Locus 97

Sequence ID sy_ha.0
Location 1,799,845 – 1,799,928
Length 83
Max. P 0.999993
window499 window500 window501 window502

overview

Window 9

Location 1,799,845 – 1,799,928
Length 83
Sequences 5
Columns 83
Reading direction forward
Mean pairwise identity 90.36
Mean single sequence MFE -36.26
Consensus MFE -36.42
Energy contribution -34.58
Covariance contribution -1.84
Combinations/Pair 1.19
Mean z-score -2.99
Structure conservation index 1.00
SVM decision value 5.67
SVM RNA-class probability 0.999992
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799845 83 - 2685015
GGUGGAGGGGGGCAGAUUCGAACUGCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCACUUCGCUACCCCUCC
...((((((((((((.......))))).....((((((.((((((.....)))))))((.....))..)))))...))))))) ( -38.60)
>sy_sa.0 1767557 83 - 2516575
GGUGGAGGGGGGCAGAUUCGAACUGCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCACUUCGCUACCCCUCC
...((((((((((((.......))))).....((((((.((((((.....)))))))((.....))..)))))...))))))) ( -38.60)
>sy_au.0 2228142 83 + 2809422
GGUGGAGGGGGGCAGAUUCGAACUGCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCACUUCGCUACCCCUCC
...((((((((((((.......))))).....((((((.((((((.....)))))))((.....))..)))))...))))))) ( -38.60)
>sp_ag.0 1154212 83 + 2160267
AAUGGAAAGAGAGGGAUUCGAACCCCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCUCUUCGCUAUCUUUCC
...(((((((..(((.((((......)))))))(((((.((((((.....)))))).((.....)).)))))....))))))) ( -31.40)
>sp_pn.0 1279118 83 - 2038615
AAUGGAGAGAGAGGGAUUCGAACCCCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCUCUUCGCUAUCUCUCC
...(((((((..(((.((((......)))))))(((((.((((((.....)))))).((.....)).)))))....))))))) ( -34.10)
>consensus
GGUGGAGGGGGGCAGAUUCGAACUGCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCACUUCGCUACCCCUCC
...((((((((((((.......))))).....((((((.((((((.....)))))))((.....))..)))))...))))))) (-36.42 = -34.58 +  -1.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,799,845 – 1,799,928
Length 83
Sequences 5
Columns 83
Reading direction reverse
Mean pairwise identity 90.36
Mean single sequence MFE -37.06
Consensus MFE -38.04
Energy contribution -35.56
Covariance contribution -2.48
Combinations/Pair 1.24
Mean z-score -2.91
Structure conservation index 1.03
SVM decision value 5.72
SVM RNA-class probability 0.999993
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799845 83 - 2685015
GGAGGGGUAGCGAAGUGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGCAGUUCGAAUCUGCCCCCCUCCACC
(((((((((((......))))...((((((((((((.((((((......))))))..))))))))...)))).)))))))... ( -39.60)
>sy_sa.0 1767557 83 - 2516575
GGAGGGGUAGCGAAGUGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGCAGUUCGAAUCUGCCCCCCUCCACC
(((((((((((......))))...((((((((((((.((((((......))))))..))))))))...)))).)))))))... ( -39.60)
>sy_au.0 2228142 83 + 2809422
GGAGGGGUAGCGAAGUGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGCAGUUCGAAUCUGCCCCCCUCCACC
(((((((((((......))))...((((((((((((.((((((......))))))..))))))))...)))).)))))))... ( -39.60)
>sp_ag.0 1154212 83 + 2160267
GGAAAGAUAGCGAAGAGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGGGGUUCGAAUCCCUCUCUUUCCAUU
(((((((.((.((((..((.....))((((((.......)))))).))))((((((((....)))))))))).)))))))... ( -31.90)
>sp_pn.0 1279118 83 - 2038615
GGAGAGAUAGCGAAGAGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGGGGUUCGAAUCCCUCUCUCUCCAUU
(((((((.((.((((..((.....))((((((.......)))))).))))((((((((....)))))))))).)))))))... ( -34.60)
>consensus
GGAGGGGUAGCGAAGUGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGCAGUUCGAAUCUGCCCCCCUCCACC
(((((((...(((((..((.....))((((((.......)))))).))))).....(((((.......))))))))))))... (-38.04 = -35.56 +  -2.48) 
