Locus 9943

Sequence ID dm3.chr3R
Location 9,988,092 – 9,988,206
Length 114
Max. P 0.918393
window13666 window13667

overview

Window 6

Location 9,988,092 – 9,988,206
Length 114
Sequences 6
Columns 142
Reading direction forward
Mean pairwise identity 62.61
Shannon entropy 0.60393
G+C content 0.49691
Mean single sequence MFE -31.55
Consensus MFE -16.59
Energy contribution -16.21
Covariance contribution -0.38
Combinations/Pair 1.42
Mean z-score -1.25
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.26
SVM RNA-class probability 0.918393
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9988092 114 + 27905053
AUGUUCCUGCUGGCAGACAAAUGAGCGCCACCAUUAAACGCUUCUGAAAUAUGCUGGCGAAUCAUUCACAACCGGAGCAGCAGAAAGAACAGGAGCAGAAGCAGGAGCAGCAGC----------------------------
.(((((((((((((............)))..........(((((((.....(((((.(..................)))))).......)))))))...)))))))))).....---------------------------- ( -35.87, z-score =  -1.80, R)
>droSim1.chr3R 16075920 90 - 27517382
CUGUUCCUGCUGGCAGACAAAUGAGCGCCACCAUUAAACGCUUCUGAAAUAUGCUGGCGAAUCAUUCACAACCGGAGCAGAAGCAGGAGC----------------------------------------------------
..(((((((((.((.......(((.(((((.(((......(....)....))).)))))..)))(((......)))))...)))))))))---------------------------------------------------- ( -27.20, z-score =  -1.49, R)
>droSec1.super_0 9092304 90 - 21120651
CUGUUCCUGCUGGCAGACAAAUGAGCGCCACCAUUAAACGCUUCUGAAAUAUGCUGGCGAAUCGUUCACAACCGGAGCAGGAGCAGGAGC----------------------------------------------------
(((((((((((((......(((((.(((((.(((......(....)....))).)))))..))))).....))..)))))))))))....---------------------------------------------------- ( -31.10, z-score =  -2.09, R)
>droYak2.chr3R 12391728 108 - 28832112
CUGUUCCUGCUGGCAGACAAAUGAGCGCCACCAUUAAACGCUUCUGAAAUAUGCUGGCGAAUCAUUCACCACCGGAGCAGGAGCAGCCACAGAGGCAGAAGCAGUAGC----------------------------------
((((..(((.((((.....((((........))))....(((((((.....((.(((.((.....)).))).))...))))))).)))))))..))))..........---------------------------------- ( -33.90, z-score =  -1.10, R)
>dp4.chr2 17399095 87 - 30794189
CUUCUCCUGCUGGUAGACAAAUGAGCACUGCCAUUAAAUGCGUUUGAAAUAUGCUGGCAAAUCCCUCACAGCUGCAGCUGGAGUUGG-------------------------------------------------------
...((((.((((.(((.....((((...(((((......((((.......))))))))).....))))...))))))).))))....------------------------------------------------------- ( -24.30, z-score =  -0.58, R)
>droGri2.scaffold_14846 82089 142 + 266023
UUUUAGCUGCUGGUAGACAAAUGAGCAAUGCCAUGGAAUACGUUUGAAAUAUGCUGGCAAAUCAUUUACAUCAGCCACAGUCUUGCCAGUUUGUUGGUUUUCCAAUAAAUCUGAAAUUGCUGAAACUGGCGUAGCUUCGAGC
....((((((((((....((((((....(((((.....................)))))..))))))..))))((((((((..(..(((((((((((....)))))))).)))..)..))))....))))))))))...... ( -36.90, z-score =  -0.46, R)
>consensus
CUGUUCCUGCUGGCAGACAAAUGAGCGCCACCAUUAAACGCUUCUGAAAUAUGCUGGCGAAUCAUUCACAACCGGAGCAGGAGCAGGAGC____________________________________________________
(((((((.((..(((.......(((((...........))).)).......)))..))((.....))......))))))).............................................................. (-16.59 = -16.21 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,988,092 – 9,988,206
