Locus 5630

Sequence ID dm3.chr3LHet
Location 2,536,892 – 2,536,986
Length 94
Max. P 0.999090
window7729 window7730

overview

Window 9

Location 2,536,892 – 2,536,986
Length 94
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 67.40
Shannon entropy 0.54227
G+C content 0.44145
Mean single sequence MFE -21.47
Consensus MFE -18.60
Energy contribution -20.40
Covariance contribution 1.80
Combinations/Pair 1.20
Mean z-score -2.37
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.27
SVM RNA-class probability 0.998152
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 2536892 94 + 2555491
----------------------AAUAUCCAUUCCUAUGCUAAGCGGCCGCCCUGUGCUUUACAGUGCGCCGCCUAAUACAUGUGAAUGUAUA---UCCUAU-UCUUAAUUACGUACUUUU
----------------------.((((.(((((.((((.((.(((((.((.(((((...))))).))))))).))...)))).))))).)))---).....-.................. ( -23.90, z-score =  -3.58, R)
>droSec1.super_165 61299 98 + 68140
----------------------GCUGACCACCCCUACACUAAGCGGCCGCCCUGUAAAUUACAGUGCGCCGCCUAAUACGUGUGAAUGAUUAGAUCGCCAAAAUUCAACUUUAUUAUUUU
----------------------((..................(((((.((.(((((...))))).)))))))(((((.(((....))))))))...))...................... ( -21.60, z-score =  -2.54, R)
>droSim1.chrU 5059139 90 + 15797150
----------------------UAUAACCAUCCCUACGCUAAGCAGCCGCUCUGUGCAUUACAGUACGCCGCCUAAUACAUGUGAAUGGUUA---CCCUCUAUCUUUACCCCACC-----
----------------------..(((((((...((((((....))).((..(((((......)))))..)).........))).)))))))---....................----- ( -14.60, z-score =  -0.99, R)
>droYak2.chrX_random 1718598 107 + 1802292
---------UGUAAUUUUUCUCAAUAUCCACUCCCAUGCUAAGCGGCCGCCCUGUGCGUUACAGUGCGCCGCCCAAUACAUGUGAAUGGCUA---UCCUGU-UCUUAAUUUUCUCCUUUU
---------..............(((.(((.((.((((....(((((.((.(((((...))))).)))))))......)))).)).))).))---).....-.................. ( -23.80, z-score =  -2.49, R)
>droEre2.scaffold_4929 26458487 116 + 26641161
UUUAAUUUUUCCUCAAUAUACGAAUAUCCAUUCCUACGCUAAGCGGCCGCCCUGUGCGUUACAGUGCGCCGCCUAAUACAUGUGAAUGGCUA---UCCUAU-UCUUUAAUUAUUUCUUUU
.....................(((((.(((((((........(((((.((.(((((...))))).))))))).........).))))))...---...)))-))................ ( -23.43, z-score =  -2.23, R)
>consensus
______________________AAUAUCCAUUCCUACGCUAAGCGGCCGCCCUGUGCAUUACAGUGCGCCGCCUAAUACAUGUGAAUGGCUA___UCCUAU_UCUUAACUUCAUCCUUUU
........................(((((((((.((((....(((((.((.(((((...))))).)))))))......)))).)))))))))............................ (-18.60 = -20.40 +   1.80)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,536,892 – 2,536,986
Length 94
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 67.40
Shannon entropy 0.54227
G+C content 0.44145
Mean single sequence MFE -32.56
Consensus MFE -30.06
Energy contribution -29.06
Covariance contribution -1.00
Combinations/Pair 1.37
Mean z-score -4.05
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.64
SVM RNA-class probability 0.999090
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 2536892 94 - 2555491
AAAAGUACGUAAUUAAGA-AUAGGA---UAUACAUUCACAUGUAUUAGGCGGCGCACUGUAAAGCACAGGGCGGCCGCUUAGCAUAGGAAUGGAUAUU----------------------
..................-....((---(((.(((((..((((..((((((((((.((((.....)))).)).))))))))))))..))))).)))))---------------------- ( -30.20, z-score =  -4.69, R)
>droSec1.super_165 61299 98 - 68140
AAAAUAAUAAAGUUGAAUUUUGGCGAUCUAAUCAUUCACACGUAUUAGGCGGCGCACUGUAAUUUACAGGGCGGCCGCUUAGUGUAGGGGUGGUCAGC----------------------
...........((..(...)..))...((.(((((((.....(((((((((((((.(((((...))))).)).)))))))))))...))))))).)).---------------------- ( -30.10, z-score =  -2.85, R)
>droSim1.chrU 5059139 90 - 15797150
-----GGUGGGGUAAAGAUAGAGGG---UAACCAUUCACAUGUAUUAGGCGGCGUACUGUAAUGCACAGAGCGGCUGCUUAGCGUAGGGAUGGUUAUA----------------------
-----...................(---(((((((((..((((..((((((((((.((((.....)))).)).))))))))))))..)))))))))).---------------------- ( -31.60, z-score =  -3.60, R)
>droYak2.chrX_random 1718598 107 - 1802292
AAAAGGAGAAAAUUAAGA-ACAGGA---UAGCCAUUCACAUGUAUUGGGCGGCGCACUGUAACGCACAGGGCGGCCGCUUAGCAUGGGAGUGGAUAUUGAGAAAAAUUACA---------
..................-....((---((.((((((.(((((..((((((((((.((((.....)))).)).))))))))))))).)))))).)))).............--------- ( -35.40, z-score =  -4.72, R)
>droEre2.scaffold_4929 26458487 116 - 26641161
AAAAGAAAUAAUUAAAGA-AUAGGA---UAGCCAUUCACAUGUAUUAGGCGGCGCACUGUAACGCACAGGGCGGCCGCUUAGCGUAGGAAUGGAUAUUCGUAUAUUGAGGAAAAAUUAAA
..................-...(((---((.((((((..((((..((((((((((.((((.....)))).)).))))))))))))..)))))).)))))..................... ( -35.50, z-score =  -4.40, R)
>consensus
AAAAGAAUAAAAUUAAGA_AUAGGA___UAACCAUUCACAUGUAUUAGGCGGCGCACUGUAACGCACAGGGCGGCCGCUUAGCGUAGGAAUGGAUAUU______________________
............................(((((((((..((((..((((((((((.((((.....)))).)).))))))))))))..)))))))))........................ (-30.06 = -29.06 +  -1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:52:03 2011