Fixed two bugs in one place: base Alignment/Block - realign used to cut sequence tails if the new alignment was wider than the existing one - any block modification that added new columns used to forget to add the columns to the alignment AFAIR, currently the only such modifications are IO, append_*, and realign() To fix it I've: - changed realign to use _pad_to_width() same as IO used, - and changed _pad_to_width() to behave in a blocks-safe manner: it now calls self._append_columns(), which in case of blocks calls itself recursively to add columns to parent too.