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

FIMO - Motif search tool

FIMO version 4.12.0, (Release date: Tue Jun 27 02:09:01 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 memechip_example_output_files/Klf1.fna
Database contains 904 sequences, 452000 residues

MOTIFS JASPAR_CORE_2014.meme (DNA)

MOTIF | WIDTH | BEST POSSIBLE MATCH
--- | --- | ---
MA0004.1 | 6 | CACGTG
MA0006.1 | 6 | TGCGTG
MA0008.1 | 8 | CAATTATT
MA0009.1 | 11 | CTAGGTGTGAA
MA0010.1 | 14 | GTAATAAACAAATC
MA0011.1 | 8 | TACTATTT
MA0012.1 | 11 | TAAACTAAAAG
MA0013.1 | 11 | TAGTAAACAAA
MA0015.1 | 10 | GTATATATAC
MA0016.1 | 10 | GGGGTCACGG
MA0017.1 | 14 | TGACCTTTGAACCT
MA0019.1 | 12 | AGATGCAATCCC
MA0020.1 | 6 | AAAGCA
MA0021.1 | 6 | AAAGCG
MA0022.1 | 12 | GGGGTTTTTCCG
MA0023.1 | 10 | GGGGTTTTCC
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
MA0038.1 | 10 | CAAATCACTG
MA0040.1 | 11 | TATTGTTTATT
MA0041.1 | 12 | GAATGTTTGTTT
MA0042.1 | 12 | GGATGTTTGTTT
MA0043.1 | 12 | GGTTACGTAATT
MA0044.1 | 9 | GTTGTATTC
MA0045.1 | 16 | CAACAAATGGAAAAAC
MA0046.1 | 14 | GGTTAATAATTAAC
MA0048.1 | 12 | GCGCAGCTGCGT
MA0049.1 | 10 | GCATAAAAAA
MA0051.1 | 18 | GGAAAGTGAAAGCAAAAC
MA0053.1 | 5 | AAAGC
MA0054.1 | 9 | TAACCGTTT
MA0056.1 | 6 | TGGGGA
MA0057.1 | 10 | GTAGGGGGAA
MA0059.1 | 11 | GAGCACGTGGT
MA0063.1 | 7 | TTAATTG
MA0064.1 | 5 | AAAGC
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
MA0077.1 | 9 | CCATTGTTC
MA0078.1 | 9 | TTCATTGTC
MA0081.1 | 7 | AGAGGAA
MA0082.1 | 14 | CCAAAAATGGAAAT
MA0084.1 | 9 | GTAAACAAT
MA0085.1 | 16 | TTGTGGGAAACGAGAT
MA0086.1 | 6 | CAGGTG
MA0087.1 | 7 | ATTGTTT
MA0088.1 | 20 | GATTTCCCATAATGCCTTGC
MA0089.1 | 6 | CATGAC
MA0090.1 | 12 | CACATTCCTCCG
MA0091.1 | 12 | CGACCATCTGTT
MA0092.1 | 10 | GGTCTGGCAT
MA0096.1 | 7 | ATGACGT
MA0097.1 | 12 | GATGACGTGGCC
MA0101.1 | 10 | GGGGATTTCC
MA0107.1 | 10 | GGGAATTTCC
MA0108.2 | 15 | GTATAAAAGGCGGGG
MA0109.1 | 10 | AACCTTATAT
MA0111.1 | 11 | AGGGTAACAGC
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
MA0139.1 | 19 | TGGCCACCAGGGGGCGCTA
MA0142.1 | 15 | CTTTGTTATGCAAAT
MA0149.1 | 18 | GGAAGGAAGGAAGGAAGG
MA0062.2 | 11 | CCGGAAGTGGC
MA0039.2 | 10 | TGGGTGGGGC
MA0138.2 | 21 | TTCAGCACCATGGACAGCGCC
MA0002.2 | 11 | GTCTGTGGTTT
MA0047.2 | 12 | TGTTTACTTAGG
MA0112.2 | 20 | GGCCCAGGTCACCCTGACCT
MA0065.2 | 15 | GTAGGGCAAAGGTCA
MA0151.1 | 6 | ATTAAA
MA0152.1 | 7 | TTTTCCA
MA0153.1 | 12 | TTAATATTTAAC
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
MA0163.1 | 14 | GGGGCCCAAGGGGG
MA0164.1 | 7 | CAAGCTT
MA0018.2 | 8 | TGACGTCA
MA0099.2 | 7 | TGACTCA
