biotite 1.5.0__cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

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  1. biotite/__init__.py +18 -0
  2. biotite/application/__init__.py +69 -0
  3. biotite/application/application.py +276 -0
  4. biotite/application/autodock/__init__.py +12 -0
  5. biotite/application/autodock/app.py +500 -0
  6. biotite/application/blast/__init__.py +14 -0
  7. biotite/application/blast/alignment.py +92 -0
  8. biotite/application/blast/webapp.py +428 -0
  9. biotite/application/clustalo/__init__.py +12 -0
  10. biotite/application/clustalo/app.py +223 -0
  11. biotite/application/dssp/__init__.py +12 -0
  12. biotite/application/dssp/app.py +216 -0
  13. biotite/application/localapp.py +342 -0
  14. biotite/application/mafft/__init__.py +12 -0
  15. biotite/application/mafft/app.py +116 -0
  16. biotite/application/msaapp.py +363 -0
  17. biotite/application/muscle/__init__.py +13 -0
  18. biotite/application/muscle/app3.py +227 -0
  19. biotite/application/muscle/app5.py +163 -0
  20. biotite/application/sra/__init__.py +18 -0
  21. biotite/application/sra/app.py +447 -0
  22. biotite/application/tantan/__init__.py +12 -0
  23. biotite/application/tantan/app.py +199 -0
  24. biotite/application/util.py +77 -0
  25. biotite/application/viennarna/__init__.py +18 -0
  26. biotite/application/viennarna/rnaalifold.py +310 -0
  27. biotite/application/viennarna/rnafold.py +254 -0
  28. biotite/application/viennarna/rnaplot.py +208 -0
  29. biotite/application/viennarna/util.py +77 -0
  30. biotite/application/webapp.py +76 -0
  31. biotite/copyable.py +71 -0
  32. biotite/database/__init__.py +23 -0
  33. biotite/database/afdb/__init__.py +12 -0
  34. biotite/database/afdb/download.py +197 -0
  35. biotite/database/entrez/__init__.py +15 -0
  36. biotite/database/entrez/check.py +60 -0
  37. biotite/database/entrez/dbnames.py +101 -0
  38. biotite/database/entrez/download.py +228 -0
  39. biotite/database/entrez/key.py +44 -0
  40. biotite/database/entrez/query.py +263 -0
  41. biotite/database/error.py +16 -0
  42. biotite/database/pubchem/__init__.py +21 -0
  43. biotite/database/pubchem/download.py +258 -0
  44. biotite/database/pubchem/error.py +30 -0
  45. biotite/database/pubchem/query.py +819 -0
  46. biotite/database/pubchem/throttle.py +98 -0
  47. biotite/database/rcsb/__init__.py +13 -0
  48. biotite/database/rcsb/download.py +161 -0
  49. biotite/database/rcsb/query.py +963 -0
  50. biotite/database/uniprot/__init__.py +13 -0
  51. biotite/database/uniprot/check.py +40 -0
  52. biotite/database/uniprot/download.py +126 -0
  53. biotite/database/uniprot/query.py +292 -0
  54. biotite/file.py +244 -0
  55. biotite/interface/__init__.py +19 -0
  56. biotite/interface/openmm/__init__.py +20 -0
  57. biotite/interface/openmm/state.py +93 -0
  58. biotite/interface/openmm/system.py +227 -0
  59. biotite/interface/pymol/__init__.py +201 -0
  60. biotite/interface/pymol/cgo.py +346 -0
  61. biotite/interface/pymol/convert.py +185 -0
  62. biotite/interface/pymol/display.py +267 -0
  63. biotite/interface/pymol/object.py +1228 -0
  64. biotite/interface/pymol/shapes.py +178 -0
  65. biotite/interface/pymol/startup.py +169 -0
  66. biotite/interface/rdkit/__init__.py +19 -0
  67. biotite/interface/rdkit/mol.py +490 -0
  68. biotite/interface/version.py +94 -0
  69. biotite/interface/warning.py +19 -0
  70. biotite/sequence/__init__.py +84 -0
  71. biotite/sequence/align/__init__.py +199 -0
  72. biotite/sequence/align/alignment.py +702 -0
  73. biotite/sequence/align/banded.cpython-312-x86_64-linux-gnu.so +0 -0
  74. biotite/sequence/align/banded.pyx +652 -0
  75. biotite/sequence/align/buckets.py +71 -0
  76. biotite/sequence/align/cigar.py +425 -0
  77. biotite/sequence/align/kmeralphabet.cpython-312-x86_64-linux-gnu.so +0 -0
  78. biotite/sequence/align/kmeralphabet.pyx +595 -0
  79. biotite/sequence/align/kmersimilarity.cpython-312-x86_64-linux-gnu.so +0 -0
  80. biotite/sequence/align/kmersimilarity.pyx +233 -0
  81. biotite/sequence/align/kmertable.cpython-312-x86_64-linux-gnu.so +0 -0
  82. biotite/sequence/align/kmertable.pyx +3411 -0
  83. biotite/sequence/align/localgapped.cpython-312-x86_64-linux-gnu.so +0 -0
  84. biotite/sequence/align/localgapped.pyx +892 -0
  85. biotite/sequence/align/localungapped.cpython-312-x86_64-linux-gnu.so +0 -0
  86. biotite/sequence/align/localungapped.pyx +279 -0
  87. biotite/sequence/align/matrix.py +631 -0
  88. biotite/sequence/align/matrix_data/3Di.mat +24 -0
  89. biotite/sequence/align/matrix_data/BLOSUM100.mat +31 -0
  90. biotite/sequence/align/matrix_data/BLOSUM30.mat +31 -0
  91. biotite/sequence/align/matrix_data/BLOSUM35.mat +31 -0
  92. biotite/sequence/align/matrix_data/BLOSUM40.mat +31 -0
  93. biotite/sequence/align/matrix_data/BLOSUM45.mat +31 -0
  94. biotite/sequence/align/matrix_data/BLOSUM50.mat +31 -0
  95. biotite/sequence/align/matrix_data/BLOSUM50_13p.mat +25 -0
  96. biotite/sequence/align/matrix_data/BLOSUM50_14.3.mat +25 -0
  97. biotite/sequence/align/matrix_data/BLOSUM50_5.0.mat +25 -0
  98. biotite/sequence/align/matrix_data/BLOSUM55.mat +31 -0
  99. biotite/sequence/align/matrix_data/BLOSUM60.mat +31 -0
  100. biotite/sequence/align/matrix_data/BLOSUM62.mat +31 -0
  101. biotite/sequence/align/matrix_data/BLOSUM62_13p.mat +25 -0
  102. biotite/sequence/align/matrix_data/BLOSUM62_14.3.mat +25 -0
  103. biotite/sequence/align/matrix_data/BLOSUM62_5.0.mat +25 -0
  104. biotite/sequence/align/matrix_data/BLOSUM65.mat +31 -0
  105. biotite/sequence/align/matrix_data/BLOSUM70.mat +31 -0
  106. biotite/sequence/align/matrix_data/BLOSUM75.mat +31 -0
  107. biotite/sequence/align/matrix_data/BLOSUM80.mat +31 -0
  108. biotite/sequence/align/matrix_data/BLOSUM85.mat +31 -0
  109. biotite/sequence/align/matrix_data/BLOSUM90.mat +31 -0
  110. biotite/sequence/align/matrix_data/BLOSUMN.mat +31 -0
  111. biotite/sequence/align/matrix_data/CorBLOSUM49_5.0.mat +25 -0
  112. biotite/sequence/align/matrix_data/CorBLOSUM57_13p.mat +25 -0
  113. biotite/sequence/align/matrix_data/CorBLOSUM57_14.3.mat +25 -0
  114. biotite/sequence/align/matrix_data/CorBLOSUM61_5.0.mat +25 -0
  115. biotite/sequence/align/matrix_data/CorBLOSUM66_13p.mat +25 -0
  116. biotite/sequence/align/matrix_data/CorBLOSUM67_14.3.mat +25 -0
  117. biotite/sequence/align/matrix_data/DAYHOFF.mat +32 -0
  118. biotite/sequence/align/matrix_data/GONNET.mat +26 -0
