Locus 256

Sequence ID 2L_DroMel_CAF1
Location 733,507 – 733,695
Length 188
Max. P 0.999795
window410 window411 window412 window413

overview

Window 0

Location 733,507 – 733,615
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.62
Mean single sequence MFE -27.46
Consensus MFE -26.90
Energy contribution -26.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.98
SVM decision value 3.76
SVM RNA-class probability 0.999595
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 733507 108 + 22407834
------------GCUCCUGCUUCUUCCUCCGCCUUCGGGGUUAAGGCACAUUAACCCCUUCUCCGCUCGCUUUGCCCAUUUCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCC
------------((....))..........((....((((((((......))))))))..........((((.(((((......(((((....)))))))).)))))))).......... ( -26.90)
>DroSec_CAF1 5020 108 + 1
------------GCUCCUGCUUCUUCCUCCGCCUCCGGGGUUAAGGCACAUUAACCCCUUCUCCGCUCGCUUUGCCCAUUUCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCC
------------((....))..........((....((((((((......))))))))..........((((.(((((......(((((....)))))))).)))))))).......... ( -26.90)
>DroSim_CAF1 5019 108 + 1
------------GCUCCUGCUUCUUCCUCCGCCUCCGGGGUUAAGGCACAUUAACCCCUUCUCCGCUCGCUUUGCCCAUUUCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCC
------------((....))..........((....((((((((......))))))))..........((((.(((((......(((((....)))))))).)))))))).......... ( -26.90)
>DroEre_CAF1 5140 108 + 1
------------GCUCGUGCUUCUUCCUCCGCCGCCGGGGUUAAGGCAUAUUAACCCCUUCUCCGCUCGCUUUGCCCAUUUCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCC
------------((..((((................((((((((......))))))))..........((((.(((((......(((((....)))))))).)))))))))).....)). ( -28.30)
>DroYak_CAF1 5345 120 + 1
UCUCCUGCCUCUGCUCGUGCUUCUUCCUUCGCCUCCGGGGUUAAGGCAUAUUAACCCCUUCUCCGCUCGCUUUGCCCAUUUCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCC
............((..((((................((((((((......))))))))..........((((.(((((......(((((....)))))))).)))))))))).....)). ( -28.30)
>consensus
____________GCUCCUGCUUCUUCCUCCGCCUCCGGGGUUAAGGCACAUUAACCCCUUCUCCGCUCGCUUUGCCCAUUUCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCC
............((....))..........((....((((((((......))))))))..........((((.(((((......(((((....)))))))).)))))))).......... (-26.90 = -26.90 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 733,535 – 733,655
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -34.32
Consensus MFE -33.88
Energy contribution -33.64
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -2.52
Structure conservation index 0.99
SVM decision value 3.83
SVM RNA-class probability 0.999650
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 733535 120 - 22407834
GCGAAAACCAUUUAAUGCUGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGAAAUGGGCAAAGCGAGCGGAGAAGGGGUUAAUGUGCCUUAA
((......((((((((((((.(((((........)))))))))))))))))(((((...((((((((....)))))......)))...))))).))......(((((......))))).. ( -32.50)
>DroSec_CAF1 5048 120 - 1
GCGAAAACCAUUUAAUGCUGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGAAAUGGGCAAAGCGAGCGGAGAAGGGGUUAAUGUGCCUUAA
((......((((((((((((.(((((........)))))))))))))))))(((((...((((((((....)))))......)))...))))).))......(((((......))))).. ( -32.50)
>DroSim_CAF1 5047 120 - 1
GCGAAAACCAUUUAAUGCUGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGAAAUGGGCAAAGCGAGCGGAGAAGGGGUUAAUGUGCCUUAA
((......((((((((((((.(((((........)))))))))))))))))(((((...((((((((....)))))......)))...))))).))......(((((......))))).. ( -32.50)
>DroEre_CAF1 5168 120 - 1
GCGAAAAGCAUUUAAUGCCGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGAAAUGGGCAAAGCGAGCGGAGAAGGGGUUAAUAUGCCUUAA
((.....(((((((((((((.(((((........))))))))))))))))))((((...((((((((....)))))......)))...))))..))....((((.((....)).)))).. ( -38.50)
>DroYak_CAF1 5385 120 - 1
GCGAAAACCAUUUAAUGCCGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGAAAUGGGCAAAGCGAGCGGAGAAGGGGUUAAUAUGCCUUAA
((......((((((((((((.(((((........)))))))))))))))))(((((...((((((((....)))))......)))...))))).))....((((.((....)).)))).. ( -35.60)
>consensus
GCGAAAACCAUUUAAUGCUGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGAAAUGGGCAAAGCGAGCGGAGAAGGGGUUAAUGUGCCUUAA
((......((((((((((((.(((((........)))))))))))))))))(((((...((((((((....)))))......)))...))))).))......(((((......))))).. (-33.88 = -33.64 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 733,575 – 733,695
