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- addintrons.gff3
- addintrons.out
- additional_attribute.gff3
- all_node_types.gff3
- Arabidopsis-C99826.embl
- Arabidopsis-C99826.fna
- Arabidopsis-C99826.gbk
- at-C99887-fwd.fna
- at-C99887-rev.fna
- at-C99930.fna
- at100K1
- at1MB
- Atinsert.embl
- Atinsert.fna
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- Atinsert_seqrange_13-17_rev.fna
- Atinsert_seqrange_3-7.fna
- Atinsert_single_3.fna
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- attribute_after_dot.gff3
- attribute_w_multiple_equals.gff3
- bar.fas
- bigfonts.style
- blank_attributes.gff3
- BLOSUM62
- blosum62.c
- BLOSUM62.gth
- BLOSUM62.out
- broken_hmmer.hmm
- cds_check_fail_1.gff3
- cds_check_fail_2.gff3
- cds_check_fail_3.gff3
- cds_check_fail_4.gff3
- cds_check_succ_1.gff3
- cds_check_succ_10.gff3
- cds_check_succ_11.gff3
- cds_check_succ_12.gff3
- cds_check_succ_2.gff3
- cds_check_succ_3.gff3
- cds_check_succ_4.gff3
- cds_check_succ_5.gff3
- cds_check_succ_6.gff3
- cds_check_succ_7.gff3
- cds_check_succ_8.gff3
- cds_check_succ_9.gff3
- cds_feature_with_multiple_parents.gff3
- cds_feature_with_multiple_parents_tidied.gff3
- cds_with_multiple_parents_1.gff3
- cds_with_multiple_parents_1_tidied.gff3
- cds_with_multiple_parents_2.gff3
- cds_with_multiple_parents_2_tidied.gff3
- Copysorttest.embl
- Copysorttest.fna
- Copysorttest.gbk
- corrupt.fas
- corrupt.gff3
- corrupt_gff3_header.txt
- corrupt_large.gff3
- corrupt_target_attribute.gff3
- corruptpatternfile.fna
- csa_example_consensus_spliced_alignments.gff3
- csa_example_spliced_alignments.gff3
- csr_testcase.fastq
- csr_testcase_r0.fastq
- csr_testcase_r10.fastq
- csr_testcase_r23.fastq
- csr_testcase_r96.fastq
- custom_streams_ref.txt
- cycle_simple.gff3
- dbxref.gff3
- dbxref_invalid.gff3
- dbxref_invalid2.gff3
- description_test.fastq
- description_test2.fastq
- dna_hmmer.hmm
- double_free.gff3
- Duplicate.embl
- Duplicate.fna
- Duplicate.gbk
- Duplicate.shreddered
- duplicate.XRF_abbr
- duplicate_attribute.gff3
- duplicate_attribute_fixed.gff3
- dust.fna
- dust.link5.out
- dust.out
- dust.threshold3.out
- dust.window32.out
- dynbuf.gff3
- Ecoli-section1.fna
- Ecoli-section2.fna
- ecolicmp-neg.of
- ecolicmp-se.of
- ecolicmp.of
- ecolicmp250.of
- eden.gff3
- eden.linesorted.gff3
- eden_only_annotation.gff3
- embl_test1.embl
- embl_test2.embl
- embl_test3.embl
- embl_test4.embl
- embl_test5.embl
- embl_test5.fas
- embl_test6.embl
- empty.gff3
- empty_attribute.gff3
- empty_attribute_name.gff3
- empty_attribute_value.gff3
- empty_file
- empty_id_attribute.gff3
- empty_other_attribute.gff3
- empty_parent_attribute.gff3
- empty_seq.fas
- encode_known_genes_Mar07.gff3
- encode_known_genes_Mar07.seqids
- example_1.bam
- example_1.fa
- example_1.fa.fai
- example_1.sam.extract
- example_1.sam.gz
- example_1.sorted.bam
- example_1.sorted.bam.bai
- fail_arrow_width.style
- fail_background_color.style
- fail_block_caption_font_size.style
- fail_block_caption_space.style
- fail_collapse.style
- fail_default_stroke_color.style
- fail_fill.style
- fail_group_by_parent.style
- fail_max_capt_show_width.style
- fail_max_num_lines.style
- fail_max_show_width.style
- fail_min_len_block.style
- fail_ruler_text.style
- fail_rulerfontsize.style
- fail_rulerspace.style
- fail_show_bar_height.style
- fail_show_block_captions.style
- fail_show_grid.style
- fail_show_margins.style
- fail_show_track_captions.style
- fail_split.style
- fail_stroke.style
- fail_stroke_width.style
- fail_style.style
- fail_track_caption_font_size.style
- fail_track_caption_space.style
- fail_track_title_color.style
- fail_track_vspace.style
- fail_unit.style
- fail_vspace.style
- fasta_seq.fas
- fasta_seq.gff3
- fastq_long.fastq
- fastq_problem.fasta
- fastq_problem.fastq.gz
- fastq_problem2.fasta
- fastq_problem2.fastq.gz
- fib25.fas.gz
- filter_luafilter_filtered_LTR.gff3
- filter_luafilter_filtered_orf_frame.gff3
- filter_luafilter_filtered_orf_pos.gff3
- filter_luafilter_filtered_orfs.gff3
- filter_luafilter_test.gff3
- filter_luafilter_test_no_frame_attribute.gff3
- filter_nh_file01.gff3
- filter_nh_file02.gff3
- filter_nh_file03.gff3
- filter_nh_file04.gff3
- filter_targetbest_complex_test.gff3
- filter_targetbest_complex_test.out
- filter_targetbest_multiple_test.gff3
- filter_targetbest_simple_test.gff3
- filter_targetbest_simple_test.out
- foo.32.des
- foo.32.esq
- foo.32.info_map
- foo.32.info_nomap
- foo.32.sds
- foo.32.ver0.al1
- foo.32.ver0.esq
- foo.64.des
- foo.64.esq
- foo.64.info_map
- foo.64.info_nomap
- foo.64.sds
- foo.64.ver0.al1
- foo.64.ver0.esq
- foo.fas
- foo_width4.fas
- foobar.fas
- foofoo.fas
- foofoofoo.fas
- foorcfoo.fas
- foorcfoofoo.fas
- frompos.fas
