Locus 126

Sequence ID sp_pn.0
Location 459,856 – 459,949
Length 93
Max. P 0.999895
window807 window808 window809 window810

overview

Window 7

Location 459,856 – 459,949
Length 93
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 75.80
Mean single sequence MFE -22.41
Consensus MFE -12.70
Energy contribution -13.37
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.57
SVM decision value 2.06
SVM RNA-class probability 0.986837
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 459856 93 + 2038615
UUAGCACUCUUUAUAAAAGAGUGCUAAUUUUUUGAGUUUUUGUCUUGACAUUCUCUUCUAAGGGUGUAUAAUAGAAUCAU-AAGUUAGCACUUG
..................((((((((((((..(((..((((((....(((((((......)))))))...))))))))).-)))))))))))). ( -23.60)
>sp_ag.0 103407 92 + 2160267
UUAGCACUCUUUGAAUAAGAGUGCUAAUUUUUGAUGUUUUUUCCUUGACUAUCUUUUAAAAAGGAGUAUAAUAAAAUCAU-A-GUUAGCAGUCG
(((((((((((.....))))))))))).(((((.(((...((((((..............)))))).))).)))))....-.-........... ( -20.64)
>sp_mu.0 83508 94 + 2030921
UUAGCACUCAAGCAGAAAGAGUGCUAAUUUUUUGUAUUUUUCUCUUGACAGAAAUUAGGAAUGGAGUAUAAUGGAAUUAUGAAGUUAGCAGUCG
...((......)).....((.(((((((((((((((((((..((((((......))))))..))))))))).........)))))))))).)). ( -23.00)
>consensus
UUAGCACUCUUUAAAAAAGAGUGCUAAUUUUUUGUGUUUUUCUCUUGACAAUCUUUUAAAAAGGAGUAUAAUAGAAUCAU_AAGUUAGCAGUCG
(((((((((((.....)))))))))))................................................................... (-12.70 = -13.37 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 459,856 – 459,949
Length 93
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 75.80
Mean single sequence MFE -17.67
Consensus MFE -12.30
Energy contribution -12.97
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.04
Structure conservation index 0.70
SVM decision value 4.42
SVM RNA-class probability 0.999895
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 459856 93 + 2038615
CAAGUGCUAACUU-AUGAUUCUAUUAUACACCCUUAGAAGAGAAUGUCAAGACAAAAACUCAAAAAAUUAGCACUCUUUUAUAAAGAGUGCUAA
.((((....))))-....(((((...........)))))(((..(((....)))....)))......(((((((((((.....))))))))))) ( -19.90)
>sp_ag.0 103407 92 + 2160267
CGACUGCUAAC-U-AUGAUUUUAUUAUACUCCUUUUUAAAAGAUAGUCAAGGAAAAAACAUCAAAAAUUAGCACUCUUAUUCAAAGAGUGCUAA
.(((((.....-(-(((((...))))))...(((.....))).)))))...................(((((((((((.....))))))))))) ( -18.40)
>sp_mu.0 83508 94 + 2030921
CGACUGCUAACUUCAUAAUUCCAUUAUACUCCAUUCCUAAUUUCUGUCAAGAGAAAAAUACAAAAAAUUAGCACUCUUUCUGCUUGAGUGCUAA
........................................(((((....))))).............(((((((((.........))))))))) ( -14.70)
>consensus
CGACUGCUAACUU_AUGAUUCUAUUAUACUCCAUUACAAAAGAAUGUCAAGAAAAAAACACAAAAAAUUAGCACUCUUUUUCAAAGAGUGCUAA
...................................................................(((((((((((.....))))))))))) (-12.30 = -12.97 +   0.67) 
# Strand winner: forward (0.90)

alignment

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secondary structure

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dotplot

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Window 9

Location 459,856 – 459,949
Length 93
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 75.80
Mean single sequence MFE -22.41
Consensus MFE -12.70
Energy contribution -13.37
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.57
SVM decision value 2.06
SVM RNA-class probability 0.986837
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 459856 93 + 2038615/0-94
UUAGCACUCUUUAUAAAAGAGUGCUAAUUUUUUGAGUUUUUGUCUUGACAUUCUCUUCUAAGGGUGUAUAAUAGAAUCAU-AAGUUAGCACUUG
..................((((((((((((..(((..((((((....(((((((......)))))))...))))))))).-)))))))))))). ( -23.60)
>sp_ag.0 103407 92 + 2160267/0-94
UUAGCACUCUUUGAAUAAGAGUGCUAAUUUUUGAUGUUUUUUCCUUGACUAUCUUUUAAAAAGGAGUAUAAUAAAAUCAU-A-GUUAGCAGUCG
(((((((((((.....))))))))))).(((((.(((...((((((..............)))))).))).)))))....-.-........... ( -20.64)
>sp_mu.0 83508 94 + 2030921/0-94
UUAGCACUCAAGCAGAAAGAGUGCUAAUUUUUUGUAUUUUUCUCUUGACAGAAAUUAGGAAUGGAGUAUAAUGGAAUUAUGAAGUUAGCAGUCG
...((......)).....((.(((((((((((((((((((..((((((......))))))..))))))))).........)))))))))).)). ( -23.00)
>consensus
UUAGCACUCUUUAAAAAAGAGUGCUAAUUUUUUGUGUUUUUCUCUUGACAAUCUUUUAAAAAGGAGUAUAAUAGAAUCAU_AAGUUAGCAGUCG
(((((((((((.....)))))))))))................................................................... (-12.70 = -13.37 +   0.67)

alignment

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secondary structure

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dotplot

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Window 0

Location 459,856 – 459,949
Length 93
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 75.80
Mean single sequence MFE -17.67
Consensus MFE -12.30
Energy contribution -12.97
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.04
Structure conservation index 0.70
SVM decision value 4.42
SVM RNA-class probability 0.999895
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 459856 93 + 2038615/0-94
CAAGUGCUAACUU-AUGAUUCUAUUAUACACCCUUAGAAGAGAAUGUCAAGACAAAAACUCAAAAAAUUAGCACUCUUUUAUAAAGAGUGCUAA
.((((....))))-....(((((...........)))))(((..(((....)))....)))......(((((((((((.....))))))))))) ( -19.90)
>sp_ag.0 103407 92 + 2160267/0-94
CGACUGCUAAC-U-AUGAUUUUAUUAUACUCCUUUUUAAAAGAUAGUCAAGGAAAAAACAUCAAAAAUUAGCACUCUUAUUCAAAGAGUGCUAA
.(((((.....-(-(((((...))))))...(((.....))).)))))...................(((((((((((.....))))))))))) ( -18.40)
>sp_mu.0 83508 94 + 2030921/0-94
CGACUGCUAACUUCAUAAUUCCAUUAUACUCCAUUCCUAAUUUCUGUCAAGAGAAAAAUACAAAAAAUUAGCACUCUUUCUGCUUGAGUGCUAA
........................................(((((....))))).............(((((((((.........))))))))) ( -14.70)
>consensus
CGACUGCUAACUU_AUGAUUCUAUUAUACUCCAUUACAAAAGAAUGUCAAGAAAAAAACACAAAAAAUUAGCACUCUUUUUCAAAGAGUGCUAA
...................................................................(((((((((((.....))))))))))) (-12.30 = -12.97 +   0.67) 
# Strand winner: forward (0.90)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:01:53 2006