Locus 251

Sequence ID dm3.chr2L
Location 1,826,398 – 1,826,488
Length 90
Max. P 0.733513
window340 window341

overview

Window 0

Location 1,826,398 – 1,826,488
Length 90
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 67.49
Shannon entropy 0.49253
G+C content 0.41065
Mean single sequence MFE -25.78
Consensus MFE -14.19
Energy contribution -15.50
Covariance contribution 1.31
Combinations/Pair 1.11
Mean z-score -1.35
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.733513
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1826398 90 + 23011544
UACGUUUUGUAGGCAUGUGCGGGUUUCCCAAAGGCCAAAAGCGUGGCCAGAGUGAAUAAAAGUGUACAUCUCGUAUUCAUUAGUUCGGUC------------------------------
.(((((((...(((...((.((....))))...))).)))))))((((..((((((((..((.......))..)))))))).....))))------------------------------ ( -24.70, z-score =  -2.06, R)
>droSim1.chr2L 1810634 85 + 22036055
UAAGU---GCGGGCAUGUGCGGUUUUCCCAAUGGCCAAAAGCGUGGCCAAAGUGAAUAUAAGUGUACAUCUCGUAUUCAUUGCUUUGA--------------------------------
..(((---(((((.(((((((.(((((.(..((((((......))))))..).)))...)).)))))))))))))))...........-------------------------------- ( -27.30, z-score =  -2.18, R)
>droYak2.chr2L 1799606 120 + 22324452
UAAGUUUUGUAGCCAUGUGCGGAUUUUCCAAAUGCCAAAACCGUGGCCAAAGUAAAUAUAAUUGUACACCUCAUAUCUAUUACUUCGAUUUUUAGAAUGGCACUGUAUAAAUCAUAGACU
...........(((((((((((.....))....((((......))))................))))........((((.............))))))))).((((.......))))... ( -19.72, z-score =   0.13, R)
>droEre2.scaffold_4929 1871389 118 + 26641161
UAUGUUUGGUGGGCAUGUGCGUGUUUCCCAAAGGCCAAAAGCGUGGCCAGAGUAACUAUAAUUGUACACCUCAUAUCCAUUAAUUCGAUUCUUGGAAUGGAACUGUAUAUA--AUAGACU
....(((((..(((((....)))))..)))))(((((......))))).......((((...((((((..((...((((..(((...)))..))))...))..))))))..--))))... ( -31.40, z-score =  -1.29, R)
>consensus
UAAGUUUUGUAGGCAUGUGCGGGUUUCCCAAAGGCCAAAAGCGUGGCCAAAGUAAAUAUAAGUGUACACCUCAUAUCCAUUACUUCGAUU______________________________
........(((((.((((((((.....))...(((((......)))))...............))))))))))).............................................. (-14.19 = -15.50 +   1.31)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,826,398 – 1,826,488
Length 90
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 67.49
Shannon entropy 0.49253
G+C content 0.41065
Mean single sequence MFE -22.33
Consensus MFE -12.36
Energy contribution -13.05
Covariance contribution 0.69
Combinations/Pair 1.25
Mean z-score -1.19
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.594218
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1826398 90 - 23011544
------------------------------GACCGAACUAAUGAAUACGAGAUGUACACUUUUAUUCACUCUGGCCACGCUUUUGGCCUUUGGGAAACCCGCACAUGCCUACAAAACGUA
------------------------------..(((((....((((((.(((.......))).))))))....(((((......)))))))))).......((....))............ ( -18.00, z-score =  -1.51, R)
>droSim1.chr2L 1810634 85 - 22036055
--------------------------------UCAAAGCAAUGAAUACGAGAUGUACACUUAUAUUCACUUUGGCCACGCUUUUGGCCAUUGGGAAAACCGCACAUGCCCGC---ACUUA
--------------------------------.....((..((((((..((.......))..))))))...((((((......))))))..(((.............)))))---..... ( -20.12, z-score =  -1.62, R)
>droYak2.chr2L 1799606 120 - 22324452
AGUCUAUGAUUUAUACAGUGCCAUUCUAAAAAUCGAAGUAAUAGAUAUGAGGUGUACAAUUAUAUUUACUUUGGCCACGGUUUUGGCAUUUGGAAAAUCCGCACAUGGCUACAAAACUUA
((.(((((........(((((((..((.....((((((((...(((((((.........)))))))))))))))....))...))))))).((.....))...))))))).......... ( -24.00, z-score =  -0.50, R)
>droEre2.scaffold_4929 1871389 118 - 26641161
AGUCUAU--UAUAUACAGUUCCAUUCCAAGAAUCGAAUUAAUGGAUAUGAGGUGUACAAUUAUAGUUACUCUGGCCACGCUUUUGGCCUUUGGGAAACACGCACAUGCCCACCAAACAUA
.((((((--((......((((.((((...)))).))))))))))))....((((..........(((.(((.(((((......)))))...))).)))..((....)).))))....... ( -27.20, z-score =  -1.15, R)
>consensus
______________________________AAUCGAAGUAAUGAAUACGAGAUGUACAAUUAUAUUCACUCUGGCCACGCUUUUGGCCUUUGGGAAACCCGCACAUGCCCACAAAACUUA
................................(((((....((((((((((.......))))))))))....(((((......))))))))))........................... (-12.36 = -13.05 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:09:23 2011