Unable to get a statistically significant motif

[Arun Prasanna]

Hi,

I chose to perform motif discovery on co-expressed genes. I chose the genes based on correlation value of > 0.8 between expression values. I ran local MEME with following parameters.

command: meme highly_similar.fasta -dna -o HS_zoops -mod zoops -minw 6 -maxw 50 -minsites 13 -nmotifs 50

I chose to keep -nmotifs to 50 so that I could find at least 5 to 6 motifs that are statistically significant. However, all the motifs I got was with E-Value starting from 2.8E+03 and semi-transparent in html display !. The combined p-values in motif locations show significance. 

Does this mean that, they are only coexpressed and not co-regulated at all or there is no strong signal for binding region ? Can anyone please let me know, what I am missing ?

Thanks,

AP

The sequences are below:

>AROS_01275

GGACACGCGGCATATGATAGTATTCAAAGATCTTCCCCCCAATGGGGAAGGCTAAGAAGG

ATTGTGTCACGAATCCGATCGGCAAGTAGTTGACTGCTTCTATTACTGTTTGGGAGTTAT

ACTTAGCACTGTGTTACGGCTCGCCGCCGTTGGGCGCTCGGGCTTACAGATCAATATTAG

CAGCATTAGTGAGCGAACGAAGAAACCGAAAACATGGACCGTTCATGTGAACCTGTTGAT

GTTGTCTTGAAAGTTGATGGTGAATCAGATCAACGTCATGGCTGGACAGCTGCAAAAGTG

CGTGATGCCGCCCTGTTTTCACTCGTACGATGATCCTGATTCCTGAGATGATGATGATGG

TCCCGTCGGGCGAGATCCATTTGAAAATCACAGTCGTTCATGCCTGGAATTGAATGCCAA

TTTGAATATGACGTACTGTGGCGTGGTTGCTGCAGGTCTTGTCACCCTTCTCTGTGGACC

TTCTGGTTTTCTTGATTATTCTCAAGAACGACGACATACTTTGGTCTTTACCCGAATATC

GAGTTTTCCGGATTTATGCGCTGCTTCTGTGGCCCCCTTCGCCGCGCCGTCGGGCATCTA

TTAGAAATTTTAAGTTCACGTCGCTTTCGCTCTCCATGAGGATACTCAGCGCTGGGGTCG

AGGCGTAATATAGTGTATTCGTGTCTGCCGGTAACACCGCAGGGGTTCCTTCACGCAAGG

TTTCCGGCGCGCCGCTTCCAGCTGATGATGTCCCTTTAGTAAGGGTGTATAGAGCTCGGT

TAGTTCGGATATCCTCCGAGAGTCTCCCTTGGGACACCTGCTACGGAGGAGGCTCCGAGA

CCCTGCCTATGGAAGCTACTACGGTTTTGAAAAACAAATGAATCTGATCATCAATTGTGA

ATTCGCAACTGTGGGAACTGCAGGGTCTTTATATCTAGCTCTCTGGCCGCCTTGGTTTCG

TCAAATCCCTGCCGCTTATTTTCCCCCCTCGCCTACTACT

>AROS_03021

GATGCGTATCAGCAGGATTCGAGTGGAGTTGTCCACGGTCCTCAGTCTCGCTTCGATGCC

