Dredd Blog: 2022-07-24

Saturday, July 30, 2022

Small Brains Considered - 2

Dolls Are Telling (2nd video below)

I. Background

Over at the Small Things Considered blog (a GMO people blog) they have uncovered dolls that hitchhike, take the doll bus to preferred locations, and build bridges "over air".

They, like many other microbiologists speak of microbes as if they have brains and emotions (The Doll As Metaphor, 2, 3, 4, 5, 6, 7, 8).

But more than that, they speak in a strange language which few other people understand ("Why have Mass in Latin if almost nobody understands Latin? Good question." - Latin Mass).

Like old time high priests who for centuries have dabbled in a language the laity (church members present) could not understand, the micro (little) biologists trumpeted:

"Microbial hitchhiking" ... "it remains unclear how spores are transported to their preferred microenvironments" ... "these ingenious appendages that bacterial cells use to propel themselves" ... "capable of "transport performances" ... "spores are capable of utilizing the motility machinery" ... "capable of utilizing the motility machinery of other microbes to complete necessary stages of their lifecycle" ... "cells were happily moving" ... "it is unclear how they relocate over short distances to their preferred microenvironments" ... "spores ... are transported ... to their preferred microenvironment" ... "capable of utilizing the motility machinery of other microbes to occupy advantageous environments" ... "necessitate that motile bacteria not evolve" ... "can form so-called 'fungal highways' that serve as bridges for motile bacteria over air gaps" ... [etc.]

(Heavy-duty Traffic, Microscale, promoting Muok et al. (2020) a.k.a. Microbial hitchhiking, emphasis added). Generally these anthropomorphic, metaphorical, and teleological notions are even somehow thought to be permanent and transmissible:

"Mutations are permanent, transmissible changes to the genetic material (DNA or RNA) of a cell or virus. Mutations result from errors in DNA replication during cell division and by exposure to radiation, chemicals, and other environmental stressors, or viruses and transposable elements. Most mutations that occur are single nucleotide polymorphisms which modify single bases of the DNA sequence, resulting in point mutations. Other types of mutations modify larger segments of DNA and can cause duplications, insertions, deletions, inversions, and translocations."

(Wikipedia, Molecular Evolution, emphasis added). All of these things are said to be done by entities within cells/microbes with no brains, yes, done by/in things that are even too tiny for the naked eye to see:

"There are many embarrassments that finger biologists as metaphorically playing with dolls while practicing teleology:

When organic chemists anthropomorphize molecules, they say that molecules “want to be in their lowest energy conformation”. This means that when they have energy molecules can move into different conformations, but they have a resting position that they come back to.

(On The Origin of Genieology - 2). Got teleology? Got conjuration?

Plasmid lovers mutating into 'mother nature' ("what could possibly go wrong?")?!

In a future post I plan to discuss the atomic-level application of Löwdin's hypothesis in greater detail because it is non-teleological."

(Junk DNA R Us - 4). The recent Cornell University work on proton tunneling reinforces a more likely hypothesis ("the revolutionary work of Per-Olov Löwdin").

II. My Research

I thought I would take a look deeper than they tend to, yes all the way down to the quanta, down to the atoms/molecules of the microbes which are said to do the "programming" (i.e. the Codons that "code for").

These codons are used in a nomenclature that is, IMO, loose (Quantum Biology - 11).

I pointed that out in a previous post It's In The GenBank - 3, which has appendices describing the Wuhan-1 SARS-CoV-2 virus.

Those appendices use 'U' for uracil, and 'T' for thymine to show the stark difference it makes when two letters are used instead of just one, to refer to both uracil and thymine in scientific databases.

Today's appendix (Appendix SBC 2) details the codons and amino acids in terms of the atoms they are made of:

Wuhan SARS-CoV-2
Amino Acid
Associations
With Codons
Amino Acid	Amino Acid Formula	DNA Codon & Formulas	RNA Codon & Formulas
MET (M)	C₅H₁₁N₁O₂S₁	ATG: C₅H₅N₅ C₅H₆N₂O₂ C₅H₅N₅O₁ C₁₅H₁₆N₁₂O₃	AUG: C₅H₅N₅ C₄H₄N₂O₂ C₅H₅N₅O₁ C₁₄H₁₄N₁₂O₃
GLU (E)	C₅H₉N₁O₄	GAA: C₅H₅N₅O₁ C₅H₅N₅ C₅H₅N₅ C₁₅H₁₅N₁₅O₁ GAG: C₅H₅N₅O₁ C₅H₅N₅ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₂	GAA: C₅H₅N₅O₁ C₅H₅N₅ C₅H₅N₅ C₁₅H₁₅N₁₅O₁ GAG: C₅H₅N₅O₁ C₅H₅N₅ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₂

...

(A snippet from today's appendix). The amino acid letters "(M)" ... "(E)" are from the GenBank .gbff file @ "CDS ... /translation=" areas (12 CDS areas total), which are the letters ascribed to the amino acids that the Codons are said "to code for" (whatever that means).

As you can see, the amino acids, codons, and atoms are not brains, no, they are inanimate objects (C=carbon, H=hydrogen,N=nitrogen, O=oxygen).

The amino acids (first column in the Table above) are composed of atoms which the Codons (which are said to "code for" the amino acid) do not match in terms of quantity (the underlined value at the end of each Codon atom list is the total number of atoms in that Codon).

That is, there is no coherent association between the atoms of the Codons and the atoms of the amino acid which the Codons are said "to code for" (notice also that the RNA values i.e. Codons with a 'U' in them, do not match the DNA values i.e. Codons with a 'T' in them).

III. Closing Comments

Can you figure out how the Carbon, Hydrogen, Nitrogen, and Oxygen atoms "figure out" how to build bridges and highways so as to "hitchhike" or otherwise be "happily moving" to and from their "preferred microenvironments"? (Ridiculous!).

If you know how to scientifically falsify my hypothesis (which is that their hypothesis is ridiculous), and can speak the language that falsifies my hypothesis free from doll-speak, please do so.

The next post in this series is here, the previous post in this series is here.

Small brain hitching a ride to its baby's "microenvironment" ...

