Locus 712

Sequence ID dm3.chr2L
Location 5,036,279 – 5,036,379
Length 100
Max. P 0.999771
window944 window945

overview

Window 4

Location 5,036,279 – 5,036,379
Length 100
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 74.96
Shannon entropy 0.39292
G+C content 0.47756
Mean single sequence MFE -39.41
Consensus MFE -28.31
Energy contribution -27.93
Covariance contribution -0.37
Combinations/Pair 1.13
Mean z-score -4.61
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.35
SVM RNA-class probability 0.999771
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5036279 100 + 23011544
--------CGUUUCCGAAGUUU---CCCUAGCUUUCCAGCAGAUGGCGCACGUUCCAACGACACUCUUGCGCCAUCUGUUGGAUACUG-CGUAGCGAAAGAUUUGAUACAAU
--------.((.((.((..(((---(.(((((..(((((((((((((((((((....))).......))))))))))))))))....)-).))).))))..)).)).))... ( -39.21, z-score =  -5.38, R)
>droEre2.scaffold_4929 5115271 109 + 26641161
CUUUUCUAAGUUGGCAAACUUAGUGCUAUAAUUUUCUAGCAGAUGGCGCACG--CAGAUGAUACACGUGCGCCAUCUGCUGGAUACAG-CUCAGUACUCGGAACUUGACAAC
.........((((.(((.((.((((((.......((((((((((((((((((--...........)))))))))))))))))).....-...)))))).))...))).)))) ( -45.26, z-score =  -6.12, R)
>droSec1.super_5 3122795 104 + 5866729
--------CUUUUCCGAACUUAGUGCCAUAGUUUUCCAGCAGAUGGCGCACGCUCCAAUGAUACUCUGGCGCCAUCUGUUGGAUAGUGGCUCAGUGAAAGACUUGCUACAAC
--------..............(.(((((.....(((((((((((((((.((..............)))))))))))))))))..))))).)((..(.....)..))..... ( -36.84, z-score =  -3.20, R)
>droSim1.chr2L_random 279557 104 + 909653
--------CUUUUCCGAACUUAGUGCCAUAGUUUUCCAGCAGAUGGCGCACGCUCCAAUGAUACUCUGGCGCCAUCUGUUGGAUACUGGCUCAGUGAAAGAAUUGAUACAAC
--------................((((..((..(((((((((((((((.((..............))))))))))))))))).))))))(((((......)))))...... ( -36.34, z-score =  -3.74, R)
>consensus
________CGUUUCCGAACUUAGUGCCAUAGUUUUCCAGCAGAUGGCGCACGCUCCAAUGAUACUCUGGCGCCAUCUGUUGGAUACUG_CUCAGUGAAAGAAUUGAUACAAC
..................................(((((((((((((((...................)))))))))))))))............................. (-28.31 = -27.93 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,036,279 – 5,036,379
Length 100
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 74.96
Shannon entropy 0.39292
G+C content 0.47756
Mean single sequence MFE -36.88
Consensus MFE -22.27
Energy contribution -23.28
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.30
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.25
SVM RNA-class probability 0.998064
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5036279 100 - 23011544
AUUGUAUCAAAUCUUUCGCUACG-CAGUAUCCAACAGAUGGCGCAAGAGUGUCGUUGGAACGUGCGCCAUCUGCUGGAAAGCUAGGG---AAACUUCGGAAACG--------
...((.((..(..((((.(((.(-(....((((.(((((((((((...((.((....)))).))))))))))).))))..))))).)---)))..)..)).)).-------- ( -37.50, z-score =  -3.61, R)
>droEre2.scaffold_4929 5115271 109 - 26641161
GUUGUCAAGUUCCGAGUACUGAG-CUGUAUCCAGCAGAUGGCGCACGUGUAUCAUCUG--CGUGCGCCAUCUGCUAGAAAAUUAUAGCACUAAGUUUGCCAACUUAGAAAAG
....(((.((.......)))))(-(((((((.((((((((((((((((.........)--))))))))))))))).))....)))))).(((((((....)))))))..... ( -45.10, z-score =  -5.97, R)
>droSec1.super_5 3122795 104 - 5866729
GUUGUAGCAAGUCUUUCACUGAGCCACUAUCCAACAGAUGGCGCCAGAGUAUCAUUGGAGCGUGCGCCAUCUGCUGGAAAACUAUGGCACUAAGUUCGGAAAAG--------
((..(((...(.(((.....))).)....((((.((((((((((....((.((....))))..)))))))))).))))...)))..))................-------- ( -31.70, z-score =  -1.32, R)
>droSim1.chr2L_random 279557 104 - 909653
GUUGUAUCAAUUCUUUCACUGAGCCAGUAUCCAACAGAUGGCGCCAGAGUAUCAUUGGAGCGUGCGCCAUCUGCUGGAAAACUAUGGCACUAAGUUCGGAAAAG--------
..........((((...(((..((((.(.((((.((((((((((....((.((....))))..)))))))))).)))).)....))))....)))..))))...-------- ( -33.20, z-score =  -2.30, R)
>consensus
GUUGUAUCAAUUCUUUCACUGAG_CAGUAUCCAACAGAUGGCGCAAGAGUAUCAUUGGAGCGUGCGCCAUCUGCUGGAAAACUAUGGCACUAAGUUCGGAAAAG________
.............................((((.(((((((((((.(....((....)).).))))))))))).)))).................................. (-22.27 = -23.28 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:17:50 2011