Locus 11301

Sequence ID dm3.chr3R
Location 20,198,110 – 20,198,226
Length 116
Max. P 0.579002
window15532 window15533

overview

Window 2

Location 20,198,110 – 20,198,226
Length 116
Sequences 9
Columns 117
Reading direction forward
Mean pairwise identity 79.51
Shannon entropy 0.41577
G+C content 0.54885
Mean single sequence MFE -33.80
Consensus MFE -19.12
Energy contribution -19.36
Covariance contribution 0.24
Combinations/Pair 1.11
Mean z-score -1.49
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.578347
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20198110 116 + 27905053
GACUGAG-GACUUACCCAUCUGAAAGGAGCUGCCUUCCGGAAAUACCAAAUAACGUCGUUUCCGGGACAACAGCUCCUGGCUGGCUGACUGGUUGUUCUGGUAGGAUGCGGACGCAG
.(((.((-(((..(((..((.(..((((((((..((((((((((((........)).))))))))))...))))))))..).....))..))).))))))))....(((....))). ( -40.10, z-score =  -1.63, R)
>droWil1.scaffold_181108 199615 101 - 4707319
-------CAACUUACCCAUCUGAAAGGAACUGCCCUCCGGAAAUACCAAAUAACGUCGUUUCCUCGACAACAGCUCUU--UCGCUUGACUGCCGGUUGACAACGACUUCG-------
-------...........((((..(((......))).)))).............((((((...(((((..(((.((..--......)))))...))))).))))))....------- ( -19.90, z-score =  -1.21, R)
>droSim1.chr3R 20032992 116 + 27517382
GACUGAG-GACUUACCCAUCUGAAAGGAGCUGCCCUCCGGAAAUACCAAAUAACGUCGUUUCCGGGACAACAGCUCCUGGCUGGCUGACUGGCUGUUCUGGACGGAUGCGGACGCAG
.......-......((((((((..((((((((...(((((((((((........)).)))))))))....))))))))(((..(....)..)))........)))))).))...... ( -41.50, z-score =  -2.12, R)
>droSec1.super_0 20536896 116 + 21120651
GACUGAG-GACUUACCCAUCUGAAAGGAGCUGCCCUCCGGAAAUACCAAAUAACGUCGUUUCCGGGACAACAGCUCCUGGCUGGCUGACUGGCUGUUCUGGACGGAUGCGGACGCAG
.......-......((((((((..((((((((...(((((((((((........)).)))))))))....))))))))(((..(....)..)))........)))))).))...... ( -41.50, z-score =  -2.12, R)
>droYak2.chr3R 2525299 116 - 28832112
GACUGAG-GACUUACCCAUCUGAAAGGAGCUGCCCUCCGGAAAUACCAAAUAACGUCGUUUCCGGGACAACAGCUCCUGGCUGGCUGACUGGCUGUUCUGGACGGAUGCGGACGCAG
.......-......((((((((..((((((((...(((((((((((........)).)))))))))....))))))))(((..(....)..)))........)))))).))...... ( -41.50, z-score =  -2.12, R)
>droEre2.scaffold_4820 2608498 116 - 10470090
GACUGAG-GACUUACCCAUCUGAAAGGAGCUGCCCUCCGGAAAUACCAAAUAACGUCGUUUCCGGGACAACAGCUCCUGGCUGGCUGACUGGCUGUUCUGGACGGAUGCGGACGCAG
.......-......((((((((..((((((((...(((((((((((........)).)))))))))....))))))))(((..(....)..)))........)))))).))...... ( -41.50, z-score =  -2.12, R)
>droAna3.scaffold_13088 238282 111 + 569066
GGCUAACUGACUUACCGAUCUGAAAGGAGCUGCCCUCCGGAAAUACCAAAUAGCGUCGUUUCCUGGACAACAGCUCUU------CCGACCGCCUGCCUUGAACGGAUGCGGAUUGGG
..............((((((((...(((((((...((((((((((((.....).)).)))))).)))...)))))))(------(((..((.......))..))))..)))))))). ( -33.80, z-score =  -1.54, R)
>dp4.chr2 12184087 92 - 30794189
----------CUUACCCAUCUGAAAGGAGCUGCCCUCCGGAAAUACCAAAUAGCGCCGUUUCCUGGACAACAGUUCAU--UCGACUGCGUGGCUCUUCUGGACG-------------
----------.....(((...((..(((((..(..(((((((((..(.......)..)))))).)))...(((((...--..))))).)..))))))))))...------------- ( -22.70, z-score =  -0.44, R)
>droPer1.super_3 6035751 92 - 7375914
----------CUUACCCAUCUGAAAGGAGCUGCCCUCCGGAAAUACCAAAUAGCGCCGUUUCCUGGACAACAGCUCAU--UCGACUGCGUGGCUCUUCUGGACG-------------
----------.((((.((..((((..((((((...(((((((((..(.......)..)))))).)))...)))))).)--)))..)).))))............------------- ( -21.70, z-score =  -0.07, R)
>consensus
GACUGAG_GACUUACCCAUCUGAAAGGAGCUGCCCUCCGGAAAUACCAAAUAACGUCGUUUCCGGGACAACAGCUCCUGGCUGGCUGACUGGCUGUUCUGGACGGAUGCGGACGCAG
........................((((((((...(((((((((..(.......)..)))))).)))...))))))))....................................... (-19.12 = -19.36 +   0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,198,110 – 20,198,226