Length 114
Sequences 6
Columns 142
Reading direction reverse
Mean pairwise identity 62.61
Shannon entropy 0.60393
G+C content 0.49691
Mean single sequence MFE -31.87
Consensus MFE -17.92
Energy contribution -17.98
Covariance contribution 0.06
Combinations/Pair 1.30
Mean z-score -0.95
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.850017
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9988092 114 - 27905053
----------------------------GCUGCUGCUCCUGCUUCUGCUCCUGUUCUUUCUGCUGCUCCGGUUGUGAAUGAUUCGCCAGCAUAUUUCAGAAGCGUUUAAUGGUGGCGCUCAUUUGUCUGCCAGCAGGAACAU
----------------------------((.(..((....))..).))...(((((...((((((...(((..(..(((((..(((((.(((....(......)....))).))))).)))))..)))).))))))))))). ( -32.80, z-score =   0.00, R)
>droSim1.chr3R 16075920 90 + 27517382
----------------------------------------------------GCUCCUGCUUCUGCUCCGGUUGUGAAUGAUUCGCCAGCAUAUUUCAGAAGCGUUUAAUGGUGGCGCUCAUUUGUCUGCCAGCAGGAACAG
----------------------------------------------------....(((.(((((((..(((.(..(((((..(((((.(((....(......)....))).))))).)))))..)..)))))))))).))) ( -30.80, z-score =  -1.74, R)
>droSec1.super_0 9092304 90 + 21120651
----------------------------------------------------GCUCCUGCUCCUGCUCCGGUUGUGAACGAUUCGCCAGCAUAUUUCAGAAGCGUUUAAUGGUGGCGCUCAUUUGUCUGCCAGCAGGAACAG
----------------------------------------------------....(((.(((((((..(((.(..((.((..(((((.(((....(......)....))).))))).)).))..)..)))))))))).))) ( -29.40, z-score =  -1.23, R)
>droYak2.chr3R 12391728 108 + 28832112
----------------------------------GCUACUGCUUCUGCCUCUGUGGCUGCUCCUGCUCCGGUGGUGAAUGAUUCGCCAGCAUAUUUCAGAAGCGUUUAAUGGUGGCGCUCAUUUGUCUGCCAGCAGGAACAG
----------------------------------(((((.((....))....)))))((.(((((((..(((((..(((((..(((((.(((....(......)....))).))))).)))))..)).)))))))))).)). ( -40.70, z-score =  -1.97, R)
>dp4.chr2 17399095 87 + 30794189
-------------------------------------------------------CCAACUCCAGCUGCAGCUGUGAGGGAUUUGCCAGCAUAUUUCAAACGCAUUUAAUGGCAGUGCUCAUUUGUCUACCAGCAGGAGAAG
-------------------------------------------------------....((((.((((..((.(((((.(...(((((.....................))))).).)))))..))....)))).))))... ( -23.40, z-score =  -0.22, R)
>droGri2.scaffold_14846 82089 142 - 266023
GCUCGAAGCUACGCCAGUUUCAGCAAUUUCAGAUUUAUUGGAAAACCAACAAACUGGCAAGACUGUGGCUGAUGUAAAUGAUUUGCCAGCAUAUUUCAAACGUAUUCCAUGGCAUUGCUCAUUUGUCUACCAGCAGCUAAAA
(((.((((((.....)))))))))....((((.(((.((((....)))).)))))))..((.((((((..(((..((((((..(((((..((((.......))))....)))))....)))))))))..))).))))).... ( -34.10, z-score =  -0.55, R)
>consensus
____________________________________________________GCUCCUGCUCCUGCUCCGGUUGUGAAUGAUUCGCCAGCAUAUUUCAGAAGCGUUUAAUGGUGGCGCUCAUUUGUCUGCCAGCAGGAACAG
............................................................(((((((..((..((((((((.((((((.....................))))))...))))))).)..))))))))).... (-17.92 = -17.98 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:14:25 2011