  119. biotite/sequence/align/matrix_data/IDENTITY.mat +25 -0
  120. biotite/sequence/align/matrix_data/MATCH.mat +25 -0
  121. biotite/sequence/align/matrix_data/NUC.mat +25 -0
  122. biotite/sequence/align/matrix_data/PAM10.mat +34 -0
  123. biotite/sequence/align/matrix_data/PAM100.mat +34 -0
  124. biotite/sequence/align/matrix_data/PAM110.mat +34 -0
  125. biotite/sequence/align/matrix_data/PAM120.mat +34 -0
  126. biotite/sequence/align/matrix_data/PAM130.mat +34 -0
  127. biotite/sequence/align/matrix_data/PAM140.mat +34 -0
  128. biotite/sequence/align/matrix_data/PAM150.mat +34 -0
  129. biotite/sequence/align/matrix_data/PAM160.mat +34 -0
  130. biotite/sequence/align/matrix_data/PAM170.mat +34 -0
  131. biotite/sequence/align/matrix_data/PAM180.mat +34 -0
  132. biotite/sequence/align/matrix_data/PAM190.mat +34 -0
  133. biotite/sequence/align/matrix_data/PAM20.mat +34 -0
  134. biotite/sequence/align/matrix_data/PAM200.mat +34 -0
  135. biotite/sequence/align/matrix_data/PAM210.mat +34 -0
  136. biotite/sequence/align/matrix_data/PAM220.mat +34 -0
  137. biotite/sequence/align/matrix_data/PAM230.mat +34 -0
  138. biotite/sequence/align/matrix_data/PAM240.mat +34 -0
  139. biotite/sequence/align/matrix_data/PAM250.mat +34 -0
  140. biotite/sequence/align/matrix_data/PAM260.mat +34 -0
  141. biotite/sequence/align/matrix_data/PAM270.mat +34 -0
  142. biotite/sequence/align/matrix_data/PAM280.mat +34 -0
  143. biotite/sequence/align/matrix_data/PAM290.mat +34 -0
  144. biotite/sequence/align/matrix_data/PAM30.mat +34 -0
  145. biotite/sequence/align/matrix_data/PAM300.mat +34 -0
  146. biotite/sequence/align/matrix_data/PAM310.mat +34 -0
  147. biotite/sequence/align/matrix_data/PAM320.mat +34 -0
  148. biotite/sequence/align/matrix_data/PAM330.mat +34 -0
  149. biotite/sequence/align/matrix_data/PAM340.mat +34 -0
  150. biotite/sequence/align/matrix_data/PAM350.mat +34 -0
  151. biotite/sequence/align/matrix_data/PAM360.mat +34 -0
  152. biotite/sequence/align/matrix_data/PAM370.mat +34 -0
  153. biotite/sequence/align/matrix_data/PAM380.mat +34 -0
  154. biotite/sequence/align/matrix_data/PAM390.mat +34 -0
  155. biotite/sequence/align/matrix_data/PAM40.mat +34 -0
  156. biotite/sequence/align/matrix_data/PAM400.mat +34 -0
  157. biotite/sequence/align/matrix_data/PAM410.mat +34 -0
  158. biotite/sequence/align/matrix_data/PAM420.mat +34 -0
  159. biotite/sequence/align/matrix_data/PAM430.mat +34 -0
  160. biotite/sequence/align/matrix_data/PAM440.mat +34 -0
  161. biotite/sequence/align/matrix_data/PAM450.mat +34 -0
  162. biotite/sequence/align/matrix_data/PAM460.mat +34 -0
  163. biotite/sequence/align/matrix_data/PAM470.mat +34 -0
  164. biotite/sequence/align/matrix_data/PAM480.mat +34 -0
  165. biotite/sequence/align/matrix_data/PAM490.mat +34 -0
  166. biotite/sequence/align/matrix_data/PAM50.mat +34 -0
  167. biotite/sequence/align/matrix_data/PAM500.mat +34 -0
  168. biotite/sequence/align/matrix_data/PAM60.mat +34 -0
  169. biotite/sequence/align/matrix_data/PAM70.mat +34 -0
  170. biotite/sequence/align/matrix_data/PAM80.mat +34 -0
  171. biotite/sequence/align/matrix_data/PAM90.mat +34 -0
  172. biotite/sequence/align/matrix_data/PB.license +21 -0
  173. biotite/sequence/align/matrix_data/PB.mat +18 -0
  174. biotite/sequence/align/matrix_data/RBLOSUM52_5.0.mat +25 -0
  175. biotite/sequence/align/matrix_data/RBLOSUM59_13p.mat +25 -0
  176. biotite/sequence/align/matrix_data/RBLOSUM59_14.3.mat +25 -0
  177. biotite/sequence/align/matrix_data/RBLOSUM64_5.0.mat +25 -0
  178. biotite/sequence/align/matrix_data/RBLOSUM69_13p.mat +25 -0
  179. biotite/sequence/align/matrix_data/RBLOSUM69_14.3.mat +25 -0
  180. biotite/sequence/align/multiple.cpython-312-x86_64-linux-gnu.so +0 -0
  181. biotite/sequence/align/multiple.pyx +619 -0
  182. biotite/sequence/align/pairwise.cpython-312-x86_64-linux-gnu.so +0 -0
  183. biotite/sequence/align/pairwise.pyx +585 -0
  184. biotite/sequence/align/permutation.cpython-312-x86_64-linux-gnu.so +0 -0
  185. biotite/sequence/align/permutation.pyx +313 -0
  186. biotite/sequence/align/primes.txt +821 -0
  187. biotite/sequence/align/selector.cpython-312-x86_64-linux-gnu.so +0 -0
  188. biotite/sequence/align/selector.pyx +954 -0
  189. biotite/sequence/align/statistics.py +264 -0
  190. biotite/sequence/align/tracetable.cpython-312-x86_64-linux-gnu.so +0 -0
  191. biotite/sequence/align/tracetable.pxd +64 -0
  192. biotite/sequence/align/tracetable.pyx +370 -0
  193. biotite/sequence/alphabet.py +555 -0
  194. biotite/sequence/annotation.py +836 -0
  195. biotite/sequence/codec.cpython-312-x86_64-linux-gnu.so +0 -0
  196. biotite/sequence/codec.pyx +155 -0
  197. biotite/sequence/codon.py +476 -0
  198. biotite/sequence/codon_tables.txt +202 -0
  199. biotite/sequence/graphics/__init__.py +33 -0
  200. biotite/sequence/graphics/alignment.py +1101 -0
  201. biotite/sequence/graphics/color_schemes/3di_flower.json +48 -0
  202. biotite/sequence/graphics/color_schemes/autumn.json +51 -0
  203. biotite/sequence/graphics/color_schemes/blossom.json +51 -0
  204. biotite/sequence/graphics/color_schemes/clustalx_dna.json +11 -0
  205. biotite/sequence/graphics/color_schemes/clustalx_protein.json +28 -0
  206. biotite/sequence/graphics/color_schemes/flower.json +51 -0
  207. biotite/sequence/graphics/color_schemes/jalview_buried.json +31 -0
  208. biotite/sequence/graphics/color_schemes/jalview_hydrophobicity.json +31 -0
  209. biotite/sequence/graphics/color_schemes/jalview_prop_helix.json +31 -0
  210. biotite/sequence/graphics/color_schemes/jalview_prop_strand.json +31 -0
  211. biotite/sequence/graphics/color_schemes/jalview_prop_turn.json +31 -0
  212. biotite/sequence/graphics/color_schemes/jalview_taylor.json +28 -0
  213. biotite/sequence/graphics/color_schemes/jalview_zappo.json +28 -0
  214. biotite/sequence/graphics/color_schemes/ocean.json +51 -0
  215. biotite/sequence/graphics/color_schemes/pb_flower.json +40 -0
  216. biotite/sequence/graphics/color_schemes/rainbow_dna.json +11 -0
  217. biotite/sequence/graphics/color_schemes/rainbow_protein.json +30 -0
  218. biotite/sequence/graphics/color_schemes/spring.json +51 -0
  219. biotite/sequence/graphics/color_schemes/sunset.json +51 -0
  220. biotite/sequence/graphics/color_schemes/wither.json +51 -0
  221. biotite/sequence/graphics/colorschemes.py +170 -0
  222. biotite/sequence/graphics/dendrogram.py +231 -0
