Locus 138

Sequence ID pao.1561
Location 2,977,268 – 2,977,400
Length 132
Max. P 0.963481
window623 window624 window625

overview

Window 3

Location 2,977,268 – 2,977,381
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.48
Mean single sequence MFE -33.91
Consensus MFE -16.92
Energy contribution -16.37
Covariance contribution -0.55
Combinations/Pair 1.30
Mean z-score -2.13
Structure conservation index 0.50
SVM decision value 1.42
SVM RNA-class probability 0.952174
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1561 2977268 113 + 6264404
GACCAUCC----GGUCACUCUUA-GAC-CUUCGUGUAGUAGUCUUGAAAAAACACUACAAAACGUUUGAC-GACGGAUUUUUUCCAGAGCAUGAUGGCCCCGCUCCCGCUAAUCAGGGGC
((((....----)))).((((((-(((-.....((((((.((.((....))))))))))....)))))).-...(((.....))).))).......(((((..............))))) ( -29.24)
>pss.1912 3825429 113 + 6093698
GACUGGCC----GGUCG-ACUUCUCAC-AAAUAUGUAGUGAUUUAAAAAAAGCACUACAAAACGUUUGAC-GCCCCCAGAAGUGCGAGGCAUGAUUGCCUCGCUCCCGCUAAUCAGAGGC
((.((((.----((...-((((((...-.....(((((((.(((....))).)))))))...((.....)-).....))))))((((((((....)))))))).)).)))).))...... ( -37.10)
>pfo.2115 4070631 113 + 6438405
GACUGAUU----AGUCG-UAUUA-GACGAAAGAUGUAGUGCUUGAAAAAAAGCACUACAAAACGUUUGAC-GAGCCAAAAAAGCGAAGGCAUGAUGGCCUCGCUCCCGCUAAUCAGAGGC
..((((((----((.((-..(((-((((.....((((((((((......))))))))))...))))))).-..........(((((.(((......))))))))..)))))))))).... ( -42.60)
>pf5.2365 4496836 113 + 7074893
GACUGAUU----AGUCG-UAUUA-GACCAAAUAUGUAGUGCCGCAAAAAAAGCACUACAAAACAUUUGAC-GAGCCAAAAAACCGCGGGCAUGAUGGCCUCGCUCCCGCUAAUCAGGGGC
..((((((----((.((-.....-...(((((.((((((((..........))))))))....)))))..-.............((((((......))).)))...)))))))))).... ( -33.20)
>psp.1823 3605972 112 + 5928787
GACUCACC----AGUCU-AACUA-CGC-AAUUAUGUAGUGAGAUUAAAGAAGCACUACAAAUUGUUUGAC-GACCCCGAUACCCCGAGGCAUGAUUGCCUCGCUCCCGCUGAUCGGAGGC
((((....----)))).-.....-.((-((((.(((((((...((....)).))))))))))))).....-..(((((((.....((((((....))))))((....))..))))).)). ( -34.00)
>pel.2001 3757331 117 + 5888780
-ACUGACCGCAGAGUCG-CAUUA-GACCAAAGAUGUAGUAAGCGCAAAAAAGCACUACAAAACAUUUGACAGGCUCUUUUUGGCAAAGGCAUGAUGGCCUCGCUCCCGCUAAUCAGAGGC
-.((((..((((((((.-..(((-((.......((((((..((........)))))))).....)))))..))))))....(((..((((......)))).)))...))...)))).... ( -27.30)
>consensus
GACUGACC____AGUCG_UAUUA_GAC_AAAUAUGUAGUGAUCUAAAAAAAGCACUACAAAACGUUUGAC_GACCCAAAAAACCCAAGGCAUGAUGGCCUCGCUCCCGCUAAUCAGAGGC
((((........)))).................(((((((............)))))))...(.(((((.................((((......)))).((....))...))))).). (-16.92 = -16.37 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,977,268 – 2,977,381
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.48
Mean single sequence MFE -37.04
Consensus MFE -19.63
Energy contribution -18.97
Covariance contribution -0.66
Combinations/Pair 1.32
Mean z-score -2.02
Structure conservation index 0.53
SVM decision value 1.34
SVM RNA-class probability 0.943745
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1561 2977268 113 - 6264404
GCCCCUGAUUAGCGGGAGCGGGGCCAUCAUGCUCUGGAAAAAAUCCGUC-GUCAAACGUUUUGUAGUGUUUUUUCAAGACUACUACACGAAG-GUC-UAAGAGUGACC----GGAUGGUC
((.((((.....)))).))..(((((((.(((((((((.....)))...-.....((.(((((((((((((.....)))).)))))).))).-)).-..))))))...----.))))))) ( -33.20)
>pss.1912 3825429 113 - 6093698
GCCUCUGAUUAGCGGGAGCGAGGCAAUCAUGCCUCGCACUUCUGGGGGC-GUCAAACGUUUUGUAGUGCUUUUUUUAAAUCACUACAUAUUU-GUGAGAAGU-CGACC----GGCCAGUC
......((((.((.((.((((((((....))))))))((((((.(((((-(.....))))))((((((.(((....))).))))))......-...))))))-...))----.)).)))) ( -40.50)
>pfo.2115 4070631 113 - 6438405
GCCUCUGAUUAGCGGGAGCGAGGCCAUCAUGCCUUCGCUUUUUUGGCUC-GUCAAACGUUUUGUAGUGCUUUUUUUCAAGCACUACAUCUUUCGUC-UAAUA-CGACU----AAUCAGUC