GTGAAGAGTTTACTCCATGTCGCAGTCTTCTAACTCCAACCAAACTCAACATCACTCCAT

GTTCATCAGCGCTTCATCCTCAGATTCCATCGCGCATCTTCACAAGTTCAGATGCGTGAT

TGTCTCATGTCGAATCACGGGTGAAGCGGTGATATTTTCTGTCCCAGCGTACGCTACTTA

AACACTCATTCTTGTAAGTTGTTACCTTATTCCATCACGGAGCTCAATATGTCAGCACCA

CCAGCCGTACCCACTTTGCTTCCTGCTCTAGACAACACTCTCGGGGCCCTATATATTGGC

GCCAGTCTCTCGACGTTGTACGTATAAAGACTCTCTCGCAATATTACCACCTCTCATAGC

AAGGAAGATTGTACGGGGTTATCTGCGTCCAGACGTTTCTCTACATAACTTCAAATCGGG

CACGATCTGACCGTTGGTGGTTGAAGCTTCTGGTGTTCGTTACAGTGTAGGTGACGATAT

TCTATATATCCTGGCAACGATATAATGCAACCTACTTGTAGTGTAAGTGCTTCATCCAAC

CTCTTTAGTAAACAGTCATACACTTACCTATCCCACGATAGGGATTGGATACTGTTCACC

AAGGCCTCATTCTGGCTGGCATGTATCGTTTTCTGGTAAGCAACTTCGCTAATCCAGCTG

CGCTTGTAGAAGGAGGGGTTAGCAGCGGCGCGGCGTATGTGTACGTCTTTTATTCACTTA

GCCCAATCTCATTGGCAAGATAACTAGATTGGTTATATATGCAAGTCTCGCTATTCTTTA

CCGTGGAATTACTTATGAAATTAACACTATGACAGGGACAGTCCATCGTTGGAGTCAGTA

TCGTTTTTCGACCTTCTCTCATGTCTCAATATGCTCAGAGGACCAGACCTGTTCTATGTT

TCTGGTGCAGCTGTGAGGAATAATTTACCGCCAATTCAGC

>AROS_04602

ACTGACGATGATCGACCATATCCAGTGGTAACCGTCATCGAGGTGCTTTGTTCTTTTTAA

GGCAGAGTCGCTAGTCGCCGGTAGTGTATCATCAACAAAGCACTGGAATCGGCTGATCGG

ATCGATCGCCGATCTCTTTTCTTCTGTCACGTCCAAAATTTTGTGGGGAACTGACTCGCT

CATTTCAGCTCAGTCTCTATACGTCCTGTAAGATTTGGTGTGCTGTTCTGTGATGACTGA

GCTTCAGGGATGGTGCGACCTGAGGGTGCCGCTGTTGTCTGTTTTTAAGGGATTCCGAGG

TGTCGCGTTCATCATCAAGACAGTCACGCAGTCTGGAAGGTGCGTGAAGTATCATTGGCT

ACCGTTGTTTTGCTATTCAAACTTGCTCCATATTAGTTTGCCTCAAAGGCCTAGTGCTGC

GCGCTATTTCCACGATGTAGGGACAATTTCTCATGTATATATTTCAGGTGCCTTAATACT

CAAAGCGCGGCGATTTCTCGTCCCCATTCTTCATATGCCGGTCCCTATTCGCGGGCCATA

AACTACCTCAAAGCAAAATCCTATTGTTCTACTATTACGATATATTTGGGCCATGATGAA

AGTAGACGCCGGTATCATCACGACGAGGGCTTCGCTCGCTAAGCGAATGAATGGGATGCC

GTCACGGCCACTGCCATTCCGCGTCTTACGCCCCTTCTCATCATTGTGGACCTCTGTTCC

AGCTCATTCCGTTGTTCTTTTCTCTGATACGCCGACTTCCGCTTTGAATACTCTCCAGAA

AGATCAGTATAGAGACTATTGTTTTCTTCAAGGCGCTGCAAGTCTCTAGATTACGTTGCA

TCGAGATGGTGCTCCCACAGGTAAGTAACCCTTTGCTTTGACGACAGCTGATCACACGAG

TCGCATAAGGTTTACGCAAAGAACAACAACCTCCTCAGAGTATACGTAGATACGAACATT

