Locus 9924

Sequence ID 3R_DroMel_CAF1
Location 26,554,143 – 26,554,243
Length 100
Max. P 0.986081
window15822 window15823

overview

Window 2

Location 26,554,143 – 26,554,243
Length 100
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 86.93
Mean single sequence MFE -33.54
Consensus MFE -28.60
Energy contribution -30.22
Covariance contribution 1.61
Combinations/Pair 1.04
Mean z-score -3.36
Structure conservation index 0.85
SVM decision value 2.03
SVM RNA-class probability 0.986081
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26554143 100 + 27905053
GGCCACUUUUGGCCACGGCUCCUGAAAUUGAGCCGCACAUCCUGGCUUGUACAGGCAAAUUGGCUUAAUUUCUUUUUAAUUUGCUGCCGGUUUUCCCGGC---
(((((....)))))..(((....((((((((((((.....((((.......)))).....))))))))))))..........)))(((((.....)))))--- ( -37.24)
>DroVir_CAF1 178755 79 + 1
-----CUU--GGA-------GCUGAAAUGGAGCCGC--AUCC--GG-UGCCCAGGCAAAUUGGCUUAAUUUCUUUUUAAUUUGCUUCCGCUGCUUACG-----
-----...--(.(-------((.(((.(((.((((.--...)--))-)..))).(((((((((............)))))))))))).))).).....----- ( -19.80)
>DroSec_CAF1 138284 100 + 1
GGCCACUUUUGGCCACGGCUCCUGAAAUUAAGCCGCACAUCCUGGCUUGUACAGGCAAAUUGGCUUAAUUUCUUUUUAAUUUGCUGCCGGUUUUCCCGGC---
(((((....)))))..(((....((((((((((((.....((((.......)))).....))))))))))))..........)))(((((.....)))))--- ( -37.14)
>DroSim_CAF1 139959 100 + 1
GGCCACUUUUGACCACGGCUCCUGAAAUUGAGCCGCACAUCCUGGCUUGUACAGGCAAAUUGGCUUAAUUUCUUUUUAAUUUGCUGCCGGUUUUCCCGGC---
((((............))))...((((((((((((.....((((.......)))).....)))))))))))).............(((((.....)))))--- ( -31.70)
>DroEre_CAF1 149377 100 + 1
GGCCACUUUUGGCCACGGCUCCUGAAAUUGAGCCGCACAUCCUGGCCUGUACAGGCAAAUUGGCUUAAUUUCUUUUUAAUUUGCUGCCGGUUUUCCCGGC---
(((((....)))))..(((....((((((((((((.....((((.......)))).....))))))))))))..........)))(((((.....)))))--- ( -37.24)
>DroYak_CAF1 146071 103 + 1
GGCCACUUUUGGCCACCGCUCCUGAAAUUGAGCCGCACAUCCUGGCUUGUACAGGCAAAUUGGCUUAAUUUCUUUUUAAUUUGCUGCCGGUUUUCCCGGCUUU
(((((....))))).........((((((((((((.....((((.......)))).....)))))))))))).............(((((.....)))))... ( -38.10)
>consensus
GGCCACUUUUGGCCACGGCUCCUGAAAUUGAGCCGCACAUCCUGGCUUGUACAGGCAAAUUGGCUUAAUUUCUUUUUAAUUUGCUGCCGGUUUUCCCGGC___
(((((....))))).........((((((((((((.....((((.......)))).....)))))))))))).............(((((.....)))))... (-28.60 = -30.22 +   1.61)

alignment

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secondary structure

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dotplot

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Window 3

Location 26,554,143 – 26,554,243
Length 100
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 86.93
Mean single sequence MFE -33.18
Consensus MFE -27.35
Energy contribution -28.38
Covariance contribution 1.03
Combinations/Pair 1.08
Mean z-score -3.26
Structure conservation index 0.82
SVM decision value 1.55
SVM RNA-class probability 0.962886
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26554143 100 - 27905053
---GCCGGGAAAACCGGCAGCAAAUUAAAAAGAAAUUAAGCCAAUUUGCCUGUACAAGCCAGGAUGUGCGGCUCAAUUUCAGGAGCCGUGGCCAAAAGUGGCC
---(((((.....))))).(((((((...((....)).....)))))))..(((((........)))))(((((........)))))..(((((....))))) ( -34.90)
>DroVir_CAF1 178755 79 - 1
-----CGUAAGCAGCGGAAGCAAAUUAAAAAGAAAUUAAGCCAAUUUGCCUGGGCA-CC--GGAU--GCGGCUCCAUUUCAGC-------UCC--AAG-----
-----....(((.((....))..........(((((..((((.((((((....)))-..--.)))--..))))..))))).))-------)..--...----- ( -20.90)
>DroSec_CAF1 138284 100 - 1
---GCCGGGAAAACCGGCAGCAAAUUAAAAAGAAAUUAAGCCAAUUUGCCUGUACAAGCCAGGAUGUGCGGCUUAAUUUCAGGAGCCGUGGCCAAAAGUGGCC
---(((((.....))))).............(((((((((((.((...((((.......))))..))..))))))))))).........(((((....))))) ( -38.20)
>DroSim_CAF1 139959 100 - 1
---GCCGGGAAAACCGGCAGCAAAUUAAAAAGAAAUUAAGCCAAUUUGCCUGUACAAGCCAGGAUGUGCGGCUCAAUUUCAGGAGCCGUGGUCAAAAGUGGCC
---(((((.....))))).....................((((.((((((.(((((........)))))(((((........)))))..)).))))..)))). ( -34.20)
>DroEre_CAF1 149377 100 - 1
---GCCGGGAAAACCGGCAGCAAAUUAAAAAGAAAUUAAGCCAAUUUGCCUGUACAGGCCAGGAUGUGCGGCUCAAUUUCAGGAGCCGUGGCCAAAAGUGGCC
---(((((.....))))).....................((((.(((((((....))))..((...((((((((........)))))))).)).))).)))). ( -36.40)
>DroYak_CAF1 146071 103 - 1
AAAGCCGGGAAAACCGGCAGCAAAUUAAAAAGAAAUUAAGCCAAUUUGCCUGUACAAGCCAGGAUGUGCGGCUCAAUUUCAGGAGCGGUGGCCAAAAGUGGCC
...(((((.....))))).............((((((.((((.((...((((.......))))..))..)))).)))))).........(((((....))))) ( -34.50)
>consensus
___GCCGGGAAAACCGGCAGCAAAUUAAAAAGAAAUUAAGCCAAUUUGCCUGUACAAGCCAGGAUGUGCGGCUCAAUUUCAGGAGCCGUGGCCAAAAGUGGCC
...(((((.....))))).............((((((.((((......((((.......))))......)))).)))))).........(((((....))))) (-27.35 = -28.38 +   1.03)

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 13:45:00 2006