- gap_fail1.gff3
- gap_fail2.gff3
- gap_fail3.gff3
- gap_fail4.gff3
- gap_fail5.gff3
- gap_fail6.gff3
- gap_fail7.gff3
- genbank_test.gbk
- genbank_test1.gbk
- genbank_test2.fas
- genbank_test2.gbk
- genbank_test3.gbk
- genbank_test4.gbk
- genbank_test5.gbk
- genbank_test6.gbk
- genbank_test7.gbk
- genbank_test8.gbk
- genome_stream_stdin.gff3
- gff3_file_1_short.txt
- gff3_file_1_short_sorted.txt
- gff3_numeric_a.gff
- gff3_numeric_mixed.gff3
- gff3_numeric_mixed.out
- gff3_numeric_only.gff3
- gff3_numeric_only.out
- gmap2gff3_prob.gmap
- gmap2gff3_prob.out
- graphics_curve_test_coords.txt
- graphics_test.out
- gt.supp
- gt_bioseq_fail_1.fas
- gt_bioseq_fail_2.fas
- gt_bioseq_fail_3.fas
- gt_bioseq_fail_4.fas
- gt_bioseq_fail_5.fas
- gt_bioseq_fail_6.fas
- gt_bioseq_fail_7.fas
- gt_bioseq_seqlengthdistri.out
- gt_bioseq_succ_1.fas
- gt_bioseq_succ_2.fas
- gt_bioseq_succ_3.fas
- gt_bioseq_succ_3.gc
- gt_bioseq_succ_3.out1
- gt_bioseq_succ_3.out2
- gt_bioseq_succ_3.out3
- gt_cds_descrange_multi.fas
- gt_cds_descrange_multi.in
- gt_cds_descrange_multi.out
- gt_cds_descrange_multi_fail_1.fas
- gt_cds_descrange_multi_fail_2.fas
- gt_cds_descrange_wrong_id.fas
- gt_cds_descrange_wrong_range.fas
- gt_cds_nostartcodon_nofinalstopcodon.in
- gt_cds_nostartcodon_nofinalstopcodon.out
- gt_cds_test_1.fas
- gt_cds_test_1.in
- gt_cds_test_1.out
- gt_cds_test_10.fas
- gt_cds_test_10.in
- gt_cds_test_10.out
- gt_cds_test_11.fas
- gt_cds_test_11.in
- gt_cds_test_11.out
- gt_cds_test_12.fas
- gt_cds_test_12.in
- gt_cds_test_12.out
- gt_cds_test_13.fas
- gt_cds_test_13.in
- gt_cds_test_13.out
- gt_cds_test_14.fas
- gt_cds_test_14.in
- gt_cds_test_14.out
- gt_cds_test_2.fas
- gt_cds_test_2.in
- gt_cds_test_2.out
- gt_cds_test_3.fas
- gt_cds_test_3.in
- gt_cds_test_3.out
- gt_cds_test_4.fas
- gt_cds_test_4.in
- gt_cds_test_4.out
- gt_cds_test_5.fas
- gt_cds_test_5.in
- gt_cds_test_5.out
- gt_cds_test_6.fas
- gt_cds_test_6.in
- gt_cds_test_6.out
- gt_cds_test_7.fas
- gt_cds_test_7.in
- gt_cds_test_7.out
- gt_cds_test_8.fas
- gt_cds_test_8.in
- gt_cds_test_8.out
- gt_cds_test_9.fas
- gt_cds_test_9.in
- gt_cds_test_9.out
- gt_cds_test_descrange.fas
- gt_cds_test_descrange.in
- gt_cds_test_descrange.out
- gt_chseqids_test_1.chseqids
- gt_chseqids_test_1.gff3
- gt_chseqids_test_1.out
- gt_chseqids_test_2.chseqids
- gt_chseqids_test_2.gff3
- gt_chseqids_test_2.out
- gt_chseqids_test_3.chseqids
- gt_chseqids_test_3.gff3
- gt_chseqids_test_4.chseqids
- gt_chseqids_test_4.gff3
- gt_chseqids_test_4.out
- gt_chseqids_test_5.chseqids
- gt_chseqids_test_5.gff3
- gt_chseqids_test_5.out
- gt_chseqids_test_5.sorted_out
- gt_chseqids_test_6.chseqids
- gt_chseqids_test_6.gff3
- gt_chseqids_test_6.out
- gt_csa_prob_1.debug
- gt_csa_prob_1.in
- gt_csa_prob_1.out
- gt_csa_prob_2.debug
- gt_csa_prob_2.in
- gt_csa_prob_2.out
- gt_csa_prob_3.debug
- gt_csa_prob_3.in
- gt_csa_prob_3.out
- gt_csa_prob_4.debug
- gt_csa_prob_4.in
- gt_csa_prob_4.out
- gt_csa_prob_5.in
- gt_csa_prob_5.out
- gt_csa_prob_6.in
- gt_csa_prob_6.out
- gt_csa_test_1.in
- gt_encseq_col_test1.fasta
- gt_encseq_eqlen_last_empty.fas
- gt_eval_ltr_prob_1.out
- gt_eval_ltr_prob_1.prediction
- gt_eval_ltr_prob_1.reality
- gt_eval_ltr_test_1.in
- gt_eval_ltr_test_1.out
- gt_eval_ltr_test_2.out
- gt_eval_ltr_test_2.prediction
- gt_eval_ltr_test_2.reality
- gt_eval_ltr_test_3.out
- gt_eval_ltr_test_3.prediction
- gt_eval_ltr_test_3.reality
- gt_eval_ltr_test_4.out
- gt_eval_ltr_test_4.prediction
- gt_eval_ltr_test_4.reality
- gt_eval_ltr_test_5.out
- gt_eval_ltr_test_5.prediction
- gt_eval_ltr_test_5.reality
- gt_eval_ltr_test_6.out
- gt_eval_ltr_test_6.prediction
- gt_eval_ltr_test_6.reality
- gt_eval_ltr_test_7.out
- gt_eval_ltr_test_7.prediction
- gt_eval_ltr_test_7.reality
- gt_eval_ltr_test_8.out
- gt_eval_ltr_test_8.prediction
- gt_eval_ltr_test_8.reality
- gt_eval_ltr_test_9.out
- gt_eval_ltr_test_9.prediction
- gt_eval_ltr_test_9.reality
- gt_eval_prob_1.out
- gt_eval_prob_1.out_swapped
- gt_eval_prob_1.prediction
- gt_eval_prob_1.reality
- gt_eval_test_1.in
- gt_eval_test_1.out
- gt_eval_test_10.in
- gt_eval_test_10.out
- gt_eval_test_2.nuc
- gt_eval_test_2.out
- gt_eval_test_2.prediction
- gt_eval_test_2.reality
- gt_eval_test_3.nuc
- gt_eval_test_3.out
- gt_eval_test_3.prediction
- gt_eval_test_3.reality
- gt_eval_test_4.nuc
- gt_eval_test_4.out
- gt_eval_test_4.prediction
- gt_eval_test_4.reality
- gt_eval_test_5.nuc
- gt_eval_test_5.out
- gt_eval_test_5.prediction
- gt_eval_test_5.reality
- gt_eval_test_6.nuc
- gt_eval_test_6.out
- gt_eval_test_6.prediction
- gt_eval_test_6.reality
- gt_eval_test_7.nuc
- gt_eval_test_7.out
- gt_eval_test_7.prediction
- gt_eval_test_7.reality
- gt_eval_test_8.nuc
