Locus 4129

Sequence ID X_DroMel_CAF1
Location 10,858,087 – 10,858,236
Length 149
Max. P 0.907673
window6783 window6784 window6785

overview

Window 3

Location 10,858,087 – 10,858,198
Length 111
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 88.17
Mean single sequence MFE -31.70
Consensus MFE -30.00
Energy contribution -30.94
Covariance contribution 0.94
Combinations/Pair 1.08
Mean z-score -1.27
Structure conservation index 0.95
SVM decision value 0.11
SVM RNA-class probability 0.589974
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10858087 111 + 22224390
CCUGUCUUUGCCCUUGAAG--CUCGUCAACUUGCUUGUCCACGCUGCGUAUACGUAACGUGCGUAUACGUAAUAUGGCAACUCCUUCGCUGGCCAGUCCUUCAGAGCAAAAAA
......(((((..((((((--((.((((....(((((.(((.(.(((((((((((.....))))))))))).).)))))).......)))))).))..)))))).)))))... ( -30.21)
>DroSec_CAF1 11903 98 + 1
CCUGUCUUUGCCCUUGAAGCGCUCGCCAACUUGCUUGUCCACGCUGCGUAU---------------ACGUAAUAUGGCAACACCGUCGCUGGCCAGUCCUUCAGAGCAAGAAA
....((((.((..((((((.(((.((((((.((.(((.(((.(.((((...---------------.)))).).))))))))..))...)))).))).)))))).)))))).. ( -26.70)
>DroSim_CAF1 13934 113 + 1
CCUGUCUUUGCCCUUGAAGCGCUCGCCGACUUGCUUGUCCACGCUGCGUAUACGUAACGUGCGUAUACGUAAUAUGGCAACUCCUUCGCUGGCCAGUCCUUCAGAGCAAGAGA
....(((((((..((((((.(((.((((((......)))...(((((((((((((.....)))))))))))....(....)......)).))).))).)))))).)).))))) ( -38.40)
>DroYak_CAF1 12146 111 + 1
CCUGUCUUUGCCCUUGAAG--CUCGCCAACUUGCUUGUCCACGCUGCGUAUACGUAACGUGCGUAUACGUAAUAUGGCAACUCCUUCGCUGGCCAGUCCUGCAGCGCAAGUAA
.(((.....(((..(((((--...((((....((........))(((((((((((.....)))))))))))...)))).....)))))..)))))).......((....)).. ( -31.50)
>consensus
CCUGUCUUUGCCCUUGAAG__CUCGCCAACUUGCUUGUCCACGCUGCGUAUACGUAACGUGCGUAUACGUAAUAUGGCAACUCCUUCGCUGGCCAGUCCUUCAGAGCAAGAAA
......(((((.((.((((.(((.((((....(((((.(((.(.(((((((((((.....))))))))))).).)))))).......)))))).))).)))))).)))))... (-30.00 = -30.94 +   0.94)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,858,087 – 10,858,198
Length 111
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 88.17
Mean single sequence MFE -38.07
Consensus MFE -33.26
Energy contribution -34.95
Covariance contribution 1.69
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.87
SVM decision value 1.05
SVM RNA-class probability 0.907673
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10858087 111 - 22224390
UUUUUUGCUCUGAAGGACUGGCCAGCGAAGGAGUUGCCAUAUUACGUAUACGCACGUUACGUAUACGCAGCGUGGACAAGCAAGUUGACGAG--CUUCAAGGGCAAAGACAGG
.((((((((((((((...((((.(((......))))))).....((((((((.......))))))))...(((.(((......))).)))..--)))).)))))))))).... ( -37.40)
>DroSec_CAF1 11903 98 - 1
UUUCUUGCUCUGAAGGACUGGCCAGCGACGGUGUUGCCAUAUUACGU---------------AUACGCAGCGUGGACAAGCAAGUUGGCGAGCGCUUCAAGGGCAAAGACAGG
