Locus 2554

Sequence ID dm3.chr2L
Location 19,985,059 – 19,985,189
Length 130
Max. P 0.953955
window3511 window3512

overview

Window 1

Location 19,985,059 – 19,985,189
Length 130
Sequences 5
Columns 130
Reading direction forward
Mean pairwise identity 86.70
Shannon entropy 0.23874
G+C content 0.46744
Mean single sequence MFE -38.58
Consensus MFE -27.46
Energy contribution -29.10
Covariance contribution 1.64
Combinations/Pair 1.12
Mean z-score -1.90
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.650349
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19985059 130 + 23011544
UCCUCCUUAUGGAGUUUGCCAAUGUUUUGUUUUGCUCUGCUGUGUGAACUGUGGAUGCUCACUUGGGAAAACGCCCCAAAAGUUAGCUAACAAAGUAAUGGAAGAGGAACUCCUAUGCCCAACAUUGGCC
..((((....))))...((((((((((((((..(((..(((..((((.(.......).))))(((((.......))))).))).))).))))))....(((...(((....)))....))))))))))). ( -39.10, z-score =  -2.14, R)
>droEre2.scaffold_4845 18246852 129 - 22589142
CACUCCUUGUGGAGUUUGCCAAUGGUUCGUUG-CCUCCGCGAUGGGAACUAUGGAUGCUCACUUGGGAAAGCUGCCCAAAAGUUGGCUAACAAAGCGAUAGAAGGGGCACUCCUAUCCCAAACAUUUGCA
(((.....)))((((...(((.((((((((((-(....)))))..)))))))))..))))..((((((.((.(((((......(.(((.....))).)......)))))...)).))))))......... ( -41.60, z-score =  -0.95, R)
>droYak2.chr2R 6454566 129 + 21139217
CCCUCCUUGUGGAGUUUGCCAAUGUUUUGUUA-CCUCCGCUGUGUGAACUAUGGAUGCUCACUUGGGAAAACUCCCCAAAUGUUAGCUAACAAAUAGGUAGAAGAGUAACACCUAUCCCAAACAUUUUCU
..((((....))))......((((((((((((-..((((..((....))..)))).(((.(((((((.......)))))..)).)))))))).((((((.(........)))))))...))))))).... ( -28.10, z-score =  -0.46, R)
>droSec1.super_7 3596512 128 + 3727775
CCUUCCUUAUGGAGUUUGCCAAUGUUUUGUUC-ACUCCGCUGUGUGAACUGUGGAUGCUCACUUGGGAAAACGCCCCAAAAGUUAGCUAACCAAGCAAUAGAAG-GGAACUCCUAUGCCCAACAUUGGCC
..((((....))))...(((((((((..((((-((........))))))..(((..(((.(((((((.......))))..))).)))...))).(((.(((.((-....)).))))))..))))))))). ( -41.40, z-score =  -2.80, R)
>droSim1.chr2L 19645679 128 + 22036055
CCCUCCUUAUGGAGUUUGCCAAUGUUUUGUUC-ACUCCGCUGUGUGAACUGUGGAUGCUCACUUGGGAAAACGCCCCAAAAGUUAGCUAACAAAGCAUUAGAAG-GGAACUCCUAUGCCCAACAUUGGCC
..((((....))))...(((((((((..((((-((........))))))...((..(((.(((((((.......))))..))).))).......((((.((.((-....)).))))))))))))))))). ( -42.70, z-score =  -3.18, R)
>consensus
CCCUCCUUAUGGAGUUUGCCAAUGUUUUGUUC_ACUCCGCUGUGUGAACUGUGGAUGCUCACUUGGGAAAACGCCCCAAAAGUUAGCUAACAAAGCAAUAGAAG_GGAACUCCUAUGCCCAACAUUGGCC
..((((....))))...((((((((((((((....(((((.((....)).))))).(((.(((((((.......))))..))).))).))))))...((((.((.....)).)))).....)))))))). (-27.46 = -29.10 +   1.64)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 19,985,059 – 19,985,189
