#mega
TITLE: ROTIFER 16S ALIGNMENT Garey et al.(1999) The evolutionary relationships of rotifers and acnthocephalans.  Hydrobiologia, in press.

#Artemia    CGCCUCUUAA ---------- --CUUUGGGA GGUCGAGCCU GCCC-ACUGA --------UG
#Katharina  CGCUCUUUGA AAA-----UU AUUAAUAAAG AGUCGUGCCU GCCC-AGUGA --------AA
#Homo       CACCUCUAGC AUC-----AC CAGUAUUAGA GGCACCGCCU GCCC-AGUGA C-------AC
#Xenopus    CGCCUCUUGC UUAAAAAACA UUGUAUAAGA GGUCCAGCCU GCCCAAGUGA C-------GU
#Urchin     CGCUCCCCAA AAUU----UA AAGCCUGGGG AGUCCUGCCU GCCC-AGUGA C-------UA
#Mytilus    UUCCUUUUGA ---------U GUAAGUAAAA GGUAGUCCCU GCCC-AGUGC AACUAGAGUA
#Brachionus AGCUUUGAGA ---------- -UUUAUUCAA AGUAUCUUCU GCCC-ACUGA U---------
#Monil      UUCUUGCUUU ---------- ----UUAGCA AGUAGUCCCU GCUC-AGUGA U---------
#Philodina  GCAUAUUUUU ---------- ----UAAUAU GUUAU-UUCU GCUC-AAUGA U---------
 

#Artemia    AA-------- UUAAAGGGCC GUGGUAUACU GACCAUGCGA AGGU-AGCAU AAUCAUUAGC
#Katharina  UU-------- UUAAACGGCC GCAGUACCCU GACUGUGCUA AGGU-AGCAU AAUAACUUGU
#Homo       AU-------G UUUAACGGCC GCGGUACCCU AACCGUGCAA AGGU-AGCAU AAUCACUUGU
#Xenopus    AUAU-----G UC-AACGGCC GCGGUA-UCU GACCGUGCAA AGGU-AGCGU AAUCACU-GU
#Urchin     GA------GG UUAAACGGCC GCUGUAUCUU GACCGU-CGG AGGU-AGCAU AAUCAUU-GU
#Mytilus    AUG-UCUGUU GUAAACGGCG GCGUUAACGU GAGCGUCCUA AGGU-AGCGC GAUAAUUUGC
#Brachionus ------ACAA UUUAAUGGCC GCAGUACCCU GACUGUGCUA AGGU-AGCGU GAUU-CUUGU
#Monil      --------UA UUAAAUAGCC GCGGUAAUUU GACUGUGCUA AGGU-AGCGU AAUCAUUAGU
#Philodina  ---------- UUAAAUAGCU GCAGUAAUCU GACUGUACUA AGGU-AGCAU AAUCAUUAGU
 

#Artemia    CUUUUGAUU- UGAGGCUGGA AUGAAUGGUU UGACGAGAGA UGG------U CUGUCUCUUC
#Katharina  UUUUUAAUU- GAAAGCUUGU AUGAAUGGCU UGACGUGGGC AAG------A CUGUCUCUAU
#Homo       UCCUUAAAU- AGGGACCUGU AUGAAUGGCU CCACGAGGGU UCA------G CUGUCUCUUA
#Xenopus    -CUU-AAU-- AAGAACUGGU AUGAACGGC- -CACGAAGGU UCA------A CUGUCUCCUG
#Urchin     CUUCCUAAUU AGAGACUAGU AUGAAUGGCA AGAGGGAAAU AA-------A -UGACAUUUU
#Mytilus    UUUUCAAUU- GAAGGAUGGU AUGAAAGGGU UAACGAAGAA GGU------G CUGUGUCUAA
#Brachionus UUUCUUAAU- UAGAAAUCUG UUCAAAGAAU GAAAUGAGAG AAU------- CUAUUGUUUC
#Monil      CUUUUAAUU- AAGGUCUAGA AUGAAUGGGU UAA------- ---CGACAGG GGGUGGUAAU
#Philodina  UUCUUAAUA- AGAAACUGGA AUGAA-GGAA UUUAAAAA-- ---------U UAUUUAAUUU
 

