Locus 8626

Sequence ID	dm3.chr3RHet
Location	2,162,613 – 2,162,714
Length	101
Max. P	0.965195

overview

Window 3

Location	2,162,613 – 2,162,714
Length	101
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	69.84
Shannon entropy	0.47961
G+C content	0.55337
Mean single sequence MFE	-36.88
Consensus MFE	-23.49
Energy contribution	-24.36
Covariance contribution	0.88
Combinations/Pair	1.36
Mean z-score	-1.74
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.75
SVM RNA-class probability	0.965195
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 2162613 101 + 2517507
----GGCUGUAUUUUUGUAGCUUUGGCAUCUCCCGUUACAGCGCGGCGGCAGCGUGUGGUCGCUGUCGCCGAGUGUGGUUCGAAGGAUAGCACGGAGAAGAAGUG-
----(((((((....)))))))......((((((((....)))(((((((((((......))))))))))).((((...((....))..))))))))).......- ( -41.50, z-score =  -2.27, R)
>droWil1.scaffold_181075 650107 100 - 1141854
----GGCGGCGCAUUUGU-GGUUUAAGAAGAACCGUUUUAGCGGGGCGCCAGCGUUCUAUCGCUGUCGCCGAGUGUGGUUCGGUGGAAGGCGCGCACAAGAAUUG-
----.((..(((.....(-(((((.....)))))).....)))..(((((((((......)))).((((((((.....))))))))..)))))))..........- ( -36.00, z-score =  -0.45, R)
>droAna3.scaffold_13111 1420772 105 + 1527837
CUGUGUGUGUGUGUUGUC-GCUUUAAGAAAUGUCGUUUUAGCAGGGCGACAGUGUAGUGUCGCUGUCGCCGAGUGUGGUUCGGUGGUAAGGAUAGAAAGAAGCAGG
((((.....((..(((((-(((((...(((......)))...))))))))))..)).((((..(..(((((((.....)))))))..)..)))).......)))). ( -32.30, z-score =  -2.69, R)
>droSim1.chrU 11369358 101 - 15797150
----GGCUGUAUUUUUGUAGCUUUAGCAUCUCCCGUUUCAGCGCGGCGGCAGUGUGUGUUCGCUGUCGCCGAGUGUGGCUCGAAGGUUAGCACGGAGAAGAAGUG-
----.((((.(((((((.((((...(((.(((.(((....))).((((((((((......)))))))))))))))))))))))))))))))..............- ( -37.70, z-score =  -1.55, R)
>consensus
____GGCUGUAUUUUUGU_GCUUUAACAACUCCCGUUUCAGCGCGGCGGCAGCGUGUGGUCGCUGUCGCCGAGUGUGGUUCGAAGGAAAGCACGGAGAAGAAGUG_
............((((....((.......((((((.....((.(((((((((((......))))))))))).))......)))))).......))....))))... (-23.49 = -24.36 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	2,162,613 – 2,162,714
Length	101
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	69.84
Shannon entropy	0.47961
G+C content	0.55337
Mean single sequence MFE	-24.20
Consensus MFE	-14.09
Energy contribution	-14.28
Covariance contribution	0.19
Combinations/Pair	1.27
Mean z-score	-1.76
Structure conservation index	0.58
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.42
SVM RNA-class probability	0.938750
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 2162613 101 - 2517507
-CACUUCUUCUCCGUGCUAUCCUUCGAACCACACUCGGCGACAGCGACCACACGCUGCCGCCGCGCUGUAACGGGAGAUGCCAAAGCUACAAAAAUACAGCC----
-.......((((((((...((....))..))).(.(((((.(((((......))))).))))).)........))))).......(((..........))).---- ( -26.60, z-score =  -1.34, R)
>droWil1.scaffold_181075 650107 100 + 1141854
-CAAUUCUUGUGCGCGCCUUCCACCGAACCACACUCGGCGACAGCGAUAGAACGCUGGCGCCCCGCUAAAACGGUUCUUCUUAAACC-ACAAAUGCGCCGCC----
-........(((.((((...................((((.(((((......))))).))))..........((((.......))))-......))))))).---- ( -27.80, z-score =  -1.48, R)
>droAna3.scaffold_13111 1420772 105 - 1527837
CCUGCUUCUUUCUAUCCUUACCACCGAACCACACUCGGCGACAGCGACACUACACUGUCGCCCUGCUAAAACGACAUUUCUUAAAGC-GACAACACACACACACAG
..(((((..................((.......))((((((((.(......).)))))))).....................))))-)................. ( -17.60, z-score =  -3.19, R)
>droSim1.chrU 11369358 101 + 15797150
-CACUUCUUCUCCGUGCUAACCUUCGAGCCACACUCGGCGACAGCGAACACACACUGCCGCCGCGCUGAAACGGGAGAUGCUAAAGCUACAAAAAUACAGCC----
-..(((((..((.((((........(((.....)))((((.(((.(......).))).)))))))).))...)))))..((....))...............---- ( -24.80, z-score =  -1.02, R)
>consensus
_CACUUCUUCUCCGUGCUAACCACCGAACCACACUCGGCGACAGCGACAACACACUGCCGCCCCGCUAAAACGGGAGAUCCUAAAGC_ACAAAAACACAGCC____
.........((((.......................((((.(((((......))))).)))).((......))))))............................. (-14.09 = -14.28 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:49:05 2011