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

bio-polymarker 1.3.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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/dangle_i.ds ADDED Viewed

@@ -0,0 +1,131 @@
+/* Entropy of dangling end */
+/* 3' dangling */
+AA_A 0
+AC_A 0
+AG_A 0
+AT_A 0
+AA_C 0
+AC_C 0
+AG_C 0
+AT_C 0
+AA_G 0
+AC_G 0
+AG_G 0
+AT_G 0
+AA_T 11
+AC_T -142
+AG_T 131
+AT_T 126
+CA_A 0
+CC_A 0
+CG_A 0
+CT_A 0
+CA_C 0
+CC_C 0
+CG_C 0
+CT_C 0
+CA_G 165
+CC_G 74
+CG_G 104
+CT_G 150
+CA_T 0
+CC_T 0
+CG_T 0
+CT_T 0
+GA_A 0
+GC_A 0
+GG_A 0
+GT_A 0
+GA_C 39
+GC_C 1
+GG_C 112
+GT_C 131
+GA_G 0
+GC_G 0
+GG_G 0
+GT_G 0
+GA_T 0
+GC_T 0
+GG_T 0
+GT_T 0
+TA_A 8
+TC_A -149
+TG_A 36
+TT_A -104
+TA_C 0
+TC_C 0
+TG_C 0
+TT_C 0
+TA_G 0
+TC_G 0
+TG_G 0
+TT_G 0
+TA_T 0
+TC_T 0
+TG_T 0
+TT_T 0
+/* 5' dangling */
+A_AA 0
+A_AC 0
+A_AG 0
+A_AT 0
+A_CA 0
+A_CC 0
+A_CG 0
+A_CT 0
+A_GA 0
+A_GC 0
+A_GG 0
+A_GT 0
+A_TA 76
+A_TC 130
+A_TG 150
+A_TT 5
+C_AA 0
+C_AC 0
+C_AG 0
+C_AT 0
+C_CA 0
+C_CC 0
+C_CG 0
+C_CT 0
+C_GA 100
+C_GC 119
+C_GG 109
+C_GT 138
+C_TA 0
+C_TC 0
+C_TG 0
+C_TT 0
+G_AA 0
+G_AC 0
+G_AG 0
+G_AT 0
+G_CA 171
+G_CC 126
+G_CG 140
+G_CT 109
+G_GA 0
+G_GC 0
+G_GG 0
+G_GT 0
+G_TA 0
+G_TC 0
+G_TG 0
+G_TT 0
+T_AA -23
+T_AC -33
+T_AG 16
+T_AT 200
+T_CA 0
+T_CC 0
+T_CG 0
+T_CT 0
+T_GA 0
+T_GC 0
+T_GG 0
+T_GT 0
+T_TA 0
+T_TC 0
+T_TG 0
+T_TT 0

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

@@ -0,0 +1,34 @@
+DESTABILIZING ENTHALPIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED)
+hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges
+SIZE         INTERNAL          BULGE            HAIRPIN
+-------------------------------------------------------
+1               .                0.0               .
+2              0.0               0.0               .
+3              0.0               0.0              0.0
+4              0.0               0.0              0.0
+5              0.0               0.0              0.0
+6              0.0               0.0              0.0
+7              0.0               0.0              0.0
+8              0.0               0.0              0.0
+9              0.0               0.0              0.0
+10             0.0               0.0              0.0
+11             0.0               0.0              0.0
+12             0.0               0.0              0.0
+13             0.0               0.0              0.0
+14             0.0               0.0              0.0
+15             0.0               0.0              0.0
+16             0.0               0.0              0.0
+17             0.0               0.0              0.0
+18             0.0               0.0              0.0
+19             0.0               0.0              0.0
+20             0.0               0.0              0.0
+21             0.0               0.0              0.0
+22             0.0               0.0              0.0
+23             0.0               0.0              0.0
+24             0.0               0.0              0.0
+25             0.0               0.0              0.0
+26             0.0               0.0              0.0
+27             0.0               0.0              0.0
+28             0.0               0.0              0.0
+29             0.0               0.0              0.0
+30             0.0               0.0              0.0

