Locus 5652

Sequence ID dm3.chr3L
Location 293,118 – 293,226
Length 108
Max. P 0.946568
window7762 window7763

overview

Window 2

Location 293,118 – 293,226
Length 108
Sequences 6
Columns 123
Reading direction forward
Mean pairwise identity 71.45
Shannon entropy 0.51760
G+C content 0.61026
Mean single sequence MFE -42.45
Consensus MFE -23.04
Energy contribution -25.60
Covariance contribution 2.56
Combinations/Pair 1.05
Mean z-score -1.29
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.753925
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 293118 108 + 24543557
CGUCGCCUGACGCUGAGCCCCGGGAAGGGGAUGCAGCUGGCGACUCGUCAAUGAGCACCAGUGACGAGUAAGUUGGUUCC-GGUUUCCC-CAAGACGGGCAC--CAUUGGAA-----------
.((((((....((((..((((.....))))...)))).))))))((((((.((.....)).))))))......((((.((-.((((...-..)))).)).))--))......----------- ( -45.00, z-score =  -1.71, R)
>droEre2.scaffold_4784 286079 111 + 25762168
CAACGCCUGACGCUGAGCCCCGGGAAGGGGAUGCAGCUGGCGACUCGUCAAUGAGCACCAGUGACGAGUAAGUUGGUUCC-GGUUCCCCCAAGGACGGGGGCAUCCUUUAAA-----------
(((((((....((((..((((.....))))...)))).))).((((((((.((.....)).))))))))..)))).....-((..(((((......)))))...))......----------- ( -49.10, z-score =  -2.49, R)
>droYak2.chr3L 272368 119 + 24197627
CGACGCCUGACGCGGAGCCCCAGGAAGGGGAUGCGGCUGGCGACUCGUCCACCAGCACCAGUGACGAGUAAGUUGCUUCC-GGUUCCUC-AAGGACGUGGGC--CCCUAGAAUGACCUCCAAA
(.((((((...(.((((((((.....))(((.((((((....(((((((.((........))))))))).)))))).)))-)))))).)-.))).))).)..--................... ( -42.30, z-score =   0.29, R)
>droSec1.super_2 324915 108 + 7591821
CGUCGCCUGAAGCUGAUCCCCGGGAAGGGGAUGCAGCUGGCGACUCGUCAAUGAGCACCAGUGACGAGUAAGUUGGUUCC-GGUUUCCC-CAAGACGGGCAC--CAUUCGAA-----------
.((((((...(((((((((((.....)))))).)))))))))))((((((.((.....)).))))))......((((.((-.((((...-..)))).)).))--))......----------- ( -48.20, z-score =  -3.16, R)
>droSim1.chr2R 8516777 108 + 19596830
CGUCGCCUGACGCUGAGCCCCGGGAAGGGGAUGCAGCUGGCGACUCGUCAAUGAGCACCAGUGACGAGUAAGUUGGUUCC-GGUGUACC-CAAGACGGGCAC--CAUUCGAA-----------
.((((((....((((..((((.....))))...)))).))))))((((((.((.....)).)))))).............-((((..((-(.....))))))--).......----------- ( -44.10, z-score =  -1.65, R)
>dp4.chrXR_group8 7879685 93 - 9212921
---CUCCGACAGCUGACAGCCGUCAGGUGGACGAAGCUGCUUCGCCGGCACUGAGCGAAACCGCCAUGUAAGUUGACAGAAGGGUCACCGCACCAC---------------------------
---....(((.((.....)).))).(((((.(((((...))))))).((((((.(((....))))).))..(.((((......)))).))))))..--------------------------- ( -26.00, z-score =   0.99, R)
>consensus
CGUCGCCUGACGCUGAGCCCCGGGAAGGGGAUGCAGCUGGCGACUCGUCAAUGAGCACCAGUGACGAGUAAGUUGGUUCC_GGUUCCCC_CAAGACGGGCAC__CAUUCGAA___________
...((((....((((..((((.....))))...)))).))))((((((((.((.....)).))))))))...................................................... (-23.04 = -25.60 +   2.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 293,118 – 293,226
