Locus 2739

Sequence ID 3R_DroMel_CAF1
Location 7,337,315 – 7,337,452
Length 137
Max. P 0.999934
window4452 window4453 window4454

overview

Window 2

Location 7,337,315 – 7,337,412
Length 97
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 93.14
Mean single sequence MFE -21.27
Consensus MFE -20.78
Energy contribution -20.50
Covariance contribution -0.28
Combinations/Pair 1.16
Mean z-score -1.76
Structure conservation index 0.98
SVM decision value 2.89
SVM RNA-class probability 0.997600
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7337315 97 + 27905053
GUUAUCUAGGAAUAGAAAGCUUUAUGCGUUAUAAGCUUCAACAUUCAUGUGUUAUAUAUUUAAUAACAAAAUGUUUGGCUUUUAGGCAUAUGCAUA---C
....((((....))))..((..(((((.(((.(((((..((((((....((((((.......)))))).)))))).))))).)))))))).))...---. ( -22.90)
>DroSec_CAF1 13521 100 + 1
UUUAUCUAGGACUAGAAAGCUUUAUGCGUUGUAAGCUUCAACAUUCAUGUGUUGUAUAUUUAAUAACAAAAUGGUUGGCUUUUAGGCAUAUGCAUACUAC
....((((....))))..((..(((((.(...(((((....((((....((((((.......)))))).))))...)))))..).))))).))....... ( -21.50)
>DroSim_CAF1 18093 100 + 1
UUUAUCUAGGACUAGAAAGCUUUAUGCGUUGUAAGCUUCAACAUUCAUGUGCUAUAUAUUUAAUAACAAAAUGGUUGGCUUUUAGGCAUAUGCAUACUAC
....((((....))))..((..(((((.(...(((((....((((..(((...............))).))))...)))))..).))))).))....... ( -18.06)
>DroEre_CAF1 17336 97 + 1
UUUAUCUGGGACUAGAAAGCUUUAUGCGUUGUAAGCUUCAACAUUCAUGUGUUAUAUAUUUAAUAACAAAAUGUUUGGCUUUUAAGCAUAUGCAUA---U
....((((....))))..((..(((((.(((.(((((..((((((....((((((.......)))))).)))))).))))).)))))))).))...---. ( -22.40)
>DroYak_CAF1 17935 97 + 1
UUUAUCUGGGACUAGAAAGCUUUAUGCGUUGUAAGCUUCAGCAUUCAUGUGUUAUAUAUUUAAUAACAAAAUGUUUGGCUUUUAAGCAUAUGCCUA---C
....((((....))))..((..(((((.(((.(((((..((((((....((((((.......)))))).)))))).))))).)))))))).))...---. ( -21.50)
>consensus
UUUAUCUAGGACUAGAAAGCUUUAUGCGUUGUAAGCUUCAACAUUCAUGUGUUAUAUAUUUAAUAACAAAAUGUUUGGCUUUUAGGCAUAUGCAUA___C
....((((....))))..((..(((((.(((.(((((..((((((....((((((.......)))))).)))))).))))).)))))))).))....... (-20.78 = -20.50 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,337,355 – 7,337,452
Length 97
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 90.92
Mean single sequence MFE -24.18
Consensus MFE -20.72
Energy contribution -21.20
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -2.51
Structure conservation index 0.86
SVM decision value 3.06
SVM RNA-class probability 0.998286
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7337355 97 + 27905053
ACAUUCAUGUGUUAUAUAUUUAAUAACAAAAUGUUUGGCUUUUAGGCAUAUGCAUA---CAUUGCGUAUACGCCAUGUACGCCAUCGAAUGUUAAACUUA
((((((...((((((.......)))))).......((((...((((((((((((..---...)))))))..))).))...))))..))))))........ ( -24.40)
>DroSec_CAF1 13561 100 + 1
ACAUUCAUGUGUUGUAUAUUUAAUAACAAAAUGGUUGGCUUUUAGGCAUAUGCAUACUACAUUGCGUAUUCGCCAUGUGCGCCAUUGAAUGUUAACCUUA
((((((...((((((.......)))))).((((((..((.....((((((((((........)))))))..)))....))))))))))))))........ ( -26.00)
