Locus 5418

Sequence ID 2R_DroMel_CAF1
Location 17,468,249 – 17,468,448
Length 199
Max. P 0.902682
window8640 window8641 window8642 window8643

overview

Window 0

Location 17,468,249 – 17,468,368
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.21
Mean single sequence MFE -38.51
Consensus MFE -34.19
Energy contribution -34.30
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.29
Structure conservation index 0.89
SVM decision value 0.60
SVM RNA-class probability 0.795534
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17468249 119 + 20766785
GUUUCCGCAACAUUUUCGCAUUGGCAGCG-GGAAAGUGCAUUUAAUUAAAUUUCCCUUUGUUCGAUGCGAGUGCAAAAAGCAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACA
......((((((.((((((((((((((.(-(((((...............)))))).))).))))))).(((((.....)))))(((..((......))..)))..)))).))))))... ( -41.46)
>DroSim_CAF1 4194 119 + 1
GUUUCCGCAACAUUUUCGCAGUGGCAGCG-GGAAAGUGCAUUUAAUUAAAUUUCCCUUUGUUCGAUGCGAGUGCAAAAAGCAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACA
......((((((.(((((((..(((((.(-(((((...............)))))).)))))...))).(((((.....)))))(((..((......))..)))..)))).))))))... ( -37.86)
>DroYak_CAF1 4461 120 + 1
GUAUCCGCAACAUUUUCGCAGUGGCAGCAGAGAAAGUGCAUUUAAUUAAAUUUCCCUUUGUUCGAUGCGAGUGCAAAAAGCAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACA
......((((((.(((((((.(.(((((((((.((((............))))..))))))....))).).))).....((.(((((..(....)..)))))))..)))).))))))... ( -36.20)
>consensus
GUUUCCGCAACAUUUUCGCAGUGGCAGCG_GGAAAGUGCAUUUAAUUAAAUUUCCCUUUGUUCGAUGCGAGUGCAAAAAGCAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACA
......((((((.(((((((.(.(((.((.(.((((...((((....))))....)))).).)).))).).))).....((.(((((..(....)..)))))))..)))).))))))... (-34.19 = -34.30 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,468,288 – 17,468,408
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 99.44
Mean single sequence MFE -35.27
Consensus MFE -35.49
Energy contribution -35.27
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.96
Structure conservation index 1.01
SVM decision value 1.03
SVM RNA-class probability 0.902682
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17468288 120 + 20766785
UUUAAUUAAAUUUCCCUUUGUUCGAUGCGAGUGCAAAAAGCAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACAUGCAGCCGCAAAAUGUCGGCUGCUCAUGACAACACCAACC
................(((((((......(((((.....)))))(((..(....)..))))))))))....(((((((...((((((((.....).)))))))...)).)))))...... ( -35.90)
>DroSim_CAF1 4233 120 + 1
UUUAAUUAAAUUUCCCUUUGUUCGAUGCGAGUGCAAAAAGCAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACAUGCAGCCGCAAAAUGUCGGCUGCUCAUGACAACACCAACC
................(((((((......(((((.....)))))(((..(....)..))))))))))....(((((((...((((((((.....).)))))))...)).)))))...... ( -35.90)
>DroYak_CAF1 4501 120 + 1
UUUAAUUAAAUUUCCCUUUGUUCGAUGCGAGUGCAAAAAGCAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACAUGCAGCCGCAAAAUGUUGGCUGCUCAUGACAACACCAACC
................(((((((......(((((.....)))))(((..(....)..))))))))))....(((((((...((((((((.....).)))))))...)).)))))...... ( -34.00)
>consensus
UUUAAUUAAAUUUCCCUUUGUUCGAUGCGAGUGCAAAAAGCAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACAUGCAGCCGCAAAAUGUCGGCUGCUCAUGACAACACCAACC
