Locus 12360

Sequence ID dm3.chr3R
Location 27,588,277 – 27,588,431
Length 154
Max. P 0.952072
window16987 window16988

overview

Window 7

Location 27,588,277 – 27,588,431
Length 154
Sequences 5
Columns 159
Reading direction forward
Mean pairwise identity 74.60
Shannon entropy 0.45121
G+C content 0.55927
Mean single sequence MFE -47.69
Consensus MFE -30.40
Energy contribution -31.84
Covariance contribution 1.44
Combinations/Pair 1.29
Mean z-score -1.79
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.952072
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27588277 154 + 27905053
CUUCAUUUAUGGCUCUGGGCCACAACUCCAACUUCGGUCG--UGGUAAUUGUCGAUGUCCAUCGACUCAUCAUU---CCCCCAUCGCCUUUCCCGCCAGCAGCUGCAGUUGGCCCAGAGUCUCGGCUGCAUAUGUCGCAAUGUUCGCGUAAUGAGCGCC
..........((((((((((((..(((.((.((.(((..(--((((....((((((....))))))..))))).---.)).....((.......))..).)).)).)))))))))))))))..(((.((.(((..(((.......)))..))).))))) ( -50.00, z-score =  -2.09, R)
>droSec1.super_31 242826 154 + 568655
CUUCAUUUAUGGCUCUGGGCCACAACUCCAACUUCGGUCG--UGGUAAUUGUCGAUGUCCAUCGACUCAUCAUC---CCCCCAUCGCCUUCCCCGCCAGCAGCUGCAGUUGGCCCAGAGUCUCGGCUGCAUAUGUCGCAGUAUUCGCGUAAUGAGCGCC
..........((((((((((((..(((.((.((.(((..(--((((....((((((....))))))..))))).---.)).....((.......))..).)).)).)))))))))))))))...(((((.......)))))....((((.....)))). ( -51.10, z-score =  -2.43, R)
>droYak2.chr3R 28522721 159 + 28832112
CUUCAUUUAUGGCUCUGGGCCACAACUCCAACUUCGGUUCGUUGGUAAUUGUUGAUGUCCAUCGACUCAUCAUCAUCCCCCCACCGCCUCUCCCACCACCUGCUGCAGUUGGCCCAGAGUCUCGGCUGCAUAUGUCGCAAUAUUCGCGUAAUGAGCGCC
..........((((((((((((..(((.((((....)))((.(((....((.(((((..........))))).)).....))).))..................).)))))))))))))))..(((.((.(((..(((.......)))..))).))))) ( -45.60, z-score =  -1.83, R)
>droEre2.scaffold_4820 10087827 154 - 10470090
CUUCAUUUAUAGCUCUGGGCCAGCACUCCAACUUCGGCUG-UGGUUAAUUGUUGAUGUCCAUCGACUCAUCAUC----CCCCUCCGCCUUUCCCCCCAGCUGCUGCAGUUGGCCCAGAGUCGCGGCUGCACAUGUCGCAAUAUUCGCGUAAUGAGCGCC
...........(((((((((((((...........(((.(-.((.....((.(((.(((....)))))).))..----..)).).)))..........((....)).))))))))))))).(((((.......))))).......((((.....)))). ( -53.10, z-score =  -3.15, R)
>droAna3.scaffold_12911 1867455 131 - 5364042
-----------------ACGUGGAGCUGCAACGGUGGCCA-----CAGCUGA-GAUGUCCGUCGGCUCAUCAUU---CCCCUGCAGCCCUCACCCCUGAC--CCGAAGGUAUGUUGAAUCUGCAACAGCAUCUGUCGCAAUCUCGGCGUAAUGAGCACC
-----------------..(((..((((((..((......-----.((((((-........)))))).......---))..)))))).((((..(((...--....)))((((((((...(((.((((...)))).)))...)))))))).))))))). ( -38.64, z-score =   0.53, R)
>consensus
CUUCAUUUAUGGCUCUGGGCCACAACUCCAACUUCGGUCG__UGGUAAUUGUCGAUGUCCAUCGACUCAUCAUC___CCCCCACCGCCUUUCCCCCCAGCAGCUGCAGUUGGCCCAGAGUCUCGGCUGCAUAUGUCGCAAUAUUCGCGUAAUGAGCGCC
..........((((((((((((........(((.((((............((((((....))))))...................((...........)).)))).)))))))))))))))..(((.((.(((..(((.......)))..))).))))) (-30.40 = -31.84 +   1.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 27,588,277 – 27,588,431
