They are troop transport ships to transport your troops to destinations which have deep water (dark blue) between you and that destination. you need a city with a sea port to build a dock to make them (for a city to have a sea port, it must be 1 cell away from deep water and the city info, given by the mouse-over, must say the city has a sea port). To build a dock in a sea port city, you need a 2x2 water terrain in your city to build the dock.