Locus 4816

Sequence ID dm3.chr2R
Location 15,738,449 – 15,738,543
Length 94
Max. P 0.992104
window6617 window6618

overview

Window 7

Location 15,738,449 – 15,738,540
Length 91
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 58.71
Shannon entropy 0.65066
G+C content 0.29071
Mean single sequence MFE -17.42
Consensus MFE -6.74
Energy contribution -9.55
Covariance contribution 2.81
Combinations/Pair 1.17
Mean z-score -2.40
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.52
SVM RNA-class probability 0.992104
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15738449 91 + 21146708
AUUAUUCGUAUAUAUGUUCUUGACACAUUUCUGGACAUGUUUAAUUUGUUUAAUUUUCUAAUAAGUUAUAUAUGUCAUGUGU---GACAGCUAG-------------
...................(((.(((((.....(((((((.(((((((((.........))))))))).)))))))..))))---).)))....------------- ( -18.70, z-score =  -1.97, R)
>droSim1.chr2R 14397269 94 + 19596830
AGUAUUCGUUUAUAUUUCCUUGACACAUUUACGGACAUGUUUAAUUUGUUAAAUUUUCUAAUAAGUUAGAUGUGUCAUUUUUCUCGACAGCUAG-------------
(((..(((((...........))).........((((((((((((((((((.......)))))))))))))))))).........))..)))..------------- ( -18.30, z-score =  -2.43, R)
>droSec1.super_1 13228484 82 + 14215200
AUUAUUCGUUUAUAUUUCCUUGA------------CAUGUUUAAUUUGUUAAAUUUUCUAAUAAGUUAGAUGUGUCAUUUUUCUCGACAGCUAG-------------
.......(((..........(((------------((((((((((((((((.......)))))))))))))))))))........)))......------------- ( -18.17, z-score =  -4.41, R)
>droVir3.scaffold_12875 16718275 104 - 20611582
-ACGUAUAUUAACAUUAUUAAGGCUCCAAAAACCUCUUGUUGCUCUUGCUAAGUUAACU--UAUCUUUUAAGACCCAUCUCUUUAGGAAGCCAUUUCCCACAUGCAA
-..((((.(((((.(((.((((((..(((.......)))..)).)))).))))))))..--..((((..((((......)))).)))).............)))).. ( -14.50, z-score =  -0.78, R)
>consensus
AUUAUUCGUUUAUAUUUCCUUGACACAUUUA_GGACAUGUUUAAUUUGUUAAAUUUUCUAAUAAGUUAGAUGUGUCAUUUUUCUCGACAGCUAG_____________
.................................((((((((((((((((((.......))))))))))))))))))............................... ( -6.74 =  -9.55 +   2.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,738,449 – 15,738,543
Length 94
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 60.53
Shannon entropy 0.63514
G+C content 0.29074
Mean single sequence MFE -17.04
Consensus MFE -6.74
Energy contribution -7.62
Covariance contribution 0.88
Combinations/Pair 1.44
Mean z-score -1.97
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.71
SVM RNA-class probability 0.962755
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15738449 94 + 21146708
AUUAU--UCGUAUAUAUGUUCUUGACACAUUUCUGGACAUGUUUAAUUUGUUUAAUUUUCUA-----AUAAGUUAUAUAUGUCAUGUGU---GACAGCUAGCUA
.....--..........(((.(((.(((((.....(((((((.(((((((((.........)-----)))))))).)))))))..))))---).)))..))).. ( -19.20, z-score =  -1.78, R)
>droSim1.chr2R 14397269 97 + 19596830
AGUAU--UCGUUUAUAUUUCCUUGACACAUUUACGGACAUGUUUAAUUUGUUAAAUUUUCUA-----AUAAGUUAGAUGUGUCAUUUUUCUCGACAGCUAGCUA
(((..--(((((...........))).........((((((((((((((((((.......))-----)))))))))))))))).........))..)))..... ( -18.30, z-score =  -2.02, R)
>droSec1.super_1 13228484 85 + 14215200
AUUAU--UCGUUUAUAUUUCCUUGAC------------AUGUUUAAUUUGUUAAAUUUUCUA-----AUAAGUUAGAUGUGUCAUUUUUCUCGACAGCUAGCUA
.....--..(((..........((((------------(((((((((((((((.......))-----)))))))))))))))))........)))......... ( -18.17, z-score =  -3.91, R)
>droVir3.scaffold_12875 16718281 103 - 20611582
AUUAACAUUAUUAAGGCUCCAAAAACCUCUUGUUGCUCUUGCUAAGUUAACUUAUCUUUUAAGACCCAUCUCUUUAGGAAGCCAUUUCCCACAUGCAAUAACU-
..............((((((........((((..((....))))))....((((.....)))).............)).))))....................- ( -12.50, z-score =  -0.16, R)
>consensus
AUUAU__UCGUUUAUAUUUCCUUGACACAUUU_UGGACAUGUUUAAUUUGUUAAAUUUUCUA_____AUAAGUUAGAUAUGUCAUUUUUCUCGACAGCUAGCUA
...................................((((((((((((((((................))))))))))))))))..................... ( -6.74 =  -7.62 +   0.88)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:36:33 2011