Locus 8506

Sequence ID dm3.chr3L
Location 24,099,761 – 24,099,911
Length 150
Max. P 0.997358
window11683 window11684

overview

Window 3

Location 24,099,761 – 24,099,911
Length 150
Sequences 5
Columns 153
Reading direction forward
Mean pairwise identity 88.66
Shannon entropy 0.20288
G+C content 0.53210
Mean single sequence MFE -59.33
Consensus MFE -44.23
Energy contribution -43.63
Covariance contribution -0.60
Combinations/Pair 1.19
Mean z-score -2.92
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.08
SVM RNA-class probability 0.981455
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24099761 150 + 24543557
AUGCCGUAAGCUUGUUGCGCG-CGGAGCUGAAGUUCCAAUGU--CCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACAAAUACUU
.....(((...((((.((((.-((((.(((((((((.....(--((.....(((((((((....))))))))).....)))..(((((.(((((((................))))))))))))))))))))))))).)))).)))).))).. ( -60.89, z-score =  -3.87, R)
>droEre2.scaffold_4784 25390242 152 + 25762168
AUGCCGUAAGCUUGUUGCGCGGCAAGGCUGGAGU-CCAGAGUGGCCAGUCUGAAGAUAUCAAAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACUUGUUUACGCCGUGUUGCCAGACUGGGCUUUAGUCUGGGCGCCACACCUCCUU
.((((((..((.....))))))))(((.(((.((-(((((.((.((((((((..(((((...(((((....(((....)))...)))))(((((............))))))))))..)))))))).)...).))))))).)))..))).... ( -61.50, z-score =  -2.85, R)
>droYak2.chr2L_random 2366577 152 + 4064425
AUGCCGUAAGCUUGUUGCGCGGCGGGGUUGAAGU-CCAGAGUGGCCAGUCUGACGAUAUCAGAAGAUAUCGUCAUCCAGGAAAGGUCUUGGCGUUAGUACUUGUUUACGCCGUGUUGCCAGACUGGGUUUUAGUCUGGGCGACAGAAAUGCGC
..(((((..((.....)))))))(.(.(((..((-(((((.(((((((((((((((((((....)))))))))..........(((..((((((............))))))....))))))))))...))).)))))))..)))...).).. ( -59.70, z-score =  -2.86, R)
>droSec1.super_94 48640 146 + 93855
GUGCCGUAAGCUUGUUGCGCGGCAGAGCUGAAGUACCAGUGUGUCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACUUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACA-------
.((((((..((.....))))))))..((((......))))((((((((.(((((((((((....)))))))(((....)))..(((((.(((((((................)))))))))))).....)))).))))))))....------- ( -57.89, z-score =  -2.58, R)
>droSim1.chr2h_random 2494563 150 - 3178526
AUGCCGUAAGCUUGUUGCGCGGCGGAGCUGAAGUUUAAGUGUGUCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACAAAUA---
.((((((..((.....))))))))((((....))))..((((((((((.(((((((((((....)))))))(((....)))..(((((.(((((((................)))))))))))).....)))).))))))).))).....--- ( -56.69, z-score =  -2.44, R)
>consensus
AUGCCGUAAGCUUGUUGCGCGGCGGAGCUGAAGU_CCAGUGUGGCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACUUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACAAAUAC__
.((((....((.....))....((((.(((((((.((.......((.....(((((((((....))))))))).....))...(((((.(((((((................)))))))))))))))))))))))))))))............ (-44.23 = -43.63 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,099,761 – 24,099,911
Length 150
Sequences 5
Columns 153
Reading direction reverse
Mean pairwise identity 88.66
Shannon entropy 0.20288
G+C content 0.53210
Mean single sequence MFE -54.04
Consensus MFE -43.42
Energy contribution -44.62
Covariance contribution 1.20
Combinations/Pair 1.10
Mean z-score -3.59
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.09
SVM RNA-class probability 0.997358
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24099761 150 - 24543557
AAGUAUUUGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGG--ACAUUGGAACUUCAGCUCCG-CGCGCAACAAGCUUACGGCAU
.(((((((((..(((((((((((.....))))))).......))))...)))))))))...(((............(((((((((((((....)))))))))...((((--(.........))))))))).-.((.......))....))).. ( -53.61, z-score =  -2.74, R)
>droEre2.scaffold_4784 25390242 152 - 25762168
AAGGAGGUGUGGCGCCCAGACUAAAGCCCAGUCUGGCAACACGGCGUAAACAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUUUGAUAUCUUCAGACUGGCCACUCUGG-ACUCCAGCCUUGCCGCGCAACAAGCUUACGGCAU
(((((((((((..(((.(((((.......))))))))..)))(((((............)))))...))))...((((((...((((((....))))))((((((........)))))-)))))))))))((((.((.....))...)))).. ( -55.60, z-score =  -3.00, R)
>droYak2.chr2L_random 2366577 152 - 4064425
GCGCAUUUCUGUCGCCCAGACUAAAACCCAGUCUGGCAACACGGCGUAAACAAGUACUAACGCCAAGACCUUUCCUGGAUGACGAUAUCUUCUGAUAUCGUCAGACUGGCCACUCUGG-ACUUCAACCCCGCCGCGCAACAAGCUUACGGCAU
((((.....(((.(((.(((((.......)))))))).))).((((.....((((.(((..((((...((......)).((((((((((....))))))))))...)))).....)))-))))......)))))))).....((.....)).. ( -51.60, z-score =  -4.62, R)
>droSec1.super_94 48640 146 - 93855
-------UGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUGGUACUUCAGCUCUGCCGCGCAACAAGCUUACGGCAC
-------(((.((((.((((((((((.((((((((((......((........))......))).)))))..(((.(...(((((((((....)))))))))...).)))......))..)))))).))))..)))).))).((.....)).. ( -54.90, z-score =  -3.61, R)
>droSim1.chr2h_random 2494563 150 + 3178526
---UAUUUGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUUAAACUUCAGCUCCGCCGCGCAACAAGCUUACGGCAU
---...((((.((((((((((((.....))))))))......((((((...((((.((.......)))))))))..(((((((((((((....)))))))))...(((((...........)))))))))))))))).))))((.....)).. ( -54.50, z-score =  -3.99, R)
>consensus
__GUAUUUGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGACACACUGG_ACUUCAGCUCCGCCGCGCAACAAGCUUACGGCAU
........((((.(((.((((((.....))))))))).))))((((..............))))..........(((((((((((((((....)))))))))...((((.....))))..))))))....((((.((.....))...)))).. (-43.42 = -44.62 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:46:53 2011