Locus 12211

Sequence ID dm3.chr3R
Location 26,501,835 – 26,501,928
Length 93
Max. P 0.999221
window16791 window16792

overview

Window 1

Location 26,501,835 – 26,501,928
Length 93
Sequences 10
Columns 105
Reading direction forward
Mean pairwise identity 66.70
Shannon entropy 0.67278
G+C content 0.57506
Mean single sequence MFE -30.14
Consensus MFE -14.40
Energy contribution -14.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.28
SVM RNA-class probability 0.987485
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26501835 93 + 27905053
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUCCGCCUCCGUCUCUUUGGCCCAGAACUCCGGAUUUUGGUUCGGACUUGGAGACU------------
.....(((((((((...........))))))))).(((((((((...........))).......(((((((....)))))))...)))))).------------ ( -36.00, z-score =  -2.90, R)
>droSim1.chr3R 26148935 93 + 27517382
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGCCUCCGCCUCCGUCUCUUUGGCCCAGGACUCCGGAUUUUGGUUCGGACUUGGAGACU------------
.....(((((((((...........)))))))))...((((.(((..(((.....)))..)))..(((((((....)))))))...))))...------------ ( -33.00, z-score =  -1.32, R)
>droSec1.super_4 5328326 93 + 6179234
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGCCUCCGCCUCCGUCUCUUUGGUCCAGGACUCCGGAUUUUGGUUCGGAUUUGGAGACU------------
.....(((((((((...........)))))))))...(((((..((((...((..(((((.((...)))))))..))..))))..)))))...------------ ( -34.80, z-score =  -2.01, R)
>droYak2.chr3R 27427539 93 + 28832112
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUCCGCCUCCGUCUCUUUGGUCCAGGACUCCGGACUUUGGUUCAUACUUGGAGACU------------
.....(((((((((...........))))))))).(((((((.........((..(((((.((...)))))))..))........))))))).------------ ( -33.33, z-score =  -2.67, R)
>droAna3.scaffold_12911 882804 105 - 5364042
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUCCGACUCCAUCUCCUUGGAUCUCGGACGCGGACACCAACACGGACACGGACAAGGACUUGGAGACU
.....(((((((((...........))))))))).((((((((.(((...((....))....(..((.(..(........)..).))..)..))).)))))))). ( -38.10, z-score =  -3.25, R)
>dp4.chr2 30093606 89 - 30794189
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUCCGACUCCGCCUCU---GCCUCCGAGUCCAUUCUCUGUCUCCAUCUCCUUGGA-------------
.....(((((((((...........))))))))).......(((((.((....---))....)))))...........((((......))))------------- ( -23.00, z-score =  -1.73, R)
>droPer1.super_7 959576 89 - 4445127
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUCCGACUCCGCCUCC---GCCUCCGAGUCCAUUCUCUGUCUCCAUCUCCUUGGA-------------
.....(((((((((...........))))))))).......(((((.((....---))....)))))...........((((......))))------------- ( -23.10, z-score =  -1.73, R)
>droMoj3.scaffold_6540 3692724 100 - 34148556
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUUUGGUGGCUCGAGCUGGAA-CUGGCACU--GGCACUGGAACUGACUCCGACUCCGACUCCCAAA--
.....(((((((((...........))))))))).....((((..(.(((.((..(..-......).--.))..((((......))))....))))..)))).-- ( -30.40, z-score =  -0.55, R)
>droVir3.scaffold_13047 11295268 100 + 19223366
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUUUGGCGCCUUAAACUCGAA-CUAGAACU--GGAACUGGAACUGACUCCGACUCCGACUCCCAAC--
.....(((((((((...........))))))))).((((((((..(.........)..-)))))...--(((..((((......))))..)))))).......-- ( -24.50, z-score =  -1.44, R)
>droGri2.scaffold_14624 1294876 88 + 4233967
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUUUGGUGGCGC---CUCGAA-CUCGAACU--GGGAAUCGGACUG----CGAAUCGGACCA-------
.((...((((((((...........))))))))((((.((((((..(.(---((((..-..)))...--))).))))))..)----)))...))....------- ( -25.20, z-score =   0.65, R)
>consensus
ACCUUAUGGCCGCACAUUAUCGGCAUGCGGCCAUCGUCUCCGCCUCCGUCUCCUUGGACCAGGAAUCCGGACUCUGGUUCGGACUCCGAGACU____________
.....(((((((((...........)))))))))....................................................................... (-14.40 = -14.40 +   0.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 2

