Locus 1123

Sequence ID 2R_DroMel_CAF1
Location 4,506,484 – 4,506,583
Length 99
Max. P 0.824739
window1980 window1981

overview

Window 0

Location 4,506,484 – 4,506,583
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 91.42
Mean single sequence MFE -33.40
Consensus MFE -27.35
Energy contribution -28.85
Covariance contribution 1.50
Combinations/Pair 1.04
Mean z-score -1.65
Structure conservation index 0.82
SVM decision value 0.32
SVM RNA-class probability 0.685726
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4506484 99 + 20766785
GCCCGAAGGCAGGCAGUCAACGGCCUACUUUAUGGCCACAAACUCGACUUGGCUCGAACCGAUCCCAUCCGAAGCGAGAUCCGAGCCGAGCCGCUGCAG
(((....)))..(((((....((((........))))........(.(((((((((....((((.(.........).))))))))))))).)))))).. ( -36.40)
>DroSec_CAF1 40237 96 + 1
GCCCGAAGGCAGGCAGUCAACGGCCUACUUUAUGGCCACAAACUCGACUUGGCUCGAACCGAUCCCAUCCGAAGCGAGAUCCGAGCCGAA---CUGCAG
(((....)))..(((((....((((........))))......(((.(((((((((...((........))...))))..))))).))))---)))).. ( -33.40)
>DroEre_CAF1 40175 94 + 1
GCCCGAAGGCAGGCAGUCAACGGCCUACUUUAUGGCCACAAACUCGACUUGGCUCAGACCGAGCCCAUCCGAAGCG--AUCCGAGCCGAG---CUGCAG
(((....)))..((((.....((((........))))..........((((((((.((.((..(......)...))--.)).))))))))---)))).. ( -33.30)
>DroYak_CAF1 42961 94 + 1
GCCUGAAGGCAAGCAGUCAACGGCCUACUUUAUGGCCCCCACCUCGACUUGGCUCAAACCGAUCCCAUCCGAAGUG--AUCCGAGCCGAC---CUGCAG
(((....)))..((((.....((((........))))......(((.(((((.(((...((........))...))--).))))).))).---)))).. ( -30.50)
>consensus
GCCCGAAGGCAGGCAGUCAACGGCCUACUUUAUGGCCACAAACUCGACUUGGCUCAAACCGAUCCCAUCCGAAGCG__AUCCGAGCCGAG___CUGCAG
(((....)))..((((.....((((........)))).....((((.(((((((((...((........))...))))..))))).))))...)))).. (-27.35 = -28.85 +   1.50)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 4,506,484 – 4,506,583
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 91.42
Mean single sequence MFE -41.45
Consensus MFE -34.19
Energy contribution -35.25
Covariance contribution 1.06
Combinations/Pair 1.07
Mean z-score -1.88
Structure conservation index 0.82
SVM decision value 0.69
SVM RNA-class probability 0.824739
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4506484 99 - 20766785
CUGCAGCGGCUCGGCUCGGAUCUCGCUUCGGAUGGGAUCGGUUCGAGCCAAGUCGAGUUUGUGGCCAUAAAGUAGGCCGUUGACUGCCUGCCUUCGGGC
..((..(((((.((((((((((((((....).)))))))....)))))).)))))((((..(((((........)))))..))))))..(((....))) ( -46.90)
>DroSec_CAF1 40237 96 - 1
CUGCAG---UUCGGCUCGGAUCUCGCUUCGGAUGGGAUCGGUUCGAGCCAAGUCGAGUUUGUGGCCAUAAAGUAGGCCGUUGACUGCCUGCCUUCGGGC
..((((---((.((((((((((((((....).)))))))....)))))).............((((........))))...))))))..(((....))) ( -41.40)
>DroEre_CAF1 40175 94 - 1
CUGCAG---CUCGGCUCGGAU--CGCUUCGGAUGGGCUCGGUCUGAGCCAAGUCGAGUUUGUGGCCAUAAAGUAGGCCGUUGACUGCCUGCCUUCGGGC
..((.(---((.(((((((((--((..((.....))..))))))))))).)))..((((..(((((........)))))..))))))..(((....))) ( -41.10)
>DroYak_CAF1 42961 94 - 1
CUGCAG---GUCGGCUCGGAU--CACUUCGGAUGGGAUCGGUUUGAGCCAAGUCGAGGUGGGGGCCAUAAAGUAGGCCGUUGACUGCUUGCCUUCAGGC
(((.((---((.(((((...(--((((((((...((.((.....)).))...))))))))))))))...((((((........)))))))))).))).. ( -36.40)
>consensus
CUGCAG___CUCGGCUCGGAU__CGCUUCGGAUGGGAUCGGUUCGAGCCAAGUCGAGUUUGUGGCCAUAAAGUAGGCCGUUGACUGCCUGCCUUCGGGC
..((........((((((((((((((....).)))))))....)))))).((((((.....(((((........)))))))))))))..(((....))) (-34.19 = -35.25 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:04 2006