/usr/share/doc/t-coffee-examples/sample_aln2.aln is in t-coffee-examples 11.00.8cbe486-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | CLUSTAL W (1.83) multiple sequence alignment
1cms --GEVASVPLTNYLDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNACKNHQRF
4pep ----IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQF
4ape -STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIY
3app AASGVATNTPTAN-DEEYITPVTIG--GTTLNLNFDTGSADLWVFSTELPASQQSGHSVY
2apr AGVGTVPMTDYGN-DIEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCG-SGQTKY
1cms_1 -----------------YTGSLHWVPVTVQQYWQFTVDS---VTISGVVVACEGGCQAIL
* : * ..* * :
1cms DPR-KSSTFQNLGKPLSIHYGTG-SMQGILGYDTVTVSNIVDIQQTVGLSTQEPGDVFTY
4pep NPD-DSSTFEATSQELSITYGTG-SMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYY
4ape TPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTED
3app NP--SATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQD
2apr DPN-QSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAASFASG
1cms_1 DTG-TSKLVGPSSDILNIQQAIG-ATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPS
. :. . .* . * : . : ..: . .
1cms AEFDGILGMAYPSLASEY---SIPVFDNMMNRHLVAQDLFSVYMDRNGQE--SMLTLGAI
4pep APFDGILGLAYPSISASG---ATPVFDNLWDQGLVSQDLFSVYLSSNDDSG-SVVLLGGI
4ape STIDGLLGLAFSTLNTVSPTQQKTFFDNAKAS--LDSPVFTADLGYHAPG---TYNFGFI
3app TNNDGLLGLAFSSINTVQPQSQTTFFDTVKSS--LAQPLFAVALKHQQPG---VYDFGFI
2apr PN-DGLLGLGFDTITTVR--GVKTPMDNLISQGLISRPIFGVYLGKAKNGGGGEYIFGGY
1cms_1 AYTSQDQGFCTSGFQSEN------HSQKWILGDVFIREYYSVFDRANNLVG----LAKAI
. . *: : : :. . : .
1cms DPSY
4pep DSSY
4ape DTTA
3app DSSK
2apr DSTK
1cms_1 ----
|