I would like single regex as, as was pointed out, the double regex is wasteful since the matching has to be done twice. Also I think it would be better from readability point of view :).

However you example 1 while s/(?<=\+)([0-9]+)[$bases]/$1 - 1/eg; doesn't quite work. I'm trying to remove all the numbers and the associated bases for it. Running yours left strange things in it (+-1 and +0 below).

..G..C...G.,,,...G,G,G...G,G...GG,.G.G...G.G.....G..G,........G....,GG
+GG.,,,..G...,,.G.G..G..G..G.G.GG..GG.G..,,G,
,CG,G,GG..GG.G.GGGG,,..GG...G.,G.GG.,G,G....,,.GGGGGG.GCG..G,,G,.G..G,
+,,G,.GGGG.,..G...,,,,G,,G..GGGGA.,,,,,.+-1.G.,,G,.
..G..GG,.G....+0..GG..G,,G,,G.G,,.,,,.,,.CG.,,,,.,..G.,,,.,.,,GGGGGG,,
+.....G..GGGGG.,.G,,GG.G..GG,,,....,.,..,G.,.,,,.,,
,,G,,,.,.,..,.,,,...GG,.,G.,G......,,,..,,........,..,.,,.,...,,..,.,C
+,..,,,.,,,,,....,,..,,,.,.....,.,,.,...,,.,,,-1a.,,,,,.,,,,,,..,.....
+.....,,,,,.,...,,.,,,.,,.,,,,,,
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Edit: I think adding /c in the match pattern should fix the problem with my while and possibly the (??{...}) version as well?