Locus 8620

Sequence ID 3L_DroMel_CAF1
Location 22,426,221 – 22,426,421
Length 200
Max. P 0.862506
window14122 window14123 window14124

overview

Window 2

Location 22,426,221 – 22,426,341
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.23
Mean single sequence MFE -29.23
Consensus MFE -23.64
Energy contribution -23.87
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -1.82
Structure conservation index 0.81
SVM decision value 0.82
SVM RNA-class probability 0.859027
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22426221 120 - 23771897
UUCCAGUCGGCCAGGAGAGUUUCAGGGAAUGGCAGAACAAGUCUACUAACUGGUUGUCGGUUUUUAGUUUAAGCACACUAAAUCAAUUCCCAGGCAUUGCUCUUUAAGCAGCCAAUUCAU
.(((.........)))(((((...(((((((((((....(((......)))..)))))....((((((........))))))...)))))).(((..((((.....)))))))))))).. ( -27.60)
>DroEre_CAF1 4115 101 - 1
UUCCAGUCGGUCUGGAGAGUUUCAAG-------------------CCCACUGGCAGUGGGUUUUUAGUUUAAGCACACUAAAUCAAUUCCCAGGCAUUGCUCUUUAAGCAGGCAAUUCAU
.....(((.((((((.(((((..(((-------------------(((((.....))))))))(((((........)))))...)))))))))))..((((.....)))))))....... ( -31.60)
>DroYak_CAF1 38114 99 - 1
-UUCAGUCGGUCUGGAGAGUUUUAA--------------------CCCACUGGUAGUGGGUUUUUAGUUUAAGCACACUAAAUCAAUUCCCAGGCAUUGCUCUUUAAGCAGCCAAUUCAU
-........((((((.(((((..((--------------------(((((.....)))))))((((((........))))))..))))))))))).(((((.....)))))......... ( -28.50)
>consensus
UUCCAGUCGGUCUGGAGAGUUUCAAG___________________CCCACUGGUAGUGGGUUUUUAGUUUAAGCACACUAAAUCAAUUCCCAGGCAUUGCUCUUUAAGCAGCCAAUUCAU
.........((((((.(((((........................(((((.....)))))..((((((........))))))..))))))))))).(((((.....)))))......... (-23.64 = -23.87 +   0.23)

alignment

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secondary structure

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Window 3

Location 22,426,261 – 22,426,381
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.89
Mean single sequence MFE -21.91
Consensus MFE -15.74
Energy contribution -16.63
Covariance contribution 0.89
Combinations/Pair 1.06
Mean z-score -1.78
Structure conservation index 0.72
SVM decision value 0.83
SVM RNA-class probability 0.862506
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22426261 120 + 23771897
UAGUGUGCUUAAACUAAAAACCGACAACCAGUUAGUAGACUUGUUCUGCCAUUCCCUGAAACUCUCCUGGCCGACUGGAAAUGCACACAAAUUUGUGACAUGGAAAUCAUUUAAAAUGCA
..((((..(((((.......((.....((((((.(((((.....))))).....((.((.....))..))..))))))..(((((((......)))).)))))......))))).)))). ( -20.42)
>DroEre_CAF1 4155 101 + 1
UAGUGUGCUUAAACUAAAAACCCACUGCCAGUGGG-------------------CUUGAAACUCUCCAGACCGACUGGAAAUGCACACAAAUUUCUGACAUGGAAAUCAUUUAAAAUGCA
..((((((............(((((.....)))))-------------------..........(((((.....)))))...))))))..((((((.....))))))............. ( -26.60)
>DroYak_CAF1 38154 96 + 1
UAGUGUGCUUAAACUAAAAACCCACUACCAGUGGG--------------------UUAAAACUCUCCAGACCGACUGAA----CACACAAAUUUGUGACAUAGAAAUCAUUUAAAAUGCA
..(((((...........(((((((.....)))))--------------------)).........(((.....)))..----)))))......((((........)))).......... ( -18.70)
>consensus
UAGUGUGCUUAAACUAAAAACCCACUACCAGUGGG___________________CUUGAAACUCUCCAGACCGACUGGAAAUGCACACAAAUUUGUGACAUGGAAAUCAUUUAAAAUGCA
..((((((............(((((.....))))).............................(((((.....)))))...))))))................................ (-15.74 = -16.63 +   0.89)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,426,301 – 22,426,421
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.39
Mean single sequence MFE -22.93
Consensus MFE -17.01
Energy contribution -16.57
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.74
SVM decision value 0.23
SVM RNA-class probability 0.643421
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22426301 120 + 23771897
UUGUUCUGCCAUUCCCUGAAACUCUCCUGGCCGACUGGAAAUGCACACAAAUUUGUGACAUGGAAAUCAUUUAAAAUGCAGAAAAUAUAUUGAAAAUUCAGUCAGGCACUCUGGAGUCUA
.......................((((.(((((((((((.(((((((......)))).)))........(((((.(((.......))).)))))..))))))).))).)...)))).... ( -23.40)
>DroEre_CAF1 4190 106 + 1
--------------CUUGAAACUCUCCAGACCGACUGGAAAUGCACACAAAUUUCUGACAUGGAAAUCAUUUAAAAUGCAGAAAAUAUAUUGAAAAUUCAGUCAGGCACUCUGGAGUCUA
--------------.........((((((((((((((((....((......((((((.(((.(((....)))...)))))))))......))....))))))).))...))))))).... ( -27.20)
>DroYak_CAF1 38189 101 + 1
---------------UUAAAACUCUCCAGACCGACUGAA----CACACAAAUUUGUGACAUAGAAAUCAUUUAAAAUGCAGAAAAUAUAUUGAAAAUUCAGUCAGGCACUCAGGAGUCUA
---------------.....(((((..((.(((((((((----((((......))))............(((((.(((.......))).)))))..))))))).))..))..)))))... ( -18.20)
>consensus
______________CUUGAAACUCUCCAGACCGACUGGAAAUGCACACAAAUUUGUGACAUGGAAAUCAUUUAAAAUGCAGAAAAUAUAUUGAAAAUUCAGUCAGGCACUCUGGAGUCUA
.......................((((.(((((((((((....((......(((.((.(((.(((....)))...))))).)))......))....))))))).))...)).)))).... (-17.01 = -16.57 +  -0.44)

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 13:20:32 2006