Locus 2804

Sequence ID dm3.chr2L
Location 22,487,122 – 22,487,240
Length 118
Max. P 0.848717
window3867 window3868

overview

Window 7

Location 22,487,122 – 22,487,240
Length 118
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 64.97
Shannon entropy 0.57409
G+C content 0.47349
Mean single sequence MFE -37.02
Consensus MFE -17.15
Energy contribution -19.78
Covariance contribution 2.63
Combinations/Pair 1.50
Mean z-score -1.41
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.68
SVM RNA-class probability 0.783499
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22487122 118 + 23011544
AUGAGGUACAGCCAUCUUAUUAUGCGUGGUGAGGUUCCCCACGACUUACCAGCAAUGUUUCUACACGUGAAAAGUGCUCUGGUGCACUUAUCAAUUUUGUUAUCGACAUGAGUUUUGA
(((((((......)))))))..(((.(((((((...........))))))))))(((((...(((..(((.((((((......)))))).)))....)))....)))))......... ( -30.00, z-score =  -0.69, R)
>dp4.Unknown_group_60 16977 118 - 24094
GAUAUGUAGAUCAAGUGCAUUAGAGCAGGUGACAGGCCCCAUGUGCUACUGAGCAUCUUCUUGGAUGCAUAAAGCGCAAUGGUGGCCUUCUUAAUCCUUUCCACUACAUUGGGUUUCC
...((((((.(((..(((......)))..))).((((((((((((((.....((((((....))))))....))))).)))).)))))...............))))))......... ( -39.60, z-score =  -2.18, R)
>droPer1.super_278 18306 118 + 27293
GAGAUGUAGAUCCAGUGCAUUAGAGCAGGUGACAGGCCCCAUGUGCUGCUGAGCAUCUUCUUGGAUGCAUAAAGCGCAAUGGUAGCCUUCUUCACCCCUUCAACUACAUUGGGCCUCC
.......((..((((((.....(((..(((((.((((.(((((((((..((.((((((....)))))).)).))))).))))..))))...)))))..))).....))))))..)).. ( -42.40, z-score =  -2.10, R)
>droYak2.chrU 19500048 117 + 28119190
GAGAUGUAAGCCAGGUGCAUAAGAGC-GAUGAGAGGUCCCAAGUGGUGCUAAGCAUCUUCUUGGAUGCAUAUAGCGUUAUGGUUGCGGUUUUCACCCUCUCUAGUACAUUGGGCUUCC
.......(((((..((((...((((.-(.((((((..(((((((..(((((.((((((....))))))...)))))..))..))).)))))))).)))))...))))....))))).. ( -36.10, z-score =  -0.69, R)
>consensus
GAGAUGUAGAUCAAGUGCAUUAGAGCAGGUGACAGGCCCCAUGUGCUACUAAGCAUCUUCUUGGAUGCAUAAAGCGCAAUGGUGGCCUUCUUAACCCUUUCAACUACAUUGGGCUUCC
.......(((((.((((.....(((..((((((((((((((((((((.....((((((....))))))....)))))).))).)))))..))))))..))).....)))).))))).. (-17.15 = -19.78 +   2.63)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,487,122 – 22,487,240
Length 118
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 64.97
Shannon entropy 0.57409
G+C content 0.47349
Mean single sequence MFE -36.33
Consensus MFE -13.82
Energy contribution -18.70
Covariance contribution 4.88
Combinations/Pair 1.46
Mean z-score -1.94
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.848717
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22487122 118 - 23011544
UCAAAACUCAUGUCGAUAACAAAAUUGAUAAGUGCACCAGAGCACUUUUCACGUGUAGAAACAUUGCUGGUAAGUCGUGGGGAACCUCACCACGCAUAAUAAGAUGGCUGUACCUCAU
..........(((((((......))))))).(((((((((.((((.......))))..........)))))..((.(((((....))))).)))))).....((.((.....)))).. ( -26.00, z-score =  -0.22, R)
>dp4.Unknown_group_60 16977 118 + 24094
GGAAACCCAAUGUAGUGGAAAGGAUUAAGAAGGCCACCAUUGCGCUUUAUGCAUCCAAGAAGAUGCUCAGUAGCACAUGGGGCCUGUCACCUGCUCUAAUGCACUUGAUCUACAUAUC
(....)(((......)))...((((((((.(((((.((((.(.(((....(((((......))))).....))).))))))))))......(((......)))))))))))....... ( -38.10, z-score =  -2.31, R)
>droPer1.super_278 18306 118 - 27293
GGAGGCCCAAUGUAGUUGAAGGGGUGAAGAAGGCUACCAUUGCGCUUUAUGCAUCCAAGAAGAUGCUCAGCAGCACAUGGGGCCUGUCACCUGCUCUAAUGCACUGGAUCUACAUCUC
..((..(((.((((...((..((((((...(((((.((((((((((....(((((......)))))..))).))).))))))))).))))))..))...)))).)))..))....... ( -46.70, z-score =  -2.71, R)
>droYak2.chrU 19500048 117 - 28119190
GGAAGCCCAAUGUACUAGAGAGGGUGAAAACCGCAACCAUAACGCUAUAUGCAUCCAAGAAGAUGCUUAGCACCACUUGGGACCUCUCAUC-GCUCUUAUGCACCUGGCUUACAUCUC
..(((((..........(((((((((.....)))..(((....((((...(((((......))))).))))......)))..))))))...-((......))....)))))....... ( -34.50, z-score =  -2.51, R)
>consensus
GGAAACCCAAUGUAGUUGAAAGGAUGAAGAAGGCCACCAUAGCGCUUUAUGCAUCCAAGAAGAUGCUCAGCAGCACAUGGGGCCUCUCACCUGCUCUAAUGCACUGGAUCUACAUCUC
..(((.(((.((((.(((((.((((((...(((((.(((....(((....(((((......)))))..)))......)))))))).)))))).))))).)))).))).)))....... (-13.82 = -18.70 +   4.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:23 2011