Locus 2856

Sequence ID 3R_DroMel_CAF1
Location 7,678,092 – 7,678,230
Length 138
Max. P 0.998505
window4614 window4615

overview

Window 4

Location 7,678,092 – 7,678,212
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.41
Mean single sequence MFE -20.85
Consensus MFE -6.58
Energy contribution -7.18
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.32
SVM decision value 1.36
SVM RNA-class probability 0.946070
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7678092 120 - 27905053
GCUGUCCUAGUUAAGAAGACCUAAAAUAGGUCAGUUCUUUGAAAAAUGUUUUUAAAAUAACAGAGGAAAAGUAAGAACAUUAUAAAUAACAAAAACUCGAGGGAACCCUAUUUAAUGAUA
..((((...((((....((((((...)))))).((((((.......((((........))))..........))))))........)))).........(((....))).......)))) ( -19.83)
>DroSec_CAF1 28052 108 - 1
GCUUUCCUAGUUAAGAAGACCUAAAAUAGGUCAGUUCUUUGAAAUAUGUUUUCAAAGUAACAUAGGGAAAUUAAGAUGAUUAUAAAUAACAAAAAC------------UAUUUAAUGAUA
..(((((((........((((((...)))))).(((((((((((.....)))))))).))).))))))).........((((((((((........------------))))).))))). ( -24.80)
>DroSim_CAF1 27763 108 - 1
GCUGUCCUAGUUAAUCAGACCUAAAAUAGGUCAGUUUUUCGAAAUAUGUUUUCCAAGUACCAUAGGAAUAUUAAGAUCAUUAUAAAUAACAAAAAC------------UAUUUAAUGAUA
....(((((........((((((...)))))).((.(((.((((.....)))).))).))..)))))........(((((((..((((........------------))))))))))). ( -18.10)
>DroEre_CAF1 28596 94 - 1
GCUGUCCUAGUUUAGAAGCCCUAAAAUAGGUCAG--------------------------CAUACUAAAAUUAAUAACAUAAUAAAUAACAAGAACUCGAGGCAACCCUAUUUAAUGAUA
((((.((((.(((((.....))))).)))).)))--------------------------)................(((..((((((....(....)(.(....).))))))))))... ( -17.30)
>DroYak_CAF1 28182 120 - 1
GCUGUCCUAGUUUAGAAGACCUAAAAUAGGUCAGUUCUAUGAAAUAUUUAGUCCAAGUAACACAGGGAAAUUAGGAACAUAAUAAAUAAGAUAAACUCGGGGAAAGCCUAUUUAAUGAUA
(((.((((((((((...((((((...)))))).(((((.(((.....))).(((..(.....)..))).....))))).............))))))..)))).)))............. ( -24.20)
>consensus
GCUGUCCUAGUUAAGAAGACCUAAAAUAGGUCAGUUCUUUGAAAUAUGUUUUCAAAGUAACAUAGGAAAAUUAAGAACAUUAUAAAUAACAAAAACUCG_GG_AA_CCUAUUUAAUGAUA
((((.((((.((.((.....)).)).)))).))))..................................................................................... ( -6.58 =  -7.18 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,678,132 – 7,678,230
Length 98
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.16
Mean single sequence MFE -23.26
Consensus MFE -13.39
Energy contribution -15.32
Covariance contribution 1.94
Combinations/Pair 1.21
Mean z-score -2.73
Structure conservation index 0.58
SVM decision value 3.12
SVM RNA-class probability 0.998505
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7678132 98 - 27905053
-------CAAAAA---------------UUUAUUUUUAUAGCUGUCCUAGUUAAGAAGACCUAAAAUAGGUCAGUUCUUUGAAAAAUGUUUUUAAAAUAACAGAGGAAAAGUAAGAACAU
-------......---------------(((((((((....((((.....(((((((((((((...))))))......((....))..)))))))....))))...)))))))))..... ( -17.40)
>DroSec_CAF1 28080 98 - 1
-------ACUAAA---------------UUUAUUUUGAAAGCUUUCCUAGUUAAGAAGACCUAAAAUAGGUCAGUUCUUUGAAAUAUGUUUUCAAAGUAACAUAGGGAAAUUAAGAUGAU
-------......---------------.(((((((((....(((((((........((((((...)))))).(((((((((((.....)))))))).))).))))))).))))))))). ( -26.80)
>DroSim_CAF1 27791 98 - 1
-------ACAAAA---------------UUUAUUUUGAAAGCUGUCCUAGUUAAUCAGACCUAAAAUAGGUCAGUUUUUCGAAAUAUGUUUUCCAAGUACCAUAGGAAUAUUAAGAUCAU
-------...(((---------------(.((((((((((((((.((((.................)))).))).))))))))))).))))(((..........)))............. ( -18.63)
>DroYak_CAF1 28222 120 - 1
AUUCAUUUCUAAAACUGUUUUUCAGUUUUCUAUCUUUGUGGCUGUCCUAGUUUAGAAGACCUAAAAUAGGUCAGUUCUAUGAAAUAUUUAGUCCAAGUAACACAGGGAAAUUAGGAACAU
.....((((((((((((.....))))).....((((((((((((.((((.(((((.....))))).)))).)))).........(((((.....))))).))))))))..)))))))... ( -30.20)
>consensus
_______ACAAAA_______________UUUAUUUUGAAAGCUGUCCUAGUUAAGAAGACCUAAAAUAGGUCAGUUCUUUGAAAUAUGUUUUCAAAGUAACAUAGGAAAAUUAAGAACAU
................................(((((((.....((((.........((((((...)))))).(((((((((((.....)))))))).)))..))))..))))))).... (-13.39 = -15.32 +   1.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:21 2006