>NC_000885.1_Tomato_chlorotic_dwarf_viroid
-CGGAACTAAA--CTCGTGGTTCCTGTGGTTC-ACACCTGACCTC----C-TGTGCAGAAAAGAAAAAA--GATAGGC----GGCTCGGAGGAGCGCTTCAGGGATCCCCGGGGAAACCTGGAGCGAACT---------GGCAAAA---GGCGGCAGGGAGCTTGTGGAAGGCGAAACAGGAGTAATCCCG-----TGTAGAAACAGG-GTTTTCACCCTTCCTTTCTTCTGC-----GGTTTCCTTCCTT-----TGCGCGCCACTCGACCCCTCGCCCCCTT-GCGCTGTCGCTTCGGCAACTACCCGGTGGAAACAACTGAAGCTC-CCGAG-----AACCGCTTTTTCTCTATCTTG---CTGCTACCGGGGCGAGGGTGTTTAGCCCTTGGAACCGCAGTT--GGTTCCT---------
>NC_001340.1_Apple_scar_skin_viroid
---GGTAAACA-CCGTGCGGTTCCTGTGGTT-CGCCCCGCCAACGCAGATAGATAAAGAAAACGAGG-AGAAGAA-------GGAACTC-----ACCTGTCGTCGTCGACGAAGG------CCGGTGAGA------------AAGGAGCTG----CCAGCACTAACCGGACGGCGCCCTCGCACCAGTTCC------GCTGTGGGT--------TCGCCT------ACAAGAACGTACGGTGTTGAGGCCCTG----------------TCCGCCGC-TGCGCTGCCACC---TACTCTCGCGCCGCTAGTCGAGCGGACTCCGGGTGGAGCCCCCTGTT---CTCTCACGCTCTTTTTCTTTGACGCAGCGGCGGGTGG-GTTCCCAG--GGTAAAAC---ACAATAGGTGTTTCCC------
>NC_001351.1_Hop_stunt_viroid
-------------------------CTGGGGAATTCTCGAGTTGCCGCAT-GGGCAAGCAAAGAAAAAACAAGGCAGG---GAGGAGACTTAC-CTGAGAAAGGAGCCCCGGGGCAACTCTTCTCAGAAT-------------CCAGCGAGAGGCGT-AGGAGAGAGGGCCGCGG--------TGCTCTG------------GAGTAGAGGCTTCTTGCTTCGAAACACCATC------GATCGTCCCTTCT-----------------TCTTTTACCTTCTCCTGGCTCTTCCGATGAGACGCGACC-GGTGGCATCACCTCTCGGTT--CGTCTTCCAACCTGCTTTTTGTCTAT-CTAAG-CCTCTGCCGCGGATCCTCTCTTGAGCCCCT------------------------------
>NC_001462.1_Coconut_cadang-cadang_viroid
------------------------------------CTGGGGAAAT-CTA-CAGGGCACCCCAAAA-ACCACTGCA-G----GAGAGGCCGCT-----TGAGGGATCCCCGGGGAAACGTCAAGCGAATC--------------TGGGAAGGGAGCGTACCTGG----GTCGAT---------CGTGCGC-------------GTTGGAGGAGA-CTCCTTCGTAGCTTCGA-------------CGCCCGG-----------------CCGCC-CCTCCTCG-----A--CCGCTTGGGAGACTACCCGGTGGATACAACTCAC---G-CGGCTCTTACCTG--TTGTTAGTAAAAAAAGGT-GTCCCTTTGTAGCCCCT-------------------------------------------
>NC_001464.1_Citrus_exocortis_viroid
-CGGGATCTTT--CTTGAGGTTCCTGTGGTGC-TCACCTGACCCTG-----CAGGCAGGAAAAGAAAAAAGAGGCG-G----CGGGGGAAGAAGTCCTTCAGGGATCCCCGGGGAAACCTGGAGGAAGTC--------GAGGTCGGGG--GGGACAGCTGCTTCGGTCGCCGCGGATCACTGGCGTCCAG------CGGAGAAACAGGAGCTCGTCTCCTTCCTTTCGCTGCT-----GGCTCCACATCCGAT---CGTCGCTGAAGCGCCTCGCCCCCTCGCCCGGAGCTTCTCTCTGGATACTACCCGGTGGAAACAACTGAAGCTT-CAACCCCA--AACCGCTTTTCTTATATCTTCA--CTGCTCTCCGGGCGAGGGTGAA-AGCCCTCGGAACCCTAGATTGGGTCCCT---------