# Strand winner: reverse (0.81)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,799,845 – 1,799,928
Length 83
Sequences 5
Columns 83
Reading direction forward
Mean pairwise identity 90.36
Mean single sequence MFE -36.26
Consensus MFE -36.42
Energy contribution -34.58
Covariance contribution -1.84
Combinations/Pair 1.19
Mean z-score -2.99
Structure conservation index 1.00
SVM decision value 5.67
SVM RNA-class probability 0.999992
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799845 83 - 2685015/0-83
GGUGGAGGGGGGCAGAUUCGAACUGCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCACUUCGCUACCCCUCC
...((((((((((((.......))))).....((((((.((((((.....)))))))((.....))..)))))...))))))) ( -38.60)
>sy_sa.0 1767557 83 - 2516575/0-83
GGUGGAGGGGGGCAGAUUCGAACUGCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCACUUCGCUACCCCUCC
...((((((((((((.......))))).....((((((.((((((.....)))))))((.....))..)))))...))))))) ( -38.60)
>sy_au.0 2228142 83 + 2809422/0-83
GGUGGAGGGGGGCAGAUUCGAACUGCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCACUUCGCUACCCCUCC
...((((((((((((.......))))).....((((((.((((((.....)))))))((.....))..)))))...))))))) ( -38.60)
>sp_ag.0 1154212 83 + 2160267/0-83
AAUGGAAAGAGAGGGAUUCGAACCCCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCUCUUCGCUAUCUUUCC
...(((((((..(((.((((......)))))))(((((.((((((.....)))))).((.....)).)))))....))))))) ( -31.40)
>sp_pn.0 1279118 83 - 2038615/0-83
AAUGGAGAGAGAGGGAUUCGAACCCCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCUCUUCGCUAUCUCUCC
...(((((((..(((.((((......)))))))(((((.((((((.....)))))).((.....)).)))))....))))))) ( -34.10)
>consensus
GGUGGAGGGGGGCAGAUUCGAACUGCCGAACCCGAAGGAGCGGAUUUACAGUCCGCCGCGUUUAGCCACUUCGCUACCCCUCC
...((((((((((((.......))))).....((((((.((((((.....)))))))((.....))..)))))...))))))) (-36.42 = -34.58 +  -1.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,799,845 – 1,799,928
Length 83
Sequences 5
Columns 83
Reading direction reverse
Mean pairwise identity 90.36
Mean single sequence MFE -37.06
Consensus MFE -38.04
Energy contribution -35.56
Covariance contribution -2.48
Combinations/Pair 1.24
Mean z-score -2.91
Structure conservation index 1.03
SVM decision value 5.72
SVM RNA-class probability 0.999993
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799845 83 - 2685015/0-83
GGAGGGGUAGCGAAGUGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGCAGUUCGAAUCUGCCCCCCUCCACC
(((((((((((......))))...((((((((((((.((((((......))))))..))))))))...)))).)))))))... ( -39.60)
>sy_sa.0 1767557 83 - 2516575/0-83
GGAGGGGUAGCGAAGUGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGCAGUUCGAAUCUGCCCCCCUCCACC
(((((((((((......))))...((((((((((((.((((((......))))))..))))))))...)))).)))))))... ( -39.60)
>sy_au.0 2228142 83 + 2809422/0-83
GGAGGGGUAGCGAAGUGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGCAGUUCGAAUCUGCCCCCCUCCACC
(((((((((((......))))...((((((((((((.((((((......))))))..))))))))...)))).)))))))... ( -39.60)
>sp_ag.0 1154212 83 + 2160267/0-83
GGAAAGAUAGCGAAGAGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGGGGUUCGAAUCCCUCUCUUUCCAUU
(((((((.((.((((..((.....))((((((.......)))))).))))((((((((....)))))))))).)))))))... ( -31.90)
>sp_pn.0 1279118 83 - 2038615/0-83
GGAGAGAUAGCGAAGAGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGGGGUUCGAAUCCCUCUCUCUCCAUU
(((((((.((.((((..((.....))((((((.......)))))).))))((((((((....)))))))))).)))))))... ( -34.60)
>consensus
GGAGGGGUAGCGAAGUGGCUAAACGCGGCGGACUGUAAAUCCGCUCCUUCGGGUUCGGCAGUUCGAAUCUGCCCCCCUCCACC
(((((((...(((((..((.....))((((((.......)))))).))))).....(((((.......))))))))))))... (-38.04 = -35.56 +  -2.48) 
# Strand winner: reverse (0.81)

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 18:57:30 2006