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Chicken vs C.savignyi Translated Blat Results

Chicken (Gallus gallus, Galgal4) and C.savignyi (Ciona savignyi, CSAV2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 71. Chicken 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

ParameterChickenC.savignyi
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 38,523 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Chicken

Uncovered: 1,043,073,605 out of 1,046,932,099
Covered: 3,858,494 out of 1,046,932,099

Uncovered: 22,449,858 out of 25,934,237
Matches: 2,389,748 out of 25,934,237
Mismatches: 1,094,445 out of 25,934,237
Insertions: 186 out of 25,934,237

C.savignyi

Uncovered: 174,278,053 out of 176,989,013
Covered: 2,710,960 out of 176,989,013

Uncovered: 11,545,811 out of 13,806,906
Matches: 1,544,696 out of 13,806,906
Mismatches: 716,271 out of 13,806,906
Insertions: 128 out of 13,806,906