#Adenien Riboswitch
>D88802.1
AUUAUCACU-UGUAUAACCUCAAUAAUAUGGUUUGAGGGUGUCUACCAGGAACCGUAAAAUCCUGAUUACAAAAUUUGUUUAUG-ACAUUUUUUGUAAUCAGGAUUUU
>AAXV01000018.1
AUUUGAAC--UGUAUAACCUCAAUAAUAUGGAUUGAGGGUCUCUACCAGGAACCAUAAAAUCCUGACUACAAAA----CUUUGU-UUCAUUUUUGUAGUCAGGAUUUU
>AAEK01000052.1
-UGAGAAUCAUGUAUAACUCCAAGAAUAUGGCUUGGGGGUCUCUACCAGGAACCAAUAACUCCUGACUACAAAAU--GCGUAUU-AUAGCGUUUGUAGUCAGGAGUUU
>BA000016.3
AUUUUGCUU-CGUAUAACUCUAAUGAUAUGGAUUAGAGGUCUCUACCAAGAACCGAGAAUUCUUGAUUACGAAGAAAGCUUAUUUGCUUUCUUCGUAAUCAAGAAUU-
>CP000851.1
-UUAACACUUCGUAUAAUCUCAAUGAUAUGGUUUGAGAGUUUCUACCAAGAGCCCUAAACUCUUGAUUAUGAAGACUUUACUUU-AUGUAAUGCUAAUUUAACAAGUU

#Native functional structures from the adenine riboswitch of the ydhL gene of Bacillus subtilis
AUUAUCACU-UGUAUAACCUCAAUAAUAUGGUUUGAGGGUGUCUACCAGGAACCGUAAAAUCCUGAUUACAAAAUUUGUUUAUG-ACAUUUUUUGUAAUCAGGAUUUU
........(-((((...((((((.........))))))........(((((.........)))))..)))))....((((...)-)))....................
.........-.......((((((.........))))))..................((((((((((((((((((..((((...)-)))..))))))))))))))))))

#Predicted
........(-((((...(((((((.......)))))))........(((((.........)))))..))))).........(((-((((...))))))).........
.......((-((.....(((((((.......)))))))........))))......((((((((((((((((((..........-.....))))))))))))))))))


#TPP
>AL009126.3
GCAGAACAAUUCAAUA-UGUAUUCGUUUAACCACUAGGGGUGUCCUUCAUAAGGGCUGAGAUAAAAGUGUG--ACUUUUAGACCCUCAUAACUUGAACAGGUUCAGACCUGCGUAGGGAAGUGGAG-CGGUAUU--UGUGUUAUUUUACUAUG---CCAAUUCCAAACCACUUUUCCUUGCGGGAAAGUGGUUU
>CP000002.3
AUAAACUGAAUGAACA-AGAAAUGUUUU--CCACUAGGGGAGUCCUUGAUAAGGGCUGAGAUAAAAGUUUG--ACUUUUAGACCCUCAUAACCUGAACAGGUUCAAACCUGCGUAGGGAAGUGGCA-CGGUAUU--UGAGU-AUGUAUAUAUG---CAAAUUCCAAACCACUUU-CCUUGCGGGAAAGUGGUUU
>CP000764.1
-ACUAUCAAAACUAUAUAGUUCUCAUCUAUCCACUAGGGGUGCCGAU-AUU--GGCUGAGAUUAAAGUUUA--UCUUUGAGACCCUUAGUACCUGAUCUGGUUCGUACCAGCGUAGGGAAGUGGAAAUGACAA---AAUAUGAUAUUUAUAUA---UCUAGGCCACUUUCUUUAC-CUACUAAGGAAGUGGCUU
>AAEK01000033.1
GAAUA-CAAUACGAAA-AUUAAAUAUUUAUCCACUAGGGGGGCCUAUUAUA--GGCUGAGAUCAAA-UGGG--AAUUUGAGACUCUUAGUACCUGAUCUGGUUAAUGCCAGCGUAGGGAAGUGGAAAAGACAUUGCUAUUUCAUGUAUAAAUACUGUCAAUUUCACUUUCUUUACGCCUGUAAAGAAA------
>ABCF01000004.1
-AAUGCAUAUAAAUAAAUAGCCGAGCAAAACCACUGGGGGAGCCUUUUAAA--GGCUGAGAUUAAAGUGUACUACUUUAAGACCCUUUGAACCUGAUCUAGUUCAUACUAGCGGAGGGAAGUGUAGUCUGAAUGAUUGAAU-AUUUCAAAAAAUCACUCAAGCCGCCUUCCCGU-GCAAUCAGGGAGGCG----

#Native functional structures from the TPP riboswitch of the thiamin gene of Bacillus subtilis
GCAGAACAAUUCAAUA-UGUAUUCGUUUAACCACUAGGGGUGUCCUUCAUAAGGGCUGAGAUAAAAGUGUG--ACUUUUAGACCCUCAUAACUUGAACAGGUUCAGACCUGCGUAGGGAAGUGGAG-CGGUAUU--UGUGUUAUUUUACUAUG---CCAAUUCCAAACCACUUUUCCUUGCGGGAAAGUGGUUU
...(((((((.(....-.).))).))))..(((((.(((((((((((...)))))).....((((((....--.)))))).))))).....((((..(((((....)))))..))))..)))))..-.(((((.--.(((......))).)))---))......(((((((((((((....)))))))))))))
................-...........(((((((.(((((((((((...)))))).....((((((....--.)))))).))))).......((((....))))..((((((..(..((((((..-.((.(((--.((((.........)))---).))).))...))))))..)..))))))..))))))).

