MAST version 4.1.1 (Release date: Tue Apr 21 15:00:06 PDT 2009)

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

If you use this program in your research, please cite:

Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(48-54), 1998.

	DATABASE ./seed.fasta (peptide)
	Last updated on Mon May 17 22:04:24 2010
	Database contains 49 sequences, 5526 residues

	MOTIFS ./memeout.txt (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    41   PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
	  2    34   IWHAIAQKKPWSGDIKNYRKDGTHFWNRLHISPM
	  3    27   GEHHYFVGMQWDITEEHEYEQRLEKHR

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1     2
	----- ----- -----
	   2   0.10
	   3   0.15  0.11
	No overly similar pairs (correlation > 0.60) found.

	Random model letter frequencies (from non-redundant database):
	A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 
	L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 
	W 0.013 Y 0.033 

• Each of the following 38 sequences has E-value less than 10.
• The E-value of a sequence is the expected number of sequences in a random database of the same size that would match the motifs as well as the sequence does and is equal to the combined p-value of the sequence times the number of sequences in the database.
• The combined p-value of a sequence measures the strength of the match of the sequence to all the motifs and is calculated by
  • finding the score of the single best match of each motif to the sequence (best matches may overlap),
  • calculating the sequence p-value of each score,
  • forming the product of the p-values,
  • taking the p-value of the product.
• The sequence p-value of a score is defined as the probability of a random sequence of the same length containing some match with as good or better a score.
• The score for the match of a position in a sequence to a motif is computed by by summing the appropriate entry from each column of the position-dependent scoring matrix that represents the motif.
• Sequences shorter than one or more of the motifs are skipped.
• The table is sorted by increasing E-value.

• The ordering and spacing of all non-overlapping motif occurrences are shown for each high-scoring sequence listed in Section I.
• A motif occurrence is defined as a position in the sequence whose match to the motif has POSITION p-value less than 0.0001.
• The POSITION p-value of a match is the probability of a single random subsequence of the length of the motif scoring at least as well as the observed match.
• For each sequence, all motif occurrences are shown unless there are overlaps. In that case, a motif occurrence is shown only if its p-value is less than the product of the p-values of the other (lower-numbered) motif occurrences that it overlaps.
• The table also shows the E-value of each sequence.
• Spacers and motif occurences are indicated by
• Spacers and motif occurences are indicated by
• Spacers and motif occurences are indicated by

  • n

    occurrence of motif `n' with p-value less than 0.0001.

  • 1

    Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.

• The positions and p-values of the non-overlapping motif occurrences are shown above the actual sequence for each of the high-scoring sequences from Section I.
• A motif occurrence is defined as a position in the sequence whose match to the motif has POSITION p-value less than 0.0001 as defined in Section II.
• For each sequence, the first line specifies the name of the sequence.
• The second (and possibly more) lines give a description of the sequence.
• Following the description line(s) is a line giving the length, combined p-value, and E-value of the sequence as defined in Section I.
• The next line reproduces the motif diagram from Section II.
• The entire sequence is printed on the following lines.
• Motif occurrences are indicated directly above their positions in the sequence on lines showing
  • the motif number of the occurrence,
  • the position p-value of the occurrence,
  • the best possible match to the motif, and
  • columns whose match to the motif has a positive score (indicated by a plus sign).

                       [1]                                        [2]
                       2.0e-30                                    1.3e-26
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY  IWHAIAQKKPWSGD
                       +++++ ++++++++++++++++++++++++++++++++ ++  ++++++++++++++
1    EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGV

     
     
     IKNYRKDGTHFWNRLHISPM
     ++++++++++++++++++++
76   LVNRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDT

                       [1]                                        [2]
                       4.6e-30                                    8.3e-24
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY  IWHAIAQKKPWSGD
                       +++++++++++++++++++++++++++++ +++++++++++  ++++++++++++++
1    GLFFTMVEQASVAISLTDARANITYANPAFCRQTGYSLAQLLNQNPRLLASSQTPREIYQEMWQTLLQRQPWRGQ

