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Table 4 Accuracies for Kiryu et al.'s dataset. SPS and MCC values (%) for Kiryu et al.'s dataset are presented. Each family has 10 RNA sequences. Family: Rfam family name. %id: average sequence identity. length: average sequence length (bases) in each family. Average(all): the results of the average value of the SPS or MCC for all families. Average(sub): the average SPS or MCC for the subset of families with an average sequence length of less than or equal to 100 bases. Because PMmulti and Stemloc were unable to align all data, the proportion of data that was aligned is given in parentheses as no. of sequences aligned/total no. of sequences. FoldalignM consists of two modes: FoldalgnM_FoldalignM and FoldalignM McCaskill, which are separately evaluated and indicated as FoldalignM(1) and FoldalignM(2) respectively.

From: A fast structural multiple alignment method for long RNA sequences

SPS:Family

%id

length(nt)

MXSCARNA

Murlet

ProbCons

MAFFT

ClustalW

StrAl

RNAlara

UnaL2

73

54

92

95

95

91

84

86

87

SECIS

41

64

70

73

68

44

35

59

53

tRNA

45

73

87

90

87

76

62

75

91

sno_14q_I_II

64

75

82

92

92

91

80

75

72

SRP_bact

47

93

58

61

61

60

61

48

56

THI

55

105

77

83

82

78

58

65

65

S_box

66

107

86

88

88

82

82

77

77

5S_rRNA

57

116

84

85

85

81

82

79

83

Retroviral_psi

92

117

97

97

97

97

96

97

97

RFN

66

140

89

91

90

91

83

80

86

5_8S_rRNA

61

154

85

88

87

84

78

81

75

U1

59

157

74

77

75

73

71

66

66

Lysine

49

181

75

77

75

66

60

68

59

U2

62

182

71

74

73

68

65

67

69

T-box

45

244

44

50

50

43

34

32

15

IRES_HCV

94

261

96

96

96

96

96

83

96

SRP_euk_arch

40

291

42

42

40

36

34

40

39

Average(all)

  

77

80

79

74

68

69

70

Average(sub)

  

82

86

85

80

73

75

77

SPS:Family

RNASampler

Locarna

FoldalignM(1)

FoldalignM(2)

MARNA

PMmulti

Stemloc

  

UnaL2

72

88

68

60

83 (5/5)

69 (5/5)

82 (5/5)

  

SECIS

54

49

42

41

47 (5/5)

35 (5/5)

82 (5/5)

  

tRNA

82

79

84

66

54 (5/5)

69 (5/5)

91 (5/5)

  

sno_14q_I_II

64

57

45

34

49 (5/5)

39 (3/5)

77 (5/5)

  

SRP_bact

54

52

55

51

43 (5/5)

36 (4/5)

47 (3/5)

  

THI

68

65

65

62

62 (4/5)

58 (5/5)

71 (5/5)

  

S_box

76

63

57

57

78 (5/5)

44 (5/5)

84 (5/5)

  

5S_rRNA

77

79

74

70

71 (5/5)

57 (5/5)

77 (3/5)

  

Retroviral_psi

96

95

91

91

96 (5/5)

87 (5/5)

75 (5/5)

  

RFN

82

72

73

63

77 (5/5)

58 (4/5)

80 (5/5)

  

5_8S_rRNA

69

75

56

31

64 (5/5)

58 (5/5)

73 (1/5)

  

U1

63

68

  

50 (5/5)

    

Lysine

71

55

  

58 (5/5)

    

U2

65

64

  

65 (1/5)

    

T-box

32

15

  

22 (5/5)

    

IRES_HCV

93

75

  

92 (3/5)

    

SRP_euk_arch

33

40

  

37 (5/5)

    

Average(all)

68

64

  

62

    

Average(sub)

72

70

64

57

52

60

76

  

MCC:Family

%id

length(nt)

MXSCARNA

Murlet

ProbCons

MAFFT

ClustalW

StrAl

RNAlara

UnaL2

73

54

42

41

46

36

24

32

44

SECIS

41

64

78

78

59

20

23

45

70

tRNA

45

73

93

97

91

85

65

85

97

sno_14q_I_II

64

75

87

91

91

91

66

75

87

SRP_bact

47

93

66

56

46

49

54

52

69

THI

55

105

71

70

70

62

38

48

58

S_box

66

107

90

89

87

79

77

75

76

5S_rRNA

57

116

75

67

62

64

53

66

69

Retroviral_psi

92

117

86

86

86

84

86

86

86

RFN

66

140

67

71

72

73

71

60

70

5_8S_rRNA

61

154

38

43

35

16

14

26

33

U1

59

157

69

61

57

56

61

52

56

Lysine

49

181

83

81

71

33

52

61

64

U2

62

182

74

71

56

38

39

58

68

T-box

45

244

72

78

80

51

41

26

0

IRES_HCV

94

261

63

62

62

63

26

34

63

SRP_euk_arch

40

291

70

63

40

21

23

38

33

Average(all)

  

72

71

65

54

48

54

61

Average(sub)

  

72

72

68

60

52

59

69

MCC:Family

RNASampler

Locarna

FoldalignM(1)

FoldalignM(2)

MARNA

PMmulti

Stemloc

  

UnaL2

51

42

57

50

36

18

39

  

SECIS

78

80

75

80

40

64

77

  

tRNA

94

96

95

89

51

91

98

  

sno_14q_I_II

84

95

95

86

79

77

87

  

SRP_bact

73

74

80

75

47

44

64

  

THI

72

60

50

51

59

41

77

  

S_box

86

82

83

87

83

55

88

  

5S_rRNA

62

75

72

73

59

58

66

  

Retroviral_psi

86

88

76

89

84

73

87

  

RFN

69

69

67

70

65

58

72

  

5_8S_rRNA

38

40

43

41

21

14

34

  

U1

64

73

  

45

    

Lysine

86

80

  

66

    

U2

79

65

  

66

    

T-box

44

1

  

2

    

IRES_HCV

63

47

  

61

    

SRP_euk_arch

62

64

  

52

    

Average(all)

70

66

  

54

    

Average(sub)

72

73

72

72

60

54

72

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