Locus 4828

Sequence ID 2R_DroMel_CAF1
Location 15,852,934 – 15,853,041
Length 107
Max. P 0.841000
window7756 window7757

overview

Window 6

Location 15,852,934 – 15,853,041
Length 107
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 89.92
Mean single sequence MFE -37.02
Consensus MFE -29.44
Energy contribution -29.28
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.77
Structure conservation index 0.80
SVM decision value 0.75
SVM RNA-class probability 0.841000
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15852934 107 + 20766785
-----UUCGUCCAGCUUU--AGCUGUUGUUGGAGCUUCGAAUUUGUAUGUUGCCUUUGACACCAGCUAAAGGGGUUACGUGUCUGCCACUUCAGAGGCAUGCUGCCACGCCCCC-
-----..........(((--(((((.(((..((((..((........))..).)))..))).))))))))(((((...((((.((((........)))).)).))...))))).- ( -33.60)
>DroSec_CAF1 10342 107 + 1
-----UUUGGCCAGCUCU--AGCUGUUGUUGGAGCUUCGAAUUUGUAUGUUGCCUUUGACACCAGCUAAAGGGGUUACGUGUCUGCCACUUCAGUGGCAUGCUGCCGCGCCCCC-
-----((((((.((((((--(((....)))))))))...........((((......))))...))))))(((((...((((.((((((....)))))).)).))...))))).- ( -39.50)
>DroEre_CAF1 11734 112 + 1
UUGUAUGUAGUCAGCUUU--AGCUGUUGUUGGAGCUUCGAAUUUGUAUGUUGCCUUUGACACCAGCUAAAGGGGUUACGUGUCUGCCACUUCAGAGGCAUGCUGCCACGCCCCC-
...((((((..(..((((--(((((.(((..((((..((........))..).)))..))).))))))))).)..))))))((((......))))(((.....)))........- ( -34.90)
>DroYak_CAF1 11467 107 + 1
-----UGCAGCCCGCUUU--AGCUGUUGUUGGAGCUUCGAAUUUGUAUGUUGCCUUUGACACCAGCUAAAGGGGUUACGUGUCUGCCACUUCAGAGGCAUGCUGCCACGCCCCC-
-----.(((((((.((((--(((((.(((..((((..((........))..).)))..))).))))))))).))....((.((((......)))).))..))))).........- ( -39.50)
>DroAna_CAF1 11757 113 + 1
CCG--UUUUUCCGGCUCUAUGGCUGUUGUUGGAGCUUCGAAUUUGUAUGUUGCCUUUGACACCAGCUAAAGGGGUUACGUGUCUGCCACUUCAGUGGCAUCCUGUUCCGCCCCCU
(((--......))).....((((((.(((..((((..((........))..).)))..))).))))))..(((((.(((.(..((((((....))))))..))))...))))).. ( -37.60)
>consensus
_____UUUAGCCAGCUUU__AGCUGUUGUUGGAGCUUCGAAUUUGUAUGUUGCCUUUGACACCAGCUAAAGGGGUUACGUGUCUGCCACUUCAGAGGCAUGCUGCCACGCCCCC_
....................(((((.(((..((((..((........))..).)))..))).)))))...(((((.....(..((((........))))..)......))))).. (-29.44 = -29.28 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,852,934 – 15,853,041
Length 107
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 89.92
Mean single sequence MFE -34.76
Consensus MFE -25.64
Energy contribution -26.44
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.74
SVM decision value 0.36
SVM RNA-class probability 0.706072
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15852934 107 - 20766785
-GGGGGCGUGGCAGCAUGCCUCUGAAGUGGCAGACACGUAACCCCUUUAGCUGGUGUCAAAGGCAACAUACAAAUUCGAAGCUCCAACAACAGCU--AAAGCUGGACGAA-----
-(((((((((....)))))))))...(((.....)))....((.(((((((((.(((....(((..(..........)..)))...))).)))))--))))..)).....----- ( -33.00)
>DroSec_CAF1 10342 107 - 1
-GGGGGCGCGGCAGCAUGCCACUGAAGUGGCAGACACGUAACCCCUUUAGCUGGUGUCAAAGGCAACAUACAAAUUCGAAGCUCCAACAACAGCU--AGAGCUGGCCAAA-----
-((((..(((......((((((....))))))....)))..))))((((((((.(((....(((..(..........)..)))...))).)))))--)))..........----- ( -35.50)
>DroEre_CAF1 11734 112 - 1
-GGGGGCGUGGCAGCAUGCCUCUGAAGUGGCAGACACGUAACCCCUUUAGCUGGUGUCAAAGGCAACAUACAAAUUCGAAGCUCCAACAACAGCU--AAAGCUGACUACAUACAA
-(((((((((....)))))))))...(((((((...........(((((((((.(((....(((..(..........)..)))...))).)))))--))))))).))))...... ( -33.30)
>DroYak_CAF1 11467 107 - 1
-GGGGGCGUGGCAGCAUGCCUCUGAAGUGGCAGACACGUAACCCCUUUAGCUGGUGUCAAAGGCAACAUACAAAUUCGAAGCUCCAACAACAGCU--AAAGCGGGCUGCA-----
-(((((((((....)))))))))...(((.....)))(((.((((((((((((.(((....(((..(..........)..)))...))).)))))--)))).))).))).----- ( -40.80)
>DroAna_CAF1 11757 113 - 1
AGGGGGCGGAACAGGAUGCCACUGAAGUGGCAGACACGUAACCCCUUUAGCUGGUGUCAAAGGCAACAUACAAAUUCGAAGCUCCAACAACAGCCAUAGAGCCGGAAAAA--CGG
((((((((.....(..((((((....))))))..).)))..)))))...((((.(((....(((..(..........)..)))...))).)))).......(((......--))) ( -31.20)
>consensus
_GGGGGCGUGGCAGCAUGCCUCUGAAGUGGCAGACACGUAACCCCUUUAGCUGGUGUCAAAGGCAACAUACAAAUUCGAAGCUCCAACAACAGCU__AAAGCUGGCCAAA_____
..((((((.(((.....))).)(((((((.....)))(((...(((((..(....)..))))).....)))...))))..))))).....((((......))))........... (-25.64 = -26.44 +   0.80)

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 11:30:15 2006