Locus 1062

Sequence ID dm3.chr2L
Location 7,957,956 – 7,958,065
Length 109
Max. P 0.984845
window1450 window1451

overview

Window 0

Location 7,957,956 – 7,958,065
Length 109
Sequences 4
Columns 121
Reading direction forward
Mean pairwise identity 66.67
Shannon entropy 0.51933
G+C content 0.28077
Mean single sequence MFE -23.09
Consensus MFE -11.24
Energy contribution -16.18
Covariance contribution 4.94
Combinations/Pair 1.17
Mean z-score -2.33
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.18
SVM RNA-class probability 0.984845
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7957956 109 + 23011544
------------CGUACAUCUGACAGCUAUCAAAAAUUUGAAAUGUGUUCAUACAUUAUUUGGAAAUUUUGUUUAGCUGCAAGCUCAUUAUGAUAAAUAGAUACCAUUUAUAAUCGUUUGU
------------...........((((((.(((((.(((.((((((((....))).))))).))).)))))..))))))(((((..(((((((..............))))))).))))). ( -21.74, z-score =  -1.44, R)
>droEre2.scaffold_4929 16880385 114 + 26641161
UUCGUAUAUCUUAGUA-AUCCGGCAGCUAUCGAAAAUUUGAAAUUUGUGU-----UCAUUUUGAAUUUUUGUU-AGCUGUCAGAUCAAUAUGAUAAAUAUAUCUGAACAUUAAUCGUUUGU
......((((.((...-(((.((((((((.((((((((..((((......-----..))))..)))))))).)-))))))).)))...)).)))).........((((.......)))).. ( -28.50, z-score =  -3.62, R)
>droYak2.chr2L 17389301 119 - 22324452
UUCAUACAACUUAGUA-AUCUGGCAGCUAUUAAAAAUUGAAAAUGUGUUCAUACAUUAUAUUGAAUUUUUGUU-AGCUGUCAAAUCGUAAUGAUAAAAAUAACUGAAUAUUAAUCGUUUGC
..((.((...((((((-.(((((((((((.((((((((.((((((((....))))))...)).)))))))).)-)))))))).(((.....)))..........)).))))))..)).)). ( -24.10, z-score =  -2.37, R)
>droSim1.chr2L 7753379 85 + 22036055
------------CGUACAUCUGACAGCUAUCA-----------------------UUAUUUGGAAUUUUUGUU-AGCUGUCAGCUCAUUAUGAUAAAUAGAUACCAAUUAUAAUCGUUUGA
------------((.((..((((((((((.((-----------------------..(........)..)).)-)))))))))...((((((((............)))))))).)).)). ( -18.00, z-score =  -1.90, R)
>consensus
____________AGUA_AUCUGACAGCUAUCAAAAAUUUGAAAUGUGUUC_____UUAUUUGGAAUUUUUGUU_AGCUGUCAGAUCAUUAUGAUAAAUAGAUACCAAUAAUAAUCGUUUGU
...................(((((((((..(((((((((((((((...........)))))))))))))))...)))))))))...................................... (-11.24 = -16.18 +   4.94)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,957,956 – 7,958,065
Length 109
Sequences 4
Columns 121
Reading direction reverse
Mean pairwise identity 66.67
Shannon entropy 0.51933
G+C content 0.28077
Mean single sequence MFE -20.01
Consensus MFE -7.72
Energy contribution -10.79
Covariance contribution 3.06
Combinations/Pair 1.16
Mean z-score -2.31
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.913522
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7957956 109 - 23011544
ACAAACGAUUAUAAAUGGUAUCUAUUUAUCAUAAUGAGCUUGCAGCUAAACAAAAUUUCCAAAUAAUGUAUGAACACAUUUCAAAUUUUUGAUAGCUGUCAGAUGUACG------------
(((...........((((((......))))))......((.(((((((...(((((((......(((((......)))))..)))))))...))))))).)).)))...------------ ( -17.70, z-score =  -0.82, R)
>droEre2.scaffold_4929 16880385 114 - 26641161
ACAAACGAUUAAUGUUCAGAUAUAUUUAUCAUAUUGAUCUGACAGCU-AACAAAAAUUCAAAAUGA-----ACACAAAUUUCAAAUUUUCGAUAGCUGCCGGAU-UACUAAGAUAUACGAA
.....((...(((((......)))))((((.((.(((((((.(((((-(.(.((((((..((((..-----......))))..)))))).).)))))).)))))-)).)).))))..)).. ( -23.40, z-score =  -3.79, R)
>droYak2.chr2L 17389301 119 + 22324452
GCAAACGAUUAAUAUUCAGUUAUUUUUAUCAUUACGAUUUGACAGCU-AACAAAAAUUCAAUAUAAUGUAUGAACACAUUUUCAAUUUUUAAUAGCUGCCAGAU-UACUAAGUUGUAUGAA
((((..(((.((((......))))...))).....((((((.(((((-(..(((((((......(((((......)))))...)))))))..)))))).)))))-)......))))..... ( -20.30, z-score =  -1.71, R)
>droSim1.chr2L 7753379 85 - 22036055
UCAAACGAUUAUAAUUGGUAUCUAUUUAUCAUAAUGAGCUGACAGCU-AACAAAAAUUCCAAAUAA-----------------------UGAUAGCUGUCAGAUGUACG------------
....(((.((((...(((((......)))))..)))).(((((((((-(.((..............-----------------------)).)))))))))).)))...------------ ( -18.64, z-score =  -2.93, R)
>consensus
ACAAACGAUUAAAAUUCAGAUAUAUUUAUCAUAAUGAGCUGACAGCU_AACAAAAAUUCAAAAUAA_____GAACACAUUUCAAAUUUUUGAUAGCUGCCAGAU_UACG____________
....................................(((((((((((...((((((((.........................))))))))..)))))))))))................. ( -7.72 = -10.79 +   3.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:24:51 2011