Read1 ACCGAG Read2 ACCGAG Read3 AC*GAG Read4 ACCGAG Read5 AC*GAG Consensus AC-GAG
Now we have a more complex case. Two disagreements out of five readings. Care
should be taken to check these traces. Also note the strand of each reading.
If the database is highly repetitive, and Read1, Read2, and
Read4 are all from one strand, with Read3 and Read5 from
the opposite strand then there is a chance that a misassembly has occurred or
that the problem is a strand dependent sequencing artifact.
Typically this is clear when using the "Highlight disagreements" mode. See section Highlight Disagreements. By selecting this mode and by also highlighting the reading names (see section The sequence names display) scanning along the contig will quickly show whether there are other disagreements in common with these two readings versus the other three (which would support the evidence of misassembly).
If any misassembled readings have been spotted then mark them for disassembly (see section Remove Readings) and they'll no longer cause conflicts in the consensus. If the problem is a simple case of needing to edit, then making the edit in the consensus will require only one key stroke instead of the two needed to edit the individual readings.