In this work we study the r-mode instability windows and the gravitational wave signatures of neutron stars in the slow rotation approximation using the equation of state obtained from the density dependent M3Y effective interaction. We consider the neutron star matter to be βequilibrated neutron-proton-electron matter at the core with a rigid crust. The fiducial gravitational and viscous timescales, the critical frequencies and the time evolutions of the frequencies and the rates of frequency change are calculated for a range of neutron star masses. We show that the young and hot rotating neutron stars lie in the r-mode instability region. We also emphasize that if the dominant dissipative mechanism of the r-mode is the shear viscosity along the boundary layer of the crust-core interface, then the neutron stars with low L value lie in the r-mode instability region and hence emit gravitational radiation.