Locus 6227

Sequence ID 2L_DroMel_CAF1
Location 17,316,626 – 17,316,785
Length 159
Max. P 0.994186
window9950 window9951 window9952

overview

Window 0

Location 17,316,626 – 17,316,746
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.25
Mean single sequence MFE -33.44
Consensus MFE -27.58
Energy contribution -28.50
Covariance contribution 0.92
Combinations/Pair 1.06
Mean z-score -2.72
Structure conservation index 0.82
SVM decision value 2.46
SVM RNA-class probability 0.994186
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17316626 120 + 22407834
UUACUUUUGUGGCAUUGCUUACUAAUUGAAUUUAUGUACAAAAUUUCGAAACAAAAGUUUGUUUGCCUCAAAGGAGGCGAAAUGUGGCGAAAGGAGGUUUGUAUAAGGUGGGAUUUCGAA
...(((((((.(((((((((.....(((((.((........)).))))).....))))....(((((((....)))))))))))).)))))))(((((((..........)))))))... ( -28.20)
>DroSec_CAF1 14216 120 + 1
UUACUUUUGUGGCAUUGCUUACUAAUUGAAUUUAUGUACAAAAUUUUGAAACAAAAGUUUGUUUGCCUCCAAGGAGGCGAAAUGUGGCGAAAGGAGGUUGCUAUAAGGUGGGAUUUCGAA
...(((((((.(((((.....................(((((.(((((...))))).)))))(((((((....)))))))))))).)))))))((((((.(........).))))))... ( -34.10)
>DroSim_CAF1 15751 120 + 1
UUACUUUUGUGGCAUUGCUUACUAAUUGAAUUUAUGUACAAAAUUUUGAAACAAAAGUUUGUUUGCCUCCAAGGAGGCGAAAUGUGGCGAAAGGAGGUUGCUAUAAGGUGGGAUUUCGAA
...(((((((.(((((.....................(((((.(((((...))))).)))))(((((((....)))))))))))).)))))))((((((.(........).))))))... ( -34.10)
>DroEre_CAF1 16204 119 + 1
UUACUUUUGUGGCAUUGCUUACUAAUUGAAUUUAUGUACAAAAUUUUGAAACAAAAGUUUGU-UGCCUCCAAGGAGGCGGAGUGUGGCGAAAGCAGGUUGCUAUAAGGUGGCAAUUCGAA
...(((((((.(((((.(...................(((((.(((((...))))).)))))-.(((((....)))))).))))).)))))))(..((((((((...))))))))..).. ( -36.20)
>DroYak_CAF1 8492 120 + 1
UUACUUUUGUGGCAUUGCUUACUAAUUGAAUUUAUGUAGAAAAUUUUGAAACAAAAGUUUGUUUGCCUCGAAGGAGGCGGAAUGUGGCGAAAGGAGCUUGCUAAAAGGUGGGAUUUCGAA
...(((((((.(((((.((((((((......))).)))).........((((((....))))))(((((....)))))).))))).)))))))((.((..((....))..))...))... ( -34.60)
>consensus
UUACUUUUGUGGCAUUGCUUACUAAUUGAAUUUAUGUACAAAAUUUUGAAACAAAAGUUUGUUUGCCUCCAAGGAGGCGAAAUGUGGCGAAAGGAGGUUGCUAUAAGGUGGGAUUUCGAA
...(((((((.(((((...........((((((.(((.............))).))))))..(((((((....)))))))))))).)))))))((((((.(........).))))))... (-27.58 = -28.50 +   0.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,316,626 – 17,316,746
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.25
Mean single sequence MFE -17.45
Consensus MFE -15.80
Energy contribution -15.64
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -1.21
Structure conservation index 0.91
SVM decision value 0.28
SVM RNA-class probability 0.667855
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17316626 120 - 22407834
UUCGAAAUCCCACCUUAUACAAACCUCCUUUCGCCACAUUUCGCCUCCUUUGAGGCAAACAAACUUUUGUUUCGAAAUUUUGUACAUAAAUUCAAUUAGUAAGCAAUGCCACAAAAGUAA
.................(((........(((((.........(((((....)))))((((((....)))))))))))((((((.(((..................)))..))))))))). ( -15.77)
>DroSec_CAF1 14216 120 - 1
UUCGAAAUCCCACCUUAUAGCAACCUCCUUUCGCCACAUUUCGCCUCCUUGGAGGCAAACAAACUUUUGUUUCAAAAUUUUGUACAUAAAUUCAAUUAGUAAGCAAUGCCACAAAAGUAA
..(((((.....................))))).........(((((....)))))......((((((((..((.....((((...(((......)))....))))))..)))))))).. ( -17.20)
>DroSim_CAF1 15751 120 - 1
