Locus 72

Sequence ID 3L_DroMel_CAF1
Location 279,263 – 279,439
Length 176
Max. P 0.983184
window101 window102 window103

overview

Window 1

Location 279,263 – 279,371
Length 108
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 85.06
Mean single sequence MFE -30.49
Consensus MFE -20.32
Energy contribution -20.56
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.66
Structure conservation index 0.67
SVM decision value 1.13
SVM RNA-class probability 0.919708
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 279263 108 + 23771897
GUAUACAUAUCGGUAAACUUUCAAUU-----------AGUUUGGUUGGGACUUAAAUUCCGGAAGAAAUGUGUGUGUAUUUGCGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCU
..((((((.((..((((((.......-----------)))))).((((((......))))))..)).))))))((((....)))).(((((((((....)))))))))((((...)))) ( -29.60)
>DroSec_CAF1 51403 107 + 1
GCAUACGUCUCGAUAAACU-UCAAUU-----------AGUUUGCUUGGGACUUAAAUUCCGGAAGAAAUGUGUCUGUUUUUACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCU
((((..(((((((((((((-......-----------)))))).)))))))........(....)..))))((((((....))...(((((((((....)))))))))..))))..... ( -32.40)
>DroSim_CAF1 47198 107 + 1
GCAUACGUCUCGAUAAACU-UCAAUU-----------AGUUUACUUGGGACUUAAAUUCCGGAAGAGAUGUGUCUGUUUUUACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCU
......(((((((((((((-......-----------)))))).)))))))............(((((.((.(((((....))...(((((((((....)))))))))))).))))))) ( -35.70)
>DroEre_CAF1 50899 106 + 1
GCAUACGGAUGGAUAAACU-UCAACU------------CUUUGGUGGGGAAUUUAAUUCCGGAAGAUAUGAGUCUAUCUUUACGCAAAUUGCAGCGAAAGCUGUAAUUACAGACUCUCU
((.((.((((((((.....-(((..(------------((((.(.(((........)))).)))))..))))))))))).)).)).(((((((((....)))))))))........... ( -31.10)
>DroYak_CAF1 47557 118 + 1
GCAUACGGAUCGAUCAACU-UUACUUUACUUUUUCUUACUUUGGUUGGGACUUAAAUUCCGGAAGAUAUGUGUCUAUUUUUACGCAAUUUGCAGCGAAAGCUGUAAUUACAGACUCUCU
((...((((....((((((-......................)))))).........))))(((((((......)))))))..))...(((((((....)))))))............. ( -23.67)
>consensus
GCAUACGUAUCGAUAAACU_UCAAUU___________AGUUUGGUUGGGACUUAAAUUCCGGAAGAAAUGUGUCUGUUUUUACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCU
..............................................((((......))))(..((...(((((........)))))(((((((((....))))))))).....))..). (-20.32 = -20.56 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 279,292 – 279,407
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 90.52
Mean single sequence MFE -28.82
Consensus MFE -21.44
Energy contribution -21.68
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.32
Structure conservation index 0.74
SVM decision value 0.93
SVM RNA-class probability 0.885002
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 279292 115 + 23771897
UUGGUUGGGACUUAAAUUCCGGAAGAAAUGUGUGUGUAUUUGCGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCUCUUGAUACCAAUACAAGUCAAAAUGGCAUUUAUAAU
(((((.((((......))))(..(((..((((((......))))))(((((((((....)))))))))......)))..).....))))).....(((.....)))......... ( -29.90)
>DroSec_CAF1 51431 115 + 1
UUGCUUGGGACUUAAAUUCCGGAAGAAAUGUGUCUGUUUUUACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCUCUUAAUACCAAUACAAGUCAAAAUGGCAUUUAUAAU
.((((...(((((......(....)...(((((........)))))(((((((((....)))))))))((((.....))))............))))).....))))........ ( -29.60)
