Locus 755

Sequence ID 2L_DroMel_CAF1
Location 2,161,901 – 2,162,042
Length 141
Max. P 0.859375
window1241 window1242 window1243

overview

Window 1

Location 2,161,901 – 2,162,002
Length 101
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 72.81
Mean single sequence MFE -24.57
Consensus MFE -17.56
Energy contribution -17.88
Covariance contribution 0.31
Combinations/Pair 1.08
Mean z-score -1.52
Structure conservation index 0.71
SVM decision value 0.82
SVM RNA-class probability 0.859375
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2161901 101 + 22407834
CUAU---------GCUAUUUAUUGAAUGCCAAUCAAAGCCCACCUCAUGAGUAUACCCAGCAAUUGGCGCCCACUGUGGGGCCCAACCUUACGUCCCAUUUAGGCGCUUC
...(---------(((.....((((.......)))).((.((.....)).))......))))...((((((....(((((((..........)))))))...)))))).. ( -24.00)
>DroSec_CAF1 3727 79 + 1
-----------------UUUAUU--------------GCAUACCUUAUGAGUAAGCCCAGCAAUUGGCGCCCACUGUGGGGCGCAACCUUACAUCCCAUUUAUGUGCUUC
-----------------......--------------(((((......(((((((..(((...)))((((((......))))))...))))).)).......)))))... ( -20.02)
>DroEre_CAF1 3764 110 + 1
UUAUUGAUUACUAGCUUUUUGAUGCAUGCCAAUCAAAACCUACCGCAUGUGCAUACCCAGCAAUUGGCGCCCAAUGUGGGGCCCAACCUUAAGUCCCAUUUAGGCGCUUC
.............(((...((.(((((((...............))))))))).....)))....((((((....(((((((..........)))))))...)))))).. ( -29.36)
>DroYak_CAF1 3832 110 + 1
UUACUGAUUACUAGCUUUUUAUUGCAUGCCAAUCUAAGCCUACCUCGUGUACAUGCCCAACAAUUGGCGCCCAAUGUGGGGCCCAACCUUAAGUCCCAUUUAGGCGCUUC
.((((((......((((...((((.....))))..)))).....))).)))..............((((((....(((((((..........)))))))...)))))).. ( -24.90)
>consensus
UUAU_________GCUUUUUAUUGCAUGCCAAUCAAAGCCUACCUCAUGAGCAUACCCAGCAAUUGGCGCCCAAUGUGGGGCCCAACCUUAAGUCCCAUUUAGGCGCUUC
.................................................................((((((....(((((((..........)))))))...)))))).. (-17.56 = -17.88 +   0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,161,901 – 2,162,002
Length 101
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 72.81
Mean single sequence MFE -30.38
Consensus MFE -18.31
Energy contribution -19.00
Covariance contribution 0.69
Combinations/Pair 1.23
Mean z-score -1.54
Structure conservation index 0.60
SVM decision value 0.08
SVM RNA-class probability 0.571330
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2161901 101 - 22407834
GAAGCGCCUAAAUGGGACGUAAGGUUGGGCCCCACAGUGGGCGCCAAUUGCUGGGUAUACUCAUGAGGUGGGCUUUGAUUGGCAUUCAAUAAAUAGC---------AUAG
...(((((((..((((.(.((....)).).))))...)))))(((((((...((((.((((.....)))).)))).)))))))............))---------.... ( -30.80)
>DroSec_CAF1 3727 79 - 1
GAAGCACAUAAAUGGGAUGUAAGGUUGCGCCCCACAGUGGGCGCCAAUUGCUGGGCUUACUCAUAAGGUAUGC--------------AAUAAA-----------------
...(((.((..(((((..((..(((.((((((......)))))).....)))..))...)))))...)).)))--------------......----------------- ( -23.30)
>DroEre_CAF1 3764 110 - 1
