In this file, I decrypt some messages sent to me by students.
> Example_sub:= "RWLFWARATEJLTJBNJLMYJLWJBKCLWBDLWDDTGJBMOTDJLTWFFKWACTJLWJLWDVMKATDJLTFWADGMYJLTHKDFWADGYMBJLMNGWADGMYOTWBGWGHMJLTBCMAYTGGMBRWLFWASBTGKDTDMXTBJLTCMNACKFWADJLNGJLTHKDFWADGNADTBLTBEWJCLWGHMJLTBCMAYTGGMBJLTHKDFWADGLWDYWFFTAJMBKCLWBDWGFMBDBWLFMYDLWBWWJFTWGJJLTFWADGELKCLLWDGMYWBGNBBTADTBTDJMLKHGLTRATEJLTQTATXMFTACTMYLKGWCJKMAGWADJLTATTDYMBJLTHQNJKJCTBJWKAFOLWDQTTAWSWKAYNFSWJLJMYMFFME";
> 

  Example_sub := "RWLFWARATEJLTJBNJLMYJLWJBKCLWBDLWDDTGJBMOTDJLTWF\
        FKWACTJLWJLWDVMKATDJLTFWADGMYJLTHKDFWADGYMBJLMNGWADGMYOTWB\
        GWGHMJLTBCMAYTGGMBRWLFWASBTGKDTDMXTBJLTCMNACKFWADJLNGJLTHK\
        DFWADGNADTBLTBEWJCLWGHMJLTBCMAYTGGMBJLTHKDFWADGLWDYWFFTAJM\
        BKCLWBDWGFMBDBWLFMYDLWBWWJFTWGJJLTFWADGELKCLLWDGMYWBGNBBTA\
        DTBTDJMLKHGLTRATEJLTQTATXMFTACTMYLKGWCJKMAGWADJLTATTDYMBJL\
        THQNJKJCTBJWKAFOLWDQTTAWSWKAYNFSWJLJMYMFFME"

> Example_Vigenere:="ZOJYOAHJKZBGXLSVZOJQTSDQTLXYNVXJUDJFAWYJKMNTYASQTVZVRHBXUSZPZLJTYOTYKKZRUBWUKJTPJTTTTPSIGSQJKJFTXPJFCHXCLSFKRHSFGWFEQVKLUBWPKFWCZPTPYIZVNLQQURJFMYNOGUIVUSIWYOJJGKHQSLYQLPLJZAMGWBJGTAZTTLIQAAYJKSTEGSBCXSTEQOFFXBNPKKMKYMFOOSDYOAMVGEJUJLGCAJMGJONUYPXVKYXCTKMCJKWKBLSJOTXGRMFPJONUVHWGTAXKTATNOCNPMPSCYOJNZLWVNHYYGZGCYPHCRSDCRHWIKIFUQLYYUYPKTNKTUTXWTBUVUZZPJVBPZVUCEAMGZHCGYOJERHNOKKYJKFXVOSQQCLICTKYJKFIKJUYFGYJHONMVHHHMCPYJEVZJUDJXKYNFGYJJKATNJTJKSHDFOLGWZPBKRSFVRLFUZIWKTNIQCUFUUSIKKYTHKCNNHLKQXLNFU";

  Example_Vigenere := "ZOJYOAHJKZBGXLSVZOJQTSDQTLXYNVXJUDJFAWYJKMN\
        TYASQTVZVRHBXUSZPZLJTYOTYKKZRUBWUKJTPJTTTTPSIGSQJKJFTXPJFC\
        HXCLSFKRHSFGWFEQVKLUBWPKFWCZPTPYIZVNLQQURJFMYNOGUIVUSIWYOJ\
        JGKHQSLYQLPLJZAMGWBJGTAZTTLIQAAYJKSTEGSBCXSTEQOFFXBNPKKMKY\
        MFOOSDYOAMVGEJUJLGCAJMGJONUYPXVKYXCTKMCJKWKBLSJOTXGRMFPJON\
        UVHWGTAXKTATNOCNPMPSCYOJNZLWVNHYYGZGCYPHCRSDCRHWIKIFUQLYYU\
        YPKTNKTUTXWTBUVUZZPJVBPZVUCEAMGZHCGYOJERHNOKKYJKFXVOSQQCLI\
        CTKYJKFIKJUYFGYJHONMVHHHMCPYJEVZJUDJXKYNFGYJJKATNJTJKSHDFO\
        LGWZPBKRSFVRLFUZIWKTNIQCUFUUSIKKYTHKCNNHLKQXLNFU"

> second_part:=(item,list) -> list;

                 second_part := (item, list) -> list

The frequency function tells how many times an item appears in a list
> frequency:=(item,list)->if nops(list) = 0 then (item,0) else if list[1] = item then (item,1+second_part(frequency(item,list[2..nops(list)]))) else frequency(item,list[2..nops(list)]) end if end if;

  frequency := proc(item, list)
option operator, arrow;
    if nops(list) = 0 then item, 0
    else
        if list[1] = item then item, 1 + second_part(
            frequency(item, list[2 .. nops(list)]))
        else frequency(item, list[2 .. nops(list)])
        end if
    end if
end proc

> with(StringTools);

  [AndMap, Capitalize, Char, CharacterMap, Chomp, CommonPrefix,

        CommonSuffix, Compare, CompareCI, Drop, Explode,

        FirstFromLeft, FirstFromRight, FormatMessage, Group, Implode,

        IsASCII, IsAlpha, IsAlphaNumeric, IsBinaryDigit,

        IsControlCharacter, IsDigit, IsGraphic, IsHexDigit,

        IsIdentifier, IsIdentifier1, IsLower, IsOctalDigit, IsPrefix,

        IsPrintable, IsPunctuation, IsSpace, IsSuffix, IsUpper, Join,

        LeftFold, Levenshtein, LongestCommonSubSequence,

        LongestCommonSubString, LowerCase, Map, OrMap, Ord, Random,

        RegMatch, RegSub, Remove, Reverse, RightFold, Search,

        SearchAll, Select, SelectRemove, Soundex, Split, Squeeze,

        SubString, Substitute, SubstituteAll, Take, Trim, TrimLeft,

        TrimRight, UpperCase]

> frequency("A",Explode(Example_Vigenere));

                               "A", 13

The frequency_table function generates a frequency table telling how many times each item in the first list appears in the second.
> frequency_table := (S,T) -> map((subs(s=(S),(x->frequency(x,s))),(T)));

  frequency_table :=

        (S, T) -> map(subs(s = S, x -> frequency(x, s)), T)

> Alphabet:="ABCDEFGHIJKLMNOPQRSTUVWXYZ";

               Alphabet := "ABCDEFGHIJKLMNOPQRSTUVWXYZ"

> M:=frequency_table(Explode(Example_sub),Explode(Alphabet));

  M := ["A", 27, "B", 25, "C", 12, "D", 29, "E", 5, "F", 20, "G", 24,

        "H", 7, "I", 0, "J", 33, "K", 16, "L", 37, "M", 27, "N", 8,

        "O", 3, "P", 0, "Q", 3, "R", 4, "S", 3, "T", 42, "U", 0, "V",

        1, "W", 40, "X", 2, "Y", 13, "Z", 0]

I develop the "bubble sort algorithm.
> bubble_insert := (a,b,L) -> if nops(L) < 2 then [a,b] else if b<L[2] then [L[1],L[2],op(bubble_insert(a,b,L[3..nops(L)]))] else [a,b,op(L)] end if end if;

  bubble_insert := proc(a, b, L)
option operator, arrow;
    if nops(L) < 2 then [a, b]
    else
        if b < L[2] then [L[1], L[2],
            op(bubble_insert(a, b, L[3 .. nops(L)]))]
        else [a, b, op(L)]
        end if
    end if
end proc

This function sorts frequency tables, putting the most frequent items first.
> sort_frequency_table:= L -> if nops(L) < 2 then L else bubble_insert(L[1],L[2],sort_frequency_table(L[3..nops(L)])) end if;

  sort_frequency_table := proc(L)
option operator, arrow;
    if nops(L) < 2 then L
    else bubble_insert(L[1], L[2],
        sort_frequency_table(L[3 .. nops(L)]))
    end if
end proc

