Locus 140

Sequence ID pao.1081
Location 1,942,978 – 1,943,066
Length 88
Max. P 0.972571
window628 window629

overview

Window 8

Location 1,942,978 – 1,943,066
Length 88
Sequences 6
Columns 88
Reading direction forward
Mean pairwise identity 74.33
Mean single sequence MFE -28.62
Consensus MFE -16.98
Energy contribution -16.87
Covariance contribution -0.11
Combinations/Pair 1.35
Mean z-score -2.08
Structure conservation index 0.59
SVM decision value 1.70
SVM RNA-class probability 0.972571
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1081 1942978 88 + 6264404
CUGUCAGGGGGUUGACAGCUUCGGCUAUGAUAAGCGCUUUGAUUUGCCCGGCCUACCCUGGUCGGGCGAGAGCAUGACCAAGGAUCCC
.......((((((...(((....))).........((((....((((((((((......)))))))))))))).........)))))) ( -35.20)
>pst.2222 2166153 69 - 6397126
UUGUCAGGGGCUUGACAGCUUCGGCUAUGAUAAGCGCUUUGAUUUAGUCGGCCUACCCUGGCCGCGCAC-------------------
..((((((((((((.((((....))..)).))))).)))))))...(((((((......))))).))..------------------- ( -27.20)
>psp.999 1939825 69 + 5928787
UUGUCAGGGACUUGACAGCUUCGGCUAUGAUAAGCGCUUUGAUUUAGUCGGCCUACCCUGGCCGCGCAC-------------------
..(((((....)))))(((....))).......((((...(((...)))((((......))))))))..------------------- ( -25.60)
>pss.1026 1968676 84 + 6093698
UUGUCAGGGACUUGACAGCUUCGGCUAUGAUAAGCGCUUUGAUUUAGUCGGCCUACCCUGGCCGCGCAC--GUAUGUCCAAGGAUC--
..(((..((((...(((((....))).......((((...(((...)))((((......))))))))..--))..))))...))).-- ( -30.90)
>ppk.1676 3301562 84 + 6181863
CUGUCAGCAGCUUGACUGCUUCGGCUAUGAUAGGCCCUUUGAUUCAAUCGGCCUACCCAGGCUGGACAC--ACGCAUUCAAGGAUC--
(((....)))(((((.((((((((((.((.((((((..(((...)))..))))))..)))))))))...--..))).)))))....-- ( -27.30)
>pel.1192 2184291 69 + 5888780
CUGUCGGCAGCUUGACUGCUUCGGCUAUGAUAGGCCCUUUGAUUCAAUCGGCCUACCCGGGCCGGCUAC-------------------
..(((((((((......)))((((....(.((((((..(((...)))..)))))))))))))))))...------------------- ( -25.50)
>consensus
CUGUCAGGGGCUUGACAGCUUCGGCUAUGAUAAGCGCUUUGAUUUAGUCGGCCUACCCUGGCCGCGCAC___________________
((((((..((((.((.....)))))).))))))((((...(((...)))((((......))))))))..................... (-16.98 = -16.87 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,942,978 – 1,943,066
Length 88
Sequences 6
Columns 88
Reading direction reverse
Mean pairwise identity 74.33
Mean single sequence MFE -24.00
Consensus MFE -16.91
Energy contribution -17.22
Covariance contribution 0.31
Combinations/Pair 1.11
Mean z-score -0.95
Structure conservation index 0.70
SVM decision value 0.23
SVM RNA-class probability 0.643381
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1081 1942978 88 - 6264404
GGGAUCCUUGGUCAUGCUCUCGCCCGACCAGGGUAGGCCGGGCAAAUCAAAGCGCUUAUCAUAGCCGAAGCUGUCAACCCCCUGACAG
.((..((((((((..((....))..))))))))....))..((........))(((......))).....((((((......)))))) ( -26.50)
>pst.2222 2166153 69 + 6397126
-------------------GUGCGCGGCCAGGGUAGGCCGACUAAAUCAAAGCGCUUAUCAUAGCCGAAGCUGUCAAGCCCCUGACAA
-------------------..((.((((...((((((((............).)))))))...))))..))(((((......))))). ( -20.70)
>psp.999 1939825 69 - 5928787
-------------------GUGCGCGGCCAGGGUAGGCCGACUAAAUCAAAGCGCUUAUCAUAGCCGAAGCUGUCAAGUCCCUGACAA
-------------------..((.((((...((((((((............).)))))))...))))..))(((((......))))). ( -20.70)
>pss.1026 1968676 84 - 6093698
--GAUCCUUGGACAUAC--GUGCGCGGCCAGGGUAGGCCGACUAAAUCAAAGCGCUUAUCAUAGCCGAAGCUGUCAAGUCCCUGACAA
--....(..((((....--..((((((((......))))((.....))...)))).....(((((....)))))...))))..).... ( -24.00)
>ppk.1676 3301562 84 - 6181863
--GAUCCUUGAAUGCGU--GUGUCCAGCCUGGGUAGGCCGAUUGAAUCAAAGGGCCUAUCAUAGCCGAAGCAGUCAAGCUGCUGACAG
--...............--.((((..((...((((((((..(((...)))..))))))))...))...(((((.....))))))))). ( -25.50)
>pel.1192 2184291 69 - 5888780
-------------------GUAGCCGGCCCGGGUAGGCCGAUUGAAUCAAAGGGCCUAUCAUAGCCGAAGCAGUCAAGCUGCCGACAG
-------------------.....((((...((((((((..(((...)))..))))))))...))))..((((.....))))...... ( -26.60)
>consensus
___________________GUGCCCGGCCAGGGUAGGCCGACUAAAUCAAAGCGCUUAUCAUAGCCGAAGCUGUCAAGCCCCUGACAA
...................((...((((...((((((((............).)))))))...))))..)).((((......)))).. (-16.91 = -17.22 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:14:37 2007