Locus 8830

Sequence ID dm3.chr3R
Location 1,950,201 – 1,950,306
Length 105
Max. P 0.727079
window12122 window12123

overview

Window 2

Location 1,950,201 – 1,950,306
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 71.09
Shannon entropy 0.47352
G+C content 0.39125
Mean single sequence MFE -22.61
Consensus MFE -12.69
Energy contribution -12.89
Covariance contribution 0.20
Combinations/Pair 1.12
Mean z-score -1.26
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.605272
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1950201 105 + 27905053
--------------GCAUGUAUUGCCAACGCCAUUAAAAUAAAGUCUCCCCAAAAGUCUGCAAAGCUUUCUCGUUCGCCCGGCCCUCUUUCAAAACAUCAGAUGAUACUUUUGGGGGAU-
--------------(((.....)))..................(((.((((((((((..((...((..........))...)).............(((....))))))))))))))))- ( -20.90, z-score =  -0.20, R)
>droEre2.scaffold_4770 2209219 120 + 17746568
AUAAUGAACUGGUCUCUAGUAUUGCCAACGCCAUUCAAAUAAAAUCUCCCCAAAAGUCUGCAAAGCUUUUUUAUUAGCCCGGCCCUCUUUCAAAAUAUCAGAUGAUACUUUUGGAGGGGU
....((((.((((................))))))))........(((((((((((...((...(((........)))...))............((((....))))))))))).)))). ( -23.39, z-score =  -0.05, R)
>droYak2.chr3R 17893302 120 + 28832112
AUAAUAAACUGGUCUCCAGUUUUACCAACGCCAUUCAAAUAAAAUCUCCCCAAAAGUCUGCAAUGCGUUUUCAUUCUUCUGGCUUUUUUUCAAAAUAUCAGAUGAUACUUUUGGAGGGGU
.....(((((((...))))))).........................(((((((((((.(.((((......)))))....))))))).(((((((((((....)))).))))))))))). ( -24.50, z-score =  -1.46, R)
>droSec1.super_6 2051102 87 + 4358794
---------------------AUGGCAACGCCAUUAAAAUAAAGUCUCCCCAAAAGUCUGCUAAAAUUUCUCGUUC-----------UUUCAAAACAUUGGAUGAUACUUUUGGGGGGU-
---------------------(((((...)))))...........((((((((((((.............((((((-----------............)))))).)))))))))))).- ( -23.14, z-score =  -2.59, R)
>droSim1.chr3R 1977483 87 + 27517382
--------------------AUUGCCAACGCCAUUAAAA-AAAAUCUCCCCAAAAGUCUGCAAAAAUGUCUCGUUC-----------UUUCAAAACAUUGGAUGAUACUUUUGGGGGGU-
--------------------...................-.....((((((((((((..(((....))).((((((-----------............)))))).)))))))))))).- ( -21.10, z-score =  -2.00, R)
>consensus
_______________C__GUAUUGCCAACGCCAUUAAAAUAAAAUCUCCCCAAAAGUCUGCAAAGCUUUCUCGUUC__C_GGC__U_UUUCAAAACAUCAGAUGAUACUUUUGGGGGGU_
.............................................((((((((((((.............(((((.........................))))).)))))))))))).. (-12.69 = -12.89 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,950,201 – 1,950,306
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.09
Shannon entropy 0.47352
G+C content 0.39125
Mean single sequence MFE -25.85
Consensus MFE -14.44
Energy contribution -13.56
Covariance contribution -0.88
Combinations/Pair 1.27
Mean z-score -1.40
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.727079
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1950201 105 - 27905053
-AUCCCCCAAAAGUAUCAUCUGAUGUUUUGAAAGAGGGCCGGGCGAACGAGAAAGCUUUGCAGACUUUUGGGGAGACUUUAUUUUAAUGGCGUUGGCAAUACAUGC--------------
-.(((((((((((((((....))).............((..(((..........)))..))..)))))))))).)).............((((.(......)))))-------------- ( -24.80, z-score =   0.28, R)
>droEre2.scaffold_4770 2209219 120 - 17746568
ACCCCUCCAAAAGUAUCAUCUGAUAUUUUGAAAGAGGGCCGGGCUAAUAAAAAAGCUUUGCAGACUUUUGGGGAGAUUUUAUUUGAAUGGCGUUGGCAAUACUAGAGACCAGUUCAUUAU
.((((....((((((((....))))))))..(((((.((..((((........))))..))...)))))))))..........((((((((.((((.....)))).).))).)))).... ( -30.00, z-score =  -0.80, R)
>droYak2.chr3R 17893302 120 - 28832112
ACCCCUCCAAAAGUAUCAUCUGAUAUUUUGAAAAAAAGCCAGAAGAAUGAAAACGCAUUGCAGACUUUUGGGGAGAUUUUAUUUGAAUGGCGUUGGUAAAACUGGAGACCAGUUUAUUAU
(((.((((((((((.((.((((...((((....))))..)))).))........((...))..))))))))))..((((.....))))......))).(((((((...)))))))..... ( -27.00, z-score =  -1.23, R)
>droSec1.super_6 2051102 87 - 4358794
-ACCCCCCAAAAGUAUCAUCCAAUGUUUUGAAA-----------GAACGAGAAAUUUUAGCAGACUUUUGGGGAGACUUUAUUUUAAUGGCGUUGCCAU---------------------
-...((((((((((...........(((((...-----------...)))))...........)))))))))).............(((((...)))))--------------------- ( -22.15, z-score =  -2.40, R)
>droSim1.chr3R 1977483 87 - 27517382
-ACCCCCCAAAAGUAUCAUCCAAUGUUUUGAAA-----------GAACGAGACAUUUUUGCAGACUUUUGGGGAGAUUUU-UUUUAAUGGCGUUGGCAAU--------------------
-...((((((((((..((...(((((((((...-----------...)))))))))..))...)))))))))).......-........((....))...-------------------- ( -25.30, z-score =  -2.83, R)
>consensus
_ACCCCCCAAAAGUAUCAUCUGAUGUUUUGAAA_A__GCC_G__GAACGAGAAAGCUUUGCAGACUUUUGGGGAGAUUUUAUUUUAAUGGCGUUGGCAAUAC__G_______________
....((((((((((...........(((((.................)))))...........))))))))))............................................... (-14.44 = -13.56 +  -0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:52:59 2011