>DroSim_CAF1 47226 115 + 1
UUACUUGGGACUUAAAUUCCGGAAGAGAUGUGUCUGUUUUUACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCUCUUAAUACCAAUACAAGUCAAAAUGGCAUUUAUAAU
..((((((((.......)))((((((((.(.((((((....))...(((((((((....)))))))))..)))).)))))))....))....))))).................. ( -31.60)
>DroEre_CAF1 50926 115 + 1
UUGGUGGGGAAUUUAAUUCCGGAAGAUAUGAGUCUAUCUUUACGCAAAUUGCAGCGAAAGCUGUAAUUACAGACUCUCUCUUAAUACCAAUACACGUCAAUAUGUUAUUUGUAAU
((((((.(((((...)))))..((((...((((((...........(((((((((....)))))))))..))))))..))))..))))))......................... ( -30.12)
>DroYak_CAF1 47596 115 + 1
UUGGUUGGGACUUAAAUUCCGGAAGAUAUGUGUCUAUUUUUACGCAAUUUGCAGCGAAAGCUGUAAUUACAGACUCUCUCUUAAUACCCAUACACGUCAAUAGGUUAUUCAUAAU
.((..((((..........(....)...(((((........)))))..(((((((....)))))))....................))))..))..................... ( -22.90)
>consensus
UUGGUUGGGACUUAAAUUCCGGAAGAAAUGUGUCUGUUUUUACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCUCUUAAUACCAAUACAAGUCAAAAUGGCAUUUAUAAU
......((((......))))(..(((..(((((........)))))(((((((((....)))))))))......)))..)................................... (-21.44 = -21.68 +   0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 279,332 – 279,439
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 93.23
Mean single sequence MFE -22.84
Consensus MFE -18.24
Energy contribution -18.20
Covariance contribution -0.04
Combinations/Pair 1.12
Mean z-score -2.52
Structure conservation index 0.80
SVM decision value 1.94
SVM RNA-class probability 0.983184
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 279332 107 + 23771897
UGCGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCUCUUGAUACCAAUACAAGUCAAAAUGGCAUUUAUAAUGAGGUAAAGUACCCCACAACGUCAUUUAAUAU
......(((((((((....)))))))))((((.....))))((((..........(((.....)))........((.((((...)))).))....))))........ ( -23.90)
>DroSec_CAF1 51471 106 + 1
UACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCUCUUAAUACCAAUACAAGUCAAAAUGGCAUUUAUAAUGAGGUAAAGUACC-CACAACGUCAUUUAAUAU
......(((((((((....)))))))))((((.....))))..................(((((((........((.((((...))))-))....)))))))..... ( -23.30)
>DroSim_CAF1 47266 106 + 1
UACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCUCUUAAUACCAAUACAAGUCAAAAUGGCAUUUAUAAUGAGGUAAAGUACC-CACAGCGUCAUUUAAUAU
.((((.(((((((((....)))))))))((((.....))))..............(((.....)))........((.((((...))))-))..)))).......... ( -25.90)
>DroEre_CAF1 50966 106 + 1
UACGCAAAUUGCAGCGAAAGCUGUAAUUACAGACUCUCUCUUAAUACCAAUACACGUCAAUAUGUUAUUUGUAAUGAGGCAAAGUACC-CACAACGUCAUUUAAUAU
...((.(((((((((....)))))))))...........((((.(((.((((.((((....)))))))).))).))))))........-.................. ( -22.90)
>DroYak_CAF1 47636 106 + 1
UACGCAAUUUGCAGCGAAAGCUGUAAUUACAGACUCUCUCUUAAUACCCAUACACGUCAAUAGGUUAUUCAUAAUGAGGCAAAGUACC-CACAACGUCAUUUAAUAU
...((...(((((((....))))))).......(((......((((.((.............)).))))......)))))........-.................. ( -18.22)
>consensus
UACGCAAAUUGCAGCGAAAGCUGUAAUUAGAGACUCUCUCUUAAUACCAAUACAAGUCAAAAUGGCAUUUAUAAUGAGGUAAAGUACC_CACAACGUCAUUUAAUAU
......(((((((((....)))))))))...(((((((....(((.(((.............))).)))......))))....((........)))))......... (-18.24 = -18.20 +  -0.04)

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 09:31:37 2006