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

@@ -0,0 +1,31 @@
+SIZE	INTERNAL	BULGE	HAIRPIN
+1	.	-128.9	.
+2	.	-93.5	.
+3	-103.1	-99.9	-112.8
+4	-116	-103.1	-112.8
+5	-128.9	-106.4	-106.4
+6	-141.8	-112.8	-128.9
+7	-148.3	-119.2	-135.4
+8	-154.7	-125.7	-138.6
+9	-157.9	-132.1	-145
+10	-157.9	-138.6	-148.3
+11	-162.6	-143.2	-152.9
+12	-167.6	-145	-161.2
+13	-171.5	-148.9	-165
+14	-174.1	-154.7	-164.4
+15	-177.4	-158.1	-167.7
+16	-180.5	-161.2	-170.8
+17	-183.4	-164.1	-173.8
+18	-187	-167.6	-177.3
+19	-189.6	-170.2	-179.9
+20	-190.2	-170.8	-183.7
+21	-192.5	-173.2	-186.1
+22	-194.8	-175.5	-188.4
+23	-197	-177.6	-190.5
+24	-199	-179.7	-192.6
+25	-203.1	-180.5	-196.6
+26	-205	-182.4	-198.5
+27	-206.8	-184.2	-200.4
+28	-208.6	-186	-202.1
+29	-210.3	-187.7	-203.8
+30	-212.8	-190.2	-203.1

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

@@ -0,0 +1,257 @@
+/*	values	in	articles	are	modified	as	follows:	dS	*(-10)	and	dH	*(-10)	*/
+AA_AA	inf
+AA_AC	inf
+AA_AG	inf
+AA_AT	inf
+AA_CA	inf
+AA_CC	inf
+AA_CG	inf
+AA_CT	inf
+AA_GA	inf
+AA_GC	inf
+AA_GG	inf
+AA_GT	inf
+AA_TA	inf
+AA_TC	inf
+AA_TG	inf
+AA_TT	-7900
+AC_AA	inf
+AC_AC	inf
+AC_AG	inf
+AC_AT	inf
+AC_CA	inf
+AC_CC	inf
+AC_CG	inf
+AC_CT	inf
+AC_GA	inf
+AC_GC	inf
+AC_GG	inf
+AC_GT	inf
+AC_TA	inf
+AC_TC	inf
+AC_TG	-8400
+AC_TT	inf
+AG_AA	inf
+AG_AC	inf
+AG_AG	inf
+AG_AT	inf
+AG_CA	inf
+AG_CC	inf
+AG_CG	inf
+AG_CT	inf
+AG_GA	inf
+AG_GC	inf
+AG_GG	inf
+AG_GT	inf
+AG_TA	inf
+AG_TC	-7800
+AG_TG	inf
+AG_TT	inf
+AT_AA	inf
+AT_AC	inf
+AT_AG	inf
+AT_AT	inf
+AT_CA	inf
+AT_CC	inf
+AT_CG	inf
+AT_CT	inf
+AT_GA	inf
+AT_GC	inf
+AT_GG	inf
+AT_GT	inf
+AT_TA	-7200
+AT_TC	inf
+AT_TG	inf
+AT_TT	inf
+CA_AA	inf
+CA_AC	inf
+CA_AG	inf
+CA_AT	inf
+CA_CA	inf
+CA_CC	inf
+CA_CG	inf
+CA_CT	inf
+CA_GA	inf
+CA_GC	inf
+CA_GG	inf
+CA_GT	-8500
+CA_TA	inf
+CA_TC	inf
+CA_TG	inf
+CA_TT	inf
+CC_AA	inf
+CC_AC	inf
+CC_AG	-52
+CC_AT	inf
+CC_CA	inf
