Locus 5602

Sequence ID	dm3.chr3LHet
Location	1,825,279 – 1,825,431
Length	152
Max. P	0.572463

overview

Window 3

Location	1,825,279 – 1,825,379
Length	100
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	66.81
Shannon entropy	0.54577
G+C content	0.56148
Mean single sequence MFE	-39.88
Consensus MFE	-19.75
Energy contribution	-20.69
Covariance contribution	0.94
Combinations/Pair	1.30
Mean z-score	-1.11
Structure conservation index	0.50
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.16
SVM RNA-class probability	0.572463
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 1825279 100 - 2555491
AUAGGGAUAGCUCAGGUGAACAUCCAUCGCGCCAAGCCGGCCUCGGCCGCGCU--------------GGUACGGA--UGUUCACAAAACCCUGGUACAGGAACCCUGGUAUAACUA
.(((((.........((((((((((...(..(((.((((((....)))).)))--------------))..))))--))))))).....((((...))))..)))))......... ( -42.60, z-score =  -3.37, R)
>droYak2.chr2L_random 2590217 115 - 4064425
CUUUGGGUGCUGCAGCUCAAUCUUCAUAAAAGCAAGGUCACGUCGGCGGAACUCCUCAUCGCCCUGGAGCAAGGGUCCGCCGACAUUAC-UUGGGCCAAGAGCCAUGGAUUGCCUC
..((((((......))))))..(((((.....((((.....(((((((((.(.(((..((......))...)))))))))))))....)-)))(((.....))))))))....... ( -36.60, z-score =   0.02, R)
>dp4.Unknown_singleton_3068 3252 116 - 4253
CUAAGGGUGCUGCAGCUCAACCUCCAUAAAAGCAAAAUAGCGUCGGCGGAGCUCCUCAUUGCCAUGGGGCAAGGGACCGCUGACAUAGCUUUAGUCCAGGAGCCGUGGAUUGCGUC
...........((((..((..((((......((......))((((((((...((((..(((((....)))))))))))))))))..............))))...))..))))... ( -40.40, z-score =  -0.51, R)
>droPer1.super_146 15091 116 + 80581
CUAAGGGUGCUGCAACUCAAUCUUCAUAAAAGCAAGGUAGCGUCGGCGGAGCUCCUCAUUGCCAUGGAGCAAGGGCCCGCCGACAUAGCUUUAGUCCAGGAGCCGUGGAUUGCGUC
....((((......)))).............(((((((...((((((((.((.(((...(((......))))))))))))))))...)))))(((((((....).))))))))... ( -39.90, z-score =  -0.59, R)
>consensus
CUAAGGGUGCUGCAGCUCAACCUCCAUAAAAGCAAGGUAGCGUCGGCGGAGCUCCUCAUUGCCAUGGAGCAAGGG_CCGCCGACAUAACUUUAGUCCAGGAGCCGUGGAUUGCCUC
((((((.((((...................)))).......((((((((.(((((..........)))))......))))))))..................))))))........ (-19.75 = -20.69 +   0.94)

alignment

secondary structure

dotplot

Window 4

Location	1,825,339 – 1,825,431
Length	92
Sequences	4
Columns	92
Reading direction	reverse
Mean pairwise identity	57.71
Shannon entropy	0.66169
G+C content	0.49702
Mean single sequence MFE	-28.05
Consensus MFE	-5.71
Energy contribution	-6.58
Covariance contribution	0.87
Combinations/Pair	1.54
Mean z-score	-2.27
Structure conservation index	0.20
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.02
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>dm3.chr3LHet 1825339 92 - 2555491
AUGAUCGGGGCAUCUCCGGAUCAGUAACGCCGAUCAUCUAAUGGUCGGGAGUAUAGGGAUAGCUCAGGUGAACAUCCAUCGCGCCAAGCCGG
.(((((.(((....))).)))))...((.((((((((...))))))))..))....((...((...((((......))))..))....)).. ( -26.00, z-score =   0.58, R)
>droYak2.chr2L_random 2590292 83 - 4064425
ACAGUCAA-------CCUUUCGAAUGGAGAUGA--GCUCAGUAGCCAUGCCACUUUGGGUGCUGCAGCUCAAUCUUCAUAAAAGCAAGGUCA
.......(-------((((.(..((((((((((--((((((((.(((........))).))))).))))).))))))))....).))))).. ( -32.80, z-score =  -3.97, R)
>dp4.Unknown_singleton_3068 3328 83 - 4253
AUAGUCAA-------CCUGUCGUGUGAGGUUGA--GUUAGCCACCCAUGACGCUAAGGGUGCUGCAGCUCAACCUCCAUAAAAGCAAAAUAG
........-------......(((.((((((((--(((.(((((((..........)))))..))))))))))))))))............. ( -28.90, z-score =  -3.68, R)
>droPer1.super_146 15167 83 + 80581
AUAGUCAA-------CCCGUCGUGCGAGGUUGA--GUUUGCCACCCAUGACACUAAGGGUGCUGCAACUCAAUCUUCAUAAAAGCAAGGUAG
........-------.((....(((((((((((--(((.(((((((..........)))))..))))))))))))).......))).))... ( -24.51, z-score =  -2.02, R)
>consensus
AUAGUCAA_______CCUGUCGAGUGAGGUUGA__GUUUACCACCCAUGACACUAAGGGUGCUGCAGCUCAACCUCCAUAAAAGCAAGGUAG
.........................((((((((........(((((..........))))).......))))))))................ ( -5.71 =  -6.58 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:51:34 2011