Locus 120

Sequence ID pao.1535
Location 2,923,148 – 2,923,305
Length 157
Max. P 0.999898
window576 window577 window578 window579

overview

Window 6

Location 2,923,148 – 2,923,219
Length 71
Sequences 6
Columns 75
Reading direction forward
Mean pairwise identity 53.94
Mean single sequence MFE -28.45
Consensus MFE -23.00
Energy contribution -19.85
Covariance contribution -3.15
Combinations/Pair 1.96
Mean z-score -6.12
Structure conservation index 0.81
SVM decision value 1.72
SVM RNA-class probability 0.973936
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1535 2923148 71 + 6264404
CGGAACGAAAAAAGGGCCCGAAGGCCCUUUCU-CAAUGAUCUACAGACUUCA--UUGGAACUCU-AUAGAUCUAU
......((..((((((((....)))))))).)-)...((((((.(((.(((.--...))).)))-.))))))... ( -23.90)
>pau.1474 3878868 64 - 6537648
CGAAACGAAAAAAGGGCCCUAAGGCCCUUUUUUCAAUGAUCUACAGGC----------AAGCCU-GUGGAUCUAU
......((((((((((((....))))))))))))...((((((((((.----------...)))-)))))))... ( -36.40)
>pss.1735 3473676 70 + 6093698
AGAAACGAAAAAAGACGCCUAGGCGUCUUUUU-UGCUGAUUCACAAAGCCCG---GAGGGUUCA-GUGAAUCAAU
.......(((((((((((....))))))))))-)..((((((((..(((((.---..)))))..-)))))))).. ( -30.90)
>pf5.2155 4107880 70 + 7074893
AGAAACGAAAAAAGGACCCGAAGGUCCUUUUU-UCGAUCGCUGCAGAAUUCG---UGGAACUCU-GCAGCGCUAU
.....(((((((((((((....))))))))))-)))..(((((((((.(((.---..))).)))-)))))).... ( -36.00)
>psp.1406 3222012 71 - 5928787
AAAAACGAAAAAAGACGCCUAAGCGUCUUUUU-UGUUAAUCCCAUAUGCCUC---UUGUGCAUACAUGGAUUUAU
...(((.(((((((((((....))))))))))-))))(((((..((((((..---..).)))))...)))))... ( -22.60)
>pst.1796 3397686 63 + 6397126
-------AAAAAAGAGGCAUAAGCCUCUUUUU-C-UGGUUUCCACACACUUCAAUUGAAGCGCG-UUGAA--AAU
-------.((((((((((....))))))))))-.-...((((.((.(.((((....)))).).)-).)))--).. ( -20.90)
>consensus
AGAAACGAAAAAAGAGCCCUAAGCCCCUUUUU_CAAUGAUCCACAAAACUCC___UGGAACUCU_GUGGAUCUAU
........((((((((((....)))))))))).....((((((((((.(((......))).))).)))))))... (-23.00 = -19.85 +  -3.15)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,923,148 – 2,923,219
Length 71
Sequences 6
Columns 75
Reading direction reverse
Mean pairwise identity 53.94
Mean single sequence MFE -32.77
Consensus MFE -29.50
Energy contribution -25.88
Covariance contribution -3.62
Combinations/Pair 2.04
Mean z-score -7.31
Structure conservation index 0.90
SVM decision value 1.62
SVM RNA-class probability 0.967977
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1535 2923148 71 - 6264404
AUAGAUCUAU-AGAGUUCCAA--UGAAGUCUGUAGAUCAUUG-AGAAAGGGCCUUCGGGCCCUUUUUUCGUUCCG
...(((((((-(((.(((...--.))).))))))))))...(-((((((((((....)))))))))))....... ( -36.40)
>pau.1474 3878868 64 + 6537648
AUAGAUCCAC-AGGCUU----------GCCUGUAGAUCAUUGAAAAAAGGGCCUUAGGGCCCUUUUUUCGUUUCG
...((((.((-(((...----------.))))).))))...((((((((((((....))))))))))))...... ( -33.40)
>pss.1735 3473676 70 - 6093698
AUUGAUUCAC-UGAACCCUC---CGGGCUUUGUGAAUCAGCA-AAAAAGACGCCUAGGCGUCUUUUUUCGUUUCU
..((((((((-.((.(((..---.))).)).))))))))(((-((((((((((....))))))))))).)).... ( -28.70)
>pf5.2155 4107880 70 - 7074893
AUAGCGCUGC-AGAGUUCCA---CGAAUUCUGCAGCGAUCGA-AAAAAGGACCUUCGGGUCCUUUUUUCGUUUCU
....((((((-(((((((..---.)))))))))))))..(((-((((((((((....)))))))))))))..... ( -43.40)
>psp.1406 3222012 71 + 5928787
AUAAAUCCAUGUAUGCACAA---GAGGCAUAUGGGAUUAACA-AAAAAGACGCUUAGGCGUCUUUUUUCGUUUUU
...(((((.(((((((....---...))))))))))))((((-((((((((((....))))))))))).)))... ( -25.40)
>pst.1796 3397686 63 - 6397126
AUU--UUCAA-CGCGCUUCAAUUGAAGUGUGUGGAAACCA-G-AAAAAGAGGCUUAUGCCUCUUUUUU-------
..(--(((.(-((((((((....))))))))).))))...-(-((((((((((....)))))))))))------- ( -29.30)
>consensus
