Repeat annotation of Linum trigynum

The detection of the repeats has been done with RepeatMasker/RepeatModeler (https://www.repeatmasker.org/) using a custom repeat library.

The genome has been deposited to ENA with the accession id: GCA_964030455 (Project PRJEB67577). See link below.

It is part of this article: Gutiérrez-Valencia, J., Zervakis, P. I., Postel, Z., Fracassetti, M., Losvik, A., Mehrabi, S., ... & Slotte, T. (2024). Genetic causes and genomic consequences of breakdown of distyly in Linum trigynum. Molecular Biology and Evolution, msae087. https://doi.org/10.1093/molbev/msae087

Example of the data:

1306 15.6 6.2 0.0 HSU08988 6563 6781 (22462) C MER7A DNA/MER2_type (0) 336 103

1306 = Smith-Waterman score of the match, usually complexity adjusted. The SW scores are not always directly comparable. Sometimes the complexity adjustment has been turned off, and a variety of scoring-matrices are used.

15.6 = % substitutions in matching region compared to the consensus

6.2 = % of bases opposite a gap in the query sequence (deleted bp)

0.0 = % of bases opposite a gap in the repeat consensus (inserted bp)

HSU08988 = name of query sequence

6563 = starting position of match in query sequence

7714 = ending position of match in query sequence

(22462) = no. of bases in query sequence past the ending position of match

C = match is with the Complement of the consensus sequence in the database