Locus 160

Sequence ID pao.1011
Location 1,803,035 – 1,803,233
Length 198
Max. P 0.997941
window707 window708 window709 window710

overview

Window 7

Location 1,803,035 – 1,803,135
Length 100
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 57.35
Mean single sequence MFE -43.45
Consensus MFE -28.19
Energy contribution -27.50
Covariance contribution -0.69
Combinations/Pair 1.19
Mean z-score -4.69
Structure conservation index 0.65
SVM decision value 2.36
SVM RNA-class probability 0.992928
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1011 1803035 100 + 6264404
------CUCAUUCAAUGGCUUAUUGUUAUCCAUGUCUCA--------------UUCUGAAAAGAAAUAUAACAAGUGAAUUGAGCAAGAAGUUGCGCAGUGCUGUGCAACUUUUUGCGCA
------.....(((((..(...(((((((..........--------------((((....))))..)))))))..).)))))(((((((((((((((....)))))))))))))))... ( -32.10)
>pau.2014 2705870 99 - 6537648
------CGCAUCCGACGGAUAAUUGUUAUCCAUGUCUCG--------------UUUUGAAU-GAAAAAUAACAAGUGAAUUGAGCAAGAAGUUGCGCAGUGCUGUGCAACUUUUUGCGCA
------.((.(((((((((((.....)))))..)))..(--------------((((....-..))))).....).)).....(((((((((((((((....))))))))))))))))). ( -32.70)
>pfo.1173 2331605 118 + 6438405
CACGUCCCCGGGAGCCGGGGACUCCACCGCUCUGGAUCGAGGCUUUGAGCGUUUUUUGAUCAGCCAGGUAGC--UCGAAGUGCGCAAGAAGUUGCGCAGUACUGCGCAACUUCUUGCGCA
...((((((((...))))))))((((......)))).....(((((((((....((((......))))..))--)))))))(((((((((((((((((....))))))))))))))))). ( -66.40)
>pst.3233 216137 95 - 6397126
UACGCCCGCAGUCG-CGGCGACUUGAUCCCCUUACGUUG-----UAAAAAAGCUUUUGGUU-------------------UGCGCAAGAAGUUGCGCACUGUUGCGCAACUUCUUGCGCA
..((((.((....)-))))).........((..(.(((.-----......))).)..))..-------------------((((((((((((((((((....)))))))))))))))))) ( -42.60)
>consensus
______CGCAGUCGACGGCGAAUUGAUAUCCAUGUCUCG______________UUUUGAAU_GAAA_AUAAC__GUGAAUUGAGCAAGAAGUUGCGCAGUGCUGCGCAACUUCUUGCGCA
................((.(.......).)).................................................((((((((((((((((((....)))))))))))))))))) (-28.19 = -27.50 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,803,035 – 1,803,135
Length 100
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 57.35
Mean single sequence MFE -39.14
Consensus MFE -24.15
Energy contribution -25.65
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -3.99
Structure conservation index 0.62
SVM decision value 2.97
SVM RNA-class probability 0.997941
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1011 1803035 100 - 6264404
UGCGCAAAAAGUUGCACAGCACUGCGCAACUUCUUGCUCAAUUCACUUGUUAUAUUUCUUUUCAGAA--------------UGAGACAUGGAUAACAAUAAGCCAUUGAAUGAG------
...((((.(((((((.((....)).))))))).))))(((((....(((((((...((((.......--------------.)))).....)))))))......))))).....------ ( -23.80)
>pau.2014 2705870 99 + 6537648
UGCGCAAAAAGUUGCACAGCACUGCGCAACUUCUUGCUCAAUUCACUUGUUAUUUUUC-AUUCAAAA--------------CGAGACAUGGAUAACAAUUAUCCGUCGGAUGCG------
.((((((.(((((((.((....)).))))))).))))...((((.((((((.......-......))--------------))))..(((((((.....))))))).)))))).------ ( -28.62)
>pfo.1173 2331605 118 - 6438405
UGCGCAAGAAGUUGCGCAGUACUGCGCAACUUCUUGCGCACUUCGA--GCUACCUGGCUGAUCAAAAAACGCUCAAAGCCUCGAUCCAGAGCGGUGGAGUCCCCGGCUCCCGGGGACGUG
((((((((((((((((((....))))))))))))))))))......--.(((((.((((.................))))((......))..))))).((((((((...))))))))... ( -61.03)
>pst.3233 216137 95 + 6397126
UGCGCAAGAAGUUGCGCAACAGUGCGCAACUUCUUGCGCA-------------------AACCAAAAGCUUUUUUA-----CAACGUAAGGGGAUCAAGUCGCCG-CGACUGCGGGCGUA
((((((((((((((((((....))))))))))))))))))-------------------........((.......-----(..(....)..).........(((-(....))))))... ( -43.10)
>consensus
UGCGCAAAAAGUUGCACAGCACUGCGCAACUUCUUGCGCAAUUCAC__GUUAU_UUUC_AAUCAAAA______________CGAGACAUGGAGAACAAGUAGCCGUCGAAUGCG______
((((((((((((((((((....))))))))))))))))))................................................................................ (-24.15 = -25.65 +   1.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,803,135 – 1,803,233
Length 98
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 69.08
Mean single sequence MFE -31.63
Consensus MFE -18.00
Energy contribution -14.47
Covariance contribution -3.54
Combinations/Pair 1.44
Mean z-score -2.13
Structure conservation index 0.57
SVM decision value 2.74
SVM RNA-class probability 0.996730
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1011 1803135 98 + 6264404
GUAGUGUUCAGGCCAGUAUUUUCAAGG---GCUGUGGACUGUUAUUGGGGAUGUUUCUUGGUUUUCAUUGUGCAACUUCUUGCACAAU--CGCUAUUACGCUC
((((((...(((((((((((..(((..---((........))..)))..))))....)))))))..(((((((((....)))))))))--))))))....... ( -26.90)
>pau.2014 2705969 98 - 6537648
GUAGUGUCCAGGCCAGUAUUUUCAAGG---GCUGUGGGCUGUUAUUGGGGAUGUUUCUUGGUUUUCAUUGUGCAACUUCUUGCACAAU--CGCUAUUACGCUC
((((((.(((((....((((..(((..---((........))..)))..))))...))))).....(((((((((....)))))))))--))))))....... ( -27.40)
>pfo.1349 3754958 100 - 6438405
CUUGGCUGUAAGCCACGAUAUAGAGGGCUUGCCGUGG-CUUUCACCGUGAUUUUAUUACGGGC--AACUGCGCAACUUUUUGCGCAGUUCCGCCAAUCCGAUC
.(((((((.((((((((....((....))...)))))-))).))(((((((...)))))))(.--((((((((((....)))))))))).))))))....... ( -40.60)
>consensus
GUAGUGUCCAGGCCAGUAUUUUCAAGG___GCUGUGG_CUGUUAUUGGGGAUGUUUCUUGGUUUUCAUUGUGCAACUUCUUGCACAAU__CGCUAUUACGCUC
...((...(((.((((......).((.....)).))).)))...(((((((...))))))).....(((((((((....))))))))).........)).... (-18.00 = -14.47 +  -3.54)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,803,135 – 1,803,233
Length 98
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 69.08
Mean single sequence MFE -24.21
Consensus MFE -14.59
Energy contribution -13.38
Covariance contribution -1.22
Combinations/Pair 1.24
Mean z-score -1.46
Structure conservation index 0.60
SVM decision value 0.78
SVM RNA-class probability 0.850045
Prediction RNA

