Locus 7899

Sequence ID dm3.chr3L
Location 18,316,612 – 18,316,757
Length 145
Max. P 0.701568
window10870 window10871

overview

Window 0

Location 18,316,612 – 18,316,757
Length 145
Sequences 4
Columns 163
Reading direction forward
Mean pairwise identity 64.99
Shannon entropy 0.55937
G+C content 0.29915
Mean single sequence MFE -27.22
Consensus MFE -13.46
Energy contribution -13.78
Covariance contribution 0.31
Combinations/Pair 1.36
Mean z-score -1.23
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.701568
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18316612 145 + 24543557
UUGCAAAUGUUAAUAAUACAAACUAAAGACGUUCGACUUCUAAGUAAGAUUUUAUAUUCAAUCAAUGAUUUACAUUUUAAAAUAUAUUUCAUUCGGCACGCUAAG------------------CCAAAGGGAAUUUUCCUCUGUGCUUGAUCUUACUUAGGAA
...(.((((((................)))))).)..((((((((((((((..........(((((((..((.(((....))).))..))))).))......(((------------------(((.(((((...))))).)).)))))))))))))))))). ( -27.99, z-score =  -1.91, R)
>droEre2.scaffold_4784 10188028 148 - 25762168
--------UUGGAUUAUUAACGAUGUACGAACCUAAUGACGAAAAAGUAUUUUAUAUUCAACCGAAUAUUUACAUUAUAUA-AAUAUUUCAUCCGGCGCUCCUUAGCCAAAUUGUUAAGCAACUCAAAGGGGAUUUUCCUUU-UACUUAGUA--AUGUAG---
--------.((.((((((((................((((((....(((....((((((....)))))).)))........-............(((........)))...))))))........(((((((....))))))-)..))))))--)).)).--- ( -23.30, z-score =   0.08, R)
>droSec1.super_19 311973 162 + 1257711
UUGCAAAUGUUAAUAAUACAAGCUAAAUAUGGUCGACUUCUAAGUAAGCUUUAAUAUUCAAGCAAAGAUUUACAUUUUAAAAUAGAUUUCAUUCGGCACGCUUUGCCUAA-UUCUCAAGCCACUCAAAGGAAAUUUUCCUCUGUGGUUGAUUUUACUUAGUAA
.....................(((((.((..(((((..((((.....((((........)))).(((((....)))))....))))..))....((((.....))))...-......((((((....((((.....))))..)))))))))..)).))))).. ( -28.80, z-score =  -0.49, R)
>droSim1.chr3L 17648952 139 + 22553184
UUGCAAAUGUUAAUAAUACAAACUAAACACAGUCGACUUCUAAGUAAGAUUUUAUAUUCAACCAAAGAGUUACAUUUUUAA-UAAAUUUU----GGCAAGCCAC-------------------UCAAAGGAAAUUUUCCUUUGUGGUUGAUCUUACUUAGUAA
.......................................((((((((((((..........((((((.((((......)))-)...))))----))..((((((-------------------..((((((.....))))))))))))))))))))))))... ( -28.80, z-score =  -2.59, R)
>consensus
UUGCAAAUGUUAAUAAUACAAACUAAACACAGUCGACUUCUAAGUAAGAUUUUAUAUUCAACCAAAGAUUUACAUUUUAAA_UAUAUUUCAUUCGGCACGCCAUG__________________UCAAAGGAAAUUUUCCUCUGUGCUUGAUCUUACUUAGUAA
.......................................((((((((((((...........................................((....))......................((((((((...)))))))).....))))))))))))... (-13.46 = -13.78 +   0.31)

alignment

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secondary structure

Postscript

dotplot

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Window 1

Location 18,316,612 – 18,316,757
Length 145
Sequences 4
Columns 163
Reading direction reverse
Mean pairwise identity 64.99
Shannon entropy 0.55937
G+C content 0.29915
Mean single sequence MFE -31.45
Consensus MFE -11.00
Energy contribution -11.62
Covariance contribution 0.62
Combinations/Pair 1.22
Mean z-score -1.87
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.627159
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18316612 145 - 24543557
UUCCUAAGUAAGAUCAAGCACAGAGGAAAAUUCCCUUUGG------------------CUUAGCGUGCCGAAUGAAAUAUAUUUUAAAAUGUAAAUCAUUGAUUGAAUAUAAAAUCUUACUUAGAAGUCGAACGUCUUUAGUUUGUAUUAUUAACAUUUGCAA
...(((((((((((.((((.((((((.......)))))))------------------)))................(((((((...((((.....))))....)))))))..))))))))))).((((((((.......))))).))).............. ( -33.00, z-score =  -2.92, R)
>droEre2.scaffold_4784 10188028 148 + 25762168
---CUACAU--UACUAAGUA-AAAGGAAAAUCCCCUUUGAGUUGCUUAACAAUUUGGCUAAGGAGCGCCGGAUGAAAUAUU-UAUAUAAUGUAAAUAUUCGGUUGAAUAUAAAAUACUUUUUCGUCAUUAGGUUCGUACAUCGUUAAUAAUCCAA--------
---......--.........-...(((...(((...(..(((((.....)))))..)....)))(.(((.(((((((((((-.....)))))..((((((....))))))..........))))))....))).)...............)))..-------- ( -22.70, z-score =   0.92, R)
>droSec1.super_19 311973 162 - 1257711
UUACUAAGUAAAAUCAACCACAGAGGAAAAUUUCCUUUGAGUGGCUUGAGAA-UUAGGCAAAGCGUGCCGAAUGAAAUCUAUUUUAAAAUGUAAAUCUUUGCUUGAAUAUUAAAGCUUACUUAGAAGUCGACCAUAUUUAGCUUGUAUUAUUAACAUUUGCAA
...((((((((..((((((((((((((.....))))))..)))).))))...-((((((((((..(((....(((((....)))))....)))...))))))))))..........))))))))................((.(((.......)))...)).. ( -35.90, z-score =  -1.88, R)
>droSim1.chr3L 17648952 139 - 22553184
UUACUAAGUAAGAUCAACCACAAAGGAAAAUUUCCUUUGA-------------------GUGGCUUGCC----AAAAUUUA-UUAAAAAUGUAACUCUUUGGUUGAAUAUAAAAUCUUACUUAGAAGUCGACUGUGUUUAGUUUGUAUUAUUAACAUUUGCAA
...((((((((((((((((((((((((.....))))))).-------------------.(((....))----).......-.................)))))))........))))))))))..(.(((.(((...((((....))))...))).)))).. ( -34.20, z-score =  -3.59, R)
>consensus
UUACUAAGUAAGAUCAACCACAAAGGAAAAUUCCCUUUGA__________________CAAAGCGUGCCGAAUGAAAUAUA_UUUAAAAUGUAAAUCUUUGGUUGAAUAUAAAAUCUUACUUAGAAGUCGACCGUGUUUAGCUUGUAUUAUUAACAUUUGCAA
...((((((((.........((((((.......)))))).............................................................((((........))))))))))))....................................... (-11.00 = -11.62 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:35:35 2011