--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multimer_output/msas/A/mgnify_hits.sto	Tue Sep 13 22:04:12 2022 +0000
@@ -0,0 +1,94 @@
+# STOCKHOLM 1.0
+
+#=GS MGYP000836687451/13-154  DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+#=GS MGYP000585341746/6-147   DE [subseq from] PL=10 UP=0 BIOMES=0000000000001
+#=GS MGYP001069732337/11-152  DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
+#=GS MGYP000701481948/1-69    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP001122892151/78-175  DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000539442244/1-72    DE [subseq from] PL=00 UP=0 BIOMES=0101000000000
+#=GS MGYP000498009340/6-38    DE [subseq from] PL=10 UP=0 BIOMES=0000000011000
+#=GS MGYP000498009340/63-137  DE [subseq from] PL=10 UP=0 BIOMES=0000000011000
+#=GS MGYP000607955645/4-146   DE [subseq from] PL=00 UP=1 BIOMES=0000000011000
+#=GS MGYP000809681506/4-146   DE [subseq from] PL=00 UP=1 BIOMES=0000000011000
+#=GS MGYP001138391873/7-146   DE [subseq from] PL=00 UP=1 BIOMES=1000000000000
+#=GS MGYP000131797357/13-155  DE [subseq from] PL=10 UP=0 BIOMES=0000000000001
+#=GS MGYP000536366561/97-193  DE [subseq from] PL=11 UP=0 BIOMES=0000000011000
+#=GS MGYP000318290004/2-70    DE [subseq from] PL=00 UP=0 BIOMES=0101000000000
+#=GS MGYP001111532658/13-154  DE [subseq from] PL=01 UP=0 BIOMES=0000000000001
+#=GS MGYP000722267483/2-47    DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
+#=GS MGYP000079462051/73-112  DE [subseq from] PL=00 UP=0 BIOMES=0101000000000
+#=GS MGYP000413961247/1-72    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000729474694/1-75    DE [subseq from] PL=10 UP=0 BIOMES=0000000011000
+#=GS MGYP000459697661/48-117  DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP001121356039/36-177  DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
+#=GS MGYP000132531679/62-95   DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
+#=GS MGYP000427472264/214-245 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000620445737/4-47    DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+#=GS MGYP000639461158/65-143  DE [subseq from] PL=01 UP=0 BIOMES=0000000000001
+#=GS MGYP000507092441/12-54   DE [subseq from] PL=10 UP=0 BIOMES=0000000011000
+#=GS MGYP000607025940/8-103   DE [subseq from] PL=01 UP=0 BIOMES=0000000000001
+#=GS MGYP000362522003/1-32    DE [subseq from] PL=00 UP=0 BIOMES=0101000000000
+#=GS MGYP000322610494/7-50    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000442294717/26-101  DE [subseq from] PL=10 UP=0 BIOMES=1000000000000
+#=GS MGYP000214952500/50-125  DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000321112601/3-73    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000386264740/2-52    DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
+#=GS MGYP000172242919/33-125  DE [subseq from] PL=10 UP=0 BIOMES=0000000011000
+#=GS MGYP000669192840/12-82   DE [subseq from] PL=00 UP=0 BIOMES=0101000000000
+#=GS MGYP000212149699/2-51    DE [subseq from] PL=00 UP=0 BIOMES=0000000010100
+#=GS MGYP000559925714/32-112  DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000335830788/32-110  DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000306499386/2-53    DE [subseq from] PL=00 UP=0 BIOMES=0101000000000
