Locus 118

Sequence ID pao.1533
Location 2,918,563 – 2,918,689
Length 126
Max. P 0.968268
window570 window571 window572

overview

Window 0

Location 2,918,563 – 2,918,679
Length 116
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.33
Mean single sequence MFE -50.88
Consensus MFE -36.95
Energy contribution -37.78
Covariance contribution 0.83
Combinations/Pair 1.12
Mean z-score -4.19
Structure conservation index 0.73
SVM decision value 1.62
SVM RNA-class probability 0.967784
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1533 2918563 116 + 6264404
AAAAAGCCCCGUAACUCAC-UGAGCUACGGGG-CUUUCC-UGUUGGAGGCUGAGGUCGGAAUCGAACCGGCGUUCACGGAUUUGCAAUCCGGUGCAUAACCACUCUGCUACUCAGCCUU
..(((((((((((.(((..-.))).)))))))-))))..-.....((((((((((((((.......)))))((...(((((.....)))))..))...............))))))))) ( -50.40)
>pau.1477 3872503 116 - 6537648
AAAAAGCCCCGUAACUCAC-UGAGCUACGGGG-CUUUCC-UGUUGGAGGCUGAGGUCGGAAUCGAACCGGCGUUCACGGAUUUGCAAUCCGGUGCAUAACCACUCUGCUACUCAGCCUU
..(((((((((((.(((..-.))).)))))))-))))..-.....((((((((((((((.......)))))((...(((((.....)))))..))...............))))))))) ( -50.40)
>pel.1299 3520912 117 - 5888780
GAAAAACCCCGCAGA-CCUGUGAUCUGCGGGG-UUUCGAAUGAUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGACGGAUUUGCAAUCCGGAGCAUAACCACUUUGCUACUCGGCCUC
...((((((((((((-.......)))))))))-))).........((((((((((((((.......))))).....(((((.....))))).((((.........)))).))))))))) ( -53.80)
>ppk.2263 4427473 106 + 6181863
GAAAAACCCCGCAAC-CUCAAUGGCUGCGGGGCUUUCGAAUGGUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGACGGAUUUGCAAUCCGGAGCAUAACCACUUUG------------
((((..(((((((.(-(.....)).))))))).))))....(((((..((((.(.(((....))).)))))((...(((((.....)))))..))....)))))...------------ ( -41.80)
>pf5.2093 3982007 116 + 7074893
AAAAAACCCCGUAGA-CGU-UAAUCUACGGGG-UUUUCAAGGGUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGGCGGAUUUGCAAUCCGCUGCAUAACCAUUUUGCUACUCGGCCCC
..(((((((((((((-...-...)))))))))-)))).......((.((((((((((((.......)))))((((.(((((.....)))))))))...............))))))))) ( -54.40)
>pst.1776 3351504 116 + 6397126
AAAAAACCCCGCAGA-CGU-UAAUCUGCGGGG-CUUUGAAUAGUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGGCGGAUUUGCAAUCCGCUGCAUAACCAUUUUGCUACUCGGCCUC
..(((.(((((((((-...-...)))))))))-.)))........((((((((((((((.......)))))((((.(((((.....)))))))))...............))))))))) ( -54.50)
>consensus
AAAAAACCCCGCAAA_CAC_UGAGCUACGGGG_CUUUCAAUGGUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGACGGAUUUGCAAUCCGGUGCAUAACCACUUUGCUACUCGGCCUC
..(((((((((((............))))))).))))........((((((((((((((.......)))))((...(((((.....)))))..))...............))))))))) (-36.95 = -37.78 +   0.83)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,918,563 – 2,918,679
Length 116
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.33
Mean single sequence MFE -51.38
Consensus MFE -39.11
Energy contribution -38.00
Covariance contribution -1.11
Combinations/Pair 1.26
Mean z-score -4.46
Structure conservation index 0.76
SVM decision value 1.62
SVM RNA-class probability 0.968268
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1533 2918563 116 - 6264404
AAGGCUGAGUAGCAGAGUGGUUAUGCACCGGAUUGCAAAUCCGUGAACGCCGGUUCGAUUCCGACCUCAGCCUCCAACA-GGAAAG-CCCCGUAGCUCA-GUGAGUUACGGGGCUUUUU
.((((((((...(.((((.(......(((((.(..(......)..)...))))).).)))).)..))))))))......-((((((-(((((((((((.-..))))))))))))))))) ( -52.00)
>pau.1477 3872503 116 + 6537648
AAGGCUGAGUAGCAGAGUGGUUAUGCACCGGAUUGCAAAUCCGUGAACGCCGGUUCGAUUCCGACCUCAGCCUCCAACA-GGAAAG-CCCCGUAGCUCA-GUGAGUUACGGGGCUUUUU
.((((((((...(.((((.(......(((((.(..(......)..)...))))).).)))).)..))))))))......-((((((-(((((((((((.-..))))))))))))))))) ( -52.00)
>pel.1299 3520912 117 + 5888780
GAGGCCGAGUAGCAAAGUGGUUAUGCUCCGGAUUGCAAAUCCGUCUACGCCGGUUCGAUUCCGACCUCGGCCUCCAUCAUUCGAAA-CCCCGCAGAUCACAGG-UCUGCGGGGUUUUUC
