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Mouse vs C.intestinalis Translated Blat alignments

Mouse (Mus musculus, GRCm38) 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 68. Mouse 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

Mouse 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} {default_soft_masking => 1}


Number of alignment blocks: 56,875

Genome coverage (bp) Coding exon coverage (bp)
Mus musculus

Uncovered: 2,724,751,033 out of 2,730,871,774
Covered: 6,120,741 out of 2,730,871,774

Uncovered: 31,873,249 out of 35,991,038
Matches: 2,807,594 out of 35,991,038
Mismatches: 1,310,042 out of 35,991,038
Insertions: 153 out of 35,991,038

Ciona intestinalis

Uncovered: 112,268,134 out of 115,212,710
Covered: 2,944,576 out of 115,212,710

Uncovered: 13,625,906 out of 16,105,584
Matches: 1,676,688 out of 16,105,584
Mismatches: 802,448 out of 16,105,584
Insertions: 542 out of 16,105,584