Locus 3473

Sequence ID 3L_DroMel_CAF1
Location 10,211,535 – 10,211,679
Length 144
Max. P 0.962765
window5422 window5423

overview

Window 2

Location 10,211,535 – 10,211,650
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -30.60
Consensus MFE -24.10
Energy contribution -23.42
Covariance contribution -0.68
Combinations/Pair 1.19
Mean z-score -1.60
Structure conservation index 0.79
SVM decision value 0.27
SVM RNA-class probability 0.661479
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10211535 115 - 23771897
GGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAACCAAAGGUAGAUCAUUUCACUGUCACUGCAAAGAGGUAAUGAAUGGGCCAUAGAAAUUAGGUUCUUCAAGCGAAAGA
((((...((((((((......))))))))........(((...))).))))(((((..(((....)))..)))))..((((.(((((..(....)..)))))))))..(....). ( -27.90)
>DroSec_CAF1 87672 115 - 1
GGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAACCAAAGGUAGAUCAUUUCACUGUCAUUGCAAAGUGGUAAUGAAUGGGCCAUGGAAAUUAUGUUCUUCAACCCAAAGA
((((...((((((((......))))))))........(((...))).)))).........(((((((......))))))).((((....((((......))))....)))).... ( -30.90)
>DroSim_CAF1 92024 115 - 1
GGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAACCAAAGGUAGAUCAUUUCACUGUCACUGCAAAGUGCUAAUGAAUGGGCCAUAGAAAUUAUGUUCUUCAACCGAAAGA
((((...((((((((......))))))))......).)))...(((.(((((((.((((..........))))..)))))..((..(((((...)))))..)))).)))...... ( -27.90)
>DroEre_CAF1 93054 115 - 1
GGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAAGCAAAGGUAGAUCAUUUCCCAGUCACUGCAAAGUGGUCUUGAAUGAGCCAUAGAAAUUAGGCUCUUCAACCGAAAGU
..((...((((((((......))))))))..............((((((((((((..(((...)))..)))))))))((((.(((((..(....)..)))))))))))))).... ( -36.10)
>DroYak_CAF1 92443 115 - 1
GGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGUACCAAAGGUAGAUCAUUUCACUGUCACUGCAAAGUGGUCAUGAGUGAGCCAUAGAAAUGAUGUUCUUCAAGCAAAAGA
.((((..((((((((......))))))))...((((((((...)))...(((((.((.(((((((....))))).)))))))))))))).....))))................. ( -30.20)
>consensus
GGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAACCAAAGGUAGAUCAUUUCACUGUCACUGCAAAGUGGUAAUGAAUGGGCCAUAGAAAUUAUGUUCUUCAACCGAAAGA
((((...((((((((......))))))))....((....))......))))..........((((....))))....((((.((((...(....)...))))))))......... (-24.10 = -23.42 +  -0.68)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,211,575 – 10,211,679
Length 104
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 96.93
Mean single sequence MFE -29.34
Consensus MFE -27.20
Energy contribution -27.44
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.93
SVM decision value 1.54
SVM RNA-class probability 0.962765
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10211575 104 - 23771897
AUCGGAGGCGGUUCCAAAUUAA-AGGACUAGGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAACCAAAGGUAGAUCAUUUCACUGUCACUGCAAAGAGGU
..(((.((((((((((......-..(((...)))...((((((((......))))))))....)))))))...(((.((.....)))))))).)))......... ( -31.00)
>DroSec_CAF1 87712 104 - 1
AUCGGAGGCGGUUCCAAAUUAA-AGGACUAGGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAACCAAAGGUAGAUCAUUUCACUGUCAUUGCAAAGUGGU
......((((((((((......-..(((...)))...((((((((......))))))))....)))))))...(((.((.....))))))))............. ( -29.30)
>DroSim_CAF1 92064 104 - 1
AUCGGAGGCGGUUCCAAAUUAA-AGGACUAGGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAACCAAAGGUAGAUCAUUUCACUGUCACUGCAAAGUGCU
..(((.((((((((((......-..(((...)))...((((((((......))))))))....)))))))...(((.((.....)))))))).)))......... ( -31.00)
>DroEre_CAF1 93094 104 - 1
AUCGGAGGCGGUUCCAAAUUAA-AGGACUAGGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAAGCAAAGGUAGAUCAUUUCCCAGUCACUGCAAAGUGGU
...(((((.(((.((.......-.))))).((((...((((((((......))))))))....((....))......)))).)))))...(((((....))))). ( -27.20)
>DroYak_CAF1 92483 105 - 1
AUCGGAGGCGGUUCCAAAUUAAAAGGACUAGGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGUACCAAAGGUAGAUCAUUUCACUGUCACUGCAAAGUGGU
..(((.(((((((((.........)))...((((...((((((((......)))))))).......((((...)))))))).....)))))).)))......... ( -28.20)
>consensus
AUCGGAGGCGGUUCCAAAUUAA_AGGACUAGGUCAAAAGUGCCGCCGCAAAGUGGCACUCAAAUGGAACCAAAGGUAGAUCAUUUCACUGUCACUGCAAAGUGGU
..(((.((((((((((.........(((...)))...((((((((......))))))))....))))))).......((.....))...))).)))......... (-27.20 = -27.44 +   0.24)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:58 2006