Table 2

Alignments available from the CRW Site. These alignments were used to generate conservation diagrams (rRNA only) and correspond to the alignments used in the nucleotide frequency tables.

Molecule

Alignment

# of Sequences

rRNA (5S / 16S / 23S)

T (Three Domains/Two Organelles)

686/6389/922

3 (Three Phylogenetic Domains)

-- / 5591 / 585

A (Archaea)

53/171/39

B (Bacteria)

323/4213/431

C (Eukaryota chloroplast)

-- / 127 / 52

E (Eukaryota nuclear)

299/1937/115

M (Eukaryota mitochondria)

-- / 899 / 295

Group I Intron

A (IA1, IA2, and IA3 subgroups)

82

B (IB1, IB2, IB3, and IB4 subgroups)

72

C (IC1 and IC2 subgroups)

305

Z (IC3 subgroup)

125

D (ID subgroup)

19

E (IE subgroup)

46

U (all other group I introns)

41

Group II Intron

A (IIA subgroup) / B (IIB subgroup)

171/571

tRNA

A (Alanine tRNAs) / C (Cysteine tRNAs)

64/19

D (Aspartic Acid tRNAs) / E (Glutamic Acid tRNAs)

35/49

F (Phenylalanine tRNAs) / G (Glycine tRNAs)

54/69

H (Histidine tRNAs) / I (Isoleucine tRNAs)

38/56

K (Lysine tRNAs) / M (Methionine tRNAs)

53/36

N (Asparagine tRNAs) / P (Proline tRNAs)

35/55

Q (Glutamine tRNAs) / R (Arginine tRNAs)

35/62

T (Threonine tRNAs) / V (Valine tRNAs)

49/65

W (Tryptophan tRNAs) / X (Methionine Initiator tRNAs)

30/65

Y (Tyrosine tRNAs) / Z (All Type 1 tRNAs)

47 / 895

Cannone et al. BMC Bioinformatics 2002 3:2   doi:10.1186/1471-2105-3-2