Locus 10265

Sequence ID	dm3.chr3R
Location	12,554,800 – 12,554,903
Length	103
Max. P	0.745279

overview

Window 4

Location	12,554,800 – 12,554,903
Length	103
Sequences	7
Columns	115
Reading direction	forward
Mean pairwise identity	81.00
Shannon entropy	0.37106
G+C content	0.59630
Mean single sequence MFE	-41.26
Consensus MFE	-23.42
Energy contribution	-25.29
Covariance contribution	1.87
Combinations/Pair	1.07
Mean z-score	-1.79
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.32
SVM RNA-class probability	0.643691
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12554800 103 + 27905053
UGUUGGGCCAUGUGUCUGGGCCACUUUGUGUUGUCGUCGUUGGCGACG------UCGACGUCUUGCAACUUUGGUCUCCUCGACCGCCAGUCGCAGU------GCGAGUCCAACG
.((((((((.((((.((((..........((((.(((((....)))))------.)))).............((((.....)))).)))).))))..------..).))))))). ( -40.60, z-score =  -1.75, R)
>droSim1.chr3R 18602140 109 - 27517382
UGUUGGGCCAUGUGUCUGGGCCACUUUGUGUUGUCGUCGUUGGCGACG------UCGACGUCUUGCAACUUUGGUCUCCUCGACCGCCAGUCGCAGUCGCAGUGCGAGUCCAACG
.(((((((..((((.((((..........((((.(((((....)))))------.)))).............((((.....)))).)))).)))).((((...))))))))))). ( -44.00, z-score =  -1.88, R)
>droSec1.super_12 530575 109 - 2123299
UGUUGGGCCAUGUGUCUGGGCCACUUUGUGUUGUCGUCGUUGGCGACG------UCGAAGUCUUGCAACUUUGGUCUCCUCGACCGCCAGUCGCAGUCGCAGUUCGAGUCCAACG
.(((((((..((((.((((((.((((((((((((((....))))))))------.))))))...))......((((.....)))).)))).)))).(((.....)))))))))). ( -43.40, z-score =  -2.58, R)
>droYak2.chr3R 16997441 109 - 28832112
UGUUGGGCCAUGUGUCUGGGCCACUUUGUGUUGUCGUCGUUGGCGACG------UCGACGUCUUGCAACUUUGGUCUCCUCGACCGCCAGUCGCAGUCGCAGUGCGAGUCCAACG
.(((((((..((((.((((..........((((.(((((....)))))------.)))).............((((.....)))).)))).)))).((((...))))))))))). ( -44.00, z-score =  -1.88, R)
>droEre2.scaffold_4770 8670220 109 - 17746568
UGUUGGGCCAUGUGUCUGGGCCACUUUGUGUUGUCGUCGUUGGCGACGGCGACGUCGACGUCUUGCAACUUUGGUCUCCUCGACCGCCAGUCGCAGU------GCGAGUCCAACG
.((((((((.((((.((((((.((.((((((((((((((....))))))))))).))).))...))......((((.....)))).)))).))))..------..).))))))). ( -47.80, z-score =  -2.37, R)
>droAna3.scaffold_13340 16366017 107 - 23697760
UGCUGGGCCAUGUGUCUGGGCCACUUUGUGUUGUCGUCGUCGUUGUCGACG--UCCAACGUCUUGCAACUUUGGUCUCCG-GGCCGGCAGUC-CAACCG----AGGAGUCCAACG
((((((.(((......))).)))......((((.(((((.......)))))--..)))).....)))...((((.((((.-((..((....)-)..)).----.)))).)))).. ( -34.70, z-score =   0.46, R)
>dp4.chr2 17539441 79 + 30794189
---UGGCCCAUGUGUCUGGGCCACUUUGUGUUGUCGUCGUUG------------UCGAGGUCUUGCAACGC-GGACCCGUGGUCGG--AGUC-CAACG-----------------
---(((((((......)))))))....((((((((.(((...------------.))).)....)))))))-(((((((....)))--.)))-)....----------------- ( -34.30, z-score =  -2.54, R)
>consensus
UGUUGGGCCAUGUGUCUGGGCCACUUUGUGUUGUCGUCGUUGGCGACG______UCGACGUCUUGCAACUUUGGUCUCCUCGACCGCCAGUCGCAGUCG____GCGAGUCCAACG
.(((((((..((((.((((..........((((((((((................)))))....)))))...((((.....)))).)))).))))............))))))). (-23.42 = -25.29 +   1.87)

