Locus 5104

Sequence ID dm3.chr2R
Location 17,780,524 – 17,780,650
Length 126
Max. P 0.523515
window7003 window7004

overview

Window 3

Location 17,780,524 – 17,780,627
Length 103
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.75
Shannon entropy 0.38444
G+C content 0.32729
Mean single sequence MFE -18.61
Consensus MFE -12.11
Energy contribution -14.03
Covariance contribution 1.92
Combinations/Pair 1.11
Mean z-score -1.28
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr2R 17780524 103 - 21146708
GGGUCGAGUGCUUUUCAGUUUUCGAUCAAUUUCAAUUUGGCUUAGCCAAUUAGUUUGUAUAAAUAUUUAAGCUUUUUGCAGCUCAAUUUAGGUCCUCUUUUUA-----------
.(((((((.(((....))).))))))).((((.((((.((((..((.((..((((((..........))))))..)))))))).)))).))))..........----------- ( -19.50, z-score =  -1.23, R)
>droSim1.chr2R 16415988 103 - 19596830
GGGUCGAGUGCUUUUCAGUUUUCGAUCAAUUUCAAUUUGGCUUAGCUAAUUAGUUUGUAUAAAUAUUUAAGCUUUUGGCAGUUCAAUUUAGGUCAUCUUUUUA-----------
.(((((((.(((....))).)))))))..........((((((((((((..((((((..........)))))).))))).........)))))))........----------- ( -21.30, z-score =  -2.53, R)
>droSec1.super_9 1095597 103 - 3197100
GGGUCGAGUGCUUUUCAGUUUUCGAUCAAUUUCAAUUUGGCUUAGCUAAUUAGUUUGUAUAAAUAUUUAAGCUUUUGGCAGUUCAAUUUACGUCCUCUUUUUA-----------
.(((((((.(((....))).)))))))......((((..(((..(((((..((((((..........)))))).))))))))..))))...............----------- ( -19.30, z-score =  -1.63, R)
>droYak2.chr2R 9734912 103 + 21139217
GGGUCGAGUGGCUUUCAAUCUUCGAUCAAUUUCAAUUUGGCUCAGCUAAUUAGUUUGUAUAAAUAUUUAAGCUUUUGGCAGCUCAAUUUAGGUCCUUCUUUUA-----------
((..(...(((((..........((((((.......)))).)).(((((..((((((..........)))))).)))))))).)).....)..))........----------- ( -19.20, z-score =  -0.70, R)
>droEre2.scaffold_4845 11914308 103 - 22589142
GGGUCGAGUGCCCCUCAGUCUUCGAUCAAUUUCAAUUUGGCUUAGCUAAUUAGUUUGGAUAAAUAUUUAAGCUUUUGGCAGCUCAAUUUACGUCCUCUUUUUG-----------
.(((((((.((......)).)))))))......((((.((((..(((((..(((((((((....))))))))).))))))))).))))...............----------- ( -23.80, z-score =  -1.69, R)
>droAna3.scaffold_13266 11159715 102 - 19884421
------------UUUCAAUUUCCUCUAAUUUCUAAUUAUUCAAAAUUAAUUAGUUUGUCCAAAUAUUUAAACUUUUGACAGCCCAAUUUUGUUUUUUGCUCUGGUCCUGAUUUC
------------..(((..............(((((((........)))))))...(.(((.......((((..(((......)))....)))).......))).).))).... (  -8.54, z-score =   0.11, R)
>consensus
GGGUCGAGUGCUUUUCAGUUUUCGAUCAAUUUCAAUUUGGCUUAGCUAAUUAGUUUGUAUAAAUAUUUAAGCUUUUGGCAGCUCAAUUUAGGUCCUCUUUUUA___________
.(((((((.((......)).)))))))......((((.((((..(((((..((((((..........)))))).))))))))).)))).......................... (-12.11 = -14.03 +   1.92)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,780,540 – 17,780,650
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 92.73
Shannon entropy 0.12515
G+C content 0.32614
Mean single sequence MFE -19.67
Consensus MFE -17.84
Energy contribution -18.00
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.19
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.523515
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17780540 110 - 21146708
UACAUUUUUCAAAUCCUUUCAAAGGGUCGAGUGCUUUUCAGUUUUCGAUCAAUUUCAAUUUGGCUUAGCCAAUUAGUUUGUAUAAAUAUUUAAGCUUUUUGCAGCUCAAU
...((((..(((((..........(((((((.(((....))).))))))).........(((((...)))))...)))))...)))).....((((......)))).... ( -18.70, z-score =  -1.18, R)
>droSim1.chr2R 16416004 110 - 19596830
UACAUUUUUCAAAUCCUUUCAAAGGGUCGAGUGCUUUUCAGUUUUCGAUCAAUUUCAAUUUGGCUUAGCUAAUUAGUUUGUAUAAAUAUUUAAGCUUUUGGCAGUUCAAU
........((((((..........(((((((.(((....))).))))))).......))))))....(((((..((((((..........)))))).)))))........ ( -18.93, z-score =  -1.34, R)
>droSec1.super_9 1095613 110 - 3197100
UACAUUUUUCAAAACCUUUCAAAGGGUCGAGUGCUUUUCAGUUUUCGAUCAAUUUCAAUUUGGCUUAGCUAAUUAGUUUGUAUAAAUAUUUAAGCUUUUGGCAGUUCAAU
........................(((((((.(((....))).))))))).........((((((..(((((..((((((..........)))))).))))))).)))). ( -18.50, z-score =  -1.00, R)
>droYak2.chr2R 9734928 110 + 21139217
UACAUUUUUCAUAUCCCUUCACAGGGUCGAGUGGCUUUCAAUCUUCGAUCAAUUUCAAUUUGGCUCAGCUAAUUAGUUUGUAUAAAUAUUUAAGCUUUUGGCAGCUCAAU
..............((((....))))..((((..............((((((.......)))).)).(((((..((((((..........)))))).))))).))))... ( -18.80, z-score =  -0.85, R)
>droEre2.scaffold_4845 11914324 109 - 22589142
UACAUUUUUCAUAU-CCUCCACAGGGUCGAGUGCCCCUCAGUCUUCGAUCAAUUUCAAUUUGGCUUAGCUAAUUAGUUUGGAUAAAUAUUUAAGCUUUUGGCAGCUCAAU
..............-.........(((((((.((......)).))))))).........((((((..(((((..(((((((((....))))))))).)))))))).))). ( -23.40, z-score =  -1.57, R)
>consensus
UACAUUUUUCAAAUCCUUUCAAAGGGUCGAGUGCUUUUCAGUUUUCGAUCAAUUUCAAUUUGGCUUAGCUAAUUAGUUUGUAUAAAUAUUUAAGCUUUUGGCAGCUCAAU
........................(((((((.((......)).))))))).........((((((..(((((..((((((..........)))))).)))))))).))). (-17.84 = -18.00 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:41:54 2011