Locus 5500

Sequence ID 3R_DroMel_CAF1
Location 14,469,474 – 14,469,673
Length 199
Max. P 0.745406
window8979 window8980 window8981

overview

Window 9

Location 14,469,474 – 14,469,594
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -41.17
Consensus MFE -37.75
Energy contribution -38.20
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.96
Structure conservation index 0.92
SVM decision value 0.46
SVM RNA-class probability 0.745406
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14469474 120 + 27905053
GCGAUUGGAUCGCUCGAUGGAUGCCCUUUUAUGGCAGAACAGCCCGCUGGCGCGAACUUGCCUGUCAUCUGCUACAAAUCAGCUGUCAUAAGUCCGAUCCAAUCGGAUCCGAUCCGAUCC
..((((((((((..(....(((((...(((.(((((((((((((....)))(((....))).)))..))))))).)))...)).)))....)..))))))))))(((((......))))) ( -41.50)
>DroSim_CAF1 27341 120 + 1
GCGAUUGGAUCGCUCGAUGGAUGCCCUUUUAUGGCAGAACAGCCCGCUGGCGCGAACUUGCCUGUCAUCUGCUACAAAUCAGCUGUCAUAAGCCCGAUCCAAUCGGAUCCGAUCCGAUCC
..((((((((((((..((((..((...(((.(((((((((((((....)))(((....))).)))..))))))).)))...))..)))).)))..(((((....))))).))))))))). ( -41.80)
>DroYak_CAF1 30167 117 + 1
GCGAUUGGAUCGCUCGAUGGAUGCCCGUUAAUGGCAGAACAGCCCGCUGGCGCGAACUUGCCUGUCAUCUGCUACAAAUCAGCUGUCAUAAGCCCCAUCCAAUCGGAUCCGAUCCGA---
(.(((((((((...(((((((((...((..(((((((....(((....)))(((....))))))))))..)).........(((......)))..))))).))))))))))))))..--- ( -40.20)
>consensus
GCGAUUGGAUCGCUCGAUGGAUGCCCUUUUAUGGCAGAACAGCCCGCUGGCGCGAACUUGCCUGUCAUCUGCUACAAAUCAGCUGUCAUAAGCCCGAUCCAAUCGGAUCCGAUCCGAUCC
..((((((((((.(((((((((.........(((((((((((((....)))(((....))).)))..))))))).......(((......)))...)))).)))))...)))))))))). (-37.75 = -38.20 +   0.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,469,474 – 14,469,594
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -46.00
Consensus MFE -40.27
Energy contribution -41.93
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -2.03
Structure conservation index 0.88
SVM decision value 0.23
SVM RNA-class probability 0.643895
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14469474 120 - 27905053
GGAUCGGAUCGGAUCCGAUUGGAUCGGACUUAUGACAGCUGAUUUGUAGCAGAUGACAGGCAAGUUCGCGCCAGCGGGCUGUUCUGCCAUAAAAGGGCAUCCAUCGAGCGAUCCAAUCGC
(((((......)))))((((((((((..((((((...(((..(((((.(((((......(((.((((((....)))))))))))))).)))))..)))...))).))))))))))))).. ( -47.10)
>DroSim_CAF1 27341 120 - 1
GGAUCGGAUCGGAUCCGAUUGGAUCGGGCUUAUGACAGCUGAUUUGUAGCAGAUGACAGGCAAGUUCGCGCCAGCGGGCUGUUCUGCCAUAAAAGGGCAUCCAUCGAGCGAUCCAAUCGC
(((((......)))))(((((((((..(((((((...(((..(((((.(((((......(((.((((((....)))))))))))))).)))))..)))...))).))))))))))))).. ( -48.10)
>DroYak_CAF1 30167 117 - 1
---UCGGAUCGGAUCCGAUUGGAUGGGGCUUAUGACAGCUGAUUUGUAGCAGAUGACAGGCAAGUUCGCGCCAGCGGGCUGUUCUGCCAUUAACGGGCAUCCAUCGAGCGAUCCAAUCGC
---...(((.(((((.(.((.((((((((((......((((.....)))).((((.((((..(((((((....)))))))..)))).))))...)))).)))))).)))))))).))).. ( -42.80)
>consensus
GGAUCGGAUCGGAUCCGAUUGGAUCGGGCUUAUGACAGCUGAUUUGUAGCAGAUGACAGGCAAGUUCGCGCCAGCGGGCUGUUCUGCCAUAAAAGGGCAUCCAUCGAGCGAUCCAAUCGC
(((((......)))))((((((((((..((((((...(((..(((((.(((((......(((.((((((....)))))))))))))).)))))..)))...))).))))))))))))).. (-40.27 = -41.93 +   1.67)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,469,554 – 14,469,673
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.33
Mean single sequence MFE -36.97
Consensus MFE -29.34
Energy contribution -30.01
Covariance contribution 0.67
Combinations/Pair 1.06
Mean z-score -1.92
Structure conservation index 0.79
SVM decision value 0.04
SVM RNA-class probability 0.551235
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14469554 119 - 27905053
UCAAAGAUUGUGUGGCUGUUAGUUGGGUUUUUGAAAGUGAUUGUAACAAUCGCCGAAAUAAUGCUGCCC-GACUCACAUUGGAUCGGAUCGGAUCCGAUUGGAUCGGACUUAUGACAGCU
.............((((((((((((((((((((...(((((((...)))))))))))).......))))-))).....((.((((.(((((....))))).)))).))....)))))))) ( -39.71)
>DroSim_CAF1 27421 120 - 1
UCAAAGAUUGUGUGGCUGUUAGUUGGGUUUUUGAAAGUGAUUGUAACAAUCGCCGAAAUAAUGCUGCCCGGACCCACAUUGGAUCGGAUCGGAUCCGAUUGGAUCGGGCUUAUGACAGCU
.............((((((((((.....(((((...(((((((...))))))))))))....)).((((((..(((.((((((((......))))))))))).))))))...)))))))) ( -40.70)
>DroYak_CAF1 30247 110 - 1
UCAAAGAUUAUGUUGCUCUUAGUUGGGGCUUUGAAAGUGAUUGUAACAAUCGCCGAAAUAAUGCUUCCCCAAC----------UCGGAUCGGAUCCGAUUGGAUGGGGCUUAUGACAGCU
.......(((((..(((((..(((((((.((((...(((((((...))))))))))).........)))))))----------((.(((((....))))).)).))))).)))))..... ( -30.50)
>consensus
UCAAAGAUUGUGUGGCUGUUAGUUGGGUUUUUGAAAGUGAUUGUAACAAUCGCCGAAAUAAUGCUGCCC_GAC_CACAUUGGAUCGGAUCGGAUCCGAUUGGAUCGGGCUUAUGACAGCU
..............(((((((((((((((((((...(((((((...)))))))))))).......)))).)))........((((.(((((....))))).)))).......))))))). (-29.34 = -30.01 +   0.67)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:46 2006