> sort_frequency_table(M);

  ["T", 42, "W", 40, "L", 37, "J", 33, "D", 29, "A", 27, "M", 27, "B",

        25, "G", 24, "F", 20, "K", 16, "Y", 13, "C", 12, "N", 8, "H",

        7, "E", 5, "R", 4, "O", 3, "Q", 3, "S", 3, "X", 2, "V", 1,

        "I", 0, "P", 0, "U", 0, "Z", 0]

This is a better function for enciphering and deciphering with the Substitution Cipher.
> partial_sub_cipher:=(list1,list2)->if nops(list1) < 2 or nops(list2) = 0 then list2
> else if list1[1] = list2[1] then [list1[2],op(partial_sub_cipher(list1,list2[2..nops(list2)]))]
> else [op(partial_sub_cipher(list1[3..nops(list1)],[list2[1]])),op(partial_sub_cipher(list1,list2[2..nops(list2)]))]end if end if;

  partial_sub_cipher := proc(list1, list2)
option operator, arrow;
    if nops(list1) < 2 or nops(list2) = 0 then list2
    else
        if list1[1] = list2[1] then [list1[2], op(
            partial_sub_cipher(list1, list2[2 .. nops(list2)]))
            ]
        else [op(partial_sub_cipher(list1[3 .. nops(list1)],
            [list2[1]])), op(partial_sub_cipher(list1,
            list2[2 .. nops(list2)]))]
        end if
    end if
end proc

Here are some examples of trial attempts to work on 
> Implode(partial_sub_cipher(["T", "e", "W","t","A","h","X","z"],Explode(Example_sub)));

  "RtLFthRheEJLeJBNJLMYJLtJBKCLtBDLtDDeGJBMOeDJLetFFKthCeJLtJLtDVM\
        KheDJLeFthDGMYJLeHKDFthDGYMBJLMNGthDGMYOetBGtGHMJLeBCMhYeG\
        GMBRtLFthSBeGKDeDMzeBJLeCMNhCKFthDJLNGJLeHKDFthDGNhDeBLeBE\
        tJCLtGHMJLeBCMhYeGGMBJLeHKDFthDGLtDYtFFehJMBKCLtBDtGFMBDBt\
        LFMYDLtBttJFetGJJLeFthDGELKCLLtDGMYtBGNBBehDeBeDJMLKHGLeRh\
        eEJLeQehezMFehCeMYLKGtCJKMhGthDJLeheeDYMBJLeHQNJKJCeBJtKhF\
        OLtDQeehtStKhYNFStJLJMYMFFME"

> 
> Implode(partial_sub_cipher(["T","t","W","e","L","a"],Explode(Example_sub)));

  "ReaFeARAtEJatJBNJaMYJaeJBKCaeBDaeDDtGJBMOtDJateFFKeACtJaeJaeDVM\
        KAtDJatFeADGMYJatHKDFeADGYMBJaMNGeADGMYOteBGeGHMJatBCMAYtG\
        GMBReaFeASBtGKDtDMXtBJatCMNACKFeADJaNGJatHKDFeADGNADtBatBE\
        eJCaeGHMJatBCMAYtGGMBJatHKDFeADGaeDYeFFtAJMBKCaeBDeGFMBDBe\
        aFMYDaeBeeJFteGJJatFeADGEaKCaaeDGMYeBGNBBtADtBtDJMaKHGatRA\
        tEJatQtAtXMFtACtMYaKGeCJKMAGeADJatAttDYMBJatHQNJKJCtBJeKAF\
        OaeDQttAeSeKAYNFSeJaJMYMFFME"

> dropL := (item,list) -> if nops(list) = 0 then list else if list[1] = item then dropL(item,list[2..nops(list)]) else [list[1],op(dropL(item,list[2..nops(list)]))]end if end if;
> 
> 

  dropL := proc(item, list)
option operator, arrow;
    if nops(list) = 0 then list
    else
        if list[1] = item then
            dropL(item, list[2 .. nops(list)])
        else
            [list[1], op(dropL(item, list[2 .. nops(list)]))]
        end if
    end if
end proc

This function generates a frequency table of the items in the list L.  It doesn't need an "alphabet" argument.
> self_count := L -> if nops(L) = 0 then L else [op(frequency_table(L,[L[1]])),op(self_count(dropL(L[1],L[2..nops(L)])))] end if;

  self_count := proc(L)
option operator, arrow;
    if nops(L) = 0 then L
    else [op(frequency_table(L, [L[1]])),
        op(self_count(dropL(L[1], L[2 .. nops(L)])))]
    end if
end proc

> self_count(Explode(Example_sub));

  ["R", 4, "W", 40, "L", 37, "F", 20, "A", 27, "T", 42, "E", 5, "J",

        33, "B", 25, "N", 8, "M", 27, "Y", 13, "K", 16, "C", 12, "D",

        29, "G", 24, "O", 3, "V", 1, "H", 7, "S", 3, "X", 2, "Q", 3]

> self_count(["a","a","b","a"]);

                           ["a", 3, "b", 1]

> 
This function generates a list of "digrams" (two letter sequences) from the text list L.
> digrams := L -> if nops(L) < 2 then [] else [[L[1],L[2]],op(digrams(L[2..nops(L)]))] end if;

  digrams := proc(L)
option operator, arrow;
    if nops(L) < 2 then []
    else [[L[1], L[2]], op(digrams(L[2 .. nops(L)]))]
    end if
end proc

> digrams (Explode(Alphabet));

  [["A", "B"], ["B", "C"], ["C", "D"], ["D", "E"], ["E", "F"],

        ["F", "G"], ["G", "H"], ["H", "I"], ["I", "J"], ["J", "K"],

        ["K", "L"], ["L", "M"], ["M", "N"], ["N", "O"], ["O", "P"],

        ["P", "Q"], ["Q", "R"], ["R", "S"], ["S", "T"], ["T", "U"],

        ["U", "V"], ["V", "W"], ["W", "X"], ["X", "Y"], ["Y", "Z"]]

> self_count(digrams(Explode(Example_sub)));

