Rosalind Challenge 9: Finding a Motif in DNA
# http://rosalind.info/problems/subs/
#
#------------------------------------------------#

print("Rosalind Challenge 9: Finding a Motif in DNA\n")

s = Seq("ACAAGCTGAGTTGCTGAGTCGCTGAGTCCGCTGAGTATCGGCTGAGTACTTGCTGAGTCAGCTGAGTGCTGAGTCGCTGAGTTAATATGGCTGAGTAGCTGAGTTACTAGCTGAGTCGCTGAGTGAGCCGCTGAGTCACCGCATCGTGCATACGCTGAGTACGCGCTGAGTATGCTGAGTGCTGAGTCGGGAGGAAATAAAGCTGAGTTGCTGAGTGCTGAGTTTCTGCTGAGTGCTGAGTGCTGAGTGGCTGAGTAAGAAGCTGAGTAGTGCTGAGTTTGTCGCTGAGTGCTGAGTTCGGCTGAGTGCTGAGTGCTGAGTGCTGAGTTACAGCTGAGTAGAAAGGGGCTGAGTGCTGAGTAGCTGAGTCGTGCTGAGTCGCTGAGTGCTGAGTAGCTGAGTAGGCTGAGTAGCTGAGTGCTGAGTGCTGAGTAAGCTGAGTGTATCGGTGGCTGAGTAAGCTGAGTGCTGAGTTGCGCCGCTGAGTCGCTGAGTTGTTGCTGAGTCGCTGAGTGCTGAGTTGGCTGAGTTGAGCTGAGTCTTGCTGAGTTTCGCTGAGTGCTGAGTGCTGAGTAGAGGGGCTGAGTACTGCTGAGTGCTGAGTTGTATGCTGAGTGCTGAGTGGGCCGCTGAGTGCTGAGTGAGGGGCTGAGTGCTGAGTTGCTGAGTAGCTGAGTGCTGAGTGCTGAGTGCTGAGTGCTGAGTGCTGAGTGCTGGCTGAGTAGGCTGAGTTGCGCTGAGTGCTGAGTTGGTTTGCTGAGTAGCTGAGTGGCTGAGTATGCTGAGTTCGCTGAGTGATCCTCGGCTGAGTGCTGAGTCCGCTGAGTGGCTGAGTGCTGAGTATACTGCTGAGTGCTGAGTTGCTGAGTTTAGCTGAGTGCTGAGTGGCTGAGTAGCCTGCTGAGTGGACGGTGCTGAGTCCCAGCTGAGTAGCTGAGTGCTGAGTAGCTGAGTGGCTGAGTATTCAAGCTGAGTGCTGAGTGCTGAGTGCTGAGT")
t = Seq("GCTGAGTGC")

locations = []
count = 0
loc = 0

while (count < len(s)):
    loc = s.find(t, start=count)
    if (loc > 0):
        count = loc + 1
        locations.append(loc + 1) # adding plus 1 since the result needs to be in count from 1 format
    else:
        count = count + 1
    
print(' '.join(map(str,locations)))

print("\n---\n")