Locus 4790

Sequence ID	dm3.chr2R
Location	15,642,896 – 15,643,029
Length	133
Max. P	0.905331

overview

Window 9

Location	15,642,896 – 15,643,029
Length	133
Sequences	3
Columns	135
Reading direction	forward
Mean pairwise identity	67.75
Shannon entropy	0.45258
G+C content	0.52213
Mean single sequence MFE	-37.16
Consensus MFE	-25.81
Energy contribution	-24.05
Covariance contribution	-1.76
Combinations/Pair	1.41
Mean z-score	-0.93
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.26
SVM RNA-class probability	0.617243
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15642896 133 + 21146708
CAGCAGGCAGCAAAAAGUUGUGGACGAGGCCAACAACACGCGGUGUUCCCAAGCGGUCCCCCAUCUAAGUACUAA--CCGCGCCCGACGCUGCUUAAUUUCGGUGAUCGGACGAGAACCGAUGUAUUCAGCGUGG
.....(((........(((((((......)).)))))..(((((((......))((....))............)--)))))))(.((((((..((...(((((..((....))..)))))..))..)))))).) ( -41.90, z-score =  -0.40, R)
>anoGam1.chr2L 13355143 130 + 48795086
CUGAGAAAAGCAAAAAGGUG---AAGAUGCCAACGACACAUGGUUUUCCCAAGUGGUCACCCACCUAAGUACUAG--CCAUGCCCGAUGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACAUGG
.((((((((((((...(((.---.....)))..((...(((((((.......((((....)))).........))--)))))..))...))))))....(((((..((....))..)))))..))))))...... ( -32.79, z-score =  -0.06, R)
>apiMel3.GroupUn 283677414 112 + 399230636
-----------------------AAGAAACCAACAACACACGGUGUUCCCAAGCGGUCAACCGAGAAGGGACUAAAACCGUGCCCGACGUAGCUUGACUUUGGUGAUCGAACGAGAACCAGUAGUUCCUACGUGG
-----------------------...............((((((..((((...(((....)))....)))).....)))))).((.((((((...(((((((((..((....))..))))).)))).)))))))) ( -36.80, z-score =  -2.33, R)
>consensus
C_G_____AGCAAAAAG_UG___AAGAAGCCAACAACACACGGUGUUCCCAAGCGGUCACCCAACUAAGUACUAA__CCGUGCCCGACGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACGUGG
......................................(((((.........((((....)))).............))))).((.((((((...(((.(((((..((....))..))))).)))..)))))))) (-25.81 = -24.05 +  -1.76)

alignment

secondary structure

dotplot

Window 0

Location	15,642,896 – 15,643,029
Length	133
Sequences	3
Columns	135
Reading direction	reverse
Mean pairwise identity	67.75
Shannon entropy	0.45258
G+C content	0.52213
Mean single sequence MFE	-40.37
Consensus MFE	-32.85
Energy contribution	-30.53
Covariance contribution	-2.32
Combinations/Pair	1.30
Mean z-score	-1.12
Structure conservation index	0.81
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.18
SVM RNA-class probability	0.905331
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15642896 133 - 21146708
CCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGG--UUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGUCCACAACUUUUUGCUGCCUGCUG
..((((((......(((((..((....))..))))).......))))))(((((((((--(..((.(((((.(((....))).))))).)))))))..(((((.(((...))).)))))........)))))... ( -47.52, z-score =  -1.18, R)
>anoGam1.chr2L 13355143 130 - 48795086
CCAUGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACAUCGGGCAUGG--CUAGUACUUAGGUGGGUGACCACUUGGGAAAACCAUGUGUCGUUGGCAUCUU---CACCUUUUUGCUUUUCUCAG
((((((((..(((..((((..((....))..))))..)))...)))))).))((((((--......(((((((((....)))))))))....))))))...(..((((....---........))))...).... ( -39.40, z-score =  -1.47, R)
>apiMel3.GroupUn 283677414 112 - 399230636
CCACGUAGGAACUACUGGUUCUCGUUCGAUCACCAAAGUCAAGCUACGUCGGGCACGGUUUUAGUCCCUUCUCGGUUGACCGCUUGGGAACACCGUGUGUUGUUGGUUUCUU-----------------------
((((((((..(((..((((..((....))..)))).)))....)))))).))(((((((.....((((....(((....)))...))))..)))))))..............----------------------- ( -34.20, z-score =  -0.70, R)
>consensus
CCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCACGG__UUAGUACUUAGAUGGGUGACCGCUUGGGAACACCGUGUGUUGUUGGCAUCUU___CA_CUUUUUGCU_____C_G
((((((((.......((((..((....))..))))........)))))).))((((((.....((.(((((.(((....))).))))).)).))))))..................................... (-32.85 = -30.53 +  -2.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:36:02 2011