  [["R", "W"], 2, ["W", "L"], 3, ["L", "F"], 3, ["F", "W"], 8,

        ["W", "A"], 11, ["A", "R"], 1, ["R", "A"], 2, ["A", "T"], 5,

        ["T", "E"], 2, ["E", "J"], 2, ["J", "L"], 20, ["L", "T"], 15,

        ["T", "J"], 2, ["J", "B"], 3, ["B", "N"], 1, ["N", "J"], 2,

        ["L", "M"], 2, ["M", "Y"], 7, ["Y", "J"], 2, ["L", "W"], 11,

        ["W", "J"], 5, ["B", "K"], 2, ["K", "C"], 3, ["C", "L"], 4,

        ["W", "B"], 5, ["B", "D"], 3, ["D", "L"], 2, ["W", "D"], 5,

        ["D", "D"], 1, ["D", "T"], 4, ["T", "G"], 4, ["G", "J"], 3,

        ["B", "M"], 1, ["M", "O"], 1, ["O", "T"], 2, ["T", "D"], 5,

        ["D", "J"], 5, ["T", "W"], 3, ["W", "F"], 2, ["F", "F"], 3,

        ["F", "K"], 1, ["K", "W"], 1, ["A", "C"], 3, ["C", "T"], 3,

        ["D", "V"], 1, ["V", "M"], 1, ["M", "K"], 1, ["K", "A"], 3,

        ["T", "F"], 2, ["A", "D"], 10, ["D", "G"], 7, ["G", "M"], 5,

        ["T", "H"], 4, ["H", "K"], 3, ["K", "D"], 4, ["D", "F"], 3,

        ["G", "Y"], 1, ["Y", "M"], 3, ["M", "B"], 6, ["B", "J"], 5,

        ["M", "N"], 2, ["N", "G"], 2, ["G", "W"], 4, ["Y", "O"], 1,

        ["B", "G"], 2, ["W", "G"], 4, ["G", "H"], 2, ["H", "M"], 2,

        ["M", "J"], 2, ["T", "B"], 7, ["B", "C"], 2, ["C", "M"], 3,

        ["M", "A"], 3, ["A", "Y"], 3, ["Y", "T"], 2, ["G", "G"], 2,

        ["B", "R"], 1, ["A", "S"], 1, ["S", "B"], 1, ["B", "T"], 3,

        ["G", "K"], 1, ["D", "M"], 1, ["M", "X"], 1, ["X", "T"], 1,

        ["T", "C"], 1, ["N", "A"], 2, ["C", "K"], 1, ["K", "F"], 1,

        ["L", "N"], 1, ["G", "N"], 2, ["B", "L"], 1, ["B", "E"], 1,

        ["E", "W"], 1, ["J", "C"], 2, ["G", "L"], 2, ["D", "Y"], 2,

        ["Y", "W"], 2, ["F", "T"], 3, ["T", "A"], 6, ["A", "J"], 1,

        ["J", "M"], 3, ["D", "W"], 1, ["G", "F"], 1, ["F", "M"], 3,

        ["D", "B"], 1, ["B", "W"], 2, ["Y", "D"], 1, ["W", "W"], 1,

        ["J", "F"], 1, ["J", "J"], 1, ["G", "E"], 1, ["E", "L"], 1,

        ["L", "K"], 3, ["L", "L"], 1, ["N", "B"], 1, ["B", "B"], 1,

        ["M", "L"], 1, ["K", "H"], 1, ["H", "G"], 1, ["T", "R"], 1,

        ["T", "Q"], 1, ["Q", "T"], 2, ["T", "X"], 1, ["X", "M"], 1,

        ["M", "F"], 2, ["T", "M"], 1, ["Y", "L"], 1, ["K", "G"], 1,

        ["W", "C"], 1, ["C", "J"], 1, ["J", "K"], 2, ["K", "M"], 1,

        ["A", "G"], 1, ["T", "T"], 2, ["H", "Q"], 1, ["Q", "N"], 1,

        ["K", "J"], 1, ["J", "W"], 1, ["W", "K"], 2, ["A", "F"], 1,

        ["F", "O"], 1, ["O", "L"], 1, ["D", "Q"], 1, ["A", "W"], 1,

        ["W", "S"], 1, ["S", "W"], 2, ["Y", "N"], 1, ["N", "F"], 1,

        ["F", "S"], 1, ["L", "J"], 1, ["M", "E"], 1]

> sort_frequency_table(%);

  [["J", "L"], 20, ["L", "T"], 15, ["W", "A"], 11, ["L", "W"], 11,

        ["A", "D"], 10, ["F", "W"], 8, ["M", "Y"], 7, ["D", "G"], 7,

        ["T", "B"], 7, ["M", "B"], 6, ["T", "A"], 6, ["A", "T"], 5,

        ["W", "J"], 5, ["W", "B"], 5, ["W", "D"], 5, ["T", "D"], 5,

        ["D", "J"], 5, ["G", "M"], 5, ["B", "J"], 5, ["C", "L"], 4,

        ["D", "T"], 4, ["T", "G"], 4, ["T", "H"], 4, ["K", "D"], 4,

        ["G", "W"], 4, ["W", "G"], 4, ["W", "L"], 3, ["L", "F"], 3,

        ["J", "B"], 3, ["K", "C"], 3, ["B", "D"], 3, ["G", "J"], 3,

        ["T", "W"], 3, ["F", "F"], 3, ["A", "C"], 3, ["C", "T"], 3,

        ["K", "A"], 3, ["H", "K"], 3, ["D", "F"], 3, ["Y", "M"], 3,

        ["C", "M"], 3, ["M", "A"], 3, ["A", "Y"], 3, ["B", "T"], 3,

        ["F", "T"], 3, ["J", "M"], 3, ["F", "M"], 3, ["L", "K"], 3,

        ["R", "W"], 2, ["R", "A"], 2, ["T", "E"], 2, ["E", "J"], 2,

        ["T", "J"], 2, ["N", "J"], 2, ["L", "M"], 2, ["Y", "J"], 2,

        ["B", "K"], 2, ["D", "L"], 2, ["O", "T"], 2, ["W", "F"], 2,

        ["T", "F"], 2, ["M", "N"], 2, ["N", "G"], 2, ["B", "G"], 2,

        ["G", "H"], 2, ["H", "M"], 2, ["M", "J"], 2, ["B", "C"], 2,

        ["Y", "T"], 2, ["G", "G"], 2, ["N", "A"], 2, ["G", "N"], 2,

        ["J", "C"], 2, ["G", "L"], 2, ["D", "Y"], 2, ["Y", "W"], 2,

        ["B", "W"], 2, ["Q", "T"], 2, ["M", "F"], 2, ["J", "K"], 2,

        ["T", "T"], 2, ["W", "K"], 2, ["S", "W"], 2, ["A", "R"], 1,

        ["B", "N"], 1, ["D", "D"], 1, ["B", "M"], 1, ["M", "O"], 1,

        ["F", "K"], 1, ["K", "W"], 1, ["D", "V"], 1, ["V", "M"], 1,

        ["M", "K"], 1, ["G", "Y"], 1, ["Y", "O"], 1, ["B", "R"], 1,

        ["A", "S"], 1, ["S", "B"], 1, ["G", "K"], 1, ["D", "M"], 1,

        ["M", "X"], 1, ["X", "T"], 1, ["T", "C"], 1, ["C", "K"], 1,

        ["K", "F"], 1, ["L", "N"], 1, ["B", "L"], 1, ["B", "E"], 1,

        ["E", "W"], 1, ["A", "J"], 1, ["D", "W"], 1, ["G", "F"], 1,

        ["D", "B"], 1, ["Y", "D"], 1, ["W", "W"], 1, ["J", "F"], 1,

        ["J", "J"], 1, ["G", "E"], 1, ["E", "L"], 1, ["L", "L"], 1,

        ["N", "B"], 1, ["B", "B"], 1, ["M", "L"], 1, ["K", "H"], 1,

        ["H", "G"], 1, ["T", "R"], 1, ["T", "Q"], 1, ["T", "X"], 1,

        ["X", "M"], 1, ["T", "M"], 1, ["Y", "L"], 1, ["K", "G"], 1,

        ["W", "C"], 1, ["C", "J"], 1, ["K", "M"], 1, ["A", "G"], 1,

        ["H", "Q"], 1, ["Q", "N"], 1, ["K", "J"], 1, ["J", "W"], 1,

        ["A", "F"], 1, ["F", "O"], 1, ["O", "L"], 1, ["D", "Q"], 1,

        ["A", "W"], 1, ["W", "S"], 1, ["Y", "N"], 1, ["N", "F"], 1,

        ["F", "S"], 1, ["L", "J"], 1, ["M", "E"], 1]

> trigrams:= L->if nops(L) < 3 then [] else [[L[1],L[2],L[3]],op(trigrams(L[2..nops(L)]))] end if;

  trigrams := proc(L)
option operator, arrow;
    if nops(L) < 3 then []
    else [[L[1], L[2], L[3]], op(trigrams(L[2 .. nops(L)]))]
    end if
end proc

> self_count(trigrams(Explode(Example_sub)));

