Locus 1421

Sequence ID X_DroMel_CAF1
Location 4,289,337 – 4,289,449
Length 112
Max. P 0.917412
window2265 window2266

overview

Window 5

Location 4,289,337 – 4,289,449
Length 112
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 79.27
Mean single sequence MFE -29.03
Consensus MFE -12.34
Energy contribution -12.14
Covariance contribution -0.20
Combinations/Pair 1.20
Mean z-score -2.16
Structure conservation index 0.43
SVM decision value 0.47
SVM RNA-class probability 0.748358
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4289337 112 + 22224390
AGAACCUAAUUGAGGUUGAACCAAUUAGUGGCG------GGUCGCCGGGGAUCUUUGCCCC-ACAAAAAAAGAGCCAAGGCAAAUAGAUAGGCAAACAAGAGCCUACAACAAGUUCGCC
.....(((((((.(......)))))))).((((------..(.(((..((.(((((.....-......))))).))..))).......(((((........)))))......)..)))) ( -32.30)
>DroSec_CAF1 75755 94 + 1
AGAACCUAAUUGAGGUUGAACCAAUUAGUGGCG------GGUCGCCGGGGAUCUUUGCCCC-A----AAAAGAGCUAAGGC------------AAACAAGAGCCUACAAUA--UUCGCC
.....(((((((.(......)))))))).((((------(((....((((.......))))-.----..........((((------------........)))).....)--)))))) ( -26.00)
>DroSim_CAF1 70060 94 + 1
AGAACCUAAUUGAGGUUGAACCAAUUAGUGGCG------GGUCGCCGGGGAUCUUUGCCCC-A----AAAAGAGCCAAGGC------------AAACAAGAGCCUACAAUA--UUCGCC
.....(((((((.(......)))))))).((((------(.((...((((.......))))-.----....)).)).((((------------........))))......--...))) ( -26.90)
>DroEre_CAF1 82925 107 + 1
AGAACCUAAUUGAGGUUGAACCAAUUAGUGGCG------GGUCGCCAGGGAUCUUUGGCCCGA----AAAAAGGCCAAAGAAAAUAGGUAUGCAAGUAAGAGCCUACAAAA--GUCGCC
.....(((((((.(......))))))))(((((------...)))))(((((((((((((...----.....)))))))))......(((.((........)).)))....--.)).)) ( -30.70)
>DroYak_CAF1 77265 112 + 1
AGAACCUAAUUGAGAUUAAACCAAUUAGUGGGAUCUUAAAUUAGCCAGGGAUCUUUGACCC-A----AAAAGGGUCAAGGAAAAUAGGUAUAUAAACAAGAGCCUACAAUA--UGCGUC
......((((((.(......)))))))(((((.((((......(((.....((((((((((-.----....)))))))))).....)))........)))).)))))....--...... ( -29.24)
>consensus
AGAACCUAAUUGAGGUUGAACCAAUUAGUGGCG______GGUCGCCGGGGAUCUUUGCCCC_A____AAAAGAGCCAAGGCAAAUAG_UA___AAACAAGAGCCUACAAUA__UUCGCC
.....(((((((.(......))))))))(((((.........))))).((.(((((............))))).))........................................... (-12.34 = -12.14 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,289,337 – 4,289,449
Length 112
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 79.27
Mean single sequence MFE -30.09
Consensus MFE -15.74
Energy contribution -16.82
Covariance contribution 1.08
Combinations/Pair 1.23
Mean z-score -2.31
Structure conservation index 0.52
SVM decision value 1.11
SVM RNA-class probability 0.917412
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4289337 112 - 22224390
GGCGAACUUGUUGUAGGCUCUUGUUUGCCUAUCUAUUUGCCUUGGCUCUUUUUUUGU-GGGGCAAAGAUCCCCGGCGACC------CGCCACUAAUUGGUUCAACCUCAAUUAGGUUCU
((((........((((((........))))))....(((((...((.........))-((((.......)))))))))..------)))).((((((((.......))))))))..... ( -32.80)
>DroSec_CAF1 75755 94 - 1
GGCGAA--UAUUGUAGGCUCUUGUUU------------GCCUUAGCUCUUUU----U-GGGGCAAAGAUCCCCGGCGACC------CGCCACUAAUUGGUUCAACCUCAAUUAGGUUCU
((((..--..((((.((....(.(((------------(((((((......)----)-)))))))).)...)).))))..------)))).((((((((.......))))))))..... ( -27.90)
>DroSim_CAF1 70060 94 - 1
GGCGAA--UAUUGUAGGCUCUUGUUU------------GCCUUGGCUCUUUU----U-GGGGCAAAGAUCCCCGGCGACC------CGCCACUAAUUGGUUCAACCUCAAUUAGGUUCU
((((..--..((((.((....(.(((------------((((..(......)----.-.))))))).)...)).))))..------)))).((((((((.......))))))))..... ( -28.70)
>DroEre_CAF1 82925 107 - 1
GGCGAC--UUUUGUAGGCUCUUACUUGCAUACCUAUUUUCUUUGGCCUUUUU----UCGGGCCAAAGAUCCCUGGCGACC------CGCCACUAAUUGGUUCAACCUCAAUUAGGUUCU
((((..--...((((((......))))))..((.....((((((((((....----..)))))))))).....)).....------)))).((((((((.......))))))))..... ( -35.60)
>DroYak_CAF1 77265 112 - 1
GACGCA--UAUUGUAGGCUCUUGUUUAUAUACCUAUUUUCCUUGACCCUUUU----U-GGGUCAAAGAUCCCUGGCUAAUUUAAGAUCCCACUAAUUGGUUUAAUCUCAAUUAGGUUCU
(((...--.......((.(((((........((.....((.(((((((....----.-))))))).)).....))......))))).))..((((((((.......))))))))))).. ( -25.44)
>consensus
GGCGAA__UAUUGUAGGCUCUUGUUU___UA_CUAUUUGCCUUGGCUCUUUU____U_GGGGCAAAGAUCCCCGGCGACC______CGCCACUAAUUGGUUCAACCUCAAUUAGGUUCU
((((........((((((....))))))..............................((((.......)))).............)))).((((((((.......))))))))..... (-15.74 = -16.82 +   1.08)

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 10:09:01 2006