GAAGCGCCUAAAUGGGACUUAAGGUUGGGCCCCACAUUGGGCGCCAAUUGCUGGGUAUGCACAUGCGGUAGGUUUUGAUUGGCAUGCAUCAAAAAGCUAGUAAUCAAUAA
...((((((((.((((.((((....)))).))))..))))))))..((((((((((((((.((..(((......)))..)))))))).........))))))))...... ( -34.10)
>DroYak_CAF1 3832 110 - 1
GAAGCGCCUAAAUGGGACUUAAGGUUGGGCCCCACAUUGGGCGCCAAUUGUUGGGCAUGUACACGAGGUAGGCUUAGAUUGGCAUGCAAUAAAAAGCUAGUAAUCAGUAA
..(((((((((.((((.((((....)))).))))..))))))(((((((..(((((...(((.....))).))))))))))))............)))............ ( -33.30)
>consensus
GAAGCGCCUAAAUGGGACGUAAGGUUGGGCCCCACAGUGGGCGCCAAUUGCUGGGCAUACACAUGAGGUAGGCUUUGAUUGGCAUGCAAUAAAAAGC_________AUAA
.....(((((.(((((.((...((((((((((......)))).))))))...)).....)))))....)))))..................................... (-18.31 = -19.00 +   0.69)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,161,922 – 2,162,042
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.81
Mean single sequence MFE -29.44
Consensus MFE -19.80
Energy contribution -21.04
Covariance contribution 1.24
Combinations/Pair 1.10
Mean z-score -1.95
Structure conservation index 0.67
SVM decision value 0.60
SVM RNA-class probability 0.796322
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2161922 120 + 22407834
AAUCAAAGCCCACCUCAUGAGUAUACCCAGCAAUUGGCGCCCACUGUGGGGCCCAACCUUACGUCCCAUUUAGGCGCUUCCGCUUCCAUAUCCGGAUACUUAACGUAAUAAAAGUUGACA
..((((...........((((((.....(((....((((((....(((((((..........)))))))...))))))...)))(((......)))))))))............)))).. ( -30.40)
>DroSec_CAF1 3733 113 + 1
-------GCAUACCUUAUGAGUAAGCCCAGCAAUUGGCGCCCACUGUGGGGCGCAACCUUACAUCCCAUUUAUGUGCUUCCGCUUUCAUAUCCGGAUACUUAAGGUAAUAAAAGUUGACA
-------((.((((....).))).)).((((.....((((((......)))))).((((((.((((....((((.((....))...))))...))))...)))))).......))))... ( -32.60)
>DroSim_CAF1 3739 101 + 1
-------GCAUACCUUAUGA------------AUUGGCGCCCACUGUGGGGCGCAACCUUACAUCCCAUUUAUGUGCUUCCGCUUUCAUAUCCGGAUACUUAAUGUAAUAAAAGUUGACA
-------((((.........------------....((((((......))))))........((((....((((.((....))...))))...)))).....)))).............. ( -22.30)
>DroEre_CAF1 3794 120 + 1
AAUCAAAACCUACCGCAUGUGCAUACCCAGCAAUUGGCGCCCAAUGUGGGGCCCAACCUUAAGUCCCAUUUAGGCGCUUCCGCUAUCAUAUCCGGAUACUUAAUAAAGUAACAGUUGACA
..((((......(((.(((((.((....(((....((((((....(((((((..........)))))))...))))))...)))))))))).))).(((((....)))))....)))).. ( -33.80)
>DroYak_CAF1 3862 120 + 1
AAUCUAAGCCUACCUCGUGUACAUGCCCAACAAUUGGCGCCCAAUGUGGGGCCCAACCUUAAGUCCCAUUUAGGCGCUUCCGCUAUCAUAUCCGGAUACUUAACAUAAUAACAGUUGACA
..............................(((((((((((....(((((((..........)))))))...))))).((((..........))))...............))))))... ( -28.10)
>consensus
AAUC_AAGCCUACCUCAUGAGCAUACCCAGCAAUUGGCGCCCACUGUGGGGCCCAACCUUACGUCCCAUUUAGGCGCUUCCGCUUUCAUAUCCGGAUACUUAACGUAAUAAAAGUUGACA
...........................((((....((((((....(((((((..........)))))))...))))))((((..........)))).................))))... (-19.80 = -21.04 +   1.24)

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 09:44:52 2006