I'm using as examples the mouse and human sequences for Rhodopsin (the protein in retinal rod cells that detects photons).
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} *)
Your method works to scroll through the alignment:
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}]

Or for a more traditional representation:
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}]

Manipulate
issues, I don't know a protein from a rock. If you showed the code to create Chains A and B, then maybe you'd have a lot more folks that could help. $\endgroup$ – JimB Jun 26 '19 at 18:50Length = Length[seqAlign]
? RedefiningLength
is not a good idea. $\endgroup$ – Rohit Namjoshi Jun 26 '19 at 19:15ProteinData[]
or some other built-in curated data source. Can you not update your question with examples for A and B? $\endgroup$ – Michael E2 Jun 26 '19 at 22:02