Locus 46

Sequence ID sy_ha.0
Location 1,408,601 – 1,408,716
Length 115
Max. P 0.997998
window211 window212 window213 window214

overview

Window 1

Location 1,408,601 – 1,408,716
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.44
Mean single sequence MFE -30.17
Consensus MFE -26.64
Energy contribution -26.09
Covariance contribution -0.55
Combinations/Pair 1.15
Mean z-score -2.23
Structure conservation index 0.88
SVM decision value 2.45
SVM RNA-class probability 0.994129
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1408601 115 + 2685015/0-120
UUUAUCGCCGAAGGUGCAAGU---UAACUACUAAACUCUCAGGCAAAAGGAUAAUACUGCUACGCAUUCCUGGAUUA--AGUGUAUAAACAGGGUAGCUAUUUGCUACUCUGUUUUUUAU
...((((((((..((...(((---.....)))..))..)).)))...((((......(((...))).)))).)))..--.(((...((((((((((((.....))))))))))))..))) ( -29.80)
>sy_au.0 1179415 116 - 2809422/0-120
UCUAUCGCCGAAGGUGCAAGUAAUUUAUUACGAAACUCUCAGGCAAAAGGAUAAUACUGUAACGCGUUCCUGAAUUGGUGAUUUAUAAACAGGGUAGCGAUU-GCUAUCCUGUUUUU---
...((((((((.(((....((((....))))...))).(((((.((..(.............)...))))))).))))))))....((((((((((((....-))))))))))))..--- ( -32.42)
>sy_sa.0 1259195 109 + 2516575/0-120
UCCAUCGCCGAAGGUGCAAGU----UUUUACGAAACUCUCAGGCAAAAGGAUAAUACUGUAACGCAUUCCUGAAAUA-----UUACAA-CAGGGUAGUU-UAGGCUACCCUGUUUUUUUA
....(((((((..((....((----....))...))..)).)))...((((................))))))....-----....((-(((((((((.-...)))))))))))...... ( -28.29)
>consensus
UCUAUCGCCGAAGGUGCAAGU___UUAUUACGAAACUCUCAGGCAAAAGGAUAAUACUGUAACGCAUUCCUGAAUUA____UUUAUAAACAGGGUAGCUAUU_GCUACCCUGUUUUUU__
....(((((((..((....((........))...))..)).)))...((((................)))))).............((((((((((((.....))))))))))))..... (-26.64 = -26.09 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,408,601 – 1,408,716
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.44
Mean single sequence MFE -28.43
Consensus MFE -25.22
Energy contribution -26.67
Covariance contribution 1.45
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.89
SVM decision value 2.46
SVM RNA-class probability 0.994161
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1408601 115 + 2685015/0-120
AUAAAAAACAGAGUAGCAAAUAGCUACCCUGUUUAUACACU--UAAUCCAGGAAUGCGUAGCAGUAUUAUCCUUUUGCCUGAGAGUUUAGUAGUUA---ACUUGCACCUUCGGCGAUAAA
.....((((((.(((((.....))))).)))))).......--......((((((((......))))..)))).(((((.(((.((..(((.....---)))...))))).))))).... ( -28.50)
>sy_au.0 1179415 116 - 2809422/0-120
---AAAAACAGGAUAGC-AAUCGCUACCCUGUUUAUAAAUCACCAAUUCAGGAACGCGUUACAGUAUUAUCCUUUUGCCUGAGAGUUUCGUAAUAAAUUACUUGCACCUUCGGCGAUAGA
---..(((((((.((((-....)))).)))))))....(((........((((..((......))....))))...(((.(((.((...((((....))))....))))).))))))... ( -25.70)
>sy_sa.0 1259195 109 + 2516575/0-120
UAAAAAAACAGGGUAGCCUA-AACUACCCUG-UUGUAA-----UAUUUCAGGAAUGCGUUACAGUAUUAUCCUUUUGCCUGAGAGUUUCGUAAAA----ACUUGCACCUUCGGCGAUGGA
......((((((((((....-..))))))))-))....-----.........(((((......))))).(((..(((((.(((.((...((((..----..))))))))).))))).))) ( -31.10)
>consensus
__AAAAAACAGGGUAGC_AAUAGCUACCCUGUUUAUAAA____UAAUUCAGGAAUGCGUUACAGUAUUAUCCUUUUGCCUGAGAGUUUCGUAAUAA___ACUUGCACCUUCGGCGAUAGA
.....((((((((((((.....))))))))))))...............((((((((......))))..)))).(((((.(((.((...((((........))))))))).))))).... (-25.22 = -26.67 +   1.45) 
