Locus 1491

Sequence ID dm3.chr2L
Location 11,508,911 – 11,509,011
Length 100
Max. P 0.993051
window2034 window2035

overview

Window 4

Location 11,508,911 – 11,509,011
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 95.60
Shannon entropy 0.07493
G+C content 0.33200
Mean single sequence MFE -21.78
Consensus MFE -18.10
Energy contribution -19.10
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.772049
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11508911 100 + 23011544
UUGGCUUAGAAUGUCGCCAGAGAAGGAAAUCUAGUUCCAAACGGUAUAUAUAAAUUAGAUAUAUAAAUUGUGGAAGCAUUUUCCAUUUUUGUGAUUAAAG
............(((((.(((((.(((((.....(((((.....(((((((.......))))))).....)))))....))))).))))))))))..... ( -21.30, z-score =  -1.90, R)
>droSim1.chr2L 11324801 100 + 22036055
UUGGCGUAGAAUGUCGCCAGAGAAGGAAAUCUAGUUCCAAACGGUAUAUAUAAAUUAGAUAUAUAAAUUGUGGAAGCAUUUUCCAUGUUUGUGAUUAAAG
((((((........))))))...........((((..(((((..(((((((.......)))))))....(((((((...))))))))))))..))))... ( -23.10, z-score =  -2.58, R)
>droYak2.chr2L 7915399 100 + 22324452
UCGGCGUAGAAUGCCGCCAGAGAAGAAAAUCUAGUUCCAAACGGUAUAUAUAAAUAAGAUAUAUAAAUUGUGGAAGCAUUUUCCAUGUUUGUGAUAAAAG
..((((........))))(((........))).((..(((((..(((((((.......)))))))....(((((((...))))))))))))..))..... ( -20.30, z-score =  -2.01, R)
>droEre2.scaffold_4929 12717782 100 - 26641161
UCGGCGUAGAAUGUCGCCAGAGAAGAAAAUCUAGUUCCAAACGGUAUAUAUAAAUAAGAUAUAUAAAUUGUGGAAGCAUUUUCCAUGUUUGUGAUACGAG
..((((........))))(((........))).(((((((((..(((((((.......)))))))....(((((((...)))))))))))).)).))... ( -21.10, z-score =  -1.73, R)
>droSec1.super_3 6906027 100 + 7220098
UUGGCGUAGAAUGUCGCCAGAGAAGGAAAUCUAGUUCCAAACGGUAUAUAUAAAUUAGAUAUAUAAAUUGUGGAAGCAUUUUCCAUGUUUGUGAUUAAAG
((((((........))))))...........((((..(((((..(((((((.......)))))))....(((((((...))))))))))))..))))... ( -23.10, z-score =  -2.58, R)
>consensus
UUGGCGUAGAAUGUCGCCAGAGAAGGAAAUCUAGUUCCAAACGGUAUAUAUAAAUUAGAUAUAUAAAUUGUGGAAGCAUUUUCCAUGUUUGUGAUUAAAG
..((((........)))).............((((..(((((..(((((((.......)))))))....(((((((...))))))))))))..))))... (-18.10 = -19.10 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,508,911 – 11,509,011
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 95.60
Shannon entropy 0.07493
G+C content 0.33200
Mean single sequence MFE -18.66
Consensus MFE -17.10
Energy contribution -16.82
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -3.05
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.58
SVM RNA-class probability 0.993051
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11508911 100 - 23011544
CUUUAAUCACAAAAAUGGAAAAUGCUUCCACAAUUUAUAUAUCUAAUUUAUAUAUACCGUUUGGAACUAGAUUUCCUUCUCUGGCGACAUUCUAAGCCAA
................(((((.((.(((((.....(((((((.......))))))).....))))).))..))))).....((((..........)))). ( -16.50, z-score =  -2.17, R)
>droSim1.chr2L 11324801 100 - 22036055
CUUUAAUCACAAACAUGGAAAAUGCUUCCACAAUUUAUAUAUCUAAUUUAUAUAUACCGUUUGGAACUAGAUUUCCUUCUCUGGCGACAUUCUACGCCAA
................(((((.((.(((((.....(((((((.......))))))).....))))).))..))))).....(((((........))))). ( -18.70, z-score =  -3.52, R)
>droYak2.chr2L 7915399 100 - 22324452
CUUUUAUCACAAACAUGGAAAAUGCUUCCACAAUUUAUAUAUCUUAUUUAUAUAUACCGUUUGGAACUAGAUUUUCUUCUCUGGCGGCAUUCUACGCCGA
......((.(((((.(((((.....))))).....((((((.......))))))....))))))).(((((........)))))((((.......)))). ( -20.70, z-score =  -3.51, R)
>droEre2.scaffold_4929 12717782 100 + 26641161
CUCGUAUCACAAACAUGGAAAAUGCUUCCACAAUUUAUAUAUCUUAUUUAUAUAUACCGUUUGGAACUAGAUUUUCUUCUCUGGCGACAUUCUACGCCGA
((.((.((.(((((.(((((.....))))).....((((((.......))))))....))))))))).))...........(((((........))))). ( -18.70, z-score =  -2.55, R)
>droSec1.super_3 6906027 100 - 7220098
CUUUAAUCACAAACAUGGAAAAUGCUUCCACAAUUUAUAUAUCUAAUUUAUAUAUACCGUUUGGAACUAGAUUUCCUUCUCUGGCGACAUUCUACGCCAA
................(((((.((.(((((.....(((((((.......))))))).....))))).))..))))).....(((((........))))). ( -18.70, z-score =  -3.52, R)
>consensus
CUUUAAUCACAAACAUGGAAAAUGCUUCCACAAUUUAUAUAUCUAAUUUAUAUAUACCGUUUGGAACUAGAUUUCCUUCUCUGGCGACAUUCUACGCCAA
................(((((.((.(((((.....(((((((.......))))))).....))))).))..))))).....(((((........))))). (-17.10 = -16.82 +  -0.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:32:56 2011