Locus 5628

Sequence ID 3L_DroMel_CAF1
Location 15,446,237 – 15,446,342
Length 105
Max. P 0.988666
window8890 window8891

overview

Window 0

Location 15,446,237 – 15,446,342
Length 105
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 78.71
Mean single sequence MFE -38.90
Consensus MFE -22.77
Energy contribution -22.37
Covariance contribution -0.40
Combinations/Pair 1.18
Mean z-score -3.31
Structure conservation index 0.59
SVM decision value 2.13
SVM RNA-class probability 0.988666
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15446237 105 + 23771897
GCGGGGUGGGUCAAUUUAAUGGAAAUUUUUAUUGAAAGCCAACAAAGCGCUCAAUGGGCCAGCUAAUGGCGUUAGUUGGCCCAAAUGGGCCAAGUCGCUGGGGGA-------------
(((((((...(((((..(((....)))...)))))..)))......(.(((((.(((((((((((((...)))))))))))))..))))))...)))).......------------- ( -40.60)
>DroVir_CAF1 172011 94 + 1
AGAAU-GGGGCCAUUUUAAUGGAAAUUUUUAUUGAAAGCCAACAAAGCGCUCAAUGGCCCAGCUAAUGGCGUUAGUUGGCC-AAC-------------UGGAGGA---------ACCA
....(-((..((.((((((((((....))))))))))((((((..(((((.((.((((...)))).))))))).)))))).-...-------------....)).---------.))) ( -31.20)
>DroPse_CAF1 174444 116 + 1
GGGCUGCGGGUCAUUUCAGUGGAAAUU-UUAUUGAAAGCCAGCAAAGCGCUCAAUGGACCAGCUAAUGGCGUUAGUUGGCCCAAAUGGUCAAA-AGGCAAGGGCAGACCGAGAGAACU
(((((((.(((..((((((((((...)-)))))))))))).))..)))((((..(((.(((((((((...))))))))).)))....(((...-.)))..))))...))......... ( -37.50)
>DroEre_CAF1 174397 105 + 1
GCGGGGCGGGUCAAUUUAAUGGAAAUUUUUAUUGAAAGCCAACAAAGCGCUCAAUGGGCCAGCUAAUGGCGUUAGUUGGCCCAAAUGGGCCAAGUCGCUGGGGGA-------------
(((((((...(((((..(((....)))...)))))..)))......(.(((((.(((((((((((((...)))))))))))))..))))))...)))).......------------- ( -42.20)
>DroAna_CAF1 315872 104 + 1
GGGCGGCGGGUCAUUUUAAUGGAAAUUUUUAUUGAAAGCCAACAAAGCGCUCAAUGGGCCAGCUAAUGGCGUUAGUUGGCCCAAAUGGGCAAAGUCGCUAGGGG--------------
.((((((.(((..((((((((((....)))))))))))))........(((((.(((((((((((((...)))))))))))))..)))))...)))))).....-------------- ( -44.40)
>DroPer_CAF1 172564 116 + 1
GGGCUGCGGGUCAUUUCAGUGGAAAUU-UUAUUGAAAGCCAGCAAAGCGCUCAAUGGACCAGCUAAUGGCGUUAGUUGGCCCAAGUGGUCAAA-AGGCAAGGGCAGACCGAGAGAACU
(((((((.(((..((((((((((...)-)))))))))))).))..)))((((..(((.(((((((((...))))))))).)))....(((...-.)))..))))...))......... ( -37.50)
>consensus
GGGCGGCGGGUCAUUUUAAUGGAAAUUUUUAUUGAAAGCCAACAAAGCGCUCAAUGGGCCAGCUAAUGGCGUUAGUUGGCCCAAAUGGGCAAA_UCGCUAGGGGA_____________
....(((.......(((((((((....))))))))).((((((..(((((.((.(((.....))).))))))).))))))................)))................... (-22.77 = -22.37 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,446,237 – 15,446,342
Length 105
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 78.71
Mean single sequence MFE -27.67
Consensus MFE -18.90
Energy contribution -19.07
Covariance contribution 0.17
Combinations/Pair 1.05
Mean z-score -1.89
Structure conservation index 0.68
SVM decision value 1.08
SVM RNA-class probability 0.911536
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15446237 105 - 23771897
-------------UCCCCCAGCGACUUGGCCCAUUUGGGCCAACUAACGCCAUUAGCUGGCCCAUUGAGCGCUUUGUUGGCUUUCAAUAAAAAUUUCCAUUAAAUUGACCCACCCCGC
-------------.......(((...(((..((...((((((.((((.....)))).))))))((((((.(((.....))).)))))).................))..)))...))) ( -27.60)
>DroVir_CAF1 172011 94 - 1
UGGU---------UCCUCCA-------------GUU-GGCCAACUAACGCCAUUAGCUGGGCCAUUGAGCGCUUUGUUGGCUUUCAAUAAAAAUUUCCAUUAAAAUGGCCCC-AUUCU
(((.---------.((((((-------------(((-(((........))))...))))))..((((((.(((.....))).))))))..................))..))-).... ( -24.10)
>DroPse_CAF1 174444 116 - 1
AGUUCUCUCGGUCUGCCCUUGCCU-UUUGACCAUUUGGGCCAACUAACGCCAUUAGCUGGUCCAUUGAGCGCUUUGCUGGCUUUCAAUAA-AAUUUCCACUGAAAUGACCCGCAGCCC
.((((....((((.((....))..-...))))...(((((((.((((.....)))).)))))))..))))(((..((.((((((((....-.........))))).).)).))))).. ( -29.52)
>DroEre_CAF1 174397 105 - 1
-------------UCCCCCAGCGACUUGGCCCAUUUGGGCCAACUAACGCCAUUAGCUGGCCCAUUGAGCGCUUUGUUGGCUUUCAAUAAAAAUUUCCAUUAAAUUGACCCGCCCCGC
-------------.......(((((..((((((..(((((((.((((.....)))).))))))).)).).)))..)).(((..(((((...............)))))...))).))) ( -28.36)
>DroAna_CAF1 315872 104 - 1
--------------CCCCUAGCGACUUUGCCCAUUUGGGCCAACUAACGCCAUUAGCUGGCCCAUUGAGCGCUUUGUUGGCUUUCAAUAAAAAUUUCCAUUAAAAUGACCCGCCGCCC
--------------......(((.....((.((..(((((((.((((.....)))).))))))).)).))(((((((((.....)))))))......(((....)))....))))).. ( -26.90)
>DroPer_CAF1 172564 116 - 1
AGUUCUCUCGGUCUGCCCUUGCCU-UUUGACCACUUGGGCCAACUAACGCCAUUAGCUGGUCCAUUGAGCGCUUUGCUGGCUUUCAAUAA-AAUUUCCACUGAAAUGACCCGCAGCCC
.((((....((((.((....))..-...))))...(((((((.((((.....)))).)))))))..))))(((..((.((((((((....-.........))))).).)).))))).. ( -29.52)
>consensus
_____________UCCCCCAGCGA_UUUGCCCAUUUGGGCCAACUAACGCCAUUAGCUGGCCCAUUGAGCGCUUUGUUGGCUUUCAAUAAAAAUUUCCAUUAAAAUGACCCGCAGCCC
....................................((((((.((((.....)))).))))))((((((.(((.....))).)))))).............................. (-18.90 = -19.07 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:58 2006