Locus 4279

Sequence ID	dm3.chr2R
Location	11,895,572 – 11,895,662
Length	90
Max. P	0.957771

overview

Window 3

Location	11,895,572 – 11,895,662
Length	90
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	59.50
Shannon entropy	0.65333
G+C content	0.36341
Mean single sequence MFE	-19.42
Consensus MFE	-8.56
Energy contribution	-9.19
Covariance contribution	0.63
Combinations/Pair	1.29
Mean z-score	-1.03
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.41
SVM RNA-class probability	0.685566
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11895572 90 + 21146708
----------GUAUAAUUGUAUAAGUAAGUCAAUAA--AGCACUAUAUGGGCUUGUUCCGUAUUAUGAACAUGGGAACUUCCCAUAAAGUUUGUGUAACCAG
----------..........................--.....(((((..((((((((........))))(((((.....))))).))))..)))))..... ( -17.70, z-score =  -0.65, R)
>droSec1.super_1 9394535 102 + 14215200
GUAUAUUUCUACGUAGCCCGAUAUAAGGAUCAAUCUCCAGCACUGUAUGGGCUCGUUCCACAUUAUGAACAUGGGAACUUCCCAUAAAGUUUGUGUAACUAG
(((......)))(.(((((.(((((.(((......))).....)))))))))))(((.((((..((....(((((.....)))))...)).)))).)))... ( -23.70, z-score =  -1.15, R)
>droSim1.chr2R 10633957 102 + 19596830
GUAUAUUUGUACGUAGCCCGAUAUAAGGAUCAAUCUCCAGCACUGUAUGGGCUCGUUCCACAUUAUGAACAUGGGAACUUCCCAUAAAGUUUGUUUAACUAG
((.(((.((((((.(((((.(((((.(((......))).....)))))))))))))...)))..))).))(((((.....)))))..((((.....)))).. ( -23.70, z-score =  -1.24, R)
>apiMel3.GroupUn 38812131 88 + 399230636
-------ACAGAACUUUCAAAAAUGAAGGUAAUCUAAAUGUAUUAU-UAGUAUGAUUCCAUAUCCGGAA------AGCUAACCUUCAAGUUAUCACAAACAA
-------................(((((((...((((........)-))).....((((......))))------.....))))))).(((......))).. ( -12.60, z-score =  -1.10, R)
>consensus
_______UCUACAUAGCCCGAUAUAAAGAUCAAUCACCAGCACUAUAUGGGCUCGUUCCACAUUAUGAACAUGGGAACUUCCCAUAAAGUUUGUGUAACCAG
.....................................(((.(((.((((((...(((((..............)))))..)))))).))))))......... ( -8.56 =  -9.19 +   0.63)

alignment

secondary structure

dotplot

Window 4

Location	11,895,572 – 11,895,662
Length	90
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	59.50
Shannon entropy	0.65333
G+C content	0.36341
Mean single sequence MFE	-21.38
Consensus MFE	-10.99
Energy contribution	-10.80
Covariance contribution	-0.19
Combinations/Pair	1.52
Mean z-score	-1.31
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.65
SVM RNA-class probability	0.957771
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11895572 90 - 21146708
CUGGUUACACAAACUUUAUGGGAAGUUCCCAUGUUCAUAAUACGGAACAAGCCCAUAUAGUGCU--UUAUUGACUUACUUAUACAAUUAUAC----------
..(((((.....(((.((((((..(((((..(((.....))).)))))...)))))).)))...--....))))).................---------- ( -18.00, z-score =  -1.59, R)
>droSec1.super_1 9394535 102 - 14215200
CUAGUUACACAAACUUUAUGGGAAGUUCCCAUGUUCAUAAUGUGGAACGAGCCCAUACAGUGCUGGAGAUUGAUCCUUAUAUCGGGCUACGUAGAAAUAUAC
....((((....(((.((((((..((((((((.......))).)))))...)))))).)))(((.((.((........)).)).)))...))))........ ( -27.80, z-score =  -2.01, R)
>droSim1.chr2R 10633957 102 - 19596830
CUAGUUAAACAAACUUUAUGGGAAGUUCCCAUGUUCAUAAUGUGGAACGAGCCCAUACAGUGCUGGAGAUUGAUCCUUAUAUCGGGCUACGUACAAAUAUAC
.(((((......(((.((((((..((((((((.......))).)))))...)))))).)))...(((......)))........)))))............. ( -26.20, z-score =  -1.76, R)
>apiMel3.GroupUn 38812131 88 - 399230636
UUGUUUGUGAUAACUUGAAGGUUAGCU------UUCCGGAUAUGGAAUCAUACUA-AUAAUACAUUUAGAUUACCUUCAUUUUUGAAAGUUCUGU-------
...............(((((((.....------(((((....))))).....(((-(........))))...)))))))................------- ( -13.50, z-score =   0.13, R)
>consensus
CUAGUUACACAAACUUUAUGGGAAGUUCCCAUGUUCAUAAUAUGGAACGAGCCCAUACAGUGCUGGAGAUUGACCCUCAUAUCGGACUACGCAGA_______
.(((((......(((.((((((..((((((((.......))).)))))...)))))).)))......(((..........))).)))))............. (-10.99 = -10.80 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:26:07 2011