Locus 4955

Sequence ID dm3.chr2R
Location 16,660,199 – 16,660,298
Length 99
Max. P 0.938137
window6812 window6813

overview

Window 2

Location 16,660,199 – 16,660,298
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 78.17
Shannon entropy 0.33056
G+C content 0.53742
Mean single sequence MFE -25.10
Consensus MFE -19.45
Energy contribution -19.20
Covariance contribution -0.25
Combinations/Pair 1.16
Mean z-score -1.88
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.42
SVM RNA-class probability 0.938137
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16660199 99 + 21146708
CCCGUGCUCCAAGGUCCAUCGUCCGGAGUCUGUAGUCCGUACACCGGACUUGGUCUACUCAAAGUUAUCUUAAGUGCUCCGAGUGGAAACUGUCAGCCG
..((.(((...((..(((..((((((.((.((.....)).)).)))))).)))(((((((..(((..........)))..)))))))..))...))))) ( -28.50, z-score =  -1.26, R)
>droSim1.chr2R 15316036 78 + 19596830
---------------------CCCGUGCUCCAAAGUCCGUACUCCGGACUUGGUCUACUCAAAGUUAUCUUAAGUGCUCCGAGUGGAAACUGUCAGCCG
---------------------..((.(((((((.(((((.....)))))))))(((((((..(((..........)))..))))))).......))))) ( -23.70, z-score =  -2.92, R)
>droSec1.super_1 14207451 78 + 14215200
---------------------CCCGUGCUCCAAAGUCCGUACUCCGGACUUGGUCUACUCAAAGUUAUCUUAAGUGCUCCGAGUGGAAACUGUCAGCCG
---------------------..((.(((((((.(((((.....)))))))))(((((((..(((..........)))..))))))).......))))) ( -23.70, z-score =  -2.92, R)
>droYak2.chr2R 8602266 85 - 21139217
--------------GCCGUGACCCGAAGUCCUUGGUCCGGAGCUCGGACUUGGUCUACUCAAAGUUAUCUUAAGUGCUCCGAGUGGAAACUGUCAGCCG
--------------.(((.((((..........))))))).(((..(((....(((((((..(((..........)))..)))))))....)))))).. ( -24.50, z-score =  -0.42, R)
>consensus
_____________________CCCGUACUCCAAAGUCCGUACUCCGGACUUGGUCUACUCAAAGUUAUCUUAAGUGCUCCGAGUGGAAACUGUCAGCCG
.............................(((.((((((.....)))))))))(((((((..(((..........)))..)))))))............ (-19.45 = -19.20 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 16,660,199 – 16,660,298
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 78.17
Shannon entropy 0.33056
G+C content 0.53742
Mean single sequence MFE -27.10
Consensus MFE -18.92
Energy contribution -19.93
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.664297
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16660199 99 - 21146708
CGGCUGACAGUUUCCACUCGGAGCACUUAAGAUAACUUUGAGUAGACCAAGUCCGGUGUACGGACUACAGACUCCGGACGAUGGACCUUGGAGCACGGG
(((((..(((..((((.((((((((((((((.....)))))))......((((((.....))))))...).))))))....))))..))).))).)).. ( -32.50, z-score =  -1.53, R)
>droSim1.chr2R 15316036 78 - 19596830
CGGCUGACAGUUUCCACUCGGAGCACUUAAGAUAACUUUGAGUAGACCAAGUCCGGAGUACGGACUUUGGAGCACGGG---------------------
(((((.......((.((((((((............)))))))).))(((((((((.....))))).))))))).))..--------------------- ( -25.90, z-score =  -2.22, R)
>droSec1.super_1 14207451 78 - 14215200
CGGCUGACAGUUUCCACUCGGAGCACUUAAGAUAACUUUGAGUAGACCAAGUCCGGAGUACGGACUUUGGAGCACGGG---------------------
(((((.......((.((((((((............)))))))).))(((((((((.....))))).))))))).))..--------------------- ( -25.90, z-score =  -2.22, R)
>droYak2.chr2R 8602266 85 + 21139217
CGGCUGACAGUUUCCACUCGGAGCACUUAAGAUAACUUUGAGUAGACCAAGUCCGAGCUCCGGACCAAGGACUUCGGGUCACGGC--------------
..((((............(((((((((((((.....))))))).(((...)))...))))))((((..........)))).))))-------------- ( -24.10, z-score =  -0.19, R)
>consensus
CGGCUGACAGUUUCCACUCGGAGCACUUAAGAUAACUUUGAGUAGACCAAGUCCGGAGUACGGACUAUGGACCACGGG_____________________
...(((......((.((((((((............)))))))).))(((((((((.....)))))).)))....)))...................... (-18.92 = -19.93 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:39:13 2011