Locus 9328

Sequence ID 3R_DroMel_CAF1
Location 24,789,958 – 24,790,058
Length 100
Max. P 0.879466
window14924 window14925

overview

Window 4

Location 24,789,958 – 24,790,058
Length 100
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 79.48
Mean single sequence MFE -32.47
Consensus MFE -19.36
Energy contribution -21.08
Covariance contribution 1.72
Combinations/Pair 1.04
Mean z-score -2.20
Structure conservation index 0.60
SVM decision value 0.91
SVM RNA-class probability 0.879466
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24789958 100 + 27905053
AGCAGUUGAG--CAGUGGAGAUGCAGCUCCUGGCAU-CGGUUCC-UUCUGGUCCUGUUCCUUUCCGGGAGCCGCUCCUUCAGGAACUUUCAACAACUUCCUAUG
....((((((--.(((((((..((.((((((((...-(((..((-....))..))).......)))))))).))..))))....)))))))))........... ( -33.50)
>DroSec_CAF1 6345 97 + 1
---AGUUGAG--CGGUGGAGAUGCAGCUCCUGGCAU-CGGUUCC-UUCUGGUCCUGUUCCUUUCCGGGAGCUGCUCCUUCAGGAACUUUCAACAACUUCCUAUG
---.((((((--.(.(((((..(((((((((((...-(((..((-....))..))).......)))))))))))..)))))....).))))))........... ( -38.50)
>DroSim_CAF1 6321 100 + 1
AGCAGUUGAG--CGGUGGAGAUGCAGCUCCUGGCAU-CGGUUCC-UUCUGGUCCUGUUCCUUUCCGGGAGCUGCUCCUUCAGGAACUUUCAACAACUUCCUAUG
....((((((--.(.(((((..(((((((((((...-(((..((-....))..))).......)))))))))))..)))))....).))))))........... ( -38.50)
>DroEre_CAF1 1053 97 + 1
AGAUGAAGAAACUGCUG------CAGCUCCUGGCUGCCGGUUCC-GUUUGGUCCUGUUCCUUUCCGGGAGCUGCUCCUUCAGGAACUUUCAACAACUUCCUAUG
....((((........(------((((((((((....(((..((-....))..))).......)))))))))))(((....)))...........))))..... ( -31.10)
>DroYak_CAF1 1071 102 + 1
AGAUGAUGAGACUGCUGCUGCAGCAGCUCCUGGCUU-UGGUUCC-UUCUGGUCCUGUUCCUUUCCGGGAGCUGCUCCUUCAGGAACUUUCAACAACUUCCUAUG
...((.(((((.(.(((..(.((((((((((((...-(((..((-....))..))).......)))))))))))).)..))).)..))))).)).......... ( -33.50)
>DroPer_CAF1 516 84 + 1
AGAUGAAGAAAUUAC------UGCAGCUCCUGGCAU-UGAAACCAGUCUGGGGCU-------------AGAAGCUCCUUCAGGAACUUUCAACAACUUCCUAUG
....((((.......------...(((.((..(.((-((....)))))..)))))-------------.((((.(((....))).))))......))))..... ( -19.70)
>consensus
AGAAGAUGAG__CGCUGGAGAUGCAGCUCCUGGCAU_CGGUUCC_UUCUGGUCCUGUUCCUUUCCGGGAGCUGCUCCUUCAGGAACUUUCAACAACUUCCUAUG
......................(((((((((((....(((..((.....))..))).......)))))))))))......(((((.((.....)).)))))... (-19.36 = -21.08 +   1.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,789,958 – 24,790,058
Length 100
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 79.48
Mean single sequence MFE -30.20
Consensus MFE -21.21
Energy contribution -22.13
Covariance contribution 0.92
Combinations/Pair 1.10
Mean z-score -1.59
Structure conservation index 0.70
SVM decision value 0.65
SVM RNA-class probability 0.810097
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24789958 100 - 27905053
CAUAGGAAGUUGUUGAAAGUUCCUGAAGGAGCGGCUCCCGGAAAGGAACAGGACCAGAA-GGAACCG-AUGCCAGGAGCUGCAUCUCCACUG--CUCAACUGCU
.......(((.(((((.((((((....)))((((((((.((...((.......((....-))..)).-...)).))))))))......))).--.))))).))) ( -30.70)
>DroSec_CAF1 6345 97 - 1
CAUAGGAAGUUGUUGAAAGUUCCUGAAGGAGCAGCUCCCGGAAAGGAACAGGACCAGAA-GGAACCG-AUGCCAGGAGCUGCAUCUCCACCG--CUCAACU---
..((((((.((.....)).))))))..(((((((((((.((...((.......((....-))..)).-...)).))))))))...)))....--.......--- ( -30.10)
>DroSim_CAF1 6321 100 - 1
CAUAGGAAGUUGUUGAAAGUUCCUGAAGGAGCAGCUCCCGGAAAGGAACAGGACCAGAA-GGAACCG-AUGCCAGGAGCUGCAUCUCCACCG--CUCAACUGCU
..((((((.((.....)).))))))..(((((((((((.((...((.......((....-))..)).-...)).))))))))...)))...(--(......)). ( -31.60)
>DroEre_CAF1 1053 97 - 1
CAUAGGAAGUUGUUGAAAGUUCCUGAAGGAGCAGCUCCCGGAAAGGAACAGGACCAAAC-GGAACCGGCAGCCAGGAGCUG------CAGCAGUUUCUUCAUCU
...(((((..(((((...(((((....)))))((((((.((...((.......))...(-(....))....)).)))))).------)))))..)))))..... ( -32.00)
>DroYak_CAF1 1071 102 - 1
CAUAGGAAGUUGUUGAAAGUUCCUGAAGGAGCAGCUCCCGGAAAGGAACAGGACCAGAA-GGAACCA-AAGCCAGGAGCUGCUGCAGCAGCAGUCUCAUCAUCU
...(((..(((((((.....(((....)))((((((((.((...((.......))....-(....).-...)).))))))))..)))))))..)))........ ( -31.40)
>DroPer_CAF1 516 84 - 1
CAUAGGAAGUUGUUGAAAGUUCCUGAAGGAGCUUCU-------------AGCCCCAGACUGGUUUCA-AUGCCAGGAGCUGCA------GUAAUUUCUUCAUCU
...((((((((((((.(((((((....)))))))..-------------.....(((.(((((....-..)))))...)))))------))))))))))..... ( -25.40)
>consensus
CAUAGGAAGUUGUUGAAAGUUCCUGAAGGAGCAGCUCCCGGAAAGGAACAGGACCAGAA_GGAACCG_AUGCCAGGAGCUGCAUCUCCACCA__CUCAACAUCU
..((((((.((.....)).)))))).....((((((((.((.........(..((.....))..)......)).))))))))...................... (-21.21 = -22.13 +   0.92)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:52 2006