Locus 3471

Sequence ID 2R_DroMel_CAF1
Location 11,653,499 – 11,653,649
Length 150
Max. P 0.867539
window5663 window5664 window5665

overview

Window 3

Location 11,653,499 – 11,653,609
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.53
Mean single sequence MFE -29.95
Consensus MFE -25.45
Energy contribution -25.32
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -1.85
Structure conservation index 0.85
SVM decision value 0.86
SVM RNA-class probability 0.867539
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11653499 110 - 20766785
GGAGCGACAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGCAAAGACGGCCAAAAGUAGUGUGGCUGCACUUGUCUAAAUCAAAUUGGCCCACAA-AAGCUCAGUCGAUG---------
.((((((((....(((((......)))))......)))).........((((((..((((.....))))..(((.......))).)))))).....-..))))........--------- ( -26.90)
>DroSim_CAF1 26866 120 - 1
GGAGCGACAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGUGAAGACGGCCAAAAGUAGUGUGGCUGCACUUGUCUAAAUCAAAUUGGCCCACAAAAAGCUCAGUUGAUGCAAGUAAUC
.((((((((....(((((......)))))......)))).(((.....((((((..((((.....))))..(((.......))).))))))))).....))))................. ( -27.80)
>DroEre_CAF1 25771 118 - 1
GGAGCGACAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGCA--GACGGCCAAAAGUAGUGUGGCUGCACUUGUCUGAAACAAUUUGGCCCACAAAAAGCUCAGUCGAUUAAAUUAAUC
.((((((((....(((((......)))))......))))....--...(((((((.((((.....))))..((((.....)))))))))))........))))................. ( -28.80)
>DroYak_CAF1 26369 120 - 1
GGAGUGAUAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGCAACGACGGCCAAAAGUAGUGUGGCUGCACUUGGGUAAGCCCAUUUGGCCCACAAAAAGCUCGACCGAUUUAAUUCAUC
...................((((((.((((...(((((((....))))(((((((.((((.....))))...((((....)))))))))))........)))...)))).)))))).... ( -36.30)
>consensus
GGAGCGACAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGCAAAGACGGCCAAAAGUAGUGUGGCUGCACUUGUCUAAAUCAAAUUGGCCCACAAAAAGCUCAGUCGAUG_AAUUAAUC
.((((((((....(((((......)))))......)))).........((((((..((((.....))))..(((.......))).))))))........))))................. (-25.45 = -25.32 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,653,529 – 11,653,649
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.64
Mean single sequence MFE -24.32
Consensus MFE -21.02
Energy contribution -21.27
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.86
SVM decision value 0.12
SVM RNA-class probability 0.594273
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11653529 120 + 20766785
UUUAGACAAGUGCAGCCACACUACUUUUGGCCGUCUUUGCCGACACUAUUCCAAAUUAAUUUAUUUGUUAUUGUCGCUCCGUUUGGACUUGUUUCCCAAGCUAUCCACGAUGUCCAUCUA
..((((..((((......)))).....(((.((((...((.((((..((..(((((......)))))..))))))))...((((((.........)))))).......)))).))))))) ( -24.80)
>DroSim_CAF1 26906 120 + 1
UUUAGACAAGUGCAGCCACACUACUUUUGGCCGUCUUCACCGACACUAUUCCAAAUUAAUUUAUUUGUUAUUGUCGCUCCGUUUGGACCUGUUUCCCAAGCAAUCCGCGAUGUCCAUCUA
..((((..((((......)))).....(((.((((.....(((((..((..(((((......)))))..)))))))....((((((.........)))))).......)))).))))))) ( -25.20)
>DroEre_CAF1 25811 118 + 1
UUCAGACAAGUGCAGCCACACUACUUUUGGCCGUC--UGCCGACACUAUUCCAAAUUAAUUUAUUUGUUAUUGUCGCUCCGUUUGGUCUCGUUUUCCAAGCUAUCCGCGAUGUCCAUCUA
...(((..((((......)))).....(((.((((--.(((((((..((..(((((......)))))..)))))))....((((((.........)))))).....)))))).)))))). ( -25.80)
>DroYak_CAF1 26409 120 + 1
CUUACCCAAGUGCAGCCACACUACUUUUGGCCGUCGUUGCCGACACUAUUCCAAAUUAAUUUAUUUGUUAUUAUCACUCCGUUUGGUCUCGUUUCCCAAGCAAUCCGCGAUGUCCAUCUA
........((((......)))).....(((.((((((....((....((..(((((......)))))..))..)).....((((((.........)))))).....)))))).))).... ( -21.50)
>consensus
UUUAGACAAGUGCAGCCACACUACUUUUGGCCGUCUUUGCCGACACUAUUCCAAAUUAAUUUAUUUGUUAUUGUCGCUCCGUUUGGACUCGUUUCCCAAGCAAUCCGCGAUGUCCAUCUA
........((((......)))).....(((.((((......((((..((..(((((......)))))..)))))).....((((((.........)))))).......)))).))).... (-21.02 = -21.27 +   0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,653,529 – 11,653,649
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.64
Mean single sequence MFE -30.05
Consensus MFE -26.31
Energy contribution -25.62
Covariance contribution -0.69
Combinations/Pair 1.19
Mean z-score -1.47
Structure conservation index 0.88
SVM decision value 0.17
SVM RNA-class probability 0.614668
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11653529 120 - 20766785
UAGAUGGACAUCGUGGAUAGCUUGGGAAACAAGUCCAAACGGAGCGACAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGCAAAGACGGCCAAAAGUAGUGUGGCUGCACUUGUCUAAA
....((((((..(((....((...(....)...(((....))).(((((....(((((......)))))......))))))).....((((((.........))))))))).)))))).. ( -30.00)
>DroSim_CAF1 26906 120 - 1
UAGAUGGACAUCGCGGAUUGCUUGGGAAACAGGUCCAAACGGAGCGACAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGUGAAGACGGCCAAAAGUAGUGUGGCUGCACUUGUCUAAA
....(((((((((((((((.....(....).)))))........(((((....(((((......)))))......))))))))).(.((((((.........)))))))...)))))).. ( -33.40)
>DroEre_CAF1 25811 118 - 1
UAGAUGGACAUCGCGGAUAGCUUGGAAAACGAGACCAAACGGAGCGACAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGCA--GACGGCCAAAAGUAGUGUGGCUGCACUUGUCUGAA
.....(((((..((((....((((.....)))).(((.((...((((((....(((((......)))))......))))(((.--....)))....)).)).)))))))...)))))... ( -29.00)
>DroYak_CAF1 26409 120 - 1
UAGAUGGACAUCGCGGAUUGCUUGGGAAACGAGACCAAACGGAGUGAUAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGCAACGACGGCCAAAAGUAGUGUGGCUGCACUUGGGUAAG
....(((...((((.....))...(....)))..)))..(.(((((.......(((((......))))).......((((....))))(((((.........))))).))))).)..... ( -27.80)
>consensus
UAGAUGGACAUCGCGGAUAGCUUGGGAAACAAGACCAAACGGAGCGACAAUAACAAAUAAAUUAAUUUGGAAUAGUGUCGGCAAAGACGGCCAAAAGUAGUGUGGCUGCACUUGUCUAAA
....((((((..((((....((((.....)))).(((.((.....((((....(((((......)))))......))))(((.......))).......)).)))))))...)))))).. (-26.31 = -25.62 +  -0.69)

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 10:56:23 2006