Locus 12118

Sequence ID dm3.chr3R
Location 25,805,424 – 25,805,539
Length 115
Max. P 0.998417
window16659 window16660

overview

Window 9

Location 25,805,424 – 25,805,539
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 53.98
Shannon entropy 0.64060
G+C content 0.31620
Mean single sequence MFE -22.78
Consensus MFE -8.00
Energy contribution -8.67
Covariance contribution 0.67
Combinations/Pair 1.19
Mean z-score -3.21
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.35
SVM RNA-class probability 0.998417
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25805424 115 + 27905053
CCAAGAU-AAAGAGU-UGGACUAAUACCUUUUUAUCAUUUAUUAAGUGCAUGGCAUUUGGCUUUACAGAAGCCCUUGGAUUCGUCCAACCAUUCAGUAACUUUUUAUUAAUCAUAUA---
....(((-(((((((-(((((.(((.((...............((((((...))))))((((((...))))))...))))).)))).((......))))))))))))).........--- ( -24.90, z-score =  -2.22, R)
>droYak2.chr3R 8162257 105 - 28832112
--AUGAUCAAAUGAU-UGAAUUAAUACUUUUUUAUCGACCUUUAAUUG----------GGCUUCUCAGAAGCCCUUG-AUGCUUUUUACUAUUCACUUAUUAAUCACUUAU-AUACACAC
--.((((..(((((.-(((((...........((((((.........(----------((((((...))))))))))-))).........))))).))))).)))).....-........ ( -18.05, z-score =  -3.45, R)
>droSim1.chr3R 25473655 96 + 27517382
--CGAAUAAAAGGGCAUAAACUAAUGCCCUUUUAUCAUUUAUUAAAAGCAUGGCAUUUGGCUUAACAGAAGCCCUC--ACUAACUUUAUUAGUUAUAUAC--------------------
--.((.(((((((((((......)))))))))))))...............(((.((((......)))).)))...--..(((((.....))))).....-------------------- ( -25.40, z-score =  -3.95, R)
>consensus
__AAGAU_AAAGGGU_UGAACUAAUACCUUUUUAUCAUUUAUUAAAUGCAUGGCAUUUGGCUUAACAGAAGCCCUUG_AUUCAUUUUACUAUUCACUUACU__U_A_U_AU_AUA_A___
....(((.(((((((.(......).))))))).)))......................(((((.....)))))............................................... ( -8.00 =  -8.67 +   0.67)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 25,805,424 – 25,805,539
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 53.98
Shannon entropy 0.64060
G+C content 0.31620
Mean single sequence MFE -23.67
Consensus MFE -7.33
Energy contribution -6.67
Covariance contribution -0.66
Combinations/Pair 1.29
Mean z-score -2.35
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.45
SVM RNA-class probability 0.939215
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25805424 115 - 27905053
---UAUAUGAUUAAUAAAAAGUUACUGAAUGGUUGGACGAAUCCAAGGGCUUCUGUAAAGCCAAAUGCCAUGCACUUAAUAAAUGAUAAAAAGGUAUUAGUCCA-ACUCUUU-AUCUUGG
---......................((((.((((((((.........(((((.....))))).((((((.......................)))))).)))))-))).)))-)...... ( -23.60, z-score =  -1.30, R)
>droYak2.chr3R 8162257 105 + 28832112
GUGUGUAU-AUAAGUGAUUAAUAAGUGAAUAGUAAAAAGCAU-CAAGGGCUUCUGAGAAGCC----------CAAUUAAAGGUCGAUAAAAAAGUAUUAAUUCA-AUCAUUUGAUCAU--
........-....((((((((....(((((.((.....))..-...(((((((...))))))----------)..........................)))))-.....))))))))-- ( -20.80, z-score =  -2.67, R)
>droSim1.chr3R 25473655 96 - 27517382
--------------------GUAUAUAACUAAUAAAGUUAGU--GAGGGCUUCUGUUAAGCCAAAUGCCAUGCUUUUAAUAAAUGAUAAAAGGGCAUUAGUUUAUGCCCUUUUAUUCG--
--------------------((((...((((((...))))))--...(((((.....))))).......))))...........(((((((((((((......)))))))))))))..-- ( -26.60, z-score =  -3.09, R)
>consensus
___U_UAU_AU_A_U_A__AGUAAAUGAAUAGUAAAAAGAAU_CAAGGGCUUCUGUAAAGCCAAAUGCCAUGCAAUUAAUAAAUGAUAAAAAGGUAUUAGUUCA_ACCCUUU_AUCAU__
...............................................(((((.....)))))......................(((.(((.(((..........))).))).))).... ( -7.33 =  -6.67 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:56:04 2011