RubyGems - bio-polymarker - Versions diffs - 1.3.2 - Mend

bio-polymarker 1.3.2

Files changed (177) hide show

checksums.yaml +7 -0
data/.travis.yml +24 -0
data/Gemfile +23 -0
data/README.md +205 -0
data/Rakefile +61 -0
data/SECURITY.md +16 -0
data/VERSION +1 -0
data/bin/bfr.rb +128 -0
data/bin/blast_triads.rb +166 -0
data/bin/blast_triads_promoters.rb +192 -0
data/bin/count_variations.rb +36 -0
data/bin/filter_blat_by_target_coverage.rb +69 -0
data/bin/filter_exonerate_by_identity.rb +38 -0
data/bin/find_best_blat_hit.rb +33 -0
data/bin/find_best_exonerate.rb +17 -0
data/bin/get_longest_hsp_blastx_triads.rb +66 -0
data/bin/hexaploid_primers.rb +168 -0
data/bin/homokaryot_primers.rb +183 -0
data/bin/mafft_triads.rb +120 -0
data/bin/mafft_triads_promoters.rb +403 -0
data/bin/map_markers_to_contigs.rb +66 -0
data/bin/marker_to_vcf.rb +241 -0
data/bin/markers_in_region.rb +42 -0
data/bin/mask_triads.rb +169 -0
data/bin/polymarker.rb +410 -0
data/bin/polymarker_capillary.rb +443 -0
data/bin/polymarker_deletions.rb +350 -0
data/bin/snp_position_to_polymarker.rb +101 -0
data/bin/snps_between_bams.rb +107 -0
data/bin/tag_stats.rb +75 -0
data/bin/vcfLineToTable.rb +56 -0
data/bin/vcfToPolyMarker.rb +82 -0
data/bio-polymarker.gemspec +227 -0
data/conf/defaults.rb +1 -0
data/conf/primer3_config/dangle.dh +128 -0
data/conf/primer3_config/dangle.ds +128 -0
data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
data/conf/primer3_config/interpretations/loops_i.dh +34 -0
data/conf/primer3_config/interpretations/loops_i.ds +31 -0
data/conf/primer3_config/interpretations/stack_i.dh +257 -0
data/conf/primer3_config/interpretations/stack_i.ds +256 -0
data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
data/conf/primer3_config/loops.dh +30 -0
data/conf/primer3_config/loops.ds +30 -0
data/conf/primer3_config/stack.dh +256 -0
data/conf/primer3_config/stack.ds +256 -0
data/conf/primer3_config/stackmm.dh +256 -0
data/conf/primer3_config/stackmm.ds +256 -0
data/conf/primer3_config/tetraloop.dh +77 -0
data/conf/primer3_config/tetraloop.ds +77 -0
data/conf/primer3_config/triloop.dh +16 -0
data/conf/primer3_config/triloop.ds +16 -0
data/conf/primer3_config/tstack.dh +256 -0
