Locus 15259

Sequence ID dm3.chrX
Location 18,152,838 – 18,152,942
Length 104
Max. P 0.999966
window21022 window21023

overview

Window 2

Location 18,152,838 – 18,152,942
Length 104
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 63.91
Shannon entropy 0.66114
G+C content 0.47406
Mean single sequence MFE -36.63
Consensus MFE -14.62
Energy contribution -15.52
Covariance contribution 0.90
Combinations/Pair 1.40
Mean z-score -4.58
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 5.24
SVM RNA-class probability 0.999959
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18152838 104 + 22422827
--------AGAGACAUC-UCAAAGAGA--ACCCUACCAAGCCUUGCAC-UGAUCUAUCUAUACAUAUCGUAGAUCUCUGCCAGGCUUGGUAGUGUAUCUCUACAGGAUAUCAUGCC
--------...((.(((-(...(((((--((.(((((((((((.(((.-.(((((((...........)))))))..))).))))))))))).)).)))))...)))).))..... ( -43.10, z-score =  -6.23, R)
>droEre2.scaffold_4690 8480911 91 + 18748788
----------------------AGAGAC-ACUCGCCCAAGCCUCCCAC-AGAUCUAUGCACACAU-UCAUAGAUCUCUGCCAGACUUGGCAGCGUAUCUCUUCGGGAUCUCAUUCC
----------------------.((((.-....((....)).((((..-(((((((((.......-.)))))))))(((((......)))))...........))))))))..... ( -28.20, z-score =  -3.42, R)
>droYak2.chrX 16783544 103 + 21770863
--------AGAGACAUCCUCCUAAAGAUAACUCUCUCAAGCCUUGCAC-AGAUCUAU----ACAUAUCAUAGAUCUCUGCCAGACUUGGUAGCGCAUCUCCUCGGCAUCUCAUUCC
--------.((((...((......((((..(.((..((((.((.(((.-((((((((----.......)))))))).))).)).))))..)).).))))....))..))))..... ( -25.80, z-score =  -2.55, R)
>droSec1.super_8 465743 100 + 3762037
--------AGAGACAUC-UCAAAGAGA--ACUCUACCAAGCCUUGCAC-CGAUCUAU----ACAUAUCGUAGAUCUCUGCCAGGCUUGGUAGUGUAUCUCUACAGGAUCUCAUGCA
--------.((((..((-(...(((((--((.(((((((((((.(((.-.(((((((----.......)))))))..))).))))))))))).)).)))))...)))))))..... ( -45.20, z-score =  -7.03, R)
>droSim1.chrX_random 4718484 100 + 5698898
--------AGAGACAUC-UCAAAGAGA--ACUCUACCAAGCCUUGCAC-CGAUCUAU----ACAAAUCGUAGAUCUCUGCCAGGCUUGGUAGUGUAUCUCUACAGGAUCUCAUGCC
--------.((((..((-(...(((((--((.(((((((((((.(((.-.(((((((----.......)))))))..))).))))))))))).)).)))))...)))))))..... ( -45.20, z-score =  -7.38, R)
>dp4.chrXL_group3a 123639 104 + 2690836
AGUUAAGCUGGGACUUA-GCUAAAAGAACAUACUCACUGGCGAUGGACGCGGUGUAA----GAGCCGAAAGGGGGUCUGACCCUUUAGAAGGCAGUUCACGGCGAAGCU-------
((((..(((((((((..-................(((((.((.....)))))))...----..(((.((((((.......))))))....)))))))).))))..))))------- ( -32.30, z-score =  -0.87, R)
>consensus
________AGAGACAUC_UCAAAGAGA__ACUCUACCAAGCCUUGCAC_CGAUCUAU____ACAUAUCAUAGAUCUCUGCCAGGCUUGGUAGCGUAUCUCUACAGGAUCUCAUGCC
......................(((((...(.((.(((((.((.(((...(((((((...........)))))))..))).)).))))).)).)..)))))............... (-14.62 = -15.52 +   0.90)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,152,838 – 18,152,942
