For instance, suppose that one of the alignments computed for your two sequences begins as follows. In this portion of the alignment, there are three gap-free pieces. This would be depicted in the pip by three horizontal line segments that indicate the positions in the first sequence and the percent identity. Icons along the top of the box have the following meanings. White pointed boxes are L1 repeats.
Black triangles are MIRs.
Black pointed boxes are LINE2s. Dark gray triangles and pointed boxes are other kinds of interspersed repeats, such as LTR elements and DNA transposons. Error messages begin with lines indicating how far the computation proceeded, and should end with a line explaining the cause of the failure. Normally, the email message should be sent within a few minutes of your submission. However, it is possible that your email program might refuse to accept the message from PipMaker in cases where a huge amount of output is produced.