Locus 4783

Sequence ID	dm3.chr2R
Location	15,637,754 – 15,637,892
Length	138
Max. P	0.998712

overview

Window 9

Location	15,637,754 – 15,637,892
Length	138
Sequences	3
Columns	138
Reading direction	forward
Mean pairwise identity	76.09
Shannon entropy	0.33691
G+C content	0.50686
Mean single sequence MFE	-42.26
Consensus MFE	-36.99
Energy contribution	-37.00
Covariance contribution	0.01
Combinations/Pair	1.25
Mean z-score	-1.09
Structure conservation index	0.88
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.73
SVM RNA-class probability	0.801404
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15637754 138 + 21146708
CAAAAAGUUGUGGACGAGGCCAACAACACGCGGUGUUCCCAAGCGGUCCCCCAUCUAAGUACUAACCGCGCCCGACGCUGCUUAAUUUCGGUGAUCGGACGAGAACCGAUGUAUUCAGCGUGGUAUGGUCGUUGGCGA
..................((((((.((.((((((((......))((....))............)))))).((.((((((..((...(((((..((....))..)))))..))..))))))))....)).)))))).. ( -44.30, z-score =  -0.01, R)
>anoGam1.chr2L 13363129 135 + 48795086
CAAAAAGGU---GAAGAUGCCAACGACACAUGGUUUUCCCAAGUGGUCACCCACCUAAGUACUAGCCAUGCCCGAUGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACAUGGUAUGGUCGUUGACAA
.........---.....((.(((((((.(((((((.......((((....)))).........))))))).((.((((((...(((.(((((..((....))..))))).)))..))))))))....))))))).)). ( -41.49, z-score =  -1.23, R)
>apiMel3.GroupUn 327590579 129 - 399230636
---------AAAAAAGAAACCAACAACACACGGUGUUCCCAAGCGGUCACCCAUUCAAGUAUUAACCGUGCCCGACGUAGCUUGACUUUGGUGAUCGAACGAGAACCAGUAGUUCCUACGUGGUAUGGUCGUUGGCGA
---------..........(((((.......((((..((.....)).)))).............((((((((..((((((...(((((((((..((....))..))))).)))).)))))))))))))).)))))... ( -41.00, z-score =  -2.03, R)
>consensus
CAAAAAG_U___GAAGAAGCCAACAACACACGGUGUUCCCAAGCGGUCACCCAUCUAAGUACUAACCGUGCCCGACGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACGUGGUAUGGUCGUUGGCGA
..................((((((.......((((...((....)).)))).............((((((((..((((((...(((.(((((..((....))..))))).)))..)))))))))))))).)))))).. (-36.99 = -37.00 +   0.01)

alignment

secondary structure

dotplot

Window 0

Location	15,637,754 – 15,637,892
Length	138
Sequences	3
Columns	138
Reading direction	reverse
Mean pairwise identity	76.09
Shannon entropy	0.33691
G+C content	0.50686
Mean single sequence MFE	-51.11
Consensus MFE	-49.44
Energy contribution	-45.79
Covariance contribution	-3.65
Combinations/Pair	1.32
Mean z-score	-3.47
Structure conservation index	0.97
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.46
SVM RNA-class probability	0.998712
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15637754 138 - 21146708
UCGCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGUCCACAACUUUUUG
..(((((((((....((((((((......(((((..((....))..))))).......)))))).))(((((((..((.(((((.(((....))).))))).)))))))))))))))))).................. ( -55.02, z-score =  -3.33, R)
>anoGam1.chr2L 13363129 135 - 48795086
UUGUCAACGACCAUACCAUGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACAUCGGGCAUGGCUAGUACUUAGGUGGGUGACCACUUGGGAAAACCAUGUGUCGUUGGCAUCUUC---ACCUUUUUG
.((((((((((....((((((((..(((..((((..((....))..))))..)))...)))))).))((((((......(((((((((....)))))))))....)))))))))))))))).....---......... ( -52.80, z-score =  -4.47, R)
>apiMel3.GroupUn 327590579 129 + 399230636
UCGCCAACGACCAUACCACGUAGGAACUACUGGUUCUCGUUCGAUCACCAAAGUCAAGCUACGUCGGGCACGGUUAAUACUUGAAUGGGUGACCGCUUGGGAACACCGUGUGUUGUUGGUUUCUUUUUU---------
..(((((((((....((((((((..(((..((((..((....))..)))).)))....)))))).))(((((((.....((..(.(((....))).)..))...)))))))))))))))).........--------- ( -45.50, z-score =  -2.60, R)
>consensus
UCGCCAACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCACGGUUAGUACUUAGAUGGGUGACCGCUUGGGAACACCGUGUGUUGUUGGCAUCUUC___A_CUUUUUG
..(((((((((....((((((((.......((((..((....))..))))........)))))).))(((((((.....(((((.(((....))).)))))...)))))))))))))))).................. (-49.44 = -45.79 +  -3.65)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:35:54 2011