>NC_001471.1_Coconut_tinangaja_viroid
------------------------------------CTGGGGAATT-CC--CACGGCTCGGCAAAATAAAAGCACA-A----GAGCGACTGCT-----AGAGGGATCCCCGGGGAAACCCCTAGC-AACC--------------GAGGTAGGGAGCGTACCTGGTGTCGCCGATT--------CGTGCTG-------------GTTGGGCTTCG-TCCCTTCCGAGCTTCGAT--------CCGACGCCCGG-----------------CCGCTTCCTCGCCG-----AAGCTGCTACGGAGACTACCCGGTGGATACAACTCTTT--G-CAGCGC---CCTG--TG--TAATAAAAGCTCGA-GTCCGGTTTGCGCCCCT-------------------------------------------
>NC_001553.1_Tomato_apical_stunt_viroid
-CGGGATCTTT--CGTGAGGTTCCTGTGGTGC-TCACCTGACCCTG-----CAGGCATCAAGAAAAAAGATAGGAGCG----GGAAGGAAGAAGTCCTTCAGGGATCCCCGGGGAAACCTGGAGGAAGTC--------GAGGTCGGGG--GCTTCGGATCATTCC-TGGTTGAGA--CAGGAGTAATCCC------AGCTGAAACAGG-GTTTTCACCCTTCCTTTC--TTCT-----GGTTTC-CTTCCTCT---CGCCG--GAAGGTCTTCGGCCC-TCGCCCGGAGCTTCTCTCTGGAGACTACCCGGTGGAAACAACTGAAGCTT-CCACTTCC--ACGCTCTTTTTCTCTATCTTTG--TTGCTCTCCGGGCGAGGGTGAA-AGCCCGTGGAACCCTGAAT--GGTCCCT---------
>NC_001558.1_Tomato_planta_macho_viroid
-CGGGATCTTTTCCTTGTGGTTCCTGTGGTAC-ACACCTGACCTCC-----TGACCAGAAAAGAAAAAA---GAATTG----CGGCCAAAGGAGCGCTTCAGGGATCCCCGGGGAAACCTGGAGCGAACT--------------GGCGAAGGAGTCGCGGCTGGGGAGTCTCCCAGACAGGAGTAATCCC------CGCTGAAACAGG-GTTTTCACCCTTCCTTTCTTCGG-------GTTTCCTTCCTC-----TGCGGTCGACACCCTCGCCCGCTTCTCTTGCGCTGTCGCTTCGGAGACTACCCGGTGGAAACAACTGAAGCTC-CCAAGC-----GCCGCTTTTTCTCTATCTTG---CTGGCTCCGGGGCGAGGGTGGAAAACCCTGGAACCCTTCGAAAAGGGTCCCT--------
>NC_001651.1_Citrus_bent_leaf_viroid
----CGGAGACTTCTTGTGGTTCCTGTGGTGTCACCCCTCAGCCCTACCTGCGAAAGAAAAAAGAGTTAGAAGGCGGCAGA-GGAGCTG-----ACTGGTCGTCGTCGACGAAGG------CTCGTCAGC------------TGCGGAG-G----TTGGGGTCGA--------------CTGGCCTCCGGT------GGCGAAGTTGAGCTC--TGCCTT------CTAAGCTGTAACCGGACC--GGTCCCC----------------TTCACCCG-AGCGCT---------GCTTGC-----CGCTAGTCGCGCGGACTTCAAGTCTTCCTCCCGAGC-CGCTTTTCTTTTCTCCTGATTTC-CGTAGCAGCGGGGAGAGGGTGAAGCCCCTGAACC---CTGAG----GGCTCCT------
>NC_001830.1_Pear_blister_canker_viroid
