Locus 1191

Sequence ID 2L_DroMel_CAF1
Location 3,229,711 – 3,229,900
Length 189
Max. P 0.981410
window1929 window1930 window1931 window1932

overview

Window 9

Location 3,229,711 – 3,229,820
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 97.61
Mean single sequence MFE -30.98
Consensus MFE -29.32
Energy contribution -29.56
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.95
SVM decision value 1.89
SVM RNA-class probability 0.981410
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3229711 109 - 22407834
GUCCUGCCGCCACUACUUUGGUCCUGCCCUGCAGCCAGUUGUGGUGGUAGUACAACUAACGUCAUAAUCAAAGUGCCUGAACCUUGAACCAGUCGCACAAUAAAAGUAA
((.((((((((((....((((..((((...))))))))..)))))))))).))...................(((((((..........)))..))))........... ( -32.00)
>DroSec_CAF1 63728 109 - 1
GUCCUGCCGCCACUACAUUGGCCCUGCCCUGCAGCCAGUUGUGGUGGUAGUACAACUAACGUCAUAAUCAAAGUGCCUGAACCUUGAACCAGUCGCACAAUAAAAGUAA
((.((((((((((...((((((..(((...))))))))).)))))))))).))...................(((((((..........)))..))))........... ( -33.80)
>DroSim_CAF1 62257 109 - 1
GUCCUGCCGCCACUACUUUGGUCCUGCCCUGCAGCCAGUUGUGGUGGUAGUACAACUAACGUCAUAAUCAAAGUGCCUGAACCUUGAACCAGUCGCACAAUAAAAGUAA
((.((((((((((....((((..((((...))))))))..)))))))))).))...................(((((((..........)))..))))........... ( -32.00)
>DroEre_CAF1 60235 109 - 1
GUCCUGCCGCCACUCCUUUGGUCCUGCCCUGCAGCCAGUUGUGGUGGUAGUAGAACUAACGUCAUAAUCAAAGUGCCUGAACCUUGAACCAGUCGCACAAUAAAAGUAA
...((((((((((....((((..((((...))))))))..))))))))))((..((....))..))......(((((((..........)))..))))........... ( -30.80)
>DroYak_CAF1 59187 109 - 1
GUCCUGCCGCCACUCCUUUGGUCCUGCCCUGCAGCCAGUUGUGCUGGUGGUACAACUAACGUCAUAAUCAAAGUGCCUGAACCUUGAACCAGUCGCACAAUAAAAGUAA
((..(((((((((.(..((((..((((...))))))))..).).))))))))..))................(((((((..........)))..))))........... ( -26.30)
>consensus
GUCCUGCCGCCACUACUUUGGUCCUGCCCUGCAGCCAGUUGUGGUGGUAGUACAACUAACGUCAUAAUCAAAGUGCCUGAACCUUGAACCAGUCGCACAAUAAAAGUAA
((.((((((((((....((((..((((...))))))))..)))))))))).))...................(((((((..........)))..))))........... (-29.32 = -29.56 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,229,750 – 3,229,860
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 96.55
Mean single sequence MFE -40.32
Consensus MFE -35.14
Energy contribution -35.74
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.87
SVM decision value 0.27
SVM RNA-class probability 0.661848
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3229750 110 + 22407834
UGAUUAUGACGUUAGUUGUACUACCACCACAACUGGCUGCAGGGCAGGACCAAAGUAGUGGCGGCAGGACGAAGUUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCAC
((....((..(((((((((.........)))))))))..))...))((.(((.......((((((((((......))).))))))).((((((....))))))))))).. ( -39.10)
>DroSec_CAF1 63767 110 + 1
UGAUUAUGACGUUAGUUGUACUACCACCACAACUGGCUGCAGGGCAGGGCCAAUGUAGUGGCGGCAGGACGAAGCUCCUUGCCCCUGGCACUGACACCAGUGUUGCCCAC
......((..(((((((((.........)))))))))..))(((((((((((......))))(((((((......))).)))))))(((((((....))))))))))).. ( -43.40)
>DroSim_CAF1 62296 110 + 1
UGAUUAUGACGUUAGUUGUACUACCACCACAACUGGCUGCAGGGCAGGACCAAAGUAGUGGCGGCAGGACGAAGCUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCAC
((....((..(((((((((.........)))))))))..))...))((.(((.......((((((((((......))).))))))).((((((....))))))))))).. ( -39.10)
>DroEre_CAF1 60274 110 + 1
UGAUUAUGACGUUAGUUCUACUACCACCACAACUGGCUGCAGGGCAGGACCAAAGGAGUGGCGGCAGGACGAAGCUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCAC
..............(((((.(..(((.......)))..).))))).((....(((((((..((......))..))))))).))((..((((((....))))))..))... ( -38.10)
>DroYak_CAF1 59226 110 + 1
UGAUUAUGACGUUAGUUGUACCACCAGCACAACUGGCUGCAGGGCAGGACCAAAGGAGUGGCGGCAGGACGAAGCUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCAC
......((..(((((((((.(.....).)))))))))..)).((((.......((((((..((......))..))))))))))((..((((((....))))))..))... ( -41.91)
>consensus
UGAUUAUGACGUUAGUUGUACUACCACCACAACUGGCUGCAGGGCAGGACCAAAGUAGUGGCGGCAGGACGAAGCUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCAC
((....((..(((((((((.........)))))))))..))...))((.(((.......((((((((((......))).))))))).((((((....))))))))))).. (-35.14 = -35.74 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,229,750 – 3,229,860