+#=GS MGYP000450732916/70-150  DE [subseq from] PL=01 UP=0 BIOMES=0000000000001
+#=GS MGYP000694104832/9-83    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000114577797/2-45    DE [subseq from] PL=01 UP=0 BIOMES=0000000000001
+#=GS MGYP001143026688/10-61   DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+#=GS MGYP000969813914/167-286 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+
+chain_A                          MVLSPADKTNVKAAWGKVG-A-HAGEYGAEA-LERMFLSFPTTKTYFPHF-DLS-----H-----G-----SA-----QVKGHGKKVADALTNAVAHVDDMPNALSALSDL---HAHKLRVDPVNFKLLSHCLLVTLAAH-LPAEFTPAVHASLDKFLASVSTVLTSKYR
+MGYP000836687451/13-154          MVLSPADKTNVKAAWGKVG-A-HAGEYGAEA-LERMFLSFPTTKTYFPHF-DLS-----H-----G-----SA-----QVKGHGKKVADALTNAVAHVDDMPNALSALSDL---HAHKLRVDPVNFKLLSHCLLVTLAAH-LPAEFTPAVHASLDKFLASVSTVLTSKYR
+MGYP000585341746/6-147           MVLSGEDKSNIKAAWGKIG-G-HGAEYVAEA-LERMFASFPTTKTYFPHF-DVS-----H-----G-----SA-----QVKGHGKKIADALASAAGHLDDLPGALSALSDL---HAHKLRVDPVNFKLLSHCLLVTLASH-HPADFTPAVHASLDKFLASVSTVLTSKYR
+MGYP001069732337/11-152          MVLSAEDKKNIVQFWEFVK-G-HEEAHGAEA-LHRMFESSPETKIYFANK-DLS-----G-----G-----SA-----FLHAHGKKVMCALTKAVGHLDDINGALSALSDK---HAQELMVDPANFPKLNHNIMVTFAVH-CKQRLTPQVHTSLDKFLCAVAHALTCKYR
+MGYP000701481948/1-69            -----------------------------------MFLSFPTTKTYFPHF-DLS-----H-----G-----SA-----QVKGHGKKVADALTNAVAHVDDMPNALSALSDL---HAHKLRVDPVNFKV------------------------------------------
+MGYP001122892151/78-175          -----GARRGPQGAWAVGGGP-RCWELTAPAPRPRLFLSHPQTKTYFPHF-DLS-----H-----G-----SA-----QVKGHGKKVADALTNAVAHVDDMPNALSALSDL---HAHKLRGDQVNFKV------------------------------------------
+MGYP000539442244/1-72            -----------------------------------MFLSFPTTKTYFPHF-DLS-----H-----G-----SA-----QVKGHGAKVAAALTKAVEHLDDLPGALSELSDL---HAHKLRVDPVNFKVSSR---------------------------------------
+MGYP000498009340/6-38            MALSAEDRALVRALWKKLG-S-NVGVYTTEA-LERC--------------------------------------------------------------------------------------------------------------------------------------
+MGYP000498009340/63-137          --------------------------------SRRTFLAFPATKTYFSHL-DLS-----P-----G-----SS-----QVRAHGQKVADALSLAVERLDDLPHALSALSHL---HACQLRVDPASFQV-SGC--------------------------------------
+MGYP000607955645/4-146           --LTDAEKAAVSGLWGKVN----ADEVGGEA-LGRLLVVYPWTQRYFDSFGDLS-----SASAIMG-----NA-----KVKAHGKKVITAFNDGLNHLDSLKGTFASLSEL---HCDKLHVDPENFRLLGNMIVIVLGHH-LGKDFTPAAQAAFQKVVAGVAAALAHKY-
+MGYP000809681506/4-146           --LTPEEKSAVTALWGKVN----VDEVGGEA-LGRLLVVYPWTQRFFESFGDLSTPDAVM-----G-----NP-----KVKAHGKKVLGAFSDGLAHLDNLKGTFATLSEL---HCDKLHVDPENFRLLGNVLVCVLAHH-FGKEFTPPVQAAYQKVVAGVANALAHKY-
+MGYP001138391873/7-146           -----EDKATITSLWGKVN-V-E--DAGGET-LGRLLVVYPWTQRFFDSFGNLS-----S-----A-----SAIMGNPKVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSEL---HCDKLHVDPENFKLLGNVLVTVLAIH-FGKEFTPEVQASWQKMVTGVASALSSRY-
+MGYP000131797357/13-155          --LSAEEKEAVLGLWGKVN----VDEVGGEA-LGRLLVVYPWTQRFFESFGDLS-----NADAVMG-----NP-----KVKAHGKKVLQSFSDGLKHLDNLKGTFAKLSEL---HCDQLHVDPENFRLLGNVIVVVLARR-LGHDFNPDVQAAFQKVVAGVANALAHKY-
+MGYP000536366561/97-193          -------RRGPQGAWAVGG-RPRCWELTAPAPRPRLFLSHPQTKTYFPHF-DLH-----P-----G-----SA-----QLRAHGSKVVAAVGDAVKSIDDIGGALSKLSEL---HAYILRVDPVNFKVR-----------------------------------------
