-- dump date 20140619_151522 -- class Genbank::repeat_region -- table repeat_region_note -- id note 410289000001 DU1, len: 29667 bases. Duplicated Region DU1. In Mycobacterium bovis BCG Pasteur, the region corresponding to Mycobacterium tuberculosis H37Rv positions:4398597-16733 (comprising the origin of replication) has been duplicated as tandem repeat at position: 4361588..16732 and 16733..46399. No difference has been found beetwen the two copies 410289000002 REP'-1, len: 315 nt. Equivalent to REP', len: 315 nt, from Mycobacterium tuberculosis strain H37Rv, (100.0% identity in 315 nt overlap). Probable pseudogene fragment, len: 105 aa; similar to many Mycobacterium tuberculosis proteins inside REP13E12 elements eg. TR:Q50655 (EMBL:Z95390) MTCY13E12.20 (317 aa), FASTA scores; opt: 324 z-score: 432.5 E(): 6.8e-17, 43.4% identity in 99 aa overlap, but no possible startsite 410289000003 REP-2, len: 1504 nt. Equivalent to REP, len: 1503 nt, from Mycobacterium tuberculosis strain H37Rv, (97.0% identity in 1504 nt overlap). REP251, member of REP13E12 family 410289000004 15 bp perfect inverted repeat, IRR, ATTCGGTGTAAGTGG, flanking IS element IS1554 410289000005 15 bp perfect inverted repeat, IRL, ATTCGGTGTAAGTGG, flanking IS element IS1554 410289000006 49 bp imperfect inverted repeat, IRL, GGGTTCAGAGCTGTTGCGTGTTGAGTGTGTTTTAGTGTGCGTTAGTGTG, flanking IS element IS1535 410289000007 17 bp perfect inverted repeat, IRL, GTTGAGTGTGTTTTAGT, flanking IS element IS1535 410289000008 49 bp imperfect inverted repeat, IRR, CCGTTGAGTGTGTTTTAGTTGCACTCTCATGCGGCGTCCCCTTTGCGGG, flanking IS element IS1535 410289000009 17 bp perfect inverted repeat, IRR, GTTGAGTGTGTTTTAGT, flanking IS element IS1535 410289000010 15 bp perfect inverted repeat, IRL, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000011 15 bp perfect inverted repeat, IRR, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000012 4 bp direct repeat, CTAG, generated by IS element on insertion. Proposed by Mariani et al. 1993. J. Gen. Microbiol. 139:1767-1772. Note that as the motif is palindromic it could be part of the inverted repeat itself 410289000013 17 bp imperfect inverted repeat, IRR, GGCGTGTCTCCCAATTT, flanking IS element. Proposed by Mariani et al. 1993. J. Gen. Microbiol. 139: 1767-1772 410289000014 17 bp imperfect inverted repeat, IRL, GGCGTGTCTCCCAAATT, flanking IS element. Proposed by Mariani et al. 1993. J. Gen. Microbiol. 139: 1767-1772 410289000015 4 bp direct repeat, CTAG, generated by IS element on insertion. Proposed by Mariani et al. 1993. J. Gen. Microbiol. 139 :1767-1772. Note that as motif palindromic could be part of inverted repeat itself 410289000016 8 bp direct repeat, TGACACCA, flanking IS element IS1081 410289000017 15 bp perfect inverted repeat, IRR, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000018 15 bp perfect inverted repeat, IRL, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000019 8 bp direct repeat, TGACACCA, flanking IS element IS1081 410289000020 20 bp imperfect inverted repeat, IRR, AGCAGACGCAAAAGCCCCCA, flanking IS element IS1557 410289000021 20 bp imperfect inverted repeat, IRL, AGCAGACGCGAAAGCCCCCA, flanking IS element IS1557 410289000022 REP-5, len: 1363 nt. Equivalent to REP, len: 1298 nt, from Mycobacterium tuberculosis strain H37Rv, (96.6% identity in 1363 nt overlap). REP336, member of REP13E12 family. 410289000023 REP-6, len: 1379 nt. Equivalent to REP, len: 1362 nt, from Mycobacterium tuberculosis strain H37RV, (65.3% identity in 1364 nt overlap). REPI125, member of REP13E12 family. 410289000024 REP-7, nt 1448. Equivalent to REP, len: 1362 nt, from Mycobacterium tuberculosis strain H37Rv, (99.9% identity in 1362 nt overlap). Member of REP13E12 family, copy REP-7 410289000025 Variable number tandem repeat region (VNTR), len: 285 nt. Contains 5 copies of 57 bp repeat, GACGACCCGGGTCGGCACGACCCGGGAAGGAACCGGGCAAATCAAGCACAGCCCGGC, there are also 5 copies in Mycobacterium bovis but only 3 copies in Mycobacterium tuberculosis H37Rv 410289000026 13 bp imperfect inverted repeat, IRR, GCAGTCGTAAAAG, flanking IS element IS1558 410289000027 13 bp imperfect inverted repeat, IRL, GCAGTCGCAAAAG, flanking IS element IS1558 410289000028 15 bp perfect inverted repeat, IRR, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000029 15 bp perfect inverted repeat, IRL, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000030 4921 bp DR, direct repeat region composed of 49 repeat_units of 36 bases pairs, one of them has been interrupted by the insertion of an IS6110 elements 410289000031 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000032 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000033 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000034 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000035 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000036 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000037 direct repeat, 35 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000038 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000039 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000040 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000041 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000042 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000043 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000044 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000045 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000046 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000047 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000048 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000049 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000050 3' part direct repeat, CCCCGAGAGGGGACGGAAAC, of sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000051 3 bp direct repeat, GGG, flanking IS element IS6110 410289000052 28 bp perfect inverted repeat, IRR, TGAACCGCCCCGGCAATGTCCGGAGACTC, flanking IS element IS6110 410289000053 28 bp perfect inverted repeat, IRL, TGAACCGCCCCGGCAATGTCCGGAGACTC, flanking IS element IS6110 410289000054 3 bp direct repeat, GGG, flanking IS element IS6110 410289000055 5' part direct repeat, GTCGTCAGACCCAAAA, of sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000056 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000057 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000058 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000059 direct repeat, 35 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000060 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000061 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000062 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000063 direct repeat, 32 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000064 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000065 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000066 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000067 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000068 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000069 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000070 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000071 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000072 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000073 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000074 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000075 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000076 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000077 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000078 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000079 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000080 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000081 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000082 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000083 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000084 direct repeat, 36 out of 36 bp identical to sequence GTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC 410289000085 5 bp direct repeat, CCGTT, flanking IS element IS1533 410289000086 54 bp imperfect inverted repeat, IRL, TGTCGACGGCACGTGAAAACTGACCCCGGCGCGGCACCCGAATTTTGACCCCCT, flanking IS element IS1533 410289000087 54 bp imperfect inverted repeat, IRR, TGTCAACGGCACCCGAAAACTGACCCCCTGACGGCATCTGAAAATTGACCCCCT, flanking IS element IS1533 410289000088 5 bp direct repeat, CCGTT, flanking IS element IS1533 410289000089 6 bp perfect inverted repeat, IRR, TGAGTG, flanking IS element IS1538 410289000090 6 bp perfect inverted repeat, IRL, TGAGTG, flanking IS element IS1538 410289000091 8 bp direct repeat, CCAGTCGC, flanking IS element IS1081 410289000092 15 bp perfect inverted repeat, IRR, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000093 15 bp perfect inverted repeat, IRL, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000094 8 bp direct repeat, CCAGTCGC, flanking IS element IS1081 410289000095 8 bp direct repeat, AGGAGGAG, flanking IS element IS1081 410289000096 15 bp perfect inverted repeat, IRL, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000097 15 bp perfect inverted repeat, IRR, TCGCGTGATCCTTCG, flanking IS element IS1081 410289000098 8 bp direct repeat, AGGAGGAG, flanking IS element IS1081 410289000099 63 bp imperfect inverted repeat, IRR, TGTCAGCGGCAACCGAAAACTGATCAGGTGTCGGCAAGGTGGTTTCTAGGCGGTGTCG C AACA, flanking IS element IS1603 410289000100 63 bp imperfect inverted repeat, IRL, TGTCGGCGGCAACTGAATACTGACCAGAGCGCGGCAAGGTGGGTTCTAGTCAACGTCG C AACA, flanking IS element IS1603 410289000101 DU2, len: 36163 bases. Duplicated Region DU2. In Mycobacterium bovis BCG Pasteur, a 99152 bp region corresponding to Mycobacterium tuberculosis H37Rv positions: 3590903..3690128 has been duplicated as tandem repeat at position: 3543385..3642536 and 3642537..3678699. An internal deletion of 62989 bp, corresponding to nucleotides 3560959..3623947 in the first copy and to Mycobacterium tuberculosis H37Rv positions: 3608477..3671539, occured in the second copy between nucleotide 3660110..3660111. There is only one diference between the 2 copies: base A at position 3557713 is replaced by G at position 3656865 410289000102 2 bp direct repeat, GT, flanking IS element IS1560 410289000103 25 bp inverted repeat, IRL, TAATTACTAGGACCTGAAAAAGTCG, flanking IS element IS1560 410289000104 25 bp inverted repeat, IRR, TAATTACTAAGACCTGAAAAAGTCG, flanking IS element IS1560 410289000105 2 bp direct repeat, GT, flanking IS element IS1560 410289000106 REP-8, len: 1393 nt. Equivalent to REP, len: 1372 nt, from Mycobacterium tuberculosis strain H37Rv, (98.8% identity in 1368 nt overlap). REP13E12, 1371 bp repeat, copies in Mycobacterium tuberculosis cosmids; cY336 from: 14471 to: 15821 (approx. 100% identity); cY251 from: 11693 to: 13109 (approx. 100% identity); cI65 from: 14515 to: 15905 (approx 75% identity); cI125 from: 27240 to: 28597 (approx. 65% Identity); cY22G8 from: 13352 to 14689 (approx. 65% identity); and cY9F9 from: 9019 to: 10451 (approx. 65% identity); also nearly identical to EM_BA :MB35021 U35021 Mycobacterium bovis BCG DNA flanking deletion region 3 from: 56 to: 1466 410289000107 49 bp imperfect inverted repeat, IRL, CGGCAACTGAATACTGACCAGAGCGCGGCAACTGAAAATTGACCAGCTT, flanking IS element IS1534 410289000108 49 bp imperfect inverted repeat, IRR, CGGCAACCGAAAACTGATCAGGTGTCGGCAATCGAAAATTGACCAGCTT, flanking IS element IS1534 410289000109 13 bp imperfect inverted repeat, IRR, GAGTTCGTCGGTG, flanking IS element IS1553 410289000110 13 bp imperfect inverted repeat, IRL, GAGATCGTCGGTG, flanking IS element IS1553 410289000111 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000112 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000113 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000114 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000115 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000116 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000117 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000118 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000119 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000120 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000121 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga 410289000122 direct repeat, 57bp sequence: tcgcgagcccggcgcagccgggcgaagcgggtcggcacgcatcggaccccgtgacga