Length 116
Sequences 9
Columns 117
Reading direction reverse
Mean pairwise identity 79.51
Shannon entropy 0.41577
G+C content 0.54885
Mean single sequence MFE -35.12
Consensus MFE -22.13
Energy contribution -22.67
Covariance contribution 0.53
Combinations/Pair 1.12
Mean z-score -1.27
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.579002
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20198110 116 - 27905053
CUGCGUCCGCAUCCUACCAGAACAACCAGUCAGCCAGCCAGGAGCUGUUGUCCCGGAAACGACGUUAUUUGGUAUUUCCGGAAGGCAGCUCCUUUCAGAUGGGUAAGUC-CUCAGUC
(((.(..(..((((.....((........)).....(..((((((((((...(((((((...((.....))...)))))))..))))))))))..)....))))..)..-).))).. ( -33.70, z-score =  -0.68, R)
>droWil1.scaffold_181108 199615 101 + 4707319
-------CGAAGUCGUUGUCAACCGGCAGUCAAGCGA--AAGAGCUGUUGUCGAGGAAACGACGUUAUUUGGUAUUUCCGGAGGGCAGUUCCUUUCAGAUGGGUAAGUUG-------
-------....(((((((((....))))).)....((--((((((((((.((..(((((...((.....))...))))).)).))))))).))))).)))..........------- ( -26.90, z-score =  -0.39, R)
>droSim1.chr3R 20032992 116 - 27517382
CUGCGUCCGCAUCCGUCCAGAACAGCCAGUCAGCCAGCCAGGAGCUGUUGUCCCGGAAACGACGUUAUUUGGUAUUUCCGGAGGGCAGCUCCUUUCAGAUGGGUAAGUC-CUCAGUC
(((.(..(..(((((((..(((..((......)).....((((((((((.(((.(((((...((.....))...)))))))).))))))))))))).)))))))..)..-).))).. ( -40.90, z-score =  -2.11, R)
>droSec1.super_0 20536896 116 - 21120651
CUGCGUCCGCAUCCGUCCAGAACAGCCAGUCAGCCAGCCAGGAGCUGUUGUCCCGGAAACGACGUUAUUUGGUAUUUCCGGAGGGCAGCUCCUUUCAGAUGGGUAAGUC-CUCAGUC
(((.(..(..(((((((..(((..((......)).....((((((((((.(((.(((((...((.....))...)))))))).))))))))))))).)))))))..)..-).))).. ( -40.90, z-score =  -2.11, R)
>droYak2.chr3R 2525299 116 + 28832112
CUGCGUCCGCAUCCGUCCAGAACAGCCAGUCAGCCAGCCAGGAGCUGUUGUCCCGGAAACGACGUUAUUUGGUAUUUCCGGAGGGCAGCUCCUUUCAGAUGGGUAAGUC-CUCAGUC
(((.(..(..(((((((..(((..((......)).....((((((((((.(((.(((((...((.....))...)))))))).))))))))))))).)))))))..)..-).))).. ( -40.90, z-score =  -2.11, R)
>droEre2.scaffold_4820 2608498 116 + 10470090
CUGCGUCCGCAUCCGUCCAGAACAGCCAGUCAGCCAGCCAGGAGCUGUUGUCCCGGAAACGACGUUAUUUGGUAUUUCCGGAGGGCAGCUCCUUUCAGAUGGGUAAGUC-CUCAGUC
(((.(..(..(((((((..(((..((......)).....((((((((((.(((.(((((...((.....))...)))))))).))))))))))))).)))))))..)..-).))).. ( -40.90, z-score =  -2.11, R)
>droAna3.scaffold_13088 238282 111 - 569066
CCCAAUCCGCAUCCGUUCAAGGCAGGCGGUCGG------AAGAGCUGUUGUCCAGGAAACGACGCUAUUUGGUAUUUCCGGAGGGCAGCUCCUUUCAGAUCGGUAAGUCAGUUAGCC
.((...((((..((......))...))))..((------((((((((((.(((.(((((..((........)).)))))))).))))))).))))).....)).............. ( -36.70, z-score =  -1.22, R)
>dp4.chr2 12184087 92 + 30794189
-------------CGUCCAGAAGAGCCACGCAGUCGA--AUGAACUGUUGUCCAGGAAACGGCGCUAUUUGGUAUUUCCGGAGGGCAGCUCCUUUCAGAUGGGUAAG----------
-------------((((..((((.(((..(((((...--....)))))......(....))))(((.(((((.....))))).))).....))))..))))......---------- ( -25.10, z-score =   0.29, R)
>droPer1.super_3 6035751 92 + 7375914
-------------CGUCCAGAAGAGCCACGCAGUCGA--AUGAGCUGUUGUCCAGGAAACGGCGCUAUUUGGUAUUUCCGGAGGGCAGCUCCUUUCAGAUGGGUAAG----------
-------------...........(((.....(((((--(.((((((((.(((.(((((..((........)).)))))))).))))))))..))).))).)))...---------- ( -30.10, z-score =  -0.99, R)
>consensus
CUGCGUCCGCAUCCGUCCAGAACAGCCAGUCAGCCAGCCAGGAGCUGUUGUCCCGGAAACGACGUUAUUUGGUAUUUCCGGAGGGCAGCUCCUUUCAGAUGGGUAAGUC_CUCAGUC
........................(((.(((..........((((((((.(((.(((((..((........)).)))))))).))))))))......))).)))............. (-22.13 = -22.67 +   0.53)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:40:18 2011