Table 1.

Stem-loop structures co-predicted by three different methods in nearly the same genomic regions of the SARS-CoV-2.

	Ab-initio-based method		SM-based method		BLASTN method
1	Sequences	Location	Sequences	Location	Sequences	Location
2	5′GCCUUUGGAGGCUGUGUGUUCUCUUAUGUUGGUUGCCAUAACAAGUGUGCCUAUUGGGUUCCACGUGCUAGCGCUAACAUAGGUUGUAACCAUACAGGUGUUGUUGGAGAAGGUUCCGAAGGU 3′	1498–1621	5′CUUUGGAGGCUGUGUGUUCUCUUAUGUUGGUUGCCAUAACAAGUGUGCCUAUUGGGUUCCACGUGCUAGCGCUAACAUAGGUUGUAACCAUACAGGUGUUGUU 3′	1479–1582	5′UCUUAUGUUGGUUGCCAUAACAAGUGUGCCUAUUGGGUUCCACGUGCUAGCGCUAA 3′	1499–1554
3	5′UGAACUUGAUGAAAGGAUUGAUAAAGUACUUAAUGAGAAGUGCUCUGCCUAUACAGUUGAACUCGGUACAGAAGUAAAUGAGUUCGCCUGUGUUGUGGCAGAUGCUGUCAUAAAAACUUUGCAACCAGUAUCUGAAUUA 3′	2832–2972	5′AAGUACUUAAUGAGAAGUGCUCUGCCUAUACAGUUGAACUCGGUACAGAAGUAAAUGAGUUCGCCUGUGUUGUGGCAGAUGCUGUCAUAAAAACUUUGCAA 3′	2816–2917	5′CACCACUGGGCAUUGAUUUAGAUGAGUGGAGUAUGG 3′	2884–2919
4	5′GUGAUACAUUCUGUGCUGGUAGUACAUUUAUUAGUGAUGAAGUUGCGAGAGACUUGUCACUACAGUUUAAAAGACCAAUAAAUCCUACUGACCAGUCUUCUUACAUCGUUGAUAGUGUUACAGUGAAGAAUGGUUCCAU 3′	7736–7876	5′CUGACCAGUCUUCUUACAUCGUUGAUAGUGUUACAGUGAAGAAUGGUUCCAUCCAUCUUUACUUUGAUAAAGCUGGUCAAAAGACUUAUGAAAGACAUUCUCU 3′	7715–7718	5′UUUGAUAAAGCUGGUCAAAAGACUUAUGAAAGACAUUCUCUCUCUCAUU 3′	7778–7826
5	5′AGUCUUCUUACAUCGUUGAUAGUGUUACAGUGAAGAAUGGUUCCAUCCAUCUUUACUUUGAUAAAGCUGGUCAAAAGACU 3′	7831–7911	5′UAAUAACACUAAAGGUUCAUUGCCUAUUAAUGUUAUAGUUUUUGAUGGUAAAUCAAAAUGUGAAGAAUCAUCUGCAAAAUCAGCGUCUGUUUACUACA 3′	7851–7949	5′AAAGGUUCAUUGCCUAUUAAUGUUAUAGUUUUUGAUGGUAAAUCAAA 3′	7862–7908
6	5′UAUUUUAGUGGAGCAAUGGAUACAACUAGCUACAGAGAAGCUGCUUGUUGUCAUCUCGCAAAGGCUCUCAAUGACUUCAGUA 3′	10051–10133	5′AACCACCACAAACCUCUAUCACCUCAGCUGUUUUGCAGAGUGGUUUUAGAAAAAUGGCAUUCCCAUCUGGUAAAGUUGAGGGUUGUAUGGUACAAGUAACUUG 3′	10016–10119	5′CUGGUAAAGUUGAGGGUUGUAUGGUACAAGUAACUUGUGGUACAACU 3′	10083–10129
