Locus 8825

Sequence ID dm3.chr3R
Location 1,918,595 – 1,918,706
Length 111
Max. P 0.900144
window12115 window12116

overview

Window 5

Location 1,918,595 – 1,918,700
Length 105
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 74.03
Shannon entropy 0.38914
G+C content 0.32949
Mean single sequence MFE -18.89
Consensus MFE -14.60
Energy contribution -14.72
Covariance contribution 0.12
Combinations/Pair 1.14
Mean z-score -1.47
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.900144
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1918595 105 + 27905053
UCCCCUAAUGCGUGUGUGGAAAACAAAAGCUAACCUACC-------UAUCAUUGUUUUCUCUGGAAUCUUGAAUGCACUUUAAUGUGUUUAAAGGCUUUCAAAUAGGAGAGA
((.((((..........(((((((((.............-------.....)))))))))........(((((.((.((((((.....)))))))).))))).)))).)).. ( -20.57, z-score =  -0.47, R)
>droEre2.scaffold_4770 2177284 101 + 17746568
----------UAAUAUUCACAACCAAAAGCUGACCUACACAAGGAAUACGAUUGUUUUCUCUGAAAUCUUGGGGGCACUUUAAGAUUUUUAA-GGCUUUCAAAUAGGAGAUA
----------.......................((((..((..(((.((....)).)))..)).....(((..(((.(((..........))-))))..))).))))..... ( -17.20, z-score =  -0.31, R)
>droSec1.super_6 2020056 90 + 4358794
---------------UAAAAAAACAAAAGCUAACCUACC-------UAUCAUUGAUUUCUCUAAAAUGUUGAAGGCACUUUAAUGUGUUUAAAGGCUUUCAAAUAGGAAUGG
---------------..................((..((-------(((((((...........))))((((((((.((((((.....)))))))))))))))))))...)) ( -18.90, z-score =  -2.56, R)
>droSim1.chr3R 1945731 90 + 27517382
---------------UAAAAAAACAAAAGCUAACCUACC-------UAUCAUUGAUUUCUCUAAAAUGUUGAAGGCACUUUAAUGUGUUUAAAGGCUUUCAAAUAGGAAUGG
---------------..................((..((-------(((((((...........))))((((((((.((((((.....)))))))))))))))))))...)) ( -18.90, z-score =  -2.56, R)
>consensus
_______________UAAAAAAACAAAAGCUAACCUACC_______UAUCAUUGAUUUCUCUAAAAUCUUGAAGGCACUUUAAUGUGUUUAAAGGCUUUCAAAUAGGAAAGA
.................................((((............((((...........))))((((((((.((((((.....)))))))))))))).))))..... (-14.60 = -14.72 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,918,605 – 1,918,706
Length 101
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 77.52
Shannon entropy 0.34573
G+C content 0.33495
Mean single sequence MFE -20.17
Consensus MFE -15.00
Energy contribution -15.88
Covariance contribution 0.88
Combinations/Pair 1.15
Mean z-score -1.31
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.647699
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1918605 101 + 27905053
CGUGUGUGGAAAACAAAAGCUAACCUACC-------UAUCAUUGUUUUCUCUGGAAUCUUGAAUGCACUUUAAUGUGUUUAAAGGCUUUCAAAUAGGAGAGAAAGUGA
.((.(((.....)))...)).........-------..(((((.((((((((......(((((.((.((((((.....)))))))).)))))...))))))))))))) ( -22.90, z-score =  -1.38, R)
>droEre2.scaffold_4770 2177287 101 + 17746568
---UAUUCACAACCAAAAGCUGACCUACACAAGGAAUACGAUUGUUUUCUCUGAAAUCUUGGGGGCACUUUAAGAUUUUUAA-GGCUUUCAAAUAGGAGAUAGAG---
---....................((((..((..(((.((....)).)))..)).....(((..(((.(((..........))-))))..))).))))........--- ( -17.20, z-score =   0.08, R)
>droSec1.super_6 2020058 94 + 4358794
-------AAAAAACAAAAGCUAACCUACC-------UAUCAUUGAUUUCUCUAAAAUGUUGAAGGCACUUUAAUGUGUUUAAAGGCUUUCAAAUAGGAAUGGAAGUGA
-------...........(((..((..((-------(((((((...........))))((((((((.((((((.....)))))))))))))))))))...)).))).. ( -20.30, z-score =  -1.98, R)
>droSim1.chr3R 1945733 94 + 27517382
-------AAAAAACAAAAGCUAACCUACC-------UAUCAUUGAUUUCUCUAAAAUGUUGAAGGCACUUUAAUGUGUUUAAAGGCUUUCAAAUAGGAAUGGAAGUGA
-------...........(((..((..((-------(((((((...........))))((((((((.((((((.....)))))))))))))))))))...)).))).. ( -20.30, z-score =  -1.98, R)
>consensus
_______AAAAAACAAAAGCUAACCUACC_______UAUCAUUGAUUUCUCUAAAAUCUUGAAGGCACUUUAAUGUGUUUAAAGGCUUUCAAAUAGGAAAGAAAGUGA
......................................(((((..((((.(((.....((((((((.((((((.....)))))))))))))).)))))))...))))) (-15.00 = -15.88 +   0.88)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:52:54 2011