#Predicted
................-.............(((((((((.((((((...))--))))....(((((((...--)))))))..)))).....((((..(((((....)))))..))))..)))))..........--.................---..........(((((((........)))))))......
................-.............(((((((((.((((((...))--))))....(((((((...--)))))))..))))...((((......))))...........(((((.((((..........--.................---......)))).)))))..............)))))...


#Lysine
>J03294.1
GAAGAUAGAGGU-GCGAACUUCAAGAGUAUGCCUUUGGAGAAAGAUGGAUUCUG-UGAAAAAGGCUGAAAGGGGAGCGUCGCCGAAGCAAAUAAAACCCCAUCGGUAUUAUUUGCUGGCCGUGCAUUGAAUAAAUGUAAGGCUGUCAAGAAAUCAUUUUCUUGGAGGGCUAUCUCGUUGUUCAUAAUCAUUUAUGAUGAUUAAUUGAU--AAGCAAUGAGAGUAUUCCUCUCAUUGC
>CP000002.3
GAAGAUAGAGGU-GCGAACUUCAAGAGUAGGCUUGAUGAGGAAGAUGGAUUCCGAUGAAGAAAGCCGAAAGGGGAGCGUCGCCGAAGCGGGGAAAAAUCCACUCGUUUUUCCUGCUGGCUUUACAUUGAAUAAAUGUGAGGCUGUCAAGAAAUCAUUU-CUUGGAGAGCUAUCUCGUUGUUUAAGAUCAUCGGCAUU--UUUGUUGGUUAAAGCAAUGAGGGAAUUC-UCUCGUUGC
>AAOX01000015.1
GAAGGUAGAGGU-GCAAACUUCAUCAGUAAAAGCUUGGAGAAAGAUGAGUUUCCGUGAAAAGCUUUGAAAGGGAAUGUUUGCCGAAGAAAAGGAAGUCUCAUUU-CUUUCUUUUCUGGUCCUGUAUUGAAUAAAUACUGGAUUGUCAAGACAGCGCCGUCUUGGAGAGCUAUCUCACUGUGUGGGCAUAUUU-UAUAUGUAUUUAAAACACAGCAAUGGGAUGGUUAUUCUCAUUG-
>M93419.1
GAAGAUAGAGGU-GCGAACUUCAUCAGUAAAAGCUUGGAGAAGAAUGAGCUUCAAUGAAAAGCUUUGAAAGGGAACGUUCGCCGAAGUGAAGAAAAACUCAUUU-UUUUCUUUGCUGGUCCUGCAUUUAAGAGAUGCCGGAUUGUCAAGGCGGUGCCGCCUUGGAGAGCUAUCUCACUGUGUCUGCGUAUUU-UAC---UACGUUAUCCACAGCAAUGAGGUAGCU-UUCUCAUUGC
>CP001186.1
AAAGGUAGAGGCCGCGAUAGGAAAGAGUAAGCUAUGGGAGAUUUAAUGGAAUCUGUGAUCAUAGGUUGAAAGGGACUAUUGCCGAAAUAUAAGAAUAACCAUCUUAUUCAUAUAUUGGGACUACAUUGAAUAAAUGUAGUACUGUCAUAAGAUUUAUUUUAUGGAGAGCUAUUUGGAGAUGUUGAUGCGGUUUCUUA--UUUUGAGGAGAUAACAACUCGUUUAUU-UUUUCAAUAU

#Native functional structures from the lysine riboswitch of the lysC gene of Bacillus subtilis
GAAGAUAGAGGU-GCGAACUUCAAGAGUAUGCCUUUGGAGAAAGAUGGAUUCUG-UGAAAAAGGCUGAAAGGGGAGCGUCGCCGAAGCAAAUAAAACCCCAUCGGUAUUAUUUGCUGGCCGUGCAUUGAAUAAAUGUAAGGCUGUCAAGAAAUCAUUUUCUUGGAGGGCUAUCUCGUUGUUCAUAAUCAUUUAUGAUGAUUAAUUGAU--AAGCAAUGAGAGUAUUCCUCUCAUUGC
..((((((..(.-((((.((((........((((((...(((.......)))..-....)))))).......))))..)))))..(((((((((.(((.....))).)))))))))((((.((((((.....)))))).)))).((((((((....))))))))....))))))......((((((((((.....)))))))..))).--..((((((((((.....))))))))))
.....(((..(.-((((.((((........((((((...(((.......)))..-....)))))).......))))..)))))..(((((((((.(((.....))).)))))))))((((.((((((.....)))))).)))).((((((((....))))))))....)))(((((((((((((((((((.....)))))))..))..--.))))))))))................

