Locus 4197

Sequence ID 3L_DroMel_CAF1
Location 12,262,176 – 12,262,298
Length 122
Max. P 0.962033
window6505 window6506

overview

Window 5

Location 12,262,176 – 12,262,271
Length 95
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 86.34
Mean single sequence MFE -21.82
Consensus MFE -17.74
Energy contribution -18.48
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.81
SVM decision value 1.28
SVM RNA-class probability 0.939636
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12262176 95 + 23771897
CCGUCCAUUUGCAUUUAGAUUGCGCCCCACUCCAG--GCGGCCAGCAU---------CCACGAAU---CUCCCAAAGCUGGCUAACCCGCAAAA-CCCCUUAACCCAAUG
.......(((((..........((((........)--)))((((((..---------........---........))))))......))))).-............... ( -21.17)
>DroSec_CAF1 15669 103 + 1
CCGUCCAUUUGCAUUUAGAUUGCGCCCCACUCCAGGGGCGGCCAGCAUAC---ACAUCCACCAAU---CCCCCAAAGCUGGCUAACCCGCAAAA-CCCCUUAACCCAAUG
.......(((((..........((((((......))))))((((((....---............---........))))))......))))).-............... ( -28.16)
>DroSim_CAF1 18107 103 + 1
CCGUCCAUUUGCAUUUAGAUUGCGCCCCACUCCAGUGGCGGCCAGCAUCC---ACAUCCACCAAU---CCCCCAAAGCUGGCUAACCCGCAAAA-CCCCUUAACCCAAUG
.......(((((..........((((.(......).))))((((((....---............---........))))))......))))).-............... ( -21.06)
>DroYak_CAF1 16599 108 + 1
UCGUCCAUUUGCAUUUAGAUUGCGCCCCACUCCAA--GCGGCCAGCAUCCUCCACUCCCCUCAAAUACCCCCAAAAGCUGGCGAACCCGCAAAAGCCCCCAAACCCAAUG
.......(((((..........(((..........--)))((((((..............................))))))......)))))................. ( -16.91)
>consensus
CCGUCCAUUUGCAUUUAGAUUGCGCCCCACUCCAG__GCGGCCAGCAUCC___ACAUCCACCAAU___CCCCCAAAGCUGGCUAACCCGCAAAA_CCCCUUAACCCAAUG
.......(((((..........((((.(......).))))((((((..............................))))))......)))))................. (-17.74 = -18.48 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 12,262,208 – 12,262,298
Length 90
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 85.17
Mean single sequence MFE -20.43
Consensus MFE -16.78
Energy contribution -17.04
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.82
SVM decision value 1.53
SVM RNA-class probability 0.962033
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12262208 90 + 23771897
CAG--GCGGCCAGCAU---------CCACGAAU---CUCCCAAAGCUGGCUAACCCGCAAAA-CCCCUUAACCCAAUGAUGCCAAACAACUGGCACAAGUGACUU
..(--(.(((((((..---------........---........)))))))...))......-.............((.(((((......)))))))........ ( -19.67)
>DroSec_CAF1 15701 98 + 1
CAGGGGCGGCCAGCAUAC---ACAUCCACCAAU---CCCCCAAAGCUGGCUAACCCGCAAAA-CCCCUUAACCCAAUGAUGCCAAACAACUGGCACAAGUGAUUU
..(((..(((((((....---............---........)))))))..)))......-.............((.(((((......)))))))........ ( -25.96)
>DroSim_CAF1 18139 98 + 1
CAGUGGCGGCCAGCAUCC---ACAUCCACCAAU---CCCCCAAAGCUGGCUAACCCGCAAAA-CCCCUUAACCCAAUGAUGCCAAACAACUGGCACAAGUGACUU
..((((.(((((((....---............---........)))))))...))))....-.............((.(((((......)))))))........ ( -23.26)
>DroYak_CAF1 16631 103 + 1
CAA--GCGGCCAGCAUCCUCCACUCCCCUCAAAUACCCCCAAAAGCUGGCGAACCCGCAAAAGCCCCCAAACCCAAUGAUGCCAAACAACUGCCACAAGUGACUU
...--(((((((((..............................))))))......((....))...............)))......(((......)))..... ( -12.81)
>consensus
CAG__GCGGCCAGCAUCC___ACAUCCACCAAU___CCCCCAAAGCUGGCUAACCCGCAAAA_CCCCUUAACCCAAUGAUGCCAAACAACUGGCACAAGUGACUU
.....(((((((((..............................)))))).....)))..................((.(((((......)))))))........ (-16.78 = -17.04 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:34 2006