---------CTTTCCTGAGGTTCCTGTGGTG---CTCCCCTGACCTGCGTTCCAAAAAGCGAAAAAGTGAGAGGCCCTAG--GGGCTTC-----TCGGCTCGTCGTCGACGAAGG------GTC------------------TAGAAGC-C----TGGGCGCTGG--------------CTGGAGCGCGCG------GCTGTGAGTAATCGC--TCCTTT------GGAGAAGAAAACCAG--C--GTTGCTT----------------CCTGCCTG-AGCCTC---------GTCTTCTGTCCCGCTAGTCGAGCGGACAACCCGAGCACCGCCGAAGCGCTTTTTTCTTTTATAGCAGCTTGGCTTCGCGGCGAGGGTGGAAGTTTACCGCGGACCC---CCGAGAGGAGGCCCTCGGGTCC
>NC_001920.1_Grapevine_yellow_speckle_viroid_1
-CGGATCACTTTCCT-GTGGTTCCTGTGGTTACACCTCGGAAGGCCGCCGCGGACCTGCAAAGAAGAAGATAGGGGCAGAG-GGGGAGT-----GAGCCTCGTCGTCGACGAAGGGGTGCACTCCAAAGC------------TCCGAACTG--GCGTCGTCCGGCTCTCCTCGGAGCCTCGCTGCTCTGGG------CGGAAGAGTCTTCTGACTTTTCTAGC---CTATTCAGCATTGCGCTCTTGAGGC------------------CCGGCGAAACGCGGTTCGTCTGCTGAGGATGCCTCCGCTAGTCGAGCGGACTTGGTCTCTTCCGCCCAAAGCCCTTTTTCTTTCAACTGAGCTTGTTCCAACGCGC-CCCGCGAGTGCAATCCCCGGAAC-CCCTGCAAAGA--GGTCCT-----
>NC_002015.1_Chrysanthemum_stunt_viroid
-CGGGA-CTTA--CTTGTGGTTCCTGTGGTGC-ACTCCTGACCCTG-----CTGCTATAGCAAAGAAAAAGAAATG-------AGGCGAAGAAGTCCTTCAGGGATCCCCGGGGAAACCTGGAGGAAGTCCGAC----GAGATCGCGGTTGGGGCTTAGGACCCCACTCCTGCGAGACAGGAGTAATCCT-----------AAACAGG-GTTTTCACCCTTCCTTTAGTTTCC-----TTCCTCTCCTGGAGA---GGTCT----TCTGCCCTAGCCCGGTCTTCGAAGCTTC-CTTTGGCTACTACCCGGTGGAAACAACTGAAGCTT-CAACGCC---------TTTTTTTCCAACCTTC--TTTAGCACCGGGCCAGGGAGTT-AGCCCTTGGAACCTTAGTATTGTTCCCT---------
>NC_002030.1_Potato_spindle_tuber_viroid
-CGGAACTAAA--CTCGTGGTTCCTGTGGTTC-ACACCTGACCTC----C-TGAGCAGAAAAGAAAAAA--GA-AGGC----GGCTCGGAGGAGCGCTTCAGGGATCCCCGGGGAAACCTGGAGCGAACT---------GGCAAAAAAGGACGGTGGGGAGTGCCCAGCGGCCGA--CAGGAGTAATTCC------CGCCGAAACAGG-GTTTTCACCCTTCCTTTCTTCGG-------GTGTCCTTCCTCG----CGCCCGCAGGACCACCCCTCGCCCCCTTTGCGCTGTCGCTTCGGCTACTACCCGGTGGAAACAACTGAAGCTC-CCGAG-----AACCGCTTTTTCTCTATCTTA---CTTGCTTCGGGGCGAGGGTGTTTAGCCCTTGGAACCGCAGTT--GGTTCCT---------
>NC_003264.1_Citrus_dwarfing_viroid
---GGAAAACT-CCGTGTGGTTCCTGTGGGG-CACACCCCC-TTGCCGAAAATAAAACGCAGAGAGG--GAAAAG-------GGAACTT-----ACCTGTCGTCGTCGACGAAGG------CAGCTAAGT------------T-------G----GTGACG------------------CCGAGTGGAGTA------A-AGACGG-AGAG----TCTCCG------CTAGTCGGAAA--GACTC-CGCATCCT----------------CCGGCTGA-CCCGCT---------AAGCTC---GCCGCTAGTCGAGCGGACTTCAGTGAGTCGCCCTAATC---CTAATCTGTTTTTATCTA---GGCTAGAAGGGGATTGGGCCTCCAG--GGTAAAAC---ACGATTGGTGTTTTCCCC----
