Connection Between Alignment and HMMs. A state model for alignment -AGGCTATCACCTGACCTCCAGGCCGA--TGCCC--- TAG-CTATCAC--GACCGC-GGTCGATTTGCCCGACC IMMJMMMMMMMJJMMMMMMJMMMMMMMIIMMMMMIII.
Pairwise alignment 2: Scoring matrices and gaps BLAST, BLAT and FASTA
