Locus 13193

Sequence ID dm3.chrX
Location 4,839,709 – 4,839,870
Length 161
Max. P 0.979550
window18147 window18148

overview

Window 7

Location 4,839,709 – 4,839,870
Length 161
Sequences 4
Columns 163
Reading direction forward
Mean pairwise identity 82.93
Shannon entropy 0.27937
G+C content 0.38864
Mean single sequence MFE -36.00
Consensus MFE -24.61
Energy contribution -27.55
Covariance contribution 2.94
Combinations/Pair 1.07
Mean z-score -2.41
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.937131
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4839709 161 + 22422827
ACUGCUGAAAUCGAAUUAAGAAAUCAUAUUCAAAUUGCAUAUGCACUUCGAGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGCUCUGCUGCCUUUUCAAAUUUUCAAU--CCAUUUUCCGGACUACGAAUGUUUUCCAGCAUGAUCGGAAUCUACAACUCCC
...((((((.(((((....(((......)))....(((....))).)))))(.(((((((((.....)))))))))).))))))(((((((.................(--((.......)))....(((....)))))))).))..(((.........))). ( -34.40, z-score =  -2.13, R)
>droSim1.chrX 3742300 160 + 17042790
ACUGCUGGAAUCGAAUUAAGAAAUCAUAUUCAAAUUGCAUAUGCACUUCGAGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGCACUGCUGCCCAUUCA-AUUUUCAGU--CCAUUUUCCGGAUUCCGGAUGUUUUCCAGCAUGAUCGGAAUCUACAACUCCC
..(((((((.(((((....(((......)))....(((....))).)))))(.(((((((((.....)))))))))).)))))))..((((........-.....))))--.........(((((((((((((......))))..)))))))))......... ( -39.72, z-score =  -2.40, R)
>droSec1.super_4 4281104 140 - 6179234
ACUGCUGGAAUCGAAUUAAGAAAUCAUAUUCAAAUUGCAUAUGCACUUCGAGCGUAGGAAAAUCUGUUUUUCCUACCAUUAA------------------AUUUUCAAU--CCAUUUUCCGGAUUCCGGAUGUUUUGCAGCAUGAUCGGAAUCUACUCCC---
.....((((.(((((....(((......)))....(((....))).)))))(.(((((((((.....)))))))))).....------------------........)--)))......(((((((((((((......))))..)))))))))......--- ( -34.90, z-score =  -2.28, R)
>droEre2.scaffold_4690 2202506 148 + 18748788
ACUGCUGAAAUCGAAUUAAGAAAUCAUAUUCAAAUUGCAUAUGCACUUUAAGCGUAGGAAAAUUUGUUUUUCCUACCAUUCAAGUGC----------UGCCUUCUCAAUUGCCAUUUUCCGGAU-----AUGUUUUCCAGCAUGAUCGGAAACUCCAUCUCCC
..(((((............((((.(((((((((((.(((...((((((.((..(((((((((.....)))))))))..)).))))))----------............))).))))...))))-----))).))))))))).(((.((.....))))).... ( -34.96, z-score =  -2.85, R)
>consensus
ACUGCUGAAAUCGAAUUAAGAAAUCAUAUUCAAAUUGCAUAUGCACUUCGAGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGCUCU__________CA_AUUUUCAAU__CCAUUUUCCGGAUUCCGGAUGUUUUCCAGCAUGAUCGGAAUCUACAACUCCC
...((((((.(((((....(((......)))....(((....))).)))))(.(((((((((.....)))))))))).))))))....................................(((((((((((((......))))..)))))))))......... (-24.61 = -27.55 +   2.94)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,839,709 – 4,839,870
Length 161
Sequences 4
Columns 163
Reading direction reverse
Mean pairwise identity 82.93
Shannon entropy 0.27937
G+C content 0.38864
Mean single sequence MFE -44.35
Consensus MFE -31.48
Energy contribution -31.98
Covariance contribution 0.50
Combinations/Pair 1.17
Mean z-score -2.68
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.02
SVM RNA-class probability 0.979550
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4839709 161 - 22422827
GGGAGUUGUAGAUUCCGAUCAUGCUGGAAAACAUUCGUAGUCCGGAAAAUGG--AUUGAAAAUUUGAAAAGGCAGCAGAGCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCUCGAAGUGCAUAUGCAAUUUGAAUAUGAUUUCUUAAUUCGAUUUCAGCAGU
.((((((...)))))).....((((((((..(((((.(((((((.....)))--))))............(((......))))))))(((((((((.....)))))))))..(((((.(((....)))....(((......)))....))))))))))))).. ( -44.60, z-score =  -2.09, R)
>droSim1.chrX 3742300 160 - 17042790
GGGAGUUGUAGAUUCCGAUCAUGCUGGAAAACAUCCGGAAUCCGGAAAAUGG--ACUGAAAAU-UGAAUGGGCAGCAGUGCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCUCGAAGUGCAUAUGCAAUUUGAAUAUGAUUUCUUAAUUCGAUUCCAGCAGU
.((((((...)))))).....((((((((....(((((...)))))......--........(-((((((((((((...))).....(((((((((.....)))))))))))))(((((.(((((.(.....).))))))))))...)))))))))))))).. ( -50.00, z-score =  -2.91, R)
>droSec1.super_4 4281104 140 + 6179234
---GGGAGUAGAUUCCGAUCAUGCUGCAAAACAUCCGGAAUCCGGAAAAUGG--AUUGAAAAU------------------UUAAUGGUAGGAAAAACAGAUUUUCCUACGCUCGAAGUGCAUAUGCAAUUUGAAUAUGAUUUCUUAAUUCGAUUCCAGCAGU
---((((.....))))......(((((......(((((...)))))...(((--((((((...------------------......(((((((((.....)))))))))..(((((.(((....))).)))))..............))))).))))))))) ( -41.20, z-score =  -3.05, R)
>droEre2.scaffold_4690 2202506 148 - 18748788
GGGAGAUGGAGUUUCCGAUCAUGCUGGAAAACAU-----AUCCGGAAAAUGGCAAUUGAGAAGGCA----------GCACUUGAAUGGUAGGAAAAACAAAUUUUCCUACGCUUAAAGUGCAUAUGCAAUUUGAAUAUGAUUUCUUAAUUCGAUUUCAGCAGU
..(((((.(((((...((((((.(((((......-----.))))).........(((.(((..(((----------((((((....((((((((((.....))))))))).)...))))))...)))..))).)))))))))....))))).)))))...... ( -41.60, z-score =  -2.65, R)
>consensus
GGGAGUUGUAGAUUCCGAUCAUGCUGGAAAACAUCCGGAAUCCGGAAAAUGG__AUUGAAAAU_UG__________AGAGCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCUCGAAGUGCAUAUGCAAUUUGAAUAUGAUUUCUUAAUUCGAUUCCAGCAGU
.(((((.....))))).....((((((((....((((.....))))...(((.....((((..........................(((((((((.....)))))))))..(((((.(((....))).)))))......)))).....))).)))))))).. (-31.48 = -31.98 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:33 2011