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Mouse vs C.intestinalis Translated Blat Results

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

ParameterValue
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

ParameterMouseC.intestinalis
Chunk size1,000,00025,000
Overlap10,00010,000
Group set size100,000,00010,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 56,875 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Mouse

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

C.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