Locus 8008

Sequence ID 3L_DroMel_CAF1
Location 21,123,367 – 21,123,518
Length 151
Max. P 0.999090
window13079 window13080 window13081

overview

Window 9

Location 21,123,367 – 21,123,487
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.25
Mean single sequence MFE -39.58
Consensus MFE -36.30
Energy contribution -36.50
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -1.24
Structure conservation index 0.92
SVM decision value 0.48
SVM RNA-class probability 0.751356
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21123367 120 + 23771897
UAGUUAGGCAUGUAAGAAGCACUAGAAGAAGACCCAUAGCCGUAGCCAUAGGUAUGGUAGCCGGUGUAACCCGAUCUGUAGGGUUGCGGCGGAUAGUGUGACAUUGUCGGCGUAAGAUGU
..(((.(((((((.....((((((..............((((((.(....).))))))..(((.((((((((........)))))))).))).)))))).))).)))))))......... ( -39.20)
>DroSec_CAF1 174080 120 + 1
UAGUUAGGCAUGUAAGAAGCACUAGAAGAAGACCCAUAGCCGUAGCCAUAGGGAUGGUAACCGGUGUAACCCGAUCUGUAGGGUUGCGGCGGAUAGUGCGACAUUGUCGGCGCAAGAUGA
......(((((((.....((((((........(((((.((....)).)).))).......(((.((((((((........)))))))).))).)))))).))).))))..(....).... ( -39.90)
>DroSim_CAF1 85778 120 + 1
UAGUUAGGCAUGUAAGAAGCACUAGAAGAAGACCCAUAGCCGUAGCCAUAGGGAUGGUAGCCGGUGUAACCCGAUCUGUAGGGUUGCGGCGGAUAGUGCGACAUUGUCGGCGCAAGAUGA
......(((((((.....((((((........(((((.((....)).)).))).......(((.((((((((........)))))))).))).)))))).))).))))..(....).... ( -39.60)
>DroEre_CAF1 96486 120 + 1
UAGUUGGGCAUGUAAGAAGCACCUGCAGAAGACCCAUAUCCAUAGCCAUAGGGAUGGUAGCCGGUGUAGCCCGAUCUGUAGGGCUGCGGCGGAUAGUGCGACAUCGUCGGAUGCGGAUGA
....(((((.((((.(......)))))...).))))(((((...(((((....)))))..(((.((((((((........)))))))).)))...((.((((...)))).))..))))). ( -42.00)
>DroYak_CAF1 67455 120 + 1
UAGUUGGGCAUGUAAGAAGCACUAGAAGAAGACCCAUAGCCAUAGCCAUAGGGAUGGUAGCCGGUGUAACCCGACCUGUAGGGCUGCGGCGGAUAGUGCGACAUCGUCGGCGUCUGAUGA
..((..(((.........((((((..............(((((..((...)).)))))..(((.((((.(((........))).)))).))).))))))(((...)))...)))..)).. ( -37.20)
>consensus
UAGUUAGGCAUGUAAGAAGCACUAGAAGAAGACCCAUAGCCGUAGCCAUAGGGAUGGUAGCCGGUGUAACCCGAUCUGUAGGGUUGCGGCGGAUAGUGCGACAUUGUCGGCGCAAGAUGA
......(((((((.....((((((....................(((((....)))))..(((.((((((((........)))))))).))).)))))).)))).)))............ (-36.30 = -36.50 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,123,367 – 21,123,487
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.25
Mean single sequence MFE -33.90
Consensus MFE -31.36
Energy contribution -31.24
Covariance contribution -0.12
Combinations/Pair 1.15
Mean z-score -2.12
Structure conservation index 0.93
SVM decision value 3.37
SVM RNA-class probability 0.999090
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21123367 120 - 23771897
ACAUCUUACGCCGACAAUGUCACACUAUCCGCCGCAACCCUACAGAUCGGGUUACACCGGCUACCAUACCUAUGGCUACGGCUAUGGGUCUUCUUCUAGUGCUUCUUACAUGCCUAACUA
.....(((.((.(((...))).(((((...((((.(((((........)))))....))))......(((((((((....))))))))).......)))))..........)).)))... ( -32.70)
>DroSec_CAF1 174080 120 - 1
UCAUCUUGCGCCGACAAUGUCGCACUAUCCGCCGCAACCCUACAGAUCGGGUUACACCGGUUACCAUCCCUAUGGCUACGGCUAUGGGUCUUCUUCUAGUGCUUCUUACAUGCCUAACUA
.......(((..(((...)))((((((...((((.(((((........)))))....)))).......((((((((....))))))))........))))))........)))....... ( -33.60)
>DroSim_CAF1 85778 120 - 1
