Locus 1717

Sequence ID dm3.chr2L
Location 13,194,996 – 13,195,094
Length 98
Max. P 0.646162
window2344 window2345

overview

Window 4

Location 13,194,996 – 13,195,094
Length 98
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 67.80
Shannon entropy 0.54725
G+C content 0.31563
Mean single sequence MFE -19.23
Consensus MFE -9.25
Energy contribution -9.89
Covariance contribution 0.64
Combinations/Pair 1.30
Mean z-score -1.12
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.01
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr2L 13194996 98 + 23011544
GCUAUCAGUAAUUCCAUCU------AUAGGUCUGGAAAGGUUUCAAUUGCUUAUUUGCAACAAUUUCUUUUGU----CUUUAAC---GUACUGAUAGUCUAGUUGGCCAUU---
((((((((((.(((((...------.......)))))..(((.....(((......)))((((......))))----....)))---.)))))))))).............--- ( -19.10, z-score =  -1.13, R)
>droSim1.chr2L 12989412 98 + 22036055
GCUAUCAGUAACUCCAUCU------AUAGGUCUUGAAAGGUCUCAAUUGUUUAUUUGCAACAAUCUCUUUUAU----CUUUAAU---GUACUGAUAGUCAAGUUGGCCAUU---
((((((((((....(((..------..(((...(((((((......((((......)))).....))))))).----)))..))---))))))))))).............--- ( -16.90, z-score =  -0.91, R)
>droSec1.super_16 1349549 99 + 1878335
GCUAUCAGUAACUCCAUCU------AUAGGUCUUGAAAGGUCUCAAUUGGUUAUAUGCAACAAUCUGUUUUAU----CUUUAACUG-AUACUG-UAGUCAAGUUGAGAGUC---
(((.....(((((....((------((((....(((......)))((..((((.(((.(((.....))).)))----...))))..-)).)))-)))...)))))..))).--- ( -15.80, z-score =   0.76, R)
>droYak2.chr2L 9618604 114 + 22324452
GCUAUCAGUAACUCUAUCACAAGAAAUAGCUCUUGAUAGAUAUCAAUUGAUUUCACCAAUCUAUUUUAUCUAUGGGCUAAUAUUAAUGUAUUGAUAGUUAAGAAUGUUUUAAAA
((((((((((..(((......)))..((((((...(((((((..(((.((((.....)))).))).))))))))))))).........))))))))))................ ( -23.50, z-score =  -2.12, R)
>droEre2.scaffold_4929 14395788 108 - 26641161
GCUAUCAGUAAUUCUAUCACAACAAAUAGCUCUUGAUAGGCAUCAAUUGGUU--GACAAUCUUUCUUUGUUAU----CAAUAGCUUUAUAUUGAUAGUCAAUUUAGUUUUAAAU
((((((((((..(((((((..............))))))).....((((((.--(((((.......)))))))----)))).......))))))))))................ ( -20.84, z-score =  -2.20, R)
>consensus
GCUAUCAGUAACUCCAUCU______AUAGGUCUUGAAAGGUAUCAAUUGGUUAUAUGCAACAAUCUCUUUUAU____CUUUAAC___GUACUGAUAGUCAAGUUGGCCAUA___
((((((((((...............(((((..(((((....))))).(((......))).........)))))...............))))))))))................ ( -9.25 =  -9.89 +   0.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,194,996 – 13,195,094
Length 98
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 67.80
Shannon entropy 0.54725
G+C content 0.31563
Mean single sequence MFE -17.01
Consensus MFE -9.98
Energy contribution -9.98
Covariance contribution 0.00
Combinations/Pair 1.17
Mean z-score -0.82
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.646162
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13194996 98 - 23011544
---AAUGGCCAACUAGACUAUCAGUAC---GUUAAAG----ACAAAAGAAAUUGUUGCAAAUAAGCAAUUGAAACCUUUCCAGACCUAU------AGAUGGAAUUACUGAUAGC
---..............(((((((((.---.......----........(((((((.......))))))).......(((((.......------...))))).))))))))). ( -18.80, z-score =  -2.04, R)
>droSim1.chr2L 12989412 98 - 22036055
---AAUGGCCAACUUGACUAUCAGUAC---AUUAAAG----AUAAAAGAGAUUGUUGCAAAUAAACAAUUGAGACCUUUCAAGACCUAU------AGAUGGAGUUACUGAUAGC
---..............((((((((((---......(----(.......(((((((.......)))))))........))....((...------....)).).))))))))). ( -17.46, z-score =  -1.31, R)
>droSec1.super_16 1349549 99 - 1878335
---GACUCUCAACUUGACUA-CAGUAU-CAGUUAAAG----AUAAAACAGAUUGUUGCAUAUAACCAAUUGAGACCUUUCAAGACCUAU------AGAUGGAGUUACUGAUAGC
---(((((.((.(((((...-..((.(-(((((....----(((.(((.....)))...)))....)))))).))...)))))..(...------.).)))))))......... ( -12.40, z-score =   1.11, R)
>droYak2.chr2L 9618604 114 - 22324452
UUUUAAAACAUUCUUAACUAUCAAUACAUUAAUAUUAGCCCAUAGAUAAAAUAGAUUGGUGAAAUCAAUUGAUAUCUAUCAAGAGCUAUUUCUUGUGAUAGAGUUACUGAUAGC
.................((((((..((........(((((.(((((((.(((.((((.....)))).)))..)))))))...).))))..(((......)))))...)))))). ( -17.90, z-score =  -0.33, R)
>droEre2.scaffold_4929 14395788 108 + 26641161
AUUUAAAACUAAAUUGACUAUCAAUAUAAAGCUAUUG----AUAACAAAGAAAGAUUGUC--AACCAAUUGAUGCCUAUCAAGAGCUAUUUGUUGUGAUAGAAUUACUGAUAGC
.................((((((.((.....(((((.----((((((((........(((--((....)))))((((....)).))..)))))))))))))...)).)))))). ( -18.50, z-score =  -1.55, R)
>consensus
___AAAAACCAACUUGACUAUCAGUAC___GUUAAAG____AUAAAAAAGAUUGUUGCAAAUAACCAAUUGAGACCUUUCAAGACCUAU______AGAUGGAGUUACUGAUAGC
.................(((((((((..........................................(((((....)))))...((((........))))...))))))))). ( -9.98 =  -9.98 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:37:15 2011