Inferred VCF ref for a PRG does not match a start-to-end PRG path

[leoisl]

This is a minor issue. It can be described as inferring a VCF ref from a PRG, and then using this VCF ref for subsequent pandora map/compare, and pandora complaining that it does not match the PRG, e.g.:

[2023-01-14 13:04:25.770326] [0x0000145b453cd700] [warning] Input vcf_ref path did not start/end at the beginning/end of PRG CP050286.1_00072.fa.msa
[2023-01-14 13:06:17.166907] [0x0000145b4e711700] [warning] Input vcf_ref path did not start/end at the beginning/end of PRG CP033559.1_00077.fa.msa
[2023-01-14 13:06:22.984843] [0x0000145b4e30f700] [warning] Input vcf_ref path did not start/end at the beginning/end of PRG NZ_CP042833.1_00216.fa.msa

This is happening in roundhound (see https://github.com/LeahRoberts/roundhound/issues/86), but is a minor issue because it just affects 3 genes. I suspect this might be related with a deletion at the start of the first site, but might be wrong. As it is minor, we decided not to fix this right now. However, data to reproduce this follows:

VCF ref:

>CP050286.1_00072.fa.msa
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG

PRG:

PRG:
>CP050286.1_00072.fa.msa
 5  7  8 ATGGACGCTCCGGACT 7 ATGGGAAACAGGTCAACTTC 9 GCGGACGGTCCGGACTA 10 ACGGGCGGCCGGGAGTG 9 TGGGAAACAGGTCAACTTC 11 A 12 G 11 CGGGCGGC 13 CGGAG 14 CGGGAG 14 CGGGAC 13  6 ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTTATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAG 6 G 5 TGTGGGG 15 A 16 G 15 ACAGGTCAACTT 17 CGCGGACG 18 TACGGACT 17 GCCCGGACT 19 ATG 20 GTG 20 AT 19 GGAAACAGGTCAA 21  23 C 24 T 23 TTCGCGGGCGGCCGGGACTGTGGG 22 CTTTACGGACGGCCCGGACTATGGC 21 AAACAGGTCAAC 25 TTTA 26 TCCG 26 TTA 25 CGGACGGCCCGGACT 27 ATGGC 28 GTGGG 27 AAACAGGT 29  31 CAAC 32 CA 31 TCCGCGGA 33 CG 34 C 33 GCGCGGACTG 30 TAACTTTGCAGACGGCCCGGACTA 29 TGGGAAACAGGTCAACTCCGCGGACGGCCCGGACT 35 ATGGGG 36 GTGGGA 35 AACAGGTCAACT 37 TTGCAGACGG 39 CCG 40 C 39  38 ACGCGGACGGCCC 37 GGACTATGGGAAACGGGTCAACTTTGCAGACGGC 41 CCGGACTATG 43 GG 44 G 43  42 GCGGACTGTGGGA 41 AACAGGTCAACT 45  47 CCGC 48 CCGCGT 47 GGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTC 49 CG 50 C 49  46 CCGCGGACGGCCCG 46 ACGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCG 45 GACTATGGGAAACAGGTCAACT 51 CCGCGGACGG 53 CCCG 54 TCCG 53  52 TTGCAGACGGCCGG 52 CCGCGACGGCCC 51 GACTATGGGAAAC 55 AGGTCAAC 57 TCCGCG 58 TCGCG 57  56 GGGTTATCTTTGCA 55 GACGGCC 59  61 C 62 T 61 GGACTATGGGAAA 63 A 64 C 63  60 CGACTAGGGAAA 59 AGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGG 65 C 66 T 65 CAACTTTGCAGACGGCC 67 G 68 C 67 GGACTGTGGGAAACAGGT 69 C 70 A 69 AACTACGCAGACAGCCGGGA 71 T 72 A 71 TGTGGGAAA 73 CAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGT 75 T 76 TC 75 CCCCCATATGTCAGCAACAAACTA 77 AGGGGGAGGGAAAATAA 78 A 77  74 CAGGTCAAGTTAG 74 TAG 73

MSA

>CP050286.1_00072
ATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCATATGTCAGCAACAAACTAAGGGGGAGGGAAAATAA
>CP052145.1_00048
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_AP022115.1_00041
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGGGACAGGTCAACTTTACGGACTGCCCGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCCCGGACTGTGGGAAACAGGTTAACTTTGCAGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTGTGGGAAACAGGTCAACTACGCGGACGGCCCGGACTATGGGAAACGGGTCAACTTTGCAGACGGCGCGGACTGTGGGAAACAGGTCAACTACGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTTATCTTTGCAGACGGCCCGGACTATGGGAAACAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGTCAACTTTGCAGACGGCCCGGACTGTGGGAAACAGGTAAACTACGCAGACAGCCGGGAATGTGGGAAATAG
>NZ_CP018455.1_00044
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_CP023934.1_00066
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_CP025463.1_00050
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_CP026133.1_00056
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA
>NZ_CP034125.1_00095
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_CP034322.1_00072
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCTGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA
>NZ_CP040535.1_00227
ATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGAAACAGGTCAATTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTACGGACGGCCCGGACTATGGCAAACAGGTCATCCGCGGACGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGAACAGGTCAACTCCGCGTGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGACTATGGGAAACAGGTCAACTCCGCGACGGCCCGACTATGGGAAACAGGTCAACTCGCGGACGGCCCGACTAGGGAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA
>NZ_CP054734.1_00106
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA
>NZ_CP063835.1_00125
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_CP064253.1_00005
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTTATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_MH263653.1_00121
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_MH643787.1_00069
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA
>NZ_MH643792.1_00135
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_MK036888.1_00125
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_MK312241.1_00102
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTTATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_MK312247.1_00086
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_MK312249.1_00087
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA
>NZ_MN182746.1_00120
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA
>NZ_MN823986.1_00097
ATGGACGCTCCGGACTATGGGAAACAGGTCAACTTCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTTCACGGGCGGCCGGGAGTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAG
>NZ_MT232812.1_00012
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA
>cpe010_5_00027
GTGTGGGGAACAGGTCAACTTCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTTCGCGGGCGGCCGGGACTGTGGGAAACAGGTCAACTTTACGGACGGCCCGGACTATGGCAAACAGGTCAACTCCGCGGACGGCGCGGACTGTGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGGAACAGGTCAACTTTGCAGACGGCCGGGACTATGGGAAACGGGTCAACTTTGCAGACGGCCCGGACTATGGGAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGTCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAACAGGTCAACTCCGCGGACGGCCCGGACTATGGGAAAAAGGTCAACTTTGCAGACGGCCCGGACTATGGGAAACAGGCCAACTTTGCAGACGGCCGGGACTGTGGGAAACAGGTCAACTACGCAGACAGCCGGGATTGTGGGAAACAGGTCAAGTTAGGCAAGCACTATGGGAAATACAGCAAGTTTAGTTCCCCCCATATGTCAGCAACAAACTAA