Length 130
Sequences 5
Columns 130
Reading direction reverse
Mean pairwise identity 86.70
Shannon entropy 0.23874
G+C content 0.46744
Mean single sequence MFE -42.80
Consensus MFE -31.54
Energy contribution -33.82
Covariance contribution 2.28
Combinations/Pair 1.03
Mean z-score -2.49
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.60
SVM RNA-class probability 0.953955
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19985059 130 - 23011544
GGCCAAUGUUGGGCAUAGGAGUUCCUCUUCCAUUACUUUGUUAGCUAACUUUUGGGGCGUUUUCCCAAGUGAGCAUCCACAGUUCACACAGCAGAGCAAAACAAAACAUUGGCAAACUCCAUAAGGAGGA
.((((((((((((...(((....)))..))).....((((((.(((.....((((((.....))))))((((((.......))))))..)))..))))))....)))))))))...((((....)))).. ( -43.70, z-score =  -3.23, R)
>droEre2.scaffold_4845 18246852 129 + 22589142
UGCAAAUGUUUGGGAUAGGAGUGCCCCUUCUAUCGCUUUGUUAGCCAACUUUUGGGCAGCUUUCCCAAGUGAGCAUCCAUAGUUCCCAUCGCGGAGG-CAACGAACCAUUGGCAAACUCCACAAGGAGUG
(((.((((...(.((((((((.....)))))))).)((((((.(((.(((..((((..((((........)))).)))).)))(((......)))))-))))))).)))).))).(((((....))))). ( -39.90, z-score =  -0.97, R)
>droYak2.chr2R 6454566 129 - 21139217
AGAAAAUGUUUGGGAUAGGUGUUACUCUUCUACCUAUUUGUUAGCUAACAUUUGGGGAGUUUUCCCAAGUGAGCAUCCAUAGUUCACACAGCGGAGG-UAACAAAACAUUGGCAAACUCCACAAGGAGGG
.(..(((((((.(((((((((.........)))))))))((((.((.....(((((((...)))))))((((((.......)))))).......)).-)))).)))))))..)...((((....)))).. ( -38.20, z-score =  -2.04, R)
>droSec1.super_7 3596512 128 - 3727775
GGCCAAUGUUGGGCAUAGGAGUUCC-CUUCUAUUGCUUGGUUAGCUAACUUUUGGGGCGUUUUCCCAAGUGAGCAUCCACAGUUCACACAGCGGAGU-GAACAAAACAUUGGCAAACUCCAUAAGGAAGG
.((((((((((((((((((((....-)))))).)))))((...(((....(((((((.....)))))))..)))..))...((((((........))-))))..)))))))))....(((....)))... ( -44.90, z-score =  -2.76, R)
>droSim1.chr2L 19645679 128 - 22036055
GGCCAAUGUUGGGCAUAGGAGUUCC-CUUCUAAUGCUUUGUUAGCUAACUUUUGGGGCGUUUUCCCAAGUGAGCAUCCACAGUUCACACAGCGGAGU-GAACAAAACAUUGGCAAACUCCAUAAGGAGGG
.((((((((((((((((((((....-))))).)))).......(((....(((((((.....)))))))..)))..))...((((((........))-))))..)))))))))...((((....)))).. ( -47.30, z-score =  -3.44, R)
>consensus
GGCCAAUGUUGGGCAUAGGAGUUCC_CUUCUAUUGCUUUGUUAGCUAACUUUUGGGGCGUUUUCCCAAGUGAGCAUCCACAGUUCACACAGCGGAGG_GAACAAAACAUUGGCAAACUCCAUAAGGAGGG
.(((((((((..(..((((((.....))))))...(((((((.........((((((.....))))))((((((.......))))))..))))))).....)..)))))))))...((((....)))).. (-31.54 = -33.82 +   2.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:53:29 2011