Sentence:  "Claius" presently went to a Fisherman, & having agreed with him, and provided some apparrell for the naked stranger, he imbarked, and the Shepheards with him: and were no sooner gone beyond the mouth of the haven, but that some way into the sea they might discerne (as it were) a stayne of the waters colour, and by times some sparkes and smoke mounting <WSD>thereout</WSD>. 
Meaning of the word marked with <WSD> tags:  Out of it, out from it.