Locus 10057

Sequence ID dm3.chr3R
Location 10,912,980 – 10,913,104
Length 124
Max. P 0.997063
window13825 window13826 window13827

overview

Window 5

Location 10,912,980 – 10,913,079
Length 99
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 76.53
Shannon entropy 0.34578
G+C content 0.50561
Mean single sequence MFE -22.93
Consensus MFE -14.12
Energy contribution -15.88
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -3.19
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.84
SVM RNA-class probability 0.995745
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10912980 99 + 27905053
CCCCGCCUGGGGAAACCCCCCAUGUCCCCCCCCCCUUCCUUUAACCGC-----ACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACAC
.......(((((.....)))))((((....................((-----....))..................(((((((((....))))))))))))). ( -24.60, z-score =  -4.48, R)
>droSim1.chr3R 16971427 88 - 27517382
----------------CCCCGCCGGGGCAAACCCCCCCUUUGAACCACCGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGC
----------------.......((((....))))..............((......))................(((((((((((....)))))))))))... ( -20.90, z-score =  -2.62, R)
>droSec1.super_0 10097754 88 - 21120651
----------------CCCCGCCGGGGGAAACCCCCCCUUUGAACCGCCGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGC
----------------.......((((....))))...........((.((......))................(((((((((((....))))))))))).)) ( -25.40, z-score =  -3.14, R)
>droEre2.scaffold_4770 10448081 83 + 17746568
----------------CCCCGCCGCCGGAGAAACCCCCUUGGAGCCGC-----ACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGC
----------------....((.(((.(((.......))).).)).))-----......................(((((((((((....)))))))))))... ( -20.80, z-score =  -2.52, R)
>consensus
________________CCCCGCCGGCGCAAACCCCCCCUUUGAACCGC_____ACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGC
.......................(((((.....))))).....................................(((((((((((....)))))))))))... (-14.12 = -15.88 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 10,913,008 – 10,913,104
Length 96
Sequences 7
Columns 111
Reading direction forward
Mean pairwise identity 71.37
Shannon entropy 0.49352
G+C content 0.41610
Mean single sequence MFE -20.53
Consensus MFE -13.32
Energy contribution -13.40
Covariance contribution 0.08
Combinations/Pair 1.05
Mean z-score -2.32
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.85
SVM RNA-class probability 0.995843
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10913008 96 + 27905053
CCCCCCCUUCCUUUAAC-CGCACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACACUAU-AUGCAAGUAGACGACAGCCCAG-------------
.................-.((....((((((((......))).(((((((((((....))))))))))).....)-))))..((.....)).))....------------- ( -17.00, z-score =  -3.45, R)
>droSim1.chr3R 16971448 92 - 27517382
-----CUUUGAACCACCGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCCAU-AUGCAAGUAGACAACAGCCCAG-------------
-----............((......((((((((......))).(((((((((((....))))))))))).....)-))))..((.....)).))....------------- ( -16.90, z-score =  -2.26, R)
>droSec1.super_0 10097775 92 - 21120651
-----CUUUGAACCGCCGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCCAU-AUGCAAGUAGACGACAGCCCAG-------------
-----.........((.((......))....((((((......(((((((((((....))))))))))).((...-..)).)))))).....))....------------- ( -17.30, z-score =  -1.55, R)
>droYak2.chr3R 13323620 87 - 28832112
----------CUUGGAGCCGCACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCUAU-AUGCAAGUAGACAGCCGACAGC-------------
----------.((((....((....))....((((((......(((((((((((....))))))))))).((...-..)).))))))...))))....------------- ( -20.20, z-score =  -1.62, R)
>droEre2.scaffold_4770 10448102 80 + 17746568
----------CUUGGAGCCGCACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCCAU-AUGCAAGUAGACAGC--------------------
