Locus 4576

Sequence ID 2R_DroMel_CAF1
Location 14,957,112 – 14,957,299
Length 187
Max. P 0.999734
window7335 window7336 window7337

overview

Window 5

Location 14,957,112 – 14,957,219
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 93.46
Mean single sequence MFE -36.26
Consensus MFE -30.63
Energy contribution -30.91
Covariance contribution 0.28
Combinations/Pair 1.16
Mean z-score -2.04
Structure conservation index 0.84
SVM decision value 1.97
SVM RNA-class probability 0.984407
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14957112 107 + 20766785
GACGUGCGCACAACAGCACGAUAGUUGGAUAACAGCACGACAACAGCACGUGUCGUGCGUUUUUUAGGUCCAUUUGUGCGCCUCAGCGCGGCCACACUAUCCUUUCC
...((((........))))((((((((((((((.((((((((........)))))))))))......)))))...(((.(((.......))))))))))))...... ( -36.80)
>DroSec_CAF1 34461 107 + 1
GCCGUGCGCACAACAGCACGAUAGUUCGAUAACAGCACGACAACAGCACGUGUCGUGCGUUUUUUAGGUUCAUUUGUGCGCUUCAGCGCGGCCACACUAACCUUUCC
(((((((........((((((....((...(((.((((((((........))))))))))).....)).....))))))......)))))))............... ( -35.54)
>DroSim_CAF1 16806 107 + 1
GCCGUGCGCACAACAGCACGAUAGUUCGAUAACAGCACGACAACAGCACGUGUCGUGCGUUUUUUAGGUCCAUUUGUGCGCUUCAGCGCGGUCACACUAACCUUUCC
(((((((........((((((....((...(((.((((((((........))))))))))).....)).....))))))......)))))))............... ( -33.44)
>DroEre_CAF1 27704 107 + 1
AGCGUGCGCACAACAGCACGAUAGUCCGAUAACAGCACGACAACAGCACGUGUCGAGCGUUUUUUAGGCCCAUUCGUGCGCUUCAGUGCGGCCACACUAACCUUUCC
((.((((((((....((((((..(((..(.(((.((.(((((........))))).)))))..)..)))....))))))......)))))..))).))......... ( -32.10)
>DroYak_CAF1 16303 107 + 1
GGCGAGCGCACAACAGCACGAUAGUCCGAUAACAGCACGACAACAGCACGUGUCGUGCGUUAUUUAGGCCCAUUCGUGCGCUUCGGCGCGGCCACACUAACCUUUCC
(((..((((......((((((..(((.((((((.((((((((........))))))))))))))..)))....))))))......)))).))).............. ( -43.40)
>consensus
GCCGUGCGCACAACAGCACGAUAGUUCGAUAACAGCACGACAACAGCACGUGUCGUGCGUUUUUUAGGUCCAUUUGUGCGCUUCAGCGCGGCCACACUAACCUUUCC
..(((((........))))).((((.........((((((((........))))))))........((((.......((((....))))))))..))))........ (-30.63 = -30.91 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,957,152 – 14,957,259
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 95.31
Mean single sequence MFE -29.58
Consensus MFE -25.50
Energy contribution -26.10
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.86
SVM decision value 1.06
SVM RNA-class probability 0.908161
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14957152 107 - 20766785
AAAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGAUAGUGUGGCCGCGCUGAGGCGCACAAAUGGACCUAAAAAACGCACGACACGUGCUGUUG
.....(((((.(((((..((.....(((.(......).)))....))..)))))..)))))...((((.((....))).)))....((((((((...))))).))). ( -27.10)
>DroSec_CAF1 34501 106 - 1
-AAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCUGAAGCGCACAAAUGAACCUAAAAAACGCACGACACGUGCUGUUG
-.....((((.(((((.(((.....(((.(......).)))....))).)))))..))))((....))..................((((((((...))))).))). ( -28.50)
>DroSim_CAF1 16846 106 - 1
-AAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGACCGCGCUGAAGCGCACAAAUGGACCUAAAAAACGCACGACACGUGCUGUUG
-.....((((.(((((.(((.....(((.(......).)))....))).)))))..))))((....))..................((((((((...))))).))). ( -27.90)
>DroEre_CAF1 27744 106 - 1
-AAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCACUGAAGCGCACGAAUGGGCCUAAAAAACGCUCGACACGUGCUGUUG
-.....((((.(((((.(((.....(((.(......).)))....))).)))))..)))).....((((((((..(((((.........)))))...))))).))). ( -32.60)
>DroYak_CAF1 16343 107 - 1
AAAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCCGAAGCGCACGAAUGGGCCUAAAUAACGCACGACACGUGCUGUUG
......((((.(((((.(((.....(((.(......).)))....))).)))))..))))(((.(..(....)..).))).....(((((((((...))))).)))) ( -31.80)
>consensus
_AAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCUGAAGCGCACAAAUGGACCUAAAAAACGCACGACACGUGCUGUUG
.....(((((.(((((.(((.....(((.(......).)))....))).)))))..))))).........................((((((((...))))).))). (-25.50 = -26.10 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,957,192 – 14,957,299
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 94.94
Mean single sequence MFE -23.88
Consensus MFE -21.78
Energy contribution -21.90
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -2.51
Structure conservation index 0.91
SVM decision value 3.97
SVM RNA-class probability 0.999734
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14957192 107 - 20766785
AUAAACGAUUUAAAAGUGGUUAAAUAAAAAUAUCGGCAAAAAAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGAUAGUGUGGCCGCGCUGAGG
...(((.(((....))).)))...........(((((.........((((.(((((..((.....(((.(......).)))....))..)))))..))))))))).. ( -21.90)
>DroSec_CAF1 34541 106 - 1
AUAAACGAUUUAAAAGUGGUUAAAUAAAAAUAUCGGCAAA-AAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCUGAAG
...(((.(((....))).)))...........(((((...-.....((((.(((((.(((.....(((.(......).)))....))).)))))..))))))))).. ( -24.90)
>DroSim_CAF1 16886 106 - 1
AUAAACGAUUUAAAAGUGGUUAAAUAAAAAUAUCGGCAAA-AAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGACCGCGCUGAAG
...(((.(((....))).)))...........(((((...-.....((((.(((((.(((.....(((.(......).)))....))).)))))..))))))))).. ( -24.30)
>DroEre_CAF1 27784 106 - 1
AUAGACGGUUUAAAAGUGGUUAAAUAAAAACAUCGGCAAA-AAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCACUGAAG
.....((((......((((((...........((.((...-.....)).))(((((.(((.....(((.(......).)))....))).)))))))))))))))... ( -23.10)
>DroYak_CAF1 16383 107 - 1
AUGGACGGUUAAAAAGUGGUUAAAUAAAAAUAUCAGCAAAAAAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCCGAAG
.....((((.......((((...........))))...........((((.(((((.(((.....(((.(......).)))....))).)))))..))))))))... ( -25.20)
>consensus
AUAAACGAUUUAAAAGUGGUUAAAUAAAAAUAUCGGCAAA_AAAACGCGGAGCACUCACCGGAAACUUGUAAGAAAAGAAGGAAAGGUUAGUGUGGCCGCGCUGAAG
...(((.(((....))).)))...........(((((.........((((.(((((.(((.....(((.(......).)))....))).)))))..))))))))).. (-21.78 = -21.90 +   0.12)

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 11:23:31 2006