Locus 12723

Sequence ID dm3.chrX
Location 1,730,410 – 1,730,510
Length 100
Max. P 0.996174
window17494 window17495

overview

Window 4

Location 1,730,410 – 1,730,510
Length 100
Sequences 7
Columns 120
Reading direction forward
Mean pairwise identity 77.25
Shannon entropy 0.38360
G+C content 0.36726
Mean single sequence MFE -32.61
Consensus MFE -17.39
Energy contribution -17.07
Covariance contribution -0.32
Combinations/Pair 1.24
Mean z-score -3.34
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.89
SVM RNA-class probability 0.996174
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1730410 100 + 22422827
------AUACAUACAUGCCCAGGCCUGUUGGUGUAUCU-AGAACAAUUUAUAGAUA-AAAUCUAUUCAAUUGUUGAUCUUAAUUUAGAACAA-------CGAGUGGGUUGUGUGA-----
------...((((((.(((((.(((....))).(((((-(..........))))))-............((((((.(((......))).)))-------))).))))))))))).----- ( -27.30, z-score =  -2.64, R)
>droSim1.chrX 1222914 100 + 17042790
------AUACAUACAUGCCCAGGUCUGUUGGUGUAUCU-AGAACAAUUUAUAGAUA-AAAUCUAUUCAAUUGUUGAUCUUAAUUUAGAACAA-------CGAGUGGGUUGUGUGA-----
------...((((((.(((((.((((((...(((....-...)))....)))))).-............((((((.(((......))).)))-------))).))))))))))).----- ( -27.10, z-score =  -2.59, R)
>droSec1.super_10 1531289 100 + 3036183
------AUACAUACAUGCCCAGGUCUGUUGGUGUAUCU-AGAACAAUUUAUAGAUA-AAAUCUAUUCAAUUGUUGAUCUUAAUUUAGAACAA-------CGAGUGGGUUGUGUGA-----
------...((((((.(((((.((((((...(((....-...)))....)))))).-............((((((.(((......))).)))-------))).))))))))))).----- ( -27.10, z-score =  -2.59, R)
>droYak2.chrX 1574913 96 + 21770863
----------AUACACACCCAGGCCUGUUGGUUUAUCU-AGCACAAUUUAUAGAUA-AAAUCUAUUCAAUUGUUGAUCUUAAUUUAGAACAA-------CGAGUGGGUUGUGUGA-----
----------.((((((((((.(((....)))((((((-(..........))))))-)...........((((((.(((......))).)))-------))).)))).)))))).----- ( -26.50, z-score =  -2.85, R)
>droEre2.scaffold_4644 1709500 96 + 2521924
----------AUACAUACCCAGGCCUGUUGGUGUAUCU-AGCACAAUUUAUAGAUA-AAAUCUAUUCAAUUGUUGAUCUUAAUUUAGAACAA-------CGAGUGGGUUGUGUGA-----
----------.((((((((((.(((....))).(((((-(..........))))))-............((((((.(((......))).)))-------))).)))).)))))).----- ( -24.30, z-score =  -1.91, R)
>dp4.chrXL_group1a 6608367 120 + 9151740
ACACACACACUCUCUCGCCCACACUCGAGUGUGUGUUUUAGAACAGUUUAUAGAUACAAAUCUAUUCAAUUGUUGAUCUUUAUUUAGAUUGGUGGGGGGCGGGAGGGCUGUGUGUGGGUC
.(((((((((((((((((((.((((................(((((((.((((((....))))))..)))))))(((((......)))))))))..))))))))))).)))))))).... ( -51.60, z-score =  -6.20, R)
>droPer1.super_25 744298 120 - 1448063
AUACACACACUCUCUCGUCCACACUCGAGUGUGUGUUUUAGAACAGUUUAUAGAUACAAAUCUAUUCAAUUGUUGAUCUUUAUUUAGAAUGGUGGGGGGCGGGAGGGCUGUGUGUGGGUC
.(((((((((((((((((((.((((................(((((((.((((((....))))))..)))))))..(((......)))..))))..))))))))))).)))))))).... ( -44.40, z-score =  -4.60, R)
>consensus
______AUACAUACAUGCCCAGGCCUGUUGGUGUAUCU_AGAACAAUUUAUAGAUA_AAAUCUAUUCAAUUGUUGAUCUUAAUUUAGAACAA_______CGAGUGGGUUGUGUGA_____
...........(((((((((.....................(((((((.((((((....))))))..)))))))..(((......)))................)))).)))))...... (-17.39 = -17.07 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,730,410 – 1,730,510
