Locus 15399

Sequence ID dm3.chrX
Location 18,849,725 – 18,849,854
Length 129
Max. P 0.995797
window21209 window21210 window21211

overview

Window 9

Location 18,849,725 – 18,849,817
Length 92
Sequences 3
Columns 92
Reading direction forward
Mean pairwise identity 90.23
Shannon entropy 0.12976
G+C content 0.47287
Mean single sequence MFE -25.53
Consensus MFE -23.37
Energy contribution -23.70
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.21
SVM RNA-class probability 0.985733
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18849725 92 + 22422827
GACAGGGGGCAGUUAAUGAGGCGUGACGGCCAAACAUAUAGUUAGCAUUAACUAUAACCGAAUCGAUCCGAUUCCAUUCGAUUCGUUUCGCC
.......(((((((((((.(((......))).(((.....)))..)))))))).....((((((((...........))))))))....))) ( -25.60, z-score =  -1.79, R)
>droSec1.super_8 1153746 82 + 3762037
GACAGGGGGCAGUUAAUGAGGCGUGACGGCCAAACAUAUAGUUAGCAUUAACUAUAACCGAAUCGAUCCGAUUCGAUUCGCC----------
.......(((((((((((.(((......))).(((.....)))..))))))))......(((((((......))))))))))---------- ( -25.50, z-score =  -2.88, R)
>droSim1.chrX 14568070 82 + 17042790
GACAGGGGGCAGUUAAUGAGGCGUGACGGCCAAACAUAUAGUUAGCAUUAACUAUAACCGAAUCGAUCCGAUUCGAUUCGCC----------
.......(((((((((((.(((......))).(((.....)))..))))))))......(((((((......))))))))))---------- ( -25.50, z-score =  -2.88, R)
>consensus
GACAGGGGGCAGUUAAUGAGGCGUGACGGCCAAACAUAUAGUUAGCAUUAACUAUAACCGAAUCGAUCCGAUUCGAUUCGCC__________
....((..(.((((((((.(((......))).(((.....)))..)))))))).)..))(((((((......)))))))............. (-23.37 = -23.70 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,849,725 – 18,849,817
Length 92
Sequences 3
Columns 92
Reading direction reverse
Mean pairwise identity 90.23
Shannon entropy 0.12976
G+C content 0.47287
Mean single sequence MFE -24.50
Consensus MFE -19.53
Energy contribution -20.53
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.776688
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18849725 92 - 22422827
GGCGAAACGAAUCGAAUGGAAUCGGAUCGAUUCGGUUAUAGUUAAUGCUAACUAUAUGUUUGGCCGUCACGCCUCAUUAACUGCCCCCUGUC
(((.(((((((((((((.((......)).))))))))(((((((....))))))).))))).)))........................... ( -24.50, z-score =  -1.28, R)
>droSec1.super_8 1153746 82 - 3762037
----------GGCGAAUCGAAUCGGAUCGAUUCGGUUAUAGUUAAUGCUAACUAUAUGUUUGGCCGUCACGCCUCAUUAACUGCCCCCUGUC
----------(((.((((((((((...))))))))))..((((((((..(((.....))).(((......))).)))))))))))....... ( -24.50, z-score =  -2.55, R)
>droSim1.chrX 14568070 82 - 17042790
----------GGCGAAUCGAAUCGGAUCGAUUCGGUUAUAGUUAAUGCUAACUAUAUGUUUGGCCGUCACGCCUCAUUAACUGCCCCCUGUC
----------(((.((((((((((...))))))))))..((((((((..(((.....))).(((......))).)))))))))))....... ( -24.50, z-score =  -2.55, R)
>consensus
__________GGCGAAUCGAAUCGGAUCGAUUCGGUUAUAGUUAAUGCUAACUAUAUGUUUGGCCGUCACGCCUCAUUAACUGCCCCCUGUC
..........(((.((((((((((...))))))))))..((((((((..(((.....))).(((......))).)))))))))))....... (-19.53 = -20.53 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,849,752 – 18,849,854
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 91.22
Shannon entropy 0.11704
G+C content 0.48622
Mean single sequence MFE -29.17
Consensus MFE -27.10
Energy contribution -27.43
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.10
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.85
SVM RNA-class probability 0.995797
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18849752 102 + 22422827
GGCCAAACAUAUAGUUAGCAUUAACUAUAACCGAAUCGAUCCGAUUCCAUUCGAUUCGUUUCGCCCGCCAGGGAGGCCAGAAUUAAUUGCGGAGCAGCCUGA
((((.....((((((((....))))))))..((((.(((..(((......)))..))).))))(((....))).))))..........((......)).... ( -29.10, z-score =  -1.91, R)
>droSec1.super_8 1153773 92 + 3762037
GGCCAAACAUAUAGUUAGCAUUAACUAUAACCGAAUCGAUCCGAUUCGAUUCG----------CCCGCCAGGGAGGCCAGAAUUAAUUGCCGAGCAGCCAGA
((((.....((((((((....))))))))..((((((((......))))))))----------(((....))).))))........((((...))))..... ( -29.20, z-score =  -3.70, R)
>droSim1.chrX 14568097 92 + 17042790
GGCCAAACAUAUAGUUAGCAUUAACUAUAACCGAAUCGAUCCGAUUCGAUUCG----------CCCGCCAGGGAGGCCAGAAUUAAUUGCCGAGCAGCCAGA
((((.....((((((((....))))))))..((((((((......))))))))----------(((....))).))))........((((...))))..... ( -29.20, z-score =  -3.70, R)
>consensus
GGCCAAACAUAUAGUUAGCAUUAACUAUAACCGAAUCGAUCCGAUUCGAUUCG__________CCCGCCAGGGAGGCCAGAAUUAAUUGCCGAGCAGCCAGA
((((.....((((((((....))))))))..((((((((......))))))))..........(((....))).))))........((((...))))..... (-27.10 = -27.43 +   0.33)

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 01:58:29 2011