ACGTN 136417072

The name of the motif.

The alternate name of the motif.

The width of the motif. No gaps are allowed in motifs supplied to MCAST as it only works for motifs of a fixed width.

The name of the (FASTA) sequence database file.

The name of the position specific priors file.

The name of the binned distribution of priors file.

The number of sequences in the database.

The number of letters in the sequence database.

The name of the file containing the (MEME-formatted) motifs used in the search.

The block diagram shows the motif matches comprising a motif cluster detected by MCAST.

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 p-value of a motif match is the probability of a single random subsequence of the length of the motif scoring at least as well as the observed match.

A selected portion of the input sequence with the matching motifs displayed above it.

For each matching motif the strand of the match (+/-), the consensus sequence of the motif, the p-value of the individual motif match (see also help button for "Cluster Score") and the sequence logo of the motif is shown.

You can select the portion of the sequence to be displayed by sliding the two buttons below the sequence block diagram so that the portion you want to see is between the two needles attached to the buttons. By default the two buttons move together, but you can drag one individually by holding shift before you start the drag.

The name of the alphabet symbol.

The frequency of the alphabet symbol as defined by the background model.

The full sequence identifier.

This lists the name of the sequence, typically the chromosome or contig name.

MCAST was run with --parse-genomic-coord specified and has split the sequence identifier into sequence name, sequence start and sequence end.

This lists the first genomic offset (1-based) of the displayed region.

MCAST was run with --parse-genomic-coord specified and has split the sequence identifier into sequence name, sequence start and sequence end in genome coordinates.

This lists the first sequence offset (1-based) of the displayed region.

This lists the last genomic offset (1-based) of the displayed region.

MCAST was run with --parse-genomic-coord specified and has split the sequence identifier into sequence name, sequence start and sequence end in genome coordinates.

This lists the last sequence offset (1-based) of the displayed region.

The start of the motif cluster relative to the start of the sequence (1-based).

The last position of the motif cluster relative to the start of the sequence (1-based).

The score that the hidden Markov model created by MCAST assigned to the motif cluster.

This is the sum of the scores of the individual motif matches in the cluster, plus a gap penalty, g, multiplied by the total size of the inter-motif gaps in the cluster. Individual motif match scores are log2(P(s)/p), where s is the log-odds score of the motif match, P(s) is the p-value of the motif match, and p is the user-specified p-value threshold (default: 0.0005).

The p-value of the motif cluster score.

MCAST estimates p-values by fitting an exponential distribution the observed motif cluster scores.

The E-value of the motif cluster score.

MCAST estimates this by multiplying the p-value of the motif cluster score times the (estimated) number of random matches found in the search.

The q-value of the motif cluster score.

MCAST estimates q-values from the motif cluster score p-values using the method of Benjamini and Hochberg (Journal of the Royal Statistical Society B, 57:289-300, 1995).

Motif1
p-value8.23e-7
Start23
End33
Cluster Start:
Cluster Stop:
Cluster Score:
p-value:
E-value:
q-value:
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

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

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]

