Locus 22

Sequence ID pao.2997
Location 5,666,125 – 5,666,233
Length 108
Max. P 0.998106
window123 window124

overview

Window 3

Location 5,666,125 – 5,666,233
Length 108
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 72.41
Mean single sequence MFE -38.38
Consensus MFE -24.27
Energy contribution -24.72
Covariance contribution 0.45
Combinations/Pair 1.28
Mean z-score -3.30
Structure conservation index 0.63
SVM decision value 2.89
SVM RNA-class probability 0.997592
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2997 5666125 108 + 6264404
CGGGCGAAAAGGGCCGCUAUUGUCGCAAAGCACAAAACAAAAGGCACGGCGGGGGCCGUGCCUUUUGUCUAUCGCGGUGAUUUGUCG--CAGCGCCGGUGGCGCCGCGGA
..((((((....(((((..((((.((...)))))).((((((((((((((....)))))))))))))).....)))))..))))))(--(.(((((...))))).))... ( -52.10)
>pf5.275 6548833 86 - 7074893
CGGAAAAAAAGUGGGGGCAUUUUCUCAGAGCGCGACACAAAAGGCACGGCAAGAGCCGUGCCUUUUAUGUAUCAGGUCAAUUUGUC------------------------
...........((((((....))))))((.(...(((.((((((((((((....)))))))))))).)))....).))........------------------------ ( -30.30)
>pst.3040 5820544 103 + 6397126
CGCUAUAAAAGUGCGCGCAUUUUCUCAGAGCGCGACGCAAAAGGCACGGCAAGCGCCGUGCCUUUUGUCUAUCGAGGCGAUUUGUUAUAAAAAAC--GUUGCGCC-----
((((...((((((....)))))).....))))(((.((((((((((((((....))))))))))))))...))).((((...((((......)))--)...))))----- ( -42.80)
>psp.252 5461780 87 - 5928787
CGCAAUAAAAGUGCCGGCAUUUUCUCAGAGCGCGACGCAAAAGGCACGGCAAGAGCCGUGCCUUUUGUCUAUCGUGCCGAUUUGCCG-----------------------
.(((.......)))(((((...((...(.((((((.((((((((((((((....))))))))))))))...)))))))))..)))))----------------------- ( -42.30)
>pss.264 5641743 87 - 6093698
CGCAAUAAAAGUGCCGGCAUUUUCUCAGAGCUCGACGCAAAAGGCACGGCGAGAGCCGUGCCUUUUGUCUAUCGAGGCGAUUUGCCA-----------------------
.(((.......))).((((...((.(....(((((.((((((((((((((....))))))))))))))...)))))).))..)))).----------------------- ( -41.60)
>pfo.232 5962001 86 - 6438405
CGGAAAAAAAGUGCGGGCAUUUUCUCAGAGCGCGACGCAAAAGGCACGGAUGCAGGUCAGCCUUUUGUCUAUCGGGUCAAUUUGUC------------------------
..((...((((((....)))))).)).((.(.(((.(((((((((...(((....))).)))))))))...)))).))........------------------------ ( -21.20)
>consensus
CGCAAUAAAAGUGCCGGCAUUUUCUCAGAGCGCGACGCAAAAGGCACGGCAAGAGCCGUGCCUUUUGUCUAUCGAGGCGAUUUGUC________________________
...............((((((..(((.((.......((((((((((((((....))))))))))))))...)))))..))..))))........................ (-24.27 = -24.72 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,666,125 – 5,666,233
Length 108
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 72.41
Mean single sequence MFE -36.77
Consensus MFE -22.42
Energy contribution -23.00
Covariance contribution 0.58
Combinations/Pair 1.18
Mean z-score -3.43
Structure conservation index 0.61
SVM decision value 3.01
SVM RNA-class probability 0.998106
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2997 5666125 108 - 6264404
UCCGCGGCGCCACCGGCGCUG--CGACAAAUCACCGCGAUAGACAAAAGGCACGGCCCCCGCCGUGCCUUUUGUUUUGUGCUUUGCGACAAUAGCGGCCCUUUUCGCCCG
..(((((((((...)))))))--)).........(((((.((((((((((((((((....))))))))))))))))......)))))......((((......))))... ( -52.20)
>pf5.275 6548833 86 + 7074893
------------------------GACAAAUUGACCUGAUACAUAAAAGGCACGGCUCUUGCCGUGCCUUUUGUGUCGCGCUCUGAGAAAAUGCCCCCACUUUUUUUCCG
------------------------.............(..((((((((((((((((....))))))))))))))))..).....(((((((..........))))))).. ( -30.70)
>pst.3040 5820544 103 - 6397126
-----GGCGCAAC--GUUUUUUAUAACAAAUCGCCUCGAUAGACAAAAGGCACGGCGCUUGCCGUGCCUUUUGCGUCGCGCUCUGAGAAAAUGCGCGCACUUUUAUAGCG
-----((((....--(((......)))....))))......(.(((((((((((((....))))))))))))))(((((((...........))))).)).......... ( -39.80)
>psp.252 5461780 87 + 5928787
-----------------------CGGCAAAUCGGCACGAUAGACAAAAGGCACGGCUCUUGCCGUGCCUUUUGCGUCGCGCUCUGAGAAAAUGCCGGCACUUUUAUUGCG
-----------------------(((((..(((((.((((.(.(((((((((((((....)))))))))))))))))).)))..)).....)))))(((.......))). ( -41.80)
>pss.264 5641743 87 + 6093698
-----------------------UGGCAAAUCGCCUCGAUAGACAAAAGGCACGGCUCUCGCCGUGCCUUUUGCGUCGAGCUCUGAGAAAAUGCCGGCACUUUUAUUGCG
-----------------------.((((..(((.((((((.(.(((((((((((((....))))))))))))))))))))...))).....)))).(((.......))). ( -39.10)
>pfo.232 5962001 86 + 6438405
------------------------GACAAAUUGACCCGAUAGACAAAAGGCUGACCUGCAUCCGUGCCUUUUGCGUCGCGCUCUGAGAAAAUGCCCGCACUUUUUUUCCG
------------------------........((.(((((.(.((((((((..............))))))))))))).).)).(((((((((....))..))))))).. ( -17.04)
>consensus
________________________GACAAAUCGCCCCGAUAGACAAAAGGCACGGCUCUUGCCGUGCCUUUUGCGUCGCGCUCUGAGAAAAUGCCCGCACUUUUAUUCCG
....................................((((...(((((((((((((....))))))))))))).))))................................ (-22.42 = -23.00 +   0.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:05:30 2007