Locus 5

Sequence ID	dm3.chr2LHet
Location	181,214 – 181,304
Length	90
Max. P	0.987914

overview

Window 7

Location	181,214 – 181,304
Length	90
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	65.29
Shannon entropy	0.58415
G+C content	0.47028
Mean single sequence MFE	-28.28
Consensus MFE	-14.18
Energy contribution	-16.68
Covariance contribution	2.50
Combinations/Pair	1.09
Mean z-score	-1.88
Structure conservation index	0.50
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.04
SVM RNA-class probability	0.980030
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2LHet 181214 90 + 368872
-------GUUGCAAGUGCAUACACAGCACUUUGACACAGCAC---UUGCUACAAUUCUUGAAGACGAAAGCAGUCCUGCCGCACCAGCACUUUCAUAUAU--
-------((.((((((((.....(((....))).....))))---)))).))......(((((......(((....))).((....))..))))).....-- ( -19.30, z-score =  -0.63, R)
>droSim1.chrU 12069185 90 - 15797150
CAACACUGUUGCAA-UGCUGACGCAGCA-GUGGACAGGAUGUCGAUUGCGCCAGUUCUGGUAAACAAAACUAGAACUGCCGCAGCAGCAUUU----------
...(((((((((..-.......))))))-)))....((((((.(.(((((.((((((((((.......)))))))))).)))))).))))))---------- ( -38.70, z-score =  -4.33, R)
>droYak2.chrX 1098450 100 - 21770863
CUACUAUGUUGCAAGUGCAGACACAGCACUUUGACAGGAUGUCGAUUGCGACAGUUCUUGCAGACGAACCCAGAACUGCCGCACCAGCAUUUCCAUAUAU--
......(((((.((((((.......)))))))))))((((((.(..((((.(((((((.............))))))).)))).).)))..)))......-- ( -26.62, z-score =  -1.90, R)
>droVir3.scaffold_13324 2893931 101 - 2960039
ACACUAUGUUGCAA-UGCUGAUCCAGCACAUUAACAGGAAGUUGGUUGUGACAGUUCUCGUGCAAGACACUUGAACUGCUGCAACGGCAAUUUGUCAGAUAC
.((((.(((((...-(((((...)))))...)))))...)).))(((((..((((((..(((.....)))..))))))..)))))(((.....)))...... ( -28.50, z-score =  -0.67, R)
>consensus
C_ACUAUGUUGCAA_UGCAGACACAGCACUUUGACAGGAUGUCGAUUGCGACAGUUCUUGUAGACGAAACCAGAACUGCCGCACCAGCAUUUUCAUAUAU__
.........(((((((((.......))))))...............((((.(((((((.((.......)).))))))).))))...)))............. (-14.18 = -16.68 +   2.50)

alignment

secondary structure

dotplot

Window 8

Location	181,214 – 181,304
Length	90
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	65.29
Shannon entropy	0.58415
G+C content	0.47028
Mean single sequence MFE	-31.35
Consensus MFE	-16.82
Energy contribution	-19.19
Covariance contribution	2.38
Combinations/Pair	1.05
Mean z-score	-1.86
Structure conservation index	0.54
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.30
SVM RNA-class probability	0.987914
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2LHet 181214 90 - 368872
--AUAUAUGAAAGUGCUGGUGCGGCAGGACUGCUUUCGUCUUCAAGAAUUGUAGCAA---GUGCUGUGUCAAAGUGCUGUGUAUGCACUUGCAAC-------
--...........((((((..(((((.(.((((.(((........)))..)))))..---.)))))..)))((((((.......)))))))))..------- ( -27.20, z-score =  -0.75, R)
>droSim1.chrU 12069185 90 + 15797150
----------AAAUGCUGCUGCGGCAGUUCUAGUUUUGUUUACCAGAACUGGCGCAAUCGACAUCCUGUCCAC-UGCUGCGUCAGCA-UUGCAACAGUGUUG
----------.(((((((.(((((((((.(((((((((.....))))))))).......(((.....))).))-))))))).)))))-))............ ( -34.60, z-score =  -3.13, R)
>droYak2.chrX 1098450 100 + 21770863
--AUAUAUGGAAAUGCUGGUGCGGCAGUUCUGGGUUCGUCUGCAAGAACUGUCGCAAUCGACAUCCUGUCAAAGUGCUGUGUCUGCACUUGCAACAUAGUAG
--......(((..((.(((((((((((((((..((......)).))))))))))).)))).)))))........((((((((.(((....))))))))))). ( -36.60, z-score =  -3.08, R)
>droVir3.scaffold_13324 2893931 101 + 2960039
GUAUCUGACAAAUUGCCGUUGCAGCAGUUCAAGUGUCUUGCACGAGAACUGUCACAACCAACUUCCUGUUAAUGUGCUGGAUCAGCA-UUGCAACAUAGUGU
.................((((..(((((((..(((.....)))..)))))))..))))..(((...((((...((((((...)))))-)...)))).))).. ( -27.00, z-score =  -0.49, R)
>consensus
__AUAUAUGAAAAUGCUGGUGCGGCAGUUCUAGUUUCGUCUACAAGAACUGUCGCAAUCGACAUCCUGUCAAAGUGCUGUGUCAGCA_UUGCAACAUAGU_G
.............(((...((((((((((((.............))))))))))))...............((((((.......)))))))))......... (-16.82 = -19.19 +   2.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:04:46 2011