Locus 14408

Sequence ID dm3.chrX
Location 13,139,707 – 13,139,802
Length 95
Max. P 0.992375
window19835 window19836

overview

Window 5

Location 13,139,707 – 13,139,802
Length 95
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 71.78
Shannon entropy 0.41563
G+C content 0.50359
Mean single sequence MFE -32.85
Consensus MFE -21.46
Energy contribution -23.90
Covariance contribution 2.44
Combinations/Pair 1.11
Mean z-score -2.52
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.54
SVM RNA-class probability 0.992375
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 13139707 95 + 22422827
--------AUGAGUUGAAGUGCUGGAAGCAAAUGGAAGAGGUUUUUCUGGUCUCCAGUUGCCCGACACUCACAGCUCCCCAGCACUUUAGCUCCACGAUUUCC-----------------
--------..(((((((((((((((.(((........(.(((....((((...))))..))))(.....)...)))..)))))))))))))))..........----------------- ( -34.40, z-score =  -3.08, R)
>droSim1.chrX 10061783 79 + 17042790
--------GUGAGUUGAAGUGCUGCAAGCAAAUGGAAGAGGUUUUUCUGGUCUCCAGUUGCCCGACACUUUUAGCUCCACGAUUUCC---------------------------------
--------(((((((((((((.((...((((.((((...((.....))....)))).)))).)).))).))))))).))).......--------------------------------- ( -20.70, z-score =  -0.58, R)
>droSec1.super_21 883730 95 + 1102487
--------GUGAGUUGAAGUGCUGGAAGCAAAUGGAAGAGGUUUUUCUGGUCUCCAGUUGCCCGACACUUUUAGCUCCGCAGCACUUUAGCUCCACGAUUUCC-----------------
--------(((((((((((((((((.((((((..(..(.(((....((((...))))..))))..)...))).))).).))))))))))))).))).......----------------- ( -34.80, z-score =  -3.02, R)
>droYak2.chrX 7411766 120 + 21770863
GUGAGUGAGUGAGUUGAAGUGCUGGGAGCAAAUCGAAGAGGUUUUUCUGGUCCCCAGUUGCCCGACACUCGUAGCUCCCCAGCACUUAAGCUCCCCGCUUUCCGAACUCCAAUUCCCAUU
..(((((.(.(((((.(((((((((((((....(((.(.(((....((((...))))..)))).....)))..))).)))))))))).)))))).))))).................... ( -41.50, z-score =  -3.43, R)
>consensus
________GUGAGUUGAAGUGCUGGAAGCAAAUGGAAGAGGUUUUUCUGGUCUCCAGUUGCCCGACACUCUUAGCUCCCCAGCACUUUAGCUCCACGAUUUCC_________________
..........(((((((((((((((.(((.....(..(.(((....((((...))))..))))..).......))).).))))))))))))))........................... (-21.46 = -23.90 +   2.44)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 13,139,707 – 13,139,802
Length 95
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 71.78
Shannon entropy 0.41563
G+C content 0.50359
Mean single sequence MFE -29.65
Consensus MFE -20.84
Energy contribution -21.90
Covariance contribution 1.06
Combinations/Pair 1.22
Mean z-score -1.05
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.591894
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 13139707 95 - 22422827
-----------------GGAAAUCGUGGAGCUAAAGUGCUGGGGAGCUGUGAGUGUCGGGCAACUGGAGACCAGAAAAACCUCUUCCAUUUGCUUCCAGCACUUCAACUCAU--------
-----------------..........(((...((((((((((.(((.(((.....(((....)))(((...........)))...)))..)))))))))))))...)))..-------- ( -29.30, z-score =  -0.69, R)
>droSim1.chrX 10061783 79 - 17042790
---------------------------------GGAAAUCGUGGAGCUAAAAGUGUCGGGCAACUGGAGACCAGAAAAACCUCUUCCAUUUGCUUGCAGCACUUCAACUCAC--------
---------------------------------..........(((....(((((((((((((.((((....(((......))))))).)))))))..))))))...)))..-------- ( -20.80, z-score =  -1.10, R)
>droSec1.super_21 883730 95 - 1102487
-----------------GGAAAUCGUGGAGCUAAAGUGCUGCGGAGCUAAAAGUGUCGGGCAACUGGAGACCAGAAAAACCUCUUCCAUUUGCUUCCAGCACUUCAACUCAC--------
-----------------..........(((...((((((((.(((((...(((((.(((....)))(((...........)))...))))))))))))))))))...)))..-------- ( -28.60, z-score =  -1.45, R)
>droYak2.chrX 7411766 120 - 21770863
AAUGGGAAUUGGAGUUCGGAAAGCGGGGAGCUUAAGUGCUGGGGAGCUACGAGUGUCGGGCAACUGGGGACCAGAAAAACCUCUUCGAUUUGCUCCCAGCACUUCAACUCACUCACUCAC
..((((.....(((((.(((((((.....))))..((((((((.(((..((((....((....))((((..........))))))))....))))))))))))))))))).....)))). ( -39.90, z-score =  -0.95, R)
>consensus
_________________GGAAAUCGUGGAGCUAAAGUGCUGGGGAGCUAAAAGUGUCGGGCAACUGGAGACCAGAAAAACCUCUUCCAUUUGCUUCCAGCACUUCAACUCAC________
...........................(((...((((((((.(((((...(((((.(((....)))(((...........)))...))))))))))))))))))...))).......... (-20.84 = -21.90 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:39:37 2011