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Search Results

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Top Scoring Clusters

CCMCRCCC
BTTATCW
MCRCCCA
RARGAAA
AKAAAM
CTGTSTS
AGGGCGK
CCTKCCY
TTAAAAW
AAATAH
CATYTCC
CAGMCAC
CACAGY
CTGGRGA
SACGTGA
Name 
Start 
Stop 
E-value 
Block Diagram 
0
50
100
150
200
250
chr225869259258695131.1e+0
+
25869259
25869259
25869593
Cluster Start:
25869324
Cluster Stop:
25869447
Cluster Score:
19.9762
p-value:
1.0e-3
E-value:
1.1e+0
q-value:
6.5e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr61364168421364170962.0e+0
+
136416842
136416842
136417248
Cluster Start:
136416875
Cluster Stop:
136417063
Cluster Score:
20.5688
p-value:
1.9e-3
E-value:
2.0e+0
q-value:
6.5e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr921940139219403933.1e+0
+
21940139
21940139
21940546
Cluster Start:
21940151
Cluster Stop:
21940381
Cluster Score:
16.2056
p-value:
3.0e-3
E-value:
3.1e+0
q-value:
6.5e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr1471023761710240153.5e+0
+
71023761
71023761
71024163
Cluster Start:
71023800
Cluster Stop:
71023975
Cluster Score:
20.9224
p-value:
3.3e-3
E-value:
3.5e+0
q-value:
6.5e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr565255925652561794.0e+0
+
65255925
65255925
65256362
Cluster Start:
65255972
Cluster Stop:
65256132
Cluster Score:
21.5795
p-value:
3.8e-3
E-value:
4.0e+0
q-value:
6.5e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr397461906974621604.0e+0
+
97461906
97461906
97462165
Cluster Start:
97461942
Cluster Stop:
97462123
Cluster Score:
20.8021
p-value:
3.9e-3
E-value:
4.0e+0
q-value:
6.5e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr874937870749381244.9e+0
+
74937870
74937870
74938207
Cluster Start:
74937913
Cluster Stop:
74938080
Cluster Score:
15.1771
p-value:
4.7e-3
E-value:
4.9e+0
q-value:
6.8e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr16868701786872716.9e+0
+
8687017
8687017
8687306
Cluster Start:
8687059
Cluster Stop:
8687229
Cluster Score:
20.4206
p-value:
6.6e-3
E-value:
6.9e+0
q-value:
7.1e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr81228957291228959837.4e+0
+
122895729
122895729
122896006
Cluster Start:
122895779
Cluster Stop:
122895932
Cluster Score:
19.9923
p-value:
7.1e-3
E-value:
7.4e+0
q-value:
7.1e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr565203390652036447.5e+0
+
65203390
65203390
65203704
Cluster Start:
65203447
Cluster Stop:
65203587
Cluster Score:
18.4525
p-value:
7.2e-3
E-value:
7.5e+0
q-value:
7.1e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr41182413971182416518.1e+0
+
118241397
118241397
118241764
Cluster Start:
118241407
Cluster Stop:
118241641
Cluster Score:
18.9397
p-value:
7.8e-3
E-value:
8.1e+0
q-value:
7.1e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

chr41345379351345381899.0e+0
+
134537935
134537935
134538434
Cluster Start:
134537974
Cluster Stop:
134538057
Cluster Score:
11.0457
p-value:
8.6e-3
E-value:
9.0e+0
q-value:
7.2e-1
Annotated Sequence

Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.

CCMCRCCC
BTTATCW
MCRCCCA
RARGAAA
AKAAAM
CTGTSTS
AGGGCGK
CCTKCCY
TTAAAAW
AAATAH
CATYTCC
CAGMCAC
CACAGY
CTGGRGA
SACGTGA

Inputs & Settings

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Alphabet

Name 
Bg. 
Bg. 
Name 
Adenine0.282A~T0.267Thymine
Cytosine0.222C~G0.229Guanine

Sequences

The following sequence database was supplied to MCAST.

Database
PSP/Wig file
PSP Distribution file
Sequence Count
Letter Count
Klf1.fna--904452000
Total904452000

Motifs

The following motif database was supplied to MCAST.

Database
Klf1.dreme

Which contained the following motifs.

Name 
Alt. Name 
Width 
1.CCMCRCCCDREME-18
2.BTTATCWDREME-27
3.MCRCCCADREME-37
4.RARGAAADREME-47
5.AKAAAMDREME-56
6.CTGTSTSDREME-67
7.AGGGCGKDREME-77
8.CCTKCCYDREME-87
9.TTAAAAWDREME-97
10.AAATAHDREME-106
11.CATYTCCDREME-117
12.CAGMCACDREME-127
13.CACAGYDREME-136
14.CTGGRGADREME-147
15.SACGTGADREME-157

Other Settings

Alpha 1
Hard mask No
Max Gap 50
Max Stored Scores 100000
Motif p-value threshold 0.0005
Output Threshold E-value10
Parse Genomic Coordinates Yes
Synthetic Scores No
Min Match Score 3.26677
Cost Factor 1
Gap Open Cost 0.0653353
Gap Extend Cost 0.0653353
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MCAST version 4.11.4
(Release date: Thu Mar 30 17:02:08 2017 -0700)
Reference
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]
Command line summary
Ran in 1.80073 seconds on Tue Apr 4 16:21:18 2017 on glutamine.gs.washington.edu