Locus 78

Sequence ID sy_ha.0
Location 2,282,663 – 2,282,780
Length 117
Max. P 0.999984
window380 window381 window382 window383

overview

Window 0

Location 2,282,663 – 2,282,780
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.55
Mean single sequence MFE -30.57
Consensus MFE -21.17
Energy contribution -20.85
Covariance contribution -0.32
Combinations/Pair 1.31
Mean z-score -5.31
Structure conservation index 0.69
SVM decision value 4.62
SVM RNA-class probability 0.999930
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2282663 117 + 2685015/0-120
AUUUUGCUCGAAGUACUGUGACAGUACCUAGUCCUUACCGUUACAAGUACAUUAAUAUUCAUUUCCCAUAAAAACCAAGUAU--AUAGA-GUGUCUCCUCACCCUACAUACUUGGUUUUU
............((((((((((.(((.........))).))))).)))))...................(((((((((((((--.(((.-(((......))).))).))))))))))))) ( -31.90)
>sy_au.0 2081207 105 - 2809422/0-120
AUUUUGCUCGAAGUACUAUGACUGUACCUAGUCCUUACUGUCAUAUGUACAAUAAUAUUCAUUUCCCAUAAAAGCCAAGUGU--AU-------------UACCAUGUGCACUUGGUUUUU
............((((((((((.(((.........))).)))))).))))...................(((((((((((((--((-------------......))))))))))))))) ( -30.40)
>sy_sa.0 2141536 117 + 2516575/0-120
UUUUUGCUCGA-GUAUAUUUUUAGUACCUAGUCCUUACUAAU-UAUGUACAAUUA-AUUCAUUUCCCGUAAAAACCAAGUAAUGAUGAAUGUGUCUCCUCACUUCAAUUACUUGGUUUUU
...........-((((((..((((((.........)))))).-.)))))).....-.............((((((((((((((..((((.(((......))))))))))))))))))))) ( -29.40)
>consensus
AUUUUGCUCGAAGUACUAUGACAGUACCUAGUCCUUACUGUUAUAUGUACAAUAAUAUUCAUUUCCCAUAAAAACCAAGUAU__AU__A_GUGUCUCCUCACCAUAAAUACUUGGUUUUU
............((((((((((.(((.........))).)))))).))))...................(((((((((((((........(((......))).....))))))))))))) (-21.17 = -20.85 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,282,663 – 2,282,780
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.55
Mean single sequence MFE -28.73
Consensus MFE -16.61
Energy contribution -19.07
Covariance contribution 2.46
Combinations/Pair 1.29
Mean z-score -3.23
Structure conservation index 0.58
SVM decision value 4.67
SVM RNA-class probability 0.999937
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2282663 117 + 2685015/0-120
AAAAACCAAGUAUGUAGGGUGAGGAGACAC-UCUAU--AUACUUGGUUUUUAUGGGAAAUGAAUAUUAAUGUACUUGUAACGGUAAGGACUAGGUACUGUCACAGUACUUCGAGCAAAAU
(((((((((((((((((((((......)))-)))))--)))))))))))))...................(((((.((.((((((.........)))))).)))))))............ ( -39.30)
>sy_au.0 2081207 105 - 2809422/0-120
AAAAACCAAGUGCACAUGGUA-------------AU--ACACUUGGCUUUUAUGGGAAAUGAAUAUUAUUGUACAUAUGACAGUAAGGACUAGGUACAGUCAUAGUACUUCGAGCAAAAU
((((.(((((((.........-------------..--.))))))).))))...................((((.((((((.(((.........))).))))))))))............ ( -19.50)
>sy_sa.0 2141536 117 + 2516575/0-120
AAAAACCAAGUAAUUGAAGUGAGGAGACACAUUCAUCAUUACUUGGUUUUUACGGGAAAUGAAU-UAAUUGUACAUA-AUUAGUAAGGACUAGGUACUAAAAAUAUAC-UCGAGCAAAAA
((((((((((((((((((.((.(....).))))))..)))))))))))))).((((.(((....-..)))((((...-.(((((....)))))))))..........)-)))........ ( -27.40)
>consensus
AAAAACCAAGUAAAUAAGGUGAGGAGACAC_U__AU__AUACUUGGUUUUUAUGGGAAAUGAAUAUUAUUGUACAUAUAACAGUAAGGACUAGGUACUGUCAAAGUACUUCGAGCAAAAU
(((((((((((((((((((((......))).)))))..)))))))))))))...................((((.(((.((((((.........)))))).)))))))............ (-16.61 = -19.07 +   2.46) 
