Molecule and ligation finding program
For the starter, you can create small function which will get input since your code requires too much user input.

Just making that one function will reduce repetitive code of raw_input() and printing it's msg.

Also, your code will be more readable.

Code:

def get_input(msg):
    print msg
    val = int(raw_input())
    return val

number = get_input("Please put the amount of BPs: ")

solution = (number * 660)
Avo = (6.022 * (10 ** 23))
Grams_Avo = ( solution / Avo)

conc = float(get_input("Put in Concentration (ng/ul): "))

multiple = (10 ** -9)
amount = (conc * multiple)
total = float(amount / Grams_Avo)
print "Amount of molecules:  %s" % total

plasmid = float(get_input("Amount of ul used by the plasmid: "))
particles = float(plasmid * total)

ratio = get_input("What ratio amount will you use?: ")

molecules_needed = float(particles * ratio)
print molecules_needed

oligo = float(get_input("Conc. of your oligo?: "))
oligo_num = float(oligo * multiple) # amount

G = get_input("Enter number of G in Oligo: ")

A = get_input("Enter number of A in Oligo: ")

T = get_input("Enter number of T in Oligo: ")

C = get_input("Enter number of C in Oligo: ")

sumG = (G * 329)
sumA = (A * 313)
sumT = (T * 304)
sumC = (C * 289)
daoligo = (sumG + sumA + sumT + sumC) # g/mol

print "Total amount of your insert %s" % daoligo

oligototal = float(oligo_num / (daoligo/Avo)) # molecules for insert
complete = float(molecules_needed/oligototal) #amount of insert needed from stock ul

m = """
    What dilution will you use?
    1. Stock
    2. 1:10
    3. 1:20
    4. 1:30
    5. 1:50
    """

code = float(raw_input())
code =  get_input(m)

if code == 1:
    print complete #stock
elif code == 2:
    code2 = (oligototal/10)
    complete1 = float(molecules_needed/code2)
    print complete1 #1:10
elif code == 3:
    code3 = (oligototal/20)
    complete2 = float(molecules_needed/code3)
    print complete2 #1:20
elif code == 4:
    code4 = (oligototal/30)
    complete3 = float(molecules_needed/code4)
    print complete3 #1:30
elif code == 5:
    code_5 = (oligototal/50)
    complete4 = float(molecules_needed/code_5)
    print complete4


Output

Please put the amount of BPs: 
12
Put in Concentration (ng/ul): 
1
Amount of molecules:  76035353535.4
Amount of ul used by the plasmid: 
2
What ratio amount will you use?: 
3
4.56212121212e+11
Conc. of your oligo?: 
4
Enter number of G in Oligo: 
4
Enter number of A in Oligo: 
6
Enter number of T in Oligo: 
7
Enter number of C in Oligo: 
8
Total amount of your insert 7634
9

    What dilution will you use?
    1. Stock
    2. 1:10
    3. 1:20
    4. 1:30
    5. 1:50

1
1.44583333333