Locus 14

Sequence ID pao.3201
Location 6,044,699 – 6,044,896
Length 197
Max. P 0.964154
window106 window107 window108

overview

Window 6

Location 6,044,699 – 6,044,817
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.25
Mean single sequence MFE -29.85
Consensus MFE -22.42
Energy contribution -22.12
Covariance contribution -0.31
Combinations/Pair 1.09
Mean z-score -3.19
Structure conservation index 0.75
SVM decision value 1.25
SVM RNA-class probability 0.935842
Prediction RNA

Download alignment: ClustalW | MAF

>pao.3201 6044699 118 + 6264404
CUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAGUUCAAUACUGC--UUGGGUUUUGAGAAAACCCUAAACUUGGCUCAGCAAUCGCAUUCUCUUAAAAAGAGAUAAAACUC
.........(((......((((((((.(...........((((.....)))).--..((((((.....))))))....).))))))))....)))..(((((.....)))))........ ( -30.90)
>pau.3340 6317618 118 + 6537648
CUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAGUUCAAUACUGC--UUGGGUUUUGAGAAAACCCUAAACUUGGCUCAGCAAUCGCAUUCUCUUAAAAAGAGAUAAAACUC
.........(((......((((((((.(...........((((.....)))).--..((((((.....))))))....).))))))))....)))..(((((.....)))))........ ( -30.90)
>ppk.94 6005017 100 - 6181863
CUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAGUUCAAUACUGC--UUGGGUUUUUAAGAAACCCUAAACUUGGCUCAGCAAUCUCAAAUGAC------------------
..((.....)).......((((((((.(...........((((.....)))).--..(((((((...)))))))....).))))))))..............------------------ ( -23.40)
>psp.1833 3636649 105 + 5928787
CUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAGUUCAAACAUCUAACUGGGUUUUGAGAAAACCCUAAACUUGGCUCAGCAAUCGUUGGCUAC---------------AUC
.....(((((((......((((((((.(....((((....)))).............((((((.....))))))....).))))))))....)))))))...---------------... ( -32.50)
>pfo.3002 5731515 103 + 6438405
CUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAGUUCAAACAUCU--UUGGGUUUUUAAGAAACCCUAAACUUGGCUCAGCAAUCGUUGGUUAC---------------AUC
.((..(((((((......((((((((.(....((((....)))).........--..(((((((...)))))))....).))))))))....)))))))..)---------------).. ( -30.90)
>pf5.3378 6387908 103 + 7074893
CUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAGUUCAAACAUCU--UUGGGUUUUGAGAAAACCCUAAACUUGGCUCAGCAAUCGUUGGUUAC---------------AUC
.((..(((((((......((((((((.(....((((....)))).........--..((((((.....))))))....).))))))))....)))))))..)---------------).. ( -30.50)
>consensus
CUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAGUUCAAAAAUCC__UUGGGUUUUGAGAAAACCCUAAACUUGGCUCAGCAAUCGCAGGCUAC_______________AUC
.........(((......((((((((.(....((((....)))).............(((((((...)))))))....).))))))))....)))......................... (-22.42 = -22.12 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,044,699 – 6,044,817
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.25
Mean single sequence MFE -35.82
Consensus MFE -27.12
Energy contribution -27.12
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.95
Structure conservation index 0.76
SVM decision value 1.17
SVM RNA-class probability 0.925233
Prediction RNA

