Locus 6299

Sequence ID 2R_DroMel_CAF1
Location 19,748,062 – 19,748,199
Length 137
Max. P 0.938840
window10069 window10070

overview

Window 9

Location 19,748,062 – 19,748,169
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.56
Mean single sequence MFE -40.38
Consensus MFE -27.83
Energy contribution -28.70
Covariance contribution 0.87
Combinations/Pair 1.04
Mean z-score -2.31
Structure conservation index 0.69
SVM decision value 1.30
SVM RNA-class probability 0.938840
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19748062 107 - 20766785
G-------GAAGCUGGGAG-CUGGGAGCUAAG----GGAGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUGUAAAGGAAUCGUUUAAAAUAAAUGACAGGCGGAC-CCC
.-------...(((...((-(.....)))...----..))).((((.(((.(...(((((.(((....))).))))).............(((((((...)))))))..).))).)-))) ( -36.50)
>DroSec_CAF1 851 114 - 1
GGGAGCUGGAAGCUGGGAG-CUGGGAGCUAAG----GGAGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUGUAAAGGAAUCGUUUAAAAUAAAUGACAGGCCGGC-CCC
(((.(((((...(((....-...((((((((.----(..((((....)).))..).)))))(((....))))))................(((((((...)))))))))).)))))-))) ( -45.10)
>DroSim_CAF1 3356 100 - 1
GG--------------GAG-CUGGGAGCUAAG----GGAGCAGGGGACCGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUGUAAAGGAAUCGUUUAAAAUAAAUGACAGGCGAGC-CCC
((--------------(.(-((.(..(((((.----(..((.(....)..))..).)))))(((....)))(((.((....))...))).(((((((...)))))))....).)))-))) ( -35.80)
>DroYak_CAF1 3459 117 - 1
GU-GGCAAGUGGCAGG-GGGUAG-GGGCAUGGGGCAGGGGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUGUAAAGGAAUCGUUUAAAAUAAAUGACAGGCGGGCCCCC
..-.((.....)).((-((((..-..((.((..(((.((.(((....))).)...(((((.(((....))).))))).).))).......(((((((...))))))))).))..)))))) ( -44.10)
>consensus
GG______GAAGCUGGGAG_CUGGGAGCUAAG____GGAGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUGUAAAGGAAUCGUUUAAAAUAAAUGACAGGCGGGC_CCC
......................(((.(((...........(((....)))((...(((((.(((....))).))))).............(((((((...)))))))...)).))).))) (-27.83 = -28.70 +   0.87)

alignment

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secondary structure

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dotplot

Postscript

Window 0

Location 19,748,101 – 19,748,199
Length 98
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 79.75
Mean single sequence MFE -35.12
Consensus MFE -26.80
Energy contribution -27.05
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.76
SVM decision value 0.29
SVM RNA-class probability 0.672295
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19748101 98 - 20766785
CUGUACUACUAUAUAGCUGAAACUGAAGCUG-------GAAGCUGGGAG-CUGGGAGCUAAG----GGAGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUG
.(((.(((((...(((((........)))))-------..)).)))...-...((((((((.----(..((((....)).))..).)))))(((....)))))).))).. ( -34.30)
>DroSec_CAF1 890 105 - 1
CUGUACUACUAUAUAGCUGAAAACGAAGCUGGGAGCUGGAAGCUGGGAG-CUGGGAGCUAAG----GGAGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUG
.(((.(((((...(((((........)))))..)).))).(((.....)-)).((((((((.----(..((((....)).))..).)))))(((....)))))).))).. ( -36.90)
>DroSim_CAF1 3395 91 - 1
CUGUACUACUAUAUAGCUGAAAACGAAGCUGG--------------GAG-CUGGGAGCUAAG----GGAGCAGGGGACCGGCGACGUUGGCGGCGAAAGCCUCCGACAUG
.............(((((........)))))(--------------..(-((((..(((...----..)))......)))))..)(((((.(((....))).)))))... ( -32.40)
>DroYak_CAF1 3499 104 - 1
CAGUA---CUAUAUAGCUGAAACUGAAGCUGU-GGCAAGUGGCAGG-GGGUAG-GGGCAUGGGGCAGGGGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUG
..(..---((((.(..(((...(((..(((..-....)))..))).-...)))-..).))))..)...(.(((....))).)...(((((.(((....))).)))))... ( -36.90)
>consensus
CUGUACUACUAUAUAGCUGAAAACGAAGCUGG______GAAGCUGGGAG_CUGGGAGCUAAG____GGAGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUG
.............(((((........)))))...................................(..((((....)).))..)(((((.(((....))).)))))... (-26.80 = -27.05 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:43 2006