Locus 3660

Sequence ID X_DroMel_CAF1
Location 9,796,440 – 9,796,534
Length 94
Max. P 0.638136
window5998 window5999

overview

Window 8

Location 9,796,440 – 9,796,534
Length 94
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.06
Mean single sequence MFE -39.10
Consensus MFE -28.56
Energy contribution -28.90
Covariance contribution 0.34
Combinations/Pair 1.06
Mean z-score -1.61
Structure conservation index 0.73
SVM decision value -0.03
SVM RNA-class probability 0.520159
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9796440 94 + 22224390
GGCACAGAAGGGUCCCACGGU-------------------------GUGGGCCACUCAUUAUGCGCUGCCGCUUUAUGGCGCCCAAAUCUGUGCUACGAAAAUUGUAUUAAAAUUUU-UU
((((((((.((((.(((..(.-------------------------((((((((.......)).))..)))).)..))).))))...))))))))..(((((((.......))))))-). ( -30.80)
>DroSec_CAF1 11114 120 + 1
GACACAGAAGGGUCCCUCGGUGGCGGGAAGGGCGGCUCGAAGGCGUGGGGGCCACUCAUUAUGCGCUGCCGCUUUAUGGCGCCCAAAUCUGUGCUACGAAAAUUGUAUUAAAAUUUUAUU
..((((((.((((.((.(((..(((.((.(((.(((((..........))))).))).))...)))..)))......)).))))...)))))).....((((((.......))))))... ( -39.70)
>DroSim_CAF1 12247 120 + 1
GGCACAGAAGGGUCCCUCGGUGGCGGGAAGGGCGGCUCGAGGGCGUGGGGGCCACUCAUUAUGCGCUGCCGCUUUAUGGUGCCCAAAUCUGUGCUACGAAAAUUGUAUUAAAAUUUUAUU
((((((((.(((..((.....(((((..((.(((....((((((......))).)))....))).)).)))))....))..)))...))))))))...((((((.......))))))... ( -46.80)
>consensus
GGCACAGAAGGGUCCCUCGGUGGCGGGAAGGGCGGCUCGA_GGCGUGGGGGCCACUCAUUAUGCGCUGCCGCUUUAUGGCGCCCAAAUCUGUGCUACGAAAAUUGUAUUAAAAUUUUAUU
((((((((..((.((((((....((((........))))......))))))))........((.((.((((.....)))))).))..))))))))...((((((.......))))))... (-28.56 = -28.90 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 9,796,440 – 9,796,534
Length 94
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.06
Mean single sequence MFE -33.70
Consensus MFE -24.72
Energy contribution -25.50
Covariance contribution 0.78
Combinations/Pair 1.05
Mean z-score -1.79
Structure conservation index 0.73
SVM decision value 0.22
SVM RNA-class probability 0.638136
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9796440 94 - 22224390
AA-AAAAUUUUAAUACAAUUUUCGUAGCACAGAUUUGGGCGCCAUAAAGCGGCAGCGCAUAAUGAGUGGCCCAC-------------------------ACCGUGGGACCCUUCUGUGCC
..-.......................(((((((...(((((((((...(((....)))...))).))).(((((-------------------------...))))).))).))))))). ( -29.70)
>DroSec_CAF1 11114 120 - 1
AAUAAAAUUUUAAUACAAUUUUCGUAGCACAGAUUUGGGCGCCAUAAAGCGGCAGCGCAUAAUGAGUGGCCCCCACGCCUUCGAGCCGCCCUUCCCGCCACCGAGGGACCCUUCUGUGUC
..........................(((((((...(((((.(.....(((....)))....((((.(((......))))))).).))))).((((........))))....))))))). ( -34.30)
>DroSim_CAF1 12247 120 - 1
AAUAAAAUUUUAAUACAAUUUUCGUAGCACAGAUUUGGGCACCAUAAAGCGGCAGCGCAUAAUGAGUGGCCCCCACGCCCUCGAGCCGCCCUUCCCGCCACCGAGGGACCCUUCUGUGCC
..........................(((((((...((((........(((....)))....((((.(((......)))))))....)))).((((........))))....))))))). ( -37.10)
>consensus
AAUAAAAUUUUAAUACAAUUUUCGUAGCACAGAUUUGGGCGCCAUAAAGCGGCAGCGCAUAAUGAGUGGCCCCCACGCC_UCGAGCCGCCCUUCCCGCCACCGAGGGACCCUUCUGUGCC
..........................(((((((...(((..((.....(((....)))....((.(((((..........................))))))).))..))).))))))). (-24.72 = -25.50 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:02 2006