Locus 140

Sequence ID sp_pn.0
Location 1,704,345 – 1,704,428
Length 83
Max. P 0.999934
window857 window858 window859 window860

overview

Window 7

Location 1,704,345 – 1,704,428
Length 83
Sequences 3
Columns 83
Reading direction forward
Mean pairwise identity 76.71
Mean single sequence MFE -19.70
Consensus MFE -15.21
Energy contribution -16.10
Covariance contribution 0.89
Combinations/Pair 1.06
Mean z-score -3.52
Structure conservation index 0.77
SVM decision value 4.66
SVM RNA-class probability 0.999934
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1704345 83 + 2038615
AUAGAUAUUAUUAGCACUCUUUGAACUGGAGUGCUAAUUCAUAAUUCUAUUGUAUCACUUGGUCAGAAAUAGUCAAGAAAAAA
(((((....(((((((((((.......))))))))))).......))))).......(((((..(....)..)))))...... ( -22.40)
>sp_mu.0 1835232 83 + 2030921
CCAUAGAUUUUUAGCACUCCAAUAUACUGAGUGCUAAUUACAUAUAUUAUUGUAUCACUUGGUCAAAAAUAGUCAAGAAAAAA
.....((...(((((((((.........))))))))).((((........)))))).(((((..(....)..)))))...... ( -15.30)
>sp_ag.0 2058164 82 + 2160267
UUUGAU-UUUUUAGCACUCUUAUACAGAGAGUGCUAACUACAAAAACUAUUCUAUCACUUGGUCAGAAUUAGUCAAGAGAAAA
((((((-(..(((((((((((.....)))))))))))...........((((((((....))).))))).)))))))...... ( -21.40)
>consensus
AUAGAUAUUUUUAGCACUCUUAUAAACAGAGUGCUAAUUACAAAUACUAUUGUAUCACUUGGUCAGAAAUAGUCAAGAAAAAA
..........((((((((((.......))))))))))....................(((((..(....)..)))))...... (-15.21 = -16.10 +   0.89)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,704,345 – 1,704,428
Length 83
Sequences 3
Columns 83
Reading direction reverse
Mean pairwise identity 76.71
Mean single sequence MFE -16.53
Consensus MFE -13.42
Energy contribution -13.20
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.81
SVM decision value 2.10
SVM RNA-class probability 0.988073
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1704345 83 + 2038615
UUUUUUCUUGACUAUUUCUGACCAAGUGAUACAAUAGAAUUAUGAAUUAGCACUCCAGUUCAAAGAGUGCUAAUAAUAUCUAU
....((((....((((.((.....)).))))....))))......((((((((((.........))))))))))......... ( -15.90)
>sp_mu.0 1835232 83 + 2030921
UUUUUUCUUGACUAUUUUUGACCAAGUGAUACAAUAAUAUAUGUAAUUAGCACUCAGUAUAUUGGAGUGCUAAAAAUCUAUGG
.....................(((.....((((........)))).(((((((((.........))))))))).......))) ( -14.90)
>sp_ag.0 2058164 82 + 2160267
UUUUCUCUUGACUAAUUCUGACCAAGUGAUAGAAUAGUUUUUGUAGUUAGCACUCUCUGUAUAAGAGUGCUAAAAA-AUCAAA
.........(((((.(((((.(.....).))))))))))((((...((((((((((.......))))))))))...-..)))) ( -18.80)
>consensus
UUUUUUCUUGACUAUUUCUGACCAAGUGAUACAAUAGUAUUUGUAAUUAGCACUCAAUAUAUAAGAGUGCUAAAAAUAUCUAA
...((.((((............)))).)).................(((((((((.........))))))))).......... (-13.42 = -13.20 +  -0.22) 
# Strand winner: forward (0.91)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,704,345 – 1,704,428
Length 83
Sequences 3
Columns 83
Reading direction forward
Mean pairwise identity 76.71
Mean single sequence MFE -19.70
Consensus MFE -15.21
Energy contribution -16.10
Covariance contribution 0.89
Combinations/Pair 1.06
Mean z-score -3.52
Structure conservation index 0.77
SVM decision value 4.66
SVM RNA-class probability 0.999934
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1704345 83 + 2038615/0-83
AUAGAUAUUAUUAGCACUCUUUGAACUGGAGUGCUAAUUCAUAAUUCUAUUGUAUCACUUGGUCAGAAAUAGUCAAGAAAAAA
(((((....(((((((((((.......))))))))))).......))))).......(((((..(....)..)))))...... ( -22.40)
>sp_mu.0 1835232 83 + 2030921/0-83
CCAUAGAUUUUUAGCACUCCAAUAUACUGAGUGCUAAUUACAUAUAUUAUUGUAUCACUUGGUCAAAAAUAGUCAAGAAAAAA
.....((...(((((((((.........))))))))).((((........)))))).(((((..(....)..)))))...... ( -15.30)
>sp_ag.0 2058164 82 + 2160267/0-83
UUUGAU-UUUUUAGCACUCUUAUACAGAGAGUGCUAACUACAAAAACUAUUCUAUCACUUGGUCAGAAUUAGUCAAGAGAAAA
((((((-(..(((((((((((.....)))))))))))...........((((((((....))).))))).)))))))...... ( -21.40)
>consensus
AUAGAUAUUUUUAGCACUCUUAUAAACAGAGUGCUAAUUACAAAUACUAUUGUAUCACUUGGUCAGAAAUAGUCAAGAAAAAA
..........((((((((((.......))))))))))....................(((((..(....)..)))))...... (-15.21 = -16.10 +   0.89)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,704,345 – 1,704,428
Length 83
Sequences 3
Columns 83
Reading direction reverse
Mean pairwise identity 76.71
Mean single sequence MFE -16.53
Consensus MFE -13.42
Energy contribution -13.20
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.81
SVM decision value 2.10
SVM RNA-class probability 0.988073
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1704345 83 + 2038615/0-83
UUUUUUCUUGACUAUUUCUGACCAAGUGAUACAAUAGAAUUAUGAAUUAGCACUCCAGUUCAAAGAGUGCUAAUAAUAUCUAU
....((((....((((.((.....)).))))....))))......((((((((((.........))))))))))......... ( -15.90)
>sp_mu.0 1835232 83 + 2030921/0-83
UUUUUUCUUGACUAUUUUUGACCAAGUGAUACAAUAAUAUAUGUAAUUAGCACUCAGUAUAUUGGAGUGCUAAAAAUCUAUGG
.....................(((.....((((........)))).(((((((((.........))))))))).......))) ( -14.90)
>sp_ag.0 2058164 82 + 2160267/0-83
UUUUCUCUUGACUAAUUCUGACCAAGUGAUAGAAUAGUUUUUGUAGUUAGCACUCUCUGUAUAAGAGUGCUAAAAA-AUCAAA
.........(((((.(((((.(.....).))))))))))((((...((((((((((.......))))))))))...-..)))) ( -18.80)
>consensus
UUUUUUCUUGACUAUUUCUGACCAAGUGAUACAAUAGUAUUUGUAAUUAGCACUCAAUAUAUAAGAGUGCUAAAAAUAUCUAA
...((.((((............)))).)).................(((((((((.........))))))))).......... (-13.42 = -13.20 +  -0.22) 
# Strand winner: forward (0.91)

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 19:02:32 2006