Locus 5213

Sequence ID dm3.chr2R
Location 18,573,984 – 18,574,078
Length 94
Max. P 0.992715
window7152 window7153

overview

Window 2

Location 18,573,984 – 18,574,078
Length 94
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 83.56
Shannon entropy 0.28538
G+C content 0.37334
Mean single sequence MFE -25.03
Consensus MFE -20.46
Energy contribution -20.50
Covariance contribution 0.04
Combinations/Pair 1.21
Mean z-score -1.88
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.935690
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18573984 94 + 21146708
---GUGCGUUUUACUAGUAUAC------AAAAGUCCCUUUUACAAAAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAA-CUUCAGGUCAUGUAAAAGGGAC
---((((.........))))..------....((((((((((((....(((((((.....)))))))...(((.((.....-.)))))....)))))))))))) ( -24.70, z-score =  -3.09, R)
>droEre2.scaffold_4845 19934116 104 + 22589142
CUAUUGCGUUUUACUAGUACACAUUUGCAAGAGUCCCUUUUACAAAAGCUACGUUUUCUAAGCACAGAAACUGCAAUAAAAAUUUCAGGUUGUGUAAAGGGGGC
...(((((.................)))))..(((((((((((....(((..........)))((((...(((.(((....))).))).))))))))))))))) ( -23.93, z-score =  -1.16, R)
>droYak2.chr2R 16039422 100 + 21139217
---AUAAGUUUUACUAGUAUGCAUUUGCAAAAGCCCCUUCUACAAAAGCUAUGUUUUCUCAGCAUGGAAACUGCAAUAAAA-CUUUAGGUGGUGCAAAGGGGGC
---................(((....)))...(((((((...((..(.(((.(((((....(((.(....))))...))))-)..))).)..))...))))))) ( -24.90, z-score =  -0.55, R)
>droSec1.super_9 1876263 100 + 3197100
---GUGAGUAUUAUUAGUCUACAUUUGCAAAAGUCCCUUUUACAAGAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAA-CUUCAGGUCGUGUAAAAGGGGC
---((((.((....)).)).))..........((((((((((((.((.((..(((((....(((.......)))...))))-)...)).)).)))))))))))) ( -26.90, z-score =  -2.51, R)
>droSim1.chr2R 17167970 100 + 19596830
---GUGAGUAUUACUAGUCUACAUUUGCAAAAGUCCCUUUUACAAAAGCUUUGUUUUCUAAGCAUAGAAACUGCAACGAAA-CUUCAGGUCUUGUAAAAGGGAC
---(..(((.............)))..)....(((((((((((((.(.((..(((((....(((.......)))...))))-)...)).).))))))))))))) ( -24.72, z-score =  -2.11, R)
>consensus
___GUGAGUUUUACUAGUAUACAUUUGCAAAAGUCCCUUUUACAAAAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAA_CUUCAGGUCGUGUAAAAGGGGC
................................((((((((((((....(((((((.....)))))))...(((.((.......)))))....)))))))))))) (-20.46 = -20.50 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,573,984 – 18,574,078
Length 94
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 83.56
Shannon entropy 0.28538
G+C content 0.37334
Mean single sequence MFE -26.14
Consensus MFE -21.54
Energy contribution -21.66
Covariance contribution 0.12
Combinations/Pair 1.29
Mean z-score -2.69
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.56
SVM RNA-class probability 0.992715
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18573984 94 - 21146708
GUCCCUUUUACAUGACCUGAAG-UUUCGUUGCAGUUUCUAUGCUUAGAAAACAUAGCUUUUGUAAAAGGGACUUUU------GUAUACUAGUAAAACGCAC---
((((((((((((.((.(((...-((((...(((.......)))...))))...))).)).))))))))))))....------...................--- ( -26.80, z-score =  -3.51, R)
>droEre2.scaffold_4845 19934116 104 - 22589142
GCCCCCUUUACACAACCUGAAAUUUUUAUUGCAGUUUCUGUGCUUAGAAAACGUAGCUUUUGUAAAAGGGACUCUUGCAAAUGUGUACUAGUAAAACGCAAUAG
(((((.((((((.((.(((...((((((..((((...))))...))))))...))).)).)))))).)))(((..((((....))))..))).....))..... ( -20.80, z-score =  -0.73, R)
>droYak2.chr2R 16039422 100 - 21139217
GCCCCCUUUGCACCACCUAAAG-UUUUAUUGCAGUUUCCAUGCUGAGAAAACAUAGCUUUUGUAGAAGGGGCUUUUGCAAAUGCAUACUAGUAAAACUUAU---
(((((.((((((....(((..(-((((....((((......))))..))))).)))....)))))).)))))...(((....)))................--- ( -25.60, z-score =  -1.78, R)
>droSec1.super_9 1876263 100 - 3197100
GCCCCUUUUACACGACCUGAAG-UUUCGUUGCAGUUUCUAUGCUUAGAAAACAUAGCUCUUGUAAAAGGGACUUUUGCAAAUGUAGACUAAUAAUACUCAC---
..((((((((((.((.(((...-((((...(((.......)))...))))...))).)).))))))))))...(((((....)))))..............--- ( -25.90, z-score =  -3.09, R)
>droSim1.chr2R 17167970 100 - 19596830
GUCCCUUUUACAAGACCUGAAG-UUUCGUUGCAGUUUCUAUGCUUAGAAAACAAAGCUUUUGUAAAAGGGACUUUUGCAAAUGUAGACUAGUAAUACUCAC---
(((((((((((((((.((....-((((...(((.......)))...))))....)).))))))))))))))).(((((....)))))..............--- ( -31.60, z-score =  -4.32, R)
>consensus
GCCCCUUUUACACGACCUGAAG_UUUCGUUGCAGUUUCUAUGCUUAGAAAACAUAGCUUUUGUAAAAGGGACUUUUGCAAAUGUAUACUAGUAAAACUCAC___
((((((((((((.((.(((....((((...(((.......)))...))))...))).)).))))))))))))................................ (-21.54 = -21.66 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:44:00 2011