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Example of HMMs: protein alignment 1 Black: original sequence m0 start 2 m1 m2 m3 m4 m5 m6 m7 end Blue: add new amino acid i0 i1 i2 i3 i4 i5 i6 m0 m1 m2 m3 m4 m5 m6 start 3 m7 end Green: delete amino acid d1 d2 d3 d4 d5 d6 i0 i1 i2 i3 i4 i5 i6 m0 m1 m2 m3 m4 m5 m6 start 4 m7 end