Locus 42

Sequence ID pao.359
Location 630,395 – 630,526
Length 131
Max. P 0.962914
window201 window202 window203

overview

Window 1

Location 630,395 – 630,453
Length 58
Sequences 6
Columns 62
Reading direction forward
Mean pairwise identity 80.60
Mean single sequence MFE -24.15
Consensus MFE -17.82
Energy contribution -17.98
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.93
Structure conservation index 0.74
SVM decision value 1.44
SVM RNA-class probability 0.954080
Prediction RNA

Download alignment: ClustalW | MAF

>pao.359 630395 58 + 6264404
UAGAAAGCGCAAAGCCGCGCAGU-GCGCGGCU-UUG--AAGGUGGUGGGCCCACACGGACUC
.......(((((((((((((...-))))))))-)))--...((((.....)))).))..... ( -24.80)
>pau.363 640368 58 + 6537648
UAGAAAGCGCAAAGCCGCGCAAU-GCGCGGCU-UUG--AAGGUGGUGGGCCCACACGGACUC
.......(((((((((((((...-))))))))-)))--...((((.....)))).))..... ( -24.80)
>pss.2807 586743 59 - 6093698
CAAAAACAAAAAAGCCGCGCAAU-GCGCGGCUUUCA--AAGGUGGUGGGCCCACACGGACUC
..........((((((((((...-))))))))))..--...((((.....))))........ ( -21.10)
>pel.208 431574 58 + 5888780
CAAAAACGCAAAAGCCGCGCAAU-GCGCGGCU-UCG--AAGAUGGUGGGCCCACACGGACUC
......((...(((((((((...-))))))))-)..--......(((....))).))..... ( -19.30)
>pf5.3416 619064 59 - 7074893
CAGAAAAGCGAAAGCCGCGCAUU-GCGCGGCUUUCU--UGUUUGGUGGGCCCACACGGACUU
.........(((((((((((...-))))))))))).--.((((((((....))).))))).. ( -28.10)
>pfo.3036 646722 62 - 6438405
CAGAUACGAAAAAGCCGCACAUAAGCGCGGCUUUUUCAUGUUUGGUGGGCCCACACGGACUU
((((((.(((((((((((.(....).))))))))))).))))))(((....)))........ ( -26.80)
>consensus
CAGAAACGAAAAAGCCGCGCAAU_GCGCGGCU_UCG__AAGGUGGUGGGCCCACACGGACUC
............((((((((....))))))))............(((....)))........ (-17.82 = -17.98 +   0.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 630,395 – 630,453
Length 58
Sequences 6
Columns 62
Reading direction reverse
Mean pairwise identity 80.60
Mean single sequence MFE -25.60
Consensus MFE -18.50
Energy contribution -18.37
Covariance contribution -0.14
Combinations/Pair 1.08
Mean z-score -3.31
Structure conservation index 0.72
SVM decision value 1.55
SVM RNA-class probability 0.962914
Prediction RNA

Download alignment: ClustalW | MAF

>pao.359 630395 58 - 6264404
GAGUCCGUGUGGGCCCACCACCUU--CAA-AGCCGCGC-ACUGCGCGGCUUUGCGCUUUCUA
(((..(((((((.....))))...--.((-((((((((-...)))))))))))))..))).. ( -26.30)
>pau.363 640368 58 - 6537648
GAGUCCGUGUGGGCCCACCACCUU--CAA-AGCCGCGC-AUUGCGCGGCUUUGCGCUUUCUA
(((..(((((((.....))))...--.((-((((((((-...)))))))))))))..))).. ( -26.30)
>pss.2807 586743 59 + 6093698
GAGUCCGUGUGGGCCCACCACCUU--UGAAAGCCGCGC-AUUGCGCGGCUUUUUUGUUUUUG
......(.((((.....)))))..--.(((((((((((-...)))))))))))......... ( -23.00)
>pel.208 431574 58 - 5888780
GAGUCCGUGUGGGCCCACCAUCUU--CGA-AGCCGCGC-AUUGCGCGGCUUUUGCGUUUUUG
(((..(((((((.....))))...--.((-((((((((-...)))))))))).)))..))). ( -23.20)
>pf5.3416 619064 59 + 7074893
AAGUCCGUGUGGGCCCACCAAACA--AGAAAGCCGCGC-AAUGCGCGGCUUUCGCUUUUCUG
((((..((.(((.....))).)).--.(((((((((((-...)))))))))))))))..... ( -25.90)
>pfo.3036 646722 62 + 6438405
AAGUCCGUGUGGGCCCACCAAACAUGAAAAAGCCGCGCUUAUGUGCGGCUUUUUCGUAUCUG
......((.(((.....))).))(((((((((((((((....)))))))))))))))..... ( -28.90)
>consensus
GAGUCCGUGUGGGCCCACCACCUU__CAA_AGCCGCGC_AUUGCGCGGCUUUUCCGUUUCUG
..((((....))))................((((((((....))))))))............ (-18.50 = -18.37 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 3

Location 630,453 – 630,526
Length 73
Sequences 6
Columns 77
Reading direction reverse
Mean pairwise identity 87.30
Mean single sequence MFE -22.42
Consensus MFE -20.10
Energy contribution -20.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.90
SVM decision value 0.44
SVM RNA-class probability 0.737080
Prediction RNA

Download alignment: ClustalW | MAF

>pao.359 630453 73 - 6264404
UCCGCCG----ACCUUCUGGGGGCCUAUAGCUCAGUCGGUUAGAGCAGAGGACUCAUAAUCCUUUGGUCCACGGUUC
...((((----.((....))(((((....((((.........))))((((((.......))))))))))).)))).. ( -24.80)
>pau.363 640426 67 - 6537648
----CCG----AC--UCUGGGGGCCUAUAGCUCAGUCGGUUAGAGCAGAGGACUCAUAAUCCUUUGGUCCACGGUUC
----(((----((--(....((((.....))))))))))...((.(((((((.......))))))).))........ ( -21.70)
>pss.2807 586802 68 + 6093698
-----CGACCUA----CUGAGGGCCCAUAGCUCAGUUGGUUAGAGCAGAGGACUCAUAAUCCUUUGGUCCACGGUUC
-----.((((.(----(((((.........)))))).)))).((.(((((((.......))))))).))........ ( -22.50)
>pel.208 431632 66 - 5888780
-------ACCUG----CUGAGGGCCUAUAGCUCAGUCGGUUAGAGCAGAGGACUCAUAAUCCUUUGGUCCACGGUUC
-------....(----(((.(((((....((((.........))))((((((.......))))))))))).)))).. ( -21.90)
>pf5.3416 619123 66 + 7074893
-------GCCUA----CUGAGGGCCUAUAGCUCAGUUGGUUAGAGCAGAGGACUCAUAAUCCUUUGGUCCACGGUUC
-------....(----(((.(((((....((((.........))))((((((.......))))))))))).)))).. ( -21.60)
>psp.2723 5323393 68 - 5928787
-----CGGCCUA----CUGAGGGCCCAUAGCUCAGUUGGUUAGAGCAGAGGACUCAUAAUCCUUUGGUCCACGGUUC
-----.((((.(----(((((.........)))))).)))).((.(((((((.......))))))).))........ ( -22.00)
>consensus
_____CG_CCUA____CUGAGGGCCUAUAGCUCAGUCGGUUAGAGCAGAGGACUCAUAAUCCUUUGGUCCACGGUUC
................(((.(((((....((((.........))))((((((.......))))))))))).)))... (-20.10 = -20.10 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:06:53 2007