Locus 5343

Sequence ID dm3.chr2R
Location 19,615,796 – 19,615,956
Length 160
Max. P 0.968775
window7325 window7326 window7327

overview

Window 5

Location 19,615,796 – 19,615,916
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 69.60
Shannon entropy 0.46422
G+C content 0.54043
Mean single sequence MFE -38.30
Consensus MFE -22.21
Energy contribution -22.40
Covariance contribution 0.19
Combinations/Pair 1.29
Mean z-score -1.22
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.594743
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19615796 120 - 21146708
GUUCUGCCGAGCUCUGCCAGAUUUCUGGCACUCGCUUCCCGCCACCAAUGGCUGGCUGGUGGCCAUGGCUACCGUGGCUCGCAGCCCCCUUUUCAAUAAAGAUUUUAGCUGCAAUCAGGA
.(((((..((((..((((((....))))))..(((..((.((((....)))).))..((((((....)))))))))))))(((((...((((.....))))......)))))...))))) ( -46.80, z-score =  -2.30, R)
>droSim1.chr2R 18181879 111 - 19596830
GCUCUGCCGAGCUCUGCCAGAUUUCUGGCACUCGGCUCCC-------AUGGCU--CUGGUGGCCAUGGCUACCGUGGCUCGCAGCCCCCCUUUCAAUAAAGAUUUGAGCUGCAAUCAGGA
.....((((((...((((((....))))))))))))..((-------..((((--.(((((((....))))))).)))).(((((.......((((.......))))))))).....)). ( -47.51, z-score =  -2.72, R)
>droYak2.chr2R 19593728 95 - 21139217
---GUUCCGAGUUUUGCUGGAUUUCUGGCACAUCA------------AUGG----CCGGUGGUCAUGGCUACUGUG----GCAGCCACCUGU--AAUAAGGAUUUAUGCUGCAAUCAAGA
---......(((...(((((((..(((((.((...------------.)))----))))..))).)))).)))(..----(((....(((..--....))).....)))..)........ ( -27.10, z-score =   0.12, R)
>droEre2.scaffold_4845 20978629 99 - 22589142
---GGGCGGCACUGUGCUGCAUUUCUGUUCCCACC------------AUCA----AUGGUGGCCAUGGCUACUGGGGCUCGCAGCCACCUUU--AGUAAAGAUUUAAGCUGCAAUCAGUA
---(((((((.....)))))..........(((((------------(...----.))))))))...((((..(((((.....))).))..)--)))..........((((....)))). ( -31.80, z-score =   0.02, R)
>consensus
___CUGCCGAGCUCUGCCAGAUUUCUGGCACUCCC____________AUGG____CUGGUGGCCAUGGCUACCGUGGCUCGCAGCCACCUUU__AAUAAAGAUUUAAGCUGCAAUCAGGA
.....(((......((((((....))))))..........................(((((((....))))))).)))..(((((......................)))))........ (-22.21 = -22.40 +   0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,615,836 – 19,615,956
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.36
Shannon entropy 0.34782
G+C content 0.53525
Mean single sequence MFE -37.11
Consensus MFE -17.93
Energy contribution -19.60
Covariance contribution 1.67
Combinations/Pair 1.12
Mean z-score -2.20
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.579694
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19615836 120 + 21146708
GAGCCACGGUAGCCAUGGCCACCAGCCAGCCAUUGGUGGCGGGAAGCGAGUGCCAGAAAUCUGGCAGAGCUCGGCAGAACAUCAAGCAAUUGUUGUACCCGUUGGUCCGAGUUUAUUAAA
(..((((((..(((...((((((((.......))))))))..((.((...((((((....))))))..)))))))...(((.(((....))).)))..))).)))..)............ ( -45.60, z-score =  -2.38, R)
>droSim1.chr2R 18181919 111 + 19596830
GAGCCACGGUAGCCAUGGCCACCAG--AGCCAU-------GGGAGCCGAGUGCCAGAAAUCUGGCAGAGCUCGGCAGAGCAUCAAGCAAUUGCCGCACCCGUUGGUCCGAGUUUAUUAAA
(..((((((...((((((((....)--.)))))-------))..((((((((((((....)))))...)))))))...((..(((....)))..))..))).)))..)............ ( -46.80, z-score =  -3.95, R)
>droYak2.chr2R 19593764 96 + 21139217
--GCCACAGUAGCCAUGACCACCGG----CCAU------------UGAUGUGCCAGAAAUCCAGCAAAACUCGG---AACAUCAAGCAA--AUUGC-UCCGUAGGUCCGAACUUAUUAAA
--..............((((..(((----...(------------((((((.((((.............)).))---.)))))))((..--...))-.)))..))))............. ( -18.92, z-score =  -0.27, R)
>consensus
GAGCCACGGUAGCCAUGGCCACCAG__AGCCAU_______GGGA_CCGAGUGCCAGAAAUCUGGCAGAGCUCGGCAGAACAUCAAGCAAUUGUUGCACCCGUUGGUCCGAGUUUAUUAAA
.......(((.((....)).)))...........................((((((....))))))((((((((...(((.....((.......))....)))...))))))))...... (-17.93 = -19.60 +   1.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,615,836 – 19,615,956
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.36
Shannon entropy 0.34782
G+C content 0.53525
Mean single sequence MFE -39.70
Consensus MFE -28.00
Energy contribution -26.57
Covariance contribution -1.43
Combinations/Pair 1.30
Mean z-score -2.22
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.80
SVM RNA-class probability 0.968775
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19615836 120 - 21146708
UUUAAUAAACUCGGACCAACGGGUACAACAAUUGCUUGAUGUUCUGCCGAGCUCUGCCAGAUUUCUGGCACUCGCUUCCCGCCACCAAUGGCUGGCUGGUGGCCAUGGCUACCGUGGCUC
.........(((((..((.((((((.......)))))).)).....)))))...((((((....))))))..((((..((((((....)))).))..))))(((((((...))))))).. ( -42.90, z-score =  -2.18, R)
>droSim1.chr2R 18181919 111 - 19596830
UUUAAUAAACUCGGACCAACGGGUGCGGCAAUUGCUUGAUGCUCUGCCGAGCUCUGCCAGAUUUCUGGCACUCGGCUCCC-------AUGGCU--CUGGUGGCCAUGGCUACCGUGGCUC
........((.(((((((..(((.((((((...((.....))..))))(((...((((((....))))))))).)).)))-------.))).)--)))))((((((((...)))))))). ( -48.00, z-score =  -3.57, R)
>droYak2.chr2R 19593764 96 - 21139217
UUUAAUAAGUUCGGACCUACGGA-GCAAU--UUGCUUGAUGUU---CCGAGUUUUGCUGGAUUUCUGGCACAUCA------------AUGG----CCGGUGGUCAUGGCUACUGUGGC--
................(((((((-((((.--..(((((.....---.))))).))))).(((..(((((.((...------------.)))----))))..))).......)))))).-- ( -28.20, z-score =  -0.90, R)
>consensus
UUUAAUAAACUCGGACCAACGGGUGCAACAAUUGCUUGAUGUUCUGCCGAGCUCUGCCAGAUUUCUGGCACUCGA_UCCC_______AUGGCU__CUGGUGGCCAUGGCUACCGUGGCUC
........(((((......))))).........(((((.........)))))..((((((....))))))..........................(((((((....)))))))...... (-28.00 = -26.57 +  -1.43)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:46:26 2011