Locus 8783

Sequence ID dm3.chr3R
Location 1,596,385 – 1,596,475
Length 90
Max. P 0.972913
window12061 window12062

overview

Window 1

Location 1,596,385 – 1,596,475
Length 90
Sequences 8
Columns 109
Reading direction forward
Mean pairwise identity 65.44
Shannon entropy 0.63706
G+C content 0.47803
Mean single sequence MFE -24.39
Consensus MFE -12.90
Energy contribution -13.34
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -1.42
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.88
SVM RNA-class probability 0.972913
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1596385 90 + 27905053
UCUACGCAGUUGCUGUGUGCCAGAUGCGACCGCAAAUGGCACGUAAAAAGAAACAUGCAGUUCCAGGCUAAUGGUUGAGUCGCCCCCAUU-------------------
.....((.(..(((((((((((..(((....)))..))))))((........))..)))))..).((((........)))))).......------------------- ( -26.10, z-score =  -0.89, R)
>droEre2.scaffold_4770 1863058 87 + 17746568
--UACGAAGUUUCUGUGUGCCAGAUGCGACCGCAAAUGGCACGUAAAAAGAAACAUCCAGUUCCAGGCUAAUGGUUGAGGCACCACAUC--------------------
--...((.((((((.(((((((..(((....)))..))))))).....)))))).))..((..(((.(....).)))..))........-------------------- ( -27.00, z-score =  -2.38, R)
>droYak2.chr3R 17550703 108 + 28832112
UUUACGUAGUUGCUGUGUGCCAGAUGCGACCGCAAAUGGCACGUAAAAGGAAACAUCCAGUUCCCGGCUAAUGGUAGUGGCAC-ACCAUACCACAACCACAACCAUACC
.....((((..((((.((((((..(((....)))..))))))......(....)...))))..).((....((((.((((...-......)))).))))...)).))). ( -32.20, z-score =  -1.65, R)
>droSec1.super_6 1705460 103 + 4358794
UCUACGCAGUUGCUGUGUGCCAGAUGCGACCGCAAAUGGCACGUAAAAAGAAACAUUCUGUUCCAGGCUAAUGGUUGAGUCGCCGCCAUUCCACAGCCACAUC------
........((.(((((((((((..(((....)))..)))))).......................((..((((((.(.....).))))))))))))).))...------ ( -30.30, z-score =  -1.20, R)
>droSim1.chr3R 1627593 103 + 27517382
UCUACGCAGUUGCUGUGUGCCAGAUGCGACCGCAAAUGGCACGUAAAAAGAAACAUCCAGUUCCAGGCAAAUGGUUGAGUCGCCCCCAUUCCACAGCCACAUC------
........((.(((((((((((..(((....)))..)))))).......((..((.(((............))).))..))...........))))).))...------ ( -28.20, z-score =  -1.40, R)
>droAna3.scaffold_13340 5192744 92 - 23697760
UCCUCGUAAUUAUUGUGUGCCAGAUGCGACCACAAAUGGCACGUAAAAAGAAACAUUCAACGUAAUGUUUCAGCCACUCACACAGCUACAGU-----------------
.....(((....((((((((((..((......))..))))))))))...((((((((......))))))))...............)))...----------------- ( -20.30, z-score =  -1.54, R)
>dp4.chr2 17426309 68 + 30794189
CCCACGUAAUUAUUAUGUGCCAGAUGCGACCGCAGAUGGGUCGUAAAAAGAAGCAUUCAAUGUAAUGG-----------------------------------------
..((((((.....))))))(((..(((((((.......))))))).......((((...))))..)))----------------------------------------- ( -15.50, z-score =  -1.07, R)
>droPer1.super_0 11272987 68 + 11822988
CCCACGUAAUUAUUAUGUGCCAGAUGCGACCGCAAAUGGGUCGUAAAAAGAAGCAUUCAAUGUAAUGG-----------------------------------------
..((((((.....))))))(((..(((((((.......))))))).......((((...))))..)))----------------------------------------- ( -15.50, z-score =  -1.20, R)
>consensus
UCUACGUAGUUGCUGUGUGCCAGAUGCGACCGCAAAUGGCACGUAAAAAGAAACAUUCAGUUCCAGGCUAAUGGUUGAGUCACC_CCAU____________________
.............(((((((((..(((....)))..)))))))))................................................................ (-12.90 = -13.34 +   0.44)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 1,596,385 – 1,596,475
