Locus 5229

Sequence ID 2L_DroMel_CAF1
Location 14,772,099 – 14,772,243
Length 144
Max. P 0.911092
window8324 window8325 window8326 window8327

overview

Window 4

Location 14,772,099 – 14,772,207
Length 108
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 85.85
Mean single sequence MFE -24.36
Consensus MFE -17.38
Energy contribution -16.62
Covariance contribution -0.76
Combinations/Pair 1.30
Mean z-score -2.08
Structure conservation index 0.71
SVM decision value 0.62
SVM RNA-class probability 0.803169
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14772099 108 + 22407834
CUAU-UUUUCUU-AUACCAUAAAAACUUAUAAAGAAGACUGUAAUUUUUAUCCGUGUAGAUACCCAUAUACACGUUUAUACGAACGUGUACGUUAGCUACAAGUGGACAA
....-.....((-((((.(((((((.(((((........))))))))))))..))))))....((((.(((((((((....))))))))).((.....))..)))).... ( -19.50)
>DroSec_CAF1 18629 108 + 1
CUAU-UUUUCUU-UUAUCAUAAAACCUUAUAAGGAAGUCAGUAAUUUUUAUCCGUGUAGAUAGCCGUAUACACGUUUAUACGAACGUGUACGUUAGCUACAAGUGGACAA
((..-(((((((-.((...........)).)))))))..)).........(((.(((((.((((....(((((((((....))))))))).)))).)))))...)))... ( -22.60)
>DroSim_CAF1 16353 109 + 1
CUAU-UUUUUUUAUUAUCAUAAAACCUUAUAGAGGAAUCUAUAAUUUUUAUCCGUGUAGAUACCCGUAUACACGUUUAUACGAACGUGUACGUUAGCUACAAGUGGACAA
....-..............(((((..(((((((....))))))).)))))(((.(((((.....(((..((((((((....)))))))))))....)))))...)))... ( -23.70)
>DroEre_CAF1 12788 108 + 1
CAAUCUUUCCUC-AUUUCAUAAGAAGUUAGAA-GGGGACUUCAAUUUCUCUCCGUGUAGAUACCCGUAUACACGUUCAUACGAACGUGUACGUUAGCUACAAGUGGACAA
.......(((.(-........(((((((.(((-(....))))))))))).....(((((.....(((..((((((((....)))))))))))....))))).).)))... ( -32.70)
>DroYak_CAF1 15679 108 + 1
CUAU-UUCUUUU-AUUUCACAAAACGCUAAAAUGAAGACUGUAAUUUUUUUCGGUGUAGAUACCCGUAUACACGUUCAUACGAACGUGUACGUUAGCUACAAGUGGACAA
....-.......-..(((((.....(((((.....................(((.((....)))))..(((((((((....)))))))))..))))).....)))))... ( -23.30)
>consensus
CUAU_UUUUCUU_AUAUCAUAAAACCUUAUAAAGAAGACUGUAAUUUUUAUCCGUGUAGAUACCCGUAUACACGUUUAUACGAACGUGUACGUUAGCUACAAGUGGACAA
................((((........(((((((.........)))))))...(((((.....(((..((((((((....)))))))))))....))))).)))).... (-17.38 = -16.62 +  -0.76)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,772,099 – 14,772,207
Length 108
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 85.85
Mean single sequence MFE -24.60
Consensus MFE -18.06
Energy contribution -18.34
Covariance contribution 0.28
Combinations/Pair 1.09
Mean z-score -1.73
Structure conservation index 0.73
SVM decision value 0.23
SVM RNA-class probability 0.643948
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14772099 108 - 22407834
UUGUCCACUUGUAGCUAACGUACACGUUCGUAUAAACGUGUAUAUGGGUAUCUACACGGAUAAAAAUUACAGUCUUCUUUAUAAGUUUUUAUGGUAU-AAGAAAA-AUAG
