Locus 4862

Sequence ID X_DroMel_CAF1
Location 12,644,914 – 12,645,087
Length 173
Max. P 0.790619
window7937 window7938 window7939

overview

Window 7

Location 12,644,914 – 12,645,018
Length 104
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.47
Mean single sequence MFE -25.87
Consensus MFE -17.95
Energy contribution -18.07
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.69
SVM decision value 0.16
SVM RNA-class probability 0.613014
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12644914 104 - 22224390
GAACAUAUUU-UUUGUAACCUACAUUUUUGGCAAAUGAAAGUUGCCGGGUGUUGUUGCAUCUUUUGCCAGCGAGCUCCUUUCAUUUCACUUUCCCAGAAAUAGU---------------A
..........-.........(((((((((((.(((((((((..((....(((((..(((.....)))))))).))..))))))))).......)))))))).))---------------) ( -22.10)
>DroSim_CAF1 689 118 - 1
GAACAUAUUUUUUUGUAACCUACAUUUUUGGCAAAUGAAAGUUGCCGGGUGUUGUUGCAUCUCUUG-CAGCGAGCUCCUUUCAUUUUACUUACCCAGAAAUACAUACCCUAUUAC-CAGU
..(((........))).......((((((((.(((((((((.....((((.((((((((.....))-))))))))))))))))))).......))))))))..............-.... ( -24.10)
>DroYak_CAF1 866 118 - 1
GAACAUAUUU-UUCGUAACCUACAUUUUUGGCAAAUGAAAGUUGCCGGGUGUUGUUGCAUCUUUUG-CAGCGCGCUCCUUUCAUUUUACUUGCCCCAAAAUGCAUACCCUAUUAUGCAUU
..........-..................((((((((((((.....((((((.((((((.....))-))))))))))))))))).....)))))....((((((((......)))))))) ( -31.40)
>consensus
GAACAUAUUU_UUUGUAACCUACAUUUUUGGCAAAUGAAAGUUGCCGGGUGUUGUUGCAUCUUUUG_CAGCGAGCUCCUUUCAUUUUACUUACCCAGAAAUACAUACCCUAUUA__CA_U
.......................((((((((.(((((((((..(((((((((....))))).........)).))..))))))))).......))))))))................... (-17.95 = -18.07 +   0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,644,979 – 12,645,087
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.70
Mean single sequence MFE -33.27
Consensus MFE -25.15
Energy contribution -24.93
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.64
Structure conservation index 0.76
SVM decision value 0.59
SVM RNA-class probability 0.790619
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12644979 108 + 22224390
UUUCAUUUGCCAAAAAUGUAGGUUACAAA-AAAUAUGUUCCGCUGGCACUUGAGC---AGCCAAGUGGGUCGCUGUUCUAAGUGCUCAGUUGG--------GUUGUUUCAUUUUUUUUUU
...(((((.....)))))........(((-(((.(((.(((((((((((((((((---(((..........))))))).)))))).))).)))--------)......))).)))))).. ( -28.70)
>DroSim_CAF1 767 106 + 1
UUUCAUUUGCCAAAAAUGUAGGUUACAAAAAAAUAUGUUCCGCUGGCACUUGAGC---AGCCAAGUGGGUCGCUGUUCUAAGUGCUCAGUUGG--------GUUUUU---UUUUGUUUUU
...(((((.....)))))......(((((((((...(..(.((((((((((((((---(((..........))))))).)))))).)))).).--------.).)))---)))))).... ( -33.00)
>DroYak_CAF1 945 116 + 1
UUUCAUUUGCCAAAAAUGUAGGUUACGAA-AAAUAUGUUCCGCUGGCACUUGAGCAGCAGCCAAGUGGGUCGCUGUUCUAAGUGCUCAGUUGGGAAGGAGGGUUCUU---UCUUUUUUUU
((((....(((.........)))...)))-)........(((((((((((((((((((.(((.....))).))))))).)))))).))).)))(((((((((.....---))))))))). ( -38.10)
>consensus
UUUCAUUUGCCAAAAAUGUAGGUUACAAA_AAAUAUGUUCCGCUGGCACUUGAGC___AGCCAAGUGGGUCGCUGUUCUAAGUGCUCAGUUGG________GUUCUU___UUUUUUUUUU
.((((..(((((.....((.((..(((........))).)))))))))..))))......((((.((((.((((......)))))))).))))........................... (-25.15 = -24.93 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,644,979 – 12,645,087
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.70
Mean single sequence MFE -25.73
Consensus MFE -16.77
Energy contribution -17.10
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.82
Structure conservation index 0.65
SVM decision value 0.10
SVM RNA-class probability 0.583251
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12644979 108 - 22224390
AAAAAAAAAAUGAAACAAC--------CCAACUGAGCACUUAGAACAGCGACCCACUUGGCU---GCUCAAGUGCCAGCGGAACAUAUUU-UUUGUAACCUACAUUUUUGGCAAAUGAAA
.....(((((((.......--------((..(((.((((((.((.((((.(......).)))---).))))))))))).)).(((.....-..)))......)))))))........... ( -24.10)
>DroSim_CAF1 767 106 - 1
AAAAACAAAA---AAAAAC--------CCAACUGAGCACUUAGAACAGCGACCCACUUGGCU---GCUCAAGUGCCAGCGGAACAUAUUUUUUUGUAACCUACAUUUUUGGCAAAUGAAA
....((((((---(((...--------.(..(((.((((((.((.((((.(......).)))---).)))))))))))..)......)))))))))......(((((.....)))))... ( -25.20)
>DroYak_CAF1 945 116 - 1
AAAAAAAAGA---AAGAACCCUCCUUCCCAACUGAGCACUUAGAACAGCGACCCACUUGGCUGCUGCUCAAGUGCCAGCGGAACAUAUUU-UUCGUAACCUACAUUUUUGGCAAAUGAAA
........((---((((.......((((...(((.((((((.((.(((((.((.....)).))))).))))))))))).))))....)))-)))........(((((.....)))))... ( -27.90)
>consensus
AAAAAAAAAA___AAAAAC________CCAACUGAGCACUUAGAACAGCGACCCACUUGGCU___GCUCAAGUGCCAGCGGAACAUAUUU_UUUGUAACCUACAUUUUUGGCAAAUGAAA
...........................(((((((.((((((((...(((.(......).)))....)).))))))))).((.(((........)))..)).......))))......... (-16.77 = -17.10 +   0.33)

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 11:34:45 2006