Locus 1903

Sequence ID 2L_DroMel_CAF1
Location 5,209,846 – 5,209,955
Length 109
Max. P 0.862931
window3051 window3052

overview

Window 1

Location 5,209,846 – 5,209,955
Length 109
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.86
Mean single sequence MFE -27.77
Consensus MFE -21.56
Energy contribution -21.89
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.34
Structure conservation index 0.78
SVM decision value 0.84
SVM RNA-class probability 0.862931
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5209846 109 + 22407834
CCAGAGUAUCUAUACCCAUUACU----------CGUUAAAUGAAAAUGGGUAUGUUGUAUUCCUAGAAAAGUAUGCAACUGAUAGAUGGACCUUCUGAAUACGACA-CAUUGUUUUUUGU
.(((((.....(((((((((..(----------(((...)))).)))))))))((((((((((((....(((.....)))..)))..((.....))))))))))).-.......))))). ( -23.70)
>DroSec_CAF1 86842 115 + 1
-CAGACUAUCUAUACCCAUUACUGAAAAUUACCCAUUAAAUGAAAAUGGGUAUGUUGUAUUCCUAGAAAAGUAUGCAACAGAUAGAUGGACCUUCUGGAUACGCCAUCAUGGG----UGU
-..........((((((((..........((((((((.......))))))))((((((((..((.....)).))))))))....(((((.((....)).....))))))))))----))) ( -32.70)
>DroSim_CAF1 59805 110 + 1
-CAGACUAUCUAUACCCAUUACU--------UUCAUAAAAUGAAAAUGGGUAUGUUGUAUUCCCAGAAAAGUAUGCAACUGAUAGAUGGACCUUCUGGAUACGCCA-CAUUGUUCUUUGU
-(((((((((.(((((((((...--------(((((...))))))))))))))(((((((.(........).))))))).)))))..((((..(.(((.....)))-.)..)))))))). ( -26.90)
>consensus
_CAGACUAUCUAUACCCAUUACU__________CAUUAAAUGAAAAUGGGUAUGUUGUAUUCCUAGAAAAGUAUGCAACUGAUAGAUGGACCUUCUGGAUACGCCA_CAUUGUU_UUUGU
.(((((((((((((((((((........................)))))))..(((((((.(........).)))))))..))))))))....))))....................... (-21.56 = -21.89 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,209,846 – 5,209,955
Length 109
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.86
Mean single sequence MFE -26.33
Consensus MFE -19.78
Energy contribution -19.56
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.97
Structure conservation index 0.75
SVM decision value 0.29
SVM RNA-class probability 0.671070
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5209846 109 - 22407834
ACAAAAAACAAUG-UGUCGUAUUCAGAAGGUCCAUCUAUCAGUUGCAUACUUUUCUAGGAAUACAACAUACCCAUUUUCAUUUAACG----------AGUAAUGGGUAUAGAUACUCUGG
........((..(-((((((((((.((((((.((.(.....).))...))))))....))))))...((((((((((((.......)----------)).))))))))).)))))..)). ( -27.00)
>DroSec_CAF1 86842 115 - 1
ACA----CCCAUGAUGGCGUAUCCAGAAGGUCCAUCUAUCUGUUGCAUACUUUUCUAGGAAUACAACAUACCCAUUUUCAUUUAAUGGGUAAUUUUCAGUAAUGGGUAUAGAUAGUCUG-
..(----((((((((((.....((....)).)))))....(((((.((.(((....))).)).)))))((((((((.......))))))))..........))))))............- ( -28.00)
>DroSim_CAF1 59805 110 - 1
ACAAAGAACAAUG-UGGCGUAUCCAGAAGGUCCAUCUAUCAGUUGCAUACUUUUCUGGGAAUACAACAUACCCAUUUUCAUUUUAUGAA--------AGUAAUGGGUAUAGAUAGUCUG-
....(((.....(-(((.....((....)).))))(((((.((((.((.(((....))).)).))))((((((((((((((...)))))--------...))))))))).)))))))).- ( -24.00)
>consensus
ACAAA_AACAAUG_UGGCGUAUCCAGAAGGUCCAUCUAUCAGUUGCAUACUUUUCUAGGAAUACAACAUACCCAUUUUCAUUUAAUG__________AGUAAUGGGUAUAGAUAGUCUG_
.......................((((..(((.........((((.((.(((....))).)).))))(((((((((........................))))))))).)))..)))). (-19.78 = -19.56 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:07 2006