- gt_eval_test_8.out
- gt_eval_test_8.prediction
- gt_eval_test_8.reality
- gt_eval_test_9.in
- gt_eval_test_9.out
- gt_evalviz_test.out
- gt_evalviz_test.prediction
- gt_evalviz_test.reality
- gt_extractfeat_mappings.fas
- gt_extractfeat_mappings.gff3
- gt_extractfeat_mappings.md5.gff3
- gt_extractfeat_mappings_md5.fas
- gt_extractfeat_mappings_ref.fas
- gt_extractfeat_mappings_ref.md5.fas
- gt_extractfeat_mappings_sep1.fas
- gt_extractfeat_mappings_sep2.fas
- gt_extractfeat_mappings_seprm.lua
- gt_extractfeat_mappings_seprm_bar.fas
- gt_extractfeat_mappings_seprm_baz.fas
- gt_extractfeat_mappings_seprm_foo.fas
- gt_extractfeat_mappings_seprm_quux.fas
- gt_extractfeat_matchdescstart_1.fas
- gt_extractfeat_matchdescstart_1.gff3
- gt_extractfeat_matchdescstart_1.out
- gt_extractfeat_matchdescstart_2.fas
- gt_extractfeat_phase.fas
- gt_extractfeat_phase.gff3
- gt_extractfeat_phase.out
- gt_extractfeat_phase_fix.gff3
- gt_extractfeat_phase_fix.out
- gt_extractfeat_retainids.fas
- gt_extractfeat_retainids.gff3
- gt_extractfeat_retainids_join.fas
- gt_extractfeat_seqid.fas
- gt_extractfeat_seqid_target.fas
- gt_extractfeat_seqid_target.gff3
- gt_extractfeat_succ_1.fas
- gt_extractfeat_succ_1.fas.gz
- gt_extractfeat_succ_1.gff3
- gt_extractfeat_succ_1.out
- gt_extractfeat_succ_2.fas
- gt_extractfeat_succ_2.gff3
- gt_extractfeat_succ_2.out1
- gt_extractfeat_succ_2.out2
- gt_extractfeat_succ_2.out3
- gt_extractfeat_succ_3.fas
- gt_extractfeat_succ_3.gff3
- gt_extractfeat_succ_3.out
- gt_extractfeat_target.fas
- gt_fingerprint_extract.out
- gt_gff3_addintrons_overlapping_exons.gff3
- gt_gff3_addintrons_overlapping_exons_with_introns.gff3
- gt_gff3_fail_1.gff3
- gt_gff3_illegal_feature_start.gff3
- gt_gff3_illegal_region_start.gff3
- gt_gff3_linesort.in.gff3
- gt_gff3_linesort.out.gff3
- gt_gff3_linesort2.in.gff3
- gt_gff3_linesort2.out.gff3
- gt_gff3_offset_test.gff3
- gt_gff3_offset_test.out-1
- gt_gff3_offset_test.out-999
- gt_gff3_offset_test.out1000
- gt_gff3_offsetfile_test.gff3
- gt_gff3_offsetfile_test.offsetfile
- gt_gff3_offsetfile_test.out
- gt_gff3_phases1.gff3
- gt_gff3_phases1.out
- gt_gff3_phases2.gff3
- gt_gff3_phases3.gff3
- gt_gff3_phases3.out
- gt_gff3_phases4.gff3
- gt_gff3_phases5.gff3
- gt_gff3_phases6.gff3
- gt_gff3_phases7.gff3
- gt_gff3_prob_1.gff3
- gt_gff3_prob_10.in
- gt_gff3_prob_10.out
- gt_gff3_prob_11.in
- gt_gff3_prob_11.out
- gt_gff3_prob_12.gff3
- gt_gff3_prob_13.gff3
- gt_gff3_prob_2.in
- gt_gff3_prob_2.out
- gt_gff3_prob_3.gff3
- gt_gff3_prob_4.gff3
- gt_gff3_prob_5.in
- gt_gff3_prob_5.out
- gt_gff3_prob_6.in
- gt_gff3_prob_7.in
- gt_gff3_prob_7.sorted
- gt_gff3_prob_7.unsorted
- gt_gff3_prob_8.in
- gt_gff3_prob_8.out
- gt_gff3_prob_9.in
- gt_gff3_prob_9.out
- gt_gff3_range_check.gff3
- gt_gff3_range_check2.gff3
- gt_gff3_range_check3.gff3
- gt_gff3_test_1.in
- gt_gff3_test_1.out
- gt_gff3_test_10.gff3
- gt_gff3_test_11.gff3
- gt_gff3_test_12.gff3
- gt_gff3_test_13.gff3
- gt_gff3_test_14.gff3
- gt_gff3_test_15.gff3
- gt_gff3_test_15.out
- gt_gff3_test_16.gff3
- gt_gff3_test_17.gff3
- gt_gff3_test_18.gff3
- gt_gff3_test_19.gff3
- gt_gff3_test_2.gff3
- gt_gff3_test_20.gff3
- gt_gff3_test_21.gff3
- gt_gff3_test_22.gff3
- gt_gff3_test_23.gff3
- gt_gff3_test_24.gff3
- gt_gff3_test_25.gff3
- gt_gff3_test_25.out
- gt_gff3_test_26.gff3
- gt_gff3_test_27.gff3
- gt_gff3_test_3.gff3
- gt_gff3_test_4.gff3
- gt_gff3_test_5.gff3
- gt_gff3_test_6.gff3
- gt_gff3_test_7.gff3
- gt_gff3_test_8.gff3
- gt_gff3_test_9.gff3
- gt_gff3_undefined_range.gff3
- gt_gff3_undefined_range_parent.gff3
- gt_gff3_undefined_range_tidy.gff3
- gt_gff3_whitespace_problem.gff3
- gt_gtf_to_gff3_test.gff3
- gt_gtf_to_gff3_test.gtf
- gt_gtf_to_gff3_test_fail_no_flank.gtf
- gt_gtf_to_gff3_test_inconsistent_strand1.gtf
- gt_gtf_to_gff3_test_inconsistent_strand2.gtf
- gt_gtf_to_gff3_test_stop_codon_in_cds.gff3
- gt_gtf_to_gff3_test_stop_codon_in_cds.gtf
- gt_gtf_to_gff3_test_stop_codon_in_cds2.gff3
- gt_gtf_to_gff3_test_stop_codon_in_cds2.gtf
- gt_linspace_align_affine_test_1.fas
- gt_linspace_align_affine_test_2.fas
- gt_linspace_align_affine_test_3.fas
- gt_linspace_align_global_affine_special_cases.out
- gt_linspace_align_global_affine_test_1.out
- gt_linspace_align_global_affine_test_2.out
- gt_linspace_align_global_linear_special_cases.out
- gt_linspace_align_global_test_1.out
- gt_linspace_align_global_test_2.out
- gt_linspace_align_local_affine_special_cases.out
- gt_linspace_align_local_affine_test_1.out
- gt_linspace_align_local_linear_special_cases.out
- gt_linspace_align_local_test_1.out
- gt_linspace_align_local_test_2.out
- gt_linspace_align_local_test_3.out
- gt_linspace_align_special_cases_test_1.fas
- gt_linspace_align_special_cases_test_2.fas
