<pre>Figure 2 alignment: MSF format

 nad1_f2.msf  MSF: 319  Type: N  January 01, 1776  12:00  Check: 61 ..

 Name: AF1831           Len:   319  Check:  5666  Weight:  1.00
 Name: EC2282           Len:   319  Check:  3250  Weight:  1.00
 Name: NU1M_HUMAN       Len:   319  Check:  1656  Weight:  1.00
 Name: Rv3152           Len:   319  Check:  3943  Weight:  1.00
 Name: nad1_PRA         Len:   319  Check:  5546  Weight:  1.00

//

         AF1831  IMPGLGVLTL YLLYIVWYER KLTARIQWRV GPLEVARPIR GAIQALADGI
         EC2282  AVVILLVVVT CGAFMSFGER RLLGLFQNRY GPNRVG--WG GSLQLVADMI
     NU1M_HUMAN  LLLLIVPILI AMAFLMLTER KILGYMQLRK GPNVVG--PY GLLQPFADAM
         Rv3152  AVFVFLMLTV LVAILA--ER KLLGRMQLRP GPNRVG--PK GALQSLADGI
       nad1_PRA  ILGLVLPLLI CVAYLTLLER KVIAAMQQRK GPNVVG--VF GLLQPLADGL

         AF1831  RYFFQEAIVH REAHRPYFVQ LPILAFIPVL LPIMFIPAGS AVG-------
         EC2282  KMFFKEDWIP KFSDRVIFTL APMIAFTSLL LAFAIVPVSP GWVV------
     NU1M_HUMAN  KLFTKEPLKP ATSTITLYIT APTLALTIAL LLWTPLPMPN PLV-------
         Rv3152  KLALKESITP GGIDRFVYFV APIISVIPAF TAFAFIPFGP EVSVFGHRTP
       nad1_PRA  KLLLKETIVP TRANSAIFIL APILTFMLSL VSWAVIPIDD GMVI------

         AF1831  ---IYTPNAI QLTVTFIALI PITIVAIGWA SNSRFAYIGS VREAFMYFAY
         EC2282  ---ADLNIGI LFFLMMAGLA VYAVLFAGWS SNNKYSLLGA MRASAQTLSY
     NU1M_HUMAN  ----NLNLGL LFILATSSLA VYSILWSGWA SNSNYALIGA LRAVAQTISY
         Rv3152  LQITDLPVAV LFILGLSAIG VYGIVLGGWA SGSTYPLLGG VRSTAQVISY
       nad1_PRA  ---ADLNIGL LYILSVSSLG VYGIITSGWS SNSKYAFLGS LRSAAQMVSY

         AF1831  EVPFIIAVIS MIFLYGSGDA YVAVEKQSAI PGALLNPIAF IVYLIAMLMA
         EC2282  EVFLGLSLMG VVAQAGSFNM TDIVNSQAHV WNVIPQFFGF ITFAIAGVAV
     NU1M_HUMAN  EVTLAIILLS TLLMSGSFNL STLITTQEHL WLLLPSWPLA MMWFISTLAE
         Rv3152  EVAMGLSFAT VFLMAGTMST SQIVAAQDGV WYAFLLLPSF VIYLISMVGE
       nad1_PRA  EVSIGLIIIT VLMCAGSLNL TQIVRCQESM WYIIPLFPLF VMFFISILAE

         AF1831  TSRLPFEIPE ADQEIAFGPF VEYSGILFGL VMVLAYEKLY IMTLLFTILF
         EC2282  CHRHPFDQPE AEQELADGYH IEYSGMKFGL FFVGEYIGIV TISALMVTLF
     NU1M_HUMAN  TNRTPFDLAE GESELVSGFN IEYAAGPFAL FFMAEYTNII MMNTLTTTIF
         Rv3152  TNRAPFDLPE AEGELVAGFH TEYSSLKFAM FMLAEYVNMT TVSALAATLF
       nad1_PRA  TNRSPFDLPE AEAELVAGYN VEYSAMGFAL FFLGEYANMI LMCSMCTILF

         AF1831  LGGWSGIYCP L-----LGDL NGPLWMFIKT IVVISILVIV RSIYARYRLD
         EC2282  FGGWQGPLLP -------P-- --FIWFALKT AFFMMMFILI RASLPRPRYD
     NU1M_HUMAN  LGTTYDALSP EL----YT-- ---TYFVTKT LLLTSLFLWI RTAYPRFRYD
         Rv3152  FGGWHAPWPL NMWASANTGW WPLIWFTAKV WGFLFIYFWL RATLPRLRYD
       nad1_PRA  LGGWLAPLNI LPFTL-IPG- --SIWFGLKV VFLLFVFIWV RATFPRYRYD