# Strand winner: forward (0.94)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,408,601 – 1,408,713
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.43
Mean single sequence MFE -25.53
Consensus MFE -21.99
Energy contribution -21.22
Covariance contribution -0.77
Combinations/Pair 1.24
Mean z-score -1.58
Structure conservation index 0.86
SVM decision value 2.44
SVM RNA-class probability 0.993923
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1408601 112 + 2685015/18-138
AGU---UAACUACUAAACUCUCAGGCAAAAGGAUAAUACUGCUACGCAUUCCUGGAUUA--AGUGUAUAAACAGGGUAGCUAUUUGCUACUCUGUUUUUUAUA---AAAAUUAUAGGGGG
...---...........(((((.......((((......(((...))).)))).((((.--..((((.((((((((((((.....))))))))))))..))))---..))))...))))) ( -27.20)
>sy_au.0 1179415 112 - 2809422/18-138
AGUAAUUUAUUACGAAACUCUCAGGCAAAAGGAUAAUACUGUAACGCGUUCCUGAAUUGGUGAUUUAUAAACAGGGUAGCGAUU-GCUAUCCUGUUUUU-------AUAAUUUUAAGGGG
.((((....))))....((((((((.((..(.............)...)))))))......((((...((((((((((((....-))))))))))))..-------..))))....))). ( -24.92)
>sy_sa.0 1259195 109 + 2516575/18-138
AGU----UUUUACGAAACUCUCAGGCAAAAGGAUAAUACUGUAACGCAUUCCUGAAAUA-----UUACAA-CAGGGUAGUU-UAGGCUACCCUGUUUUUUUAUUAUAUAAUCUUUAGGAG
...----..........((((((((.......(((....)))........)))))((((-----..(.((-(((((((((.-...))))))))))).)..)))).............))) ( -24.46)
>consensus
AGU___UUAUUACGAAACUCUCAGGCAAAAGGAUAAUACUGUAACGCAUUCCUGAAUUA____UUUAUAAACAGGGUAGCUAUU_GCUACCCUGUUUUUU______AUAAUUUUAAGGGG
.................((((((((.....(.............).....))))).............((((((((((((.....))))))))))))....................))) (-21.99 = -21.22 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,408,601 – 1,408,713
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.43
Mean single sequence MFE -22.87
Consensus MFE -17.37
Energy contribution -19.37
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.76
SVM decision value 2.98
SVM RNA-class probability 0.997998
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1408601 112 + 2685015/18-138
CCCCCUAUAAUUUU---UAUAAAAAACAGAGUAGCAAAUAGCUACCCUGUUUAUACACU--UAAUCCAGGAAUGCGUAGCAGUAUUAUCCUUUUGCCUGAGAGUUUAGUAGUUA---ACU
....((((((((((---((....((((((.(((((.....))))).)))))).......--......((((((((......))))..))))......))))))))..))))...---... ( -23.20)
>sy_au.0 1179415 112 - 2809422/18-138
CCCCUUAAAAUUAU-------AAAAACAGGAUAGC-AAUCGCUACCCUGUUUAUAAAUCACCAAUUCAGGAACGCGUUACAGUAUUAUCCUUUUGCCUGAGAGUUUCGUAAUAAAUUACU
.........(((((-------..(((((((.((((-....)))).)))))))................(((((((......))......(((......))).))))))))))........ ( -19.80)
>sy_sa.0 1259195 109 + 2516575/18-138
CUCCUAAAGAUUAUAUAAUAAAAAAACAGGGUAGCCUA-AACUACCCUG-UUGUAA-----UAUUUCAGGAAUGCGUUACAGUAUUAUCCUUUUGCCUGAGAGUUUCGUAAAA----ACU
..........((((..(((.....((((((((((....-..))))))))-))....-----..((((((((((((......))))).........))))))))))..))))..----... ( -25.60)
>consensus
CCCCUUAAAAUUAU______AAAAAACAGGGUAGC_AAUAGCUACCCUGUUUAUAAA____UAAUUCAGGAAUGCGUUACAGUAUUAUCCUUUUGCCUGAGAGUUUCGUAAUAA___ACU
.......................((((((((((((.....))))))))))))............(((((((((((......))))).........))))))................... (-17.37 = -19.37 +   2.00) 
# Strand winner: forward (1.00)

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 18:53:33 2006