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//home/cluster1/data/bu01/1121861/jlex/alignment/alignments.xml~
<!--*******************************************************--> <alignment> <date>2005-03-24</date> <purpose>To align the "red" alleles of the founder strains 26695 and J99. </purpose> <file>26695_j99-red_alleles</file> <sequence> <strain>26695</strain> <description>L1-1/3-Red-SN></description> </sequence> <sequence> <strain>26695</strain> <description>L2-1/2-Red-SN></description> </sequence> <sequence> <strain>26695</strain> <description>L1-3/3-Red-NK></description> </sequence> <sequence> <strain>J99</strain> <description>L1-1/1-Red-NK></description> </sequence> <sequence> <strain>26695</strain> <description>L2-2/2-Red-NK></description> </sequence> <conclusions>As demonstrated, there is significan identity between red alleles across strains. HP1187 and HP0118 share the most identity - 99% HP1188 shares the lowest identity with other strains which is expected as there is a frame shift. jhp0110 shares the least amount of identity with the other genes with the exception of 1188.</conclusions> <plans>1. Align the green alleles, the conserved regions, and the intergenic regions of 26695 and J99.</plans> </alignment>