Download alignment: ClustalW | MAF

>pao.1011 1803135 98 - 6264404
GAGCGUAAUAGCG--AUUGUGCAAGAAGUUGCACAAUGAAAACCAAGAAACAUCCCCAAUAACAGUCCACAGC---CCUUGAAAAUACUGGCCUGAACACUAC
..((......)).--(((((((((....)))))))))..........................(((...(((.---((...........)).)))...))).. ( -16.70)
>pau.2014 2705969 98 + 6537648
GAGCGUAAUAGCG--AUUGUGCAAGAAGUUGCACAAUGAAAACCAAGAAACAUCCCCAAUAACAGCCCACAGC---CCUUGAAAAUACUGGCCUGGACACUAC
..((......)).--(((((((((....)))))))))...........................(.(((..((---(..(....)....))).))).)..... ( -17.00)
>pfo.1349 3754958 100 + 6438405
GAUCGGAUUGGCGGAACUGCGCAAAAAGUUGCGCAGUU--GCCCGUAAUAAAAUCACGGUGAAAG-CCACGGCAAGCCCUCUAUAUCGUGGCUUACAGCCAAG
.......((((((.((((((((((....))))))))))--.)((((.........))))((.(((-((((((.............))))))))).))))))). ( -38.92)
>consensus
GAGCGUAAUAGCG__AUUGUGCAAGAAGUUGCACAAUGAAAACCAAGAAACAUCCCCAAUAACAG_CCACAGC___CCUUGAAAAUACUGGCCUGAACACUAC
....((.........(((((((((....))))))))).........................(((.(((...................))).)))...))... (-14.59 = -13.38 +  -1.22)

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 21:16:06 2007