Locus 5345

Sequence ID dm3.chr2R
Location 19,630,883 – 19,630,980
Length 97
Max. P 0.998222
window7332 window7333

overview

Window 2

Location 19,630,883 – 19,630,980
Length 97
Sequences 7
Columns 104
Reading direction forward
Mean pairwise identity 67.14
Shannon entropy 0.57906
G+C content 0.46904
Mean single sequence MFE -20.57
Consensus MFE -13.17
Energy contribution -14.27
Covariance contribution 1.11
Combinations/Pair 1.17
Mean z-score -2.20
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.29
SVM RNA-class probability 0.998222
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19630883 97 + 21146708
-----ACCCUCCUCUCCACAAGUGAGAACAUCAAACAAAUGUGUUCACA--UAUCUUCGCCUCGAGGGAAAGUGCAUUGCACCUUCCCAGCACCCAACACCCAA
-----................(((((.((((.......)))).))))).--..............(((((.((((...)))).)))))................ ( -19.90, z-score =  -2.09, R)
>droEre2.scaffold_4845 20994029 89 + 22589142
-----ACCCCCAGCUCA-CGAGUGAGAACAUCAAACAAAUGUCUUCACA--UAUCUCCGGCUCGAGGGAAAGUGCAUUGCACCUUCCCAACUCCCAG-------
-----....(.((((..-.((((((..((((.......))))..)))).--..))...)))).).(((((.((((...)))).))))).........------- ( -22.10, z-score =  -2.38, R)
>droYak2.chr2R 19609028 96 + 21139217
-----ACCCCCCGCUCC-GGAGUGAGAACAUCAAACAAAUGUCUUCACA--UAUCUCCAACUCGAGGGAAAGUGCAUUGCACCUUCCCAGCUCGCAACUCCCAA
-----.......(((..-(((((((..((((.......))))..)))).--....))).......(((((.((((...)))).))))))))............. ( -23.70, z-score =  -2.51, R)
>droSec1.super_9 2911094 94 + 3197100
-CCCCCCACAUCAUCUCACAAGUGAGAACAUCAAACAAAUGUGUUCACA--UAUCUCCGCCUCGAGGGAAAGUGCAUUGCACCUUCCCAACACCCAA-------
-............(((((....))))).............(((((....--..((........))(((((.((((...)))).))))))))))....------- ( -20.50, z-score =  -2.82, R)
>droSim1.chr2R 18197137 95 + 19596830
CCCCCCCUCAUCCUCUUACAAGUGAGAACAUCAAACAAAUGUGUUCACA--UAUCUCCGCCUCGAGGGAAAGUGCAUUGCACCUUCCCAACACCCAA-------
.....................(((((.((((.......)))).))))).--..............(((((.((((...)))).))))).........------- ( -19.90, z-score =  -2.82, R)
>dp4.chr3 10413701 90 - 19779522
-------CCACUCCAUCAAAAAUACAUAGAUUUUUGGAGUGCCCACACAAAUAUCUGAGAGCAAAGGGAAAGUGCAUUGCACCUUUUCUUUAAGAAA-------
-------.(((((((...(((((......)))))))))))).....................((((..((.((((...)))).))..))))......------- ( -19.40, z-score =  -1.62, R)
>droPer1.super_4 2473676 90 - 7162766
-------CCACUCCAUCAAAAAUACAUAGAUCUUUGGAGUGCCCACACAAAUAUCUGAGAGCAAAGGGAAAGUGCAUUGCACCUUUUCUUUAAGAAA-------
-------.(((((((...................))))))).....................((((..((.((((...)))).))..))))......------- ( -18.51, z-score =  -1.17, R)
>consensus
_____ACCCACCCCUUCACAAGUGAGAACAUCAAACAAAUGUCUUCACA__UAUCUCCGACUCGAGGGAAAGUGCAUUGCACCUUCCCAACACCCAA_______
.....................(((((.((((.......)))).))))).................(((((.((((...)))).)))))................ (-13.17 = -14.27 +   1.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,630,883 – 19,630,980