Appendix SBC 2

This is an appendix to: Small Brains Considered - 2

Wuhan SARS-CoV-2
Amino Acid
Associations
With Codons
Amino Acid	Amino Acid Formula	DNA Codon & Formulas	RNA Codon & Formulas
MET (M)	C₅H₁₁N₁O₂S₁	ATG: C₅H₅N₅ C₅H₆N₂O₂ C₅H₅N₅O₁ C₁₅H₁₆N₁₂O₃	AUG: C₅H₅N₅ C₄H₄N₂O₂ C₅H₅N₅O₁ C₁₄H₁₄N₁₂O₃
GLU (E)	C₅H₉N₁O₄	GAA: C₅H₅N₅O₁ C₅H₅N₅ C₅H₅N₅ C₁₅H₁₅N₁₅O₁ GAG: C₅H₅N₅O₁ C₅H₅N₅ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₂	GAA: C₅H₅N₅O₁ C₅H₅N₅ C₅H₅N₅ C₁₅H₁₅N₁₅O₁ GAG: C₅H₅N₅O₁ C₅H₅N₅ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₂
SER (S)	C₃H₇N₁O₃	TCT: C₅H₆N₂O₂ C₄H₅N₃O₁ C₅H₆N₂O₂ C₁₄H₁₇N₇O₅ TCC: C₅H₆N₂O₂ C₄H₅N₃O₁ C₄H₅N₃O₁ C₁₃H₁₆N₈O₄ TCA: C₅H₆N₂O₂ C₄H₅N₃O₁ C₅H₅N₅ C₁₄H₁₆N₁₀O₃ TCG: C₅H₆N₂O₂ C₄H₅N₃O₁ C₅H₅N₅O₁ C₁₄H₁₆N₁₀O₄ AGT: C₅H₅N₅ C₅H₅N₅O₁ C₅H₆N₂O₂ C₁₅H₁₆N₁₂O₃ AGC: C₅H₅N₅ C₅H₅N₅O₁ C₄H₅N₃O₁ C₁₄H₁₅N₁₃O₂	UCU: C₄H₄N₂O₂ C₄H₅N₃O₁ C₄H₄N₂O₂ C₁₂H₁₃N₇O₅ UCC: C₄H₄N₂O₂ C₄H₅N₃O₁ C₄H₅N₃O₁ C₁₂H₁₄N₈O₄ UCA: C₄H₄N₂O₂ C₄H₅N₃O₁ C₅H₅N₅ C₁₃H₁₄N₁₀O₃ UCG: C₄H₄N₂O₂ C₄H₅N₃O₁ C₅H₅N₅O₁ C₁₃H₁₄N₁₀O₄ AGU: C₅H₅N₅ C₅H₅N₅O₁ C₄H₄N₂O₂ C₁₄H₁₄N₁₂O₃ AGC: C₅H₅N₅ C₅H₅N₅O₁ C₄H₅N₃O₁ C₁₄H₁₅N₁₃O₂
LEU (L)	C₆H₁₃N₁O₂	CTT: C₄H₅N₃O₁ C₅H₆N₂O₂ C₅H₆N₂O₂ C₁₄H₁₇N₇O₅ CTC: C₄H₅N₃O₁ C₅H₆N₂O₂ C₄H₅N₃O₁ C₁₃H₁₆N₈O₄ CTA: C₄H₅N₃O₁ C₅H₆N₂O₂ C₅H₅N₅ C₁₄H₁₆N₁₀O₃ CTG: C₄H₅N₃O₁ C₅H₆N₂O₂ C₅H₅N₅O₁ C₁₄H₁₆N₁₀O₄ TTA: C₅H₆N₂O₂ C₅H₆N₂O₂ C₅H₅N₅ C₁₅H₁₇N₉O₄ TTG: C₅H₆N₂O₂ C₅H₆N₂O₂ C₅H₅N₅O₁ C₁₅H₁₇N₉O₅	CUU: C₄H₅N₃O₁ C₄H₄N₂O₂ C₄H₄N₂O₂ C₁₂H₁₃N₇O₅ CUC: C₄H₅N₃O₁ C₄H₄N₂O₂ C₄H₅N₃O₁ C₁₂H₁₄N₈O₄ CUA: C₄H₅N₃O₁ C₄H₄N₂O₂ C₅H₅N₅ C₁₃H₁₄N₁₀O₃ CUG: C₄H₅N₃O₁ C₄H₄N₂O₂ C₅H₅N₅O₁ C₁₃H₁₄N₁₀O₄ UUA: C₄H₄N₂O₂ C₄H₄N₂O₂ C₅H₅N₅ C₁₃H₁₃N₉O₄ UUG: C₄H₄N₂O₂ C₄H₄N₂O₂ C₅H₅N₅O₁ C₁₃H₁₃N₉O₅
VAL (V)	C₅H₁₁N₁O₂	GTT: C₅H₅N₅O₁ C₅H₆N₂O₂ C₅H₆N₂O₂ C₁₅H₁₇N₉O₅ GTC: C₅H₅N₅O₁ C₅H₆N₂O₂ C₄H₅N₃O₁ C₁₄H₁₆N₁₀O₄ GTA: C₅H₅N₅O₁ C₅H₆N₂O₂ C₅H₅N₅ C₁₅H₁₆N₁₂O₃ GTG: C₅H₅N₅O₁ C₅H₆N₂O₂ C₅H₅N₅O₁ C₁₅H₁₆N₁₂O₄	GUU: C₅H₅N₅O₁ C₄H₄N₂O₂ C₄H₄N₂O₂ C₁₃H₁₃N₉O₅ GUC: C₅H₅N₅O₁ C₄H₄N₂O₂ C₄H₅N₃O₁ C₁₃H₁₄N₁₀O₄ GUA: C₅H₅N₅O₁ C₄H₄N₂O₂ C₅H₅N₅ C₁₄H₁₄N₁₂O₃ GUG: C₅H₅N₅O₁ C₄H₄N₂O₂ C₅H₅N₅O₁ C₁₄H₁₄N₁₂O₄
PRO (P)	C₅H₉N₁O₂	CCT: C₄H₅N₃O₁ C₄H₅N₃O₁ C₅H₆N₂O₂ C₁₃H₁₆N₈O₄ CCC: C₄H₅N₃O₁ C₄H₅N₃O₁ C₄H₅N₃O₁ C₁₂H₁₅N₉O₃ CCA: C₄H₅N₃O₁ C₄H₅N₃O₁ C₅H₅N₅ C₁₃H₁₅N₁₁O₂ CCG: C₄H₅N₃O₁ C₄H₅N₃O₁ C₅H₅N₅O₁ C₁₃H₁₅N₁₁O₃	CCU: C₄H₅N₃O₁ C₄H₅N₃O₁ C₄H₄N₂O₂ C₁₂H₁₄N₈O₄ CCC: C₄H₅N₃O₁ C₄H₅N₃O₁ C₄H₅N₃O₁ C₁₂H₁₅N₉O₃ CCA: C₄H₅N₃O₁ C₄H₅N₃O₁ C₅H₅N₅ C₁₃H₁₅N₁₁O₂ CCG: C₄H₅N₃O₁ C₄H₅N₃O₁ C₅H₅N₅O₁ C₁₃H₁₅N₁₁O₃
GLY (G)	C₂H₅N₁O₂	GGT: C₅H₅N₅O₁ C₅H₅N₅O₁ C₅H₆N₂O₂ C₁₅H₁₆N₁₂O₄ GGC: C₅H₅N₅O₁ C₅H₅N₅O₁ C₄H₅N₃O₁ C₁₄H₁₅N₁₃O₃ GGA: C₅H₅N₅O₁ C₅H₅N₅O₁ C₅H₅N₅ C₁₅H₁₅N₁₅O₂ GGG: C₅H₅N₅O₁ C₅H₅N₅O₁ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₃	GGU: C₅H₅N₅O₁ C₅H₅N₅O₁ C₄H₄N₂O₂ C₁₄H₁₄N₁₂O₄ GGC: C₅H₅N₅O₁ C₅H₅N₅O₁ C₄H₅N₃O₁ C₁₄H₁₅N₁₃O₃ GGA: C₅H₅N₅O₁ C₅H₅N₅O₁ C₅H₅N₅ C₁₅H₁₅N₁₅O₂ GGG: C₅H₅N₅O₁ C₅H₅N₅O₁ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₃
PHE (F)	C₉H₁₁N₁O₂	TTT: C₅H₆N₂O₂ C₅H₆N₂O₂ C₅H₆N₂O₂ C₁₅H₁₈N₆O₆ TTC: C₅H₆N₂O₂ C₅H₆N₂O₂ C₄H₅N₃O₁ C₁₄H₁₇N₇O₅	UUU: C₄H₄N₂O₂ C₄H₄N₂O₂ C₄H₄N₂O₂ C₁₂H₁₂N₆O₆ UUC: C₄H₄N₂O₂ C₄H₄N₂O₂ C₄H₅N₃O₁ C₁₂H₁₃N₇O₅
ASN (N)	C₄H₈N₂O₃	AAT: C₅H₅N₅ C₅H₅N₅ C₅H₆N₂O₂ C₁₅H₁₆N₁₂O₂ AAC: C₅H₅N₅ C₅H₅N₅ C₄H₅N₃O₁ C₁₄H₁₅N₁₃O₁	AAU: C₅H₅N₅ C₅H₅N₅ C₄H₄N₂O₂ C₁₄H₁₄N₁₂O₂ AAC: C₅H₅N₅ C₅H₅N₅ C₄H₅N₃O₁ C₁₄H₁₅N₁₃O₁
LYS (K)	C₆H₁₄N₂O₂	AAA: C₅H₅N₅ C₅H₅N₅ C₅H₅N₅ C₁₅H₁₅N₁₅ AAG: C₅H₅N₅ C₅H₅N₅ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₁	AAA: C₅H₅N₅ C₅H₅N₅ C₅H₅N₅ C₁₅H₁₅N₁₅ AAG: C₅H₅N₅ C₅H₅N₅ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₁
THR (T)	C₄H₉N₁O₃	ACT: C₅H₅N₅ C₄H₅N₃O₁ C₅H₆N₂O₂ C₁₄H₁₆N₁₀O₃ ACC: C₅H₅N₅ C₄H₅N₃O₁ C₄H₅N₃O₁ C₁₃H₁₅N₁₁O₂ ACA: C₅H₅N₅ C₄H₅N₃O₁ C₅H₅N₅ C₁₄H₁₅N₁₃O₁ ACG: C₅H₅N₅ C₄H₅N₃O₁ C₅H₅N₅O₁ C₁₄H₁₅N₁₃O₂	ACU: C₅H₅N₅ C₄H₅N₃O₁ C₄H₄N₂O₂ C₁₃H₁₄N₁₀O₃ ACC: C₅H₅N₅ C₄H₅N₃O₁ C₄H₅N₃O₁ C₁₃H₁₅N₁₁O₂ ACA: C₅H₅N₅ C₄H₅N₃O₁ C₅H₅N₅ C₁₄H₁₅N₁₃O₁ ACG: C₅H₅N₅ C₄H₅N₃O₁ C₅H₅N₅O₁ C₁₄H₁₅N₁₃O₂
HIS (H)	C₆H₉N₃O₂	CAT: C₄H₅N₃O₁ C₅H₅N₅ C₅H₆N₂O₂ C₁₄H₁₆N₁₀O₃ CAC: C₄H₅N₃O₁ C₅H₅N₅ C₄H₅N₃O₁ C₁₃H₁₅N₁₁O₂	CAU: C₄H₅N₃O₁ C₅H₅N₅ C₄H₄N₂O₂ C₁₃H₁₄N₁₀O₃ CAC: C₄H₅N₃O₁ C₅H₅N₅ C₄H₅N₃O₁ C₁₃H₁₅N₁₁O₂
GLN (Q)	C₅H₁₀N₂O₃	CAA: C₄H₅N₃O₁ C₅H₅N₅ C₅H₅N₅ C₁₄H₁₅N₁₃O₁ CAG: C₄H₅N₃O₁ C₅H₅N₅ C₅H₅N₅O₁ C₁₄H₁₅N₁₃O₂	CAA: C₄H₅N₃O₁ C₅H₅N₅ C₅H₅N₅ C₁₄H₁₅N₁₃O₁ CAG: C₄H₅N₃O₁ C₅H₅N₅ C₅H₅N₅O₁ C₁₄H₁₅N₁₃O₂
ARG (R)	C₆H₁₄N₄O₂	CGT: C₄H₅N₃O₁ C₅H₅N₅O₁ C₅H₆N₂O₂ C₁₄H₁₆N₁₀O₄ CGC: C₄H₅N₃O₁ C₅H₅N₅O₁ C₄H₅N₃O₁ C₁₃H₁₅N₁₁O₃ CGA: C₄H₅N₃O₁ C₅H₅N₅O₁ C₅H₅N₅ C₁₄H₁₅N₁₃O₂ CGG: C₄H₅N₃O₁ C₅H₅N₅O₁ C₅H₅N₅O₁ C₁₄H₁₅N₁₃O₃ AGA: C₅H₅N₅ C₅H₅N₅O₁ C₅H₅N₅ C₁₅H₁₅N₁₅O₁ AGG: C₅H₅N₅ C₅H₅N₅O₁ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₂	CGU: C₄H₅N₃O₁ C₅H₅N₅O₁ C₄H₄N₂O₂ C₁₃H₁₄N₁₀O₄ CGC: C₄H₅N₃O₁ C₅H₅N₅O₁ C₄H₅N₃O₁ C₁₃H₁₅N₁₁O₃ CGA: C₄H₅N₃O₁ C₅H₅N₅O₁ C₅H₅N₅ C₁₄H₁₅N₁₃O₂ CGG: C₄H₅N₃O₁ C₅H₅N₅O₁ C₅H₅N₅O₁ C₁₄H₁₅N₁₃O₃ AGA: C₅H₅N₅ C₅H₅N₅O₁ C₅H₅N₅ C₁₅H₁₅N₁₅O₁ AGG: C₅H₅N₅ C₅H₅N₅O₁ C₅H₅N₅O₁ C₁₅H₁₅N₁₅O₂
ASP (D)	C₄H₇N₁O₄	GAT: C₅H₅N₅O₁ C₅H₅N₅ C₅H₆N₂O₂ C₁₅H₁₆N₁₂O₃ GAC: C₅H₅N₅O₁ C₅H₅N₅ C₄H₅N₃O₁ C₁₄H₁₅N₁₃O₂	GAU: C₅H₅N₅O₁ C₅H₅N₅ C₄H₄N₂O₂ C₁₄H₁₄N₁₂O₃ GAC: C₅H₅N₅O₁ C₅H₅N₅ C₄H₅N₃O₁ C₁₄H₁₅N₁₃O₂
ALA (A)	C₃H₇N₁O₂	GCT: C₅H₅N₅O₁ C₄H₅N₃O₁ C₅H₆N₂O₂ C₁₄H₁₆N₁₀O₄ GCC: C₅H₅N₅O₁ C₄H₅N₃O₁ C₄H₅N₃O₁ C₁₃H₁₅N₁₁O₃ GCA: C₅H₅N₅O₁ C₄H₅N₃O₁ C₅H₅N₅ C₁₄H₁₅N₁₃O₂ GCG: C₅H₅N₅O₁ C₄H₅N₃O₁ C₅H₅N₅O₁ C₁₄H₁₅N₁₃O₃	GCU: C₅H₅N₅O₁ C₄H₅N₃O₁ C₄H₄N₂O₂ C₁₃H₁₄N₁₀O₄ GCC: C₅H₅N₅O₁ C₄H₅N₃O₁ C₄H₅N₃O₁ C₁₃H₁₅N₁₁O₃ GCA: C₅H₅N₅O₁ C₄H₅N₃O₁ C₅H₅N₅ C₁₄H₁₅N₁₃O₂ GCG: C₅H₅N₅O₁ C₄H₅N₃O₁ C₅H₅N₅O₁ C₁₄H₁₅N₁₃O₃
CYS (C)	C₃H₇N₁O₂S₁	TGT: C₅H₆N₂O₂ C₅H₅N₅O₁ C₅H₆N₂O₂ C₁₅H₁₇N₉O₅ TGC: C₅H₆N₂O₂ C₅H₅N₅O₁ C₄H₅N₃O₁ C₁₄H₁₆N₁₀O₄	UGU: C₄H₄N₂O₂ C₅H₅N₅O₁ C₄H₄N₂O₂ C₁₃H₁₃N₉O₅ UGC: C₄H₄N₂O₂ C₅H₅N₅O₁ C₄H₅N₃O₁ C₁₃H₁₄N₁₀O₄
TYR (Y)	C₉H₁₁N₁O₃	TAT: C₅H₆N₂O₂ C₅H₅N₅ C₅H₆N₂O₂ C₁₅H₁₇N₉O₄ TAC: C₅H₆N₂O₂ C₅H₅N₅ C₄H₅N₃O₁ C₁₄H₁₆N₁₀O₃	UAU: C₄H₄N₂O₂ C₅H₅N₅ C₄H₄N₂O₂ C₁₃H₁₃N₉O₄ UAC: C₄H₄N₂O₂ C₅H₅N₅ C₄H₅N₃O₁ C₁₃H₁₄N₁₀O₃
ILE (I)	C₆H₁₃N₁O₂	ATT: C₅H₅N₅ C₅H₆N₂O₂ C₅H₆N₂O₂ C₁₅H₁₇N₉O₄ ATC: C₅H₅N₅ C₅H₆N₂O₂ C₄H₅N₃O₁ C₁₄H₁₆N₁₀O₃ ATA: C₅H₅N₅ C₅H₆N₂O₂ C₅H₅N₅ C₁₅H₁₆N₁₂O₂	AUU: C₅H₅N₅ C₄H₄N₂O₂ C₄H₄N₂O₂ C₁₃H₁₃N₉O₄ AUC: C₅H₅N₅ C₄H₄N₂O₂ C₄H₅N₃O₁ C₁₃H₁₄N₁₀O₃ AUA: C₅H₅N₅ C₄H₄N₂O₂ C₅H₅N₅ C₁₄H₁₄N₁₂O₂
TRP (W)	C₁₁H₁₂N₂O₂	TGG: C₅H₆N₂O₂ C₅H₅N₅O₁ C₅H₅N₅O₁ C₁₅H₁₆N₁₂O₄	UGG: C₄H₄N₂O₂ C₅H₅N₅O₁ C₅H₅N₅O₁ C₁₄H₁₄N₁₂O₄

Monday, July 25, 2022

Quantum Biology - 11

Fig. 1 Close up of a cell's brain?

I. Preference Appendices

I read two doll-oriented papers recently; one from western civilization scientists (Germany & Russia), the other from near-eastern civilization scientists (India).

The papers reveal how cultural/religious beliefs impact scientific research.

The western civilization versions focus on anthropomorphic selections in the brains of microbes (cells with DNA/RNA):

"Translational pressure means preference towards codons [prefer: "to like, choose, or want one thing rather than another" (dictionary)] that are most suitable for translation in a given context ... a growing body of evidence suggests that [Translational pressure] is not the main driver of synonymous codon preference. [IOW 'preference' means that a single cell prefers some codons more than other codons]" (p.1)

"A predominant factor ... is believed ... Additional factors ... might contribute ... could also be produced by ... however, the extent of such ... is still a matter of controversy ... speculated to ... no proof has been presented ... remains to be proven" [yet ...] "The concept of synonymous and non-synonymous genetic variation is central to evolutionary studies." (p. 7)

(Causes and Implications of Codon Usage Bias in RNA, emphasis added). This honesty ("no proof ... remains to be proven") seems clumsy, as far as I am concerned.

It seems to me that it is more scientific to know the 'what' and the 'where' before stumbling over the 'why' when one considers DNA/RNA dynamics.

Mentioning the 'why' in scientific papers, especially when 'the why' is unknown, is a bit clumsy and it detracts from the honesty.

The 'what', the Codons and the viruses listed in that paper, are discussed in today's appendices (Appendix_01, Appendix_02, Appendix_03, Appendix_04, Appendix_05, Appendix_06, Appendix_07, Appendix_08, Appendix_09, Appendix_codons, Appendix_combo_counts, Appendix_CUB_counts).

The "01 - 09" appendices detail the Codon positions within 54 viruses specified in the paper (each virus genome is linked to; click on the link for GenBank virus information).

The "Appendix_codons" appendix is a list of the Codons in the DNA Codon and RNA Codon Tables along with the counts of atoms in the nucleotides of each Codon.

Notice the difference between the two (emphasized by bold), in terms of atomic weight and the impact that could have on the Löwdin hypothesis (The Doll As Metaphor - 4).

I tried to point this out to "the powers that be" (It's In The GenBank - 4).

The "Appendix_combo_counts" details the Codon counts (by family) of the 54 viruses discussed in the paper.

The "Appendix_CUB_counts" details the number of codons in each of the 54 viruses, from most to least contained in the virus (links to each virus included).

II. Western Cells Have Brains?

This is especially so when one is on the edge of saying that a cell can contemplate which codon out of the 64 available is a better choice than the other 63, and therefore that cell somehow prefers (i.e. "to like, choose, or want one thing rather than another") the chosen one.

One of the appendices in today's post includes a list of those 64 codons, the atoms which each nucleotide (molecule) in each codon is made of, and a "Total Atoms" column listing all of the atoms in the three nucleotides (molecules) of that codon:

"Atomic Composition of Codons
Codon	Atoms 1	Atoms 2	Atoms 3	Total Atoms
GCT	C₅H₅N₅O₁	C₄H₅N₃O₁	C₅H₆N₂O₂	C₁₄H₁₆N₁₀O₄
GCC	C₅H₅N₅O₁	C₄H₅N₃O₁	C₄H₅N₃O₁	C₁₃H₁₅N₁₁O₃

..."

(List of Codon Atoms, sample). The "Atoms 1" applies to the first nucleotide in the Codon, the "Atoms 2" applies to the second nucleotide in the Codon, and "Atoms 3" applies to the third nucleotide in the Codon (they are the quanta of the the codon's three molecules).

The "Total Atoms" column is the total of, for example, the 'C' (carbon), 'H' (hydrogen), 'N' (nitrogen), and 'O' (oxygen) atoms in that Codon.

I am pointing out that what the CUB club scientists are really talking about "deep down", is a myth, i.e a myth that a cell makes a choice as to the molecules/atoms that make-up that Codon (The Doll As Metaphor - 3).

III. Near-Eastern Cells Have Magic?

The paper from India is an another, but more extreme, example of animism usage in science:

"In the Indian-origin religions, namely Hinduism, Buddhism, Jainism, and Sikhism, the animistic aspects of nature worship ... are part of the core belief system."

(Wikipedia, Animism). What is a bit strange about this, for one thing, is that they nevertheless are full-on chemical genetic engineering aficionados (e.g. GMO):

"Today, Genetic Engineering is one of the top career choices made by students in engineering courses.

What is Genetic Engineering?

Genetic Engineering is also referred as genetic modification. It is a process of manually adding new DNA to a living organism through artificial methods."

