Locus 64

Sequence ID Eco_1
Location 3,309,260 – 3,309,437
Length 177
Max. P 0.988095
window199 window200 window201 window202

overview

Window 9

Location 3,309,260 – 3,309,380
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -41.10
Consensus MFE -40.42
Energy contribution -40.53
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.32
Structure conservation index 0.98
SVM decision value 1.57
SVM RNA-class probability 0.964612
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3309260 120 - 1
GCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGCGGCUAAUGAGAGGCUUUACCCACAUAGAGCUGGGUUAGGGUUGUCAUUAGUCGCGAGG
(((((..((.(....)....))...))))).......((.((((.......)))).)).((((((((((((.((.(((.(((((........))))).))).)).))))))))))))... ( -41.20)
>Sfl_1 1 120 - 1
GCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGCGGCUAAUGAGAGGCUUUACCCACAUAGAGCUGGGUUAGGGUUGUCAUUAGUCGCGAGG
(((((..((.(....)....))...))))).......((.((((.......)))).)).((((((((((((.((.(((.(((((........))))).))).)).))))))))))))... ( -41.20)
>Sty_1 1 116 - 1
GCAAUUCGCUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGCGGCUAAUGAGAGGCUUUACCCAUAU----CAGGGUUAGGGUUGUCAUUAGUCGCGAGG
(((((..((.(....)....))...))))).......((.((((.......)))).)).((((((((((((.((.(((.((((....----..)))).))).)).))))))))))))... ( -40.90)
>consensus
GCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGCGGCUAAUGAGAGGCUUUACCCACAUAGAGCUGGGUUAGGGUUGUCAUUAGUCGCGAGG
(((((..((.(....)....))...))))).......((.((((.......)))).)).((((((((((((.((.(((.(((((........))))).))).)).))))))))))))... (-40.42 = -40.53 +   0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,309,300 – 3,309,419
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.54
Mean single sequence MFE -42.60
Consensus MFE -39.77
Energy contribution -40.00
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -2.31
Structure conservation index 0.93
SVM decision value 1.12
SVM RNA-class probability 0.918401
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3309300 119 - 1
A-AGGGGGCCUGAGUGGCCCCUUUUUUCAAGCUGACGGCAGCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGCGGCUAAUGAGAGGCUUUA
(-((((((((.....)))))))))((((((((((.((((((((((.((..(....)...)).)))))))).......((.((((.......)))).)).)))))))..)))))....... ( -42.90)
>Sfl_1 41 119 - 1
A-AGGGGGCCUGAGUGGCCCCUUUUUUCAAGCUGACGGCAGCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGCGGCUAAUGAGAGGCUUUA
(-((((((((.....)))))))))((((((((((.((((((((((.((..(....)...)).)))))))).......((.((((.......)))).)).)))))))..)))))....... ( -42.90)
>Sty_1 37 120 - 1
AGAGGGGGCCUUCAUGGCCCCUUUUUUCCAGCAGAUGGCAGCAAUUCGCUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGCGGCUAAUGAGAGGCUUUA
((((((((((.....))))))))))....(((..(((((((((((.((..(....)...)).)))))))))))......((((((((.((........)))))).....)))).)))... ( -42.00)
>consensus
A_AGGGGGCCUGAGUGGCCCCUUUUUUCAAGCUGACGGCAGCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGCGGCUAAUGAGAGGCUUUA
..((((((((.....))))))))(((((((((((.((((((((((.((..(....)...)).)))))))).......((.((((.......)))).)).)))))))..))))))...... (-39.77 = -40.00 +   0.23)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,309,318 – 3,309,437
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.99
Mean single sequence MFE -33.50
Consensus MFE -30.72
Energy contribution -30.50
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.88
Structure conservation index 0.92
SVM decision value 0.38
SVM RNA-class probability 0.711780
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3309318 119 + 1
GCGCGAACCUCUGCAACGGAAGAUCAUUCAUAGCAACAAUACAUUAGUUUCCAGUGAAUUGCUGCCGUCAGCUUGAAAAAAGGGGCCACUCAGGCCCCCU-UUUCUGAAACUCGCAAGAA
..((((......((.((((.((...((((((.(.(((.........)))..).))))))..)).))))..))..(((((..((((((.....)))))).)-))))......))))..... ( -32.70)
>Sfl_1 59 119 + 1
GCGCGAACCUCUGCAACGGAAGAUCAUUCAUAGCAACAAUACAUUAGUUUCCAGUGAAUUGCUGCCGUCAGCUUGAAAAAAGGGGCCACUCAGGCCCCCU-UUUCUGAAACUCGCAAGAA
..((((......((.((((.((...((((((.(.(((.........)))..).))))))..)).))))..))..(((((..((((((.....)))))).)-))))......))))..... ( -32.70)
>Sty_1 55 120 + 1
GCGCGAACCUCUGCAACGGAAGAUCAUUCAUAGCAACAAUACAUUAGUUUCCAGCGAAUUGCUGCCAUCUGCUGGAAAAAAGGGGCCAUGAAGGCCCCCUCUUUCUGAAACUCGAAAGAA
(((((......)))..(....)..........)).............(((((((((...((....))..)))))))))...((((((.....)))))).((((((........)))))). ( -35.10)
>consensus
GCGCGAACCUCUGCAACGGAAGAUCAUUCAUAGCAACAAUACAUUAGUUUCCAGUGAAUUGCUGCCGUCAGCUUGAAAAAAGGGGCCACUCAGGCCCCCU_UUUCUGAAACUCGCAAGAA
(((((......)))..(....)..........))............(((((((((.....))))..........((((...((((((.....))))))...)))).)))))((....)). (-30.72 = -30.50 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,309,318 – 3,309,437
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.99
Mean single sequence MFE -47.80
Consensus MFE -45.67
Energy contribution -45.57
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -4.12
Structure conservation index 0.96
SVM decision value 2.11
SVM RNA-class probability 0.988095
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3309318 119 - 1
UUCUUGCGAGUUUCAGAAA-AGGGGGCCUGAGUGGCCCCUUUUUUCAAGCUGACGGCAGCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGC
.....(((((..((.((((-((((((((.....))))))))))))...((.((((((((((((.((..(....)...)).))))))))...(((.....))))))))).))..))))).. ( -47.90)
>Sfl_1 59 119 - 1
UUCUUGCGAGUUUCAGAAA-AGGGGGCCUGAGUGGCCCCUUUUUUCAAGCUGACGGCAGCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGC
.....(((((..((.((((-((((((((.....))))))))))))...((.((((((((((((.((..(....)...)).))))))))...(((.....))))))))).))..))))).. ( -47.90)
>Sty_1 55 120 - 1
UUCUUUCGAGUUUCAGAAAGAGGGGGCCUUCAUGGCCCCUUUUUUCCAGCAGAUGGCAGCAAUUCGCUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGC
......((((..((.(((((((((((((.....)))))))))))))..((..(((((((((((.((..(....)...)).))))))))))).((((......)))))).))..))))... ( -47.60)
>consensus
UUCUUGCGAGUUUCAGAAA_AGGGGGCCUGAGUGGCCCCUUUUUUCAAGCUGACGGCAGCAAUUCACUGGAAACUAAUGUAUUGUUGCUAUGAAUGAUCUUCCGUUGCAGAGGUUCGCGC
....((((((..((.((((.((((((((.....)))))))).))))..((.((((((((((((.((..(....)...)).))))))))...(((.....))))))))).))..)))))). (-45.67 = -45.57 +  -0.11)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:04:54 2006