Locus 3263

Sequence ID dm3.chr2R
Location 3,875,040 – 3,875,144
Length 104
Max. P 0.959130
window4492 window4493

overview

Window 2

Location 3,875,040 – 3,875,144
Length 104
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 83.44
Shannon entropy 0.25462
G+C content 0.41477
Mean single sequence MFE -25.19
Consensus MFE -19.10
Energy contribution -19.73
Covariance contribution 0.62
Combinations/Pair 1.15
Mean z-score -2.32
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.56
SVM RNA-class probability 0.949908
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3875040 104 + 21146708
---------CAC-UAUGUACUACAUAAGAACUACAUAUGUACAAGGAGCGCCACUAAUUCGAACAGAAAGGCGGUCGAAUUAAGCGGGGCAACCUGCCGGAUUAAUAACAAUUU
---------..(-(.(((((..................)))))))((.((((.....(((.....))).)))).)).((((..(((((....)))))..))))........... ( -25.57, z-score =  -2.63, R)
>droEre2.scaffold_4929 7887738 112 - 26641161
UGUUCACCACAUGUGUGUACUAUAUACAAAU--CAUCCAUACAAGGAUCGCCCCUAAUUCAAACAGAAUGGCGGUCGAAUUAAGCAGGGAAACCUACGGGAUUAAUAACAAUAU
((((.......(((((((...)))))))...--.((((.......(((((((....((((.....))))))))))).......(.(((....))).).))))....)))).... ( -26.30, z-score =  -1.80, R)
>droSec1.super_1 1512296 102 + 14215200
---------CAC-UAUGUACUACAUAAGUACUACAUAUGUACAAGGAGCGCCACUAAUUCGAACAGAAAGGAGG--GAAUUAAGCGGGGCAACCUGCCGGAUUAAUAACAAUUU
---------.((-((((((.(((....))).)))))).))..........((.((..(((.....)))...)))--)((((..(((((....)))))..))))........... ( -22.70, z-score =  -1.96, R)
>droSim1.chr2R 2582228 102 + 19596830
---------CAC-UAUGUACUACAUAAGUACUACAUAUGUACAAGGAGCGCCACUAAUUCGAACAGAAAGGCGG--GAAUUAAGCGGGGCAACCUGCGGGAUUAAUAACAAUCU
---------.((-((((((.(((....))).)))))).))....(((.((((.....(((.....))).)))).--.((((..(((((....)))))..))))........))) ( -26.20, z-score =  -2.89, R)
>consensus
_________CAC_UAUGUACUACAUAAGAACUACAUAUGUACAAGGAGCGCCACUAAUUCGAACAGAAAGGCGG__GAAUUAAGCGGGGCAACCUGCCGGAUUAAUAACAAUUU
..........((.((((((.(((....))).)))))).))........((((.....(((.....))).))))....((((..(((((....)))))..))))........... (-19.10 = -19.73 +   0.62)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,875,040 – 3,875,144
Length 104
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 83.44
Shannon entropy 0.25462
G+C content 0.41477
Mean single sequence MFE -26.80
Consensus MFE -20.56
Energy contribution -21.75
Covariance contribution 1.19
Combinations/Pair 1.19
Mean z-score -2.35
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.66
SVM RNA-class probability 0.959130
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3875040 104 - 21146708
AAAUUGUUAUUAAUCCGGCAGGUUGCCCCGCUUAAUUCGACCGCCUUUCUGUUCGAAUUAGUGGCGCUCCUUGUACAUAUGUAGUUCUUAUGUAGUACAUA-GUG---------
.................(((((..((.(((((.(((((((.((......)).)))))))))))).))..)))))((.((((((.(.(....).).))))))-)).--------- ( -27.30, z-score =  -2.62, R)
>droEre2.scaffold_4929 7887738 112 + 26641161
AUAUUGUUAUUAAUCCCGUAGGUUUCCCUGCUUAAUUCGACCGCCAUUCUGUUUGAAUUAGGGGCGAUCCUUGUAUGGAUG--AUUUGUAUAUAGUACACACAUGUGGUGAACA
.((((((...((((((((((((....))))).((((((((.((......)).))))))))))))..((((......)))).--..)))...))))))(((....)))....... ( -24.30, z-score =   0.27, R)
>droSec1.super_1 1512296 102 - 14215200
AAAUUGUUAUUAAUCCGGCAGGUUGCCCCGCUUAAUUC--CCUCCUUUCUGUUCGAAUUAGUGGCGCUCCUUGUACAUAUGUAGUACUUAUGUAGUACAUA-GUG---------
.................(((((..((.(((((.(((((--...(......)...)))))))))).))..)))))((.((((((.(((....))).))))))-)).--------- ( -26.10, z-score =  -2.99, R)
>droSim1.chr2R 2582228 102 - 19596830
AGAUUGUUAUUAAUCCCGCAGGUUGCCCCGCUUAAUUC--CCGCCUUUCUGUUCGAAUUAGUGGCGCUCCUUGUACAUAUGUAGUACUUAUGUAGUACAUA-GUG---------
.(((((....)))))..(((((..((.(((((.(((((--..((......))..)))))))))).))..)))))((.((((((.(((....))).))))))-)).--------- ( -29.50, z-score =  -4.04, R)
>consensus
AAAUUGUUAUUAAUCCCGCAGGUUGCCCCGCUUAAUUC__CCGCCUUUCUGUUCGAAUUAGUGGCGCUCCUUGUACAUAUGUAGUACUUAUGUAGUACAUA_GUG_________
.................(((((..((.(((((.(((((((.(........).)))))))))))).))..)))))((.((((((.(((....))).)))))).)).......... (-20.56 = -21.75 +   1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:06:57 2011