Locus 13455

Sequence ID dm3.chrX
Location 6,640,800 – 6,640,991
Length 191
Max. P 0.981764
window18529 window18530 window18531 window18532

overview

Window 9

Location 6,640,800 – 6,640,911
Length 111
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 76.96
Shannon entropy 0.37538
G+C content 0.53780
Mean single sequence MFE -37.20
Consensus MFE -24.32
Energy contribution -24.20
Covariance contribution -0.12
Combinations/Pair 1.27
Mean z-score -2.44
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.08
SVM RNA-class probability 0.981764
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6640800 111 + 22422827
UCACAAAAAAAAAAAAAACGAGGCGGGAUCAAGGGUAGCGUGAUCAUGAUGAUCAUGAUCAUCAAGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG---UGACUAUGGCCAG
.....................(((..(((((.((((.(((((....(((((((....)))))))..))))).))))....))))).)))...((((((---(....))))))). ( -39.80, z-score =  -4.57, R)
>droEre2.scaffold_4690 15566930 91 + 18748788
--------------UCAUAGAGGCGGGAUCAAGGGCAGC---------AUGGUCAUGAUCAGCGAGCAUGCAGCUCAAGAUGCUUAGCCGAGUGGCCGAGGUGACUGCGGCUGG
--------------.......(((((.(((..((((.((---------(((.((.........)).))))).))))..))).))..)))....(((((((....)).))))).. ( -35.80, z-score =  -1.59, R)
>droYak2.chrX 2603905 88 + 21770863
--------------UCAUAGAGGCGGGAUCAAGGGCAGC---------AUGAUCAUGAUCAGCACGCAUGCAGCUCGAGAUGAUCAGCUGAGUGGCCG---UGACUGUGGCCAG
--------------((((((..((((..(((....((((---------.(((((((..(((((.........))).)).)))))))))))..))))))---)..)))))).... ( -29.70, z-score =  -0.14, R)
>droSec1.super_4 6025782 103 - 6179234
--------UCACAAAAACCGAGGCGGGAUCAAGGGCAGCCUGAUCAUGAUGAUCAUGAUCACCAGGCAUGCAGCUCAAGAUGAUCCGCCGAAUGGCCG---UGACUAUGGCCAA
--------.............(((((.((((((.((((((((((((((.....)))))))...)))).)))..)).....)))))))))...((((((---(....))))))). ( -41.50, z-score =  -3.16, R)
>droSim1.chrX_random 2112183 103 + 5698898
--------UCACAAAAACCGAGGCGGGAUCAAGGGCAGCCUGAUCAUGAUGAUCAUGAUCACCAGGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG---UGACUAUGGCCAG
--------.............(((..(((((((.((((((((((((((.....)))))))...)))).)))..)).....))))).)))...((((((---(....))))))). ( -39.20, z-score =  -2.72, R)
>consensus
__________A_AAAAACCGAGGCGGGAUCAAGGGCAGC_UGAUCAUGAUGAUCAUGAUCACCAAGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG___UGACUAUGGCCAG
.....................(((..(((((.((((.((.((.......((((....)))).....)).)).))))....))))).)))...((((((.........)))))). (-24.32 = -24.20 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,640,840 – 6,640,951
Length 111
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 77.55
Shannon entropy 0.38142
G+C content 0.48098
Mean single sequence MFE -37.14
Consensus MFE -17.48
Energy contribution -16.84
Covariance contribution -0.64
Combinations/Pair 1.38
Mean z-score -2.13
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.629301
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6640840 111 + 22422827
UGAUCAUGAUGAUCAUGAUCAUCAAGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG---UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAAUAGUUCAAUUCUG
