Locus 12103

Sequence ID dm3.chr3R
Location 25,668,833 – 25,668,927
Length 94
Max. P 0.999078
window16639 window16640

overview

Window 9

Location 25,668,833 – 25,668,927
Length 94
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 66.11
Shannon entropy 0.50184
G+C content 0.28026
Mean single sequence MFE -14.85
Consensus MFE -7.82
Energy contribution -8.45
Covariance contribution 0.63
Combinations/Pair 1.06
Mean z-score -1.23
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.600173
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25668833 94 + 27905053
UUUGGCCAUCAUCUAAAUUCAAAGAUUUGUUUUUAAUUAUU---CUAAACUCAACUUAUUUUGGCCAAUUAAGACAAUCAUAAUGGUAGAAUGUUUA---------------
.(((((((..((((........))))(((..((((......---.))))..))).......)))))))...(((((.((.........)).))))).--------------- ( -14.10, z-score =  -0.88, R)
>droSim1.chr3R 25343150 78 + 27517382
UUUGGCCAGCAUCUAAAUUCAGAGAUUUGUUUUUAAUUAUU---CUAAAUUCAACUUACUUUGGCCAAUUAAGAUUGUU-UA------------------------------
.((((((((.((((........))))(((..((((......---.))))..)))......))))))))...........-..------------------------------ ( -13.00, z-score =  -1.26, R)
>droSec1.super_4 4519218 78 + 6179234
UUUGGCCAGCAUCUAAAUUCAGAGAUUUGUUUUUAAUUAUU---CUAAAUUCAACUUACUUUGGCCAAUUAAGAUUGUU-UA------------------------------
.((((((((.((((........))))(((..((((......---.))))..)))......))))))))...........-..------------------------------ ( -13.00, z-score =  -1.26, R)
>droEre2.scaffold_4820 8136474 110 - 10470090
UUUGGCCAGCAUCUUAAUUCAGCGACUUAUGUUUAAUAUUUGCACUUAACUUA-UUUACUUUGGCCA-UUAAAACGAUGGCCAUUUAAGACCAUCAUACGAGAGAUUAUUUA
..(((......((((((....((((..(((.....))).))))..........-.......((((((-((.....)))))))).))))))))).....(....)........ ( -19.30, z-score =  -1.54, R)
>consensus
UUUGGCCAGCAUCUAAAUUCAGAGAUUUGUUUUUAAUUAUU___CUAAACUCAACUUACUUUGGCCAAUUAAGACUAUU_UA______________________________
.(((((((...(((........))).(((..((((..........))))..))).......)))))))............................................ ( -7.82 =  -8.45 +   0.63)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 25,668,833 – 25,668,927
Length 94
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 66.11
Shannon entropy 0.50184
G+C content 0.28026
Mean single sequence MFE -19.66
Consensus MFE -12.62
Energy contribution -12.75
Covariance contribution 0.12
Combinations/Pair 1.17
Mean z-score -2.88
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.63
SVM RNA-class probability 0.999078
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25668833 94 - 27905053
---------------UAAACAUUCUACCAUUAUGAUUGUCUUAAUUGGCCAAAAUAAGUUGAGUUUAG---AAUAAUUAAAAACAAAUCUUUGAAUUUAGAUGAUGGCCAAA
---------------...(((.((.........)).))).....(((((((.......((((((((((---(.................)))))))))))....))))))). ( -15.73, z-score =  -1.29, R)
>droSim1.chr3R 25343150 78 - 27517382
------------------------------UA-AACAAUCUUAAUUGGCCAAAGUAAGUUGAAUUUAG---AAUAAUUAAAAACAAAUCUCUGAAUUUAGAUGCUGGCCAAA
------------------------------..-...........(((((((..(((..((((((((((---(.................))))))))))).)))))))))). ( -18.83, z-score =  -3.87, R)
>droSec1.super_4 4519218 78 - 6179234
------------------------------UA-AACAAUCUUAAUUGGCCAAAGUAAGUUGAAUUUAG---AAUAAUUAAAAACAAAUCUCUGAAUUUAGAUGCUGGCCAAA
------------------------------..-...........(((((((..(((..((((((((((---(.................))))))))))).)))))))))). ( -18.83, z-score =  -3.87, R)
>droEre2.scaffold_4820 8136474 110 + 10470090
UAAAUAAUCUCUCGUAUGAUGGUCUUAAAUGGCCAUCGUUUUAA-UGGCCAAAGUAAA-UAAGUUAAGUGCAAAUAUUAAACAUAAGUCGCUGAAUUAAGAUGCUGGCCAAA
...............(((((((((......))))))))).....-((((((..(((..-(.((((.(((((...............).)))).)))).)..))))))))).. ( -25.26, z-score =  -2.48, R)
>consensus
______________________________UA_AACAAUCUUAAUUGGCCAAAGUAAGUUGAAUUUAG___AAUAAUUAAAAACAAAUCUCUGAAUUUAGAUGCUGGCCAAA
............................................(((((((..((....(((((((((......................))))))))).))..))))))). (-12.62 = -12.75 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:55:47 2011