Locus 525

Sequence ID X_DroMel_CAF1
Location 1,514,296 – 1,514,441
Length 145
Max. P 0.995771
window821 window822 window823 window824

overview

Window 1

Location 1,514,296 – 1,514,401
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.28
Mean single sequence MFE -21.72
Consensus MFE -16.98
Energy contribution -16.98
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.78
SVM decision value 0.22
SVM RNA-class probability 0.639650
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1514296 105 + 22224390
UCGACAAAAUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGGUUCGUUCUCUUCAGA-------------AAGCAUAAAAUAA--AACACGAAGAGCACAACGAACCGGAAACCACG
.....................................((((((((((((((((((((...-------------.............--.....))))))...)))))))))))))).... ( -27.90)
>DroSec_CAF1 3780 105 + 1
UCGACAAAAUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGCAGA-------------AAGCAUAAAAUAA--AACACGAAGAGCACAACGAACCGGAAACCACG
.....................................(((((((.((((((((((.....-------------.............--.......))))...)))))).))))))).... ( -17.71)
>DroSim_CAF1 5002 105 + 1
UCGACAAAAUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGCAGA-------------AAGCAGAAAAUAA--AACACGAAGAGCACAACGAACCGGAAACCACG
.....................................(((((((.((((((.(((((...-------------..)))))......--.....(.....)..)))))).))))))).... ( -20.20)
>DroEre_CAF1 3805 105 + 1
ACGACAAAAUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGAAGA-------------AAGCAUAUAAUAA--AGAAAUAAGAGCACAACGAACCGGAAACCACG
.....................................(((((((.((((((((((.....-------------.............--.......))))...)))))).))))))).... ( -17.71)
>DroYak_CAF1 5328 120 + 1
UCGACAAAAUUAACAGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGGAGAAUAUUCUGCAUUAAAGCAGAAAUUAAAUAGAAAGAAGAGCACAACGAACCGGAAACCACG
(((........(((.......))).......)))...(((((((.((((((((((......((((((((......)))))......)))......))))...)))))).))))))).... ( -25.06)
>consensus
UCGACAAAAUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGCAGA_____________AAGCAUAAAAUAA__AACACGAAGAGCACAACGAACCGGAAACCACG
.....................................(((((((.((((((((((........................................))))...)))))).))))))).... (-16.98 = -16.98 +   0.00)

alignment

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secondary structure

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Window 2

Location 1,514,296 – 1,514,401
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.28
Mean single sequence MFE -32.64
Consensus MFE -27.22
Energy contribution -27.06
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.86
Structure conservation index 0.83
SVM decision value 1.27
SVM RNA-class probability 0.938230
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1514296 105 - 22224390
CGUGGUUUCCGGUUCGUUGUGCUCUUCGUGUU--UUAUUUUAUGCUU-------------UCUGAAGAGAACGAACCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGA
....((((((((((((((...(((((((.((.--.........))..-------------..))))))))))))))))))))).((..(((((((...((....)).)))))))..)).. ( -35.70)
>DroSec_CAF1 3780 105 - 1
CGUGGUUUCCGGUUCGUUGUGCUCUUCGUGUU--UUAUUUUAUGCUU-------------UCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGA
....((((((((((((((.(((.....((((.--.......))))..-------------...)))...)))))))))))))).((..(((((((...((....)).)))))))..)).. ( -30.40)
>DroSim_CAF1 5002 105 - 1
CGUGGUUUCCGGUUCGUUGUGCUCUUCGUGUU--UUAUUUUCUGCUU-------------UCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGA
....(((((((((((((((..(.....)..).--.....((((((..-------------...)))))))))))))))))))).((..(((((((...((....)).)))))))..)).. ( -34.60)
>DroEre_CAF1 3805 105 - 1
CGUGGUUUCCGGUUCGUUGUGCUCUUAUUUCU--UUAUUAUAUGCUU-------------UCUUCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGU
....((((((((((((((...((((.......--.............-------------.....)))))))))))))))))).((..(((((((...((....)).)))))))..)).. ( -27.51)
>DroYak_CAF1 5328 120 - 1
CGUGGUUUCCGGUUCGUUGUGCUCUUCUUUCUAUUUAAUUUCUGCUUUAAUGCAGAAUAUUCUCCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCUGUUAAUUUUGUCGA
....((((((((((((((.....................((((((......))))))..(((....))))))))))))))))).((..(((((((...(....)...)))))))..)).. ( -35.00)
>consensus
CGUGGUUUCCGGUUCGUUGUGCUCUUCGUGUU__UUAUUUUAUGCUU_____________UCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGA
....((((((((((((((...((((........................................)))))))))))))))))).((..(((((((...(....)...)))))))..)).. (-27.22 = -27.06 +  -0.16)