         AF1831  QALRIGWTSM LALSIVALV
         EC2282  QVMSFGWKIC LPLTLINLL
     NU1M_HUMAN  QLMHLLWKNF LPLTLALLM
         Rv3152  QFMALGWKLL IPVSLVWVM
       nad1_PRA  QLMRLGWKIF LPFSLGWVL

Figure 2 alignment: FASTA format

>AF1831
IMPGLGVLTLYLLYIVWYERKLTARIQWRVGPLEVARPIRGAIQALADGIRYFFQEAIVHREAHRPYFVQLPILAFIPV
LLPIMFIPAGSAVG----------IYTPNAIQLTVTFIALIPITIVAIGWASNSRFAYIGSVREAFMYFAYEVPFIIAV
ISMIFLYGSGDAYVAVEKQSAIPGALLNPIAFIVYLIAMLMATSRLPFEIPEADQEIAFGPFVEYSGILFGLVMVLAYE
KLYIMTLLFTILFLGGWSGIYCPL-----LGDLNGPLWMFIKTIVVISILVIVRSIYARYRLDQALRIGWTSMLALSIV
ALV
>EC2282
AVVILLVVVTCGAFMSFGERRLLGLFQNRYGPNRVG--WGGSLQLVADMIKMFFKEDWIPKFSDRVIFTLAPMIAFTSL
LLAFAIVPVSPGWVV---------ADLNIGILFFLMMAGLAVYAVLFAGWSSNNKYSLLGAMRASAQTLSYEVFLGLSL
MGVVAQAGSFNMTDIVNSQAHVWNVIPQFFGFITFAIAGVAVCHRHPFDQPEAEQELADGYHIEYSGMKFGLFFVGEYI
GIVTISALMVTLFFGGWQGPLLP-------P----FIWFALKTAFFMMMFILIRASLPRPRYDQVMSFGWKICLPLTLI
NLL
>NU1M_HUMAN
LLLLIVPILIAMAFLMLTERKILGYMQLRKGPNVVG--PYGLLQPFADAMKLFTKEPLKPATSTITLYITAPTLALTIA
LLLWTPLPMPNPLV-----------NLNLGLLFILATSSLAVYSILWSGWASNSNYALIGALRAVAQTISYEVTLAIIL
LSTLLMSGSFNLSTLITTQEHLWLLLPSWPLAMMWFISTLAETNRTPFDLAEGESELVSGFNIEYAAGPFALFFMAEYT
NIIMMNTLTTTIFLGTTYDALSPEL----YT-----TYFVTKTLLLTSLFLWIRTAYPRFRYDQLMHLLWKNFLPLTLA
LLM
>Rv3152
AVFVFLMLTVLVAILA--ERKLLGRMQLRPGPNRVG--PKGALQSLADGIKLALKESITPGGIDRFVYFVAPIISVIPA
FTAFAFIPFGPEVSVFGHRTPLQITDLPVAVLFILGLSAIGVYGIVLGGWASGSTYPLLGGVRSTAQVISYEVAMGLSF
ATVFLMAGTMSTSQIVAAQDGVWYAFLLLPSFVIYLISMVGETNRAPFDLPEAEGELVAGFHTEYSSLKFAMFMLAEYV
NMTTVSALAATLFFGGWHAPWPLNMWASANTGWWPLIWFTAKVWGFLFIYFWLRATLPRLRYDQFMALGWKLLIPVSLV
WVM
>nad1_PRA
ILGLVLPLLICVAYLTLLERKVIAAMQQRKGPNVVG--VFGLLQPLADGLKLLLKETIVPTRANSAIFILAPILTFMLS
LVSWAVIPIDDGMVI---------ADLNIGLLYILSVSSLGVYGIITSGWSSNSKYAFLGSLRSAAQMVSYEVSIGLII
ITVLMCAGSLNLTQIVRCQESMWYIIPLFPLFVMFFISILAETNRSPFDLPEAEAELVAGYNVEYSAMGFALFFLGEYA
NMILMCSMCTILFLGGWLAPLNILPFTL-IPG---SIWFGLKVVFLLFVFIWVRATFPRYRYDQLMRLGWKIFLPFSLG
WVL


</pre><pre>Figure 1 alignment: MSF format

 nad4_f1.msf  MSF: 171  Type: N  January 01, 1776  12:00  Check: 2713 ..