- gt_linspace_align_test_1.fas
- gt_linspace_align_test_2.fas
- gt_linspace_align_test_3.fas
- gt_linspace_align_test_4.fas
- gt_loccheck_containment_fail.gff3
- gt_merge_prob_1.in1
- gt_merge_prob_1.in2
- gt_merge_prob_1.out
- gt_merge_prob_2.in1
- gt_merge_prob_2.in2
- gt_merge_prob_2.out
- gt_mmapandread_test_1.in
- gt_mmapandread_test_2.in
- gt_mmapandread_test_3.in
- gt_mmapandread_test_4.in
- gt_mutate_test_1.fas
- gt_mutate_test_1.out
- gt_mutate_test_2.fas
- gt_mutate_test_2.out
- gt_mutate_test_both.out
- gt_regioncov_test_1.out
- gt_regioncov_test_2.out
- gt_select_encode.out
- gt_select_test.out
- gt_select_test_contain.1000-8999
- gt_select_test_contain.1000-9000
- gt_select_test_contain.1001-9000
- gt_seqlensort_test.fas
- gt_seqlensort_test_sorted.fas
- gt_seqorder_test.fas
- gt_seqorder_test_revsort.fas
- gt_seqorder_test_sort.fas
- gt_seqorder_test_sorthdr.fas
- gt_seqorder_test_sortlength.fas
- gt_sequniq_rev_bug.fas
- gt_sequniq_rev_bug.out
- gt_sketch_multiline_without_parent.gff3
- gt_sketch_textwidth.gff3
- gt_sketch_textwidth_0.recmaps
- gt_sketch_textwidth_1.recmaps
- gt_sketch_textwidth_2.recmaps
- gt_splicesiteinfo_prob_1.gff3
- gt_splicesiteinfo_test_1.fas
- gt_splicesiteinfo_test_1.gff3
- gt_splicesiteinfo_test_1.out
- gt_splicesiteinfo_test_2.fas
- gt_splicesiteinfo_test_2.gff3
- gt_splicesiteinfo_test_2.out
- gt_splicesiteinfo_test_3.gff3
- gt_splicesiteinfo_test_4.fas
- gt_splicesiteinfo_test_4.gff3
- gt_splicesiteinfo_test_4.out
- gt_splicesiteinfo_test_5.fas
- gt_splicesiteinfo_test_5.gff3
- gt_splicesiteinfo_test_5.out
- gt_splicesiteinfo_test_6.gff3
- gt_splicesiteinfo_test_6.mapping
- gt_stat_cdslengthdistri.out
- gt_stat_exonnumberdistri_encode.out
- gt_stat_exonnumberdistri_standard.out
- gt_stat_source.out
- gt_stat_test_1.out
- gt_stat_test_2.out
- gt_stat_test_3.out
- gt_stat_test_4.out
- gt_stat_test_5.out
- gt_stat_test_6.out
- gt_translate.in
- gt_translate.out
- gt_uniq_test_1.gff3
- gt_uniq_test_1.out
- gt_uniq_test_2.gff3
- gt_uniq_test_2.out
- gt_uniq_test_3.gff3
- gt_uniq_test_3.out
- gt_uniq_test_4.gff3
- gt_uniq_test_4.out
- gt_uniq_test_5.gff3
- gt_uniq_test_5.out
- gt_uniq_test_6.gff3
- gt_uniq_test_6.out
- gt_view.sh
- gt_view_prob_1.gff3
- gt_view_prob_2.gff3
- header.gff3
- header_3_1_21.gff3
- identity_score_matrix
- illegal_is_circular_value.gff3
- illegal_uppercase_attribute.gff3
- inconsistent_sequence_ids.gff3
- interfeat_pseudo.gff3
- interfeat_pseudo.out
- invalidregex.XRF_abbr
- invalidtag.XRF_abbr
- is_circular_example.gff3
- is_circular_example_with_sequence_region.gff3
- linesort_test_1.gff3
- linesort_test_1.out
- linesort_test_2.gff3
- linesort_test_2.out
- linesort_test_3.gff3
- linesort_test_3.out
- lua_aaseq.fas
- lua_dnaseq.fas
- marker.fas
- marker.out
- match_part_gap.gff3
- matchtool_blast.db
- matchtool_blast.match
- matchtool_blast.match.bz2
- matchtool_blast.match.gz
- matchtool_blast.out
- matchtool_blast_corrupt.match
- matchtool_blast_empty.match
- matchtool_blast_empty.out
- matchtool_blast_neg.match
- matchtool_blast_too_few.match
- matchtool_blast_too_many.match
- matchtool_blastalln.out
- matchtool_blastallp.out
- matchtool_blastn.db
- matchtool_blastn.out
- matchtool_blastn.query
- matchtool_blastp.db
- matchtool_blastp.out
- matchtool_blastp.query
- matchtool_open.match
- matchtool_open.match.bz2
- matchtool_open.match.gz
- matchtool_open.out
- matchtool_open_corrupt.match
- matchtool_open_empty.match
- matchtool_open_empty.out
- matchtool_open_neg.match
- matchtool_open_too_few.match
- matchtool_open_too_many.match
- matchtool_see-ext.match
- md5_seqid_missing_seqid.gff3
- md5_seqid_too_short.gff3
- md5_seqid_wrong_separator.gff3
- merge_with_seq.gff3
- mergefeat.gff3
- mergefeat.out
- mergefeat_no_merge.gff3
- meta_directives.gff3
- mini_peptide_repeats.fas
- minimal_fasta.gff3
- minimal_fasta_without_directive.gff3
- missing_gff3_header.gff3
- missingabbr.XRF_abbr
- multi_feature_different_sequence_id.gff3
- multi_feature_multi.gff3
- multi_feature_orphan_fail.gff3
- multi_feature_orphan_succ.gff3
- multi_feature_simple.gff3
- multi_feature_simple_reverted.gff3
- multi_feature_undefined_parent.gff3
- multi_feature_with_different_parent_1.gff3
- multi_feature_with_different_parent_1_tidy.gff3
- multi_feature_with_different_parent_2.gff3
- multi_feature_with_different_parent_2_tidy.gff3
- multiple_header_lines.gff3
- multiple_top_level_parents.gff3
- not_sorted.gff3
- nowildcardatend.fna
- nowildcardatend_rev.fna
- order_sketch_out.txt
- orphaned_parent.gff3
- png_devel_1.gff3
- png_devel_10.gff3
- png_devel_11.gff3
- png_devel_12.gff3
- png_devel_2.gff3
- png_devel_3.gff3
- png_devel_4.gff3
- png_devel_5.gff3
- png_devel_6.gff3