  [["R", "W", "L"], 2, ["W", "L", "F"], 3, ["L", "F", "W"], 2,

        ["F", "W", "A"], 8, ["W", "A", "R"], 1, ["A", "R", "A"], 1,

        ["R", "A", "T"], 2, ["A", "T", "E"], 2, ["T", "E", "J"], 2,

        ["E", "J", "L"], 2, ["J", "L", "T"], 13, ["L", "T", "J"], 1,

        ["T", "J", "B"], 1, ["J", "B", "N"], 1, ["B", "N", "J"], 1,

        ["N", "J", "L"], 1, ["J", "L", "M"], 2, ["L", "M", "Y"], 1,

        ["M", "Y", "J"], 2, ["Y", "J", "L"], 2, ["J", "L", "W"], 3,

        ["L", "W", "J"], 2, ["W", "J", "B"], 1, ["J", "B", "K"], 1,

        ["B", "K", "C"], 2, ["K", "C", "L"], 3, ["C", "L", "W"], 3,

        ["L", "W", "B"], 3, ["W", "B", "D"], 2, ["B", "D", "L"], 1,

        ["D", "L", "W"], 2, ["L", "W", "D"], 5, ["W", "D", "D"], 1,

        ["D", "D", "T"], 1, ["D", "T", "G"], 1, ["T", "G", "J"], 1,

        ["G", "J", "B"], 1, ["J", "B", "M"], 1, ["B", "M", "O"], 1,

        ["M", "O", "T"], 1, ["O", "T", "D"], 1, ["T", "D", "J"], 3,

        ["D", "J", "L"], 4, ["L", "T", "W"], 1, ["T", "W", "F"], 1,

        ["W", "F", "F"], 2, ["F", "F", "K"], 1, ["F", "K", "W"], 1,

        ["K", "W", "A"], 1, ["W", "A", "C"], 1, ["A", "C", "T"], 2,

        ["C", "T", "J"], 1, ["T", "J", "L"], 1, ["W", "J", "L"], 2,

        ["W", "D", "V"], 1, ["D", "V", "M"], 1, ["V", "M", "K"], 1,

        ["M", "K", "A"], 1, ["K", "A", "T"], 1, ["A", "T", "D"], 1,

        ["L", "T", "F"], 2, ["T", "F", "W"], 2, ["W", "A", "D"], 8,

        ["A", "D", "G"], 6, ["D", "G", "M"], 3, ["G", "M", "Y"], 3,

        ["L", "T", "H"], 4, ["T", "H", "K"], 3, ["H", "K", "D"], 3,

        ["K", "D", "F"], 3, ["D", "F", "W"], 3, ["D", "G", "Y"], 1,

        ["G", "Y", "M"], 1, ["Y", "M", "B"], 2, ["M", "B", "J"], 3,

        ["B", "J", "L"], 4, ["L", "M", "N"], 1, ["M", "N", "G"], 1,

        ["N", "G", "W"], 1, ["G", "W", "A"], 2, ["M", "Y", "O"], 1,

        ["Y", "O", "T"], 1, ["O", "T", "W"], 1, ["T", "W", "B"], 1,

        ["W", "B", "G"], 2, ["B", "G", "W"], 1, ["G", "W", "G"], 1,

        ["W", "G", "H"], 2, ["G", "H", "M"], 2, ["H", "M", "J"], 2,

        ["M", "J", "L"], 2, ["L", "T", "B"], 3, ["T", "B", "C"], 2,

        ["B", "C", "M"], 2, ["C", "M", "A"], 2, ["M", "A", "Y"], 2,

        ["A", "Y", "T"], 2, ["Y", "T", "G"], 2, ["T", "G", "G"], 2,

        ["G", "G", "M"], 2, ["G", "M", "B"], 2, ["M", "B", "R"], 1,

        ["B", "R", "W"], 1, ["W", "A", "S"], 1, ["A", "S", "B"], 1,

        ["S", "B", "T"], 1, ["B", "T", "G"], 1, ["T", "G", "K"], 1,

        ["G", "K", "D"], 1, ["K", "D", "T"], 1, ["D", "T", "D"], 1,

        ["T", "D", "M"], 1, ["D", "M", "X"], 1, ["M", "X", "T"], 1,

        ["X", "T", "B"], 1, ["T", "B", "J"], 2, ["L", "T", "C"], 1,

        ["T", "C", "M"], 1, ["C", "M", "N"], 1, ["M", "N", "A"], 1,

        ["N", "A", "C"], 1, ["A", "C", "K"], 1, ["C", "K", "F"], 1,

        ["K", "F", "W"], 1, ["A", "D", "J"], 2, ["J", "L", "N"], 1,

        ["L", "N", "G"], 1, ["N", "G", "J"], 1, ["G", "J", "L"], 1,

        ["D", "G", "N"], 1, ["G", "N", "A"], 1, ["N", "A", "D"], 1,

        ["A", "D", "T"], 2, ["D", "T", "B"], 2, ["T", "B", "L"], 1,

        ["B", "L", "T"], 1, ["T", "B", "E"], 1, ["B", "E", "W"], 1,

        ["E", "W", "J"], 1, ["W", "J", "C"], 1, ["J", "C", "L"], 1,

        ["L", "W", "G"], 1, ["D", "G", "L"], 1, ["G", "L", "W"], 1,

        ["W", "D", "Y"], 1, ["D", "Y", "W"], 1, ["Y", "W", "F"], 1,

        ["F", "F", "T"], 1, ["F", "T", "A"], 2, ["T", "A", "J"], 1,

        ["A", "J", "M"], 1, ["J", "M", "B"], 1, ["M", "B", "K"], 1,

        ["B", "D", "W"], 1, ["D", "W", "G"], 1, ["W", "G", "F"], 1,

        ["G", "F", "M"], 1, ["F", "M", "B"], 1, ["M", "B", "D"], 1,

        ["B", "D", "B"], 1, ["D", "B", "W"], 1, ["B", "W", "L"], 1,

        ["L", "F", "M"], 1, ["F", "M", "Y"], 1, ["M", "Y", "D"], 1,

        ["Y", "D", "L"], 1, ["W", "B", "W"], 1, ["B", "W", "W"], 1,

        ["W", "W", "J"], 1, ["W", "J", "F"], 1, ["J", "F", "T"], 1,

        ["F", "T", "W"], 1, ["T", "W", "G"], 1, ["W", "G", "J"], 1,

        ["G", "J", "J"], 1, ["J", "J", "L"], 1, ["D", "G", "E"], 1,

        ["G", "E", "L"], 1, ["E", "L", "K"], 1, ["L", "K", "C"], 1,

        ["C", "L", "L"], 1, ["L", "L", "W"], 1, ["W", "D", "G"], 1,

        ["M", "Y", "W"], 1, ["Y", "W", "B"], 1, ["B", "G", "N"], 1,

        ["G", "N", "B"], 1, ["N", "B", "B"], 1, ["B", "B", "T"], 1,

        ["B", "T", "A"], 1, ["T", "A", "D"], 1, ["T", "B", "T"], 1,

        ["B", "T", "D"], 1, ["D", "J", "M"], 1, ["J", "M", "L"], 1,

        ["M", "L", "K"], 1, ["L", "K", "H"], 1, ["K", "H", "G"], 1,

        ["H", "G", "L"], 1, ["G", "L", "T"], 1, ["L", "T", "R"], 1,

        ["T", "R", "A"], 1, ["L", "T", "Q"], 1, ["T", "Q", "T"], 1,

        ["Q", "T", "A"], 1, ["T", "A", "T"], 2, ["A", "T", "X"], 1,

        ["T", "X", "M"], 1, ["X", "M", "F"], 1, ["M", "F", "T"], 1,

        ["T", "A", "C"], 1, ["C", "T", "M"], 1, ["T", "M", "Y"], 1,

        ["M", "Y", "L"], 1, ["Y", "L", "K"], 1, ["L", "K", "G"], 1,

        ["K", "G", "W"], 1, ["G", "W", "C"], 1, ["W", "C", "J"], 1,

        ["C", "J", "K"], 1, ["J", "K", "M"], 1, ["K", "M", "A"], 1,

        ["M", "A", "G"], 1, ["A", "G", "W"], 1, ["L", "T", "A"], 1,

        ["A", "T", "T"], 1, ["T", "T", "D"], 1, ["T", "D", "Y"], 1,

        ["D", "Y", "M"], 1, ["T", "H", "Q"], 1, ["H", "Q", "N"], 1,

        ["Q", "N", "J"], 1, ["N", "J", "K"], 1, ["J", "K", "J"], 1,

        ["K", "J", "C"], 1, ["J", "C", "T"], 1, ["C", "T", "B"], 1,

        ["B", "J", "W"], 1, ["J", "W", "K"], 1, ["W", "K", "A"], 2,

        ["K", "A", "F"], 1, ["A", "F", "O"], 1, ["F", "O", "L"], 1,

        ["O", "L", "W"], 1, ["W", "D", "Q"], 1, ["D", "Q", "T"], 1,

        ["Q", "T", "T"], 1, ["T", "T", "A"], 1, ["T", "A", "W"], 1,

        ["A", "W", "S"], 1, ["W", "S", "W"], 1, ["S", "W", "K"], 1,

        ["K", "A", "Y"], 1, ["A", "Y", "N"], 1, ["Y", "N", "F"], 1,

        ["N", "F", "S"], 1, ["F", "S", "W"], 1, ["S", "W", "J"], 1,

        ["J", "L", "J"], 1, ["L", "J", "M"], 1, ["J", "M", "Y"], 1,

        ["M", "Y", "M"], 1, ["Y", "M", "F"], 1, ["M", "F", "F"], 1,

        ["F", "F", "M"], 1, ["F", "M", "E"], 1]

