Locus 5624

Sequence ID dm3.chr3LHet
Location 2,445,663 – 2,445,739
Length 76
Max. P 0.999119
window7721 window7722

overview

Window 1

Location 2,445,663 – 2,445,739
Length 76
Sequences 8
Columns 77
Reading direction forward
Mean pairwise identity 63.25
Shannon entropy 0.75884
G+C content 0.59916
Mean single sequence MFE -27.74
Consensus MFE -15.97
Energy contribution -16.62
Covariance contribution 0.66
Combinations/Pair 1.40
Mean z-score -1.79
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.66
SVM RNA-class probability 0.999119
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 2445663 76 + 2555491
GACUGGCGUCAAAGUACCGUUACGAGUGAGGCGACGGCGUUGUAGCGCUGUCGCCUAAAGUAGUCCAGCUAGCGUG-
(.(((((.(((..(((....)))...)))(((((((((((....)))))))))))............))))))...- ( -31.40, z-score =  -2.30, R)
>droSim1.chrU 10271674 62 - 15797150
UACACUUGCCAAAAUACAAUUACGAGUGAGGCGACGGUGCUGUCGCGCUGUCGCCGAGUGUA---------------
(((((((.......(((........))).(((((((((((....))))))))))))))))))--------------- ( -28.50, z-score =  -4.12, R)
>droSec1.super_60 150380 76 + 163194
GACUGGCGCCAAAGUACCGUUACGAGUGAGGCGACGGCGUUGUCGCGCUGUCGCCAAGUGUAGUCCAGCUAGGGUG-
..(((((..((..(((....)))...)).(((((((((((....)))))))))))............)))))....- ( -30.40, z-score =  -1.29, R)
>droYak2.chrU 19814955 58 - 28119190
GACUGGCGCCAAAGUACCGCAACGAGUGAGGCGACGACGUUGUCGUCCAG----CUAGCGUG---------------
(.((((((((....(((((...)).))).)))((((((...))))))..)----)))))...--------------- ( -19.40, z-score =  -0.58, R)
>droAna3.scaffold_12944 226763 65 - 272910
---------CAAAGUACCGUUGU-AGCGAGGCGACAGCGUUGUAUCGCUGUCGCCGAUCGAGGUUUGGUAGUAUG--
---------...(.(((((....-..(((((((((((((......))))))))))..))).....))))).)...-- ( -28.40, z-score =  -4.36, R)
>droWil1.scaffold_181154 1830346 76 + 4610121
GACUGGCGCCUAGGUGCCGUA-CGAGUGAGGCGACAGCGUUGUCGCGCUGUCGCCGAGUGUAGUCCAGCUUGGCGUC
....((((((.((.((...((-((.....(((((((((((....)))))))))))...))))...)).)).)))))) ( -38.30, z-score =  -2.68, R)
>droVir3.scaffold_12958 1410437 71 - 3547706
----GGCGCCAAAAUACUGUA-CGAGUGAGGGGACGGCGUUGUCGCGCUGACGCCGAGUGUAGUCCAGCUUG-CGUG
----.((((......((((((-(......(....)((((((........))))))..))))))).......)-))). ( -20.82, z-score =   1.34, R)
>droMoj3.scaffold_6500 31239524 67 + 32352404
--------CGGUGGUGUCCUU-UGAGCGAGGCGACGGCGGUGUCGCGCUGUCGCUGAGUGUAGUCCAACUUG-CGUU
--------..(..(((..((.-...((..((((((((((......))))))))))..))..))..))..)..-)... ( -24.70, z-score =  -0.36, R)
>consensus
GACUGGCGCCAAAGUACCGUUACGAGUGAGGCGACGGCGUUGUCGCGCUGUCGCCGAGUGUAGUCCAGCUUG_CG__
.............................((((((((((......))))))))))...................... (-15.97 = -16.62 +   0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 2,445,663 – 2,445,739
Length 76
Sequences 8
Columns 77
Reading direction reverse
Mean pairwise identity 63.25
Shannon entropy 0.75884
G+C content 0.59916
Mean single sequence MFE -21.38
Consensus MFE -9.86
Energy contribution -11.00
Covariance contribution 1.14
Combinations/Pair 1.11
Mean z-score -1.40
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.14
SVM RNA-class probability 0.983731
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 2445663 76 - 2555491
-CACGCUAGCUGGACUACUUUAGGCGACAGCGCUACAACGCCGUCGCCUCACUCGUAACGGUACUUUGACGCCAGUC
-.......(((((........(((((((.(((......))).))))))).....(((....))).......))))). ( -23.00, z-score =  -1.03, R)
>droSim1.chrU 10271674 62 + 15797150
---------------UACACUCGGCGACAGCGCGACAGCACCGUCGCCUCACUCGUAAUUGUAUUUUGGCAAGUGUA
---------------(((((..((((((.(.((....)).).))))))..........((((......))))))))) ( -20.60, z-score =  -2.01, R)
>droSec1.super_60 150380 76 - 163194
-CACCCUAGCUGGACUACACUUGGCGACAGCGCGACAACGCCGUCGCCUCACUCGUAACGGUACUUUGGCGCCAGUC
-.......((..((.(((....((((((.(((......))).)))))).....((...))))).))..))....... ( -23.10, z-score =  -0.55, R)
>droYak2.chrU 19814955 58 + 28119190
---------------CACGCUAG----CUGGACGACAACGUCGUCGCCUCACUCGUUGCGGUACUUUGGCGCCAGUC
---------------..((((((----...((((((...))))))(((.((.....)).)))...))))))...... ( -16.60, z-score =   0.16, R)
>droAna3.scaffold_12944 226763 65 + 272910
--CAUACUACCAAACCUCGAUCGGCGACAGCGAUACAACGCUGUCGCCUCGCU-ACAACGGUACUUUG---------
--.....((((......(((..((((((((((......)))))))))))))..-.....)))).....--------- ( -24.52, z-score =  -5.92, R)
>droWil1.scaffold_181154 1830346 76 - 4610121
GACGCCAAGCUGGACUACACUCGGCGACAGCGCGACAACGCUGUCGCCUCACUCG-UACGGCACCUAGGCGCCAGUC
(.((((..((((.((.......((((((((((......))))))))))......)-).)))).....)))).).... ( -30.82, z-score =  -2.34, R)
>droVir3.scaffold_12958 1410437 71 + 3547706
CACG-CAAGCUGGACUACACUCGGCGUCAGCGCGACAACGCCGUCCCCUCACUCG-UACAGUAUUUUGGCGCC----
....-...((..((.(((.....(((....)))(((......)))..........-....))).))..))...---- ( -15.10, z-score =   1.31, R)
>droMoj3.scaffold_6500 31239524 67 - 32352404
AACG-CAAGUUGGACUACACUCAGCGACAGCGCGACACCGCCGUCGCCUCGCUCA-AAGGACACCACCG--------
(((.-...)))((.........(((((..(.(((((......)))))))))))..-..((...)).)).-------- ( -17.30, z-score =  -0.85, R)
>consensus
__CG_CAAGCUGGACUACACUCGGCGACAGCGCGACAACGCCGUCGCCUCACUCGUAACGGUACUUUGGCGCCAGUC
......................((((((.(((......))).))))))............................. ( -9.86 = -11.00 +   1.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:51:56 2011