Locus 14872

Sequence ID dm3.chrX
Location 15,999,928 – 16,000,081
Length 153
Max. P 0.998373
window20481 window20482 window20483 window20484

overview

Window 1

Location 15,999,928 – 16,000,046
Length 118
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 93.84
Shannon entropy 0.08488
G+C content 0.33424
Mean single sequence MFE -31.57
Consensus MFE -28.54
Energy contribution -29.43
Covariance contribution 0.89
Combinations/Pair 1.03
Mean z-score -2.62
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.00
SVM RNA-class probability 0.978405
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15999928 118 + 22422827
AAGCGC-GCGUAGUAGCUAUUUUUGGAGACUAAACUACCGCCAUCUGUUGGUGUUUAUUCAAAACAGACGUAAAAAAGUAUGUUACACAAAAUAAAUUUUUUGUGUAGUUACUAUAUUU
......-..(((((((((..(((((((...(((((.((((.(....).))))))))))))))))..((((((......))))))((((((((......))))))))))))))))).... ( -29.00, z-score =  -2.22, R)
>droSim1.chrX 12341025 119 + 17042790
AAGCGCUGCGUAGUAGCCAUUUUUGGAGACUUAAUUGUCGCCAUCUGUUGGUGUUUAUUCACAACAGACGUGUAAAAGUAUGUUACACAAAAUAAAUUUUUUGUGUAGUUACUAUAUUU
.........((((((((.((((((((.(((......))).)).(((((((.((......))))))))).....))))))....(((((((((......))))))))))))))))).... ( -33.10, z-score =  -3.02, R)
>droSec1.super_47 57761 119 + 216421
AAGCGCUGCGUAGUAGCCAUUUUUGGAGGCUUAAUUGUCGCCAUCUGUUGGUGUUUAUUCACAACAGACGUGAAAAAGUAUGUUACACAAAAUAAUUUUUUUGUGUAGUUACUAUAUUU
.........((((((((.((((((((.(((......))).)).(((((((.((......))))))))).....))))))....(((((((((......))))))))))))))))).... ( -32.60, z-score =  -2.62, R)
>consensus
AAGCGCUGCGUAGUAGCCAUUUUUGGAGACUUAAUUGUCGCCAUCUGUUGGUGUUUAUUCACAACAGACGUGAAAAAGUAUGUUACACAAAAUAAAUUUUUUGUGUAGUUACUAUAUUU
.........((((((((.((((((((.(((......))).)).(((((((.((......))))))))).....))))))....(((((((((......))))))))))))))))).... (-28.54 = -29.43 +   0.89)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,999,928 – 16,000,046
Length 118
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 93.84
Shannon entropy 0.08488
G+C content 0.33424
Mean single sequence MFE -28.37
Consensus MFE -24.38
Energy contribution -24.82
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -3.34
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.56
SVM RNA-class probability 0.992715
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15999928 118 - 22422827
AAAUAUAGUAACUACACAAAAAAUUUAUUUUGUGUAACAUACUUUUUUACGUCUGUUUUGAAUAAACACCAACAGAUGGCGGUAGUUUAGUCUCCAAAAAUAGCUACUACGC-GCGCUU
......((((..(((((((((......)))))))))...))))......((((((((.((......))..))))))))((((((((..(((...........)))))))).)-)).... ( -26.80, z-score =  -2.66, R)
>droSim1.chrX 12341025 119 - 17042790
AAAUAUAGUAACUACACAAAAAAUUUAUUUUGUGUAACAUACUUUUACACGUCUGUUGUGAAUAAACACCAACAGAUGGCGACAAUUAAGUCUCCAAAAAUGGCUACUACGCAGCGCUU
......((((..(((((((((......)))))))))...))))......(((((((((((......)).)))))))))(((.......(((..(((....)))..)))......))).. ( -28.72, z-score =  -3.51, R)
>droSec1.super_47 57761 119 - 216421
AAAUAUAGUAACUACACAAAAAAAUUAUUUUGUGUAACAUACUUUUUCACGUCUGUUGUGAAUAAACACCAACAGAUGGCGACAAUUAAGCCUCCAAAAAUGGCUACUACGCAGCGCUU
......((((..(((((((((......)))))))))...))))......(((((((((((......)).)))))))))(((.......((((.........)))).........))).. ( -29.59, z-score =  -3.84, R)
>consensus
AAAUAUAGUAACUACACAAAAAAUUUAUUUUGUGUAACAUACUUUUUCACGUCUGUUGUGAAUAAACACCAACAGAUGGCGACAAUUAAGUCUCCAAAAAUGGCUACUACGCAGCGCUU