  223. biotite/sequence/graphics/features.py +544 -0
  224. biotite/sequence/graphics/logo.py +102 -0
  225. biotite/sequence/graphics/plasmid.py +712 -0
  226. biotite/sequence/io/__init__.py +12 -0
  227. biotite/sequence/io/fasta/__init__.py +22 -0
  228. biotite/sequence/io/fasta/convert.py +283 -0
  229. biotite/sequence/io/fasta/file.py +265 -0
  230. biotite/sequence/io/fastq/__init__.py +19 -0
  231. biotite/sequence/io/fastq/convert.py +117 -0
  232. biotite/sequence/io/fastq/file.py +507 -0
  233. biotite/sequence/io/genbank/__init__.py +17 -0
  234. biotite/sequence/io/genbank/annotation.py +269 -0
  235. biotite/sequence/io/genbank/file.py +573 -0
  236. biotite/sequence/io/genbank/metadata.py +336 -0
  237. biotite/sequence/io/genbank/sequence.py +173 -0
  238. biotite/sequence/io/general.py +201 -0
  239. biotite/sequence/io/gff/__init__.py +26 -0
  240. biotite/sequence/io/gff/convert.py +128 -0
  241. biotite/sequence/io/gff/file.py +449 -0
  242. biotite/sequence/phylo/__init__.py +36 -0
  243. biotite/sequence/phylo/nj.cpython-312-x86_64-linux-gnu.so +0 -0
  244. biotite/sequence/phylo/nj.pyx +221 -0
  245. biotite/sequence/phylo/tree.cpython-312-x86_64-linux-gnu.so +0 -0
  246. biotite/sequence/phylo/tree.pyx +1169 -0
  247. biotite/sequence/phylo/upgma.cpython-312-x86_64-linux-gnu.so +0 -0
  248. biotite/sequence/phylo/upgma.pyx +164 -0
  249. biotite/sequence/profile.py +561 -0
  250. biotite/sequence/search.py +117 -0
  251. biotite/sequence/seqtypes.py +720 -0
  252. biotite/sequence/sequence.py +373 -0
  253. biotite/setup_ccd.py +197 -0
  254. biotite/structure/__init__.py +135 -0
  255. biotite/structure/alphabet/__init__.py +25 -0
  256. biotite/structure/alphabet/encoder.py +332 -0
  257. biotite/structure/alphabet/encoder_weights_3di.kerasify +0 -0
  258. biotite/structure/alphabet/i3d.py +109 -0
  259. biotite/structure/alphabet/layers.py +86 -0
  260. biotite/structure/alphabet/pb.license +21 -0
  261. biotite/structure/alphabet/pb.py +170 -0
  262. biotite/structure/alphabet/unkerasify.py +128 -0
  263. biotite/structure/atoms.py +1562 -0
  264. biotite/structure/basepairs.py +1403 -0
  265. biotite/structure/bonds.cpython-312-x86_64-linux-gnu.so +0 -0
  266. biotite/structure/bonds.pyx +2036 -0
  267. biotite/structure/box.py +724 -0
  268. biotite/structure/celllist.cpython-312-x86_64-linux-gnu.so +0 -0
  269. biotite/structure/celllist.pyx +864 -0
  270. biotite/structure/chains.py +310 -0
  271. biotite/structure/charges.cpython-312-x86_64-linux-gnu.so +0 -0
  272. biotite/structure/charges.pyx +520 -0
  273. biotite/structure/compare.py +683 -0
  274. biotite/structure/density.py +109 -0
  275. biotite/structure/dotbracket.py +213 -0
  276. biotite/structure/error.py +39 -0
  277. biotite/structure/filter.py +591 -0
  278. biotite/structure/geometry.py +817 -0
  279. biotite/structure/graphics/__init__.py +13 -0
  280. biotite/structure/graphics/atoms.py +243 -0
  281. biotite/structure/graphics/rna.py +298 -0
  282. biotite/structure/hbond.py +425 -0
  283. biotite/structure/info/__init__.py +24 -0
  284. biotite/structure/info/atom_masses.json +121 -0
  285. biotite/structure/info/atoms.py +98 -0
  286. biotite/structure/info/bonds.py +149 -0
  287. biotite/structure/info/ccd.py +200 -0
  288. biotite/structure/info/components.bcif +0 -0
  289. biotite/structure/info/groups.py +128 -0
  290. biotite/structure/info/masses.py +121 -0
  291. biotite/structure/info/misc.py +137 -0
  292. biotite/structure/info/radii.py +267 -0
  293. biotite/structure/info/standardize.py +185 -0
  294. biotite/structure/integrity.py +213 -0
  295. biotite/structure/io/__init__.py +29 -0
  296. biotite/structure/io/dcd/__init__.py +13 -0
  297. biotite/structure/io/dcd/file.py +67 -0
  298. biotite/structure/io/general.py +243 -0
  299. biotite/structure/io/gro/__init__.py +14 -0
  300. biotite/structure/io/gro/file.py +343 -0
  301. biotite/structure/io/mol/__init__.py +20 -0
  302. biotite/structure/io/mol/convert.py +112 -0
  303. biotite/structure/io/mol/ctab.py +420 -0
  304. biotite/structure/io/mol/header.py +120 -0
  305. biotite/structure/io/mol/mol.py +149 -0
  306. biotite/structure/io/mol/sdf.py +940 -0
  307. biotite/structure/io/netcdf/__init__.py +13 -0
  308. biotite/structure/io/netcdf/file.py +64 -0
  309. biotite/structure/io/pdb/__init__.py +20 -0
  310. biotite/structure/io/pdb/convert.py +389 -0
  311. biotite/structure/io/pdb/file.py +1380 -0
  312. biotite/structure/io/pdb/hybrid36.cpython-312-x86_64-linux-gnu.so +0 -0
  313. biotite/structure/io/pdb/hybrid36.pyx +242 -0
  314. biotite/structure/io/pdbqt/__init__.py +15 -0
  315. biotite/structure/io/pdbqt/convert.py +113 -0
  316. biotite/structure/io/pdbqt/file.py +688 -0
  317. biotite/structure/io/pdbx/__init__.py +23 -0
  318. biotite/structure/io/pdbx/bcif.py +674 -0
  319. biotite/structure/io/pdbx/cif.py +1091 -0
  320. biotite/structure/io/pdbx/component.py +251 -0
  321. biotite/structure/io/pdbx/compress.py +362 -0
  322. biotite/structure/io/pdbx/convert.py +2113 -0
  323. biotite/structure/io/pdbx/encoding.cpython-312-x86_64-linux-gnu.so +0 -0
  324. biotite/structure/io/pdbx/encoding.pyx +1078 -0
  325. biotite/structure/io/trajfile.py +696 -0
  326. biotite/structure/io/trr/__init__.py +13 -0
  327. biotite/structure/io/trr/file.py +43 -0
  328. biotite/structure/io/util.py +38 -0
  329. biotite/structure/io/xtc/__init__.py +13 -0
  330. biotite/structure/io/xtc/file.py +43 -0
  331. biotite/structure/mechanics.py +72 -0
  332. biotite/structure/molecules.py +337 -0
  333. biotite/structure/pseudoknots.py +622 -0
  334. biotite/structure/rdf.py +245 -0
  335. biotite/structure/repair.py +302 -0
  336. biotite/structure/residues.py +716 -0
  337. biotite/structure/rings.py +451 -0
  338. biotite/structure/sasa.cpython-312-x86_64-linux-gnu.so +0 -0
  339. biotite/structure/sasa.pyx +322 -0
  340. biotite/structure/segments.py +328 -0
  341. biotite/structure/sequence.py +110 -0
  342. biotite/structure/spacegroups.json +1567 -0
  343. biotite/structure/spacegroups.license +26 -0
  344. biotite/structure/sse.py +306 -0
  345. biotite/structure/superimpose.py +511 -0
  346. biotite/structure/tm.py +581 -0
  347. biotite/structure/transform.py +736 -0
  348. biotite/structure/util.py +160 -0
  349. biotite/version.py +34 -0
  350. biotite/visualize.py +375 -0
  351. biotite-1.5.0.dist-info/METADATA +162 -0