#Artemia    GAUU---AAA UUGAAGUU-A AUCUUUAAGU GAAAAAGCUU AAAUGUACUU GGAGGGCGAU
#Katharina  UACAU-UAAA UAAAAAUUAA UUUUUAA-GU GAAGAAGCUU AAAUAAUCUC AAAAGACGAA
#Homo       CUUUUAACCA GUGAAAUUGA CCUGCCC-GU GAAGAGGCGG GCAUGACACA GCAAGACGAG
#Xenopus    CAUCCAAUCC AUUAAACUGA C--CUCC-GU GCAGAGGCGG GGAUAGAACC AUAGAACGAG
#Urchin     UUCUAUAGCC CUUAAUACUA CCUCCCC-GU GAAGAGGCGG GGAUAAAACG GUUAGACGAG
#Mytilus    AAAUUCAAU- UU-AAACUAA CUUUAAG-GU GAAGAGGCCU UUAUGUAAAA GAAGGACGAC
#Brachionus UAUAACAA-- GUGAAUUUAA AAUGUU-AGU GAAAAUUCUG ACAAGUCCUU AAAAGACGAG
#Monil      AGGAUAAUUU AAUGAAGUUU UAGUUUAAGU GAAAAUACUU A-AUAUUAUU UAAAGACGGA
#Philodina  UUAAUAAUUU UAUUAAGUUU UAUUUUAAGU GAAAAUACUU AAAAUUUAAG UUUAGACGAU
 

#Artemia    AAGACCCUAU AGAUCUUU-A CAUUUAAUUC UUUUG----- UCUUGCGG-U AGGUAAUUAG
#Katharina  AAGACCCUAU CGAGCUUU-A AAUUUAUGUA UAAAU----- -AAAAUCU-- ---UUUAGAA
#Homo       AAGACCCUAU GGAGCUUU-A AUUUAUUAAU GCAAA----- CAA------- ---UACCUAA
#Xenopus    AAG-CCCUAU GGAGCUUU-A AACUAAAGAA CUGCC----- AAGUUGAAC- --CUAACCCA
#Urchin     AAGACCCUGU GGAGCUUUUA AGCGGAAGUU AAAUU----- -UUAACACAC UUACCUUGUG
#Mytilus    AAGACCCUAU GAAGCUUU-A UCUUAAUUGG AGCUC----- UCA------- ----------
#Brachionus AAGACCCCAU AAAACUU--A AUUUGAUCUC UUUCU----- ---------- ----------
#Monil      AAGACCCUGG AA-GUUUU-A UAAUAU---- ---------- ---------- ----------
#Philodina  AAGACCCUAU AA-AUUUU-A AAUU------ ---------- ---------- ----------
 

#Artemia    AC-------- ---------- ---------- ---------- ---------- -AGAGUAAAA
#Katharina  AA--ACAAAA U--------- ---------- ---------- ---------- -UUAUAUC--
#Homo       CA--AACCCA --CAGGUC-C UAAACUAC-- -CAAACC--- ---------- -UGCAUUAA-
#Xenopus    UA--AGGAAA UAACAAUU-A AACA-AGC-- -AGAAAC--- ---------- -UGACCUAA-
#Urchin     AC--UAACUA AUAUACCUAU CCAACAGUAA GUUUUAA--- --------AC AUUUUAGCA-
#Mytilus    ---------- ---------- ---------- ---------- ---------- -GGCUCUUA-
#Brachionus ---------- ---------- ---------- ---------- ---------- -UAAGAGUUU
#Monil      ---------- ---------- ---------- ---------- ---------- ----------
#Philodina  ---------- ---------- ---------- ---------- ---------- ----------
 

