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You can see here that there is very little (or indeed any) overlap which is why there is a gap. Gaps cause the stitcher to go mad which is why this pano is so large (and presumably took forever to blend and to upload). Could it be that your gigapan unit is not calibrated correctly?
The snapshot area you've picked out is actually where I removed complete row from, to try and reduced it from a full 360 just to try and get it to upload and see what happened, but there are other "breaks", more work needed, a lot more work needed, oh dear!
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