Three data sets providing assistance and guidance of data processing using Kmasker plants. Also, we perform a comparison of Kmasker plants functionality with the KAT tool. This DOI holds input and output data of this analysis. Example_1 uses an Aegilops speltoides dataset and results show that tested repeat sequences have B chromosome origin. Example_2 uses the winter barley specific gene VRN-H2 and results show that it is absent in spring barley cultivar Morex. Example_3 uses the full barley gene set and compares winter and spring barley presence/absence. Related commands and updates of this tutorial are provided on GitHub in the tutorial section of Kmasker plants. For the most recent version of this tutorial please have a look to the project page (https://github.com/tschmutzer/kmasker).