Locus 2807

Sequence ID X_DroMel_CAF1
Location 7,490,020 – 7,490,207
Length 187
Max. P 0.977480
window4602 window4603 window4604

overview

Window 2

Location 7,490,020 – 7,490,140
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.82
Mean single sequence MFE -33.38
Consensus MFE -28.38
Energy contribution -28.98
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.36
Structure conservation index 0.85
SVM decision value 0.32
SVM RNA-class probability 0.688694
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7490020 120 - 22224390
UGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAAGCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUUUGGAAAUUAGUCGGUGGGCUAGUGCUGCUGCUGCUGCUGC
(((((((......)))))))..(((((((..(((((......)))))..)))))))(((((.((((((..((((....))))...(((((((....)))))))))..)))).)).))).. ( -37.20)
>DroSec_CAF1 23047 117 - 1
UGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAAGCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUUUGGAAAUUAGUCGGUGAGCUAGUGCUGCUG---CUGCUGC
(((((((......)))))))..(((((((..(((((......)))))..)))))))(((((.((((.(((.........)))...((((((......)))))).)))).)---).))).. ( -33.90)
>DroSim_CAF1 25039 117 - 1
UGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAAGCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUUUGGAAAUUAGUCGGUGGGCUAGUGCUGCUG---CUGCUGC
(((((((......)))))))..(((((((..(((((......)))))..)))))))(((((.((((.(((.........)))...(((((((....))))))).)))).)---).))).. ( -36.60)
>DroEre_CAF1 24147 117 - 1
UGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAACCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUUUGGAAAUUAGUCGGUGGGCUAGUGCUGCUG---CUUCUGC
(((((((......))))))).....(((((((.(((((....((...((....)).))..)))))((((.((((....))))...(((((((....)))))))..)))))---)))))). ( -32.10)
>DroYak_CAF1 26864 106 - 1
UGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAACCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUUUGGAAAUUAGUCGUUGGGCUAGUGCU--------------
(((((((......)))))))..........((((((((....((...((....)).))..)))))))).................(((((((....)))))))...-------------- ( -27.10)
>consensus
UGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAAGCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUUUGGAAAUUAGUCGGUGGGCUAGUGCUGCUG___CUGCUGC
(((((((......)))))))..(((((((..(((((......)))))..)))))))(((((((....))))..............(((((((....)))))))))).............. (-28.38 = -28.98 +   0.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,490,060 – 7,490,173
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.03
Mean single sequence MFE -33.12
Consensus MFE -28.42
Energy contribution -29.02
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.86
SVM decision value 1.79
SVM RNA-class probability 0.977480
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7490060 113 - 22224390
UCCGUUGAUUUGUUC-----GGUUUGGUUUGGGGUU--UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAAGCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUU
...........((((-----.......(((.((...--(((((((((......)))))))))..)).)))((((((((....((...((....))..)).))))))))......)))).. ( -33.80)
>DroSec_CAF1 23084 113 - 1
UCCGUUGAUUUGUUC-----GGUUUGGUUUGGGGUU--UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAAGCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUU
...........((((-----.......(((.((...--(((((((((......)))))))))..)).)))((((((((....((...((....))..)).))))))))......)))).. ( -33.80)
>DroSim_CAF1 25076 113 - 1
UCCGUUGAUUUGUUC-----GGUUUGGUUUGGGGUU--UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAAGCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUU
...........((((-----.......(((.((...--(((((((((......)))))))))..)).)))((((((((....((...((....))..)).))))))))......)))).. ( -33.80)
>DroEre_CAF1 24184 113 - 1
UCCGUUGAUUUGUUC-----GGUUUGGCCUGGGGUU--UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAACCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUU
...........((((-----((.....))...(((.--(((((((((......))))))))).)))....((((((((....((...((....)).))..))))))))......)))).. ( -33.40)
>DroYak_CAF1 26890 120 - 1
UCCGUUGAUUUGCUCAGUUUGGUUUGGUUUGGGGUUUUUUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAACCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUU
(((........((.(((......)))))....(((...(((((((((......))))))))).)))))).((((((((....((...((....)).))..))))))))............ ( -30.80)
>consensus
UCCGUUGAUUUGUUC_____GGUUUGGUUUGGGGUU__UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAAAAGCAGGACUUCGGUGGGCGUUGCAGGCAAUAAAGAACUU
...(((..((((((..................(((...(((((((((......))))))))).)))....((((((((....((...((....))..)).)))))))))))))).))).. (-28.42 = -29.02 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,490,100 – 7,490,207
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.77
Mean single sequence MFE -28.62
Consensus MFE -24.30
Energy contribution -24.90
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.85
SVM decision value 1.79
SVM RNA-class probability 0.977174
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7490100 107 - 22224390
------AAGCACCAAAUGGCAAUGACUUCUGCUUCGAUUUUCCGUUGAUUUGUUC-----GGUUUGGUUUGGGGUU--UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAA
------((((.((((((((((........)))).(((....(((..........)-----)).)))))))))(((.--(((((((((......))))))))).)))....))))...... ( -26.90)
>DroSec_CAF1 23124 107 - 1
------AAGCACCAAAUGGCAAUGACUUUUGCUUCGAUUUUCCGUUGAUUUGUUC-----GGUUUGGUUUGGGGUU--UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAA
------((((.(((((((((((......))))).(((....(((..........)-----)).)))))))))(((.--(((((((((......))))))))).)))....))))...... ( -28.60)
>DroSim_CAF1 25116 107 - 1
------AAGCACCAAAUGGCAAUGACUUUUGCUUCGAUUUUCCGUUGAUUUGUUC-----GGUUUGGUUUGGGGUU--UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAA
------((((.(((((((((((......))))).(((....(((..........)-----)).)))))))))(((.--(((((((((......))))))))).)))....))))...... ( -28.60)
>DroEre_CAF1 24224 113 - 1
ACACCAAAACACCAAAUGGCAAUGACUUUUGCUUCGAUUUUCCGUUGAUUUGUUC-----GGUUUGGCCUGGGGUU--UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAA
...((......(((...(((...((((...((.(((((.....)))))...))..-----))))..))))))(((.--(((((((((......))))))))).)))))............ ( -27.50)
>DroYak_CAF1 26930 118 - 1
G--CCCAAGCACCAAAUGGCAAUGACUUUUGCUUCGAUUUUCCGUUGAUUUGCUCAGUUUGGUUUGGUUUGGGGUUUUUUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAA
.--..(((((.(((((((((...((((...((.(((((.....)))))...))..))))..)))..))))))(((...(((((((((......))))))))).)))....)))))..... ( -31.50)
>consensus
______AAGCACCAAAUGGCAAUGACUUUUGCUUCGAUUUUCCGUUGAUUUGUUC_____GGUUUGGUUUGGGGUU__UUUGUGCAAUUUUAUUUGUAUAAAUACCGGAAGCUUGCAAAA
......((((((((((((((((......)))))(((((.....))))).............)))))))....(((...(((((((((......))))))))).)))....))))...... (-24.30 = -24.90 +   0.60)

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 10:43:58 2006