Locus 553

Sequence ID 2L_DroMel_CAF1
Location 1,725,453 – 1,725,613
Length 160
Max. P 0.999749
window893 window894 window895

overview

Window 3

Location 1,725,453 – 1,725,573
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.33
Mean single sequence MFE -53.80
Consensus MFE -50.82
Energy contribution -51.14
Covariance contribution 0.32
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.94
SVM decision value 1.68
SVM RNA-class probability 0.971491
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1725453 120 + 22407834
CGGUCUUGAUCUGGCCGGUGGACAGACCGACGACCAGGUCACCGAUGAACGAGUCCUCGGUCUCACCGGAACGGUGGGAGACCAUGGUGCCCCAGCCGUUCUUCUUGGCCAGCAGAUGGG
(.((((....((((((((((...(((((((.(((..(.(((....))).)..))).)))))))))))(((((((((((..((....))..)))).)))))))....)))))).)))).). ( -56.00)
>DroSec_CAF1 7606 120 + 1
CGGUCUUGAUCUGGCCGGUGGACAGACCGACGACCAGGUCACCGAUGAACGAGUCCUCGGUCUCGCCGGAACGGUGGGAGACCAUGGUGCCCCAGCCGUUCUUCUUGGCCAGCAGAUGGG
(.((((....((((((((((...(((((((.(((..(.(((....))).)..))).)))))))))))(((((((((((..((....))..)))).)))))))....)))))).)))).). ( -55.60)
>DroSim_CAF1 7784 120 + 1
CGGUCUUGAUCUGGCCGGUGGACAGACCGACGACCAAGUCACCGAUGAACGAGUCCUCGGUCUCGCCGGAACGGUGGGAGACCAUGGUGCCCCAGCCGUUCUUCUUGGCCAGCAGAUGGG
(.((((....((((((((((...(((((((.(((....(((....)))....))).)))))))))))(((((((((((..((....))..)))).)))))))....)))))).)))).). ( -55.00)
>DroEre_CAF1 7632 120 + 1
CGGUCUUGAUCUGGCCGGUGGACAGGCCCACGACCAGGUCACCGAUGAACGAGUCCUCGGUCUCGCCGGAGCGGUGGGAGACCAUGGUGCCCCAACCGUUCUGCUUGGCCAGCAGAUGGG
(.((((....(((((((((((((.((((........))))..(((.((.....)).)))))).))))(((((((((((..((....))..))).))))))))....)))))).)))).). ( -52.10)
>DroYak_CAF1 8290 120 + 1
CGGUCUUGAUCUGGCCGGUGGACAGACCCACGACCAGGUCACCGAUGAACGAGUCCUCGGUCUCGCCGGAACGGUGAGAGACCAUGGUACCCCAGCCGUUCUGCUUGGCCAGCAGAUGAG
.((((.((((((((.((.(((......))))).))))))))((((.((.....)).))))((((((((...))))))))))))(((((......)))))((((((.....)))))).... ( -50.30)
>consensus
CGGUCUUGAUCUGGCCGGUGGACAGACCGACGACCAGGUCACCGAUGAACGAGUCCUCGGUCUCGCCGGAACGGUGGGAGACCAUGGUGCCCCAGCCGUUCUUCUUGGCCAGCAGAUGGG
(.((((....((((((((((...(((((((.(((....(((....)))....))).)))))))))))(((((((((((..((....))..)))).)))))))....)))))).)))).). (-50.82 = -51.14 +   0.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,725,453 – 1,725,573
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.33
Mean single sequence MFE -54.66
Consensus MFE -51.70
Energy contribution -52.18
Covariance contribution 0.48
Combinations/Pair 1.05
Mean z-score -2.39
Structure conservation index 0.95
SVM decision value 4.00
SVM RNA-class probability 0.999749
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1725453 120 - 22407834
CCCAUCUGCUGGCCAAGAAGAACGGCUGGGGCACCAUGGUCUCCCACCGUUCCGGUGAGACCGAGGACUCGUUCAUCGGUGACCUGGUCGUCGGUCUGUCCACCGGCCAGAUCAAGACCG
....(((.((((((.....((((((.(((((.((....)).))))))))))).(((((((((((.((((.(.(((....))).).)))).)))))))...))))))))))....)))... ( -58.90)
>DroSec_CAF1 7606 120 - 1
CCCAUCUGCUGGCCAAGAAGAACGGCUGGGGCACCAUGGUCUCCCACCGUUCCGGCGAGACCGAGGACUCGUUCAUCGGUGACCUGGUCGUCGGUCUGUCCACCGGCCAGAUCAAGACCG
....(((.((((((.....((((((.(((((.((....)).))))))))))).(((.(((((((.((((.(.(((....))).).)))).))))))))))....))))))....)))... ( -56.40)
>DroSim_CAF1 7784 120 - 1