> sort_frequency_table(%);

  [["J", "L", "T"], 13, ["F", "W", "A"], 8, ["W", "A", "D"], 8,

        ["A", "D", "G"], 6, ["L", "W", "D"], 5, ["D", "J", "L"], 4,

        ["L", "T", "H"], 4, ["B", "J", "L"], 4, ["W", "L", "F"], 3,

        ["J", "L", "W"], 3, ["K", "C", "L"], 3, ["C", "L", "W"], 3,

        ["L", "W", "B"], 3, ["T", "D", "J"], 3, ["D", "G", "M"], 3,

        ["G", "M", "Y"], 3, ["T", "H", "K"], 3, ["H", "K", "D"], 3,

        ["K", "D", "F"], 3, ["D", "F", "W"], 3, ["M", "B", "J"], 3,

        ["L", "T", "B"], 3, ["R", "W", "L"], 2, ["L", "F", "W"], 2,

        ["R", "A", "T"], 2, ["A", "T", "E"], 2, ["T", "E", "J"], 2,

        ["E", "J", "L"], 2, ["J", "L", "M"], 2, ["M", "Y", "J"], 2,

        ["Y", "J", "L"], 2, ["L", "W", "J"], 2, ["B", "K", "C"], 2,

        ["W", "B", "D"], 2, ["D", "L", "W"], 2, ["W", "F", "F"], 2,

        ["A", "C", "T"], 2, ["W", "J", "L"], 2, ["L", "T", "F"], 2,

        ["T", "F", "W"], 2, ["Y", "M", "B"], 2, ["G", "W", "A"], 2,

        ["W", "B", "G"], 2, ["W", "G", "H"], 2, ["G", "H", "M"], 2,

        ["H", "M", "J"], 2, ["M", "J", "L"], 2, ["T", "B", "C"], 2,

        ["B", "C", "M"], 2, ["C", "M", "A"], 2, ["M", "A", "Y"], 2,

        ["A", "Y", "T"], 2, ["Y", "T", "G"], 2, ["T", "G", "G"], 2,

        ["G", "G", "M"], 2, ["G", "M", "B"], 2, ["T", "B", "J"], 2,

        ["A", "D", "J"], 2, ["A", "D", "T"], 2, ["D", "T", "B"], 2,

        ["F", "T", "A"], 2, ["T", "A", "T"], 2, ["W", "K", "A"], 2,

        ["W", "A", "R"], 1, ["A", "R", "A"], 1, ["L", "T", "J"], 1,

        ["T", "J", "B"], 1, ["J", "B", "N"], 1, ["B", "N", "J"], 1,

        ["N", "J", "L"], 1, ["L", "M", "Y"], 1, ["W", "J", "B"], 1,

        ["J", "B", "K"], 1, ["B", "D", "L"], 1, ["W", "D", "D"], 1,

        ["D", "D", "T"], 1, ["D", "T", "G"], 1, ["T", "G", "J"], 1,

        ["G", "J", "B"], 1, ["J", "B", "M"], 1, ["B", "M", "O"], 1,

        ["M", "O", "T"], 1, ["O", "T", "D"], 1, ["L", "T", "W"], 1,

        ["T", "W", "F"], 1, ["F", "F", "K"], 1, ["F", "K", "W"], 1,

        ["K", "W", "A"], 1, ["W", "A", "C"], 1, ["C", "T", "J"], 1,

        ["T", "J", "L"], 1, ["W", "D", "V"], 1, ["D", "V", "M"], 1,

        ["V", "M", "K"], 1, ["M", "K", "A"], 1, ["K", "A", "T"], 1,

        ["A", "T", "D"], 1, ["D", "G", "Y"], 1, ["G", "Y", "M"], 1,

        ["L", "M", "N"], 1, ["M", "N", "G"], 1, ["N", "G", "W"], 1,

        ["M", "Y", "O"], 1, ["Y", "O", "T"], 1, ["O", "T", "W"], 1,

        ["T", "W", "B"], 1, ["B", "G", "W"], 1, ["G", "W", "G"], 1,

        ["M", "B", "R"], 1, ["B", "R", "W"], 1, ["W", "A", "S"], 1,

        ["A", "S", "B"], 1, ["S", "B", "T"], 1, ["B", "T", "G"], 1,

        ["T", "G", "K"], 1, ["G", "K", "D"], 1, ["K", "D", "T"], 1,

        ["D", "T", "D"], 1, ["T", "D", "M"], 1, ["D", "M", "X"], 1,

        ["M", "X", "T"], 1, ["X", "T", "B"], 1, ["L", "T", "C"], 1,

        ["T", "C", "M"], 1, ["C", "M", "N"], 1, ["M", "N", "A"], 1,

        ["N", "A", "C"], 1, ["A", "C", "K"], 1, ["C", "K", "F"], 1,

        ["K", "F", "W"], 1, ["J", "L", "N"], 1, ["L", "N", "G"], 1,

        ["N", "G", "J"], 1, ["G", "J", "L"], 1, ["D", "G", "N"], 1,

        ["G", "N", "A"], 1, ["N", "A", "D"], 1, ["T", "B", "L"], 1,

        ["B", "L", "T"], 1, ["T", "B", "E"], 1, ["B", "E", "W"], 1,

        ["E", "W", "J"], 1, ["W", "J", "C"], 1, ["J", "C", "L"], 1,

        ["L", "W", "G"], 1, ["D", "G", "L"], 1, ["G", "L", "W"], 1,

        ["W", "D", "Y"], 1, ["D", "Y", "W"], 1, ["Y", "W", "F"], 1,

        ["F", "F", "T"], 1, ["T", "A", "J"], 1, ["A", "J", "M"], 1,

        ["J", "M", "B"], 1, ["M", "B", "K"], 1, ["B", "D", "W"], 1,

        ["D", "W", "G"], 1, ["W", "G", "F"], 1, ["G", "F", "M"], 1,

        ["F", "M", "B"], 1, ["M", "B", "D"], 1, ["B", "D", "B"], 1,

        ["D", "B", "W"], 1, ["B", "W", "L"], 1, ["L", "F", "M"], 1,

        ["F", "M", "Y"], 1, ["M", "Y", "D"], 1, ["Y", "D", "L"], 1,

        ["W", "B", "W"], 1, ["B", "W", "W"], 1, ["W", "W", "J"], 1,

        ["W", "J", "F"], 1, ["J", "F", "T"], 1, ["F", "T", "W"], 1,

        ["T", "W", "G"], 1, ["W", "G", "J"], 1, ["G", "J", "J"], 1,

        ["J", "J", "L"], 1, ["D", "G", "E"], 1, ["G", "E", "L"], 1,

        ["E", "L", "K"], 1, ["L", "K", "C"], 1, ["C", "L", "L"], 1,

        ["L", "L", "W"], 1, ["W", "D", "G"], 1, ["M", "Y", "W"], 1,

        ["Y", "W", "B"], 1, ["B", "G", "N"], 1, ["G", "N", "B"], 1,

        ["N", "B", "B"], 1, ["B", "B", "T"], 1, ["B", "T", "A"], 1,

        ["T", "A", "D"], 1, ["T", "B", "T"], 1, ["B", "T", "D"], 1,

        ["D", "J", "M"], 1, ["J", "M", "L"], 1, ["M", "L", "K"], 1,

        ["L", "K", "H"], 1, ["K", "H", "G"], 1, ["H", "G", "L"], 1,

        ["G", "L", "T"], 1, ["L", "T", "R"], 1, ["T", "R", "A"], 1,

        ["L", "T", "Q"], 1, ["T", "Q", "T"], 1, ["Q", "T", "A"], 1,

