Locus 7982

Sequence ID 3R_DroMel_CAF1
Location 21,403,313 – 21,403,460
Length 147
Max. P 0.993105
window12851 window12852 window12853 window12854

overview

Window 1

Location 21,403,313 – 21,403,431
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 87.01
Mean single sequence MFE -19.87
Consensus MFE -14.22
Energy contribution -15.67
Covariance contribution 1.45
Combinations/Pair 1.04
Mean z-score -2.23
Structure conservation index 0.72
SVM decision value 0.20
SVM RNA-class probability 0.632160
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21403313 118 + 27905053
CAAUAAUAAAUCCAAUUACAAAUUUCGAUUUUCCAGCCAGCAAAGAUGCCGCCCAUCCAUAAUAGAUUACAUUUCUGCUCUCUAUAGACUGGCAAACAUUUGCCAAUUGGCAAACAAA
.......(((((.((........)).)))))....((((((...((((.....))))....(((((...((....))...))))).).))))).....((((((....)))))).... ( -20.40)
>DroSim_CAF1 94091 118 + 1
CAAUAAUAAAUCCAAUUACAAAUUUCGAUUUUCCAGCCAGCAAAGAUGAAGUCCAUCCAUAAUAGAUUACAUUUCUGCUCUCUAUAGACUGGCAAACAUUUGCCAAUUGGCAAACAAA
.......(((((.((........)).)))))....(((((((.(((((.((((.((.....)).)))).))))).)))...........((((((....))))))..))))....... ( -22.10)
>DroYak_CAF1 97657 111 + 1
-------AAAUCGAAUUUGAAAUUCCGAUUACCCGUCUAGCAAAGAUAAAGUCCAUCCAUAAUACAUUACAUUUCUGCUUUCUAUAGAUUGGCAAACAUUUGCCAAUUGGCAAACAAA
-------.((((((((.....))).)))))....(((.((((.((((.......................)))).)))).......(((((((((....))))))))))))....... ( -17.10)
>consensus
CAAUAAUAAAUCCAAUUACAAAUUUCGAUUUUCCAGCCAGCAAAGAUGAAGUCCAUCCAUAAUAGAUUACAUUUCUGCUCUCUAUAGACUGGCAAACAUUUGCCAAUUGGCAAACAAA
...................................(((((((.(((((.((((.((.....)).)))).))))).)))...........((((((....))))))..))))....... (-14.22 = -15.67 +   1.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,403,313 – 21,403,431
Length 118
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 87.01
Mean single sequence MFE -29.93
Consensus MFE -22.51
Energy contribution -23.73
Covariance contribution 1.23
Combinations/Pair 1.06
Mean z-score -2.19
Structure conservation index 0.75
SVM decision value 0.30
SVM RNA-class probability 0.678069
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21403313 118 - 27905053
UUUGUUUGCCAAUUGGCAAAUGUUUGCCAGUCUAUAGAGAGCAGAAAUGUAAUCUAUUAUGGAUGGGCGGCAUCUUUGCUGGCUGGAAAAUCGAAAUUUGUAAUUGGAUUUAUUAUUG
........(((.(..(((((.(((((((.((((((((((((((....)))..))).)))))))).))))).)).)))))..).))).(((((.((........)).)))))....... ( -33.10)
>DroSim_CAF1 94091 118 - 1
UUUGUUUGCCAAUUGGCAAAUGUUUGCCAGUCUAUAGAGAGCAGAAAUGUAAUCUAUUAUGGAUGGACUUCAUCUUUGCUGGCUGGAAAAUCGAAAUUUGUAAUUGGAUUUAUUAUUG
...(((((((....)))))))....((((((..(((((..(((....)))..)))))...(((((.....)))))..))))))....(((((.((........)).)))))....... ( -31.20)
>DroYak_CAF1 97657 111 - 1
UUUGUUUGCCAAUUGGCAAAUGUUUGCCAAUCUAUAGAAAGCAGAAAUGUAAUGUAUUAUGGAUGGACUUUAUCUUUGCUAGACGGGUAAUCGGAAUUUCAAAUUCGAUUU-------
.....(((((..((((((((.((..((((.(((((((.(.(((....)))....).)))))))))).)...)).))))))))...)))))(((((........)))))...------- ( -25.50)
>consensus
UUUGUUUGCCAAUUGGCAAAUGUUUGCCAGUCUAUAGAGAGCAGAAAUGUAAUCUAUUAUGGAUGGACUUCAUCUUUGCUGGCUGGAAAAUCGAAAUUUGUAAUUGGAUUUAUUAUUG
