I.  COSII.xls contains the following sheets:
	(1)  "1698 COSII" lists all 1698 COSII genes.  Each row represents one COSII group containing three to five sequences ('-' means no ortholog identified in this species) and written as the following format:
(Arabidopsis id)	(copy number)	(new tomato build id)	(copy number)	(lycopersicon combined build id)	(potato unigene build 1 id)	(copy number)	(pepper unigene build 1 id)	(copy number)	(coffee unigene build 1 id)	(copy number)	

	(2)  "mapping primer" lists all mapping primers used for F2 2000 map ('-' or blank cell means no primers designed for the COSII group).  The primers are named after the Arabidopsis ortholgo with prefix "C2_".

	(3)  "outer primer" constains the primers designed further away from the predicted introns than those mapping primers.  None of them are used for mapping.

	(4)  "F2 2000 map" contains mapping information.  Hopefully this sheet is self-explanatory.

	(5)  "various PCR" contains PCR results in various species using those mapping primers.  Please ignore colors of the cells for the moment.  


II.  Directories of COSII-v2.0/ and COSII-v3.0/ contains sequence analysis of COSII groups.  In COSII-v2.0, tomato unigene sequences of lycopersicon combined build were used; while in COSII-v3.0, tomato unigene sequences of new tomato build were used.  But in the future analysis, only sequences of new tomato build will be used.  All files are named after Arabidopsis id and the file type as following:
Atxgxxxxx.x.cds.txt:  fasta file of original unigene seqs and Arabidopsis CDS seq;  
Atxgxxxxx.x.cds.txt.modify:  fasta file of edited unigene seqs and Arabidopsis CDS seq (from TAIR and not edited);
CdsTxt/Atxgxxxxx.x.pep.txt:  fasta format; translated peptide seqs from edited seqs in the corresponding ".cds.txt.modify" file;
CdsTxt/Atxgxxxxx.x.pep.aln:  clustalw format; alignment of translated peptide seqs in the corresponding ".pep.txt" file;
CdsTxt/Atxgxxxxx.x.pep.fasta:  fasta format; converted from the corresponding ".pep.aln" file;
CdsTxt/Atxgxxxxx.x.cds.txt.modify.aligned2aa:  text file; DNA-protein alignment;
CdsFasta/Atxgxxxxx.x.cds.fasta:  fasta format; DNA alignment;
CdsTxt/Atxgxxxxx.x.ATH1.blastx:  blast format; BLASTX result of original unigene seqs against Arabidopsis protein database from TAIR;
intron_txt/Atxgxxxxx.x.intron.txt:  fasta format; edited seqs with "=====" representing predicted introns;
phylogeny/Atxgxxxxx.x.cds.nex:  nexus format; input file for PAUP;
phylogeny/Atxgxxxxx.x.ml.tre:  phylogenetic tree file;  output file of PAUP;


III.  examples/ gives all the files for the COSII group "At1g14820.1"

