Locus 2103

Sequence ID 3R_DroMel_CAF1
Location 5,998,192 – 5,998,299
Length 107
Max. P 0.999959
window3439 window3440

overview

Window 9

Location 5,998,192 – 5,998,299
Length 107
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 68.77
Mean single sequence MFE -22.61
Consensus MFE -13.59
Energy contribution -15.90
Covariance contribution 2.31
Combinations/Pair 1.09
Mean z-score -2.14
Structure conservation index 0.60
SVM decision value 2.73
SVM RNA-class probability 0.996636
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5998192 107 + 27905053
GGAAUUUUAUUGUAUACGCAGAGAAAAAGAGGUUCCUGUACUC-----AACCAUAUUAUGAACUCUGAUUAAACUCUGAUUUAUCUCUGUGUACCUAUAAACGUCAGAUUUA
.((..(((((....((((((((((...((((.(((..(((...-----.....)))...)))))))(((((.....)))))..))))))))))...)))))..))....... ( -20.30)
>DroSec_CAF1 10158 107 + 1
GGGAUUUCAUAGGAUGCACAGAAAAAAAGAGGUUCCUGUACUC-----AACCAUAUUAUGAACUCUGAUUAAACUCUUAUUUAUCUCUGUGCACCUAUAAACGUCAGAUUUA
..(((((.(((((.(((((((((((.(((((((((..(((...-----.....)))...))))..........))))).)))...))))))))))))).)).)))....... ( -23.00)
>DroSim_CAF1 8814 81 + 1
GCUAUUUCAUAGGGUACACAGAGAAAAAGAGGUUCCU-----------------------------GAUUAA--UCUGAUUUAUCUCUGUGCACCUAUAAACGUCAGAUUUA
........(((((...((((((((.(((.(((((...-----------------------------....))--)))..))).))))))))..))))).............. ( -20.30)
>DroYak_CAF1 11579 96 + 1
GGUAAUUUAUAAGAUGCACAGAGAAAAAGUUGUUCUCAUACUAGAUAUAGCAAUUCUAUGA--------------CUGGUU--UCUCUGUGCAGCUAUAAACGUCGGAUUUA
.....((((((...((((((((((((.(((..(.......(((....))).......)..)--------------))..))--))))))))))..))))))........... ( -26.84)
>consensus
GGUAUUUCAUAGGAUACACAGAGAAAAAGAGGUUCCUGUACUC_____AACCAUAUUAUGA_____GAUUAA__UCUGAUUUAUCUCUGUGCACCUAUAAACGUCAGAUUUA
.....((((((((.((((((((((...((((..........................................))))......))))))))))))))))))........... (-13.59 = -15.90 +   2.31)

alignment

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secondary structure

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dotplot

Postscript

Window 0

Location 5,998,192 – 5,998,299
Length 107
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 68.77
Mean single sequence MFE -24.27
Consensus MFE -16.93
Energy contribution -16.49
Covariance contribution -0.44
Combinations/Pair 1.33
Mean z-score -2.86
Structure conservation index 0.70
SVM decision value 4.88
SVM RNA-class probability 0.999959
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5998192 107 - 27905053
UAAAUCUGACGUUUAUAGGUACACAGAGAUAAAUCAGAGUUUAAUCAGAGUUCAUAAUAUGGUU-----GAGUACAGGAACCUCUUUUUCUCUGCGUAUACAAUAAAAUUCC
.......((..(((((..((((.((((((......((((((((((((............)))))-----))).........))))...)))))).))))...)))))..)). ( -18.90)
>DroSec_CAF1 10158 107 - 1
UAAAUCUGACGUUUAUAGGUGCACAGAGAUAAAUAAGAGUUUAAUCAGAGUUCAUAAUAUGGUU-----GAGUACAGGAACCUCUUUUUUUCUGUGCAUCCUAUGAAAUCCC
...........((((((((((((((((((.....(((((((((((((............)))))-----))).........)))))..)))))))))).))))))))..... ( -29.90)
>DroSim_CAF1 8814 81 - 1
UAAAUCUGACGUUUAUAGGUGCACAGAGAUAAAUCAGA--UUAAUC-----------------------------AGGAACCUCUUUUUCUCUGUGUACCCUAUGAAAUAGC
.....(((...((((((((((((((((((.(((...((--....))-----------------------------((....)).))).)))))))))).)))))))).))). ( -23.10)
>DroYak_CAF1 11579 96 - 1
UAAAUCCGACGUUUAUAGCUGCACAGAGA--AACCAG--------------UCAUAGAAUUGCUAUAUCUAGUAUGAGAACAACUUUUUCUCUGUGCAUCUUAUAAAUUACC
..........((((((((.((((((((((--((..((--------------(........(((((....)))))........))).))))))))))))..)))))))).... ( -25.19)
>consensus
UAAAUCUGACGUUUAUAGGUGCACAGAGAUAAAUCAGA__UUAAUC_____UCAUAAUAUGGUU_____GAGUACAGGAACCUCUUUUUCUCUGUGCAUCCUAUAAAAUACC
...........((((((((((((((((((...........................................................))))))))))).)))))))..... (-16.93 = -16.49 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:30 2006