Locus 15457

Sequence ID dm3.chrX
Location 19,160,029 – 19,160,230
Length 201
Max. P 0.997205
window21302 window21303 window21304 window21305

overview

Window 2

Location 19,160,029 – 19,160,121
Length 92
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 78.23
Shannon entropy 0.28990
G+C content 0.60191
Mean single sequence MFE -43.00
Consensus MFE -24.70
Energy contribution -25.03
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.96
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.76
SVM RNA-class probability 0.966322
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19160029 92 + 22422827
--------GCUGCGUCUGCGG----CAUUCCCAUUCUGAUUCCGCCUGGCGGUUCCUACAAGGCCGCCACCAGAGGUUCCAUAACGGGAAUGCAACGGAGCAGC------
--------(((((.((((..(----(((((((.((.((...((..((((.(((.((.....))..))).)))).))...)).)).))))))))..)))))))))------ ( -44.10, z-score =  -4.18, R)
>droSec1.super_8 1454332 97 + 3762037
AGCGCUCUGCUGCGGCUGCGG----CAUUCCCAUUCUGAUUCCGCCAGGCGGUUCCUACAAGGCCGCCACCAGA---UCCAUAACGGGAAUGUAUCGGAGCAGC------
........(((((..(((..(----(((((((.((.((..((.(...(((((((.......)))))))..).))---..)).)).))))))))..))).)))))------ ( -36.70, z-score =  -1.02, R)
>droEre2.scaffold_4690 9418889 107 + 18748788
CGCGCUCUUCUGCGGAUGGCAUUCCCAUUCCCAUUCUGAUUCUGGCUGGCGGUUCCUACAAGGCCGCCACCAGA---UCCAAAACGGGAAUGCAACGGGGCAGCGAUGUC
((((((((..((((((......))).((((((.((.((..(((((.((((((((.......)))))))))))))---..)).)).)))))))))..))))).)))..... ( -48.20, z-score =  -3.69, R)
>consensus
_GCGCUCUGCUGCGGCUGCGG____CAUUCCCAUUCUGAUUCCGCCUGGCGGUUCCUACAAGGCCGCCACCAGA___UCCAUAACGGGAAUGCAACGGAGCAGC______
........(((((...((.......(((((((...............(((((((.......)))))))....(......).....)))))))...))..)))))...... (-24.70 = -25.03 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,160,029 – 19,160,121
Length 92
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 78.23
Shannon entropy 0.28990
G+C content 0.60191
Mean single sequence MFE -46.77
Consensus MFE -32.40
Energy contribution -32.51
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -3.45
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.06
SVM RNA-class probability 0.997205
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19160029 92 - 22422827
------GCUGCUCCGUUGCAUUCCCGUUAUGGAACCUCUGGUGGCGGCCUUGUAGGAACCGCCAGGCGGAAUCAGAAUGGGAAUG----CCGCAGACGCAGC--------
------(((((((.((.(((((((((((.(((..((((((((((...((.....))..)))))))).))..))).))))))))))----).)).)).)))))-------- ( -48.70, z-score =  -4.76, R)
>droSec1.super_8 1454332 97 - 3762037
------GCUGCUCCGAUACAUUCCCGUUAUGGA---UCUGGUGGCGGCCUUGUAGGAACCGCCUGGCGGAAUCAGAAUGGGAAUG----CCGCAGCCGCAGCAGAGCGCU
------((.(((.((...((((((((((.(((.---((((.((((((((.....))..))))).).)))).))).))))))))))----.)).))).))(((.....))) ( -40.50, z-score =  -1.35, R)
>droEre2.scaffold_4690 9418889 107 - 18748788
GACAUCGCUGCCCCGUUGCAUUCCCGUUUUGGA---UCUGGUGGCGGCCUUGUAGGAACCGCCAGCCAGAAUCAGAAUGGGAAUGGGAAUGCCAUCCGCAGAAGAGCGCG
.....(((.((.(..(((((((((((((((((.---(((((((((((((.....))..)))))).))))).))))))))))))).(((......)))))))..).))))) ( -51.10, z-score =  -4.24, R)
>consensus
______GCUGCUCCGUUGCAUUCCCGUUAUGGA___UCUGGUGGCGGCCUUGUAGGAACCGCCAGGCGGAAUCAGAAUGGGAAUG____CCGCAGCCGCAGCAGAGCGC_
......(((((.......((((((((((...((...((((..(((((((.....))..)))))...)))).))..))))))))))............)))))........ (-32.40 = -32.51 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,160,047 – 19,160,155
Length 108
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 68.34