TCACGCGCGTTTTCTCTATGCGTCTTAAGAGCTTGCAGGA

>AROS_14610

TCCAGTCGACCATGGGATATGACGAAGATCGGCAAGAGAAATATTGAGACTGGTATACTA

TATATGATGCAGAGGAAGAGACAGAGTAAAACAGAGAACCGTGGTAATGATGTTCACATC

CCAAACGCGTGATATGTCTGGCCTATCGAACTGAGGTCCGGCAGCGATACTGAAAGCTTG

GAATCTTAATGCATTCAATAACAAATCTAAATGAAGAGATTCTAGGATCAGAAACACAAA

AAACGGGCATTCCGTTTCTCCGCTTTCAGCGCAGAAAACCCGAGTTGCATATGTTGAACT

CGATGAGAACTTGAAGGGGCAGAAAAGGGTAGAGTGGCCCTGAGATGGTGGTTGAATCTG

AGATAGGAACGGACCGAGGTTCCGAATCCGGCAACTCGGGAACAGACAAGGACAAACAAC

GCGCCGTCCTTATCCAGATTCCATTGACTTTGAAGTTTGCCGCTGATACCATATGAGTCT

TTCTTCTTTTTATTCAGTTTATGTCGCGCCGAAAATCACCTATACAATTTCCTCTGATCC

TGAAATCAGATTTGCCGTTCGGAGTTCTGATTTCTCTGTTTTTCAAAAACGGATGCGATC

TCATGCGTCAGGGTGGTCTCCTGGCGAGCCGAAGAGGACTTGATTTCCAAAAGGTCTGTG

TAGTTGTTACGATAAAAACTGATCCGGCAGTTAGGAGAATAGCCCTAAGATCTGGCAATC

TTGGTCTTTTCTCATACGTCGACCTAGGCCTTATACTCCGTGGAAGCTCGATCTGTTTCA

ATGGTAAGTCTTTCTACCGTATGGTTTCTAATATACTAAGCAGTTTACATGTAGATTATT

TAAATAATAAAATTTTATCAGGCGCTCGGTCAGCCTGGAAGAGCGCTGAAGAGCTTCTCC

AAGAATAAACGCCCGACGATCTCGTGAAATTGATAAGTTGATATAAGTAGGTTTGAATAA

GTGGATCCACCCTCCCGCGTTTACTTGCTACGCTTCCACT

>AROS_17511

ACTCTGCCGACAGCTCATTTCCGAGTGGTCTCAGCGCTCTTCCACAGACGACGATCTGCA

TGATATCTATCGTGACATTCGGAAGAAATGTAATTGTTTGCCTTTTTCCCGGATCATTAT

ATTACTGAATTTACGATATAGACACCAATAACCATGCCGTAGCAGGCAGATGGAGATCGA

TGACCCGCGAGAGCAGCAAGTACAGCGTGGTATCAGAAACTGAAGAGAATTTCTATTCTC

GTGTCACTGAGGCGGTGTTGAATGTGTTGCGTGTTGCCGGGTGGTCGCCTGCAGACGCGA

AGGGCACTCTCATGCAGACTTTTGGCAAACGTGTTTCTGCGATCGTGAAGGCGGCAATGA

AACTAGATCGGGCTATGGGCGAGGGTATCACGTCTCAAGACCTAGTGGTGTATACCGCAC

ACTTCGATGACCATTTTGACTCTAACACGATGGTCGATGCATATGGGAACCAGAAGGCGG

ACGGCGACGTTGTGGCGTGTACATGTGAACTTGGGCTTAAAGTCTCCGGCGGGAGCAATA

TCTTGTTGAAGACTGGTGTCGTACTATACTCTGCATTTTTAACATAATGATTCAGGATAG

GTTTGTTTCCAGATACGGCATCGTGTACCTTAGTTTCGACCTGTAATCTTCCTCGTGGTT

CTAATGCATTCAATTTGTACCTTTTCAAGTGCACGTGTGAAAGAGTGAAATGCAGTTGAT

GTTCTTTAGATTGAGACAAGCTTTCATGGATCGCTTTGAGAGCCATACCGGTCACATAAC

TACTTTGGCCAGCTCTCACAAGGATCGAACTAGTGCAGACACAGCCCTCACATCCTCGAT