data/conf/primer3_config/tstack2.dh +256 -0
data/conf/primer3_config/tstack2.ds +256 -0
data/conf/primer3_config/tstack_tm_inf.ds +256 -0
data/lib/bio/BFRTools.rb +465 -0
data/lib/bio/BIOExtensions.rb +153 -0
data/lib/bio/PolyploidTools/ChromosomeArm.rb +63 -0
data/lib/bio/PolyploidTools/ExonContainer.rb +245 -0
data/lib/bio/PolyploidTools/Marker.rb +175 -0
data/lib/bio/PolyploidTools/Mask.rb +116 -0
data/lib/bio/PolyploidTools/NoSNPSequence.rb +292 -0
data/lib/bio/PolyploidTools/PrimerRegion.rb +30 -0
data/lib/bio/PolyploidTools/SNP.rb +804 -0
data/lib/bio/PolyploidTools/SNPMutant.rb +86 -0
data/lib/bio/PolyploidTools/SNPSequence.rb +55 -0
data/lib/bio/db/blast.rb +114 -0
data/lib/bio/db/exonerate.rb +333 -0
data/lib/bio/db/primer3.rb +820 -0
data/lib/bio-polymarker.rb +28 -0
data/test/data/7B_amplicon_test.fa +12 -0
data/test/data/7B_amplicon_test.fa.fai +1 -0
data/test/data/7B_amplicon_test_reference.fa +110 -0
data/test/data/7B_amplicon_test_reference.fa.fai +3 -0
data/test/data/7B_marker_test.txt +1 -0
data/test/data/BS00068396_51.fa +2 -0
data/test/data/BS00068396_51_blast.tab +4 -0
data/test/data/BS00068396_51_contigs.aln +1412 -0
data/test/data/BS00068396_51_contigs.dnd +7 -0
data/test/data/BS00068396_51_contigs.fa +8 -0
data/test/data/BS00068396_51_contigs.fa.fai +4 -0
data/test/data/BS00068396_51_contigs.fa.nhr +0 -0
data/test/data/BS00068396_51_contigs.fa.nin +0 -0
data/test/data/BS00068396_51_contigs.fa.nsq +0 -0
data/test/data/BS00068396_51_contigs.nhr +0 -0
data/test/data/BS00068396_51_contigs.nin +0 -0
data/test/data/BS00068396_51_contigs.nsq +0 -0
data/test/data/BS00068396_51_exonerate.tab +6 -0
data/test/data/BS00068396_51_for_polymarker.txt +1 -0
data/test/data/BS00068396_51_genes.txt +14 -0
data/test/data/IWGSC_CSS_1AL_scaff_1455974.fa +112 -0
data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa +2304 -0
data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai +11 -0
data/test/data/LIB1716.bam +0 -0
data/test/data/LIB1716.bam.bai +0 -0
data/test/data/LIB1719.bam +0 -0
data/test/data/LIB1719.bam.bai +0 -0
data/test/data/LIB1721.bam +0 -0
data/test/data/LIB1721.bam.bai +0 -0
data/test/data/LIB1722.bam +0 -0