        ["A", "T", "X"], 1, ["T", "X", "M"], 1, ["X", "M", "F"], 1,

        ["M", "F", "T"], 1, ["T", "A", "C"], 1, ["C", "T", "M"], 1,

        ["T", "M", "Y"], 1, ["M", "Y", "L"], 1, ["Y", "L", "K"], 1,

        ["L", "K", "G"], 1, ["K", "G", "W"], 1, ["G", "W", "C"], 1,

        ["W", "C", "J"], 1, ["C", "J", "K"], 1, ["J", "K", "M"], 1,

        ["K", "M", "A"], 1, ["M", "A", "G"], 1, ["A", "G", "W"], 1,

        ["L", "T", "A"], 1, ["A", "T", "T"], 1, ["T", "T", "D"], 1,

        ["T", "D", "Y"], 1, ["D", "Y", "M"], 1, ["T", "H", "Q"], 1,

        ["H", "Q", "N"], 1, ["Q", "N", "J"], 1, ["N", "J", "K"], 1,

        ["J", "K", "J"], 1, ["K", "J", "C"], 1, ["J", "C", "T"], 1,

        ["C", "T", "B"], 1, ["B", "J", "W"], 1, ["J", "W", "K"], 1,

        ["K", "A", "F"], 1, ["A", "F", "O"], 1, ["F", "O", "L"], 1,

        ["O", "L", "W"], 1, ["W", "D", "Q"], 1, ["D", "Q", "T"], 1,

        ["Q", "T", "T"], 1, ["T", "T", "A"], 1, ["T", "A", "W"], 1,

        ["A", "W", "S"], 1, ["W", "S", "W"], 1, ["S", "W", "K"], 1,

        ["K", "A", "Y"], 1, ["A", "Y", "N"], 1, ["Y", "N", "F"], 1,

        ["N", "F", "S"], 1, ["F", "S", "W"], 1, ["S", "W", "J"], 1,

        ["J", "L", "J"], 1, ["L", "J", "M"], 1, ["J", "M", "Y"], 1,

        ["M", "Y", "M"], 1, ["Y", "M", "F"], 1, ["M", "F", "F"], 1,

        ["F", "F", "M"], 1, ["F", "M", "E"], 1]

> Implode(partial_sub_cipher(["J","t","L","h","T","e","W","a","A","n","D","d","Q","b","M","o","Y","f","B", "r","G","s","N","u","O","y","F","l","C","c","K","i","V","j","H","m","E","w","R","k","X","v","S","p"],Explode(Example_sub)));

  "kahlanknewthetruthofthatrichardhaddestroyedthealliancethathadjo\
        inedthelandsofthemidlandsforthousandsofyearsasmotherconfes\
        sorkahlanpresidedoverthecouncilandthusthemidlandsunderherw\
        atchasmotherconfessorthemidlandshadfallentorichardaslordra\
        hlofdharaatleastthelandswhichhadsofarsurrenderedtohimshekn\
        ewthebenevolenceofhisactionsandtheneedforthembutitcertainl\
        yhadbeenapainfulpathtofollow"

> sort_frequency_table(M);  # this is the frequency table from above -- I used it for reference.

  ["T", 42, "W", 40, "L", 37, "J", 33, "D", 29, "A", 27, "M", 27, "B",

        25, "G", 24, "F", 20, "K", 16, "Y", 13, "C", 12, "N", 8, "H",

        7, "E", 5, "R", 4, "O", 3, "Q", 3, "S", 3, "X", 2, "V", 1,

        "I", 0, "P", 0, "U", 0, "Z", 0]

> # it was the trigram frequency table that gave me the right insight on this -- once I saw that
> # JLT was "the" and WAD was "and" the rest was a matter of recognizing words. Not quite --
> # I spotted "b" because of the word "been", then I used frequency to guess "o" and guessed "f"
> # because I thought I saw "of" -- then it reduced to deciphering words.
A step by step deciphering follows:
First, JLT is probably "the"
> Implode(partial_sub_cipher(["J","t","L","h","T","e"],Explode(Example_sub)));

  "RWhFWARAeEthetBNthMYthWtBKChWBDhWDDeGtBMOeDtheWFFKWACethWthWDVM\
        KAeDtheFWADGMYtheHKDFWADGYMBthMNGWADGMYOeWBGWGHMtheBCMAYeG\
        GMBRWhFWASBeGKDeDMXeBtheCMNACKFWADthNGtheHKDFWADGNADeBheBE\
        WtChWGHMtheBCMAYeGGMBtheHKDFWADGhWDYWFFeAtMBKChWBDWGFMBDBW\
        hFMYDhWBWWtFeWGttheFWADGEhKChhWDGMYWBGNBBeADeBeDtMhKHGheRA\
        eEtheQeAeXMFeACeMYhKGWCtKMAGWADtheAeeDYMBtheHQNtKtCeBtWKAF\
        OhWDQeeAWSWKAYNFSWthtMYMFFME"

I omit some false starts here.  As soon as I tried WAD = "and", plaintext started popping out!
> Implode(partial_sub_cipher(["J","t","L","h","T","e","W","a","A","n","D","d"],Explode(Example_sub)));

  "RahFanRneEthetBNthMYthatBKChaBdhaddeGtBMOedtheaFFKanCethathadVM\
        KnedtheFandGMYtheHKdFandGYMBthMNGandGMYOeaBGaGHMtheBCMnYeG\
        GMBRahFanSBeGKdedMXeBtheCMNnCKFandthNGtheHKdFandGNndeBheBE\
        atChaGHMtheBCMnYeGGMBtheHKdFandGhadYaFFentMBKChaBdaGFMBdBa\
        hFMYdhaBaatFeaGttheFandGEhKChhadGMYaBGNBBendeBedtMhKHGheRn\
        eEtheQeneXMFenCeMYhKGaCtKMnGandtheneedYMBtheHQNtKtCeBtaKnF\
        OhadQeenaSaKnYNFSathtMYMFFME"

I decided by inspection that "Q" was probably "b" (I saw "been").
> Implode(partial_sub_cipher(["J","t","L","h","T","e","W","a","A","n","D","d","Q","b"],Explode(Example_sub)));

  "RahFanRneEthetBNthMYthatBKChaBdhaddeGtBMOedtheaFFKanCethathadVM\
        KnedtheFandGMYtheHKdFandGYMBthMNGandGMYOeaBGaGHMtheBCMnYeG\
        GMBRahFanSBeGKdedMXeBtheCMNnCKFandthNGtheHKdFandGNndeBheBE\
        atChaGHMtheBCMnYeGGMBtheHKdFandGhadYaFFentMBKChaBdaGFMBdBa\
        hFMYdhaBaatFeaGttheFandGEhKChhadGMYaBGNBBendeBedtMhKHGheRn\
        eEthebeneXMFenCeMYhKGaCtKMnGandtheneedYMBtheHbNtKtCeBtaKnF\
        OhadbeenaSaKnYNFSathtMYMFFME"

I got M = "o" by looking at the frequency table.
> Implode(partial_sub_cipher(["J","t","L","h","T","e","W","a","A","n","D","d","Q","b","M","o"],Explode(Example_sub)));

