$ perl bio.pl sequence.fa
Position: 29 String: TAA
Position: 48 String: TGA
Position: 73 String: TAA
Position: 134 String: TGA
Position: 201 String: TAA
Position: 221 String: TGA
Position: 248 String: TAA
Position: 288 String: TGA
Position: 309 String: TAG
Position: 324 String: TGA
Position: 332 String: TAA
Position: 378 String: TAA
Position: 381 String: TAG
Position: 395 String: TGA
Position: 408 String: TGA
Position: 448 String: TAA
Position: 505 String: TGA
Position: 512 String: TAA
Position: 621 String: TGA
Position: 700 String: TGA
Position: 722 String: TAA
Position: 743 String: TAA
Position: 752 String: TGA
Position: 857 String: TAA
Position: 864 String: TAA
Position: 957 String: TAG
Position: 974 String: TAA
Position: 1002 String: TGA
Position: 1019 String: TAA
Position: 1052 String: TGA
Position: 1198 String: TGA
Position: 1210 String: TAG
Position: 1253 String: TGA
Position: 1265 String: TAA