Locus 4733

Sequence ID 2R_DroMel_CAF1
Location 15,537,777 – 15,537,908
Length 131
Max. P 0.966965
window7616 window7617

overview

Window 6

Location 15,537,777 – 15,537,880
Length 103
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 84.40
Mean single sequence MFE -38.76
Consensus MFE -23.18
Energy contribution -24.86
Covariance contribution 1.68
Combinations/Pair 1.12
Mean z-score -3.40
Structure conservation index 0.60
SVM decision value 1.60
SVM RNA-class probability 0.966965
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15537777 103 - 20766785
AAAAAGCGCAUUUGCAUACAGUCGAGGCUGGGAGCUGUGAGCUGGGAUCUUAGCUCUUGGCUCUUGGCUGUGUGCUGACCAAAAAUGGCAGAAGCCGCCAUGC
.......((....(((((((((((((((..(((((((.((.......)).)))))))..)).))))))))))))).........(((((.......))))))) ( -47.10)
>DroSec_CAF1 331565 96 - 1
AAAAAGCGCAUUUGCAUACAGUCGAGGCUGGGAGC-------UGGGAUCUUGGCUCUUGGCUCUUAGCUGUGUGCUGACCAAAAAUGGCAGAAGCCGCCAUGC
.......((....(((((((((..((((..(((((-------..(....)..)))))..)).))..))))))))).........(((((.......))))))) ( -42.80)
>DroSim_CAF1 311437 89 - 1
AAAAAGCGCAUUUGCAUACAGUCGAGGCUGGGAGC-------UGGGAUCUUGGCUCUUGG-------CUGUGUGCUGACCAAAAAUGGCAGAAGCCGCCAUGC
.......((....(((((((((((((((..(((..-------.....)))..)).)))))-------)))))))).........(((((.......))))))) ( -37.20)
>DroEre_CAF1 319936 89 - 1
AAAAAGCGCAUUUGCAUACGGUCGAGGUUGGGAGCUGG-------UAGCUGGGAUCU-------UGGCUGUGUGCUGACCAAAAAUGGCAGAAGCCGCCAUGC
.......((....((((((((((((((((...(((...-------..)))..)))))-------))))))))))).........(((((.......))))))) ( -32.50)
>DroYak_CAF1 330508 96 - 1
AAAAAGCGCAUUUGCAUACAGUUGAGGUUGGGAGCUGGUAGCUGGUAGCUGGGAUCU-------UGGCUGUGUGCUGACCAAAAAUGGCAGAAGCCGCCAUGC
.......((....(((((((((..(((((...(((((.(....).)))))..)))))-------..))))))))).........(((((.......))))))) ( -34.20)
>consensus
AAAAAGCGCAUUUGCAUACAGUCGAGGCUGGGAGCUG_____UGGGAUCUUGGCUCUUGG____UGGCUGUGUGCUGACCAAAAAUGGCAGAAGCCGCCAUGC
.......((....(((((((((((...(..((((((...............))))))..)....))))))))))).........(((((.......))))))) (-23.18 = -24.86 +   1.68)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,537,803 – 15,537,908
Length 105
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 75.21
Mean single sequence MFE -38.28
Consensus MFE -16.38
Energy contribution -18.06
Covariance contribution 1.68
Combinations/Pair 1.17
Mean z-score -1.97
Structure conservation index 0.43
SVM decision value 0.69
SVM RNA-class probability 0.824789
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15537803 105 - 20766785
UUGGUCUCGCUCCG----ACCGGCCG---ACAAACAAAAAGCGCAUUUGCAUACAGUCGAGGCUGGGAGCUGUGAGCUGGGAUCUUAGCUCUUGGCUCUUGGCUGUGUGCUG
(((((((((...))----)..)))))---)..................(((((((((((((((..(((((((.((.......)).)))))))..)).))))))))))))).. ( -46.10)
>DroSec_CAF1 331591 90 - 1
--------CGACAA----ACCGACCG---ACAAACAAAAAGCGCAUUUGCAUACAGUCGAGGCUGGGAGC-------UGGGAUCUUGGCUCUUGGCUCUUAGCUGUGUGCUG
--------......----........---...................(((((((((..((((..(((((-------..(....)..)))))..)).))..))))))))).. ( -36.00)
>DroSim_CAF1 311463 91 - 1
UUGGUCUCGCUCCG----ACCGGCCG---ACAAACAAAAAGCGCAUUUGCAUACAGUCGAGGCUGGGAGC-------UGGGAUCUUGGCUCUUGG-------CUGUGUGCUG
(((((((((...))----)..)))))---)..................(((((((((((((((..(((..-------.....)))..)).)))))-------)))))))).. ( -36.20)
>DroEre_CAF1 319962 94 - 1
UUGCUCCCGGUCCG----GCCGGCCGACAACAAACAAAAAGCGCAUUUGCAUACGGUCGAGGUUGGGAGCUGG-------UAGCUGGGAUCU-------UGGCUGUGUGCUG
..(((((((..(((----((((((................))((....))...)))))).)..)))))))...-------((((..(....)-------..))))....... ( -34.49)
>DroYak_CAF1 330534 105 - 1
UUGCUCUCGGUCCGACCAGCCGGCCGGCAACAAACAAAAAGCGCAUUUGCAUACAGUUGAGGUUGGGAGCUGGUAGCUGGUAGCUGGGAUCU-------UGGCUGUGUGCUG
.(((.((.((.(((......)))))(....)........)).)))...(((((((((..(((((...(((((.(....).)))))..)))))-------..))))))))).. ( -38.60)
>consensus
UUGCUCUCGGUCCG____ACCGGCCG___ACAAACAAAAAGCGCAUUUGCAUACAGUCGAGGCUGGGAGCUG_____UGGGAUCUUGGCUCUUGG____UGGCUGUGUGCUG
................................................(((((((((((...(..((((((...............))))))..)....))))))))))).. (-16.38 = -18.06 +   1.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:03 2006