  352. biotite-1.5.0.dist-info/RECORD +354 -0
  353. biotite-1.5.0.dist-info/WHEEL +6 -0
  354. biotite-1.5.0.dist-info/licenses/LICENSE.rst +30 -0
biotite/sequence/align/matrix_data/BLOSUMN.mat ADDED
@@ -0,0 +1,31 @@
1
+ # Matrix made by matblas from blosumn.iij
2
+ # * column uses minimum score
3
+ # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
4
+ # Blocks Database = /data/blocks_5.0/blocks.dat
5
+ # Cluster Percentage: >= -2
6
+ # Entropy = 1.5172, Expected = -1.1484
7
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
8
+ A 6 -2 -2 -3 -2 -1 -2 -1 -3 -3 -3 -2 -2 -4 -1 1 -1 -4 -4 -1 -3 -2 -1 -7
9
+ R -2 7 -1 -3 -6 0 -2 -4 -1 -5 -4 2 -3 -4 -3 -2 -2 -5 -4 -4 -2 -1 -2 -7
10
+ N -2 -1 7 1 -4 -1 -1 -2 0 -5 -5 -1 -4 -5 -4 0 -1 -6 -4 -4 4 -1 -2 -7
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+ D -3 -3 1 7 -6 -2 1 -3 -2 -6 -6 -2 -5 -5 -3 -2 -2 -7 -5 -5 4 0 -3 -7
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+ C -2 -6 -4 -6 9 -5 -7 -5 -6 -2 -3 -5 -3 -3 -5 -2 -2 -5 -4 -2 -5 -6 -4 -7
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+ Q -1 0 -1 -2 -5 7 1 -4 0 -4 -3 1 -1 -4 -2 -1 -2 -4 -3 -4 -1 4 -2 -7
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+ E -2 -2 -1 1 -7 1 6 -4 -1 -5 -5 0 -4 -5 -3 -1 -2 -5 -4 -4 0 5 -2 -7
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+ G -1 -4 -2 -3 -5 -4 -4 6 -4 -6 -6 -3 -5 -5 -4 -1 -3 -5 -6 -5 -2 -4 -3 -7
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+ H -3 -1 0 -2 -6 0 -1 -4 9 -5 -4 -2 -3 -3 -4 -2 -3 -4 1 -5 -1 -1 -3 -7
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+ I -3 -5 -5 -6 -2 -4 -5 -6 -5 6 1 -4 1 -1 -5 -4 -2 -4 -3 2 -5 -5 -2 -7
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+ L -3 -4 -5 -6 -3 -3 -5 -6 -4 1 5 -4 2 0 -5 -4 -3 -4 -3 0 -5 -4 -2 -7
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+ K -2 2 -1 -2 -5 1 0 -3 -2 -4 -4 6 -2 -4 -2 -1 -2 -6 -4 -4 -1 0 -2 -7
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+ M -2 -3 -4 -5 -3 -1 -4 -5 -3 1 2 -2 8 -1 -4 -3 -2 -2 -3 0 -5 -3 -2 -7
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+ F -4 -4 -5 -5 -3 -4 -5 -5 -3 -1 0 -4 -1 7 -5 -4 -3 0 3 -2 -5 -5 -3 -7
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+ P -1 -3 -4 -3 -5 -2 -3 -4 -4 -5 -5 -2 -4 -5 8 -2 -3 -5 -5 -4 -4 -3 -3 -7
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+ S 1 -2 0 -2 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 6 1 -4 -3 -3 -1 -1 -1 -7
24
+ T -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -3 -2 -2 -3 -3 1 6 -5 -3 -1 -2 -2 -1 -7
25
+ W -4 -5 -6 -7 -5 -4 -5 -5 -4 -4 -4 -6 -2 0 -5 -4 -5 11 1 -3 -6 -4 -4 -7
26
+ Y -4 -4 -4 -5 -4 -3 -4 -6 1 -3 -3 -4 -3 3 -5 -3 -3 1 8 -3 -4 -4 -3 -7
27
+ V -1 -4 -4 -5 -2 -4 -4 -5 -5 2 0 -4 0 -2 -4 -3 -1 -3 -3 5 -5 -4 -2 -7
28
+ B -3 -2 4 4 -5 -1 0 -2 -1 -5 -5 -1 -5 -5 -4 -1 -2 -6 -4 -5 4 1 -2 -7
29
+ Z -2 -1 -1 0 -6 4 5 -4 -1 -5 -4 0 -3 -5 -3 -1 -2 -4 -4 -4 1 4 -2 -7
30
+ X -1 -2 -2 -3 -4 -2 -2 -3 -3 -2 -2 -2 -2 -3 -3 -1 -1 -4 -3 -2 -2 -2 -2 -7
31
+ * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
biotite/sequence/align/matrix_data/CorBLOSUM49_5.0.mat ADDED
@@ -0,0 +1,25 @@
1
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
2
+ A 5 -2 -1 -2 0 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5
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+ R -2 7 0 -2 -4 1 0 -3 0 -3 -3 3 -2 -3 -3 -1 -1 -2 -2 -3 -1 0 -1 -5
4
+ N -1 0 7 2 -2 0 0 -1 1 -3 -3 0 -2 -3 -2 1 0 -3 -2 -3 4 0 -1 -5
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+ D -2 -2 2 8 -4 0 2 -2 0 -4 -4 0 -3 -4 -1 0 -1 -4 -3 -4 5 2 -1 -5
6
+ C 0 -4 -2 -4 13 -3 -4 -3 -2 -2 -2 -4 -1 -2 -3 -1 -1 -3 -2 -1 -3 -4 -2 -5
7
+ Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 -1 -3 -1 0 -1 -2 -1 -3 0 4 -1 -5
8
+ E -1 0 0 2 -4 2 7 -3 -1 -4 -3 1 -2 -4 -1 -1 -1 -3 -2 -3 1 5 -1 -5
9
+ G 0 -3 -1 -2 -3 -2 -3 8 -2 -4 -5 -2 -4 -4 -2 0 -2 -3 -4 -4 -1 -3 -2 -5
10
+ H -2 0 1 0 -2 1 -1 -2 10 -4 -2 0 -2 -2 -3 -1 -2 -1 2 -3 0 0 -1 -5
11
+ I -2 -3 -3 -4 -2 -3 -4 -4 -4 6 2 -3 1 0 -3 -3 -1 -2 -1 4 -4 -3 -1 -5
12
+ L -2 -3 -3 -4 -2 -2 -3 -5 -2 2 5 -3 3 1 -3 -3 -2 -1 -1 1 -3 -3 -1 -5
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+ K -1 3 0 0 -4 2 1 -2 0 -3 -3 6 -2 -4 -2 0 -1 -3 -2 -3 0 1 -1 -5
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+ M -1 -2 -2 -3 -1 -1 -2 -4 -2 1 3 -2 7 1 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
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+ F -3 -3 -3 -4 -2 -3 -4 -4 -2 0 1 -4 1 8 -3 -3 -2 2 4 -1 -4 -4 -2 -5
16
+ P -1 -3 -2 -1 -3 -1 -1 -2 -3 -3 -3 -2 -3 -3 10 -1 -1 -3 -3 -3 -2 -1 -2 -5
17
+ S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 -1 -1 -5
18
+ T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 2 6 -3 -2 0 -1 -1 -1 -5
19
+ W -3 -2 -3 -4 -3 -2 -3 -3 -1 -2 -1 -3 -2 2 -3 -4 -3 15 3 -3 -3 -3 -2 -5
20
+ Y -2 -2 -2 -3 -2 -1 -2 -4 2 -1 -1 -2 -1 4 -3 -2 -2 3 9 -1 -2 -2 -1 -5
21
+ V 0 -3 -3 -4 -1 -3 -3 -4 -3 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5
22
+ B -2 -1 4 5 -3 0 1 -1 0 -4 -3 0 -3 -4 -2 0 -1 -3 -2 -4 5 1 -1 -5
23
+ Z -1 0 0 2 -4 4 5 -3 0 -3 -3 1 -2 -4 -1 -1 -1 -3 -2 -3 1 4 -1 -5
24
+ X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5
25
+ * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
biotite/sequence/align/matrix_data/CorBLOSUM57_13p.mat ADDED
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+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
2
+ A 5 -1 -1 -2 -2 -1 -1 0 -2 -1 -1 -1 0 -2 -1 1 0 -2 -2 0 -1 -1 0 -5
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+ R -1 7 0 0 -4 2 1 -2 0 -2 -2 3 -1 -2 -1 0 0 -1 -2 -2 0 1 -1 -5
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+ N -1 0 7 2 -3 1 0 0 1 -2 -3 1 -2 -2 -1 1 0 -2 -2 -2 4 0 -1 -5
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+ D -2 0 2 8 -3 1 3 -1 -1 -3 -3 0 -3 -3 -1 0 -1 -3 -3 -3 6 2 -1 -5
6
+ C -2 -4 -3 -3 16 -3 -4 -4 -3 -3 -3 -4 -3 -2 -3 -2 -3 -3 -3 -2 -3 -4 -3 -5
7
+ Q -1 2 1 1 -3 5 2 -2 0 -2 -2 2 0 -2 -1 0 0 -1 -1 -2 1 3 0 -5
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+ E -1 1 0 3 -4 2 6 -2 -1 -3 -3 1 -2 -3 0 0 0 -2 -2 -2 2 5 -1 -5
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+ G 0 -2 0 -1 -4 -2 -2 9 -3 -4 -4 -2 -3 -3 -1 0 -2 -3 -4 -3 -1 -2 -1 -5
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+ H -2 0 1 -1 -3 0 -1 -3 12 -3 -3 0 -2 -2 -2 -1 -2 -2 0 -3 0 0 -1 -5
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+ I -1 -2 -2 -3 -3 -2 -3 -4 -3 6 3 -2 2 1 -3 -2 -1 -1 -1 4 -3 -2 -1 -5
