Locus 1045

Sequence ID 2R_DroMel_CAF1
Location 4,302,034 – 4,302,162
Length 128
Max. P 0.931024
window1848 window1849

overview

Window 8

Location 4,302,034 – 4,302,134
Length 100
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 84.11
Mean single sequence MFE -27.70
Consensus MFE -18.56
Energy contribution -19.56
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.67
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4302034 100 - 20766785
CAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAGCCCUCAUCCUGCAUCCACCAUCC-------UACA-GCCGCCAUCCAAGUGGCAACGCACGGCAGACGCCGG
........(((....((.((((((.(((........)))))))))..))...........-------....-(((((.......)))))...)))((((....)))). ( -33.20)
>DroSec_CAF1 57271 100 - 1
CAGCCUCCUGCAUCCGCUGAUGAGUGGCCACAUCCAGCCACCAUCCAGCAUCCACCAUCC-------UACA-GCCGCCAUCCAAGUGGCAACGCACGGCAGACGCCGG
........(((....(((((((.(((((........)))))))).))))...........-------....-(((((.......)))))...)))((((....)))). ( -34.70)
>DroSim_CAF1 60700 86 - 1
CAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAGCCAC--------------CAUCC-------UACA-GCCGCCAUCCAAGUGGCAACGCACGGCAGACGCCGG
........(((....(((((((.(((((........)))))--------------)))).-------...)-)).(((((....)))))...)))((((....)))). ( -30.60)
>DroEre_CAF1 56690 100 - 1
CAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAUCCUCCAUUCACAAUCCACCAUCC-------ACCACUCCGCCCUCCAAGUGGCAACGCACGGCAGACGCCG-
.........((.((.((((..((((((.................................-------.))))))..........(((....))).)))).)).))..- ( -20.28)
>DroYak_CAF1 58097 107 - 1
CAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAUCCACUAUCCGCCAUCUACCAUCCUGCAUCUACCA-UCCUCCAUCCAAGUAGCAACGCACGGCAGACGCCGG
........(((....((.((((.(((((..................)))))....))))..))..((((..-............))))....)))((((....)))). ( -19.71)
>consensus
CAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAGCCACCAUCCACCAUCCACCAUCC_______UACA_GCCGCCAUCCAAGUGGCAACGCACGGCAGACGCCGG
........(((..(((((((((.(((((............................................)))))))))..)))))....)))((((....)))). (-18.56 = -19.56 +   1.00) 

alignment

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secondary structure

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dotplot

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Window 9

Location 4,302,064 – 4,302,162
Length 98
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 83.79
Mean single sequence MFE -36.51
Consensus MFE -30.26
Energy contribution -30.66
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.83
SVM decision value 1.21
SVM RNA-class probability 0.931024
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4302064 98 - 20766785
GAGGAAGUGGCUACGGGUGUCCAGGGGUCAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAGCCCUCAUCCUGCAUCCACCAUCC-------UACA-GCCGCC
......((((((..(((((..((((((....)).)))))))))((.((((((.(((........)))))))))..))...........-------...)-))))). ( -39.80)
>DroSec_CAF1 57301 98 - 1
GAGGAAGUGGCUACGGGUGUCCAGGGGUCAGCCUCCUGCAUCCGCUGAUGAGUGGCCACAUCCAGCCACCAUCCAGCAUCCACCAUCC-------UACA-GCCGCC
......((((((..(((((..((((((....)).)))))))))(((((((.(((((........)))))))).))))...........-------...)-))))). ( -41.30)
>DroSim_CAF1 60730 84 - 1
GAGGAAGUGGCUACGGGUGUCCAGGGGUCAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAGCCAC--------------CAUCC-------UACA-GCCGCC
......((((((.((((((..((((((....)).))))))))))..((((.(((((........)))))--------------)))).-------...)-))))). ( -37.60)
>DroEre_CAF1 56719 99 - 1
GAGGACUUGGCUACGGGUGUCCAGGGGUCAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAUCCUCCAUUCACAAUCCACCAUCC-------ACCACUCCGCC
..(((..((((((((((((..((((((....)).))))))))).(....).)))))))..))).........................-------........... ( -28.90)
>DroYak_CAF1 58127 105 - 1
GAGGAAGUGGCUAGGGGUGUCCAGGGGUCAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAUCCACUAUCCGCCAUCUACCAUCCUGCAUCUACCA-UCCUCC
(((((..(((.((((((((..((((((....)).)))))))))((.((((.(((((..................)))))....))))..))..))))))-))))). ( -34.97)
>consensus
GAGGAAGUGGCUACGGGUGUCCAGGGGUCAGCCUCCUGCAUCCGCUGAUGAGUGGCCACCUCCAGCCACCAUCCACCAUCCACCAUCC_______UACA_GCCGCC
..(((.(((((((((((((..((((((....)).))))))))).(....).)))))))).)))........................................... (-30.26 = -30.66 +   0.40) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:02 2006