Locus 6612

Sequence ID 2R_DroMel_CAF1
Location 20,704,910 – 20,705,026
Length 116
Max. P 0.702187
window10522 window10523

overview

Window 2

Location 20,704,910 – 20,705,026
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.37
Mean single sequence MFE -37.14
Consensus MFE -23.70
Energy contribution -24.54
Covariance contribution 0.84
Combinations/Pair 1.13
Mean z-score -2.24
Structure conservation index 0.64
SVM decision value 0.35
SVM RNA-class probability 0.702187
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20704910 116 + 20766785
AAAGACGAUUUGAGUAGGAUGCUUCUGGCACGCGACGAUUUGUAUUUAAGAAAUAGGUUUUGGGAGUGUGCCAAGAAUUUAGCGUGCCAUCAGCCUCUCAGCUUGAUCUUAUUUGU----
.(((((((.(((((.(((.((....((((((((.....((((....))))...((((((((.((......)).)))))))))))))))).)).)))))))).))).))))......---- ( -33.60)
>DroSec_CAF1 138550 116 + 1
AAAGAGGAUUCGAGUAGGAUGCUUCUGGCACGCGACGAUUUGUAUUUAAGAAAUAGGUUUUGGGAGUGUGCCAAGUAUUUAGCGUGGCAUCAGCCUCUCUGCUCGAUCUUAUUUGU----
....(((((.(((((((((((((..((((((((..(((..(.((((.....)))).)..)))...))))))))))))))....(.(((....))).).))))))))))))......---- ( -40.70)
>DroSim_CAF1 142265 116 + 1
AAAGAGGAUUCGAGUAGGAUGCUUCUGGCACGCGACGAUUUUUAUUUAAGAAAUAGGUUUUGGGAGUGUGCCAAGUAUUUAGCGUGGCAUCAGCCUCUCUGCUCGAUCUUAUUUGU----
....(((((.(((((((((((((..((((((((..(((..((((((.....))))))..)))...))))))))))))))....(.(((....))).).))))))))))))......---- ( -41.40)
>DroEre_CAF1 179297 116 + 1
AAAGACAAUUCGAGGAGGAUGCUCCUGGCACGCGACGAGUUGAGUUUAAGAAUUGGGAUUUGGGAGUGUGCCAAGAGUUUAGCGUGCCAUCAGCCUCUGCCC----AUUUUUUUGUUUUU
((((((((...((((.(((.(((..(((((((((((.......)))((((..((((.((........)).))))...))))))))))))..))).)))..))----.))...)))))))) ( -35.20)
>DroYak_CAF1 144482 113 + 1
AAAG---AUUCGAUAAGGAUGCUCCAGGCACGCGACGAGUUGAGUUUAAGAAUUAGGAUUUGGGAGUGUGCCAAGAUUUUAGCGUGCCAUCAGCCUCUGCGCUCGAAUUUUUUUGU----
((((---((((((...(((.(((...((((((((((.......))).......((((((((.((......)).)))))))))))))))...))).)))....))))))))))....---- ( -34.80)
>consensus
AAAGACGAUUCGAGUAGGAUGCUUCUGGCACGCGACGAUUUGUAUUUAAGAAAUAGGUUUUGGGAGUGUGCCAAGAAUUUAGCGUGCCAUCAGCCUCUCCGCUCGAUCUUAUUUGU____
.........((((((.(((.(((..((((((((..(.((((.........)))).)..(((((.......)))))......))))))))..))).)))..)))))).............. (-23.70 = -24.54 +   0.84)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,704,910 – 20,705,026
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.37
Mean single sequence MFE -25.69
Consensus MFE -17.84
Energy contribution -20.04
Covariance contribution 2.20
Combinations/Pair 1.08
Mean z-score -1.72
Structure conservation index 0.69
SVM decision value 0.07
SVM RNA-class probability 0.570973
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20704910 116 - 20766785
----ACAAAUAAGAUCAAGCUGAGAGGCUGAUGGCACGCUAAAUUCUUGGCACACUCCCAAAACCUAUUUCUUAAAUACAAAUCGUCGCGUGCCAGAAGCAUCCUACUCAAAUCGUCUUU
----......(((((.....(((((((.((.((((((((.......((((.......))))....((((.....)))).........))))))))....)).))).))))....))))). ( -27.50)
>DroSec_CAF1 138550 116 - 1
----ACAAAUAAGAUCGAGCAGAGAGGCUGAUGCCACGCUAAAUACUUGGCACACUCCCAAAACCUAUUUCUUAAAUACAAAUCGUCGCGUGCCAGAAGCAUCCUACUCGAAUCCUCUUU
----........(((((((.((.((.(((..((.(((((.......((((.......))))....((((.....)))).........))))).))..))).)))).)))).)))...... ( -25.10)
>DroSim_CAF1 142265 116 - 1
----ACAAAUAAGAUCGAGCAGAGAGGCUGAUGCCACGCUAAAUACUUGGCACACUCCCAAAACCUAUUUCUUAAAUAAAAAUCGUCGCGUGCCAGAAGCAUCCUACUCGAAUCCUCUUU
----........(((((((.((.((.(((..((.(((((.......((((.......))))....((((.....)))).........))))).))..))).)))).)))).)))...... ( -25.40)
>DroEre_CAF1 179297 116 - 1
AAAAACAAAAAAAU----GGGCAGAGGCUGAUGGCACGCUAAACUCUUGGCACACUCCCAAAUCCCAAUUCUUAAACUCAACUCGUCGCGUGCCAGGAGCAUCCUCCUCGAAUUGUCUUU
..............----(((((((((..(((((....)....((((((((((.(................................).))))))))))))))..))))....))))).. ( -26.25)
>DroYak_CAF1 144482 113 - 1
----ACAAAAAAAUUCGAGCGCAGAGGCUGAUGGCACGCUAAAAUCUUGGCACACUCCCAAAUCCUAAUUCUUAAACUCAACUCGUCGCGUGCCUGGAGCAUCCUUAUCGAAU---CUUU
----........((((((.....((.(((...(((((((.......((((.......))))..............((.......)).)))))))...))).))....))))))---.... ( -24.20)
>consensus
____ACAAAUAAGAUCGAGCAGAGAGGCUGAUGGCACGCUAAAUUCUUGGCACACUCCCAAAACCUAUUUCUUAAAUACAAAUCGUCGCGUGCCAGAAGCAUCCUACUCGAAUCCUCUUU
..............(((((.((.((.(((..((((((((.......((((.......))))..............((.......)).))))))))..))).)))).)))))......... (-17.84 = -20.04 +   2.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:05 2006