Locus 60

Sequence ID sy_ha.0
Location 878,122 – 878,241
Length 119
Max. P 1.000000
window270 window271 window272 window273

overview

Window 0

Location 878,122 – 878,241
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 66.94
Mean single sequence MFE -29.37
Consensus MFE -21.38
Energy contribution -20.83
Covariance contribution -0.55
Combinations/Pair 1.22
Mean z-score -1.87
Structure conservation index 0.73
SVM decision value 4.26
SVM RNA-class probability 0.999852
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 878122 119 - 2685015/0-120
AUGGUAUCUAAUUACAAGACAAAAUAAAAAGAACGCCGUCAUAACAGCGUUCUCA-ACCUAAAAAUAUAUGUAAUUUUUAGUUAAUAGCGUCCUGGGAGGGAUUCGAACCCCCGACCGAU
.((((.........((.(((.........(((((((.((....)).)))))))..-..((((((((.......))))))))........))).))((.(((.......))))).)))).. ( -27.90)
>sy_au.0 1191692 119 + 2809422/0-120
AUACUAUAUUACUGAAAUUCAAAACAAAAAGAGCCCCGUAAUCACGGAACUCUUUUGUUUGGUAAUGCGUAUAAAAAU-ACCUAUAAACGUCCUGGGAGGGAUUCGAACCCCCGACCGAU
((((..((((((..((..........(((((((..((((....))))..))))))).))..)))))).))))......-..........(((..(((.((........)))))))).... ( -27.70)
>sy_sa.0 1707858 118 + 2516575/0-120
AUUGUAUCGCAUUGUAG-AUAAAAUAAAAGAAACCCCGUCGUUACGGGGUUUCCUAGUUUGA-AUUGUGCGCUAUUUAACGCUAUUAGUGUCCUGGGAGGGAUUCGAACCCCCGACCGAU
...(((.(((((.....-...((((....((((((((((....))))))))))...))))..-...))))).)))...((((.....))))..(((..(((.........)))..))).. ( -32.52)
>consensus
AUAGUAUCUAAUUGAAA_ACAAAAUAAAAAGAACCCCGUCAUAACGGAGUUCUCU_GUUUGA_AAUGUGUGUAAUUUU_AGCUAUUAGCGUCCUGGGAGGGAUUCGAACCCCCGACCGAU
.............................((((((((((....))))))))))....................................(((..(((.((........)))))))).... (-21.38 = -20.83 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 1