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
MA0217.1 | 5 | TAACA
MA0218.1 | 6 | TTGAAC
MA0219.1 | 7 | TTAATGA
MA0220.1 | 7 | TTAATTA
MA0221.1 | 7 | CTAATGA
MA0222.1 | 8 | TTTTGACA
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
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
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
MA0094.2 | 8 | TTTAATTA
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
MA0445.1 | 11 | TCCATTGTTCT
MA0446.1 | 11 | TGTTTGCTTAA
MA0447.1 | 10 | ATTACGTAAT
MA0448.1 | 7 | TTAATTA
MA0449.1 | 10 | GGCACGTGCC
MA0450.1 | 9 | GGGGCGTGA
MA0451.1 | 12 | AAACTAGAGCAC
MA0453.1 | 12 | TATGCAAATTAG
MA0454.1 | 11 | AACAGTAGCAG
MA0456.1 | 12 | GACCCCCCGCTG
MA0457.1 | 7 | TTAATTA
MA0458.1 | 11 | TTGTTTACATT
MA0459.1 | 10 | AAAAGTCAAA
MA0460.1 | 9 | AAGGATAAT
MA0141.2 | 12 | AGGTCAAGGTCA
MA0145.2 | 14 | CCAGTTCAAACCAG
MA0146.2 | 14 | GGGGCCGAGGCCTG
MA0461.1 | 8 | CAGATGGC
MA0462.1 | 11 | GAAATGACTCA
MA0463.1 | 14 | TTTCCTAGAAAGCA
MA0464.1 | 11 | CTCACGTGCAC
MA0465.1 | 11 | AAGCCATAAAA
MA0466.1 | 11 | TATTGCACAAT
MA0467.1 | 11 | AAGAGGATTAG
MA0468.1 | 11 | TAATTTAATCA
MA0469.1 | 15 | CTCCCGCCCCCACTC
MA0470.1 | 11 | GGGCGGGAAGG
MA0471.1 | 11 | GGGCGGGAAGG
MA0472.1 | 15 | CCCCCGCCCACGCAC
MA0473.1 | 13 | GAACCAGGAAGTG
MA0474.1 | 11 | ACAGGAAGTGG
MA0475.1 | 11 | ACAGGAAGTGG
MA0476.1 | 11 | TGTGACTCATT
MA0477.1 | 11 | GGTGACTCATG
MA0478.1 | 11 | GGATGACTCAT
MA0479.1 | 11 | TCCAATCCACA
MA0480.1 | 11 | TCCTGTTTACA
MA0481.1 | 15 | CAAAAGTAAACAAAG
MA0482.1 | 11 | TCTTATCTCCC
MA0483.1 | 11 | AAATCACAGCA
MA0484.1 | 15 | AGAGTCCAAAGTCCA
MA0485.1 | 13 | GGCCATAAATCAC
MA0486.1 | 15 | CTTCTAGAAGGTTCT
MA0488.1 | 13 | AAGATGATGTCAT
MA0489.1 | 14 | AGGAGATGACTCAT
MA0490.1 | 11 | GGATGACTCAT
MA0491.1 | 11 | GGTGACTCATC
MA0492.1 | 15 | AAAGATGATGTCATC
MA0493.1 | 11 | GGCCACACCCA
MA0494.1 | 19 | TGACCTAAAGTAACCTCTG
MA0495.1 | 18 | GCTGAGTCAGCAATTTTT
MA0496.1 | 15 | CTGAGTCAGCAATTT
MA0497.1 | 15 | ATGCTAAAAATAGAA
MA0498.1 | 15 | AGCTGTCACTCACCT
MA0499.1 | 13 | TGCAGCTGTCCCT
MA0500.1 | 11 | GACAGCTGCAG
MA0501.1 | 15 | ATGACTCAGCAATTT
MA0502.1 | 15 | AAATGGACCAATCAG
MA0503.1 | 11 | AGCCACTCAAG
MA0504.1 | 15 | AGGGGTCAGAGGTCA
MA0505.1 | 15 | AAGTTCAAGGTCAGC
MA0506.1 | 11 | GCGCCTGCGCA
MA0507.1 | 13 | TTCATTTGCATAT
MA0508.1 | 15 | AGAAAGTGAAAGTGA
MA0509.1 | 14 | GTTGCCATGGCAAC
MA0510.1 | 15 | CTCCCTGGCAACAGC
MA0511.1 | 15 | GGGGTTTGTGGTTTG
MA0512.1 | 11 | CAAAGGTCAGA
MA0513.1 | 13 | CTGTCTGTCACCT
MA0514.1 | 10 | CCTTTGTTTT
MA0515.1 | 10 | CCATTGTTTT
MA0516.1 | 15 | GCCCCGCCCCCTCCC
MA0517.1 | 15 | TCAGTTTCATTTTCC
