Locus 4719

Sequence ID 3R_DroMel_CAF1
Location 12,390,912 – 12,391,032
Length 120
Max. P 0.913505
window7752 window7753

overview

Window 2

Location 12,390,912 – 12,391,032
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.83
Mean single sequence MFE -60.35
Consensus MFE -38.72
Energy contribution -39.92
Covariance contribution 1.20
Combinations/Pair 1.33
Mean z-score -2.56
Structure conservation index 0.64
SVM decision value 1.05
SVM RNA-class probability 0.907370
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12390912 120 + 27905053
GGAGAACCUGGUGAGCCAGGAGAGCCCGGAUCUUUGGGUCCACGAGGAUUGGACGGACUGCCCGGUGAGCCGGGCAUCGAAGGACCACCGGGACUGCCAGGAUACCAGGGUCCACCAGGA
......(((((((..((.((..(((((((.((((((((((((.......)))))....(((((((....))))))))))))))....))))).)).)).((...))..))..))))))). ( -57.50)
>DroGri_CAF1 41063 120 + 1
GGUGACGCGGGCGAGCCUGGAGAGCCGGGCUCCUUGGGUCCACGUGGCUUAGAUGGUUUACCGGGCGAGCCGGGAAUUGAGGGACCACCUGGUCUGCCGGGCUAUCAAGGACCACCAGGU
.(((((.((((.((((((((....)))))))))))).)).)))(((((((.(((((....((.((((..(((((...((......)))))))..)))).))))))).))).))))..... ( -57.20)
>DroEre_CAF1 59767 120 + 1
GGAGAACCUGGCGAGCCAGGAGAGCCCGGAUCUUUGGGUCCGCGAGGAUUGGACGGACUGCCCGGUGAGCCGGGCAUCGAAGGACCGCCGGGGCUGCCGGGAUACCAGGGUCCACCAGGA
......(((((.(..((.((..(((((.........(((((....)))))((.(((..(((((((....)))))))((....))))))).))))).))((....))..))..).))))). ( -60.50)
>DroWil_CAF1 22006 120 + 1
GGCGAGCCUGGAGAACCAGGUGAACCCGGUUCGCUGGGUCCCAGAGGUUUGGAUGGUUUACCAGGCGAGCCUGGCAUUGAAGGACCUCCCGGUUUGCCUGGCUACCAAGGUCCUCCUGGU
((((((((.((((((((.((....)).)))))....(((((((((((((((..(((....)))..)))))))....)))..)))))))).)))))))).....((((.((....)))))) ( -54.40)
>DroYak_CAF1 57036 120 + 1
GGAGAACCUGGUGAGCCAGGAGAGCCCGGAUCUUUGGGUCCGCGAGGAUUAGACGGACUGCCCGGGGAGCCGGGCAUCGAAGGACCACCGGGACUGCCGGGAUACCAGGGUCCACCAGGU
.....((((((((..((.((..(((((((.(((((((((((((........).))))))((((((....))))))..))))))....))))).)).))((....))..))..)))))))) ( -63.10)
>DroAna_CAF1 41610 120 + 1
GGAGAGGCAGGCGAGCCGGGAGAACCCGGUUCGUUGGGUCCCCGUGGCCUGGACGGCCUGCCUGGAGAGCCGGGCAUCGAAGGACCUCCCGGUCUGCCAGGAUACCAGGGACCGCCUGGC
....((((.(((((((((((....))))))))))).((((((...((((.....))))..((((((((.(((((..((....))...)))))))).)))))......))))))))))... ( -69.40)
>consensus
GGAGAACCUGGCGAGCCAGGAGAGCCCGGAUCUUUGGGUCCACGAGGAUUGGACGGACUGCCCGGCGAGCCGGGCAUCGAAGGACCACCGGGUCUGCCGGGAUACCAGGGUCCACCAGGU
......(((((((..((.((....(((((.(((((.((((((.......)))))....(((((((....))))))).).)))))...)))))....)).((...))..))..))))))). (-38.72 = -39.92 +   1.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 12,390,912 – 12,391,032
