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Human vs C.intestinalis Translated Blat alignments

Human (Homo sapiens, GRCh37) 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 66. Human 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

Human 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: 55,364

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 3,093,055,442 out of 3,098,825,702
Covered: 5,770,260 out of 3,098,825,702

Uncovered: 31,265,821 out of 35,313,516
Matches: 2,761,631 out of 35,313,516
Mismatches: 1,285,958 out of 35,313,516
Insertions: 106 out of 35,313,516

Ciona intestinalis

Uncovered: 112,255,264 out of 115,212,710
Covered: 2,957,446 out of 115,212,710

Uncovered: 13,626,470 out of 16,105,584
Matches: 1,677,126 out of 16,105,584
Mismatches: 801,585 out of 16,105,584
Insertions: 403 out of 16,105,584