Locus 7486

Sequence ID 2L_DroMel_CAF1
Location 20,790,437 – 20,790,536
Length 99
Max. P 0.663138
window12033 window12034

overview

Window 3

Location 20,790,437 – 20,790,536
Length 99
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 87.54
Mean single sequence MFE -33.17
Consensus MFE -24.08
Energy contribution -26.57
Covariance contribution 2.50
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.73
SVM decision value 0.27
SVM RNA-class probability 0.663138
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20790437 99 + 22407834
UCG---------------UCUUGCUGUUCCACCAUCCUCACUGCGUUUGGUAGCCGGAUAGCUCAUAAGUUAAUGGAGAUCUCGUCAUCUCAUCAGUCGCAAACGCAGUGUGAG
...---------------................((..((((((((((.(..((.((.(((((....)))))...(((((......))))).)).))..))))))))))).)). ( -25.60)
>DroSec_CAF1 13760 109 + 1
UCGACAGCGGUGGAAUCAUCUUGCUGUUCCACCAUCCUCACUGCGUUUGGUAGCCGGAUAGCUCAUAAGUUAAUGGAGAUCUCGUC-----AUCAGUCGCAAACGCAGUGUGAG
........(((((((.((......))))))))).((..(((((((((((....(((..(((((....))))).))).(((......-----))).....))))))))))).)). ( -35.40)
>DroSim_CAF1 16235 109 + 1
UCGACAGUGGUGGAAUCAUCUUGCUGUUCCACCAUCCUCACUGCGUUUGGUAGCCGGAUAGCUCAUAAGUUAAUGGAGAUCUCGUC-----AUCAGUCGCAAACGCAGUGUGAG
......(((((((((.((......))))))))))).(.(((((((((((....(((..(((((....))))).))).(((......-----))).....))))))))))).).. ( -36.70)
>DroYak_CAF1 14720 106 + 1
UCGAAA---GUGGAAUCGUCUUGCUGUUCCACCAUCUUCACUGCGUUUGCUACCCGGAUAGCUCAUAACUUAAUGGAGAUCUCGUC-----AUCAGUCGCAAACGCAGUGUGAU
......---(((((((.(.....).))))))).(((..((((((((((((.((...(((..(.(((......)))((....)))..-----))).)).)))))))))))).))) ( -35.00)
>consensus
UCGACA___GUGGAAUCAUCUUGCUGUUCCACCAUCCUCACUGCGUUUGGUAGCCGGAUAGCUCAUAAGUUAAUGGAGAUCUCGUC_____AUCAGUCGCAAACGCAGUGUGAG
........((((((((.........)))))))).((..(((((((((((....(((..(((((....))))).))).((.((.((......)).)))).))))))))))).)). (-24.08 = -26.57 +   2.50)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 20,790,437 – 20,790,536
Length 99
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 87.54
Mean single sequence MFE -34.05
Consensus MFE -21.25
Energy contribution -23.50
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -2.03
Structure conservation index 0.62
SVM decision value -0.03
SVM RNA-class probability 0.515892
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20790437 99 - 22407834
CUCACACUGCGUUUGCGACUGAUGAGAUGACGAGAUCUCCAUUAACUUAUGAGCUAUCCGGCUACCAAACGCAGUGAGGAUGGUGGAACAGCAAGA---------------CGA
....(((((((((((.(..(((((((((......)))).))))).......((((....)))).))))))))))))....((.((...)).))...---------------... ( -26.90)
>DroSec_CAF1 13760 109 - 1
CUCACACUGCGUUUGCGACUGAU-----GACGAGAUCUCCAUUAACUUAUGAGCUAUCCGGCUACCAAACGCAGUGAGGAUGGUGGAACAGCAAGAUGAUUCCACCGCUGUCGA
....(((((((((((.(..((((-----(..(....)..))))).......((((....)))).)))))))))))).((.((((((((((......)).))))))))))..... ( -35.80)
>DroSim_CAF1 16235 109 - 1
CUCACACUGCGUUUGCGACUGAU-----GACGAGAUCUCCAUUAACUUAUGAGCUAUCCGGCUACCAAACGCAGUGAGGAUGGUGGAACAGCAAGAUGAUUCCACCACUGUCGA
....(((((((((((.(..((((-----(..(....)..))))).......((((....)))).)))))))))))).((.((((((((((......)).))))))))))..... ( -36.20)
>DroYak_CAF1 14720 106 - 1
AUCACACUGCGUUUGCGACUGAU-----GACGAGAUCUCCAUUAAGUUAUGAGCUAUCCGGGUAGCAAACGCAGUGAAGAUGGUGGAACAGCAAGACGAUUCCAC---UUUCGA
....(((((((((((((.((.((-----(((..(((....)))..))))).)))(((....)))))))))))))))..((.(((((((..(.....)..))))))---).)).. ( -37.30)
>consensus
CUCACACUGCGUUUGCGACUGAU_____GACGAGAUCUCCAUUAACUUAUGAGCUAUCCGGCUACCAAACGCAGUGAGGAUGGUGGAACAGCAAGAUGAUUCCAC___UGUCGA
....(((((((((((........................(((......)))((((....))))..))))))))))).....(((((((...........)))))))........ (-21.25 = -23.50 +   2.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:01 2006