----------((((.(...((....))................(((((((((((....)))))))))))......-.).))))........-------------------- ( -16.90, z-score =  -1.19, R)
>dp4.chr2 20891719 100 + 30794189
-----------CUCCGAGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGAGUCGAUGAUAUGCACAAGCAGUAGACAAACGCUUUGCUUUGG
-----------..(((((((.....(((((.....((((...((((((((((((....))))))))))))...)))))))))..((((.((......))))))))).)))) ( -27.70, z-score =  -3.07, R)
>droPer1.super_3 3643660 100 + 7375914
-----------CUCCGAGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGAGUCGAUGAUAUGCACAAGCAGUAGACAAACGCUUUGCUUUGG
-----------..(((((((.....(((((.....((((...((((((((((((....))))))))))))...)))))))))..((((.((......))))))))).)))) ( -27.70, z-score =  -3.07, R)
>consensus
__________CUUCGACGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCCAU_AUGCAAGUAGACAGCAGACAAG_____________
.........................((((((((......))))(((((((((((....))))))))))).......))))............................... (-13.32 = -13.40 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 10,913,008 – 10,913,104
Length 96
Sequences 7
Columns 111
Reading direction reverse
Mean pairwise identity 71.37
Shannon entropy 0.49352
G+C content 0.41610
Mean single sequence MFE -25.74
Consensus MFE -15.11
Energy contribution -15.01
Covariance contribution -0.10
Combinations/Pair 1.26
Mean z-score -2.61
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.03
SVM RNA-class probability 0.997063
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10913008 96 - 27905053
-------------CUGGGCUGUCGUCUACUUGCAU-AUAGUGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGCG-GUUAAAGGAAGGGGGGG
-------------.....((.((.((((((.((((-((......(((((((((....))))))))).....(((((....))))).)))))))-))....))).)).)).. ( -22.60, z-score =  -1.27, R)
>droSim1.chr3R 16971448 92 + 27517382
-------------CUGGGCUGUUGUCUACUUGCAU-AUGGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCGGUGGUUCAAAG-----
-------------.(((((..((((.(((.(((((-(.(....)(((((((((....)))))))))...............)))))).))).))))..)))))...----- ( -29.20, z-score =  -3.69, R)
>droSec1.super_0 10097775 92 + 21120651
-------------CUGGGCUGUCGUCUACUUGCAU-AUGGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCGGCGGUUCAAAG-----
-------------.(((((((((((.(((.(((((-(.(....)(((((((((....)))))))))...............)))))).))).)))))))))))...----- ( -34.10, z-score =  -5.06, R)
>droYak2.chr3R 13323620 87 + 28832112
-------------GCUGUCGGCUGUCUACUUGCAU-AUAGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGCGGCUCCAAG----------
-------------.((...((((((.(((..((((-........(((((((((....)))))))))..((((......))))))))))).))))))...))---------- ( -23.10, z-score =  -2.08, R)
>droEre2.scaffold_4770 10448102 80 - 17746568
--------------------GCUGUCUACUUGCAU-AUGGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGCGGCUCCAAG----------
--------------------(((((.(((..((((-(.(....)(((((((((....)))))))))...............)))))))).)))))......---------- ( -22.20, z-score =  -2.74, R)
>dp4.chr2 20891719 100 - 30794189
CCAAAGCAAAGCGUUUGUCUACUGCUUGUGCAUAUCAUCGACUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCUCGGAG-----------
((..((((..((((..(((...(((....))).......)))..(((((((((....)))))))))..................))))...)))).))..----------- ( -24.50, z-score =  -1.72, R)
>droPer1.super_3 3643660 100 - 7375914
CCAAAGCAAAGCGUUUGUCUACUGCUUGUGCAUAUCAUCGACUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCUCGGAG-----------
((..((((..((((..(((...(((....))).......)))..(((((((((....)))))))))..................))))...)))).))..----------- ( -24.50, z-score =  -1.72, R)
>consensus
_____________CUGGGCUGCUGUCUACUUGCAU_AUGGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCGUCGAAG__________
.............................((((((....((((.(((((((((....)))))))))..((((......))))))))..))))))................. (-15.11 = -15.01 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:16:36 2011