(((((.....)))))((((((((.(((.....)))...))))))))......((((((---(....)))))))..((((((.((.((((((.......)))))).)).)))))) ( -39.90, z-score =  -2.87, R)
>droEre2.scaffold_4690 15566955 101 + 18748788
--------AUGGUCAUGAUCAGCGAGCAUGCAGCUCAAGAUGCUUAGCCGAGUGGCCGAGGUGACUGCGGCUGGCCAGAACUGAGCUAUUCGCGAAAGGAACUACUUUG-----
--------.((((....))))(((((.....((((((...((.((((((((((.((....)).))).))))))).))....)))))).))))).((((......)))).----- ( -33.90, z-score =  -0.54, R)
>droYak2.chrX 2603930 98 + 21770863
--------AUGAUCAUGAUCAGCACGCAUGCAGCUCGAGAUGAUCAGCUGAGUGGCCG---UGACUGUGGCCAGUCAGAAUGGAACUAUUCGAGCAAAGGAUCACUGUA-----
--------.......(((((.(((....))).(((((((..(.((..((((.((((((---......)))))).))))....)).)..)))))))....))))).....----- ( -36.30, z-score =  -2.03, R)
>droSec1.super_4 6025814 111 - 6179234
UGAUCAUGAUGAUCAUGAUCACCAGGCAUGCAGCUCAAGAUGAUCCGCCGAAUGGCCG---UGACUAUGGCCAACCAGAAUGGAUCUAUUCGAGAUGAGAAUAACUCAUUUCUG
((((((((.....))))))))...(((.....)))...((.((((((.....((((((---(....))))))).......))))))...))((((((((.....)))))))).. ( -37.40, z-score =  -2.77, R)
>droSim1.chrX_random 2112215 111 + 5698898
UGAUCAUGAUGAUCAUGAUCACCAGGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG---UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAAUAACUCAUUUCUG
((((((((.....))))))))...(((..((.(.((.....)).).))....((((((---(....)))))))))).(((((....)))))((((((((.....)))))))).. ( -38.20, z-score =  -2.43, R)
>consensus
UGAUCAUGAUGAUCAUGAUCACCAAGCAUGCAGCUCAAGAUGAUCAGCCGAAUGGCCG___UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAAUAACUCAAUUCUG
..........((((.((((((...(((.....))).....))))))...(..((((((.........))))))..)......)))).........((((.....))))...... (-17.48 = -16.84 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,640,879 – 6,640,991
Length 112
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 68.95
Shannon entropy 0.53382
G+C content 0.46301
Mean single sequence MFE -34.48
Consensus MFE -13.58
Energy contribution -15.02
Covariance contribution 1.44
Combinations/Pair 1.42
Mean z-score -2.36
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.939998
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6640879 112 + 22422827
AUGAUCAGCCGAAUGGCCG---UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAAUAGUUCAAUUCUGUUUCACUGCAAGUCGCCAGUAUUGAUGAUCAGUUGAUUAG
.((((((((.((.((((((---(....)))))))..((((((.((.((((((.......)))))).)).))))))....(((((.....).))))........)).)))))))). ( -35.60, z-score =  -2.58, R)
>droEre2.scaffold_4690 15566986 91 + 18748788
AUGCUUAGCCGAGUGGCCGAGGUGACUGCGGCUGGCCAGAACUGAGCUAUUCGCGAAAGGAACUACU-----UUGGUUCGGU--------CAAGUAUUGCUGAU-----------
((((((((((((((.((....)).))).)))))((((.((((..((.(((((.(....)))).)).)-----)..)))))))--------))))))).......----------- ( -34.30, z-score =  -2.29, R)
>droYak2.chrX 2603961 98 + 21770863
AUGAUCAGCUGAGUGGCCG---UGACUGUGGCCAGUCAGAAUGGAACUAUUCGAGCAAAGGAUCACUGUAUGUAAGUCUACUA-------UCGAUGAUGAUUGCUAGG-------
.(((((.(((((.((((((---......)))))).)).(((((....))))).)))....)))))...............(((-------.((((....)))).))).------- ( -26.40, z-score =  -0.40, R)
>droSec1.super_4 6025853 110 - 6179234
AUGAUCCGCCGAAUGGCCG---UGACUAUGGCCAACCAGAAUGGAUCUAUUCGAGAUGAGAAUAACUCAUUUCUGGUUCACUGCAAGU--CCAGUAUUGGUGAUCAGUUGAUAAG
