Locus 2409

Sequence ID 3R_DroMel_CAF1
Location 6,756,555 – 6,756,674
Length 119
Max. P 0.573081
window3913 window3914

overview

Window 3

Location 6,756,555 – 6,756,674
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 84.06
Mean single sequence MFE -25.07
Consensus MFE -19.71
Energy contribution -19.43
Covariance contribution -0.27
Combinations/Pair 1.07
Mean z-score -1.56
Structure conservation index 0.79
SVM decision value -0.05
SVM RNA-class probability 0.506904
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756555 119 + 27905053
UCAGUUUUUUCCACCGGUUUUCCUUACCCUGCAGCUUAACUGCCCAAGUGGGUAGAUAGGGUUUCUUAAGAAUAUGGAAAGUUAUGUAUCAUAUCUGAUAUAUAUGUAUACUCUAUUUA
......(((((((...(((((....((((((........((((((....)))))).))))))......))))).))))))).(((((((((....)))))))))............... ( -28.40)
>DroSec_CAF1 20737 103 + 1
UCGGUUUUUUCCACCGGCUUUCCAUACCCUGCAGCUUAACUGCCAAAAAGGGUAGAUAGGGUUUCUUAGAAAUGUAG------AUGUAUCAUAUCUGAUAUAU------ACUCUA----
(((((.......))))).......((((((((((.....)))).....))))))..((((((.(((((....)).))------)(((((((....))))))).------))))))---- ( -24.40)
>DroSim_CAF1 25117 107 + 1
UCAGUUUUUUCCACCGGCUUUCCAUACCCUGCAGCUUAACUGCCAAAGUGGGUAGAUAGGGUUCCUUAAGAAUGUAG------AUGUAUCAUAUCUGAUAUAU------ACUCUAUUUU
...............((...(((.(((((.((((.....))))......)))))....)))..))...((((((.((------((((((((....))))))))------.)).)))))) ( -22.40)
>consensus
UCAGUUUUUUCCACCGGCUUUCCAUACCCUGCAGCUUAACUGCCAAAGUGGGUAGAUAGGGUUUCUUAAGAAUGUAG______AUGUAUCAUAUCUGAUAUAU______ACUCUAUUU_
...((((((...(((((....)).(((((.((((.....))))......))))).....))).....)))))).........(((((((((....)))))))))............... (-19.71 = -19.43 +  -0.27)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 4

Location 6,756,555 – 6,756,674
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 84.06
Mean single sequence MFE -24.67
Consensus MFE -19.36
Energy contribution -18.70
Covariance contribution -0.66
Combinations/Pair 1.12
Mean z-score -1.66
Structure conservation index 0.78
SVM decision value 0.08
SVM RNA-class probability 0.573081
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756555 119 - 27905053
UAAAUAGAGUAUACAUAUAUAUCAGAUAUGAUACAUAACUUUCCAUAUUCUUAAGAAACCCUAUCUACCCACUUGGGCAGUUAAGCUGCAGGGUAAGGAAAACCGGUGGAAAAAACUGA
....(((.((((.(((((.......))))))))).....(((((((...........(((((......((....))((((.....)))))))))..((....)).)))))))...))). ( -28.50)
>DroSec_CAF1 20737 103 - 1
----UAGAGU------AUAUAUCAGAUAUGAUACAU------CUACAUUUCUAAGAAACCCUAUCUACCCUUUUUGGCAGUUAAGCUGCAGGGUAUGGAAAGCCGGUGGAAAAAACCGA
----((((..------...(((((....)))))..)------)))..((((((((.....))...((((((.....((((.....))))))))))))))))..((((.......)))). ( -23.50)
>DroSim_CAF1 25117 107 - 1
AAAAUAGAGU------AUAUAUCAGAUAUGAUACAU------CUACAUUCUUAAGGAACCCUAUCUACCCACUUUGGCAGUUAAGCUGCAGGGUAUGGAAAGCCGGUGGAAAAAACUGA
....((((..------...(((((....)))))..)------)))..((((...((...((....(((((......((((.....)))).))))).))....))...))))........ ( -22.00)
>consensus
_AAAUAGAGU______AUAUAUCAGAUAUGAUACAU______CUACAUUCUUAAGAAACCCUAUCUACCCACUUUGGCAGUUAAGCUGCAGGGUAUGGAAAGCCGGUGGAAAAAACUGA
....(((.((.........(((((....)))))..............(((....))))).)))((((((.......((((.....))))..(((.......)))))))))......... (-19.36 = -18.70 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:03 2006