CCATTCACATAATCCCATGTGAAGAAACACGCCGCCATGCTAAAGTAACGTTCAGGTGAG

CGGTGCGTGTCAGGCCCGACATACACGTGGAATGCACATCTTAGCGACATACTACGAAGC

ACTCTTGCTATTCAGCACCATCTTCGCCTTCTGGCTTGCT

>AROS_05141

TTTTGCACAGAAACTCACGAATCGTGCCGATGCACGGCTGCGTATTGAAGCTTTCGAGCA

CATTGCGTTCGATGGCGCATTTCAACTCGAATGCATGTCTTCCGATGATTCTGACTCCGA

AGACGACGGTTTGCTGTGTTCTCGAGGGTATCCCTGGCGCAGTAAACGCTTAATCAGATT

GTACGAGATCCTGGACAGGGAAGACATCGGGGACAAGGCGTCCAAACCCAAGAGGGGTGT

TGGAAAGAAGGACCGAGCAGTTGGTCCATTGAAGGAAGGCTTCTGTCTCCCTCCCAAAGG

TGTGGCCAGCTGGATGGTCAGTCGACGATGGATAGCCGAAACTCAATTGACGAGGTCCGA

CTTACCGCGTTGGCTTGAATCGATTGTCAATGACCTGCCTGATTTTGATTCCACGGTCCA

GAAATGTGTTATTCTGGATGACGATAGCGACGACGAATACTTTCAGCGTACGAACTCTAA

TACGACTTCAAACTTGCAACCGTTACCTATGCATTACAGTATCACTAATAACTCTTCTCT

GCAATACGCTCTTTCTTGATCACTTATATATATGATTGTAGCCACTATGATGAACATCCA

GTACACGATGTCCCGCATTTAGTAAACCGTACGCGTATCATTTGCATCTCAACATGATAG

CAGGTGGGTTCCTTAGATGTTGTCTTGCAAGTATCGCGTCAAATGTTGGTCTAAGCAGGA

GGAGAGCGCCTTTGAACTAGGCTTATAGTGCCCAATCGGAATTCTTGTCCTTGTACGATT

TAACGCTAGGAATCAGGTTCGAAGTCCAAATCATCAGCCCTGTCAACTGCGACGGTCCGC

TCAGGCAGAATCCTTGCACATATGACAGCAAAGAGTCTCCCGTGGGCCGCATTGCCGTCA

CCAGCTTTGATTGCACAGGTCAGTTGAACAGAGAATCTCTGTCACGAACGAGTATATATT

GCATGAAGTTGTACTACTCCGACCCACTCATCTCCTCCTG

>AROS_08316

ATACCGTTTTCAGCGAGGAATATTACGATGCCGAATCGCTTCCCTGGGTGACTGCGAAGA

CTGGTGTAATGGCGGGTGAAGTTCGTAGTGCCGGTGGCGGTGGGTTCACTTCGGGCAATG

TCACTTTCGTGAACGTCCACAATGCCGGGTTTGTCTTAACTTCAGTTCTTGTATATTGAT

TAACTCACTATGCTCGGATCTTTCCAAATAGACACATGGTTCCGTACGATCAATCTGAGG

CTGCCCTGGTTTGTTAAATTTTATCGTATTTCTTACGGTACTGACTATTCATGTCTTGCT

AGGATCTGATTACTCGGTGGATTAAGGATAGCCCCCTGTCATAAGTGTATCATTGAGGAT

TCAGTTTGTTAGTACGTGTATAGAATGAATGTAGACTGGTATAACGTCTCCACTGATTAA

AGTTCGCATCATCTGTTGTATATGGCATGTGAAGGTGGCGCTTGCTCTGCTTCTTCGCCT

TCCACAGGATATTCAGGTGATCTACCACGTCAATCGCTTGTATGTATTAAGCGTACGTCT

TGGAGTTACCCGCCAGCAGCTACAGTAGCCGACGCCCACATATTTGCAACGGTCTGGTGG

TTTCAATCTATCAGTATTCTTAATATTGATATTTGATGTGAGGGAAGGCTGACGCGGTAG

ATCCAGGCAGACCTCTTATTCCTGCACAACGATTACTTTCTTCCATTGGATCCGGACTGC

TCGACATGCGCTTCTGGCCTCGAATTCTTCAAGATGTAATAGTCAAAAACTCGTAAACTA