+MGYP000318290004/2-70            --------------------------------------AFPSSKTYFLHL-NLS-----P-----G-----SA-----QVAAHGQKVADALSLAVNHLDDLPGTLSYLREL---HTHKLRVDPVFFKVSSR---------------------------------------
+MGYP001111532658/13-154          ----DAERSAITSLWGKID----VGEIGPQA-LARLLIVYPWAQRYFKAFGDLS-----TNAAIMG-----NP-----KVAQHGKTVMGGLENAVKNLDNIKQTYAKLSVM---HSEKLHVDPDNFRVLAECISLCVAAKFCPSVFTADVQEAWQKFLAVVVSALRRQY-
+MGYP000722267483/2-47            ---------------------------------------------------------------------------------------------------------------------------LARQLLSHSLLVTLASH-LPSDFTPAVHASLDKFLANVSTVLTSKYR
+MGYP000079462051/73-112          ---------------------------------------------------------------------------------------------------------------------------------SLDMLVTLAAH-LPAEFTPAVHASLDKFLASVSTVLTSKYR
+MGYP000413961247/1-72            -----------------------------------MLVVYPQTKTYFSHWKDVS-----P-----G-----SA-----AIRKHGLTVMTGYMDAVEKIDDIANGLLTLSEL---HAFTLRVDPANFKVCD----------------------------------------
+MGYP000729474694/1-75            -----------------------------------MLVVYPQTKTYFSHWSDIT-----P-----G-----SA-----PVMKHGRTVMGGVATAVGVIDDLIGGLLTLSEL---HAFQLRIDPANFKVKTYYI-------------------------------------
+MGYP000459697661/48-117          ----------------------------------RLFTVYPSTKVYFPHL-SAC-----Q-----D-----AT-----QLLSHGQRMLAAVGAAVQHVDNLRAALSPLADL---HALVLRVDPANFPV------------------------------------------
+MGYP001121356039/36-177          --LTKDDKKYVCDVWSHIN-C---EQVGGDA-LIRLICVDPWTRRYFLKFGDLS-----C-----AEAIIHNA-----HLAAHGVKVLKSIGDAITHIDDLRGHYADLSAF---HSKKFHVDPANFWLFAGIVSVTVGMA-LGEDYTAHKQACFERFLHDVCRALSHG--
+MGYP000132531679/62-95           -------------------------------------------------------------------------------------------LQATMHVDDMPNALSALSDL---HAHKLRVDPVNFKV------------------------------------------
+MGYP000427472264/214-245         MVLSPADKTNVKAAWGKVG-A-HAGEYGAEA-LER---------------------------------------------------------------------------------------------------------------------------------------
+MGYP000620445737/4-47            -----------------------------------------------------------------------------------------------------------------------------FQLLSHCILVTLACH-MKDEFTPVAHAAMDKYLSAFAAVLAEKYR
+MGYP000639461158/65-143          ------------------------------S-LRRLLIVYPWTQRFFDNFGNLS-----SPTAIIG-----NP-----KVRAHGKKVLSSFGEAVKNLDNIKNTYAKLSEL---HCEKLHVDPENFRV------------------------------------------
+MGYP000507092441/12-54           ------------------------------------------------------------------------------------------------------------------------------QLLSHCLLVTLAAR-FPADFTAEAHAAWAKFLSVVSSVLTEKYR
+MGYP000607025940/8-103           --------------------------------LCRLLIVYPWTQRFFASFGNLS-----SATAIIG-----NP-----MVRAHGKKVLTSFGDAVKNLDNIKNTFSQLSEL---HCDKLHVDPENFRVRCS-WLGPIPMH-LQEEILP----------------------
+MGYP000362522003/1-32            MVLSAADKGNVKAAWGKVG-G-HAAEYGAEA-LER---------------------------------------------------------------------------------------------------------------------------------------
+MGYP000322610494/7-50            -----------------------------------------------------------------------------------------------------------------------------SQLLAHCLLVELAIM-FPAEFTPVVHVSMDKFFAALGLALAEKYR
