/usr/share/doc/t-coffee-examples/combined_aln.aln is in t-coffee-examples 10.00.r1613-1.
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 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 | CLUSTAL FORMAT for T-COFFEE Version_4.39 [http://www.tcoffee.org], CPU=0.57 sec, SCORE=95, Nseq=10, Len=259
1cms --GEVASVPLTNYLDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNACKNHQRF
4pep ----IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQF
2apr AGVGTVPMTDYGN-DIEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCG-SGQTKY
3app AASGVATNTPTAN-DEEYITPVTIG--GTTLNLNFDTGSADLWVFSTELPASQQSGHSVY
4ape -STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIY
1cms_1 -----------------YTGSLHWVPVTVQQYWQFTVDS---VTISGVVVACEGGCQAIL
hmgt_mouse ------------------------------------------------------------
hmgb_chite ------------------------------------------------------------
hmgl_wheat ------------------------------------------------------------
hmgl_trybr ------------------------------------------------------------
1cms DPR-KSSTFQNLGKPLSIHYGTG-SMQGILGYDTVTVSNIVDIQQTVGLSTQEPGDVFTY
4pep NPD-DSSTFEATSQELSITYGTG-SMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYY
2apr DPN-QSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAASFASG
3app NP--SATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQD
4ape TPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTED
1cms_1 DTG-TSKLVGPSSDILNIQQAIG-ATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPS
hmgt_mouse ------------------------------------------------------------
hmgb_chite ------------------------------------------------------------
hmgl_wheat ------------------------------------------------------------
hmgl_trybr ------------------------------------------------------------
1cms AEFDGILGMAYPSLASEY---SIPVFDNMMNRHLVAQDLFSVYMDRNGQE--SMLTLGAI
4pep APFDGILGLAYPSISASG---ATPVFDNLWDQGLVSQDLFSVYLSSNDDSG-SVVLLGGI
2apr PN-DGLLGLGFDTITTVR--GVKTPMDNLISQGLISRPIFGVYLGKAKNGGGGEYIFGGY
3app TNNDGLLGLAFSSINTVQPQSQTTFFDTVKSS--LAQPLFAVALKHQQPG---VYDFGFI
4ape STIDGLLGLAFSTLNTVSPTQQKTFFDNAKAS--LDSPVFTADLGYHAPG---TYNFGFI
1cms_1 AYTSQDQGFCTSGFQSEN------HSQKWILGDVFIREYYSVFDRANNLVG----LAKAI
hmgt_mouse ------------------------------------------------------------
hmgb_chite -----------------------------------------------------------a
hmgl_wheat ----------------------------------------------------------dp
hmgl_trybr ----------------------------------------------------------kk
1cms DPSY--------------------------------------------------------
4pep DSSY--------------------------------------------------------
2apr DSTK--------------------------------------------------------
3app DSSK--------------------------------------------------------
4ape DTTA--------------------------------------------------------
1cms_1 ------------------------------------------------------------
hmgt_mouse ---kpkrprsayniyvsesfq---eakddsa-qgkl-klvneawknlspeekqayiqlak
hmgb_chite --dkpkrplsaymlwlnsaresikrenpdfk-vtevakkggelwrglk--dkseweakaa
hmgl_wheat --nkpkrapsaffvfmgefreefkqknpknksvaavgkaagerwkslsesekapyvakan
hmgl_trybr dsnapkramtsfmffssdfr----skhsdls-ivemskaagaawkelgpeerkvyeemae
1cms -------------------
4pep -------------------
2apr -------------------
3app -------------------
4ape -------------------
1cms_1 -------------------
hmgt_mouse ddrirydnemksweeqmae
hmgb_chite takqnyiralqeyern-gg
hmgl_wheat klkgeynkaiaaynkgesa
hmgl_trybr kdkerykrem---------
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