Locus 7

Sequence ID sp_pn.0
Location 1,976,049 – 1,976,112
Length 63
Max. P 0.963992
window66 window67 window68 window69

overview

Window 6

Location 1,976,049 – 1,976,112
Length 63
Sequences 3
Columns 71
Reading direction forward
Mean pairwise identity 79.51
Mean single sequence MFE -17.61
Consensus MFE -9.86
Energy contribution -9.09
Covariance contribution -0.77
Combinations/Pair 1.25
Mean z-score -2.20
Structure conservation index 0.56
SVM decision value 0.11
SVM RNA-class probability 0.586389
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1976049 63 + 2038615
AAUCGAGUAGGGGAUAAUCUCUAGCCCCUCUCACACCACC--------GUACGUGCCGUUCGGCAUACGGC
....(((.(((((.((.....)).))))))))......((--------((..(((((....))))))))). ( -23.80)
>sp_ag.0 1244583 63 + 2160267
AAUCGAGUAGAGGCUAAUCUCUAGCCCCUCUCACACCACC--------GUACGUGCCGUUCGGCAUACGGC
....(((.((.(((((.....))))).)))))......((--------((..(((((....))))))))). ( -23.50)
>sp_mu.0 1052832 71 + 2030921
AAUCAAGUAGAGGCUAAUCUCUAACUCCUCUCACACCAUCACACCAGCGUACGUACUAUUAGACAUAUAGC
......(((((((.............))))).)).....................((((.......)))). (  -5.52)
>consensus
AAUCGAGUAGAGGCUAAUCUCUAGCCCCUCUCACACCACC________GUACGUGCCGUUCGGCAUACGGC
......(((((((.............))))).))....................(((((.......))))) ( -9.86 =  -9.09 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,976,049 – 1,976,112
Length 63
Sequences 3
Columns 71
Reading direction reverse
Mean pairwise identity 79.51
Mean single sequence MFE -23.03
Consensus MFE -17.49
Energy contribution -16.50
Covariance contribution -0.99
Combinations/Pair 1.33
Mean z-score -2.13
Structure conservation index 0.76
SVM decision value 1.56
SVM RNA-class probability 0.963992
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1976049 63 + 2038615
GCCGUAUGCCGAACGGCACGUAC--------GGUGGUGUGAGAGGGGCUAGAGAUUAUCCCCUACUCGAUU
((((((((((....))))..)))--------)))....(((((((((.(((...))).))))).))))... ( -24.90)
>sp_ag.0 1244583 63 + 2160267
GCCGUAUGCCGAACGGCACGUAC--------GGUGGUGUGAGAGGGGCUAGAGAUUAGCCUCUACUCGAUU
((((((((((....))))..)))--------)))....(((((((((((((...))))))))).))))... ( -28.50)
>sp_mu.0 1052832 71 + 2030921
GCUAUAUGUCUAAUAGUACGUACGCUGGUGUGAUGGUGUGAGAGGAGUUAGAGAUUAGCCUCUACUUGAUU
((((.((.((((((......(((((((......)))))))......)))))).))))))............ ( -15.70)
>consensus
GCCGUAUGCCGAACGGCACGUAC________GGUGGUGUGAGAGGGGCUAGAGAUUAGCCUCUACUCGAUU
(((((.......))))).....................(((((((((((((...))))))))).))))... (-17.49 = -16.50 +  -0.99) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 1,976,049 – 1,976,112
Length 63
Sequences 3
Columns 71
Reading direction forward
Mean pairwise identity 79.51
Mean single sequence MFE -17.61
Consensus MFE -9.86
Energy contribution -9.09
Covariance contribution -0.77
Combinations/Pair 1.25
Mean z-score -2.20
Structure conservation index 0.56
SVM decision value 0.11
SVM RNA-class probability 0.586389
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1976049 63 + 2038615/0-71
AAUCGAGUAGGGGAUAAUCUCUAGCCCCUCUCACACCACC--------GUACGUGCCGUUCGGCAUACGGC
....(((.(((((.((.....)).))))))))......((--------((..(((((....))))))))). ( -23.80)
>sp_ag.0 1244583 63 + 2160267/0-71
AAUCGAGUAGAGGCUAAUCUCUAGCCCCUCUCACACCACC--------GUACGUGCCGUUCGGCAUACGGC
....(((.((.(((((.....))))).)))))......((--------((..(((((....))))))))). ( -23.50)
>sp_mu.0 1052832 71 + 2030921/0-71
AAUCAAGUAGAGGCUAAUCUCUAACUCCUCUCACACCAUCACACCAGCGUACGUACUAUUAGACAUAUAGC
......(((((((.............))))).)).....................((((.......)))). (  -5.52)
>consensus
AAUCGAGUAGAGGCUAAUCUCUAGCCCCUCUCACACCACC________GUACGUGCCGUUCGGCAUACGGC
......(((((((.............))))).))....................(((((.......))))) ( -9.86 =  -9.09 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 1,976,049 – 1,976,112
Length 63
Sequences 3
Columns 71
Reading direction reverse
Mean pairwise identity 79.51
Mean single sequence MFE -23.03
Consensus MFE -17.49
Energy contribution -16.50
Covariance contribution -0.99
Combinations/Pair 1.33
Mean z-score -2.13
Structure conservation index 0.76
SVM decision value 1.56
SVM RNA-class probability 0.963992
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1976049 63 + 2038615/0-71
GCCGUAUGCCGAACGGCACGUAC--------GGUGGUGUGAGAGGGGCUAGAGAUUAUCCCCUACUCGAUU
((((((((((....))))..)))--------)))....(((((((((.(((...))).))))).))))... ( -24.90)
>sp_ag.0 1244583 63 + 2160267/0-71
GCCGUAUGCCGAACGGCACGUAC--------GGUGGUGUGAGAGGGGCUAGAGAUUAGCCUCUACUCGAUU
((((((((((....))))..)))--------)))....(((((((((((((...))))))))).))))... ( -28.50)
>sp_mu.0 1052832 71 + 2030921/0-71
GCUAUAUGUCUAAUAGUACGUACGCUGGUGUGAUGGUGUGAGAGGAGUUAGAGAUUAGCCUCUACUUGAUU
((((.((.((((((......(((((((......)))))))......)))))).))))))............ ( -15.70)
>consensus
GCCGUAUGCCGAACGGCACGUAC________GGUGGUGUGAGAGGGGCUAGAGAUUAGCCUCUACUCGAUU
(((((.......))))).....................(((((((((((((...))))))))).))))... (-17.49 = -16.50 +  -0.99) 
# Strand winner: reverse (1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:51:21 2006