60     .    :    .    :    .    :    .    :    .    :    .    :
      1      MKKTVFRLNFLTACVSLGIASQAWAGHTYFGIDYQYYRDFAENKGKFTVGAKNIE
        +++++++++++++++++++++++++++++++++++++++++| | | ||| |  || |  
     61 VWARD                                    YLDLAQNKGVFKAGATNVS

    120     .    :    .    :    .    :    .    :    .    :    .    :
     56 VYNKEGQLVGTSMTKAPMIDFSVVSRNGVAALVGDQYIVSVAHNGGYNDVDFGAEGRNPD
           | ||  --     |  |||  |  |     |  | |   |||-------------  
     85 IQLKNGQTF  NFPNVPIPDFSPASNKGATTSIGGAYSVTATHNG             TT

    180     .    :    .    :    .    :    .    :    .    :    .    :
    116 QHRFTYQIVKRNNYQAWERKHPYDGDYHMPRLHKFVTEAEPV                  
         |    |      |    |  -- ||    || ||| |   |++++++++++++++++++
    130 HHAISTQNWGQSSYKYIDRMT  NGDFAVTRLDKFVVETTGVKNSVDFSLNSHDALERYG

                      ~~~ 120 residues removed ~~~

    360     .    :    .    :    .    :    .    :    .    :    .    :
    224 GTVNLSGNVVSPNHYGPLPTGGSKGDSGSPMFIYDAKKKQWLINAVL             
        ++++++++++++|   |       |||||    ||  || |     |+++++++++++++
    242             NNTTPFYNETTGGDSGSGFYLYDNVKKEWVMLGTLFGIASSGADVGSI

                      ~~~ 120 residues removed ~~~

    540     .    :    .    :    .    :    .    :    .    :    .    :
    339 AKSEVGTVKLFNPSLNQTAKEHVKAAAGYNIYQPRMEYGKNIYLGDQGKGTLTIENNINQ
        +++++++++++++++++++++++++++++++++++++++++++|   | |     |  | 
    342                                            LSFSGGGSINFDNDVNI

    600     .    :    .    :    .    :    .    :    .    :    .    :
    399 GAGGLYFEGNFVVKGKQNNITWQGAGVSIGQDATVEWKVHNPENDRLSKIGIGTLLVNGK
        | ||| |          || |  |||  ||   || | |     | | ||| ||| ||  
    359 GSGGLIFDAGHHYTVTGNNKTFKGAGLDIGDNTTVDWNVKGVVGDNLHKIGAGTLNVNVS

    660     .    :    .    :    .    :    .    :    .    :    .    :
    459 GKNLGSLSAGNGKVILDQQADEAGQKQAFKEVGIVSGRATVQLNSTDQVDPNN    IYF
          |-- |  | | | |   ------- ||      ||   |  |       ||----| |
    419 QGN  NLKTGDGLVVLNSA       NAFDNIYMASGHGVVKINHSAALNQNNDYRGIFF

    720     .    :    .    :    .    :    .    :    .    :    .    :
    515 GFRGGRLDLNGHSLTFKRIQNTDEGAMIVN                              
           || |||||    |  |  || || | |++++++++++++++++++++++++++++++
    470 TENGGTLDLNGYDQSFNKIAATDIGALITNSAVQKAVLSVNNQSHYMYHGSVSGNTEINH


Fig. 5.  A portion of a general alignment of two protein sequences.
The portion consists of three similar regions separated by two
difference blocks, each with more than 120 residues.