for dir in */;
do cd $dir;
cd $(ls | grep '^iteration[0-9]\+$' | cut -c10-| sort -n| tail -n1 | sed 's|^|iteration|');
assembly=$(find -maxdepth 1 -type d -name "cMTNT*assembly" | head -1); cd $assembly
results=$(find -maxdepth 1 -type d -name "cMTNT*results" | head -1); cd $results;
echo $dir; 
cp cMTNT*Nna_out*cMTNT*.unpadded* /pool/genomics/tsuchiyam/mitogenomes/results;
cd /pool/genomics/tsuchiyam/mitogenomes/interleaved;
done;

Description:
for all subfolders in the current directory;
go to each directory;
go to the directory (cd) that matches the following description (grep):
	starts (^) with 'iteration', followed by numbers [0-9]
	the plus symbol means that the previous pattern will appear at least once before the end ($) of the name
	cut -c10-: excludes the first nine characters, start on character 10
	sort -n: sort the result from 'cut' (above)
	tail -n1: select the last (n1) element of the sorted list
	sed 's|^|iteration|': add the word "iteration" to the result of tail (above)
	OBS: we need to use ls so the folder that matches the requirement is listed and we can cd to it
create the variable $assembly (same applies for $results)
	find -maxdepth 1 (maxdepth determines how many levels down to search; level 1 is the root)
		-type d (directory)
		-name 
		-head (print the result of the search)
copy the file that matches the description to an specified location
go to folder
close the loop