Locus 404

Sequence ID dm3.chr2L
Location 2,800,569 – 2,800,728
Length 159
Max. P 0.908620
window551 window552 window553

overview

Window 1

Location 2,800,569 – 2,800,688
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 66.48
Shannon entropy 0.47273
G+C content 0.29134
Mean single sequence MFE -20.07
Consensus MFE -8.99
Energy contribution -11.33
Covariance contribution 2.34
Combinations/Pair 1.16
Mean z-score -2.22
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.20
SVM RNA-class probability 0.908620
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2800569 119 + 23011544
AAAAAUCAAAACAAAUUACUUAUCUAACGAUAAGCCAAAAUAGUAUGACUGUGAAAUUAAAUCUUUUUCAAUAGAUCCGAUCCAUCCAGGCAAUUUAUUUGGUUUUGGAAAUGCAUUAU
.....(((((((......((((((....))))))...((((((..((.(((.((.(((..((((........))))..)))...))))).))..)))))).)))))))........... ( -19.90, z-score =  -1.39, R)
>droSec1.super_5 959824 96 + 5866729
ACAAAUCAAAACAAAUUACUUAUCUAACGAUAAGACAAAAUAGUAUAGCUGUGACAUUAAAUCAC-----------------------AGCAAUUUAUUUUGUUUUGGAAAUGCAUGAU
.....((((((((((.((((((((....)))))).............(((((((.......))))-----------------------)))....)).))))))))))........... ( -26.30, z-score =  -5.69, R)
>droEre2.scaffold_4929 2847084 113 + 26641161
GCAAAUCAAAACAAAUUACUUACCUAAAGUGAAGUUAACACGGCAUUAAUGUGACAUUAUAUUUCUCUCAAAGGAUCUAA-----CCGCUCAAUUU-UCUUGCUUUGAAUGCGCAUCAU
(((..(((((.(((.((((((.....)))))).........(((..(((((...))))).............((......-----)))))......-..))).))))).)))....... ( -14.00, z-score =   0.42, R)
>consensus
ACAAAUCAAAACAAAUUACUUAUCUAACGAUAAGACAAAAUAGUAUAACUGUGACAUUAAAUCUCU_UCAA__GAUC__A_____CC_AGCAAUUUAUUUUGUUUUGGAAAUGCAUCAU
.....(((((((((....((((((....)))))).....((((.....))))...............................................)))))))))........... ( -8.99 = -11.33 +   2.34)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,800,569 – 2,800,688
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 66.48
Shannon entropy 0.47273
G+C content 0.29134
Mean single sequence MFE -24.13
Consensus MFE -8.48
Energy contribution -9.93
Covariance contribution 1.45
Combinations/Pair 1.16
Mean z-score -2.25
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.610657
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2800569 119 - 23011544
AUAAUGCAUUUCCAAAACCAAAUAAAUUGCCUGGAUGGAUCGGAUCUAUUGAAAAAGAUUUAAUUUCACAGUCAUACUAUUUUGGCUUAUCGUUAGAUAAGUAAUUUGUUUUGAUUUUU
............((((((((((.....((.(((...((((..(((((........)))))..))))..))).))......))))(((((((....))))))).....))))))...... ( -23.70, z-score =  -1.49, R)
>droSec1.super_5 959824 96 - 5866729
AUCAUGCAUUUCCAAAACAAAAUAAAUUGCU-----------------------GUGAUUUAAUGUCACAGCUAUACUAUUUUGUCUUAUCGUUAGAUAAGUAAUUUGUUUUGAUUUGU
............((((.((((((((((((((-----------------------(((((.....)))))))).............((((((....)))))).))))))))))).)))). ( -27.70, z-score =  -5.41, R)
>droEre2.scaffold_4929 2847084 113 - 26641161
AUGAUGCGCAUUCAAAGCAAGA-AAAUUGAGCGG-----UUAGAUCCUUUGAGAGAAAUAUAAUGUCACAUUAAUGCCGUGUUAACUUCACUUUAGGUAAGUAAUUUGUUUUGAUUUGC
.......(((.(((((((((((-(......((((-----(.......(((....)))...(((((...)))))..)))))......)))((((.....))))...)))))))))..))) ( -21.00, z-score =   0.14, R)
>consensus
AUAAUGCAUUUCCAAAACAAAAUAAAUUGCC_GG_____U__GAUC__UUGA_AGAGAUUUAAUGUCACAGUAAUACUAUUUUGACUUAUCGUUAGAUAAGUAAUUUGUUUUGAUUUGU
............(((((((((...................................(((.....))).................(((((((....)))))))..)))))))))...... ( -8.48 =  -9.93 +   1.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,800,609 – 2,800,728
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 66.42
Shannon entropy 0.54010
G+C content 0.35715
Mean single sequence MFE -23.67
Consensus MFE -11.59
Energy contribution -11.90
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -1.52
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.85
SVM RNA-class probability 0.834899
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2800609 119 + 23011544
UAGUAUGACUGUGAAAUUAAAUCUUUUUCAAUAGAUCCGAUCCAUCCAGGCAAUUUAUUUGGUUUUGGAAAUGCAUUAUUAAAAGGUCGUGCCUACUUUUGGGCUGACAAGUCCAUCUU
..((((((((.(((((.........)))))..........((((.(((((.......)))))...))))...............)))))))).......((((((....)))))).... ( -26.10, z-score =  -0.80, R)
>droSim1.chr2L 2758276 93 + 22036055
---------------------UCUCUUUCAAUAGAUCUAUCCACGC-----AAUUUAUUUUGUUUUGGAAAUGCAUGAUUAAAAAGUCGUGUCUACUUUUGGGCUGACAUGUCCAUCUU
---------------------..........((((....((((.((-----((......))))..))))....(((((((....)))))))))))....(((((......))))).... ( -19.00, z-score =  -1.66, R)
>droSec1.super_5 959864 96 + 5866729
--------------UAGUAUAGCUGUGACAUUAAAUCACAGC---------AAUUUAUUUUGUUUUGGAAAUGCAUGAUUAAAAAGUCGUGUCUACUUUUGGGCUGACAAGUCCAUCUU
--------------.((((..(((((((.......)))))))---------.....................((((((((....)))))))).))))..((((((....)))))).... ( -25.50, z-score =  -2.71, R)
>droEre2.scaffold_4929 2847124 113 + 26641161
CGGCAUUAAUGUGACAUUAUAUUUCUCUCAAAGGAUCUAACCGCUC-----AAUUU-UCUUGCUUUGAAUGCGCAUCAUGCAAAAGUAUUGCCUACUUUUGGGCUGACAUGCCCAACUU
..((((..(((((.((((..............((......))((..-----.....-....))....))))))))).))))(((((((.....)))))))((((......))))..... ( -24.10, z-score =  -0.93, R)
>consensus
_______________AUUAUAUCUCUUUCAAUAGAUCUAACC_CUC_____AAUUUAUUUUGUUUUGGAAAUGCAUGAUUAAAAAGUCGUGCCUACUUUUGGGCUGACAAGUCCAUCUU
........................................................................(((((((......))))))).......(((((......))))).... (-11.59 = -11.90 +   0.31)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:12:20 2011