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+ L -1 -2 -3 -3 -3 -2 -3 -4 -3 3 6 -2 3 1 -3 -3 -2 0 -1 1 -3 -2 -1 -5
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+ K -1 3 1 0 -4 2 1 -2 0 -2 -2 6 -1 -3 -1 0 0 -2 -2 -2 0 2 -1 -5
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+ M 0 -1 -2 -3 -3 0 -2 -3 -2 2 3 -1 7 1 -2 -1 -1 0 -1 1 -2 -1 0 -5
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+ F -2 -2 -2 -3 -2 -2 -3 -3 -2 1 1 -3 1 9 -3 -2 -2 3 4 0 -3 -3 -1 -5
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+ P -1 -1 -1 -1 -3 -1 0 -1 -2 -3 -3 -1 -2 -3 11 0 -1 -2 -3 -2 -1 0 -1 -5
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+ S 1 0 1 0 -2 0 0 0 -1 -2 -3 0 -1 -2 0 4 2 -2 -2 -1 1 0 0 -5
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+ T 0 0 0 -1 -3 0 0 -2 -2 -1 -2 0 -1 -2 -1 2 5 -1 -1 0 0 0 0 -5
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+ W -2 -1 -2 -3 -3 -1 -2 -3 -2 -1 0 -2 0 3 -2 -2 -1 15 3 -1 -2 -2 -1 -5
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+ V 0 -2 -2 -3 -2 -2 -2 -3 -3 4 1 -2 1 0 -2 -1 0 -1 -1 5 -2 -2 0 -5
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+ B -1 0 4 6 -3 1 2 -1 0 -3 -3 0 -2 -3 -1 1 0 -2 -2 -2 5 2 -1 -5
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+ Z -1 1 0 2 -4 3 5 -2 0 -2 -2 2 -1 -3 0 0 0 -2 -2 -2 2 4 0 -5
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+ X 0 -1 -1 -1 -3 0 -1 -1 -1 -1 -1 -1 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5
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+ * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
biotite/sequence/align/matrix_data/CorBLOSUM57_14.3.mat ADDED
@@ -0,0 +1,25 @@
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+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
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+ A 5 -1 -2 -1 1 0 -1 0 -1 -1 -1 -1 0 -2 -1 1 0 -2 -3 0 -1 -1 0 -5
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+ R -1 7 0 0 -3 2 1 -2 1 -3 -3 4 -2 -3 -1 -1 -1 -2 -2 -3 0 2 -1 -5
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+ C 1 -3 -1 -2 17 -2 -3 -1 -1 -1 -1 -3 0 -1 -2 0 0 -1 -1 1 -2 -3 -1 -5
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biotite/sequence/align/matrix_data/CorBLOSUM61_5.0.mat ADDED
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+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
2
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biotite/sequence/align/matrix_data/CorBLOSUM66_13p.mat ADDED
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+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
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biotite/sequence/align/matrix_data/CorBLOSUM67_14.3.mat ADDED
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+ A 5 -1 -2 -2 1 -1 -1 0 -1 -2 -2 -2 -1 -2 -1 1 0 -2 -3 -1 -2 -1 0 -5
3
+ R -1 7 0 0 -3 2 1 -2 1 -3 -3 3 -2 -3 -1 -1 -1 -1 -2 -3 0 1 -1 -5
4
+ N -2 0 8 2 -1 1 0 1 1 -3 -3 0 -2 -3 -1 1 0 -2 -2 -2 5 0 -1 -5
5
+ D -2 0 2 9 -3 1 3 -1 0 -4 -4 0 -3 -4 0 0 -1 -3 -3 -4 6 3 -1 -5
6
+ C 1 -3 -1 -3 15 -3 -3 -2 -2 -1 -1 -3 0 -1 -3 0 0 -1 -2 1 -2 -3 -1 -5
7
+ Q -1 2 1 1 -3 6 3 -2 1 -3 -2 2 -1 -3 -1 0 0 -2 -2 -3 1 4 0 -5
8
+ E -1 1 0 3 -3 3 8 -3 0 -4 -4 1 -3 -5 -1 -1 -1 -3 -3 -3 2 6 -1 -5
9
+ G 0 -2 1 -1 -2 -2 -3 9 -1 -5 -4 -2 -3 -4 -1 0 -2 -2 -4 -4 0 -2 -1 -5
10
+ H -1 1 1 0 -2 1 0 -1 11 -2 -2 0 -2 -1 -2 -1 -1 0 2 -2 1 0 -1 -5
11
+ I -2 -3 -3 -4 -1 -3 -4 -5 -2 6 2 -4 2 1 -3 -3 -1 -1 -2 4 -4 -4 -1 -5
12
+ L -2 -3 -3 -4 -1 -2 -4 -4 -2 2 5 -3 3 2 -3 -3 -2 1 -1 1 -4 -3 -1 -5
13
+ K -2 3 0 0 -3 2 1 -2 0 -4 -3 8 -2 -4 -1 -1 -1 -3 -3 -3 0 2 -1 -5
14
+ M -1 -2 -2 -3 0 -1 -3 -3 -2 2 3 -2 7 2 -3 -2 -1 1 0 1 -3 -2 -1 -5
15
+ F -2 -3 -3 -4 -1 -3 -5 -4 -1 1 2 -4 2 9 -4 -3 -2 4 4 0 -4 -4 -1 -5
16
+ P -1 -1 -1 0 -3 -1 -1 -1 -2 -3 -3 -1 -3 -4 12 0 -1 -2 -4 -3 -1 -1 -1 -5
17
+ S 1 -1 1 0 0 0 -1 0 -1 -3 -3 -1 -2 -3 0 6 3 -2 -3 -2 1 -1 -1 -5
18
+ T 0 -1 0 -1 0 0 -1 -2 -1 -1 -2 -1 -1 -2 -1 3 6 -2 -2 0 0 -1 0 -5
19
+ W -2 -1 -2 -3 -1 -2 -3 -2 0 -1 1 -3 1 4 -2 -2 -2 15 4 -1 -3 -3 -1 -5
20
+ Y -3 -2 -2 -3 -2 -2 -3 -4 2 -2 -1 -3 0 4 -4 -3 -2 4 12 -2 -3 -3 -1 -5
21
+ V -1 -3 -2 -4 1 -3 -3 -4 -2 4 1 -3 1 0 -3 -2 0 -1 -2 5 -3 -3 -1 -5
22
+ B -2 0 5 6 -2 1 2 0 1 -4 -4 0 -3 -4 -1 1 0 -3 -3 -3 5 2 -1 -5
23
+ Z -1 1 0 3 -3 4 6 -2 0 -4 -3 2 -2 -4 -1 -1 -1 -3 -3 -3 2 5 -1 -5
24
+ X 0 -1 -1 -1 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 -1 -1 -5
25
+ * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
biotite/sequence/align/matrix_data/DAYHOFF.mat ADDED
@@ -0,0 +1,32 @@
1
+ #Date: Wed, 18 Sep 91 17:36:51 EDT
2
+ #From: altschul@ray.nlm.nih.gov (Stephen Altschul)
3
+ #To: gish@ray.nlm.nih.gov
4
+ #Subject: Vanilla-flavored PAM-250
5
+ #
6
+ # substitution scores for B, Z, X, and * were obtained with "pam" version 1.0.5
7
+ #
8
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
9
+ A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -3 0 0 0 0 -8
10
+ R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
11
+ N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
12
+ D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
13
+ C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8
14
+ Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
15
+ E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8
16
+ G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
17
+ H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
18
+ I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
19
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8
20
+ K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8
21
+ M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8
22
+ F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
23
+ P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
24
+ S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8
25
+ T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
26
+ W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
27
+ Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
28
+ V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8
29
+ B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8
30
+ Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
31
+ X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
32
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
biotite/sequence/align/matrix_data/GONNET.mat ADDED
@@ -0,0 +1,26 @@
1
+ # PAM 250 matrix recommended by Gonnet, Cohen & Benner
2
+ # Science June 5, 1992.
