Locus 12652

Sequence ID dm3.chrX
Location 1,412,604 – 1,412,701
Length 97
Max. P 0.637089
window17392 window17393

overview

Window 2

Location 1,412,604 – 1,412,701
Length 97
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 63.28
Shannon entropy 0.60223
G+C content 0.47857
Mean single sequence MFE -26.61
Consensus MFE -10.59
Energy contribution -12.15
Covariance contribution 1.56
Combinations/Pair 1.29
Mean z-score -1.41
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.637089
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1412604 97 + 22422827
AGGUGUUGAGCCAGGAGAAUUACGCUCC-CAACUCCGCGCCAGCUGUGCAGUUGUUUCCCCUAACCUGGAAGGUAUGCCAACUCAAUCUACGGUCUCC-
.(((((.(((...((((.......))))-...))).))))).((((((..((((.((((........))))((....))....)))).))))))....- ( -26.20, z-score =  -0.29, R)
>droYak2.chrU 8888291 89 - 28119190
UGGA-ACACUCCAGCAGAGAUACGAGCUAUGAUUGCCUCAAGGCAAUACGAUUCUCUUGGCCUUUCGGCAAUGCAAAUCUUGGUAAAACC---------
((((-....))))((.(((((..(((...((((((((....)))))).))...)))...(((....))).......))))).))......--------- ( -22.10, z-score =  -1.05, R)
>droSec1.super_1989 535 97 - 3922
UGGACAUACUCCAGCAGAGAUACGAGCCAUGAUUGCCUCAAGGCAAUACGAUUCUUUUGGCCUUUCA-CAAGG-AAGUCUUGGUAAAACCAGCUCUGCU
((((.....))))((((((......((((..((((((....))))))..((((..((((........-)))).-.)))).))))........)))))). ( -29.24, z-score =  -2.12, R)
>droSim1.chr2L 20995059 97 + 22036055
UGGACAUACUCCAGCAGAGAUACGAGCUAUGAUUGCCUCAAGGCAAUAAGAUUCUUUUGGCCUUUCA-CAAAG-AAGUCUUGGUAACACCAGCUCUGCU
((((.....))))((((((............((((((....))))))((((((..((((........-)))).-.))))))((.....))..)))))). ( -28.90, z-score =  -2.18, R)
>consensus
UGGACAUACUCCAGCAGAGAUACGAGCCAUGAUUGCCUCAAGGCAAUACGAUUCUUUUGGCCUUUCA_CAAGG_AAGUCUUGGUAAAACCAGCUCUGC_
.(((.....))).((((((............((((((....))))))..((((......((......))......)))).............)))))). (-10.59 = -12.15 +   1.56)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 1,412,604 – 1,412,701
Length 97
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 63.28
Shannon entropy 0.60223
G+C content 0.47857
Mean single sequence MFE -29.83
Consensus MFE -11.30
Energy contribution -12.11
Covariance contribution 0.81
Combinations/Pair 1.38
Mean z-score -1.41
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.531272
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1412604 97 - 22422827
-GGAGACCGUAGAUUGAGUUGGCAUACCUUCCAGGUUAGGGGAAACAACUGCACAGCUGGCGCGGAGUUG-GGAGCGUAAUUCUCCUGGCUCAACACCU
-(....).........((((((((..(((........)))(....)...))).)))))((.(..((((..-((((.......))))..))))..).)). ( -31.50, z-score =  -0.49, R)
>droYak2.chrU 8888291 89 + 28119190
---------GGUUUUACCAAGAUUUGCAUUGCCGAAAGGCCAAGAGAAUCGUAUUGCCUUGAGGCAAUCAUAGCUCGUAUCUCUGCUGGAGUGU-UCCA
---------((..(..((((((..(((...(((....)))...(((....(.((((((....)))))))....))))))..)))..)))...).-.)). ( -26.10, z-score =  -1.43, R)
>droSec1.super_1989 535 97 + 3922
AGCAGAGCUGGUUUUACCAAGACUU-CCUUG-UGAAAGGCCAAAAGAAUCGUAUUGCCUUGAGGCAAUCAUGGCUCGUAUCUCUGCUGGAGUAUGUCCA
(((((((.(((((((.(((((....-.))))-.).)))))))...((..(((((((((....)))))).)))..))....)))))))(((.....))). ( -34.30, z-score =  -2.85, R)
>droSim1.chr2L 20995059 97 - 22036055
AGCAGAGCUGGUGUUACCAAGACUU-CUUUG-UGAAAGGCCAAAAGAAUCUUAUUGCCUUGAGGCAAUCAUAGCUCGUAUCUCUGCUGGAGUAUGUCCA
(((((((.(((.((((..((((.((-((((.-((......))))))))))))((((((....))))))..)))).).)).)))))))(((.....))). ( -27.40, z-score =  -0.88, R)
>consensus
_GCAGAGCUGGUUUUACCAAGACUU_CCUUG_UGAAAGGCCAAAAGAAUCGUAUUGCCUUGAGGCAAUCAUAGCUCGUAUCUCUGCUGGAGUAUGUCCA
.((((((..((.....))..........(((((..(((((...............)))))..))))).............)))))).(((.....))). (-11.30 = -12.11 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:06:15 2011