- png_devel_7.gff3
- png_devel_8.gff3
- png_devel_9.gff3
- png_prob_1.gff3
- png_prob_2.gff3
- png_prob_3.gff3
- png_prob_4.gff3
- png_prob_5.gff3
- png_test_1.gff3
- png_test_3.gff3
- problematic.fas
- pseudo_feature_minimal.gff3
- Q1.gz
- query-fwd.match
- query-rev.match
- Query1
- Query2
- Query3
- Random-Small.embl
- Random-Small.fna
- Random-Small.gbk
- Random.embl
- Random.fna
- Random.gbk
- Random.magicmatch
- Random159.embl
- Random159.fna
- Random159.gbk
- Random160.embl
- Random160.fna
- Random160.gbk
- Random80.fna
- RandomN.embl
- RandomN.fna
- RandomN.gbk
- RandomN.magicmatch
- rcr_testreads.fq
- rcr_testreads_on_seq.bam
- rcr_testreads_on_seq.bam.bai
- rcr_testreads_on_seq.sam
- rcr_testseq.fa
- rcr_testseq.fa.fai
- Reads1.fna
- Reads2-spmitv.txt
- Reads2.fna
- Reads3.fna
- Reference1
- Reference2
- regionmapping_1.lua
- regionmapping_2.lua
- regionmapping_3.lua
- regionmapping_4.lua
- regionmapping_5.lua
- regionmapping_6.lua
- Repfind-example.fna
- resetsource.gff3
- resetsource.out
- retain_1.gff3
- retain_2.gff3
- retain_both.gff3
- retainids.gff3
- reverse_feature_order.gff3
- reverse_feature_order.out
- reverse_feature_order_multiple_parents.gff3
- reverse_feature_order_multiple_parents.out
- reverse_standard_gene_as_tree.gff3
- revision_numbers.gff3
- revision_numbers.out
- sain.fna
- Scaffold_102.fa
- Scaffold_102.gff3
- Scaffold_102.joined.out
- Scaffold_102.out
- script_example.out
- script_filter_output.txt
- see-ext-ani-at1MB-U8.txt
- see-ext-at1MB-400-al-from-dtrace.matches
- see-ext-at1MB-400-cigar.matches
- see-ext-at1MB-400-cigarX.matches
- see-ext-at1MB-400-dtrace.matches
- see-ext-at1MB-400-evalue-bitscore.matches
- see-ext-at1MB-400-seqdesc.matches
- see-ext-at1MB-400-seqlength.matches
- see-ext-at1MB-400-trace.matches
- see-ext-at1MB-500-al.matches
- see-ext-at1MB-500-alignment-seed_in_algn.matches
- see-ext-at1MB-500-failed_seed.matches
- see-ext-at1MB-Atinsert100-evalue-bitscore-cigar-seqlength.matches
- see-ext-at1MB-Atinsert100-evalue-bitscore-cigarX-seqlength.matches
- see-ext-at1MB-maxmat250.matches
- see-ext-at1MB-mincoverage200-tabsep.matches
- see-ext-at1MB-U8-200-al-from-dtrace.matches
- see-ext-at1MB-u8-failed_seed-evalue.matches
- see-ext-at1MB-u8-maxmat30.matches
- see-ext-at1MB-u8.matches
- see-ext-at1MB.matches
- see-ext-fastq_long-u8.matches
- see-ext-fastq_long.matches
- see-ext-paired-u8.matches
- see-ext-paired.matches
- see-ext-U8-evalue-bitscore.matches
- seedextend1.out.gz
- seedextend2.out.gz
- seedextend3.out
- self_referential.gff3
- seqfilter_prot_wildcard.fas
- seqfilter_prot_wildcard_no_wildcards.fas
- sequence_region_1.gff3
- sequence_region_2.gff3
- sequence_region_joined.gff3
- sequence_region_negative_end.gff3
- sequence_region_negative_start.gff3
- shorten_desc.clipped.fas
- shorten_desc.embl
- shorten_desc.fas
- shorten_desc.gbk
- shorthand.XRF_abbr
- simple_orphan.gff3
- Small.embl
- Small.fna
- Small.gbk
- small_poly.fas
- Smalldup.fna
- solid_color_reads.fastq
- splice_site_prob.gff3
- splice_site_prob.out
- Splintoptions
- standard_fasta_example.fas
- standard_fasta_example.gff3
- standard_fasta_example_only_annotation.gff3
- standard_fasta_example_rejoined.gff3
- standard_fasta_example_with_id.gff3
- standard_fasta_example_with_id.out
- standard_gene_as_dag.gff3
- standard_gene_as_dag_sorted.gff3
- standard_gene_as_tree.blocks
- standard_gene_as_tree.gff3
- standard_gene_as_tree.header
- standard_gene_as_tree.hotspots
- standard_gene_as_tree.recmaps
- standard_gene_as_tree.types
- standard_gene_simple.gff3
- standard_gene_with_introns_as_tree.gff3
- sw100K1.fsa
- sw100K1.magicmatch
- sw100K2.fsa
- sw100K2.magicmatch
- target_attribute_swapped_range.gff3
- target_attribute_without_strand.gff3
- terminator_separation.gff3
- test.XRF_abbr
- test1.fasta
- test1.fastq
- test10_multiline.fastq
- test2_wrong_begin.fastq
- test3_different_seqnames.fastq
- test4_different_seqlengths.fastq
- test5_tricky.fastq
- test6_premature_end.fastq
- test7_empty_seq.fastq
- test9_uneven_length.fastq
- test_1_multiset.txt
- test_1_result.txt
- test_1_text.txt
- test_2_multiset.txt
- test_2_result.txt
- test_2_text.txt
- test_3_multiset.txt
- test_3_result.txt
- test_3_text.txt
- testspec.lua
- testspec_fi.lua
- trackname1.out
- trackname1.style
- transcript.gff3
- transcript.png
- transcript.style
- transient_edges_bug.gff3
- trembl-difflenkey.faa
- trembl-emptykey.faa
- trembl-eqlen.faa
- trembl-keys.txt
- trembl-wrongkey.txt
- trembl.faa
- trkeys-result.txt
- trkeys.txt
- tRNA.dos.fas
- trna_glutamine.embl
- trna_glutamine.fna
- trna_glutamine.gbk
- trna_glutamine.out
- TTT-small-wrongchar.embl
- TTT-small-wrongchar.fna
- TTT-small-wrongchar.gbk
- TTT-small.embl
