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Mouse vs Xenopus Translated Blat Results

Mouse (Mus musculus, GRCm38) and Xenopus (Xenopus tropicalis, JGI_4.2) 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

Chunk size1,000,00025,000
Group set size100,000,00010,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 232,673 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)

Uncovered: 2,703,980,936 out of 2,730,871,774
Covered: 26,890,838 out of 2,730,871,774

Uncovered: 17,690,031 out of 35,991,038
Matches: 13,437,167 out of 35,991,038
Mismatches: 4,855,360 out of 35,991,038
Insertions: 8,480 out of 35,991,038


Uncovered: 1,491,229,058 out of 1,511,717,716
Covered: 20,488,658 out of 1,511,717,716

Uncovered: 15,196,094 out of 30,481,746
Matches: 11,294,326 out of 30,481,746
Mismatches: 3,986,378 out of 30,481,746
Insertions: 4,948 out of 30,481,746