Locus 9

Sequence ID sp_ag.0
Location 1,833,033 – 1,833,106
Length 73
Max. P 0.881055
window72 window73 window74 window75

overview

Window 2

Location 1,833,033 – 1,833,106
Length 73
Sequences 3
Columns 73
Reading direction forward
Mean pairwise identity 99.09
Mean single sequence MFE -25.40
Consensus MFE -25.40
Energy contribution -25.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 1.00
SVM decision value 0.92
SVM RNA-class probability 0.881055
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 1833033 73 + 2160267
GGCGGUAUAGCCAAGUGGUAAGGCACGGCUCUGCAAAAGCUUGAUCGUCGGUUCAAAUCCGUCUACCGCCUUU
(((((((....(((((.(((..((...))..)))....)))))...(.(((.......))).))))))))... ( -25.40)
>sp_mu.0 1904602 73 + 2030921
GGCGGUAUAGCCAAGUGGUAAGGCACGGCUCUGCAAAAGCUUGAUCGUCGGUUCAAAUCCGUCUACCGCCUUU
(((((((....(((((.(((..((...))..)))....)))))...(.(((.......))).))))))))... ( -25.40)
>sp_pn.0 1752047 73 + 2038615
GGCGGUAUAGCCAAGUGGUAAGGCACGGCUCUGCAAAAGCUUGAUCGUCGGUUCAAAUCCGUCUACCGCCUUC
(((((((....(((((.(((..((...))..)))....)))))...(.(((.......))).))))))))... ( -25.40)
>consensus
GGCGGUAUAGCCAAGUGGUAAGGCACGGCUCUGCAAAAGCUUGAUCGUCGGUUCAAAUCCGUCUACCGCCUUU
(((((((....(((((.(((..((...))..)))....)))))...(.(((.......))).))))))))... (-25.40 = -25.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,833,033 – 1,833,106
Length 73
Sequences 3
Columns 73
Reading direction reverse
Mean pairwise identity 99.09
Mean single sequence MFE -23.10
Consensus MFE -23.10
Energy contribution -23.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 1.00
SVM decision value 0.08
SVM RNA-class probability 0.572485
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 1833033 73 + 2160267
AAAGGCGGUAGACGGAUUUGAACCGACGAUCAAGCUUUUGCAGAGCCGUGCCUUACCACUUGGCUAUACCGCC
...(((((((.((((..((((........))))((....))....))))(((.........)))..))))))) ( -23.10)
>sp_mu.0 1904602 73 + 2030921
AAAGGCGGUAGACGGAUUUGAACCGACGAUCAAGCUUUUGCAGAGCCGUGCCUUACCACUUGGCUAUACCGCC
...(((((((.((((..((((........))))((....))....))))(((.........)))..))))))) ( -23.10)
>sp_pn.0 1752047 73 + 2038615
GAAGGCGGUAGACGGAUUUGAACCGACGAUCAAGCUUUUGCAGAGCCGUGCCUUACCACUUGGCUAUACCGCC
...(((((((.((((..((((........))))((....))....))))(((.........)))..))))))) ( -23.10)
>consensus
AAAGGCGGUAGACGGAUUUGAACCGACGAUCAAGCUUUUGCAGAGCCGUGCCUUACCACUUGGCUAUACCGCC
...(((((((.((((..((((........))))((....))....))))(((.........)))..))))))) (-23.10 = -23.10 +  -0.00) 
# Strand winner: forward (0.54)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 1,833,033 – 1,833,106
Length 73
Sequences 3
Columns 73
Reading direction forward
Mean pairwise identity 99.09
Mean single sequence MFE -25.40
Consensus MFE -25.40
Energy contribution -25.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 1.00
SVM decision value 0.92
SVM RNA-class probability 0.881055
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 1833033 73 + 2160267/0-73
GGCGGUAUAGCCAAGUGGUAAGGCACGGCUCUGCAAAAGCUUGAUCGUCGGUUCAAAUCCGUCUACCGCCUUU
(((((((....(((((.(((..((...))..)))....)))))...(.(((.......))).))))))))... ( -25.40)
>sp_mu.0 1904602 73 + 2030921/0-73
GGCGGUAUAGCCAAGUGGUAAGGCACGGCUCUGCAAAAGCUUGAUCGUCGGUUCAAAUCCGUCUACCGCCUUU
(((((((....(((((.(((..((...))..)))....)))))...(.(((.......))).))))))))... ( -25.40)
>sp_pn.0 1752047 73 + 2038615/0-73
GGCGGUAUAGCCAAGUGGUAAGGCACGGCUCUGCAAAAGCUUGAUCGUCGGUUCAAAUCCGUCUACCGCCUUC
(((((((....(((((.(((..((...))..)))....)))))...(.(((.......))).))))))))... ( -25.40)
>consensus
GGCGGUAUAGCCAAGUGGUAAGGCACGGCUCUGCAAAAGCUUGAUCGUCGGUUCAAAUCCGUCUACCGCCUUU
(((((((....(((((.(((..((...))..)))....)))))...(.(((.......))).))))))))... (-25.40 = -25.40 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 1,833,033 – 1,833,106
Length 73
Sequences 3
Columns 73
Reading direction reverse
Mean pairwise identity 99.09
Mean single sequence MFE -23.10
Consensus MFE -23.10
Energy contribution -23.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 1.00
SVM decision value 0.08
SVM RNA-class probability 0.572485
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 1833033 73 + 2160267/0-73
AAAGGCGGUAGACGGAUUUGAACCGACGAUCAAGCUUUUGCAGAGCCGUGCCUUACCACUUGGCUAUACCGCC
...(((((((.((((..((((........))))((....))....))))(((.........)))..))))))) ( -23.10)
>sp_mu.0 1904602 73 + 2030921/0-73
AAAGGCGGUAGACGGAUUUGAACCGACGAUCAAGCUUUUGCAGAGCCGUGCCUUACCACUUGGCUAUACCGCC
...(((((((.((((..((((........))))((....))....))))(((.........)))..))))))) ( -23.10)
>sp_pn.0 1752047 73 + 2038615/0-73
GAAGGCGGUAGACGGAUUUGAACCGACGAUCAAGCUUUUGCAGAGCCGUGCCUUACCACUUGGCUAUACCGCC
...(((((((.((((..((((........))))((....))....))))(((.........)))..))))))) ( -23.10)
>consensus
AAAGGCGGUAGACGGAUUUGAACCGACGAUCAAGCUUUUGCAGAGCCGUGCCUUACCACUUGGCUAUACCGCC
...(((((((.((((..((((........))))((....))....))))(((.........)))..))))))) (-23.10 = -23.10 +  -0.00) 
# Strand winner: forward (0.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:51:26 2006