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Rat vs C.intestinalis Translated Blat alignments

Rat (Rattus norvegicus, Rnor_5.0) and C.intestinalis (Ciona intestinalis, KH) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 70. Rat was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Configuration parameters

Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

Rat C.intestinalis
Chunk size 1,000,000 25,000
Overlap 10,000 10,000
Group set size 100,000,000 10,000,000
Masking options {default_soft_masking => 1}


Number of alignment blocks: 59,386

Genome coverage (bp) Coding exon coverage (bp)
Rattus norvegicus

Uncovered: 2,903,362,095 out of 2,909,698,938
Covered: 6,336,843 out of 2,909,698,938

Uncovered: 30,000,128 out of 34,224,882
Matches: 2,883,704 out of 34,224,882
Mismatches: 1,340,857 out of 34,224,882
Insertions: 193 out of 34,224,882

Ciona intestinalis

Uncovered: 112,295,581 out of 115,226,814
Covered: 2,931,233 out of 115,226,814

Uncovered: 13,644,248 out of 16,105,584
Matches: 1,663,721 out of 16,105,584
Mismatches: 797,132 out of 16,105,584
Insertions: 483 out of 16,105,584