Locus 4863

Sequence ID 3L_DroMel_CAF1
Location 13,601,688 – 13,601,906
Length 218
Max. P 0.996950
window7674 window7675 window7676

overview

Window 4

Location 13,601,688 – 13,601,791
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.78
Mean single sequence MFE -26.03
Consensus MFE -13.60
Energy contribution -13.49
Covariance contribution -0.11
Combinations/Pair 1.11
Mean z-score -1.95
Structure conservation index 0.52
SVM decision value 0.19
SVM RNA-class probability 0.628077
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13601688 103 + 23771897
AUACACAACAAUAACUGUCAGAGGAAAACUGUUGGGUGCUGCUGGUC-------CACC---CCAA-------AGAAGCGGCAUUUAUUGUUGUUAUUAUUGCAUUAUCCGUUGCAUACUC
....(((((((((((((.(((.......))).)))((((((((((..-------..))---....-------...))))))))))))))))))......((((........))))..... ( -24.91)
>DroSec_CAF1 8605 100 + 1
AUACACAACAAUAACUGUCAGUGGAAAACUGUUGGGUG---CUGGUC-------CACC---CCAA-------AGAAGCGGCAUUUAUUGUUGUUAUUAUUGCAUUAUCCGUUGCAUACUU
....((((((((((.(((((((.....)))...(((((---......-------))))---)...-------......)))).))))))))))......((((........))))..... ( -26.40)
>DroSim_CAF1 17864 102 + 1
AUACACAACAAUAACUGUCAGAGGAAAACUGCUGGGUGC-GCUGGUC-------CACC---CCAA-------AGAAGCGGCAUUUAUUGUUGUUAUUAUUGCAUUAUCCGUUGCAUACUU
....((((((((((.((((..((.....))((((((((.-.......-------))))---)...-------...))))))).))))))))))......((((........))))..... ( -26.60)
>DroEre_CAF1 11418 100 + 1
AUACACAACAAUAACUGUCAGGGAGAAACGGGUGGGUGC---UACUC-------CACC---CGAA-------AGAAGCGGCAUUUAUUGUUGUUAUUAUUGCAUUAUCCGUUGCAUACUU
....((((((((((.((((.........((((((((...---...))-------))))---))..-------......)))).))))))))))......((((........))))..... ( -30.83)
>DroYak_CAF1 14760 117 + 1
AUACACAACAAUAACUGUCGGGGAGAAACUGGUGGCUGC---CCCUCUCCUUUCCACCCCCCAAAAAUAAAUAAAAGCGGCAUUUAUUGUUGUUAUUAUUGCAUUAUCCGUUGCAUACUU
....((((((((((.(((((((((((....(((....))---)..))))))..........................))))).))))))))))......((((........))))..... ( -26.86)
>DroAna_CAF1 44449 84 + 1
AUACACAAUAAUAACUGUCAGGA--------------G---UUGGCC-------CGCC---CA---------GAUAGCAGCGUUUAUUGUUGUUAUUAUUGCAUUAUCCGCUGCACUCUU
...................((((--------------(---((((..-------...)---))---------....((((((..((.(((.((....)).))).))..)))))))))))) ( -20.60)
>consensus
AUACACAACAAUAACUGUCAGGGGAAAACUGGUGGGUGC__CUGGUC_______CACC___CCAA_______AGAAGCGGCAUUUAUUGUUGUUAUUAUUGCAUUAUCCGUUGCAUACUU
....((((((((((.((((...........................................................)))).))))))))))......((((........))))..... (-13.60 = -13.49 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,601,751 – 13,601,871
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -25.85
Consensus MFE -23.93
Energy contribution -24.43
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.93
SVM decision value 2.77
SVM RNA-class probability 0.996950
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13601751 120 - 23771897
AGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGAGAGUAUGCAACGGAUAAUGCAAUAAUAACAACAAUAAAUG
.((...(((((...(((.((((((((..(((((..(......)..)))))..))))))))....(((((....))))).......)))..)))))...)).................... ( -25.50)
>DroSec_CAF1 8665 120 - 1
AGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGAAAGUAUGCAACGGAUAAUGCAAUAAUAACAACAAUAAAUG
.((...(((((...(((.((((((((..(((((..(......)..)))))..))))))))....(((((....))))).......)))..)))))...)).................... ( -25.50)
>DroSim_CAF1 17926 120 - 1
AGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGAAAGUAUGCAACGGAUAAUGCAAUAAUAACAACAAUAAAUG
