Sequence Comparison Analysis

Insthoviricetes

Pair Frequencies

Genera	ii (Identical Pairs)	si (Transitionsal Pairs)	sv (Transversional Pairs)	R (si/sv)
Alphainfluenzavirus	11041	1406	797	1.8
Betainfluenzavirus	13546	507	90	5.7
Gammainfluenzavirus	12237	315	120	2.6
Deltainfluenzavirus	12367	256	34	7.4
Influenza virus	7400	2163	2551	0.8
Orthomyxoviridae	5685	2192	2689	0.8
Articulavirales	5615	2186	2686	0.8
Insthoviricetes	5615	2186	2686	0.8

1. ii (Identical Pairs): Base pairs in DNA that are the same when two sequences are compared. They indicate the degree of similarity or genetic relationship between the sequences.

2. si (Transitional Pairs): Substitutions between purines (A and G) or between pyrimidines (C and T) in DNA. These mutations are more common because of the chemical structure similarities between purines and between pyrimidines.

3. sv (Transversional Pairs): Substitutions between a purine and a pyrimidine (e.g., A to C or T, G to C or T) in DNA. These are less common due to the more significant chemical structure changes involved.

4. R (si/sv): The ratio of transitional to transversional pairs. This ratio helps in understanding the predominance of mutation types in DNA and can indicate evolutionary pressures or repair mechanisms.

Polymorphic Sites

Genera	Total sites	Conserved sites	Variable site	Parsim-Info sites	Singleton sites	CpG
Alphainfluenzavirus	13851	7814	5997	4992	996	1484
Betainfluenzavirus	14556	12349	2061	1741	320	3310
Gammainfluenzavirus	13868	11901	1005	168	837	3202
Deltainfluenzavirus	12804	11533	1267	730	537	3204
Influenza virus	16864	4074	12414	11870	541	116
Orthomyxoviridae	25853	1801	18883	16438	1940	0
Articulavirales	26217	1845	19373	16611	2065	0
Insthoviricetes	26217	1845	19373	16611	2065	0

1. Conserved Sites: DNA sequence positions that remain unchanged across different individuals or species, indicating evolutionary importance and functional significance.

2. Variable Site: Positions in DNA sequences where variations are observed when comparing different individuals or species, used to study genetic diversity.

3. Parsim-Info Sites: Sites that provide information for the least number of evolutionary changes, useful in phylogenetic construction for simplifying evolutionary assumptions.

4. Singleton Sites: Positions in a DNA sequence that show a mutation in only one individual within a population, potentially indicating recent mutation events.

5. CpG Sites: Specific DNA regions where a cytosine is followed by a guanine, often involved in gene regulation through methylation processes.

Genetic Distance

Genera	Alphainfluenzavirus	Betainfluenzavirus	Gammainfluenzavirus	Deltainfluenzavirus	Others
Alphainfluenzavirus	0.152	0.678	0.803	0.823	1.035
Betainfluenzavirus	0.678	0.043	0.666	0.67	1.081
Gammainfluenzavirus	0.803	0.666	0.027	0.42	1.113
Deltainfluenzavirus	0.823	0.67	0.42	0.022	1.151
Others	1.035	1.081	1.113	1.151	1.059

"Others" refers to all other genera within Insthoviricetes, excluding Alphainfluenzavirus, Betainfluenzavirus, Gammainfluenzavirus, and Deltainfluenzavirus.