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Index of /EvidentialGene/plants/cacao/genome

      Name                                  Last modified       Size  

[DIR] Parent Directory 08-Apr-2019 15:34 - [TXT] assembly_align_summary.txt 23-Aug-2011 17:09 3k [TXT] cacao11allasm.chr.gff 26-Aug-2011 16:11 54k [TXT] cacao11allasm_nomito.fa.count 14-Dec-2011 20:30 31k [   ] cacao11allasm_nomito.fa.gz 20-Aug-2011 16:23 96.4M [TXT] cacao11allasm_repmask_nomito.fa.count 14-Dec-2011 20:30 31k [   ] cacao11allasm_repmask_nomito.fa.gz 06-Dec-2011 23:22 115M

Theobroma cacao assembly (Matina cultivar)

cacao11allasm.fa   : genome assembly
cacao11allasm_repmask.fa.gz is soft-masked with repeats + plant transposons (Repbase 2011 May).

Genes_gff       size            Alias
scaffold_1      38988864        Alias=chromosome_1
scaffold_2      42436413        Alias=chromosome_2
scaffold_3      34397752        Alias=chromosome_3
scaffold_4      33492547        Alias=chromosome_4
scaffold_5      40442896        Alias=chromosome_5
scaffold_6      27290986        Alias=chromosome_6
scaffold_7      24379470        Alias=chromosome_7
scaffold_8      21543242        Alias=chromosome_8
scaffold_9      42035188        Alias=chromosome_9
scaffold_10r    25448839        Alias=chromosome_10;Alias=scaffold_10
 .. 701 small scaffolds ..
cacao1chloroplast       160604  Alias=chloroplast
cacao1mito      544287  Alias=mito
cacao1rdna_scaffold_175 10639   Alias=rdna
scaffold_10r is the name I used for scaffold_10 or chromosome 10.
The chloroplast genome is T_cacao_cp, a curated one from Chris Saski,
rather than assembled from reads.  Mitochondrial genome is from
assembly as  M16_mito_v1.0.  The rDNA scaffold is from assembly 
marked as ribosomal DNA.
M16_mito_v1.0 has been withdrawn from public use for the time being (6 Dec 2011)
cacao11allasm.fa is replaced by cacao11allasm_nomito.fa
Full genome assembly from Theobroma_cacao/20110822
included in  cacao11allasm_nomito.fa.gz 
M16_mito_v1.0.fasta     << Withdrawn
T_cacao_cp.fasta	<< Included
sequences/Theobroma_cacao.main_genome.scaffolds.fasta   << Included
sequences/Theobroma_cacao.rDNA.scaffolds.fasta		<< Included
sequences/Theobroma_cacao.chloroplast.scaffolds.fasta   << Not included
sequences/Theobroma_cacao.exclude.scaffolds.fasta	<< Not included
sequences/Theobroma_cacao.mitochondrial.scaffolds.fasta << Not included
sequences/Theobroma_cacao.repeat.scaffolds.fasta	<< Not included

Developed at the Genome Informatics Lab of Indiana University Biology Department