 Name: EC2280           Len:   171  Check:  1731  Weight:  1.00
 Name: NU6M_HUMAN       Len:   171  Check:  4145  Weight:  1.00
 Name: NU6M_XENLA       Len:   171  Check:  6839  Weight:  1.00
 Name: Rv3154           Len:   171  Check:  4621  Weight:  1.00
 Name: nad6_PRA         Len:   171  Check:  5377  Weight:  1.00

//

         EC2280  MEFAFYICGL IAILATLRVI THTNPVHALL YLIISLLAIS GVFFSLGAYF
     NU6M_HUMAN  MMYALFLLSV GLVMGFVGFS SKPSPIYGGL VLIVSGVVGC VIILNFGGGY
     NU6M_XENLA  MIYMVSVSMM VLVLGLVAVA SNPSPFYAAL GLVLAAGAGC LVIVSFGSSF
         Rv3154  EAVMFWVLSA LALLGAVGVV LAVNAVYSAM FLAMTMIILA VFYMAQDALF
       nad6_PRA  E-ILFYFFSF LALSSATLVI ASSNPIHSVL FLVLVFCSTS GLFILIEAEF

         EC2280  AGALEIIVYA GAIMVLFVFV VMMLNLGGSE IEQERQWLKP QVWIGPAILS
     NU6M_HUMAN  MGLMVFLIYL GGMMVVFGYT TAMAIEEYPE AWGSGVEVLV SVLVGLAMEV
     NU6M_XENLA  LSIVLFLIYL GGMLVVFAYS AARA-KPYPE AWGS--WSVV FYVLVYLIGV
         Rv3154  LGVVQVVVYT GAVMMLFLFV LMLIGVDSAE SLKETLRGQR VAAVLTGVGF
       nad6_PRA  IAMIFIMVYV GAIAVLFLFV VMMLNVRLVQ FNVNMLRYLP LGGVIGLIFL

         EC2280  AIM------- LVVIVYAILG VNDQGIDGT- ----PISAKA VGITLFGPYV
     NU6M_HUMAN  GLVLWVKEYD GVVVVVNFNS VGSWMIYEGE GSGLIREDPI GAGALYDYGR
     NU6M_XENLA  LVW------Y LFLGGVEVDG MNKSSELGS- ---YVMRGDW VGVALMYSCW
         Rv3154  GVL------- LISTIGQVAT RGFAGLTVAN ---ANGNVEG LAALIFSRYL
       nad6_PRA  LELFLIIDSD LIPLFGLNIN NNIAPFQWAD TIDSITNVEA IGKLLYTHYF

         EC2280  LAVELASMLL LAGLVVAFHV G
     NU6M_HUMAN  WLVVVTGWTL FVGVYIVIEI A
     NU6M_XENLA  WVIIVYWW-- -VSIIINFVC G
         Rv3154  WAFELTSALL ITAAVGAMVL A
       nad6_PRA  YLFLVSGMIL LVAMIGAIVL T

Figure 1 alignment: FASTA format

>EC2280
MEFAFYICGLIAILATLRVITHTNPVHALLYLIISLLAISGVFFSLGAYFAGALEIIVYAGAIMVLFVFVVMMLNLGGS
EIEQERQWLKPQVWIGPAILSAIM-------LVVIVYAILGVNDQGIDGT-----PISAKAVGITLFGPYVLAVELASM
LLLAGLVVAFHVG
>NU6M_HUMAN
MMYALFLLSVGLVMGFVGFSSKPSPIYGGLVLIVSGVVGCVIILNFGGGYMGLMVFLIYLGGMMVVFGYTTAMAIEEYP
EAWGSGVEVLVSVLVGLAMEVGLVLWVKEYDGVVVVVNFNSVGSWMIYEGEGSGLIREDPIGAGALYDYGRWLVVVTGW
TLFVGVYIVIEIA
>NU6M_XENLA
MIYMVSVSMMVLVLGLVAVASNPSPFYAALGLVLAAGAGCLVIVSFGSSFLSIVLFLIYLGGMLVVFAYSAARA-KPYP
EAWGS--WSVVFYVLVYLIGVLVW------YLFLGGVEVDGMNKSSELGS----YVMRGDWVGVALMYSCWWVIIVYWW
---VSIIINFVCG
>Rv3154
EAVMFWVLSALALLGAVGVVLAVNAVYSAMFLAMTMIILAVFYMAQDALFLGVVQVVVYTGAVMMLFLFVLMLIGVDSA
ESLKETLRGQRVAAVLTGVGFGVL-------LISTIGQVATRGFAGLTVAN---ANGNVEGLAALIFSRYLWAFELTSA
LLITAAVGAMVLA
>nad6_PRA
E-ILFYFFSFLALSSATLVIASSNPIHSVLFLVLVFCSTSGLFILIEAEFIAMIFIMVYVGAIAVLFLFVVMMLNVRLV
QFNVNMLRYLPLGGVIGLIFLLELFLIIDSDLIPLFGLNINNNIAPFQWADTIDSITNVEAIGKLLYTHYFYLFLVSGM
ILLVAMIGAIVLT


</pre>