#Artemia    CAAUGUUCGG UUGGGGCGAC GGUAAGAA-C AGAAUAAACA CU-UACAA-C A---------
#Katharina  -CAUUUUUAG UUGGGGCGAC AAAAGAAC-- AAAUAAAGCU UC-UUUUUAU UAU-------
#Homo       -AAAUUUCGG UUGGGGCGAC CUCGGAGC-A GAACCCAACC UC-CGAGCAG UAC-------
#Xenopus    -AGUUUUCGG UUGGGGCGAC CACGGAGA-A UAAAAAAUCC UC-CUUGA-A GAA-------
#Urchin     AAAGCUUUGG UUGGGGCAAC -GCGGAGU-A AGAA-GACCC UC-CGCUA-A UAA-------
#Mytilus    UACGAUUUUG AUGGGAGAUC AGUAGAAA-- -UAA--GUCU UC-UACUA-U CA--------
#Brachionus AAAAUUUAAA -UGGGGACUU UAGAGUAU-- AAUAAUAACU CA-AAGACCU AUAUUU----
#Monil      UUUAUUU-CA UUGGGGUAAU GGCUGGAGCU UAGGUUUU-- ---------- ----------
#Philodina  AUAUUUU-CU UUGGGGUAAA GUAAAUUUAU AUUAA----- ---------- ----------
 

#Artemia    ---------- ---------- ---------- ---------- ---------- ----------
#Katharina  ---------- ---------- ---------- ---------- ---------- ----------
#Homo       ---------- ---------- ---------- ---------- ---------- ----------
#Xenopus    ---------- ---------- ---------- ---------- ---------- ----------
#Urchin     ---------- ---------- ---------- ---------- ---------- ----------
#Mytilus    ---------- ---------- ---------- ---------- ---------- ----------
#Brachionus ---------- ---------- ---------- ---------- ---------- ----------
#Monil      ---------- ---------- ---------- ---------- ---------- ----------
#Philodina  ---------- ---------- ---------- ---------- ---------- ----------
 

#Artemia    ---------- ---------- ---------- ---------- ---------- -----UAAA-
#Katharina  ---------- ---------- ---------- ---------- ---------- ----------
#Homo       ---------- ---------- ---------- ---------- ---------- ----AUGCCA
#Xenopus    ---------- ---------- ---------- -------UAG GGCCUACCAC CCUUUCACCA
#Urchin     ---------- ---------- ---------- ---------- ----GAUAUU ACUAUAAAAA
#Mytilus    ---------- ---------- ---------- ---------- ---------- ------UAUU
#Brachionus ---------- ---------- ---------- ---------- ---------- ----------
#Monil      ---------- ---------- ---------- ---------- ---------- ----------
#Philodina  ---------- ---------- ---------- ---------- ---------- ----------
 

#Artemia    ------CACA ---UC-AAUA AA-------- ----UGACC- -AUUGAUCC- --UUA-GAUG
#Katharina  ---------- -------GUA AA-------U UU-AUAAAUU UAUAGAGCCA U-AAUU-AUG
#Homo       AGACUUCACC AGUCAAAGCG A------ACU AC-CAUACUC AAUUGAUCCA A-UAAC-UUG
#Xenopus    AGAAC-CACC AUUCUAAGUA ACAA-AAUUU AU-GACUAUA -AUUGAUCCA GUCCU-ACUG
#Urchin     GAA-U-UACG G-UUCUACAA UCAAAA--UG AAAGAAU--- ----GAUCCA C-UAAG-GUG
#Mytilus    AAUCU-UACU AGUAUUUCCU AA-------- ---------- ---------- ---CUU-UAU
#Brachionus ---------- ---------- ---------- ---------- ---------- ---------A
#Monil      ---------- ---------- ---------- ---------- ---------- ---------A
#Philodina  ---------- ---------- ---------- ---------- ---------- ---------A
 

