Locus 475

Sequence ID X_DroMel_CAF1
Location 1,388,835 – 1,388,990
Length 155
Max. P 0.992285
window729 window730 window731 window732 window733

overview

Window 9

Location 1,388,835 – 1,388,928
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 87.81
Mean single sequence MFE -31.32
Consensus MFE -26.66
Energy contribution -26.48
Covariance contribution -0.19
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.85
SVM decision value 1.29
SVM RNA-class probability 0.940611
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1388835 93 + 22224390
UUGCGAUUCGGGCAGCUAAAUUAAUUAAAAAUGUUGGAGCACUUCUACGGUGCUCCUCGCACUGCUUGAGCGGCUCAAAGGAUCCCGGGAUCC
..((..(((((((((................(((.((((((((.....))))))))..))))))))))))..)).....(((((....))))) ( -32.69)
>DroSec_CAF1 16156 93 + 1
UUGCGAUUCGGGCAGCUAAAUUAAUUAAAAAUGUUGGAGCACUUCCACGGUGCUCCUCGCACUGCUUGAGCGGCUCAAAGGAUCCCGGGAUCC
..((..(((((((((................(((.((((((((.....))))))))..))))))))))))..)).....(((((....))))) ( -32.69)
>DroEre_CAF1 15088 93 + 1
CGGCGCUUCGGGCAGCUAAAUUAAUUAAAAUUGCUCAAGCACUUCCCCGGUGCUUCUCGCACUGCUUGAGCGGCUCAAAGGAUCCGGGGAUCC
.(.((((.(((((((...((((......))))((..(((((((.....)))))))...)).))))))))))).).....(((((....))))) ( -32.60)
>DroYak_CAF1 4413 84 + 1
---------GGGCAGCUAAAUUAAUUAAAAAUGCUGCAGCACUUUCCCAGUGCUCCUCGCACUGCUUGAGCGGCUCAAAGGAUCCGGGGAUCC
---------..(((((................)))))(((.(((...((((((.....))))))...)))..)))....(((((....))))) ( -27.29)
>consensus
UUGCGAUUCGGGCAGCUAAAUUAAUUAAAAAUGCUGGAGCACUUCCACGGUGCUCCUCGCACUGCUUGAGCGGCUCAAAGGAUCCCGGGAUCC
.........((((.(((..............(((.((((((((.....))))))))..)))(.....)))).))))...(((((....))))) (-26.66 = -26.48 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,388,835 – 1,388,928
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 87.81
Mean single sequence MFE -29.38
Consensus MFE -24.40
Energy contribution -24.65
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -1.39
Structure conservation index 0.83
SVM decision value 0.01
SVM RNA-class probability 0.540178
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1388835 93 - 22224390
GGAUCCCGGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGAGCACCGUAGAAGUGCUCCAACAUUUUUAAUUAAUUUAGCUGCCCGAAUCGCAA
(((((....)))))((((((...))))))...((((((((((((.......))))))).......((((.....)))).........))))). ( -28.00)
>DroSec_CAF1 16156 93 - 1
GGAUCCCGGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGAGCACCGUGGAAGUGCUCCAACAUUUUUAAUUAAUUUAGCUGCCCGAAUCGCAA
(((((....)))))((((((...))))))...((((((((((((.......))))))).......((((.....)))).........))))). ( -28.00)
>DroEre_CAF1 15088 93 - 1
GGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGAAGCACCGGGGAAGUGCUUGAGCAAUUUUAAUUAAUUUAGCUGCCCGAAGCGCCG
(((((....)))))...(.((.(((((((((((((.....))))........)))))))))................(((......)))))). ( -31.80)
>DroYak_CAF1 4413 84 - 1
GGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGAGCACUGGGAAAGUGCUGCAGCAUUUUUAAUUAAUUUAGCUGCCC---------
(((((....))))).....((.(((.((.((((((.....)))))).((((((((....))))))))......)).))).))..--------- ( -29.70)
>consensus
GGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGAGCACCGGGGAAGUGCUCCAACAUUUUUAAUUAAUUUAGCUGCCCGAAUCGCAA
(((((....))))).(((((...)))))(((((....(((((((.......)))))))........(((.....))))))))........... (-24.40 = -24.65 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,388,854 – 1,388,953
Length 99
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 85.90
Mean single sequence MFE -37.90
Consensus MFE -33.19
Energy contribution -33.50
Covariance contribution 0.31
Combinations/Pair 1.08
Mean z-score -2.05
Structure conservation index 0.88
SVM decision value 1.31
SVM RNA-class probability 0.940665
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1388854 99 + 22224390
AUUAAUUAAAAAUGUUGGAGCACUUCUACGGUGCUCCUCGCACUGCUUGAGCGGCUCAAAGGAUCCCGGGAUCCUGUGUGCCCG------UGUCCGUGCCCGUGU
................((((((((.....))))))))..((((.((....))(((.((.((((((....)))))).)).)))..------.....))))...... ( -37.30)
>DroSec_CAF1 16175 93 + 1
AUUAAUUAAAAAUGUUGGAGCACUUCCACGGUGCUCCUCGCACUGCUUGAGCGGCUCAAAGGAUCCCGGGAUCCUGUGUGCCCG------------UGCCCGUGU
................((((((((.....))))))))..((((.((....))(((.((.((((((....)))))).)).))).)------------)))...... ( -37.30)
>DroEre_CAF1 15107 105 + 1
