Locus 5323

Sequence ID dm3.chr2R
Location 19,469,287 – 19,469,377
Length 90
Max. P 0.959354
window7296 window7297

overview

Window 6

Location 19,469,287 – 19,469,377
Length 90
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 75.18
Shannon entropy 0.38049
G+C content 0.46169
Mean single sequence MFE -28.58
Consensus MFE -12.28
Energy contribution -14.24
Covariance contribution 1.96
Combinations/Pair 1.09
Mean z-score -3.03
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959354
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19469287 90 + 21146708
UGACUUGACUGACACUCCUUAGUCUUAGUCAUUAGCCAACUAACUGGCA------------AAUGGCUUGGUAUCUUCGCCCGUCAUUUGUGUGGGCUAGAU----
(((((.((((((......))))))..)))))((((((.....((..(((------------((((((..(((......))).))))))))))).))))))..---- ( -30.50, z-score =  -3.23, R)
>droSim1.chr2R 18040539 77 + 19596830
UGACUUGACUGACACUCCUUAGUCUUAGUCAUUAGCCAACUAACUGGCA------------AAUGGCGUGGUAUCUUCGCCCGCUAGAU-----------------
(((((.((((((......))))))..)))))...((((......)))).------------..(((((.(((......))))))))...----------------- ( -26.20, z-score =  -3.78, R)
>droSec1.super_9 2750511 77 + 3197100
UGACUUGACUGACACUCCUUAGUCUUAGUCAUUAGCCAACUAACUGGCA------------AAUGGCGUGGUAUCUUCGCCCGCUAGAU-----------------
(((((.((((((......))))))..)))))...((((......)))).------------..(((((.(((......))))))))...----------------- ( -26.20, z-score =  -3.78, R)
>droYak2.chr2R 19443681 106 + 21139217
UGACUUGACUGACACUCCUUAGUCUUAGUCAUUAGCCAACUGGCAAACGGGCAAACUGGCAAAUGUCUUGGUAUCUUCGCCCGCCAUUUGUGUGGGCUAGAUAAAU
.(((.(((((((.(((....))).)))))))...((((....((......))....))))....)))....(((((..(((((((....).)))))).)))))... ( -33.50, z-score =  -2.37, R)
>droEre2.scaffold_4845 20829327 90 + 22589142
UGACUUGAGUGACACUCCUUAGUCUUAGUCAUUAGCCAACUGACAAACG----------------UCUUGGUAUCUUCGCCCGCCAUUUGUGUGGGCUAGAUAGAU
.((((.(((.....)))...))))...(((....(((((..(((....)----------------)))))))((((..(((((((....).)))))).)))).))) ( -26.50, z-score =  -2.02, R)
>consensus
UGACUUGACUGACACUCCUUAGUCUUAGUCAUUAGCCAACUAACUGGCA____________AAUGGCUUGGUAUCUUCGCCCGCCAUUUGUGUGGGCUAGAU____
(((((.((((((......))))))..)))))...((((......))))...............((((..(((......))).)))).................... (-12.28 = -14.24 +   1.96)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 19,469,287 – 19,469,377
Length 90
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 75.18
Shannon entropy 0.38049
G+C content 0.46169
Mean single sequence MFE -24.30
Consensus MFE -16.69
Energy contribution -15.37
Covariance contribution -1.32
Combinations/Pair 1.32
Mean z-score -1.39
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.709612
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19469287 90 - 21146708
----AUCUAGCCCACACAAAUGACGGGCGAAGAUACCAAGCCAUU------------UGCCAGUUAGUUGGCUAAUGACUAAGACUAAGGAGUGUCAGUCAAGUCA
----...(((((.((.....((((.((((((............))------------)))).)))))).))))).(((((.(.(((....))).).)))))..... ( -23.30, z-score =  -1.28, R)
>droSim1.chr2R 18040539 77 - 19596830
-----------------AUCUAGCGGGCGAAGAUACCACGCCAUU------------UGCCAGUUAGUUGGCUAAUGACUAAGACUAAGGAGUGUCAGUCAAGUCA
-----------------..(((((.((((((............))------------)))).))))).(((((..(((((.(.(((....))).).)))))))))) ( -22.40, z-score =  -1.62, R)
>droSec1.super_9 2750511 77 - 3197100
-----------------AUCUAGCGGGCGAAGAUACCACGCCAUU------------UGCCAGUUAGUUGGCUAAUGACUAAGACUAAGGAGUGUCAGUCAAGUCA
-----------------..(((((.((((((............))------------)))).))))).(((((..(((((.(.(((....))).).)))))))))) ( -22.40, z-score =  -1.62, R)
>droYak2.chr2R 19443681 106 - 21139217
AUUUAUCUAGCCCACACAAAUGGCGGGCGAAGAUACCAAGACAUUUGCCAGUUUGCCCGUUUGCCAGUUGGCUAAUGACUAAGACUAAGGAGUGUCAGUCAAGUCA
...(((((.((((.(.(....)).))))..)))))....(((....((((..(.((......)).)..))))...(((((.(.(((....))).).))))).))). ( -30.40, z-score =  -1.56, R)
>droEre2.scaffold_4845 20829327 90 - 22589142
AUCUAUCUAGCCCACACAAAUGGCGGGCGAAGAUACCAAGA----------------CGUUUGUCAGUUGGCUAAUGACUAAGACUAAGGAGUGUCACUCAAGUCA
...(((((.((((.(.(....)).))))..)))))...((.----------------((((.(((....))).)))).))..((((...(((.....))).)))). ( -23.00, z-score =  -0.85, R)
>consensus
____AUCUAGCCCACACAAAUGGCGGGCGAAGAUACCAAGCCAUU____________UGCCAGUUAGUUGGCUAAUGACUAAGACUAAGGAGUGUCAGUCAAGUCA
....................((((.((((............................)))).))))..(((((..(((((.(.(((....))).).)))))))))) (-16.69 = -15.37 +  -1.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:46:01 2011