Locus 15911

Sequence ID	dm3.chrYHet
Location	164,789 – 164,893
Length	104
Max. P	0.996763

overview

Window 2

Location	164,789 – 164,893
Length	104
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	65.87
Shannon entropy	0.56429
G+C content	0.42057
Mean single sequence MFE	-25.16
Consensus MFE	-10.06
Energy contribution	-10.50
Covariance contribution	0.44
Combinations/Pair	1.40
Mean z-score	-1.71
Structure conservation index	0.40
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.57
SVM RNA-class probability	0.746471
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrYHet 164789 104 + 347038
GAGGUCACAUACCACGAAGCUACAAAUAGAAUGUAGCUUAGAUGCAAAUGAGCGACUCAUCCUCUCUCUACAAAUACUCUCUGCUAUGCAGGAGUAUAUGCAGG
((((............((((((((.......))))))))........(((((...)))))))))...((.((.((((((.((((...)))))))))).)).)). ( -29.40, z-score =  -2.37, R)
>droSim1.chrU 4193992 104 - 15797150
GAGGACACAUACCACAAAGCCACAAAUAGAAUGUAGCUUAGCUGCCAAUGAGCGACUGAUCCUCUCUCUACAAAUACUCUCUGUUAUGGAAGAGUAUAUGCAGG
(((((((.........((((.(((.......))).)))).(((.......)))...)).)))))...((.((.(((((((((.....)).))))))).)).)). ( -23.90, z-score =  -0.99, R)
>droSec1.super_556 3953 104 - 14122
GAGCCCACAUACAACAAAGCUACAAAUAUAAUGUAGCUUAGCUACAAAUGAGCGACUCAUCCUCUCUCUACAUAUACUCUCUGCUAUGCAGGAGUACAUGUAAG
(((.............((((((((.......)))))))).(((.(....))))..)))..........(((((.(((((.((((...))))))))).))))).. ( -28.50, z-score =  -3.92, R)
>droVir3.scaffold_12970 500675 92 + 11907090
----AUACUUGC-AUAUUG-UGUAUAUGAAAAGAAGCAUUUAUGCGCUUGUGUGCCUGUUGCU-UGCCUGCCCCGAUGCAAAUGUA-ACAAGAUUUUGGG----
----......((-((((.(-((((((..............)))))))..)))))).((((((.-....(((......)))...)))-)))..........---- ( -18.84, z-score =   0.43, R)
>consensus
GAGGACACAUACCACAAAGCUACAAAUAGAAUGUAGCUUAGAUGCAAAUGAGCGACUCAUCCUCUCUCUACAAAUACUCUCUGCUAUGCAAGAGUAUAUGCAGG
...................................(((((........))))).................((((((((((..........)))))))))).... (-10.06 = -10.50 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	164,789 – 164,893
Length	104
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	65.87
Shannon entropy	0.56429
G+C content	0.42057
Mean single sequence MFE	-32.16
Consensus MFE	-16.44
Energy contribution	-20.12
Covariance contribution	3.69
Combinations/Pair	1.34
Mean z-score	-2.49
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.98
SVM RNA-class probability	0.996763
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrYHet 164789 104 - 347038
CCUGCAUAUACUCCUGCAUAGCAGAGAGUAUUUGUAGAGAGAGGAUGAGUCGCUCAUUUGCAUCUAAGCUACAUUCUAUUUGUAGCUUCGUGGUAUGUGACCUC
.(((((.((((((((((...)))).)))))).)))))...(((((((((...)))))(..(((((((((((((.......)))))))...))).)))..))))) ( -38.30, z-score =  -3.67, R)
>droSim1.chrU 4193992 104 + 15797150
CCUGCAUAUACUCUUCCAUAACAGAGAGUAUUUGUAGAGAGAGGAUCAGUCGCUCAUUGGCAGCUAAGCUACAUUCUAUUUGUGGCUUUGUGGUAUGUGUCCUC
.(((((.((((((((........)))))))).)))))...((((((((...(((....))).((.((((((((.......)))))))).))....)).)))))) ( -35.10, z-score =  -2.74, R)
>droSec1.super_556 3953 104 + 14122
CUUACAUGUACUCCUGCAUAGCAGAGAGUAUAUGUAGAGAGAGGAUGAGUCGCUCAUUUGUAGCUAAGCUACAUUAUAUUUGUAGCUUUGUUGUAUGUGGGCUC
.((((((((((((((((...)))).))))))))))))..............((((((.((((((.((((((((.......)))))))).)))))).)))))).. ( -41.80, z-score =  -4.77, R)
>droVir3.scaffold_12970 500675 92 - 11907090
----CCCAAAAUCUUGU-UACAUUUGCAUCGGGGCAGGCA-AGCAACAGGCACACAAGCGCAUAAAUGCUUCUUUUCAUAUACA-CAAUAU-GCAAGUAU----
----.............-...((((((((...((.(((.(-((((....((.(....).)).....)))))))).)).......-....))-))))))..---- ( -13.44, z-score =   1.23, R)
>consensus
CCUGCAUAUACUCCUGCAUAGCAGAGAGUAUUUGUAGAGAGAGGAUCAGUCGCUCAUUUGCAGCUAAGCUACAUUCUAUUUGUAGCUUUGUGGUAUGUGUCCUC
.(((((((((((((((.....))).)))))))))))).(((.((.....)).)))....((.((.((((((((.......)))))))).)).)).......... (-16.44 = -20.12 +   3.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:08:10 2011