3
+ # Values rounded to nearest integer
4
+ C S T P A G N D E Q H R K M I L V F Y W X *
5
+ C 12 0 0 -3 0 -2 -2 -3 -3 -2 -1 -2 -3 -1 -1 -2 0 -1 0 -1 -3 -8
6
+ S 0 2 2 0 1 0 1 0 0 0 0 0 0 -1 -2 -2 -1 -3 -2 -3 0 -8
7
+ T 0 2 2 0 1 -1 0 0 0 0 0 0 0 -1 -1 -1 0 -2 -2 -4 0 -8
8
+ P -3 0 0 8 0 -2 -1 -1 0 0 -1 -1 -1 -2 -3 -2 -2 -4 -3 -5 -1 -8
9
+ A 0 1 1 0 2 0 0 0 0 0 -1 -1 0 -1 -1 -1 0 -2 -2 -4 0 -8
10
+ G -2 0 -1 -2 0 7 0 0 -1 -1 -1 -1 -1 -4 -4 -4 -3 -5 -4 -4 -1 -8
11
+ N -2 1 0 -1 0 0 4 2 1 1 1 0 1 -2 -3 -3 -2 -3 -1 -4 0 -8
12
+ D -3 0 0 -1 0 0 2 5 3 1 0 0 0 -3 -4 -4 -3 -4 -3 -5 -1 -8
13
+ E -3 0 0 0 0 -1 1 3 4 2 0 0 1 -2 -3 -3 -2 -4 -3 -4 -1 -8
14
+ Q -2 0 0 0 0 -1 1 1 2 3 1 2 2 -1 -2 -2 -2 -3 -2 -3 -1 -8
15
+ H -1 0 0 -1 -1 -1 1 0 0 1 6 1 1 -1 -2 -2 -2 0 2 -1 -1 -8
16
+ R -2 0 0 -1 -1 -1 0 0 0 2 1 5 3 -2 -2 -2 -2 -3 -2 -2 -1 -8
17
+ K -3 0 0 -1 0 -1 1 0 1 2 1 3 3 -1 -2 -2 -2 -3 -2 -4 -1 -8
18
+ M -1 -1 -1 -2 -1 -4 -2 -3 -2 -1 -1 -2 -1 4 2 3 2 2 0 -1 -1 -8
19
+ I -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -2 -2 -2 2 4 3 3 1 -1 -2 -1 -8
20
+ L -2 -2 -1 -2 -1 -4 -3 -4 -3 -2 -2 -2 -2 3 3 4 2 2 0 -1 -1 -8
21
+ V 0 -1 0 -2 0 -3 -2 -3 -2 -2 -2 -2 -2 2 3 2 3 0 -1 -3 -1 -8
22
+ F -1 -3 -2 -4 -2 -5 -3 -4 -4 -3 0 -3 -3 2 1 2 0 7 5 4 -2 -8
23
+ Y 0 -2 -2 -3 -2 -4 -1 -3 -3 -2 2 -2 -2 0 -1 0 -1 5 8 4 -2 -8
24
+ W -1 -3 -4 -5 -4 -4 -4 -5 -4 -3 -1 -2 -4 -1 -2 -1 -3 4 4 14 -4 -8
25
+ X -3 0 0 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -2 -4 -1 -8
26
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
biotite/sequence/align/matrix_data/IDENTITY.mat ADDED
@@ -0,0 +1,25 @@
1
+ A R N B D C Q Z E G H I L K M F P S T W Y V X *
2
+ A 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
3
+ R -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
4
+ N -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
5
+ B -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
6
+ D -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
7
+ C -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
8
+ Q -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
9
+ Z -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
10
+ E -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
11
+ G -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
12
+ H -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
13
+ I -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
14
+ L -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
15
+ K -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
16
+ M -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
17
+ F -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
18
+ P -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000
19
+ S -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000
20
+ T -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000
21
+ W -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000
22
+ Y -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000
23
+ V -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000
24
+ X -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0 -10000
25
+ * -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0
biotite/sequence/align/matrix_data/MATCH.mat ADDED
@@ -0,0 +1,25 @@
1
+ A R N B D C Q Z E G H I L K M F P S T W Y V X *
2
+ A 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
3
+ R -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
4
+ N -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
5
+ B -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
6
+ D -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
7
+ C -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
8
+ Q -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
9
+ Z -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
10
+ E -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
11
+ G -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
12
+ H -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
13
+ I -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
14
+ L -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
15
+ K -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
16
+ M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1
17
+ F -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1
18
+ P -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1
19
+ S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1
20
+ T -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1
21
+ W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1
22
+ Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1
23
+ V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1
24
+ X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1
25
+ * -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
biotite/sequence/align/matrix_data/NUC.mat ADDED
@@ -0,0 +1,25 @@
1
+ #
2
+ # This matrix was created by Todd Lowe 12/10/92
3
+ #
4
+ # Uses ambiguous nucleotide codes, probabilities rounded to
5
+ # nearest integer
6
+ #
7
+ # Lowest score = -4, Highest score = 5
8
+ #
9
+ A T G C S W R Y K M B V H D N
10
+ A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2
11
+ T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2
12
+ G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2
13
+ C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2
14
+ S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1
15
+ W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1
16
+ R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1
17
+ Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1
18
+ K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1
19
+ M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1
20
+ B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1
21
+ V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1
22
+ H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1
23
+ D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1
24
+ N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
25
+
biotite/sequence/align/matrix_data/PAM10.mat ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 10 substitution matrix, scale = ln(2)/2 = 0.346574
5
+ #
6
+ # Expected score = -8.27, Entropy = 3.43 bits
7
+ #
8
+ # Lowest score = -23, Highest score = 13
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 7 -10 -7 -6 -10 -7 -5 -4 -11 -8 -9 -10 -8 -12 -4 -3 -3 -20 -11 -5 -6 -6 -6 -23
12
+ R -10 9 -9 -17 -11 -4 -15 -13 -4 -8 -12 -2 -7 -12 -7 -6 -10 -5 -14 -11 -11 -7 -9 -23
13
+ N -7 -9 9 -1 -17 -7 -5 -6 -2 -8 -10 -4 -15 -12 -9 -2 -5 -11 -7 -12 7 -6 -6 -23
14
+ D -6 -17 -1 8 -21 -6 0 -6 -7 -11 -19 -8 -17 -21 -12 -7 -8 -21 -17 -11 7 -1 -9 -23
15
+ C -10 -11 -17 -21 10 -20 -20 -13 -10 -9 -21 -20 -20 -19 -11 -6 -11 -22 -7 -9 -18 -20 -13 -23
16
+ Q -7 -4 -7 -6 -20 9 -1 -10 -2 -11 -8 -6 -7 -19 -6 -8 -9 -19 -18 -10 -6 7 -8 -23
17
+ E -5 -15 -5 0 -20 -1 8 -7 -9 -8 -13 -7 -10 -20 -9 -7 -9 -23 -11 -10 -1 7 -8 -23
18
+ G -4 -13 -6 -6 -13 -10 -7 7 -13 -17 -14 -10 -12 -12 -10 -4 -10 -21 -20 -9 -6 -8 -8 -23
19
+ H -11 -4 -2 -7 -10 -2 -9 -13 10 -13 -9 -10 -17 -9 -7 -9 -11 -10 -6 -9 -4 -4 -8 -23
20
+ I -8 -8 -8 -11 -9 -11 -8 -17 -13 9 -4 -9 -3 -5 -12 -10 -5 -20 -9 -1 -9 -9 -8 -23
21
+ L -9 -12 -10 -19 -21 -8 -13 -14 -9 -4 7 -11 -2 -5 -10 -12 -10 -9 -10 -5 -12 -10 -9 -23
22
+ K -10 -2 -4 -8 -20 -6 -7 -10 -10 -9 -11 7 -4 -20 -10 -7 -6 -18 -12 -13 -5 -6 -8 -23
23
+ M -8 -7 -15 -17 -20 -7 -10 -12 -17 -3 -2 -4 12 -7 -11 -8 -7 -19 -17 -4 -16 -8 -9 -23
24
+ F -12 -12 -12 -21 -19 -19 -20 -12 -9 -5 -5 -20 -7 9 -13 -9 -12 -7 -1 -12 -14 -20 -12 -23
25
+ P -4 -7 -9 -12 -11 -6 -9 -10 -7 -12 -10 -10 -11 -13 8 -4 -7 -20 -20 -9 -10 -7 -8 -23
26
+ S -3 -6 -2 -7 -6 -8 -7 -4 -9 -10 -12 -7 -8 -9 -4 7 -2 -8 -10 -10 -4 -8 -6 -23
