Locus 10406

Sequence ID dm3.chr3R
Location 13,618,731 – 13,618,863
Length 132
Max. P 0.762614
window14310 window14311

overview

Window 0

Location 13,618,731 – 13,618,829
Length 98
Sequences 8
Columns 112
Reading direction reverse
Mean pairwise identity 73.43
Shannon entropy 0.49111
G+C content 0.52082
Mean single sequence MFE -29.34
Consensus MFE -12.84
Energy contribution -12.57
Covariance contribution -0.26
Combinations/Pair 1.31
Mean z-score -1.88
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.61
SVM RNA-class probability 0.762614
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13618731 98 - 27905053
-------CGAGCAAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAUUUUUAAC
-------((((....((((((.(((....))).....))))))....))))...((((((..((((-------...(((.....)))(((....)))))))...)))))).. ( -28.40, z-score =  -1.79, R)
>droSim1.chr3R 19645688 98 + 27517382
-------CGAGCGAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAUUUUUAAC
-------((((....((((((.(((....))).....))))))....))))...((((((..((((-------...(((.....)))(((....)))))))...)))))).. ( -28.40, z-score =  -1.38, R)
>droSec1.super_12 1587860 98 + 2123299
-------CGAGCGAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACCUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAUUUUUAAC
-------((((....((((((.(((....))).....))))))....))))...((((((..((((-------...(((.....)))(((....)))))))...)))))).. ( -28.40, z-score =  -1.38, R)
>droYak2.chr3R 2197689 105 - 28832112
GUUCAUCCAAGUUAAGCUGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACUUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAUUUUUAAC
....(((((((((.(((((.....)))))...(((..(((((......)))))..)))))))).((-------...(((.....)))(((....)))))))))......... ( -30.80, z-score =  -2.70, R)
>droEre2.scaffold_4770 9734196 98 + 17746568
-------CAAGUAAAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACUUCGC-------AAUGGGACAAUCCCGAGACGUCUCGCGGAUAUUUUUAAC
-------........((((((.(((....))).....))))))...........((((((.(((((-------...(((.....)))(((....))))))))..)))))).. ( -25.60, z-score =  -1.43, R)
>droAna3.scaffold_13340 12913556 93 + 23697760
-------------------CACUGCAGCUGCACCUUUAUCGAGCCAACUCGAUCUAGGCCCAGUGCACAAAAAAAAGAGACAAUCCCGAGACGUCUUGGGGAUAUUUUUAAC
-------------------...((((.(((..(((..((((((....))))))..)))..)))))))........(((((.(.(((((((....))))))).).)))))... ( -29.30, z-score =  -3.77, R)
>dp4.chr2 25969142 96 - 30794189
-------------UGGGCAGCCAGCAGCUGCACCUUUAUCGCUCACACUGGAUCUGGGCGCUCCAGCGACAAACACGAGACGCGCGCCA---GUCUUGGGGAUAUUUUUAAC
-------------.(((((((.....))))).))..((((.((((....(((.((((((((((...((.......)).)).)))).)))---))))))))))))........ ( -31.90, z-score =  -1.32, R)
>droPer1.super_6 1302705 96 - 6141320
-------------UGGGCAGCCAGCAGCUGCACCUUUAUCGCUCACACUGGAUCUGGGCGCUCCAGCGACAAACACGAGACGCGCGCCA---GUCUUGGGGAUAUUUUUAAC
-------------.(((((((.....))))).))..((((.((((....(((.((((((((((...((.......)).)).)))).)))---))))))))))))........ ( -31.90, z-score =  -1.32, R)
>consensus
_______C_AG__AAGCCGAUCUGCAGCUGCACCUUUAUCGGCACAACUCGAUCUAGGAACUUCGC_______AAUGGGACAAUCCCGAGACGUCUCGCGGAUAUUUUUAAC
.......................((....)).(((..(((((......)))))..))).................((((((...........)))))).............. (-12.84 = -12.57 +  -0.26)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,618,763 – 13,618,863
