Locus 3974

Sequence ID dm3.chr2R
Location 9,370,228 – 9,370,319
Length 91
Max. P 0.993763
window5438 window5439

overview

Window 8

Location 9,370,228 – 9,370,319
Length 91
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 87.70
Shannon entropy 0.21436
G+C content 0.49729
Mean single sequence MFE -32.34
Consensus MFE -27.42
Energy contribution -27.66
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.35
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.90
SVM RNA-class probability 0.974021
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9370228 91 + 21146708
AGCGCUGCACUUUCCAGUGGAAAAUUUCACGACGCAACCAAAACAAACGCCGUUUGCCGCUGGAAAAUGCAGCAGCAACAG----AGAGCAAGUG----------
.((((((((.((((((((((........(((.((.............)).)))...)))))))))).)))))).)).....----..........---------- ( -30.42, z-score =  -2.49, R)
>droEre2.scaffold_4845 6143405 105 - 22589142
UGCGCUGCACUUUCCAGUGGAAAAUUUCACGACGCAACCAAAACAAACGCCGUUUGCCGCUGGAAAAUGCAGCAGCAACAGCAACAAAGCAACAGAGAGUAAGUG
(((((((((.((((((((((........(((.((.............)).)))...)))))))))).)))))).((....))......))).............. ( -32.82, z-score =  -2.43, R)
>droYak2.chr2R 13555239 105 - 21139217
UCCGCUGCACUUUCCAGUGGAAAAUUUGACGCUGCAACCAAAACAAACGCCGUUUGCCGCUGAAAAAUGCAGCGGCAACAGCAACAACGCAACAGAGAGUAAGUG
..((((..(((((((((((..........)))))..............((.(((.(((((((.......)))))))))).))............)))))).)))) ( -32.40, z-score =  -2.07, R)
>droSec1.super_1 6889504 102 + 14215200
UGCGCUGCACUUUCCAGUGGAAUAUUUCACGACGCAACCAAAACAAACGCCGUUUGCCGCUGGAAAAUGCAGCAGCAGCAAC---AAAGCAACAGAGAGCAAGUG
(((((((((.((((((((((........(((.((.............)).)))...)))))))))).))))))....((...---...))........))).... ( -33.02, z-score =  -2.37, R)
>droSim1.chr2R 7820833 102 + 19596830
UGCGCUGCACUUUCCAGUGGAAUAUUUCACGACGCAACCAAAACAAACGCCGUUUGCCGCUGGAAAAUGCAGCAGCAGCAAC---AAAGCAACAGAGAGCAAGUG
(((((((((.((((((((((........(((.((.............)).)))...)))))))))).))))))....((...---...))........))).... ( -33.02, z-score =  -2.37, R)
>consensus
UGCGCUGCACUUUCCAGUGGAAAAUUUCACGACGCAACCAAAACAAACGCCGUUUGCCGCUGGAAAAUGCAGCAGCAACAGC___AAAGCAACAGAGAGCAAGUG
.((((((((.((((((((((........(((.((.............)).)))...)))))))))).)))))).))............................. (-27.42 = -27.66 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,370,228 – 9,370,319
Length 91
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 87.70
Shannon entropy 0.21436
G+C content 0.49729
Mean single sequence MFE -39.02
Consensus MFE -33.46
Energy contribution -33.90
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.89
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.64
SVM RNA-class probability 0.993763
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9370228 91 - 21146708
----------CACUUGCUCU----CUGUUGCUGCUGCAUUUUCCAGCGGCAAACGGCGUUUGUUUUGGUUGCGUCGUGAAAUUUUCCACUGGAAAGUGCAGCGCU
----------..........----.....((.((((((((((((((.((...(((((((...........)))))))........)).)))))))))))))))). ( -36.70, z-score =  -3.36, R)
>droEre2.scaffold_4845 6143405 105 + 22589142
CACUUACUCUCUGUUGCUUUGUUGCUGUUGCUGCUGCAUUUUCCAGCGGCAAACGGCGUUUGUUUUGGUUGCGUCGUGAAAUUUUCCACUGGAAAGUGCAGCGCA
...............((......))...(((.((((((((((((((.((...(((((((...........)))))))........)).))))))))))))))))) ( -38.50, z-score =  -2.66, R)
>droYak2.chr2R 13555239 105 + 21139217
CACUUACUCUCUGUUGCGUUGUUGCUGUUGCCGCUGCAUUUUUCAGCGGCAAACGGCGUUUGUUUUGGUUGCAGCGUCAAAUUUUCCACUGGAAAGUGCAGCGGA
.........(((((((((((((((((((((((((((.......))))))).)))))))............))))).....(((((((...))))))))))))))) ( -40.10, z-score =  -2.63, R)
>droSec1.super_1 6889504 102 - 14215200
CACUUGCUCUCUGUUGCUUU---GUUGCUGCUGCUGCAUUUUCCAGCGGCAAACGGCGUUUGUUUUGGUUGCGUCGUGAAAUAUUCCACUGGAAAGUGCAGCGCA
....(((.....((.((...---...)).)).((((((((((((((.((...(((((((...........)))))))........)).))))))))))))))))) ( -39.90, z-score =  -2.90, R)
>droSim1.chr2R 7820833 102 - 19596830
CACUUGCUCUCUGUUGCUUU---GUUGCUGCUGCUGCAUUUUCCAGCGGCAAACGGCGUUUGUUUUGGUUGCGUCGUGAAAUAUUCCACUGGAAAGUGCAGCGCA
....(((.....((.((...---...)).)).((((((((((((((.((...(((((((...........)))))))........)).))))))))))))))))) ( -39.90, z-score =  -2.90, R)
>consensus
CACUUACUCUCUGUUGCUUU___GCUGUUGCUGCUGCAUUUUCCAGCGGCAAACGGCGUUUGUUUUGGUUGCGUCGUGAAAUUUUCCACUGGAAAGUGCAGCGCA
.............................((.((((((((((((((.((...(((((((...........)))))))........)).)))))))))))))))). (-33.46 = -33.90 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:20:15 2011