Locus 10819

Sequence ID dm3.chr3R
Location 16,706,650 – 16,706,748
Length 98
Max. P 0.973628
window14864 window14865 window14866

overview

Window 4

Location 16,706,650 – 16,706,745
Length 95
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 85.88
Shannon entropy 0.22199
G+C content 0.47046
Mean single sequence MFE -30.64
Consensus MFE -26.26
Energy contribution -27.14
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -1.60
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.829503
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16706650 95 + 27905053
-----------UGCUUUCUGUUUUGACAUUCAUUUGCCAAAGUC--CACAGAAAGCGUUUGCAAUUUGCCGAGGCAUCAUUGCGCAACUGGGGAGCCGGCAGUGAACU
-----------.(((((((((((((.((......)).))))...--.)))))))))(((((((((.(((....)))..)))))((..((((....))))..)))))). ( -31.00, z-score =  -1.31, R)
>droEre2.scaffold_4770 12795195 100 - 17746568
UGCCAUUUGAAUACUUUCUGUUUUGACAUUCAUUUGCGAAAGUC--CACAGAAAGCGUUUGCAAUUUGCCGAGGCAU---UGCGCAACUGGGGAGCCAGC---GAACU
(((.....(((..((((((((...(((.(((......))).)))--.))))))))..)))((((..(((....))))---)))))).((((....)))).---..... ( -30.40, z-score =  -1.59, R)
>droYak2.chr3R 5508487 100 + 28832112
UGCCAUUUGAAUACUUUCUGUUUUGACAUUCAUUUGCGAAAGUC--CACAGAAAGCGUUUGCAAUUUGCCGACGCAU---UGCGCAACUGGGAAGCAAGC---GAACU
.............((((((((...(((.(((......))).)))--.))))))))(((((((...((.(((..((..---...))...))).))))))))---).... ( -25.50, z-score =  -0.51, R)
>droSec1.super_27 771431 94 - 799419
-----------UGCUUUCUGUUUUGACAUUCAUUUGGGAAAGUCCCCACAGAAAGCGUUUGCAAUUUGCCGAGGCAUCAUUGCGCAACUGGGGAGUCAGC---GAACU
-----------.(((((((((...(((.(((......))).)))...)))))))))((((((.((((.(((..((........))...))).))))..))---)))). ( -32.10, z-score =  -2.08, R)
>droSim1.chr3R 22763179 94 - 27517382
-----------UGCUUUCUGUUUUGACAUUCAUUUGGGAAAGUCCCCACAGAAAGCGUUUGCAAUUUGCCGAGGCAUCAUUGCGCAACUGGGGAGCCAGC---GAACU
-----------.(((((((((...(((.(((......))).)))...)))))))))(((((((((.(((....)))..)))))....((((....)))).---)))). ( -34.20, z-score =  -2.52, R)
>consensus
___________UGCUUUCUGUUUUGACAUUCAUUUGCGAAAGUC__CACAGAAAGCGUUUGCAAUUUGCCGAGGCAUCAUUGCGCAACUGGGGAGCCAGC___GAACU
............(((((((((...(((.(((......))).)))...)))))))))((((((((..(((....)))...))))....((((....))))....)))). (-26.26 = -27.14 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,706,650 – 16,706,745
Length 95
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 85.88
Shannon entropy 0.22199
G+C content 0.47046
Mean single sequence MFE -32.00
Consensus MFE -26.72
Energy contribution -27.52
Covariance contribution 0.80
Combinations/Pair 1.06
Mean z-score -2.40
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.89
SVM RNA-class probability 0.973628
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16706650 95 - 27905053
AGUUCACUGCCGGCUCCCCAGUUGCGCAAUGAUGCCUCGGCAAAUUGCAAACGCUUUCUGUG--GACUUUGGCAAAUGAAUGUCAAAACAGAAAGCA-----------
...(((.((((((((....))))).))).)))(((....)))..........(((((((((.--...(((((((......)))))))))))))))).----------- ( -30.90, z-score =  -1.78, R)
>droEre2.scaffold_4770 12795195 100 + 17746568
AGUUC---GCUGGCUCCCCAGUUGCGCA---AUGCCUCGGCAAAUUGCAAACGCUUUCUGUG--GACUUUCGCAAAUGAAUGUCAAAACAGAAAGUAUUCAAAUGGCA
.....---(((((....)))))((((((---((((....)))..))))....(((((((((.--(((.((((....)))).)))...))))))))).........))) ( -31.90, z-score =  -2.34, R)
>droYak2.chr3R 5508487 100 - 28832112