MA0518.1 | 14 | TTTCCAGGAAATGG
MA0519.1 | 11 | ATTTCCAAGAA
MA0520.1 | 15 | CATTTCCTGAGAAAT
MA0521.1 | 11 | AACAGCTGCAG
MA0522.1 | 11 | CACAGCTGCAG
MA0523.1 | 14 | AAAGATCAAAGGAA
MA0524.1 | 15 | CATGGCCCCAGGGCA
MA0525.1 | 20 | AGACATGCCCAGACATGCCC
MA0526.1 | 11 | GTCATGTGACC
MA0527.1 | 15 | CTCTCGCGAGATCTG
MA0528.1 | 21 | GGAGGAGGAGGGGGAGGAGGA
MA0007.2 | 15 | AAGAACAGAATGTTC
MA0102.3 | 11 | ATTGCACAATA
MA0024.2 | 11 | CGGGCGGGAGG
MA0154.2 | 11 | GTCCCCAGGGA
MA0162.2 | 14 | CCCCCGCCCCCGCC
MA0076.2 | 11 | CCACTTCCGGC
MA0258.2 | 15 | AGGTCACCCTGACCT
MA0098.2 | 15 | CCCACTTCCTGTCTC
MA0148.3 | 15 | TCCATGTTTACTTTG
MA0035.3 | 11 | TTCTTATCTGT
MA0036.2 | 14 | AGATTCTTATCTGT
MA0037.2 | 8 | AGATAAGA
MA0114.2 | 15 | CTGGACTTTGGACTC
MA0050.2 | 21 | TTTTACTTTCACTTTCACTTT
MA0058.2 | 10 | AAGCACATGG
MA0052.2 | 15 | AGCTAAAAATAGCAT
MA0100.2 | 10 | CCAACTGCCA
MA0147.2 | 10 | CCATGTGCTT
MA0104.3 | 8 | GCCACGTG
MA0150.2 | 15 | CAGCATGACTCAGCA
MA0105.3 | 11 | GGGAATTTCCC
MA0060.2 | 18 | AGAGTGCTGATTGGTCCA
MA0014.2 | 19 | GAGGGCAGCCAAGCGTGAC
MA0080.3 | 15 | AAAAAGAGGAAGTGA
MA0143.3 | 8 | CCTTTGTT
MA0079.3 | 11 | GCCCCGCCCCC
MA0083.2 | 18 | CATGCCCAAATAAGGCAA
MA0137.3 | 11 | TTTCCAGGAAA
MA0144.2 | 11 | CTTCTGGGAAA
MA0140.2 | 18 | CTTATCTGTGAGGAGCAG
MA0003.2 | 15 | CATTGCCTCAGGGCA
MA0106.2 | 15 | ACATGCCCAGACATG
MA0093.2 | 11 | GCCACGTGACC
MA0095.2 | 12 | CAAGATGGCGGC
MA0103.2 | 9 | CCTCACCTG
MA0529.1 | 15 | TCGAAACTATCGATA
MA0216.2 | 11 | GGCCATAAAAA
MA0530.1 | 15 | GATGACTCGGCAAAT
MA0531.1 | 15 | CCGCTAGATGGCGCC
MA0452.2 | 14 | TTTAACCCTTTTTC
MA0532.1 | 15 | CGGAATTCCAGGAAA
MA0533.1 | 21 | GCCCAAAAGTATGCAACAAAT
MA0534.1 | 15 | GAGTTCATTGACCTT
MA0237.2 | 14 | TCGGCTCCTTTGAT
MA0535.1 | 15 | CAGGCGCCGCCGCCG
MA0536.1 | 11 | TATCGATAGTT
MA0247.2 | 10 | TTTCAAGTGG
MA0537.1 | 11 | AAAAGTGAAAA
MA0538.1 | 15 | GTGTGTGTGTGCGTG
MA0540.1 | 16 | TGTCCCTGCGCGATAA
MA0541.1 | 15 | CGCGCGCGCGAAATT
MA0542.1 | 8 | TCTTATCA
MA0543.1 | 15 | AGAGAGACGCAGAGA
MA0544.1 | 12 | GTGTCGGCCGCT
MA0545.1 | 11 | GAACAGCTGTC
MA0546.1 | 10 | AAAGTAAACA
MA0547.1 | 15 | AAAATGATGACAATT
MA0548.1 | 15 | TTTCCATTTTTGGAA
MA0549.1 | 11 | CGCACGTGTGA
MA0550.1 | 14 | AAGCCACGTGTCCA
MA0551.1 | 16 | AATGCCACGTGGCATT
MA0552.1 | 14 | AGAAGGTCACGTGG
MA0553.1 | 8 | CCTCGTAC
MA0554.1 | 21 | TTTTTTTTTTTTTTTTTTTTT
MA0555.1 | 20 | ATTACCAAAAATGGAAAGAA
MA0556.1 | 15 | TTCCAAAAATGGAAA
MA0557.1 | 12 | CTCACGCGCTCA
MA0558.1 | 21 | AATTTCCAAAAATAGAAAGAA
MA0559.1 | 14 | CCAAAAAAGGAAAA
MA0560.1 | 10 | AGCCACGTGA
MA0561.1 | 8 | CACGTGGC
MA0562.1 | 8 | TCACGTGG
MA0563.1 | 11 | TCCATTTTTGG
