satDNA Analyzer v1.2 - Universidad de Granada

   ATH_AVG  ATAGTA_TMTCTCGA-TT

   CEL_AVG  ATMCCAATATCTCGAATT

Global_AVG  ATAGYAATATCTCGA-TT

ATH_1  ATAGTANTCTCTCGA-TT
ATH_5  ATAGTANCC-GTCGA-TT
ATH_3  ATAGTANTCTCTCGA-TG
ATH_2  ATAGTAATATCTCGA-TC
ATH_4  ATAGTAATATCTCGA-TT
ATH_6  ATAGTAATATCTCGA-TT


CEL_6  ATAGCAACATCTCGAATT
CEL_4  ATACC-AT-TCTCGAGTT
CEL_5  ATACCAATATCTCGAATT
CEL_1  CCCCCAAGATCTCGAATT
CEL_2  ACCCCTATCTCTCGAACT
CEL_3  ATCCCAATA-TTCGAATT

Legend: Strachan Type I, Type II, Type III, Type IV, Type V, Type VI;
         Shared polymorphism, Shared polymorphism due to indels, Irrelevant position; Irrelevant position due to indels; Ignored position.

Location of positions for species ATH and species CEL

Strachan Type I	7, 12, 13, 14, 15,
Strachan Type II	1, 17,
Strachan Type III	2, 3, 18,
Strachan Type IV	4,
Strachan Type V	5,
Strachan Type VI
Shared Polymorphism	8, 9,
Shared Polymorphism due to indels	10,
Irrelevant positions	11,
Irrelevant positions due to indels	6, 16,

Shared polymorphisms not excluded
Pairwise option
Statistics

For species ATH
Number of nucleotide substitutions per site:

	ATH_1	ATH_5	ATH_3	ATH_2	ATH_4	ATH_6
ATH_1	--	0.1333	0.0625	0.125	0.0625	0.0625
ATH_5	0.1333	--	0.2	0.2667	0.2	0.2
ATH_3	0.0625	0.2	--	0.125	0.125	0.125
ATH_2	0.125	0.2667	0.125	--	0.05882	0.05882
ATH_4	0.0625	0.2	0.125	0.05882	--	0
ATH_6	0.0625	0.2	0.125	0.05882	0	--

Number of nucleotide substitutions per site (JC):

	ATH_1	ATH_5	ATH_3	ATH_2	ATH_4	ATH_6
ATH_1	--	0.1468	0.06526	0.1367	0.06526	0.06526
ATH_5	0.1468	--	0.2326	0.3295	0.2326	0.2326
ATH_3	0.06526	0.2	--	0.1367	0.1367	0.1367
ATH_2	0.1367	0.2667	0.125	--	0.06126	0.06126
ATH_4	0.06526	0.2	0.125	0.05882	--	-0
ATH_6	0.06526	0.2	0.125	0.05882	0	--

Average Number of Nucleotide Differences (K): 1.867
Nucleotide Diversity (π):0.1203
Nucleotide Diversity (π(JC)): 0.136

For species CEL
Number of nucleotide substitutions per site:

	CEL_6	CEL_4	CEL_5	CEL_1	CEL_2	CEL_3
CEL_6	--	0.1875	0.1111	0.2778	0.3889	0.2353
CEL_4	0.1875	--	0.0625	0.3125	0.25	0.2
CEL_5	0.1111	0.0625	--	0.2222	0.2778	0.1176
CEL_1	0.2778	0.3125	0.2222	--	0.2778	0.2353
CEL_2	0.3889	0.25	0.2778	0.2778	--	0.2941
CEL_3	0.2353	0.2	0.1176	0.2353	0.2941	--

Number of nucleotide substitutions per site (JC):

	CEL_6	CEL_4	CEL_5	CEL_1	CEL_2	CEL_3
CEL_6	--	0.2158	0.1203	0.347	0.5482	0.2824
CEL_4	0.2158	--	0.06526	0.4042	0.3041	0.2326
CEL_5	0.1203	0.0625	--	0.2635	0.347	0.128
CEL_1	0.347	0.3125	0.2222	--	0.347	0.2824
CEL_2	0.5482	0.25	0.2778	0.2778	--	0.3734
CEL_3	0.2824	0.2	0.1176	0.2353	0.2941	--

