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Can anyone explain....  beatnk96  Bioinformatics  2  11262013 07:15 AM 

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10152020, 10:25 AM  #1 
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Location: California Join Date: Sep 2020
Posts: 3

Can somebody more learned than me help explain what these two questions are asking?
So I am tackling an introductory bioinformatics course and I am kind of confused on what the following questions are asking to be honest, not really asking for homework help, but to simply explain how I would go about solving these?
Here is one Q: https://imgur.com/cw2jeUc I am not sure if I am supposed to draw 5 different trees for the 5 different positions here? Isn't the answer WWWWW? Cos if you do 5 trees, position 10 is the most parsimonious and doesn't have any mutations but i don't know if I did this wrong... Here is a second Q: https://imgur.com/1ebAvRW I am given two structures here, I calculated the energy for the structure on the left using the tables provided for example at the top their is a 6 base hairpin so table shows that as 4.3 then we have UG to UA and that is 0.5 then their is a 6 base internal loop and that has 2.5 energy. Anyways I did this for the rest of structure 1 and added up all the numbers and got 2.3 so I'm pretty sure its correct. But I am not sure how to do structure 2... Starting at the top its a 6 base hairpin no problems, then we have UG to UA and that's no problem, but then the internal loop is that a 3 base loop or a 4 base loop? Cos the C is under A I'm not sure if its included in the loop. That's it from me guys, thanks! 
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