Identifying JCVI watermark sequences in mycoides using GEvo

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Region Notes
Annotation talks about how a piece of e. coli made it into this area. Not the greener region (GC rich). When that sequence is extracted and blasted against E. coli, get a very high quality hit (95%). http://genomevolution.org/CoGe//CoGeBlast.pl?chr=contig_sMmYCp235-1&upstream=308819&downstream=309545&dsid=59166&rc=0&gstid=1
http://genomevolution.org/CoGe//SeqView.pl?dsid=59166&chr=contig_sMmYCp235-1&start=389504&stop=390368&gstid=1. There is an obvious "new thing" that is annotated as a hypothetical protein predicted by glimmer. Gene it replaces is a transposon (which wouldn't be missed). This sequence does not match anything in K12 MG1655. Its sequence, when 6-frame translated, yields one frame that contains several "CVI" amino acid sequences. This sequence hasn't been seen in other aa sequences from this genome. Obvious email/web address did not jump out.
http://genomevolution.org/CoGe//SeqView.pl?dsid=59166&chr=contig_sMmYCp235-1&start=565568&stop=566608&gstid=1 . Did not match anything in E. coli. No obvious words. Disrupted (removed) WT ABC transporters.
http://genomevolution.org/CoGe//SeqView.pl?dsid=59166&chr=contig_sMmYCp235-1&start=725610&stop=726650&gstid=1 . Did not match anything in E. coli. Did contain VCI. Interrupted WT "Type III restriction-modification system is named MmyCI"
http://genomevolution.org/CoGe//SeqView.pl?dsid=59166&chr=contig_sMmYCp235-1&start=958651&stop=959707&gstid=1 . Did not match anything in E. coli. Did contain VCI. Interrupting a WT transposon. Hit nothing else in NCBI NR database.