Locus 5377

Sequence ID	dm3.chr2R
Location	19,897,302 – 19,897,394
Length	92
Max. P	0.938553

overview

Window 4

Location	19,897,302 – 19,897,394
Length	92
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	63.67
Shannon entropy	0.55276
G+C content	0.55667
Mean single sequence MFE	-32.95
Consensus MFE	-16.74
Energy contribution	-17.68
Covariance contribution	0.94
Combinations/Pair	1.31
Mean z-score	-1.41
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.93
SVM RNA-class probability	0.855269
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19897302 92 + 21146708
GAAGGAGUUACCUCCUUAGCAGGAGAAGCAACCGCACGGGGUUGAGGUGGAGGAGCAACCUCUUUUACUGGUGAAGUAACCACUUGC--GGUUG-------
.((((((....))))))...........((((((((.(.(((((.((((((((((....)))))))))).......))))).).)))--)))))------- ( -34.20, z-score =  -2.09, R)
>droGri2.scaffold_15252 3023931 101 + 17193109
GGAGGAGUCGCUUCCUUAACCGGAGGAGGAGUCGCUUCCUUGACCGGAGGAGGAGUCGCUUCCUUGACCAGAGGAGGUGUCGCUUGCUUGACUGGAGGAGU
(((((.(.(.(((((((.....))))))).).).)))))....((((((.(((.(.(((((((((.....))))))))).).))).))...))))...... ( -39.50, z-score =   0.00, R)
>droYak2.chr2R 19875745 80 + 21139217
------------UCCUUAACAGAAGAAGCGACCGCUGGAGGCUGAGGUGGAGGAGCAACCUCCUUUACUGGAGAAGUAACCACUUGC--GGCGG-------
------------................((.(((((((..(((..((((((((((....)))))))))).....)))..)))...))--)))).------- ( -27.00, z-score =  -1.21, R)
>droSim1.chr2R 18443173 80 + 19596830
------------UCCUUAGCAGGAGAAGCAACCGCAGUGGGUUGAGGUGGAGGAGCAACCUCUUUUACUGGUGAAGUAACCACUGGC--GGUUG-------
------------((((....))))....((((((((((((.(((.((((((((((....))))))))))..))).....))))).))--)))))------- ( -31.10, z-score =  -2.33, R)
>consensus
____________UCCUUAACAGGAGAAGCAACCGCAGGGGGUUGAGGUGGAGGAGCAACCUCCUUUACUGGAGAAGUAACCACUUGC__GGCUG_______
...........((((......))))...(((((((....(((((.((((((((((....)))))))))).......)))))....))..)))))....... (-16.74 = -17.68 +   0.94)

alignment

secondary structure

dotplot

Window 5

Location	19,897,302 – 19,897,394
Length	92
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	63.67
Shannon entropy	0.55276
G+C content	0.55667
Mean single sequence MFE	-28.00
Consensus MFE	-12.29
Energy contribution	-12.48
Covariance contribution	0.19
Combinations/Pair	1.30
Mean z-score	-2.00
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.45
SVM RNA-class probability	0.938553
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19897302 92 - 21146708
-------CAACC--GCAAGUGGUUACUUCACCAGUAAAAGAGGUUGCUCCUCCACCUCAACCCCGUGCGGUUGCUUCUCCUGCUAAGGAGGUAACUCCUUC
-------(((((--(((.(.(((((((.....)))....(((((.(.....).))))))))).).))))))))..((((((....)))))).......... ( -29.90, z-score =  -2.91, R)
>droGri2.scaffold_15252 3023931 101 - 17193109
ACUCCUCCAGUCAAGCAAGCGACACCUCCUCUGGUCAAGGAAGCGACUCCUCCUCCGGUCAAGGAAGCGACUCCUCCUCCGGUUAAGGAAGCGACUCCUCC
.........(((........)))(((......)))..((((..((..((((...((((...((((......))))...))))...))))..))..)))).. ( -29.00, z-score =  -0.19, R)
>droYak2.chr2R 19875745 80 - 21139217
-------CCGCC--GCAAGUGGUUACUUCUCCAGUAAAGGAGGUUGCUCCUCCACCUCAGCCUCCAGCGGUCGCUUCUUCUGUUAAGGA------------
-------.((((--((.(.(((........))).)...((((((((...........)))))))).)))).))....((((....))))------------ ( -23.70, z-score =  -1.02, R)
>droSim1.chr2R 18443173 80 - 19596830
-------CAACC--GCCAGUGGUUACUUCACCAGUAAAAGAGGUUGCUCCUCCACCUCAACCCACUGCGGUUGCUUCUCCUGCUAAGGA------------
-------(((((--((.((((((((((.....)))))..(((((.(.....).)))))...))))))))))))....((((....))))------------ ( -29.40, z-score =  -3.89, R)
>consensus
_______CAACC__GCAAGUGGUUACUUCACCAGUAAAAGAGGUUGCUCCUCCACCUCAACCCCCAGCGGUUGCUUCUCCUGCUAAGGA____________
.......(((((..((.(.(((........))).)...(((((.....))))).............)))))))....((((....))))............ (-12.29 = -12.48 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:47:07 2011