+CC_CC	inf
+CC_CG	-36
+CC_CT	inf
+CC_GA	inf
+CC_GC	inf
+CC_GG	-8000
+CC_GT	inf
+CC_TA	inf
+CC_TC	inf
+CC_TG	inf
+CC_TT	inf
+CG_AA	inf
+CG_AC	inf
+CG_AG	inf
+CG_AT	inf
+CG_CA	inf
+CG_CC	inf
+CG_CG	inf
+CG_CT	inf
+CG_GA	inf
+CG_GC	-10600
+CG_GG	inf
+CG_GT	inf
+CG_TA	inf
+CG_TC	inf
+CG_TG	inf
+CG_TT	inf
+CT_AA	inf
+CT_AC	inf
+CT_AG	inf
+CT_AT	inf
+CT_CA	inf
+CT_CC	inf
+CT_CG	inf
+CT_CT	inf
+CT_GA	-7800
+CT_GC	inf
+CT_GG	inf
+CT_GT	inf
+CT_TA	inf
+CT_TC	inf
+CT_TG	inf
+CT_TT	inf
+GA_AA	inf
+GA_AC	inf
+GA_AG	inf
+GA_AT	inf
+GA_CA	inf
+GA_CC	inf
+GA_CG	inf
+GA_CT	-8200
+GA_GA	inf
+GA_GC	inf
+GA_GG	inf
+GA_GT	inf
+GA_TA	inf
+GA_TC	inf
+GA_TG	inf
+GA_TT	inf
+GC_AA	inf
+GC_AC	inf
+GC_AG	inf
+GC_AT	inf
+GC_CA	inf
+GC_CC	inf
+GC_CG	-9800
+GC_CT	inf
+GC_GA	inf
+GC_GC	inf
+GC_GG	inf
+GC_GT	inf
+GC_TA	inf
+GC_TC	inf
+GC_TG	inf
+GC_TT	inf
+GG_AA	inf
+GG_AC	inf
+GG_AG	inf
+GG_AT	inf
+GG_CA	inf
+GG_CC	-8000
+GG_CG	inf
+GG_CT	inf
+GG_GA	inf
+GG_GC	inf
+GG_GG	inf
+GG_GT	inf
+GG_TA	inf
+GG_TC	inf
+GG_TG	inf
+GG_TT	inf
+GT_AA	inf
+GT_AC	inf
+GT_AG	inf
+GT_AT	inf
+GT_CA	-8400
+GT_CC	inf
+GT_CG	inf
+GT_CT	inf
+GT_GA	inf
+GT_GC	inf
+GT_GG	inf
+GT_GT	inf
+GT_TA	inf
+GT_TC	inf
+GT_TG	inf
+GT_TT	inf
+TA_AA	inf
+TA_AC	inf
+TA_AG	inf
+TA_AT	-7200
+TA_CA	inf
+TA_CC	inf
+TA_CG	inf
+TA_CT	inf
+TA_GA	inf
+TA_GC	inf
+TA_GG	inf
+TA_GT	inf
+TA_TA	inf
+TA_TC	inf
+TA_TG	inf
+TA_TT	inf
+TC_AA	inf
+TC_AC	inf
+TC_AG	-8200
+TC_AT	inf
+TC_CA	inf
+TC_CC	inf
+TC_CG	inf
+TC_CT	inf
+TC_GA	inf
+TC_GC	inf
+TC_GG	inf
+TC_GT	inf
+TC_TA	inf
+TC_TC	inf
+TC_TG	inf
+TC_TT	inf
+TG_AA	inf
+TG_AC	-8500
+TG_AG	inf
+TG_AT	inf
+TG_CA	inf
+TG_CC	inf
+TG_CG	inf
+TG_CT	inf
+TG_GA	inf
+TG_GC	inf
+TG_GG	inf
+TG_GT	inf
+TG_TA	inf
+TG_TC	inf
+TG_TG	inf
+TG_TT	inf
+TT_AA	-7900
+TT_AC	inf
+TT_AG	inf
+TT_AT	inf
+TT_CA	inf
+TT_CC	inf
+TT_CG	inf
+TT_CT	inf
+TT_GA	inf
+TT_GC	inf
+TT_GG	inf
+TT_GT	inf
+TT_TA	inf
+TT_TC	inf
+TT_TG	inf
+TT_TT	inf