AUAGAUCCAC_AGAGCUCCA___CGAGCUCUGUAGAUCAACA_AAAAAGAGCCUUAGGCCCCUUUUUUCGUUUCU
...(((((((.(((((((......)))))))))))))).....((((((((((....))))))))))........ (-29.50 = -25.88 +  -3.62)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,923,219 – 2,923,305
Length 86
Sequences 6
Columns 86
Reading direction forward
Mean pairwise identity 95.52
Mean single sequence MFE -30.08
Consensus MFE -29.90
Energy contribution -29.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.99
SVM decision value 3.88
SVM RNA-class probability 0.999684
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1535 2923219 86 + 6264404
AUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAUCGUCU
.....(((((((((..(((.......)))(((((((((....)))...))))))((((........))))..))))))).)).... ( -30.40)
>pau.1474 3878932 86 - 6537648
AUCUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAUCGUCU
.....(((((((((..(((.......)))(((((((((....)))...))))))((((........))))..))))))).)).... ( -30.40)
>pss.1735 3473746 83 + 6093698
GUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAUUG---
.......(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))....--- ( -29.90)
>pf5.2155 4107950 83 + 7074893
GUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAACG---
....(..(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))..).--- ( -30.00)
>pfo.2462 4728948 83 + 6438405
AUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAUG---
.......(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))....--- ( -29.90)
>pst.1796 3397749 83 + 6397126
AUCUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAUUG---
.......(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))....--- ( -29.90)
>consensus
AUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAUCG___
.......(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))....... (-29.90 = -29.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,923,219 – 2,923,305
Length 86
Sequences 6
Columns 86
Reading direction reverse
Mean pairwise identity 95.52
Mean single sequence MFE -33.92
Consensus MFE -33.60
Energy contribution -33.60
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.99
SVM decision value 4.44
SVM RNA-class probability 0.999898
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1535 2923219 86 - 6264404
AGACGAUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAU
....((.(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))))..... ( -34.20)
>pau.1474 3878932 86 + 6537648
AGACGAUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAGAU
....((.(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))))..... ( -34.20)
>pss.1735 3473746 83 - 6093698
---CAAUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAC
---....(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))....... ( -33.60)
>pf5.2155 4107950 83 - 7074893
---CGUUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAC
---.(..(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))..).... ( -34.30)
>pfo.2462 4728948 83 - 6438405
---CAUUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAU
---....(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))....... ( -33.60)
>pst.1796 3397749 83 - 6397126
---CAAUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAGAU
---....(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))....... ( -33.60)
>consensus
___CAAUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAU
.......(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))....... (-33.60 = -33.60 +   0.00)

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 21:13:44 2007