Locus 2800

Sequence ID dm3.chr2L
Location 22,463,501 – 22,463,569
Length 68
Max. P 0.997980
window3856 window3857

overview

Window 6

Location 22,463,501 – 22,463,569
Length 68
Sequences 3
Columns 75
Reading direction forward
Mean pairwise identity 62.22
Shannon entropy 0.53974
G+C content 0.49732
Mean single sequence MFE -22.60
Consensus MFE -16.95
Energy contribution -17.07
Covariance contribution 0.12
Combinations/Pair 1.44
Mean z-score -2.21
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.23
SVM RNA-class probability 0.997980
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22463501 68 + 23011544
GGAAUGUGAUCGAAACGUUGCCCGAU-------CAAACGAUCGUAAAACUACGAUCAAGUGACAGCUGGGAUUGC
(((((((.......))))).))((((-------(....(((((((....))))))).(((....)))..))))). ( -17.10, z-score =  -1.31, R)
>droEre2.scaffold_4929 246337 68 - 26641161
GGAAUGUGGCCGAAACAGUGCCCGAUCGUUUUACGAUCAAGCUAACAGCUACGCUUGUGGGGCAUUGU-------
((.......))...((((((((((((((.....))))).(((.....))).........)))))))))------- ( -24.40, z-score =  -2.30, R)
>droSim1.chr3h_random 1448966 75 - 1452968
GGAAUGUGGACGAAACAGUGCCCGAUUGUUUUGCGAUCGAGCUAACAACCAAGCUUGUUGGGCACUGAGGACUGA
...............(((((((((((((.....)))))(((((........)))))...))))))))........ ( -26.30, z-score =  -3.03, R)
>consensus
GGAAUGUGGACGAAACAGUGCCCGAU_GUUUU_CGAUCGAGCUAACAACUACGCUUGUGGGGCACUGAGGA_UG_
...............(((((((((((((.....)))))(((((........)))))...))))))))........ (-16.95 = -17.07 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 22,463,501 – 22,463,569
Length 68
Sequences 3
Columns 75
Reading direction reverse
Mean pairwise identity 62.22
Shannon entropy 0.53974
G+C content 0.49732
Mean single sequence MFE -18.27
Consensus MFE -8.46
Energy contribution -8.02
Covariance contribution -0.43
Combinations/Pair 1.46
Mean z-score -1.75
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.876832
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22463501 68 - 23011544
GCAAUCCCAGCUGUCACUUGAUCGUAGUUUUACGAUCGUUUG-------AUCGGGCAACGUUUCGAUCACAUUCC
.........(((((((..((((((((....))))))))..))-------))..)))................... ( -15.50, z-score =  -1.15, R)
>droEre2.scaffold_4929 246337 68 + 26641161
-------ACAAUGCCCCACAAGCGUAGCUGUUAGCUUGAUCGUAAAACGAUCGGGCACUGUUUCGGCCACAUUCC
-------(((.(((((...((((..........))))(((((.....)))))))))).))).............. ( -19.70, z-score =  -1.84, R)
>droSim1.chr3h_random 1448966 75 + 1452968
UCAGUCCUCAGUGCCCAACAAGCUUGGUUGUUAGCUCGAUCGCAAAACAAUCGGGCACUGUUUCGUCCACAUUCC
........((((((((.........(((((((.((......))..)))))))))))))))............... ( -19.60, z-score =  -2.25, R)
>consensus
_CA_UCCACAAUGCCCCACAAGCGUAGUUGUUAGCUCGAUCG_AAAAC_AUCGGGCACUGUUUCGACCACAUUCC
........((.(((((..((((((........))))))..............))))).))............... ( -8.46 =  -8.02 +  -0.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:14 2011