Base Position Track Settings
Genome Base Position   (All Mapping and Sequencing Tracks)

Display mode:   

 Show ruler

 Show scale bar

 Show assembly next to scale bar

Zoom factor:  1.5x    3x    10x    100x    base   

Motifs to highlight:   (Comma separated list, e.g.: GT,AG for splice sites)

 Show reverse complements of motifs also

Options for slides and presentations:


Display:   assembly   position


The Base Position feature in the Genome Browser annotations track image shows the genomic coordinates of the displayed region and -- when zoomed in to the base level -- the base composition of the sequence underlying the annotation tracks display. To quickly zoom in to the base level, click the base zoom-in button. The base button may also be used to automatically zoom the window to maximize the base display when the image is resized. Click the arrow to the left of the base display to show the base complement. To toggle between dense and full display mode, click anywhere on the base composition line.

In dense display mode, clicking anywhere on the genome coordinate line will zoom-in the display, centered on the coordinate of the click. The degree of the zoom may be configured through the Zoom configuration buttons (the default is 3X). In full display mode, the track shows three frames of translation when viewed at the base level. Methionines (including potential start codons) are displayed in green and labeled "M". Stop codons are colored red and labeled with "*". Codons within or on the boundaries of gaps, or at the ends of the chromosome, are colored black and labeled with an "X" to indicate an error (e.g. a truncated codon). All other codons are shown in alternating shades of gray to indicate codon boundaries and are labeled by the amino acids they represent. To view the translation on the reverse strand, click the arrow to complement the base display.

To add a title to the top of the display browser display image, enter the text in the Title textbox. To display the name and date of the assembly, check the Assembly checkbox. To display the position and chromosome, check the Position checkbox.