Locus 2936

Sequence ID X_DroMel_CAF1
Location 7,853,351 – 7,853,528
Length 177
Max. P 0.639829
window4813 window4814 window4815 window4816

overview

Window 3

Location 7,853,351 – 7,853,469
Length 118
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 87.57
Mean single sequence MFE -24.97
Consensus MFE -20.20
Energy contribution -20.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.81
SVM decision value 0.03
SVM RNA-class probability 0.547861
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7853351 118 - 22224390
AAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAAAGCUCAAGCAGAAGUGGAAGCCGAAGCGAAAUAACAAAGCAAAUAAACAAACAAAACGGCCAGGGGAAAGGACUGAAG
........((((((((....))))))))((((((((.....((....))....)))))...))).((...........))................(((((........)).)))... ( -24.40)
>DroEre_CAF1 38132 118 - 1
AAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAAAGCUCAAGCAGAAGUGGAAGCCGAAGCGAAAUAACAAAGCAAAUAAACAAACAAAACGGGCAAAGGAAAGGACUUAAG
.......(((((((((....))))))))).((((.......((....))..........(((...((...........))...........(.....))))........))))..... ( -24.70)
>DroAna_CAF1 22915 112 - 1
AAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAAAGCCCGAGCAAAAGUGGAAGCCGAGGCGGAAUAACAAAGCAAAUAAACAAACAACAAGGGAAG------UGGCCAAAA
.......(((((((((....))))))))).(.((((.....(((((.((..........)))).)))(......)...........................)------))).).... ( -25.80)
>consensus
AAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAAAGCUCAAGCAGAAGUGGAAGCCGAAGCGAAAUAACAAAGCAAAUAAACAAACAAAACGGGCAG_GGAAAGGACUAAAG
........((((((((....))))))))((((((((.....((....))....)))))...))).((...........))...................................... (-20.20 = -20.20 +  -0.00)

alignment

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secondary structure

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Window 4

Location 7,853,389 – 7,853,509
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -26.83
Consensus MFE -25.37
Energy contribution -25.37
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.95
SVM decision value -0.03
SVM RNA-class probability 0.518280
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7853389 120 - 22224390
CAGCAGCCAAGUGCCCACAAAUACAUUCAAAUUUAAUUGAAAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAAAGCUCAAGCAGAAGUGGAAGCCGAAGCGAAAUAACAAAGC
..((..(((.((((..((.......(((((......)))))......(((((((((....))))))))).))..))))...((....)).....)))..))................... ( -25.60)
>DroYak_CAF1 33683 120 - 1
CAGCAGCCAAGUGCCCACAAAUACAUUCAAAUUUAAUUGAAAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAAAGCUCAAGCAGAAGUGGAAGCCGAAGCGAAAUAACAAAGC
..((..(((.((((..((.......(((((......)))))......(((((((((....))))))))).))..))))...((....)).....)))..))................... ( -25.60)
>DroAna_CAF1 22947 120 - 1
CAGCAGCCAAGUGCCCACAAAUACAUUCAAAUUUAAUUGAAAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAAAGCCCGAGCAAAAGUGGAAGCCGAGGCGGAAUAACAAAGC
......((..((((..((.......(((((......)))))......(((((((((....))))))))).))..))))...(((((.((..........)))).)))))........... ( -29.30)
>consensus
CAGCAGCCAAGUGCCCACAAAUACAUUCAAAUUUAAUUGAAAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAAAGCUCAAGCAGAAGUGGAAGCCGAAGCGAAAUAACAAAGC
..((..(((.((((..((.......(((((......)))))......(((((((((....))))))))).))..))))...((....)).....)))..))................... (-25.37 = -25.37 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,853,429 – 7,853,528
Length 99
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.53
Mean single sequence MFE -24.53
Consensus MFE -20.60
Energy contribution -20.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.84
SVM decision value 0.01
SVM RNA-class probability 0.540558
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7853429 99 + 22224390
UUAUGCGGACGAUUGGCAACAAAAGCUGCCAAUUUGUAUUUCAAUUAAAUUUGAAUGUAUUUGUGGGCACUUGGCUGCUGCUUUCUCC-------CCAGCUUUUCC--------------
...((.(((.((..((((.((.(((.((((.((..(((((((((......))))).))))..)).)))))))...)).)))).)))))-------.))........-------------- ( -23.80)
>DroYak_CAF1 33723 100 + 1
UUAUGCGGACGAUUGGCAACAAAAGCUGCCAAUUUGUAUUUCAAUUAAAUUUGAAUGUAUUUGUGGGCACUUGGCUGCUGCUUUUCCC-------CCAGCUUUUCCC-------------
....((((..((..((((.((.(((.((((.((..(((((((((......))))).))))..)).)))))))...)).))))..))..-------)).)).......------------- ( -24.10)
>DroAna_CAF1 22987 120 + 1
UUAUGCGGACGAUUGGCAACAAAAGCUGCCAAUUUGUAUUUCAAUUAAAUUUGAAUGUAUUUGUGGGCACUUGGCUGCUGCUUUUCUCUUUUUCUUUAUCUUUUUCCCUCGGCCUUCGUC
.......(((((..(((.....(((.((((.((..(((((((((......))))).))))..)).)))))))(((....))).............................))).))))) ( -25.70)
>consensus
UUAUGCGGACGAUUGGCAACAAAAGCUGCCAAUUUGUAUUUCAAUUAAAUUUGAAUGUAUUUGUGGGCACUUGGCUGCUGCUUUUCCC_______CCAGCUUUUCCC_____________
....((((.((.(((....)))(((.((((.((..(((((((((......))))).))))..)).)))))))...))))))....................................... (-20.60 = -20.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,853,429 – 7,853,528
Length 99
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.53
Mean single sequence MFE -24.16
Consensus MFE -19.20
Energy contribution -19.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.79
SVM decision value 0.22
SVM RNA-class probability 0.639829
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7853429 99 - 22224390
--------------GGAAAAGCUGG-------GGAGAAAGCAGCAGCCAAGUGCCCACAAAUACAUUCAAAUUUAAUUGAAAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAA
--------------((....((((.-------........))))..))..((((..((.......(((((......)))))......(((((((((....))))))))).))..)))).. ( -24.60)
>DroYak_CAF1 33723 100 - 1
-------------GGGAAAAGCUGG-------GGGAAAAGCAGCAGCCAAGUGCCCACAAAUACAUUCAAAUUUAAUUGAAAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAA
-------------.((....((((.-------........))))..))..((((..((.......(((((......)))))......(((((((((....))))))))).))..)))).. ( -24.60)
>DroAna_CAF1 22987 120 - 1
GACGAAGGCCGAGGGAAAAAGAUAAAGAAAAAGAGAAAAGCAGCAGCCAAGUGCCCACAAAUACAUUCAAAUUUAAUUGAAAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAA
(((((.((((...((...............................))..).)))..........(((((......))))).......((((((((....)))))))))))))....... ( -23.28)
>consensus
_____________GGGAAAAGCUGG_______GGGAAAAGCAGCAGCCAAGUGCCCACAAAUACAUUCAAAUUUAAUUGAAAUACAAAUUGGCAGCUUUUGUUGCCAAUCGUCCGCAUAA
.......................................((....))...((((..((.......(((((......)))))......(((((((((....))))))))).))..)))).. (-19.20 = -19.20 +  -0.00)

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 10:47:08 2006