Locus 1470

Sequence ID 2R_DroMel_CAF1
Location 5,614,370 – 5,614,519
Length 149
Max. P 0.876949
window2503 window2504

overview

Window 3

Location 5,614,370 – 5,614,488
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 87.37
Mean single sequence MFE -25.10
Consensus MFE -16.99
Energy contribution -17.83
Covariance contribution 0.84
Combinations/Pair 1.11
Mean z-score -1.87
Structure conservation index 0.68
SVM decision value 0.01
SVM RNA-class probability 0.539076
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5614370 118 - 20766785
UCCAAAAUGUUUGAAACCCCAUACAAAUGUUCUUUACUGAAGCUAACAACUAGUUUCAAAGACCCAGUAACAUUGGCAGAAGCAAUUAUAAAUGCUGAUUUCUGCGCAGUUGCCUAAA
.......(((.((......)).))).....((((...((((((((.....))))))))))))....(((((..(((((((((((........))))....))))).)))))))..... ( -23.40)
>DroSec_CAF1 3952 117 - 1
UCCAAACUGUUUGAAAAC-CAUACAAAUGUUGUUUGCUGAAGCUAACAACUAGUUUCAGAGACCCAGUAACAUUUGCAGAAGCAAUUAUAAAUGCCGAGUUCUGCGCAGUUGUCUGAA
....((((((........-.....(((((((((((.(((((((((.....))))))))))))).....)))))))(((((((((........)))....))))))))))))....... ( -30.00)
>DroSim_CAF1 3976 118 - 1
UCCAAACUGUUUGAAAACCCAUACAAAUGUUGUACGCUGAAGCUAACAACUAGUUUCAGAGACCCAGUAACAUUUGCAGAAGCAAUUAUAAAUGCUGAGUUCUGCGCAGUUGUCUAAA
....((((((..............(((((((((...(((((((((.....)))))))))..)).....)))))))(((((((((........))))....)))))))))))....... ( -29.40)
>DroEre_CAF1 4154 118 - 1
UCAAAAUUGUUUCAAAACCUAUACAAAUGUUCUUCUCUGCAGCUUACAACUAGUUUUAGAUACCCAGUAACAUUUGCAGAAGCAAUUAUAAAUACUGAGUUCUGCGCAGUUGUCUAAA
....(((((((((..........((((((((((..((((.((((.......)))).)))).....)).))))))))..)))))))))......((((.(.....).))))........ ( -18.80)
>DroYak_CAF1 3954 111 - 1
UAAAAAUUGUUUGAAAACCCAUAGAAAUGGUCUUUGCUAAAGCUAAAAACUAGUUUUAGAGACCCAGUAACAUUUGCACAAGCAAUUAU-------GAGUUCUGCGCAGUUGUCUAAA
....((((((.....(((.(((((....(((((...(((((((((.....)))))))))))))).........((((....))))))))-------).)))....))))))....... ( -23.90)
>consensus
UCCAAACUGUUUGAAAACCCAUACAAAUGUUCUUUGCUGAAGCUAACAACUAGUUUCAGAGACCCAGUAACAUUUGCAGAAGCAAUUAUAAAUGCUGAGUUCUGCGCAGUUGUCUAAA
....((((((..............(((((((.....(((((((((.....))))))))).........)))))))((((((..................))))))))))))....... (-16.99 = -17.83 +   0.84)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,614,408 – 5,614,519
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.28
Mean single sequence MFE -23.82
Consensus MFE -12.71
Energy contribution -13.91
Covariance contribution 1.20
Combinations/Pair 1.17
Mean z-score -2.43
Structure conservation index 0.53
SVM decision value 0.90
SVM RNA-class probability 0.876949
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5614408 111 - 20766785
CUACAUUGAAAUGGUUAGGUGAAAA-AU--------AGUCUCCAAAAUGUUUGAAACCCCAUACAAAUGUUCUUUACUGAAGCUAACAACUAGUUUCAAAGACCCAGUAACAUUGGCAGA
..(((((...((((...(((...((-((--------(..........)))))...)))))))...)))))((((...((((((((.....)))))))))))).(((((...))))).... ( -20.30)
>DroSec_CAF1 3990 110 - 1
CUACAUUCAAAUGGUUAUGUGAAAA-AU--------AAUCUCCAAACUGUUUGAAAAC-CAUACAAAUGUUGUUUGCUGAAGCUAACAACUAGUUUCAGAGACCCAGUAACAUUUGCAGA
.....(((((((((((.((.((...-..--------....)))))))))))))))...-....((((((((((((.(((((((((.....))))))))))))).....)))))))).... ( -27.50)
>DroSim_CAF1 4014 111 - 1
CUACAUUCAAAUGGUUAUGUGAAAA-AU--------AAUCUCCAAACUGUUUGAAAACCCAUACAAAUGUUGUACGCUGAAGCUAACAACUAGUUUCAGAGACCCAGUAACAUUUGCAGA
.....(((((((((((.((.((...-..--------....)))))))))))))))........((((((((((...(((((((((.....)))))))))..)).....)))))))).... ( -26.20)
>DroEre_CAF1 4192 119 - 1
UUACUUUUAAAUGUUUAAAUGAACAGAU-AAAAGCUUCUCUCAAAAUUGUUUCAAAACCUAUACAAAUGUUCUUCUCUGCAGCUUACAACUAGUUUUAGAUACCCAGUAACAUUUGCAGA
...((((((..(((((....)))))..)-))))).............................((((((((((..((((.((((.......)))).)))).....)).)))))))).... ( -17.50)
>DroYak_CAF1 3985 120 - 1
UUACAUUUAAAUGAUUAGAUGGAGAGAUGAAAAGCUUCUCUAAAAAUUGUUUGAAAACCCAUAGAAAUGGUCUUUGCUAAAGCUAAAAACUAGUUUUAGAGACCCAGUAACAUUUGCACA
((((.((((((..(((...(((((((.(....)..)))))))..)))..)))))).............(((((...(((((((((.....))))))))))))))..)))).......... ( -27.60)
>consensus
CUACAUUCAAAUGGUUAGGUGAAAA_AU________AAUCUCCAAACUGUUUGAAAACCCAUACAAAUGUUCUUUGCUGAAGCUAACAACUAGUUUCAGAGACCCAGUAACAUUUGCAGA
.....(((((((((((....((................))....)))))))))))........((((((((.....(((((((((.....))))))))).........)))))))).... (-12.71 = -13.91 +   1.20)

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 10:05:37 2006