Locus 6327

Sequence ID dm3.chr3L
Location 5,613,581 – 5,613,690
Length 109
Max. P 0.884700
window8701 window8702

overview

Window 1

Location 5,613,581 – 5,613,690
Length 109
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 71.86
Shannon entropy 0.52692
G+C content 0.39032
Mean single sequence MFE -22.72
Consensus MFE -11.43
Energy contribution -10.97
Covariance contribution -0.46
Combinations/Pair 1.68
Mean z-score -1.65
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.884700
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5613581 109 + 24543557
UAACAAAUUACGCGUACACAGGAUGGAGGUAUCCAUCCUUCCUGUUGCUCAACAAAGCUGAAUAACAACCCUCUCGGAUUCCAUGAUUACCAAAAUAAAAUCUAAGACG-------
...........(((.(((.((((((((....))))))))...)))))).......................(((..((((..((..........))..))))..)))..------- ( -20.00, z-score =  -1.40, R)
>droSim1.chr3L 5131852 109 + 22553184
AAACAAAUUACGCUUACUCAGGAUGGAGGUAUCCAUCCUUCCUGUUCCUCGACAAAGCUGAAUAACAACCCUCUCGGAUUCCAUGAUUACCGGAAUAAAAUCUAAGACG-------
...........((((....((((((((....))))))))...((((....)))))))).............(((..((((((.........))).....)))..)))..------- ( -21.40, z-score =  -1.00, R)
>droSec1.super_2 5550080 109 + 7591821
AAACAAAUUACGCUUAUUCAGGAUGGAGGUAUCCAUCCUUCCUGUUGCUCAACAAAGCUGAAUAACAACCCUCUCGGAUUCCAUGAUUACCAGAAUAAAAUCUAAGACG-------
...........(.((((((((((((((....)))))))........(((......))))))))))).....(((..((((...((.....))......))))..)))..------- ( -21.80, z-score =  -1.72, R)
>droYak2.chr3L 6178098 109 + 24197627
UAACAAAUUACGCUUACUCAGGAUGGAGGUAUCCAUCCUUCCUGUUGCUCAACAAAGCCGAAUAGCAACCCUCUCGGAUUCCCUGAUUGCCAGAGUAAAAUCUAUGACC-------
.............((((((((((((((....))))))))....((((((...(......)...))))))....((((.....))))......))))))...........------- ( -25.20, z-score =  -1.64, R)
>droEre2.scaffold_4784 8301359 109 + 25762168
UAACAAAUUACGUUUGCUCAGGAUGGAGGUAUCCAUCCAUCCUGUUGCUCAACAAAGCUGGAUAAUAAUCCUCUUGGAUUCCCUGAUCACCAGAAUAAAAUCUAAGACC-------
...........(((.((.(((((((((((...)).)))))))))..))..)))......((((....))))(((((((((..(((.....))).....)))))))))..------- ( -31.10, z-score =  -3.40, R)
>droWil1.scaffold_180698 7581372 108 - 11422946
--------CAAACUGACAAUGAAUUGAGGAGUUUAAGCUUCCACAUUUUUUAAAAUAAUGUGUGGAAUUCUUAAGAAACAACAAAAGGAUUCACAUUUAAAGUAAAUCUACAUAUA
--------..........(((..(((..(..((((((.((((((((.((.......)).))))))))..))))))...)..)))..(((((.((.......)).))))).)))... ( -16.80, z-score =  -0.75, R)
>consensus
UAACAAAUUACGCUUACUCAGGAUGGAGGUAUCCAUCCUUCCUGUUGCUCAACAAAGCUGAAUAACAACCCUCUCGGAUUCCAUGAUUACCAGAAUAAAAUCUAAGACG_______
....................(((((((....)))))))...(((.((.(((......((((............))))......))).)).)))....................... (-11.43 = -10.97 +  -0.46)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,613,581 – 5,613,690
Length 109
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 71.86
Shannon entropy 0.52692
G+C content 0.39032
Mean single sequence MFE -28.79
Consensus MFE -15.64
Energy contribution -14.45
Covariance contribution -1.19
Combinations/Pair 1.60
Mean z-score -1.48
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.883736
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5613581 109 - 24543557
-------CGUCUUAGAUUUUAUUUUGGUAAUCAUGGAAUCCGAGAGGGUUGUUAUUCAGCUUUGUUGAGCAACAGGAAGGAUGGAUACCUCCAUCCUGUGUACGCGUAAUUUGUUA
-------(.(((..((((((((..(....)..))))))))..))).)(((((...(((((...))))))))))....((((((((....))))))))................... ( -29.10, z-score =  -1.43, R)
>droSim1.chr3L 5131852 109 - 22553184
-------CGUCUUAGAUUUUAUUCCGGUAAUCAUGGAAUCCGAGAGGGUUGUUAUUCAGCUUUGUCGAGGAACAGGAAGGAUGGAUACCUCCAUCCUGAGUAAGCGUAAUUUGUUU
-------((.((((......((((((.......)))))).(((.(((((((.....))))))).))).....(((((.(((.((...))))).)))))..)))))).......... ( -29.20, z-score =  -0.91, R)
>droSec1.super_2 5550080 109 - 7591821
-------CGUCUUAGAUUUUAUUCUGGUAAUCAUGGAAUCCGAGAGGGUUGUUAUUCAGCUUUGUUGAGCAACAGGAAGGAUGGAUACCUCCAUCCUGAAUAAGCGUAAUUUGUUU
-------((.((((.......(((((..........(((((....)))))........((((....))))..)))))((((((((....))))))))...)))))).......... ( -29.80, z-score =  -1.63, R)
>droYak2.chr3L 6178098 109 - 24197627
-------GGUCAUAGAUUUUACUCUGGCAAUCAGGGAAUCCGAGAGGGUUGCUAUUCGGCUUUGUUGAGCAACAGGAAGGAUGGAUACCUCCAUCCUGAGUAAGCGUAAUUUGUUA
-------....(((((((...(((((.....)))))(((((....)))))(((((((.((((....)))).......((((((((....)))))))))))).)))..))))))).. ( -34.10, z-score =  -1.69, R)
>droEre2.scaffold_4784 8301359 109 - 25762168
-------GGUCUUAGAUUUUAUUCUGGUGAUCAGGGAAUCCAAGAGGAUUAUUAUCCAGCUUUGUUGAGCAACAGGAUGGAUGGAUACCUCCAUCCUGAGCAAACGUAAUUUGUUA
-------(((((((((......))))).)))).((((((((....)))))....))).((((....))))..(((((((((.((...)))))))))))((((((.....)))))). ( -35.00, z-score =  -2.62, R)
>droWil1.scaffold_180698 7581372 108 + 11422946
UAUAUGUAGAUUUACUUUAAAUGUGAAUCCUUUUGUUGUUUCUUAAGAAUUCCACACAUUAUUUUAAAAAAUGUGGAAGCUUAAACUCCUCAAUUCAUUGUCAGUUUG--------
........(((((((.......))))))).....((((....(((((..(((((((...............))))))).)))))......))))..............-------- ( -15.56, z-score =  -0.59, R)
>consensus
_______CGUCUUAGAUUUUAUUCUGGUAAUCAUGGAAUCCGAGAGGGUUGUUAUUCAGCUUUGUUGAGCAACAGGAAGGAUGGAUACCUCCAUCCUGAGUAAGCGUAAUUUGUUA
..........................((........(((((....)))))........((((....))))..(((((.(((.(....).))).))))).....))........... (-15.64 = -14.45 +  -1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:05:34 2011