Locus 4134

Sequence ID 3R_DroMel_CAF1
Location 11,274,710 – 11,274,807
Length 97
Max. P 0.920405
window6622 window6623

overview

Window 2

Location 11,274,710 – 11,274,807
Length 97
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 80.95
Mean single sequence MFE -41.25
Consensus MFE -26.78
Energy contribution -27.45
Covariance contribution 0.67
Combinations/Pair 1.25
Mean z-score -1.41
Structure conservation index 0.65
SVM decision value -0.02
SVM RNA-class probability 0.522506
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11274710 97 + 27905053
GUGAGACGGAGACCAUCGAGUGCGGAUCGUCCUCGACGUAACCGGAGUAGAAGCAGCCUAGGUGGCGCUGCUCCGCCUCCGCCUCCGUCUCCGGUCC
(.(((((((((....(((((..((...))..)))))......(((((..(.((((((((....)).)))))).)..))))).))))))))))..... ( -44.70)
>DroPse_CAF1 15077 95 + 1
GCGAAACGGCCACCGCCGAGUGGGAGUCGCCUUCGACGUAGCCCUUGUAGUAGCAGCCCAGAUAGUGCUGCUGCUCCUGGUCCU--GUUCCUGCUCC
.......(((....)))(((..(((((((....)))).(((..((.(.(((((((((.(.....).))))))))).).))..))--).)))..))). ( -36.80)
>DroSec_CAF1 9738 97 + 1
GUGAGACGGAGACCAUCGAGUGCGGAUCGUCCUCGACGUAGCCGGAGUAUAAGCAGCCCAGAUGGCGCUGUUCCGCCUCAGCCUCCGUCUCCGGUCC
(.(((((((((....(((((..((...))..))))).(.((.((((......(((((((....)).))))))))).)))...))))))))))..... ( -39.60)
>DroSim_CAF1 9661 97 + 1
GUGAGACGGAGACCAUCGAGUGCGGAUCGUCCUCGACGUAGCCGGAGUAGAAGCAGCCCAGGUGGCGCUGCUCCGCCUCCGCCUCCGUCUCCGGUCC
(.(((((((((....(((((..((...))..)))))......(((((..(.((((((((....)).)))))).)..))))).))))))))))..... ( -47.20)
>DroYak_CAF1 8447 91 + 1
GUGAGACGGAGACCAUCGAGUGCGGAUCGUCCUCGACGUAGCCGGAGUAGAAGCAGCCCAGGUGGCGCUGCUCCGCCUCC------GUCUCCGGUCC
(.(((((((((....(((((..((...))..)))))......((((((((..((.((....)).)).)))))))).))))------))))))..... ( -42.40)
>DroPer_CAF1 15194 95 + 1
GCGAAACGGCCACCGCCGAGUGGGAGUCGCCUUCGACGUAGCCCUUGUAGUAGCAGCCCAGAUAGUGCUGCUGCUCCUGGUCCU--GUUCCUGCUCC
.......(((....)))(((..(((((((....)))).(((..((.(.(((((((((.(.....).))))))))).).))..))--).)))..))). ( -36.80)
>consensus
GUGAGACGGAGACCAUCGAGUGCGGAUCGUCCUCGACGUAGCCGGAGUAGAAGCAGCCCAGAUGGCGCUGCUCCGCCUCCGCCU__GUCUCCGGUCC
......(((((((..(((((.(((...))).))))).......((((..(.((((((((....)).)))))).)..))))......))))))).... (-26.78 = -27.45 +   0.67)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 11,274,710 – 11,274,807
Length 97
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 80.95
Mean single sequence MFE -46.08
Consensus MFE -32.28
Energy contribution -32.67
Covariance contribution 0.39
Combinations/Pair 1.21
Mean z-score -2.55
Structure conservation index 0.70
SVM decision value 1.13
SVM RNA-class probability 0.920405
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11274710 97 - 27905053
GGACCGGAGACGGAGGCGGAGGCGGAGCAGCGCCACCUAGGCUGCUUCUACUCCGGUUACGUCGAGGACGAUCCGCACUCGAUGGUCUCCGUCUCAC
......(((((((((((((((..((((((((.........))))))))..)))).....(((((((..((...))..)))))))))))))))))).. ( -54.00)
>DroPse_CAF1 15077 95 - 1
GGAGCAGGAAC--AGGACCAGGAGCAGCAGCACUAUCUGGGCUGCUACUACAAGGGCUACGUCGAAGGCGACUCCCACUCGGCGGUGGCCGUUUCGC
...((.(((((--.......(.((.((((((.((....)))))))).)).)...(((((((((((.((......))..))))).))))))))))))) ( -33.60)
>DroSec_CAF1 9738 97 - 1
GGACCGGAGACGGAGGCUGAGGCGGAACAGCGCCAUCUGGGCUGCUUAUACUCCGGCUACGUCGAGGACGAUCCGCACUCGAUGGUCUCCGUCUCAC
......(((((((((((..((.((((..((((((.....))).))).....)))).)).(((((((..((...))..)))))))))))))))))).. ( -47.40)
>DroSim_CAF1 9661 97 - 1
GGACCGGAGACGGAGGCGGAGGCGGAGCAGCGCCACCUGGGCUGCUUCUACUCCGGCUACGUCGAGGACGAUCCGCACUCGAUGGUCUCCGUCUCAC
......(((((((((((((((..((((((((.((....))))))))))..)))).....(((((((..((...))..)))))))))))))))))).. ( -57.80)
>DroYak_CAF1 8447 91 - 1
GGACCGGAGAC------GGAGGCGGAGCAGCGCCACCUGGGCUGCUUCUACUCCGGCUACGUCGAGGACGAUCCGCACUCGAUGGUCUCCGUCUCAC
((((.((((((------((((..((((((((.((....))))))))))..)))).....(((((((..((...))..)))))))))))))))))... ( -50.10)
>DroPer_CAF1 15194 95 - 1
GGAGCAGGAAC--AGGACCAGGAGCAGCAGCACUAUCUGGGCUGCUACUACAAGGGCUACGUCGAAGGCGACUCCCACUCGGCGGUGGCCGUUUCGC
...((.(((((--.......(.((.((((((.((....)))))))).)).)...(((((((((((.((......))..))))).))))))))))))) ( -33.60)
>consensus
GGACCGGAGAC__AGGCGGAGGCGGAGCAGCGCCACCUGGGCUGCUUCUACUCCGGCUACGUCGAGGACGAUCCGCACUCGAUGGUCUCCGUCUCAC
......(((((......((((..((((((((.((....))))))))))..))))((...(((((((...........)))))))....))))))).. (-32.28 = -32.67 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:03 2006