Locus 134

Sequence ID sp_mu.0
Location 1,211,960 – 1,212,032
Length 72
Max. P 0.998216
window836 window837 window838 window839

overview

Window 6

Location 1,211,960 – 1,212,032
Length 72
Sequences 3
Columns 72
Reading direction forward
Mean pairwise identity 90.74
Mean single sequence MFE -23.33
Consensus MFE -21.36
Energy contribution -21.70
Covariance contribution 0.34
Combinations/Pair 1.10
Mean z-score -2.37
Structure conservation index 0.92
SVM decision value 1.28
SVM RNA-class probability 0.939949
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1211960 72 + 2030921
UAUCCCCUGCCGGAAUCGAACCAGCAACUGCUCCUUAGGAGGGAGAUGUUAUAUCCAUUUAACUAAGGGGAC
..((((((....((((.((...((((....(((((.....))))).))))...)).)))).....)))))). ( -21.00)
>sp_ag.0 1601483 72 - 2160267
UGUCCCCUGCCGGAAUCGAACCAGCAAUUACUCCUUAGGAGGGAGUUGUUAUAUCCAUUGAACUAAGGGGAC
.(((((((((.((.......)).))(((.((((((.....)))))).)))...............))))))) ( -23.90)
>sp_pn.0 1173376 72 + 2038615
UGCCCCCUGCAGGAAUCGAACCUGCAACUACUCCUUAGGAGGGAGUUGUUAUAUCCAUUGAACUAAGGGAGC
.((.(((((((((.......)))))(((.((((((.....)))))).)))...............)))).)) ( -25.10)
>consensus
UGUCCCCUGCCGGAAUCGAACCAGCAACUACUCCUUAGGAGGGAGUUGUUAUAUCCAUUGAACUAAGGGGAC
.(((((((((.((.......)).))(((.((((((.....)))))).)))...............))))))) (-21.36 = -21.70 +   0.34)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,211,960 – 1,212,032
Length 72
Sequences 3
Columns 72
Reading direction reverse
Mean pairwise identity 90.74
Mean single sequence MFE -26.27
Consensus MFE -26.76
Energy contribution -26.10
Covariance contribution -0.66
Combinations/Pair 1.20
Mean z-score -3.28
Structure conservation index 1.02
SVM decision value 3.04
SVM RNA-class probability 0.998216
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1211960 72 + 2030921
GUCCCCUUAGUUAAAUGGAUAUAACAUCUCCCUCCUAAGGAGCAGUUGCUGGUUCGAUUCCGGCAGGGGAUA
(((((((...............(((..((((.......))))..)))(((((.......)))))))))))). ( -23.40)
>sp_ag.0 1601483 72 - 2160267
GUCCCCUUAGUUCAAUGGAUAUAACAACUCCCUCCUAAGGAGUAAUUGCUGGUUCGAUUCCGGCAGGGGACA
((((((....................(((((.......)))))...((((((.......)))))))))))). ( -27.00)
>sp_pn.0 1173376 72 + 2038615
GCUCCCUUAGUUCAAUGGAUAUAACAACUCCCUCCUAAGGAGUAGUUGCAGGUUCGAUUCCUGCAGGGGGCA
(((((((...............(((.(((((.......))))).)))(((((.......)))))))))))). ( -28.40)
>consensus
GUCCCCUUAGUUCAAUGGAUAUAACAACUCCCUCCUAAGGAGUAGUUGCUGGUUCGAUUCCGGCAGGGGACA
(((((((...............(((.(((((.......))))).)))(((((.......)))))))))))). (-26.76 = -26.10 +  -0.66) 
# Strand winner: reverse (0.94)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,211,960 – 1,212,032
Length 72
Sequences 3
Columns 72
Reading direction forward
Mean pairwise identity 90.74
Mean single sequence MFE -23.33
Consensus MFE -21.36
Energy contribution -21.70
Covariance contribution 0.34
Combinations/Pair 1.10
Mean z-score -2.37
Structure conservation index 0.92
SVM decision value 1.28
SVM RNA-class probability 0.939949
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1211960 72 + 2030921/0-72
UAUCCCCUGCCGGAAUCGAACCAGCAACUGCUCCUUAGGAGGGAGAUGUUAUAUCCAUUUAACUAAGGGGAC
..((((((....((((.((...((((....(((((.....))))).))))...)).)))).....)))))). ( -21.00)
>sp_ag.0 1601483 72 - 2160267/0-72
UGUCCCCUGCCGGAAUCGAACCAGCAAUUACUCCUUAGGAGGGAGUUGUUAUAUCCAUUGAACUAAGGGGAC
.(((((((((.((.......)).))(((.((((((.....)))))).)))...............))))))) ( -23.90)
>sp_pn.0 1173376 72 + 2038615/0-72
UGCCCCCUGCAGGAAUCGAACCUGCAACUACUCCUUAGGAGGGAGUUGUUAUAUCCAUUGAACUAAGGGAGC
.((.(((((((((.......)))))(((.((((((.....)))))).)))...............)))).)) ( -25.10)
>consensus
UGUCCCCUGCCGGAAUCGAACCAGCAACUACUCCUUAGGAGGGAGUUGUUAUAUCCAUUGAACUAAGGGGAC
.(((((((((.((.......)).))(((.((((((.....)))))).)))...............))))))) (-21.36 = -21.70 +   0.34)

alignment

Postscript

secondary structure

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dotplot

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Window 9

Location 1,211,960 – 1,212,032
Length 72
Sequences 3
Columns 72
Reading direction reverse
Mean pairwise identity 90.74
Mean single sequence MFE -26.27
Consensus MFE -26.76
Energy contribution -26.10
Covariance contribution -0.66
Combinations/Pair 1.20
Mean z-score -3.28
Structure conservation index 1.02
SVM decision value 3.04
SVM RNA-class probability 0.998216
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1211960 72 + 2030921/0-72
GUCCCCUUAGUUAAAUGGAUAUAACAUCUCCCUCCUAAGGAGCAGUUGCUGGUUCGAUUCCGGCAGGGGAUA
(((((((...............(((..((((.......))))..)))(((((.......)))))))))))). ( -23.40)
>sp_ag.0 1601483 72 - 2160267/0-72
GUCCCCUUAGUUCAAUGGAUAUAACAACUCCCUCCUAAGGAGUAAUUGCUGGUUCGAUUCCGGCAGGGGACA
((((((....................(((((.......)))))...((((((.......)))))))))))). ( -27.00)
>sp_pn.0 1173376 72 + 2038615/0-72
GCUCCCUUAGUUCAAUGGAUAUAACAACUCCCUCCUAAGGAGUAGUUGCAGGUUCGAUUCCUGCAGGGGGCA
(((((((...............(((.(((((.......))))).)))(((((.......)))))))))))). ( -28.40)
>consensus
GUCCCCUUAGUUCAAUGGAUAUAACAACUCCCUCCUAAGGAGUAGUUGCUGGUUCGAUUCCGGCAGGGGACA
(((((((...............(((.(((((.......))))).)))(((((.......)))))))))))). (-26.76 = -26.10 +  -0.66) 
# Strand winner: reverse (0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:02:16 2006