27
+ T -3 -10 -5 -8 -11 -9 -9 -10 -11 -5 -10 -6 -7 -12 -7 -2 8 -19 -9 -6 -6 -9 -7 -23
28
+ W -20 -5 -11 -21 -22 -19 -23 -21 -10 -20 -9 -18 -19 -7 -20 -8 -19 13 -8 -22 -13 -21 -16 -23
29
+ Y -11 -14 -7 -17 -7 -18 -11 -20 -6 -9 -10 -12 -17 -1 -20 -10 -9 -8 10 -10 -9 -13 -11 -23
30
+ V -5 -11 -12 -11 -9 -10 -10 -9 -9 -1 -5 -13 -4 -12 -9 -10 -6 -22 -10 8 -11 -10 -8 -23
31
+ B -6 -11 7 7 -18 -6 -1 -6 -4 -9 -12 -5 -16 -14 -10 -4 -6 -13 -9 -11 7 -3 -8 -23
32
+ Z -6 -7 -6 -1 -20 7 7 -8 -4 -9 -10 -6 -8 -20 -7 -8 -9 -21 -13 -10 -3 7 -8 -23
33
+ X -6 -9 -6 -9 -13 -8 -8 -8 -8 -8 -9 -8 -9 -12 -8 -6 -7 -16 -11 -8 -8 -8 -8 -23
34
+ * -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 1
biotite/sequence/align/matrix_data/PAM100.mat ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 100 substitution matrix, scale = ln(2)/2 = 0.346574
5
+ #
6
+ # Expected score = -1.99, Entropy = 1.18 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 12
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 4 -3 -1 -1 -3 -2 0 1 -3 -2 -3 -3 -2 -5 1 1 1 -7 -4 0 -1 -1 -1 -9
12
+ R -3 7 -2 -4 -5 1 -3 -5 1 -3 -5 2 -1 -6 -1 -1 -3 1 -6 -4 -3 -1 -2 -9
13
+ N -1 -2 5 3 -5 -1 1 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -3 4 0 -1 -9
14
+ D -1 -4 3 5 -7 0 4 -1 -1 -4 -6 -1 -5 -8 -3 -1 -2 -9 -6 -4 4 3 -2 -9
15
+ C -3 -5 -5 -7 9 -8 -8 -5 -4 -3 -8 -8 -7 -7 -4 -1 -4 -9 -1 -3 -6 -8 -5 -9
16
+ Q -2 1 -1 0 -8 6 2 -3 3 -4 -2 0 -2 -7 -1 -2 -2 -7 -6 -3 0 5 -2 -9
17
+ E 0 -3 1 4 -8 2 5 -1 -1 -3 -5 -1 -4 -8 -2 -1 -2 -9 -5 -3 3 4 -2 -9
18
+ G 1 -5 -1 -1 -5 -3 -1 5 -4 -5 -6 -3 -4 -6 -2 0 -2 -9 -7 -3 -1 -2 -2 -9
19
+ H -3 1 2 -1 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
20
+ I -2 -3 -3 -4 -3 -4 -3 -5 -4 6 1 -3 1 0 -4 -3 0 -7 -3 3 -3 -3 -2 -9
21
+ L -3 -5 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 0 -5 -4 -3 -9
22
+ K -3 2 1 -1 -8 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -6 -6 -4 0 -1 -2 -9
23
+ M -2 -1 -4 -5 -7 -2 -4 -4 -4 1 3 0 9 -1 -4 -3 -1 -6 -5 1 -4 -2 -2 -9
24
+ F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -7 -1 8 -6 -4 -5 -1 4 -3 -6 -7 -4 -9
25
+ P 1 -1 -2 -3 -4 -1 -2 -2 -1 -4 -4 -3 -4 -6 7 0 -1 -7 -7 -3 -3 -1 -2 -9
26
+ S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -3 -4 0 4 2 -3 -4 -2 0 -2 -1 -9
27
+ T 1 -3 0 -2 -4 -2 -2 -2 -3 0 -3 -1 -1 -5 -1 2 5 -7 -4 0 -1 -2 -1 -9
28
+ W -7 1 -5 -9 -9 -7 -9 -9 -4 -7 -3 -6 -6 -1 -7 -3 -7 12 -2 -9 -6 -8 -6 -9
29
+ Y -4 -6 -2 -6 -1 -6 -5 -7 -1 -3 -3 -6 -5 4 -7 -4 -4 -2 9 -4 -4 -6 -4 -9
30
+ V 0 -4 -3 -4 -3 -3 -3 -3 -3 3 0 -4 1 -3 -3 -2 0 -9 -4 5 -4 -3 -2 -9
31
+ B -1 -3 4 4 -6 0 3 -1 1 -3 -5 0 -4 -6 -3 0 -1 -6 -4 -4 4 2 -2 -9
32
+ Z -1 -1 0 3 -8 5 4 -2 1 -3 -4 -1 -2 -7 -1 -2 -2 -8 -6 -3 2 5 -2 -9
33
+ X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
biotite/sequence/align/matrix_data/PAM110.mat ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 110 substitution matrix, scale = ln(2)/2 = 0.346574
5
+ #
6
+ # Expected score = -1.81, Entropy = 1.07 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 12
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 3 -3 -1 -1 -3 -1 0 1 -3 -1 -3 -3 -2 -4 1 1 1 -7 -4 0 -1 -1 -1 -9
12
+ R -3 7 -1 -4 -4 1 -3 -4 1 -3 -4 2 -1 -5 -1 -1 -2 1 -5 -4 -2 -1 -2 -9
13
+ N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -5 -2 -3 3 0 -1 -9
14
+ D -1 -4 2 5 -7 1 4 0 0 -3 -6 -1 -5 -7 -3 -1 -1 -8 -5 -4 4 3 -2 -9
15
+ C -3 -4 -5 -7 9 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 -1 -3 -9 -1 -3 -6 -7 -4 -9
16
+ Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -6 -3 0 4 -1 -9
17
+ E 0 -3 1 4 -7 2 5 -1 -1 -3 -5 -1 -3 -7 -2 -1 -2 -9 -5 -3 3 4 -2 -9
18
+ G 1 -4 0 0 -5 -3 -1 5 -4 -4 -6 -3 -4 -5 -2 0 -2 -8 -7 -2 0 -2 -2 -9
19
+ H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
20
+ I -1 -3 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -4 -3 0 -7 -2 3 -3 -3 -2 -9
21
+ L -3 -4 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 1 -5 -3 -2 -9
22
+ K -3 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -5 -5 -4 0 -1 -2 -9
23
+ M -2 -1 -3 -5 -7 -1 -3 -4 -4 1 3 0 8 -1 -4 -2 -1 -6 -5 1 -4 -2 -2 -9
24
+ F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -6 -4 -4 -1 4 -3 -6 -7 -4 -9
25
+ P 1 -1 -2 -3 -4 0 -2 -2 -1 -4 -4 -3 -4 -6 6 0 -1 -7 -7 -2 -2 -1 -2 -9
26
+ S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -2 -4 0 3 2 -3 -3 -2 0 -1 -1 -9
27
+ T 1 -2 0 -1 -3 -2 -2 -2 -3 0 -3 -1 -1 -4 -1 2 5 -6 -3 0 -1 -2 -1 -9
28
+ W -7 1 -5 -8 -9 -6 -9 -8 -4 -7 -3 -5 -6 -1 -7 -3 -6 12 -2 -8 -6 -7 -5 -9
29
+ Y -4 -5 -2 -5 -1 -6 -5 -7 -1 -2 -3 -5 -5 4 -7 -3 -3 -2 8 -4 -3 -5 -3 -9
30
+ V 0 -4 -3 -4 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -4 5 -3 -3 -2 -9
31
+ B -1 -2 3 4 -6 0 3 0 1 -3 -5 0 -4 -6 -2 0 -1 -6 -3 -3 4 2 -1 -9
32
+ Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -7 -1 -1 -2 -7 -5 -3 2 4 -2 -9
33
+ X -1 -2 -1 -2 -4 -1 -2 -2 -2 -2 -2 -2 -2 -4 -2 -1 -1 -5 -3 -2 -1 -2 -2 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
biotite/sequence/align/matrix_data/PAM120.mat ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574
5
+ #
6
+ # Expected score = -1.64, Entropy = 0.979 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 12
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 3 -3 -1 0 -3 -1 0 1 -3 -1 -3 -2 -2 -4 1 1 1 -7 -4 0 0 -1 -1 -8
12
+ R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
13
+ N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -4 -2 -3 3 0 -1 -8
14
+ D 0 -3 2 5 -7 1 3 0 0 -3 -5 -1 -4 -7 -3 0 -1 -8 -5 -3 4 3 -2 -8
15
+ C -3 -4 -5 -7 9 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -8 -1 -3 -6 -7 -4 -8
16
+ Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -5 -3 0 4 -1 -8
17
+ E 0 -3 1 3 -7 2 5 -1 -1 -3 -4 -1 -3 -7 -2 -1 -2 -8 -5 -3 3 4 -1 -8
18
+ G 1 -4 0 0 -4 -3 -1 5 -4 -4 -5 -3 -4 -5 -2 1 -1 -8 -6 -2 0 -2 -2 -8
19
+ H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -3 -1 -3 1 1 -2 -8
20
+ I -1 -2 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
21
+ L -3 -4 -4 -5 -7 -2 -4 -5 -3 1 5 -4 3 0 -3 -4 -3 -3 -2 1 -4 -3 -2 -8
22
+ K -2 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -2 -1 -1 -5 -5 -4 0 -1 -2 -8
23
+ M -2 -1 -3 -4 -6 -1 -3 -4 -4 1 3 0 8 -1 -3 -2 -1 -6 -4 1 -4 -2 -2 -8
24
+ F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -5 -3 -4 -1 4 -3 -5 -6 -3 -8
25
+ P 1 -1 -2 -3 -4 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -7 -6 -2 -2 -1 -2 -8
26
+ S 1 -1 1 0 0 -2 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
27
+ T 1 -2 0 -1 -3 -2 -2 -1 -3 0 -3 -1 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
28
+ W -7 1 -4 -8 -8 -6 -8 -8 -3 -6 -3 -5 -6 -1 -7 -2 -6 12 -2 -8 -6 -7 -5 -8
29
+ Y -4 -5 -2 -5 -1 -5 -5 -6 -1 -2 -2 -5 -4 4 -6 -3 -3 -2 8 -3 -3 -5 -3 -8
30
+ V 0 -3 -3 -3 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -3 5 -3 -3 -1 -8
31
+ B 0 -2 3 4 -6 0 3 0 1 -3 -4 0 -4 -5 -2 0 0 -6 -3 -3 4 2 -1 -8
32
+ Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
33
+ X -1 -2 -1 -2 -4 -1 -1 -2 -2 -1 -2 -2 -2 -3 -2 -1 -1 -5 -3 -1 -1 -1 -2 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
biotite/sequence/align/matrix_data/PAM130.mat ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 130 substitution matrix, scale = ln(2)/2 = 0.346574
5
+ #
6
+ # Expected score = -1.48, Entropy = 0.895 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 12
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
12
+ R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
13
+ N 0 -1 4 2 -4 0 1 0 2 -2 -3 1 -3 -4 -1 1 0 -4 -2 -3 3 0 -1 -8
14
+ D 0 -3 2 5 -6 1 3 0 0 -3 -5 -1 -4 -7 -2 0 -1 -7 -5 -3 4 3 -1 -8
15
+ C -3 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
16
+ Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -6 0 -1 -2 -6 -5 -3 0 4 -1 -8
17
+ E 0 -3 1 3 -6 2 5 -1 0 -2 -4 -1 -3 -6 -2 -1 -1 -8 -5 -3 2 4 -1 -8
18
+ G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -4 -5 -2 1 -1 -7 -6 -2 0 -1 -2 -8
19
+ H -2 1 2 0 -4 3 0 -3 7 -3 -3 -1 -3 -2 -1 -2 -2 -3 0 -3 1 1 -1 -8
20
+ I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
21
+ L -3 -4 -3 -5 -7 -2 -4 -5 -3 1 5 -4 3 1 -3 -4 -2 -2 -2 1 -4 -3 -2 -8
22
+ K -2 2 1 -1 -6 0 -1 -3 -1 -2 -4 5 0 -6 -2 -1 0 -5 -5 -4 0 0 -1 -8
23
+ M -2 -1 -3 -4 -6 -1 -3 -4 -3 2 3 0 8 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
24
+ F -4 -5 -4 -7 -5 -6 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
25
+ P 1 -1 -1 -2 -3 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -6 -6 -2 -2 -1 -1 -8
26
+ S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
27
+ T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
28
+ W -6 1 -4 -7 -8 -6 -8 -7 -3 -6 -2 -5 -5 -1 -6 -2 -6 12 -1 -7 -5 -7 -5 -8
29
+ Y -4 -5 -2 -5 -1 -5 -5 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -5 -3 -8
30
+ V 0 -3 -3 -3 -2 -3 -3 -2 -3 3 1 -4 1 -2 -2 -2 0 -7 -3 5 -3 -3 -1 -8
31
+ B 0 -2 3 4 -5 0 2 0 1 -3 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
32
+ Z 0 -1 0 3 -6 4 4 -1 1 -3 -3 0 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
33
+ X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 -1 -1 -5 -3 -1 -1 -1 -1 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
biotite/sequence/align/matrix_data/PAM140.mat ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 140 substitution matrix, scale = ln(2)/2 = 0.346574
5
+ #
6
+ # Expected score = -1.35, Entropy = 0.820 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 12
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
12
+ R -2 6 -1 -3 -4 1 -2 -4 1 -2 -4 3 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -1 -8
13
+ N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -8
14
+ D 0 -3 2 4 -6 1 3 0 0 -3 -5 -1 -4 -6 -2 0 -1 -7 -5 -3 4 3 -1 -8
15
+ C -2 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
16
+ Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -2 -5 -5 -2 1 4 -1 -8
17
+ E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -3 -6 -1 -1 -1 -8 -4 -2 2 4 -1 -8
18
+ G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -3 -5 -1 1 -1 -7 -6 -2 0 -1 -1 -8
19
+ H -2 1 2 0 -4 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -8
20
+ I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -2 -2 -1 -8
21
+ L -2 -4 -3 -5 -7 -2 -4 -5 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -8
22
+ K -2 3 1 -1 -6 0 -1 -3 -1 -2 -3 5 0 -6 -2 -1 0 -4 -5 -3 0 0 -1 -8
23
+ M -2 -1 -2 -4 -6 -1 -3 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
24
+ F -4 -5 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
25
+ P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -6 -2 -2 -1 -1 -8
26
+ S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 0 -8
27
+ T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -5 -3 0 0 -1 -1 -8
28
+ W -6 1 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 -1 -6 -2 -5 12 -1 -7 -5 -6 -5 -8
29
+ Y -4 -5 -2 -5 -1 -5 -4 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -4 -3 -8
30
+ V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -2 0 -7 -3 5 -3 -2 -1 -8
31
+ B 0 -2 3 4 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
32
+ Z 0 -1 1 3 -6 4 4 -1 1 -2 -3 0 -2 -6 -1 -1 -1 -6 -4 -2 2 4 -1 -8
33
+ X -1 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -5 -3 -1 -1 -1 -1 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
biotite/sequence/align/matrix_data/PAM150.mat ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 150 substitution matrix, scale = ln(2)/2 = 0.346574
5
+ #
6
+ # Expected score = -1.25, Entropy = 0.754 bits
7
+ #
8
+ # Lowest score = -7, Highest score = 12
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -6 -3 0 0 0 -1 -7
12
+ R -2 6 -1 -2 -4 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -2 1 -4 -3 -2 0 -1 -7
13
+ N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -7
14
+ D 0 -2 2 4 -6 1 3 0 0 -3 -5 -1 -3 -6 -2 0 -1 -7 -4 -3 3 2 -1 -7
15
+ C -2 -4 -4 -6 9 -6 -6 -4 -3 -2 -6 -6 -5 -5 -3 0 -3 -7 0 -2 -5 -6 -3 -7
16
+ Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -7
17
+ E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -2 -6 -1 -1 -1 -7 -4 -2 2 4 -1 -7
18
+ G 1 -3 0 0 -4 -2 -1 4 -3 -3 -4 -2 -3 -5 -1 1 -1 -7 -5 -2 0 -1 -1 -7
19
+ H -2 1 2 0 -3 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -7
20
+ I -1 -2 -2 -3 -2 -3 -2 -3 -3 5 1 -2 2 0 -3 -2 0 -5 -2 3 -2 -2 -1 -7
21
+ L -2 -3 -3 -5 -6 -2 -4 -4 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
22
+ K -2 3 1 -1 -6 0 -1 -2 -1 -2 -3 4 0 -6 -2 -1 0 -4 -4 -3 0 0 -1 -7
23
+ M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -3 1 -3 -2 -1 -7
24
+ F -4 -4 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -3 -1 5 -2 -5 -5 -3 -7
25
+ P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -5 -2 -2 -1 -1 -7
26
+ S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
27
+ T 1 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 4 -5 -3 0 0 -1 -1 -7
28
+ W -6 1 -4 -7 -7 -5 -7 -7 -3 -5 -2 -4 -5 -1 -6 -2 -5 12 -1 -6 -5 -6 -4 -7
29
+ Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
30
+ V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
31
+ B 0 -2 3 3 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -2 3 2 -1 -7
32
+ Z 0 0 1 2 -6 4 4 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 4 -1 -7
33
+ X -1 -1 -1 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -4 -3 -1 -1 -1 -1 -7
34
+ * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
biotite/sequence/align/matrix_data/PAM160.mat ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 160 substitution matrix, scale = ln(2)/2 = 0.346574
5
+ #
6
+ # Expected score = -1.14, Entropy = 0.694 bits
7
+ #
8
+ # Lowest score = -7, Highest score = 12
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -3 1 1 1 -5 -3 0 0 0 0 -7
12
+ R -2 6 -1 -2 -3 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -1 1 -4 -3 -1 0 -1 -7
13
+ N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -3 -1 1 0 -4 -2 -2 2 1 0 -7
14
+ D 0 -2 2 4 -5 1 3 0 0 -3 -4 0 -3 -6 -2 0 -1 -6 -4 -3 3 2 -1 -7
15
+ C -2 -3 -4 -5 9 -5 -5 -3 -3 -2 -6 -5 -5 -5 -3 0 -2 -7 0 -2 -4 -5 -3 -7
16
+ Q -1 1 0 1 -5 5 2 -2 2 -2 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -7
17
+ E 0 -2 1 3 -5 2 4 0 0 -2 -3 -1 -2 -5 -1 0 -1 -7 -4 -2 2 3 -1 -7
18
+ G 1 -3 0 0 -3 -2 0 4 -3 -3 -4 -2 -3 -4 -1 1 -1 -7 -5 -2 0 -1 -1 -7
19
+ H -2 1 2 0 -3 2 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -2 1 1 -1 -7
20
+ I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 0 -2 -2 0 -5 -2 3 -2 -2 -1 -7
21
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
22
+ K -2 3 1 0 -5 0 -1 -2 -1 -2 -3 4 0 -5 -2 -1 0 -4 -4 -3 0 0 -1 -7
23
+ M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 0 -2 -2 -1 -4 -3 1 -3 -2 -1 -7
24
+ F -3 -4 -3 -6 -5 -5 -5 -4 -2 0 1 -5 0 7 -4 -3 -3 -1 5 -2 -4 -5 -3 -7
25
+ P 1 -1 -1 -2 -3 0 -1 -1 -1 -2 -3 -2 -2 -4 5 1 0 -5 -5 -2 -1 -1 -1 -7
26
+ S 1 -1 1 0 0 -1 0 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
27
+ T 1 -1 0 -1 -2 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -7
28
+ W -5 1 -4 -6 -7 -5 -7 -7 -3 -5 -2 -4 -4 -1 -5 -2 -5 12 -1 -6 -5 -6 -4 -7
29
+ Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
30
+ V 0 -3 -2 -3 -2 -2 -2 -2 -2 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
31
+ B 0 -1 2 3 -4 1 2 0 1 -2 -4 0 -3 -4 -1 0 0 -5 -3 -2 3 2 -1 -7
32
+ Z 0 0 1 2 -5 3 3 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 3 -1 -7
33
+ X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -7
34
+ * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1