Location 878,122 – 878,241
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 66.94
Mean single sequence MFE -35.14
Consensus MFE -27.50
Energy contribution -24.63
Covariance contribution -2.87
Combinations/Pair 1.48
Mean z-score -2.89
Structure conservation index 0.78
SVM decision value 7.21
SVM RNA-class probability 1.000000
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 878122 119 - 2685015/0-120
AUCGGUCGGGGGUUCGAAUCCCUCCCAGGACGCUAUUAACUAAAAAUUACAUAUAUUUUUAGGU-UGAGAACGCUGUUAUGACGGCGUUCUUUUUAUUUUGUCUUGUAAUUAGAUACCAU
...(((.(((((.......))))).((((((........((((((((.......))))))))..-.(((((((((((....)))))))))))........)))))).........))).. ( -36.90)
>sy_au.0 1191692 119 + 2809422/0-120
AUCGGUCGGGGGUUCGAAUCCCUCCCAGGACGUUUAUAGGU-AUUUUUAUACGCAUUACCAAACAAAAGAGUUCCGUGAUUACGGGGCUCUUUUUGUUUUGAAUUUCAGUAAUAUAGUAU
...((..((((((....)))))).))..((.(((((..(((-(.............))))(((((((((((((((((....))))))))).))))))))))))).))............. ( -33.12)
>sy_sa.0 1707858 118 + 2516575/0-120
AUCGGUCGGGGGUUCGAAUCCCUCCCAGGACACUAAUAGCGUUAAAUAGCGCACAAU-UCAAACUAGGAAACCCCGUAACGACGGGGUUUCUUUUAUUUUAU-CUACAAUGCGAUACAAU
((((((((((((........)))))...))).......(((((....))))).....-.......((((((((((((....)))))))))))).........-........))))..... ( -35.40)
>consensus
AUCGGUCGGGGGUUCGAAUCCCUCCCAGGACGCUAAUAGCU_AAAAUUACACACAUU_UCAAAC_AGAGAACCCCGUAAUGACGGGGUUCUUUUUAUUUUGU_UUACAAUAAGAUACAAU
...((..((((((....)))))).))..................................((((..(((((((((((....)))))))))))...))))..................... (-27.50 = -24.63 +  -2.87) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 878,122 – 878,240
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.43
Mean single sequence MFE -36.13
Consensus MFE -31.30
Energy contribution -31.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.76
Structure conservation index 0.87
SVM decision value 1.48
SVM RNA-class probability 0.957286
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 878122 118 - 2685015/80-200
GUUAAUAGCGUCCUGGGAGGGAUUCGAACCCCCGACCGAUGGCUUAGAAGGCCAUUGCUCUAUCCAGCUGAGCUACCAGGACAUGAA--UUUUUAACACAAGAAUUAUUAUAGCUAAAGA
.....((((((((((((.(((........))))....(((((((.....)))))))((((.........))))..)))))))...((--(((((.....)))))))......)))).... ( -37.10)
>sy_au.0 1191692 117 + 2809422/80-200
CCUAUAAACGUCCUGGGAGGGAUUCGAACCCCCGACCGAUGGCUUAGAAGGCCAUUGCUCUAUCCAGCUGAGCUACCAGGACACGU---UUAACAACACAAGAAUUAUUAUAUCUAAAUG
....(((((((((((((.(((........))))....(((((((.....)))))))((((.........))))..)))))))..))---)))............................ ( -32.50)
>sy_sa.0 1707858 120 + 2516575/80-200
GCUAUUAGUGUCCUGGGAGGGAUUCGAACCCCCGACCGAUGGCUUAGAAGGCCAUUGCUCUAUCCAGCUGAGCUACCAGGACAUAUUGUUUUUGAACACAAAAAUAAUUAUAUCUAACUU
.......((((((((((.(((........))))....(((((((.....)))))))((((.........))))..)))))))))((((((((((....))))))))))............ ( -38.80)
>consensus
GCUAUUAGCGUCCUGGGAGGGAUUCGAACCCCCGACCGAUGGCUUAGAAGGCCAUUGCUCUAUCCAGCUGAGCUACCAGGACAUGU___UUUUCAACACAAGAAUUAUUAUAUCUAAAUA
.........((((((((.(((........))))....(((((((.....)))))))((((.........))))..)))))))...................................... (-31.30 = -31.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 878,122 – 878,240
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.43
Mean single sequence MFE -34.93
Consensus MFE -32.09
Energy contribution -32.20
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.70
Structure conservation index 0.92
SVM decision value 0.70
SVM RNA-class probability 0.826260
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 878122 118 - 2685015/80-200
UCUUUAGCUAUAAUAAUUCUUGUGUUAAAAA--UUCAUGUCCUGGUAGCUCAGCUGGAUAGAGCAAUGGCCUUCUAAGCCAUCGGUCGGGGGUUCGAAUCCCUCCCAGGACGCUAUUAAC
....((((.....((((......))))....--.....(((((((((((...))))....((.(.(((((.......))))).).))(((((.......))))))))))))))))..... ( -34.00)
>sy_au.0 1191692 117 + 2809422/80-200
CAUUUAGAUAUAAUAAUUCUUGUGUUGUUAA---ACGUGUCCUGGUAGCUCAGCUGGAUAGAGCAAUGGCCUUCUAAGCCAUCGGUCGGGGGUUCGAAUCCCUCCCAGGACGUUUAUAGG
....(((((.(((((((......))))))).---....(((((((((((...))))....((.(.(((((.......))))).).))(((((.......))))))))))))))))).... ( -34.10)
>sy_sa.0 1707858 120 + 2516575/80-200
AAGUUAGAUAUAAUUAUUUUUGUGUUCAAAAACAAUAUGUCCUGGUAGCUCAGCUGGAUAGAGCAAUGGCCUUCUAAGCCAUCGGUCGGGGGUUCGAAUCCCUCCCAGGACACUAAUAGC
..(((((.....(((.((((((....)))))).))).((((((((((((...))))....((.(.(((((.......))))).).))(((((.......))))))))))))))))))... ( -36.70)
>consensus
AAUUUAGAUAUAAUAAUUCUUGUGUUAAAAA___ACAUGUCCUGGUAGCUCAGCUGGAUAGAGCAAUGGCCUUCUAAGCCAUCGGUCGGGGGUUCGAAUCCCUCCCAGGACGCUAAUAGC
......(((((((......)))))))...........((((((((((((...))))....((.(.(((((.......))))).).))(((((.......)))))))))))))........ (-32.09 = -32.20 +   0.11) 
# Strand winner: reverse (0.71)

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 18:54:22 2006