Locus 6874

Sequence ID 3R_DroMel_CAF1
Location 18,180,046 – 18,180,158
Length 112
Max. P 0.824210
window11160 window11161

overview

Window 0

Location 18,180,046 – 18,180,158
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.10
Mean single sequence MFE -25.92
Consensus MFE -20.44
Energy contribution -20.24
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -1.52
Structure conservation index 0.79
SVM decision value 0.18
SVM RNA-class probability 0.623127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18180046 112 + 27905053
AACAAAGCCAACGUCAAUCUUAUUUAUUGAUUGGCUUUUAGUUUACGCAA--------AGAUGGCAAUUCGAUUCGAACAGAAAUCUGUGUGCGCAAAAUAGAUUGCAAGCUCAAAAUUG
...(((((((..((((((.......))))))))))))).(((((..(((.--------((((..(..((((...))))..)..))))...)))((((......)))))))))........ ( -25.60)
>DroSec_CAF1 2917 112 + 1
AACAAAGCCAACGUCAAUCUUAUUUAUUGAUUGGCUUUUAGUUUAUGCAA--------AGAUGGCAAUUCGAUUCGAGCAGAAAUCUGUGUGUGCAAAGUAAAUUGCAAGCUCAAAAUUG
......((((.((((((((.........))))))).....((....))..--------.).))))..........((((((....)).....(((((......))))).))))....... ( -24.30)
>DroSim_CAF1 2000 112 + 1
AAAAAAGCAAACGUCAAUCUUAUUUAUUGAUUGGCUUUUAGUUUAUGCAA--------AGAUGGCAAUUCGAUUCGAACAGAAAUCUGUGUGCGCAAAAUAGAUUGCAAGCUCAAAAUUG
......((((..(((((((.........))))))).((((.(((.((((.--------((((..(..((((...))))..)..))))...)))).))).))))))))............. ( -22.90)
>DroEre_CAF1 1974 112 + 1
AACAAAGCCAACGUCAAUCUUAUUUAUUGAUUGGCUUUUAGUUUAUGCAA--------AGAUCGCAAUUCGAUUCGAGCAGAAAUCUGUGUGCGCAAAAUAGAUUGCAAGCACAAAAUGG
...(((((((..((((((.......)))))))))))))((((((.(((..--------.(((((.....)))))...))).))).)))(((((((((......))))..)))))...... ( -26.40)
>DroYak_CAF1 2058 120 + 1
AACAAAGCCAACGUCAAUCUUAUUUAUUGAUUGGCUUUCAGUUUAUGCAAAGAUGCAAAGAUGGCAAUUCGAUUCGUGCAGAAAUCUGUGUGCGCAAAAUAGAUUGCAAGCGCCAAAUGG
...(((((((..((((((.......)))))))))))))..((((.((((....)))).))))(((.........((..(((....)))..)).((((......))))....)))...... ( -30.40)
>consensus
AACAAAGCCAACGUCAAUCUUAUUUAUUGAUUGGCUUUUAGUUUAUGCAA________AGAUGGCAAUUCGAUUCGAGCAGAAAUCUGUGUGCGCAAAAUAGAUUGCAAGCUCAAAAUUG
...(((((((..((((((.......)))))))))))))..((((..(((..........((.......)).......((((....)))).)))((((......))))))))......... (-20.44 = -20.24 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,180,046 – 18,180,158
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.10
Mean single sequence MFE -24.54
Consensus MFE -19.88
Energy contribution -20.28
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.81
SVM decision value 0.69
SVM RNA-class probability 0.824210
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18180046 112 - 27905053
CAAUUUUGAGCUUGCAAUCUAUUUUGCGCACACAGAUUUCUGUUCGAAUCGAAUUGCCAUCU--------UUGCGUAAACUAAAAGCCAAUCAAUAAAUAAGAUUGACGUUGGCUUUGUU
......................((((((((...((((..(.(((((...))))).)..))))--------.))))))))...(((((((((((((.......)))))..))))))))... ( -24.80)
>DroSec_CAF1 2917 112 - 1
CAAUUUUGAGCUUGCAAUUUACUUUGCACACACAGAUUUCUGCUCGAAUCGAAUUGCCAUCU--------UUGCAUAAACUAAAAGCCAAUCAAUAAAUAAGAUUGACGUUGGCUUUGUU
....(((((((.(((((......))))).....((....)))))))))......(((.....--------..))).......(((((((((((((.......)))))..))))))))... ( -24.10)
>DroSim_CAF1 2000 112 - 1
CAAUUUUGAGCUUGCAAUCUAUUUUGCGCACACAGAUUUCUGUUCGAAUCGAAUUGCCAUCU--------UUGCAUAAACUAAAAGCCAAUCAAUAAAUAAGAUUGACGUUUGCUUUUUU
.....(((.((((((((......))))(((...((((..(.(((((...))))).)..))))--------.))).........)))))))(((((.......)))))............. ( -17.80)
>DroEre_CAF1 1974 112 - 1
CCAUUUUGUGCUUGCAAUCUAUUUUGCGCACACAGAUUUCUGCUCGAAUCGAAUUGCGAUCU--------UUGCAUAAACUAAAAGCCAAUCAAUAAAUAAGAUUGACGUUGGCUUUGUU
....(((((((..((((......))))(((....(((((......)))))....))).....--------..)))))))...(((((((((((((.......)))))..))))))))... ( -27.80)
>DroYak_CAF1 2058 120 - 1
CCAUUUGGCGCUUGCAAUCUAUUUUGCGCACACAGAUUUCUGCACGAAUCGAAUUGCCAUCUUUGCAUCUUUGCAUAAACUGAAAGCCAAUCAAUAAAUAAGAUUGACGUUGGCUUUGUU
.....((((((..((((......)))))).....(((((......))))).....))))....((((....)))).......(((((((((((((.......)))))..))))))))... ( -28.20)
>consensus
CAAUUUUGAGCUUGCAAUCUAUUUUGCGCACACAGAUUUCUGCUCGAAUCGAAUUGCCAUCU________UUGCAUAAACUAAAAGCCAAUCAAUAAAUAAGAUUGACGUUGGCUUUGUU
.........((..((((......))))(((....(((((......)))))....)))...............))........(((((((((((((.......)))))..))))))))... (-19.88 = -20.28 +   0.40)

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 12:32:10 2006