data/test/data/LIB1722.bam.bai +0 -0
data/test/data/PST130_7067.csv +1 -0
data/test/data/PST130_7067.fa +2 -0
data/test/data/PST130_7067.fa.fai +1 -0
data/test/data/PST130_7067.fa.ndb +0 -0
data/test/data/PST130_7067.fa.nhr +0 -0
data/test/data/PST130_7067.fa.nin +0 -0
data/test/data/PST130_7067.fa.not +0 -0
data/test/data/PST130_7067.fa.nsq +0 -0
data/test/data/PST130_7067.fa.ntf +0 -0
data/test/data/PST130_7067.fa.nto +0 -0
data/test/data/PST130_reverse_primer.csv +1 -0
data/test/data/S22380157.fa +16 -0
data/test/data/S22380157.fa.fai +1 -0
data/test/data/S22380157.vcf +67 -0
data/test/data/S58861868/LIB1716.bam +0 -0
data/test/data/S58861868/LIB1716.sam +651 -0
data/test/data/S58861868/LIB1719.bam +0 -0
data/test/data/S58861868/LIB1719.sam +805 -0
data/test/data/S58861868/LIB1721.bam +0 -0
data/test/data/S58861868/LIB1721.sam +1790 -0
data/test/data/S58861868/LIB1722.bam +0 -0
data/test/data/S58861868/LIB1722.sam +1271 -0
data/test/data/S58861868/S58861868.fa +16 -0
data/test/data/S58861868/S58861868.fa.fai +1 -0
data/test/data/S58861868/S58861868.vcf +76 -0
data/test/data/S58861868/header.txt +9 -0
data/test/data/S58861868/merged.bam +0 -0
data/test/data/S58861868/merged_reheader.bam +0 -0
data/test/data/S58861868/merged_reheader.bam.bai +0 -0
data/test/data/Test3Aspecific.csv +2 -0
data/test/data/Test3Aspecific_contigs.fa +6 -0
data/test/data/bfr_out_test.csv +5 -0
data/test/data/chr1A_C1145499T/chr1A_C1145499T.csv +1 -0
data/test/data/chr1A_G540414846C/chr1A_G540414846C.csv +1 -0
data/test/data/chr1A_G540414846C/chr1A_G540414846C.fa +2 -0
data/test/data/chr1A_T517634750C/chr1A_T517634750C.csv +1 -0
data/test/data/chr2D_C112180134A/chr2D_C112180134A.csv +1 -0
data/test/data/chr4D_C14473543T/chr4D_C14473543T.csv +1 -0
data/test/data/chr4D_C14473543T/chr4D_C14473543T.fa +2 -0
data/test/data/headerMergeed.txt +9 -0
data/test/data/headerS2238015 +1 -0
data/test/data/mergedLibs.bam +0 -0
data/test/data/mergedLibsReheader.bam +0 -0
data/test/data/mergedLibsSorted.bam +0 -0
data/test/data/mergedLibsSorted.bam.bai +0 -0
data/test/data/patological_cases5D.csv +1 -0
data/test/data/primer_3_input_header_test +5 -0
data/test/data/short_primer_design_test.csv +10 -0