Length 100
Sequences 8
Columns 116
Reading direction forward
Mean pairwise identity 68.26
Shannon entropy 0.58094
G+C content 0.57489
Mean single sequence MFE -36.99
Consensus MFE -13.62
Energy contribution -14.19
Covariance contribution 0.56
Combinations/Pair 1.37
Mean z-score -1.63
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.599746
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13618763 100 + 27905053
-----UCCCAUUGC--GAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUUGCUCGGA--------GGAGCUGAGGAGCA-AGGAGCAGGCGAGGAUAA
-----..((.((((--...((((((.((((.(((((..((......))..)))))...)))).(((((((((...--------.))))...))))).-))))))..)))))).... ( -41.70, z-score =  -2.72, R)
>droSim1.chr3R 19645720 100 - 27517382
-----UCCCAUUGC--GAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUCGCUCGGA--------GGAGCAGAGGAGCA-AGGAGCAGGCGAGGAUCA
-----..((.((((--...((((((.((((.(((((..((......))..)))))...)))).(((((((((...--------.))))...))))).-))))))..)))))).... ( -43.20, z-score =  -2.97, R)
>droSec1.super_12 1587892 100 - 2123299
-----UCCCAUUGC--GAGGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUCGCUCGGA--------GGAGCAGAGGAGCA-AGGAGCAGGCGAGGAUCA
-----..((.((((--...((((((.((((.(((((..((......))..)))))...)))).(((((((((...--------.))))...))))).-))))))..)))))).... ( -43.20, z-score =  -2.97, R)
>droYak2.chr3R 2197721 109 + 28832112
-----UCCCAUUGC--GAAGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCAGCUUAACUUGGAUGAACAGAGAAGCAGAGGAGCAGAGUAGCAGGCGAGGAUCA
-----((((.((((--...((((((.((((.(((((..((......))..)))))...)))).((((...(((......)))..))))..))))))......))))..).)))... ( -37.30, z-score =  -2.72, R)
>droEre2.scaffold_4770 9734228 101 - 17746568
-----UCCCAUUGC--GAAGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUUACUUGGA--------GGAGCAGAGGAGCAGAAGAGCAGGCGAAGAUCA
-----((((..(((--...((((((.((((.(((((..((......))..)))))...)))).(((((.......--------)))))..))))))......))))).))...... ( -33.20, z-score =  -1.29, R)
>droAna3.scaffold_13340 12913588 91 - 23697760
UCUCUUUUUUUUGUGCACUGGGCCUAGAUCGAGUUGGCUCGAUAAAGGUGCAGCUGCAG--UGG--AAAGUGGAA--------GGGGCAUCAG-GCA-UGGGGUA-----------
.((((((((((..(((((((.((((..((((((....))))))..)))).))).))).)--..)--)))...)))--------)))((..((.-...-))..)).----------- ( -31.90, z-score =  -1.83, R)
>dp4.chr2 25969182 87 + 30794189
----------UCGCU-GGAGCGCCCAGAUCCAGUGUGAGCGAUAAAGGUGCAGCUGCUGGCUGCCCAGA---GAAU-------GGGGCAGGGGGGCA-GGGGGCAGACA-------
----------..(((-...((.(((....(((((((..(((.......))).)).)))))((((((...---....-------.))))))))).)).-...))).....------- ( -32.40, z-score =   0.50, R)
>droPer1.super_6 1302745 87 + 6141320
----------UCGCU-GGAGCGCCCAGAUCCAGUGUGAGCGAUAAAGGUGCAGCUGCUGGCUGCCCAGA---GAAU-------GGGGCGGGGGGGCA-GGGGGCAGGCA-------
----------..(((-...((.(((....(((((((..(((.......))).)).)))))((((((...---....-------.)))))).......-))).)).))).------- ( -33.00, z-score =   0.92, R)
>consensus
_____UCCCAUUGC__GAAGUUCCUAGAUCGAGUUGUGCCGAUAAAGGUGCAGCUGCAGAUCGGCUUAACUCGGA________GGAGCAGAGGAGCA_AGGAGCAGGCGAGGAUCA
...................((.(((......(((((..((......))..)))))((...((.(((...................))).))...))..))).))............ (-13.62 = -14.19 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:23:21 2011