Locus 12848

Sequence ID dm3.chrX
Location 2,608,365 – 2,608,472
Length 107
Max. P 0.769916
window17665 window17666

overview

Window 5

Location 2,608,365 – 2,608,467
Length 102
Sequences 4
Columns 121
Reading direction forward
Mean pairwise identity 54.11
Shannon entropy 0.71182
G+C content 0.56486
Mean single sequence MFE -32.78
Consensus MFE -13.14
Energy contribution -13.57
Covariance contribution 0.44
Combinations/Pair 1.43
Mean z-score -0.93
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.600883
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2608365 102 + 22422827
-------------------GCGCUGAUAAGGAUUUCAGACGAUUUCCUUACCUCCACGCCGGGAGAGGGCCAGAAGGACGUGCCCACCACGGAGAGCACAAAAUUGCAGAACCUGCACAGC
-------------------..((((.((((((..((....))..)))))).(((....(((((...(((((........).)))).)).))).)))........(((((...))))))))) ( -30.90, z-score =  -1.69, R)
>droSec1.super_10 2369896 78 + 3036183
-------------------GCGUUGAUAUGCAUUUCAGACGAUUUCCGUACCUCCACGCCGGGAGAGGGUCAGGAGGUCGUGGAGAACCUGAACCGC------------------------
-------------------((((....)))).((((..(((((((((...((((..(....)..))))....))))))))).))))...........------------------------ ( -25.60, z-score =  -0.73, R)
>droYak2.chrX 16028972 120 - 21770863
ACAGCAAGCGACAGUGGCAGCGUC-AUAUGGAUUUCAAGCGAUUCCCUUGCCUCCUCACAGGGGGAGGCCCAGGGAGUCAAUGCUACCAAGGAGCUGGCAGACUUCGAGACUUUGUACUGC
.((((........((((((((...-.............))((((((((.((((((((....))))))))..))))))))..))))))......))))((((((...........)).)))) ( -45.03, z-score =  -1.65, R)
>droEre2.scaffold_4690 34823 108 + 18748788
-------ACGACA-----AGCGAC-AUUUGGAUUUCAGAGGACUCUCUUGCCUCCUCGCAGGACGGGGCCCAAGGAGUCAUUGCUACCGAAGAGAGAGCAGACUUCGAGAACCCCUACAGG
-------......-----.((((.-....(((....((((....))))....))))))).....((((..(..((((((..((((..(.....)..))))))))))..)..))))...... ( -29.60, z-score =   0.37, R)
>consensus
___________________GCGUC_AUAUGGAUUUCAGACGAUUCCCUUACCUCCACGCAGGGAGAGGCCCAGGAAGUCAUGGCUACCAAGGAGAGCGCAGACUUCGAGAACCUGUACAGC
........................................(((((((..(((((.((....)).)))))...))))))).......................................... (-13.14 = -13.57 +   0.44)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 6

Location 2,608,370 – 2,608,472
Length 102
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 53.98
Shannon entropy 0.71563
G+C content 0.56241
Mean single sequence MFE -34.08
Consensus MFE -13.14
Energy contribution -13.57
Covariance contribution 0.44
Combinations/Pair 1.43
Mean z-score -1.17
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.769916
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 2608370 102 + 22422827
------------------GAUAAGGAUUUCAGACGAUUUCCUUACCUCCACGCCGGGAGAGGGCCAGAAGGACGUGCCCACCACGGAGAGCACAAAAUUGCAGAACCUGCACAGCCGCAA
------------------..((((((..((....))..)))))).((((......))))..(((.........((((.(.(....).).)))).....(((((...)))))..))).... ( -28.50, z-score =  -1.37, R)
>droSec1.super_10 2369901 78 + 3036183
------------------GAUAUGCAUUUCAGACGAUUUCCGUACCUCCACGCCGGGAGAGGGUCAGGAGGUCGUGGAGAACCUGAACCGCCGCAA------------------------
------------------.....((..((((((((((((((...((((..(....)..))))....)))))))))(.....))))))..)).....------------------------ ( -23.80, z-score =  -0.20, R)
>droYak2.chrX 16028977 120 - 21770863
AAGCGACAGUGGCAGCGUCAUAUGGAUUUCAAGCGAUUCCCUUGCCUCCUCACAGGGGGAGGCCCAGGGAGUCAAUGCUACCAAGGAGCUGGCAGACUUCGAGACUUUGUACUGCCGCAA
..(((.(((((.(((.(((...(.((..((....((((((((.((((((((....))))))))..))))))))..(((((.(.....).)))))))..)).)))).)))))))).))).. ( -50.00, z-score =  -2.72, R)
>droEre2.scaffold_4690 34828 108 + 18748788
------------AAGCGACAUUUGGAUUUCAGAGGACUCUCUUGCCUCCUCGCAGGACGGGGCCCAAGGAGUCAUUGCUACCGAAGAGAGAGCAGACUUCGAGAACCCCUACAGGCGCAA
------------..(((......((.((((..(((((((.((((...(((((.....)))))..))))))))).(((((..(.....)..))))).))..)))).))((....))))).. ( -34.00, z-score =  -0.39, R)
>consensus
__________________CAUAUGGAUUUCAGACGAUUCCCUUACCUCCACGCAGGGAGAGGCCCAGGAAGUCAUGGCUACCAAGGAGAGCGCAAACUUCGAGAACCUGUACAGCCGCAA
..................................(((((((..(((((.((....)).)))))...)))))))............................................... (-13.14 = -13.57 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:09:58 2011