Locus 5629

Sequence ID dm3.chr3LHet
Location 2,536,384 – 2,536,611
Length 227
Max. P 0.950889
window7727 window7728

overview

Window 7

Location 2,536,384 – 2,536,498
Length 114
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 68.47
Shannon entropy 0.55751
G+C content 0.53662
Mean single sequence MFE -35.45
Consensus MFE -19.24
Energy contribution -19.84
Covariance contribution 0.60
Combinations/Pair 1.58
Mean z-score -0.83
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.522259
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 2536384 114 + 2555491
UUCGGCAUGGUAAAUGGCAUCGGAAACGGAGGUUGGUUGCUUCCUCUCCACUGGUACUGCGACCAGACGCCUGUUUCCCUAUGGUUUUCAACUGUCUGGGGCUCUUCUCUCUCC---
(((((.(((((....(((...((((((((.(.((((((((..((........))....)))))))).)..)))))))).....)))....))))))))))..............--- ( -31.50, z-score =   0.33, R)
>droSim1.chrU 5056725 117 + 15797150
CUUGGCAUGGCAAAUGGCAUUGAAAACGGAGGAGGAUUGUUUCCUCCCCAAUGGUACUGCGACCAAAUGCCUGUUUCUCUGUGAGCUUCCAAAAUCGGUGGCUCUUCCUUCUUCUGA
....(((.((.((((((((((......((.((((((.....))))))))..((((......)))))))))).)))))).)))(((((.((......)).)))))............. ( -38.40, z-score =  -2.09, R)
>droSec1.super_165 59835 114 + 68140
UUUGGCAUAGUAAAUGGCAUCGGAAACGGAGGUUGGUCGUUUCCUCCCCACCGGUACUGCGGCCAACCGCCUGUUUCCCUAUGGGUUCCACUUGGUUGGGACUCCUCUUUCUCC---
..((.(((.....))).))..((((((((.((((((((((..((........))....))))))))))..))))))))....((((((((......))))))))..........--- ( -43.40, z-score =  -2.15, R)
>droYak2.chr2h_random 2814463 114 - 3774259
CUUUGCAU---AAACGGCAUUGGAAACGGAGGAGGGUUAGUCCCUCCCCACUGAUACUGGGACCAAAUGCCCGUCUCCCGGUGAGCCUCCAACGUUUGGGGCUUCUCUUUCUCCUGA
...(((..---.....)))..(((...((((..((((..(((((..............))))).....))))..)))).(..(((((.(((.....))))))))..)....)))... ( -37.04, z-score =  -0.16, R)
>droEre2.scaffold_4929 21783330 99 + 26641161
------------------UUCGGCAUUGGAAACGGACUGCUUCCUCCCCACUGGUACUGCGACCAGACGCGUGUUUCCCUGUGGGUUUUCAACACCUGGGACUCUUCCUUCUCCUGA
------------------...((..(((((((((((.....)))...((((.((.((((((......)))).))...)).))))))))))))..)).((((....))))........ ( -26.90, z-score =  -0.07, R)
>consensus
CUUGGCAU_G_AAAUGGCAUCGGAAACGGAGGAGGGUUGCUUCCUCCCCACUGGUACUGCGACCAAACGCCUGUUUCCCUGUGGGUUUCCAACGUCUGGGGCUCUUCUUUCUCCUGA
.....................((((((((.....((((((..((........))....))))))......))))))))....((((((((......))))))))............. (-19.24 = -19.84 +   0.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,536,498 – 2,536,611
Length 113
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 66.22
Shannon entropy 0.55117
G+C content 0.45532
Mean single sequence MFE -28.29
Consensus MFE -19.08
Energy contribution -19.52
Covariance contribution 0.44
Combinations/Pair 1.55
Mean z-score -1.20
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.950889
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 2536498 113 - 2555491
AUAGCUUGCAGGGAAAAUAACUUGGUGGCCUUGGCAGAAACCAAUUCAACUCAGAAAGCACAGGAGUCAACGGAGUCAACAGAUAAGGCUACUGAGGAAGUUCGAAAACAAGU
...(((((....(((.....((..(((((((((.(.(((.....))).((((.....((......)).....)))).....).)))))))))..))....))).....))))) ( -27.20, z-score =  -0.99, R)
>droSim1.chrU 5056842 113 - 15797150
AUAGCCUGUAGGGAGGAAAAGUUAGUUGCCUUAGAAGGUGGCGGCUCAGAACCUAAAACUCAAGGGUCGGUAGAGUCGCGAGAUAAGGCUAUUAAAGAAACUGAGAAACAGGA
....(((((.....((.....(((((.((((((.....(.(((((((.((.(((........))).))....))))))).)..)))))).))))).....)).....))))). ( -33.00, z-score =  -1.98, R)
>droSec1.super_165 59949 107 - 68140
AUAGCUUGCAGGGAAAGGAACCUGUUAGCCUUGGCGGAA------UCAGAUCGGAAAGCACAGGACUCAACGGAGUCAAAAGAUAAGGCUACUGAGGAAGUUCAGAAACAAGA
...(((.(((((........))))).)))((((.(.(((------(....((((..(((....(((((....)))))..........))).))))....)))).)...)))). ( -28.74, z-score =  -1.62, R)
>droYak2.chr2h_random 2814577 113 + 3774259
AUAGUUUGUAGAGAGGAGAAGUUAACGGCUGUAGAAAGUGUCGGCUUAGAACCCAAAACGCAGAGGUCGUUGGAGUCGCGAGACAAAGCCAUUAAAGAAACUCAGAAACAGGA
...((((.(.(((.............(((..........)))(((((.....((((...((....))..)))).(((....))).)))))..........)))).)))).... ( -24.20, z-score =  -0.22, R)
>consensus
AUAGCUUGCAGGGAAAAGAACUUAGUGGCCUUAGAAGAAG_CGGCUCAGAACCGAAAACACAGGAGUCAACGGAGUCAAGAGAUAAGGCUACUAAAGAAACUCAGAAACAAGA
....(((((...(((.....((((((((((((.........((((((................)))))).....(((....)))))))))))))))....)))....))))). (-19.08 = -19.52 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:52:01 2011