UUCGAAAUCCCACCUUAUAGCAACCUCCUUUCGCCACAUUUCGCCUCCUUGGAGGCAAACAAACUUUUGUUUCAAAAUUUUGUACAUAAAUUCAAUUAGUAAGCAAUGCCACAAAAGUAA
..(((((.....................))))).........(((((....)))))......((((((((..((.....((((...(((......)))....))))))..)))))))).. ( -17.20)
>DroEre_CAF1 16204 119 - 1
UUCGAAUUGCCACCUUAUAGCAACCUGCUUUCGCCACACUCCGCCUCCUUGGAGGCA-ACAAACUUUUGUUUCAAAAUUUUGUACAUAAAUUCAAUUAGUAAGCAAUGCCACAAAAGUAA
...................(((...(((((.(..........(((((....))))).-(((((.(((((...))))).)))))...............).))))).)))........... ( -21.60)
>DroYak_CAF1 8492 120 - 1
UUCGAAAUCCCACCUUUUAGCAAGCUCCUUUCGCCACAUUCCGCCUCCUUCGAGGCAAACAAACUUUUGUUUCAAAAUUUUCUACAUAAAUUCAAUUAGUAAGCAAUGCCACAAAAGUAA
.............(((((.(((.(((................(((((....)))))((((((....)))))).............................)))..)))...)))))... ( -15.50)
>consensus
UUCGAAAUCCCACCUUAUAGCAACCUCCUUUCGCCACAUUUCGCCUCCUUGGAGGCAAACAAACUUUUGUUUCAAAAUUUUGUACAUAAAUUCAAUUAGUAAGCAAUGCCACAAAAGUAA
..........................................(((((....)))))......((((((((..((........(((.(((......)))))).....))..)))))))).. (-15.80 = -15.64 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,316,666 – 17,316,785
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.22
Mean single sequence MFE -31.94
Consensus MFE -26.40
Energy contribution -26.80
Covariance contribution 0.40
Combinations/Pair 1.12
Mean z-score -2.20
Structure conservation index 0.83
SVM decision value 1.99
SVM RNA-class probability 0.984824
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17316666 119 + 22407834
AAAUUUCGAAACAAAAGUUUGUUUGCCUCAAAGGAGGCGAAAUGUGGCGAAAGGAGGUUUGUAUAAGGUGGGAUUUCGAAGAAAAGGCAACACAUGUGUGCGAUUGAAAUCAGUU-UUGG
......((((((....(((..((((((((....))))))))....))).......................((((((((.(...(.(((.....))).).)..)))))))).)))-))). ( -27.10)
>DroSec_CAF1 14256 119 + 1
AAAUUUUGAAACAAAAGUUUGUUUGCCUCCAAGGAGGCGAAAUGUGGCGAAAGGAGGUUGCUAUAAGGUGGGAUUUCGAAGAAAAGGCAACACAUGUGUGCGAUUGAAAUCAGUU-UUGG
.....(..((((.........((((((((....)))))))).((((((((.......))))))))......((((((((.(...(.(((.....))).).)..)))))))).)))-)..) ( -31.50)
>DroSim_CAF1 15791 119 + 1
AAAUUUUGAAACAAAAGUUUGUUUGCCUCCAAGGAGGCGAAAUGUGGCGAAAGGAGGUUGCUAUAAGGUGGGAUUUCGAAGAAAAGGCAACACAUGUGUGCGAUUGAAAUCAGUU-UUGG
.....(..((((.........((((((((....)))))))).((((((((.......))))))))......((((((((.(...(.(((.....))).).)..)))))))).)))-)..) ( -31.50)
>DroEre_CAF1 16244 118 + 1
AAAUUUUGAAACAAAAGUUUGU-UGCCUCCAAGGAGGCGGAGUGUGGCGAAAGCAGGUUGCUAUAAGGUGGCAAUUCGAAGAACAGGCGCCACAUGUGUGCGAUUGAAAUCAGUU-CUGG
(((((((......))))))).(-((((((....))))))).((((((((....(..((((((((...))))))))..).........))))))))......(((((....)))))-.... ( -35.32)
>DroYak_CAF1 8532 120 + 1
AAAUUUUGAAACAAAAGUUUGUUUGCCUCGAAGGAGGCGGAAUGUGGCGAAAGGAGCUUGCUAAAAGGUGGGAUUUCGAAGAACAGGCACCACAUGUGUGCGAUUGAAAUCAAUUUUUGG
...........((((((((.(((((((((....)))))....(((..(((((....((..((....))..)).)))))....))).(((((....).)))).....)))).)))))))). ( -34.30)
>consensus
AAAUUUUGAAACAAAAGUUUGUUUGCCUCCAAGGAGGCGAAAUGUGGCGAAAGGAGGUUGCUAUAAGGUGGGAUUUCGAAGAAAAGGCAACACAUGUGUGCGAUUGAAAUCAGUU_UUGG
...((((((((..........((((((((....)))))))).((((((((.......))))))))........)))))))).....(((.((....)))))(((((....)))))..... (-26.40 = -26.80 +   0.40)

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 12:05:47 2006