Locus 76

Sequence ID sy_ha.0
Location 2,017,441 – 2,017,500
Length 59
Max. P 0.999283
window375 window376 window377 window378

overview

Window 5

Location 2,017,441 – 2,017,500
Length 59
Sequences 3
Columns 62
Reading direction forward
Mean pairwise identity 74.59
Mean single sequence MFE -17.43
Consensus MFE -16.72
Energy contribution -17.17
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -4.75
Structure conservation index 0.96
SVM decision value 3.48
SVM RNA-class probability 0.999283
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2017441 59 - 2685015
ACAAAAAUAUAA---AAGCUCCCUACAAAGUUUACAUUCAUUAAUGUCUACUUUGUAGGAAG
............---......((((((((((..(((((....)))))..))))))))))... ( -17.60)
>sy_au.0 1825579 62 - 2809422
ACUAGAACAUAAAUAAGGCUCCCUUCAAAAUUUUCAUUUUUCAAUGUCUACUUUGAAGGGAG
..................(((((((((((.....((((....)))).....))))))))))) ( -16.70)
>sy_sa.0 2095301 61 + 2516575
AUACUGAUAUAAA-AAAGCUCCCGUCUAAGUUUUCAUUUUUCAAUGUCAACUUUAACGGGAG
.............-....(((((((..(((((..((((....))))..)))))..))))))) ( -18.00)
>consensus
ACAAAAAUAUAAA_AAAGCUCCCUUCAAAGUUUUCAUUUUUCAAUGUCUACUUUGAAGGGAG
..................(((((((((((((...((((....))))...))))))))))))) (-16.72 = -17.17 +   0.45)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,017,441 – 2,017,500
Length 59
Sequences 3
Columns 62
Reading direction reverse
Mean pairwise identity 74.59
Mean single sequence MFE -21.87
Consensus MFE -21.75
Energy contribution -20.53
Covariance contribution -1.21
Combinations/Pair 1.29
Mean z-score -5.85
Structure conservation index 0.99
SVM decision value 1.85
SVM RNA-class probability 0.980130
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2017441 59 - 2685015
CUUCCUACAAAGUAGACAUUAAUGAAUGUAAACUUUGUAGGGAGCUU---UUAUAUUUUUGU
(((((((((((((..(((((....)))))..)))))))))))))...---............ ( -22.00)
>sy_au.0 1825579 62 - 2809422
CUCCCUUCAAAGUAGACAUUGAAAAAUGAAAAUUUUGAAGGGAGCCUUAUUUAUGUUCUAGU
(((((((((((((...((((....))))...))))))))))))).................. ( -21.50)
>sy_sa.0 2095301 61 + 2516575
CUCCCGUUAAAGUUGACAUUGAAAAAUGAAAACUUAGACGGGAGCUUU-UUUAUAUCAGUAU
((((((((.(((((..((((....))))..))))).))))))))....-............. ( -22.10)
>consensus
CUCCCUUCAAAGUAGACAUUGAAAAAUGAAAACUUUGAAGGGAGCUUU_UUUAUAUUAUUGU
(((((((((((((...((((....))))...))))))))))))).................. (-21.75 = -20.53 +  -1.21) 
# Strand winner: reverse (0.99)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,017,441 – 2,017,500
Length 59
Sequences 3
Columns 62
Reading direction forward
Mean pairwise identity 74.59
Mean single sequence MFE -17.43
Consensus MFE -16.72
Energy contribution -17.17
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -4.75
Structure conservation index 0.96
SVM decision value 3.48
SVM RNA-class probability 0.999283
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2017441 59 - 2685015/0-62
ACAAAAAUAUAA---AAGCUCCCUACAAAGUUUACAUUCAUUAAUGUCUACUUUGUAGGAAG
............---......((((((((((..(((((....)))))..))))))))))... ( -17.60)
>sy_au.0 1825579 62 - 2809422/0-62
ACUAGAACAUAAAUAAGGCUCCCUUCAAAAUUUUCAUUUUUCAAUGUCUACUUUGAAGGGAG
..................(((((((((((.....((((....)))).....))))))))))) ( -16.70)
>sy_sa.0 2095301 61 + 2516575/0-62
AUACUGAUAUAAA-AAAGCUCCCGUCUAAGUUUUCAUUUUUCAAUGUCAACUUUAACGGGAG
.............-....(((((((..(((((..((((....))))..)))))..))))))) ( -18.00)
>consensus
ACAAAAAUAUAAA_AAAGCUCCCUUCAAAGUUUUCAUUUUUCAAUGUCUACUUUGAAGGGAG
..................(((((((((((((...((((....))))...))))))))))))) (-16.72 = -17.17 +   0.45)

alignment

Postscript

secondary structure

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dotplot

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Window 8

Location 2,017,441 – 2,017,500
Length 59
Sequences 3
Columns 62
Reading direction reverse
Mean pairwise identity 74.59
Mean single sequence MFE -21.87
Consensus MFE -21.75
Energy contribution -20.53
Covariance contribution -1.21
Combinations/Pair 1.29
Mean z-score -5.85
Structure conservation index 0.99
SVM decision value 1.85
SVM RNA-class probability 0.980130
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2017441 59 - 2685015/0-62
CUUCCUACAAAGUAGACAUUAAUGAAUGUAAACUUUGUAGGGAGCUU---UUAUAUUUUUGU
(((((((((((((..(((((....)))))..)))))))))))))...---............ ( -22.00)
>sy_au.0 1825579 62 - 2809422/0-62
CUCCCUUCAAAGUAGACAUUGAAAAAUGAAAAUUUUGAAGGGAGCCUUAUUUAUGUUCUAGU
(((((((((((((...((((....))))...))))))))))))).................. ( -21.50)
>sy_sa.0 2095301 61 + 2516575/0-62
CUCCCGUUAAAGUUGACAUUGAAAAAUGAAAACUUAGACGGGAGCUUU-UUUAUAUCAGUAU
((((((((.(((((..((((....))))..))))).))))))))....-............. ( -22.10)
>consensus
CUCCCUUCAAAGUAGACAUUGAAAAAUGAAAACUUUGAAGGGAGCUUU_UUUAUAUUAUUGU
(((((((((((((...((((....))))...))))))))))))).................. (-21.75 = -20.53 +  -1.21) 
# Strand winner: reverse (0.99)

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 18:55:49 2006