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.83
Mean single sequence MFE -53.43
Consensus MFE -36.89
Energy contribution -37.34
Covariance contribution 0.45
Combinations/Pair 1.30
Mean z-score -2.45
Structure conservation index 0.69
SVM decision value 1.09
SVM RNA-class probability 0.913505
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12390912 120 - 27905053
UCCUGGUGGACCCUGGUAUCCUGGCAGUCCCGGUGGUCCUUCGAUGCCCGGCUCACCGGGCAGUCCGUCCAAUCCUCGUGGACCCAAAGAUCCGGGCUCUCCUGGCUCACCAGGUUCUCC
.(((((((..((..((...(((((..(((...(.(((((..((((((((((....))))))).............))).))))))...))))))))....)).))..)))))))...... ( -51.71)
>DroGri_CAF1 41063 120 - 1
ACCUGGUGGUCCUUGAUAGCCCGGCAGACCAGGUGGUCCCUCAAUUCCCGGCUCGCCCGGUAAACCAUCUAAGCCACGUGGACCCAAGGAGCCCGGCUCUCCAGGCUCGCCCGCGUCACC
(((.((((..(((.((.((((.(((...(((.(((((..........((((.....))))............))))).))).((...)).))).)))).)).)))..)))).).)).... ( -42.35)
>DroEre_CAF1 59767 120 - 1
UCCUGGUGGACCCUGGUAUCCCGGCAGCCCCGGCGGUCCUUCGAUGCCCGGCUCACCGGGCAGUCCGUCCAAUCCUCGCGGACCCAAAGAUCCGGGCUCUCCUGGCUCGCCAGGUUCUCC
.(((((((..((..((...(((((..((....))((........(((((((....)))))))((((((.........))))))))......)))))....)).))..)))))))...... ( -54.00)
>DroWil_CAF1 22006 120 - 1
ACCAGGAGGACCUUGGUAGCCAGGCAAACCGGGAGGUCCUUCAAUGCCAGGCUCGCCUGGUAAACCAUCCAAACCUCUGGGACCCAGCGAACCGGGUUCACCUGGUUCUCCAGGCUCGCC
....(((((((((((((.((...))..)))..)))))))))).......(((..((((((.......((((......)))).......((((((((....)))))))).))))))..))) ( -49.90)
>DroYak_CAF1 57036 120 - 1
ACCUGGUGGACCCUGGUAUCCCGGCAGUCCCGGUGGUCCUUCGAUGCCCGGCUCCCCGGGCAGUCCGUCUAAUCCUCGCGGACCCAAAGAUCCGGGCUCUCCUGGCUCACCAGGUUCUCC
((((((((..((..((...(((((..(((....(((........(((((((....)))))))((((((.........)))))))))..))))))))....)).))..))))))))..... ( -54.60)
>DroAna_CAF1 41610 120 - 1
GCCAGGCGGUCCCUGGUAUCCUGGCAGACCGGGAGGUCCUUCGAUGCCCGGCUCUCCAGGCAGGCCGUCCAGGCCACGGGGACCCAACGAACCGGGUUCUCCCGGCUCGCCUGCCUCUCC
(.(((((((((((((....(((((.((((((((..(((....))).))))).))))))))..((((.....)))).))))))))....((.(((((....))))).))))))).)..... ( -68.00)
>consensus
ACCUGGUGGACCCUGGUAUCCCGGCAGACCCGGUGGUCCUUCGAUGCCCGGCUCACCGGGCAGUCCGUCCAAUCCUCGCGGACCCAAAGAUCCGGGCUCUCCUGGCUCGCCAGGUUCUCC
.(((((((..((..((...(((((........(.(((((.....(((((((....)))))))(......).........))))))......)))))....)).))..)))))))...... (-36.89 = -37.34 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:20 2006