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/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