I've checked all 42,288 of the length 872 n=6 superpermutations in this "treelike" solution set from Robin Houston against all 96 length 873 "standard" superpermutations in Nathaniel Johnston's original (before discovery of length 872 solutions) file (at
http://www.njohnston.ca/superperm6.txt) to evaluate the spans where a "standard" superpermutation can match any of these length 872 superpermutations.
The maximum span of alignment anywhere is 145. That is, they can match exactly for just at or under 1/6 of the way. So, they can bag about 120 of the 720 permutations in the exact same way and a length 872 superpermutation must find its advantage over the "standard" superpermutation in bagging the remaining 5/6 of the permutations.
In the over four million pairings, this result is far from unique, though.
From spot checking, it appears each "standard" superpermutation tends to find 526 partners from the "treelike" solution set with which to achieve alignment of length 145.
Plenty of cases of alignment 144 also exist.
For a given pair of "standard" superpermutation and length 872 superpermutation from the "treelike" set, such spans of alignment like 145 or 144 can only be achieved once. That is, a superpermutation pair can and frequently does match for the first 145 or 144 digits, and then they go separate ways, but they do not resume such matching for the last 1/6 of the way, for example.
After a matching span of 145 or 144 digits, the longest you can find the same pair to resume matching exactly is a span of 35 or 36 digits, respectively.
I just wrote a little bit of C++ code to find these alignment results, and I was pleased the computational time for comparing 4,059,648 pairs of n = 6 superpermutations was not more than a few minutes.
If we consider the 1st, 2nd, 3rd, and 4th longest stretches of exact matching for a given pairing, the following cases, each of which has just a handful (eight or so) total instances in the over four million pairings, might be argued as "most aligned":
145-35-8-3,
144-36-8-4,
145-28-12-7
For each of these cases, I'm sharing below one of the explicit pairings, and I have adjusted white space to highlight where they match and where they don't. In particular, I have indented the matching stretches.
Please consider this first case:
1234561234516234512634512364512346512341562341526341523641523461523416523412563412536412534612534162534126534123564123546123541623541263541236541
23146523146253146235146231546231456231426531426351426
31542631
452631425631423651423615423614523614253614235614231654231645231642531642351642315642312456312453612453162453126453124653124356124351624351264351246351243651243156243152643152463152436152431652431256431254631254361254316254312654312134562134526134521634521364521346521342561342516342513642513462513426513421563421536421534621534261534216534213564213546213542613542163542136542132456132451632451362451326451324651324156324153624153264153246153241653
24135624135264135246135241635241365
24132564132546132541632541362541326541321456321453621453261453216453214653214356214352614352164352146352143652143256143251643251463251436251432651432156432154632154362154326154321654321
1234561234516234512634512364512346512341562341526341523641523461523416523412563412536412534612534162534126534123564123546123541623541263541236541
32654312564321564325164325614325641325643125463215462
31542631
542361542316542315642315462135462153462154362154632514623514263514236514235614235164235146253142653142563142536142531642531462513462514362514632541632546132546312456321456231456213456214356214536241536245136245316245361245362145632415632451632456132456312465321465231465213465214365214635214653241653246153246513246531246351243651243561243516243512643512463152436152431652431562431526431524631254361254316254312654321654326154326514326541362541365
24135624135264135246135241635241365
4213645216342516342156342165342163542163452164352164532614523614526314526134256134265134261534261354261345261435261453264153264513264531264532164523164521364251364215364213564213654123
The top part is a length 873 superpermutation (for n=6) from Nathaniel Johnston's original file of 96 such superpermutations, and the bottom part is a length 872 superpermutation from Robin Houston's "treelike" solution set of 42,288 such superpermutations.
I've indented lines where this pair of superpermutations matches exactly for spans exceeding the length of an individual permutation.
This pair starts off identical for a span of 145, then later matches exactly again for a span of 8, and then sometime later aligns for a span of 35.
Second case:
123456123451623451263451236451234651234156234152634152364152346152341652341256341253641253461253416253412653412356412354612354162354126354123654
1231456231452631452361452316452314652314256314253614253164253146253142653142356142351642351462351426351423651
42315642
315462315426315423615423165423124563124536124531624531264531246531243561243516243512643512463512436512431562431526431524631524361524316524312564312546312543612543162543126543121345621345261345216345213645213465213425613425163425136425134625134265134215634215364215346215342615342165342135642135462135426135421635421365421324561324516324513624513264513246513241563241536241532641532461532416532413562413526413524613524163524136524132564132546132541632541362541326541321456321453621453261453216453214653214356214352614352164352146352143652143
256143251643251463251436251432651432
156432154632154362154326154321654321
123456123451623451263451236451234651234156234152634152364152346152341652341256341253641253461253416253412653412356412354612354162354126354123654
2136524136254136245136241536241356214356213456213546215346215436215463215462315462135642153642156342156432156
42315642
135624136521436521346521364521365423165423615426315426135246132546132456132465132461532461352641325641326541326451326415326413526143526134526135426153426154326154236514235614253614523614532614536214536124536142563145263145623145632145631246531426531462531465231465321645312645316245316425316452316453216543216534216532416352146352164352163452163542163524163254163245163241563241653214653124635124365124356124351624351264351246315243615243165243156243152643152463125436125431625431265431256431254631245631425613425163425136425134625134265134
256143251643251463251436251432651432
56142351642351462351426351423654123
Again, the top part is a length 873 superpermutation (for n=6) from Nathaniel Johnston's original file of 96 such superpermutations, and the bottom part is a length 872 superpermutation from Robin Houston's "treelike" solution set of 42,288 such superpermutations.
Again, I've indented lines where this pair of superpermutations matches exactly for spans exceeding the length of an individual permutation.
This pair starts off identical for a span of 144, then later matches exactly again for a span of 8, and then sometime later aligns for a span of 36.
Similarly, the third case:
1234561234516234512634512364512346512341562341526341523641523461523416523412563412536412534612534162534126534123564123546123541623541263541236541
23145623145263145236145231645231465231425631425
3614253164253146253142653142
35614235164235146235142635142365142315642315462315426315423615423165423124563124536124531624531264531246531243561243516243512643512463512436512431562431526431524631524361524316524312564312546312543612543162543126543121346521346251346215346213546213
4562134
265134261534261354261345261342561342165342163542163452163425163421563421365421364521364251364215364213564213245613245163245136245132645132465132415632415362415326415324615324165324135624135264135246135
241635241365
24132564132546132541632541362541326541321456321453621453261453216453214653214356214352614352164352146352143652143256143251643251463251436251432651432156432154632154362154326154321654321
1234561234516234512634512364512346512341562341526341523641523461523416523412563412536412534612534162534126534123564123546123541623541263541236541
32654312654321654326153426153246153264153261452
3614253164253146253142653142
56314253614235614236514236154231654231564231546231542631542361452631452613452614352614532615432651432654136254316254361245316245312645312465312456312453612435612436512436152431652431562431526431524631524361254362153462153642153624153621456321456231
4562134
562143562145362154362514362541365241356241352641352461352416325461325463125463215463251463521465321465231465213465214365214635124635142635146235146325416324513624513264513246513245613245163241563241653
241635241365
4213564213546213542613542163452164351264351624351642351643256143256413256431256432156432516435216453216452316452136452163425136425134625134265134256134251634215634216534216354213654123
This pair starts off identical for a span of 145, then later matches exactly again for a span of 28, then later again aligns for a span of 7, and then sometime later aligns for a span of 12.