Locus 5549

Sequence ID	dm3.chr3LHet
Location	500,139 – 500,256
Length	117
Max. P	0.836737

overview

Window 2

Location	500,139 – 500,253
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	53.51
Shannon entropy	0.84726
G+C content	0.43684
Mean single sequence MFE	-33.87
Consensus MFE	-7.70
Energy contribution	-8.06
Covariance contribution	0.36
Combinations/Pair	1.87
Mean z-score	-1.87
Structure conservation index	0.23
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.86
SVM RNA-class probability	0.836737
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 500139 114 - 2555491
CUAGAACUCUGCUAACAAAGGUGACAUCAAUGAAAGAUGUACCUCUGUCAUUAUUGAACGUCGGUUUGAACCCGUCGUUUAGCAAUGCGAGAUCUAGCAGGUUCAUGGUAUCGA
(((((((.(((((((((.(((((.((((.......))))))))).)))((((.(((((((.(((.......))).))))))).)))).......)))))))))).)))...... ( -37.60, z-score =  -3.42, R)
>dp4.chrXR_group5 67475 114 - 740492
CUAGUUGAGUACUUAUGUAGGUGAGGUCUAUGAUGGAUGUGGUAUUUGCUCUGCUGAAAGUUGGGUUGCAACCAGCGUUUUUUACGACUAUGUCCAGGGAGGCAAAAGCCUCCA
.......((..(((((....)))))..))....((((((((((........(((((...((((.....))))))))).........)))))))))).((((((....)))))). ( -34.13, z-score =  -0.96, R)
>droPer1.super_166 55330 114 + 96193
CUAGUCGAGUACUUAUGUAGGUGAGGUCUAUGAUGGCUGUGGUACCUGCUCUGCUGAAUGUUGGGUUGGAACCAGCGUUUUUUAGGACUAUGUCCAGGGAGGCAAAAGCCUCCA
.(((((..........(((((((.((((......))))....))))))).(((..(((((((((.......)))))))))..)))))))).......((((((....)))))). ( -43.80, z-score =  -2.89, R)
>droWil1.scaffold_181145 347793 114 - 2682060
CCAGGCUCGUGCUUGAAAAGGUAACAUCAAUUUUUGAGUUACGUCCUGCUUUGCUGAAUGUUUGUGUGCUGCCGAUAUUCAGUAAACUCACGUUUCUCGAGGCAAAGGAGUCCA
...(((((.(((((....)))))........(((((((..((((...(.(((((((((((((.((.....)).))))))))))))))..))))..))))))).....))))).. ( -35.80, z-score =  -2.42, R)
>triCas2.ChLG10 1594212 114 - 8806720
CAUUAUUUUUUCAGACACUAGUGAGGUCAAUGUAUAAUGAUCCGUUUGUGCGCUCUAGUGUAGGUACUUUACCGUCAUUUAAUACGCUCAUAUUCAUAAAUUCUGCAAGUUCCA
.......(((.((((.....(((((.....(((((((((((.......(((((....)))))((((...))))))))))..)))))......)))))....)))).)))..... ( -18.00, z-score =   0.36, R)
>consensus
CUAGACGAGUACUUACAAAGGUGAGGUCAAUGAUGGAUGUACCACUUGCUCUGCUGAAUGUUGGUUUGCAACCGGCGUUUAGUAAGACCAUGUCCAGCGAGGCAAAAGCCUCCA
.........(((((....))))).........................((((((((((((((((.......)))))))))............((....)))))))))....... ( -7.70 =  -8.06 +   0.36)

alignment

secondary structure

dotplot

Window 3

Location	500,142 – 500,256
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	52.02
Shannon entropy	0.87700
G+C content	0.43684
Mean single sequence MFE	-32.21
Consensus MFE	-7.70
Energy contribution	-8.06
Covariance contribution	0.36
Combinations/Pair	1.87
Mean z-score	-1.34
Structure conservation index	0.24
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.00
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>dm3.chr3LHet 500142 114 - 2555491
CCACUAGAACUCUGCUAACAAAGGUGACAUCAAUGAAAGAUGUACCUCUGUCAUUAUUGAACGUCGGUUUGAACCCGUCGUUUAGCAAUGCGAGAUCUAGCAGGUUCAUGGUAU
..((((((((.(((((((((.(((((.((((.......))))))))).)))((((.(((((((.(((.......))).))))))).)))).......)))))))))).)))).. ( -39.70, z-score =  -4.34, R)
>dp4.chrXR_group5 67478 114 - 740492
CUGCUAGUUGAGUACUUAUGUAGGUGAGGUCUAUGAUGGAUGUGGUAUUUGCUCUGCUGAAAGUUGGGUUGCAACCAGCGUUUUUUACGACUAUGUCCAGGGAGGCAAAAGCCU
.(((.(((.....)))...)))(((...((((....((((((((((........(((((...((((.....))))))))).........))))))))))...))))....))). ( -30.13, z-score =   0.24, R)
>droPer1.super_166 55333 114 + 96193
CUGCUAGUCGAGUACUUAUGUAGGUGAGGUCUAUGAUGGCUGUGGUACCUGCUCUGCUGAAUGUUGGGUUGGAACCAGCGUUUUUUAGGACUAUGUCCAGGGAGGCAAAAGCCU
(((.(((((..........(((((((.((((......))))....))))))).(((..(((((((((.......)))))))))..))))))))....)))..((((....)))) ( -37.60, z-score =  -1.17, R)
>droWil1.scaffold_181145 347796 114 - 2682060
GGGCCAGGCUCGUGCUUGAAAAGGUAACAUCAAUUUUUGAGUUACGUCCUGCUUUGCUGAAUGUUUGUGUGCUGCCGAUAUUCAGUAAACUCACGUUUCUCGAGGCAAAGGAGU
(((((((((....))))).....(((((.(((.....))))))))))))(((((((..((((((..((.(((((........))))).))..))))))..)))))))....... ( -35.60, z-score =  -1.70, R)
>triCas2.ChLG10 1594215 114 - 8806720
UUCCAUUAUUUUUUCAGACACUAGUGAGGUCAAUGUAUAAUGAUCCGUUUGUGCGCUCUAGUGUAGGUACUUUACCGUCAUUUAAUACGCUCAUAUUCAUAAAUUCUGCAAGUU
..........(((.((((.....(((((.....(((((((((((.......(((((....)))))((((...))))))))))..)))))......)))))....)))).))).. ( -18.00, z-score =   0.28, R)
>consensus
CUGCUAGACGAGUACUUACAAAGGUGAGGUCAAUGAUGGAUGUACCACUUGCUCUGCUGAAUGUUGGUUUGCAACCGGCGUUUAGUAAGACCAUGUCCAGCGAGGCAAAAGCCU
............(((((....))))).........................((((((((((((((((.......)))))))))............((....))))))))).... ( -7.70 =  -8.06 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:50:36 2011