DATABASE SEARCH RESULTS | ALIGNMENTS | MOTIF DIAGRAMS | EXPLANATION OF OUTPUT | PROGRAM PARAMETERS |
Program: mhmmscan File contents: Database search results Motif file: crp0.meme.html HMM file: mcast_out/crp0.meme.html.mhmm Sequence file: crp0.fasta Create date: Tue Jun 7 15:29:50 2011For further information on how to interpret these results or to get a copy of the MEME Suite software, please access http://meme.sdsc.edu.
ID | E-value | Score | Hits | Span | Start | End | Description |
lac | nan | 20.55 | 2 | 35 | 9 | 43 | |
trn9cat | nan | 13.71 | 2 | 66 | 36 | 101 | |
ilv | nan | 12.71 | 2 | 56 | 5 | 60 | |
ara | nan | 9.70 | 1 | 18 | 59 | 76 | |
male | nan | 9.42 | 2 | 35 | 14 | 48 | |
malt | nan | 9.28 | 1 | 18 | 41 | 58 | |
deop2 | nan | 8.46 | 1 | 18 | 60 | 77 | |
pbr322 | nan | 7.29 | 1 | 18 | 57 | 74 | |
uxu1 | nan | 6.94 | 1 | 18 | 17 | 34 | |
ce1cg | nan | 6.58 | 1 | 18 | 65 | 82 | |
tnaa | nan | 5.90 | 1 | 18 | 75 | 92 | |
gale | nan | 5.90 | 1 | 18 | 46 | 63 | |
cya | nan | 5.36 | 1 | 18 | 50 | 67 | |
crp | nan | 5.25 | 1 | 18 | 67 | 84 | |
ompa | nan | 4.74 | 1 | 18 | 48 | 65 | |
malk | nan | 4.74 | 1 | 18 | 61 | 78 | |
tdc | nan | 4.44 | 1 | 18 | 82 | 99 |
E-value Score | |
nan 20.55 | 5.4e-07 2.4e-07 *________+1______* *_____-3__* AATTGTGACGTTGTTCAC......GGCACCCCAGG +A TGTGA+ T+G TCAC GGCACCCCAGG 1 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCAC |
nan 13.71 | 4.7e-07 9.0e-06 *_____+3__* *________+1______* CCTGGGGTCCC.....................................AATTGTGACGTTGTTCAC CCTGG+GTCCC AA TG GACGTTG+TC 1 CTGTGACGGAAGATCACTTCGCAGAATAAATAAATCCTGGTGTCCCTGTTGATACCGGGAAGCCCTGGGCCAACTTTTGGCGAAAATGAGACGTTGATCGGCACG |
nan 12.71 | 7.1e-06 1.6e-06 *___+2_* *________-1______* CGGCGGGG..............................GTGATCTACGTCACAATT CGGCGGGG GTGATC+AC+ C CAATT 1 GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAAAATTTTCCATTGTCTCCCCTGTAAAGCTGT |
nan 9.70 | 6.0e-07 *________-1______* GTGATCTACGTCACAATT +TG +C CGTCACA TT 1 GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACTTTGCTATGCCATAGCATTTTTATCCATAAG |
nan 9.42 | 1.6e-05 1.6e-05 *________+1______* *___+2_* AATTGTGACGTTGTTCAC.........CGGCGGGG ++ TGT AC+ +G+TCAC CGG+GGGG 1 ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGGTTGCCGTATAAAGAAACTAGAGTCCGTTTA |
nan 9.28 | 8.1e-07 *________+1______* AATTGTGACGTTGTTCAC AATTGTGAC+ +GT CA+ 1 GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAAAACGTCATCGCTTGCATTAGAAAGGTTTCT |
nan 8.46 | 1.4e-06 *________+1______* AATTGTGACGTTGTTCAC AATTGTGA GT +TC + 1 AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATCGAAGTGTGTTGCGGAGTAGATGTTAGAATA |
nan 7.29 | 3.2e-06 *________-1______* GTGATCTACGTCACAATT GTGA+ TAC+ CACA +T 1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTC |
nan 6.94 | 4.1e-06 *________+1______* AATTGTGACGTTGTTCAC + TTGTGA GT GTT AC 1 CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAGAACTTATACGCCATCTCATCCGATGCAAGC |
nan 6.58 | 5.2e-06 *________-1______* GTGATCTACGTCACAATT +TGATC + TCACAA++ 1 TAATNTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTTCACAAAAATGGAAGTCCACAGTCTTGACAG |
nan 5.90 | 8.4e-06 *________-1______* GTGATCTACGTCACAATT GTGAT TCACA TT 1 TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTGTGATTCGATTCACATTTAAACAATTTCAGA |
nan 5.90 | 8.4e-06 *________-1______* GTGATCTACGTCACAATT +T TC A+GTCACA TT 1 GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTGTTATGCTATGGTTATTTCATACCATAAGCC |
nan 5.36 | 1.2e-05 *________+1______* AATTGTGACGTTGTTCAC A TGT A +TTG+TCAC 1 ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGACCATTTTTTCGTCGTGAAACTAAAAAAACC |
nan 5.25 | 1.3e-05 *________-1______* GTGATCTACGTCACAATT G A+ ACGTCACA T+ 1 CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGACGTCACATTACCGTGCAGTACAGTTGATAGC |
