Locus 15560

Sequence ID dm3.chrX
Location 19,575,355 – 19,575,501
Length 146
Max. P 0.888653
window21456 window21457

overview

Window 6

Location 19,575,355 – 19,575,501
Length 146
Sequences 4
Columns 148
Reading direction forward
Mean pairwise identity 68.95
Shannon entropy 0.50578
G+C content 0.56634
Mean single sequence MFE -48.22
Consensus MFE -25.95
Energy contribution -27.70
Covariance contribution 1.75
Combinations/Pair 1.25
Mean z-score -1.60
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.888653
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19575355 146 + 22422827
GGCAACGAUUACAGCCACGCCUUGCAAUCCGAAGACGCCUGUUGUCUGCUGUAUACCUUAUGUAUACAGACUCCUGGCGAUUCUGG--GGGAAAUGGUGGGUCUGCCUCCUCCGAUUUCCGUGGAAGUGCAUUCGCCCAGAAUGCCGC
(((..............((((...........(((((.....))))).((((((((.....))))))))......))))(((((((--(.(((.(((.(((......))).)))(((((....)))))...))).))))))))))).. ( -50.10, z-score =  -1.33, R)
>droEre2.scaffold_4690 9802310 111 + 18748788
---------------------------------GGCUACCCACAUCUGCUUGGCACUUGAUGUGUGCC-ACGCCAUGCGCGUUGAACUAGGAAACUAGAGG---GCCUCCUCCGAUUUCCGUGGAAGUGGACUCGCCCAGAACGCCGU
---------------------------------((....))......((.((((((.......)))))-).)).(((.(((((...((((....)))).((---((....(((.(((((....))))))))...))))..)))))))) ( -41.40, z-score =  -2.00, R)
>droSec1.super_8 1854910 144 + 3762037
GGC--UGAUUACAGUCACGCCUUGCAAUCCGAAGACGCCUGUCGUCCAUUGUAUACCCUAUGUAUACAGACUCCUAGCGAGUCUGG--GGGCAAUGGAGGGCCUGCCUCCUCCGAUUUCCGUGGAAGUGCAUUCGCCCAGAAUGCCGC
(((--((((....)))).)))..((((((.((.((.((..(((.((((((((...(((...(....)((((((.....))))))))--).)))))))).)))..)).)).)).)))).........(.((((((.....))))))))) ( -50.70, z-score =  -1.50, R)
>droSim1.chrX_random 5128952 137 + 5698898
GGC--UGAUUACAGCCACGCCUUGCAAUGCGAAGACGCCU-------AUUGUAUACCCUAUGUAUACAGACUCCUGGCGAGUCUGG--GGGCAAUGGAGGGCCUGCCUCCUCCGAUUUCCGUGGAAGUGCAUUCGCCCAGAAUGCCGC
(((--((....)))))..(((((((((((((....)))..-------)))))..............(((((((.....))))))))--))))..(((((((......)))))))(((((....)))))((((((.....))))))... ( -50.70, z-score =  -1.57, R)
>consensus
GGC__UGAUUACAGCCACGCCUUGCAAUCCGAAGACGCCUGUCGUCUACUGUAUACCCUAUGUAUACAGACUCCUGGCGAGUCUGG__GGGAAAUGGAGGGCCUGCCUCCUCCGAUUUCCGUGGAAGUGCAUUCGCCCAGAAUGCCGC
............................................(((((.((((((.....))))))((((((.....)))))).....((((((((((((......))))))).)))))))))).(.((((((.....))))))).. (-25.95 = -27.70 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 7

Location 19,575,355 – 19,575,501
Length 146
Sequences 4
Columns 148
Reading direction reverse
Mean pairwise identity 68.95
Shannon entropy 0.50578
G+C content 0.56634
Mean single sequence MFE -49.73
Consensus MFE -27.95
Energy contribution -30.57
Covariance contribution 2.62
Combinations/Pair 1.14
Mean z-score -1.48
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.872003
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19575355 146 - 22422827
GCGGCAUUCUGGGCGAAUGCACUUCCACGGAAAUCGGAGGAGGCAGACCCACCAUUUCCC--CCAGAAUCGCCAGGAGUCUGUAUACAUAAGGUAUACAGCAGACAACAGGCGUCUUCGGAUUGCAAGGCGUGGCUGUAAUCGUUGCC
(((((((((((((.((((((.((((..((.....))..)))))))(......)..))).)--))))))).((((.(.(.((((((((.....))))))))).........(((((....)).)))....).)))).......))))). ( -50.10, z-score =  -1.28, R)
>droEre2.scaffold_4690 9802310 111 - 18748788
ACGGCGUUCUGGGCGAGUCCACUUCCACGGAAAUCGGAGGAGGC---CCUCUAGUUUCCUAGUUCAACGCGCAUGGCGU-GGCACACAUCAAGUGCCAAGCAGAUGUGGGUAGCC---------------------------------
..(((....((((((((....)))....((((((..((((....---))))..))))))..)))))((.(((((.((.(-(((((.......)))))).))..))))).)).)))--------------------------------- ( -44.30, z-score =  -2.04, R)
>droSec1.super_8 1854910 144 - 3762037
GCGGCAUUCUGGGCGAAUGCACUUCCACGGAAAUCGGAGGAGGCAGGCCCUCCAUUGCCC--CCAGACUCGCUAGGAGUCUGUAUACAUAGGGUAUACAAUGGACGACAGGCGUCUUCGGAUUGCAAGGCGUGACUGUAAUCA--GCC
..(((.....((((...(((.((((..((.....))..))))))).))))(((((((...--.(((((((.....)))))))(((((.....))))))))))))..(((((((((((........)))))))..)))).....--))) ( -51.90, z-score =  -1.04, R)
>droSim1.chrX_random 5128952 137 - 5698898
GCGGCAUUCUGGGCGAAUGCACUUCCACGGAAAUCGGAGGAGGCAGGCCCUCCAUUGCCC--CCAGACUCGCCAGGAGUCUGUAUACAUAGGGUAUACAAU-------AGGCGUCUUCGCAUUGCAAGGCGUGGCUGUAAUCA--GCC
..((((....((((...(((.((((..((.....))..))))))).)))).....)))).--..((((((.....))))))((((((.....))))))...-------..(((((((.((...)))))))))(((((....))--))) ( -52.60, z-score =  -1.57, R)
>consensus
GCGGCAUUCUGGGCGAAUGCACUUCCACGGAAAUCGGAGGAGGCAGGCCCUCCAUUGCCC__CCAGACUCGCCAGGAGUCUGUAUACAUAAGGUAUACAACAGACGACAGGCGUCUUCGGAUUGCAAGGCGUGGCUGUAAUCA__GCC
..((((....((((...(((.((((..((.....))..))))))).)))).....)))).....((((((.....))))))((((((.....))))))............(((((((........)))))))................ (-27.95 = -30.57 +   2.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:01:46 2011