Gene Sequence Tag Alignment Legend
All alignment images are generated independently of one another.

Top of image

|     |	Ticks represent intervals of 200 bases.

Gene line

	A horizontal black line denotes the length of the gene in the alignment. The name of the gene is located on the left-hand side of this line.
	Magenta shows the coding sequence (CDS) region of the gene.
	Green shows that the CDS region of the gene has incomplete information, such as uncertain start and/or stop locations.
	A vertical white line in a colored section denotes a gap position generated by the alignment process.

CDS by exons line
     The offset representation shows the locations of genomic segments of the gene.
     This representation is meant to make the location of possible exon boundaries visible.

	Cyan represents genomic sequence outside of the CDS, such as 5' and/or 3' UTR regions.
	Blue represents genomic sequence inside of the CDS and shows possible exon boundaries.
	A vertical white line in a colored section denotes a gap position generated by the alignment process.

Sequence tag lines
     The sequence tag name is located on the left side of the image.
      A name containing (R) denotes a reverse complemented tag.

	Red denotes the location of a sequence tag in the alignment.
	A red enclosed white space represents that portion of the cell line not used in the displayed alignment:

			represent areas outside the gene.
			represent areas within the gene.
			represent areas that are at the boundaries of the gene and extend beyond.

represents areas between displayed sections.

	A vertical black line denotes a mismatch position in the alignment between the gene and sequence tag sequences.
	A vertical purple line denotes an insertion position in the sequence tag that generates a gap in the gene sequence shown in the alignment.
	A vertical white line in a colored section denotes a gap position generated by the alignment process.