Locus 769

Sequence ID dm3.chr2L
Location 5,453,067 – 5,453,139
Length 72
Max. P 0.999542
window1036 window1037

overview

Window 6

Location 5,453,067 – 5,453,139
Length 72
Sequences 9
Columns 82
Reading direction forward
Mean pairwise identity 56.38
Shannon entropy 0.88107
G+C content 0.55933
Mean single sequence MFE -16.75
Consensus MFE -7.68
Energy contribution -7.88
Covariance contribution 0.20
Combinations/Pair 1.60
Mean z-score -2.11
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.99
SVM RNA-class probability 0.999542
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5453067 72 + 23011544
---UAUAGCAUACACCUCCG-AAAGUGGAUAGCGCCAACUGGCGCAUCAAACCCA------CCCCCAGACUCAUCCUUACCC
---.........(((.....-...)))(((.(((((....)))))))).......------..................... ( -13.70, z-score =  -2.25, R)
>droSim1.chr2L 5255845 72 + 22036055
---UAUAGCAUACACCUCCG-AAAGUGGGUAGCGCCAACUGGCGCAUCAAACCCA------CCACCAGACUCAUCCUUACCC
---.................-...((((((.(((((....))))).....)))))------).................... ( -18.10, z-score =  -2.95, R)
>droSec1.super_5 3527258 72 + 5866729
---UAUAGCAUACACCUCCG-AAAGUGGGUAGCGCCAACUGUAGCAUCAAACCCA------CCACCAGACUCAUCCUUUCCC
---....((.((((((..(.-...)..)))((......)))))))..........------..................... (  -9.60, z-score =  -0.19, R)
>droYak2.chr2L 8580350 78 - 22324452
---CACACAGUACACCUCCG-AGAGUGGGUAGCGCCAACUGGCGCAUCGAGCCCAAAUUCACCCCCUGACUCAUCCUUUCCC
---................(-((((.((((.(((((....)))))...(((......))))))).))..))).......... ( -19.80, z-score =  -1.73, R)
>droEre2.scaffold_4929 5537266 57 + 26641161
------------------AGUAAAGUGGGUAGCGCCAACUGGCGCAUCGAACUCAC-----CCCU--GACUCAUCCUUUUCC
------------------(((..((.((((.(((((....)))))...(....)))-----))))--.)))........... ( -16.10, z-score =  -1.87, R)
>droAna3.scaffold_12916 6479557 72 - 16180835
---CACAUAAGCCGCCUCUAAAAAGUGGGAAGCGCCAACUGGCGCACAGAACUCAU-----CCCCUAAACUCACUCCUCU--
---....................((.((((.(((((....)))))...(....).)-----)))))..............-- ( -16.10, z-score =  -1.99, R)
>dp4.chr4_group1 4758334 69 + 5278887
UACUCGAAGGUGCACCUUCG-------CGUAGCGCCAACCGGCGCACAAGACUCGGAACCACCCCCAUCCCGACUC------
(((.((((((....))))))-------.)))(((((....)))))....((.((((.............)))).))------ ( -25.22, z-score =  -3.99, R)
>droPer1.super_5 6354019 69 - 6813705
UACUCGAAGGUGCACCUUCG-------CGUAGCGCCAACCGGCGCACAAGACUCGGAACCACCCCCAUCCCGACUC------
(((.((((((....))))))-------.)))(((((....)))))....((.((((.............)))).))------ ( -25.22, z-score =  -3.99, R)
>droGri2.scaffold_15252 5913488 64 - 17193109
---UAAAGAGUACACCUCUC--AUGGAAGUCACAGUGAAAGUCAUUCCAUCCCCAC-----CCCCUCCACACAC--------
---....(((.......)))--((((((...((.......))..))))))......-----.............-------- (  -6.90, z-score =  -0.02, R)
>consensus
___UAUAGAAUACACCUCCG_AAAGUGGGUAGCGCCAACUGGCGCAUCAAACCCA______CCCCCAGACUCAUCCUU_CCC
...............................(((((....)))))..................................... ( -7.68 =  -7.88 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,453,067 – 5,453,139
