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2 genomes BUD3416 4 proteins
a Hsa
Halobacterium
sp. NRC-1		 b Hma
Haloarcula
marismortui		 f Hvo
Haloferax
volcanii		 g Hbo
Halogeometricum
borinquense		 h Hmu
Halomicrobium
mukohataei		 i Hut
Halorhabdus
utahensis		 j Hla
Halorubrum
lacusprofundi		 q Nph
Natronomonas
pharaonis		 x Hwa
Haloquadratum
walsbyi
-

rrnAC0735

rrnAC3329

 - -

Hmu0762

Hmu1008

 - - - -

Pairwise sequence scores
Consensus score1709 rrnAC3329 Hmu1008 rrnAC0735 Hmu0762
1285rrnAC3329 1677 1186 1062 1048
1323Hmu1008 1186 1607 947 1204
1314rrnAC0735 1062 947 1684 1295
1434Hmu0762 1048 1204 1295 1726 

231 symbols
consensus       -------MNRREFVRTAGG-AGAAAAASAAGAAAAQEEEGGDGGG-GGTPDYGGFLDSVG
#oth            11111112211212...112...21122.1.112...11.11.111112..1.11.11.1
rrnAC3329       MTDGRADVS::G:L:::--::::T::SA:::T:T:::--:TE::::::P::F:::::Q::
Hmu1008         :::::::------M:::--:::::T::G:::TV:::::::::::::::::::::W:G::S
rrnAC0735       :::::::::::::::::::A:::::TL::T::::::::-::::AK:-TV:::::::::::
Hmu0762         :::::::::::::::::::V:::S:::::T:::V:::::::::::G:::::::DW:G::S

consensus       NFDGETVDATGQDSTTVEVGVQANGGAFGFGPAAVHVDNGATVQFEWTGNGGRHNVVSDG
#oth            .1.1111......12.....1......1....1.1..............1..1.......
rrnAC3329       :Y::SVA::::::TA:::::::::::::::::P:I:::::::::::::::::G:::::::
Hmu1008         :::-::::::::::::::::T::::::::::::::::::::::::::::E::::::::::
rrnAC0735       ::::S::::::::TV::::::::::::Y::::P:::::::::::::::::::G:::::::
Hmu0762         :::::::::::::::::::::::::::::::::::::::::::::::::E::::::::::

consensus       DGPLDSGDAVSSAGVNYEHTFEEDGIYPYYCVPHEGLNMKGAIVVGSDYPTADSGGGGGG
#oth            1......111211..1.............2....11.1........21...221..21..
rrnAC3329       E::::::S:::::::::::::::::::::V:::::::G::::::::T::::KS:::::::
Hmu1008         ::::::::::ETT::E::::::::::::::::::KS::::::::::::::::::::::::
rrnAC0735       :::::::STA:::::::::::::::::::L::::::::::::::::EE:::QTI::--::
Hmu0762         ::::::::::DTT::E::::::::::::::::::KS::::::::::::::::::::D:::

consensus       EGEGGDPEAAGVPIQPHFLGVAAGLAMVATLGLAFFFLKYGEDYNTPEGNN
#oth            31232212322..212131.2111211222111112221..1123.21111
rrnAC3329       S:SS:P::---::NSAKT::::TSFV::::::::Y::IR::G::E:::---
Hmu1008         G:G::SSA:PA::ESIKS:::::SVV:T::::::YV:M:::G::D:::---
rrnAC0735       PV:-V::HY:::::::::V:FG::::VIIP:IFT::Q:::::SPH:SG:::
Hmu0762         :V:TL:::E::::::::WV:IG::::::VSTIFT:YL:::::SA::KG:::