Locus 4791

Sequence ID	dm3.chr2R
Location	15,643,262 – 15,643,397
Length	135
Max. P	0.815386

overview

Window 1

Location	15,643,262 – 15,643,397
Length	135
Sequences	3
Columns	137
Reading direction	forward
Mean pairwise identity	65.04
Shannon entropy	0.49895
G+C content	0.52358
Mean single sequence MFE	-37.94
Consensus MFE	-24.51
Energy contribution	-22.75
Covariance contribution	-1.76
Combinations/Pair	1.44
Mean z-score	-1.09
Structure conservation index	0.65
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.78
SVM RNA-class probability	0.815386
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15643262 135 + 21146708
AGGCAGCAGGCAGCAAAAAGUUGUGGACGAGGCCAACAACACGCGGUGUUCCCAAGCGGUCCCCCAUCUAAGUACUAA--CCGCGCCCGACGCUGCUUAAUUUCGGUGAUCGGACGAGAACCGAUGUAUUCAGCGUG
.(((....((.((((....(((((((......)).)))))......)))).))..(((((.................)--)))))))..((((((..((...(((((..((....))..)))))..))..)))))). ( -42.53, z-score =  -0.20, R)
>anoGam1.chr2L 13355639 132 + 48795086
AGGCUGAGAAAAGCAAAAAGGUGAAGAUG---CCAACGACACAUGGUUUUCCCAAGUGGUCACCCACCUAAGUACUAG--CCAUGCCCGAUGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACAUG
..(((......))).....(.((((((((---((.....(((.(((.....))).)))(((...((((.((((...((--((((.....)))..)))..)))).))))....))).......)))))))))).)... ( -35.80, z-score =  -0.65, R)
>apiMel3.GroupUn 283677416 109 + 399230636
----------------------------GAAACCAACAACACACGGUGUUCCCAAGCGGUCAACCGAGAAGGGACUAAAACCGUGCCCGACGUAGCUUGACUUUGGUGAUCGAACGAGAACCAGUAGUUCCUACGUG
----------------------------.............((((((..((((...(((....)))....)))).....))))))....((((((...(((((((((..((....))..))))).)))).)))))). ( -35.50, z-score =  -2.42, R)
>consensus
AGGC_G_____AGCAAAAAG_UG__GA_GA__CCAACAACACACGGUGUUCCCAAGCGGUCACCCAACUAAGUACUAA__CCGUGCCCGACGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACGUG
.........................................(((((.........((((....)))).............)))))....((((((...(((.(((((..((....))..))))).)))..)))))). (-24.51 = -22.75 +  -1.76)

alignment

secondary structure

dotplot

Window 2

Location	15,643,262 – 15,643,397
Length	135
Sequences	3
Columns	137
Reading direction	reverse
Mean pairwise identity	65.04
Shannon entropy	0.49895
G+C content	0.52358
Mean single sequence MFE	-39.44
Consensus MFE	-29.85
Energy contribution	-27.53
Covariance contribution	-2.32
Combinations/Pair	1.32
Mean z-score	-0.67
Structure conservation index	0.76
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.54
SVM RNA-class probability	0.736917
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15643262 135 - 21146708
CACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGG--UUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGUCCACAACUUUUUGCUGCCUGCUGCCU
.((((((......(((((..((....))..))))).......))))))(((((((((--(..((.(((((.(((....))).))))).)))))))..(((((.(((...))).)))))........)))))...... ( -47.52, z-score =  -0.75, R)
>anoGam1.chr2L 13355639 132 - 48795086
CAUGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACAUCGGGCAUGG--CUAGUACUUAGGUGGGUGACCACUUGGGAAAACCAUGUGUCGUUGG---CAUCUUCACCUUUUUGCUUUUCUCAGCCU
...(((((......((((..((....))..))))..(..((((((....((((((((--......(((((((((....)))))))))....))))))((.....)---).......))...))))))..)))))).. ( -39.60, z-score =  -1.25, R)
>apiMel3.GroupUn 283677416 109 - 399230636
CACGUAGGAACUACUGGUUCUCGUUCGAUCACCAAAGUCAAGCUACGUCGGGCACGGUUUUAGUCCCUUCUCGGUUGACCGCUUGGGAACACCGUGUGUUGUUGGUUUC----------------------------
.((((((..(((..((((..((....))..)))).)))....))))))...(((((((.....((((....(((....)))...))))..)))))))............---------------------------- ( -31.20, z-score =  -0.01, R)
>consensus
CACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCACGG__UUAGUACUUAGAUGGGUGACCGCUUGGGAACACCGUGUGUUGUUGG__UC_UC__CA_CUUUUUGCU_____C_GCCU
.((((((.......((((..((....))..))))........))))))...((((((.....((.(((((.(((....))).))))).)).))))))........................................ (-29.85 = -27.53 +  -2.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:36:04 2011