Locus 84

Sequence ID sy_ha.0
Location 2,471,227 – 2,471,345
Length 118
Max. P 0.998728
window423 window424 window425

overview

Window 3

Location 2,471,227 – 2,471,345
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.14
Mean single sequence MFE -29.14
Consensus MFE -19.61
Energy contribution -18.73
Covariance contribution -0.88
Combinations/Pair 1.19
Mean z-score -2.42
Structure conservation index 0.67
SVM decision value 3.20
SVM RNA-class probability 0.998728
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2471227 118 + 2685015/0-120
AAAUUGACUUGAACGUG-UGAUCAUAAAAAUGAUCUUUCAAGCGCUUUUUGCCGUGGGUAGAAAGUGCUUUUUUUAUUGAGAAAUUUAAAAAGC-ACCAAAAAUAAAAAUGGAGGUGUCU
(((((..((..(..(..-.((((((....))))))...)((((((((((((((...))))))))))))))......)..)).))))).....((-(((...............))))).. ( -30.26)
>sy_au.0 2204346 113 - 2809422/0-120
AAAUUGACUUGAACGUGAUGAUC-----UAUGAUCUUUCAAGCACUUUUUGCCGUGGGUAGAAAGUGCUUUUUUUAUU-AAUUUUAAAAAAAGC-ACCAAAAAUUUAAAUGGAGGUGUCU
...((((...((.((((......-----)))).))..))))((((((((((((...))))))))))))((((((((..-.....))))))))((-(((...............))))).. ( -26.76)
>sy_sa.0 2279440 115 + 2516575/0-120
AAAUUGACUUGAACGUGAAGAUU-----UUAGAUCUUUCAAGCACUUUUUGCCGUGGGUAGAAAGUGUUUUUUUUAUUGGAUAAUCUGAGGAACUGACGAACGUCAAUCCACAGAACUUC
................((((...-----((((((..(((((((((((((((((...))))))))))))........)))))..))))))(((..((((....)))).)))......)))) ( -30.40)
>consensus
AAAUUGACUUGAACGUGAUGAUC_____UAUGAUCUUUCAAGCACUUUUUGCCGUGGGUAGAAAGUGCUUUUUUUAUUGAAUAAUAUAAAAAGC_ACCAAAAAUAAAAAUGGAGGUGUCU
...(((.............((((........))))....((((((((((((((...))))))))))))))...........................))).................... (-19.61 = -18.73 +  -0.88) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,471,227 – 2,471,345
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.54
Mean single sequence MFE -22.17
Consensus MFE -18.63
Energy contribution -18.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.84
SVM decision value 0.95
SVM RNA-class probability 0.888558
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2471227 118 + 2685015/40-160
UCAAUAAAAAAAGCACUUUCUACCCACGGCAAAAAGCGCUUGAAAGAUCAUUUUUAUGAUCA-CACGUUCAAGUCAAUUUUAGCCUCGGCAGGAU-AAUUUUUAAGUUAUACUAUAACUC
.......(((((.....((((.((...(((.((((..(((((((.((((((....)))))).-....)))))))...)))).)))..)).)))).-..))))).((((((...)))))). ( -24.60)
>sy_au.0 2204346 112 - 2809422/40-160
U-AAUAAAAAAAGCACUUUCUACCCACGGCAAAAAGUGCUUGAAAGAUCAUA-----GAUCAUCACGUUCAAGUCAAUUUUAGCCUCGGCAGGAU-AAAUUUUAAGUUAUAA-AUAACUC
.-......((((.....((((.((...(((.((((.((((((((.((((...-----))))......)))))).)).)))).)))..)).)))).-...)))).(((((...-.))))). ( -19.20)
>sy_sa.0 2279440 114 + 2516575/40-160
CCAAUAAAAAAAACACUUUCUACCCACGGCAAAAAGUGCUUGAAAGAUCUAA-----AAUCUUCACGUUCAAGUCAAUUUUAGCCUCGGUAGGAUCAAAUUUUAAGUUAUUA-CUAACUC
.................(((((((...(((.((((.((((((((((((....-----.)))).....)))))).)).)))).)))..)))))))..........(((((...-.))))). ( -22.70)
>consensus
UCAAUAAAAAAAGCACUUUCUACCCACGGCAAAAAGUGCUUGAAAGAUCAUA_____GAUCAUCACGUUCAAGUCAAUUUUAGCCUCGGCAGGAU_AAAUUUUAAGUUAUAA_AUAACUC
........((((.....((((.((...(((.((((..(((((((.((((........))))......)))))))...)))).)))..)).)))).....)))).(((((.....))))). (-18.63 = -18.97 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,471,227 – 2,471,345
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.54
Mean single sequence MFE -27.57
Consensus MFE -25.29
Energy contribution -24.63
Covariance contribution -0.66
Combinations/Pair 1.10
Mean z-score -1.83
Structure conservation index 0.92
SVM decision value 0.86
SVM RNA-class probability 0.868351
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2471227 118 + 2685015/40-160
GAGUUAUAGUAUAACUUAAAAAUU-AUCCUGCCGAGGCUAAAAUUGACUUGAACGUG-UGAUCAUAAAAAUGAUCUUUCAAGCGCUUUUUGCCGUGGGUAGAAAGUGCUUUUUUUAUUGA
(((((((...))))))).......-...(((((.((((.((((.((.((((((....-.((((((....)))))).)))))))).)))).))).).)))))................... ( -28.50)
>sy_au.0 2204346 112 - 2809422/40-160
GAGUUAU-UUAUAACUUAAAAUUU-AUCCUGCCGAGGCUAAAAUUGACUUGAACGUGAUGAUC-----UAUGAUCUUUCAAGCACUUUUUGCCGUGGGUAGAAAGUGCUUUUUUUAUU-A
(((((((-(((.....)))).(((-(.(((....))).))))..)))))).....(((.((((-----...))))..)))(((((((((((((...))))))))))))).........-. ( -25.90)
>sy_sa.0 2279440 114 + 2516575/40-160
GAGUUAG-UAAUAACUUAAAAUUUGAUCCUACCGAGGCUAAAAUUGACUUGAACGUGAAGAUU-----UUAGAUCUUUCAAGCACUUUUUGCCGUGGGUAGAAAGUGUUUUUUUUAUUGG
((((((.-...))))))..............((((((((((((((..(........)..))))-----)))).))))..((((((((((((((...))))))))))))))........)) ( -28.30)
>consensus
GAGUUAU_UUAUAACUUAAAAUUU_AUCCUGCCGAGGCUAAAAUUGACUUGAACGUGAUGAUC_____UAUGAUCUUUCAAGCACUUUUUGCCGUGGGUAGAAAGUGCUUUUUUUAUUGA
((((((.....))))))...........(((((.((((.((((.((.((((((......((((........)))).)))))))).)))).))).).)))))................... (-25.29 = -24.63 +  -0.66) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:56:28 2006