Locus 2686

Sequence ID 2R_DroMel_CAF1
Location 9,484,089 – 9,484,216
Length 127
Max. P 0.961526
window4422 window4423 window4424

overview

Window 2

Location 9,484,089 – 9,484,199
Length 110
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 81.40
Mean single sequence MFE -37.30
Consensus MFE -31.56
Energy contribution -31.62
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -1.79
Structure conservation index 0.85
SVM decision value 0.86
SVM RNA-class probability 0.867738
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9484089 110 - 20766785
CGCAAGGCUUCAGCAGCACGGACUGUGCUGUUAGGCGCACACUAACAGAGCUGUUGGAUAACCACCUGGCGCCAUCUGCCGGAAAGCGAAAGUGU-UGAA--CAGAAAUUGUA
(....)((((.((((((((.....))))))))))))........((((..(((((.(((......((((((.....))))))...((....))))-).))--)))...)))). ( -36.60)
>DroSim_CAF1 5947 102 - 1
CGCAAGGCUUCGGCAGCACGGACUGUGCUGUUAGGCGCACACUAACAGAGCUGUUAGAUAACCAGCUGGCGCCAUCUGCCGGAAAGCGAAAGCACUUUUA--CA---------
.....(((...((((((((.....)))))))).(((((...((((((....)))))).....(....))))))....))).....((....)).......--..--------- ( -36.10)
>DroEre_CAF1 5773 104 - 1
CGCAAGGCUUCAGCAGCACACACUGUGCUGUUAGGCGCAUACUAACAGAGCCGUUGGCCCACCUGUUGGCGCCAUCUGCCGGAAAGCGAGUGCACUUUAAGCAA---------
(((..(((...((((((((.....)))))))).(((((....((((((.(((...)))....)))))))))))....))).....)))..(((.......))).--------- ( -37.20)
>DroYak_CAF1 5899 102 - 1
CGCAAGGCUUCAGCAGCACGCACUGUGCUGUUAGGCGCGCUCUAACAGAGCUGUUAGAACGCCUGCUGGCGCCAUCUGCCGGAAAACGAGGGCCCUUUAA--AA---------
.....((((((((((((((.....))))))))(((((...(((((((....))))))).))))).((((((.....)))))).....)).))))......--..--------- ( -39.30)
>consensus
CGCAAGGCUUCAGCAGCACGCACUGUGCUGUUAGGCGCACACUAACAGAGCUGUUAGAUAACCAGCUGGCGCCAUCUGCCGGAAAGCGAAAGCACUUUAA__AA_________
(((..(((...((((((((.....)))))))).(((((...((((((....)))))).....(....))))))....))).....)))......................... (-31.56 = -31.62 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,484,126 – 9,484,216
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 87.41
Mean single sequence MFE -30.75
Consensus MFE -22.29
Energy contribution -22.22
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -1.44
Structure conservation index 0.72
SVM decision value 0.00
SVM RNA-class probability 0.534333
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9484126 90 + 20766785
GGCGCCAGGUGGUUAUCCAACAGCUCUGUUAGUGUGCGCCUAACAGCACAGUCCGUGCUGCUGAAGCCUUGCGACUGCUGUAGAAAAUUA
(((((.((((((....))..((((...(((((.(....))))))(((((.....)))))))))..)))).))).)).............. ( -27.60)
>DroSim_CAF1 5976 90 + 1
GGCGCCAGCUGGUUAUCUAACAGCUCUGUUAGUGUGCGCCUAACAGCACAGUCCGUGCUGCCGAAGCCUUGCGACUGCUGUUGAAAAUUA
(((((((.........((((((....)))))))).)))))...((((((((((((.(((.....)))..)).))))).)))))....... ( -30.40)
>DroEre_CAF1 5804 90 + 1
GGCGCCAACAGGUGGGCCAACGGCUCUGUUAGUAUGCGCCUAACAGCACAGUGUGUGCUGCUGAAGCCUUGCGAUUGCUCUAGAGAAAUA
(((((..((..(..((((...))).)..)..))..)))))...((((((.....))))))(((.(((.........))).)))....... ( -28.20)
>DroYak_CAF1 5928 90 + 1
GGCGCCAGCAGGCGUUCUAACAGCUCUGUUAGAGCGCGCCUAACAGCACAGUGCGUGCUGCUGAAGCCUUGCGAUUGCUGUAGAAAAAUA
((((((....)))(((((((((....)))))))))..)))..((((((...((((.(((.....)))..))))..))))))......... ( -36.80)
>consensus
GGCGCCAGCAGGUGAUCCAACAGCUCUGUUAGUGUGCGCCUAACAGCACAGUCCGUGCUGCUGAAGCCUUGCGACUGCUGUAGAAAAAUA
((((((....))).......((((...(((((.......)))))(((((.....)))))))))..)))..((....))............ (-22.29 = -22.22 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,484,126 – 9,484,216
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 87.41
Mean single sequence MFE -31.73
Consensus MFE -27.29
Energy contribution -27.60
Covariance contribution 0.31
Combinations/Pair 1.08
Mean z-score -2.22
Structure conservation index 0.86
SVM decision value 1.53
SVM RNA-class probability 0.961526
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9484126 90 - 20766785
UAAUUUUCUACAGCAGUCGCAAGGCUUCAGCAGCACGGACUGUGCUGUUAGGCGCACACUAACAGAGCUGUUGGAUAACCACCUGGCGCC
............(.((((....)))).)((((((((.....)))))))).(((((...((((((....)))))).....(....)))))) ( -30.60)
>DroSim_CAF1 5976 90 - 1
UAAUUUUCAACAGCAGUCGCAAGGCUUCGGCAGCACGGACUGUGCUGUUAGGCGCACACUAACAGAGCUGUUAGAUAACCAGCUGGCGCC
............(.((((....)))).)((((((((.....)))))))).(((((...((((((....)))))).....(....)))))) ( -30.80)
>DroEre_CAF1 5804 90 - 1
UAUUUCUCUAGAGCAAUCGCAAGGCUUCAGCAGCACACACUGUGCUGUUAGGCGCAUACUAACAGAGCCGUUGGCCCACCUGUUGGCGCC
..........((((...(....))))).((((((((.....)))))))).(((((....((((((.(((...)))....))))))))))) ( -29.40)
>DroYak_CAF1 5928 90 - 1
UAUUUUUCUACAGCAAUCGCAAGGCUUCAGCAGCACGCACUGUGCUGUUAGGCGCGCUCUAACAGAGCUGUUAGAACGCCUGCUGGCGCC
..........(((((..(....)((((.((((((((.....))))))))))))(((.(((((((....))))))).))).)))))..... ( -36.10)
>consensus
UAAUUUUCUACAGCAAUCGCAAGGCUUCAGCAGCACGCACUGUGCUGUUAGGCGCACACUAACAGAGCUGUUAGAUAACCAGCUGGCGCC
............(.((((....)))).)((((((((.....)))))))).(((((...((((((....)))))).....(....)))))) (-27.29 = -27.60 +   0.31)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:23 2006