data/test/data/some_tests/some_tests.csv +201 -0
data/test/data/test_from_mutant.csv +3 -0
data/test/data/test_iselect.csv +196 -0
data/test/data/test_iselect_reference.fa +1868 -0
data/test/data/test_iselect_reference.fa.fai +934 -0
data/test/data/test_primer3_error.csv +4 -0
data/test/data/test_primer3_error_contigs.fa +10 -0
data/test/test_bfr.rb +135 -0
data/test/test_blast.rb +47 -0
data/test/test_exon_container.rb +17 -0
data/test/test_exonearate.rb +48 -0
data/test/test_integration.rb +76 -0
data/test/test_snp_parsing.rb +121 -0
data/test/test_wrong_selection.sh +5 -0
metadata +356 -0

data/conf/primer3_config/interpretations/tstack_i.ds ADDED Viewed

@@ -0,0 +1,256 @@
+AA_AA inf
+AA_AC inf
+AA_AG inf
+AA_AT 63
+AA_CA inf
+AA_CC inf
+AA_CG inf
+AA_CT 70
+AA_GA inf
+AA_GC inf
+AA_GG inf
+AA_GT 58
+AA_TA 78
+AA_TC 40
+AA_TG 44
+AA_TT 0
+AC_AA inf
+AC_AC inf
+AC_AG 225
+AC_AT inf
+AC_CA inf
+AC_CC inf
+AC_CG 71
+AC_CT inf
+AC_GA inf
+AC_GC inf
+AC_GG 114
+AC_GT inf
+AC_TA 38
+AC_TC 5
+AC_TG 0
+AC_TT 17
+AG_AA inf
+AG_AC 107
+AG_AG inf
+AG_AT inf
+AG_CA inf
+AG_CC 60
+AG_CG inf
+AG_CT inf
+AG_GA inf
+AG_GC 155
+AG_GG inf
+AG_GT inf
+AG_TA 59
+AG_TC 0
+AG_TG 21
+AG_TT 87
+AT_AA 78
+AT_AC inf
+AT_AG inf
+AT_AT inf
+AT_CA 38
+AT_CC inf
+AT_CG inf
+AT_CT inf
+AT_GA 59
+AT_GC inf
+AT_GG inf
+AT_GT inf
+AT_TA 0
+AT_TC 63
+AT_TG 94
+AT_TT 65
+CA_AA inf
+CA_AC inf
+CA_AG inf
+CA_AT 59
+CA_CA inf
+CA_CC inf
+CA_CG inf
+CA_CT 13
+CA_GA 107
+CA_GC 59
+CA_GG 96
+CA_GT 0
+CA_TA inf
+CA_TC inf
+CA_TG inf
+CA_TT 12
+CC_AA inf
+CC_AC inf
+CC_AG 138
+CC_AT inf
+CC_CA inf
+CC_CC inf
+CC_CG 106
+CC_CT inf
+CC_GA 60
+CC_GC 51
+CC_GG 0
+CC_GT 80
+CC_TA inf
+CC_TC inf
+CC_TG 78
+CC_TT inf
+CG_AA inf
+CG_AC 59
+CG_AG inf
+CG_AT inf
+CG_CA inf
+CG_CC 51
+CG_CG inf
+CG_CT inf
+CG_GA 155
+CG_GC 0
+CG_GG 95
+CG_GT 90
+CG_TA inf
+CG_TC 106
+CG_TG inf
+CG_TT inf
+CT_AA 40
+CT_AC inf
+CT_AG inf
+CT_AT inf
+CT_CA 5
+CT_CC inf
+CT_CG inf
+CT_CT inf
+CT_GA 0
+CT_GC 106
+CT_GG 187
+CT_GT 169
+CT_TA 63
+CT_TC inf
+CT_TG inf
+CT_TT inf
+GA_AA inf
+GA_AC inf
+GA_AG inf
+GA_AT 47
+GA_CA 225
+GA_CC 138
+GA_CG 111
+GA_CT 0
+GA_GA inf
+GA_GC inf
+GA_GG inf
+GA_GT 27
+GA_TA inf