AGUUC---GCUUGCUUCCCAGUUGCGCA---AUGCGUCGGCAAAUUGCAAACGCUUUCUGUG--GACUUUCGCAAAUGAAUGUCAAAACAGAAAGUAUUCAAAUGGCA
.....---((((((......(((((((.---..))).)))).....))))..(((((((((.--(((.((((....)))).)))...))))))))).........)). ( -27.70, z-score =  -0.94, R)
>droSec1.super_27 771431 94 + 799419
AGUUC---GCUGACUCCCCAGUUGCGCAAUGAUGCCUCGGCAAAUUGCAAACGCUUUCUGUGGGGACUUUCCCAAAUGAAUGUCAAAACAGAAAGCA-----------
.((..---((((......)))).))(((((..(((....))).)))))....(((((((((...(((.(((......))).)))...))))))))).----------- ( -33.60, z-score =  -3.43, R)
>droSim1.chr3R 22763179 94 + 27517382
AGUUC---GCUGGCUCCCCAGUUGCGCAAUGAUGCCUCGGCAAAUUGCAAACGCUUUCUGUGGGGACUUUCCCAAAUGAAUGUCAAAACAGAAAGCA-----------
.((..---(((((....))))).))(((((..(((....))).)))))....(((((((((...(((.(((......))).)))...))))))))).----------- ( -35.90, z-score =  -3.49, R)
>consensus
AGUUC___GCUGGCUCCCCAGUUGCGCAAUGAUGCCUCGGCAAAUUGCAAACGCUUUCUGUG__GACUUUCGCAAAUGAAUGUCAAAACAGAAAGCA___________
.(((....((.((((....))))))(((((..(((....))).))))).)))(((((((((...(((.(((......))).)))...)))))))))............ (-26.72 = -27.52 +   0.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,706,652 – 16,706,748
Length 96
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 87.10
Shannon entropy 0.20401
G+C content 0.47371
Mean single sequence MFE -28.78
Consensus MFE -22.90
Energy contribution -23.94
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -2.08
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.08
SVM RNA-class probability 0.887595
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16706652 96 - 27905053
CCAAGUUCACUGCCGGCUCCCCAGUUGCGCAAUGAUGCCUCGGCAAAUUGCAAACGCUUUCUGU--GGACUUUGGCAAAUGAAUGUCAAAACAGAAAG----------
....(((((.((((((.(((.(((..(((((((..(((....))).)))))....))...))).--)))..))))))..)))))..............---------- ( -26.60, z-score =  -0.96, R)
>droEre2.scaffold_4770 12795198 100 + 17746568
CCAAGUUC---GCUGGCUCCCCAGUUGCGCA---AUGCCUCGGCAAAUUGCAAACGCUUUCUGU--GGACUUUCGCAAAUGAAUGUCAAAACAGAAAGUAUUCAAAUG
....((..---(((((....))))).))(((---((((....)))..))))....(((((((((--.(((.((((....)))).)))...)))))))))......... ( -30.90, z-score =  -3.04, R)
>droYak2.chr3R 5508490 100 - 28832112
CCAAGUUC---GCUUGCUUCCCAGUUGCGCA---AUGCGUCGGCAAAUUGCAAACGCUUUCUGU--GGACUUUCGCAAAUGAAUGUCAAAACAGAAAGUAUUCAAAUG
.((((...---.)))).......(((..(((---((((....)))..)))).)))(((((((((--.(((.((((....)))).)))...)))))))))......... ( -27.30, z-score =  -1.72, R)
>droSec1.super_27 771433 95 + 799419
CCAAGUUC---GCUGACUCCCCAGUUGCGCAAUGAUGCCUCGGCAAAUUGCAAACGCUUUCUGUGGGGACUUUCCCAAAUGAAUGUCAAAACAGAAAG----------
....((..---((((......)))).))(((((..(((....))).))))).....((((((((...(((.(((......))).)))...))))))))---------- ( -28.40, z-score =  -2.29, R)
>droSim1.chr3R 22763181 95 + 27517382
CCAAGUUC---GCUGGCUCCCCAGUUGCGCAAUGAUGCCUCGGCAAAUUGCAAACGCUUUCUGUGGGGACUUUCCCAAAUGAAUGUCAAAACAGAAAG----------
....((..---(((((....))))).))(((((..(((....))).))))).....((((((((...(((.(((......))).)))...))))))))---------- ( -30.70, z-score =  -2.39, R)
>consensus
CCAAGUUC___GCUGGCUCCCCAGUUGCGCAAUGAUGCCUCGGCAAAUUGCAAACGCUUUCUGU__GGACUUUCGCAAAUGAAUGUCAAAACAGAAAG__________
....(((....((.((((....))))))(((((..(((....))).))))).))).((((((((...(((.(((......))).)))...)))))))).......... (-22.90 = -23.94 +   1.04)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:31:02 2011