GGGCTGCGAACGGTTAGAAGTCCCATATACTTCCCTCGATTAACCAGGCGGCGTTTCCTT

CCCGAGGATTCACAACGTCATCTGTTACCAAAGCTGAGGATACCTACCCTGGTATATCGT

GCATATCGTCGTATAAAAACCATCGTTGTATACCTCACATCCTCATCTCCTCCTCTGCGA

GAAGACCGAGCCTCCCAAACCCAGCCAGTCGACCACCAAC

>AROS_14226

CTGCATCGGTCACGGATACCACGTCGAGCACGTAAGTTATTCCATGTTCCCGACTCCCGA

TTTGAACCTGACTCATTTAATCTATAGCTTCGACGCATCTTACAACGACGTGAGCAAAGT

CACGATAAAGATGACTGCTCCCGAAGGCAAGACTTGTACGGCTGTGGTGCGTCTCTTTCA

ATCTTGTGATCATAAGCGGCTCCGTGACCTTTCCTTGTTAGACCAACACCAAGACTTGTA

ATATTCAGGCGACGGGCCAGATCCGCTACCTCGCGACCGGCTGGATTTGGTTCAACTACA

ACTCTGCGACTCAAGGCCACTATAAATGTTAGTATTCATGCAAGCACCTGGTTGCATGAT

CTAATTCGTTTTTTCTTCTAGGGGCTGTCAGCATTGAAGCCGTCCTCACAAACCAGGATG

ACCGCTCTAGCTTTGCCACCTTCAAGGGTTCTATGGTTGCGAACACCGAGACCAGCTATG

CTGGCAATTGTCAATAAATCTGACGTCACAGTCGGTGACTGTGCAGGTCCAGTATAAAGC

CGCAGCCTTTGTACAACGTCAACTAACGAAAACACCTCTTTGGTTATCTGTCCGGCATTG

ATTGATCCTATTTAGTCTGTTATTTATAATATTCTATAAACGACGAACATCCACTCTCCT

TCTTAACACTCACGTTTAGTTTATCATTTCGATTGCATAGCAGTAAGATGCATTCTTGTA

TGATACCTTTATCAGATAGGTAGATTCTCATGCTTCGATAGCTTCATTATCATGATGTAA

CTATGTCAAACTGATCCAGAGGATACCGTAGTCGCACCTTTCAGCGCTTCCAATATATTC

CCTAATCAATCATCATTCACCACAGTCCGTACTGATAGTTGCCTCCAAATTGAACCGGAG

ACAGGTAAAACAGGCAGTGAGCCGGGTCGCATGATGTCCGCGAGTCCCCGGGCGATGCTT

CTCTCCCTTTCCCCTCTTCTGCCCTACCTGTTTTACACCC

>AROS_16786

CTGACCCGAATGTCATTTTGAGTAGATACTTGAGACAGTCACGCGAGGGGAACTTGGACT

GTTTTGGGTTCAAATCTCGTCGCCACGTCTGGGAGCCCATCGATGGTGAGTCAGTGGTGA

GTTCGATCTCGTCACTTTTTCTTCTCTTCTTATTTCTCAGTTCAAACTTCGGGCTCTATC

GTCACACGCACCTGGGGGGCATTTATTAAATCCAATAACAAGAAGGTAAGCGCCTTTTCC

CCTTCTCGCTTTTGATTTCGGCTAAAGAATAATCTTTGCAGATTATAATATTGCATGGAA

GTGAGCCGTATTCGCCTTTCTTTGAATAACCTTTTTCGCAGTTAGGTTCTCGTTCTTTCG

GAGGATGTATACGGGGTTGGCTTGTGCGATTTTTGGTATATTTGACGTGCATAGACTATG

CTGGTTGTTTCCTTGTACACGCCTCGCTAACAAATTGTTTATTTTGTCTACTTGGTGGCC

CGAAGACATTAGATTAAGTATGTAATGTACGGCGAGTCTTTCTTCTTATAAGGATGCTCT

ATCTCACCGTTTTAAATAGAAAGCTCGAACCTTTCATTCCGAATCAGTGTCGCATGATGT

ATGCTCGGAAGTTGGATGCATCCAGTTTGACTGCCTGTAAGAATGATGGATCTATGCGTC

