Locus 56

Sequence ID sy_ha.0
Location 1,786,422 – 1,786,539
Length 117
Max. P 0.997014
window255 window256 window257

overview

Window 5

Location 1,786,422 – 1,786,539
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.99
Mean single sequence MFE -25.87
Consensus MFE -16.63
Energy contribution -17.30
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.07
Structure conservation index 0.64
SVM decision value 2.78
SVM RNA-class probability 0.997014
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1786422 117 + 2685015/0-120
UUAAAUGUAAAAGAACUCUAAGUUCAAUUAAAAAGGGACGG-AAUUACCGCGGUACCACCCUUGUUAACUCAACUUAGAGUUCUCUCAU--AUAUAAUAUUACUUUGUAAAAAUCAGUGA
....(((....(((((((((((((.(.((((.(((((.(((-.....))).(....).))))).)))).).)))))))))))))..)))--.(((((.......)))))........... ( -28.70)
>sy_au.0 1598539 116 - 2809422/0-120
UAAAAAUUUAAAAAACUCUAAGUUAAAUUAAAA-GGGACG--AUUGCUCGCGGUACCACCCUUAUUAACUCAACUUAGAGUUCUCUCAUU-ACAUUAUUUAAAUAUUAAAAAGCCAGUGA
.............(((((((((((.(.((((((-(((...--((((....))))....))))).)))).).)))))))))))........-............................. ( -21.20)
>sy_sa.0 1650268 117 + 2516575/0-120
UAUACAAUAAAAGAACCCUAAGUUCAAUUAACA-GGGACGAUAUUGACCGCGUUACCACCCUGGUUAACUCAACUUAGAGUUCUCUCAUUUAUGUUAUAUAAAUUGUGACAA--CAGUGA
...........(((((.(((((((.(.((((((-((((((..........))).....)))).))))).).))))))).))))).(((((..(((((((.....))))))).--.))))) ( -27.70)
>consensus
UAAAAAAUAAAAGAACUCUAAGUUCAAUUAAAA_GGGACG__AUUGACCGCGGUACCACCCUUGUUAACUCAACUUAGAGUUCUCUCAUU_AUAUUAUAUAAAUUUUAAAAA__CAGUGA
...........(((((((((((((.(.((((...(((.((........)).(....).)))...)))).).))))))))))))).................................... (-16.63 = -17.30 +   0.67)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,786,422 – 1,786,539
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.99
Mean single sequence MFE -38.93
Consensus MFE -29.50
Energy contribution -29.18
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -5.57
Structure conservation index 0.76
SVM decision value 2.44
SVM RNA-class probability 0.994017
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1786422 117 + 2685015/0-120
UCACUGAUUUUUACAAAGUAAUAUUAUAU--AUGAGAGAACUCUAAGUUGAGUUAACAAGGGUGGUACCGCGGUAAUU-CCGUCCCUUUUUAAUUGAACUUAGAGUUCUUUUACAUUUAA
.............................--.(((((((((((((((((.((((((.(((((((((((....)))...-))).))))).)))))).)))))))))))))))))....... ( -40.00)
>sy_au.0 1598539 116 - 2809422/0-120
UCACUGGCUUUUUAAUAUUUAAAUAAUGU-AAUGAGAGAACUCUAAGUUGAGUUAAUAAGGGUGGUACCGCGAGCAAU--CGUCCC-UUUUAAUUUAACUUAGAGUUUUUUAAAUUUUUA
..............(((((.....)))))-....((((((((((((((((((((((.(((((((((..(....)..))--)).)))-))))))))))))))))))))))))......... ( -35.30)
>sy_sa.0 1650268 117 + 2516575/0-120
UCACUG--UUGUCACAAUUUAUAUAACAUAAAUGAGAGAACUCUAAGUUGAGUUAACCAGGGUGGUAACGCGGUCAAUAUCGUCCC-UGUUAAUUGAACUUAGGGUUCUUUUAUUGUAUA
....((--((((..........))))))..(((((((((((((((((((.(((((((.(((((((((..........))))).)))-)))))))).)))))))))))))))))))..... ( -41.50)
>consensus
UCACUG__UUUUAAAAAUUUAUAUAAUAU_AAUGAGAGAACUCUAAGUUGAGUUAACAAGGGUGGUACCGCGGUCAAU__CGUCCC_UUUUAAUUGAACUUAGAGUUCUUUUAAUUUUUA
................................(((((((((((((((((.((((((.(((((.......((((......))))))).)))))))).)))))))))))))))))....... (-29.50 = -29.18 +  -0.33) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,786,422 – 1,786,539
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.83
Mean single sequence MFE -22.07
Consensus MFE -16.51
Energy contribution -13.30
Covariance contribution -3.21
Combinations/Pair 1.44
Mean z-score -0.84
Structure conservation index 0.75
SVM decision value -0.02
SVM RNA-class probability 0.524359
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1786422 117 + 2685015/78-198
UCAGACAAGUAGGAGAUAAUAAACUUUUUACAGCGAAUUAGG-GUUGGUGAAAGCCUAAUAAAAGUCUAUCUCUUAUAUCACUGAUUUUUACAAAGUAAUAUUAUAU--AUGAGAGAACU
..((((..(((((((.........))))))).....((((((-.((.....)).))))))....)))).((((((((((...((((..((((...)))).)))).))--))))))))... ( -24.60)
>sy_au.0 1598539 119 - 2809422/78-198
ACAGACGCGUAAUAUACAUUUAACUUUUCACAGCGAAUUAGGUAAUGGUGAGAGCCUAGUAAAAGCAUGUAUGUUAUAUCACUGGCUUUUUAAUAUUUAAAUAAUGU-AAUGAGAGAACU
.(((....(((((((((((....(((((.((.((.......))...(((....)))..))))))).)))))))))))....))).(((((..(((((.....)))))-...))))).... ( -21.20)
>sy_sa.0 1650268 117 + 2516575/78-198
ACAGACACGUUUGAAACGAAACACAUAUCAAAGCGAGUUAGG-AAUAGUGAGAGCCUUUCAUAUGUGCGUUUCUAAUAUCACUG--UUGUCACAAUUUAUAUAACAUAAAUGAGAGAACU
........(((.((((((...(((((((.....(......)(-((..((....))..)))))))))))))))).)))......(--((.((...((((((.....))))))..)).))). ( -20.40)
>consensus
ACAGACACGUAAGAAACAAUAAACUUUUCACAGCGAAUUAGG_AAUGGUGAGAGCCUAAUAAAAGUAUGUAUCUUAUAUCACUG__UUUUAAAAAUUUAUAUAAUAU_AAUGAGAGAACU
.(((....((((((((((....((((((....((..((((.....))))....)).....)))))).))))))))))....))).................................... (-16.51 = -13.30 +  -3.21) 
# Strand winner: reverse (0.83)

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 18:54:09 2006