Locus 8774

Sequence ID dm3.chr3R
Location 1,521,276 – 1,521,379
Length 103
Max. P 0.890221
window12046 window12047

overview

Window 6

Location 1,521,276 – 1,521,374
Length 98
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 56.55
Shannon entropy 0.71117
G+C content 0.35465
Mean single sequence MFE -20.05
Consensus MFE -7.40
Energy contribution -9.65
Covariance contribution 2.25
Combinations/Pair 1.15
Mean z-score -1.51
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.884497
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1521276 98 - 27905053
--------AAGCACUUUUCACGCAGAAAUCCACUGCACUAACAAGCAGUCUACUGCUUUAAAGAUUGCAGACGACUUAC--UUCUUAC--UUCUUGCAAUCUGUUCUUUC----
--------.............((((.......))))......((((((....))))))...((((((((((.(......--......)--.)).))))))))........---- ( -20.20, z-score =  -1.98, R)
>droEre2.scaffold_4845 3103060 84 - 22589142
-------UUGGCACAUGUGGGAUAGACACCAGCUACUGUAACCGACAUUUAAGUACAUU-----UUUCUUA----UUUCUCUUUUUUUCAUUAUCAAACU--------------
-------((((...((((.((....(((........)))..)).)))).((((......-----...))))----..................))))...-------------- (  -6.10, z-score =   1.51, R)
>droSec1.super_6 1637310 113 - 4358794
UAUGCAAGCUGAAUUUUUCAAGCAGAAAUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUUUUCUUGCUAUCCUUUCAAUAAACGUU-ACUUUC
...(((((((((((((((.((((((......(((((........)))))...)))))).))))))).))).............)))))...................-...... ( -23.01, z-score =  -1.29, R)
>droSim1.chr3R 1556091 114 - 27517382
UAUACAAGCAGGAUUUUUCAAGUAUAGUUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUUUUCUUGCUAUCCUUUCAAUAAAUUUUGACUUUC
......(((((((......((((..(((((..(((((((...((((((....)))))).....)))))))..))))))))).)))))))......((((......))))..... ( -30.90, z-score =  -4.26, R)
>consensus
_______GCAGCACUUUUCAAGCAGAAAUCCACUGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAGACGAGCUACUUUUCUUGCUAUCCUUUCAAUAAAUUUU_AC____
................................(((((((...((((((....)))))).....)))))))............................................ ( -7.40 =  -9.65 +   2.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,521,280 – 1,521,379
Length 99
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 57.06
Shannon entropy 0.68535
G+C content 0.36588
Mean single sequence MFE -23.48
Consensus MFE -8.26
Energy contribution -8.95
Covariance contribution 0.69
Combinations/Pair 1.17
Mean z-score -1.74
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.890221
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1521280 99 - 27905053
--------UGC-AGAAGCACUUUUCACGCAGAAAUCCAC-UGCACUAACAAGCAGUCUACUGCUUUAAAGAUUGCAG-ACGACUUACU--UCUUACU--UCUUG-CAAUCUGUUC--
--------(((-(((((....((((.....))))....(-((((((...((((((....))))))...))..)))))-..........--.....))--)).))-))........-- ( -21.90, z-score =  -1.47, R)
>droEre2.scaffold_4845 3103060 90 - 22589142
------------------------UGAGUGUUGGCACAUGUGGGAUAGACACCAGC-UACUGUAACCGACAUUUAAGUACAUUUUUCUUAUUUCUCUUUUUUUCAUUAUCAAACU--
------------------------((((((((((.(((.((((............)-))))))..))))))))))........................................-- ( -14.40, z-score =  -0.25, R)
>droSec1.super_6 1637316 113 - 4358794
UGAAGCUAUGCAAGCUGAAUUUUUCAAGCAGAAAUCCAC-UGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAG-ACGAGCUACUUUUCUUGCUAUCCUUU-CAAUAAACGUU-
(((((..(((((((((((((((((.((((((......((-(((........)))))...)))))).))))))).)))-.............))))).))..)))-)).........- ( -25.31, z-score =  -1.28, R)
>droSim1.chr3R 1556097 114 - 27517382
AGAAGCUAUACAAGCAGGAUUUUUCAAGUAUAGUUCCAC-UGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAG-ACGAGCUACUUUUCUUGCUAUCCUUU-CAAUAAAUUUUG
.((((((.....)))(((((....((((..((((((..(-((((((...((((((....)))))).....)))))))-..)))))).....))))..)))))))-)........... ( -32.30, z-score =  -3.98, R)
>consensus
________UGC_AGCAG_AUUUUUCAAGCAGAAAUCCAC_UGCAAUAACAAGCAGUAUACUGCUUUAAAGAUUGCAG_ACGAGCUACUUUUCUUGCUAUCCUUU_CAAUAAAUUU__
........................................((((((...((((((....)))))).....))))))......................................... ( -8.26 =  -8.95 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:51:56 2011