- TTT-small.fna
- TTT-small.gbk
- TTTN.fna
- two_fasta_seqs.gff3
- two_fasta_seqs_without_sequence_regions.gff3
- U89959_cds.fas
- U89959_cds.gff3
- U89959_cds_1.fas
- U89959_cds_10.fas
- U89959_cds_11.fas
- U89959_cds_12.fas
- U89959_cds_13.fas
- U89959_cds_14.fas
- U89959_cds_16.fas
- U89959_cds_2.fas
- U89959_cds_21.fas
- U89959_cds_22.fas
- U89959_cds_23.fas
- U89959_cds_24.fas
- U89959_cds_25.fas
- U89959_cds_3.fas
- U89959_cds_4.fas
- U89959_cds_5.fas
- U89959_cds_6.fas
- U89959_cds_9.fas
- U89959_csas.gff3
- U89959_csas.gff3md5
- U89959_csas.gff3md5old
- U89959_ests.checklist
- U89959_ests.checklist_uniq
- U89959_ests.fas
- U89959_ests.magicmatch
- U89959_ests_gi_8690080_soft_masked.fas
- U89959_ests_gi_8690080_unmasked.checklist
- U89959_ests_no_wildcards.fas
- U89959_ests_unique.fas
- U89959_genomic.fas
- U89959_genomic.magicmatch
- U89959_ginums.corrupt
- U89959_ginums.out
- U89959_ginums.txt
- U89959_sas.gff3
- U89959_sas.gff3md5
- U89959_sas.gff3md5old
- U89959_sas.minus_targets
- undefined_parent.gff3
- unknown_meta_directive.gff3
- unknown_meta_directive_without_argument.gff3
- unsorted_gff3_file.txt
- uppercase_attributes.gff3
- Verysmall.embl
- Verysmall.fna
- Verysmall.gbk
- wildcardatend.fna
- wildcardatend_rev.fna
blosum62.c @HEAD — raw · history · blame
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 | #include <limits.h> int main(int argc, char *argv[]) { int score_matrix[CHAR_MAX][CHAR_MAX] = {{0}}; score_matrix['L']['L'] = 4; score_matrix['L']['V'] = 1; score_matrix['L']['I'] = 2; score_matrix['L']['F'] = 0; score_matrix['L']['K'] = -2; score_matrix['L']['R'] = -2; score_matrix['L']['E'] = -3; score_matrix['L']['D'] = -4; score_matrix['L']['A'] = -1; score_matrix['L']['G'] = -4; score_matrix['L']['S'] = -2; score_matrix['L']['T'] = -1; score_matrix['L']['N'] = -3; score_matrix['L']['Q'] = -2; score_matrix['L']['Y'] = -1; score_matrix['L']['W'] = -2; score_matrix['L']['P'] = -3; score_matrix['L']['H'] = -3; score_matrix['L']['M'] = 2; score_matrix['L']['C'] = -1; score_matrix['L']['X'] = -1; score_matrix['V']['L'] = 1; score_matrix['V']['V'] = 4; score_matrix['V']['I'] = 3; score_matrix['V']['F'] = -1; score_matrix['V']['K'] = -2; score_matrix['V']['R'] = -3; score_matrix['V']['E'] = -2; score_matrix['V']['D'] = -3; score_matrix['V']['A'] = 0; score_matrix['V']['G'] = -3; score_matrix['V']['S'] = -2; score_matrix['V']['T'] = 0; score_matrix['V']['N'] = -3; score_matrix['V']['Q'] = -2; score_matrix['V']['Y'] = -1; score_matrix['V']['W'] = -3; score_matrix['V']['P'] = -2; score_matrix['V']['H'] = -3; score_matrix['V']['M'] = 1; score_matrix['V']['C'] = -1; score_matrix['V']['X'] = -1; score_matrix['I']['L'] = 2; score_matrix['I']['V'] = 3; score_matrix['I']['I'] = 4; score_matrix['I']['F'] = 0; score_matrix['I']['K'] = -3; score_matrix['I']['R'] = -3; score_matrix['I']['E'] = -3; score_matrix['I']['D'] = -3; score_matrix['I']['A'] = -1; score_matrix['I']['G'] = -4; score_matrix['I']['S'] = -2; score_matrix['I']['T'] = -1; score_matrix['I']['N'] = -3; score_matrix['I']['Q'] = -3; score_matrix['I']['Y'] = -1; score_matrix['I']['W'] = -3; score_matrix['I']['P'] = -3; score_matrix['I']['H'] = -3; score_matrix['I']['M'] = 1; score_matrix['I']['C'] = -1; score_matrix['I']['X'] = -1; score_matrix['F']['L'] = 0; score_matrix['F']['V'] = -1; score_matrix['F']['I'] = 0; score_matrix['F']['F'] = 6; score_matrix['F']['K'] = -3; score_matrix['F']['R'] = -3; score_matrix['F']['E'] = -3; score_matrix['F']['D'] = -3; score_matrix['F']['A'] = -2; score_matrix['F']['G'] = -3; score_matrix['F']['S'] = -2; score_matrix['F']['T'] = -2; score_matrix['F']['N'] = -3; score_matrix['F']['Q'] = -3; score_matrix['F']['Y'] = 3; score_matrix['F']['W'] = 1; score_matrix['F']['P'] = -4; score_matrix['F']['H'] = -1; score_matrix['F']['M'] = 0; score_matrix['F']['C'] = -2; score_matrix['F']['X'] = -1; score_matrix['K']['L'] = -2; score_matrix['K']['V'] = -2; score_matrix['K']['I'] = -3; score_matrix['K']['F'] = -3; score_matrix['K']['K'] = 5; score_matrix['K']['R'] = 2; score_matrix['K']['E'] = 1; score_matrix['K']['D'] = -1; score_matrix['K']['A'] = -1; score_matrix['K']['G'] = -2; score_matrix['K']['S'] = 0; score_matrix['K']['T'] = -1; score_matrix['K']['N'] = 0; score_matrix['K']['Q'] = 1; score_matrix['K']['Y'] = -2; score_matrix['K']['W'] = -3; score_matrix['K']['P'] = -1; score_matrix['K']['H'] = -1; score_matrix['K']['M'] = -1; score_matrix['K']['C'] = -3; score_matrix['K']['X'] = -1; score_matrix['R']['L'] = -2; score_matrix['R']['V'] = -3; score_matrix['R']['I'] = -3; score_matrix['R']['F'] = -3; score_matrix['R']['K'] = 2; score_matrix['R']['R'] = 5; score_matrix['R']['E'] = 