Locus 3208

Sequence ID dm3.chr2R
Location 3,431,809 – 3,431,952
Length 143
Max. P 0.828880
window4409 window4410

overview

Window 9

Location 3,431,809 – 3,431,912
Length 103
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 83.13
Shannon entropy 0.28384
G+C content 0.63643
Mean single sequence MFE -45.38
Consensus MFE -37.66
Energy contribution -39.54
Covariance contribution 1.88
Combinations/Pair 1.06
Mean z-score -1.51
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.828880
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3431809 103 - 21146708
UGCCGGCUGACAGCUGGCACCCCUCUCCUCCUUUGGACUCUCCGCUCACACCCACCAUCCGCCAAGGUGAGUGAGCAAGGCGGU-GAUGAGAAGGGUUGGCGGG-------
(((((((.....))))))).(((.((..((((((....((.((((((.(((.((((.........)))).))).)...))))).-))...))))))..)).)))------- ( -41.20, z-score =  -0.40, R)
>droEre2.scaffold_4929 7474038 105 + 26641161
UGCCGGCUGACAGCUGGCUACCCUCCCCUCCACA-GACUCUCCGCCCAC---CACCCCC-GUCAAGGUGAGUGAGCAAGGCGGU-GAUGAGGAGGCUUGAGGGGGUACCAU
.((((((.....))))))..(((((.(((((.((-...((.((((((((---((((...-.....)))).))).....))))).-)))).)))))...)))))........ ( -47.60, z-score =  -1.80, R)
>droYak2.chr2L 16108642 106 - 22324452
UGCCGGCUGACAGCUGGCUGCCCUCCCCUCCUCA-GAAUCUCCGCCCAC---CACCCCCUGCCAAGGUGAGUUAGCAAGGCGGU-GAUGAGGAGGCUUGCGGGGGUACCAU
.((((((.....))))))((((((((((((((((-...((.((((((((---(............)))).(....)..))))).-))))))))))...).))))))).... ( -48.30, z-score =  -1.68, R)
>droSec1.super_1 1094136 102 - 14215200
UGCCGGCUGACAGCUGGCAUCCCUCUCCUCCUUAGGACUCUCCGCUCACACCCACCAUCCGCCAAGGUGAGUGAGCAAGGCGGU-UAUGAGGAGGGUUGCGGG--------
(((((((.....))))))).(((.((((((((((.((((((..((((((...((((.........)))).))))))..)).)))-).)))))))))..).)))-------- ( -46.30, z-score =  -2.24, R)
>droSim1.chr2R 2156348 104 - 19596830
UGCCGGCUGACAGCUGACACCCCUCUCCUCCUUAGGACUCUCCGCUCACACCCACCAUCCGCCAAGGUGAGUGAGCAAGGCGGUAGAUGAGGAGGUUUUGGGGG-------
((.((((.....)))).))((((...((((((((..(((((..((((((...((((.........)))).))))))..)).)))...))))))))....)))).------- ( -43.50, z-score =  -1.45, R)
>consensus
UGCCGGCUGACAGCUGGCACCCCUCUCCUCCUUAGGACUCUCCGCUCACACCCACCAUCCGCCAAGGUGAGUGAGCAAGGCGGU_GAUGAGGAGGCUUGCGGGG_______
.((((((.....))))))..(((((.((((((((....((.((((((((...((((.........)))).))))))..)).))....))))))))...)))))........ (-37.66 = -39.54 +   1.88)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 0

Location 3,431,834 – 3,431,952
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 89.97
Shannon entropy 0.17538
G+C content 0.58021
Mean single sequence MFE -48.50
Consensus MFE -41.50
Energy contribution -41.42
Covariance contribution -0.08
Combinations/Pair 1.14
Mean z-score -1.42
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.608533
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3431834 118 + 21146708
UUGCUCACUCACCUUGGCGGAUGGUGGGUGUGAGCGGAGAGUCCAAAGGAGGAGAGGGGUGCCAGCUGUCAGCCGGCAAAUGGCUUUCACUUUCCUUCCACAGCCAUCCAAGCGUGGU
........(((((((((......((((.((((...((.....))...((((((((((((.((((..((((....))))..)))).))).))))))))))))).))))))))).)))). ( -47.20, z-score =  -0.82, R)
>droEre2.scaffold_4929 7474070 113 - 26641161
UUGCUCACUCACCUUGACGGG-GGUG---GUGGGCGGAGAGUC-UGUGGAGGGGAGGGUAGCCAGCUGUCAGCCGGCAAAUGGCUUUCACUUUCCUUCCACAGCCAUCCAGGUGUGGU
..((((((.(((((......)-))))---))))))(((..(.(-(((((((((((((..(((((..((((....))))..)))))....)))))))))))))))..)))......... ( -59.30, z-score =  -4.05, R)
>droYak2.chr2L 16108674 114 + 22324452
UUGCUAACUCACCUUGGCAGGGGGUG---GUGGGCGGAGAUUC-UGAGGAGGGGAGGGCAGCCAGCUGUCAGCCGGCAAAUGGCUUUCACUUUCCUUUCACAGCAAUCCGAGUGUGGU
..(((.((.((((((.....))))))---)).)))(((....(-((.((((((((((..(((((..((((....))))..)))))....)))))))))).)))...)))......... ( -44.50, z-score =  -0.76, R)
>droSec1.super_1 1094160 118 + 14215200
UUGCUCACUCACCUUGGCGGAUGGUGGGUGUGAGCGGAGAGUCCUAAGGAGGAGAGGGAUGCCAGCUGUCAGCCGGCAAAUGGCUUUCACUUUCCUUCCACAGCCAUCCAAGUGUGGU
........(((((((((......((((.((((...((.....))...((((((((((((.((((..((((....))))..)))).))).))))))))))))).))))))))).)))). ( -47.50, z-score =  -1.18, R)
>droSim1.chr2R 2156374 118 + 19596830
UUGCUCACUCACCUUGGCGGAUGGUGGGUGUGAGCGGAGAGUCCUAAGGAGGAGAGGGGUGUCAGCUGUCAGCCGGCAAAUGGCUUUCACUUUCCUUCCACAGCCAUCCAAGUGUGGU
........(((((((((......((((.((((...((.....))...((((((((((((.((((..((((....))))..)))).))).))))))))))))).))))))))).)))). ( -44.00, z-score =  -0.29, R)
>consensus
UUGCUCACUCACCUUGGCGGAUGGUGGGUGUGAGCGGAGAGUCCUAAGGAGGAGAGGGGUGCCAGCUGUCAGCCGGCAAAUGGCUUUCACUUUCCUUCCACAGCCAUCCAAGUGUGGU
..((((((.((((.........))))...))))))(((..((.....((((((((((((.((((..((((....))))..)))).))).)))))))))....))..)))......... (-41.50 = -41.42 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:05:48 2011