Locus 11730

Sequence ID dm3.chr3R
Location 23,379,347 – 23,379,486
Length 139
Max. P 0.868450
window16113 window16114

overview

Window 3

Location 23,379,347 – 23,379,446
Length 99
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 74.47
Shannon entropy 0.48850
G+C content 0.44364
Mean single sequence MFE -21.86
Consensus MFE -13.30
Energy contribution -13.80
Covariance contribution 0.50
Combinations/Pair 1.31
Mean z-score -1.38
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.99
SVM RNA-class probability 0.868450
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23379347 99 + 27905053
AAUGUUUCCA-UACAA---AUGAUGACUCAAGCGAUGACCUAUCUGAAACUUUGAAAAGAGCCAACUAAUUGCGACAUCAUCGUUGGCGCCUAGCCAACAGCA
..(((.....-.))).---..(((((.....(((((((....)).....((((....)))).......)))))....)))))((((((.....)))))).... ( -21.40, z-score =  -1.55, R)
>droPer1.super_0 2838353 81 + 11822988
---------AUUGUUGAU-GUCAUAAUACAGAUGAUUCACCGUCAAAGAUGUUGCAU----UCAAAAAGUCGUGACGAAAUCUCUGGCGCCCCCC--------
---------.........-.........((((.((((...(((((..(((.(((...----.)))...))).))))).)))))))).........-------- ( -14.10, z-score =   0.01, R)
>droSim1.chr3R 23110508 99 + 27517382
AAUGUUUCCA-UACAA---UGGAUGACUCAAGCGAUGACCUAUCUAAAACUUUGACUAGCGCCAACUAAUUGCGACAUCAUCGUUGGCGCCUAGCCAACAGCA
...(((((((-(...)---)))).)))....(((((((.(((((.........)).)))(((.........)))...)))))((((((.....)))))).)). ( -23.90, z-score =  -2.04, R)
>droSec1.super_22 13123 99 + 1066717
AAUGUUUCCA-UACAA---GUGAUGACUCAAGCGAUGACCUAUCUAAAACUUUGACUAGCGCCAACUAAUUGCGACAUCAUCGUUGGCGCCUAGCCAACAGCA
...(((..((-(....---)))..)))....(((((((.(((((.........)).)))(((.........)))...)))))((((((.....)))))).)). ( -21.80, z-score =  -1.26, R)
>droYak2.chr3R 5721973 100 - 28832112
AAUGUUUUCAAUACAA---GCGAUGACUCAAGCAAUGACCCCUCUACAGCUUUGACUAGCGCCAACUAAUUGCGACAUCAUCGUUGGCGCCUAGCCAACAGCA
................---(((((((.....(((((............(((......)))........)))))....)))))((((((.....)))))).)). ( -25.25, z-score =  -2.20, R)
>droEre2.scaffold_4820 5810058 103 - 10470090
AAUGUUUUCAAUACAAGUGAUGAUGACUCAAGCGAUGACCUCUCUAAAACGUUGACUAGCGCCAACUAAUUGCGACAUCAUCGUUGGCGCCUAGCCAACAGCA
...(((.(((.((....)).))).)))....(((((((..((.(......((((........)))).....).))..)))))((((((.....)))))).)). ( -24.70, z-score =  -1.25, R)
>consensus
AAUGUUUCCA_UACAA___GUGAUGACUCAAGCGAUGACCUAUCUAAAACUUUGACUAGCGCCAACUAAUUGCGACAUCAUCGUUGGCGCCUAGCCAACAGCA
.....................(((((.....(((((................................)))))....)))))((((((.....)))))).... (-13.30 = -13.80 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 23,379,380 – 23,379,486
Length 106
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 77.89
Shannon entropy 0.41573
G+C content 0.49142
Mean single sequence MFE -34.89
Consensus MFE -20.28
Energy contribution -21.04
Covariance contribution 0.76
Combinations/Pair 1.41
Mean z-score -1.47
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.595236
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23379380 106 - 27905053
--UGUAAUUCGAGCUGGAGGCACUGG--AUCCGAUGGCUUUAAU-UGCUGUUGGCUAGGCGCCAACGAUGAUGUCGCAAUUAGUUGGCUCUUUUCAAAGUUUCAGAUAGGU
--......((...((((((((.((((--..((((((((......-.))))))))))))))((((((..((((......))))))))))...........))))))...)). ( -30.70, z-score =  -0.52, R)
>dp4.chr2 9025547 105 - 30794189
UGUUUUUCUCGACUCCCUGUUGACGGACACUUGAUGCCGCAAGCGGGGGGCCGCCUAGGCGCCAGAGAUUUCGUCACGACUUUUUGA----AUGCAACAUCUUUGACGG--
......((((....(((((((..(((.((.....)))))..)))))))(((.((....))))).))))...(((((.......(((.----...)))......))))).-- ( -32.42, z-score =  -0.82, R)
>droSim1.chr3R 23110541 106 - 27517382
--UGUAAUUCGAGCUGGAGGCACUGG--AUCCGAUGGCUAUAAU-UGCUGUUGGCUAGGCGCCAACGAUGAUGUCGCAAUUAGUUGGCGCUAGUCAAAGUUUUAGAUAGGU
--.((((((..(((((..((......--..))..)))))..)))-)))..((((((((.(((((((..((((......))))))))))))))))))).............. ( -33.90, z-score =  -1.36, R)
>droSec1.super_22 13156 106 - 1066717
--UGUAAUUCGAGCUGGAUGCACUGG--AUCCGAUGGCUAUAAU-UGCUGUUGGCUAGGCGCCAACGAUGAUGUCGCAAUUAGUUGGCGCUAGUCAAAGUUUUAGAUAGGU
--.((((((..((((((((.(...).--))))...))))..)))-)))..((((((((.(((((((..((((......))))))))))))))))))).............. ( -34.20, z-score =  -1.57, R)
>droYak2.chr3R 5722007 106 + 28832112
--UGUAAUUCGAGCCGGAGGCACUGG--AUCCGAUGGCUUUAAU-UGCUGUUGGCUAGGCGCCAACGAUGAUGUCGCAAUUAGUUGGCGCUAGUCAAAGCUGUAGAGGGGU
--.((((((.((((((..((......--..))..)))))).)))-)))..((((((((.(((((((..((((......))))))))))))))))))).............. ( -38.80, z-score =  -1.79, R)
>droEre2.scaffold_4820 5810095 106 + 10470090
--UGUAAUUCGAGCUGGAGGCAGUGG--AUCCGAUGGCUUUAAU-UGCUGUUGGCUAGGCGCCAACGAUGAUGUCGCAAUUAGUUGGCGCUAGUCAACGUUUUAGAGAGGU
--.((((((.((((((..((......--..))..)))))).)))-))).(((((((((.(((((((..((((......))))))))))))))))))))............. ( -39.30, z-score =  -2.78, R)
>consensus
__UGUAAUUCGAGCUGGAGGCACUGG__AUCCGAUGGCUUUAAU_UGCUGUUGGCUAGGCGCCAACGAUGAUGUCGCAAUUAGUUGGCGCUAGUCAAAGUUUUAGAUAGGU
................(((((.........((((((((........))))))))...(((((((((................))))))))).......)))))........ (-20.28 = -21.04 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:48:27 2011