Locus 11687

Sequence ID dm3.chr3R
Location 23,107,971 – 23,108,074
Length 103
Max. P 0.821891
window16056 window16057

overview

Window 6

Location 23,107,971 – 23,108,074
Length 103
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 76.63
Shannon entropy 0.43579
G+C content 0.35866
Mean single sequence MFE -22.07
Consensus MFE -11.10
Energy contribution -11.72
Covariance contribution 0.62
Combinations/Pair 1.39
Mean z-score -1.98
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.821891
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23107971 103 + 27905053
AUAAUGAU--UUUUCAAGUUUUGUUUUCCGCUCGUC---UGCCAUUCUCCGUGAAGUGAAGAAGACUCUAACGGAAAGUUUCAGACUAUCUAUAAUCUUUAAAUUCAA------
....(((.--...))).................(((---((..(((.(((((..(((.......)))...))))).)))..)))))......................------ ( -16.10, z-score =   0.19, R)
>droAna3.scaffold_13340 4114613 99 - 23697760
AUAAUAAUGAUUUUCAAGUUUUUUUUUCAUUUCAUUCAUUGCCAUUCGUCAUGA---------UUCGUAAGCUGCGACUUUCCGUAUUCAUUUUUUUACGAGAAUCGU------
......(((((((((.(((((.....((((..(..............)..))))---------.....)))))(((......)))..............)))))))))------ ( -13.34, z-score =  -0.52, R)
>droEre2.scaffold_4820 5544013 106 - 10470090
AUAAUGAU--UUUUCAAGUUCUGUUUUCCGCUCGUCCACUGCCAUUCACCGUGAAAUGAAGAAGACACGAGCGGAAAGUUUCAGACUAUCUCUAAUCUACAGAUCCAA------
.....(((--(.....(((.(((((((((((((((...((....((((........))))..))..))))))))))))...))))))......))))...........------ ( -25.00, z-score =  -1.85, R)
>droYak2.chr3R 5446462 112 - 28832112
AUAAUGAU--UUUUCAAGUUCUGUUUUCCGCUCGUCCACUGCCAUUUACCGUAAAAUGAAAAAUACACGAGCGGAAACUUUCAGACUAUCUCUAAUCUUUAUCUUUAUAUCCAA
((((.(((--(.....(((.(((.(((((((((((.......(((((......)))))........)))))))))))....))))))......)))).))))............ ( -24.56, z-score =  -4.58, R)
>droSec1.super_13 1862048 106 + 2104621
AUAAUGAU--UUUUCAAGUUCUGUUUUCCGCUCGUCCACUGCCAUUCACCGUGAAGUGAAGAAGACACGAGCGGAAAGUUUCAGACUAUCUUUAAUCUUCAAAUUCAA------
.....(((--(.....(((.(((((((((((((((...((....(((((......)))))..))..))))))))))))...))))))......))))...........------ ( -28.30, z-score =  -3.05, R)
>droSim1.chr3R_random 36634 106 + 1307089
AUAAUGAU--UUUUCAAGUUCUGUUUUCCGCUCGUCCACUGCCAUUCACCGUGAAGUGAAGAAGACUCGAGCGGAAAGUUUCUGACUAUCUUUAAUCUUUAAAUUCAA------
.(((.(((--(.....((((...(((((((((((....((....(((((......)))))..))...))))))))))).....))))......)))).))).......------ ( -25.10, z-score =  -2.06, R)
>consensus
AUAAUGAU__UUUUCAAGUUCUGUUUUCCGCUCGUCCACUGCCAUUCACCGUGAAGUGAAGAAGACACGAGCGGAAAGUUUCAGACUAUCUUUAAUCUUUAAAUUCAA______
...................((((.(((((((((((.........(((.....)))...........)))))))))))....))))............................. (-11.10 = -11.72 +   0.62)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 7

Location 23,107,971 – 23,108,074
Length 103
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 76.63
Shannon entropy 0.43579
G+C content 0.35866
Mean single sequence MFE -24.53
Consensus MFE -13.07
Energy contribution -13.88
Covariance contribution 0.81
Combinations/Pair 1.43
Mean z-score -1.59
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.619974
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23107971 103 - 27905053
------UUGAAUUUAAAGAUUAUAGAUAGUCUGAAACUUUCCGUUAGAGUCUUCUUCACUUCACGGAGAAUGGCA---GACGAGCGGAAAACAAAACUUGAAAA--AUCAUUAU
------.(((.(((..((((((....)))))).....((((((((...((((.((...(((....)))...)).)---))).))))))))...........)))--.))).... ( -21.20, z-score =  -1.13, R)
>droAna3.scaffold_13340 4114613 99 + 23697760
------ACGAUUCUCGUAAAAAAAUGAAUACGGAAAGUCGCAGCUUACGAA---------UCAUGACGAAUGGCAAUGAAUGAAAUGAAAAAAAAACUUGAAAAUCAUUAUUAU
------.(((((.(((((..........)))))..)))))..(((..((..---------......))...))).........(((((................)))))..... (  -8.39, z-score =   1.56, R)
>droEre2.scaffold_4820 5544013 106 + 10470090
------UUGGAUCUGUAGAUUAGAGAUAGUCUGAAACUUUCCGCUCGUGUCUUCUUCAUUUCACGGUGAAUGGCAGUGGACGAGCGGAAAACAGAACUUGAAAA--AUCAUUAU
------..((.(((((((((((....)))))).....(((((((((((.((((((((((......))))).)).)).).)))))))))))))))).))......--........ ( -31.50, z-score =  -2.26, R)
>droYak2.chr3R 5446462 112 + 28832112
UUGGAUAUAAAGAUAAAGAUUAGAGAUAGUCUGAAAGUUUCCGCUCGUGUAUUUUUCAUUUUACGGUAAAUGGCAGUGGACGAGCGGAAAACAGAACUUGAAAA--AUCAUUAU
............((((.((((.(((....((((....(((((((((((.((((..((((((......)))))).)))).))))))))))).)))).)))....)--))).)))) ( -31.10, z-score =  -3.90, R)
>droSec1.super_13 1862048 106 - 2104621
------UUGAAUUUGAAGAUUAAAGAUAGUCUGAAACUUUCCGCUCGUGUCUUCUUCACUUCACGGUGAAUGGCAGUGGACGAGCGGAAAACAGAACUUGAAAA--AUCAUUAU
------...........((((......((((((....(((((((((((.(((((((((((....)))))).)).)).).))))))))))).))).))).....)--)))..... ( -29.70, z-score =  -2.40, R)
>droSim1.chr3R_random 36634 106 - 1307089
------UUGAAUUUAAAGAUUAAAGAUAGUCAGAAACUUUCCGCUCGAGUCUUCUUCACUUCACGGUGAAUGGCAGUGGACGAGCGGAAAACAGAACUUGAAAA--AUCAUUAU
------.(((.(((...(((((....)))))......((((((((((...((((((((((....)))))).)).))....))))))))))...........)))--.))).... ( -25.30, z-score =  -1.40, R)
>consensus
______UUGAAUUUAAAGAUUAAAGAUAGUCUGAAACUUUCCGCUCGUGUCUUCUUCACUUCACGGUGAAUGGCAGUGGACGAGCGGAAAACAGAACUUGAAAA__AUCAUUAU
................((((((....)))))).....((((((((((............(((((.((.....)).)))))))))))))))........................ (-13.07 = -13.88 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:47:38 2011