Situation

REF  AGCATGTTAGATAAGATAG-----------CTGTGCTAGTAGGCAGTCAGCGCCAT
READ AGCATGTTAGATAAGATAGCCCCCCCCCCCCTGTGCTAGTAGGCAGTCAGCGCCAT

Resulting alignments

Left
      0     .    :    .     
        AGCATGTTAGATAAGATAG
        |||||||||||||||||||
        AGCATGTTAGATAAGATAG


Right
      0     .    :    .    :    .  
        CTGTGCTAGTAGGCAGTCAGCGCCAT
        ||||||||||||||||||||||||||
        CTGTGCTAGTAGGCAGTCAGCGCCAT



refSplitPosition   == 19
readSplitLPosition == 19
readSplitRPosition == 30

Reference Left  AGCATGTTAGATAAGATAG
Reference Right CTGTGCTAGTAGGCAGTCAGCGCCAT

Read Left       AGCATGTTAGATAAGATAG
Read Center     CCCCCCCCCCC
Read Right      CTGTGCTAGTAGGCAGTCAGCGCCAT