Length 104
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 63.91
Shannon entropy 0.66114
G+C content 0.47406
Mean single sequence MFE -39.48
Consensus MFE -20.65
Energy contribution -22.49
Covariance contribution 1.84
Combinations/Pair 1.28
Mean z-score -4.01
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 5.33
SVM RNA-class probability 0.999966
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18152838 104 - 22422827
GGCAUGAUAUCCUGUAGAGAUACACUACCAAGCCUGGCAGAGAUCUACGAUAUGUAUAGAUAGAUCA-GUGCAAGGCUUGGUAGGGU--UCUCUUUGA-GAUGUCUCU--------
.....(((((((...(((((.((.(((((((((((.(((..(((((((..........).)))))).-.))).))))))))))).))--)))))..).-))))))...-------- ( -44.60, z-score =  -4.82, R)
>droEre2.scaffold_4690 8480911 91 - 18748788
GGAAUGAGAUCCCGAAGAGAUACGCUGCCAAGUCUGGCAGAGAUCUAUGA-AUGUGUGCAUAGAUCU-GUGGGAGGCUUGGGCGAGU-GUCUCU----------------------
(((......)))...((((((((..((((((((((..((.(((((((((.-.......)))))))))-.))..)))))).)))).))-))))))---------------------- ( -40.60, z-score =  -4.67, R)
>droYak2.chrX 16783544 103 - 21770863
GGAAUGAGAUGCCGAGGAGAUGCGCUACCAAGUCUGGCAGAGAUCUAUGAUAUGU----AUAGAUCU-GUGCAAGGCUUGAGAGAGUUAUCUUUAGGAGGAUGUCUCU--------
.....((((((((..((((((((.((..(((((((.(((.(((((((((.....)----))))))))-.))).)))))))..)).).)))))))....)).)))))).-------- ( -41.30, z-score =  -4.40, R)
>droSec1.super_8 465743 100 - 3762037
UGCAUGAGAUCCUGUAGAGAUACACUACCAAGCCUGGCAGAGAUCUACGAUAUGU----AUAGAUCG-GUGCAAGGCUUGGUAGAGU--UCUCUUUGA-GAUGUCUCU--------
.....(((((.((..(((((.((.(((((((((((.(((..((((((........----.)))))).-.))).))))))))))).))--)))))...)-)..))))).-------- ( -43.40, z-score =  -4.95, R)
>droSim1.chrX_random 4718484 100 - 5698898
GGCAUGAGAUCCUGUAGAGAUACACUACCAAGCCUGGCAGAGAUCUACGAUUUGU----AUAGAUCG-GUGCAAGGCUUGGUAGAGU--UCUCUUUGA-GAUGUCUCU--------
.....(((((.((..(((((.((.(((((((((((.(((..((((((........----.)))))).-.))).))))))))))).))--)))))...)-)..))))).-------- ( -43.40, z-score =  -4.81, R)
>dp4.chrXL_group3a 123639 104 - 2690836
-------AGCUUCGCCGUGAACUGCCUUCUAAAGGGUCAGACCCCCUUUCGGCUC----UUACACCGCGUCCAUCGCCAGUGAGUAUGUUCUUUUAGC-UAAGUCCCAGCUUAACU
-------.(((.......((((.(((....((((((.......)))))).))).(----((((...(((.....)))..)))))...))))....)))-(((((....)))))... ( -23.60, z-score =  -0.41, R)
>consensus
GGCAUGAGAUCCCGUAGAGAUACACUACCAAGCCUGGCAGAGAUCUACGAUAUGU____AUAGAUCG_GUGCAAGGCUUGGGAGAGU__UCUCUUUGA_GAUGUCUCU________
...............(((((....(((((((((((.(((..((((((.............))))))...))).))))))))))).....)))))...................... (-20.65 = -22.49 +   1.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:55:58 2011