mouse = "MNGTEGPNFYVPFSNVTGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYV
TVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVL
AIERYVVVCKPMSNFRFGENHAIMGVVFTWIMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNE
SFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIFFLICWLPYASV
AFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMLNKQFRNCMLTTLCCGKNPLGDDDASATASKTE
TSQVAPA";
human = "MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYV
TVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVL
AIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNE
SFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASV
AFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTE
TSQVAPA";

s = SequenceAlignment[mouse, human]

(* {MNGTEGPNFYVPFSN,{V,A},TGVVRSPFE,{Q,Y},
PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV,
{F,L},GGFT,{T,S},TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGV,
{V,A},FTW,{I,V},MALACAAPPL,{V,A},GWSRYIPEG,{M,L},
QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI,{V,I},
IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVI,{F,A},
FLICW,{L,V},PYASVAFYIFTHQGSNFGPIFMT,{L,I},PAFFAKS,
{SS,AA},IYNPVIYIM,{L,M},NKQFRNCMLTT,{L,I},CCGKNPLGDD,{D,E},ASAT,{A,V},SKTETSQVAPA} *)

Manipulate[
 seqLength = Length[s];
 shownSize = 5;
 Grid[{If[ListQ[#], Column[#, Frame -> All, Spacings -> 1], #] & /@
    s[[x ;; x + shownSize]]}, Frame -> All], {x, 1,
  seqLength - shownSize, 1}]

aln1 = "";
aln2 = "";
ident = "";
Do[{
  If[Length[n] == 0,
   {
    aln1 = aln1 <> n,
    aln2 = aln2 <> n,
    Do[ident = ident <> "*", {StringLength[n]}]
    },
   {
    While[StringLength[n[[1]]] != StringLength[n[[2]]], {
      If[StringLength[n[[1]]] < StringLength[n[[2]]],
       n[[1]] = n[[1]] <> "-",
       n[[2]] = n[[2]] <> "-"]
      }],
    Do[ident = ident <> " ", {Max[Map[StringLength, n]]}],
    aln1 = aln1 <> n[[1]],
    aln2 = aln2 <> n[[2]]
    }
   ]
  }, {n, s}]

Manipulate[
 seqLength2 = StringLength[ident];
 shownSize2 = 40;
 Grid[Characters[{ident, aln1, aln2}][[All, n ;; n + shownSize2]]]
 , {n, 1, seqLength2 - shownSize2, 1}]