Locus 8209

Sequence ID dm3.chr3L
Location 21,036,067 – 21,036,182
Length 115
Max. P 0.812430
window11281 window11282 window11283

overview

Window 1

Location 21,036,067 – 21,036,169
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 94.31
Shannon entropy 0.09862
G+C content 0.45957
Mean single sequence MFE -28.92
Consensus MFE -24.26
Energy contribution -24.46
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.56
SVM RNA-class probability 0.743115
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21036067 102 - 24543557
GAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGAGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUGAUUGCAAUGAUGAUUGCCAGUUGC
..((((.((((((((.((((..((((.......)))))))).)))).....(((((.(((....))))))))..))))...(((((....)))))...)))) ( -26.10, z-score =  -1.32, R)
>droSim1.chr3L 20390013 95 - 22553184
GAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGCGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG---GCAAUGAUGAUUGCCAU----
.......((((.(((.(((...((((.......)))).))).)))))))..(((((.(((....))))))))...(((---(((((....))))))))---- ( -28.10, z-score =  -2.03, R)
>droSec1.super_11 924452 99 - 2888827
GAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGCGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG---GCAAUGAUGAUUGCCGUUUCC
.......((((.(((.(((...((((.......)))).))).)))))))..(((((.(((....))))))))..((((---(((((....)))))))))... ( -28.90, z-score =  -1.81, R)
>droYak2.chr3L 4705150 99 + 24197627
GAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGAGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG---GCAGUGAUGAUUGCCAGUUGC
..((((.((((.(((.((((..((((.......)))))))).)))))))..(((((.(((....))))))))....((---(((((....))))))).)))) ( -31.00, z-score =  -2.59, R)
>droEre2.scaffold_4784 20717741 99 - 25762168
GAGCGAACAUUUGUCUGCCUUCCCACGGCAAAAGUGGAGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG---GCAGUGAUGAUUGCCAGUUGC
..((((.((((.((..((((..((((.......))))))))..))))))..(((((.(((....))))))))....((---(((((....))))))).)))) ( -30.50, z-score =  -2.12, R)
>consensus
GAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGAGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG___GCAAUGAUGAUUGCCAGUUGC
..((((((....))))))........(((((..((.(..((.....((.(.(((((.(((....)))))))).).))....))..).))..)))))...... (-24.26 = -24.46 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,036,090 – 21,036,182
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 92.16
Shannon entropy 0.12826
G+C content 0.45006
Mean single sequence MFE -18.52
Consensus MFE -17.34
Energy contribution -17.34
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.09
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.603563
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21036090 92 + 24543557
UCAUCAUCAUCGUGUCAAUACAUCGAUGGUCAUUAUUAGCCUCCACUUUUGCCGUGGGAAGGCAAACAAAUGUUCGCUCGAUAUAUAUUCAU
..(((((((((((((....))).)))))))........((((((((.......))))..))))................))).......... ( -19.80, z-score =  -1.32, R)
>droSim1.chr3L 20390030 79 + 22553184
-CAUCAUCAUCGUGUCAAUACAUCGAUGGUCAUUAUUAGCCGCCACUUUUGCCGUGGGAAGGCAAACAAAUGUUCGCUCG------------
-....((((((((((....))).)))))))........(((.((((.......))))...))).................------------ ( -18.00, z-score =  -0.83, R)
>droSec1.super_11 924473 79 + 2888827
-CAUCAUCAUCGUGUCAAUACAUCGAUGGUCAUUAUUAGCCGCCACUUUUGCCGUGGGAAGGCAAACAAAUGUUCGCUCG------------
-....((((((((((....))).)))))))........(((.((((.......))))...))).................------------ ( -18.00, z-score =  -0.83, R)
>droYak2.chr3L 4705171 79 - 24197627
-CAUCAUCAUCGUGUCAAUACAUCGAUGGUCAUUAUUAGCCUCCACUUUUGCCGUGGGAAGGCAAACAAAUGUUCGCUCA------------
-....((((((((((....))).)))))))........((((((((.......))))..)))).................------------ ( -18.40, z-score =  -1.47, R)
>droEre2.scaffold_4784 20717762 79 + 25762168
-CAUCAUCAUCGUGUCAAUACAUCGAUGGUCAUUAUUAGCCUCCACUUUUGCCGUGGGAAGGCAGACAAAUGUUCGCUCG------------
-....((((((((((....))).)))))))........((((((((.......))))..)))).................------------ ( -18.40, z-score =  -1.00, R)
>consensus
_CAUCAUCAUCGUGUCAAUACAUCGAUGGUCAUUAUUAGCCUCCACUUUUGCCGUGGGAAGGCAAACAAAUGUUCGCUCG____________
.....((((((((((....))).)))))))........(((.((((.......))))...)))............................. (-17.34 = -17.34 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,036,090 – 21,036,182
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 92.16
Shannon entropy 0.12826
G+C content 0.45006
Mean single sequence MFE -20.40
Consensus MFE -18.98
Energy contribution -19.58
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.812430
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21036090 92 - 24543557
AUGAAUAUAUAUCGAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGAGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUGA
.........(((((......((((.(((.((((..((((.......)))))))).)))))))..(((((.(((....)))))))).))))). ( -23.10, z-score =  -1.90, R)
>droSim1.chr3L 20390030 79 - 22553184
------------CGAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGCGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG-
------------........((((.(((.(((...((((.......)))).))).)))))))..(((((.(((....))))))))......- ( -19.10, z-score =  -0.94, R)
>droSec1.super_11 924473 79 - 2888827
------------CGAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGCGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG-
------------........((((.(((.(((...((((.......)))).))).)))))))..(((((.(((....))))))))......- ( -19.10, z-score =  -0.94, R)
>droYak2.chr3L 4705171 79 + 24197627
------------UGAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGAGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG-
------------........((((.(((.((((..((((.......)))))))).)))))))..(((((.(((....))))))))......- ( -20.60, z-score =  -2.05, R)
>droEre2.scaffold_4784 20717762 79 - 25762168
------------CGAGCGAACAUUUGUCUGCCUUCCCACGGCAAAAGUGGAGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG-
------------........((((.((..((((..((((.......))))))))..))))))..(((((.(((....))))))))......- ( -20.10, z-score =  -1.53, R)
>consensus
____________CGAGCGAACAUUUGUUUGCCUUCCCACGGCAAAAGUGGAGGCUAAUAAUGACCAUCGAUGUAUUGACACGAUGAUGAUG_
....................((((.(((.((((..((((.......)))))))).)))))))..(((((.(((....))))))))....... (-18.98 = -19.58 +   0.60)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:41:20 2011