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  • Repeats named with trailing underscore eg. ID4 vs ID4_, tRNA-Gln-CAA vs tRNA-Gln-CAA_

    I'm looking for repeats in my mouse ChIP-seq data using RepBase and RepeatMasker. I've downloaded the repeat information and found some repeats with the same names except one version has a trailing underscore and one does not. In RepBase a bunch of the tRNA repeats are like this, the two versions having different consensus sequences, for example:

    Code:
    >tRNA-Gln-CAA	tRNA	Vertebrata
    ggtcccatggtgtaatggttagcactctggactttgaatccagcaatccgagttcgaatctcggtgggac
    ctcca
    >tRNA-Gln-CAA_	tRNA	Vertebrata
    taggacatggtgtaataggtagcacggagaattttgaattctcaggggtaggttcaattcctatagttct
    Another example, RepeatMasker has both ID4 and ID4_ while RepBase has just ID4_.

    Do these underscores mean something specific or are they just repeats that are similar so whoever was in charge of naming them just decided to name them like this?

  • #2
    The best way to find out for certain would be to email the people at RepBase and ask because it does not appear to be documented on their website, and it isn't clear from the annotation files. I would be very interested to know what this means, so please post the answer if you find out what the trailing underscore indicates.

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