Locus 5526

Sequence ID	dm3.chr3LHet
Location	169,942 – 170,093
Length	151
Max. P	0.882119

overview

Window 5

Location	169,942 – 170,053
Length	111
Sequences	3
Columns	118
Reading direction	forward
Mean pairwise identity	58.55
Shannon entropy	0.58280
G+C content	0.56329
Mean single sequence MFE	-47.77
Consensus MFE	-8.67
Energy contribution	-7.80
Covariance contribution	-0.87
Combinations/Pair	1.53
Mean z-score	-3.25
Structure conservation index	0.18
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.04
SVM RNA-class probability	0.880043
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 169942 111 + 2555491
------UAAAAACCCAUUGCCGCAACUUGGUUAGCCCGGGAUGACCCUAACCGUAAGGGGCUGAGCGGGGCCAGAACGAAGUGGUAUCUUCGUUACCUUUAGCAGGCCAAGUCACCC-
------............(((((..((((.((((((((((....)))....(....)))))))).)))).....(((((((......))))))).......)).)))..........- ( -36.50, z-score =  -0.50, R)
>droVir3.scaffold_12823 181988 109 - 2474545
------UAUAACGUCACCGGGACAACCCGGU--GGCAAGGGUGAUCCAAACAGAAGAAACCUGAGCGGAUCGCGCACCAAAUGGUAUGUGCGCUACCUCAAAAAGGG-AUUUCAUCCC
------......(((((((((....))))))--)))..(((((((((...(((.......)))...)))))((((((..........)))))).))))......(((-((...))))) ( -43.50, z-score =  -4.24, R)
>droGri2.scaffold_4812 5858 115 + 6386
AGAGCUCCUGCCACCAAGGGGUCAACCCGGU--GGGCUGGAUGACCCGAACCGGAGAAAUCUCUGCGGUUCAAGGGUCAAGUGGUACCUCCGGUACCUCCAGCAGGG-ACUCAACCCC
.(((..(((.(((((..(((.....))))))--))((((((((((((((((((.(((....))).))))))..))))))...((((((...))))))))))))))).-.)))...... ( -63.30, z-score =  -5.01, R)
>consensus
______UAUAACACCAACGGGACAACCCGGU__GGCCAGGAUGACCCAAACCGAAGAAACCUGAGCGGAUCAAGAACCAAGUGGUAUCUCCGCUACCUCAAGCAGGG_AAUUCACCCC
............(((.(((((......((((......(((.....))).))))......)))))...)))............((((.......))))..................... ( -8.67 =  -7.80 +  -0.87)

alignment

secondary structure

dotplot

Window 6

Location	169,942 – 170,053
Length	111
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	58.55
Shannon entropy	0.58280
G+C content	0.56329
Mean single sequence MFE	-47.37
Consensus MFE	-11.45
Energy contribution	-8.69
Covariance contribution	-2.76
Combinations/Pair	1.71
Mean z-score	-2.49
Structure conservation index	0.24
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.37
SVM RNA-class probability	0.665841
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 169942 111 - 2555491
-GGGUGACUUGGCCUGCUAAAGGUAACGAAGAUACCACUUCGUUCUGGCCCCGCUCAGCCCCUUACGGUUAGGGUCAUCCCGGGCUAACCAAGUUGCGGCAAUGGGUUUUUA------
-..(..(((((((((.....))).(((((((......))))))).((((((.....((((......)))).(((....))))))))).))))))..)...............------ ( -37.30, z-score =   0.01, R)
>droVir3.scaffold_12823 181988 109 + 2474545
GGGAUGAAAU-CCCUUUUUGAGGUAGCGCACAUACCAUUUGGUGCGCGAUCCGCUCAGGUUUCUUCUGUUUGGAUCACCCUUGCC--ACCGGGUUGUCCCGGUGACGUUAUA------
(((((...))-))).....((((..((((((..........))))))((((((..((((.....))))..))))))..))))..(--((((((....)))))))........------ ( -45.70, z-score =  -4.15, R)
>droGri2.scaffold_4812 5858 115 - 6386
GGGGUUGAGU-CCCUGCUGGAGGUACCGGAGGUACCACUUGACCCUUGAACCGCAGAGAUUUCUCCGGUUCGGGUCAUCCAGCCC--ACCGGGUUGACCCCUUGGUGGCAGGAGCUCU
......(((.-.(((((((((((((((...))))))...((((((..((((((..(((....)))))))))))))))))))))((--((((((....)))...))))).)))..))). ( -59.10, z-score =  -3.33, R)
>consensus
GGGGUGAAAU_CCCUGCUAGAGGUAACGAAGAUACCACUUGGUCCUCGAACCGCUCAGAUUUCUACGGUUAGGGUCAUCCAGGCC__ACCGGGUUGACCCAAUGGCGUUAUA______
.(((........(((.....)))...(((.(((........))).))).)))......(((....(..(((((...............)))))..).......)))............ (-11.45 =  -8.69 +  -2.76)

alignment

secondary structure

dotplot

Window 7

Location	169,975 – 170,093
Length	118
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	60.45
Shannon entropy	0.57992
G+C content	0.56497
Mean single sequence MFE	-47.70
Consensus MFE	-16.37
Energy contribution	-14.83
Covariance contribution	-1.53
Combinations/Pair	1.53
Mean z-score	-2.22
Structure conservation index	0.34
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.05
SVM RNA-class probability	0.882119
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 169975 118 - 2555491
CUAGCGGCUGUUGUGUCUUGGCCAGAGACAAAGCUUCUGCGGGUGACUUGGCCUGCUAAAGGUAACGAAGAUACCACUUCGUUCUGGCCCCGCUCAGCCCCUUACGGUUAGGGUCAUC
.....(((((..(((....(((((((.......(((..((((((......))))))..)))...((((((......))))))))))))).))).)))))(((((....)))))..... ( -43.70, z-score =  -1.40, R)
>droVir3.scaffold_12823 182019 118 + 2474545
CUGGCUGCACAGGCUCCCUGGCCAUGCGCAAGGCUUCAUCGGGAUGAAAUCCCUUUUUGAGGUAGCGCACAUACCAUUUGGUGCGCGAUCCGCUCAGGUUUCUUCUGUUUGGAUCACC
...((.((((.((((....)))).(((((...((((((..(((((...)))))....)))))).)))))...........))))))((((((..((((.....))))..))))))... ( -46.50, z-score =  -2.60, R)
>droGri2.scaffold_4812 5895 118 - 6386
CCUCCUCCCUGGGCUCUUUGGCCUUUUUCAGGGCUUCAUCGGGGUUGAGUCCCUGCUGGAGGUACCGGAGGUACCACUUGACCCUUGAACCGCAGAGAUUUCUCCGGUUCGGGUCAUC
(((((.(((((((((....)))).....)))))(((((.(((((......))))).))))).....))))).......((((((..((((((..(((....))))))))))))))).. ( -52.90, z-score =  -2.67, R)
>consensus
CUAGCUGCACAGGCUCCUUGGCCAUACACAAGGCUUCAUCGGGAUAAAAUCCCUGCUAGAGGUAACGAAGAUACCACUUGGUCCUCGAACCGCUCAGAUUUCUACGGUUAGGGUCAUC
((....(((.(((...((((((..........(((((..(((((......)))))...)))))..(((.(((........))).)))....)).))))...))).)))..))...... (-16.37 = -14.83 +  -1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:50:07 2011