Locus 69

Sequence ID sy_sa.0
Location 1,945,819 – 1,945,890
Length 71
Max. P 1.000000
window357 window358 window359 window360

overview

Window 7

Location 1,945,819 – 1,945,890
Length 71
Sequences 3
Columns 72
Reading direction forward
Mean pairwise identity 70.37
Mean single sequence MFE -12.65
Consensus MFE -11.90
Energy contribution -12.23
Covariance contribution 0.34
Combinations/Pair 1.18
Mean z-score -2.97
Structure conservation index 0.94
SVM decision value 5.97
SVM RNA-class probability 0.999996
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1945819 71 + 2516575
AUGCCCUUUUAC-AAUAUCCUAGACACAAAAACAACCCUUUAACUAUUGGAGUUAAAGGGUUUGUUAAUUAA
............-.................(((((((((((((((.....)))))))))).)))))...... ( -17.00)
>sy_ha.0 2593435 72 + 2685015
AUGCCCUUUUUCGAAUUUACAAAUUACAAAAACAACCCUCUAACCAUUGUGGUUAAAGGGUUUUAUAAUUCA
............(((((................((((((.(((((.....))))).))))))....))))). ( -14.35)
>sy_au.0 1905995 72 - 2809422
GCGCCCUUUUUUUAUUUUCAAUACCACAAAAAUAACCCCUUAAUCGUUUUCAUUAAAGGGUAUUUCUAUUUA
..................................((((.(((((.......))))).))))........... (  -6.60)
>consensus
AUGCCCUUUUUC_AAUUUCCAAAACACAAAAACAACCCUUUAACCAUUGUAGUUAAAGGGUUUUUUAAUUAA
..................................(((((((((((.....)))))))))))........... (-11.90 = -12.23 +   0.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,945,819 – 1,945,890
Length 71
Sequences 3
Columns 72
Reading direction reverse
Mean pairwise identity 70.37
Mean single sequence MFE -18.85
Consensus MFE -14.67
Energy contribution -14.23
Covariance contribution -0.44
Combinations/Pair 1.33
Mean z-score -3.72
Structure conservation index 0.78
SVM decision value 7.16
SVM RNA-class probability 1.000000
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1945819 71 + 2516575
UUAAUUAACAAACCCUUUAACUCCAAUAGUUAAAGGGUUGUUUUUGUGUCUAGGAUAUU-GUAAAAGGGCAU
......(((((.((((((((((.....)))))))))))))))...((((((........-......)))))) ( -18.64)
>sy_ha.0 2593435 72 + 2685015
UGAAUUAUAAAACCCUUUAACCACAAUGGUUAGAGGGUUGUUUUUGUAAUUUGUAAAUUCGAAAAAGGGCAU
.(((((((((((((((((((((.....)))))))))))....)))))))))).................... ( -22.20)
>sy_au.0 1905995 72 - 2809422
UAAAUAGAAAUACCCUUUAAUGAAAACGAUUAAGGGGUUAUUUUUGUGGUAUUGAAAAUAAAAAAAGGGCGC
...((((((((((((((((((.......))))))))).)))))))))......................... ( -15.70)
>consensus
UAAAUUAAAAAACCCUUUAACCACAAUGGUUAAAGGGUUGUUUUUGUGAUUUGGAAAUU_GAAAAAGGGCAU
..........((((((((((((.....))))))))))))................................. (-14.67 = -14.23 +  -0.44) 
# Strand winner: reverse (0.81)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,945,819 – 1,945,890
Length 71
Sequences 3
Columns 72
Reading direction forward
Mean pairwise identity 70.37
Mean single sequence MFE -12.65
Consensus MFE -11.90
Energy contribution -12.23
Covariance contribution 0.34
Combinations/Pair 1.18
Mean z-score -2.97
Structure conservation index 0.94
SVM decision value 5.97
SVM RNA-class probability 0.999996
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1945819 71 + 2516575/0-72
AUGCCCUUUUAC-AAUAUCCUAGACACAAAAACAACCCUUUAACUAUUGGAGUUAAAGGGUUUGUUAAUUAA
............-.................(((((((((((((((.....)))))))))).)))))...... ( -17.00)
>sy_ha.0 2593435 72 + 2685015/0-72
AUGCCCUUUUUCGAAUUUACAAAUUACAAAAACAACCCUCUAACCAUUGUGGUUAAAGGGUUUUAUAAUUCA
............(((((................((((((.(((((.....))))).))))))....))))). ( -14.35)
>sy_au.0 1905995 72 - 2809422/0-72
GCGCCCUUUUUUUAUUUUCAAUACCACAAAAAUAACCCCUUAAUCGUUUUCAUUAAAGGGUAUUUCUAUUUA
..................................((((.(((((.......))))).))))........... (  -6.60)
>consensus
AUGCCCUUUUUC_AAUUUCCAAAACACAAAAACAACCCUUUAACCAUUGUAGUUAAAGGGUUUUUUAAUUAA
..................................(((((((((((.....)))))))))))........... (-11.90 = -12.23 +   0.34)

alignment

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secondary structure

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dotplot

Postscript

Window 0

Location 1,945,819 – 1,945,890
Length 71
Sequences 3
Columns 72
Reading direction reverse
Mean pairwise identity 70.37
Mean single sequence MFE -18.85
Consensus MFE -14.67
Energy contribution -14.23
Covariance contribution -0.44
Combinations/Pair 1.33
Mean z-score -3.72
Structure conservation index 0.78
SVM decision value 7.16
SVM RNA-class probability 1.000000
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1945819 71 + 2516575/0-72
UUAAUUAACAAACCCUUUAACUCCAAUAGUUAAAGGGUUGUUUUUGUGUCUAGGAUAUU-GUAAAAGGGCAU
......(((((.((((((((((.....)))))))))))))))...((((((........-......)))))) ( -18.64)
>sy_ha.0 2593435 72 + 2685015/0-72
UGAAUUAUAAAACCCUUUAACCACAAUGGUUAGAGGGUUGUUUUUGUAAUUUGUAAAUUCGAAAAAGGGCAU
.(((((((((((((((((((((.....)))))))))))....)))))))))).................... ( -22.20)
>sy_au.0 1905995 72 - 2809422/0-72
UAAAUAGAAAUACCCUUUAAUGAAAACGAUUAAGGGGUUAUUUUUGUGGUAUUGAAAAUAAAAAAAGGGCGC
...((((((((((((((((((.......))))))))).)))))))))......................... ( -15.70)
>consensus
UAAAUUAAAAAACCCUUUAACCACAAUGGUUAAAGGGUUGUUUUUGUGAUUUGGAAAUU_GAAAAAGGGCAU
..........((((((((((((.....))))))))))))................................. (-14.67 = -14.23 +  -0.44) 
# Strand winner: reverse (0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:55:35 2006