<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">This is the RepBase entry (from this file …/RepeatMasker/Libraries/RepeatMasker.lib) —><div class=""><br class=""></div><div class=""><div class="">>RLG_scAle_3_1-LTR#LTR/Copia @Saccharum_hybrid_cultivar [S:] RepbaseID: RLG_scAle_3_1-LTR</div><div class="">tgttagaagattatgttaatatcttctgtataaggtaggggatctgtgtg</div><div class="">accacgagatccggtggattggcttgcaagtcaagttgtaatctatgtaa</div><div class="">atctaaccttcttgttgtacaagcccaaggggctatatattaacatgtac</div><div class="">cgagtacctgagaggtatctcgttccatctatttctaca</div></div><div class=""><br class=""></div><div class="">There are 64 RLG entries associated with Copia in the RepBase library for RepeatMasker. I’m not a repeat expert, so I can’t address whether this is an error or not. But if you think there is something amiss, you could contact RepBase.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 2, 2017, at 8:19 AM, Matt Simenc <<a href="mailto:mcsimenc@gmail.com" class="">mcsimenc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">TE Superfamily RLG are aka Gypsy, but RLG is associated with Copia annotations in our RepeatMasker annotations. Has anyone else seen this before?</div><div class=""><br class=""></div><span style="font-size:12.8px" class=""><div class=""><span style="font-size:12.8px" class=""><br class=""></span></div>Azfi_s0077</span><span class="gmail-m_-8372810666362642339Apple-tab-span" style="font-size:12.8px;white-space:pre-wrap"> </span><span style="font-size:12.8px" class=""> repeatmasker</span><span class="gmail-m_-8372810666362642339Apple-tab-span" style="font-size:12.8px;white-space:pre-wrap"> </span><span style="font-size:12.8px" class="">match</span><span class="gmail-m_-8372810666362642339Apple-tab-span" style="font-size:12.8px;white-space:pre-wrap">
</span><span style="font-size:12.8px" class="">1400976</span><span class="gmail-m_-8372810666362642339Apple-tab-span" style="font-size:12.8px;white-space:pre-wrap"> </span><span style="font-size:12.8px" class="">1401715</span><span class="gmail-m_-8372810666362642339Apple-tab-span" style="font-size:12.8px;white-space:pre-wrap">
</span><span style="font-size:12.8px" class="">521</span><span class="gmail-m_-8372810666362642339Apple-tab-span" style="font-size:12.8px;white-space:pre-wrap"> </span><span style="font-size:12.8px" class="">+</span><span class="gmail-m_-8372810666362642339Apple-tab-span" style="font-size:12.8px;white-space:pre-wrap">
</span><span style="font-size:12.8px" class="">.</span><span class="gmail-m_-8372810666362642339Apple-tab-span" style="font-size:12.8px;white-space:pre-wrap"> </span><span style="font-size:12.8px" class="">ID=Azfi_s0077:hit:59234:1.3.0.</span><wbr style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">14;Name=species:</span><b style="font-size:12.8px" class="">RLG_scAle_3_1-</b><wbr style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">I|genus:LTR%252FCopia;Target=</span><wbr style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">species:</span><b style="font-size:12.8px" class="">RLG_scAle_3_</b><span style="font-size:12.8px" class="">1-I|genus:</span><b style="font-size:12.8px" class=""><wbr class="">LTR%252FCopia</b><span style="font-size:12.8px" class="">1522 2556 +</span><div class=""><span style="font-size:12.8px" class=""><br class=""></span></div><div class=""><span style="font-size:12.8px" class=""><br class=""></span></div><div class=""><br class=""></div><div class=""><span style="font-size:12.8px" class="">Matt Simenc</span></div></div>
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