(Sarvgyan, emphasis added). Note that "The headquarters of Ananda Marga Gurukula (an unincorporated international Neohumanist university in the making) is located at Ananda Nagar in the Purulia District of West Bengal, India" (AMGK; cf. Wikipedia: Prabhat Ranjan Sarkar).

I pointed out some of this conundrum ("why artificial-ize the gods?") in a previous post:

"Examples of Intelligence ... For a remarkably long time, the atoms keep some ‘memory’ of their previous quantum mechanical origin ... These, what are called ‘intelligent molecules’ ... Some mysterious traveler is hiding in the background ... Viruses can choose their victims ... a virus cooperates ... How could the trees think of this practical solution and implement it? ... Plants may have intelligence, but are they also able to learn? ... Remarkably, the plants remembered their training ... How do plants transmit their intelligence, learn and remember, since they don’t have brains and a neural system? ... Cooperation is a widely spread phenomenon ... To go with the flow may be a sign of intelligence, but the conscious choice to sometimes cheat and sometimes cooperate hints at intelligence... we know by research, that both human beings and insects have brains and are smart"

(The Doll As Metaphor - 5, quoting from "Evolving Intelligence").

Thus, the characterization of "cells intelligently choosing their Codons" (like humans choosing their favorite liver, heart, lungs, etc.) is but one illogical deduction from the word salad rhetoric in the India paper (Codon usage bias).

Is nothing sacred?

IV. Back To Non-Teleological, Non-Anthropomorphic Science

Can you see that I see a drift in molecular biology from "just the facts ma'am" to "playing with dolls", i.e. using play pretend on inanimate objects that become like "selfish genes" (what next "my lawnmower is so selfish"?).

There are even scientists now in word battles where both use teleological, anthropomorphic ideology to try to cancel each other out (see e.g. The Unselfish Gene vs The Selfish Gene).

Hopefully, soon their dolls will soon have no stuffing in them.

But I digress.

The issue of "codon usage bias" (CUB) was discussed in a recent series (Junk DNA R Us, 2, 3, 4).

Today, let's take a look at CUB from the perspective of atoms while remembering that a codon is:

"A sequence of three consecutive nucleotides in a DNA or RNA molecule that codes for a specific amino acid."

(Codon Definition). The codons are made of nucleotides, and those nucleotides are ... drum roll ... molecules ... and those molecules are made up of ... drum roll .... inanimate objects we call atoms.

V. Closing Comments

That is what quantum science is about, that is what quantum biology is about (Quantum Biology, 2, 3, 4, 5, 6, 7, 8, 9, 10).

The nucleotide's atoms are not alive, the molecules of the Codon are not alive, the Codons are not alive, and the DNA is not alive.

They are quantum mechanical machines (The New Paradigm: The Physical Universe Is Mostly Machine - 2).

IMO, it is about time for virologists and microbiologists to develop and use a realistic nomenclature and stop playing with dolls:

My interpretation of that statement is that Dr. Penrose thinks that evolutionary biologists utilize too much teleological language, and other observers agree with Penrose:

Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena ... except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes.

(Teleological Explanations in Biology, emphasis added). The piece "Teleological Notions in Biology" adds further insight.

This teleological factor lingers in the literature even after many years have passed since "the modern synthesis":

The modern evolutionary synthesis is a 20th-century union of ideas from several biological specialties which provides a widely accepted account of evolution. It is also referred to as the new synthesis, the modern synthesis, the evolutionary synthesis, millennium synthesis and the neo-Darwinian synthesis.

The synthesis, produced between 1936 and 1947, reflects the consensus about how evolution proceeds. The previous development of population genetics, between 1918 and 1932, was a stimulus, as it showed that Mendelian genetics was consistent with natural selection and gradual evolution. The synthesis is still, to a large extent, the current paradigm in evolutionary biology.

The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century.

(Wikipedia, emphasis added). That has led me to zero in on 1) teleology, 2) the modern synthesis, and 3) the issue of the impact of quantum mechanical concepts on evolutionary biology.

(On The Origin of Genieology - 2; cf. Quantum Biology - 7).

The next post in this series is here, the previous post in this series is here.

QB_11 Appx 1

This is an appendix to: Quantum Biology - 11

01) Codon Usage Bias:
About: Respiratory syncytial virus, complete genome (15191bp)
VERSION: U39661.1
CODONS & LOCATIONS:
GCT: 184,222,391,1143,1308,1347,1492,1553,1575,1680,1695,
1735,1762,1869,1952,1962,2121,2124,2184,2199,2268,
2282,2309,2360,2396,2697,2791,2831,2927,3264,3278,
3281,3389,3472,3535,3665,3914,3968,4363,4441,4451,
4744,4946,4957,5004,5203,5208,5399,5677,5698,5759,
5770,5851,5896,5916,6047,6088,6139,6160,6170,6263,
6694,6842,6878,7183,7269,7401,7619,7680,7762,7812,
8416,8495,8555,8813,8843,8863,8954,9360,9366,9547,
9566,9569,9578,9592,9694,9791,9923,10088,10409,10551,
10673,10832,10883,10955,10972,11111,11279,11489,11621,
11654,11675,11729,11830,11992,12179,12530,12636,12648,
12712,12956,13076,13126,13284,13547,13717,13903,14143,
14195,14246,14276,14393,14451,14543,14591,14892,14998
GCT count: 127

GCC: 295,338,406,616,796,906,954,1074,1755,1887,2010,2128,
2508,2575,2623,2852,3160,3168,3183,3340,3361,3484,
3506,3588,3794,3883,4121,4256,4318,4565,4830,4845,
4900,5093,5110,5261,5345,5357,5482,5583,5640,5950,
6076,6423,6865,7136,7258,7285,7665,7792,7867,7932,
8031,8137,8455,9294,9782,9857,9907,10048,10141,11022,
11410,11933,12286,12437,12483,12564,12642,13245,13335,
13729,13826,14284,14581
GCC count: 75

GCA: 48,103,106,165,216,228,256,269,539,599,837,851,893,
941,947,963,1045,1128,1150,1201,1222,1259,1285,1413,
1589,1632,1653,1656,1824,1846,1896,1901,1929,1970,
1974,2031,2064,2116,2134,2187,2193,2253,2334,2384,
2424,2744,2816,2900,2933,2966,3227,3320,3365,3467,
3476,3489,3531,3539,3572,3806,3866,3961,3980,4193,
4261,4308,4388,4468,4486,4504,4561,4647,4653,4681,
4773,4797,4827,4851,4878,4893,5036,5089,5176,5179,
5185,5188,5473,5576,5622,5659,5668,5680,5741,5746,
5753,5910,5922,5927,5935,6020,6070,6083,6105,6200,
6258,6269,6352,6374,6480,6523,6579,6667,6776,6809,
6839,6884,6901,7014,7022,7099,7141,7280,7292,7310,
7342,7366,7570,7595,7675,7733,7765,7858,7874,7985,
8035,8084,8330,8984,9058,9651,9698,9807,9834,10320,
10355,10360,10394,10490,10572,10586,10636,10698,10708,
10712,10961,10976,11012,11016,11065,11238,11300,11387,
11592,11705,11724,11756,11800,11867,12075,12171,12186,
12344,12365,12405,12478,12518,12576,12796,12904,13116,
13121,13253,13319,13379,13755,13876,13884,13899,13912,
14015,14033,14109,14204,14325,14329,14343,14457,14507,
14612,14675,14729,14751,14773
GCA count: 203

GCG: 3,13,28,1395,1629,2810,5566,6947,9375,11688,14050
GCG count: 11

CGT: 1440,1725,3244,4417,4640,4741,6846,6916,7150,8040,
8763,10025,10034,10514,11142,11629,12224,13307,14373,
14735,15189
CGT count: 21

CGC: (0)

CGA: 2731,3259,3310,3974,4454,5468,5507,5947,6642,6716,
6721,7158,7452,7582,7609,7737,8130,8280,8512,9131,
9634,9811,10189,10592,10798,11450,14074,14407,15159
CGA count: 29

CGG: 1218,1914,2834,3189,6942,7797,9530,10043,11095,11827,
11893,13626,13785
CGG count: 13

AGA: 55,95,132,413,583,586,661,675,682,698,721,739,775,
790,936,1014,1105,1114,1121,1181,1229,1301,1304,1356,
1365,1370,1389,1445,1460,1522,1526,1533,1559,1568,
1580,1665,1799,1839,1851,2027,2144,2151,2171,2213,
2243,2258,2264,2294,2306,2377,2380,2393,2410,2443,
2451,2458,2485,2491,2503,2550,2554,2588,2611,2614,
2656,2665,2686,2689,2710,2724,2747,2752,2846,2867,
2872,2881,2891,2918,2923,2936,2961,2971,2980,3007,
3111,3114,3199,3220,3301,3307,3382,3443,3461,3527,
3622,3725,3740,3748,3904,3922,3928,3997,4126,4151,
4242,4297,4448,4619,4627,4690,4697,4702,4889,4903,
4909,4936,5053,5220,5245,5284,5297,5351,5388,5426,
5601,5721,5776,5808,5847,5874,5880,5904,5953,5956,
6023,6034,6037,6111,6210,6228,6308,6316,6324,6440,
6475,6558,6637,6646,6831,6929,7017,7121,7124,7133,
7288,7407,7495,7534,7561,7631,7687,7708,7749,7777,
7782,7785,7815,7929,7946,7951,8026,8048,8081,8106,
8207,8229,8317,8545,8618,8635,8652,8710,8713,8751,
8767,8772,8799,8807,8810,8818,8869,8875,8880,8902,
8908,8938,9013,9039,9169,9245,9302,9371,9418,9466,
9472,9508,9511,9514,9524,9562,9582,9599,9619,9624,
9746,9769,9776,9851,9869,9902,9941,9994,9998,10130,
10165,10205,10208,10216,10229,10324,10328,10346,10376,
10398,10448,10462,10470,10480,10564,10727,10741,10756,
10778,10828,10912,10931,11043,11057,11132,11182,11206,
11212,11224,11252,11462,11465,11485,11542,11554,11563,
11570,11642,11667,11699,11776,11782,11809,11834,11871,
11925,11938,11947,11967,12013,12023,12092,12231,12271,
12299,12321,12325,12334,12373,12397,12432,12500,12536,
12586,12604,12664,12692,12720,12811,12909,12991,13015,
13024,13083,13150,13177,13216,13354,13396,13406,13426,
13510,13561,13597,13606,13647,13713,13742,13762,13807,
13925,13984,13999,14081,14093,14200,14336,14398,14419,
14561,14586,14599,14691,14707,14816,14824,14854
AGA count: 331

AGG: 356,1102,1226,1334,1361,1689,1692,1747,1859,1955,1996,
2163,2421,2566,2756,2785,2942,2949,3031,3826,3862,
4208,4672,5326,5417,5443,5825,5855,5968,6028,6057,
6098,6114,6334,6509,6512,6611,6615,6861,6965,6987,
7041,7313,7585,7827,7918,7990,8356,8527,8560,8695,
8961,9141,9234,9447,9880,9917,10018,10342,10366,10801,
10864,10942,11035,11191,11337,11659,11715,11975,11999,
12032,12086,12235,12381,12409,12751,12999,13108,13206,
13248,13273,13541,13669,13816,13951,14023,14029,14103,
14469,14500,14662,14932,15102,15105
AGG count: 94

AAT: 10,42,51,77,141,153,176,196,200,213,242,247,252,300,
303,306,319,324,335,351,371,379,402,410,420,428,433,
461,468,477,481,490,510,518,524,528,542,546,593,602,
606,610,643,705,708,757,764,825,857,866,875,887,919,
975,994,1002,1024,1031,1068,1081,1090,1097,1131,1139,
1164,1204,1248,1272,1295,1311,1318,1331,1382,1416,
1452,1463,1468,1505,1511,1537,1550,1562,1616,1640,
1648,1698,1701,1713,1718,1783,1828,1884,1933,1944,
1979,2005,2017,2086,2138,2166,2217,2286,2298,2319,
2328,2337,2367,2403,2416,2427,2482,2522,2546,2579,
2633,2681,2713,2717,2735,2769,2779,2788,2887,2905,
2912,2945,2996,3012,3035,3047,3083,3163,3171,3196,
3230,3288,3293,3331,3351,3392,3415,3428,3481,3492,
3509,3565,3594,3602,3675,3683,3709,3743,3767,3783,
3791,3803,3811,3873,3894,3953,4073,4099,4165,4173,
4179,4196,4199,4212,4221,4227,4265,4273,4280,4294,
4311,4333,4351,4354,4366,4372,4410,4460,4477,4591,
4598,4601,4610,4635,4650,4719,4758,4765,4778,4805,
4823,4952,4965,5078,5136,5139,5193,5409,5421,5593,
5609,5625,5631,5643,5656,5818,5830,5839,5861,5944,
5977,5992,6001,6007,6129,6178,6338,6349,6391,6398,
6411,6415,6433,6450,6460,6468,6504,6536,6555,6664,
6713,6738,6769,6800,6813,6893,6907,6913,6921,6961,
6991,7009,7050,7053,7057,7091,7117,7154,7163,7174,
7180,7190,7201,7221,7239,7254,7336,7356,7362,7372,
7386,7438,7523,7528,7557,7573,7588,7598,7605,7624,
7651,7661,7752,7840,7853,7924,7936,7960,7999,8095,
8143,8146,8163,8191,8222,8246,8261,8294,8299,8339,
8380,8407,8413,8448,8467,8483,8489,8498,8552,8576,
8594,8611,8624,8632,8645,8660,8677,8701,8707,8786,
8803,8821,8852,8886,8894,8932,8966,8970,8993,9019,
9042,9046,9055,9079,9092,9105,9173,9185,9195,9206,
9210,9266,9270,9287,9308,9319,9353,9383,9386,9443,
9460,9493,9500,9519,9539,9572,9587,9638,9643,9647,
9661,9684,9688,9707,9719,9729,9763,9803,9819,9890,
9893,9920,10069,10079,10106,10133,10157,10176,10182,
10200,10239,10244,10248,10274,10298,10369,10387,10402,
10425,10474,10495,10506,10511,10520,10526,10535,10575,
10580,10647,10690,10693,10751,10869,10876,10888,10892,
10901,10905,10909,10982,10992,11028,11083,11255,11270,
11275,11294,11312,11316,11366,11375,11405,11576,11596,
11618,11625,11680,11692,11696,11740,11789,11804,11875,
11882,11901,12037,12069,12078,12110,12148,12159,12190,
12201,12206,12283,12296,12331,12348,12387,12412,12444,
12510,12523,12545,12572,12652,12669,12677,12716,12730,
12817,12831,12840,12854,12867,12884,12890,12895,12929,
12950,13055,13073,13142,13170,13174,13233,13313,13323,
13421,13432,13445,13455,13460,13467,13481,13496,13514,
13550,13557,13565,13568,13578,13610,13622,13632,13637,
13655,13676,13687,13690,13709,13725,13735,13748,13772,
13801,13820,13830,13864,13880,13922,13931,13960,13993,
14006,14039,14150,14180,14280,14308,14340,14363,14367,
14377,14385,14415,14423,14497,14510,14528,14540,14547,
14570,14615,14665,14669,14738,14790,14798,14810,14837,
14880,14903,14926,14957,14961,14964,14968,14974,14988,
15020,15036,15043,15051,15059,15077,15085,15108,15112,
15118,15124,15129
AAT count: 556