  "RahFanRneEthetBNthoYthatBKChaBdhaddeGtBoOedtheaFFKanCethathadVo\
        KnedtheFandGoYtheHKdFandGYoBthoNGandGoYOeaBGaGHotheBConYeG\
        GoBRahFanSBeGKdedoXeBtheCoNnCKFandthNGtheHKdFandGNndeBheBE\
        atChaGHotheBConYeGGoBtheHKdFandGhadYaFFentoBKChaBdaGFoBdBa\
        hFoYdhaBaatFeaGttheFandGEhKChhadGoYaBGNBBendeBedtohKHGheRn\
        eEthebeneXoFenCeoYhKGaCtKonGandtheneedYoBtheHbNtKtCeBtaKnF\
        OhadbeenaSaKnYNFSathtoYoFFoE"

Y="f" came from my recognition of an instance of "of".
> Implode(partial_sub_cipher(["J","t","L","h","T","e","W","a","A","n","D","d","Q","b","M","o","Y","f"],Explode(Example_sub)));

  "RahFanRneEthetBNthofthatBKChaBdhaddeGtBoOedtheaFFKanCethathadVo\
        KnedtheFandGoftheHKdFandGfoBthoNGandGofOeaBGaGHotheBConfeG\
        GoBRahFanSBeGKdedoXeBtheCoNnCKFandthNGtheHKdFandGNndeBheBE\
        atChaGHotheBConfeGGoBtheHKdFandGhadfaFFentoBKChaBdaGFoBdBa\
        hFofdhaBaatFeaGttheFandGEhKChhadGofaBGNBBendeBedtohKHGheRn\
        eEthebeneXoFenCeofhKGaCtKonGandtheneedfoBtheHbNtKtCeBtaKnF\
        OhadbeenaSaKnfNFSathtofoFFoE"

I recognized the word "for" and got B ="r".
> Implode(partial_sub_cipher(["J","t","L","h","T","e","W","a","A","n","D","d","Q","b","M","o","Y","f","B","r"],Explode(Example_sub)));

  "RahFanRneEthetrNthofthatrKChardhaddeGtroOedtheaFFKanCethathadVo\
        KnedtheFandGoftheHKdFandGforthoNGandGofOearGaGHotherConfeG\
        GorRahFanSreGKdedoXertheCoNnCKFandthNGtheHKdFandGNnderherE\
        atChaGHotherConfeGGortheHKdFandGhadfaFFentorKChardaGFordra\
        hFofdharaatFeaGttheFandGEhKChhadGofarGNrrenderedtohKHGheRn\
        eEthebeneXoFenCeofhKGaCtKonGandtheneedfortheHbNtKtCertaKnF\
        OhadbeenaSaKnfNFSathtofoFFoE"

I got G = "s" and N = "u" by recognizing "surrendered".  The rest of the deciphering is easy by word recognition.
> Implode(partial_sub_cipher(["J","t","L","h","T","e","W","a","A","n","D","d","Q","b","M","o","Y","f","B","r","G","s","N","u"],Explode(Example_sub)));

  "RahFanRneEthetruthofthatrKChardhaddestroOedtheaFFKanCethathadVo\
        KnedtheFandsoftheHKdFandsforthousandsofOearsasHotherConfes\
        sorRahFanSresKdedoXertheCounCKFandthustheHKdFandsunderherE\
        atChasHotherConfessortheHKdFandshadfaFFentorKChardasFordra\
        hFofdharaatFeasttheFandsEhKChhadsofarsurrenderedtohKHsheRn\
        eEthebeneXoFenCeofhKsaCtKonsandtheneedfortheHbutKtCertaKnF\
        OhadbeenaSaKnfuFSathtofoFFoE"

> 
> #self_count(trigrams(Explode(Example_Vigenere)));  #I don't know why this is so slow.
> 
> 

> #sort_frequency_table(%);  YJK and YOJ are repeated, for example.
We are now going to apply the Kasiski test:  if we look at repeated trigram (or longer segments) it is likely that they represent
the same text shifted by a multiple of the key length!  To get these positions, we develop the following function:
> # function which returns list of positions of an item in a list.
> find := (item,list) ->if nops(list) = 0 then [] else if list[1]=item then [1,op(map ((x->x+1),
> find(item,list[2..nops(list)])))] else map ((x->x+1),find(item,list[2..nops(list)])) end if end if;
> 
> 
> 

  find := proc(item, list)
option operator, arrow;
    if nops(list) = 0 then []
    else
        if list[1] = item then [1, op(map(x -> x + 1,
            find(item, list[2 .. nops(list)])))]
        else map(x -> x + 1,
            find(item, list[2 .. nops(list)]))
        end if
    end if
end proc

> find("a",Explode("hahaha"));

                              [2, 4, 6]

> find(["Y","J","K"],trigrams(Explode(Example_Vigenere)));

                         [39, 191, 379, 395]

> gcd(191-39,379-39);gcd(191-39,395-39);

                                  4


                                  4

> find(["Y","O","J"],trigrams(Explode(Example_Vigenere)));

                           [157, 297, 369]

> gcd(297-157,369-157);

                                  4

The evidence of the Kasiski text strongly suggests that the length of the key is 4.
> #  I think the key length must be 4.
> 
The sample_list function takes every nth element of a list starting with the (m mod n)th element.
> sample_list:=(a,b,list)->if list = [] then [] else if a mod b = 1 then [list[1],op(sample_list(a-1,b,list[2..nops(list)]))]
> else sample_list(a-1,b,list[2..nops(list)]) end if end if;

  sample_list := proc(a, b, list)
option operator, arrow;
    if list = [] then []
    else
        if a mod b = 1 then [list[1],
            op(sample_list(a - 1, b, list[2 .. nops(list)]))]
        else sample_list(a - 1, b, list[2 .. nops(list)])
        end if
    end if
end proc

> sample_list(1,2,Explode("hahaha"));

                           ["h", "h", "h"]

> sample_list(2,2,Explode("hahaha"));

                           ["a", "a", "a"]

This is weird maple syntax for summing numbers in a list.
> foldl(`+`,0,op([1,2,3,4]));

                                  10

This computes "n choose 2".
> choose2 := n -> (n*(n-1))/2;

                    choose2 := n -> 1/2 n (n - 1)

ioc stands for "index of coincidence" -- this one gets the i.o.c. from the list of frequencies.
> ioc:= L -> evalf(  foldl(`+`,0,op( map (choose2, L) ) )    /  (choose2(foldl(`+`,0,op(L)))     ));

                          foldl(`+`, 0, op(map(choose2, L)))
        ioc := L -> evalf(----------------------------------)
                            choose2(foldl(`+`, 0, op(L)))

This generates a frequency table from a list then computes the i.o.c.
> IOC := L -> ioc(sample_list(2,2,self_count(L)));

          IOC := L -> ioc(sample_list(2, 2, self_count(L)))

Note that the substitution cipher example has the same IOC that we expect from English text.
> IOC(Explode(Example_sub));

                             .06973338859

The IOC of the full Vigenere text is low.
> IOC(Explode(Example_Vigenere));

                             .04342993445

Now our aim is to discover the key length by computing IOC of sampled text (every n letters).
> IOC(sample_list(1,2,Explode(Example_Vigenere)));  # key length 2 looks unlikely.

                             .05114004405

> IOC(sample_list(1,3,Explode(Example_Vigenere)));  # key length 3looks unlikely.

