Locus 2465

Sequence ID dm3.chr2L
Location 19,270,844 – 19,270,975
Length 131
Max. P 0.978982
window3389 window3390

overview

Window 9

Location 19,270,844 – 19,270,944
Length 100
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 58.15
Shannon entropy 0.74510
G+C content 0.37169
Mean single sequence MFE -22.36
Consensus MFE -8.58
Energy contribution -9.94
Covariance contribution 1.36
Combinations/Pair 1.22
Mean z-score -1.32
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.878697
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19270844 100 + 23011544
-----------AUUCAA-AUCGGAUUCUUCAUUCAU---AAGGUAC--CCCACCGCUAGGUGGAGCUGAUGUGUAAUCUCGAUAACUAUUGUUUUGUAUAUUAGCAUAUCAGCUACC
-----------......-...((((.....))))..---..(((..--.(((((....)))))((((((((((((((..(((.(((....))))))...))).)))))))))))))) ( -27.80, z-score =  -3.06, R)
>droSim1.chr2L 18962013 112 + 22036055
-----AUUCGAAUCGAAAUAUUCAUUAAAAAGUUGUAAAAACAAGUUACCCACAGCUAGGUGGCGCUAGUGUGUAAUCUCGAAAAUCAUUGUUUUGCAUUUUAGCAUAUCAGCUACC
-----....((((......)))).......(((((.........((((((........))))))(((((.((((((...(((......)))..)))))).)))))....)))))... ( -23.30, z-score =  -1.80, R)
>droSec1.super_7 2899725 108 + 3727775
-------UUGUUUUCAAUAUCAAAUUUCAAAUACAUGAUAACAAUC--ACCACCGCUAGGUGGCGCUAGUGUGUAAUCUCGAAAACUAUUGUUUUGUAUAUUAUCAUAUCAGCUACC
-------(((((.(((...................))).)))))..--.(((((....))))).(((.(((((((((....(((((....)))))....)))).))))).))).... ( -21.21, z-score =  -2.01, R)
>droYak2.chr2R 5778553 105 + 21139217
----AAACCGAUGCAUUAAUAAAAUUGUAAUGACAAACGAAUGUAC---CCAAAGCUAGGUGGGGCUACUGUGUAAUAUCGAACACUAUUGCUGUGCAUAUUUUCAGCUACC-----
----......((((((........((((....)))).........(---(((........))))((....((((........))))....)).)))))).............----- ( -16.60, z-score =   1.14, R)
>droEre2.scaffold_4845 17578010 101 - 22589142
GAACAAAUGAACAAGUUCAUAAAAGAGUUUUGACAAUUGAAUGCAC---CCACCGCUAGGUGGAGCUAUUGUGCAAUCUCGAAAACUGUUGCGCUGCAUAUUUC-------------
......(((((....)))))....................(((((.---(((((....))))).......(((((((..........)))))))))))).....------------- ( -22.90, z-score =  -0.85, R)
>consensus
_____A_UCGAAUCCAAAAUAAAAUUGUAAAGACAUAAGAACGAAC___CCACCGCUAGGUGGAGCUAGUGUGUAAUCUCGAAAACUAUUGUUUUGCAUAUUAGCAUAUCAGCUACC
.................................................(((((....)))))...((((((((((...(((......)))..)))))))))).............. ( -8.58 =  -9.94 +   1.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,270,875 – 19,270,975
Length 100
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 60.66
Shannon entropy 0.63189
G+C content 0.40618
Mean single sequence MFE -24.80
Consensus MFE -9.59
Energy contribution -10.65
Covariance contribution 1.06
Combinations/Pair 1.20
Mean z-score -2.20
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.978982
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19270875 100 + 23011544
-----------CCCACCGCUAGGUGGAGCUGAUGUGUAAUCUCGAUAACUAUUGUUUUGUAUAUUAGCAUAUCAGCUACCUCGCACUUUCAUAAUCAAAGU-CGAAUAACUA
-----------.(((((....)))))((((((((((((((..(((.(((....))))))...))).)))))))))))...(((.(((((.......)))))-)))....... ( -30.00, z-score =  -4.29, R)
>droSec1.super_7 2899753 112 + 3727775
UGAUAACAAUCACCACCGCUAGGUGGCGCUAGUGUGUAAUCUCGAAAACUAUUGUUUUGUAUAUUAUCAUAUCAGCUACCUCGCACAUUCAUAACUAUAAUAUUAAUUUCUU
((((....)))).....((.(((((((....(((((((((....(((((....)))))....)))).)))))..))))))).))............................ ( -21.50, z-score =  -1.97, R)
>droYak2.chr2R 5778589 85 + 21139217
------AUGUACCCAAAGCUAGGUGGGGCUACUGUGUAAUAUCGAACACUAUUGCUGUGCAUAUU-----UUCAGCUACCUAGCACUUUCAUAAGC----------------
------...........((((((((((((....((((........))))....))).((......-----..)).)))))))))............---------------- ( -20.40, z-score =  -0.28, R)
>droEre2.scaffold_4845 17578050 89 - 22589142
------AUGCACCCACCGCUAGGUGGAGCUAUUGUGCAAUCUCGAAAACUGUUGCGCUGCAUAUU-------UCGCAGUUUCACAAGCUGAUCGAAAUACUG----------
------.((((.(((((....))))).......(((((((..........)))))))))))((((-------((((((((.....)))))..)))))))...---------- ( -27.30, z-score =  -2.26, R)
>consensus
______AUGUACCCACCGCUAGGUGGAGCUAAUGUGUAAUCUCGAAAACUAUUGCUUUGCAUAUU_____AUCAGCUACCUCGCACUUUCAUAAACAUA_U___________
............(((((....))))).((((((((((((...(((......)))..)))))))))........))).................................... ( -9.59 = -10.65 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:51:42 2011