AAC: 19,23,33,82,179,209,332,383,397,445,458,534,555,624,
636,717,732,779,817,830,880,1008,1034,1037,1049,1176,
1186,1264,1430,1433,1481,1496,1499,1515,1643,1758,
1984,2052,2055,2203,2206,2229,2275,2342,2387,2390,
2477,2497,2515,2527,2542,2570,2592,2646,2659,2668,
2678,2740,3001,3017,3020,3095,3102,3108,3119,3123,
3127,3131,3144,3149,3178,3238,3248,3252,3398,3411,
3455,3550,3583,3610,3637,3644,3649,3691,3715,3755,
3772,3775,3857,3949,3987,4002,4039,4080,4095,4104,
4109,4217,4237,4251,4269,4291,4345,4348,4397,4401,
4427,4432,4492,4498,4517,4520,4539,4548,4607,4614,
4632,4656,4668,4678,4811,4854,4871,4874,4916,4922,
4976,4988,5009,5012,5030,5045,5061,5066,5069,5072,
5083,5104,5107,5115,5119,5127,5131,5163,5198,5229,
5236,5249,5272,5276,5288,5305,5312,5320,5360,5367,
5378,5382,5406,5447,5459,5501,5521,5538,5543,5547,
5597,5613,5628,5652,5710,5733,5736,5802,5844,5870,
5901,5941,5960,5989,6012,6124,6154,6195,6220,6233,
6253,6277,6285,6302,6313,6360,6387,6429,6457,6575,
6600,6604,6622,6633,6699,6742,6750,6793,6828,6888,
7046,7129,7212,7319,7351,7411,7444,7455,7539,7693,
7705,7845,7850,7877,7889,7894,7913,7996,8003,8007,
8052,8061,8088,8098,8112,8194,8252,8255,8264,8286,
8349,8400,8432,8439,8445,8509,8606,8655,8665,8856,
8891,8912,8926,9006,9025,9028,9110,9113,9121,9149,
9237,9259,9335,9344,9402,9432,9505,9551,9554,9710,
9716,9899,9949,9965,9987,10235,10262,10289,10292,10332,
10415,10502,10532,10600,10632,10748,10761,10815,10923,
10948,11038,11080,11088,11150,11286,11309,11346,11356,
11392,11438,11528,11547,11587,11612,11632,11735,11760,
11908,11912,11944,11981,11986,12020,12053,12166,12212,
12220,12246,12280,12310,12318,12377,12424,12470,12583,
12626,12689,12735,12777,12792,12859,12981,13036,13290,
13349,13366,13387,13449,13502,13528,13533,13574,13600,
13618,13758,13835,13839,14064,14162,14210,14213,14250,
14290,14297,14428,14440,14653,14685,14757,14780,14821,
14831,14888,14899,14907,14916,14948,15008,15062,15073,
15149,15154
AAC count: 368

GAT: 62,98,122,156,233,374,453,499,504,666,669,753,784,
925,988,1167,1239,1254,1392,1399,1425,1602,1610,1613,
1662,1685,1862,1873,1907,2181,2225,2301,2558,2630,
2675,2720,2762,2837,2849,2878,3038,3050,3062,3065,
3072,3368,3451,3521,3545,4029,4342,4384,4482,4802,
5142,5865,6065,6327,6418,6436,6650,6671,6805,7087,
7096,7209,7230,7427,7726,7900,8071,8149,8323,8327,
8366,8369,8471,8597,8828,8942,9166,9189,9328,9378,
9477,9654,9658,9788,10001,10006,10061,10072,10082,
10111,10196,10232,10253,10405,10457,10523,10619,10628,
10730,10770,10847,10964,11060,11146,11162,11165,11372,
11381,11432,11474,11534,11567,11638,11645,11779,11792,
11971,12026,12353,12557,12599,12611,12755,12761,12784,
12873,12967,12973,13029,13040,13136,13413,13417,13463,
13738,13792,13796,14114,14168,14273,14402,14551,14594,
14609,14629,14920,15097,15162
GAT count: 152

GAC: 150,192,417,464,580,619,631,646,724,1108,1593,2081,
2249,2820,2908,2915,3044,3314,3432,3656,3850,3854,
4710,5588,6661,6733,6784,6819,6973,7066,7265,7774,
7903,7921,8159,8308,8462,8743,8758,8898,9256,9277,
9397,9704,9756,9814,10117,10315,10822,10898,11139,
11200,11327,11606,11670,12152,12826,12917,12960,13640,
13658,13682,14154,14185,14896,15175
GAC count: 66

TGT: 145,169,260,266,272,311,343,423,689,1192,1281,1288,
1339,1351,1406,1477,1486,1605,1623,1774,1802,1808,
1876,1967,1991,2074,2105,2222,2237,2473,2563,2988,
3024,3087,3345,3503,3513,3560,3575,3606,3671,3736,
3834,3943,4087,4143,4233,4406,4509,4660,4969,5021,
5158,5168,5214,5692,5796,5836,6053,6060,6189,6206,
6239,6249,6288,6345,6357,6369,6383,6497,6528,6552,
6568,6595,6628,6658,6703,6730,6834,6870,6954,6978,
6984,7005,7035,7076,7244,7377,7550,7577,7636,7683,
7700,7800,7861,7955,7965,8018,8115,8171,8204,8217,
8394,8502,8530,8549,9050,9218,9253,9314,9338,9422,
9486,9605,9741,9828,9846,9886,9928,9981,10009,10265,
10303,10339,10350,10607,10613,10642,10684,10738,10808,
11098,11306,11397,11415,11442,11503,11559,11839,12017,
12082,12121,12141,12360,12466,12506,12629,12683,12801,
12835,12880,13047,13095,13133,13160,13200,13277,13345,
13402,13664,13701,13767,13789,13936,13955,14009,14266,
14270,14287,14332,14351,14446,14514,14642,14679,14695,
14698,14803,14883,14940,15013,15141
TGT count: 182

TGC: (0)

CAA: 36,138,280,348,440,658,840,861,884,959,981,1135,1157,
1215,1489,1544,2013,2059,2210,2290,2500,2585,2608,
2643,2653,2727,3175,3213,3568,3597,3696,3787,3887,
4135,4245,4305,4489,4536,4664,4751,4859,4897,5017,
5024,5057,5075,5101,5258,5266,5291,5317,5323,5342,
5375,5434,5439,5479,5490,5606,5649,5707,5997,6132,
6216,6608,6758,6824,7103,7690,7908,8102,8225,8249,
8258,8336,8452,8621,8833,8935,8989,9003,9022,9102,
9135,9241,9779,10154,10277,10379,10583,10811,10861,
10958,11170,11651,11749,11898,12302,12313,12623,12769,
12788,12814,13220,14537,14566,14682
CAA count: 107

CAG: 793,1586,1936,2102,2234,3075,3615,3733,3846,4020,5550,
5703,6674,7298,8669,8729,8916,9125,9627,10336,10926,
12489,12493,12657,13180,13329,14055,14257,14358,14520
CAG count: 30

GAA: 159,787,848,1078,1118,1457,1473,1721,1770,1779,2351,
2765,2897,2957,2984,3524,3634,3680,3764,3958,4277,
5154,5242,6118,6763,7981,9283,9773,10172,10412,10436,
10486,11122,11846,11921,12050,12089,12274,12988,13010,
13060,13192,13375,14177,14477,14741
GAA count: 46

GAG: 116,1420,2314,4024,5635,6182,7323,7768,7808,7818,9724,
9841,10037,10192,11006,11074,11176,12043,13130,14132,
14302
GAG count: 21

GGT: 91,813,929,1327,1571,1671,1818,1842,1893,1922,2022,
2035,2154,2840,2857,2861,3337,4090,5782,5786,6653,
6969,7186,7389,7612,7627,8579,9075,9087,9155,9215,
9450,9469,9701,9766,9854,9945,10306,10454,10662,10790,
10793,10895,11262,11423,11426,11429,12099,12227,12253,
12257,12420,12596,13296,13342,14174,14223,14472,14793,
14851,15133
GGT count: 61

GGC: 12901
GGC count: 1

GGA: 368,1071,3028,3235,3911,3994,4118,6572,7759,8486,10939,
12394,14322,14732
GGA count: 14

GGG: 45,596,1125,1565,1659,1918,2141,2331,3224,4190,4644,
5619,7567,8860,12357,13020,14036
GGG count: 17

CAT: 112,204,237,514,560,627,678,686,729,760,800,806,922,
972,998,1042,1059,1195,1211,1268,1314,1376,1437,1812,
2043,2068,2347,2372,2433,2467,2530,2662,2703,2799,
2826,2875,2976,3091,3139,3270,3354,3358,3438,3448,
3499,3653,3661,3706,3730,3814,3841,3877,3991,4017,
4033,4052,4067,4070,4113,4130,4140,4147,4187,4202,
4284,4288,4339,4369,4378,4381,4424,4464,4544,4558,
4570,4574,4604,4722,4733,4738,4783,4790,4835,4841,
4883,4981,4997,5279,5363,5527,5533,5557,5919,6407,
6501,6584,6780,6854,6875,6924,6932,6995,7070,7171,
7197,7206,7250,7394,7404,7415,7422,7449,7461,7472,
7483,7615,7639,7648,7672,7968,7973,8014,8055,8066,
8091,8134,8185,8267,8289,8303,8397,8424,8427,8476,
8569,8628,8641,8690,8733,8929,8975,9062,9069,9072,
9083,9152,9176,9230,9324,9348,9457,9608,9612,10075,
10150,10169,10540,10558,10667,10701,10733,10784,10825,
10936,10952,11297,11509,11531,11601,11817,12009,12126,
12249,12261,12391,12725,12742,12926,12937,13043,13051,
13103,13237,13280,13361,13370,13438,13492,13520,13586,
13698,13811,13859,13887,13916,14020,14069,14117,14188,
14219,14390,14575,14578,14718,14768,14840,14862,14954,
14994,15091
CAT count: 210

CAC: 71,329,387,551,640,651,672,692,713,736,966,1019,1052,
1171,1208,1298,1322,1373,1791,1959,2094,2158,2436,
2795,3057,3099,3135,3274,3324,3421,3553,3628,3759,
3778,3799,3964,4059,4064,4076,4224,4329,4473,4526,
4555,4685,4693,4816,4865,4913,4931,4984,4991,4994,
5042,5096,5122,5148,5252,5255,5339,5348,5372,5395,
5402,5414,5430,5454,5518,5685,5715,5930,5984,6150,
6365,6542,6563,6689,7194,7295,7302,7477,7884,7940,
8077,8233,8277,8377,8782,8996,9440,9559,10095,10146,
10561,10687,10839,11482,11498,11770,11962,12129,12241,
12267,12453,12551,12748,13593,13650,13846,13890,14929,
15002
CAC count: 112

ATT: 58,109,263,276,834,1236,1292,1449,1518,1619,1947,2048,
2111,2240,2671,2700,2759,3829,3939,4300,4420,4623,
4727,4730,4838,5570,5573,5662,5724,5811,5877,5907,
6015,6280,6402,6726,6753,6789,6950,7001,7147,7167,
7339,7487,7547,7655,7978,8043,8333,8360,8389,8436,
8480,8520,8534,8572,8724,8848,8921,9118,9163,9200,
9248,9290,9406,9436,9482,9616,9667,9883,10213,10224,
10390,10418,10477,10483,10610,10654,10676,10843,10968,
11068,11103,11209,11233,11332,11378,11419,11520,11635,
11743,11795,11951,12040,12062,12340,12448,12474,12569,
12580,12608,12619,12695,12698,12745,12764,12844,12898,
12921,12963,13004,13165,13188,13210,13384,13525,13544,
13721,13777,13896,13919,13939,14044,14047,14106,14129,
14165,14216,14229,14434,14524,14606,14618,14721,14982,
15016,15030,15146,15165
ATT count: 139

ATC: 485,531,916,1402,1529,1786,2271,2278,2413,2470,2518,
2692,3004,3152,3418,3983,4182,4230,4551,4787,4939,
5039,5211,5385,5476,5504,5671,5729,5762,5821,6073,
6093,6147,6174,6273,6493,6625,6678,6850,6957,7316,
7397,7746,7830,8011,8074,8109,8166,8283,8352,8505,
9392,9595,9631,9972,10015,10284,10309,10603,11053,
11185,11820,11890,12106,12137,12155,12913,13229,13705,
14159,14557,14783,14857,14865,14871
ATC count: 75

ATA: 187,361,472,745,769,869,978,1085,1111,1343,1583,1626,
1750,1821,2147,2177,2650,2843,3156,3206,3241,3401,
3686,3718,3899,3935,4391,4413,4748,4770,4925,5223,
5497,5789,5981,6224,6380,6546,7225,7234,7275,7508,
7711,7823,8270,8372,8383,8601,8746,8945,9097,9221,
9425,9863,10091,10137,10161,10258,10704,10722,10774,
10835,10916,11049,11091,11156,11266,11400,11446,11492,
11523,11766,11915,11996,12113,12144,12162,12176,12427,
12614,12632,12704,12977,13032,13080,13392,13435,13473,
13536,13582,13613,14012,14078,14312,14711,14726,14754,
14845,14944,15024,15047,15138
ATA count: 102

CTT: 88,495,507,577,750,896,933,1146,1674,1831,1925,2077,
2246,2638,3298,3435,3517,3819,3908,4005,4011,4056,
4324,4359,4435,4501,4531,4761,5173,5485,5674,6043,
6192,6377,6519,6684,7381,7433,7592,7714,7742,8320,
8538,8674,8721,8738,8792,8948,8978,9034,9274,9680,
9713,9912,9937,9969,9975,10064,10429,10442,10745,10988,
11046,11159,11350,11359,11369,11513,11584,11857,11885,
11928,11941,12096,12102,12401,12416,12701,12847,12933,
13069,13146,13241,13301,13310,13338,13476,13486,13854,
13869,13908,13988,14226,14261,14485,14492,14635,14639,
14868,14977,15179
CTT count: 101