0; score_matrix['R']['D'] = -2; score_matrix['R']['A'] = -1; score_matrix['R']['G'] = -2; score_matrix['R']['S'] = -1; score_matrix['R']['T'] = -1; score_matrix['R']['N'] = 0; score_matrix['R']['Q'] = 1; score_matrix['R']['Y'] = -2; score_matrix['R']['W'] = -3; score_matrix['R']['P'] = -2; score_matrix['R']['H'] = 0; score_matrix['R']['M'] = -1; score_matrix['R']['C'] = -3; score_matrix['R']['X'] = -1; score_matrix['E']['L'] = -3; score_matrix['E']['V'] = -2; score_matrix['E']['I'] = -3; score_matrix['E']['F'] = -3; score_matrix['E']['K'] = 1; score_matrix['E']['R'] = 0; score_matrix['E']['E'] = 5; score_matrix['E']['D'] = 2; score_matrix['E']['A'] = -1; score_matrix['E']['G'] = -2; score_matrix['E']['S'] = 0; score_matrix['E']['T'] = -1; score_matrix['E']['N'] = 0; score_matrix['E']['Q'] = 2; score_matrix['E']['Y'] = -2; score_matrix['E']['W'] = -3; score_matrix['E']['P'] = -1; score_matrix['E']['H'] = 0; score_matrix['E']['M'] = -2; score_matrix['E']['C'] = -4; score_matrix['E']['X'] = -1; score_matrix['D']['L'] = -4; score_matrix['D']['V'] = -3; score_matrix['D']['I'] = -3; score_matrix['D']['F'] = -3; score_matrix['D']['K'] = -1; score_matrix['D']['R'] = -2; score_matrix['D']['E'] = 2; score_matrix['D']['D'] = 6; score_matrix['D']['A'] = -2; score_matrix['D']['G'] = -1; score_matrix['D']['S'] = 0; score_matrix['D']['T'] = -1; score_matrix['D']['N'] = 1; score_matrix['D']['Q'] = 0; score_matrix['D']['Y'] = -3; score_matrix['D']['W'] = -4; score_matrix['D']['P'] = -1; score_matrix['D']['H'] = -1; score_matrix['D']['M'] = -3; score_matrix['D']['C'] = -3; score_matrix['D']['X'] = -1; score_matrix['A']['L'] = -1; score_matrix['A']['V'] = 0; score_matrix['A']['I'] = -1; score_matrix['A']['F'] = -2; score_matrix['A']['K'] = -1; score_matrix['A']['R'] = -1; score_matrix['A']['E'] = -1; score_matrix['A']['D'] = -2; score_matrix['A']['A'] = 4; score_matrix['A']['G'] = 0; score_matrix['A']['S'] = 1; score_matrix['A']['T'] = 0; score_matrix['A']['N'] = -2; score_matrix['A']['Q'] = -1; score_matrix['A']['Y'] = -2; score_matrix['A']['W'] = -3; score_matrix['A']['P'] = -1; score_matrix['A']['H'] = -2; score_matrix['A']['M'] = -1; score_matrix['A']['C'] = 0; score_matrix['A']['X'] = 0; score_matrix['G']['L'] = -4; score_matrix['G']['V'] = -3; score_matrix['G']['I'] = -4; score_matrix['G']['F'] = -3; score_matrix['G']['K'] = -2; score_matrix['G']['R'] = -2; score_matrix['G']['E'] = -2; score_matrix['G']['D'] = -1; score_matrix['G']['A'] = 0; score_matrix['G']['G'] = 6; score_matrix['G']['S'] = 0; score_matrix['G']['T'] = -2; score_matrix['G']['N'] = 0; score_matrix['G']['Q'] = -2; score_matrix['G']['Y'] = -3; score_matrix['G']['W'] = -2; score_matrix['G']['P'] = -2; score_matrix['G']['H'] = -2; score_matrix['G']['M'] = -3; score_matrix['G']['C'] = -3; score_matrix['G']['X'] = -1; score_matrix['S']['L'] = -2; score_matrix['S']['V'] = -2; score_matrix['S']['I'] = -2; score_matrix['S']['F'] = -2; score_matrix['S']['K'] = 0; score_matrix['S']['R'] = -1; score_matrix['S']['E'] = 0; score_matrix['S']['D'] = 0; score_matrix['S']['A'] = 1; score_matrix['S']['G'] = 0; score_matrix['S']['S'] = 4; score_matrix['S']['T'] = 1; score_matrix['S']['N'] = 1; score_matrix['S']['Q'] = 0; score_matrix['S']['Y'] = -2; score_matrix['S']['W'] = -3; score_matrix['S']['P'] = -1; score_matrix['S']['H'] = -1; score_matrix['S']['M'] = -1; score_matrix['S']['C'] = -1; score_matrix['S']['X'] = 0; score_matrix['T']['L'] = -1; score_matrix['T']['V'] = 0; score_matrix['T']['I'] = -1; score_matrix['T']['F'] = -2; score_matrix['T']['K'] = -1; score_matrix['T']['R'] = -1; score_matrix['T']['E'] = -1; score_matrix['T']['D'] = -1; score_matrix['T']['A'] = 0; score_matrix['T']['G'] = -2; score_matrix['T']['S'] = 1; score_matrix['T']['T'] = 5; score_matrix['T']['N'] = 0; score_matrix['T']['Q'] = -1; score_matrix['T']['Y'] = -2; score_matrix['T']['W'] = -2; score_matrix['T']['P'] = -1; score_matrix['T']['H'] = -2; score_matrix['T']['M'] = -1; score_matrix['T']['C'] = -1; score_matrix['T']['X'] = 0; score_matrix['N']['L'] = -3; score_matrix['N']['V'] = -3; score_matrix['N']['I'] = -3; score_matrix['N']['F'] = -3; score_matrix['N']['K'] = 0; score_matrix['N']['R'] = 0; score_matrix['N']['E'] = 0; score_matrix['N']['D'] = 1; score_matrix['N']['A'] = -2; score_matrix['N']['G'] = 0; score_matrix['N']['S'] = 1; score_matrix['N']['T'] = 0; score_matrix['N']['N'] = 6; score_matrix['N']['Q'] = 0; score_matrix['N']['Y'] = -2; score_matrix['N']['W'] = -4; score_matrix['N']['P'] = -2; score_matrix['N']['H'] = 1; score_matrix['N']['M'] = -2; score_matrix['N']['C'] = -3; score_matrix['N']['X'] = -1; score_matrix['Q']['L'] = -2; score_matrix['Q']['V'] = -2; score_matrix['Q']['I'] = -3; score_matrix['Q']['F'] = -3; score_matrix['Q']['K'] = 