Fig. 6. Alignment of the downstream regions of the internal transcribed spacer from M. vaginatus and M. steenstrupii. Box A Spacer (bold type) and D4 (red font) are invariant. V3 (bold type) is a stem and loop structure that demonstrates marked sequence variability, especially within M. steenstrupii (compare the terminal loop sequence, indicated by red font). These sequences are contiguous with those in Fig. 5b.
Box A Spacer D4 <----------------------------------- M. vaginatus SEV2MC1-3F CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCAUCAUCAA------GCAGGUAAGUCUUCUG------- WD1MC2-5D CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUAUCAUCCG------- FB1MC1-3C CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUGUCAUCCG------- FB2MC3-4C CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCGAUCAUCCG------- FI5MC4-2E CUCUAGCCA-GAACCUUGAAAACUGCAUAGGAAUUAAGUCA---UCAAA-----GCGUGUUUAUCAUCCG------- MOA4MC3-3C CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUGUCAUCCG------- MERMC1-1C CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUAUCAUCCG------- SEV2MC1-3E CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCUUGCCUAUCGUCGG------- MERMC1-1B CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUAUCAUCCG------- CSV2MC1-6B CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUUGAUCAUCCG------- MOA4MC3-3B CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUGUCAUCCG------- MOA4MC3-3D CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUGUCAUCCG------- FB1MC1-3E CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUGUCAUCCG------- WD1MC2-5C CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUAUCAUCCG------- FB2MC3-4B CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCUUGUUUAUCGUCCG------- FI5MC4-2F CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUUUAUCAUCCG------- CSV2MC1-6C CUCUAGUCA-GAACCUUGAAAACUGCAUAGAAAUUAAGUCA---UCAAA-----GCGUGUCUAUCAUCCG-------
M. steenstrupii DG6MC1-3E GUCCAGUGAAGAACCUUGAAAACUGCAUAGCCAUUAAGU-A---ACAAA----GGCAGGUAAGACCGCUGAUAC--- USPCMC1-2D AUCCAGUCA-GCACCUUGAAAACUGCAUAGCAAU-AAGUCA---ACAAA-----GCAGGUAAGAGUAAAGACACU-- MOA1MC1-1F AUCCAGUCA-GCACCUUGAAAACUGCAUAGCAAU-AAGUCA---ACAAA-----GUAGGUAAGAAGAAAGACACU-- MOA2MC2-3B AUCCAGUCA-GCACCUUGAAAACUGCAUAGCAAU-AAGUCA---ACAAA-----GCAGGUAAGACUCAAGACACU-- USPCMC1-2E -UCCAGCGA-GAACCUUGAAAACUGCAUAGCAACAAA----------AAUUCUGUCAGGUA-GAUA--AG-CUGCCC USPCMC1-2F CUCCAGCGA-GAACCUUGAAAACUGCAUAGCAACAAA----------GAUUCUGUCAGGUA-GAUA---G---CGUU DG6MC1-3D CUCCAGCGA-GAACCUUGAAAACUGCAUAGCAACAAA----------AAUUCUGUCAGGUA-GAUA---G---CUUU MOA2MC2-2A -UCCAGUCA-GAACCUUGAAAACUGCAUAGCAACU-AGUCAGGUAGAAA--CUGUCA-GUA-GUCAGUAGUC----- MOA1MC1-1D -UCCAGUCA-GAACCUUGAAAACUGCAUAGCGACU-AGUCAGGUAUAAA--CUGUCA-GUA-GUCAGUAGUC----- MOA1MC1-1E -UCCAGUCA-GAACCUUGAAAACUGCAUAGCAAU-AAGUCA---ACAAA----GU-AGGUAAGAAGAAAGACAC---
----------------V3--------------------------------------------------------> M. vaginatus SEV2MC1-3F ----------A---GAAAUCA-----GGAA-------------------------AUCUUACUGAGC---GACCUC WD1MC2-5D ----------A---UUACUCG-----UUCG-------------------------AUAAGAC-AAGC---GACACC FB1MC1-3C ----------AA--GCAAUCG-----UUCG-------------------------GUAUGAC-AAGC---GACACC FB2MC3-4C ----------A---UUGCUCG-----GAGG-------------------------AUGGCAC-AAGC---GACACC FI5MC4-2E ----------A---UUGCUCG-----GAAG-------------------------AUAUGAC-AAGC---GACACC MOA4MC3-3C ----------A---UUGCUCG-----GAAG-------------------------AUAUGGC-AAGC---GACACC MERMC1-1C ----------A---UUGCUCG-----GAAG-------------------------AUAUGAC-AAGC---GACACC SEV2MC1-3E ----------A---UUGCUCG-----UUCG-------------------------AUAGGAC-AAGC---GACACC MERMC1-1B ----------A---UUGCUCG-----GAAG-------------------------AUAUGAC-AAGC---GACACC CSV2MC1-6B ----------A---UUGCUCG-----GAAG-------------------------ACAUCAC-AAGC---GACACC MOA4MC3-3B ----------AA--GCAAUCG-----UUCG-------------------------AUAUGAC-AAGC---GACACC MOA4MC3-3D ----------AA--GCAAUCG-----UUCG-------------------------AUAUGAC-AAGC---GACACC FB1MC1-3E ----------AA--GCAAUCG-----UUCG-------------------------GUAUGAC-AAGC---GACACC WD1MC2-5C ----------A---UUACUCG-----UUCG-------------------------AUAAGAC-AAGC---GACACC FB2MC3-4B ----------AA--GCAAUCG-----UUCG-------------------------GUAUGAC-AAGC---GACACC FI5MC4-2F ----------A---UUGCUCG-----GAAG-------------------------AUAUGAC-AAGC---GACACC CSV2MC1-6C ----------A---UUGCUCG-----GGAG-------------------------AUAUGAC-AAGC---GACACC
M. steenstrupii DG6MC1-3E --------------CUAAUAA----------------------------------GUGUCAG-AUUCUUAUAAAGA USPCMC1-2D --------------C-AAUAA---------------------------------AGUGUCUG-CAUCUUAU-CAGU MOA1MC1-1F ---------------UAAUAA---------------------------------AGUGUCUG-UAUCUUAU-CAGU MOA2MC2-3B ---------------UAAUAC---------------------------------AGUGUCUG-CAUCUUAU-CAGG USPCMC1-2E AAAG-AGAAAAACGCUU-UAAAAA--------------C-GUAAA-G-CUCUUUAGUAGCCA--AUC----ACAGA USPCMC1-2F AAAG-----------ACAUAAG----------------CUUU--ACGCUA----AGUA-------UC----ACAGA DG6MC1-3D AAAG----------CUUAUGG-----------------CUUU-AA-GGUA----AGUA-------UC----ACAGA MOA2MC2-2A --AGUAG-------GCAAGUCG--CUACAGACAA----CUUUCAA-CCGAC---AGUGG-AU--AUC----ACAGA MOA1MC1-1D --AGUAG-------GCAAGUCG--CUACAGACAA----CUUUCAA-CCGAC---AGUGGGAU--AUC----ACAGA MOA1MC1-1E --------------UUAAUA------------AAGUGUCU---------------GUAUCUU--AUC----A--GG