AUUAAUUAAAAUUGCUCAAGCACUUCCCCGGUGCUUCUCGCACUGCUUGAGCGGCUCAAAGGAUCCGGGGAUCCUGUGUGCCAGUGCCCGUGCCUGUGCCCGUGU
.............(((((((((........((((.....)))))))))))))(((.((.((((((....)))))).)).)))...((.((.((....)).)).)) ( -38.70)
>DroYak_CAF1 4423 105 + 1
AUUAAUUAAAAAUGCUGCAGCACUUUCCCAGUGCUCCUCGCACUGCUUGAGCGGCUCAAAGGAUCCGGGGAUCCUGUGUGCCAGUGGCGGUGGCUGUGCCCGUGU
.............(((((.((.(((...((((((.....))))))...))).(((.((.((((((....)))))).)).))).)).)))))(((...)))..... ( -38.30)
>consensus
AUUAAUUAAAAAUGCUGGAGCACUUCCACGGUGCUCCUCGCACUGCUUGAGCGGCUCAAAGGAUCCCGGGAUCCUGUGUGCCAG______UG_CUGUGCCCGUGU
................((((((((.....))))))))..((((.((....))(((.((.((((((....)))))).)).))).............))))...... (-33.19 = -33.50 +   0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,388,854 – 1,388,953
Length 99
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 85.90
Mean single sequence MFE -39.20
Consensus MFE -33.00
Energy contribution -33.50
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -2.83
Structure conservation index 0.84
SVM decision value 2.32
SVM RNA-class probability 0.992285
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1388854 99 - 22224390
ACACGGGCACGGACA------CGGGCACACAGGAUCCCGGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGAGCACCGUAGAAGUGCUCCAACAUUUUUAAUUAAU
......((((.....------..(((.((.((((((....)))))).)).)))((....)).))))..(((((((.......)))))))................ ( -37.70)
>DroSec_CAF1 16175 93 - 1
ACACGGGCA------------CGGGCACACAGGAUCCCGGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGAGCACCGUGGAAGUGCUCCAACAUUUUUAAUUAAU
......(((------------(.(((.((.((((((....)))))).)).)))((....)).))))..(((((((.......)))))))................ ( -37.70)
>DroEre_CAF1 15107 105 - 1
ACACGGGCACAGGCACGGGCACUGGCACACAGGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGAAGCACCGGGGAAGUGCUUGAGCAAUUUUAAUUAAU
......((.(((((((((((...(((.((.((((((....)))))).)).)))))))...(.((((.....)))).).....))))))).))............. ( -41.00)
>DroYak_CAF1 4423 105 - 1
ACACGGGCACAGCCACCGCCACUGGCACACAGGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGAGCACUGGGAAAGUGCUGCAGCAUUUUUAAUUAAU
....((((...((....))....(((.((.((((((....)))))).)).)))))))...((((((.....)))))).((((((((....))))))))....... ( -40.40)
>consensus
ACACGGGCACAG_CA______CGGGCACACAGGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGAGCACCGGGGAAGUGCUCCAACAUUUUUAAUUAAU
......((((.............(((.((.((((((....)))))).)).)))((....)).))))..(((((((.......)))))))................ (-33.00 = -33.50 +   0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,388,888 – 1,388,990
Length 102
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 89.72
Mean single sequence MFE -37.72
Consensus MFE -34.72
Energy contribution -34.98
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.18
Structure conservation index 0.92
SVM decision value 1.84
SVM RNA-class probability 0.979691
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1388888 102 - 22224390
CAAGCUUAGUUCCCCUUGCGCAACUUGCUCAUUUUCAACACGGGCACGGACA------CGGGCACACAGGAUCCCGGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGA
.............((((((((....(((((...........)))))((....------))(((.((.((((((....)))))).)).)))((....)).)))))))). ( -37.00)
>DroSec_CAF1 16209 96 - 1
CAAGCUUAGUUCCCCUUGCGCAACUUGCUCAUUUCCCACACGGGCA------------CGGGCACACAGGAUCCCGGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGA
.............((((((((..((((..(....(((....)))..------------..(((.((.((((((....)))))).)).))))..))))..)))))))). ( -37.10)
>DroEre_CAF1 15141 108 - 1
CAAGCUUAGUUCCCCUUGCGCAACUUGCUCAUUUCCCACACGGGCACAGGCACGGGCACUGGCACACAGGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGAA
..............(((((((....((((.....(((....)))....)))).((((...(((.((.((((((....)))))).)).))))))).....))))))).. ( -38.60)
>DroYak_CAF1 4457 108 - 1
CAAGCUUAGUUCCCCUUGCGCAACUUGCUCAUUUCCCACACGGGCACAGCCACCGCCACUGGCACACAGGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGA
.............((((((((.....(((((...(((....)))....((((.......))))....((((((....)))))).))))).((....)).)))))))). ( -38.20)
>consensus
CAAGCUUAGUUCCCCUUGCGCAACUUGCUCAUUUCCCACACGGGCACAG_CA______CGGGCACACAGGAUCCCCGGAUCCUUUGAGCCGCUCAAGCAGUGCGAGGA
.............((((((((....(((((...........)))))..............(((.((.((((((....)))))).)).)))((....)).)))))))). (-34.72 = -34.98 +   0.25)

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 09:45:30 2006