# Strand winner: forward (0.97)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,282,663 – 2,282,779
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.51
Mean single sequence MFE -32.63
Consensus MFE -21.21
Energy contribution -20.89
Covariance contribution -0.32
Combinations/Pair 1.31
Mean z-score -5.74
Structure conservation index 0.65
SVM decision value 3.97
SVM RNA-class probability 0.999733
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2282663 116 + 2685015/9-129
GAAGUACUGUGACAGUACCUAGUCCUUACCGUUACAAGUACAUUAAUAUUCAUUUCCCAUAAAAACCAAGUAU--AUAGA-GUGUCUCCUCACCCUACAUACUUGGUUUUU-AUCAUGUU
...((((((((((.(((.........))).))))).))))).................(((((((((((((((--.(((.-(((......))).))).)))))))))))))-))...... ( -34.50)
>sy_au.0 2081207 104 - 2809422/9-129
GAAGUACUAUGACUGUACCUAGUCCUUACUGUCAUAUGUACAAUAAUAUUCAUUUCCCAUAAAAGCCAAGUGU--AU-------------UACCAUGUGCACUUGGUUUUU-AUAAUGCU
...((((((((((.(((.........))).)))))).)))).................(((((((((((((((--((-------------......)))))))))))))))-))...... ( -33.60)
>sy_sa.0 2141536 117 + 2516575/9-129
GA-GUAUAUUUUUAGUACCUAGUCCUUACUAAU-UAUGUACAAUUA-AUUCAUUUCCCGUAAAAACCAAGUAAUGAUGAAUGUGUCUCCUCACUUCAAUUACUUGGUUUUUUAUUGUGUU
..-((((((..((((((.........)))))).-.)))))).....-...(((.......((((((((((((((..((((.(((......)))))))))))))))))))))....))).. ( -29.80)
>consensus
GAAGUACUAUGACAGUACCUAGUCCUUACUGUUAUAUGUACAAUAAUAUUCAUUUCCCAUAAAAACCAAGUAU__AU__A_GUGUCUCCUCACCAUAAAUACUUGGUUUUU_AUAAUGUU
...((((((((((.(((.........))).)))))).))))...................(((((((((((((........(((......))).....)))))))))))))......... (-21.21 = -20.89 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,282,663 – 2,282,779
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.51
Mean single sequence MFE -30.30
Consensus MFE -16.71
Energy contribution -19.17
Covariance contribution 2.46
Combinations/Pair 1.29
Mean z-score -3.73
Structure conservation index 0.55
SVM decision value 5.34
SVM RNA-class probability 0.999984
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2282663 116 + 2685015/9-129
AACAUGAU-AAAAACCAAGUAUGUAGGGUGAGGAGACAC-UCUAU--AUACUUGGUUUUUAUGGGAAAUGAAUAUUAAUGUACUUGUAACGGUAAGGACUAGGUACUGUCACAGUACUUC
....(.((-(((((((((((((((((((((......)))-)))))--))))))))))))))).)...............(((((.((.((((((.........)))))).)))))))... ( -42.50)
>sy_au.0 2081207 104 - 2809422/9-129
AGCAUUAU-AAAAACCAAGUGCACAUGGUA-------------AU--ACACUUGGCUUUUAUGGGAAAUGAAUAUUAUUGUACAUAUGACAGUAAGGACUAGGUACAGUCAUAGUACUUC
....((((-((((.(((((((.........-------------..--.))))))).))))))))...............((((.((((((.(((.........))).))))))))))... ( -23.80)
>sy_sa.0 2141536 117 + 2516575/9-129
AACACAAUAAAAAACCAAGUAAUUGAAGUGAGGAGACACAUUCAUCAUUACUUGGUUUUUACGGGAAAUGAAU-UAAUUGUACAUA-AUUAGUAAGGACUAGGUACUAAAAAUAUAC-UC
.........((((((((((((((((((.((.(....).))))))..)))))))))))))).............-.....((((...-.(((((....)))))))))...........-.. ( -24.60)
>consensus
AACAUAAU_AAAAACCAAGUAAAUAAGGUGAGGAGACAC_U__AU__AUACUUGGUUUUUAUGGGAAAUGAAUAUUAUUGUACAUAUAACAGUAAGGACUAGGUACUGUCAAAGUACUUC
.........(((((((((((((((((((((......))).)))))..)))))))))))))...................((((.(((.((((((.........)))))).)))))))... (-16.71 = -19.17 +   2.46) 
# Strand winner: forward (0.98)

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 18:55:53 2006