Locus 4918

Sequence ID X_DroMel_CAF1
Location 12,800,393 – 12,800,531
Length 138
Max. P 0.963142
window8021 window8022

overview

Window 1

Location 12,800,393 – 12,800,507
Length 114
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 78.16
Mean single sequence MFE -27.30
Consensus MFE -18.15
Energy contribution -17.90
Covariance contribution -0.25
Combinations/Pair 1.30
Mean z-score -2.19
Structure conservation index 0.66
SVM decision value 1.55
SVM RNA-class probability 0.963142
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12800393 114 + 22224390
-CCUUAAGCCUGGCAGUAACAAAUACUUGUGCAUAAACACAAACACACACACACACACGUGUUUGUGUGUGACACAAGGAUGCUAUCCUGCGCACUGCUAAUUGAAUCAGAAACC
-..((((...(((((((........(((((((((..((((((((((............))))))))))))).))))))(.(((......))))))))))).)))).......... ( -33.40)
>DroSim_CAF1 8340 112 + 1
-CGGUAAGCCAGGCAGUAACAAAUACUCGUGCAUAAACACA--CAUACACACAUACACGUGGUUGUGUGUGACACAAGGAUGCUAUCCUGCGCACUGCUAAUUGAAUCAGAAACC
-.((....)).((((((...........((((.....((((--((((..(((......)))..)))))))).....(((((...)))))))))))))))................ ( -30.70)
>DroEre_CAF1 6636 104 + 1
-ACUUAAGCCUGGCAGCAACAAAUACAUGUGCA----------CGAGCAUACACACAUGCGAGUAUGUGUGACACAAGGAUGCUAUCCUGCGCACUGCUAAUUGAAUCAGAAACC
-..((((...((((((...........((((((----------..(((((.((((((((....)))))))).(....).)))))....)))))))))))).)))).......... ( -26.70)
>DroYak_CAF1 7706 100 + 1
GCCUUAAGCCUGGUAGUAACAAAA-CA----AA----------CAGAUACACAUACAUUCAUAUGUGUGUGACACAAGGAUGGUAUUCAGCGCAUUGCUAAUUGAAUCAGAAACC
.((((....(((...((......)-).----..----------)))...(((((((((....)))))))))....)))).(((((((.(((.....))))))...))))...... ( -18.40)
>consensus
_CCUUAAGCCUGGCAGUAACAAAUACAUGUGCA__________CAAACACACACACACGCGUUUGUGUGUGACACAAGGAUGCUAUCCUGCGCACUGCUAAUUGAAUCAGAAACC
..........(((((((..................................((((((((....)))))))).....(((((...)))))....)))))))............... (-18.15 = -17.90 +  -0.25)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 12,800,427 – 12,800,531
Length 104
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 83.66
Mean single sequence MFE -24.60
Consensus MFE -19.42
Energy contribution -18.93
Covariance contribution -0.50
Combinations/Pair 1.22
Mean z-score -2.27
Structure conservation index 0.79
SVM decision value 1.46
SVM RNA-class probability 0.956300
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12800427 104 + 22224390
AACACAAACACACACACACACACGUGUUUGUGUGUGACACAAGGAUGCUAUCCUGCGCACUGCUAAUUGAAUCAGAAACCGCACCAUGAAAUCAGCAGGCAAAC
........((((((((.(((....))).)))))))).....(((((...)))))..((.(((((.(((...(((............)))))).))))))).... ( -27.90)
>DroSim_CAF1 8374 102 + 1
AACACA--CAUACACACAUACACGUGGUUGUGUGUGACACAAGGAUGCUAUCCUGCGCACUGCUAAUUGAAUCAGAAACCGCACCAUGAAAUCAGCAGGCAAAC
..((((--((((..(((......)))..)))))))).....(((((...)))))..((.(((((.(((...(((............)))))).))))))).... ( -27.10)
>DroEre_CAF1 6668 96 + 1
--------CGAGCAUACACACAUGCGAGUAUGUGUGACACAAGGAUGCUAUCCUGCGCACUGCUAAUUGAAUCAGAAACCGCACCAUGAAAUCAGCAGGCAAAC
--------...((...((((((((....)))))))).....(((((...)))))))((.(((((.(((...(((............)))))).))))))).... ( -25.50)
>DroYak_CAF1 7734 95 + 1
--------CAGAUACACAUACAUUCAUAUGUGUGUGACACAAGGAUGGUAUUCAGCGCAUUGCUAAUUGAAUCAGAAACCGCACCAUAAAAUC-GCAAGCAAAC
--------..(((.(((((((((....)))))))))......((.((((((((((.((...))...)))))).....))))..)).....)))-.......... ( -17.90)
>consensus
________CAAACACACACACACGCGUUUGUGUGUGACACAAGGAUGCUAUCCUGCGCACUGCUAAUUGAAUCAGAAACCGCACCAUGAAAUCAGCAGGCAAAC
................((((((((....)))))))).....(((((...)))))..((.(((((.(((.....................))).))))))).... (-19.42 = -18.93 +  -0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:02 2006