Locus 2364

Sequence ID 2R_DroMel_CAF1
Location 8,588,440 – 8,588,569
Length 129
Max. P 0.764667
window3903 window3904

overview

Window 3

Location 8,588,440 – 8,588,541
Length 101
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 75.84
Mean single sequence MFE -31.23
Consensus MFE -14.48
Energy contribution -15.87
Covariance contribution 1.39
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.46
SVM decision value 0.51
SVM RNA-class probability 0.764667
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8588440 101 + 20766785
GGUUUCAUUAAUGGAUUAG----------GAAGCGGAACUGAG-ACUGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUGUUCAGAUAGCCGCUGACCG
..................(----------(.(((((..(((..-.((((((.....(((((((..((((((...))))))))))))).....)))))).))))))))..)). ( -31.50)
>DroVir_CAF1 20380 96 + 1
ACUUUCCCUC-----UCAG-----------AAAUAGGUUUCAUAUGUGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUAAAAAUGUUUAGAUAUCCGCUGACCA
..........-----....-----------.....((((..((((.(((((......((((((..((((((...))))))))))))......))))).)))).....)))). ( -21.00)
>DroPse_CAF1 22823 110 + 1
GGUUUCAUUAAGG--UUAGAGGGGGACUGUAACUGGAACUGAGAACAGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUAUUCAGAUAUCCUCUGACCA
...........((--((((((((...(((....(((((((((.....((......)).)))))))))(((((....)))))..............)))...)))))))))). ( -36.20)
>DroGri_CAF1 20424 99 + 1
GUUUUCCCAC-----CCAG---GA-----GACAUAGGUCUGUGAUGUAGACUUACCCAUCAGUUUCAUCACUUCAUGGUGGCUGAUGAAAAUGUUGAGAUAUGCGCUGACCG
((((((....-----...)---))-----)))...((((.(((((((.(((.....(((((((..(((((.....)))))))))))).....)))...)))).))).)))). ( -29.50)
>DroAna_CAF1 14803 101 + 1
AGUUUCAUUAGUGGAUUAG----------GAAAUGAGACUGGA-ACUGGACUCACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUGUUCAGAUAGCCGCUGACGG
...((((....))))..((----------(..((((((((((.-..(((......)))))))))))))..)))(((((((((((.((((....))))..)))))))).))). ( -33.00)
>DroPer_CAF1 23129 110 + 1
GGUUUCAUUAAGG--UUAGAGGGGGACUGUAACUGGAACUGAGAACAGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUAUUCAGAUAUCCUCUGACCA
...........((--((((((((...(((....(((((((((.....((......)).)))))))))(((((....)))))..............)))...)))))))))). ( -36.20)
>consensus
GGUUUCAUUAA_G__UUAG__________GAAAUGGAACUGAGAACUGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUGUUCAGAUAUCCGCUGACCA
.............................................((((((.....(((((((..((((((...))))))))))))).....)))))).............. (-14.48 = -15.87 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 8,588,462 – 8,588,569
Length 107
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.32
Mean single sequence MFE -37.97
Consensus MFE -21.47
Energy contribution -22.08
Covariance contribution 0.61
Combinations/Pair 1.15
Mean z-score -1.78
Structure conservation index 0.57
SVM decision value 0.32
SVM RNA-class probability 0.689129
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8588462 107 + 20766785
GCGGAACUGAG-ACUGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUGUUCAGAUAGCCGCUGACCG------------AAGUGGAAAUGGUUAGGCAUAGGAGCAG
((((((((((.-..(((......)))))))))))....(((.((((((((((.((((....))))..)))))))(((((.------------..((....)))))))..)))))).)).. ( -34.50)
>DroVir_CAF1 20396 120 + 1
AUAGGUUUCAUAUGUGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUAAAAAUGUUUAGAUAUCCGCUGACCAAAGGUAGCUGCCAAGUGAUCCAAGAGAUCCAGAGCAGCUG
...((((..((((.(((((......((((((..((((((...))))))))))))......))))).)))).....)))).....(((((((...(.((((.....)))))...))))))) ( -33.60)
>DroPse_CAF1 22853 120 + 1
CUGGAACUGAGAACAGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUAUUCAGAUAUCCUCUGACCAAAGGCGUCCGCCAAGAGGCCAACGAGAGGCAGAGGAGCAG
(((...(((((....((.....))(((((((..((((((...)))))))))))))......)))))...(((((((.((.....(((..(((....)))..)))...))))))))).))) ( -40.80)
>DroEre_CAF1 54711 107 + 1
GCGGAAAUGAG-ACUGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUGUUCAGAUAGCCGCUGACCG------------AGGUGGACAUGGUUAGGCAUAGGAGCAG
((.....((((-(((((.........)))))))))((((((((.((((((((.((((....))))..))))))))...))------------))))))..................)).. ( -37.10)
>DroAna_CAF1 14825 119 + 1
AUGAGACUGGA-ACUGGACUCACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUGUUCAGAUAGCCGCUGACGGAGGGCGUCCGCCAAGUGGAAAUGGUCAGGAAGAGGAGCCA
((((((((((.-..(((......)))))))))))))..(..(((((((((((.((((....))))..)))))))).)))..)(((.(((((((........))))..)))......))). ( -41.00)
>DroPer_CAF1 23159 120 + 1
CUGGAACUGAGAACAGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUAUUCAGAUAUCCUCUGACCAAAGGCGUCCGCCAAGAGGCCAACGAGAGGCAGAGGAGCAG
(((...(((((....((.....))(((((((..((((((...)))))))))))))......)))))...(((((((.((.....(((..(((....)))..)))...))))))))).))) ( -40.80)
>consensus
AUGGAACUGAG_ACUGGACUUACCCAUCAGUUUCAUCACCUCGUGGUGGCUGAUGAAAAUGUUCAGAUAGCCGCUGACCAAAGGCGUCCGCCAAGUGGACAAGGAGAGGCAGAGGAGCAG
.............((((((.....(((((((..((((((...))))))))))))).....))))))....(((((.......(((....))).)))))...................... (-21.47 = -22.08 +   0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:05 2006