CTC: 394,437,991,1056,1243,1386,1597,2099,2595,2939,2991,
3641,3823,4084,4161,4375,4714,4808,4961,5301,5308,
5451,5462,5465,5524,5530,5689,6489,6590,6772,6857,
7030,7083,8311,8404,8542,9066,9180,9410,9489,10098,
10568,10650,10680,10873,11469,11746,11823,12738,12863,
12876,13154,13507
CTC count: 53

CTA: 701,854,902,1541,1707,1740,1766,1834,2039,2439,2511,
2619,2823,3053,3386,3404,3722,4014,4045,4049,4155,
5001,5335,5392,5514,5773,5792,6142,6245,6319,6938,
7062,7217,7306,7418,7501,7721,8153,8214,8345,8648,
8682,8718,8778,8839,9000,9262,9428,9454,9962,10022,
10030,10101,10466,10554,10850,11129,11458,11685,11786,
11814,11904,12056,12132,12264,12369,12540,12561,12708,
12996,13157,13197,13203,13590,13782,13851,13947,14253,
14649,14714,14828,15081
CTA count: 82

CTG: 872,1027,2364,3752,4315,4394,4706,4794,4972,5239,7441,
10625,10997,11342,11664,11702,11712,11918,12066,12870,
13554,14099
CTG count: 22

TTA: 74,135,566,803,950,1093,1278,1635,1795,1879,1911,1939,
2000,2864,3078,3210,3327,3371,3495,3618,3668,4321,
4755,4819,5765,5972,6185,6341,6486,7346,7480,7512,
7542,7643,7697,8211,8566,8775,8789,8883,8951,8958,
9159,9226,9297,9305,9497,9535,9795,9823,9932,9952,
9990,10421,10670,10979,11243,11282,11303,11537,11709,
11842,11852,12292,12486,12645,12672,12773,12806,12941,
12953,12984,13111,13259,13357,13489,13629,13694,13843,
14123,14138,14443,14465,14482,14786,14807,14910,15067,
15115
TTA count: 89

TTG: 219,695,944,1161,1855,7262,7601,7658,7771,7805,9203,
9341,11573,11720,12117,12639
TTG count: 16

AAA: 6,39,125,173,590,1379,1409,1547,1556,1710,2190,2322,
2325,2454,2884,2952,3192,3216,3304,3699,3880,3925,
4176,4595,5217,5232,5269,5294,5354,5561,5579,5884,
6031,6305,6443,6706,6910,7025,7038,7359,7553,7729,
7993,8022,8058,8140,8524,8591,8704,8795,8872,8981,
9009,9145,9356,9463,9527,9575,10052,10055,10764,11032,
11290,11353,11609,11978,12029,12277,12440,12589,13223,
13270,13304,13442,13643,13673,13981,14437,14621,14656,
14659,14913,14971,14985,15040
AAA count: 85

AAG: 65,225,449,1153,1275,1987,2354,2602,2626,2773,3702,
3931,4168,4512,5329,5756,5814,5833,6135,6157,6203,
6483,6515,7112,7491,7717,7755,8197,8563,9670,9674,
9798,10085,10498,10547,11227,11579,11752,12463,12780,
12820,12850,14462,14875
AAG count: 44

ATG: 365,821,890,2706,2930,3334,6881,7870,8458,9280,9414,
9785,10114,10596,10787,10819,12047,12384,13139,13409,
14777
ATG count: 21

TTT: 742,1805,1815,1865,2357,2605,3977,4008,4042,5145,5151,
5695,6040,6050,6681,6747,6935,7144,7430,7505,8342,
9838,9860,10012,10040,10123,10185,10312,10589,10657,
11197,11362,11455,11989,12217,12306,12554,12823,13007,
13065,13099,13213,13332,13470,13893,14135,14243,14410,
14626,14745,14951,15054,15094,15170,15182
TTT count: 55

TTC: 899,1005,1064,1189,2089,3068,3255,3285,3869,6298,6464,
6710,7498,8182,9677,10373,10383,11477,11550,13928,
14813,15185
TTC count: 22

CCT: 810,2407,3317,3919,4523,4928,5033,5646,6102,6108,6213,
7272,7369,7881,8156,8410,8582,9978,10127,10295,10433,
10719,11615,11648,12515,12686,13603,14003,14126,14192,
14355,14504
CCT count: 32

CCC: 1743,2447,2539,3425,3557,4919,4942,6587,6796,7080,
7669,9760,10715,11107,11435
CCC count: 15

CCA: 655,1198,2400,3267,4445,5086,5226,5965,7943,8421,11732,
12503,12527,15121
CCA count: 14

CCG: (0)

TCT: 1668,2174,3580,3625,5494,5616,7458,8492,9664,11179,
11230,12337,12887,12970,13399,14603
TCT count: 16

TCC: 85,969,3348,6454,6619,6904,9192,14517,14991
TCC count: 9

TCA: 613,1508,2430,3458,4906,5050,5750,6167,8314,8442,10945,
12328,13287,13326,14748
TCA count: 15

TCG: 4848
TCG count: 1

AGT: 128,285,314,843,1233,1904,2108,2462,2494,2599,2803,
2806,2813,3041,3464,3838,3890,4495,4587,4862,5554,
5893,6079,6236,6394,6446,6471,6531,7897,8119,8201,
8516,8615,8685,8825,8836,9332,9542,10270,10280,10439,
10544,10616,10919,10985,11125,11173,11516,11849,11878,
12059,12182,12289,12497,12661,12944,13184,13256,13873,
13943,13964,14059,14096,14120,14293,14346,14380,14488,
14533,14702,14936
AGT count: 71

AGC: (0)

ACT: 2261,2782,2894,3203,4868,5779,7564,8188,8236,8274,
8363,9031,10221,10880,11153,11763,12947,13517,14554,
14672,15005
ACT count: 21

ACC: 3105,3186,3712,4675,5665,5938,6004,6331,7531,10363,
12238,13745,14207,14632,14646
ACC count: 15

ACA: 1011,1677,3971,4036,4336,4886,6898,8638,10445,11025,
11203,11384,13452,13752,13823,14233
ACA count: 16

ACG: (0)

TGG: 4205,4949,6549,7326,9984,10639,10805,11136
TGG count: 8

TAT: 119,521,985,1251,1890,2071,2196,2488,2582,3542,3631,
5182,5799,5805,6426,6816,6998,7247,7789,8386,8755,
9128,9866,10451,10781,11009,11071,11188,11259,12533,
12548,12593,13293,13499,13661,13804,14171,14431,14834,
14848,15088
TAT count: 41

TAC: 16,68,3946,5332,5511,6242,6539,9016,9896,10517,10529,
11773,13571,13732,14147
TAC count: 15

GTT: 5913,7864,9311,9389,11495,11506,12209,12758,13226,
13679,15027
GTT count: 11

GTC: 1704,3395,4248,4457,5027,6981
GTC count: 6

GTA: 162,4158,6163,6266,6766,7177,9602,10622,12680,13316,
14370
GTA count: 11

GTG: 772,3407,6121,9138,10058,10767,15070
GTG count: 7

TAA: 3591,5858,8866,9691,9831,10179,11077,12072,13429,13996,
14305,14688,14923,15033
TAA count: 14

TAG: 563,2131,7073,9363,10120,11019,11194,14454
TAG count: 8

TGA: 1502,2776,4438,5718,8698,8905,14026
TGA count: 7

02) Codon Usage Bias:
About: Influenza C virus (C/Ann Arbor/1/50) PB2 gene for polymerase 2, complete cds (2365bp)
VERSION: NC_006307.2
CODONS & LOCATIONS:
GCT: 73,82,208,222,232,556,565,709,772,936,997,1041,1171,
1252,1457,1504,1566,1664,1731,1743,1831,1876,1989,
2009,2056,2293,2357,2363
GCT count: 28

GCC: 65,262,316,486,696,717,871,1035,1165,1297,1405,1536,
1708,1960,2019,2249,2281
GCC count: 17

GCA: 2,8,43,79,181,188,191,310,528,569,622,652,742,781,
823,847,850,856,878,1108,1134,1181,1259,1271,1303,
1318,1486,1585,1612,1684,1780,2000,2140,2182,2226,
2296
GCA count: 36

GCG: 2089,2258,2274,2303
GCG count: 4

CGT: 122,2135,2244
CGT count: 3

CGC: (0)

CGA: 466,546,960,1331,1401,2004,2172
CGA count: 7

CGG: 680,705,1065
CGG count: 3

AGA: 58,69,128,155,169,175,215,228,246,273,279,282,366,
378,394,403,408,412,420,435,442,460,469,472,492,499,
505,513,522,549,582,603,610,642,663,688,720,724,753,
768,820,913,921,927,931,942,1049,1080,1105,1137,1140,
1152,1192,1200,1233,1237,1241,1275,1281,1293,1342,
1389,1392,1431,1483,1526,1539,1548,1603,1623,1693,
1700,1784,1815,1843,1852,1870,1879,2115,2148,2179,
2197,2202,2236,2263,2315,2327,2333
AGA count: 88

AGG: 12,47,99,145,149,295,415,747,750,805,832,1002,1005,
1014,1098,1187,1215,1218,1221,1338,1420,1443,1501,
1521,1599,1643,1655,1719,1746,1752,1787,1857,1937,
1970,1983,2095,2151,2253,2290
AGG count: 39

AAT: 21,39,50,87,131,194,201,204,219,237,256,337,361,423,
426,516,531,572,586,606,637,671,676,731,793,811,853,
864,992,1053,1115,1121,1212,1224,1228,1308,1314,1347,
1358,1372,1385,1396,1425,1438,1449,1461,1467,1493,
1512,1517,1554,1576,1617,1734,1759,1776,1807,1823,
1827,1839,1849,1883,1928,1974,2029,2035,2070,2085,
2187,2208,2311,2348
AAT count: 72

AAC: 102,112,211,253,358,625,629,668,756,775,868,881,924,
957,981,1020,1311,1434,1647,1670,1704,1713,1749,1967,
2032,2120,2193,2277,2341
AAC count: 29

GAT: 90,298,372,457,735,762,786,799,814,964,1206,1321,1365,
1368,1377,1471,1573,1591,1678,1696,1762,1932,2212,
2219
GAT count: 24

GAC: 36,93,135,347,478,537,1244,1531,1636,1756,1910,2059,
2128
GAC count: 13

TGT: 105,285,303,343,352,489,542,659,699,829,841,988,1101,
1256,1362,1428,1608,1659,1796,1889,2013,2077,2109,
2160,2164,2307,2319,2336
TGT count: 28

TGC: (0)

CAA: 54,290,375,463,496,600,614,802,905,1381,1479,1544,
1737,1897,1964,2271,2287,2300
CAA count: 18

CAG: 1085,1416
CAG count: 2

GAA: 5,432,553,976,1184,1582,1726,2167,2322
GAA count: 9

GAG: 889,1128,2024,2049
GAG count: 4

GGT: 592,885,1060,1474,2190
GGT count: 5

GGC: (0)

GGA: 18,225,270,400,1454
GGA count: 5

GGG: 1464
GGG count: 1

CAT: 140,449,739,1010,1038,1352,1595,1919,1924,2080,2124
CAT count: 11

CAC: 117,164,250,276,655,971,1196,1509,1558
CAC count: 9

ATT: 15,33,332,577,916,984,1143,1176,1286,1410,1489,1650,
1689,1765,1790,1793,1865,1913,1916,1955,2040,2145
ATT count: 22

ATC: 108,158,1026,1093,1355,1673
ATC count: 6

ATA: 712,949,1089,1155,1413,2073,2092
ATA count: 7

CTT: 26,161,265,307,320,439,525,562,693,844,946,952,1496,
1561,1579,1627,1769,1773,1801,1836,1941,1947,1952,
1995,2045,2102,2132,2241,2268,2354
CTT count: 30

CTC: 482,632,1045,1569
CTC count: 4

CTA: 61,242,595,1146,1249,1631,1892,1904,2066
CTA count: 9

CTG: 509,1125,1681,1907
CTG count: 4

TTA: 446,1076,1289,1324,1810,1901,2156
TTA count: 7

TTG: 502,759,1031,1118,1979,2222
TTG count: 6

AAA: 152,683,808,835,874,1017,1071,1446,1551,1639,1716,
2229,2345
AAA count: 13

AAG: 76,900,1159,1740,1986,2053
AAG count: 6

ATG: 172,184,727,817,910,1203
ATG count: 6

TTT: 340,397,619,702,1588,1620,1862,1992,2205
TTT count: 9

TTC: 29,789,1056,1667
TTC count: 4

CCT: 559,1300,2351
CCT count: 3

CCC: 198,1846,2175
CCC count: 3

CCA: (0)

CCG: (0)

TCT: 391,968,1023
TCT count: 3

TCC: (0)

TCA: 125,1162,2284
TCA count: 3

TCG: (0)

AGT: 96,369,381,453,645,648,859,1068,1327,1334,1818,2062,
2106,2232
AGT count: 14

AGC: 313
AGC count: 1

ACT: 778,2360
ACT count: 2

ACC: 1168,1944
ACC count: 2

ACA: 765
ACA count: 1

ACG: (0)

TGG: 178,1149,1278,2112,2216
TGG count: 5

TAT: 589,1723,1804
TAT count: 3

TAC: 1112,1209,2099
TAC count: 3

GTT: 475,796,838,1873
GTT count: 4

GTC: 355
GTC count: 1

GTA: 259,826
GTA count: 2

GTG: 429,534
GTG count: 2

TAA: 519,2330
TAA count: 2

TAG: 1886
TAG count: 1

TGA: 939,1131,2016
TGA count: 3

03) Codon Usage Bias:
About: Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 2, complete sequence (2341bp)
VERSION: NC_002021.1
CODONS & LOCATIONS:
GCT: 73,301,387,439,510,715,729,1042,1140,1206,1366,1437,
1548,1654,1783,1791,1999,2099,2173,2280,2307
GCT count: 21

GCC: 60,116,237,243,271,398,435,454,485,493,837,982,1011,
1235,1405,1531,1663,1706,1808,1853,1922,1962,1978,
2188,2328
GCC count: 25

GCA: 8,12,64,80,181,211,216,295,369,442,448,685,742,748,
762,799,848,862,871,1100,1132,1144,1148,1225,1253,
1271,1381,1457,1541,1574,1648,1767,1898,1951,1966,
2005,2102,2129,2200,2289
GCA count: 40