Length 90
Sequences 8
Columns 109
Reading direction reverse
Mean pairwise identity 65.44
Shannon entropy 0.63706
G+C content 0.47803
Mean single sequence MFE -27.48
Consensus MFE -12.97
Energy contribution -13.36
Covariance contribution 0.39
Combinations/Pair 1.11
Mean z-score -1.35
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.912986
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1596385 90 - 27905053
-------------------AAUGGGGGCGACUCAACCAUUAGCCUGGAACUGCAUGUUUCUUUUUACGUGCCAUUUGCGGUCGCAUCUGGCACACAGCAACUGCGUAGA
-------------------.....((((.............))))(((((.....)))))..(((((((((((..(((....)))..))))))...((....))))))) ( -27.92, z-score =  -1.06, R)
>droEre2.scaffold_4770 1863058 87 - 17746568
--------------------GAUGUGGUGCCUCAACCAUUAGCCUGGAACUGGAUGUUUCUUUUUACGUGCCAUUUGCGGUCGCAUCUGGCACACAGAAACUUCGUA--
--------------------...(((((......))))).............((.((((((......((((((..(((....)))..))))))..)))))).))...-- ( -24.90, z-score =  -1.16, R)
>droYak2.chr3R 17550703 108 - 28832112
GGUAUGGUUGUGGUUGUGGUAUGGU-GUGCCACUACCAUUAGCCGGGAACUGGAUGUUUCCUUUUACGUGCCAUUUGCGGUCGCAUCUGGCACACAGCAACUACGUAAA
.(..((((((((((((((((((((.-...))).))))).)))))((((((.....))))))......((((((..(((....)))..))))))...)))))))..)... ( -44.40, z-score =  -3.12, R)
>droSec1.super_6 1705460 103 - 4358794
------GAUGUGGCUGUGGAAUGGCGGCGACUCAACCAUUAGCCUGGAACAGAAUGUUUCUUUUUACGUGCCAUUUGCGGUCGCAUCUGGCACACAGCAACUGCGUAGA
------((((((((((..((.(((((((.............))).(((((.....))))).........))))))..))))))))))....((.(((...))).))... ( -35.12, z-score =  -1.33, R)
>droSim1.chr3R 1627593 103 - 27517382
------GAUGUGGCUGUGGAAUGGGGGCGACUCAACCAUUUGCCUGGAACUGGAUGUUUCUUUUUACGUGCCAUUUGCGGUCGCAUCUGGCACACAGCAACUGCGUAGA
------.....(((.((((....(((....)))..))))..))).(((((.....)))))..(((((((((((..(((....)))..))))))...((....))))))) ( -35.80, z-score =  -1.48, R)
>droAna3.scaffold_13340 5192744 92 + 23697760
-----------------ACUGUAGCUGUGUGAGUGGCUGAAACAUUACGUUGAAUGUUUCUUUUUACGUGCCAUUUGUGGUCGCAUCUGGCACACAAUAAUUACGAGGA
-----------------.......((.(((((((((..((((((((......))))))))...))))((((((..(((....)))..)))))).......))))).)). ( -26.50, z-score =  -1.37, R)
>dp4.chr2 17426309 68 - 30794189
-----------------------------------------CCAUUACAUUGAAUGCUUCUUUUUACGACCCAUCUGCGGUCGCAUCUGGCACAUAAUAAUUACGUGGG
-----------------------------------------((((...((((..((((........((((((....).))))).....))))..))))......)))). ( -12.62, z-score =  -0.65, R)
>droPer1.super_0 11272987 68 - 11822988
-----------------------------------------CCAUUACAUUGAAUGCUUCUUUUUACGACCCAUUUGCGGUCGCAUCUGGCACAUAAUAAUUACGUGGG
-----------------------------------------((((...((((..((((........((((((....).))))).....))))..))))......)))). ( -12.62, z-score =  -0.66, R)
>consensus
____________________AUGG_GGCGACUCAACCAUUAGCCUGGAACUGAAUGUUUCUUUUUACGUGCCAUUUGCGGUCGCAUCUGGCACACAGCAACUACGUAGA
...................................................................((((((..(((....)))..))))))................ (-12.97 = -13.36 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:52:08 2011