>DroSim_CAF1 18133 100 + 1
ACAUUCAUGUGCUAUAUAUUUAAUAACAAAAUGGUUGGCUUUUAGGCAUAUGCAUACUACAUUGCGUAUUCGCCAUGUGCGCCAUUGAAUGUUAACCUUA
(((((((.((((.((((......((((......)))).......((((((((((........)))))))..)))))))))))...)))))))........ ( -24.90)
>DroEre_CAF1 17376 97 + 1
ACAUUCAUGUGUUAUAUAUUUAAUAACAAAAUGUUUGGCUUUUAAGCAUAUGCAUA---UAUUGCGUAUACGCCAUGUGCGCCAUUGAAUGUGAACCCUA
(((((((..((((((.......)))))).......((((......(.(((((((..---...))))))).)((.....)))))).)))))))........ ( -23.00)
>DroYak_CAF1 17975 97 + 1
GCAUUCAUGUGUUAUAUAUUUAAUAACAAAAUGUUUGGCUUUUAAGCAUAUGCCUA---CAUUGCGUAUACGCCAUGUGUGCCAUCGAAUGUUGGCCUUA
((((((...((((((.......)))))).......((((......((....)).((---(((.(((....))).))))).))))..))))))........ ( -22.60)
>consensus
ACAUUCAUGUGUUAUAUAUUUAAUAACAAAAUGUUUGGCUUUUAGGCAUAUGCAUA___CAUUGCGUAUACGCCAUGUGCGCCAUUGAAUGUUAACCUUA
((((((...((((((.......)))))).......((((.....((((((((((........)))))))..)))......))))..))))))........ (-20.72 = -21.20 +   0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,337,355 – 7,337,452
Length 97
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 90.92
Mean single sequence MFE -23.44
Consensus MFE -22.04
Energy contribution -22.40
Covariance contribution 0.36
Combinations/Pair 1.11
Mean z-score -2.69
Structure conservation index 0.94
SVM decision value 4.65
SVM RNA-class probability 0.999934
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7337355 97 - 27905053
UAAGUUUAACAUUCGAUGGCGUACAUGGCGUAUACGCAAUG---UAUGCAUAUGCCUAAAAGCCAAACAUUUUGUUAUUAAAUAUAUAACACAUGAAUGU
........(((((((.((((......(((((((..(((...---..)))))))))).....)))).......((((((.......))))))..))))))) ( -25.50)
>DroSec_CAF1 13561 100 - 1
UAAGGUUAACAUUCAAUGGCGCACAUGGCGAAUACGCAAUGUAGUAUGCAUAUGCCUAAAAGCCAACCAUUUUGUUAUUAAAUAUACAACACAUGAAUGU
........(((((((.((((((((((.(((....))).)))).))..((....))......))))......((((..........))))....))))))) ( -20.30)
>DroSim_CAF1 18133 100 - 1
UAAGGUUAACAUUCAAUGGCGCACAUGGCGAAUACGCAAUGUAGUAUGCAUAUGCCUAAAAGCCAACCAUUUUGUUAUUAAAUAUAUAGCACAUGAAUGU
........(((((((.((((((((((.(((....))).)))).))..((....))......)))).......((((((.......))))))..))))))) ( -23.30)
>DroEre_CAF1 17376 97 - 1
UAGGGUUCACAUUCAAUGGCGCACAUGGCGUAUACGCAAUA---UAUGCAUAUGCUUAAAAGCCAAACAUUUUGUUAUUAAAUAUAUAACACAUGAAUGU
........(((((((.((((......(((((((..(((...---..)))))))))).....)))).......((((((.......))))))..))))))) ( -24.30)
>DroYak_CAF1 17975 97 - 1
UAAGGCCAACAUUCGAUGGCACACAUGGCGUAUACGCAAUG---UAGGCAUAUGCUUAAAAGCCAAACAUUUUGUUAUUAAAUAUAUAACACAUGAAUGC
.........((((((.((((..((((.(((....))).)))---)((((....))))....)))).......((((((.......))))))..)))))). ( -23.80)
>consensus
UAAGGUUAACAUUCAAUGGCGCACAUGGCGUAUACGCAAUG___UAUGCAUAUGCCUAAAAGCCAAACAUUUUGUUAUUAAAUAUAUAACACAUGAAUGU
........(((((((.((((......(((((((..(((........)))))))))).....)))).......((((((.......))))))..))))))) (-22.04 = -22.40 +   0.36)

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 10:43:44 2006