Length 100
Sequences 7
Columns 120
Reading direction reverse
Mean pairwise identity 77.25
Shannon entropy 0.38360
G+C content 0.36726
Mean single sequence MFE -22.54
Consensus MFE -11.36
Energy contribution -12.34
Covariance contribution 0.98
Combinations/Pair 1.05
Mean z-score -2.14
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.754400
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1730410 100 - 22422827
-----UCACACAACCCACUCG-------UUGUUCUAAAUUAAGAUCAACAAUUGAAUAGAUUU-UAUCUAUAAAUUGUUCU-AGAUACACCAACAGGCCUGGGCAUGUAUGUAU------
-----.((.(((.(((((..(-------(((.(((......)))..(((((((..((((((..-.)))))).)))))))..-........))))..)..))))..))).))...------ ( -17.70, z-score =  -0.93, R)
>droSim1.chrX 1222914 100 - 17042790
-----UCACACAACCCACUCG-------UUGUUCUAAAUUAAGAUCAACAAUUGAAUAGAUUU-UAUCUAUAAAUUGUUCU-AGAUACACCAACAGACCUGGGCAUGUAUGUAU------
-----.((.(((.((((....-------(((((....(((.(((...((((((..((((((..-.)))))).)))))))))-.))).....)))))...))))..))).))...------ ( -17.20, z-score =  -1.04, R)
>droSec1.super_10 1531289 100 - 3036183
-----UCACACAACCCACUCG-------UUGUUCUAAAUUAAGAUCAACAAUUGAAUAGAUUU-UAUCUAUAAAUUGUUCU-AGAUACACCAACAGACCUGGGCAUGUAUGUAU------
-----.((.(((.((((....-------(((((....(((.(((...((((((..((((((..-.)))))).)))))))))-.))).....)))))...))))..))).))...------ ( -17.20, z-score =  -1.04, R)
>droYak2.chrX 1574913 96 - 21770863
-----UCACACAACCCACUCG-------UUGUUCUAAAUUAAGAUCAACAAUUGAAUAGAUUU-UAUCUAUAAAUUGUGCU-AGAUAAACCAACAGGCCUGGGUGUGUAU----------
-----..(((((.(((((..(-------(((......(((.((....((((((..((((((..-.)))))).)))))).))-.)))....))))..)..)))))))))..---------- ( -22.50, z-score =  -2.46, R)
>droEre2.scaffold_4644 1709500 96 - 2521924
-----UCACACAACCCACUCG-------UUGUUCUAAAUUAAGAUCAACAAUUGAAUAGAUUU-UAUCUAUAAAUUGUGCU-AGAUACACCAACAGGCCUGGGUAUGUAU----------
-----....(((((((((..(-------(((......(((.((....((((((..((((((..-.)))))).)))))).))-.)))....))))..)..))))).)))..---------- ( -19.10, z-score =  -1.53, R)
>dp4.chrXL_group1a 6608367 120 - 9151740
GACCCACACACAGCCCUCCCGCCCCCCACCAAUCUAAAUAAAGAUCAACAAUUGAAUAGAUUUGUAUCUAUAAACUGUUCUAAAACACACACUCGAGUGUGGGCGAGAGAGUGUGUGUGU
....((((((((.(.(((.(((((..((((.((((......))))........((((((.(((((....)))))))))))..............).))).))))).))).))))))))). ( -36.70, z-score =  -4.96, R)
>droPer1.super_25 744298 120 + 1448063
GACCCACACACAGCCCUCCCGCCCCCCACCAUUCUAAAUAAAGAUCAACAAUUGAAUAGAUUUGUAUCUAUAAACUGUUCUAAAACACACACUCGAGUGUGGACGAGAGAGUGUGUGUAU
.....(((((((.(.(((.((................................((((((.(((((....))))))))))).......(((((....)))))..)).))).)))))))).. ( -27.40, z-score =  -3.01, R)
>consensus
_____UCACACAACCCACUCG_______UUGUUCUAAAUUAAGAUCAACAAUUGAAUAGAUUU_UAUCUAUAAAUUGUUCU_AGAUACACCAACAGGCCUGGGCAUGUAUGUAU______
............((((................(((......)))..(((((((..((((((....)))))).))))))).....................))))................ (-11.36 = -12.34 +   0.98)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:07:36 2011