Download alignment: ClustalW | MAF

>pao.3201 6044699 118 - 6264404
GAGUUUUAUCUCUUUUUAAGAGAAUGCGAUUGCUGAGCCAAGUUUAGGGUUUUCUCAAAACCCAA--GCAGUAUUGAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAG
........(((((.....))))).(((.....((((((((.((((.((((((.....))))))))--)).(.((..((((....))))..))).))))))))......((....))))). ( -37.60)
>pau.3340 6317618 118 - 6537648
GAGUUUUAUCUCUUUUUAAGAGAAUGCGAUUGCUGAGCCAAGUUUAGGGUUUUCUCAAAACCCAA--GCAGUAUUGAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAG
........(((((.....))))).(((.....((((((((.((((.((((((.....))))))))--)).(.((..((((....))))..))).))))))))......((....))))). ( -37.60)
>ppk.94 6005017 100 + 6181863
------------------GUCAUUUGAGAUUGCUGAGCCAAGUUUAGGGUUUCUUAAAAACCCAA--GCAGUAUUGAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAG
------------------((((((..(.....((((((((.((((.((((((.....))))))))--)).(.((..((((....))))..))).)))))))).)..))...))))..... ( -32.60)
>psp.1833 3636649 105 - 5928787
GAU---------------GUAGCCAACGAUUGCUGAGCCAAGUUUAGGGUUUUCUCAAAACCCAGUUAGAUGUUUGAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAG
..(---------------((.((((.((.((.(((((((.......((((((.....))))))......(((.(..((((....))))..).))))))))))...)).)).)))).))). ( -37.80)
>pfo.3002 5731515 103 - 6438405
GAU---------------GUAACCAACGAUUGCUGAGCCAAGUUUAGGGUUUCUUAAAAACCCAA--AGAUGUUUGAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAG
..(---------------((..(((.((.((.(((((((.......((((((.....))))))..--..(((.(..((((....))))..).))))))))))...)).)).)))..))). ( -34.60)
>pf5.3378 6387908 103 - 7074893
GAU---------------GUAACCAACGAUUGCUGAGCCAAGUUUAGGGUUUUCUCAAAACCCAA--AGAUGUUUGAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAG
..(---------------((..(((.((.((.(((((((.......((((((.....))))))..--..(((.(..((((....))))..).))))))))))...)).)).)))..))). ( -34.70)
>consensus
GAU_______________GUAACCAACGAUUGCUGAGCCAAGUUUAGGGUUUUCUCAAAACCCAA__ACAGGAUUGAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAG
................................((((((((......((((((.....))))))..........(..((((....))))..)...)))))))).......((.....)).. (-27.12 = -27.12 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,044,817 – 6,044,896
Length 79
Sequences 6
Columns 81
Reading direction reverse
Mean pairwise identity 81.83
Mean single sequence MFE -29.45
Consensus MFE -21.10
Energy contribution -21.10
Covariance contribution 0.00
Combinations/Pair 1.22
Mean z-score -4.15
Structure conservation index 0.72
SVM decision value 1.56
SVM RNA-class probability 0.964154
Prediction RNA

Download alignment: ClustalW | MAF

>pao.3201 6044817 79 - 6264404
GCAAUUCGUGUGGGUGCUUGUGAUGUAAGACUGGUGAUCGCAA-GAUUAUCAGCAACGCAAGUAACACU-CGUGAAUUCGA
(.((((((.(((..((((((((.((.....(((((((((....-))))))))))).)))))))).))).-..))))))).. ( -29.40)
>pau.3340 6317736 79 - 6537648
GCAAUUCGUGUGGGUGCUUGUGAUGUAAGACUGGUGAUCGCAA-GAUUAUCAGCAACGCAAGUAACACU-CGUGAAUUCGA
(.((((((.(((..((((((((.((.....(((((((((....-))))))))))).)))))))).))).-..))))))).. ( -29.40)
>ppk.94 6005120 79 + 6181863
--AAUUCGUGUGGGUGCUUGUGAGUACGGACUGAUAGUCAAAAAGAUUAUCAGCAUCACAAGUGGCCAUGCGAGAAAUCAC
--..(((((((((.(((((((((.....(.(((((((((.....)))))))))).))))))))).)))))))))....... ( -36.40)
>psp.1833 3636755 77 - 5928787
--AAUUCGUGUGGGUGCUUGUGGUGUCAGACUGA-AGUCAACA-GAUUAUCAGCAACCCAAGUUACUCCGCGAGAAAUCAA
--..((((((.(((((((((.(((....(.((((-((((....-)))).))))).))))))).)))))))))))....... ( -25.70)
>pf5.3378 6388012 81 - 7074893
GCAAUUCGUGUGGGUGCUUGUGGAGUCAGACUGAUAGUCAAAAAGAUUAUCAGCAUCACAAGUUACUCCGCGAGAAAUCAA
....((((((.(((((((((((..(.....(((((((((.....))))))))))..)))))).)))))))))))....... ( -30.10)
>pst.2031 3874743 79 - 6397126
GCAAUUCGUGUGGGUGCUUGUGGUGUCAGACUGA-AGUCAACA-GAUUAUCAGCAACCCAAGUUACUCCGCGAGAAAUCAA
....((((((.(((((((((.(((....(.((((-((((....-)))).))))).))))))).)))))))))))....... ( -25.70)
>consensus
GCAAUUCGUGUGGGUGCUUGUGAUGUCAGACUGAUAGUCAAAA_GAUUAUCAGCAACACAAGUUACUCCGCGAGAAAUCAA
....(((.((((((((((((((......(.(((((((((.....))))))))))..))))))).)).))))).)))..... (-21.10 = -21.10 +   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 21:05:13 2007