((((((...(((((((...(((((((((......)))))))))...))...))))).)))))).........((((..((((((....))))))...-))))...-.... ( -21.60)
>DroSec_CAF1 18629 108 - 1
UUGUCCACUUGUAGCUAACGUACACGUUCGUAUAAACGUGUAUACGGCUAUCUACACGGAUAAAAAUUACUGACUUCCUUAUAAGGUUUUAUGAUAA-AAGAAAA-AUAG
((((((....((((((...(((((((((......)))))))))..))))))......))))))..((((..(((((.......)))))...))))..-.......-.... ( -22.60)
>DroSim_CAF1 16353 109 - 1
UUGUCCACUUGUAGCUAACGUACACGUUCGUAUAAACGUGUAUACGGGUAUCUACACGGAUAAAAAUUAUAGAUUCCUCUAUAAGGUUUUAUGAUAAUAAAAAAA-AUAG
((((((...(((((.((.((((((((((......)))))))..)))..)).))))).))))))..((((((((..(((.....))).))))))))..........-.... ( -26.40)
>DroEre_CAF1 12788 108 - 1
UUGUCCACUUGUAGCUAACGUACACGUUCGUAUGAACGUGUAUACGGGUAUCUACACGGAGAGAAAUUGAAGUCCCC-UUCUAACUUCUUAUGAAAU-GAGGAAAGAUUG
...(((.(.(((((.((.(((((((((((....))))))))..)))..)).))))).)..(((((.((((((....)-))).)).))))).......-..)))....... ( -27.10)
>DroYak_CAF1 15679 108 - 1
UUGUCCACUUGUAGCUAACGUACACGUUCGUAUGAACGUGUAUACGGGUAUCUACACCGAAAAAAAUUACAGUCUUCAUUUUAGCGUUUUGUGAAAU-AAAAGAA-AUAG
.....(((.....(((((.((((((((((....)))))))))).(((((....)).))).....................))))).....)))....-.......-.... ( -25.30)
>consensus
UUGUCCACUUGUAGCUAACGUACACGUUCGUAUAAACGUGUAUACGGGUAUCUACACGGAUAAAAAUUACAGUCUUCUUUAUAAGGUUUUAUGAUAU_AAGAAAA_AUAG
((((((...(((((.((.((((((((((......)))))))..)))..)).))))).))))))............................................... (-18.06 = -18.34 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,772,137 – 14,772,243
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 95.85
Mean single sequence MFE -25.92
Consensus MFE -22.64
Energy contribution -22.80
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.87
SVM decision value 1.07
SVM RNA-class probability 0.911092
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14772137 106 + 22407834
GUAAUUUUUAUCCGUGUAGAUACCCAUAUACACGUUUAUACGAACGUGUACGUUAGCUACAAGUGGACAAAGCCGACUAUAAGUGGCAGAAGAACGAAAACCCGAA
....(((((.(((.(((((......(..(((((((((....)))))))))..)...)))))...)))....(((.((.....))))).))))).((......)).. ( -23.00)
>DroSec_CAF1 18667 106 + 1
GUAAUUUUUAUCCGUGUAGAUAGCCGUAUACACGUUUAUACGAACGUGUACGUUAGCUACAAGUGGACAAAGCCGACUAUAAGUGGCAUAAGAACGAAAACCCGAA
....(((((((((.(((((.((((....(((((((((....))))))))).)))).)))))...)))....(((.((.....))))).))))))((......)).. ( -26.40)
>DroSim_CAF1 16392 106 + 1
AUAAUUUUUAUCCGUGUAGAUACCCGUAUACACGUUUAUACGAACGUGUACGUUAGCUACAAGUGGACAAAGCCGACUAUAAGUGGCAGAAGAACGAAAACCCGAA
....(((((.(((.(((((.....(((..((((((((....)))))))))))....)))))...)))....(((.((.....))))).))))).((......)).. ( -24.30)
>DroEre_CAF1 12826 106 + 1
UCAAUUUCUCUCCGUGUAGAUACCCGUAUACACGUUCAUACGAACGUGUACGUUAGCUACAAGUGGACAAAGCCGACUAUAAGUGGCAGAAGAACGAAAACCCGAA
