Locus 8717

Sequence ID dm3.chr3R
Location 982,527 – 982,633
Length 106
Max. P 0.616892
window11964 window11965

overview

Window 4

Location 982,527 – 982,633
Length 106
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 66.16
Shannon entropy 0.52901
G+C content 0.47405
Mean single sequence MFE -28.80
Consensus MFE -13.97
Energy contribution -14.09
Covariance contribution 0.12
Combinations/Pair 1.24
Mean z-score -1.33
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.616892
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 982527 106 + 27905053
----------UUUUGAACAAGUGGGGCAACCCCCUAUACUAUACUCUAUGUACAUACAUACUAGUCUCGUAAUGGCCACACACGAGGAUGUUUGGGCCACGUUUUCGCAUCAAGUC
----------.(((((...((.(((....))).)).(((...(((.(((((....)))))..)))...))).(((((.((.((......)).)))))))..........))))).. ( -23.70, z-score =   0.01, R)
>droSim1.chr3R 1006125 102 + 27517382
----------UUUUGGACAAGUGGGGCAACCCACUAUGCCAUACUCUAUGUACACACUU----GUCUCGUAAUGGCCACACACGAGGAUGUUUGGGCCACGUUUUCGCAUCAAGUC
----------...(((.((((((((....)))))).)))))(((.....)))...((((----(...((...(((((.((.((......)).)))))))......))...))))). ( -31.30, z-score =  -1.79, R)
>droSec1.super_6 1106294 102 + 4358794
----------UUUUGGACAAGUGGGGCAACCCACUAUGCUACACUCUAUGUACACACUU----GUCUCGUAAUGGCCACACACGAGGAUGUUUGGGCCACGUUUUCGCAUCAAGUC
----------.....(((.((((((....))))))((((.......((((.(((....)----))..)))).(((((.((.((......)).))))))).......))))...))) ( -29.50, z-score =  -1.38, R)
>dp4.chr2 8978185 108 - 30794189
UACACACGAGUAUGCCAUUUAUUCAGUAAAUAAAUAGCCCAGCCAGAGAGGGCCGUAAUAUGGGCCUUAUAAUGGAUACACACGCGGAUGUUUGUCCCAU-CAUCCGCC-------
.........((((((.(((((((.....))))))).))....(((...((((((........))))))....)))))))....(((((((..........-))))))).------- ( -30.70, z-score =  -2.15, R)
>consensus
__________UUUUGGACAAGUGGGGCAACCCACUAUGCCAUACUCUAUGUACACACAU____GUCUCGUAAUGGCCACACACGAGGAUGUUUGGGCCACGUUUUCGCAUCAAGUC
...................((((((....))))))............................((.......((((((.(((......))).))).))).......))........ (-13.97 = -14.09 +   0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 982,527 – 982,633
Length 106
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 66.16
Shannon entropy 0.52901
G+C content 0.47405
Mean single sequence MFE -30.67
Consensus MFE -15.81
Energy contribution -16.25
Covariance contribution 0.44
Combinations/Pair 1.32
Mean z-score -1.04
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.507211
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 982527 106 - 27905053
GACUUGAUGCGAAAACGUGGCCCAAACAUCCUCGUGUGUGGCCAUUACGAGACUAGUAUGUAUGUACAUAGAGUAUAGUAUAGGGGGUUGCCCCACUUGUUCAAAA----------
...((((.((((....((((((...((((....))))..))))))(((...(((..(((((....))))).)))...)))..((((....))))..))))))))..---------- ( -29.40, z-score =  -0.87, R)
>droSim1.chr3R 1006125 102 - 27517382
GACUUGAUGCGAAAACGUGGCCCAAACAUCCUCGUGUGUGGCCAUUACGAGAC----AAGUGUGUACAUAGAGUAUGGCAUAGUGGGUUGCCCCACUUGUCCAAAA----------
.(((((...((.....((((((...((((....))))..))))))..))...)----))))..((((.....))))((((.((((((....)))))))))).....---------- ( -30.40, z-score =  -1.04, R)
>droSec1.super_6 1106294 102 - 4358794
GACUUGAUGCGAAAACGUGGCCCAAACAUCCUCGUGUGUGGCCAUUACGAGAC----AAGUGUGUACAUAGAGUGUAGCAUAGUGGGUUGCCCCACUUGUCCAAAA----------
................((((((...((((....))))..))))))...(.(((----((.(((((((((...)))).)))))(((((....)))))))))))....---------- ( -28.50, z-score =  -0.70, R)
>dp4.chr2 8978185 108 + 30794189
-------GGCGGAUG-AUGGGACAAACAUCCGCGUGUGUAUCCAUUAUAAGGCCCAUAUUACGGCCCUCUCUGGCUGGGCUAUUUAUUUACUGAAUAAAUGGCAUACUCGUGUGUA
-------(((..(((-((((((((.((......)).))).))))))))...)))(((((..(((((......))))).(((((((((((...)))))))))))......))))).. ( -34.40, z-score =  -1.54, R)
>consensus
GACUUGAUGCGAAAACGUGGCCCAAACAUCCUCGUGUGUGGCCAUUACGAGAC____AAGUGUGUACAUAGAGUAUAGCAUAGUGGGUUGCCCCACUUGUCCAAAA__________
......((((......((((((...((((....))))..)))))).................(((((.....)))))))))((((((....))))))................... (-15.81 = -16.25 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:50:47 2011