nan 4.74 | 1.9e-05 *________+1______* AATTGTGACGTTGTTCAC A+ TGACG +GTTCAC 1 GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGTTTTCAACTACGTTGTAGACTTTACATCGCC |
nan 4.74 | 1.9e-05 *________+1______* AATTGTGACGTTGTTCAC ++T GTGA GTTG T C 1 GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCTTGCAAAAATCGTGGCGATTTTATGTGCGCA |
nan 4.44 | 2.3e-05 *________-1______* GTGATCTACGTCACAATT GTGA ++ CACA +T 1 GATTTTTATACTTTAACTTGTTGATATTTAAAGGTATTTAATTGTAATAACGATACTCTGGAAAGTATTGAAAGTTAATTTGTGAGTGGTCGCACATATCCTGTT |
Name | E-value | Motifs | ||||||||||
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lac | nan |
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trn9cat | nan |
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ilv | nan |
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ara | nan |
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male | nan |
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malt | nan |
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deop2 | nan |
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pbr322 | nan |
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uxu1 | nan |
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ce1cg | nan |
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tnaa | nan |
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gale | nan |
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cya | nan |
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crp | nan |
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ompa | nan |
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malk | nan |
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tdc | nan |
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SCALE |
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mhmmscan/MCAST
output has up to three sections
containing your search results:
All three sections are always present in MCAST
output.
The second two sections will not be present in
mhmmscan
output unless the -fancy option was
specified.
The results in all three sections are sorted by increasing E-value if possible, or by decreasing match score if E-values could not be computed.
DATABASE SEARCH RESULTS
The "Database Search Results" section consists of lines of the following form:
These fields contain, for each match found,
ALIGNMENTS
Each alignment lists the sequence identifier, match E-value and log-odds score along the left. On the right, it shows the alignment of the match with the sequence in groups of four segments. An example segment from an alignment is given below, followed by a description of what each line of the segment means. (The example shows p-value score mode. The row of p-values would be replaced by log-odds scores in log-odds score mode. If '--motif-scoring' is not on, the row of p-values or scores is absent.)
1.5e-07 55.02 |
2.4e-04 2.4e-04 1.3e-04 *_____+3__* *____-2__* *___+1_* TTTTTTATGCG.......................TTTTATGACT.........CTAATCCG.................................. TTTTTAT+ + TTTTAT A T +TAATC+G 220 CGGAACATTAAAATGATTTTTATTTCTATGCTAAATCTGTTGTATTTACTTTTATAAATTTAATGTGTTTAATCTGTTCACATTTTTAAATACTTCGTATGCTATCNNNN 329 |
MOTIF DIAGRAMS
The motif diagrams section shows the matches in schematic format. For each match, in the right two columns, it shows the sequence identifier and the match E-value. On the left, it shows the positions and spacings of the hits making up the match. Hits are labeled with numbers corresponding to the order the motifs were given in the query. A plus or minus sign preceding a hit indicates that the hit occurs on the given (+) or reverse complement (-) of the DNA sequence in the database.
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