Locus 3606

Sequence ID X_DroMel_CAF1
Location 9,660,313 – 9,660,538
Length 225
Max. P 0.856761
window5901 window5902

overview

Window 1

Location 9,660,313 – 9,660,426
Length 113
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 97.05
Mean single sequence MFE -25.87
Consensus MFE -24.72
Energy contribution -24.83
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.89
Structure conservation index 0.96
SVM decision value 0.63
SVM RNA-class probability 0.803892
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9660313 113 - 22224390
AGCCAAAAAAGGCCAGGUAAGCUGCACUAAAAGAAGCAACUAUUUCGUGUUCCUUAUAUUUAUAGUCAAGCGACAAUAAGUUAUAGUAAGCAAAGGCGGCAUUGAGUCAUAAC
.(((......))).......(((((.((....((((......)))).((((..((((((((((.(((....))).))))).)))))..)))).)))))))............. ( -22.90)
>DroSim_CAF1 10359 113 - 1
AGCCAAAAAAGACCAGGUAAGCUGCACUAAAAGAAGCAACUAUUUCGUGUUGCUUAUAUUUAUAGUCAAGCGACAAUAAGUUAUAGUAAGCAAAGGCGGCAUUGAGUCAUAAC
..........((((((....(((((.((....((((......))))...((((((((((((((.(((....))).))))))....))))))))))))))).))).)))..... ( -26.80)
>DroEre_CAF1 2836 113 - 1
AGCCAAAAAAGACCAGGUAAGCUGCACUAAAAGAAGCAACUAUUCUGUGUUGCUUAUAUUUAUAGUCGAGCGACAAUAAGUUAUAGUAAGCAAAGGCGGCAUUGAGUCAUAAC
..........((((((....(((((.((...((((.......))))...((((((((((((((.(((....))).))))))....))))))))))))))).))).)))..... ( -27.90)
>consensus
AGCCAAAAAAGACCAGGUAAGCUGCACUAAAAGAAGCAACUAUUUCGUGUUGCUUAUAUUUAUAGUCAAGCGACAAUAAGUUAUAGUAAGCAAAGGCGGCAUUGAGUCAUAAC
..........((((((....(((((.((.....(((((((........)))))))..((((((.(((....))).))))))............))))))).))).)))..... (-24.72 = -24.83 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 9,660,426 – 9,660,538
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 71.62
Mean single sequence MFE -25.64
Consensus MFE -13.81
Energy contribution -14.12
Covariance contribution 0.31
Combinations/Pair 1.07
Mean z-score -1.89
Structure conservation index 0.54
SVM decision value 0.81
SVM RNA-class probability 0.856761
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9660426 112 - 22224390
CCAAAGAUCCAUUCCCCUGCUC-----G---CUACGUGCCACAUUACGUAGCCGACUGGUGAGCCAGACUCCCAAAAAAAAGGAAAAAAAAAGAGCAAAAAUUUAUAGGACUACAGAAUA
....((.(((((.....(((((-----(---(((((((......))))))))...((((....))))..(((.........)))........))))).......)).)))))........ ( -25.50)
>DroAna_CAF1 24827 97 - 1
----UCCUGCACUCUCCUGUUUCGUUAG---CUACGUGCCACAUUACGUAGCCGACCUGUGCGCCAGACA---AAA----------AACAAAGGGCGAAGCCAAGCAGGAGCAG---CUA
----....((...(((((((((.((..(---(((((((......))))))))..))((...((((.....---...----------.......)))).))..)))))))))..)---).. ( -32.36)
>DroSim_CAF1 10472 105 - 1
CCAAAGAUCCAUACCCCUGCUU-----GCUGCUACGUGCCACAUUACGUAGCCGACUGGUGAGCCAGACUCCAAAA----------AAAAAAGAGCAAAAAUUUAUAGGACUACAGAAUA
....((.((((((....(((((-----.(.((((((((......)))))))).).((((....)))).........----------......)))))......))).)))))........ ( -23.30)
>DroEre_CAF1 2949 99 - 1
CCGAAGAUCCAUUCCCCUGCCU-----G---CUACGUGCCACAUUACGUAGCCGACUGGUAAGCCAGACUCCCAAA-------------AAAGAGCACAAAUUUAUAGGACUAGAGAGUA
..........((((.(..((((-----(---(((((((......))))))))...((((....)))).(((.....-------------...)))...........))).)..).)))). ( -21.40)
>consensus
CCAAAGAUCCAUUCCCCUGCUU_____G___CUACGUGCCACAUUACGUAGCCGACUGGUGAGCCAGACUCCCAAA__________AAAAAAGAGCAAAAAUUUAUAGGACUACAGAAUA
...............((((............(((((((......)))))))....((((....))))......................................))))........... (-13.81 = -14.12 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:34 2006