Locus 4293

Sequence ID dm3.chr2R
Location 11,986,346 – 11,986,414
Length 68
Max. P 0.995025
window5884 window5885

overview

Window 4

Location 11,986,346 – 11,986,414
Length 68
Sequences 6
Columns 75
Reading direction forward
Mean pairwise identity 55.02
Shannon entropy 0.84405
G+C content 0.38152
Mean single sequence MFE -16.40
Consensus MFE -5.87
Energy contribution -7.68
Covariance contribution 1.82
Combinations/Pair 1.90
Mean z-score -2.02
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.76
SVM RNA-class probability 0.995025
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11986346 68 + 21146708
-----UGUAAUGCAUUUUACAUGC-UAACGUAAAAUAGCAU-GCAGCUAAGUUCGAAAUUUCGAACCCAAUGGUC
-----((((.((((((((((....-....))))))).))))-)))((((.((((((....))))))....)))). ( -16.70, z-score =  -2.57, R)
>droEre2.scaffold_4845 8717836 67 - 22589142
-----UUCAAAGUAUUUUUCAUUG-UAAUGUAAAAUUGCCUUGAAGCUAAGUUCGAAAGCC--AACCCAUUGGUC
-----(((((.(((.(((((((..-..))).)))).))).))))).............(((--((....))))). ( -10.20, z-score =  -1.12, R)
>droSec1.super_1 9482022 69 + 14215200
-----UGUAAUGCAUUUUACAUGU-UUAUGUAAAGUGGCAUUGCAGCUGAGUUCGAAAUUUCGAACCCAUUGAUC
-----(((((((((((((((((..-..))))))))).))))))))..((.((((((....)))))).))...... ( -23.80, z-score =  -4.62, R)
>droSim1.chr2R 10721750 69 + 19596830
-----GGUAAUGAAUUUUACAUGC-UAAUGUAAAAUGUCAUUGCAGCUUUGUUCGAAAUUUCGAACCCAUUGAUC
-----.((((((((((((((((..-..))))))))).)))))))......((((((....))))))......... ( -20.90, z-score =  -4.57, R)
>dp4.chr3 16418964 68 + 19779522
-----UAUAUUGUCAGCUGUUUGC-CAGCGUA-AUCAGUGCUGCCAUACCGUGUAAGAUCUAGCGAACGAACAUC
-----....((((..(((((.((.-(((((..-.....))))).)).))(......)....)))..))))..... ( -11.10, z-score =   0.98, R)
>apiMel3.Group5 290723 75 - 13386189
UUCGUUGAGAUGUACAUCGAGCGCAUAAUGCACGACCACAAUGACGACAAUGAUGUUGUCUCAAACCUAAUUGUC
....((((((((.((((((..(((((..((......))..))).))....))))))))))))))........... ( -15.70, z-score =  -0.23, R)
>consensus
_____UGUAAUGUAUUUUACAUGC_UAAUGUAAAAUAGCAUUGCAGCUAAGUUCGAAAUCUCGAACCCAAUGAUC
......((((((((((((((((.....))))))))).)))))))......(((((......)))))......... ( -5.87 =  -7.68 +   1.82)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,986,346 – 11,986,414
Length 68
Sequences 6
Columns 75
Reading direction reverse
Mean pairwise identity 55.02
Shannon entropy 0.84405
G+C content 0.38152
Mean single sequence MFE -16.73
Consensus MFE -2.83
Energy contribution -6.25
Covariance contribution 3.42
Combinations/Pair 1.74
Mean z-score -2.14
Structure conservation index 0.17
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.752588
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11986346 68 - 21146708
GACCAUUGGGUUCGAAAUUUCGAACUUAGCUGC-AUGCUAUUUUACGUUA-GCAUGUAAAAUGCAUUACA-----
......(((((((((....)))))))))(((((-((((((........))-)))))))....))......----- ( -21.40, z-score =  -4.08, R)
>droEre2.scaffold_4845 8717836 67 + 22589142
GACCAAUGGGUU--GGCUUUCGAACUUAGCUUCAAGGCAAUUUUACAUUA-CAAUGAAAAAUACUUUGAA-----
((((....))))--((((.........))))((((((..(((((.(((..-..))).))))).)))))).----- ( -10.90, z-score =  -1.07, R)
>droSec1.super_1 9482022 69 - 14215200
GAUCAAUGGGUUCGAAAUUUCGAACUCAGCUGCAAUGCCACUUUACAUAA-ACAUGUAAAAUGCAUUACA-----
......(((((((((....)))))))))...(.(((((...(((((((..-..)))))))..))))).).----- ( -19.60, z-score =  -4.34, R)
>droSim1.chr2R 10721750 69 - 19596830
GAUCAAUGGGUUCGAAAUUUCGAACAAAGCUGCAAUGACAUUUUACAUUA-GCAUGUAAAAUUCAUUACC-----
.......((((((((....))))))........(((((.(((((((((..-..)))))))))))))).))----- ( -16.30, z-score =  -3.26, R)
>dp4.chr3 16418964 68 - 19779522
GAUGUUCGUUCGCUAGAUCUUACACGGUAUGGCAGCACUGAU-UACGCUG-GCAAACAGCUGACAAUAUA-----
..((((.(((.((((.(((......))).)))))))......-...((((-.....)))).)))).....----- ( -14.40, z-score =  -0.02, R)
>apiMel3.Group5 290723 75 + 13386189
GACAAUUAGGUUUGAGACAACAUCAUUGUCGUCAUUGUGGUCGUGCAUUAUGCGCUCGAUGUACAUCUCAACGAA
((((((...(((......)))...)))))).((.(((.(((.(((((((........)))))))))).))).)). ( -17.80, z-score =  -0.09, R)
>consensus
GACCAAUGGGUUCGAAAUUUCGAACUUAGCUGCAAUGCCAUUUUACAUUA_GCAUGUAAAAUACAUUACA_____
......(((((((((....))))))))).....(((((.(((((((((.....))))))))))))))........ ( -2.83 =  -6.25 +   3.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:26:24 2011