Table 3 Alignment results from different BLAST strategies using the ARS-UCD1.2 genome assembly and standard linearization configuration of the mitochondrial DNA.

From: Survey of mitochondrial sequences integrated into the bovine nuclear genome

BLAST

Sequence linearization

Alignmentsd

NUMT Regionse

#a

Program

Scoringc

Number

Length

(kbp)

Identity

(%)

Number

Length

(kbp)

1

Discontiguous MegaBLAST

2/–3/5/2

Standard

283

211.0

79%

115

356.7

2

Discontiguous MegaBLAST

1/–1/4/1

Standard

289

219.7

77%

121

368.1

3b

BLASTN

2/–3/5/2

Standard

431

252.4

78%

170

436.0

4

BLASTN

1/–1/4/1

Standard

478

290.2

75%

190

478.6

5

BLASTN

1/–1/2/1

Standard

471

311.5

75%

192

495.3

6

BLASTN

1/–1/0/2

Standard

460

316.2

76%

190

495.4

Consolidated results of all BLAST searches

208

510.5

  1. aBLAST # is the identification of the BLAST strategy used.
  2. bBLAST # 3 is called as “default BLAST” from here on.
  3. cScoring scheme: match/mismatch/gap opening cost/gap extension cost.
  4. dInformation about number of alignments, total alignment length and identity between sequences.
  5. eInformation about number of NUMT regions and total their total length. NUMT regions located on unplaced scaffolds were discarded from these analyses.
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