Locus 1003

Sequence ID 2L_DroMel_CAF1
Location 2,890,804 – 2,890,964
Length 160
Max. P 0.962216
window1606 window1607

overview

Window 6

Location 2,890,804 – 2,890,924
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.32
Mean single sequence MFE -29.50
Consensus MFE -26.92
Energy contribution -26.68
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -1.54
Structure conservation index 0.91
SVM decision value 1.54
SVM RNA-class probability 0.962216
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2890804 120 + 22407834
GAGGGAUCUCCUUCUAUGAGGCAACCAACACUUGCAGCAGCAGCAGCACCAGCAACGAUUUGGAUCCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUCG
(((((....))))).....(((.(((......(((.((....)).)))...((...((((((....))))))..((((((......))))))..............))...)))..))). ( -28.50)
>DroSec_CAF1 9577 117 + 1
GAGGGAUCCCCUUCUAUGAGGCAACCAACACUUGCAGCA---GCAGCACCAGCAACGAUUUGGAUCCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUUU
..(((((((((((....))))...((((....(((....---)))((....))......))))....)))))))((((((......))))))...(((((.(((.......))).))))) ( -30.70)
>DroSim_CAF1 9795 117 + 1
GAGGGAUCCCCUUCUAUGAGGCAACCAACACUUGCAGCA---GCAGCACCAGCAACGAUUUGGAUUCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUUU
..(((((((((((....))))...((((....(((....---)))((....))......))))....)))))))((((((......))))))...(((((.(((.......))).))))) ( -30.70)
>DroEre_CAF1 9660 114 + 1
GAGGGAUCCCCCUCUAUGAGGCAACCAACACUUGCAGC------AGCACCAGCAACGAUUUGGAACCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUCG
(((((....)))))..((.(....)))..((((((...------.((.........((((((....))))))..((((((......))))))..............))....)))))).. ( -29.00)
>DroYak_CAF1 9753 114 + 1
GAGGGAACACCCUCUAUGAGGCAACCAACACUUGCAGC------AGCACCAGCAACGAUUUGGAUCCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUCG
(((((....)))))..((.(....)))..((((((...------.((.........((((((....))))))..((((((......))))))..............))....)))))).. ( -28.60)
>consensus
GAGGGAUCCCCUUCUAUGAGGCAACCAACACUUGCAGCA___GCAGCACCAGCAACGAUUUGGAUCCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUCG
(((((....)))))..((.(....)))..((((((.((.......))....((...((((((....))))))..((((((......))))))..............))....)))))).. (-26.92 = -26.68 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,890,844 – 2,890,964
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.00
Mean single sequence MFE -18.47
Consensus MFE -15.20
Energy contribution -15.20
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.15
Structure conservation index 0.82
SVM decision value 0.01
SVM RNA-class probability 0.539593
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2890844 120 + 22407834
CAGCAGCACCAGCAACGAUUUGGAUCCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUCGAUUCAGUUAACAAAUUUCACCUAAAGGAAUAUCCCACAUU
.(((.((....))..((((((((((....)))).((((((......))))))......................)))))).....))).................((......))..... ( -17.80)
>DroEre_CAF1 9698 95 + 1
----AGCACCAGCAACGAUUUGGAACCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUCGAUUCAGCUACCUACUUACC---------------------
----.......((...((((((....))))))..((((((......))))))..............))...(((((((.(..........).)))))))--------------------- ( -19.10)
>DroYak_CAF1 9791 95 + 1
----AGCACCAGCAACGAUUUGGAUCCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUCGAUUCAAUUACCAAAUUACU---------------------
----.((....))...(((((((....(((((..((((((......)))))).....(((.(((.......))).))).))))).....)))))))...--------------------- ( -18.50)
>consensus
____AGCACCAGCAACGAUUUGGAUCCGGAUCCCCAUAUGGAUAUACAUAUGAAAAAACUAACUAAGCCACGGUAAGUCGAUUCAGUUACCAAAUUACA_____________________
.......(((.((...((((((....))))))..((((((......))))))..............))...))).............................................. (-15.20 = -15.20 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:45 2006