>NC_003463.1_Apple_dimple_fruit_viroid
GGAGGAAAACT-CCGTGTGGTTCCTGTGGGG-CACCCCCCTGCGCAAATGACTAAAAGAAAAATCAGCAGGTGAA-------GAGACTT-----ACCTGTCGTCGTCGACGAAGG------CTGGTAAGC------------CGTGACGCG----TGGAGGAGAGC-------------CCGGGTCGCGCT------CTTGGGGGTAA------CCCCTT------TGAGACTTGACC-GGTTC-----CTCT----------------CCCAC----CCTGCC---------GAGCTTCCTGCCGCTAGTCGAGCGGACTCCGGGTAGCT-CTCCGACC---CTCAGATTTTCTCTTAAG---GTCTGGCAGGGAGTGGAGCTCCCAG--GGTAAAAC---ACGATTGGTGTTTTCCCC----
>NC_003538.1_Columnea_latent_viroid
-CGGAACTAAA--CTCGTGGTTCCTGTGGTAC-ACACCTGACCCTGCAGC-CATGCAAAAGAAAAAAGAACGGGAGGG----AGAGCGCAAGAGCGGTCTCAGGAGCCCCGGGGCAACTCAGACCGAGCG---------GGGTCTC----GTGGTCGAGGGCGTTGCCCTGTTCAGACAGGAGTAATCCC------AGCTGAAACAGG-GTTTTCACCCTTCCTTTCTTCTG-------GTTTCCTTCCTCTG---CTTCAGCGGCCTCGCCCGGAACCTCTTGACCAGCGCAGGTGCTGACGCGACC-GGTGGCATCA-CCGAGTTGC-TCGAGCCTCAACCTCCTTTTTCTCTATCTTAGC-TTGGTCTCCGGGCGAGGGTGTTTAGCCCTTGGAACCGCAGTA--GGTTCCT---------
>NC_003539.1_Citrus_bark_cracking_viroid
------------------------------------CTGGGGAATTTCTC-TGCGGGACCAAATAAAAACAGCTTGTG----GAGGGAACATACCTGAAGAGGGATCCCCGGGGAAATCTCTTCAGACTC--------------GTCGAGGGGAGGGCGCCGCGGATCACTGGCGT---CCAGCACCGGA-------------ACAGGAGCTCGTCTCCTTCCTTCCATCGCTG-----GCTCCACATCCGA-----------------TCGTCGCTTCTTCCTTCGCGACCTGAGATAGAAACTACCCGGTGGATACAACTCTTGG-G-TTGTTCCTCCCAGGCTTGTTAATAAAAA-TGGC-CCGCGTTTGAGACCCCT-------------------------------------------
>NC_003553.1_Australian_grapevine_viroid
--TGGGCACCAACTA-GAGGTTCCTGTGGT-AC-TCACCGAAGGCCGCGAACGTAGGAAAGAAAAAGATAGAAAAGCTGGGTAAGACTCACCTGGCGACTCGTCGTCGACGAAGGG-TCCTCAGCAGAGC------------ACCGGCAGGAGGCGCTATGCAGGAACGCTAGGGGTCCTCCAGCGGAGGA------CTGAAGAAACTCCGGTTTCTTCTTTCACTCTGTAGCTGGAATCCCTGTTGCGCTTG----------------CTGGCGAAACCTG--CAGGGAAGCTAGCTGGGTCCCGCTAGTCGAGCGGACTCG-TCCCAGCGGTCCCAACCAGTTTTCTTT---ATCCTATTT-TTCCTGCGGGCGCCCGGTCGTGGTTACCCTGGAGCTCCCTGTTTGGA--GGCCC------
>NC_003611.1_Hop_latent_viroid
------------------------------------CTGGGGAATA-----CACTACGTGACTTACCTGTATGGTGGC----AAGGGCTCGAA------GAGGGATCCCCGGGGAAAC--CTACTCGAGC--------------GAGGCGGAGATCGAGCGCCAGTTCGTGCGCG-------GCGACCTG-------------AAGTTGCTTCGGCTTCTTCTTGTTCGCGTC---------CTGCGTGGAA-----------------CGGCTCCTTCTTCACAC-CAGCCGGAGTTGGAAACTACCCGGTGGATACAACTCTTG-----AGCGC---CGAGCTTTACCTGCAGAAGTTCAC-ATAAAA--AGTGCCCCT-------------------------------------------