GCG: 2,1069,1283,1585,1890
GCG count: 5

CGT: 341,1516,1697,1774
CGT count: 4

CGC: (0)

CGA: 38,201,227,353,376,912,954,1014,1201,1359,1413,1426,
1578,1702,1735,1800,2038,2191,2214
CGA count: 19

CGG: 99,592,736,970,1803,2151,2203
CGG count: 7

AGA: 102,174,184,246,249,279,381,404,427,465,475,516,552,
555,581,587,598,614,629,653,682,711,719,739,791,815,
854,857,887,936,962,1003,1024,1072,1097,1103,1117,
1180,1184,1187,1310,1322,1460,1480,1683,1738,1754,
1828,1929,2032,2062,2076,2140,2143,2185,2231,2235,
2238,2249,2258,2277,2284
AGA count: 62

AGG: 126,132,157,311,359,527,639,646,667,723,756,769,802,
831,883,905,1083,1395,1417,1485,1690,1877,1886,2095,
2224
AGG count: 25

AAT: 24,34,70,253,314,424,462,481,496,534,543,558,604,618,
636,678,702,765,827,874,898,947,958,1006,1027,1047,
1050,1065,1125,1137,1168,1197,1242,1261,1297,1349,
1378,1387,1446,1450,1496,1534,1621,1633,1659,1725,
1749,1813,1831,1859,1865,1932,1937,1941,1948,2035,
2050,2085,2117,2294,2301,2325
AAT count: 62

AAC: 15,84,129,154,192,196,204,223,257,276,337,372,430,
457,570,624,633,650,661,697,818,824,940,1060,1112,
1176,1477,1618,1630,1731,1757,1770,1822,1909,1945,
1984,2010,2081
AAC count: 38

GAT: 28,145,232,564,621,656,759,891,987,1153,1171,1245,
1248,1313,1339,1371,1398,1626,1636,1869,1873,1956,
1959,1996,2022,2154,2197,2209
GAT count: 28

GAC: 123,189,390,401,412,417,601,609,690,705,894,924,999,
1221,1304,1588,1717,1787
GAC count: 18

TGT: 150,283,363,470,531,777,786,811,879,974,1091,1256,
1265,1275,1374,1432,1527,1563,1608,1673,1760,1917,
2263,2310,2332
TGT count: 25

TGC: (0)

CAA: 67,260,384,394,708,1402,1502,1614,1680,1779,2028,2054,
2059,2092
CAA count: 14

CAG: 166,1554,1669,2147,2160
CAG count: 5

GAA: 292,334,349,506,546,584,726,951,1079,1158,1192,1846,
2113,2320
GAA count: 14

GAG: 499,538,845,1409,1593,1601,1990,2066,2170
GAG count: 9

GGT: 265,325,773,1019,1334,1342,1523,1642,1794,1972,2166,
2178
GGT count: 12

GGC: (0)

GGA: 208,1545,1571,1764,2221
GGA count: 5

GGG: 561,1862
GGG count: 2

CAT: 18,141,163,319,513,574,927,992,1229,1290,1390,1441,
1473,1490,1611,1677,1742,1839,1913,1969,2043,2135,
2253,2271,2317
CAT count: 25

CAC: 138,489,567,794,909,930,1317,1721,1904,2014,2244,2268
CAC count: 12

ATT: 288,328,346,745,1039,1278,1597,1825,1880,2105,2109,
2194,2206
ATT count: 13

ATC: 674,965,2157,2217
ATC count: 4

ATA: 76,95,135,780,808,995,1088,1818,1925,2227
ATA count: 10

CTT: 42,46,51,92,110,307,519,523,783,916,920,1209,1300,
1328,1345,1469,1639,1666,2046,2071,2121,2314
CTT count: 22

CTC: 107,171,220,902,1056,1121,1287,1353,1797,1834
CTC count: 10

CTA: 408,1033,1325,1512,2337
CTA count: 5

CTG: 503,694,1075,1238,1294,1568,2019
CTG count: 7

TTA: 421,1422,1604,1686,1894,2304
TTA count: 6

TTG: 21,451,821,842,868,979,1094,1493,1559,1745
TTG count: 10

AAA: 5,54,177,549,643,664,732,1307,1463,1981
AAA count: 10

AAG: 865
AAG count: 1

ATG: 119,298,851,1108,1453,1520,1987
ATG count: 7

TTT: 87,331,577,1362,1506,1509
TTT count: 6

TTC: 304,1537,2181
TTC count: 3

CCT: 322,1129,1843
CCT count: 3

CCC: 752,1384,2025,2124
CCC count: 4

CCA: 944,1645,1975
CCA count: 3

CCG: (0)

TCT: 1850
TCT count: 1

TCC: 1551
TCC count: 1

TCA: 366,478,1499,1582
TCA count: 4

TCG: (0)

AGT: 57,670,805,1036,1466,2297
AGT count: 6

AGC: (0)

ACT: 240,1331
ACT count: 2

ACC: 1429,1883,1901
ACC count: 3

ACA: 113,160,445,1651,1694,1728
ACA count: 6

ACG: (0)

TGG: 356,933
TGG count: 2

TAT: 268,1993,2163
TAT count: 3

TAC: 2089
TAC count: 1

GTT: 834,1030,1053,2002,2132,2241
GTT count: 6

GTC: 31
GTC count: 1

GTA: (0)

GTG: 595
GTG count: 1

TAA: 1268,1856
TAA count: 2

TAG: (0)

TGA: 1232,1356,2274
TGA count: 3

04) Codon Usage Bias:
About: Hepatitis E virus, complete genome (7176bp)
VERSION: NC_001434.1
CODONS & LOCATIONS:
GCT: 28,46,58,61,94,165,225,231,257,284,317,320,382,385,
414,421,424,440,458,532,558,565,630,682,713,782,920,
943,1010,1013,1046,1085,1105,1114,1171,1210,1242,1297,
1310,1314,1325,1415,1431,1531,1540,1593,1618,1630,
1644,1843,1846,1851,1862,1870,1878,1992,2025,2074,
2131,2260,2281,2290,2343,2363,2381,2385,2409,2451,
2494,2566,2601,2608,2627,2644,2751,2755,2836,2882,
2951,3026,3031,3034,3117,3120,3123,3204,3263,3285,
3358,3391,3439,3478,3505,3570,3619,3694,3739,3747,
3775,3798,3918,3927,3957,4053,4088,4104,4261,4273,
4287,4342,4435,4467,4475,4668,4699,4702,4714,4718,
4797,4814,4827,4872,4882,4905,4918,4992,4999,5005,
5017,5046,5100,5143,5149,5170,5258,5324,5336,5373,
5378,5408,5435,5449,5462,5594,5608,5648,5657,5690,
5700,5710,5723,5733,5898,5953,5967,6016,6142,6155,
6158,6165,6229,6248,6259,6293,6304,6355,6377,6521,
6532,6538,6551,6579,6661,6742,6754,6815,6829,6845,
6860,6890,6917,6940,6949,7032,7037,7055,7060,7113,
7137,7163
GCT count: 190

GCC: 1,10,73,82,108,161,176,244,254,260,274,329,334,364,
378,392,472,487,526,542,568,582,597,775,785,811,819,
831,884,952,985,1003,1019,1075,1093,1126,1129,1145,
1190,1229,1259,1277,1321,1366,1373,1436,1474,1490,
1504,1582,1603,1640,1651,1760,1769,1789,1807,1810,
1814,1834,1837,1873,1900,1924,1942,1954,1978,1985,
2033,2041,2146,2151,2175,2194,2197,2215,2277,2296,
2302,2308,2326,2336,2339,2377,2438,2497,2524,2527,
2547,2560,2611,2633,2682,2704,2723,2758,2773,2781,
2789,2854,2867,2872,2878,2931,2965,3010,3017,3020,
3052,3055,3074,3094,3139,3142,3181,3199,3214,3222,
3232,3266,3354,3397,3400,3466,3485,3511,3520,3530,
3566,3635,3644,3676,3697,3705,3713,3724,3752,3763,
3786,3791,3809,3822,3892,3895,3902,3913,3935,3944,
3947,3967,3997,4012,4019,4063,4079,4093,4186,4202,
4216,4237,4247,4282,4315,4348,4424,4458,4513,4560,
4597,4639,4642,4691,4724,4780,4787,4819,4823,4847,
4853,4877,5040,5105,5127,5134,5164,5173,5179,5185,
5194,5202,5205,5208,5269,5309,5330,5352,5360,5393,
5400,5405,5411,5441,5446,5468,5482,5488,5510,5520,
5564,5591,5604,5669,5706,5738,5758,5833,5843,5871,
5933,6008,6029,6101,6111,6137,6216,6300,6318,6332,
6343,6491,6501,6554,6591,6647,6653,6693,6739,6785,
6842,6882,6894,6926,6974,6980,7002,7011,7014,7023,
7068,7119
GCC count: 250

GCA: 35,54,67,126,153,403,431,605,614,644,808,1040,1064,
1163,1206,1445,1465,1577,1636,1721,1799,2058,2096,
2111,2233,2331,2461,2482,2647,2669,2818,2827,2907,
2923,2942,3045,3132,3195,3249,3298,3366,3388,3430,
3472,3559,3584,3595,3665,3879,3908,3950,4208,4351,
4354,4360,4461,4509,4565,4632,4673,4765,4869,4901,
4988,5012,5220,5276,5524,5628,5838,5851,5958,6048,
6096,6125,6382,6398,6406,6466,6643,6712,6770,6850,
6944
GCA count: 84

GCG: 70,88,207,339,351,374,396,408,482,555,619,648,765,
1152,1200,1387,1399,1481,1680,1741,1891,1907,1931,
1973,2212,2266,2323,2419,2444,2511,2519,2712,2900,
3003,3023,3135,3271,3545,3575,3626,3662,3772,3986,
4121,4339,4498,4530,4625,4793,4860,4864,5117,5215,
5223,5226,5235,5327,5383,5456,5505,5921,6076,6120,
6219,6264,6339,6632,6639,6747,6911,7154
GCG count: 71

CGT: 247,623,651,662,756,967,1036,1393,1566,1569,1633,1724,
1727,2045,2269,2412,2862,2970,2976,2982,2995,3098,
3147,3207,3292,3338,3497,3600,3852,3886,4000,4023,
4125,4258,4329,4684,4747,4806,4809,4945,4971,5345,
5417,5420,5560,5687,5751,5781,5785,5819,5882,5974,
6086,6104,6116,6288,6322,6325,6431,6832,6898
CGT count: 61

CGC: 241,3527,5176,6498,6977,7160
CGC count: 6

CGA: 180,444,696,858,871,875,932,1500,1524,1674,1686,2154,
2396,2514,2769,2841,2887,2990,3167,3186,3225,3481,
3502,3591,3899,4050,4071,4107,4517,4661,4751,4857,
4910,5049,5314,5363,5778,5808,5848,6034,6273,6415,
6473,6477,6518,6585,6664,6991
CGA count: 48

CGG: 411,447,741,815,850,887,981,1342,1677,1704,1737,1888,
1918,1998,2055,2120,2237,2299,2357,2617,2637,2661,
2688,2727,2821,3325,3334,3408,3419,4172,4554,5074,
5188,5255,5569,5678,5914,6004,6013,6061,6205,6421,
6656,6854,7005,7094
CGG count: 46

AGA: 134,476,724,744,993,1214,1250,1622,1694,1749,1764,
1796,2091,2597,2621,2761,2859,3058,3173,3314,3450,
3539,3716,3757,3828,3870,4148,4152,4178,4226,4268,
4376,4406,4428,4544,4688,4835,4838,4922,5423,5653,
5763,5907,6210,6277,6370,6723,6837,7074
AGA count: 49

AGG: 587,668,734,772,1052,1100,1181,1306,1381,1439,1470,
1487,1511,1661,1670,1856,1934,1963,2021,2123,2160,
2191,2369,2473,2578,2678,2810,3068,3434,3578,3743,
3806,4028,4076,4082,4132,4205,4295,4357,4492,4520,
4533,4650,4695,4736,5622,5890,5925,5928,6174,6390,
6444,6675,6954,7029,7080
AGG count: 56

AAT: 91,150,220,267,288,292,304,388,1023,1078,1535,1708,
1756,1774,1969,2002,2077,2425,2550,2553,2716,2776,
2830,3007,3604,3630,3679,3863,3964,4043,4159,4163,
4411,4579,5059,5064,5081,5085,5633,5644,5663,5695,
5795,5800,5990,6065,6197,6335,6374,6426,6524,6626,
6800
AAT count: 53

AAC: 76,145,193,298,463,691,706,912,1090,1224,1460,1589,
1713,2313,2416,2538,2585,2590,2793,2805,3371,3403,
3607,3803,3855,3867,4035,4117,4547,4591,4978,5088,
5296,5300,5355,5452,5531,5539,5576,5720,5803,5885,
5978,6071,6242,6455,6459,6806,6825,7090
AAC count: 50

GAT: 129,295,343,505,520,633,720,1185,1264,1357,1519,1683,
1786,2128,2491,2508,2572,2685,2731,2936,3088,3274,
3288,3309,3475,3844,3979,4312,4321,4396,4455,4503,
4618,4654,4657,4710,4741,4891,4933,4983,5261,5492,
5813,6128,6223,6283,6386,6452,6527,6686
GAT count: 50

GAC: 427,552,640,673,964,997,1026,1336,1495,1549,1609,1647,
1752,1882,2431,2664,2701,2784,2848,3163,3255,3453,
3556,3673,3685,4324,4381,4967,5008,5055,5252,5340,
5387,5474,5498,5789,6023,6133,6251,6346,6410,6470,
6563,6608,6616,6670,6821,6965,6995
GAC count: 49

TGT: 168,210,238,509,536,593,654,699,792,837,867,974,977,
1059,1071,1303,1346,1378,1450,1626,1690,1731,1866,
1948,2061,2086,2401,2455,2505,2738,2814,2875,2904,
2928,2979,3081,3252,3280,3341,3377,3516,3651,3768,
3841,3849,3876,3883,3930,4039,4046,4114,4156,4234,
4299,4370,4432,4450,4478,4612,4760,4770,4773,4914,
4925,4929,4938,5069,5092,5157,5317,5683,5854,5902,
5947,6202,6237,6349,6367,6511,6601,6613,6733,7051,
7116,7133
TGT count: 85

TGC: 710,1859,5124,5517,6937
TGC count: 5

CAA: 1000,1406,1600,2470,2594,2962,3953,5862,6720
CAA count: 9

CAG: 16,1168,1236,1282,1300,1655,1821,1981,2320,2694,2914,
3219,3385,3413,3493,3563,3640,3733,4583,4996,5033,
5390,5396,5672,6566,6594,7043,7064
CAG count: 28