+MGYP000442294717/26-101          ----------------------------------RLLVVYPWTQRFFESFGDLSTPDAVM-----G-----NP-----KVKAHGKKVLGAFSDGLAHLDNLKGTFATLSEL---HCDKLHVDPENFRV------------------------------------------
+MGYP000214952500/50-125          ----------------------------------RLLVVYPWTQRFFESFGDLSTPDAVM-----G-----NP-----KVKAHGKKVLGAFSDGLAHLDNLKGTFATLSEL---HCDKLHVDPENFRV------------------------------------------
+MGYP000321112601/3-73            ---------------------------------------YPWTQRFFESFGDLS-----SPDAVMG-----NP-----KVKAHGKKVLGAFSDGLAHLDNLKGTFSQLSEL---HCDKLHVDPENFRV------------------------------------------
+MGYP000386264740/2-52            -----------------------------------------------------------------G-----NP-----KVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSEL---HCDKLHVDPENFKVS-----------------------------------------
+MGYP000172242919/33-125          --------------------------------IDRVLIVYPWTQRYFGTFGDLS-----NAAAILG-----NA-----KVAAHGKVVLGALDKGVKNVDNVKATYTALSQL---HCLKLNVDPDNFKVNVQALC-LLGYR-TPSQ-------------------------
+MGYP000669192840/12-82           ---------------------------------------YSWTQRFFESFGDLS-----SADAILG-----NP-----KVKAHGKKVLDSFCEGLKQLDDLKGAFASLSEL---HCDKLHVDPENFRV------------------------------------------
+MGYP000212149699/2-51            -----------------------------------------------------------------G-----NP-----KVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSEL---HCDKLHVDPENFRV------------------------------------------
+MGYP000559925714/32-112          --------------------------------FHRLLVVYPWTQRFFDSFGNLS-----SPSAILG-----NP-----KVKAHGKKVLTSFGDAIKNMDNLKPAFAKLSEL---HCDKLHVDPENFKVSSG---------------------------------------
+MGYP000335830788/32-110          --------------------------------FHRLLVVYPWTQRFFDSFGNLS-----SPSAILG-----NP-----KVKAHGKKVLTSFGDAIKNMDNLKPAFAKLSEL---HCDKLHVDPENFKVS-----------------------------------------
+MGYP000306499386/2-53            -----------------------------------------------------------------G-----NP-----KVKAHGKKVLDSFCEGLKQLDDLKGAFASLSEL---HCDKLHVDPENFRVSL----------------------------------------
+MGYP000450732916/70-150          ----------------------------SPS-LYRLLIVYPWTQRFFASFGNLS-----SPTAILG-----NP-----MVRAHGKKVLSSFGEAVKNLDNIKNTYAKLSEL---HCDKLHVDPENFRV------------------------------------------
+MGYP000694104832/9-83            -----------------------------------LLIVSPWTQRHFSTFGNLS-----NAAAIMG-----NA-----KVAQHGKTVMGGLDRAVKNLDDIKNTYSALSVM---HSEKLHVDPDNFRV------------------------------------------
+MGYP000114577797/2-45            -------------------------------------------------------------------------------------KVLNAIGEAVKNIDDIRGALAKLSEL---HAYILRVDPVNFKVSGHA--------------------------------------
+MGYP001143026688/10-61           -----------------------------------------------------------------G-----NP-----KVKAHGKKVLISFGKAVMLTDDLKGTFATLSDL---HCNKLHVDPENFLVSS----------------------------------------
+MGYP000969813914/167-286         ----------VEETWRIVE-P-RADQLGTDF-FLRLFQRSPSLLELFSFK-DDKP---LS-----S-----SP-----RLRAHGSKVMATIANAVSGLRDLEALIPILANLAKKHA-EYGVQEEHFPYVGEALLGTLADA-LGTDWTPDVQTAW----------------
+#=GC RF                          xxxxxxxxxxxxxxxxxxx.x.xxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxx.....x.....x.....xx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+//