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

If you use MCAST in your research please cite the following paper:
Timothy Bailey and William Stafford Noble, "Searching for statistically significant regulatory modules", Bioinformatics (Proceedings of the European Conference on Computational Biology), 19(Suppl. 2):ii16-ii25, 2003. [full text]

Inputs | Search Results | Program information | Documentation

Inputs

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Sequence Database

The sequence database "crp0.fna" was supplied to MCAST.

Sequence Count Residue Count
18 1890

Motifs

The following motifs were supplied to MCAST from "crp0.meme"

Motif Width Best possible match Best possible RC match
1 18 AATTGTGACGTTGTTCAC GTGATCTACGTCACAATT
2 8 CGGTGGGG CCCCGCCG

Search Results

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Top Scoring Matches

MCAST could not evaluate statistics for the match scores. All the matches found by MCAST are shown below, but no signficance statistics are provided.

Motif 1
Motif 2
  Sequence Start Stop Score p-value E-value q-value    
  tdc 82 100 4.60501 nan nan nan
+
-
  uxu1 17 35 7.10103 nan nan nan
+
-
  tnaa 75 93 5.86876 nan nan nan
+
-
  ompa 48 66 5.036 nan nan nan
+
-
  ilv 5 61 12.7089 nan nan nan
+
-
  deop2 60 78 8.23625 nan nan nan
+
-
  ce1cg 17 83 6.86344 nan nan nan
+
-
  gale 46 64 6.07963 nan nan nan
+
-
  ara 59 77 10.0989 nan nan nan
+
-
  lac 9 27 10.0969 nan nan nan
+
-
  crp 67 85 5.50862 nan nan nan
+
-
  cya 50 68 5.28224 nan nan nan
+
-
  malt 41 59 9.5075 nan nan nan
+
-
  malk 61 79 4.98687 nan nan nan
+
-
  male 14 49 9.86417 nan nan nan
+
-
  trn9cat 84 102 6.10716 nan nan nan
+
-
  pbr322 57 75 7.21464 nan nan nan
+
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MCAST version
4.10.2 56c3e3f21c83859d11666a0d349867befe70ffe5 (Release date: Thu Aug 06 17:34:33 2015 -0700)
Command line summary

Background letter frequencies (from non-redundant database):
A: 0.282 C: 0.222 G: 0.229 T: 0.267

Result calculation took 0.00844 seconds.

Explanation of MCAST Results

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The MCAST results consist of

Inputs

MCAST received the following inputs.

Sequence Databases

This table summarises the sequence databases specified to MCAST.

Database
The name of the database file.
Sequence Count
The number of sequences in the database.
Residue Count
The number of residues in the database.
Motifs

Summary of the motifs specified to MCAST.

Name
The name of the motif. If the motif has been removed or removal is recommended to avoid highly similar motifs then it will be displayed in red text.
Width
The width of the motif. No gaps are allowed in motifs supplied to MCAST as it only works for motifs of a fixed width.
Best possible match
The sequence that would achieve the best possible match score and its reverse complement for nucleotide motifs.

Search Results

MCAST provides the following motif search results.

Top Scoring Sequences

This table summarises the top scoring sequences. The sequences are sorted by the Sequence q-value from most to least significant.

Sequence
The name of the sequence. This maybe be linked to search a sequence database for the sequence name.
Start
The position of the start of the match in 1-based coordinates, starting at the first position in the sequence.
Stop
The position of the end of the match in 1-based coordinates, starting at the first position in the sequence.
Score
The MCAST score for the match.
p-value
The p-value of the match score.
E-value
The E-value of the match score.
q-value
The q-value of the match score.
&more;
Click on this to show additional information about the sequence such as a description, combined p-value and the annotated sequence.
Block Diagram
The block diagram shows the best non-overlapping tiling of motif matches on the sequence.
  • The length of the line shows the length of a sequence relative to all the other sequences.
  • A block is shown where the positional p-value of a motif is less (more significant) than the significance threshold which is 0.0001 by default.
  • If a significant motif match (as specified above) overlaps other significant motif matches then it is only displayed as a block if its positional p-value is less (more significant) then the product of the positional p-values of the significant matches that it overlaps.
  • The position of a block shows where a motif has matched the sequence.
  • The width of a block shows the width of the motif relative to the length of the sequence.
  • The colour and border of a block identifies the matching motif as in the legend.
  • The height of a block gives an indication of the significance of the match as taller blocks are more significant. The height is calculated to be proportional to the negative logarithm of the positional p-value, truncated at the height for a p-value of 1e-10.
  • Hovering the mouse cursor over the block causes the display of the motif name and other details in the hovering text.
  • DNA only; blocks displayed above the line are a match on the given DNA, whereas blocks displayed below the line are matches to the reverse-complement of the given DNA.
  • DNA only; when strands are scored separately then blocks may overlap on opposing strands.