alignment

secondary structure

dotplot

Window 5

Location	12,554,800 – 12,554,903
Length	103
Sequences	7
Columns	115
Reading direction	reverse
Mean pairwise identity	81.00
Shannon entropy	0.37106
G+C content	0.59630
Mean single sequence MFE	-37.09
Consensus MFE	-24.07
Energy contribution	-25.32
Covariance contribution	1.25
Combinations/Pair	1.08
Mean z-score	-1.62
Structure conservation index	0.65
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.57
SVM RNA-class probability	0.745279
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12554800 103 - 27905053
CGUUGGACUCGC------ACUGCGACUGGCGGUCGAGGAGACCAAAGUUGCAAGACGUCGA------CGUCGCCAACGACGACAACACAAAGUGGCCCAGACACAUGGCCCAACA
.(((((((((..------..(((((((...((((.....))))..))))))).)).)))..------(((((....))))).))))......(((.(((......))).)))... ( -36.70, z-score =  -1.62, R)
>droSim1.chr3R 18602140 109 + 27517382
CGUUGGACUCGCACUGCGACUGCGACUGGCGGUCGAGGAGACCAAAGUUGCAAGACGUCGA------CGUCGCCAACGACGACAACACAAAGUGGCCCAGACACAUGGCCCAACA
.(((((((((((...)))).(((((((...((((.....))))..)))))))....)))..------(((((....))))).))))......(((.(((......))).)))... ( -38.80, z-score =  -1.43, R)
>droSec1.super_12 530575 109 + 2123299
CGUUGGACUCGAACUGCGACUGCGACUGGCGGUCGAGGAGACCAAAGUUGCAAGACUUCGA------CGUCGCCAACGACGACAACACAAAGUGGCCCAGACACAUGGCCCAACA
.((((...(((((.(((((((((.....))((((.....))))..)))))))....)))))------(((((....))))).))))......(((.(((......))).)))... ( -37.00, z-score =  -1.69, R)
>droYak2.chr3R 16997441 109 + 28832112
CGUUGGACUCGCACUGCGACUGCGACUGGCGGUCGAGGAGACCAAAGUUGCAAGACGUCGA------CGUCGCCAACGACGACAACACAAAGUGGCCCAGACACAUGGCCCAACA
.(((((((((((...)))).(((((((...((((.....))))..)))))))....)))..------(((((....))))).))))......(((.(((......))).)))... ( -38.80, z-score =  -1.43, R)
>droEre2.scaffold_4770 8670220 109 + 17746568
CGUUGGACUCGC------ACUGCGACUGGCGGUCGAGGAGACCAAAGUUGCAAGACGUCGACGUCGCCGUCGCCAACGACGACAACACAAAGUGGCCCAGACACAUGGCCCAACA
.((((.....((------..(((((((...((((.....))))..))))))).((((....))))))(((((....))))).))))......(((.(((......))).)))... ( -39.90, z-score =  -1.28, R)
>droAna3.scaffold_13340 16366017 107 + 23697760
CGUUGGACUCCU----CGGUUG-GACUGCCGGCC-CGGAGACCAAAGUUGCAAGACGUUGGA--CGUCGACAACGACGACGACAACACAAAGUGGCCCAGACACAUGGCCCAGCA
..((((.((((.----.(((((-(....))))))-.)))).))))...(((.....((((..--(((((....))))).)))).........(((.(((......))).)))))) ( -38.50, z-score =  -1.46, R)
>dp4.chr2 17539441 79 - 30794189
-----------------CGUUG-GACU--CCGACCACGGGUCC-GCGUUGCAAGACCUCGA------------CAACGACGACAACACAAAGUGGCCCAGACACAUGGGCCA---
-----------------.((((-(((.--(((....))))))(-(((((((........).------------))))).)).))))......(((((((......)))))))--- ( -29.90, z-score =  -2.40, R)
>consensus
CGUUGGACUCGC____CGACUGCGACUGGCGGUCGAGGAGACCAAAGUUGCAAGACGUCGA______CGUCGCCAACGACGACAACACAAAGUGGCCCAGACACAUGGCCCAACA
.((((...............(((((((...((((.....))))..)))))))...(((((................))))).))))......(((.(((......))).)))... (-24.07 = -25.32 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:20:37 2011