.((...(((((...(((.((((((((..(((((..(......)..)))))..))))))))....(((((....))))).......)))..)))))...)).................... ( -25.50)
>DroEre_CAF1 11478 120 - 1
AGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGAAAGUAUGCAACGGAUAAUGCAAUAAUAACAACAAUAAAUG
.((...(((((...(((.((((((((..(((((..(......)..)))))..))))))))....(((((....))))).......)))..)))))...)).................... ( -25.50)
>DroYak_CAF1 14837 120 - 1
AGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUCGAAAGUAUGCAACGGAUAAUGCAAUAAUAACAACAAUAAAUG
.((...(((((...(((.((((((((..(((((..(......)..)))))..)))))))).....((((....))))........)))..)))))...)).................... ( -24.00)
>DroAna_CAF1 44493 120 - 1
AGUUACGUCUGCCGGCAAUAAUUGCAGCUGUAUUUUUAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCCCGAAAGAGUGCAGCGGAUAAUGCAAUAAUAACAACAAUAAACG
.((...((((((......((((((((..(((((..((....))..)))))..))))))))............((((.(....).)))).))))))...)).................... ( -29.10)
>consensus
AGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGAAAGUAUGCAACGGAUAAUGCAAUAAUAACAACAAUAAAUG
.((...(((((...(((.((((((((..(((((..(......)..)))))..))))))))....(((((....))))).......)))..)))))...)).................... (-23.93 = -24.43 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,601,791 – 13,601,906
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.17
Mean single sequence MFE -29.00
Consensus MFE -25.09
Energy contribution -25.45
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.87
SVM decision value 0.87
SVM RNA-class probability 0.871260
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13601791 115 - 23771897
CC----CCC-AGUGGAACAGACGAUAAAUUUCUGCCCAAGAGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGA
..----...-.((.(..((((((.(((...(((.....))).))))))))).).))..((((((((..(((((..(......)..)))))..))))))))....(((((....))))).. ( -28.40)
>DroSec_CAF1 8705 115 - 1
CC----CCC-AGUGGAACAGACGAUAAAUUUCCGCCCAAGAGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGA
..----...-.((.(..((((((...(((((........))))).)))))).).))..((((((((..(((((..(......)..)))))..))))))))....(((((....))))).. ( -25.90)
>DroSim_CAF1 17966 115 - 1
CC----CCC-AGUGGAACAGACGAUAAAUUUCUGCCCAAGAGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGA
..----...-.((.(..((((((.(((...(((.....))).))))))))).).))..((((((((..(((((..(......)..)))))..))))))))....(((((....))))).. ( -28.40)
>DroEre_CAF1 11518 114 - 1
CC-----CC-ACUGGAACAGACGAUAAAUUUCUGCCCAAGAGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGA
..-----..-.((((..((((((.(((...(((.....))).)))))))))))))...((((((((..(((((..(......)..)))))..))))))))....(((((....))))).. ( -30.20)
>DroYak_CAF1 14877 114 - 1
CC-----CC-ACUGGAACAGACGAUAAAUUUCUGCCCAAGAGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUCGA
..-----..-.((((..((((((.(((...(((.....))).)))))))))))))...((((((((..(((((..(......)..)))))..)))))))).....((((....))))... ( -28.70)
>DroAna_CAF1 44533 119 - 1
CAGCGCUCGAGCUCGAACAGACGAUAAAUUUCAGC-CAAGAGUUACGUCUGCCGGCAAUAAUUGCAGCUGUAUUUUUAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCCCGA
..(((((((.((.((..((((((.(((...((...-...)).))))))))).))))..((((((((..(((((..((....))..)))))..)))))))).......)))..)))).... ( -32.40)
>consensus
CC____CCC_ACUGGAACAGACGAUAAAUUUCUGCCCAAGAGUUACGUCUGCCGGCAAUAAUUGCAACUGUAUUUUAAAAGAAUUAUGCACGUGCAAUUAAAUAAAGCGACAGCGCUUGA
.............((..((((((.(((...(((.....))).)))))))))))(((..((((((((..(((((..(......)..)))))..))))))))......((....)))))... (-25.09 = -25.45 +   0.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:32 2006