Shannon entropy 0.49832
G+C content 0.56648
Mean single sequence MFE -37.37
Consensus MFE -20.10
Energy contribution -22.98
Covariance contribution 2.87
Combinations/Pair 1.31
Mean z-score -1.55
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.851204
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19160047 108 - 22422827
GGUGUCAAGUUGGGUUCGAUAACCCAGCGC------CACCGCUGCUCCGUUGCAUUCCCGUUAUGGAACCUCUGGUGGCGGCCUUGUAGGAACCGCCAGGCGGAAUCAGAAUGG
((((....((((((((....))))))))..------))))..(((......)))...(((((.(((..((((((((((...((.....))..)))))))).))..))).))))) ( -42.10, z-score =  -1.28, R)
>droSec1.super_8 1454358 105 - 3762037
GGUGUCAAGUUGGGUUCGAUAACCCAGCGC------CACCGCUGCUCCGAUACAUUCCCGUUAUGGA---UCUGGUGGCGGCCUUGUAGGAACCGCCUGGCGGAAUCAGAAUGG
.(((((..((((((((....))))))))((------....))......)))))....(((((.(((.---((((.((((((((.....))..))))).).)))).))).))))) ( -38.50, z-score =  -0.79, R)
>droEre2.scaffold_4690 9418919 111 - 18748788
GGUGUCAAGUAGGGGUCGAUAACCCAUCGCCAUCGACAUCGCUGCCCCGUUGCAUUCCCGUUUUGGA---UCUGGUGGCGGCCUUGUAGGAACCGCCAGCCAGAAUCAGAAUGG
((((((..((..((((.....))))...))....))))))((.((...)).))....(((((((((.---(((((((((((((.....))..)))))).))))).))))))))) ( -43.90, z-score =  -2.19, R)
>droAna3.scaffold_12903 518696 95 - 802071
GGUGUCAAGAGUGGGUCGAUAACCCAUUC-------AAUCCAAGC---------UUCCCAUUCCAAG---UUCCUCCGCCCAGUCGAGAUAAACGCCGAGGAAUACGAGAAGUG
........((((((((.....))))))))-------.......((---------(((....((...(---((((((.((...............)).)))))))..))))))). ( -24.96, z-score =  -1.94, R)
>consensus
GGUGUCAAGUUGGGGUCGAUAACCCAGCGC______CACCGCUGCUCCGUUGCAUUCCCGUUAUGGA___UCUGGUGGCGGCCUUGUAGGAACCGCCAGGCAGAAUCAGAAUGG
((((....((((((........))))))........)))).................(((((((((....(((((((((((((.....))..)))))).))))).))))))))) (-20.10 = -22.98 +   2.87)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,160,121 – 19,160,230
Length 109
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 82.97
Shannon entropy 0.23146
G+C content 0.61276
Mean single sequence MFE -45.83
Consensus MFE -33.13
Energy contribution -34.13
Covariance contribution 1.01
Combinations/Pair 1.10
Mean z-score -1.87
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.632635
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19160121 109 - 22422827
-ACGCGUAAGGCGGUGAUGGGCGGACGGCACUUCCAUAGCCACUUCCGGUGGCUAUGUUUGGCCCGGCCUUCGAUCGGUGUCAAGUUGGGUUCGAUAACCCAGCGCCACC
-..((....((((.((((.((.((.(((..(...(((((((((.....)))))))))...)..))).)).)).)))).))))..((((((((....)))))))))).... ( -48.00, z-score =  -1.90, R)
>droSec1.super_8 1454429 102 - 3762037
--AACGAAAGGCGGUGCUGGGCGGCCGGCACUUCCACA------UCCGGUGGCUAUGUUUGGCCCGGCCUUCGAUCGGUGUCAAGUUGGGUUCGAUAACCCAGCGCCACC
--.......((.((((((((....)))))))).))...------...((((((.....((((((((..(...)..))).)))))((((((((....)))))))))))))) ( -47.80, z-score =  -2.34, R)
>droEre2.scaffold_4690 9418996 104 - 18748788
AAUGAGAGGGGCAGCGCUGGGCGGCAAGCACUUCCACA------UCCGGUGGCUAUGUUUGGCGCUGCCUUCGAUCGGUGUCAAGUAGGGGUCGAUAACCCAUCGCCAUC
...((..((((((((((..((((...(((....((...------...))..))).))))..)))))))).))..))((((........((((.....))))..))))... ( -41.70, z-score =  -1.37, R)
>consensus
_AAGCGAAAGGCGGUGCUGGGCGGCCGGCACUUCCACA______UCCGGUGGCUAUGUUUGGCCCGGCCUUCGAUCGGUGUCAAGUUGGGUUCGAUAACCCAGCGCCACC
.........((.(((((((......))))))).))............((((((.....(((((...(((.......))))))))((((((........)))))))))))) (-33.13 = -34.13 +   1.01)

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 01:59:44 2011