Locus 1170

Sequence ID dm3.chr2L
Location 8,803,072 – 8,803,166
Length 94
Max. P 0.735478
window1602 window1603

overview

Window 2

Location 8,803,072 – 8,803,166
Length 94
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 74.09
Shannon entropy 0.44236
G+C content 0.56254
Mean single sequence MFE -30.02
Consensus MFE -17.69
Energy contribution -18.70
Covariance contribution 1.01
Combinations/Pair 1.12
Mean z-score -1.33
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.626414
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8803072 94 + 23011544
CUGCCAAAGCCGAGAUGGAUGACUUGAAUGGCCGGGCAG--------AAGGACGGAAGGUUCGCCUGGAUGGAUGGGCGAGUAU-----UUCGGUUCGGCUGGAUGG
...(((.(((((((.((((..(((((..((.((((((.(--------((...(....).))))))))).....))..)))))..-----)))).)))))))...))) ( -34.30, z-score =  -2.19, R)
>droSim1.chr2L 8581203 94 + 22036055
CUGCCAAAGCCGAGAUGGAUGACUUGAAUGGCCGGGCAG--------AAGGACAGAAGGUUCGCCUGGAUGGAUGGGCGAGUAU-----UUCGGUUCGGCUGGAUGG
...(((.(((((((.((((..(((((..((.((((((..--------..((((.....)))))))))).....))..)))))..-----)))).)))))))...))) ( -32.30, z-score =  -1.64, R)
>droSec1.super_3 4275023 93 + 7220098
CUGCCAAAGCCGAGAUGGAUGACUUGAAUGGCCGGGCAG--------AAGGACAGAAGGUUCGCCUGGAUGGAUGGGCGAGUAU-----UUCGGUUCGGCUGGAUG-
...(((..((((((.((((..(((((..((.((((((..--------..((((.....)))))))))).....))..)))))..-----)))).)))))))))...- ( -31.00, z-score =  -1.33, R)
>droEre2.scaffold_4929 9391464 107 + 26641161
CUGCCAAAGCCGAGAUGGAUGACUUGGAUGGCCGGGCAGGAGGACAGAAGGACAGAAGGUUCGCCUGGAUGGAUGGGCGAGUAUAGUAUUUCGGUUCGGCUGGAUGG
..(((..((((((((((....(((((.....(((..((((.((((.............)))).))))..))).....)))))....)))))))))).)))....... ( -34.42, z-score =  -1.39, R)
>droAna3.scaffold_12916 10465326 76 + 16180835
CUGCCAAAUCCGAGAUGGAUGGCUUGGAUGGACAUUUGGAUGGAUGGAUGGUUUAGGUUUUGGCCUGGCUGGAUGG-------------------------------
...(((..((((((........))))))))).((((..(..((..((((.......))))...))...)..)))).------------------------------- ( -18.10, z-score =  -0.09, R)
>consensus
CUGCCAAAGCCGAGAUGGAUGACUUGAAUGGCCGGGCAG________AAGGACAGAAGGUUCGCCUGGAUGGAUGGGCGAGUAU_____UUCGGUUCGGCUGGAUGG
(((((...((((....((....))....))))..)))))....................((((((((......))))))))........(((((.....)))))... (-17.69 = -18.70 +   1.01)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,803,072 – 8,803,166
Length 94
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 74.09
Shannon entropy 0.44236
G+C content 0.56254
Mean single sequence MFE -20.07
Consensus MFE -10.88
Energy contribution -13.88
Covariance contribution 3.00
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.735478
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8803072 94 - 23011544
CCAUCCAGCCGAACCGAA-----AUACUCGCCCAUCCAUCCAGGCGAACCUUCCGUCCUU--------CUGCCCGGCCAUUCAAGUCAUCCAUCUCGGCUUUGGCAG
.......((((((((((.-----....(((((..........))))).....(((..(..--------..)..)))..................)))).)))))).. ( -23.50, z-score =  -2.40, R)
>droSim1.chr2L 8581203 94 - 22036055
CCAUCCAGCCGAACCGAA-----AUACUCGCCCAUCCAUCCAGGCGAACCUUCUGUCCUU--------CUGCCCGGCCAUUCAAGUCAUCCAUCUCGGCUUUGGCAG
.......((((((((((.-----....(((((..........))))).............--------......(((.......))).......)))).)))))).. ( -22.00, z-score =  -1.69, R)
>droSec1.super_3 4275023 93 - 7220098
-CAUCCAGCCGAACCGAA-----AUACUCGCCCAUCCAUCCAGGCGAACCUUCUGUCCUU--------CUGCCCGGCCAUUCAAGUCAUCCAUCUCGGCUUUGGCAG
-......((((((((((.-----....(((((..........))))).............--------......(((.......))).......)))).)))))).. ( -22.00, z-score =  -1.65, R)
>droEre2.scaffold_4929 9391464 107 - 26641161
CCAUCCAGCCGAACCGAAAUACUAUACUCGCCCAUCCAUCCAGGCGAACCUUCUGUCCUUCUGUCCUCCUGCCCGGCCAUCCAAGUCAUCCAUCUCGGCUUUGGCAG
.......((((((((((..........(((((..........)))))...........................(((.......))).......)))).)))))).. ( -22.00, z-score =  -1.30, R)
>droAna3.scaffold_12916 10465326 76 - 16180835
-------------------------------CCAUCCAGCCAGGCCAAAACCUAAACCAUCCAUCCAUCCAAAUGUCCAUCCAAGCCAUCCAUCUCGGAUUUGGCAG
-------------------------------.......(((((((.......................................)))((((.....)))).)))).. ( -10.83, z-score =  -1.20, R)
>consensus
CCAUCCAGCCGAACCGAA_____AUACUCGCCCAUCCAUCCAGGCGAACCUUCUGUCCUU________CUGCCCGGCCAUUCAAGUCAUCCAUCUCGGCUUUGGCAG
.......((((((((((..........(((((..........)))))...........................(((.......))).......)))).)))))).. (-10.88 = -13.88 +   3.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:26:58 2011