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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-3A var. Lima) Synteny results

The syntenic regions between Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-3A var. Lima) (Oryza sativa Indica Group, Os127564RS1) were extracted from their pairwise alignment in Ensembl Plants release 111. We look for stretches where the alignment blocks are in synteny. The search is run in two phases. In the first one, syntenic alignments that are closer than 200 kbp are grouped. In the second phase, the groups that are in synteny are linked provided that no more than 2 non-syntenic groups are found between them and they are less than 3Mbp apart.

Configuration parameters

No configuration parameters are available.

Statistics over 28 synteny blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 7,519,145 out of 375,049,285
Covered: 367,530,140 out of 375,049,285

Uncovered: 444,791 out of 34,818,902
Covered: 34,374,111 out of 34,818,902
Oryza sativa (Xian/Indica-3A var. Lima)

Uncovered: 20,876,805 out of 405,399,143
Covered: 384,522,338 out of 405,399,143

Uncovered: 1,320,752 out of 42,895,272
Covered: 41,574,520 out of 42,895,272