Length 108
Sequences 6
Columns 123
Reading direction reverse
Mean pairwise identity 71.45
Shannon entropy 0.51760
G+C content 0.61026
Mean single sequence MFE -42.99
Consensus MFE -24.02
Energy contribution -25.30
Covariance contribution 1.28
Combinations/Pair 1.26
Mean z-score -1.69
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946568
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 293118 108 - 24543557
-----------UUCCAAUG--GUGCCCGUCUUG-GGGAAACC-GGAACCAACUUACUCGUCACUGGUGCUCAUUGACGAGUCGCCAGCUGCAUCCCCUUCCCGGGGCUCAGCGUCAGGCGACG
-----------...(((((--(..((.((..((-((....))-(....)........))..)).))..).)))))....((((((.((((...((((.....))))..))))....)))))). ( -42.10, z-score =  -1.81, R)
>droEre2.scaffold_4784 286079 111 - 25762168
-----------UUUAAAGGAUGCCCCCGUCCUUGGGGGAACC-GGAACCAACUUACUCGUCACUGGUGCUCAUUGACGAGUCGCCAGCUGCAUCCCCUUCCCGGGGCUCAGCGUCAGGCGUUG
-----------......((...((((((....))))))..))-.....((((..((((((((.((.....)).)))))))).(((.((((...((((.....))))..))))....))))))) ( -45.60, z-score =  -2.31, R)
>droYak2.chr3L 272368 119 - 24197627
UUUGGAGGUCAUUCUAGGG--GCCCACGUCCUU-GAGGAACC-GGAAGCAACUUACUCGUCACUGGUGCUGGUGGACGAGUCGCCAGCCGCAUCCCCUUCCUGGGGCUCCGCGUCAGGCGUCG
....((.(((......(((--((((.((....)-)(((((..-(((.((.(((...........)))((((((((.....)))))))).)).)))..))))).)))))))......))).)). ( -43.60, z-score =   0.68, R)
>droSec1.super_2 324915 108 - 7591821
-----------UUCGAAUG--GUGCCCGUCUUG-GGGAAACC-GGAACCAACUUACUCGUCACUGGUGCUCAUUGACGAGUCGCCAGCUGCAUCCCCUUCCCGGGGAUCAGCUUCAGGCGACG
-----------......((--((.((.......-((....))-)).))))......((((((.((.....)).))))))(((((((((((.((((((.....)))))))))))...)))))). ( -46.21, z-score =  -3.24, R)
>droSim1.chr2R 8516777 108 - 19596830
-----------UUCGAAUG--GUGCCCGUCUUG-GGUACACC-GGAACCAACUUACUCGUCACUGGUGCUCAUUGACGAGUCGCCAGCUGCAUCCCCUUCCCGGGGCUCAGCGUCAGGCGACG
-----------((((....--((((((.....)-)))))..)-)))..........((((((.((.....)).))))))((((((.((((...((((.....))))..))))....)))))). ( -43.70, z-score =  -2.38, R)
>dp4.chrXR_group8 7879685 93 + 9212921
---------------------------GUGGUGCGGUGACCCUUCUGUCAACUUACAUGGCGGUUUCGCUCAGUGCCGGCGAAGCAGCUUCGUCCACCUGACGGCUGUCAGCUGUCGGAG---
---------------------------((((.((((((((......))))........(((.((((((((.......)))))))).)))))))))))((((((((.....))))))))..--- ( -36.70, z-score =  -1.09, R)
>consensus
___________UUCGAAUG__GUGCCCGUCUUG_GGGAAACC_GGAACCAACUUACUCGUCACUGGUGCUCAUUGACGAGUCGCCAGCUGCAUCCCCUUCCCGGGGCUCAGCGUCAGGCGACG
............................(((...((....)).)))........((((((((.((.....)).))))))))((((.((((...((((.....))))..))))....))))... (-24.02 = -25.30 +   1.28)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:52:30 2011