GAA: 1081,1425,5037,7170
GAA count: 4

GAG: 7,529,1288,1360,2068,2392,2605,2734,2998,3091,3427,
4060,4221,4390,4447,4678,4887,5029,5867,6041,6557,
6767,7097
GAG count: 23

GGT: 99,183,271,309,356,547,657,685,768,861,892,1350,1514,
1559,2009,2117,2272,2765,2985,3078,3160,3245,3349,
3622,4068,4192,4253,4443,4635,4756,4776,4956,5112,
5240,5249,5581,5713,5729,5917,5942,6079,6296,6622,
6689,6773,6789,6887,7085
GGT count: 48

GGC: 2287,3014,3071,3295,5895
GGC count: 5

GGA: 228,1197,1203,2709,2973,4541
GGA count: 6

GGG: 4175,4309,4844,5333,5438
GGG count: 5

CAT: 13,196,201,217,502,515,608,637,748,759,917,940,955,
1119,1140,1330,2014,2081,2458,2534,3084,3129,3259,
3424,3459,3489,3508,3549,3552,3647,3730,4182,4189,
4365,4470,4975,5020,5108,5291,5471,5639,5746,5963,
6169,6363,6495,6961,6983,7147
CAT count: 49

CAC: 39,121,277,313,512,574,729,804,824,924,1122,1827,1885,
1913,1938,1995,2099,2106,2201,2317,2434,2557,2654,
2719,2799,2892,3039,3048,3063,3112,3151,3237,3318,
3381,3447,3534,3834,3837,3924,3973,4137,4167,4401,
4483,4605,4609,5025,5320,5367,5431,5767,5770,5773,
5876,5970,5994,6055,6107,6145,6148,6151,6480,6547,
6571,6679,6703,6706,6811,6868,6874,6877,6932
CAC count: 72

ATT: 22,49,142,494,778,906,1390,1543,2373,2956,3463,3858,
3938,4015,4264,4438,4841,5138,5288,5822,6183,6280,
6395,6440,6447,6717,6863,6905,7109,7141
ATT count: 30

ATC: 214,958,1176,1270,1554,2169,2240,3170,3655,3668,4006,
4276,4628,5279,5513,5536,5542,5741,5858,6401
ATC count: 20

ATA: 359,1959,2182,2531,2673,4489,5985,6000,6360,6957,7102
ATA count: 11

CTT: 85,139,434,627,789,798,842,879,936,1108,1135,1245,
1333,1606,1699,1716,1781,1817,2029,2037,2114,2157,
2243,2346,2487,2501,2624,2743,2845,3103,3154,3157,
3189,3616,3690,3710,4099,4111,4140,4143,4230,4240,
4332,4419,4486,4570,5095,5272,5305,5549,5556,5585,
5600,5982,5997,6038,6245,6483,6505,6582,6619,6683,
6698,6727,6730,6760,6795,6987,7019,7125,7128
CTT count: 71

CTC: 115,158,325,490,497,571,577,752,900,970,1033,1159,
1317,1585,1612,1665,1777,2219,2252,2256,3240,3331,
3588,3659,3814,3990,3994,4292,4335,4551,4897,4941,
5130,5153,5265,5618,5911,5938,6082,6091,6179,6313,
6328,6515,6543,6604,6757,6901
CTC count: 48

CTA: 64,368,677,827,834,854,864,1233,1293,1456,1563,1802,
1830,2138,2186,2249,2352,2366,3305,3444,3781,3960,
4573,5284,5427,5612,6189,6269,6310,6598,6777,6780,
7047
CTA count: 33

CTG: 32,189,455,479,602,717,1097,1574,1928,2018,2406,2441,
2747,2833,3345,3794,4279,4587,4802,4832,4850,4964,
5199,5245,5755,6667
CTG count: 26

TTA: 104,234,561,737,1029,1043,1055,1220,1421,1596,2103,
2165,2204,2466,2918,3719,4031,4305,4601,4646,4950,
5825,6186,6574,6871,6923,7071
TTA count: 27

TTG: 263,1239,1285,2064,2581,3229,3362,3523,3736,4373,4732,
4790,6020,6535,6763
TTG count: 15

AAA: 4195,4728,7173
AAA count: 3

AAG: 25,928,1396,3394
AAG count: 4

ATG: 4,665,1508,2360,3889,4594,5792,6462
ATG count: 8

TTT: 19,111,171,186,451,466,1006,1353,1411,1745,1895,1910,
1945,1966,1988,2005,2048,2135,2389,2697,3610,4003,
4211,4318,4384,4393,4414,4537,4894,6026,7040,7106
TTT count: 32

TTC: 347,399,702,1453,2178,3613,3700,3727,3983,4243,4621,
4744,4959,5160,5230,5349,6044,6508,6998,7150,7157
TTC count: 21

CCT: 301,795,903,949,990,1068,1370,2230,2284,2569,2658,
3109,3760,3819,4250,4527,4707,5052,5553,5597,6052,
6256,6418,6736,6971,7167
CCT count: 26

CCC: 280,371,417,469,846,896,1016,1273,1527,1615,1903,2051,
2207,2224,2227,2246,2478,2541,2630,2895,2948,3042,
3106,3177,3211,4783,5478,5502,5546,5615,5716,6058,
6162,6234,6486,6929,7122
CCC count: 37

CCA: 204,1149,1339,2143,3126,3825,5121,5830,6709
CCA count: 9

CCG: 251,1256,2263,2305,2544,2939,4009,5465,6588,6636
CCG count: 10

TCT: 79,118,1194,1403,1824,1840,1951,2422,2796,3976,4387,
4495,4506,5660,7144
TCT count: 15

TCC: 539,590,909,2691,3970,4129,6908,7026
TCC count: 8

TCA: 1921,2851,5191,5414
TCA count: 4

TCG: 1363,1478,2071,5370,6213
TCG count: 5

AGT: 1217,1253,1442,1546,1792,2945,3322,3542,4056,4523,
4665,5043,5485,6436,6818,7008
AGT count: 16

AGC: 3905,6226
AGC count: 2

ACT: 43,437,801,1384,3831,5636,6194
ACT count: 7

ACC: 611,1484,2293,2641,2651,2959,3302,5182,5703,6068,6792
ACC count: 11

ACA: 1049,1111,2824,5573
ACA count: 4

ACG: 3469,3941,4085,5625
ACG count: 4

TGG: 961,2448,3581,4199,4576,4953,5078,5212
TGG count: 8

TAT: 688,1267,2575,2802,3873,4615,5167,5528,5666,5879,5950,
6560,6803
TAT count: 13

TAC: 1132,1156,2349,2614,2911,3456,4681,5588,5675,6968
TAC count: 10

GTT: 1418,2428,3682,3778,4302,5002,5146,5495,5726,5816,
6307,6650,6857,6914,6920
GTT count: 15

GTC: 523,946,2563,3328,3921,4096,5459
GTC count: 7

GTA: 3277,6629,6750
GTA count: 3

GTG: 1428,4345,4464,4721
GTG count: 4

TAA: 1658,6352
TAA count: 2

TAG: 3374
TAG count: 1

TGA: 762,1734,2172,3192,3416,4557,7077
TGA count: 7

05) Codon Usage Bias:
About: La Crosse virus segment L, complete genome (6980bp)
VERSION: NC_004108.1
CODONS & LOCATIONS:
GCT: 92,181,721,749,854,1039,1130,1354,1418,1523,1658,1667,
1685,1703,1750,1838,1846,2019,2138,2142,2150,2239,
2318,2623,2746,2756,2960,3152,3193,3257,3286,3400,
3437,3490,3531,3878,3988,4076,4196,4453,4667,4715,
4979,4997,5145,5351,5417,5524,5552,5573,5637,5770,
5927,6070,6148,6187,6249,6443,6465,6492,6755,6916
GCT count: 62

GCC: 125,155,250,654,703,874,992,1213,1232,1378,1422,1477,
1863,1905,1974,2011,2589,2715,2761,2842,2913,3037,
3216,3293,3376,3569,3707,3726,3851,3862,3896,3905,
4609,4746,4891,4931,5304,5312,5330,5862,6475
GCC count: 41

GCA: 57,107,116,186,278,363,475,608,632,642,836,871,972,
1019,1059,1152,1167,1172,1189,1252,1326,1336,1403,
1464,1549,1576,1639,1724,1740,1753,1792,1797,2015,
2052,2072,2338,2360,2472,2486,2626,2659,2667,2681,
2728,2733,2978,2993,3048,3067,3112,3137,3146,3155,
3204,3209,3236,3348,3416,3536,3686,3731,3762,3819,
3913,3935,3950,3997,4028,4146,4165,4280,4364,4368,
4428,4571,4823,4872,4946,5081,5236,5320,5323,5341,
5384,5425,5469,5611,5711,5760,5777,5782,5829,5920,
5981,6083,6098,6219,6326,6398,6500,6945,6971
GCA count: 102

GCG: 715,1088,1317,1944,2167,2385,2512,3798,4317,5538
GCG count: 10

CGT: 445,449,2695,2922,2944,3122,3523,5621,5977,6002
CGT count: 10

CGC: (0)

CGA: 136,253,354,412,547,1588,2875,3089,3100,3130,3636,
3884,4219,4523,4887,5196,5504,6076,6154,6295,6342
CGA count: 21

CGG: 577,3586,3618,4158,4849,4862,4989,5096,5659,5686,6067
CGG count: 11

AGA: 30,73,158,176,202,229,259,274,295,334,416,433,454,
491,499,589,645,730,762,791,804,808,817,882,888,918,
928,933,937,963,1084,1123,1144,1175,1210,1279,1290,
1344,1357,1366,1390,1440,1446,1449,1480,1519,1531,
1563,1568,1719,1759,1765,1835,1849,1855,1866,1989,
2008,2076,2097,2123,2160,2180,2227,2334,2364,2374,
2391,2409,2436,2475,2498,2519,2524,2543,2609,2614,
2620,2640,2643,2653,2675,2701,2742,2773,2818,2836,
2916,2937,2950,2985,2998,3002,3076,3082,3117,3168,
3178,3222,3298,3325,3329,3364,3379,3423,3480,3565,
3583,3657,3679,3694,3702,3744,3769,3871,3900,4054,
4072,4172,4206,4231,4247,4276,4284,4311,4325,4349,
4409,4458,4489,4498,4546,4563,4585,4590,4618,4664,
4672,4711,4721,4750,4894,4901,4943,5000,5020,5031,
5044,5047,5085,5119,5129,5167,5175,5218,5254,5260,
5289,5398,5437,5490,5531,5546,5560,5589,5669,5689,
5692,5742,5849,5853,5857,5880,5917,5939,6014,6022,
6141,6181,6262,6283,6316,6368,6373,6377,6415,6419,
6429,6439,6459,6478,6496,6553,6582,6650,6674,6703,
6730,6744,6775,6783,6787,6796,6841,6869,6930,6963
AGA count: 207

AGG: 95,110,129,209,342,401,468,897,1003,1066,1102,1652,
1783,1859,2061,2218,2277,2323,2406,2531,2546,2599,
2750,2801,2824,2928,3057,3160,3213,3261,3318,3496,
3651,3859,3994,4037,4041,4215,4331,4376,4404,4483,
4538,4634,4677,4693,4733,4865,4974,5063,5089,5139,
5411,5463,5729,5773,5906,5909,5933,5985,6056,6127,
6145,6212,6255,6392,6697,6819,6823,6830,6884,6900,
6967
AGG count: 73

AAT: 34,50,61,84,101,151,197,212,235,299,317,384,430,436,
514,536,540,558,573,660,687,694,746,756,770,787,795,
831,878,910,940,948,1007,1013,1016,1095,1108,1192,
1195,1206,1222,1229,1265,1268,1299,1310,1351,1384,
1406,1484,1496,1500,1513,1526,1544,1610,1629,1670,
1676,1814,1870,1925,1955,2079,2128,2135,2293,2315,
2423,2452,2528,2537,2596,2647,2671,2689,2753,2765,
2857,2860,2906,2965,2989,3009,3014,3025,3072,3085,
3127,3173,3184,3229,3233,3249,3384,3395,3433,3449,
3453,3458,3464,3485,3500,3556,3643,3665,3673,3734,
3758,3811,4004,4012,4034,4061,4087,4110,4118,4149,
4192,4235,4255,4353,4380,4437,4509,4529,4558,4575,
4615,4641,4729,4760,4777,4792,4799,4843,4904,4911,
4915,4958,4961,4993,5039,5053,5160,5202,5243,5248,
5317,5327,5345,5367,5371,5434,5442,5485,5501,5603,
5641,5645,5653,5666,5674,5680,5683,5700,5715,5766,
5793,5801,5812,5895,5899,5912,5948,5953,6032,6035,
6088,6112,6136,6165,6174,6197,6206,6215,6240,6350,
6395,6405,6482,6514,6519,6533,6558,6577,6624,6638,
6659,6678,6686,6719,6747,6836,6880,6911,6921
AAT count: 207

AAC: 23,81,268,373,397,482,555,669,776,966,998,1029,1075,
1199,1218,1226,1248,1329,1426,1437,1534,1634,1643,
1673,1714,1769,1778,1897,1900,1917,1930,2005,2033,
2175,2209,2242,2269,2287,2388,2399,2433,2444,2504,
2516,2534,2554,2557,2566,2637,2684,2706,2785,3506,
3574,3602,3626,3631,3640,3754,3788,3801,3832,3983,
4187,4228,4360,4461,4680,4702,4756,4816,4826,5112,
5212,5215,5286,5472,5614,5650,5656,5677,5696,5734,
5749,5818,5842,5902,5956,6191,6308,6337,6424,6529,
6734,6764,6778,6807,6873,6941
AAC count: 99

GAT: 113,164,215,242,488,581,584,765,861,1111,1115,1276,
1361,1397,1432,1506,1603,1922,1939,2026,2147,2183,
2198,2354,2458,2798,2864,2869,3020,3028,3044,3239,
3359,3370,3428,3475,3623,3668,3723,3822,3845,3964,
4016,4090,4104,4132,4223,4298,4516,4658,4763,4810,
4813,4982,5003,5099,5122,5431,5456,5570,5606,5990,
6010,6038,6169,6203,6226,6244,6275,6412,6593,6614,
6664,6667,6760,6811,6848,6937
GAT count: 78