GAACAATGAGTCCATGATCAGACACATGGTTTATCCCCCGCGAAACTAGTATAACTTGTA

AGTCCTCACAGAACTCTAAGCGTCTATCTCGGGTGTTGCCTGGGCTCATTCAGATGTATT

TGCGGTATTCAATGATATCTCCAATATTTCACTGTGTCGTCTTGACCAAAGGTTTCCGAA

ATATTTGGATGCTTAGAAGCGAGGCTGTTGTTAACACGTTGTTGTGGTCTAAGCGCTAGT

ACGCAGTTGCTGCGTCTGACCACGAGAATGGCATGCGTCTGCACGACGAAAGCCTCTTGG

TGCAACTCTCTGAGGTTGGTACTGTACTACGTGGACCATC

>AROS_19547

CGTCTATAATGTCTATAGGTCGCTTGCGTCACGTTGGAACACAAGCACGCCCAAGCGATG

CGACAGTTTGTGACACGCGCGAGAACTTGGCGAGAACAATCACGTGCTGGAAAAGTTTGT

GGACGAAACGGGCCGATTCGCCGCCTTTACCTCCCACTCTGATCATGGCGGACAGCCGCA

AGACAAATACGTAGTGGTGCGTTGCTCGATCACTTGAGTTCTGGACAAAAACATACTTAC

ATCTCTTCAGTTCGAAGCACCGTTCCCAATGACACGTTGATGGCACGCGAACCTGGGCAA

TTTCTGATTCGTGTGACACACAGCATCGACTCGAACGTTCATTACAACCAAGCAACCAAA

AGTCGGTCTTTTCGCGGTCGTTCTTTGTGAGGTGCAAAGATATATAATTTTCAGTTTGTA

GCGAAGAACGTGCGCACCAATACCAATACCAATACCGTAAGTCTCTGAAGTCTATATATA

CATCTCTATTCTTAGGTCCCGTTTCCAGGCTGTTCAGGACGTACCAGAAGGCATGAGAAT

GCTACCAAATTCTTGCATCGTGGTTATAAGATTCGAAGCATGATCGTTAACATTGAACGG

GACTTGGAAGGCCGAAAGATTCGGGGAACTGCACCACGTTCTTGCTGTGTTCACTGGGCG

TCCATCAGCCCTTTCTTCCGTTTAGATGCTTTGTGGTAGATAATTTCGCAGGCCGGTCGG

GCTAAGTTGGCCAAAGAGAATCCTTTTCTGACCAGATGTCCCTTCTCTTAGGTGAGAGCT

CCCTTCTAGTTCCGGTATTGGTATATGTCACTCAACAATCGCGTCATCCTAGCAGATGAG

GGATTTTGGTGCACTTACGACTTGCATCTACTCGAGAAGAGTCACGAGTAATGTGGGTCG

AGTAAGCTTCGTGGCACGCCTGCGTCTGAAATACCCTTCTGGGTTTACCCTATGAGCCGT

ATATAAGGATGCGACAAGATATCCACATTGGTGGCCCATC

>AROS_22180

CCGCTTCTTTGCTAGAAGGTAGGTAGCTCCCCGTTATTCGTAGCTTGGATTTGCACTATT

GCATTCATTTACTTGCGACACTTCCAGTGGCAGATTTAGAGGGAGATCTGCCATACCCTG

ACACCCGCCACTATTTATATCGTGATTACACCCGAAAACGCACCTTGAACGCACCGAACA

CATGAACACATCTCTTTCATTGCTAACACGTTTCTTCTGCGCATCCACATTACTCAAACA

TCGAGGGAAGGATTCGCCTTAGCCTACAATCAATCACTAAAGGGCTATTGCCCGAACATT

GCCGGTGAACGTGTAGAAACCGCTTCTGACTTCGGTAATGCTAGGATTCAATTCTCTTTC

TGCTATTCATTCAAAGCACAGGCGCATGGAAATGAGGAGTTTCCTACAAAATCTCTCTTC

GACCAGATACTTGTGACAGACCCGTGGGGCACTCCACACGCCCGTTCACATCACCGGTTT

GCGATTATCCTTTGTTGCCTTCCGTCTCAGTTCCTTGAAATGAGTTGTAAATGACGCTGA

