Locus 5147

Sequence ID 2R_DroMel_CAF1
Location 16,748,894 – 16,748,987
Length 93
Max. P 0.792856
window8232 window8233

overview

Window 2

Location 16,748,894 – 16,748,987
Length 93
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 73.26
Mean single sequence MFE -14.65
Consensus MFE -8.62
Energy contribution -9.18
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -1.70
Structure conservation index 0.59
SVM decision value 0.59
SVM RNA-class probability 0.792856
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16748894 93 + 20766785
CCAGCU------CAGGAAAAAAAACCAGGCGAAACGAAGCAAAGCAAAUUGGCUUUAAACAACAAAUUUCUUAAAGAAUUCAAGACCAAUUUGCGAGAA
....((------(.((........))..((........))...((((((((((((.((.........(((.....))))).))).)))))))))))).. ( -17.20)
>DroSec_CAF1 61100 75 + 1
CCAGU------------------------AAAAACGAAGCAUAGCAAAUUGGCUUUAAACAACAAAUUUCUUAAAGAAUUCAAGAACAAUUUGCGAGGA
((.((------------------------....))........((((((((.((((((............))))))..........))))))))..)). ( -10.50)
>DroSim_CAF1 58883 75 + 1
CCAGC------------------------AUAAACGAAGCAUAGCAAAUUGGCUUUAAACAACAAAUUUCUUAAAGAAUUCAAGACCAAUUUGCGAGGA
((.((------------------------.........))...((((((((((((.((.........(((.....))))).))).)))))))))..)). ( -14.10)
>DroEre_CAF1 58095 98 + 1
CCAGCAAAAAAUAAAUAGGAAAAGCCAGGCGAAACCAACCACAGCAAAUUGGCUUUAAACAACAAAUUUCUUAAAGAAUUCGAGACCAU-UUGUGAGGA
((..................(((((((.((.............))....))))))).....((((((.((((.........))))..))-))))..)). ( -14.52)
>DroYak_CAF1 63778 91 + 1
--------AAAUAAAUAGGAAAAGCCAGGCGAAUUGAACCAAAGCAAAUUGGCUUUAAGCAACAAAUUUCUUAAAGAAUUGGAGACCAUUUUGUGAGGA
--------............(((((((.((.............))....)))))))...........((((((.(((((.(....).))))).)))))) ( -16.92)
>consensus
CCAGC________A__A__AAAA_CCAGGCGAAACGAAGCAAAGCAAAUUGGCUUUAAACAACAAAUUUCUUAAAGAAUUCAAGACCAAUUUGCGAGGA
...........................................(((((((((((((((............)))))).........)))))))))..... ( -8.62 =  -9.18 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,748,894 – 16,748,987
Length 93
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 73.26
Mean single sequence MFE -16.03
Consensus MFE -10.22
Energy contribution -12.22
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -1.33
Structure conservation index 0.64
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16748894 93 - 20766785
UUCUCGCAAAUUGGUCUUGAAUUCUUUAAGAAAUUUGUUGUUUAAAGCCAAUUUGCUUUGCUUCGUUUCGCCUGGUUUUUUUUCCUG------AGCUGG
.....(((((((((..((((((.....((....))....))))))..)))))))))...............(..((((........)------)))..) ( -22.50)
>DroSec_CAF1 61100 75 - 1
UCCUCGCAAAUUGUUCUUGAAUUCUUUAAGAAAUUUGUUGUUUAAAGCCAAUUUGCUAUGCUUCGUUUUU------------------------ACUGG
.....(((((((((((((((.....)))))))....(((......)))))))))))..............------------------------..... ( -12.90)
>DroSim_CAF1 58883 75 - 1
UCCUCGCAAAUUGGUCUUGAAUUCUUUAAGAAAUUUGUUGUUUAAAGCCAAUUUGCUAUGCUUCGUUUAU------------------------GCUGG
.....(((((((((..((((((.....((....))....))))))..)))))))))...((.........------------------------))... ( -18.60)
>DroEre_CAF1 58095 98 - 1
UCCUCACAA-AUGGUCUCGAAUUCUUUAAGAAAUUUGUUGUUUAAAGCCAAUUUGCUGUGGUUGGUUUCGCCUGGCUUUUCCUAUUUAUUUUUUGCUGG
.....((((-((..(((..(.....)..))).))))))......(((((((((......)))))))))...(..((..................))..) ( -15.17)
>DroYak_CAF1 63778 91 - 1
UCCUCACAAAAUGGUCUCCAAUUCUUUAAGAAAUUUGUUGCUUAAAGCCAAUUUGCUUUGGUUCAAUUCGCCUGGCUUUUCCUAUUUAUUU--------
........((((((.........(((((((..........))))))).......(((..(((.......))).))).....))))))....-------- ( -11.00)
>consensus
UCCUCGCAAAUUGGUCUUGAAUUCUUUAAGAAAUUUGUUGUUUAAAGCCAAUUUGCUAUGCUUCGUUUCGCCUGG_UUUU__U__U________GCUGG
.....((((((((((.((((((.....((....))....)))))).))))))))))........................................... (-10.22 = -12.22 +   2.00)

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 11:37:45 2006