UCAUCUUGCGCCGACAAUGUCGCACUAUCCGCCGCAACCCUACAGAUCGGGUUACACCGGCUACCAUCCCUAUGGCUACGGCUAUGGGUCUUCUUCUAGUGCUUCUUACAUGCCUAACUA
.......(((..(((...)))((((((...((((.(((((........)))))....)))).......((((((((....))))))))........))))))........)))....... ( -36.10)
>DroEre_CAF1 96486 120 - 1
UCAUCCGCAUCCGACGAUGUCGCACUAUCCGCCGCAGCCCUACAGAUCGGGCUACACCGGCUACCAUCCCUAUGGCUAUGGAUAUGGGUCUUCUGCAGGUGCUUCUUACAUGCCCAACUA
......(((((.(..((.(.(.((.(((((((((.(((((........)))))....))))..((((....))))....))))))).).).))..).))))).................. ( -33.60)
>DroYak_CAF1 67455 120 - 1
UCAUCAGACGCCGACGAUGUCGCACUAUCCGCCGCAGCCCUACAGGUCGGGUUACACCGGCUACCAUCCCUAUGGCUAUGGCUAUGGGUCUUCUUCUAGUGCUUCUUACAUGCCCAACUA
......((((.......))))((((((...((((.(((((........)))))....)))).......((((((((....))))))))........)))))).................. ( -33.50)
>consensus
UCAUCUUACGCCGACAAUGUCGCACUAUCCGCCGCAACCCUACAGAUCGGGUUACACCGGCUACCAUCCCUAUGGCUACGGCUAUGGGUCUUCUUCUAGUGCUUCUUACAUGCCUAACUA
............(((...)))((((((...((((.(((((........)))))....)))).......((((((((....))))))))........)))))).................. (-31.36 = -31.24 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,123,407 – 21,123,518
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.88
Mean single sequence MFE -40.34
Consensus MFE -31.78
Energy contribution -31.38
Covariance contribution -0.40
Combinations/Pair 1.14
Mean z-score -1.70
Structure conservation index 0.79
SVM decision value 0.40
SVM RNA-class probability 0.719626
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21123407 111 + 23771897
CGUAGCCAUAGGUAUGGUAGCCGGUGUAACCCGAUCUGUAGGGUUGCGGCGGAUAGUGUGACAUUGUCGGCGUAAGAUGUU---GCGGAUGAUGAU------GACUAUGAUGCUGAUCGU
..(((((((((.((((.((.(((.((((((((........)))))))).))).)).)))).(((..((.(((........)---)).))..)))..------..)))))..))))..... ( -40.50)
>DroSec_CAF1 174120 105 + 1
CGUAGCCAUAGGGAUGGUAACCGGUGUAACCCGAUCUGUAGGGUUGCGGCGGAUAGUGCGACAUUGUCGGCGCAAGAUGAU---GCGGAUGGUGAU------------GAUGCUGAUCGU
.((.(((((....))))).))((.((((((((........)))))))).))(((...(((.(((..(((.((((......)---)))..)))..))------------).)))..))).. ( -39.30)
>DroSim_CAF1 85818 105 + 1
CGUAGCCAUAGGGAUGGUAGCCGGUGUAACCCGAUCUGUAGGGUUGCGGCGGAUAGUGCGACAUUGUCGGCGCAAGAUGAU---GCGGAUGGUGAU------------GAUGCUGAUCGU
.((.(((((....))))).))((.((((((((........)))))))).))(((...(((.(((..(((.((((......)---)))..)))..))------------).)))..))).. ( -39.60)
>DroEre_CAF1 96526 120 + 1
CAUAGCCAUAGGGAUGGUAGCCGGUGUAGCCCGAUCUGUAGGGCUGCGGCGGAUAGUGCGACAUCGUCGGAUGCGGAUGAUAUGGCGGAUGGUGCUGACUAUGCUGAUGAUGCUGAUCGU
....(((((....)))))..(((.((((((((........)))))))).))).....(((((((((((((.(((.(......).))).(((((....))))).)))))))))....)))) ( -42.90)
>DroYak_CAF1 67495 111 + 1
CAUAGCCAUAGGGAUGGUAGCCGGUGUAACCCGACCUGUAGGGCUGCGGCGGAUAGUGCGACAUCGUCGGCGUCUGAUGAU---GCGGGUGGUGAU------GAUGAUGAUGCUGAUCGU
....(((((....)))))..(((.((((.(((........))).)))).))).(((((((.((((((((.(..(((.....---.)))..).))))------)))).)).)))))..... ( -39.40)
>consensus
CGUAGCCAUAGGGAUGGUAGCCGGUGUAACCCGAUCUGUAGGGUUGCGGCGGAUAGUGCGACAUUGUCGGCGCAAGAUGAU___GCGGAUGGUGAU______G___AUGAUGCUGAUCGU
....(((((....)))))..(((.((((((((........)))))))).))).........(((((((.((.............)).)))))))..............(((....))).. (-31.78 = -31.38 +  -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 13:03:43 2006