Length 72
Sequences 9
Columns 82
Reading direction reverse
Mean pairwise identity 56.38
Shannon entropy 0.88107
G+C content 0.55933
Mean single sequence MFE -24.58
Consensus MFE -7.12
Energy contribution -7.19
Covariance contribution 0.06
Combinations/Pair 1.60
Mean z-score -1.46
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.862231
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5453067 72 - 23011544
GGGUAAGGAUGAGUCUGGGGG------UGGGUUUGAUGCGCCAGUUGGCGCUAUCCACUUU-CGGAGGUGUAUGCUAUA---
.((((...(((..((((..((------(((((.....(((((....))))).)))))))..-))))..))).))))...--- ( -30.90, z-score =  -3.99, R)
>droSim1.chr2L 5255845 72 - 22036055
GGGUAAGGAUGAGUCUGGUGG------UGGGUUUGAUGCGCCAGUUGGCGCUACCCACUUU-CGGAGGUGUAUGCUAUA---
.((((...(((..(((((.((------(((((.....(((((....))))).))))))).)-))))..))).))))...--- ( -29.80, z-score =  -3.09, R)
>droSec1.super_5 3527258 72 - 5866729
GGGAAAGGAUGAGUCUGGUGG------UGGGUUUGAUGCUACAGUUGGCGCUACCCACUUU-CGGAGGUGUAUGCUAUA---
.....((.(((..(((((.((------(((((..(.(((((....)))))).))))))).)-))))....))).))...--- ( -22.50, z-score =  -1.24, R)
>droYak2.chr2L 8580350 78 + 22324452
GGGAAAGGAUGAGUCAGGGGGUGAAUUUGGGCUCGAUGCGCCAGUUGGCGCUACCCACUCU-CGGAGGUGUACUGUGUG---
(((......((((((..((......))..))))))..(((((....)))))..))).....-((.((.....)).))..--- ( -23.10, z-score =   0.54, R)
>droEre2.scaffold_4929 5537266 57 - 26641161
GGAAAAGGAUGAGUC--AGGG-----GUGAGUUCGAUGCGCCAGUUGGCGCUACCCACUUUACU------------------
.....((...((((.--..((-----(((........(((((....))))))))))))))..))------------------ ( -15.90, z-score =  -0.37, R)
>droAna3.scaffold_12916 6479557 72 + 16180835
--AGAGGAGUGAGUUUAGGGG-----AUGAGUUCUGUGCGCCAGUUGGCGCUUCCCACUUUUUAGAGGCGGCUUAUGUG---
--......(((((((..((((-----(..........(((((....)))))))))).(((....)))..)))))))...--- ( -19.40, z-score =   0.27, R)
>dp4.chr4_group1 4758334 69 - 5278887
------GAGUCGGGAUGGGGGUGGUUCCGAGUCUUGUGCGCCGGUUGGCGCUACG-------CGAAGGUGCACCUUCGAGUA
------((.(((((((.......))))))).))....(((((....)))))(((.-------((((((....)))))).))) ( -30.50, z-score =  -2.04, R)
>droPer1.super_5 6354019 69 + 6813705
------GAGUCGGGAUGGGGGUGGUUCCGAGUCUUGUGCGCCGGUUGGCGCUACG-------CGAAGGUGCACCUUCGAGUA
------((.(((((((.......))))))).))....(((((....)))))(((.-------((((((....)))))).))) ( -30.50, z-score =  -2.04, R)
>droGri2.scaffold_15252 5913488 64 + 17193109
--------GUGUGUGGAGGGG-----GUGGGGAUGGAAUGACUUUCACUGUGACUUCCAU--GAGAGGUGUACUCUUUA---
--------....(((((((..-----(..((((.(......).))).)..)..)))))))--(((((.....)))))..--- ( -18.60, z-score =  -1.17, R)
>consensus
GGG_AAGGAUGAGUCUGGGGG______UGGGUUUGAUGCGCCAGUUGGCGCUACCCACUUU_CGGAGGUGUACGCUAUA___
.....................................(((((....)))))............................... ( -7.12 =  -7.19 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:19:05 2011