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:
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?
Code:
>tRNA-Gln-CAA tRNA Vertebrata ggtcccatggtgtaatggttagcactctggactttgaatccagcaatccgagttcgaatctcggtgggac ctcca >tRNA-Gln-CAA_ tRNA Vertebrata taggacatggtgtaataggtagcacggagaattttgaattctcaggggtaggttcaattcctatagttct
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?
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