Locus 3151

Sequence ID dm3.chr2R
Location 2,883,425 – 2,883,540
Length 115
Max. P 0.847868
window4334 window4335

overview

Window 4

Location 2,883,425 – 2,883,528
Length 103
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 71.96
Shannon entropy 0.45353
G+C content 0.47242
Mean single sequence MFE -28.20
Consensus MFE -15.47
Energy contribution -17.59
Covariance contribution 2.12
Combinations/Pair 1.21
Mean z-score -1.37
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.574853
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2883425 103 + 21146708
GAUCGGAUGCGAUGCUAACUAUUCUGAUCCCACGAACCGCUGAGCUCGGCGGCUGAGUCAU--GCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAACUAUAGUU
(((((((...............)))))))........(((..((((..(((((........--)))))))))..)))............................ ( -25.36, z-score =   0.35, R)
>droAna3.scaffold_13266 9193155 94 + 19884421
----------GUUCCGAUCUGAUCUGCUCCAUUGAACUGAUGAACUCGUCAGUCUCUCCAUUAGUCAUGGCGCUAUUAGAUCGAAUUAGUUUAUCU-CUCUAAUU
----------....(((((((((..((.((((.(((((((((....)))))))...........)))))).)).)))))))))((((((.......-..)))))) ( -27.10, z-score =  -3.77, R)
>droSec1.super_1 555721 103 + 14215200
GAUCGGAUGCGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAU--GCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAACUGUAGUU
((((((((.............)))))))).(((((.((((((....)))))).....))))--)((((((((((.((........))......)))))))))).. ( -31.62, z-score =  -1.42, R)
>droSim1.chr2R 1690474 103 + 19596830
GAUCGGAUGCGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAU--GCUGCAGUUUGGCGCAAUCCCACGAAUUUAUGAACUAUAGUU
((((((((.............)))))))).((((((.(((..((((..(((((........--)))))))))..)))...((....)).)))))).......... ( -28.72, z-score =  -0.63, R)
>consensus
GAUCGGAUGCGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAU__GCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAACUAUAGUU
((((((((.............)))))))).((((((((((((....)))))).((.((((...((....)).)))).))..........)))))).......... (-15.47 = -17.59 +   2.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,883,434 – 2,883,540
Length 106
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 68.69
Shannon entropy 0.50801
G+C content 0.47144
Mean single sequence MFE -28.77
Consensus MFE -18.01
Energy contribution -17.32
Covariance contribution -0.69
Combinations/Pair 1.44
Mean z-score -1.17
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.847868
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2883434 106 + 21146708
CGAUGCUAACUAUUCUGAUCCCACGAACCGCUGAGCUCGGCGGCUGAGUCAU--GCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAACUAUAGUUUGGCUGGGGGUG
.................(((((.....((((((....))))))...(((((.--((((.((((((.((........))......)))))).)))).))))).))))). ( -29.10, z-score =   0.21, R)
>droAna3.scaffold_13266 9193163 93 + 19884421
---------CUGAUCUGCUCCAUUGAACUGAUGAACUCGUCAGUCUCUCCAUUAGUCAUGGCGCUAUUAGAUCGAAUUAGUUUAUCU-CUCUAAUUAAAUAGA-----
---------.((((((((.((((.(((((((((....)))))))...........)))))).))....))))))((((((.......-..)))))).......----- ( -20.40, z-score =  -1.44, R)
>droSec1.super_1 555730 106 + 14215200
CGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAU--GCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAACUGUAGUUUGACAUGAGGAG
.(((........)))...((((((...((((((....))))))....((((.--(((((((((((.((........))......))))))))))).))))))).))). ( -33.70, z-score =  -2.15, R)
>droSim1.chr2R 1690483 106 + 19596830
CGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAU--GCUGCAGUUUGGCGCAAUCCCACGAAUUUAUGAACUAUAGUUUGACAUGGGGAG
.(((........)))...(((((((...(((..((((..(((((........--)))))))))..)))........((((((..........)))))).))))))).. ( -31.90, z-score =  -1.31, R)
>consensus
CGAUGCUAACUAAUCUGAUCCCAUGAACCGCUGAGCUCGGCGGCUGAGUCAU__GCUGCAGUUUGGCGCAAUCCUACGAAUUUAUGAACUAUAGUUUGACAGGGGGAG
..................(((((((..((((((....)))))).((.((((...((....)).)))).))......((((((..........)))))).))))))).. (-18.01 = -17.32 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:04:44 2011