Locus 1539

Sequence ID dm3.chr2L
Location 11,921,390 – 11,921,494
Length 104
Max. P 0.967470
window2102 window2103

overview

Window 2

Location 11,921,390 – 11,921,494
Length 104
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 82.53
Shannon entropy 0.29054
G+C content 0.32372
Mean single sequence MFE -24.75
Consensus MFE -15.49
Energy contribution -19.68
Covariance contribution 4.19
Combinations/Pair 1.07
Mean z-score -2.75
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967470
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11921390 104 + 23011544
ACUGUUUCGAACAAAUGCAAUGUUUACCAAGUUCAUGGGACUAAAAAUAAGUGCAUGGUAUUUGUUUAAAUGCCAUGCAUUUACCUCAAUGACAUUUGCAUAAC
..............((((((((((.....((((.....)))).....((((((((((((((((....)))))))))))))))).......)))).))))))... ( -30.00, z-score =  -3.53, R)
>droSim1.chr2L 11728588 104 + 22036055
AUAGUUUCGAACGAAUGCAAUGUUUACCAAGUUCAUGGGACUAAAAAUAAGUCCAUGGUAUUUUUUUAAAUGCCAUGCAUUUACCUUAAUGACAUUUGCAUAAC
..............((((((((((......((..((((((((.......)))))(((((((((....))))))))).)))..))......)))).))))))... ( -25.60, z-score =  -2.98, R)
>droSec1.super_16 120722 104 + 1878335
AUAGUUUCGAACAAAUGCAAUGUUUACCAAGUUCAUGGGACUUAAAAUAAGUGUAUGGUAUUUGUUUAAAUGCCAUGCAUUUACCUUAAUGACAUUUGCAUAAC
..............((((((((((....(((((.....)))))....((((((((((((((((....)))))))))))))))).......)))).))))))... ( -28.90, z-score =  -3.50, R)
>droYak2.chr2L 8341571 84 + 22324452
-UCGUUUUGAACAAAUGCAAUUUUUACCUAGUUCAUGGAACACAA-------------------UUUCAUUGCCAUGCAUUUACCUUAAUGGCAUUUGCAUAAC
-.............((((((..........((((...))))....-------------------......((((((............)))))).))))))... ( -14.50, z-score =  -1.00, R)
>consensus
AUAGUUUCGAACAAAUGCAAUGUUUACCAAGUUCAUGGGACUAAAAAUAAGUGCAUGGUAUUUGUUUAAAUGCCAUGCAUUUACCUUAAUGACAUUUGCAUAAC
..............((((((((((..((........)).........((((((((((((((((....)))))))))))))))).......)))).))))))... (-15.49 = -19.68 +   4.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,921,390 – 11,921,494
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 82.53
Shannon entropy 0.29054
G+C content 0.32372
Mean single sequence MFE -22.30
Consensus MFE -15.27
Energy contribution -14.90
Covariance contribution -0.37
Combinations/Pair 1.10
Mean z-score -1.68
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.559913
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11921390 104 - 23011544
GUUAUGCAAAUGUCAUUGAGGUAAAUGCAUGGCAUUUAAACAAAUACCAUGCACUUAUUUUUAGUCCCAUGAACUUGGUAAACAUUGCAUUUGUUCGAAACAGU
(((..(((((((.((.((((((((.(((((((.((((....)))).))))))).))))))......(((......)))....)).)))))))))....)))... ( -25.90, z-score =  -1.94, R)
>droSim1.chr2L 11728588 104 - 22036055
GUUAUGCAAAUGUCAUUAAGGUAAAUGCAUGGCAUUUAAAAAAAUACCAUGGACUUAUUUUUAGUCCCAUGAACUUGGUAAACAUUGCAUUCGUUCGAAACUAU
...((((((.(((.((((((.(((((((...))))))).........((((((((.......))).)))))..))))))..))))))))).............. ( -22.60, z-score =  -1.82, R)
>droSec1.super_16 120722 104 - 1878335
GUUAUGCAAAUGUCAUUAAGGUAAAUGCAUGGCAUUUAAACAAAUACCAUACACUUAUUUUAAGUCCCAUGAACUUGGUAAACAUUGCAUUUGUUCGAAACUAU
(((..((((((((..(((((((((.((.((((.((((....)))).)))).)).)))))))))...(((......)))........))))))))....)))... ( -20.60, z-score =  -1.37, R)
>droYak2.chr2L 8341571 84 - 22324452
GUUAUGCAAAUGCCAUUAAGGUAAAUGCAUGGCAAUGAAA-------------------UUGUGUUCCAUGAACUAGGUAAAAAUUGCAUUUGUUCAAAACGA-
((((((((..((((.....))))..)))))))).......-------------------...((((...(((((...(((.....)))....))))).)))).- ( -20.10, z-score =  -1.60, R)
>consensus
GUUAUGCAAAUGUCAUUAAGGUAAAUGCAUGGCAUUUAAACAAAUACCAUGCACUUAUUUUUAGUCCCAUGAACUUGGUAAACAUUGCAUUUGUUCGAAACUAU
((((((((..((((.....))))..))))))))....................................(((((...(((.....)))....)))))....... (-15.27 = -14.90 +  -0.37)

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 21:33:54 2011