................(((((((......(((((.....)))))(((..(....)..))))))))))....(((((((...((((((((.....).)))))))...)).)))))...... (-35.49 = -35.27 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,468,288 – 17,468,408
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -36.53
Consensus MFE -35.93
Energy contribution -36.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.98
SVM decision value 0.23
SVM RNA-class probability 0.644610
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17468288 120 - 20766785
GGUUGGUGUUGUCAUGAGCAGCCGACAUUUUGCGGCUGCAUGUGCAACAGUUUCUUGCCCGCCCGCAAAAGUAGGCAAUGCUUUUUGCACUCGCAUCGAACAAAGGGAAAUUUAAUUAAA
((..(.(((((.((((.(((((((.(.....)))))))).))))))))).)..))..((((((..(....)..)))..((.((..(((....)))..)).))..)))............. ( -37.60)
>DroSim_CAF1 4233 120 - 1
GGUUGGUGUUGUCAUGAGCAGCCGACAUUUUGCGGCUGCAUGUGCAACAGUUUCUUGCCCGCCCGCAAAAGUAGGCAAUGCUUUUUGCACUCGCAUCGAACAAAGGGAAAUUUAAUUAAA
((..(.(((((.((((.(((((((.(.....)))))))).))))))))).)..))..((((((..(....)..)))..((.((..(((....)))..)).))..)))............. ( -37.60)
>DroYak_CAF1 4501 120 - 1
GGUUGGUGUUGUCAUGAGCAGCCAACAUUUUGCGGCUGCAUGUGCAACAGUUUCUUGCCCGCCCGCAAAAGUAGGCAAUGCUUUUUGCACUCGCAUCGAACAAAGGGAAAUUUAAUUAAA
((..(.(((((.((((.((((((..........)))))).))))))))).)..))..((((((..(....)..)))..((.((..(((....)))..)).))..)))............. ( -34.40)
>consensus
GGUUGGUGUUGUCAUGAGCAGCCGACAUUUUGCGGCUGCAUGUGCAACAGUUUCUUGCCCGCCCGCAAAAGUAGGCAAUGCUUUUUGCACUCGCAUCGAACAAAGGGAAAUUUAAUUAAA
((..(.(((((.((((.(((((((........))))))).))))))))).)..))..((((((..(....)..)))..((.((..(((....)))..)).))..)))............. (-35.93 = -36.27 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,468,328 – 17,468,448
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -33.31
Consensus MFE -33.53
Energy contribution -33.31
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.54
Structure conservation index 1.01
SVM decision value 0.37
SVM RNA-class probability 0.710617
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17468328 120 + 20766785
CAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACAUGCAGCCGCAAAAUGUCGGCUGCUCAUGACAACACCAACCAGCAGCCCUCAACCACCAACCGAGCACCACCGAGCACCGA
...(((......(((.((((..((.......(((((((...((((((((.....).)))))))...)).))))).......)).)))).)))........((........)).))).... ( -33.94)
>DroSim_CAF1 4273 120 + 1
CAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACAUGCAGCCGCAAAAUGUCGGCUGCUCAUGACAACACCAACCAGCAGCCCUCAACCACCAACCGAGCACCACCGAGCACCGA
...(((......(((.((((..((.......(((((((...((((((((.....).)))))))...)).))))).......)).)))).)))........((........)).))).... ( -33.94)
>DroYak_CAF1 4541 118 + 1
CAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACAUGCAGCCGCAAAAUGUUGGCUGCUCAUGACAACACCAACCAGCAGCCCUCAACCACCAACCGAGCACCACCGAGCACC--
...(((......(((.((((..((.......(((((((...((((((((.....).)))))))...)).))))).......)).)))).)))........((........)).)))..-- ( -32.04)
>consensus
CAUUGCCUACUUUUGCGGGCGGGCAAGAAACUGUUGCACAUGCAGCCGCAAAAUGUCGGCUGCUCAUGACAACACCAACCAGCAGCCCUCAACCACCAACCGAGCACCACCGAGCACCGA
...(((......(((.((((..((.......(((((((...((((((((.....).)))))))...)).))))).......)).)))).)))........((........)).))).... (-33.53 = -33.31 +  -0.22)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:18 2006