Average Number of Nucleotide Differences (K): 3.933
Nucleotide Diversity (π):0.23
Nucleotide Diversity (π(JC)): 0.2841

Number of Nucleotide Differences between Species ATH and CEL

	CEL_6	CEL_4	CEL_5	CEL_1	CEL_2	CEL_3
ATH_1	0.1875	0.1429	0.1875	0.4375	0.375	0.3333
ATH_5	0.2	0.3077	0.3333	0.5333	0.5333	0.4
ATH_3	0.25	0.2143	0.25	0.5	0.4375	0.4
ATH_2	0.1765	0.2	0.1765	0.4118	0.4706	0.3125
ATH_4	0.1176	0.1333	0.1176	0.3529	0.4118	0.25
ATH_6	0.1176	0.1333	0.1176	0.3529	0.4118	0.25

Number of Nucleotide Differences between Species ATH and CEL (JC)

	CEL_6	CEL_4	CEL_5	CEL_1	CEL_2	CEL_3
ATH_1	0.2158	0.1585	0.2158	0.6566	0.5199	0.4408
ATH_5	0.2326	0.3961	0.4408	0.9313	0.9313	0.5716
ATH_3	0.3041	0.2524	0.3041	0.824	0.6566	0.5716
ATH_2	0.2012	0.2326	0.2012	0.5972	0.7405	0.4042
ATH_4	0.128	0.1468	0.128	0.477	0.5972	0.3041
ATH_6	0.128	0.1468	0.128	0.477	0.5972	0.3041

Average Number of Nucleotide Differences: ATH and CEL (K): 4.639
Average Number of Nucleotide Substitution per Site between Species ATH and CEL (Dxy): 0.2927
Average Number of Nucleotide Substitutions between Species ATH and CEL (Dxy(JC)): 0.4045
Number of Net Nucleotide Substitutions per Site between Species ATH and CEL (Da): 0.1175
Number of Net Nucleotide Substitutions per Site between Species ATH and CEL (Da(JC)): 0.1945
The expected λ/T value is: 0.002938
The expected λ/T value(JC) is: 0.004863

Transitions/Transversions:
Intraspecies values:
Species ATH Ratio of transitional to transversional differences:

	ATH_1	ATH_5	ATH_3	ATH_2	ATH_4	ATH_6
ATH_1	--	1	0	1	0	0
ATH_5	1	--	0.5	1	0.5	0.5
ATH_3	0	0.5	--	0	0	0
ATH_2	1	1	0	--	NC	NC
ATH_4	0	0.5	0	NC	--	NC
ATH_6	0	0.5	0	NC	NC	--

Proportion of transicional differences for species ATH: 0.04596
Proportion of transversional differences for species ATH: 0.09589
Ratio of transitional to transversional differences for species ATH: 0.375
Species CEL Ratio of transitional to transversional differences:

	CEL_6	CEL_4	CEL_5	CEL_1	CEL_2	CEL_3
CEL_6	--	2	1	0.25	0.75	1
CEL_4	2	--	NC	0.6667	3	2
CEL_5	1	NC	--	0.3333	0.6667	1
CEL_1	0.25	0.6667	0.3333	--	0.25	1
CEL_2	0.75	3	0.6667	0.25	--	1.5
CEL_3	1	2	1	1	1.5	--

Proportion of transicional differences for species CEL: 0.1146
Proportion of transversional differences for species CEL: 0.1319
Ratio of transitional to transversional differences for species CEL: 1.101
Species ATH and CEL Ratio of transitional to transversional differences:

	CEL_6	CEL_4	CEL_5	CEL_1	CEL_2	CEL_3
ATH_1	2	1	0.5	0.4	1	0.6667
ATH_5	0.5	1	0.6667	0.3333	1	0.5
ATH_3	1	0.5	0.3333	0.3333	0.75	0.5
ATH_2	NC	2	2	0.75	1	1.5
ATH_4	NC	1	1	0.5	0.75	1
ATH_6	NC	1	1	0.5	0.75	1

Proportion of transicional differences average between species ATH and CEL: 0.1365
Proportion of transversional differences average between species ATH and CEL: 0.1715
Ratio of transitional to transversional differences average between species ATH and CEL: 0.8707

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