     
     
     IKNYRKDGTHFWNRLHISPM
     ++++ +++++++++++++++
76   LINQARDGGLYLVDIDITPVLNPQGELEHYLAMQRDI

                       [1]                                            [2]
                       1.0e-29                                        4.0e-06
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY      IWHAIAQKKP
                       +++++++++++++++++++++++++++ +++++++++++++      + ++ +
1    AHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMATGEKRIIG

     
     
     WSGDIKNYRKDGTHFWNRLHISPM
     ++ ++  ++++++ +   + ++ +
76   IDRVVSGQRKDGSTFPMKLAVGEMRSGGERFFTGFIRDL

                       [1]
                       8.9e-12
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                         + +  + ++++++++ ++ ++++++ +++++++ +  ++
1    THLRSILHTIPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIG

                       [1]
                       1.2e-08
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                        ++ ++  +++++ ++++ + ++++++ +++   +     +
1    TLNDLIIENAADGVIAIDRQGDVTTMNPAAEVITGYQRHELVGQPYSMLFDNTQFYSPVLDTLEHGTEHVALEIS

                       [1]                                      [2]
                       1.7e-05                                  2.0e-07
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHYIWHAIAQKKPWSGDIK
                           + +++++++ ++  ++  ++ +  + +  +     + + + ++ +++++   +
1    SLPSAILNNMVTATLILDDGLAIRYANPAAELLFSQSAKRIVEQSLSQLIQHASLDLALLTQPLQSGQSITDSDV

     
     
     NYRKDGTHFWNRLHISPM
         ++ + + +++++++
76   TFVVDGRPLMLEVTVSPITWQKQLMLLVEMRKI

                       [1]
                       6.3e-09
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       + + + +++ +++++ + +++ ++++   +   ++   ++
1    AFRRAMEESLTVGMRAKDLSGRILYVNGAFCKLVGLAAEDLVGRAQPMPYWAPDFLEETLARQRQLIEGQPVPQA

                       [1]
                       9.5e-06
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       + + ++ ++ +++ +++ +++ +++++      +
1    AARRAMLDTSIDAVIVADEAGAIVEFNHAAEAIFGHTREGVIGRPMTETIIPAHYIDRHRQGFMRHLATGENHIM

                       [1]
                       2.8e-06
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       + + +   +  + ++++ + +++++++ + +  ++    +
1    NEMVRLIDTAAVPIFAVDASGVINGWNSKAAEVTGLAVEQAIGKPVSDLVEDDSVETVKNMLALALEGSEERGAE

        [2]
        5.8e-05
        IWHAIAQKKPWSGDIKNYRKDGTHFWNRLHISPM
          ++ + +++ + ++++   + ++  + + +  +
76   IRIRAFGPKRKSSPVELVVNTCCSRDMTNNVLGVCFIGQDV

                       [1]
                       8.4e-08
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                        ++++   +++  ++++    ++++++      + ++  ++
1    KMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTM

                       [1]
                       4.5e-07
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                           ++ ++  ++++ +  ++++++++   + +++  + +
1    YKYDRIFNSTHDGMIFIDINEEIILFNHMAEKMVGKKREEVIGRPIKEVIPSTKMPRILKTRVPEYNQKQLLGDH

                       [1]                                         [2]
                       3.0e-05                                     5.9e-05
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY   IWHAIAQKKPWSG
                       + + +  +++   ++ + + ++++++    +  +  +  +           +++ +
1    KRWRAIFEHNPAMYFMVDEAGIVLNVNTLGATQLGFACAELLGQSVLDVFLEEDRAFVRKCIQTCLEDVGQSRTW

     
     
     DIKNYRKDGTHFWNRLHISPM
     ++   +++++  +++ ++  +
76   DVRKVRKDGSVLWVRENAKAMLWAGDRPVILMACEDI

                       [1]
                       3.0e-06
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                        +  ++  ++ ++++ + ++ +++ +    + +++    +
1    RFTEAVLSGVGAGVIGLDSQERITILNRSAERLLGLSEVEALHRHLAEVVPETAGLLEEAEHARQRSVQGNITLT

