Locus 42

Sequence ID sy_sa.0
Location 1,223,674 – 1,223,726
Length 52
Max. P 0.988975
window200 window201 window202 window203

overview

Window 0

Location 1,223,674 – 1,223,726
Length 52
Sequences 3
Columns 53
Reading direction forward
Mean pairwise identity 84.62
Mean single sequence MFE -18.30
Consensus MFE -15.95
Energy contribution -15.73
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -5.71
Structure conservation index 0.87
SVM decision value 1.20
SVM RNA-class probability 0.929249
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1223674 52 + 2516575
GCCAAAUUAAGUCAAAGUCAAUUGAACAUUGGCUUUGACUUUUUCCUUU-UUA
........((((((((((((((.....))))))))))))))........-... ( -16.00)
>sy_ha.0 1372022 50 + 2685015
GCCAAA--AAGUCAAAGUCAAUUGAACAUUGGCUUUGACUUUUUCUUUU-AUA
...(((--((((((((((((((.....))))))))))))))))).....-... ( -18.80)
>sy_au.0 1142879 51 - 2809422
UCUGAA--AAGUCAAAGUCAAUAGAACAUUGGCUUUGGCUUUUUAUUUGGAUA
..((((--((((((((((((((.....))))))))))))))))))........ ( -20.10)
>consensus
GCCAAA__AAGUCAAAGUCAAUUGAACAUUGGCUUUGACUUUUUCUUUU_AUA
........((((((((((((((.....))))))))))))))............ (-15.95 = -15.73 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,223,674 – 1,223,726
Length 52
Sequences 3
Columns 53
Reading direction reverse
Mean pairwise identity 84.62
Mean single sequence MFE -12.93
Consensus MFE -10.87
Energy contribution -11.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.79
Structure conservation index 0.84
SVM decision value 2.14
SVM RNA-class probability 0.988975
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1223674 52 + 2516575
UAA-AAAGGAAAAAGUCAAAGCCAAUGUUCAAUUGACUUUGACUUAAUUUGGC
...-........(((((((((.((((.....)))).)))))))))........ ( -13.60)
>sy_ha.0 1372022 50 + 2685015
UAU-AAAAGAAAAAGUCAAAGCCAAUGUUCAAUUGACUUUGACUU--UUUGGC
...-.....((((((((((((.((((.....)))).)))))))))--)))... ( -16.40)
>sy_au.0 1142879 51 - 2809422
UAUCCAAAUAAAAAGCCAAAGCCAAUGUUCUAUUGACUUUGACUU--UUCAGA
..........(((((.(((((.(((((...))))).))))).)))--)).... (  -8.80)
>consensus
UAU_AAAAGAAAAAGUCAAAGCCAAUGUUCAAUUGACUUUGACUU__UUUGGC
............(((((((((.((((.....)))).)))))))))........ (-10.87 = -11.20 +   0.33) 
# Strand winner: forward (0.98)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 1,223,674 – 1,223,726
Length 52
Sequences 3
Columns 53
Reading direction forward
Mean pairwise identity 84.62
Mean single sequence MFE -18.30
Consensus MFE -15.95
Energy contribution -15.73
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -5.71
Structure conservation index 0.87
SVM decision value 1.20
SVM RNA-class probability 0.929249
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1223674 52 + 2516575/0-53
GCCAAAUUAAGUCAAAGUCAAUUGAACAUUGGCUUUGACUUUUUCCUUU-UUA
........((((((((((((((.....))))))))))))))........-... ( -16.00)
>sy_ha.0 1372022 50 + 2685015/0-53
GCCAAA--AAGUCAAAGUCAAUUGAACAUUGGCUUUGACUUUUUCUUUU-AUA
...(((--((((((((((((((.....))))))))))))))))).....-... ( -18.80)
>sy_au.0 1142879 51 - 2809422/0-53
UCUGAA--AAGUCAAAGUCAAUAGAACAUUGGCUUUGGCUUUUUAUUUGGAUA
..((((--((((((((((((((.....))))))))))))))))))........ ( -20.10)
>consensus
GCCAAA__AAGUCAAAGUCAAUUGAACAUUGGCUUUGACUUUUUCUUUU_AUA
........((((((((((((((.....))))))))))))))............ (-15.95 = -15.73 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 1,223,674 – 1,223,726
Length 52
Sequences 3
Columns 53
Reading direction reverse
Mean pairwise identity 84.62
Mean single sequence MFE -12.93
Consensus MFE -10.87
Energy contribution -11.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.79
Structure conservation index 0.84
SVM decision value 2.14
SVM RNA-class probability 0.988975
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1223674 52 + 2516575/0-53
UAA-AAAGGAAAAAGUCAAAGCCAAUGUUCAAUUGACUUUGACUUAAUUUGGC
...-........(((((((((.((((.....)))).)))))))))........ ( -13.60)
>sy_ha.0 1372022 50 + 2685015/0-53
UAU-AAAAGAAAAAGUCAAAGCCAAUGUUCAAUUGACUUUGACUU--UUUGGC
...-.....((((((((((((.((((.....)))).)))))))))--)))... ( -16.40)
>sy_au.0 1142879 51 - 2809422/0-53
UAUCCAAAUAAAAAGCCAAAGCCAAUGUUCUAUUGACUUUGACUU--UUCAGA
..........(((((.(((((.(((((...))))).))))).)))--)).... (  -8.80)
>consensus
UAU_AAAAGAAAAAGUCAAAGCCAAUGUUCAAUUGACUUUGACUU__UUUGGC
............(((((((((.((((.....)))).)))))))))........ (-10.87 = -11.20 +   0.33) 
# Strand winner: forward (0.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:53:23 2006