Locus 15298

Sequence ID dm3.chrX
Location 18,329,127 – 18,329,284
Length 157
Max. P 0.892667
window21072 window21073 window21074 window21075 window21076

overview

Window 2

Location 18,329,127 – 18,329,245
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.40
Shannon entropy 0.33922
G+C content 0.53556
Mean single sequence MFE -36.20
Consensus MFE -27.95
Energy contribution -28.07
Covariance contribution 0.12
Combinations/Pair 1.17
Mean z-score -1.48
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.816804
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18329127 118 + 22422827
CCAAUUAGCCGCCGGCCAACCAGGGCAAUUGUCUCCGU--UCAUUGAUGCACCACUCGGCGGUGCAAGUGGUGGUGGACUCGAGCAGAGGAUGUCCAUUCCCAUGGAUGUCUAAUAAUAC
.(((((.(((.(.((....)).)))))))))....(((--((.....((((((.......)))))).((((..((((((((........)).))))))..)))))))))........... ( -38.00, z-score =  -0.32, R)
>droSec1.super_8 632901 98 + 3762037
CCAAUUAGCCGCCGGUCAGCCAGGGCAAUUGUUUCCGU--UCAUUGAUGCACCACUCGGUGGUGCACG--------------------GGAUGUCCAUUCCUAUGGAUGUCUAAUAAUAC
.(((((.(((.(.((....)).)))))))))...((((--........(((((((...))))))))))--------------------)(((((((((....)))))))))......... ( -33.80, z-score =  -2.08, R)
>droSim1.chrX 14142503 98 + 17042790
CCAAUUAGUCGCCGGUCAGCCAGGGCAAUUGUUUCCGU--UCAUUGAUGCACCACUCGGUGGUGCACG--------------------GGAUGUCCAUUCCCAUGGAUGUCUAAUAAUAC
...(((((.((((((....))..))).......(((((--.......((((((((...)))))))).(--------------------(((.......))))))))).).)))))..... ( -31.80, z-score =  -1.49, R)
>droYak2.chrX 16947434 107 + 21770863
CCAAUUAGCCAGCGGGCAGCCAGUGCACUUGUUUCCAUACCCAUGGAUGCCCCGCGCCGCGUGGCAAGUGG-------------CAAGUGGUGUCCAUUCCCAUGGACGCCUAAUAAUAC
.......(((((((((((((....)).......(((((....))))))).)))))(((....)))...)))-------------)....(((((((((....)))))))))......... ( -41.20, z-score =  -2.04, R)
>consensus
CCAAUUAGCCGCCGGUCAGCCAGGGCAAUUGUUUCCGU__UCAUUGAUGCACCACUCGGCGGUGCAAG____________________GGAUGUCCAUUCCCAUGGAUGUCUAAUAAUAC
.(((((.(((.(.((....)).)))))))))................((((((((...))))))))......................((((((((((....))))))))))........ (-27.95 = -28.07 +   0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,329,127 – 18,329,245
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.40
Shannon entropy 0.33922
G+C content 0.53556
Mean single sequence MFE -36.55
Consensus MFE -26.66
Energy contribution -26.72
Covariance contribution 0.06
Combinations/Pair 1.15
Mean z-score -1.56
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.68
SVM RNA-class probability 0.786116
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18329127 118 - 22422827
GUAUUAUUAGACAUCCAUGGGAAUGGACAUCCUCUGCUCGAGUCCACCACCACUUGCACCGCCGAGUGGUGCAUCAAUGA--ACGGAGACAAUUGCCCUGGUUGGCCGGCGGCUAAUUGG
.........((..(((((....)))))..))(((((.(((.......(((((((((......)))))))))......)))--.))))).((((((((((((....)))).))).))))). ( -40.62, z-score =  -1.41, R)
>droSec1.super_8 632901 98 - 3762037
GUAUUAUUAGACAUCCAUAGGAAUGGACAUCC--------------------CGUGCACCACCGAGUGGUGCAUCAAUGA--ACGGAAACAAUUGCCCUGGCUGACCGGCGGCUAAUUGG