#Artemia    AAUAAAGAC- CAAGUUACCU UAGGGAUAAC AGCGUAAUUC U-UUUUGAGA GUUCAAAUCG
#Katharina  AUUAAAAGAA AAAGCUACCG UAGGGAUAAC AGCAGUUAUU UUUUCAGAGA GUCCUAAUCG
#Homo       ACCAACGGAA CAAGUUACCC UAGGGAUAAC AGCGCAAUCC U-AUUCUAGA GUCCAUAUCA
#Xenopus    AUCAACGAAC CAAGUUACCC UAGGGAUAAC AGCGCAAUCC A-UUUCAAAA GUUCCUAUCG
#Urchin     AUCAAAGAAA CAAGUUACCG CAGG-AUAAC AGCGUUAUCU U-UUCUGAGA GUUCACAUUG
#Mytilus    AUG-UGUGGC U-AGCUACUC UAGGGAUAAC AGCGCAAUUU C-UCCCGAAA GAUGGUAUUG
#Brachionus UAUUAUUAGC GAAGCUACUU UGGGGAUAAC AGGGUAAAAU A-UUUAGAGA GUUCAUAUCG
#Monil      GUGGGGCAGA AAAAUUACUC CAGGGAUAAC AGGACAAUUU A-GAAGGUCA GUUCGUAUGU
#Philodina  UUAUUGUUUU AAAUUACUUU AGGGGUUAAC AGGGUAAUAU U-AUUAUUAA GAUCUUAUUA
 

#Artemia    ACAAAAGAGU UUGCGAGCCU CGAUGUUGGU -UCAGGGACC CUACUCG-GU GCAGCAGC-C
#Katharina  AAGAAAAAGU UUGCGA-CCU CGAUGUUGGA -UUAAAGUAA CUUUUAA-GU GCAGAAGCUU
#Homo       ACAAUAGGGU UUACGA-CCU CGAUGUUGGA -UCAGGACAU CCCGAUG-GU GCAGCCGC-U
#Xenopus    ACAAAUGGGU UUACGA-CCU CGAUGUUGGA AUCAGGGCAU CCCAGUG-GU GCAGCCGC-U
#Urchin     ACGAAAAGGU UUGCGA-CCU CGAUGUUGGA -UCGGGACAU CCUAAGG-GU GCAGAAGC-U
#Mytilus    GAGGGGAAGA UUGCGA-CCU CGAUGUUGGC -UUUAGAUAU CCUAGAG-GC GGAGAAGC-U
#Brachionus AUAAAUAUAU CUACUA-CCU CGAUGUUGGA -UUAUCUUUU CAUAUAUAUU GUAGCAG--U
#Monil      AUUUUUAAGA UUGUUA-CCU CGAUGUUGGA -UCAUCCUUU CCCAA-G-GU ------GUUU
#Philodina  AUAAUAAUGU UUACUA-CCU CGAUGUUGGA -UCAUUAUAC UAAUUAA-GU -----AGAAU
 

#Artemia    UAGAGA-GG- CAGUCUGUUC GACUGUU-AA -ACCCCUACG UG
#Katharina  AAAAUA-AGU GGGUCUGUUC GACCCUU-AA -ACCUUUACA UG
#Homo       AUUAAA-GGU UCGUUUGUUC AACGAUU-AA -AGUCCUACG UG
#Xenopus    ACUAAA-GGU UCGUUUGUUC AACGAUU-AA -AGCCCUACG UG
#Urchin     UUUAAG-GGU UGGUCUGUUC GACCAUU-AA -AGUCCUACG UG
#Mytilus    UCUGAU-GGU GGGUCUGUUC GCCCUUU-AA -AAUCUAACA UG
#Brachionus AUAUAU-UGU UAGUCUGUUC GACUAUU-AA -AAAGUUACA U-
#Monil      UUGGGU-UCU AGGUCUGUUC GACCAU--AA -AAGGUUACG U-
#Philodina  UAAUUAAUUU UAGUCUGUUA GACUAU--AC -AAUUUUACG --