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

@@ -0,0 +1,256 @@
+AA_AA	inf
+AA_AC	inf
+AA_AG	inf
+AA_AT	inf
+AA_CA	inf
+AA_CC	inf
+AA_CG	inf
+AA_CT	inf
+AA_GA	inf
+AA_GC	inf
+AA_GG	inf
+AA_GT	inf
+AA_TA	inf
+AA_TC	inf
+AA_TG	inf
+AA_TT	-22.2
+AC_AA	inf
+AC_AC	inf
+AC_AG	inf
+AC_AT	inf
+AC_CA	inf
+AC_CC	inf
+AC_CG	inf
+AC_CT	inf
+AC_GA	inf
+AC_GC	inf
+AC_GG	inf
+AC_GT	inf
+AC_TA	inf
+AC_TC	inf
+AC_TG	-22.4
+AC_TT	inf
+AG_AA	inf
+AG_AC	inf
+AG_AG	inf
+AG_AT	inf
+AG_CA	inf
+AG_CC	inf
+AG_CG	inf
+AG_CT	inf
+AG_GA	inf
+AG_GC	-13.2
+AG_GG	inf
+AG_GT	inf
+AG_TA	inf
+AG_TC	-21.0
+AG_TG	inf
+AG_TT	inf
+AT_AA	inf
+AT_AC	inf
+AT_AG	inf
+AT_AT	inf
+AT_CA	inf
+AT_CC	inf
+AT_CG	inf
+AT_CT	inf
+AT_GA	inf
+AT_GC	inf
+AT_GG	inf
+AT_GT	inf
+AT_TA	-20.4
+AT_TC	inf
+AT_TG	inf
+AT_TT	inf
+CA_AA	inf
+CA_AC	inf
+CA_AG	inf
+CA_AT	inf
+CA_CA	inf
+CA_CC	inf
+CA_CG	inf
+CA_CT	inf
+CA_GA	inf
+CA_GC	inf
+CA_GG	inf
+CA_GT	-22.7
+CA_TA	inf
+CA_TC	inf
+CA_TG	inf
+CA_TT	inf
+CC_AA	inf
+CC_AC	inf
+CC_AG	inf
+CC_AT	inf
+CC_CA	inf
+CC_CC	inf
+CC_CG	inf
+CC_CT	inf
+CC_GA	inf
+CC_GC	inf
+CC_GG	-19.9
+CC_GT	inf
+CC_TA	inf
+CC_TC	inf
+CC_TG	inf
+CC_TT	inf
+CG_AA	inf
+CG_AC	inf
+CG_AG	inf
+CG_AT	inf
+CG_CA	inf
+CG_CC	inf
+CG_CG	inf
+CG_CT	inf
+CG_GA	inf
+CG_GC	-27.2
+CG_GG	inf
+CG_GT	inf
+CG_TA	inf
+CG_TC	inf
+CG_TG	inf
+CG_TT	inf
+CT_AA	inf
+CT_AC	inf
+CT_AG	inf
+CT_AT	inf
+CT_CA	inf
+CT_CC	inf
+CT_CG	inf
+CT_CT	inf
+CT_GA	-21.0
+CT_GC	inf
+CT_GG	inf
+CT_GT	-15.8
+CT_TA	inf
+CT_TC	inf
+CT_TG	inf
+CT_TT	inf
+GA_AA	inf
+GA_AC	inf
+GA_AG	inf
+GA_AT	inf
+GA_CA	inf
+GA_CC	inf
+GA_CG	inf
+GA_CT	-22.2
+GA_GA	inf
+GA_GC	inf
+GA_GG	inf
+GA_GT	inf
+GA_TA	inf
+GA_TC	inf
+GA_TG	inf
+GA_TT	inf
+GC_AA	inf
+GC_AC	inf
+GC_AG	inf
+GC_AT	inf
+GC_CA	inf
+GC_CC	inf
+GC_CG	-24.4
+GC_CT	inf
+GC_GA	inf
+GC_GC	inf
+GC_GG	inf
+GC_GT	inf
+GC_TA	inf
+GC_TC	inf
+GC_TG	inf
+GC_TT	inf
+GG_AA	inf
+GG_AC	inf
+GG_AG	inf
+GG_AT	inf
+GG_CA	inf
+GG_CC	-19.9
+GG_CG	-15.8
+GG_CT	inf
+GG_GA	inf
+GG_GC	inf
+GG_GG	inf
+GG_GT	inf
+GG_TA	inf
+GG_TC	inf
+GG_TG	inf
+GG_TT	inf
+GT_AA	inf
+GT_AC	inf
+GT_AG	inf
+GT_AT	inf
+GT_CA	-22.4
+GT_CC	inf
+GT_CG	inf
+GT_CT	inf
+GT_GA	inf
+GT_GC	inf
+GT_GG	inf
+GT_GT	inf
+GT_TA	inf
+GT_TC	inf
+GT_TG	inf
+GT_TT	inf
+TA_AA	inf
+TA_AC	inf
+TA_AG	inf
+TA_AT	-21.3
+TA_CA	inf
+TA_CC	inf
+TA_CG	inf
+TA_CT	inf
+TA_GA	inf
+TA_GC	inf
+TA_GG	inf
+TA_GT	inf
+TA_TA	inf
+TA_TC	inf
+TA_TG	inf
+TA_TT	inf
+TC_AA	inf
+TC_AC	inf
+TC_AG	-22.2
+TC_AT	inf
+TC_CA	inf
+TC_CC	inf
+TC_CG	inf
+TC_CT	inf
+TC_GA	inf
+TC_GC	inf
+TC_GG	inf
+TC_GT	inf
+TC_TA	inf
+TC_TC	inf
+TC_TG	inf
+TC_TT	inf
+TG_AA	inf
+TG_AC	-22.7
+TG_AG	inf
+TG_AT	inf
+TG_CA	inf
+TG_CC	inf
+TG_CG	inf
+TG_CT	inf
+TG_GA	inf
+TG_GC	inf
+TG_GG	inf
+TG_GT	inf
+TG_TA	inf
+TG_TC	inf
+TG_TG	inf
+TG_TT	inf
+TT_AA	-22.2
+TT_AC	inf
+TT_AG	inf
+TT_AT	inf
+TT_CA	inf
+TT_CC	inf
+TT_CG	inf
+TT_CT	inf
+TT_GA	-9
+TT_GC	inf
+TT_GG	inf
+TT_GT	inf
+TT_TA	inf
+TT_TC	inf
+TT_TG	inf
+TT_TT	inf