>NC_003612.1_Grapevine_yellow_speckle_viroid_2
-CGGATCATTTTCCTTGTGGTTCCTGTGGTTACACCTCGGAAGGCCTCCGCGGACCTGCAGAGAAAAGAAGAAGGGCCCAGAGGGGAAT-----GAGCCTCGTCGTCGACGAAGGGGTGCATTCCGAAGA------------GCTGGCCTG--GCGTCGTCCGGCTCCCTCGACCGCACCGGAGCGCTAG---------AAAAGGTCCTCGGACTTTCTT------CTAT-CTCCGAAGCCGGTTTGAGGC------------------CCGGCGAAACGCGGGCCTGTCTCCTAAGATGCCTCCGCTAGTCGAGCGGACTTGGCCTCTTCCGCCCGAGGACCTTTTCTTTCTAATCTTGCTTGTTCCAACGAGC-CCCGCGAGTGGAATCCCCGGAAC-CCCTGCGAAAAAGGGTCCT-----
>NC_003613.1_Iresine_viroid_1
---------------CGTGGTTCCAATGGTGC-ACCCCTGACCTGC-----AATGCAAAAAGAAAAAAA--GATGGGG----CGGCGGCTACAACGCTTCAGGGATCCCCGGGGAAACCTGGAGCGAACTCGGCAAGGAGGCCTGGCGGTAGGTGCGCGGAGTCGACCGCGTAAAGACCGGAGAACTCCTCGCGGCGGAAGAAACAGGAGCTCGACTCCTTCCTTTCTGTCGCCCGCAGGACTCACCTGGCAGCGGCGTCTTCTCCGCACCCCCGCCCGCTTCCGCGCTGGTCGCTCTGGCTACTACCCGGTGGATACAACTGTAGCTT-GAAGCCCGC-CCGCCCTTTTTCTTCATTCT----TCTGCTGCGCGGCGAGGGTGGGCTTCTAAAGGAAACCCT---------------------
>NC_003681.1_Coleus_blumei_viroid_1
--------------------------TGGCTCGAACTGACTAGAACGGTT--TTAAGAAAAAGTTCTTACCTGGAG------TTGCTTACCTGGGTTCCCTGGCAGCGCTGCAACGGAATCCAGTGCC---------CACCG--------------GAGCGCCAGT------------TCGTGCGAGA-----GTTGCTTC-------------GGCTTCTTCTTCGTGGAAC------GCTCCGCGTGTACG-----------------CCTGGTGACCCGCG-------AGCGATTGCAAAGGTCCTGGTTCGCTGACCCGGTTCGAACCTCTTTTCTAAACCCTA--GTTCAGCTTAACGAGCT---------------------------------------------------------
>NC_003682.1_Coleus_blumei_viroid_2
-CGGATCATTTTC-TTGTGGTTCCTGTGGTACACCTCCGAAGGCGCGCTAGGCGAGAAGAGAGTAAATAGAGGAGA------GAGCTTACCTGGGTTCCCTGGCAGCGCTGCAACGGAATCCAGTGCC---------CACCG--------------GAGCGCCAGT------------TCGTGCGAGA-----GCCGCTTC-------------GGCTTCTTCTTCGCGGAAC-----GGCTCCGCGTGTACG-----------------CCTGGGACCCCGCG-------AGCGATTGCAAAGGTCCCGGTTCGCTCTCCTTTTCTTTTTTACCTACTTCAG-CCGACCGCCCCGGGGAGTGAATCACCCGGGACCGCGA--AAAGCGATCCT------------------------------
>NC_003683.1_Coleus_blumei_viroid_3