+GA_TC inf
+GA_TG inf
+GA_TT 98
+GC_AA inf
+GC_AC inf
+GC_AG 111
+GC_AT inf
+GC_CA 71
+GC_CC 106
+GC_CG 0
+GC_CT 135
+GC_GA inf
+GC_GC inf
+GC_GG 192
+GC_GT inf
+GC_TA inf
+GC_TC inf
+GC_TG 161
+GC_TT inf
+GG_AA inf
+GG_AC 96
+GG_AG inf
+GG_AT inf
+GG_CA 114
+GG_CC 0
+GG_CG 192
+GG_CT 159
+GG_GA inf
+GG_GC 95
+GG_GG inf
+GG_GT inf
+GG_TA inf
+GG_TC 187
+GG_TG inf
+GG_TT inf
+GT_AA 44
+GT_AC inf
+GT_AG inf
+GT_AT inf
+GT_CA 0
+GT_CC 78
+GT_CG 161
+GT_CT 212
+GT_GA 21
+GT_GC inf
+GT_GG inf
+GT_GT inf
+GT_TA 94
+GT_TC inf
+GT_TG inf
+GT_TT inf
+TA_AA 63
+TA_AC 59
+TA_AG 47
+TA_AT 0
+TA_CA inf
+TA_CC inf
+TA_CG inf
+TA_CT 63
+TA_GA inf
+TA_GC inf
+TA_GG inf
+TA_GT 105
+TA_TA inf
+TA_TC inf
+TA_TG inf
+TA_TT 89
+TC_AA 70
+TC_AC 13
+TC_AG 0
+TC_AT 63
+TC_CA inf
+TC_CC inf
+TC_CG 135
+TC_CT inf
+TC_GA inf
+TC_GC inf
+TC_GG 159
+TC_GT inf
+TC_TA inf
+TC_TC inf
+TC_TG 212
+TC_TT inf
+TG_AA 58
+TG_AC 0
+TG_AG 27
+TG_AT 105
+TG_CA inf
+TG_CC 80
+TG_CG inf
+TG_CT inf
+TG_GA inf
+TG_GC 90
+TG_GG inf
+TG_GT inf
+TG_TA inf
+TG_TC 169
+TG_TG inf
+TG_TT inf
+TT_AA 0
+TT_AC 12
+TT_AG 98
+TT_AT 89
+TT_CA 17
+TT_CC inf
+TT_CG inf
+TT_CT inf
+TT_GA 87
+TT_GC inf
+TT_GG inf
+TT_GT inf
+TT_TA 65
+TT_TC inf
+TT_TG inf
+TT_TT inf

data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh ADDED Viewed

@@ -0,0 +1,256 @@
+AA_AA 0
+AA_AC 0
+AA_AG 0
+AA_AT 25
+AA_CA 0
+AA_CC 0
+AA_CG 0
+AA_CT 27
+AA_GA 0
+AA_GC 0
+AA_GG 0
+AA_GT 24
+AA_TA 31
+AA_TC 16
+AA_TG 19
+AA_TT 0
+AC_AA 0
+AC_AC 0
+AC_AG 80
+AC_AT 0
+AC_CA 0
+AC_CC 0
+AC_CG 32
+AC_CT 0
+AC_GA 0
+AC_GC 0
+AC_GG 46
+AC_GT 0
+AC_TA 18
+AC_TC 1
+AC_TG 0
+AC_TT 9
+AG_AA 0
+AG_AC 43
+AG_AG 0
+AG_AT 0
+AG_CA 0
+AG_CC 27
+AG_CG 0
+AG_CT 0
+AG_GA 0
+AG_GC 60
+AG_GG 0
+AG_GT 0
+AG_TA 25
+AG_TC 0
+AG_TG 11
+AG_TT 32
+AT_AA 31
+AT_AC 0
+AT_AG 0
+AT_AT 0
+AT_CA 18
+AT_CC 0
+AT_CG 0
+AT_CT 0
+AT_GA 25
+AT_GC 0
+AT_GG 0
+AT_GT 0
+AT_TA 0
+AT_TC 23
+AT_TG 35
+AT_TT 24
+CA_AA 0
+CA_AC 0
+CA_AG 0
+CA_AT 23
+CA_CA 0
+CA_CC 0
+CA_CG 0
+CA_CT 7
+CA_GA 43
+CA_GC 26
+CA_GG 39
+CA_GT 0
+CA_TA 0
+CA_TC 0
+CA_TG 0
+CA_TT 7
+CC_AA 0
+CC_AC 0
+CC_AG 50
+CC_AT 0
+CC_CA 0
+CC_CC 0
+CC_CG 39
+CC_CT 0
+CC_GA 27
+CC_GC 21
+CC_GG 0
+CC_GT 32
+CC_TA 0
