With the constraint from gravitational wave emission of a binary merger system(GW170817)and two-solar-mass pulsar observations, we investigate the r-mode instability windows of strange stars with unpaired and color-flavor-locked phase strange quark matter. Shear viscosities due to surface rubbing and electron-electron scattering are taken into account in this work. The results show that the effects of the equation of state of unpaired strange quark matter are only dominant at low temperature, but do not have significant effects on strange stars in the color-flavor-locked phase. A color-flavor-locked phase strange star,which is surrounded by an insulating nuclear crust, seems to be consistent with observational data of young pulsars. We find that an additional enhanced dissipation mechanisms might exist in SAX J1808.4–3658.Fast spinning young pulsar PSR J0537–6910 is a primary source for detecting gravitational waves from a rotating strange star, and young pulsars might be strange stars with color-flavor-locked phase strange quark matter.
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