((.(((((.((..(((((....)))))..)).--------------------.(((((((((...))))))))).)))))--)).....((((((((((((....)))).))).))))). ( -32.70, z-score =  -2.10, R)
>droSim1.chrX 14142503 98 - 17042790
GUAUUAUUAGACAUCCAUGGGAAUGGACAUCC--------------------CGUGCACCACCGAGUGGUGCAUCAAUGA--ACGGAAACAAUUGCCCUGGCUGACCGGCGACUAAUUGG
.....(((((...(((..((((.......)))--------------------)(((((((((...)))))))))......--..))).....(((((..((....))))))))))))... ( -29.70, z-score =  -1.24, R)
>droYak2.chrX 16947434 107 - 21770863
GUAUUAUUAGGCGUCCAUGGGAAUGGACACCACUUG-------------CCACUUGCCACGCGGCGCGGGGCAUCCAUGGGUAUGGAAACAAGUGCACUGGCUGCCCGCUGGCUAAUUGG
.........((.((((((....)))))).))....(-------------(((...(((....)))(((((.((.(((((.(..((....))..).)).))).)))))))))))....... ( -43.20, z-score =  -1.49, R)
>consensus
GUAUUAUUAGACAUCCAUGGGAAUGGACAUCC____________________CGUGCACCACCGAGUGGUGCAUCAAUGA__ACGGAAACAAUUGCCCUGGCUGACCGGCGGCUAAUUGG
.........((..(((((....)))))..)).......................((((((((...))))))))................((((((((((((....)))).))).))))). (-26.66 = -26.72 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,329,165 – 18,329,280
Length 115
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 71.12
Shannon entropy 0.44141
G+C content 0.57194
Mean single sequence MFE -34.10
Consensus MFE -25.45
Energy contribution -26.07
Covariance contribution 0.62
Combinations/Pair 1.22
Mean z-score -1.15
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.847459
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18329165 115 + 22422827
UCAUUGAUGCACCACUCGGCGGUGCAAGUGGUGGUGGACUCGAGCAGAGGAUGUCCAUUCCCAUGGAUGUCUAAUAAUACCCCAACAAUCGAAGUCCGUCGCCGUUGCGACUGCG
..................(((((((((.(((((..((((((((.....((((((((((....))))))))))................))).)))))..))))))))).))))). ( -41.30, z-score =  -1.78, R)
>droSec1.super_8 632939 95 + 3762037
UCAUUGAUGCACCACUCGGUGGUGCACG--------------------GGAUGUCCAUUCCUAUGGAUGUCUAAUAAUACGCCCACAAUCGAAGCCCGUCGUGGUCGCGGCUGCG
((((((.((((((((...))))))))..--------------------((((((((((....)))))))))).............)))).)).((..(((((....))))).)). ( -33.40, z-score =  -1.31, R)
>droSim1.chrX 14142541 95 + 17042790
UCAUUGAUGCACCACUCGGUGGUGCACG--------------------GGAUGUCCAUUCCCAUGGAUGUCUAAUAAUACGCCCACAAUCGAAGCCCGUCGUGGUCGCGGCUGCG
((((((.((((((((...))))))))..--------------------((((((((((....)))))))))).............)))).)).((..(((((....))))).)). ( -32.70, z-score =  -0.86, R)
>droYak2.chrX 16947474 88 + 21770863
CCAUGGAUGCCCCGCGCCGCGUGGCAAGUGG-------------CAAGUGGUGUCCAUUCCCAUGGACGCCUAAUAAUACACCCGCAAUCGAAGCCCGCCA--------------
.......((((.(((...))).))))..(((-------------(....(((((((((....))))))))).............((.......))..))))-------------- ( -29.00, z-score =  -0.64, R)
>consensus
UCAUUGAUGCACCACUCGGCGGUGCAAG____________________GGAUGUCCAUUCCCAUGGAUGUCUAAUAAUACGCCCACAAUCGAAGCCCGUCGUGGUCGCGGCUGCG
...((((((((((((...))))))).......................((((((((((....))))))))))...............))))).....(((((....))))).... (-25.45 = -26.07 +   0.62)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,329,169 – 18,329,284
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 81.54
Shannon entropy 0.23956
G+C content 0.56796