....((((((((((((((((((((......))).))))))).((((...-.))))(((...((((((((((......)))))))))).....))).-.....-)).))----)))))).. ( -39.90)
>pf5.2365 4496836 113 - 7074893
GCCCCUGAUUAGCGGGAGCGAGGCCAUCAUGCCCGCGGUUUUUUGGCUC-GUCAAAUGUUUUGUAGUGCUUUUUUUGCGGCACUACAUAUUUGGUC-UAAUA-CGACU----AAUCAGUC
....((((((((((...(((((.(((....(((...)))....))))))-))((((((...(((((((((........)))))))))))))))...-.....-)).))----)))))).. ( -39.40)
>psp.1823 3605972 112 - 5928787
GCCUCCGAUCAGCGGGAGCGAGGCAAUCAUGCCUCGGGGUAUCGGGGUC-GUCAAACAAUUUGUAGUGCUUCUUUAAUCUCACUACAUAAUU-GCG-UAGUU-AGACU----GGUGAGUC
(((.((((((.((....))((((((....))))))...).)))))((((-......((((((((((((............))))))).))))-)..-.....-.))))----)))..... ( -34.74)
>pel.2001 3757331 117 - 5888780
GCCUCUGAUUAGCGGGAGCGAGGCCAUCAUGCCUUUGCCAAAAAGAGCCUGUCAAAUGUUUUGUAGUGCUUUUUUGCGCUUACUACAUCUUUGGUC-UAAUG-CGACUCUGCGGUCAGU-
....((((((.(((((.((.((((((.((.((((((.....)))).)).))....((((...(((((((......)))).))).))))...)))))-)...)-)...))))))))))).- ( -34.50)
>consensus
GCCUCUGAUUAGCGGGAGCGAGGCCAUCAUGCCUUGGACUAUUUGGGUC_GUCAAACGUUUUGUAGUGCUUUUUUUAAAUCACUACAUAUUU_GUC_UAAUA_CGACU____GGUCAGUC
((.((((.....)))).))(((((......)))))..........................(((((((............))))))).................((((........)))) (-19.63 = -18.97 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,977,290 – 2,977,400
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.51
Mean single sequence MFE -38.56
Consensus MFE -21.53
Energy contribution -21.51
Covariance contribution -0.02
Combinations/Pair 1.33
Mean z-score -2.11
Structure conservation index 0.56
SVM decision value 1.55
SVM RNA-class probability 0.963481
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1561 2977290 110 + 6264404
-CUUCGUGUAGUAGUCUUGAAAAAACACUACAAAACGUUUGAC-GACGGAUUUUUUCCAGAGCAUGAUGGCCCCGCUCCCGCUAAUCAGGGGCUCUGAAA--------CGACGAGCUCCC
-.((((((((((.((.((....)))))))))....(((((...-...(((.....)))(((((.(((((((.........))).))))...))))).)))--------)))))))..... ( -28.30)
>pss.1912 3825451 118 + 6093698
-AAAUAUGUAGUGAUUUAAAAAAAGCACUACAAAACGUUUGAC-GCCCCCAGAAGUGCGAGGCAUGAUUGCCUCGCUCCCGCUAAUCAGAGGCUUUGCAAAAAGCCUUCGAGUCGCCGCU
-.....(((((((.(((....))).)))))))........(((-......((..(.((((((((....)))))))).)...))..((..(((((((....)))))))..)))))...... ( -40.00)
>pfo.2115 4070652 119 + 6438405
GAAAGAUGUAGUGCUUGAAAAAAAGCACUACAAAACGUUUGAC-GAGCCAAAAAAGCGAAGGCAUGAUGGCCUCGCUCCCGCUAAUCAGAGGCCCUGGCAAGGGCCUUCGAAGCGCUGCU
......((((((((((......))))))))))...((.....)-)(((......(((((.(((......))))))))..((((..((..(((((((....)))))))..))))))..))) ( -49.00)
>pf5.2365 4496857 119 + 7074893
CAAAUAUGUAGUGCCGCAAAAAAAGCACUACAAAACAUUUGAC-GAGCCAAAAAACCGCGGGCAUGAUGGCCUCGCUCCCGCUAAUCAGGGGCCCUGGCAAGGGCCUUCGGAUCGCCGCU
(((((.((((((((..........))))))))....))))).(-((.((........(((((..(((.....)))..)))))......((((((((....)))))))).)).)))..... ( -41.00)
>ppk.2374 4653090 120 + 6181863
CAAAGAUGUAGUAAGGACAAAAAAGCACUACAAAACAUUUGACAGGGUCUUUUUCCCAAGGGCAUGAUGGCCUCGCUCCCGCUAAUCAGGGGCCCUGGCAAGGGCCUUCGGGGCGCGCUC
((((..((((((..............)))))).....))))...(((.......)))..((((......))))((((((((.......((((((((....))))))))))))).)))... ( -36.95)
>pel.2001 3757355 120 + 5888780
CAAAGAUGUAGUAAGCGCAAAAAAGCACUACAAAACAUUUGACAGGCUCUUUUUGGCAAAGGCAUGAUGGCCUCGCUCCCGCUAAUCAGAGGCCCUGGCAAGGGUCUUCGGAGCGCCCUC
((((..((((((..((........)))))))).....)))).............(((..((((......)))).(((((.........((((((((....)))))))).))))))))... ( -36.10)
>consensus
CAAAGAUGUAGUAAUCGAAAAAAAGCACUACAAAACAUUUGAC_GACCCAAUAAACCAAAGGCAUGAUGGCCUCGCUCCCGCUAAUCAGAGGCCCUGGCAAGGGCCUUCGAAGCGCCCCC
......((((((..............))))))...........................((((......)))).......((...((..(((((((....)))))))..))...)).... (-21.53 = -21.51 +  -0.02)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:14:33 2007