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Table 6 Alignment ratios and multiple alignment ratios of repeats on five data sets

From: RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads

Species

Method

Num

Alignment                ratio (%)

Multiple alignment          ratio (%)

Drosophila melanogaster

RepARK CLC

818

97.43

92.42

RepARK Velvet

4561

99.28

94.04

REPdenovo

52

88.46

86.54

RepAHR

2647

97.96

95.35

Saccharomyces cerevisiae

RepARK CLC

545

97.42

25.32

RepARK Velvet

1457

98.76

41.39

REPdenovo

3

100.0

33.33

RepAHR

392

97.70

90.56

Acromyrmex echinatior

RepARK CLC

485

84.95

69.69

RepARK Velvet

3931

93.64

87.75

REPdenovo

249

65.46

61.45

RepAHR

2699

94.89

89.14

\(Homo \ sapiens\) chr14

RepARK CLC

105

97.14

95.24

RepARK Velvet

846

98.23

97.52

REPdenovo

14

100.0

100.0

RepAHR

1738

99.71

98.85

\(Mus\ musculus\)

RepARK CLC

3839

96.77

92.81

RepARK Velvet

47,232

90.47

88.20

REPdenovo

9376

50.53

48.54

RepAHR

77,891

95.56

93.05

  1. \('alignment\ \ ratio'\) indicates the ratio of the number of repeats aligned to the reference genome at least one position to the total number of repeats. \('multiple\ \ alignment\ \ ratio'\) indicates the ratio of the number of repeats aligned to the reference genome multiple positions to the total number of repeats