Locus 10299

Sequence ID dm3.chr3R
Location 12,838,834 – 12,838,927
Length 93
Max. P 0.833294
window14162 window14163

overview

Window 2

Location 12,838,834 – 12,838,927
Length 93
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 80.47
Shannon entropy 0.37061
G+C content 0.46040
Mean single sequence MFE -27.67
Consensus MFE -14.97
Energy contribution -16.80
Covariance contribution 1.83
Combinations/Pair 1.08
Mean z-score -2.17
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.833294
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12838834 93 + 27905053
UUUGUGAAGUCACAUGUUUCAAGGCUCCAACCGGUCUCUUGUUAGCCUGGUUAUUUGGCUAAACAUAUGUAGCUUCACGUGUACUUACUGUCU--
...((((((..((((((..(((((..((....))..)))))((((((.........))))))..))))))..))))))(((....))).....-- ( -28.50, z-score =  -3.37, R)
>droSim1.chr3R 18882974 95 - 27517382
UUUGUGAAGUCACAUGUUUCAAGGCUCCAACCGGUCUCUUGUUAGCCUGGUUUUUUGGCUAAACAUAUGUAGCUUCACGUGUACUUACCGUCUCU
...((((((..((((((..(((((..((....))..)))))((((((.........))))))..))))))..))))))................. ( -28.30, z-score =  -3.40, R)
>droSec1.super_12 806006 95 - 2123299
UUUGUGAAGUCACAUGUUUCAAGGCUCCAACCGGUCUCUUGUUAGCCUGGUUUUUUGGCUAAACAUAUGUAGCUUCACGUGUACUUACCGUCUCU
...((((((..((((((..(((((..((....))..)))))((((((.........))))))..))))))..))))))................. ( -28.30, z-score =  -3.40, R)
>droYak2.chr3R 17286926 93 - 28832112
UCUGUGAAGUCACAUGUUUCAAGGCUCCAACCGGUCUCUUGUUAGCCUGGUUACGUGGCCGAACAUGUGUAGGUUCACGUGUACUUGCUGGCC--
...(((((.((((((((((...(((..(((((((.((......)).))))))..)..))))))))))))..).)))))...............-- ( -27.90, z-score =  -0.65, R)
>droEre2.scaffold_4770 8954688 93 - 17746568
UCUGUGAAGUCACAUGCUUCAAGGCUCCAACCGGUCUCUUGUUAGCCUGGUUACUUGGCUAAACAUGUGUAGGUUCACGUGUACUAGCUGGCC--
....((((((.....)))))).((((..((((((.((......)).))))))....(((((.(((((((......)))))))..)))))))))-- ( -28.90, z-score =  -1.34, R)
>droAna3.scaffold_13340 16633671 81 - 23697760
UCUGUGAAGUCACAUGUUUCAAGGCUCCAACCGGUCUCUGGACA-CAGAGACAUGUG-UUACCUUUACGUGGAGAGACUCUUA------------
...((((((.((((((((((..((......)).(((....))).-..))))))))))-....))))))..((((...))))..------------ ( -24.10, z-score =  -0.88, R)
>consensus
UCUGUGAAGUCACAUGUUUCAAGGCUCCAACCGGUCUCUUGUUAGCCUGGUUAUUUGGCUAAACAUAUGUAGCUUCACGUGUACUUACUGUCU__
...(((((.(.((((((..(((((..((....))..)))))((((((.........))))))..)))))).).)))))................. (-14.97 = -16.80 +   1.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,838,834 – 12,838,927
Length 93
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 80.47
Shannon entropy 0.37061
G+C content 0.46040
Mean single sequence MFE -23.99
Consensus MFE -15.32
Energy contribution -16.72
Covariance contribution 1.39
Combinations/Pair 1.17
Mean z-score -1.39
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.510055
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12838834 93 - 27905053
--AGACAGUAAGUACACGUGAAGCUACAUAUGUUUAGCCAAAUAACCAGGCUAACAAGAGACCGGUUGGAGCCUUGAAACAUGUGACUUCACAAA
--...............((((((...(((((((((.((....(((((.((((......)).)))))))..))....))))))))).))))))... ( -24.80, z-score =  -2.61, R)
>droSim1.chr3R 18882974 95 + 27517382
AGAGACGGUAAGUACACGUGAAGCUACAUAUGUUUAGCCAAAAAACCAGGCUAACAAGAGACCGGUUGGAGCCUUGAAACAUGUGACUUCACAAA
.................((((((...(((((((((((((.........))))..((((...((....))...))))))))))))).))))))... ( -24.50, z-score =  -2.05, R)
>droSec1.super_12 806006 95 + 2123299
AGAGACGGUAAGUACACGUGAAGCUACAUAUGUUUAGCCAAAAAACCAGGCUAACAAGAGACCGGUUGGAGCCUUGAAACAUGUGACUUCACAAA
.................((((((...(((((((((((((.........))))..((((...((....))...))))))))))))).))))))... ( -24.50, z-score =  -2.05, R)
>droYak2.chr3R 17286926 93 + 28832112
--GGCCAGCAAGUACACGUGAACCUACACAUGUUCGGCCACGUAACCAGGCUAACAAGAGACCGGUUGGAGCCUUGAAACAUGUGACUUCACAGA
--...............(((((....((((((((.(((..((..(((.((((......)).)))))))..)))....))))))))..)))))... ( -23.90, z-score =  -0.37, R)
>droEre2.scaffold_4770 8954688 93 + 17746568
--GGCCAGCUAGUACACGUGAACCUACACAUGUUUAGCCAAGUAACCAGGCUAACAAGAGACCGGUUGGAGCCUUGAAGCAUGUGACUUCACAGA
--((((.(((((.(((.(((......))).))))))))....(((((.((((......)).)))))))).))).((((((....).))))).... ( -23.80, z-score =  -0.54, R)
>droAna3.scaffold_13340 16633671 81 + 23697760
------------UAAGAGUCUCUCCACGUAAAGGUAA-CACAUGUCUCUG-UGUCCAGAGACCGGUUGGAGCCUUGAAACAUGUGACUUCACAGA
------------...(((((.(........(((((..-(((..(((((((-....)))))))..).))..))))).......).)))))...... ( -22.46, z-score =  -0.74, R)
>consensus
__AGACAGUAAGUACACGUGAAGCUACAUAUGUUUAGCCAAAUAACCAGGCUAACAAGAGACCGGUUGGAGCCUUGAAACAUGUGACUUCACAAA
.................(((((....(((((((((((((.........))))..((((...((....))...)))))))))))))..)))))... (-15.32 = -16.72 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:21:17 2011