Locus 8466

Sequence ID dm3.chr3L
Location 23,112,521 – 23,112,631
Length 110
Max. P 0.999452
window11625 window11626

overview

Window 5

Location 23,112,521 – 23,112,631
Length 110
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 52.14
Shannon entropy 0.76593
G+C content 0.44120
Mean single sequence MFE -29.62
Consensus MFE -13.34
Energy contribution -16.27
Covariance contribution 2.94
Combinations/Pair 1.55
Mean z-score -2.44
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.90
SVM RNA-class probability 0.999452
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23112521 110 + 24543557
GCGUAGCUAGAGAUAGUUUUCGUCGAGCAGAUGAUCUUCUUUCCGCGCUUAAUUCACAGUUUAAUGGCCUUAAGCUAAUAGAGGAAUCUCCGAAGCGCAAAGAAGCCGCU
(((.(((((....))))).(((((.....))))).(((((((..((((((.........((((.((((.....)))).))))((.....)).))))))))))))).))). ( -29.50, z-score =  -0.25, R)
>droPer1.super_76 130794 89 - 268861
---------------------AAAAGCAAUACCAUCGGCUCUUAGCCAUGGAGUCUCAAUAUGGCAGUCUGCAACUUCUGAAUGAGUCUCCGAGGCGUAAAAAGGUCACU
---------------------...............(((.(((.(((.(((((.((((...(((.(((.....))).)))..)))).))))).))).....))))))... ( -22.90, z-score =  -1.12, R)
>droWil1.scaffold_181148 2801111 101 - 5435427
---------GGGCAGGUUUUAAUAAACUCCAAGCGGAGUUUACUGCGGUGGAGACUCAGUUCAGAAGUUUAUCGCUUAUGAAUGAGUCUCCGAAACGUAAAAGGUCCAGU
---------((((.........((((((((....)))))))).((((.((((((((((.((((.((((.....)))).))))))))))))))...))))....))))... ( -41.90, z-score =  -5.92, R)
>droVir3.scaffold_12958 1203962 99 - 3547706
-----------GUUGGUUUUCGUAAACUUAACGAUCAACUCACAGCCCUGGACAUCCAAUUUAAUAGCCUUAAACUGUUGAAUGAGUCUCCUGGGCCUAAAAAGUCCAAU
-----------((.((((.((((.......))))..)))).)).((((.(((.(..((.((((((((.......))))))))))..).))).)))).............. ( -24.20, z-score =  -2.47, R)
>consensus
___________G_UGGUUUUCAUAAACUAAACGAUCAGCUCACAGCCCUGGAGACUCAAUUUAAUAGCCUUAAACUUAUGAAUGAGUCUCCGAAGCGUAAAAAGGCCACU
............................................(((.(((((((((.((((((((((.....))))))))))))))))))).))).............. (-13.34 = -16.27 +   2.94)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 23,112,521 – 23,112,631
Length 110
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 52.14
Shannon entropy 0.76593
G+C content 0.44120
Mean single sequence MFE -28.23
Consensus MFE -12.68
Energy contribution -17.30
Covariance contribution 4.62
Combinations/Pair 1.60
Mean z-score -2.12
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.39
SVM RNA-class probability 0.998533
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23112521 110 - 24543557
AGCGGCUUCUUUGCGCUUCGGAGAUUCCUCUAUUAGCUUAAGGCCAUUAAACUGUGAAUUAAGCGCGGAAAGAAGAUCAUCUGCUCGACGAAAACUAUCUCUAGCUACGC
.(((.(((((((.(((...((((....))))....((((((..(((......)).)..))))))))).))))))).......(((.((.((......)))).)))..))) ( -31.60, z-score =  -1.12, R)
>droPer1.super_76 130794 89 + 268861
AGUGACCUUUUUACGCCUCGGAGACUCAUUCAGAAGUUGCAGACUGCCAUAUUGAGACUCCAUGGCUAAGAGCCGAUGGUAUUGCUUUU---------------------
.((((.....))))(((((((((.((((......((((...)))).......)))).))))..(((.....))))).))).........--------------------- ( -22.02, z-score =  -0.70, R)
>droWil1.scaffold_181148 2801111 101 + 5435427
ACUGGACCUUUUACGUUUCGGAGACUCAUUCAUAAGCGAUAAACUUCUGAACUGAGUCUCCACCGCAGUAAACUCCGCUUGGAGUUUAUUAAAACCUGCCC---------
...((..............(((((((((((((.(((.......))).)))).))))))))).....((((((((((....))))))))))....)).....--------- ( -32.80, z-score =  -4.97, R)
>droVir3.scaffold_12958 1203962 99 + 3547706
AUUGGACUUUUUAGGCCCAGGAGACUCAUUCAACAGUUUAAGGCUAUUAAAUUGGAUGUCCAGGGCUGUGAGUUGAUCGUUAAGUUUACGAAAACCAAC-----------
.((((((((....(((((.(((....((((((...((((((.....))))))))))))))).)))))..))))...((((.......))))...)))).----------- ( -26.50, z-score =  -1.70, R)
>consensus
AGUGGACUUUUUACGCCUCGGAGACUCAUUCAUAAGCUUAAGACUACUAAACUGAGACUCCAGCGCUGAAAGCUGAUCGUAUAGUUUACGAAAACCA_C___________
..............((((.((((((((((((((((((.....))))))))).))))))))).)))).((((((((......))))))))..................... (-12.68 = -17.30 +   4.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:46:07 2011