TTAATCTTCTTTTAACGAAACAACCCTTATTGACTCAATGTCGTGGGACGCATATGTTAA

CAGCGTGTATGCAGCCAGTTCTCCTCTCTCAAAAGTTCCATCCTCGATTCGCCAGAATTG

TTTCCTTTCCTTTTCGTGTCCGTAATCCTTCTACTACATTCTCCGTCTGTATGTCTTTCC

AAACGATTCATTCATTTGACTGACTTTCAGCAACAGTCGTCGCGTCCTCCAGCTCAAGAC

AAGCTGTAACTCGTCAAACAAGTTTTCCGCGCCGTTATTTGGTGCGTATATTGCATACTA

TATTCCCTGCTCAGTAAGCTAAGATAAGTGTAGGAATATTCGAAGAGCAACAACCGCCTT

ATCAGACTCGGTTCCTCTGTCAATATACAACGGGTTCGTCGTACAATTTCATGTTCCGCT

ATGCGCCCTAATGAGTGACAAAGTCCTTTAAATGACCGGA

>AROS_22280

GGGTGGCTTTTGGTTTCGAAGGAGGAAGAGTGCATGTTGACGGGAAGCTCTGAATCGAAC

CTTCAAGACCACTGGGCAAGTTCATCTTTCAATGAATTAATGAGGGGTGATCGATTGATC

CGTGGGAATATAGGCTGAAAACCCTGCTGCCGATAGATGTACAAGGCTTGCGTTGTGTAT

CAGTGATATCACTGATGGCGCACACTAAAGTGACACGCCGCATCGAAGCGCGAACACACA

ACGCAAGCACGGTTTTCAGATGCATCCACGTTAACGTGAACGCACGAACACGTGGAAGAA

GAACGAAATCCACCGTGCCCTGCAGTCGATTATTATATGACTATTGCTTATCTGTGGTAC

GCTTCTTACTTGGATTTTTCTCTTTCTGCTATTCGTTAAATTACAGGCGCACAGATGTGG

AGAATTTCGTGCCAATGATCTCTTGCAATGGATACCTACGAGAGGATTCTTTATTAGTTC

TATATGCTAGTCCACACCACAGATTCATGAGTATGTGTTGTTGATGCTCGTTTCAGTTTC

ATTAAACATCATTCCATAGAATGACGCGTAGTCCCGGGTCTGGTCATGACCTGCTTCATG

GGTTACATATGTCATCAACGTGCATGCAGTGCGATCTCCTCTCTCATAACCTCCCTCCTC

GATTCCCCACGATACGTTTTCTTCGTCGCATCCTTATCCCGTTTCCTACACTCCCTGTAT

GTACTTCTTTCCAAACGATCGTCCATTCAGCTAACCTTCAATGAAGGATCTCACATCATC

AAGCTCAAGTTTCGTGAAAGATATCCTCAGCGCATATTTCTGGTGGCCTCTTGGCATATT

CTACTGACCGCTTAGTAGGTCAGGATAAATATAGGAAAATTCAGGTACTGACAAGCGTTT

TCTTAGAATCGGTTCCTTTCGTGGACAGATAGTGGGTGCGTCCTCAATATTTTATGTTCT

GCTATGCTGCCTAATGCTTGAAGCCCTTAGAATCACCGAC

>AROS_22295

TCAGGTGGAGAGGCAGTATTTGTAGGTAATCGAGATGGTCCTGCACCAGAACTGGGGTGA

TGACCATCCAATGGACTGTTTGTCATATTGTAGAAAATTGAGTGTTTTGGAACTAGCTTG

ATTTGGTTTAGACCCCCTCGCGGTGGGCTCCAGAAATGTCAGCGGGATTCGGGATTAGGT

GAATTCCCTTTCAGTACAGTGCAATTGTCTGTACTGCTGTTGTAGTTCGATGGGGTCAAG

CACGAATGCTATAGATGTTCCAATCTAGTTCCTAGTGAGTGGTTTAGAGTGTGGGGAAAT

AGAGGATAGGGATGTGTTTGGTGGAAATGGGTGTACGTGAAGGGTGATGTGGTGGTGTTC

AGAATTGGTAATGTTGATAATAGTCAGGAATGGTAATGCTGTTGTTGGTCGAGAATGGTA

