sorted by increasing p-value.

Motif | Sequence Name | Strand | Start | End | p-value | Matched Sequence
--- | --- | --- | --- | --- | --- | ---

DEBUGGING INFORMATION

Command line:

    /home/james/reldist/BUILD/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_4 --bgfile memechip_example_output_files/background --motif MA0036.1 JASPAR_CORE_2009.meme memechip_example_output_files/sample-dna-Klf1.fa

Settings:

    output directory = memechip_example_output_files/fimo_out_4
    MEME file name = JASPAR_CORE_2009.meme
    sequence file name = memechip_example_output_files/sample-dna-Klf1.fa

    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

    max sequence length = 250000000
    output threshold = 0.0001
    threshold type = p-value

    max stored scores = 100000
    pseudocount = 0.1
    verbosity = 1

    selected motif = MA0036.1

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

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