Locus 122

Sequence ID sp_mu.0
Location 138,040 – 138,106
Length 66
Max. P 0.999396
window791 window792 window793 window794

overview

Window 1

Location 138,040 – 138,106
Length 66
Sequences 3
Columns 66
Reading direction forward
Mean pairwise identity 81.82
Mean single sequence MFE -10.10
Consensus MFE -6.59
Energy contribution -7.27
Covariance contribution 0.67
Combinations/Pair 1.23
Mean z-score -2.63
Structure conservation index 0.65
SVM decision value 1.31
SVM RNA-class probability 0.940424
Prediction RNA
WARNING Sequence 3: Base composition out of range.

Download alignment: ClustalW | MAF

>sp_mu.0 138040 66 - 2030921
UUUGAGCACAAAAAACGCUCGUUAAAAACUUUUUUGAGCAUAAAAAACGCUCAUAAAAAACUUUUU
...((((.........)))).........((((.(((((.........))))).))))........ ( -11.40)
>sp_ag.0 76603 66 + 2160267
UCUGAGCACAAAAAACGCUCGUAAAAAACUUUUUUGAGCACAAAAAACGCUCAUAAAAAACUUUUU
...((((.........)))).........((((.(((((.........))))).))))........ ( -11.40)
>sp_pn.0 196008 63 + 2038615
CUUGAGCAUAAAAAACGCUCGUUAAAAACUUUUU---GAAUAAAAAAUAUAGAAAAGGAACUAUUU
...((((.........))))(((.....((((((---..(((.....))).)))))).)))..... (  -7.50)
>consensus
UUUGAGCACAAAAAACGCUCGUUAAAAACUUUUUUGAGCAUAAAAAACGCUCAUAAAAAACUUUUU
...((((.........)))).........((((.(((((.........))))).))))........ ( -6.59 =  -7.27 +   0.67)

alignment

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secondary structure

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dotplot

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Window 2

Location 138,040 – 138,106
Length 66
Sequences 3
Columns 66
Reading direction reverse
Mean pairwise identity 81.82
Mean single sequence MFE -14.33
Consensus MFE -9.59
Energy contribution -11.60
Covariance contribution 2.01
Combinations/Pair 1.13
Mean z-score -2.79
Structure conservation index 0.67
SVM decision value 1.64
SVM RNA-class probability 0.969298
Prediction RNA
WARNING Sequence 3: Base composition out of range.

Download alignment: ClustalW | MAF

>sp_mu.0 138040 66 - 2030921
AAAAAGUUUUUUAUGAGCGUUUUUUAUGCUCAAAAAAGUUUUUAACGAGCGUUUUUUGUGCUCAAA
.((((..(((((.(((((((.....))))))))))))..))))...(((((.......)))))... ( -17.80)
>sp_ag.0 76603 66 + 2160267
AAAAAGUUUUUUAUGAGCGUUUUUUGUGCUCAAAAAAGUUUUUUACGAGCGUUUUUUGUGCUCAGA
(((((..(((((.((((((.......)))))))))))..)))))..(((((.......)))))... ( -16.30)
>sp_pn.0 196008 63 + 2038615
AAAUAGUUCCUUUUCUAUAUUUUUUAUUC---AAAAAGUUUUUAACGAGCGUUUUUUAUGCUCAAG
..((((........))))(((((((....---))))))).......((((((.....))))))... (  -8.90)
>consensus
AAAAAGUUUUUUAUGAGCGUUUUUUAUGCUCAAAAAAGUUUUUAACGAGCGUUUUUUGUGCUCAAA
(((((.(((((..(((((((.....)))))))))))).)))))...((((((.....))))))... ( -9.59 = -11.60 +   2.01) 
# Strand winner: reverse (0.98)

alignment

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secondary structure

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dotplot

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Window 3

Location 138,040 – 138,106
Length 66
Sequences 2
Columns 66
Reading direction forward
Mean pairwise identity 95.45
Mean single sequence MFE -11.40
Consensus MFE -11.40
Energy contribution -11.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.35
Structure conservation index 1.00
SVM decision value 3.57
SVM RNA-class probability 0.999396
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 138040 66 - 2030921/0-66
UUUGAGCACAAAAAACGCUCGUUAAAAACUUUUUUGAGCAUAAAAAACGCUCAUAAAAAACUUUUU
...((((.........)))).........((((.(((((.........))))).))))........ ( -11.40)
>sp_ag.0 76603 66 + 2160267/0-66
UCUGAGCACAAAAAACGCUCGUAAAAAACUUUUUUGAGCACAAAAAACGCUCAUAAAAAACUUUUU
...((((.........)))).........((((.(((((.........))))).))))........ ( -11.40)
>consensus
UCUGAGCACAAAAAACGCUCGUAAAAAACUUUUUUGAGCACAAAAAACGCUCAUAAAAAACUUUUU
...((((.........)))).........((((.(((((.........))))).))))........ (-11.40 = -11.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 138,040 – 138,106
Length 66
Sequences 2
Columns 66
Reading direction reverse
Mean pairwise identity 95.45
Mean single sequence MFE -17.05
Consensus MFE -16.40
Energy contribution -16.15
Covariance contribution -0.25
Combinations/Pair 1.05
Mean z-score -3.45
Structure conservation index 0.96
SVM decision value 3.19
SVM RNA-class probability 0.998700
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 138040 66 - 2030921/0-66
AAAAAGUUUUUUAUGAGCGUUUUUUAUGCUCAAAAAAGUUUUUAACGAGCGUUUUUUGUGCUCAAA
.((((..(((((.(((((((.....))))))))))))..))))...(((((.......)))))... ( -17.80)
>sp_ag.0 76603 66 + 2160267/0-66
AAAAAGUUUUUUAUGAGCGUUUUUUGUGCUCAAAAAAGUUUUUUACGAGCGUUUUUUGUGCUCAGA
(((((..(((((.((((((.......)))))))))))..)))))..(((((.......)))))... ( -16.30)
>consensus
AAAAAGUUUUUUAUGAGCGUUUUUUAUGCUCAAAAAAGUUUUUAACGAGCGUUUUUUGUGCUCAAA
.((((..(((((.(((((((.....))))))))))))..))))...(((((.......)))))... (-16.40 = -16.15 +  -0.25) 
# Strand winner: reverse (0.99)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:01:41 2006