....(((((.(((.(((((.....(((..((((((((....)))))))))))....)))))...)))....(((.((.....))))))))))..((......)).. ( -27.70)
>DroYak_CAF1 15717 106 + 1
GUAAUUUUUUUCGGUGUAGAUACCCGUAUACACGUUCAUACGAACGUGUACGUUAGCUACAAGUGGACAAAGCCGACUAUAAGUGGCAGAAGAACGAAAACCCGAA
.........(((((.((...........(((((((((....)))))))))((((.(((((.(((((......)).)))....))))).....))))...))))))) ( -28.20)
>consensus
GUAAUUUUUAUCCGUGUAGAUACCCGUAUACACGUUUAUACGAACGUGUACGUUAGCUACAAGUGGACAAAGCCGACUAUAAGUGGCAGAAGAACGAAAACCCGAA
..........(((.(((((.....(((..((((((((....)))))))))))....)))))...)))....(((.((.....))))).......((......)).. (-22.64 = -22.80 +   0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,772,137 – 14,772,243
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 95.85
Mean single sequence MFE -27.18
Consensus MFE -23.64
Energy contribution -23.92
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.59
Structure conservation index 0.87
SVM decision value 1.03
SVM RNA-class probability 0.902650
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14772137 106 - 22407834
UUCGGGUUUUCGUUCUUCUGCCACUUAUAGUCGGCUUUGUCCACUUGUAGCUAACGUACACGUUCGUAUAAACGUGUAUAUGGGUAUCUACACGGAUAAAAAUUAC
...................(((((.....)).)))(((((((...(((((((...(((((((((......)))))))))...))...))))).)))))))...... ( -25.20)
>DroSec_CAF1 18667 106 - 1
UUCGGGUUUUCGUUCUUAUGCCACUUAUAGUCGGCUUUGUCCACUUGUAGCUAACGUACACGUUCGUAUAAACGUGUAUACGGCUAUCUACACGGAUAAAAAUUAC
...................(((((.....)).)))(((((((....((((((...(((((((((......)))))))))..))))))......)))))))...... ( -26.70)
>DroSim_CAF1 16392 106 - 1
UUCGGGUUUUCGUUCUUCUGCCACUUAUAGUCGGCUUUGUCCACUUGUAGCUAACGUACACGUUCGUAUAAACGUGUAUACGGGUAUCUACACGGAUAAAAAUUAU
...................(((((.....)).)))(((((((...(((((.((.((((((((((......)))))))..)))..)).))))).)))))))...... ( -25.70)
>DroEre_CAF1 12826 106 - 1
UUCGGGUUUUCGUUCUUCUGCCACUUAUAGUCGGCUUUGUCCACUUGUAGCUAACGUACACGUUCGUAUGAACGUGUAUACGGGUAUCUACACGGAGAGAAAUUGA
.((((.(((((........(((((.....)).)))....(((...(((((.((.(((((((((((....))))))))..)))..)).))))).)))))))).)))) ( -29.50)
>DroYak_CAF1 15717 106 - 1
UUCGGGUUUUCGUUCUUCUGCCACUUAUAGUCGGCUUUGUCCACUUGUAGCUAACGUACACGUUCGUAUGAACGUGUAUACGGGUAUCUACACCGAAAAAAAUUAC
(((((......(..(....(((((.....)).)))...)..)...(((((.((.(((((((((((....))))))))..)))..)).))))))))))......... ( -28.80)
>consensus
UUCGGGUUUUCGUUCUUCUGCCACUUAUAGUCGGCUUUGUCCACUUGUAGCUAACGUACACGUUCGUAUAAACGUGUAUACGGGUAUCUACACGGAUAAAAAUUAC
...................(((((.....)).)))(((((((...(((((.((.((((((((((......)))))))..)))..)).))))).)))))))...... (-23.64 = -23.92 +   0.28)

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 11:39:14 2006