alignment

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secondary structure

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Window 3

Location 1,514,336 – 1,514,441
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.92
Mean single sequence MFE -25.13
Consensus MFE -18.84
Energy contribution -18.52
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -2.30
Structure conservation index 0.75
SVM decision value 1.10
SVM RNA-class probability 0.914829
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1514336 105 + 22224390
UCCGGUUCGUUCUCUUCAGA-------------AAGCAUAAAAUAA--AACACGAAGAGCACAACGAACCGGAAACCACGAUCGGAAUAGCCAACGUAGUGGCAAAACCUAAAUCUGAAC
(((((((((((((((((...-------------.............--.....))))))...)))))))))))..((......))....((((......))))................. ( -29.70)
>DroSec_CAF1 3820 105 + 1
UCCGAUUCGUUCUCUGCAGA-------------AAGCAUAAAAUAA--AACACGAAGAGCACAACGAACCGGAAACCACGAUCGGAAUAGCCAACGUAGUGGCAAAACCUAAAUCUGAAC
((((.((((((((((.....-------------.............--.......))))...)))))).))))..((......))....((((......))))................. ( -19.51)
>DroSim_CAF1 5042 105 + 1
UCCGAUUCGUUCUCUGCAGA-------------AAGCAGAAAAUAA--AACACGAAGAGCACAACGAACCGGAAACCACGAUCGGAAUAGCCAACGUAGUGGCAAAACCUAAAUCUGAAC
((((((.(((..(((((...-------------..)))))......--......................(....).)))))))))...((((......))))................. ( -23.20)
>DroEre_CAF1 3845 105 + 1
UCCGAUUCGUUCUCUGAAGA-------------AAGCAUAUAAUAA--AGAAAUAAGAGCACAACGAACCGGAAACCACGAUCGGAGUAGCCAACGUAGUGGCAAAACCUAAAUCUGAAC
((((.((((((((((.....-------------.............--.......))))...)))))).))))........(((((...((((......))))..........))))).. ( -20.13)
>DroYak_CAF1 5368 120 + 1
UCCGAUUCGUUCUCUGGAGAAUAUUCUGCAUUAAAGCAGAAAUUAAAUAGAAAGAAGAGCACAACGAACCGGAAACCACGGUCGGAAUAGCCGACGUAGUGGCAAAACCUAAAUCUGAAC
((((.((((((((((......((((((((......)))))......)))......))))...)))))).))))..((((.(((((.....)))))...)))).................. ( -33.10)
>consensus
UCCGAUUCGUUCUCUGCAGA_____________AAGCAUAAAAUAA__AACACGAAGAGCACAACGAACCGGAAACCACGAUCGGAAUAGCCAACGUAGUGGCAAAACCUAAAUCUGAAC
((((.((((((((((........................................))))...)))))).))))...((.(((.((....((((......))))....))...)))))... (-18.84 = -18.52 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,514,336 – 1,514,441
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.92
Mean single sequence MFE -31.56
Consensus MFE -26.70
Energy contribution -26.38
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -2.46
Structure conservation index 0.85
SVM decision value 2.61
SVM RNA-class probability 0.995771
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1514336 105 - 22224390
GUUCAGAUUUAGGUUUUGCCACUACGUUGGCUAUUCCGAUCGUGGUUUCCGGUUCGUUGUGCUCUUCGUGUU--UUAUUUUAUGCUU-------------UCUGAAGAGAACGAACCGGA
...........((.....))((((((((((.....)))).)))))).(((((((((((...(((((((.((.--.........))..-------------..)))))))))))))))))) ( -34.10)
>DroSec_CAF1 3820 105 - 1
GUUCAGAUUUAGGUUUUGCCACUACGUUGGCUAUUCCGAUCGUGGUUUCCGGUUCGUUGUGCUCUUCGUGUU--UUAUUUUAUGCUU-------------UCUGCAGAGAACGAAUCGGA
...........((.....))((((((((((.....)))).)))))).(((((((((((.(((.....((((.--.......))))..-------------...)))...))))))))))) ( -28.80)
>DroSim_CAF1 5042 105 - 1
GUUCAGAUUUAGGUUUUGCCACUACGUUGGCUAUUCCGAUCGUGGUUUCCGGUUCGUUGUGCUCUUCGUGUU--UUAUUUUCUGCUU-------------UCUGCAGAGAACGAAUCGGA
...........((.....))((((((((((.....)))).)))))).((((((((((((..(.....)..).--.....((((((..-------------...))))))))))))))))) ( -33.00)
>DroEre_CAF1 3845 105 - 1
GUUCAGAUUUAGGUUUUGCCACUACGUUGGCUACUCCGAUCGUGGUUUCCGGUUCGUUGUGCUCUUAUUUCU--UUAUUAUAUGCUU-------------UCUUCAGAGAACGAAUCGGA
...........((.....))((((((((((.....)))).)))))).(((((((((((...((((.......--.............-------------.....))))))))))))))) ( -25.91)
>DroYak_CAF1 5368 120 - 1
GUUCAGAUUUAGGUUUUGCCACUACGUCGGCUAUUCCGACCGUGGUUUCCGGUUCGUUGUGCUCUUCUUUCUAUUUAAUUUCUGCUUUAAUGCAGAAUAUUCUCCAGAGAACGAAUCGGA
...........((.....))((((((((((.....)))).)))))).(((((((((((.....................((((((......))))))..(((....)))))))))))))) ( -36.00)
>consensus
GUUCAGAUUUAGGUUUUGCCACUACGUUGGCUAUUCCGAUCGUGGUUUCCGGUUCGUUGUGCUCUUCGUGUU__UUAUUUUAUGCUU_____________UCUGCAGAGAACGAAUCGGA
...........((.....))((((((((((.....)))).)))))).(((((((((((...((((........................................))))))))))))))) (-26.70 = -26.38 +  -0.32)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:51 2006