Location 26,501,835 – 26,501,928
Length 93
Sequences 10
Columns 105
Reading direction reverse
Mean pairwise identity 66.70
Shannon entropy 0.67278
G+C content 0.57506
Mean single sequence MFE -35.54
Consensus MFE -17.40
Energy contribution -17.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.72
SVM RNA-class probability 0.999221
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26501835 93 - 27905053
------------AGUCUCCAAGUCCGAACCAAAAUCCGGAGUUCUGGGCCAAAGAGACGGAGGCGGAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
------------.((((((...((((........(((((....))))).........))))...)))))).((((((((((.........))))))))))..... ( -37.63, z-score =  -2.88, R)
>droSim1.chr3R 26148935 93 - 27517382
------------AGUCUCCAAGUCCGAACCAAAAUCCGGAGUCCUGGGCCAAAGAGACGGAGGCGGAGGCGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
------------.((((((...((((..........))))((((((...........))).))))))))).((((((((((.........))))))))))..... ( -36.80, z-score =  -1.94, R)
>droSec1.super_4 5328326 93 - 6179234
------------AGUCUCCAAAUCCGAACCAAAAUCCGGAGUCCUGGACCAAAGAGACGGAGGCGGAGGCGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
------------.((((((...((((........(((((....))))).........))))...)))))).((((((((((.........))))))))))..... ( -38.43, z-score =  -3.15, R)
>droYak2.chr3R 27427539 93 - 28832112
------------AGUCUCCAAGUAUGAACCAAAGUCCGGAGUCCUGGACCAAAGAGACGGAGGCGGAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
------------.((((((..((....))....((((((....)))))).........))))))(....).((((((((((.........))))))))))..... ( -36.70, z-score =  -3.38, R)
>droAna3.scaffold_12911 882804 105 + 5364042
AGUCUCCAAGUCCUUGUCCGUGUCCGUGUUGGUGUCCGCGUCCGAGAUCCAAGGAGAUGGAGUCGGAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
.((((((.(.(((.(.(((.((...((.((((((....)).)))).)).)).))).).))).).)))))).((((((((((.........))))))))))..... ( -43.80, z-score =  -3.42, R)
>dp4.chr2 30093606 89 + 30794189
-------------UCCAAGGAGAUGGAGACAGAGAAUGGACUCGGAGGC---AGAGGCGGAGUCGGAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
-------------(((.......((....))(((......))))))(((---(...((((.((((....))))..)))).))))...........(((....))) ( -33.00, z-score =  -3.53, R)
>droPer1.super_7 959576 89 + 4445127
-------------UCCAAGGAGAUGGAGACAGAGAAUGGACUCGGAGGC---GGAGGCGGAGUCGGAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
-------------(((.......((....))(((......))))))(((---(...((((.((((....))))..)))).))))...........(((....))) ( -32.30, z-score =  -2.99, R)
>droMoj3.scaffold_6540 3692724 100 + 34148556
--UUUGGGAGUCGGAGUCGGAGUCAGUUCCAGUGCC--AGUGCCAG-UUCCAGCUCGAGCCACCAAAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
--(((((..((..((((.((((...((.(.......--.).))...-)))).))))..))..)))))....((((((((((.........))))))))))..... ( -33.10, z-score =  -0.83, R)
>droVir3.scaffold_13047 11295268 100 - 19223366
--GUUGGGAGUCGGAGUCGGAGUCAGUUCCAGUUCC--AGUUCUAG-UUCGAGUUUAAGGCGCCAAAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
--(((.((.(((((((..((((....))))..))))--..(((...-...))).....))).))...))).((((((((((.........))))))))))..... ( -34.80, z-score =  -2.29, R)
>droGri2.scaffold_14624 1294876 88 - 4233967
-------UGGUCCGAUUCG----CAGUCCGAUUCCC--AGUUCGAG-UUCGAG---GCGCCACCAAAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
-------((((.((.((((----.((..(((.....--...)))..-))))))---.))..))))......((((((((((.........))))))))))..... ( -28.80, z-score =  -0.79, R)
>consensus
____________AGUCUCCGAGUCCGAACCAGAGUCCGGAGUCCAGGGCCAAAGAGACGGAGGCGGAGACGAUGGCCGCAUGCCGAUAAUGUGCGGCCAUAAGGU
.......................................................................((((((((((.........))))))))))..... (-17.40 = -17.40 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:57:52 2011