Locus 1226

Sequence ID 3R_DroMel_CAF1
Location 3,704,745 – 3,704,841
Length 96
Max. P 0.946293
window2004 window2005

overview

Window 4

Location 3,704,745 – 3,704,841
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 81.88
Mean single sequence MFE -16.86
Consensus MFE -10.42
Energy contribution -11.26
Covariance contribution 0.84
Combinations/Pair 1.06
Mean z-score -2.54
Structure conservation index 0.62
SVM decision value 1.36
SVM RNA-class probability 0.946293
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3704745 96 + 27905053
AAUGAAAAUUUCCGCUUAUGUAAGUACACCGAACUUACGUCAGCCAUGAUGGGAAACGAAACGCAAAGGAAAAUAAACGAAAAACAAAAUUAAAAU
........((((((((.((((((((.......)))))))).))).......(....)..........)))))........................ ( -17.90)
>DroSec_CAF1 62741 96 + 1
AAUGAAAAUUUCCGCUUAUGUAAGUACACCGAACUUACGUCAGCCAUGACGUGAAACGAAACGCAAAGGAAAAGAAGCGAAAAACAAAAUUAAAAU
........((((((((.((((((((.......)))))))).)))..((.(((........)))))..)))))........................ ( -19.10)
>DroSim_CAF1 65722 96 + 1
AAUGAAAAUUUCCGCUUAUGUAAGUACACCGAACUUACGUCAGCCAUGAUGGAAAACGAAACGCAAAGGAAAAGAAGCGAAAAACAAAAUUAAAAU
........((((((((.((((((((.......)))))))).)))......)))))......(((............)))................. ( -15.80)
>DroEre_CAF1 64328 96 + 1
AAUGAAAAUUUCCGCUUAUAUAAGUACUCCGCACUUACGUCAUCCAUGAUGGAAAACGAAACGCAAGGGAAAACACACGAAAAACAAAAUUAAAAU
........(((((.(((...(((((.......)))))(((..(((.....)))..)))......))))))))........................ ( -13.50)
>DroYak_CAF1 60917 72 + 1
AAGGAAAUUUUCCGCUUAUAAAAGUACACCGAACUUACGUCAGCCAUGAUGGAAAACGAAGUUCAAGGAAAA------------------------
.......((((((((((....)))).....((((((.(((...((.....))...)))))))))..))))))------------------------ ( -18.00)
>consensus
AAUGAAAAUUUCCGCUUAUGUAAGUACACCGAACUUACGUCAGCCAUGAUGGAAAACGAAACGCAAAGGAAAAGAAACGAAAAACAAAAUUAAAAU
........((((((((.((((((((.......)))))))).))).....((.....)).........)))))........................ (-10.42 = -11.26 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,704,745 – 3,704,841
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 81.88
Mean single sequence MFE -18.64
Consensus MFE -11.60
Energy contribution -11.36
Covariance contribution -0.24
Combinations/Pair 1.15
Mean z-score -1.96
Structure conservation index 0.62
SVM decision value 0.39
SVM RNA-class probability 0.715047
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3704745 96 - 27905053
AUUUUAAUUUUGUUUUUCGUUUAUUUUCCUUUGCGUUUCGUUUCCCAUCAUGGCUGACGUAAGUUCGGUGUACUUACAUAAGCGGAAAUUUUCAUU
.............(((((((((((...............(((..((.....))..)))((((((.......)))))))))))))))))........ ( -18.60)
>DroSec_CAF1 62741 96 - 1
AUUUUAAUUUUGUUUUUCGCUUCUUUUCCUUUGCGUUUCGUUUCACGUCAUGGCUGACGUAAGUUCGGUGUACUUACAUAAGCGGAAAUUUUCAUU
.............(((((((((.....((...((((........))))...)).....((((((.......))))))..)))))))))........ ( -17.90)
>DroSim_CAF1 65722 96 - 1
AUUUUAAUUUUGUUUUUCGCUUCUUUUCCUUUGCGUUUCGUUUUCCAUCAUGGCUGACGUAAGUUCGGUGUACUUACAUAAGCGGAAAUUUUCAUU
.............(((((((((.................(((..((.....))..)))((((((.......))))))..)))))))))........ ( -18.40)
>DroEre_CAF1 64328 96 - 1
AUUUUAAUUUUGUUUUUCGUGUGUUUUCCCUUGCGUUUCGUUUUCCAUCAUGGAUGACGUAAGUGCGGAGUACUUAUAUAAGCGGAAAUUUUCAUU
.......((((((((...(((.((.((((...((((((((((.(((.....))).)))).)))))))))).)).)))..))))))))......... ( -20.30)
>DroYak_CAF1 60917 72 - 1
------------------------UUUUCCUUGAACUUCGUUUUCCAUCAUGGCUGACGUAAGUUCGGUGUACUUUUAUAAGCGGAAAAUUUCCUU
------------------------((((((((((((((((((..((.....))..)))).))))))))....(((....))).))))))....... ( -18.00)
>consensus
AUUUUAAUUUUGUUUUUCGCUUCUUUUCCUUUGCGUUUCGUUUUCCAUCAUGGCUGACGUAAGUUCGGUGUACUUACAUAAGCGGAAAUUUUCAUU
........................(((((((((......(((..((.....))..)))((((((.......)))))).)))).)))))........ (-11.60 = -11.36 +  -0.24)

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 10:04:06 2006