Locus 9428

Sequence ID dm3.chr3R
Location 6,643,382 – 6,643,508
Length 126
Max. P 0.878458
window12930 window12931

overview

Window 0

Location 6,643,382 – 6,643,486
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 89.53
Shannon entropy 0.17910
G+C content 0.58999
Mean single sequence MFE -37.32
Consensus MFE -30.94
Energy contribution -32.34
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.878458
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6643382 104 + 27905053
AUUUCAUCCGGGUCCAGAGGGCCCGAACCGAGCUGCAGUUGUCGCCAGCGUCCUCGACCAUGGGUACCUCUACCCAUACCAGCAGUAUCGACUGUGGCGACAGA
........(((((((...)))))))......((..((((((..((..(((((...))).(((((((....)))))))....)).))..))))))..))...... ( -39.20, z-score =  -1.95, R)
>droSim1.chr3R 12794268 102 - 27517382
AUUUCAUCCGGGUCCAGAGGGCCCGAACCGAGCUGCAGUUGUCGCCAACGUCCUCGACCAUGGGUACCU--ACCCAUACCAGCAGUAUCGACUGUGGCGACAGA
........(((((((...))))))).............((((((((.............((((((....--))))))....(((((....))))))))))))). ( -37.80, z-score =  -2.06, R)
>droSec1.super_0 5813777 102 - 21120651
AUUUCAUCCGGGUCCAGAGGGCCCGAACCGAGCUGCAGUUGUCGCCAACGUCCUCGACCAUGGGUACCU--ACCCAUACCAGCAGUAUCGACUGUGGCGACAGA
........(((((((...))))))).............((((((((.............((((((....--))))))....(((((....))))))))))))). ( -37.80, z-score =  -2.06, R)
>droYak2.chr3R 10676667 91 + 28832112
AUUUCAUCCGGGUCCAGAGGGCC-GA-----GCUGUAGUUGUCGCCAGCGUCCUCGGCCAUGGA-------ACCCAUGCCAGCAGUAUCCACUGUGGCGACAGA
.........(((((((...((((-((-----(.....((((....))))...))))))).))).-------)))).(((((.((((....)))))))))..... ( -39.20, z-score =  -2.79, R)
>droEre2.scaffold_4770 2778934 96 - 17746568
AUUUCAUCCGGGUCCAGAGGGCC-GAAACGAGCUGUAGUUGUCGCCAGCGUCCUCGACCAUGGU-------ACCCAUGCCACCAGUAUCUACUGUGGCGACAGA
.........(((((((...((.(-((.....((((..(....)..))))....))).)).))).-------)))).((((((.(((....)))))))))..... ( -32.60, z-score =  -1.17, R)
>consensus
AUUUCAUCCGGGUCCAGAGGGCCCGAACCGAGCUGCAGUUGUCGCCAGCGUCCUCGACCAUGGGUACCU__ACCCAUACCAGCAGUAUCGACUGUGGCGACAGA
........(((((((...))))))).............((((((((.............((((((......))))))....(((((....))))))))))))). (-30.94 = -32.34 +   1.40)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 6,643,406 – 6,643,508
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 89.93
Shannon entropy 0.16092
G+C content 0.57442
Mean single sequence MFE -33.50
Consensus MFE -28.62
Energy contribution -29.25
Covariance contribution 0.62
Combinations/Pair 1.08
Mean z-score -1.83
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.817820
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6643406 102 + 27905053
GAACCGAGCUGCAGUUGUCGCCAGCGUCCUCGACCAUGGGUACCUCUACCCAUACCAGCAGUAUCGACUGUGGCGACAGAGCGGUGGAAAACAGAACGCUCG
....((((((((..((((((((.............(((((((....)))))))....(((((....))))))))))))).)))((.....)).....))))) ( -36.30, z-score =  -1.78, R)
>droSim1.chr3R 12794292 100 - 27517382
GAACCGAGCUGCAGUUGUCGCCAACGUCCUCGACCAUGGGUACCU--ACCCAUACCAGCAGUAUCGACUGUGGCGACAGAGCGGUGGAAAACAGAACGCUCG
....((((((((..((((((((.............((((((....--))))))....(((((....))))))))))))).)))((.....)).....))))) ( -35.30, z-score =  -2.02, R)
>droSec1.super_0 5813801 100 - 21120651
GAACCGAGCUGCAGUUGUCGCCAACGUCCUCGACCAUGGGUACCU--ACCCAUACCAGCAGUAUCGACUGUGGCGACAGAGCGGUGGAAAACAGAACGCUCG
....((((((((..((((((((.............((((((....--))))))....(((((....))))))))))))).)))((.....)).....))))) ( -35.30, z-score =  -2.02, R)
>droEre2.scaffold_4770 2778957 91 - 17746568
GAAACGAGCUGUAGUUGUCGCCAGCGUCCUCGACCAUGGU-------ACCCAUGCCACCAGUAUCUACUGUGGCGACAGAGCAGAGGAAAACAGAACG----
....((..((((.((((....)))).(((((....((((.-------..))))(((((.(((....)))))))).........)))))..))))..))---- ( -27.10, z-score =  -1.51, R)
>consensus
GAACCGAGCUGCAGUUGUCGCCAACGUCCUCGACCAUGGGUACCU__ACCCAUACCAGCAGUAUCGACUGUGGCGACAGAGCGGUGGAAAACAGAACGCUCG
.......(((((..((((((((.............((((((......))))))....(((((....))))))))))))).)))))................. (-28.62 = -29.25 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:04:15 2011