MA0564.1 | 9 | CTGCATGCA
MA0565.1 | 9 | CGCATGCGC
MA0566.1 | 8 | GCACGTGC
MA0567.1 | 8 | CGCCGCCA
MA0568.1 | 8 | GCACGTGC
MA0569.1 | 8 | ACACGTGC
MA0570.1 | 19 | GGACACGTGGCACGACGGG
MA0005.2 | 18 | ATTACCAAATTGGGTAAT
MA0571.1 | 21 | TGGCACAGTTCCCGAGGTGAA
MA0572.1 | 12 | TTCAATTATTGC
MA0110.2 | 13 | GGTCCAATTATTG
MA0573.1 | 19 | AATCGTAATGATTACTCGC
MA0574.1 | 13 | CGACGGTAGGTGG
MA0575.1 | 13 | AAGTGACAGTTAC
MA0576.1 | 13 | GGGGGGTAGGTGG
MA0577.1 | 16 | ATTGCCGTACTTTTTC
MA0578.1 | 16 | TTTTTTGTACCTTATT
MA0579.1 | 11 | GGCTCAGCGCG
MA0580.1 | 14 | CGTGAGTCACGTGA
MA0581.1 | 11 | TGCATGCACAT
MA0582.1 | 12 | CAGCAACAGAAA
MA0583.1 | 12 | ATCACCTGAGGC
MA0584.1 | 18 | TTTACCATATATAGAAAT
MA0001.2 | 18 | GTTTCCATATATAGTAAG
MA0585.1 | 18 | ATTGCCAAATTGGGTAAG
MA0586.1 | 19 | TTGCGTCCGTACAGGAGGG
MA0587.1 | 10 | GTGGACCCGG
MA0588.1 | 11 | TGGTGACGTAA
MA0589.1 | 11 | TTGACCGAGCC
MA0590.1 | 19 | TATTGACCGGCGGTCAATA
MA0591.1 | 15 | AGGATGACTCAGCAC
MA0592.1 | 11 | CCAAGGTCACA
MA0593.1 | 11 | AAGTAAACAAA
MA0594.1 | 11 | GCCATAAATCA
MA0595.1 | 10 | ATCACCCCAC
MA0596.1 | 10 | ATGGGGTGAT
MA0597.1 | 9 | CTGCCCGCA
MA0598.1 | 8 | CCTTCCTG
MA0599.1 | 10 | GCCCCGCCCC
MA0600.1 | 19 | GTTGCCATGGCAACCGCGG
MA0113.2 | 15 | AGAACAGAATGTTCT

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

SECTION I: HIGH-SCORING MOTIF OCCURENCES

- There were 0 motif occurences with a p-value less than 0.0001. The full set of motif occurences can be seen in the tab-delimited plain text output file fimo.txt, the GFF file fimo.gff which may be suitable for uploading to the UCSC Genome Table Browser (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), or the XML file fimo.xml.
- 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 q-value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.
- The table is sorted by increasing p-value.

Motif ID | Alt ID | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence
--- | --- | --- | --- | --- | --- | --- | --- | ---

DEBUGGING INFORMATION

Command line:

    /Users/cegrant/meme_4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_4 --bgfile memechip_example_output_files/background --motif MA0204.1 JASPAR_CORE_2014.meme memechip_example_output_files/Klf1.fna

Settings:

        output_directory = memechip_example_output_files/fimo_out_4
        MEME file name = JASPAR_CORE_2014.meme
        sequence file name = memechip_example_output_files/Klf1.fna

        background file name = memechip_example_output_files/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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