Locus 12057

Sequence ID dm3.chr3R
Location 25,339,547 – 25,339,668
Length 121
Max. P 0.995665
window16573 window16574

overview

Window 3

Location 25,339,547 – 25,339,668
Length 121
Sequences 4
Columns 133
Reading direction forward
Mean pairwise identity 81.28
Shannon entropy 0.29060
G+C content 0.55718
Mean single sequence MFE -49.75
Consensus MFE -39.71
Energy contribution -39.53
Covariance contribution -0.19
Combinations/Pair 1.18
Mean z-score -2.41
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.13
SVM RNA-class probability 0.983400
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25339547 121 + 27905053
---GAGCCAUGAGACAGGAAGCGCACUCGGCUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCCAGCGACGAUGUCACCGGGCAGCAACAAUUGCAGUUGCUGUUGCAG---------
---..((((((((((((.............)))))))))(((((((((((...((((((....)))))).........)))))))))))......))).((((((...((....))))))))..--------- ( -49.62, z-score =  -2.98, R)
>droSim1.chr3R 25012867 130 + 27517382
---GAGCCAUGAGACAGGAAGCGCACUCGGCUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCCAGCGACGAUGUCACCGGGCAGCAACAAUUGCAGCAGUUGCAGUUGCUGUUGCAG
---...(((((((((((.............)))))))))(((((((((((...((((((....)))))).........))))))))))).....))((((((.(((((((((...))))))))).)))))).. ( -55.92, z-score =  -3.46, R)
>droSec1.super_4 4198200 130 + 6179234
---GAGCCAUGAGACAGGAAGCGCACUCGGCUGUCUCAUCUUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCCAGCGACGAUGUCACCGGGCAGCAACAAUUGCAGCAGUUGCAGUUGCUCUUGCAG
---..((((((((((((.............)))))))))..(((((((((...((((((....)))))).........)))))))))........))).(((((((((((((...)))))))))...)))).. ( -49.52, z-score =  -2.01, R)
>dp4.chr2 2202792 120 + 30794189
GUUCGGCUAGGGGACAGGAAGCUGGCUCGCUUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCAAGCGACGAUGUCA----GCCACAGCCACUGCCACUGCCACAGCAG---------
....((((..((((((((.((....))..))))))))..((((((((((....((((((....))))))..........))))))))))..)----))).............((((....))))--------- ( -43.94, z-score =  -1.20, R)
>consensus
___GAGCCAUGAGACAGGAAGCGCACUCGGCUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCCAGCGACGAUGUCACCGGGCAGCAACAAUUGCAGCAGCUGCAGCAG_________
.....((((((((((((..((....))...)))))))))(((((((((((...((((((....)))))).........)))))))))))......))).((((...)))).(((((....)))))........ (-39.71 = -39.53 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 25,339,547 – 25,339,668
Length 121
Sequences 4
Columns 133
Reading direction reverse
Mean pairwise identity 81.28
Shannon entropy 0.29060
G+C content 0.55718
Mean single sequence MFE -52.33
Consensus MFE -39.86
Energy contribution -43.92
Covariance contribution 4.06
Combinations/Pair 1.05
Mean z-score -3.06
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.83
SVM RNA-class probability 0.995665
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25339547 121 - 27905053
---------CUGCAACAGCAACUGCAAUUGUUGCUGCCCGGUGACAUCGUCGCUGGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAGCCGAGUGCGCUUCCUGUCUCAUGGCUC---
---------.((((........)))).((((((((((((((((((...))))))))).......((((((....))))))...)))))))))(.(((((((((..(((....))).))))))))).)...--- ( -53.10, z-score =  -4.07, R)
>droSim1.chr3R 25012867 130 - 27517382
CUGCAACAGCAACUGCAACUGCUGCAAUUGUUGCUGCCCGGUGACAUCGUCGCUGGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAGCCGAGUGCGCUUCCUGUCUCAUGGCUC---
.((((.(((.........))).)))).((((((((((((((((((...))))))))).......((((((....))))))...)))))))))(.(((((((((..(((....))).))))))))).)...--- ( -56.00, z-score =  -3.85, R)
>droSec1.super_4 4198200 130 - 6179234
CUGCAAGAGCAACUGCAACUGCUGCAAUUGUUGCUGCCCGGUGACAUCGUCGCUGGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAAAGAUGAGACAGCCGAGUGCGCUUCCUGUCUCAUGGCUC---
......((((...((((.....)))).((((((((((((((((((...))))))))).......((((((....))))))...)))))))))..(((((((((..(((....))).))))))))).))))--- ( -56.90, z-score =  -3.81, R)
>dp4.chr2 2202792 120 - 30794189
---------CUGCUGUGGCAGUGGCAGUGGCUGUGGC----UGACAUCGUCGCUUGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAAGCGAGCCAGCUUCCUGUCCCCUAGCCGAAC
---------......((((((.(((((.((((((.((----(....((((((.(((.(((....((((((....))))))....)))..)))))))))....))).)..)))))..))).)).)).))))... ( -43.30, z-score =  -0.51, R)
>consensus
_________CAACUGCAACAGCUGCAAUUGUUGCUGCCCGGUGACAUCGUCGCUGGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAGCCGAGUGCGCUUCCUGUCUCAUGGCUC___
.......((((((....))))))((..((((((((((((((((((...))))))))).......((((((....))))))...)))))))))..(((((((((..(((....))).))))))))).))..... (-39.86 = -43.92 +   4.06)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:54:51 2011