Locus 4116

Sequence ID dm3.chr2R
Location 10,570,809 – 10,570,902
Length 93
Max. P 0.987058
window5645 window5646

overview

Window 5

Location 10,570,809 – 10,570,902
Length 93
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 85.24
Shannon entropy 0.26343
G+C content 0.39577
Mean single sequence MFE -22.52
Consensus MFE -20.98
Energy contribution -20.78
Covariance contribution -0.19
Combinations/Pair 1.13
Mean z-score -1.94
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.00
SVM RNA-class probability 0.978443
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10570809 93 + 21146708
GCGAAUGUGGUAGACGCUGUUGACGCCAUUGUAAUGCUAAUGGCUCAUUAGCACUUUGAUUUUUUCGCACUGGUUUUCUCUUUUUUUUUUUUU
(((((.....((((.((((.(((.(((((((......)))))))))).))))..)))).....)))))......................... ( -22.90, z-score =  -2.37, R)
>droAna3.scaffold_13266 5047219 80 - 19884421
GAGAGUGUGGUGGAUCCUGUUGACGCCAUUGUAAUGCUAAUGGCUCAUUAGCACUUUGAUUUUUUCGCUUGGUAUUUUUU-------------
..(((((....(((((.((((((.(((((((......)))))))...))))))....)))))...)))))..........------------- ( -17.90, z-score =  -0.66, R)
>droEre2.scaffold_4845 7311679 78 - 22589142
GCGAGUGUGGCAGACGCUGUUGACGCCAUUGUAAUGCUAAUGGCUCAUUAGCACUUUGAUUUUUUCGCACUGUAUUUU---------------
(((((.....((((.((((.(((.(((((((......)))))))))).))))..)))).....)))))..........--------------- ( -24.40, z-score =  -2.16, R)
>droYak2.chr2R 10503024 93 + 21139217
GCGAGUGUGGUAGACGCUGUUGACGCCAUUGUAAUGCUAAUGGCUCAUUAGCACUUUGAUUUUUUCGCACUGGAUUUUUUGUUGUUUUUUUUU
.(.(((((((....)((((.(((.(((((((......)))))))))).)))).............)))))).).................... ( -23.70, z-score =  -1.75, R)
>droSec1.super_1 8090230 89 + 14215200
GCGAAUGUGGUAGACGCUGUUGACGCCAUUGUAAUGCUAAUGGCUCAUUAGCACUUUGAUUUUUUCGCACUGGUUUUUCCUUUUUUUUU----
(((((.....((((.((((.(((.(((((((......)))))))))).))))..)))).....)))))...((.....)).........---- ( -23.30, z-score =  -2.35, R)
>droSim1.chr2R 9333828 89 + 19596830
GCGAAUGUGGUAGACGCUGUUGACGCCAUUGUAAUGCUAAUGGCUCAUUAGCACUUUGAUUUUUUCGCACUGGUUUUUUCUUUUUUUUU----
(((((.....((((.((((.(((.(((((((......)))))))))).))))..)))).....))))).....................---- ( -22.90, z-score =  -2.33, R)
>consensus
GCGAAUGUGGUAGACGCUGUUGACGCCAUUGUAAUGCUAAUGGCUCAUUAGCACUUUGAUUUUUUCGCACUGGAUUUUUCUUUUUUUUU____
(((((.....((((.((((.(((.(((((((......)))))))))).))))..)))).....)))))......................... (-20.98 = -20.78 +  -0.19)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 6

Location 10,570,809 – 10,570,902
Length 93
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 85.24
Shannon entropy 0.26343
G+C content 0.39577
Mean single sequence MFE -18.22
Consensus MFE -15.82
Energy contribution -16.32
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.26
SVM RNA-class probability 0.987058
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10570809 93 - 21146708
AAAAAAAAAAAAAGAGAAAACCAGUGCGAAAAAAUCAAAGUGCUAAUGAGCCAUUAGCAUUACAAUGGCGUCAACAGCGUCUACCACAUUCGC
.........................(((((........((((((((((...)))))))))).....(((((.....))))).......))))) ( -19.60, z-score =  -2.82, R)
>droAna3.scaffold_13266 5047219 80 + 19884421
-------------AAAAAAUACCAAGCGAAAAAAUCAAAGUGCUAAUGAGCCAUUAGCAUUACAAUGGCGUCAACAGGAUCCACCACACUCUC
-------------.........................((((((((((...))))))))))....(((.(((.....)))))).......... ( -12.80, z-score =  -1.51, R)
>droEre2.scaffold_4845 7311679 78 + 22589142
---------------AAAAUACAGUGCGAAAAAAUCAAAGUGCUAAUGAGCCAUUAGCAUUACAAUGGCGUCAACAGCGUCUGCCACACUCGC
---------------..........((((.........((((((((((...)))))))))).....(((((.....)))))........)))) ( -18.50, z-score =  -1.48, R)
>droYak2.chr2R 10503024 93 - 21139217
AAAAAAAAACAACAAAAAAUCCAGUGCGAAAAAAUCAAAGUGCUAAUGAGCCAUUAGCAUUACAAUGGCGUCAACAGCGUCUACCACACUCGC
.........................((((.........((((((((((...)))))))))).....(((((.....)))))........)))) ( -18.50, z-score =  -2.71, R)
>droSec1.super_1 8090230 89 - 14215200
----AAAAAAAAAGGAAAAACCAGUGCGAAAAAAUCAAAGUGCUAAUGAGCCAUUAGCAUUACAAUGGCGUCAACAGCGUCUACCACAUUCGC
----.........((.....))...(((((........((((((((((...)))))))))).....(((((.....))))).......))))) ( -20.30, z-score =  -2.70, R)
>droSim1.chr2R 9333828 89 - 19596830
----AAAAAAAAAGAAAAAACCAGUGCGAAAAAAUCAAAGUGCUAAUGAGCCAUUAGCAUUACAAUGGCGUCAACAGCGUCUACCACAUUCGC
----.....................(((((........((((((((((...)))))))))).....(((((.....))))).......))))) ( -19.60, z-score =  -2.97, R)
>consensus
____AAAAAAAAAGAAAAAACCAGUGCGAAAAAAUCAAAGUGCUAAUGAGCCAUUAGCAUUACAAUGGCGUCAACAGCGUCUACCACACUCGC
.........................((((.........((((((((((...)))))))))).....(((((.....)))))........)))) (-15.82 = -16.32 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:23:06 2011