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 96.55
Mean single sequence MFE -39.34
Consensus MFE -35.56
Energy contribution -35.60
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.16
Structure conservation index 0.90
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3229750 110 - 22407834
GUGGCCAACACUGGUGUCAGUGCCAGCGGCAAGGAACUUCGUCCUGCCGCCACUACUUUGGUCCUGCCCUGCAGCCAGUUGUGGUGGUAGUACAACUAACGUCAUAAUCA
(((((.....(((((......))))).((((.(((......)))))))))))).((.(((((.((((((..(((....)))..).)))))....))))).))........ ( -39.10)
>DroSec_CAF1 63767 110 - 1
GUGGGCAACACUGGUGUCAGUGCCAGGGGCAAGGAGCUUCGUCCUGCCGCCACUACAUUGGCCCUGCCCUGCAGCCAGUUGUGGUGGUAGUACAACUAACGUCAUAAUCA
...(((..(((((....)))))...(((((.....)))))((.((((((((((...((((((..(((...))))))))).)))))))))).)).......)))....... ( -41.10)
>DroSim_CAF1 62296 110 - 1
GUGGCCAACACUGGUGUCAGUGCCAGCGGCAAGGAGCUUCGUCCUGCCGCCACUACUUUGGUCCUGCCCUGCAGCCAGUUGUGGUGGUAGUACAACUAACGUCAUAAUCA
(((((.....(((((......))))).((((.(((......)))))))))))).((.(((((.((((((..(((....)))..).)))))....))))).))........ ( -39.00)
>DroEre_CAF1 60274 110 - 1
GUGGCCAACACUGGUGUCAGUGCCAGCGGCAAGGAGCUUCGUCCUGCCGCCACUCCUUUGGUCCUGCCCUGCAGCCAGUUGUGGUGGUAGUAGAACUAACGUCAUAAUCA
..(((((((((((....)))))...((((((.(((......))))))))).......))))))((((((..(((....)))..).)))))((..((....))..)).... ( -39.10)
>DroYak_CAF1 59226 110 - 1
GUGGCCAACACUGGUGUCAGUGCCAGCGGCAAGGAGCUUCGUCCUGCCGCCACUCCUUUGGUCCUGCCCUGCAGCCAGUUGUGCUGGUGGUACAACUAACGUCAUAAUCA
..(((((((((((....)))))...((((((.(((......))))))))).......))))))((((...))))..((((((((.....))))))))............. ( -38.40)
>consensus
GUGGCCAACACUGGUGUCAGUGCCAGCGGCAAGGAGCUUCGUCCUGCCGCCACUACUUUGGUCCUGCCCUGCAGCCAGUUGUGGUGGUAGUACAACUAACGUCAUAAUCA
(((((.....(((((......))))).((((.(((......)))))))))))).....(((..((((...)))))))((((((..(.(((.....))).)..)))))).. (-35.56 = -35.60 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,229,782 – 3,229,900
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 92.63
Mean single sequence MFE -43.90
Consensus MFE -38.16
Energy contribution -38.40
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.51
Structure conservation index 0.87
SVM decision value 0.97
SVM RNA-class probability 0.891417
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3229782 118 + 22407834
CUGGCUGCAGGGCAGGACCAAAGUAGUGGCGGCAGGACGAAGUUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCACCAAGGCGUUGCAGAAAAAGUGGCUAAGACCUGGAUUACAA
.(((((((...))))..)))..(((((((((((((((......))).)))))))..........(((((.((((((((.....(......).....)))))))).).))))))))).. ( -42.50)
>DroSec_CAF1 63799 118 + 1
CUGGCUGCAGGGCAGGGCCAAUGUAGUGGCGGCAGGACGAAGCUCCUUGCCCCUGGCACUGACACCAGUGUUGCCCACCAAGGCGUUGCAGAAAAAGUGGCUAAGACCUGGAUUACAG
.((((..(.(((((((((((......))))(((((((......))).)))))))(((((((....)))))))))))......((...)).......)..))))....(((.....))) ( -43.10)
>DroSim_CAF1 62328 118 + 1
CUGGCUGCAGGGCAGGACCAAAGUAGUGGCGGCAGGACGAAGCUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCACCAAGGCGCUGCAGAAAAAGUGGCUAAGACAUGGAUUACAG
.((((..(.((......))...((((((.((((((((......))).))))((..((((((....))))))..))......).)))))).......)..))))............... ( -46.10)
>DroEre_CAF1 60306 107 + 1
CUGGCUGCAGGGCAGGACCAAAGGAGUGGCGGCAGGACGAAGCUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCACCAAGGGGUUGCAGAAAAAGUGGCUAAGAC-----------
.((((..(...((((..((.(((((((..((......))..)))))))...((..((((((....))))))..))......))..)))).......)..))))....----------- ( -43.60)
>DroYak_CAF1 59258 118 + 1
CUGGCUGCAGGGCAGGACCAAAGGAGUGGCGGCAGGACGAAGCUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCACCAAGGGGUUGCAGAAAAAGUGGCUAAGACCUGGAUUACAA
..(((....((......)).(((((((..((......))..))))))))))((..((((((....))))))..))..(((.(((((..(.......)..)))....)))))....... ( -44.20)
>consensus
CUGGCUGCAGGGCAGGACCAAAGUAGUGGCGGCAGGACGAAGCUCCUUGCCGCUGGCACUGACACCAGUGUUGGCCACCAAGGCGUUGCAGAAAAAGUGGCUAAGACCUGGAUUACAA
.((((..(.((......))......(..(((((((((......))).))))((..((((((....))))))..)).........))..).......)..))))............... (-38.16 = -38.40 +   0.24)

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 09:55:55 2006