+CC_TC 0
+CC_TG 30
+CC_TT 0
+CG_AA 0
+CG_AC 26
+CG_AG 0
+CG_AT 0
+CG_CA 0
+CG_CC 21
+CG_CG 0
+CG_CT 0
+CG_GA 60
+CG_GC 0
+CG_GG 38
+CG_GT 38
+CG_TA 0
+CG_TC 39
+CG_TG 0
+CG_TT 0
+CT_AA 16
+CT_AC 0
+CT_AG 0
+CT_AT 0
+CT_CA 1
+CT_CC 0
+CT_CG 0
+CT_CT 0
+CT_GA 0
+CT_GC 39
+CT_GG 66
+CT_GT 61
+CT_TA 23
+CT_TC 0
+CT_TG 0
+CT_TT 0
+GA_AA 0
+GA_AC 0
+GA_AG 0
+GA_AT 20
+GA_CA 80
+GA_CC 50
+GA_CG 43
+GA_CT 0
+GA_GA 0
+GA_GC 0
+GA_GG 0
+GA_GT 11
+GA_TA 0
+GA_TC 0
+GA_TG 0
+GA_TT 36
+GC_AA 0
+GC_AC 0
+GC_AG 43
+GC_AT 0
+GC_CA 32
+GC_CC 39
+GC_CG 0
+GC_CT 49
+GC_GA 0
+GC_GC 0
+GC_GG 7
+GC_GT 0
+GC_TA 0
+GC_TC 0
+GC_TG 59
+GC_TT 0
+GG_AA 0
+GG_AC 39
+GG_AG 0
+GG_AT 0
+GG_CA 46
+GG_CC 0
+GG_CG 7
+GG_CT 57
+GG_GA 0
+GG_GC 38
+GG_GG 0
+GG_GT 0
+GG_TA 0
+GG_TC 66
+GG_TG 0
+GG_TT 0
+GT_AA 19
+GT_AC 0
+GT_AG 0
+GT_AT 0
+GT_CA 0
+GT_CC 30
+GT_CG 59
+GT_CT 74
+GT_GA 11
+GT_GC 0
+GT_GG 0
+GT_GT 0
+GT_TA 35
+GT_TC 0
+GT_TG 0
+GT_TT 0
+TA_AA 25
+TA_AC 23
+TA_AG 20
+TA_AT 72
+TA_CA 0
+TA_CC 0
+TA_CG 0
+TA_CT 25
+TA_GA 0
+TA_GC 0
+TA_GG 0
+TA_GT 39
+TA_TA 0
+TA_TC 0
+TA_TG 0
+TA_TT 32
+TC_AA 27
+TC_AC 7
+TC_AG 0
+TC_AT 25
+TC_CA 0
+TC_CC 0
+TC_CG 49
+TC_CT 0
+TC_GA 0
+TC_GC 0
+TC_GG 57
+TC_GT 0
+TC_TA 0
+TC_TC 0
+TC_TG 74
+TC_TT 0
+TG_AA 24
+TG_AC 0
+TG_AG 11
+TG_AT 39
+TG_CA 0
+TG_CC 32
+TG_CG 0
+TG_CT 0
+TG_GA 0
+TG_GC 38
+TG_GG 0
+TG_GT 0
+TG_TA 0
+TG_TC 61
+TG_TG 0
+TG_TT 0
+TT_AA 0
+TT_AC 7
+TT_AG 36
+TT_AT 32
+TT_CA 9
+TT_CC 0
+TT_CG 0
+TT_CT 0
+TT_GA 32
+TT_GC 0
+TT_GG 0
+TT_GT 0
+TT_TA 24
+TT_TC 0
+TT_TG 0
+TT_TT 0

data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds ADDED Viewed

@@ -0,0 +1,256 @@
+AA_AA inf
+AA_AC inf
+AA_AG inf
+AA_AT 63
+AA_CA inf
+AA_CC inf
+AA_CG inf
+AA_CT 70
+AA_GA inf
+AA_GC inf
+AA_GG inf
+AA_GT 58
+AA_TA 78
+AA_TC 40
+AA_TG 44
+AA_TT inf
+AC_AA inf
+AC_AC inf
+AC_AG 225
+AC_AT inf
+AC_CA inf
+AC_CC inf
+AC_CG 71
+AC_CT inf
+AC_GA inf
+AC_GC inf
+AC_GG 114
+AC_GT inf
+AC_TA 38
+AC_TC 5
+AC_TG inf
+AC_TT 17
+AG_AA inf
+AG_AC 107
+AG_AG inf
+AG_AT inf
+AG_CA inf
+AG_CC 60
+AG_CG inf
+AG_CT inf
+AG_GA inf
+AG_GC 155
+AG_GG inf
+AG_GT inf
+AG_TA 59
+AG_TC inf
+AG_TG 21
+AG_TT 87
+AT_AA 78
+AT_AC inf
+AT_AG inf
+AT_AT inf
+AT_CA 38
