He said, "We know from the journals that flags were hoisted from camps along the trail and presented to tribes. But what exactly did these banners look like? This question seems like a no brainer at first. However upon closer inspection things are not so clear, despite the fact that the Star Spangled Banner (with 15 stars and 15 stripes) is displayed at virtually every state and national Lewis and Clark Trail site."
After a discussion of several possibilities he postulated, "The Lewis and Clark Expedition was a US Army mission with active army officers and men in uniform. The historically logical assumption would be that the Expedition carried the US Army blue flag, if it carried an expedition flag at all. It defies logic that the Expedition would post one flag and then hand out Indian Presentation Flags of another design. The tribes would want a copy of what they saw flying as the official flag of the soldiers." He continues with, "So, the leading possibility would be that the Expedition hoisted in their camps the Lewis and Clark Indian Presentation Flag. This flag would probably have been a flag with a rather elongated field of 15 alternating stripes and 17 stars with a canton of the US Army flag."
The flag he had on display representing what he described looked very much like the one held locally (at Great Falls) by the Gopher family.