Locus 10006

Sequence ID 3R_DroMel_CAF1
Location 26,780,368 – 26,780,506
Length 138
Max. P 0.996118
window15948 window15949 window15950

overview

Window 8

Location 26,780,368 – 26,780,474
Length 106
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 80.48
Mean single sequence MFE -39.06
Consensus MFE -24.09
Energy contribution -24.17
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -3.14
Structure conservation index 0.62
SVM decision value 2.66
SVM RNA-class probability 0.996118
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26780368 106 + 27905053
GCGGU-----------UUGUGGUGUGGUGGGUGGUAUGGGAUGGCAAAGAAGGAGCAGAAGGGAUCUGCGGUUCAAAUCCCCGGAUUGCCAGCUCAUUACAAUGAAGUGCAACCGCA
(((((-----------(.((..((((((((((((((.(((((......(((...(((((.....)))))..)))..))))).....))))).))))))))).......)))))))). ( -38.00)
>DroSec_CAF1 83701 92 + 1
GCGGC-----------UUGUGGUGG--------------GGUGGCAAAGAAGGAGCAGAGGGGAUCUGCGGUUCAAAUCCCCGGAUUGCCAGCUCAUUACAAUGAAGUGCAACCGCA
((((.-----------(((((((((--------------(.((((((....((.(((((.....)))))((.......))))...)))))).))))))))))((.....)).)))). ( -37.50)
>DroSim_CAF1 87483 102 + 1
GCGGC-----------UUGUGGUGGGGU----GUGAUGGGGUGGCAAAGAAGGAGCAGAGGGGAUCUGCGGUUCAAAUCCCCGGAUUGCCAGCUCAUUACAAUGAAGUGCAACCGCA
((((.-----------(((((.(....(----((((((((.((((((....((.(((((.....)))))((.......))))...)))))).)))))))))....).))))))))). ( -44.70)
>DroEre_CAF1 85268 92 + 1
GCGGC-----------UUGUGGUGG--------------GCAGGGAUAGGAGGAGCAGAAGAGAUCUGCGGUUCAAAUCCCCGGAUUGCCAGCUCAUUACAAUGAAGUGCAACCGCA
((((.-----------(((((((((--------------((.(((((..(((..(((((.....)))))..)))..))))).((....)).)))))))))))((.....)).)))). ( -38.70)
>DroYak_CAF1 87016 103 + 1
GCGGUGGGCAUGGAUAUGGAGAUGG--------------GGAUGGAUAAAAGAAGCGGAUGGGGUCUGCGGUUCAAAUCCCCGGAUUGCCAGCUCAUUACAAUGAAGUGCAACCGCA
(((((..((((.....(((...(((--------------((((((((.......((((((...)))))).)))))..)))))).....)))..((((....)))).)))).))))). ( -36.40)
>consensus
GCGGC___________UUGUGGUGG______________GGUGGCAAAGAAGGAGCAGAAGGGAUCUGCGGUUCAAAUCCCCGGAUUGCCAGCUCAUUACAAUGAAGUGCAACCGCA
((((............((((((((..............................(((((.....)))))(((...((((....)))))))....))))))))..........)))). (-24.09 = -24.17 +   0.08)

