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Statistics about an opened sequence can be found on the Statistics tab of the Options Panel. When a region is selected in the sequence, the statistics is interactively re-calculated for this region only. The following information is available:

• Common statistics (length, molecular weight, etc.) - see the detailed description below
• Characters occurrence
• Dinucleotides occurrence - available for nucleotide sequences only

Note that all data, displayed on the Statistics tab, can be selected with the mouse and copied. Use the copy item in the context menu or a shortcut - Ctrl+C on Windows or Linux, Cmd+C on macOS.

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• Length
• GC content
• Molecular weight
• Extinction coefficient
• Melting Tmtemperature
• nmole/OD260
• μg/OD260

GC content

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The percentage of guanine (G) and cytosine (C) bases in the within the sequence or its selected region, for example:

GC-content("ACGTAC") = ((0 + 1 + 1 + 0 + 0 + 1) / 6) * 100% = 50%

If the sequence contains degenerate base characters, average values are used, for example:

GC-content("ACGNBCT") = ((0 + 1 + 1 + 1/2 + 2/3 + 1 + 0) / 7) * 100% ~= 59.52%

In this example "1/2" is used for "N" (any nucleotide), "2/3" us used for "B" (that means "C", "G", or "T" according to the IUPAC notationnucleotide code).

Molecular weight

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Molecular weight for a single-stranded molecule is calculated as the sum a sum of the atomic masses of the molecule compounds:

DNA molecular weight  = nA*251.24 + nT*242.23 + nC*227.22 + nG*267.24 + (n-1)*

62

61.97 RNA molecular weight = nA*267.

24 

24 + nU*244.20 + nC*243.22 + nG*283.24 + (n-1)*

62

61.97

Here "nA", "nT", "nC", "nG", "nU" denote the number of the corresponding nucleotide in the molecule, "n" is the number of all bases (62 is 61.97 is the weight of an internal phosphate).

Note that for degenerate base characters average value of nucleotide weight is used, for example, if the sequence also contain "Y" characters (that is "C" or "T"), the sum will include one more summand - "nY*(242.23 + 227.22)/2".

Molecular weight for  for a double-stranded molecule is calculated as the sum of the single strands molecular weights.

Extinction coefficient

TODO

Context information about a sequence can be found on the All information is contextual, i.e. it shows statistics about the currently selected region (on the selected sequence). The tab includes information about:

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• Length - number of bases in the analyzed sequence
• GC content - the molar percentage of guanine and cytosine bases in an oligonucleotide sequence
• Molar weight - is the sum of the atomic masses of the constituent atoms for 1 mole of oligonucleotide
• Molar ext. coefficient - the molar extinction coefficient is a physical constant that is unique for each sequence and describes the amount of absorbance at 260nm (A₂₆₀) of 1 mole/L DNA solution measured in 1 cm path-length cuvette
• Melting TM - melting temperature is the temperature at which an oligonucleotide duplex is 50% in single-stranded form and 50% in double-stranded form
• nmole/OD₂₆₀ - the amount of oligonucleotide in nanomoles that, when dissolved in 1 mL volume, results in 1 unit of absorbance at 260 nm with a standard 1 cm path-length cuvette
• μg/OD₂₆₀ - the amount of oligonucleotide in micrograms that, when dissolved in 1 mL volume, results in 1 unit of absorbance at 260 nm with a standard 1 cm path-length cuvette

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To calculate the Extinction coefficient, an approach proposed by Richard Owczarzy is used: http://www.owczarzy.net/extinctionDNA.htm. That is for a single-stranded molecule:

Extinction coefficient = sum(extinction coefficients of all dinucleotides) - sum(extinction coefficients of inner mononucleotides)

For example, let's calculate the molar extinction coefficient ("ε") for "ATGCA":

ε(ATGCA) = ε(AT) + ε(TG) + ε(GC) + ε(CA) - ε(T) - ε(G) - ε(C) =                       = 22800 + 19000 + 17600 + 21200 - 8700 - 11500 - 7400 =                       = 53000

As for the other statistics, average values are used in case of degenerate base characters.

Extinction coefficientfor a double-stranded molecule is calculated as a sum of the extinction coefficients of the two single strands (e_s1 + e_s2) multiplied by coefficient of (1 - hypochromicity h_260nm). The hypochromicity effect can be taken into account as follows:

h260nm = (0.287fAT + 0.059fGC)

where f_AT and f_GC are fractions of AT and GC base pairs, respectively.

Melting temperature

The melting temperature is calculated as follows. For sequences of length 15 or longer:

For shorter sequences:

Here "nA", "nT", "nC", "nG" denote the number of the corresponding nucleotide.

nmole/OD260

The amount of DNA or RNA represented in nanomoles per 1 unit of absorbance at 260 nm dissolved in 1 ml cuvette with 1 cm pathlength.

μg/OD₂₆₀

The amount of DNA or RNA represented in microgrames per 1 unit of absorbance at 260 nm dissolved in 1 ml cuvette with 1 cm pathlength.

Amino acid sequence common statistics

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