Length 154
Sequences 5
Columns 159
Reading direction reverse
Mean pairwise identity 74.60
Shannon entropy 0.45121
G+C content 0.55927
Mean single sequence MFE -54.76
Consensus MFE -33.26
Energy contribution -33.82
Covariance contribution 0.56
Combinations/Pair 1.27
Mean z-score -1.86
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947486
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27588277 154 - 27905053
GGCGCUCAUUACGCGAACAUUGCGACAUAUGCAGCCGAGACUCUGGGCCAACUGCAGCUGCUGGCGGGAAAGGCGAUGGGGG---AAUGAUGAGUCGAUGGACAUCGACAAUUACCA--CGACCGAAGUUGGAGUUGUGGCCCAGAGCCAUAAAUGAAG
(((((......(((((...)))))......)).)))..(.(((((((((((((.(((((.....(((......((.(((...---(((.....((((((....)))))).))).)))--)).))).))))).)))..)))))))))).).......... ( -55.30, z-score =  -2.22, R)
>droSec1.super_31 242826 154 - 568655
GGCGCUCAUUACGCGAAUACUGCGACAUAUGCAGCCGAGACUCUGGGCCAACUGCAGCUGCUGGCGGGGAAGGCGAUGGGGG---GAUGAUGAGUCGAUGGACAUCGACAAUUACCA--CGACCGAAGUUGGAGUUGUGGCCCAGAGCCAUAAAUGAAG
(((((......((((.....))))......)).)))..(.(((((((((((((.((((((((..(...)..)))..(((..(---(.((((..((((((....)))))).)))))).--...))).))))).)))..)))))))))).).......... ( -56.50, z-score =  -2.14, R)
>droYak2.chr3R 28522721 159 - 28832112
GGCGCUCAUUACGCGAAUAUUGCGACAUAUGCAGCCGAGACUCUGGGCCAACUGCAGCAGGUGGUGGGAGAGGCGGUGGGGGGAUGAUGAUGAGUCGAUGGACAUCAACAAUUACCAACGAACCGAAGUUGGAGUUGUGGCCCAGAGCCAUAAAUGAAG
(((((......(((((...)))))......)).)))..(.(((((((((((((.((((...((((........((.(((..(..((.((((..(((....))))))).)).)..))).)).))))..)))).)))..)))))))))).).......... ( -53.10, z-score =  -1.47, R)
>droEre2.scaffold_4820 10087827 154 + 10470090
GGCGCUCAUUACGCGAAUAUUGCGACAUGUGCAGCCGCGACUCUGGGCCAACUGCAGCAGCUGGGGGGAAAGGCGGAGGGG----GAUGAUGAGUCGAUGGACAUCAACAAUUAACCA-CAGCCGAAGUUGGAGUGCUGGCCCAGAGCUAUAAAUGAAG
(((((.(((..(((((...)))))..))).)).)))..(.(((((((((((((.((((..((....))...(((.(.((..----(((..((((((....))).)))...)))..)).-).)))...)))).)))..)))))))))))........... ( -56.00, z-score =  -1.88, R)
>droAna3.scaffold_12911 1867455 131 + 5364042
GGUGCUCAUUACGCCGAGAUUGCGACAGAUGCUGUUGCAGAUUCAACAUACCUUCGG--GUCAGGGGUGAGGGCUGCAGGGG---AAUGAUGAGCCGACGGACAUC-UCAGCUG-----UGGCCACCGUUGCAGCUCCACGU-----------------
.(((....((((.(((((.(((((((((...))))))))).))).....(((....)--))..)).))))(((((((((.((---.....((.(((.((((.(...-...))))-----)))))))).))))))))))))..----------------- ( -52.90, z-score =  -1.61, R)
>consensus
GGCGCUCAUUACGCGAAUAUUGCGACAUAUGCAGCCGAGACUCUGGGCCAACUGCAGCAGCUGGCGGGAAAGGCGGUGGGGG___GAUGAUGAGUCGAUGGACAUCAACAAUUACCA__CGACCGAAGUUGGAGUUGUGGCCCAGAGCCAUAAAUGAAG
(((((......((((.....))))......)).)))....(((((((((((((.((((.(((.........))).............((.((((((....))).))).)).................)))).)))..))))))))))............ (-33.26 = -33.82 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:00:38 2011