alignment

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secondary structure

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Window 9

Location 26,780,368 – 26,780,474
Length 106
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 80.48
Mean single sequence MFE -28.40
Consensus MFE -23.72
Energy contribution -23.40
Covariance contribution -0.32
Combinations/Pair 1.17
Mean z-score -2.37
Structure conservation index 0.84
SVM decision value 1.99
SVM RNA-class probability 0.985070
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26780368 106 - 27905053
UGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCCCUUCUGCUCCUUCUUUGCCAUCCCAUACCACCCACCACACCACAA-----------ACCGC
.(((((((((......))).(((.(.((((((...(((((........(((((.....))))))))))..)))))).).)))..................)-----------))))) ( -27.60)
>DroSec_CAF1 83701 92 - 1
UGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCCCCUCUGCUCCUUCUUUGCCACC--------------CCACCACAA-----------GCCGC
.((((((..........((((.(((..((((....(((((((((.....)))))))))..))))..))).))))....--------------........)-----------))))) ( -29.35)
>DroSim_CAF1 87483 102 - 1
UGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCCCCUCUGCUCCUUCUUUGCCACCCCAUCAC----ACCCCACCACAA-----------GCCGC
.((((((.........(((.(((.(.((((((...(((((((((.....)))))))))............)))))).).))).))----)..........)-----------))))) ( -31.57)
>DroEre_CAF1 85268 92 - 1
UGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCUCUUCUGCUCCUCCUAUCCCUGC--------------CCACCACAA-----------GCCGC
.((((((((..(((((....)))))...))....(((((((..((...(((((.....)))))...))..))))))).--------------........)-----------))))) ( -30.50)
>DroYak_CAF1 87016 103 - 1
UGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGACCCCAUCCGCUUCUUUUAUCCAUCC--------------CCAUCUCCAUAUCCAUGCCCACCGC
.((((((((..(((((....)))))...)))....((((((.((((..((.((.....)).))....))))...))))--------------))..................))))) ( -23.00)
>consensus
UGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCCCCUCUGCUCCUUCUUUGCCACC______________CCACCACAA___________GCCGC
.(((((((((......))))..((((.((....))(((((((((.....)))))))))...))))...............................................))))) (-23.72 = -23.40 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 0

Location 26,780,397 – 26,780,506
Length 109
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 83.24
Mean single sequence MFE -30.57
Consensus MFE -23.20
Energy contribution -23.80
Covariance contribution 0.60
Combinations/Pair 1.20
Mean z-score -1.70
Structure conservation index 0.76
SVM decision value 0.19
SVM RNA-class probability 0.627464
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26780397 109 - 27905053
---CGUUUGCAAUUGUUUUUUCGGCAUUCCGCUCCUGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCCCUUCUGCUCCUUCUUUGCC---AU
---....(((((((((.....(((....))).....))))))))).......((((.(((..((((....(((((((((.....)))))))))..))))..))).)))).---.. ( -32.60)
>DroSec_CAF1 83716 109 - 1
---CGUUUGCAAUUGUUUUUUCGGCAUUCCGCUCCUGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCCCCUCUGCUCCUUCUUUGCC---AC
---....(((((((((.....(((....))).....))))))))).......((((.(((..((((....(((((((((.....)))))))))..))))..))).)))).---.. ( -34.50)
>DroSim_CAF1 87508 109 - 1
---CGUUUGCAAUUGUUUUUUCGGCAUUCCGCUCCUGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCCCCUCUGCUCCUUCUUUGCC---AC
---....(((((((((.....(((....))).....))))))))).......((((.(((..((((....(((((((((.....)))))))))..))))..))).)))).---.. ( -34.50)
>DroEre_CAF1 85283 111 - 1
CUCCGUUUGCAAUUGUUUUUUCGGCAAUCCGCU-CUGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCUCUUCUGCUCCUCCUAUCCC---UG
....((..((.............((((.((((.-..))))))))...((((....))))))..))....(((((((..((...(((((.....)))))...))..)))))---)) ( -33.60)
>DroYak_CAF1 87042 109 - 1
---CGUUUGCAAUUGUUUUUUGGGCAAUCCGCUCCUGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGACCCCAUCCGCUUCUUUUAUCCA---UC
---...(((((((.(......((((((.((((....)))))))).)).)))))))).((((.((....))((((.((((.....))))))))....))))..........---.. ( -28.40)
>DroAna_CAF1 98057 99 - 1
---CGUUUGCAAUUGUUUUUU-GGUAUUCCGCUCCUGUGGCUGCAGUCCAUUGUAAUGAGCUGGCGAUCCGGGGCUUC------------UCUACAUUACAUUUUUUAAAAUGGC
---(((((.....(((..(.(-((......((.((((.(..(((((..(((....)))..)).)))..)))))))...------------.))).)..))).......))))).. ( -19.80)
>consensus
___CGUUUGCAAUUGUUUUUUCGGCAUUCCGCUCCUGCGGUUGCACUUCAUUGUAAUGAGCUGGCAAUCCGGGGAUUUGAACCGCAGAUCCCUUCUGCUCCUUCUUUGCC___AC
......(((((((.(........(((..((((....)))).)))....)))))))).((((.((....))(((((((((.....)))))))))...))))............... (-23.20 = -23.80 +   0.60)

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 13:46:54 2006