ATATAGTGTGCGATTGGTGTCAAGAATGGTTATATCGAGAATGGTAATGTGGTTGGTATT

CGAGAATGGTAATGTTGTTGTTAATCGAGAAAGGTAATATCGCTGGTGATTGAGAAGGGG

TTTGTTAAGTTCTTGAAATCTCTTGAGTCGCTGAAATATCAGGTCTTGTAATCTTGTGGT

GTAATCTGTGGGGTAATTGTCTCTGAATTTTTCTACTTCTACTTACACATATTTATACTA

TCCTACTGTTTATACCTAGGTTTGTGTAAACCAATGATTTGGCCGTGTTGTTCCAGTGCT

TATTACACTGGTTTTATCCAGCGTACATTGGCTTTAGCCTGTGTTTACACTGGTTTTTAC

CTGTGTAAGTACTAGCTTGGTCCTATGCTCCTTTTTTTTATTACTAATATTCCCTTATTA

AGTCTGGCTTCAGCCTGACAACGGTGGAACGAATCGAAGAGAGGATTGAAGCTTCGTATG

GTTACTCAGGGACGAACAGATTCATTGTTCTCCCTTTGGATGCGATGCCAGCACCTACCA

TGCGCGAGGGTCTTGCGATGGTTCTTGTCCACCTCCAGTC

[CharlesEGrant]

The traditional threshold for a significant p-value or value is 0.01 or 0.05. While this is only a convention, an E-value of 2.8E+03 is almost certainly a chance result.

I have a few comments regarding the parameters you've set on your analysis:

Are your sequences coming from the genes or the upstream regions of the genes? Regulatory motifs are sometimes found in the first intron, but more typically they're in the region up to 1000 bp from the start of the gene.

You've set '-minsites 13'. This is a very stringent condition! You are directing MEME to reject any candidate motif for which it can't find at least 13 examples. Generally you should only crank up the 'ministers' setting if MEME is reporting multiple very similar motifs.

You are also using the default background model. The single most important factor to improve MEME's performance is to use an appropriate background model. The default background model is derived from a NR database of several years ago. You may want to construct a background model more tailored to your sequence data. This post may be helpful.

Finally, MEME is weak at finding short motifs (<8 positions wide). You might also try using DREME which is better at discovering short motifs.

I did try running DREME and MEME with a background model on your sequence data, and didn't see any signal of a common motif in you sequence data.