......((((..(((((((((......)))))))))...))))......(((((((((((......)).)))))))))(((.......((((.........)))).........))).. (-24.38 = -24.82 +   0.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,999,967 – 16,000,081
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 85.84
Shannon entropy 0.19112
G+C content 0.28421
Mean single sequence MFE -24.77
Consensus MFE -22.06
Energy contribution -21.40
Covariance contribution -0.66
Combinations/Pair 1.11
Mean z-score -2.11
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.71
SVM RNA-class probability 0.962319
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15999967 114 + 22422827
CCAUCUGUUGGUGUUUAUUCAAAACAGACGUAAAAAAGUAUGUUACACAAAAUAAAUUUUUUGUGUAGUUACUAUAUUUUUAGGGUUGACUAGCGUUGUGCUAUUUUUCAGUAA
((.((((((..((......)).)))))).....(((((((((((((((((((......))))))))))....))))))))).))(..((.((((.....)))).))..)..... ( -24.40, z-score =  -1.67, R)
>droSim1.chrX 12341065 104 + 17042790
CCAUCUGUUGGUGUUUAUUCACAACAGACGUGUAAAAGUAUGUUACACAAAAUAAAUUUUUUGUGUAGUUACUAUAUUUUUAGGGUUAACUGUGAUUGUUAUAA----------
((.(((((((.((......)))))))))....((((((((((((((((((((......))))))))))....))))))))))))..((((.......))))...---------- ( -25.60, z-score =  -2.48, R)
>droSec1.super_47 57801 102 + 216421
CCAUCUGUUGGUGUUUAUUCACAACAGACGUGAAAAAGUAUGUUACACAAAAUAAUUUUUUUGUGUAGUUACUAUAUUUUUAGGGUUAACUGUGAUUGUUAU------------
((.(((((((.((......))))))))).....(((((((((((((((((((......))))))))))....))))))))).))..((((.......)))).------------ ( -24.30, z-score =  -2.19, R)
>consensus
CCAUCUGUUGGUGUUUAUUCACAACAGACGUGAAAAAGUAUGUUACACAAAAUAAAUUUUUUGUGUAGUUACUAUAUUUUUAGGGUUAACUGUGAUUGUUAUA___________
((.(((((((.((......))))))))).....(((((((((((((((((((......))))))))))....))))))))).))......(((((...)))))........... (-22.06 = -21.40 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,999,967 – 16,000,081
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 85.84
Shannon entropy 0.19112
G+C content 0.28421
Mean single sequence MFE -22.83
Consensus MFE -20.03
Energy contribution -20.37
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.69
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.34
SVM RNA-class probability 0.998373
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15999967 114 - 22422827
UUACUGAAAAAUAGCACAACGCUAGUCAACCCUAAAAAUAUAGUAACUACACAAAAAAUUUAUUUUGUGUAACAUACUUUUUUACGUCUGUUUUGAAUAAACACCAACAGAUGG
....(((....((((.....)))).)))....((((((...((((..(((((((((......)))))))))...))))))))))((((((((.((......))..)))))))). ( -23.70, z-score =  -3.81, R)
>droSim1.chrX 12341065 104 - 17042790
----------UUAUAACAAUCACAGUUAACCCUAAAAAUAUAGUAACUACACAAAAAAUUUAUUUUGUGUAACAUACUUUUACACGUCUGUUGUGAAUAAACACCAACAGAUGG
----------...((((.......)))).............((((..(((((((((......)))))))))...))))......(((((((((((......)).))))))))). ( -22.40, z-score =  -3.51, R)
>droSec1.super_47 57801 102 - 216421
------------AUAACAAUCACAGUUAACCCUAAAAAUAUAGUAACUACACAAAAAAAUUAUUUUGUGUAACAUACUUUUUCACGUCUGUUGUGAAUAAACACCAACAGAUGG
------------.((((.......)))).............((((..(((((((((......)))))))))...))))......(((((((((((......)).))))))))). ( -22.40, z-score =  -3.74, R)
>consensus
___________UAUAACAAUCACAGUUAACCCUAAAAAUAUAGUAACUACACAAAAAAUUUAUUUUGUGUAACAUACUUUUUCACGUCUGUUGUGAAUAAACACCAACAGAUGG
.........................................((((..(((((((((......)))))))))...))))......(((((((((((......)).))))))))). (-20.03 = -20.37 +   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 01:48:31 2011