Absolute hits are the number of oligos which occur in the source sequence and in the targeted sequences (i.e. in the relatives of the source sequence).
If an oligo occurs multiple times in source or target sequence, it only creates the minimum number of hits (e.g. if it occurs twice in source and three times in a target, only two hits will be counted for that target).
The theoretical maximum for absolute hits is
maxhits = minimumBasecount(source, target) - oligolen + 1
In practice that value is rarely or never reached because several oligos are skipped, namely all oligos containing IUPAC codes, N's or dots. The PT-server as well will not report matches hitting ambiguous positions or sequence endings.
The number of absolute hits is as well affected by other parameters:
using quick search will only produces around 25% of the hits as using complete search (assuming that 25% of all oligo starts with an 'A')
searching for complement or reverse will duplicate the number of possible hits. Searching for all 4 reverse/complement-combinations will produce 4 times as many hits as a plain forward search.
The relative score is absolute hits scaled versus a maximum POC (possible oligo count). You can specify which maximum POC to use with the selection button next to the score selection button:
to source POC maximum possible oligos in source
to target POC maximum possible oligos in target
to minimum POC minimum possible oligos in source or target
to maximum POC maximum possible oligos in source or target
'to source POC' will report ~100% score for partial source versus all full sequences containing the part.
'to target POC' will report ~100% score for all partial target sequences which are contained in the source sequence.
'to minimum POC' will report ~100% score if source is part of target or vice versa (this was the default method in previous ARB versions).
'to maximum POC' will report ~100% score if source and target contain each other, i.e. if they have an identical oligo distribution. If either source or target is missing some bases, the score will lower.
When using 'quick search mode' the max. relative score will be 25% (if 25% of the oligos start with 'A').
When searching for forward and reverse-complement, the theoretical max. relative score will be 200%. In practice it won't find much hits on the reverse-complement strand. So you'll get similar scores as without reverse-complement, but especially if you lower the oligo size, you'll probably reach scores above 100%.
The EDIT4 aligner currently always uses 'to minimum POC'.