.(((((.(((((.((((((---(....)))))))(((((((((....)))))((((((((.....))))))))))))..((((.....--.)))).))))))))))......... ( -37.70, z-score =  -3.31, R)
>droSim1.chrX_random 2112254 110 + 5698898
AUGAUCAGCCGAAUGGCCG---UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAAUAACUCAUUUCUGGUUCACUGCAAGU--CCAGUAUUGGUGAUCAGUUGAUAAG
.((((((.((((.((((((---(....)))))))(((((((((....)))))((((((((.....))))))))))))..((((.....--.)))).))))))))))......... ( -38.40, z-score =  -3.22, R)
>consensus
AUGAUCAGCCGAAUGGCCG___UGACUAUGGCCAGCCAGAAUGGAUCUAUUCGAGAUGAGAAUAACUCAAUUCUGGUUCACUGCAAGU__CCAGUAUUGAUGAUCAGUUGAU_AG
.((((((......((((((.........))))))(((((((......(((((.......)))))......))))))).......................))))))......... (-13.58 = -15.02 +   1.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,640,879 – 6,640,991
Length 112
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 68.95
Shannon entropy 0.53382
G+C content 0.46301
Mean single sequence MFE -28.18
Consensus MFE -13.46
Energy contribution -13.70
Covariance contribution 0.24
Combinations/Pair 1.23
Mean z-score -1.83
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.31
SVM RNA-class probability 0.924682
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6640879 112 - 22422827
CUAAUCAACUGAUCAUCAAUACUGGCGACUUGCAGUGAAACAGAAUUGAACUAUUCUCAUCUCGAAUAGAUCCAUUCUGGCUGGCCAUAGUCA---CGGCCAUUCGGCUGAUCAU
.........((((((((...((((........))))(((.((((((.((.((((((.......)))))).)).))))))..(((((.......---.)))))))))).)))))). ( -32.50, z-score =  -2.78, R)
>droEre2.scaffold_4690 15566986 91 - 18748788
-----------AUCAGCAAUACUUG--------ACCGAACCAA-----AGUAGUUCCUUUCGCGAAUAGCUCAGUUCUGGCCAGCCGCAGUCACCUCGGCCACUCGGCUAAGCAU
-----------....((.......(--------.((((((...-----(((.(((((....).)))).)))..)))).)).)(((((.(((..(....)..))))))))..)).. ( -21.20, z-score =  -0.55, R)
>droYak2.chrX 2603961 98 - 21770863
-------CCUAGCAAUCAUCAUCGA-------UAGUAGACUUACAUACAGUGAUCCUUUGCUCGAAUAGUUCCAUUCUGACUGGCCACAGUCA---CGGCCACUCAGCUGAUCAU
-------..((((........((((-------(((..((.((((.....))))))..))).))))............(((.(((((.......---.))))).)))))))..... ( -21.70, z-score =  -0.92, R)
>droSec1.super_4 6025853 110 + 6179234
CUUAUCAACUGAUCACCAAUACUGG--ACUUGCAGUGAACCAGAAAUGAGUUAUUCUCAUCUCGAAUAGAUCCAUUCUGGUUGGCCAUAGUCA---CGGCCAUUCGGCGGAUCAU
.........(((((.((..(((((.--.....)))))((((((((..((.((((((.......)))))).))..))))))))((((.......---.))))....))..))))). ( -32.80, z-score =  -2.37, R)
>droSim1.chrX_random 2112254 110 - 5698898
CUUAUCAACUGAUCACCAAUACUGG--ACUUGCAGUGAACCAGAAAUGAGUUAUUCUCAUCUCGAAUAGAUCCAUUCUGGCUGGCCAUAGUCA---CGGCCAUUCGGCUGAUCAU
.........((((((((..(((((.--.....)))))..((((((..((.((((((.......)))))).))..)))))).(((((.......---.)))))...)).)))))). ( -32.70, z-score =  -2.53, R)
>consensus
CU_AUCAACUGAUCACCAAUACUGG__ACUUGCAGUGAACCAGAAAUGAGUUAUUCUCAUCUCGAAUAGAUCCAUUCUGGCUGGCCAUAGUCA___CGGCCAUUCGGCUGAUCAU
....................................................................((((....((((.(((((...........))))).))))..)))).. (-13.46 = -13.70 +   0.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:21:46 2011