+AT_CC inf
+AT_CG inf
+AT_CT inf
+AT_GA 59
+AT_GC inf
+AT_GG inf
+AT_GT inf
+AT_TA inf
+AT_TC 63
+AT_TG 94
+AT_TT 65
+CA_AA inf
+CA_AC inf
+CA_AG inf
+CA_AT 59
+CA_CA inf
+CA_CC inf
+CA_CG inf
+CA_CT 13
+CA_GA 107
+CA_GC 59
+CA_GG 96
+CA_GT inf
+CA_TA inf
+CA_TC inf
+CA_TG inf
+CA_TT 12
+CC_AA inf
+CC_AC inf
+CC_AG 138
+CC_AT inf
+CC_CA inf
+CC_CC inf
+CC_CG 106
+CC_CT inf
+CC_GA 60
+CC_GC 51
+CC_GG inf
+CC_GT 80
+CC_TA inf
+CC_TC inf
+CC_TG 78
+CC_TT inf
+CG_AA inf
+CG_AC 59
+CG_AG inf
+CG_AT inf
+CG_CA inf
+CG_CC 51
+CG_CG inf
+CG_CT inf
+CG_GA 155
+CG_GC inf
+CG_GG 95
+CG_GT 90
+CG_TA inf
+CG_TC 106
+CG_TG inf
+CG_TT inf
+CT_AA 40
+CT_AC inf
+CT_AG inf
+CT_AT inf
+CT_CA 5
+CT_CC inf
+CT_CG inf
+CT_CT inf
+CT_GA inf
+CT_GC 106
+CT_GG 187
+CT_GT 169
+CT_TA 63
+CT_TC inf
+CT_TG inf
+CT_TT inf
+GA_AA inf
+GA_AC inf
+GA_AG inf
+GA_AT 47
+GA_CA 225
+GA_CC 138
+GA_CG 111
+GA_CT inf
+GA_GA inf
+GA_GC inf
+GA_GG inf
+GA_GT 27
+GA_TA inf
+GA_TC inf
+GA_TG inf
+GA_TT 98
+GC_AA inf
+GC_AC inf
+GC_AG 111
+GC_AT inf
+GC_CA 71
+GC_CC 106
+GC_CG inf
+GC_CT 135
+GC_GA inf
+GC_GC inf
+GC_GG 192
+GC_GT inf
+GC_TA inf
+GC_TC inf
+GC_TG 161
+GC_TT inf
+GG_AA inf
+GG_AC 96
+GG_AG inf
+GG_AT inf
+GG_CA 114
+GG_CC inf
+GG_CG 192
+GG_CT 159
+GG_GA inf
+GG_GC 95
+GG_GG inf
+GG_GT inf
+GG_TA inf
+GG_TC 187
+GG_TG inf
+GG_TT inf
+GT_AA 44
+GT_AC inf
+GT_AG inf
+GT_AT inf
+GT_CA inf
+GT_CC 78
+GT_CG 161
+GT_CT 212
+GT_GA 21
+GT_GC inf
+GT_GG inf
+GT_GT inf
+GT_TA 94
+GT_TC inf
+GT_TG inf
+GT_TT inf
+TA_AA 63
+TA_AC 59
+TA_AG 47
+TA_AT inf
+TA_CA inf
+TA_CC inf
+TA_CG inf
+TA_CT 63
+TA_GA inf
+TA_GC inf
+TA_GG inf
+TA_GT 105
+TA_TA inf
+TA_TC inf
+TA_TG inf
+TA_TT 89
+TC_AA 70
+TC_AC 13
+TC_AG inf
+TC_AT 63
+TC_CA inf
+TC_CC inf
+TC_CG 135
+TC_CT inf
+TC_GA inf
+TC_GC inf
+TC_GG 159
+TC_GT inf
+TC_TA inf
+TC_TC inf
+TC_TG 212
+TC_TT inf
+TG_AA 58
+TG_AC inf
+TG_AG 27
+TG_AT 105
+TG_CA inf
+TG_CC 80
+TG_CG inf
+TG_CT inf
+TG_GA inf
+TG_GC 90
+TG_GG inf
+TG_GT inf
+TG_TA inf
+TG_TC 169
+TG_TG inf
+TG_TT inf
+TT_AA inf
+TT_AC 12
+TT_AG 98
+TT_AT 89
+TT_CA 17
+TT_CC inf
+TT_CG inf
+TT_CT inf
+TT_GA 87
+TT_GC inf
+TT_GG inf
+TT_GT inf
+TT_TA 65
+TT_TC inf
+TT_TG inf
+TT_TT inf