Locus 2940

Sequence ID dm3.chr2RHet
Location 2,810,582 – 2,810,689
Length 107
Max. P 0.965655
window4038 window4039

overview

Window 8

Location 2,810,582 – 2,810,689
Length 107
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 52.64
Shannon entropy 0.78193
G+C content 0.52314
Mean single sequence MFE -31.62
Consensus MFE -10.25
Energy contribution -11.50
Covariance contribution 1.25
Combinations/Pair 1.56
Mean z-score -1.92
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965655
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 2810582 107 + 3288761
-------AUGCCGAAGAUCCCAUUGUACAUGAUUUUCCACAGGAUUGGUCAAAGUACCGAUCCUUGGAGAACACCUGUUGAAACUCGGUAUCUUUUUUGGCCACCUUCCGUAUC
-------..(((((((((.((...(((((((.(((((((.(((((((((......))))))))))))))))))..)))....))..)).))))...)))))............. ( -30.20, z-score =  -2.19, R)
>dp4.Unknown_singleton_2768 1291 107 - 14987
-------AGUCGCAAUAUGCCGUCGUUCAUUGCGUUGCACAGUGUGGGGCCCAGCACCGACCCCUGCGGGACGCCUGCAAAUACCUCCUAUUGCUCCGUGCCAGCCUCGGUACC
-------.(..(((((((((...(((.....)))..)))...((..((((((.(((........)))))).).))..)).........))))))..)(((((......))))). ( -31.30, z-score =   1.00, R)
>droWil1.scaffold_181136 1555138 114 + 2313701
CAUUUCCAGUCGUAAGACAGUGUCAUACAUGACAUUCCUCAAUGCUGGCCCUAUCACCGUUCCUUGAGGUUCUCCGCCUGUGAUGGUGUGUUUCCGUGGUCCAGCUGCCGUAUC
........(((....)))(((((((....))))))).......((((((((...((((((..(..(.((....)).)..)..)))))).......).)).)))))......... ( -31.30, z-score =  -1.33, R)
>triCas2.chrUn_190 48519 104 - 65089
-------AAUCUAAGAACUCCAUCAUAAAGGAUGUUCCACAAGGUCGGCCCCAAUACCGAUCCUUGUGGAACUCCACUCGUCACCUC-CAUGACUUGUCCCUCGCCCAAGUC--
-------......................(((.(((((((((((((((........)))).))))))))))))))............-...((((((.........))))))-- ( -33.70, z-score =  -5.17, R)
>consensus
_______AGUCGAAAGACACCAUCAUACAUGACGUUCCACAAGGUUGGCCCCAGCACCGAUCCUUGAGGAACUCCUCCUGAAACCUCGUAUUUCUUUGGGCCAGCCUCCGUAUC
.....................(((......)))(((((((((((((((........))))).)))))))))).......................................... (-10.25 = -11.50 +   1.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,810,582 – 2,810,689
Length 107
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 52.64
Shannon entropy 0.78193
G+C content 0.52314
Mean single sequence MFE -34.45
Consensus MFE -13.27
Energy contribution -15.03
Covariance contribution 1.75
Combinations/Pair 1.53
Mean z-score -1.15
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.879656
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 2810582 107 - 3288761
GAUACGGAAGGUGGCCAAAAAAGAUACCGAGUUUCAACAGGUGUUCUCCAAGGAUCGGUACUUUGACCAAUCCUGUGGAAAAUCAUGUACAAUGGGAUCUUCGGCAU-------
....(.((((((..(((.....((((((..((....)).)))))).(((((((((.(((......))).))))).)))).............))).)))))).)...------- ( -27.80, z-score =  -0.42, R)
>dp4.Unknown_singleton_2768 1291 107 + 14987
GGUACCGAGGCUGGCACGGAGCAAUAGGAGGUAUUUGCAGGCGUCCCGCAGGGGUCGGUGCUGGGCCCCACACUGUGCAACGCAAUGAACGACGGCAUAUUGCGACU-------
(((..(((.((((((((((.((....(((.((........)).))).)).((((((.......))))))...))))))..((.......)).))))...)))..)))------- ( -34.40, z-score =   1.41, R)
>droWil1.scaffold_181136 1555138 114 - 2313701
GAUACGGCAGCUGGACCACGGAAACACACCAUCACAGGCGGAGAACCUCAAGGAACGGUGAUAGGGCCAGCAUUGAGGAAUGUCAUGUAUGACACUGUCUUACGACUGGAAAUG
....((((.(((((.((..(....).((((.(..(..(.((....)).)..)..).))))...)).)))))..(((((..(((((....)))))...))))).).)))...... ( -31.00, z-score =  -0.96, R)
>triCas2.chrUn_190 48519 104 + 65089
--GACUUGGGCGAGGGACAAGUCAUG-GAGGUGACGAGUGGAGUUCCACAAGGAUCGGUAUUGGGGCCGACCUUGUGGAACAUCCUUUAUGAUGGAGUUCUUAGAUU-------
--..........((((((..((((((-(((....)....((((((((((((((.(((((......)))))))))))))))).)))))))))))...)))))).....------- ( -44.60, z-score =  -4.61, R)
>consensus
GAUACGGAAGCUGGCCAAAAGAAAUACGAGGUAACAACAGGAGUUCCACAAGGAUCGGUACUGGGGCCAACACUGUGGAACAUCAUGUACGACGGAAUCUUACGACU_______
.......................................((((((((((((((...(((......)))..)))))))))))))).............................. (-13.27 = -15.03 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:00:41 2011