Mean single sequence MFE -37.87
Consensus MFE -32.27
Energy contribution -32.50
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -1.75
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.892667
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18329169 115 + 22422827
UGAUGCACCACUCGGCGGUGCAAGUGGUGGUGGACUCGAGCAGAGGAUGUCCAUUCCCAUGGAUGUCUAAUAAUACCCCAACAAUCGAAGUCCGUCGCCGUUGCGACUGCGACUG
...((((((.......))))))...((((..((((((((.....((((((((((....))))))))))................))).)))))..))))(((((....))))).. ( -43.10, z-score =  -2.14, R)
>droSec1.super_8 632943 95 + 3762037
UGAUGCACCACUCGGUGGUGCACG--------------------GGAUGUCCAUUCCUAUGGAUGUCUAAUAAUACGCCCACAAUCGAAGCCCGUCGUGGUCGCGGCUGCGACUG
.((((((((((...)))))))...--------------------((((((((((....))))))))))...............))).......((((..((....))..)))).. ( -35.60, z-score =  -1.79, R)
>droSim1.chrX 14142545 95 + 17042790
UGAUGCACCACUCGGUGGUGCACG--------------------GGAUGUCCAUUCCCAUGGAUGUCUAAUAAUACGCCCACAAUCGAAGCCCGUCGUGGUCGCGGCUGCGACUG
.((((((((((...)))))))...--------------------((((((((((....))))))))))...............))).......((((..((....))..)))).. ( -34.90, z-score =  -1.32, R)
>consensus
UGAUGCACCACUCGGUGGUGCACG____________________GGAUGUCCAUUCCCAUGGAUGUCUAAUAAUACGCCCACAAUCGAAGCCCGUCGUGGUCGCGGCUGCGACUG
.((((((((((...))))))).......................((((((((((....))))))))))...............))).......((((((((....)))))))).. (-32.27 = -32.50 +   0.23)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,329,169 – 18,329,284
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 81.54
Shannon entropy 0.23956
G+C content 0.56796
Mean single sequence MFE -37.09
Consensus MFE -30.20
Energy contribution -30.20
Covariance contribution 0.00
Combinations/Pair 1.07
Mean z-score -1.50
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.662685
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18329169 115 - 22422827
CAGUCGCAGUCGCAACGGCGACGGACUUCGAUUGUUGGGGUAUUAUUAGACAUCCAUGGGAAUGGACAUCCUCUGCUCGAGUCCACCACCACUUGCACCGCCGAGUGGUGCAUCA
..(((((.((....)).)))))(((((.(((..((.((((............(((((....)))))...)))).))))))))))..(((((((((......)))))))))..... ( -40.56, z-score =  -1.32, R)
>droSec1.super_8 632943 95 - 3762037
CAGUCGCAGCCGCGACCACGACGGGCUUCGAUUGUGGGCGUAUUAUUAGACAUCCAUAGGAAUGGACAUCC--------------------CGUGCACCACCGAGUGGUGCAUCA
((((((.((((.((.......)))))).)))))).(((.((........)).(((((....)))))...))--------------------)(((((((((...))))))))).. ( -34.80, z-score =  -1.71, R)
>droSim1.chrX 14142545 95 - 17042790
CAGUCGCAGCCGCGACCACGACGGGCUUCGAUUGUGGGCGUAUUAUUAGACAUCCAUGGGAAUGGACAUCC--------------------CGUGCACCACCGAGUGGUGCAUCA
((((((.((((.((.......)))))).))))))(((..((........))..))).((((.......)))--------------------)(((((((((...))))))))).. ( -35.90, z-score =  -1.46, R)
>consensus
CAGUCGCAGCCGCGACCACGACGGGCUUCGAUUGUGGGCGUAUUAUUAGACAUCCAUGGGAAUGGACAUCC____________________CGUGCACCACCGAGUGGUGCAUCA
((((((.((((.((.......)))))).))))))..............((..(((((....)))))..))......................(((((((((...))))))))).. (-30.20 = -30.20 +   0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:56:40 2011