Locus 5372

Sequence ID dm3.chr2R
Location 19,844,964 – 19,845,060
Length 96
Max. P 0.682607
window7368 window7369

overview

Window 8

Location 19,844,964 – 19,845,060
Length 96
Sequences 4
Columns 122
Reading direction forward
Mean pairwise identity 71.35
Shannon entropy 0.44431
G+C content 0.40600
Mean single sequence MFE -26.76
Consensus MFE -16.21
Energy contribution -17.65
Covariance contribution 1.44
Combinations/Pair 1.12
Mean z-score -1.31
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.682607
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19844964 96 + 21146708
UGUUAGGGGAACUCCCGUUGUCCAGGGUUGUCAUGCCGGAUUAGUUUCACAAAUUAACUUCCGCAACCGGAAGUCAUGAAA------AU---GGAAAAUAUAACU-----------------
.((((.(((....)))(((.((((......(((((..(((.....)))........(((((((....))))))))))))..------.)---))).))).)))).----------------- ( -24.40, z-score =  -0.79, R)
>droSec1.super_9 3128849 102 + 3197100
UGUUAGGGGAACUCCCGUUGUCCAGGGCUGUCAUACCCGAUUAGUUUCAAAAAUUAACUUCCGCAACCGGAAGUCAUGAAGUGAGAUAG---GGAAAAUAUAACU-----------------
.((((.(((....)))(((.(((.(((........))).....((((((.......(((((((....))))))).......))))))..---))).))).)))).----------------- ( -27.84, z-score =  -1.36, R)
>droYak2.chr2R 19822311 119 + 21139217
UGUUAGCGGAACUCCCGUUGCCUAGGGUUGUCACUCCUGCUUAGUUUCGUAUAUUAAUUUCCGUUACCGGAAGUUAUGAAAUUUGAAAC---AAAACCUCUUACUACAACGAAAAAUAUUCU
.(((((((((((.(((........)))..))...))).)))..((((((.....(((((((((....))))))))).......))))))---...............)))............ ( -24.90, z-score =  -1.33, R)
>droEre2.scaffold_4845 21217717 111 + 22589142
UGUUAGGGGAACUCCCGUUGUCUAGGGUUGUCAUUCCUGAUUAGUUUUACAAAUCAACUUCCGUUACCGGAAGUUAUUAAAUCUGAUACUCUGGAAAUGGAAAAUACAGCU-----------
......(((....)))((((((((((((.((((.....((((.(.....).))))((((((((....))))))))........))))))))))))..(....)...)))).----------- ( -29.90, z-score =  -1.75, R)
>consensus
UGUUAGGGGAACUCCCGUUGUCCAGGGUUGUCAUUCCUGAUUAGUUUCACAAAUUAACUUCCGCAACCGGAAGUCAUGAAAU_UGAUAC___GGAAAAUAUAACU_________________
.((((((.((...(((........)))...))...))))))...(((((.....(((((((((....))))))))))))))......................................... (-16.21 = -17.65 +   1.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,844,964 – 19,845,060
Length 96
Sequences 4
Columns 122
Reading direction reverse
Mean pairwise identity 71.35
Shannon entropy 0.44431
G+C content 0.40600
Mean single sequence MFE -25.28
Consensus MFE -17.05
Energy contribution -17.18
Covariance contribution 0.13
Combinations/Pair 1.18
Mean z-score -1.04
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.622688
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19844964 96 - 21146708
-----------------AGUUAUAUUUUCC---AU------UUUCAUGACUUCCGGUUGCGGAAGUUAAUUUGUGAAACUAAUCCGGCAUGACAACCCUGGACAACGGGAGUUCCCCUAACA
-----------------.((((.....(((---(.------((((((((((((((....)))))))).....)))))).......((........)).))))....(((....))).)))). ( -22.90, z-score =  -0.72, R)
>droSec1.super_9 3128849 102 - 3197100
-----------------AGUUAUAUUUUCC---CUAUCUCACUUCAUGACUUCCGGUUGCGGAAGUUAAUUUUUGAAACUAAUCGGGUAUGACAGCCCUGGACAACGGGAGUUCCCCUAACA
-----------------.((((....((((---(....(((.....(((((((((....))))))))).....)))........((((......))))........)))))......)))). ( -26.70, z-score =  -1.28, R)
>droYak2.chr2R 19822311 119 - 21139217
AGAAUAUUUUUCGUUGUAGUAAGAGGUUUU---GUUUCAAAUUUCAUAACUUCCGGUAACGGAAAUUAAUAUACGAAACUAAGCAGGAGUGACAACCCUAGGCAACGGGAGUUCCGCUAACA
.((((...(..((((((........((((.---(((((........(((.(((((....))))).)))......))))).))))(((.((....)))))..))))))..)))))........ ( -27.24, z-score =  -1.15, R)
>droEre2.scaffold_4845 21217717 111 - 22589142
-----------AGCUGUAUUUUCCAUUUCCAGAGUAUCAGAUUUAAUAACUUCCGGUAACGGAAGUUGAUUUGUAAAACUAAUCAGGAAUGACAACCCUAGACAACGGGAGUUCCCCUAACA
-----------((((........((((((...(((..((((((....((((((((....))))))))))))))....))).....))))))....(((........)))))))......... ( -24.30, z-score =  -1.01, R)
>consensus
_________________AGUUAUAUUUUCC___GUAUCA_AUUUCAUAACUUCCGGUAACGGAAGUUAAUUUGUGAAACUAAUCAGGAAUGACAACCCUAGACAACGGGAGUUCCCCUAACA
..............................................(((((((((....))))))))).................(((((.....(((........))).)))))....... (-17.05 = -17.18 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:47:02 2011