Locus 1798

Sequence ID X_DroMel_CAF1
Location 4,975,654 – 4,975,807
Length 153
Max. P 0.887326
window2933 window2934

overview

Window 3

Location 4,975,654 – 4,975,771
Length 117
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 86.05
Mean single sequence MFE -24.77
Consensus MFE -22.02
Energy contribution -21.52
Covariance contribution -0.50
Combinations/Pair 1.10
Mean z-score -1.82
Structure conservation index 0.89
SVM decision value 0.95
SVM RNA-class probability 0.887326
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4975654 117 - 22224390
UAAAUAAAACAAAAAUGAAAAGAACAAGAAGCAUUUGAGGCAACUACAAAACAAUUUGUAGUUUACGCUUUACGCGUUCUCUACAGUUCGUCCGUAACGAAAGCACAAGUUGAGACC--
.....................((((........((((((....)).))))......(((((...((((.....))))...)))))))))(((..((((..........)))).))).-- ( -23.00)
>DroEre_CAF1 46776 107 - 1
----------AAAAAUGAAAAGAACAAGAAGCAUUUGAGGCAACUACAAAACAAUUUGUAGUUUACGCUUUACGCGUUCUCUACAGUUCGUCCGUAACGAAAGCACAAGCUGAGACC--
----------....................((...(((((((((((((((....)))))))))...)))))).))..((((.....(((((.....)))))(((....)))))))..-- ( -22.50)
>DroYak_CAF1 43315 107 - 1
----------AAAAAUGAAAAGAGCAAGAAGCAUUUGAGGCAACUACAAAACAAUUUGUAGUUUACGCUUUACGCGUUCUCUACAGUUCGUCCGUAACGAAAGCACGAGCUGAGACC--
----------.................(((((...(((((((((((((((....)))))))))...)))))).)).)))(((.((((((((.(.........).)))))))))))..-- ( -27.20)
>DroAna_CAF1 43178 114 - 1
-----AAAAAACGAACGAAAGGUACAACUCGCAUUUGAAGCAACUACAAAACAAUUUGUAGUUUACGCUUUACGCGUUCUCCACAGCUCGUCCGUAACGAGAGCCCAAGCUGAGUCUUC
-----..........(....).....((((((...(((((((((((((((....)))))))))...)))))).(.((((((....((......))...)))))).)..)).)))).... ( -26.40)
>consensus
__________AAAAAUGAAAAGAACAAGAAGCAUUUGAGGCAACUACAAAACAAUUUGUAGUUUACGCUUUACGCGUUCUCUACAGUUCGUCCGUAACGAAAGCACAAGCUGAGACC__
..............................((...(((((((((((((((....)))))))))...)))))).))..((((.....(((((.....)))))(((....))))))).... (-22.02 = -21.52 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,975,692 – 4,975,807
Length 115
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 73.83
Mean single sequence MFE -21.42
Consensus MFE -15.50
Energy contribution -15.18
Covariance contribution -0.32
Combinations/Pair 1.26
Mean z-score -1.22
Structure conservation index 0.72
SVM decision value 0.54
SVM RNA-class probability 0.774254
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4975692 115 + 22224390
GAACGCGUAAAGCGUAAACUACAAAUUGUUUUGUAGUUGCCUCAAAUGCUUCUUGUUCUUUUCAUUUUUGUUUUAUUUAUUUUUUUUCAUUCUUAU-UUUGUUGCGGCAACAGCAA
(((((.(..((((((.(((((((((....))))))))).......))))))).)))))......................................-....(((((....).)))) ( -19.40)
>DroGri_CAF1 62075 90 + 1
AAGCGCGUAAAGCGUAAACAGUAAAUUGUGUUGUCGUUGCCA----------UUGUCGUUGUCGGUGUU------------CUUGUUG---CAAUU-UUUGAUGUUGCUACAUAAA
..((((.....))))..........((((((.........((----------(((.......)))))..------------......(---((((.-......))))).)))))). ( -14.60)
>DroEre_CAF1 46814 103 + 1
GAACGCGUAAAGCGUAAACUACAAAUUGUUUUGUAGUUGCCUCAAAUGCUUCUUGUUCUUUUCAUUUUU----------U--UUGUUCUUUCUUAU-UUUGCUGCGGCAACAGCAA
(((((.(..((((((.(((((((((....))))))))).......))))))).)))))...........----------.--..............-.((((((......)))))) ( -21.40)
>DroYak_CAF1 43353 105 + 1
GAACGCGUAAAGCGUAAACUACAAAUUGUUUUGUAGUUGCCUCAAAUGCUUCUUGCUCUUUUCAUUUUU----------UUGUUGUUUCCUCUUAU-UUUGUUGCGGCAACAGCAA
....(((..((((((.(((((((((....))))))))).......))))))..))).............----------((((((((.((.(....-......).)).)))))))) ( -25.50)
>DroAna_CAF1 43218 111 + 1
GAACGCGUAAAGCGUAAACUACAAAUUGUUUUGUAGUUGCUUCAAAUGCGAGUUGUACCUUUCGUUCGUUUUUU-----CUCUCGUUUCUGCUUAUUUUUGUUGAAGCAACAGCAA
((((((((.(((((...((((((((....)))))))))))))...))))(((........))))))).......-----.....(((((.((........)).)))))........ ( -26.20)
>consensus
GAACGCGUAAAGCGUAAACUACAAAUUGUUUUGUAGUUGCCUCAAAUGCUUCUUGUUCUUUUCAUUUUU__________UUCUUGUUCCUUCUUAU_UUUGUUGCGGCAACAGCAA
..((((.....)))).(((((((((....)))))))))............................................................((((((......)))))) (-15.50 = -15.18 +  -0.32)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:05 2006