Locus 10996

Sequence ID dm3.chr3R
Location 18,021,505 – 18,021,578
Length 73
Max. P 0.946527
window15110 window15111

overview

Window 0

Location 18,021,505 – 18,021,578
Length 73
Sequences 6
Columns 74
Reading direction forward
Mean pairwise identity 66.40
Shannon entropy 0.66545
G+C content 0.49691
Mean single sequence MFE -22.45
Consensus MFE -9.61
Energy contribution -10.34
Covariance contribution 0.72
Combinations/Pair 1.15
Mean z-score -1.58
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946527
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18021505 73 + 27905053
ACCGUGCGUUGCGAUACCCUGGACAAAGGGAUUU-CUAGGGUAUGUGGCAUCGAUGGCUCCAGAGGGCGUGCAG
...(..(((..(.((((((((((..........)-))))))))))..)).......((((....)))))..).. ( -27.60, z-score =  -1.62, R)
>droAna3.scaffold_13340 9019725 57 + 23697760
CCAGUGCGUUUUCGUACCCUAGAAAGGUGGGCUUUCCAGGGUAAACUUAGUCCUAAA-----------------
..((..(.......((((((.(((((.....))))).))))))......)..))...----------------- ( -15.92, z-score =  -1.24, R)
>droEre2.scaffold_4820 414373 74 - 10470090
ACUGUGCGUUGGUAUACCCUGGAUUUGGGGAUUUUCUAGGGUAUGUUGCACUCUUGUCUCUAGCGCGCUUGCAA
...((((((((((((((((((((...........)))))))))))..(((....)))..)))))))))...... ( -26.80, z-score =  -3.07, R)
>droYak2.chr3R 18871901 74 + 28832112
ACUGUGCGUUGGUAUACCCUGGAUUUAAGGAUUUCCUAGGGUAUGUUGCAUUGUUGUCUCUAGUGAGCCUGCAA
...(((((....(((((((((((..........))).)))))))).)))))(((.(.(((....))).).))). ( -21.50, z-score =  -1.55, R)
>droSec1.super_0 18391031 73 + 21120651
ACCGUGCGCUGGGACACCCUGGACUAAGGGGUUU-AUAGGGUAUGUGGCAUUGUUGGCUGAAGAGAAUCAGCAA
.((((((.(((((((.((((......))))))))-.))).))))).).........(((((......))))).. ( -23.90, z-score =  -1.29, R)
>droSim1.chr3R 17837901 73 + 27517382
ACCGUGCGUUGAGAUACCCUGGACUAAGGGAUUU-CUAGGGUAUGUGGCAUUGUUGACUGAAGAGAACCAGCAA
.((((((.(((((((.((((......))))))))-).)).))))).)...((((((............)))))) ( -19.00, z-score =  -0.75, R)
>consensus
ACCGUGCGUUGGGAUACCCUGGACUAAGGGAUUU_CUAGGGUAUGUGGCAUUGUUGACUCAAGAGAGCCUGCAA
...((((......(((((((((.............)))))))))...))))....................... ( -9.61 = -10.34 +   0.72)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,021,505 – 18,021,578
Length 73
Sequences 6
Columns 74
Reading direction reverse
Mean pairwise identity 66.40
Shannon entropy 0.66545
G+C content 0.49691
Mean single sequence MFE -16.50
Consensus MFE -6.34
Energy contribution -6.36
Covariance contribution 0.03
Combinations/Pair 1.14
Mean z-score -1.51
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.829201
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18021505 73 - 27905053
CUGCACGCCCUCUGGAGCCAUCGAUGCCACAUACCCUAG-AAAUCCCUUUGUCCAGGGUAUCGCAACGCACGGU
.(((..((((...)).))....(.(((...(((((((.(-(.(......).)).))))))).))).)))).... ( -16.20, z-score =   0.41, R)
>droAna3.scaffold_13340 9019725 57 - 23697760
-----------------UUUAGGACUAAGUUUACCCUGGAAAGCCCACCUUUCUAGGGUACGAAAACGCACUGG
-----------------..(((..(....((((((((((((((.....)))))))))))).))....)..))). ( -17.30, z-score =  -2.13, R)
>droEre2.scaffold_4820 414373 74 + 10470090
UUGCAAGCGCGCUAGAGACAAGAGUGCAACAUACCCUAGAAAAUCCCCAAAUCCAGGGUAUACCAACGCACAGU
.(((..((((.((.......)).))))...(((((((.((...........)).)))))))......))).... ( -17.90, z-score =  -3.08, R)
>droYak2.chr3R 18871901 74 - 28832112
UUGCAGGCUCACUAGAGACAACAAUGCAACAUACCCUAGGAAAUCCUUAAAUCCAGGGUAUACCAACGCACAGU
(((((.((((....))).).....))))).(((((((.(((..........))))))))))............. ( -17.60, z-score =  -2.57, R)
>droSec1.super_0 18391031 73 - 21120651
UUGCUGAUUCUCUUCAGCCAACAAUGCCACAUACCCUAU-AAACCCCUUAGUCCAGGGUGUCCCAGCGCACGGU
..(((((......)))))..((..((((..(((((((.(-((.....)))....)))))))....).)))..)) ( -15.80, z-score =  -1.02, R)
>droSim1.chr3R 17837901 73 - 27517382
UUGCUGGUUCUCUUCAGUCAACAAUGCCACAUACCCUAG-AAAUCCCUUAGUCCAGGGUAUCUCAACGCACGGU
..(((((......)))))..((..(((...(((((((.(-(..........)).)))))))......)))..)) ( -14.20, z-score =  -0.67, R)
>consensus
UUGCAGGCUCUCUAGAGACAACAAUGCAACAUACCCUAG_AAAUCCCUUAGUCCAGGGUAUCCCAACGCACGGU
..............................(((((((.................)))))))............. ( -6.34 =  -6.36 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:34:26 2011