..((((((((((((((.((.((((((.....((((.(((..((.((.---------------...)).))..)))...)))).)))))).))).)))).))))).)))).... ( -35.80)
>DroSim_CAF1 13934 113 - 1
UCUCUUGCUCUGAAGGACUGGCCAGCGAAGGAGUUGCCAUAUUACGUAUACGCACGUUACGUAUACGCAGCGUGGACAAGCAAGUCGGCGAGCGCUUCAAGGGCAAAGACAGG
(((.((((((((((((.((.(((.((....(..((((((..((.((((((((.......)))))))).))..))).))).)..)).))).))).)))).)))))))))).... ( -40.80)
>DroYak_CAF1 12146 111 - 1
UUACUUGCGCUGCAGGACUGGCCAGCGAAGGAGUUGCCAUAUUACGUAUACGCACGUUACGUAUACGCAGCGUGGACAAGCAAGUUGGCGAG--CUUCAAGGGCAAAGACAGG
....((((.((..(((.((.((((((....(..((((((..((.((((((((.......)))))))).))..))).))).)..)))))).))--)))..)).))))....... ( -38.30)
>consensus
UUUCUUGCUCUGAAGGACUGGCCAGCGAAGGAGUUGCCAUAUUACGUAUACGCACGUUACGUAUACGCAGCGUGGACAAGCAAGUUGGCGAG__CUUCAAGGGCAAAGACAGG
....(((((((((((..((.((((((....(..((((((..((.((((((((.......)))))))).))..))).))).)..)))))).))..)))).)))))))....... (-33.26 = -34.95 +   1.69)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,858,121 – 10,858,236
Length 115
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 80.76
Mean single sequence MFE -29.31
Consensus MFE -19.20
Energy contribution -19.95
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.66
SVM decision value 0.34
SVM RNA-class probability 0.696266
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10858121 115 + 22224390
GUCCACGCUGCGUAUACGUAACGUGCGUAUACGUAAUAUGGCAACUCCUUCGCUGGCCAGUCCUUCAGAGCAAAAAAAAAAAAAAAAAAUGCGACAACAAGAAAAGCGA--AAUGGA
(.(((.(.(((((((((((.....))))))))))).).))))...(((((((((((.....))......(((.................)))............)))))--)..))) ( -26.23)
>DroSec_CAF1 11939 88 + 1
GUCCACGCUGCGUAU---------------ACGUAAUAUGGCAACACCGUCGCUGGCCAGUCCUUCAGAGCAAGAAAA------------GCGACAACAAGCAGAGCGA--AAUGGA
.((((((((((....---------------........((....))..((((((..(..(..(....)..)..)...)------------))))).....))..)))).--..)))) ( -21.40)
>DroSim_CAF1 13970 103 + 1
GUCCACGCUGCGUAUACGUAACGUGCGUAUACGUAAUAUGGCAACUCCUUCGCUGGCCAGUCCUUCAGAGCAAGAGAA------------GCGACAACAAGCAGAGCGA--AAUGGA
(.(((.(.(((((((((((.....))))))))))).).))))...(((((((((.((..(((((((.........)))------------).))).....))..)))))--)..))) ( -33.00)
>DroYak_CAF1 12180 105 + 1
GUCCACGCUGCGUAUACGUAACGUGCGUAUACGUAAUAUGGCAACUCCUUCGCUGGCCAGUCCUGCAGCGCAAGUAAA------------AGGACAACAAGAAGAGCGUAGAAUGUA
.((.(((((((((((((((.....))))))))))....((((..(......)...))))(((((...((....))...------------))))).........))))).))..... ( -36.60)
>consensus
GUCCACGCUGCGUAUACGUAACGUGCGUAUACGUAAUAUGGCAACUCCUUCGCUGGCCAGUCCUUCAGAGCAAGAAAA____________GCGACAACAAGAAGAGCGA__AAUGGA
.....((((((((((((((.....))))))))))....((((..(......)...)))).............................................))))......... (-19.20 = -19.95 +   0.75)

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 11:17:04 2006