...(((((((....))))))).....((((((.(((((..(((....)))..)))))...(((((.....))))).....)))))).(((((.((........)).)))))....... (-22.51 = -23.73 +   1.23)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,403,353 – 21,403,460
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 94.39
Mean single sequence MFE -18.83
Consensus MFE -15.85
Energy contribution -16.30
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.97
Structure conservation index 0.84
SVM decision value 0.98
SVM RNA-class probability 0.893263
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21403353 107 + 27905053
CAAAGAUGCCGCCCAUCCAUAAUAGAUUACAUUUCUGCUCUCUAUAGACUGGCAAACAUUUGCCAAUUGGCAAACAAAUGCCAAAUAAAUCAAAAUCAAACAAGAGA
....((((.....)))).....((((.......)))).(((((......((((((....)))))).((((((......))))))..................))))) ( -21.40)
>DroSim_CAF1 94131 107 + 1
CAAAGAUGAAGUCCAUCCAUAAUAGAUUACAUUUCUGCUCUCUAUAGACUGGCAAACAUUUGCCAAUUGGCAAACAAAUGCCAAAUAAAUCAAAAUCAAACAAGAGA
((.(((((.((((.((.....)).)))).))))).)).(((((......((((((....)))))).((((((......))))))..................))))) ( -22.50)
>DroYak_CAF1 97690 107 + 1
CAAAGAUAAAGUCCAUCCAUAAUACAUUACAUUUCUGCUUUCUAUAGAUUGGCAAACAUUUGCCAAUUGGCAAACAAAUACCAAAUAAAUCAAAAUCAAACAAGAGC
....................................(((((.....(((((((((....)))))))))((..........))....................))))) ( -12.60)
>consensus
CAAAGAUGAAGUCCAUCCAUAAUAGAUUACAUUUCUGCUCUCUAUAGACUGGCAAACAUUUGCCAAUUGGCAAACAAAUGCCAAAUAAAUCAAAAUCAAACAAGAGA
....((((.....))))......................((((......((((((....)))))).((((((......))))))..................)))). (-15.85 = -16.30 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,403,353 – 21,403,460
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 94.39
Mean single sequence MFE -29.10
Consensus MFE -28.46
Energy contribution -28.13
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -3.06
Structure conservation index 0.98
SVM decision value 2.37
SVM RNA-class probability 0.993105
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21403353 107 - 27905053
UCUCUUGUUUGAUUUUGAUUUAUUUGGCAUUUGUUUGCCAAUUGGCAAAUGUUUGCCAGUCUAUAGAGAGCAGAAAUGUAAUCUAUUAUGGAUGGGCGGCAUCUUUG
..........(((.(((.......(((((..((((((((....))))))))..)))))((((((((((((((....)))..))).))))))))...))).))).... ( -31.00)
>DroSim_CAF1 94131 107 - 1
UCUCUUGUUUGAUUUUGAUUUAUUUGGCAUUUGUUUGCCAAUUGGCAAAUGUUUGCCAGUCUAUAGAGAGCAGAAAUGUAAUCUAUUAUGGAUGGACUUCAUCUUUG
.........(((..((.((((((((((((..((((((((....))))))))..))))))...(((((..(((....)))..))))).)))))).))..)))...... ( -31.70)
>DroYak_CAF1 97690 107 - 1
GCUCUUGUUUGAUUUUGAUUUAUUUGGUAUUUGUUUGCCAAUUGGCAAAUGUUUGCCAAUCUAUAGAAAGCAGAAAUGUAAUGUAUUAUGGAUGGACUUUAUCUUUG
......((((..............(((((..((((((((....))))))))..)))))((((((((.(.(((....)))....).)))))))))))).......... ( -24.60)
>consensus
UCUCUUGUUUGAUUUUGAUUUAUUUGGCAUUUGUUUGCCAAUUGGCAAAUGUUUGCCAGUCUAUAGAGAGCAGAAAUGUAAUCUAUUAUGGAUGGACUUCAUCUUUG
......((((..............(((((..((((((((....))))))))..)))))((((((((((((((....)))..))).)))))))))))).......... (-28.46 = -28.13 +  -0.33)

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 12:59:35 2006