(((((((((..((..(((((...(((........)))...))).))..))(((.......)))..)))))))))........((((-((((((((((.....)-))))))))))))).. ( -53.60)
>ppk.2263 4427473 106 - 6181863
------------CAAAGUGGUUAUGCUCCGGAUUGCAAAUCCGUCUACGCCGGUUCGAUUCCGACCUCGGCCUCCACCAUUCGAAAGCCCCGCAGCCAUUGAG-GUUGCGGGGUUUUUC
------------...((((((.......(((((.....))))).....(((((.(((....))).).))))....)))))).(((((((((((((((.....)-)))))))))))))). ( -45.10)
>pf5.2093 3982007 116 - 7074893
GGGGCCGAGUAGCAAAAUGGUUAUGCAGCGGAUUGCAAAUCCGCCUACGCCGGUUCGAUUCCGACCUCGGCCUCCACCCUUGAAAA-CCCCGUAGAUUA-ACG-UCUACGGGGUUUUUU
((((((((((((((.........))).((((((.....)))))).)))...(((.((....))))))))))).))......(((((-((((((((((..-..)-)))))))))))))). ( -52.00)
>pst.1776 3351504 116 - 6397126
GAGGCCGAGUAGCAAAAUGGUUAUGCAGCGGAUUGCAAAUCCGCCUACGCCGGUUCGAUUCCGACCUCGGCCUCCACUAUUCAAAG-CCCCGCAGAUUA-ACG-UCUGCGGGGUUUUUU
((((((((((((((.........))).((((((.....)))))).)))...(((.((....)))))))))))))........((((-((((((((((..-..)-))))))))))))).. ( -53.60)
>consensus
GAGGCCGAGUAGCAAAGUGGUUAUGCACCGGAUUGCAAAUCCGUCUACGCCGGUUCGAUUCCGACCUCGGCCUCCACCAUUCAAAA_CCCCGCAGAUCA_ACG_GCUACGGGGUUUUUU
.((((((((..(((.........)))..((((...(.((((.((....)).)))).)..))))..)))))))).........((((.(((((((((........))))))))))))).. (-39.11 = -38.00 +  -1.11)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 2,918,574 – 2,918,689
Length 115
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 77.16
Mean single sequence MFE -39.80
Consensus MFE -30.70
Energy contribution -30.03
Covariance contribution -0.67
Combinations/Pair 1.14
Mean z-score -1.79
Structure conservation index 0.77
SVM decision value 1.45
SVM RNA-class probability 0.955029
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1533 2918574 115 + 6264404
UAACUCAC-UGAGCUACGGGGCUU-UCC-UGUUGGAGGCUGAGGUCGGAAUCGAACCGGCGUUCACGGAUUUGCAAUCCGGUGCAUAACCACUCUGCUACUCAGCCUU-UGAGCGAAGC
.......(-(..((..((((....-.))-))(..((((((((((((((.......)))))((...(((((.....)))))..))...............)))))))))-..)))..)). ( -39.90)
>pau.1477 3872514 115 - 6537648
UAACUCAC-UGAGCUACGGGGCUU-UCC-UGUUGGAGGCUGAGGUCGGAAUCGAACCGGCGUUCACGGAUUUGCAAUCCGGUGCAUAACCACUCUGCUACUCAGCCUU-UGAGCGAAGC
.......(-(..((..((((....-.))-))(..((((((((((((((.......)))))((...(((((.....)))))..))...............)))))))))-..)))..)). ( -39.90)
>pel.1299 3520923 109 - 5888780
CAGA-CCUGUGAUCUGCGGGGUUU-CGAAUGAUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGACGGAUUUGCAAUCCGGAGCAUAACCACUUUGCUACUCGGCCUC-AAA-------
....-(((((.....)))))....-.........((((((((((((((.......))))).....(((((.....))))).((((.........)))).)))))))))-...------- ( -41.30)
>pf5.2093 3982018 109 + 7074893
UAGA-CGU-UAAUCUACGGGGUUU-UCAAGGGUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGGCGGAUUUGCAAUCCGCUGCAUAACCAUUUUGCUACUCGGCCCC-AAA------U
....-(((-......)))......-.......(((.((((((((((((.......)))))((((.(((((.....)))))))))...............)))))))))-)..------. ( -39.00)
>pst.1776 3351515 109 + 6397126
CAGA-CGU-UAAUCUGCGGGGCUU-UGAAUAGUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGGCGGAUUUGCAAUCCGCUGCAUAACCAUUUUGCUACUCGGCCUC-AUA------C
....-(((-......)))..(((.-.....))).((((((((((((((.......)))))((((.(((((.....)))))))))...............)))))))))-...------. ( -40.70)
>pfo.1799 3506720 94 + 6438405
-------------------AGCUUGUUUAUAGUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGGCGGAUUUGCAAUCCGCUGCAUAACCAUUUUGCUACUCGGCCUCAAAA------C
-------------------...............((((((((((((((.......)))))((((.(((((.....)))))))))...............)))))))))....------. ( -38.00)
>consensus
UAGA_CAU_UGAUCUACGGGGCUU_UCAAUGGUGGAGGCCGAGGUCGGAAUCGAACCGGCGUAGACGGAUUUGCAAUCCGCUGCAUAACCACUUUGCUACUCGGCCUC_AAA______C
..................................((((((((((((((.......)))))((.(.(((((.....)))))).))...............)))))))))........... (-30.70 = -30.03 +  -0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:13:37 2007