Figure 2

Schematic explanation of the re-aligning processes. ReAlignerV retrieves the local alignments that are produced by bl2seq in decreasing order of the bit scores. Colored blocks represent the same-direction locally aligned portions. The number above each block indicates the order of the degree of bit score. ReAlignerV adopts blue blocks and discards red and yellow ones to construct the resultant alignment. The scheme illustrated here shows the case where the noncoding sequences immediately upstream of the start codon were used to assess the specificity and robustness to TEs for the 1,490 8-kb trio orthologs.