Locus 919

Sequence ID 2R_DroMel_CAF1
Location 4,061,335 – 4,061,455
Length 120
Max. P 0.990483
window1622 window1623

overview

Window 2

Location 4,061,335 – 4,061,455
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.33
Mean single sequence MFE -33.13
Consensus MFE -27.46
Energy contribution -28.50
Covariance contribution 1.04
Combinations/Pair 1.09
Mean z-score -2.28
Structure conservation index 0.83
SVM decision value 2.22
SVM RNA-class probability 0.990483
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4061335 120 + 20766785
CUGUUAAAUGCCAAGAACCAACAAAGAAAAUGCUUUGCAGCCUUUCAAGACUUAACCCUUUUGACAUUUGGCGCUGAGGGGCUCUAACAGAAGCCCCAAGGCGUACGGCACAUACUCGUA
........((((.........(((((......)))))..(((..((((((........)))))).....)))(((..(((((((.....).))))))..)))....)))).......... ( -32.30)
>DroSec_CAF1 44040 119 + 1
CUGUUAAAUGCCAAGAACCAACAAAUAAAAUGCUUUGCAGCCUUUCAAGACUUAACCCUUUUGGCAUUU-GCGCUGAGGGGCUCUAACAGAAGCCCCAAAGCGUGCGGCACAUACUCGUA
((((.(((((((((((...........(((.(((....))).))).............)))))))))))-(((((..(((((((.....).))))))..)))))))))............ ( -33.35)
>DroSim_CAF1 50652 120 + 1
CUGUUAAAUGCCAACAACCAACAAAUAAAAUGCUUUGCAGCCUUUCAAGACUUAACCCUUUUGGCAUUUGGCGCUGAGGGGCUCUAAUAGAAGCCCCAAAGCGUGCGGCACAUACUCGUA
........((((.........(((((....(((...)))(((....(((........)))..))))))))(((((..(((((((.....).))))))..)))))..)))).......... ( -34.20)
>DroEre_CAF1 45232 119 + 1
CUGUUAAAUGCCAAGAACCAACAAAUAA-AAGCUUUGCAGCCCUUCAAGACUAAACCCUUUUGGCAUUGGGCGCUUUGGGGCUAUAAGAGAAGCCCCAAAGCGUAGGGCACAUGCUUGUA
............................-((((..((..(((((((((..(((((....)))))..))))(((((((((((((........)))))))))))))))))).)).))))... ( -41.30)
>DroYak_CAF1 47984 120 + 1
CUGUUAAAUACCAAGAACCAACAAAUAAAAAGCUUUGAAGCCUUUCACGACUUAACCCUUUUGCCAUUUCGCGCUAAGGGGCUCCAACAGAAGCCCCAAAGCGUACGGCACAUACUCGUA
..............((...............(((....)))....................((((.....(((((..((((((.(....).))))))..)))))..)))).....))... ( -24.50)
>consensus
CUGUUAAAUGCCAAGAACCAACAAAUAAAAUGCUUUGCAGCCUUUCAAGACUUAACCCUUUUGGCAUUUGGCGCUGAGGGGCUCUAACAGAAGCCCCAAAGCGUACGGCACAUACUCGUA
..((((((((((((((...............(((....)))(......).........))))))))))))))(((..((((((........))))))..))).(((((.......))))) (-27.46 = -28.50 +   1.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,061,335 – 4,061,455
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.33
Mean single sequence MFE -40.70
Consensus MFE -31.76
Energy contribution -32.84
Covariance contribution 1.08
Combinations/Pair 1.06
Mean z-score -2.61
Structure conservation index 0.78
SVM decision value 1.86
SVM RNA-class probability 0.980418
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4061335 120 - 20766785
UACGAGUAUGUGCCGUACGCCUUGGGGCUUCUGUUAGAGCCCCUCAGCGCCAAAUGUCAAAAGGGUUAAGUCUUGAAAGGCUGCAAAGCAUUUUCUUUGUUGGUUCUUGGCAUUUAACAG
((((.((....))))))(((...(((((((......)))))))...)))..((((((((..((..((((((((....)))))((((((......)))))))))..))))))))))..... ( -36.90)
>DroSec_CAF1 44040 119 - 1
UACGAGUAUGUGCCGCACGCUUUGGGGCUUCUGUUAGAGCCCCUCAGCGC-AAAUGCCAAAAGGGUUAAGUCUUGAAAGGCUGCAAAGCAUUUUAUUUGUUGGUUCUUGGCAUUUAACAG
.....((..((((((((((((..(((((((......)))))))..)))).-...)))...(((..((((....(((((.(((....))).)))))....))))..))))))))...)).. ( -39.40)
>DroSim_CAF1 50652 120 - 1
UACGAGUAUGUGCCGCACGCUUUGGGGCUUCUAUUAGAGCCCCUCAGCGCCAAAUGCCAAAAGGGUUAAGUCUUGAAAGGCUGCAAAGCAUUUUAUUUGUUGGUUGUUGGCAUUUAACAG
.....((..((((((.(((((..(((((((......)))))))..)))(((((..(((.....))).......(((((.(((....))).)))))....))))).))))))))...)).. ( -37.90)
>DroEre_CAF1 45232 119 - 1
UACAAGCAUGUGCCCUACGCUUUGGGGCUUCUCUUAUAGCCCCAAAGCGCCCAAUGCCAAAAGGGUUUAGUCUUGAAGGGCUGCAAAGCUU-UUAUUUGUUGGUUCUUGGCAUUUAACAG
...((((.((((((((.((((((((((((........)))))))))))((((..........))))........).))))).)))..))))-(((..(((..(...)..)))..)))... ( -42.50)
>DroYak_CAF1 47984 120 - 1
UACGAGUAUGUGCCGUACGCUUUGGGGCUUCUGUUGGAGCCCCUUAGCGCGAAAUGGCAAAAGGGUUAAGUCGUGAAAGGCUUCAAAGCUUUUUAUUUGUUGGUUCUUGGUAUUUAACAG
...((((((.((((((.((((..((((((((....))))))))..))))....)))))).(((..((((...((((((((((....))))))))))...))))..))).))))))..... ( -46.80)
>consensus
UACGAGUAUGUGCCGUACGCUUUGGGGCUUCUGUUAGAGCCCCUCAGCGCCAAAUGCCAAAAGGGUUAAGUCUUGAAAGGCUGCAAAGCAUUUUAUUUGUUGGUUCUUGGCAUUUAACAG
.....((..(((((...((((..(((((((......)))))))..))))...........(((..((((....(((((.(((....))).)))))....))))..))))))))...)).. (-31.76 = -32.84 +   1.08)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:22 2006