                       [1]
                       1.5e-05
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       + +     +++ ++ ++ +++ ++++        + +  +
1    EFMRVLIDGTPNPIYVRDKEGRMLLCNDAYLDTFGVTADAVLGKTIPEANVVGDPALAREMHEFLLTRMSAEREP

                       [1]
                       5.2e-05
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       ++  ++ +++++ + ++ +   + ++      +++     +
1    AKLETLVSTIADGAILLDKDLRVILVNRTAIENFGWEGKNIAGSIIVDYLPEDINQQLFPILNDIIRKNFLEQSI

                       [1]
                       1.2e-06
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                         + + ++++ ++ + + ++++++++   ++   +     +
1    LEYVKFIAQIGTPTCIWRRNGQISYVNEEFEILCGWTREELLNKMTFIVEIMDDESVRDYFKTLSKVAYRDFRGS

                       [1]
                       8.5e-07
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       +++ ++ ++ +++  +  +++ +  +    + + + +  +
1    TDGEAILNALPNPVLLVAPDGRIVDANIAAESFFEISTQFLRRQSLKELVPFGSPLLALIEQVRTSGSPVNEYKV

                         [1]
                         5.1e-06
                         PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                         + + + ++  +++   ++  + ++++    + +++  + +
1    YRVPEEIHSQRSPKFAIRHTAAGIISHVDSAAVSALGYLPQDLMGRSIMDLYHHDDLPVIKEIYESVMKKGQTAG

                       [1]
                       2.3e-05
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       +++ +++ +++   +++ +  + +++  +    +    +
1    EEKNRIMDNLQEIVFQTNAKGEITYLNQAWASITGFSISECMGTMYNDYFIKEKHVADHINTQIQNKASSGMFTA

                       [1]
                       2.0e-05
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       ++       ++++++ + + ++         + ++ +++ +
1    EHFRVRIEGFGVGTWDLDLKTWALDWSDTARTLLGIGQDQPASYDLFLSRLEPDDRERVESAIKRVSERGGGFDV

                       [1]
                       1.2e-05
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       + +     + +  ++++ ++ ++++++ +   +++
1    TMLEAIIQSSDEAISVVDENGIGLLINKAYTKMTGLSEKEVIGKPANTDISEGESMHLKVLETRRPVRGVRMKVG

                       [1]
                       1.2e-05
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                         + + +++  +++ ++ +++   + +   + ++  +  +
1    IDPSVMLNALPDPVLVVDGSGDIRYVNLEAQEFFGLSAAMMEGMPLAELLPPNSPVSQLIEQVQQGRHRASQEGV

                          [1]
                          1.6e-05
                          PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                          +       +++ +++++  + +++++       + + +
1    GDYKAIIHSPNPLIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLLVREVFGSYCRLKGPDALTKFMIVLHN

                                                         [1]
                                                         5.3e-05
                                                         PDCPIIYANPAFCNMTGYEAEEI
                                                         + +   + ++   +     +  +
1    EQLSNILSSMADGVITINIDGTILVTNPPAERFLQAWYYEQNMNIKEGDNLPPEAKELFQNAVSTEKEQMIEMTL

     
     
     LGKNCRFLQGPDTDPEHY
     +++    ++++ +   ++
76   QGRSWVLLMSPLYAESHVRGAVAVLRDM

                       [1]
                       8.3e-05
                       PDCPIIYANPAFCNMTGYEAEEILGKNCRFLQGPDTDPEHY
                       ++      +++ + +++ ++ +++   +  + ++    ++
1    SFLRSFLDASPDLVFYRNEDKEFSGCNRAMELLTGKSEKQLVHLKPADVYSPEAAAKVIETDEKVFRHNVSLTYE

CPU: kodomo-count
Time 0.052003 secs.

mast ./memeout.txt -d ./seed.fasta -ev 10.000000 -mt 0.000100