Locus 3075

Sequence ID 3R_DroMel_CAF1
Location 8,108,053 – 8,108,195
Length 142
Max. P 0.979100
window4992 window4993

overview

Window 2

Location 8,108,053 – 8,108,173
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 71.22
Mean single sequence MFE -29.74
Consensus MFE -12.72
Energy contribution -12.68
Covariance contribution -0.04
Combinations/Pair 1.07
Mean z-score -2.21
Structure conservation index 0.43
SVM decision value 1.83
SVM RNA-class probability 0.979100
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8108053 120 + 27905053
ACCAGUACAUUAAUUGUGCUUAUGCCAUACAUGUCAAUGUAUCUAUUUGGUGCCAUCUUGAGGACCAUCACAUCUUGGCAAUUUUUAUUGCUGAGUAGCGAUCUCACCUCCAAGGUGCAA
(((((((((.....))))).......((((((....)))))).....))))((.(((((((((...(((.(..((..(((((....)))))..))..).)))....))).)))))))).. ( -34.60)
>DroSec_CAF1 1843 109 + 1
ACCAGUACGUUAGUUGUGUUUAUGCCAGACAUGUCAAUGUAUCUAUU-----------UGAGGACCACCGCAUCUUGGCAAUUUUUAUUGCUGAGUAGCGAUCUCACCUCCAAAGUGCAA
....(((((((.(.(((((((.....))))))).)))))))).....-----------.((((.....(((..((..(((((....)))))..))..)))......)))).......... ( -25.80)
>DroSim_CAF1 1847 100 + 1
ACCAGUACAUUAGAUGUGUUUAU---------GUCAAUGUAUCUAUU-----------UGAGGACCAUCGCAUCUUGGCAAUUUUUAUUGCUGAGUAGCGAUCUCACCUCCAAGGUGCAA
....((((..((((((..((...---------...))..))))))..-----------.((((...(((((..((..(((((....)))))..))..)))))....))))....)))).. ( -31.90)
>DroEre_CAF1 1390 112 + 1
AGCAGUACAUUGGUUA--CCUAAACCAUAAAUGCCAAAGUAUCGAA-UGGUGCCAUCCUGAGGAC-----UAUCUUGGCAAUUUUCAUUGCUGAGCAGCGAUCUCAGCGCCAAGGUGCAA
.(((......(((((.--....)))))....)))....(((((...-((((((.....(((((.(-----...((..(((((....)))))..))....).))))))))))).))))).. ( -32.90)
>DroYak_CAF1 810 91 + 1
AGCAAA-----------------------------AAUGUAACGAUUUGGUGCCAUCUUGAGGAGCAUCAUAUCUUGGCACUUUUUAUUGCUGAGUAGCGAUCUCACCGCCAAGGUGCAA
.((...-----------------------------............(((((((........).)))))).((((((((.......((((((....))))))......)))))))))).. ( -23.52)
>consensus
ACCAGUACAUUAGUUGUGCUUAU_CCA_A_AUGUCAAUGUAUCUAUUUGGUGCCAUC_UGAGGACCAUCACAUCUUGGCAAUUUUUAUUGCUGAGUAGCGAUCUCACCUCCAAGGUGCAA
......................................................................((((((((........((((((....)))))).......))))))))... (-12.72 = -12.68 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,108,093 – 8,108,195
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 84.84
Mean single sequence MFE -28.36
Consensus MFE -19.16
Energy contribution -20.16
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.68
SVM decision value 0.12
SVM RNA-class probability 0.593121
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8108093 102 + 27905053
AUCUAUUUGGUGCCAUCUUGAGGACCAUCACAUCUUGGCAAUUUUUAUUGCUGAGUAGCGAUCUCACCUCCAAGGUGCAAUUGGGGGUCAAUUGAUUUCGUA
.......((((.((.......))))))......((..(((((....)))))..))..((((..((((((((((.......)))))))).....))..)))). ( -29.30)
>DroSec_CAF1 1883 91 + 1
AUCUAUU-----------UGAGGACCACCGCAUCUUGGCAAUUUUUAUUGCUGAGUAGCGAUCUCACCUCCAAAGUGCAAUUGGGGGUCAAUUGAUUUCGAA
.....((-----------(((((.....(((..((..(((((....)))))..))..))).....((((((((.......)))))))).......))))))) ( -26.60)
>DroSim_CAF1 1878 91 + 1
AUCUAUU-----------UGAGGACCAUCGCAUCUUGGCAAUUUUUAUUGCUGAGUAGCGAUCUCACCUCCAAGGUGCAAUUGGGGGUCAAUUGAUUUCGUA
.......-----------.(((....(((((..((..(((((....)))))..))..))))))))((((((((.......)))))))).............. ( -28.70)
>DroEre_CAF1 1428 96 + 1
AUCGAA-UGGUGCCAUCCUGAGGAC-----UAUCUUGGCAAUUUUCAUUGCUGAGCAGCGAUCUCAGCGCCAAGGUGCAAUUGGGGGUCAAUUGAUUUCGUA
(((((.-((..(((..((..(....-----((((((((((((....)))((((((.......)))))))))))))))...)..))))))).)))))...... ( -28.20)
>DroYak_CAF1 821 102 + 1
AACGAUUUGGUGCCAUCUUGAGGAGCAUCAUAUCUUGGCACUUUUUAUUGCUGAGUAGCGAUCUCACCGCCAAGGUGCAAUUGGGGGUCAAUUGAUUUCGUA
..((((((((((((........).))))))(((((((((.......((((((....))))))......))))))))).)))))(..(((....)))..)... ( -29.02)
>consensus
AUCUAUUUGGUGCCAUC_UGAGGACCAUCACAUCUUGGCAAUUUUUAUUGCUGAGUAGCGAUCUCACCUCCAAGGUGCAAUUGGGGGUCAAUUGAUUUCGUA
.................................((..(((((....)))))..))..((((..((((((((((.......))))))).....)))..)))). (-19.16 = -20.16 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:29 2006