Length 97
Sequences 7
Columns 104
Reading direction reverse
Mean pairwise identity 67.14
Shannon entropy 0.57906
G+C content 0.46904
Mean single sequence MFE -27.82
Consensus MFE -17.37
Energy contribution -17.37
Covariance contribution 0.01
Combinations/Pair 1.26
Mean z-score -1.35
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.83
SVM RNA-class probability 0.970358
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19630883 97 - 21146708
UUGGGUGUUGGGUGCUGGGAAGGUGCAAUGCACUUUCCCUCGAGGCGAAGAUA--UGUGAACACAUUUGUUUGAUGUUCUCACUUGUGGAGAGGAGGGU-----
(((.(((((...((((((((((((((...))))))))))....))))..))))--).)))..(((((.....)))))((((.(((.....)))))))..----- ( -29.10, z-score =  -0.91, R)
>droEre2.scaffold_4845 20994029 89 - 22589142
-------CUGGGAGUUGGGAAGGUGCAAUGCACUUUCCCUCGAGCCGGAGAUA--UGUGAAGACAUUUGUUUGAUGUUCUCACUCG-UGAGCUGGGGGU-----
-------.........((((((((((...)))))))))).....((((.....--.((((..(((((.....)))))..))))...-....))))....----- ( -31.42, z-score =  -1.81, R)
>droYak2.chr2R 19609028 96 - 21139217
UUGGGAGUUGCGAGCUGGGAAGGUGCAAUGCACUUUCCCUCGAGUUGGAGAUA--UGUGAAGACAUUUGUUUGAUGUUCUCACUCC-GGAGCGGGGGGU-----
((.(((((.(.((((.((((((((((...))))))))))....((..((.(.(--(((....)))).).))..)))))).))))))-.)).........----- ( -34.30, z-score =  -1.92, R)
>droSec1.super_9 2911094 94 - 3197100
-------UUGGGUGUUGGGAAGGUGCAAUGCACUUUCCCUCGAGGCGGAGAUA--UGUGAACACAUUUGUUUGAUGUUCUCACUUGUGAGAUGAUGUGGGGGG-
-------(((.(((((((((((((((...))))))))))((......))))))--).))).((((((..........(((((....))))).)))))).....- ( -27.40, z-score =  -0.92, R)
>droSim1.chr2R 18197137 95 - 19596830
-------UUGGGUGUUGGGAAGGUGCAAUGCACUUUCCCUCGAGGCGGAGAUA--UGUGAACACAUUUGUUUGAUGUUCUCACUUGUAAGAGGAUGAGGGGGGG
-------....((((((........)))))).((..(((((....((((.(.(--(((....)))).).))))..((((((........)))))))))))..)) ( -27.80, z-score =  -1.17, R)
>dp4.chr3 10413701 90 + 19779522
-------UUUCUUAAAGAAAAGGUGCAAUGCACUUUCCCUUUGCUCUCAGAUAUUUGUGUGGGCACUCCAAAAAUCUAUGUAUUUUUGAUGGAGUGG-------
-------......((((..(((((((...)))))))..))))((((.((.(....).)).))))(((((((((((......)))))...))))))..------- ( -22.30, z-score =  -1.53, R)
>droPer1.super_4 2473676 90 + 7162766
-------UUUCUUAAAGAAAAGGUGCAAUGCACUUUCCCUUUGCUCUCAGAUAUUUGUGUGGGCACUCCAAAGAUCUAUGUAUUUUUGAUGGAGUGG-------
-------......((((..(((((((...)))))))..))))((((.((.(....).)).))))(((((((((((......)))))...))))))..------- ( -22.40, z-score =  -1.15, R)
>consensus
_______UUGGGUGUUGGGAAGGUGCAAUGCACUUUCCCUCGAGGCGGAGAUA__UGUGAAGACAUUUGUUUGAUGUUCUCACUUGUGAAGGGGUGGGU_____
................((((((((((...)))))))))).................((((..(((((.....)))))..))))..................... (-17.37 = -17.37 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:46:30 2011