Locus 204

Sequence ID pao.731
Location 1,292,452 – 1,292,570
Length 118
Max. P 0.987600
window798 window799 window800 window801

overview

Window 8

Location 1,292,452 – 1,292,558
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 68.21
Mean single sequence MFE -52.10
Consensus MFE -23.84
Energy contribution -28.62
Covariance contribution 4.78
Combinations/Pair 1.09
Mean z-score -2.76
Structure conservation index 0.46
SVM decision value 2.09
SVM RNA-class probability 0.987600
Prediction RNA

Download alignment: ClustalW | MAF

>pao.731 1292452 106 + 6264404
AGCGCC------------GGGCGCGCAUGGACAGCGCCACCCGGUGCUCGGCCGACCUAUGCGACCUUAUGUCGCAGUAUAGGAACGGCCCGAGCCCGCGUCGCUCGCGGGG--UUAGAG
((((((------------(((.((((.......))))..))))))))).(((((.((((((((((.....))))))...))))..))))).((.((((((.....)))))).--)).... ( -58.70)
>pau.2299 2181088 106 - 6537648
AGCGCC------------GGGCGCGCAUGGACAGCGCCACCUGGUGCUCGGCCGACCUAUGCGACCUUAUGUCGCAGUAUAGGAACGGCCCGACCCCGCGUCGCUCGCGGGG--UUAGAG
((((((------------(((.((((.......))))..))))))))).(((((.((((((((((.....))))))...))))..))))).(((((((((.....)))))))--)).... ( -61.00)
>pfo.2488 1663725 107 - 6438405
AGCGCCUACGGGCCAAUCGGCCGAGCAAAUACAGGUCUUCAGAUUG-----------UGUGCGACCUUAUGUCGCAGUAUAGAAAGGUCUUAA--CCGCACAGGUGGUAGGGGCUUAGAG
(((.(((((.((((....))))..((..((((.((((....)))).-----------..((((((.....)))))))))).....(((....)--)))).......))))).)))..... ( -36.60)
>consensus
AGCGCC____________GGGCGCGCAUGGACAGCGCCACCCGGUGCUCGGCCGACCUAUGCGACCUUAUGUCGCAGUAUAGGAACGGCCCGA_CCCGCGUCGCUCGCGGGG__UUAGAG
.(((((.............)))))........((((((....)))))).(((((.((((((((((.....))))))...))))..)))))....((((((.....))))))......... (-23.84 = -28.62 +   4.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,292,452 – 1,292,558
Length 106
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 68.21
Mean single sequence MFE -48.60
Consensus MFE -23.38
Energy contribution -27.72
Covariance contribution 4.34
Combinations/Pair 1.06
Mean z-score -2.34
Structure conservation index 0.48
SVM decision value 1.60
SVM RNA-class probability 0.966528
Prediction RNA

Download alignment: ClustalW | MAF

>pao.731 1292452 106 - 6264404
CUCUAA--CCCCGCGAGCGACGCGGGCUCGGGCCGUUCCUAUACUGCGACAUAAGGUCGCAUAGGUCGGCCGAGCACCGGGUGGCGCUGUCCAUGCGCGCCC------------GGCGCU
......--.((((((.....))))))....(((((..((((...((((((.....)))))))))).))))).(((.(((((((.(((.......))))))))------------)).))) ( -58.20)
>pau.2299 2181088 106 + 6537648
CUCUAA--CCCCGCGAGCGACGCGGGGUCGGGCCGUUCCUAUACUGCGACAUAAGGUCGCAUAGGUCGGCCGAGCACCAGGUGGCGCUGUCCAUGCGCGCCC------------GGCGCU
.....(--(((((((.....))))))))..(((((..((((...((((((.....)))))))))).))))).(((.((.((((.(((.......))))))).------------)).))) ( -56.80)
>pfo.2488 1663725 107 + 6438405
CUCUAAGCCCCUACCACCUGUGCGG--UUAAGACCUUUCUAUACUGCGACAUAAGGUCGCACA-----------CAAUCUGAAGACCUGUAUUUGCUCGGCCGAUUGGCCCGUAGGCGCU
.....(((.(((((.....((((((--((.(((....)))....((((((.....))))))..-----------.........)))).))))......((((....)))).))))).))) ( -30.80)
>consensus
CUCUAA__CCCCGCGAGCGACGCGGG_UCGGGCCGUUCCUAUACUGCGACAUAAGGUCGCAUAGGUCGGCCGAGCACCAGGUGGCGCUGUCCAUGCGCGCCC____________GGCGCU
.........((((((.....))))))....(((((..((((...((((((.....)))))))))).))))).(((........((((.......))))(((.............)))))) (-23.38 = -27.72 +   4.34)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,292,458 – 1,292,570
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.14
Mean single sequence MFE -46.60
Consensus MFE -25.28
Energy contribution -29.40
Covariance contribution 4.12
Combinations/Pair 1.09
Mean z-score -2.03
Structure conservation index 0.54
SVM decision value 1.83
SVM RNA-class probability 0.979140
Prediction RNA