CCCAUCUGCUGGCCAAGAAGAACGGCUGGGGCACCAUGGUCUCCCACCGUUCCGGCGAGACCGAGGACUCGUUCAUCGGUGACUUGGUCGUCGGUCUGUCCACCGGCCAGAUCAAGACCG
....(((.((((((.....((((((.(((((.((....)).))))))))))).(((.(((((((.((((.(.(((....))).).)))).))))))))))....))))))....)))... ( -55.20)
>DroEre_CAF1 7632 120 - 1
CCCAUCUGCUGGCCAAGCAGAACGGUUGGGGCACCAUGGUCUCCCACCGCUCCGGCGAGACCGAGGACUCGUUCAUCGGUGACCUGGUCGUGGGCCUGUCCACCGGCCAGAUCAAGACCG
....((((((.....)))))).(((((..((((((..((((((((........)).))))))(((((....))).))))))..(((((((((((....)))).))))))).))..))))) ( -52.40)
>DroYak_CAF1 8290 120 - 1
CUCAUCUGCUGGCCAAGCAGAACGGCUGGGGUACCAUGGUCUCUCACCGUUCCGGCGAGACCGAGGACUCGUUCAUCGGUGACCUGGUCGUGGGUCUGUCCACCGGCCAGAUCAAGACCG
....((((((.....))))))..((((((((..(((((..(..((((((....((((((.(....).))))))...))))))...)..)))))......)).))))))............ ( -50.40)
>consensus
CCCAUCUGCUGGCCAAGAAGAACGGCUGGGGCACCAUGGUCUCCCACCGUUCCGGCGAGACCGAGGACUCGUUCAUCGGUGACCUGGUCGUCGGUCUGUCCACCGGCCAGAUCAAGACCG
....(((.((((((.....((((((.(((((.((....)).))))))))))).((..(((((((.((((.(.(((....))).).)))).)))))))..))...))))))....)))... (-51.70 = -52.18 +   0.48)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,725,493 – 1,725,613
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.25
Mean single sequence MFE -49.86
Consensus MFE -47.56
Energy contribution -47.52
Covariance contribution -0.04
Combinations/Pair 1.11
Mean z-score -2.12
Structure conservation index 0.95
SVM decision value 3.51
SVM RNA-class probability 0.999321
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1725493 120 - 22407834
AAGGUCAACCAGAUCGGCACCGUCACCGAGUCCAUUGCCGCCCAUCUGCUGGCCAAGAAGAACGGCUGGGGCACCAUGGUCUCCCACCGUUCCGGUGAGACCGAGGACUCGUUCAUCGGU
..((((.....))))...((((....(((((((......((((....((((..(.....)..))))..))))....(((((((..((((...))))))))))).))))))).....)))) ( -48.40)
>DroSec_CAF1 7646 120 - 1
AAGGUCAACCAGAUCGGCACCGUGACCGAGUCCAUUGCCGCCCAUCUGCUGGCCAAGAAGAACGGCUGGGGCACCAUGGUCUCCCACCGUUCCGGCGAGACCGAGGACUCGUUCAUCGGU
..((((.....))))...(((((((.(((((((......((((....((((..(.....)..))))..))))....(((((((((........)).))))))).))))))).))).)))) ( -52.20)
>DroSim_CAF1 7824 120 - 1
AAGGUCAACCAGAUCGGCACCGUGACCGAAUCCAUUGCCGCCCAUCUGCUGGCCAAGAAGAACGGCUGGGGCACCAUGGUCUCCCACCGUUCCGGCGAGACCGAGGACUCGUUCAUCGGU
..((((.....))))...(((((((.(((.(((......((((....((((..(.....)..))))..))))....(((((((((........)).))))))).))).))).))).)))) ( -46.20)
>DroEre_CAF1 7672 120 - 1
AAGGUCAACCAGAUCGGCACCGUGACCGAGUCCAUUGCCGCCCAUCUGCUGGCCAAGCAGAACGGUUGGGGCACCAUGGUCUCCCACCGCUCCGGCGAGACCGAGGACUCGUUCAUCGGU
..((((.....))))...(((((((.(((((((..(((((((..((((((.....))))))..)))...))))...(((((((((........)).))))))).))))))).))).)))) ( -54.00)
>DroYak_CAF1 8330 120 - 1
AAGGUCAACCAGAUCGGUACCGUAACCGAGUCCAUUGCCGCUCAUCUGCUGGCCAAGCAGAACGGCUGGGGUACCAUGGUCUCUCACCGUUCCGGCGAGACCGAGGACUCGUUCAUCGGU
..((((.....))))...((((....(((((((...((((....((((((.....)))))).))))(((....)))(((((((...(((...))).))))))).))))))).....)))) ( -48.50)
>consensus
AAGGUCAACCAGAUCGGCACCGUGACCGAGUCCAUUGCCGCCCAUCUGCUGGCCAAGAAGAACGGCUGGGGCACCAUGGUCUCCCACCGUUCCGGCGAGACCGAGGACUCGUUCAUCGGU
..((((.....))))...(((((((.(((((((......((((....((((..(.....)..))))..))))....(((((((((........)).))))))).))))))).))).)))) (-47.56 = -47.52 +  -0.04)

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 09:39:12 2006