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -38.46
Consensus MFE -33.16
Energy contribution -33.12
Covariance contribution -0.04
Combinations/Pair 1.03
Mean z-score -2.03
Structure conservation index 0.86
SVM decision value 1.82
SVM RNA-class probability 0.978526
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 733575 120 + 22407834
UCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCCAACUUUUAAGUAUGAAAGCACAGCAUUAAAUGGUUUUCGCCGCUUCCUUCUGUUGUGUGAAAGGGGGCGUAGUGGAGCUG
(((((((((....))))).((((.((((.(((.((((((...((((((....))))))....)))))).))))))).))))(((((((((........).))))))))...))))..... ( -35.20)
>DroSec_CAF1 5088 120 + 1
UCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCCAACUUUUAAGUAUGAAAGCACAGCAUUAAAUGGUUUUCGCCGCUUCCUUCUGUUGUGCGAAAGGGGGCGUAGGGGGCCCG
....(((((....))))).((((.((((.(((.((((((...((((((....))))))....)))))).))))))).))))((((((((.((.....)).))))))))...((....)). ( -38.20)
>DroSim_CAF1 5087 120 + 1
UCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCCAACUUUUAAGUAUGAAAGCACAGCAUUAAAUGGUUUUCGCCGCUUCCUUCUGUUGUGCGAAAGGGGGCGUAGUGGGGCCG
(((((((((....))))).((((.((((.(((.((((((...((((((....))))))....)))))).))))))).))))((((((((.((.....)).))))))))...))))..... ( -36.50)
>DroEre_CAF1 5208 120 + 1
UCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCCAACUUUUAAGUAUGAAAGCACGGCAUUAAAUGCUUUUCGCCGCUUCCUUCUGUUGUGUGAAAGGGGGCGUAGUGGGGAUG
.(((..((((.........((((.(((.((((.(((((((..((((((....))))))...))))))).)))).)))))))(((((((((........).))))))))...))))..))) ( -41.20)
>DroYak_CAF1 5425 120 + 1
UCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCCAACUUUUAAGUAUGAAAGCACGGCAUUAAAUGGUUUUCGCCGCUUCCUUCUGUUGUGUGAAAGGGGGCGUAGUGGGGAUG
.(((..((((.........((((.((((.(((.(((((((..((((((....))))))...))))))).))))))).))))(((((((((........).))))))))...))))..))) ( -41.20)
>consensus
UCAUAACCAUAUUUGGUUUGGUGUAAGCGCAUCUAAUGCCAACUUUUAAGUAUGAAAGCACAGCAUUAAAUGGUUUUCGCCGCUUCCUUCUGUUGUGUGAAAGGGGGCGUAGUGGGGCUG
....(((((....))))).((((.((((.(((.((((((...((((((....))))))....)))))).))))))).))))((((((((..(.....)..))))))))............ (-33.16 = -33.12 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 733,575 – 733,695
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -32.16
Consensus MFE -29.60
Energy contribution -29.36
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -2.77
Structure conservation index 0.92
SVM decision value 4.10
SVM RNA-class probability 0.999795
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 733575 120 - 22407834
CAGCUCCACUACGCCCCCUUUCACACAACAGAAGGAAGCGGCGAAAACCAUUUAAUGCUGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGA
.(((.......(((((.(((((........)))))..).)))).....((((((((((((.(((((........))))))))))))))))).))).....(((((((....))))).)). ( -30.00)
>DroSec_CAF1 5088 120 - 1
CGGGCCCCCUACGCCCCCUUUCGCACAACAGAAGGAAGCGGCGAAAACCAUUUAAUGCUGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGA
.((((.......)))).(((((........)))))(((((........((((((((((((.(((((........))))))))))))))))))))))....(((((((....))))).)). ( -32.00)
>DroSim_CAF1 5087 120 - 1
CGGCCCCACUACGCCCCCUUUCGCACAACAGAAGGAAGCGGCGAAAACCAUUUAAUGCUGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGA
.((........(((..((((..(.....)..))))..)))(((.....((((((((((((.(((((........)))))))))))))))))))).....)).(((((....))))).... ( -30.50)
>DroEre_CAF1 5208 120 - 1
CAUCCCCACUACGCCCCCUUUCACACAACAGAAGGAAGCGGCGAAAAGCAUUUAAUGCCGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGA
(((..(((...(((((.(((((........)))))..).))))....(((((((((((((.(((((........))))))))))))))))))...................)))..))). ( -36.20)
>DroYak_CAF1 5425 120 - 1
CAUCCCCACUACGCCCCCUUUCACACAACAGAAGGAAGCGGCGAAAACCAUUUAAUGCCGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGA
(((..(((...(((..(((((.........)))))..)))(((.....((((((((((((.(((((........)))))))))))))))))))).................)))..))). ( -32.10)
>consensus
CAGCCCCACUACGCCCCCUUUCACACAACAGAAGGAAGCGGCGAAAACCAUUUAAUGCUGUGCUUUCAUACUUAAAAGUUGGCAUUAGAUGCGCUUACACCAAACCAAAUAUGGUUAUGA
...........(((..(((((.........)))))..)))(((.....((((((((((((.(((((........))))))))))))))))))))......(((((((....))))).)). (-29.60 = -29.36 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:23 2006