7	5′CAGCUGAUGCACAAUCGUUUUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUAUACAGGGCUUUUGACAUCUACAAUGAUAAAGUAGCUG 3′	13660–13710	5′AGGACGAAGAUGACAAUUUAAUUGAUUCUUACUUUGUAGUUAAGAGACACACUUUCUCUAACUACCAACAUGAAGAAACAAUUUAUAAUUUACUUAAGGAUUGU 3′	13615–13719	5′AGACACACUUUCUCUAACUACCAACAUGAAGAAACAAUUUAUAAUUUACUU 3′	13660–13710
8	5′CAGCUGAUGCACAAUCGUUUUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUAUACAGGGCUUUUGACAUCUACAAUGAUAAAGUAGCUG 3′	13660–13710	5′AGGACGAAGAUGACAAUUUAAUUGAUUCUUACUUUGUAGUUAAGAGACACACUUUCUCUAACUACCAACAUGAAGAAACAAUUUAUAAUUUACUUAAGGAUUGU 3′	13615–13719	5′ACUUUCUCUAACUACCAACAUGAAGAA 3′	13366–13692
9	5′UGGCUUAUACCCAACACUCAAUAUCUCAGAUGAGUUUUCUAGCAAUGUUGCAAAUUAUCAAAAGGUUGGUAUGCAAAAGUAUUCUACACUCCAGGGACCACCUGGUACUGGUAAGAGUCA3′	17227–17348	5′GUAGUAGAAUUAUACCUGCACGUGCUCGUGUAGAGUGUUUUGAUAAAUUCAAAGUGAAUUCAACAUUAGAACAGUAUGUCUUUUGUACUGUAAA3′	17224–17318	5′GUUUUGAUAAAUUCAAAGUGAAUUCAACAUUAGAACAGUAUGUCUUUUGUACUGUA 3′	17261–17316
10	5′GAGGGUUUUUUCACUUACAUUUGUGGGUUUAUACAACAAAAGCUAGCUCUUGGAGGUUCCGUGGCUAUAAAGAUAACAGAACAUUCUUGGAAUGCUGAUCUUUAUAAGCUCAUGGGACACUUCGCAUGGUGGACAGCCUUU3′	21397–21539	5′CUUAAAUUAAGGGGUACUGCUGUUAUGUCUUUAAAAGAAGGUCAAAUCAAUGAUAUGAUUUUAUCUCUUCUUAGUAAAGGUAGACUUAUAAUUAGAGAAAA3′	21411–21512	5′GUGACUAUUGACUAUACAGAAAUUUCAUUUAUGCUUUGGUGUAAAGAUG 3′	21433–21471
11	5′AGAAUGUUCUCUAUGAGAACCAAAAAUUGAUUGCCAACCAAUUUAAUAGUGCUAUUGGCAAAAUUCAAGACUCACUUUCU3′	24646–24726	5′GUACUUGGACAAUCAAAAAGAGUUGAUUUUUGUGGAAAGGGCUAUCAUCUUAUGUCCUUCCCUCAGUCAGCACCUCAUGGUGUAGUCUUCUUG3′	24658–24751	5′CAAAAAGAGUUGAUUUUUGUGGAAAGGGCUAUCAUCUUAUGUCCUUC 3′	24672–24718
12	5′UACAUUUGGCUAGGUUUUAUAGCUGGCUUGAUUGCCAUAGUAAUGGUGACAAUUAUGCUUUGCUGUAUGACCAGUUGCUGUAGUUGUCUCAAGGGCUGUUGUUCUUGUGGAUCCUGCUGCAAAUUUG3′	25564–25691	5′CCUCAAAAAGAGAUGGCAACUAGCACUCUCCAAGGGUGUUCACUUUGUUUGCAACUUGCUGUUGUUGUUUGUAACAGUUUACUCACACCUUUUGCUCGUUGCUGCUGGCCUUGAAGCCC3′	25583–25702	5′UGUUGUUGUUUGUAACAGUUUACUCACACCUUUUGCUCGUUGCUGCU 3′	25643–25689