GAC: 65,143,380,404,617,904,959,1271,1400,1541,1706,1887,
2119,2156,2163,2204,2489,2603,2698,2833,3103,3404,
3445,3715,3967,3976,4007,4289,4342,4477,4637,4685,
4736,4766,4802,4967,5125,5387,5480,5510,5555,5630,
5704,5725,5787,5996,6299,6385,6653,6700,6727
GAC count: 51

TGT: 6,119,139,226,321,349,367,460,736,1155,1237,1371,1410,
1455,1580,1621,1662,1729,1787,1808,1873,1890,1977,
1993,2056,2103,2110,2170,2266,2344,2426,2469,2845,
2969,2973,3005,3060,3243,3265,3345,3540,3544,3710,
3751,3775,3792,3838,3848,3920,3942,4066,4083,4140,
4413,4440,4470,4513,4554,4596,4740,4839,4875,4880,
5026,5155,5225,5295,5360,5720,5805,5872,5966,6291,
6522,6572,6600,6960
TGT count: 77

TGC: 5068
TGC count: 1

CAA: 20,739,801,828,945,1044,1055,1282,1306,1333,1374,1381,
1459,1510,1516,1552,1986,2094,2213,2574,2580,2593,
2839,2881,2925,3108,3407,3516,4314,4534,4543,4772,
4859,4884,5093,5199,5549,5563,5809,5999,6237,6363,
6739,6925
CAA count: 44

CAG: 38,2107,2439,2631,3468,3928,4098,4179,4261,4393,5271,
5446,5826,5867,5961,6454,6546
CAG count: 17

GAA: 359,569,601,1186,1474,1606,2396,2617,2720,2957,3143,
3188,3662,3691,3739,4031,4168,4199,4238,4495,5017,
5056,5078,5578,5763,5798,6323,6526,6814
GAA count: 29

GAG: 392,697,718,1136,2662,2810,3134,3253,4175,4425,4466,
4852,5150,5357,6536,6861
GAG count: 16

GGT: 173,520,614,639,651,781,900,913,922,1261,1470,1818,
2253,2261,2350,2415,2656,2872,3041,3097,3842,3917,
4307,4432,4628,5265,5300,5496,5593,6115,6258,6279,
6320,6488,6540,6587
GGT count: 36

GGC: (0)

GGA: 523,666,989,1762,3064,3226,4212,4486,6908
GGA count: 9

GGG: 1245,3939,4115,4328,5239,5993,6634,6827,6897,6933
GGG count: 10

CAT: 42,161,222,264,271,284,331,611,676,956,977,995,1033,
1179,1182,1429,1647,1800,1828,2023,2037,2304,2330,
2347,2462,2898,3289,3355,3527,3606,3614,3747,3780,
3891,3946,3959,4080,4162,4321,4604,4612,4655,4789,
4832,4919,4922,5012,5188,5205,5233,5378,5391,5395,
5403,5515,5520,5585,5598,5885,5891,6120,6332,6380,
6450,6469,6510,6566,6605,6609,6682,6714,6724
CAT count: 72

CAC: 47,622,1081,1881,1969,2100,2501,2507,3198,3315,3511,
3924,4357,4444,5035,5171,5209,5229,5276,5624,6101,
6596,6646,6711,6802,6974
CAC count: 26

ATT: 98,148,168,287,387,425,471,479,592,598,813,907,1036,
1118,1133,1147,1303,1339,1387,1572,1693,1774,1912,
1949,2222,2272,2283,2310,2371,2478,2561,2569,2736,
2794,2815,2892,2941,3140,3279,3334,3367,3388,3391,
3559,3577,3595,3697,3718,3784,3829,4020,4057,4069,
4301,4337,4386,4449,4519,4579,4690,4705,4726,4769,
4782,4820,4897,5348,5541,5832,5835,6007,6059,6079,
6357,6401,6563,6752,6799,6844
ATT count: 79

ATC: 15,69,78,303,409,733,1072,1413,1585,1613,1618,1831,
1982,1999,2194,2782,3031,3305,3835,4046,4631,4970,
5136,5407,5617,5930,6027,6229,6472
ATC count: 29

ATA: 53,132,205,245,307,325,339,376,798,867,983,1322,1347,
1490,1537,1655,1688,1709,1737,1745,1841,1964,2067,
2115,2249,2296,2402,2769,2778,2806,2953,3163,3337,
3654,3814,3855,3887,3908,3953,3979,4123,4152,4503,
4835,4846,4950,5102,5307,5707,5745,5753,5821,5838,
5845,5875,5942,6209,6329,6353,6388,6569,6707
ATA count: 62

CTT: 88,193,503,532,550,626,724,1024,1051,1098,1393,1591,
1681,1698,2088,2299,2447,2493,2586,2650,3094,3340,
3805,4126,4129,4250,4389,4416,4621,4785,4796,5107,
5185,6018,6050,6158,6194,6223,6346,6485
CTT count: 40

CTC: 346,563,951,1594,1599,3308,3970,4600,5192,6177,6793
CTC count: 11

CTA: 510,969,1160,1934,2327,2357,2367,2418,2483,2550,3246,
3352,3441,3591,3932,4050,4293,4652,4743,4806,5163,
5282,5334,6303,6621,6642,6768,6876
CTA count: 28

CTG: 648,657,711,759,851,1493,1884,3283,4422,5535,5739,
6162,6949
CTG count: 13

TTA: 26,419,441,495,690,891,1078,1241,1257,1803,2634,2678,
3149,3520,3865,3875,4203,4373,4907,4934,5006,5466,
5476,5662,5790,5973,6105,6312,6549,6630,6692,6857,
6865
TTA count: 33

TTG: 239,1295,1503,2724,2982,3053,3201,4101,4940,5627,6123,
6435
TTG count: 12

AAA: 839,1063,1105,1163,1202,2132,2789,2884,2909,2919,3181,
3321,3410,3562,3766,4135,4696,4955,5050,5116,5179,
5251,6062,6091,6094
AAA count: 25

AAG: 463,1127,1285,2245,2709,4397,4549,5581
AAG count: 8

ATG: 753,885,1140,1467,1811,1952,2030,2739,4304,4868,5493,
5633,5924,6462,6590,6656
ATG count: 16

TTT: 543,663,864,980,1487,1734,1893,1958,2002,2082,2307,
2455,2540,2606,2829,2901,3268,3682,5132,5142,5221,
5354,5381,5420,5527,6184,6232,6287,6432,6671,6790,
6894,6904
TTT count: 33

TTC: 743,1091,1313,1876,2888,3471,3503,3648,3808,4272,4624,
5363,6446
TTC count: 13

CCT: 12,595,636,2258,2466,3017,3302,3826,4025,4346,4856,
4964,6151
CCT count: 13

CCC: 291,457,673,1626,2085,4155,4419,4567,4926,4985,6131
CCC count: 11

CCA: 281,2341,2430,2878,3493,5815,6543
CCA count: 7

CCG: (0)

TCT: 485,1961,1996,3973,4334,5888,6047
TCT count: 7

TCC: 6618
TCC count: 1

TCA: 925,2895,3461,4001,5414,6053
TCA count: 6

TCG: (0)

AGT: 1,189,256,422,517,604,706,857,1010,1047,2280,2583,
3598,3610,3881,3956,4094,4183,4474,4661,4699,5059,
5182,5756,6505,6689,6771,6833,6852
AGT count: 29

AGC: 2041
AGC count: 1

ACT: 104,773,1909,2064,3373,3580,4209,4258,4753,5507,6360,
6409,6978
ACT count: 13

ACC: 9,507,3312,3420,3991,4401,5375,5936
ACC count: 8

ACA: 629,2091,2290,3079,4829,5268
ACA count: 6

ACG: 3795
ACG count: 1

TGG: 986,2947,4107,4506
TGG count: 4

TAT: 232,328,370,566,700,1069,1452,2153,2201,2412,2712,
3676,4383,4492,4526,4582,4593,4718,5292,5567,6200
TAT count: 21

TAC: 219,4708,5279,5945
TAC count: 4

GTT: 2577,2692,3413,3772,4937,5009,5023,5428,6627
GTT count: 9

GTC: (0)

GTA: 122,1443,5969,6108
GTA count: 4

GTG: 894,5337,5459,6252
GTG count: 4

TAA: 784,1756,1852,2821,3219,4480,5257,6265
TAA count: 8

TAG: (0)

TGA: 727,3034,3868,4143,6073
TGA count: 5

06) Codon Usage Bias:
About: Influenza B virus (B/Lee/1940) segment 2, complete sequence (2313bp)
VERSION: NC_002205.1
CODONS & LOCATIONS:
GCT: 10,33,178,247,356,453,624,699,707,790,840,844,943,
1383,1581,1662,1687,1768,1800,1917,1923,2090,2236,
2309
GCT count: 24

GCC: 52,154,315,388,398,413,468,643,660,904,925,1136,1171,
1280,1546,1857,1872,1899,2176,2202,2302
GCC count: 21

GCA: 30,199,286,289,485,520,616,667,673,682,794,823,856,
901,946,1115,1208,1276,1331,1375,1411,1576,1729,1738,
1748,1789,1795,1889,2015,2077,2086,2105
GCA count: 32

GCG: 481,1109,2012
GCG count: 3

CGT: 5,1554,1592,2205
CGT count: 4

CGC: (0)

CGA: 205,351,593,646,1273,1312,1950
CGA count: 7

CGG: 59,77,1044,1050,1080,1994,2165
CGG count: 7

AGA: 67,71,81,100,118,128,142,252,367,371,376,422,430,436,
474,516,532,567,574,629,633,649,693,727,769,800,808,
811,837,849,863,873,940,964,970,976,985,998,1012,1032,
1064,1083,1086,1102,1144,1191,1224,1249,1254,1482,
1566,1607,1632,1707,1710,1760,1763,1792,1813,1821,
1896,2052,2056,2062,2127,2155,2169,2227,2267,2275
AGA count: 70

AGG: 40,188,224,258,267,321,333,344,461,587,652,714,744,
747,915,951,1008,1178,1181,1231,1242,1327,1361,1431,
1522,1885,1929,1932,1935,1957,1962,2034,2045,2144,
2196,2221,2259
AGG count: 37

AAT: 15,46,86,96,104,109,166,202,218,228,244,273,282,304,
385,402,465,492,495,501,525,536,581,696,721,732,751,
764,776,780,804,816,859,890,936,960,1002,1024,1041,
1056,1071,1091,1112,1140,1165,1197,1200,1261,1270,
1324,1349,1364,1396,1400,1404,1408,1450,1504,1515,
1539,1549,1562,1584,1617,1655,1669,1721,1752,1809,
1841,1850,1880,1907,1942,1984,1998,2019,2040,2059,
2067,2074,2108,2245
AAT count: 83

AAC: 20,91,233,240,261,405,448,557,600,755,759,829,881,
992,1053,1154,1283,1304,1443,1479,1497,1623,1626,1645,
1677,1805,1833,2004,2136,2147,2162,2179
AAC count: 32

GAT: 193,325,546,561,597,783,852,870,910,919,1016,1027,
1035,1122,1161,1257,1345,1355,1392,1455,1459,1462,
1587,1597,1726,1784,2022,2119,2262
GAT count: 29

GAC: 43,183,382,931,1336,1417,1816,1837,2113,2270,2280
GAC count: 11

TGT: 62,158,277,417,489,609,786,867,895,928,1098,1105,1235,
1298,1437,1610,1715,1853,1864,1973,2097
TGT count: 21

TGC: (0)

CAA: 74,967,973,1020,1060,1309,1573,1629,1642,1877,1990,
2133
CAA count: 12

CAG: 1690,1774,1779
CAG count: 3

GAA: 49,124,147,340,478,577,590,718,1128,1150,1188,1428,
1531,1683,1703,1735,1744,1830,1926,1939,2152
GAA count: 21

GAG: 425,685,1914,2287
GAG count: 4

GGT: 299,1212,1434,1638,1659,1771,1824,2297
GGT count: 8

GGC: (0)

GGA: 498,670,797,1077,1543,1614
GGA count: 6

GGG: 395,982,1118,1352,1528,1620,2070
GGG count: 7

CAT: 113,137,255,308,318,606,621,677,690,703,739,1185,1387,
1424,1845,1947,2027,2139,2292
CAT count: 19

CAC: 456,833,876,1227,1367,1601,2255
CAC count: 7

ATT: 121,504,507,954,1038,1125,1215,1680
ATT count: 8

ATC: 208,1005,1290,1491,1569,1904,2182,2241
ATC count: 8

ATA: 735,1421,2008,2231
ATA count: 4

CTT: 134,174,213,379,392,408,542,884,988,1203,1267,1317,
1339,1507,1649,1696,2122,2188
CTT count: 18

CTC: 364,773,1220,1757,1977
CTC count: 5

CTA: 25,348,442,445,512,539,637,1370,1472,1980,2158
CTA count: 11

CTG: 329,613,898,907,1321,1475,2083
CTG count: 7

TTA: 37,236,293,1466,1535,1672,2185,2216
TTA count: 8

TTG: 1067,1699,2305
TTG count: 3

AAA: 55,433,564,570,957,1047,1131,1174,1446,1485,1500,1518,
1666,2031,2037,2172,2199,2209,2224
AAA count: 19

AAG: 1557
AAG count: 1

ATG: 1,196,311,1074,1147,1358,1892,2048
ATG count: 8

TTT: 169,337,359,979,1194,1264,1286,1342,1512,1693,1732,
1741,1860,1867,1910,2130
TTT count: 16

TTC: 162,655,2093
TTC count: 3

CCT: 296,1970,2001,2116
CCT count: 4

CCC: 471,1293,1967
CCC count: 3

CCA: 529,1095,1239,1604,1987,2193
CCA count: 6

CCG: (0)

TCT: 1414
TCT count: 1

TCC: 603,1718
TCC count: 2

TCA: 826,1168
TCA count: 2

TCG: (0)

AGT: 663,819,1245,1378,1440,1488,1953,2101,2283
AGT count: 9

AGC: (0)

ACT: 1158,1525,1635
ACT count: 3

ACC: 131,1301,1652
ACC count: 3

ACA: 221,270,711
ACA count: 3

ACG: (0)

TGG: 151,724
TGG count: 2

TAT: 1494,1827,1920
TAT count: 3

TAC: (0)

GTT: 640,1469
GTT count: 2

GTC: (0)

GTA: 439,922,2080,2212
GTA count: 4

GTG: (0)

TAA: 264,887,995
TAA count: 3

TAG: (0)

TGA: 584
TGA count: 1

Pages

Saturday, July 30, 2022

Small Brains Considered - 2

Appendix SBC 2

Monday, July 25, 2022

Quantum Biology - 11

QB_11 Appx 1