1; score_matrix['Q']['R'] = 1; score_matrix['Q']['E'] = 2; score_matrix['Q']['D'] = 0; score_matrix['Q']['A'] = -1; score_matrix['Q']['G'] = -2; score_matrix['Q']['S'] = 0; score_matrix['Q']['T'] = -1; score_matrix['Q']['N'] = 0; score_matrix['Q']['Q'] = 5; score_matrix['Q']['Y'] = -1; score_matrix['Q']['W'] = -2; score_matrix['Q']['P'] = -1; score_matrix['Q']['H'] = 0; score_matrix['Q']['M'] = 0; score_matrix['Q']['C'] = -3; score_matrix['Q']['X'] = -1; score_matrix['Y']['L'] = -1; score_matrix['Y']['V'] = -1; score_matrix['Y']['I'] = -1; score_matrix['Y']['F'] = 3; score_matrix['Y']['K'] = -2; score_matrix['Y']['R'] = -2; score_matrix['Y']['E'] = -2; score_matrix['Y']['D'] = -3; score_matrix['Y']['A'] = -2; score_matrix['Y']['G'] = -3; score_matrix['Y']['S'] = -2; score_matrix['Y']['T'] = -2; score_matrix['Y']['N'] = -2; score_matrix['Y']['Q'] = -1; score_matrix['Y']['Y'] = 7; score_matrix['Y']['W'] = 2; score_matrix['Y']['P'] = -3; score_matrix['Y']['H'] = 2; score_matrix['Y']['M'] = -1; score_matrix['Y']['C'] = -2; score_matrix['Y']['X'] = -1; score_matrix['W']['L'] = -2; score_matrix['W']['V'] = -3; score_matrix['W']['I'] = -3; score_matrix['W']['F'] = 1; score_matrix['W']['K'] = -3; score_matrix['W']['R'] = -3; score_matrix['W']['E'] = -3; score_matrix['W']['D'] = -4; score_matrix['W']['A'] = -3; score_matrix['W']['G'] = -2; score_matrix['W']['S'] = -3; score_matrix['W']['T'] = -2; score_matrix['W']['N'] = -4; score_matrix['W']['Q'] = -2; score_matrix['W']['Y'] = 2; score_matrix['W']['W'] = 11; score_matrix['W']['P'] = -4; score_matrix['W']['H'] = -2; score_matrix['W']['M'] = -1; score_matrix['W']['C'] = -2; score_matrix['W']['X'] = -2; score_matrix['P']['L'] = -3; score_matrix['P']['V'] = -2; score_matrix['P']['I'] = -3; score_matrix['P']['F'] = -4; score_matrix['P']['K'] = -1; score_matrix['P']['R'] = -2; score_matrix['P']['E'] = -1; score_matrix['P']['D'] = -1; score_matrix['P']['A'] = -1; score_matrix['P']['G'] = -2; score_matrix['P']['S'] = -1; score_matrix['P']['T'] = -1; score_matrix['P']['N'] = -2; score_matrix['P']['Q'] = -1; score_matrix['P']['Y'] = -3; score_matrix['P']['W'] = -4; score_matrix['P']['P'] = 7; score_matrix['P']['H'] = -2; score_matrix['P']['M'] = -2; score_matrix['P']['C'] = -3; score_matrix['P']['X'] = -2; score_matrix['H']['L'] = -3; score_matrix['H']['V'] = -3; score_matrix['H']['I'] = -3; score_matrix['H']['F'] = -1; score_matrix['H']['K'] = -1; score_matrix['H']['R'] = 0; score_matrix['H']['E'] = 0; score_matrix['H']['D'] = -1; score_matrix['H']['A'] = -2; score_matrix['H']['G'] = -2; score_matrix['H']['S'] = -1; score_matrix['H']['T'] = -2; score_matrix['H']['N'] = 1; score_matrix['H']['Q'] = 0; score_matrix['H']['Y'] = 2; score_matrix['H']['W'] = -2; score_matrix['H']['P'] = -2; score_matrix['H']['H'] = 8; score_matrix['H']['M'] = -2; score_matrix['H']['C'] = -3; score_matrix['H']['X'] = -1; score_matrix['M']['L'] = 2; score_matrix['M']['V'] = 1; score_matrix['M']['I'] = 1; score_matrix['M']['F'] = 0; score_matrix['M']['K'] = -1; score_matrix['M']['R'] = -1; score_matrix['M']['E'] = -2; score_matrix['M']['D'] = -3; score_matrix['M']['A'] = -1; score_matrix['M']['G'] = -3; score_matrix['M']['S'] = -1; score_matrix['M']['T'] = -1; score_matrix['M']['N'] = -2; score_matrix['M']['Q'] = 0; score_matrix['M']['Y'] = -1; score_matrix['M']['W'] = -1; score_matrix['M']['P'] = -2; score_matrix['M']['H'] = -2; score_matrix['M']['M'] = 5; score_matrix['M']['C'] = -1; score_matrix['M']['X'] = -1; score_matrix['C']['L'] = -1; score_matrix['C']['V'] = -1; score_matrix['C']['I'] = -1; score_matrix['C']['F'] = -2; score_matrix['C']['K'] = -3; score_matrix['C']['R'] = -3; score_matrix['C']['E'] = -4; score_matrix['C']['D'] = -3; score_matrix['C']['A'] = 0; score_matrix['C']['G'] = -3; score_matrix['C']['S'] = -1; score_matrix['C']['T'] = -1; score_matrix['C']['N'] = -3; score_matrix['C']['Q'] = -3; score_matrix['C']['Y'] = -2; score_matrix['C']['W'] = -2; score_matrix['C']['P'] = -3; score_matrix['C']['H'] = -3; score_matrix['C']['M'] = -1; score_matrix['C']['C'] = 9; score_matrix['C']['X'] = -2; score_matrix['X']['L'] = -1; score_matrix['X']['V'] = -1; score_matrix['X']['I'] = -1; score_matrix['X']['F'] = -1; score_matrix['X']['K'] = -1; score_matrix['X']['R'] = -1; score_matrix['X']['E'] = -1; score_matrix['X']['D'] = -1; score_matrix['X']['A'] = 0; score_matrix['X']['G'] = -1; score_matrix['X']['S'] = 0; score_matrix['X']['T'] = 0; score_matrix['X']['N'] = -1; score_matrix['X']['Q'] = -1; score_matrix['X']['Y'] = -1; score_matrix['X']['W'] = -2; score_matrix['X']['P'] = -2; score_matrix['X']['H'] = -1; score_matrix['X']['M'] = -1; score_matrix['X']['C'] = -2; score_matrix['X']['X'] = -1; return 0; } |