Locus 10177

Sequence ID dm3.chr3R
Location 11,936,420 – 11,936,510
Length 90
Max. P 0.934239
window13991 window13992

overview

Window 1

Location 11,936,420 – 11,936,510
Length 90
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 75.80
Shannon entropy 0.46597
G+C content 0.54999
Mean single sequence MFE -29.74
Consensus MFE -18.76
Energy contribution -18.10
Covariance contribution -0.66
Combinations/Pair 1.29
Mean z-score -1.39
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.851510
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11936420 90 + 27905053
CUGGCUAGCCGUUAAUGCGCCAAAAAGGCCAACAUACUGUUGGCCAGGAAGAAGAGAG-UAUGG-UAUGGCAGGGUGGUGGUGUGGCGGUGU
.......(((((((...(((((.....((((.((((((.((..(......)..)).))-)))).-..))))....)))))...))))))).. ( -31.90, z-score =  -1.93, R)
>droSim1.chr3R 17977078 90 - 27517382
CUGGCUAGCCGUUAAUGCGCCAAAAAGGCCAACAUACUGUUGGCCAGGAAGAGAAGGGGUAUGGGUAUGG--GCAUGGCAGGUUGGCGGUGU
...(((((((....((((.((.....(((((((.....))))))).............(((....)))))--))))....)))))))..... ( -31.90, z-score =  -1.44, R)
>droSec1.super_0 11097252 90 - 21120651
CUGGCUAGCCGUUAAUGCGCCAAAAAGGCCAACAUACUGUUGGCCAGGAAGAGAAGGGGUAUGGGUAUGG--GUAUGGCAGGUUGGCGGUGU
...(((((((((....))(((.....(((((((.....))))))).............((((........--))))))).)))))))..... ( -30.10, z-score =  -1.23, R)
>droEre2.scaffold_4770 11460221 75 + 17746568
CUGGCUAGCCGUUAAUGCGCCAAAAAGGCCAACAUAUUGUUGGCCAGGAAGAGG-GGGGUAUGGGUAUGGCGGUGU----------------
...(((.(((((..((((.((.....(((((((.....))))))).........-)).))))....))))))))..---------------- ( -26.94, z-score =  -1.80, R)
>droYak2.chr3R 14334356 83 - 28832112
CUGGCUAGCCGUUAAUGCGCCAAAAAGGCCAACAUAUUGUUGGCCAGGAAGAGG-GGGCUAUGGGUAUGGCGGUGUGGCAAUGU--------
...(((((((((((.(((.(((....(((((((.....)))))))......((.-...)).))))))))))))).)))).....-------- ( -30.70, z-score =  -1.53, R)
>droAna3.scaffold_13340 2059630 90 - 23697760
UUGGCUAGCCGUUAAUGCGCCAAAAAGGUGAACAGGUUGUUGGCCAGAAAGGAGGAAG--AGCGGCACGGGGAAAGCGAAAGGGCCUGGCGU
..((((.((((((..(.(.((.....(((.(((.....))).))).....)).).)..--))))))..........(....)))))...... ( -26.90, z-score =  -0.38, R)
>consensus
CUGGCUAGCCGUUAAUGCGCCAAAAAGGCCAACAUACUGUUGGCCAGGAAGAGGAGGGGUAUGGGUAUGGCGGUAUGGCAGGGUGGCGGUGU
(((((((((.((......(((.....)))......)).)))))))))............................................. (-18.76 = -18.10 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,936,420 – 11,936,510
Length 90
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 75.80
Shannon entropy 0.46597
G+C content 0.54999
Mean single sequence MFE -19.72
Consensus MFE -16.20
Energy contribution -16.53
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.17
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.39
SVM RNA-class probability 0.934239
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11936420 90 - 27905053
ACACCGCCACACCACCACCCUGCCAUA-CCAUA-CUCUCUUCUUCCUGGCCAACAGUAUGUUGGCCUUUUUGGCGCAUUAACGGCUAGCCAG
....(((((...((......)).....-.....-.............(((((((.....)))))))....))))).......((....)).. ( -19.80, z-score =  -1.39, R)
>droSim1.chr3R 17977078 90 + 27517382
ACACCGCCAACCUGCCAUGC--CCAUACCCAUACCCCUUCUCUUCCUGGCCAACAGUAUGUUGGCCUUUUUGGCGCAUUAACGGCUAGCCAG
....((((((......(((.--.......)))...............(((((((.....)))))))...)))))).......((....)).. ( -21.90, z-score =  -1.46, R)
>droSec1.super_0 11097252 90 + 21120651
ACACCGCCAACCUGCCAUAC--CCAUACCCAUACCCCUUCUCUUCCUGGCCAACAGUAUGUUGGCCUUUUUGGCGCAUUAACGGCUAGCCAG
....((((((..((......--.))......................(((((((.....)))))))...)))))).......((....)).. ( -20.20, z-score =  -1.45, R)
>droEre2.scaffold_4770 11460221 75 - 17746568
----------------ACACCGCCAUACCCAUACCCC-CCUCUUCCUGGCCAACAAUAUGUUGGCCUUUUUGGCGCAUUAACGGCUAGCCAG
----------------....(((((............-.........(((((((.....)))))))....))))).......((....)).. ( -19.61, z-score =  -2.25, R)
>droYak2.chr3R 14334356 83 + 28832112
--------ACAUUGCCACACCGCCAUACCCAUAGCCC-CCUCUUCCUGGCCAACAAUAUGUUGGCCUUUUUGGCGCAUUAACGGCUAGCCAG
--------.....(((....(((((............-.........(((((((.....)))))))....))))).......)))....... ( -20.61, z-score =  -1.27, R)
>droAna3.scaffold_13340 2059630 90 + 23697760
ACGCCAGGCCCUUUCGCUUUCCCCGUGCCGCU--CUUCCUCCUUUCUGGCCAACAACCUGUUCACCUUUUUGGCGCAUUAACGGCUAGCCAA
..(((((((......)))).....(((((...--......((.....))..(((.....))).........)))))......)))....... ( -16.20, z-score =   0.82, R)
>consensus
ACACCGCCACCCUGCCACACCGCCAUACCCAUACCCCUCCUCUUCCUGGCCAACAAUAUGUUGGCCUUUUUGGCGCAUUAACGGCUAGCCAG
...............................................(((((((.....)))))))....((((((.......))..)))). (-16.20 = -16.53 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:18:56 2011