Locus 132

Sequence ID sp_mu.0
Location 108,557 – 108,631
Length 74
Max. P 0.999995
window828 window829 window830 window831

overview

Window 8

Location 108,557 – 108,631
Length 74
Sequences 3
Columns 74
Reading direction forward
Mean pairwise identity 69.37
Mean single sequence MFE -26.67
Consensus MFE -29.54
Energy contribution -25.33
Covariance contribution -4.21
Combinations/Pair 1.67
Mean z-score -2.31
Structure conservation index 1.11
SVM decision value 5.89
SVM RNA-class probability 0.999995
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 108557 74 + 2030921
GCCGAUUUAGCUCAGCUGGUAGAGCAACGCACUCGUAACGCGUAGGUCACAGGUUCAAGUCCUGCAAUCGGCAU
(((((((..((((........)))).((((.........))))......((((.......)))).))))))).. ( -23.40)
>sp_ag.0 96461 74 + 2160267
GCCGGCUUAGCUCAGUUGGUAGAGCAUCUGAUUUGUAAUCAGAGGGUCGCGUGUUCAAGUCAUGUAGCCGGCAU
(((((((..((((........)))).((((((.....)))))).....(((((.......)))))))))))).. ( -29.00)
>sp_pn.0 904863 74 + 2038615
GCUGAUUUAGCUCAGUUGGCAGAGCGCAUCCAUGGUAAGGAUGAGGUCGCCGGUUCAAUCCCGGCAAUUAGCAU
(((((((..(((.....))).((.(.(((((.......))))).).))(((((.......)))))))))))).. ( -27.60)
>consensus
GCCGAUUUAGCUCAGUUGGUAGAGCAACUCAAUCGUAACGAGAAGGUCGCAGGUUCAAGUCCUGCAAUCGGCAU
(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).. (-29.54 = -25.33 +  -4.21)

alignment

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secondary structure

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dotplot

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Window 9

Location 108,557 – 108,631
Length 74
Sequences 3
Columns 74
Reading direction reverse
Mean pairwise identity 69.37
Mean single sequence MFE -24.10
Consensus MFE -26.32
Energy contribution -22.67
Covariance contribution -3.65
Combinations/Pair 1.62
Mean z-score -2.48
Structure conservation index 1.09
SVM decision value 5.78
SVM RNA-class probability 0.999993
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 108557 74 + 2030921
AUGCCGAUUGCAGGACUUGAACCUGUGACCUACGCGUUACGAGUGCGUUGCUCUACCAGCUGAGCUAAAUCGGC
..((((((((((((.......))))).....(((((.......))))).((((........))))..))))))) ( -23.80)
>sp_ag.0 96461 74 + 2160267
AUGCCGGCUACAUGACUUGAACACGCGACCCUCUGAUUACAAAUCAGAUGCUCUACCAACUGAGCUAAGCCGGC
..(((((((......................((((((.....)))))).((((........))))..))))))) ( -24.30)
>sp_pn.0 904863 74 + 2038615
AUGCUAAUUGCCGGGAUUGAACCGGCGACCUCAUCCUUACCAUGGAUGCGCUCUGCCAACUGAGCUAAAUCAGC
..(((..(((((((.......)))))))...(((((.......))))).((((........))))......))) ( -24.20)
>consensus
AUGCCGAUUGCAGGACUUGAACCCGCGACCUACUCAUUACAAAUGAGAUGCUCUACCAACUGAGCUAAAUCGGC
..((((((((((((.......))))).....(((((.......))))).((((........))))..))))))) (-26.32 = -22.67 +  -3.65) 
# Strand winner: forward (0.98)

alignment

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secondary structure

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dotplot

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Window 0

Location 108,557 – 108,631
Length 74
Sequences 3
Columns 74
Reading direction forward
Mean pairwise identity 69.37
Mean single sequence MFE -26.67
Consensus MFE -29.54
Energy contribution -25.33
Covariance contribution -4.21
Combinations/Pair 1.67
Mean z-score -2.31
Structure conservation index 1.11
SVM decision value 5.89
SVM RNA-class probability 0.999995
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 108557 74 + 2030921/0-74
GCCGAUUUAGCUCAGCUGGUAGAGCAACGCACUCGUAACGCGUAGGUCACAGGUUCAAGUCCUGCAAUCGGCAU
(((((((..((((........)))).((((.........))))......((((.......)))).))))))).. ( -23.40)
>sp_ag.0 96461 74 + 2160267/0-74
GCCGGCUUAGCUCAGUUGGUAGAGCAUCUGAUUUGUAAUCAGAGGGUCGCGUGUUCAAGUCAUGUAGCCGGCAU
(((((((..((((........)))).((((((.....)))))).....(((((.......)))))))))))).. ( -29.00)
>sp_pn.0 904863 74 + 2038615/0-74
GCUGAUUUAGCUCAGUUGGCAGAGCGCAUCCAUGGUAAGGAUGAGGUCGCCGGUUCAAUCCCGGCAAUUAGCAU
(((((((..(((.....))).((.(.(((((.......))))).).))(((((.......)))))))))))).. ( -27.60)
>consensus
GCCGAUUUAGCUCAGUUGGUAGAGCAACUCAAUCGUAACGAGAAGGUCGCAGGUUCAAGUCCUGCAAUCGGCAU
(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).. (-29.54 = -25.33 +  -4.21)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 1

Location 108,557 – 108,631
Length 74
Sequences 3
Columns 74
Reading direction reverse
Mean pairwise identity 69.37
Mean single sequence MFE -24.10
Consensus MFE -26.32
Energy contribution -22.67
Covariance contribution -3.65
Combinations/Pair 1.62
Mean z-score -2.48
Structure conservation index 1.09
SVM decision value 5.78
SVM RNA-class probability 0.999993
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 108557 74 + 2030921/0-74
AUGCCGAUUGCAGGACUUGAACCUGUGACCUACGCGUUACGAGUGCGUUGCUCUACCAGCUGAGCUAAAUCGGC
..((((((((((((.......))))).....(((((.......))))).((((........))))..))))))) ( -23.80)
>sp_ag.0 96461 74 + 2160267/0-74
AUGCCGGCUACAUGACUUGAACACGCGACCCUCUGAUUACAAAUCAGAUGCUCUACCAACUGAGCUAAGCCGGC
..(((((((......................((((((.....)))))).((((........))))..))))))) ( -24.30)
>sp_pn.0 904863 74 + 2038615/0-74
AUGCUAAUUGCCGGGAUUGAACCGGCGACCUCAUCCUUACCAUGGAUGCGCUCUGCCAACUGAGCUAAAUCAGC
..(((..(((((((.......)))))))...(((((.......))))).((((........))))......))) ( -24.20)
>consensus
AUGCCGAUUGCAGGACUUGAACCCGCGACCUACUCAUUACAAAUGAGAUGCUCUACCAACUGAGCUAAAUCGGC
..((((((((((((.......))))).....(((((.......))))).((((........))))..))))))) (-26.32 = -22.67 +  -3.65) 
# Strand winner: forward (0.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:02:10 2006