Download alignment: ClustalW | MAF

>pao.731 1292458 112 + 6264404
------GGGCGCGCAUGGACAGCGCCACCCGGUGCUCGGCCGACCUAUGCGACCUUAUGUCGCAGUAUAGGAACGGCCCGAGCCCGCGUCGCUCGCGGGG--UUAGAGCAAAUCGAAGCU
------.(((((.........)))))...(((((((((((((.((((((((((.....))))))...))))..))))).((.((((((.....)))))).--)).)))))..)))..... ( -53.60)
>pau.2299 2181094 110 - 6537648
------GGGCGCGCAUGGACAGCGCCACCUGGUGCUCGGCCGACCUAUGCGACCUUAUGUCGCAGUAUAGGAACGGCCCGACCCCGCGUCGCUCGCGGGG--UUAGAGCAAAUCGAAG--
------.(((((.........)))))......((((((((((.((((((((((.....))))))...))))..))))).(((((((((.....)))))))--)).)))))........-- ( -57.10)
>pfo.2488 1663737 102 - 6438405
CCAAUCGGCCGAGCAAAUACAGGUCUUCAGAUUG-----------UGUGCGACCUUAUGUCGCAGUAUAGAAAGGUCUUAA--CCGCACAGGUGGUAGGGGCUUAGAGCAAAUCG-----
......((((...........))))....(((((-----------(.((((((.....))))))........((((((..(--((((....)))))..))))))...)).)))).----- ( -29.10)
>consensus
______GGGCGCGCAUGGACAGCGCCACCCGGUGCUCGGCCGACCUAUGCGACCUUAUGUCGCAGUAUAGGAACGGCCCGA_CCCGCGUCGCUCGCGGGG__UUAGAGCAAAUCGAAG__
......((..((((.......))))..))...((((((((((.((((((((((.....))))))...))))..)))))....((((((.....))))))......))))).......... (-25.28 = -29.40 +   4.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,292,458 – 1,292,570
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.14
Mean single sequence MFE -44.83
Consensus MFE -25.83
Energy contribution -30.17
Covariance contribution 4.34
Combinations/Pair 1.07
Mean z-score -1.85
Structure conservation index 0.58
SVM decision value 1.85
SVM RNA-class probability 0.979939
Prediction RNA

Download alignment: ClustalW | MAF

>pao.731 1292458 112 - 6264404
AGCUUCGAUUUGCUCUAA--CCCCGCGAGCGACGCGGGCUCGGGCCGUUCCUAUACUGCGACAUAAGGUCGCAUAGGUCGGCCGAGCACCGGGUGGCGCUGUCCAUGCGCGCCC------
.((.(((.(((((.....--....)))))))).))((((((((.(((..((((...((((((.....)))))))))).))))))))).))(((((.(((.......))))))))------ ( -55.00)
>pau.2299 2181094 110 + 6537648
--CUUCGAUUUGCUCUAA--CCCCGCGAGCGACGCGGGGUCGGGCCGUUCCUAUACUGCGACAUAAGGUCGCAUAGGUCGGCCGAGCACCAGGUGGCGCUGUCCAUGCGCGCCC------
--........(((((..(--(((((((.....))))))))..(((((..((((...((((((.....)))))))))).))))))))))...((((.(((.......))))))).------ ( -56.20)
>pfo.2488 1663737 102 + 6438405
-----CGAUUUGCUCUAAGCCCCUACCACCUGUGCGG--UUAAGACCUUUCUAUACUGCGACAUAAGGUCGCACA-----------CAAUCUGAAGACCUGUAUUUGCUCGGCCGAUUGG
-----(((((.(((...(((...(((....(((((((--(..(((....)))..))))).)))..(((((...((-----------.....))..))))))))...))).))).))))). ( -23.30)
>consensus
__CUUCGAUUUGCUCUAA__CCCCGCGAGCGACGCGGG_UCGGGCCGUUCCUAUACUGCGACAUAAGGUCGCAUAGGUCGGCCGAGCACCAGGUGGCGCUGUCCAUGCGCGCCC______
..........(((((......((((((.....))))))....(((((..((((...((((((.....)))))))))).)))))))))).......((((.......)))).......... (-25.83 = -30.17 +   4.34)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:17:44 2007