-CGGATCATTTTCCTTGTGGTTCCTGTGGTACACCTCCGAAGGCGCGCTCGGCGAGAAGAGAGTAAATAGAAGAGA------GAGCTTACCTGGGTTCCCTGGCAGCGCTGCAACGGAATCCAGGGCGTTGG-----CCCCGATGGAGTTTCCGATGAGCACCGGTGAGAAGAAACTGTCTCGCAGAATAGAAGTCTCTTCTTGTTTGCTTTGAGACTTCTTCTCCACAGGGCTCTTCGGCTCTTCGCGGGTA-----------------CCCAGCAACCTGCTCCCACGCGGCGATTGCAAAGGACCCGGTTCGCTCTCCTTTTCTTATTTACCTGCTTCAGACCGACCGCCCCGGGGAGTGAATCACT-GGAACCGCGAGAAAAAGGATCCT------------------------------
>NC_004359.1_Citrus_viroid_VI
-GGAGGAAACT-CCGTGTGGTTCCTGTGGGT-CACCCCCCGGTTCCCTCTAATGAA----AAGAAAG--GCAAGG-------AGAACTC-----ACCTGTCGTCGTCGACGAAGG------CATGTGAGC------------TTCCACTCG----ATGAAGAGCGTCAGCGGACGGCCTCTGAGACGAGCG------ATGGACAGTAGAGCTCGTCTCTA------CCAGTCGCGTGCTGACTCTCACGCCCA----------------CCCGCACG-GCTGCTCCGAGGGAGGGGCTCTCTGCCGCTAGTCGAGCGGACTA-ACAGAGTGACTCC---C---CTGCCCTATTTTCTACGG---AGC--ACCGGCGGTGGAGTCCCCAG--GGTAAAAC---ACGATTGGTGTTTCCCC-----
>NC_010165.1_Citrus_viroid_V
-TGGGTGAACAACCTTGTGGTTCCTGTGGGT-CACCCCGCCC-CACGGAATAATAAAAGCA--GAGG-AGTAGAG-------AGTACTC-----ACCTGTCGTCGTCGACGAAGG------CCGGTGAG---------------------------CAGTA--AGCCGGACGGTCCCCTCGCGGCCGATCC------TCTG-GAGC--------TCTGCT------CTAAGATCTT-CGCTGCTGAGGCCCGC----------------GCCGCCGC-T----------------CTTCCGCGCTGCTAGTCGAGCGGACGTTGGT--GGTCTCCCTCTC---CCTGTGCAATAAAATCCA-------GGTGGCGAGTGGTGTCCCCAG--GGTAAAAC---ACGATTGGTGTTCTCCC-----
>NC_011590.1_Pepper_chat_fruit_viroid
-CCGGATTCTT--CTAAGGGTGCCTGTGGTGCCTCCCCCGAAGCC------CGCTTAGGGAAAAAGAAA----GGGGA----AGCAAGCATCTCCTGTTCAGGGATCCCCGGGGAAACCTGAACAGATCG--------------GGCGGAGAAGCGCCGTGCGGGTCCGTCTTCTGACAGGAGTAATCCC------CGCTGAAACAGG-GTTTTCACCCTTCCTTTCTTCGG-------GTTTCCTTCCTCA-----GTCGACCGGACCGCGTCGGCCTTCTCGCGCA-CTTCTGTTCGGAGACTACCCGGTGGATACAACTGACAGAG-GTGCT-----------TTTTCTTCCACCCTGCT-TCTACCGACGCGGCCGGGAGTGAAGCTACCCGGGACCCGAGA--GGATCT----------
>NC_020160.1_Dahlia_latent_viroid
-----CAGGTCTTCTAAGGGTTCCTGTGGTGCCTCCCTCCAAGGCCGCGTAGGGAAAGAAAAAGTGAAAGAAAGTGTACCTGAAGAGAGAGAGACTCTCTGAGGAGCCCCGGGGCAACTCCGAGAGTGCT-------------GCGGCAGGAGGAGCCGGGGGCGGAGGTTGTCT--------CGCTCTT------------GAG----AGCTCCGCTCCTTGTAGCTTTGA-------GACTACCGCCCTT-----------------TTGCTTCCTTCTCGCTGGCTGACTCGA--GGACGCGACC-GGTGGTA-CACCAAGAGGTCTCCACCTCCTAGGGTACTTTTTTCTAACACCGAT-TCCGTACCGAGCGCCGGAGAGTGAAGCGCCCAGGGCTCCAAAGAAGCCC-----------