                             .04337349398

> IOC(sample_list(1,4,Explode(Example_Vigenere)));

                             .06593548387

> IOC(sample_list(2,4,Explode(Example_Vigenere)));

                             .05795961185

> IOC(sample_list(3,4,Explode(Example_Vigenere)));

                             .05782848151

> IOC(sample_list(4,4,Explode(Example_Vigenere)));

                             .06045108838

> # the index of coincidence appears to confirm the conjecture that the key is of length 4.
> 
> Alph := l -> Ord(l)-Ord("A");

                  Alph := l -> :-Ord(l) - :-Ord("A")

> Alph("B");

                                  1

To find the displacement between letters in the key, we use the IOC again -- if we merge one of the 4 lists with another, shifting the second by
a guessed difference between the two key letters, we will get a high IOC when we hit the right value!  The following function implements this
merger of a list with a second shifted list.
> shiftmerge := (n,L,M) -> [op(map(Alph,L)),op(map(subs(N=n,(x->((Alph(x))+N) mod 26))   ,M))];

  shiftmerge := (n, L, M) -> [op(map(Alph, L)),

        op(map(subs(N = n, x -> (Alph(x) + N) mod 26), M))]

> 
> # using shiftmerge, I can use index of coincidence to determine shifts between letters of the key
> # the four sublists follow.
> L1 := sample_list(1,4,Explode(Example_Vigenere));

  L1 := ["Z", "O", "K", "X", "Z", "T", "T", "N", "U", "A", "K", "Y",

        "T", "R", "U", "Z", "Y", "K", "U", "K", "J", "T", "G", "K",

        "X", "C", "L", "R", "G", "Q", "U", "K", "Z", "Y", "N", "U",

        "M", "G", "U", "Y", "G", "S", "L", "Z", "W", "T", "T", "A",

        "K", "G", "X", "Q", "X", "K", "Y", "O", "O", "G", "J", "A",

        "J", "Y", "K", "T", "J", "B", "O", "R", "J", "V", "T", "T",

        "O", "M", "Y", "Z", "N", "G", "Y", "R", "R", "K", "Q", "U",

        "T", "U", "T", "U", "J", "Z", "E", "Z", "Y", "R", "K", "K",

        "O", "C", "T", "K", "J", "G", "O", "H", "C", "E", "U", "K",

        "G", "K", "J", "S", "O", "Z", "R", "R", "Z", "T", "C", "U",

        "K", "K", "H", "X", "U"]

> L2 := sample_list(2,4,Explode(Example_Vigenere));

  L2 := ["O", "A", "Z", "L", "O", "S", "L", "V", "D", "W", "M", "A",

        "V", "H", "S", "L", "O", "K", "B", "J", "T", "P", "S", "J",

        "P", "H", "S", "H", "W", "V", "B", "F", "P", "I", "L", "R",

        "Y", "U", "S", "O", "K", "L", "P", "A", "B", "A", "L", "A",

        "S", "S", "S", "O", "B", "K", "M", "S", "A", "E", "L", "J",

        "O", "P", "Y", "K", "K", "L", "T", "M", "O", "H", "A", "A",

        "C", "P", "O", "L", "H", "Z", "P", "S", "H", "I", "L", "Y",

        "N", "T", "B", "Z", "V", "V", "A", "H", "O", "H", "K", "F",

        "S", "L", "K", "F", "U", "Y", "N", "H", "P", "V", "D", "Y",

        "Y", "A", "T", "H", "L", "P", "S", "L", "I", "N", "U", "S",

        "Y", "C", "L", "L"]

> L3 := sample_list(3,4,Explode(Example_Vigenere));

  L3 := ["J", "H", "B", "S", "J", "D", "X", "X", "J", "Y", "N", "S",

        "Z", "B", "Z", "J", "T", "Z", "W", "T", "T", "S", "Q", "F",

        "J", "X", "F", "S", "F", "K", "W", "W", "T", "Z", "Q", "J",

        "N", "I", "I", "J", "H", "Y", "L", "M", "J", "Z", "I", "Y",

        "T", "B", "T", "F", "N", "M", "F", "D", "M", "J", "G", "M",

        "N", "X", "X", "M", "W", "S", "X", "F", "N", "W", "X", "T",

        "N", "S", "J", "W", "Y", "G", "H", "D", "W", "F", "Y", "P",

        "K", "X", "U", "Z", "B", "U", "M", "C", "J", "N", "Y", "X",

        "Q", "I", "Y", "I", "Y", "J", "M", "H", "Y", "Z", "J", "N",

        "J", "T", "J", "D", "G", "B", "F", "F", "W", "I", "F", "I",

        "T", "N", "K", "N"]

> L4:= sample_list(4,4,Explode(Example_Vigenere));

  L4 := ["Y", "J", "G", "V", "Q", "Q", "Y", "J", "F", "J", "T", "Q",

        "V", "X", "P", "T", "Y", "R", "U", "P", "T", "I", "J", "T",

        "F", "C", "K", "F", "E", "L", "P", "C", "P", "V", "Q", "F",

        "O", "V", "W", "J", "Q", "Q", "J", "G", "G", "T", "Q", "J",

        "E", "C", "E", "F", "P", "K", "O", "Y", "V", "U", "C", "G",

        "U", "V", "C", "C", "K", "J", "G", "P", "U", "G", "K", "N",

        "P", "C", "N", "V", "Y", "C", "C", "C", "I", "U", "Y", "K",

        "T", "W", "V", "P", "P", "C", "G", "G", "E", "O", "J", "V",

        "Q", "C", "J", "K", "F", "H", "V", "M", "J", "J", "X", "F",

        "J", "N", "K", "F", "W", "K", "V", "U", "K", "Q", "U", "K",

        "H", "N", "Q", "F"]

You should vary the first argument of the shiftmerge function until you get the right shift.  The change in IOC is dramatic!
> IOC(shiftmerge(25,L1,L2));  # 25?

                             .06127736753

> IOC(shiftmerge(1,L1,L3));  # 4?

                             .06292913590

> IOC(shiftmerge(4,L1,L4)); # 1?

                             .06257287213

> Example_Vigenere;

  "ZOJYOAHJKZBGXLSVZOJQTSDQTLXYNVXJUDJFAWYJKMNTYASQTVZVRHBXUSZPZLJ\
        TYOTYKKZRUBWUKJTPJTTTTPSIGSQJKJFTXPJFCHXCLSFKRHSFGWFEQVKLU\
        BWPKFWCZPTPYIZVNLQQURJFMYNOGUIVUSIWYOJJGKHQSLYQLPLJZAMGWBJ\
        GTAZTTLIQAAYJKSTEGSBCXSTEQOFFXBNPKKMKYMFOOSDYOAMVGEJUJLGCA\
        JMGJONUYPXVKYXCTKMCJKWKBLSJOTXGRMFPJONUVHWGTAXKTATNOCNPMPS\
        CYOJNZLWVNHYYGZGCYPHCRSDCRHWIKIFUQLYYUYPKTNKTUTXWTBUVUZZPJ\
        VBPZVUCEAMGZHCGYOJERHNOKKYJKFXVOSQQCLICTKYJKFIKJUYFGYJHONM\
        VHHHMCPYJEVZJUDJXKYNFGYJJKATNJTJKSHDFOLGWZPBKRSFVRLFUZIWKT\
        NIQCUFUUSIKKYTHKCNNHLKQXLNFU"

> 
> 
> keyguess1:= [0,26-25,26-1,26-4];

                     keyguess1 := [0, 1, 25, 22]

> map(alphabetinv,(keyguess1));

                         ["A", "B", "Z", "W"]

> LowerCase(Implode((map (alphabetinv,keyguess1))));

                                "abzw"

> 
I used shiftdecipher to generate shifts because its output is lower case.  I plugged in each number from 1 up to 20 for the first argument of shiftcipher until it came clean.
> unvigenere(shiftdecipher(20,"ABZW"),LowerCase(Example_Vigenere));

  "thewitcheswerenttheonlyoneswhoshowedupthefirstnonoutlawvoluntee\
        rshowedupoursecondmorningallhecarriedwasaflailandapackofjo\
        urneyrationsbuthelookedgrimandtoldushehadcometofighttheque\
        enturnedoutthelocalwarlockhadruinedhisfamilywithtaxesdebau\
        chedhissistersandhaddrivenhimselfandhisparentsintolivingin\
        ashelterthatwasbasicallyalargebasketworkingfromsunuptosund\
        owntopaythetaxesheclaimedtheystillowedandtheydidntdarefigh\
        tbackwithyouhoweveridarehetoldmeimaydiebutiwillatleastbrin\
        gdownasoldierofevilbeforeido"

> shiftdecipher(20,"ABZW");  #this is the correct key.

                                "ghfc"

> 
> 
> 
> 
>