#Predicted
..((((((....-((((((((........(((((((...((((......))))......)))))))........))))))))....((((((((((.........))))))))))((((((((((((.....))))))))))))((((((((....))))))))....)))))).........((((((....))))--))...........(((((((((.......)))))))))
............-((((((((........(((((((...((((......))))......)))))))........))))))))....((((((((((.........))))))))))((((((((((((.....)))))))))))).(((((((....)))))))(((((.(((((((.......((((((....))))--))...............)))))))....))))).....


#FMN
>X51510.1
UAUCCUUCGGGGCAGGGUGGAAAUCCCGACCGGCGGUAGUAAAGCACAUUUGC--UUUAGAGCCCGUGACCCGUGUGC----AUAAGCACGCGGUGGAUUCAGUUUAA-GCUGAAGCCGACAGUGAAAGUCUGGAUGGGAGAAGGAUG---AUGAGCCGCUAUGCAAAAUGUU-UAAAAAUGCAUAGUGUUAUUUCCUAUUGCGUAAAAUACCUAAAGCCCCGAAUUUUUUAUAAAUUCGGGGCUUU
>X95955.1
UAUCCUUCGGGGCUGGGUGAAAAUCCCGACCGGCGGUAAUAAGGCGCUCCUGCGCUUUACAGCCCGUGACCCGUAUGC----AUCUGUAUACGGUGGAUUCAGUGAAAAGCUGAAGCCGACAGUGAAAGUCUGGAUGGGAGAAGGAUG---A-GAGAAGCUAUGCAAAAAAUAAUCAUACUGUAUAGUCUUAUUUCCUAUGGAUUAAAACUGGUAAAGCCCCGAAUGUGUAA-ACAUUCGGGGCUUU
>BA000004.3
UAUCCUUCGGGGCUGGGUGGAAAUCCCGACCGGCGGUGAUGAAGCGAA--UGC--UUCUUAGUCCGUGACCCGGUUGCUGAUAUCAGUAAGCGGUGGACCUGGUGAAAAUCCGGGACCGACAGUGAAAGUCUGGAUGGGAGAAGGAAACGUACGGUUCAAUUUGGAAAAAUGUGCAUGAUUGCACAUCUUCUUUCUCGUGGGCAAAAAACCUACGUAUACACAAGGGAGAAGUCUGUCCAAAU----
>CP000903.1
CAUCCUUCGGGGUCGGGUGAAAUUCCCAACCGGCGGUGAUGAAGCGAU--AGC--UUCUAAGUCCGUGACCCGUUUUC---AACGCGAAAACGGUGGAUCUAGUGAAACUCUAGGGCCGACAGU-AUAGUCUGGAUGGGAGAAGGAUA---------UGUUUUCUAGUAAUUUUAUAUAGCGAAUACACUUUUAUUUCAGUAUGCAUA-UUUUUAAAGUUUCAUUUUGAAUCUUUAUAUAUGUUUUA
>L47648.1
CAAUCUUCGGGGCAGGGUGAAAUUCCCUACCGGCGGUGAUGAGCCAAU--GGC---UCUAAGCCCGCGAGCUGUCUUU---------ACAGCA--GGAUUCGGUGAGAUUCCGGAGCCGACAGU-ACAGUCUGGAUGGGAGAAG-AUGGAGGUUCAUAAGCGUUUUGAAAUUGAAUUUUUCAAACGUUUCUUUGCCU-----AGCCUAAUUUUCGAAACCCCGCUUUUAUAUAUGAAGCGGUUUUUU

#Native functional structures from the FMN riboswitch of the ribD gene of Bacillus subtilis
UAUCCUUCGGGGCAGGGUGGAAAUCCCGACCGGCGGUAGUAAAGCACAUUUGC--UUUAGAGCCCGUGACCCGUGUGC----AUAAGCACGCGGUGGAUUCAGUUUAA-GCUGAAGCCGACAGUGAAAGUCUGGAUGGGAGAAGGAUG---AUGAGCCGCUAUGCAAAAUGUU-UAAAAAUGCAUAGUGUUAUUUCCUAUUGCGUAAAAUACCUAAAGCCCCGAAUUUUUUAUAAAUUCGGGGCUUU
((((((((......(((.......))).....((((...((((((......))--))))....))))...((((((((----....))))))))....((((((....-)))))).....(((.......))).......))))))))---......................-........................................((((((((((((((.....))))))))))))))
.....((((((((.(((.......))).....((((...((((((......))--))))....))))...((((((((----....))))))))....((((((....-)))))).....(((.......)))...............---......................-...........................................)))))))).(((....)))...........

#Predicted structures
((((((((...............(((((.(((((((....(((((...--.))--))).....)))....((((((((----....))))))))....(((((.......)))))...............)))).)))))))))))))---.......((((((((..............))))))))..........................((((((((((((((.....))))))))))))))
.....((((((((.((((....))))...(((((((....(((((...--.))--))).....)))....((((((((----....))))))))....(((((.......)))))...............))))..(((((((((((.---.........((((((..............)))))))))))))))))....................))))))))......................