Click on "Start Application" to start the analysis. The input mask will look like Every request is associated with a unique ID number. All running processes have their specific ID and are handled in order of the submission time. The last 10 request IDs are displayed in "Select one of the last requests..." selection box. So you can easily navigate through them.

Notes

• The calculation of the results may take minutes up to hours. As long as the calculation is in process, you are redirected to a "waiting" page. It updates automatically every minute.
• Requests are kept for 30 days on the server. After this period all the data will be deleted.
• There is a limit of 100 open requests. That means that if you try to submit your data and there are 100 requests running, you will have to wait until the queue is ready to accept requests again.
• The maximum size of the coordinate file is 25MB - meaning max. 1.000.000 coordinate lines.

Field	Description
Target	The target against you wish to run. If you select a target the species and the input parameters are (re-)displayed, because they are related to the target.
Title	You may give the request a title, so you know better what is behind a specific reuest id. The title is displayed on top of the input mask.
Reference Genome Coordinates	Your query coordiantes of the form species chromosome start end comment (You can skip the comment field)
File	An input file with the genome coordinates or with local repeatmasker data.
Server RM Data	A list of species on the server providing repeatmasker data.
Input Paramters	Parameters for the request. Click on the header to swich them on or off.
Species	A list with selectable species - at least one of the species MUST be selected!

You must choose one of the following input data types: Reference Genome Coordinate, File or Server RM File.

When the request is finished, the main results page will be displayed first Note: Much of the result data is kept in your browser, locally on your own computer. So, if you send a big request with much more than 100.000 coordiantes it may be good to have much main memory (RAM) free on your computer - it can be several GB.

The navigation though you table is not done by a scrollbar. Use your mouse wheel, arrow keys (including the "Pos1" and "End" key!) or in the left menu the "Navigation" buttons.

You can sort the table rows either by the columns or by the "Sort" option on the left menu. If you would like that the table should be sorted by columns, there are 2 groups of sortable columns: (1) By coordinate, comment and annotation and (2) and by species. They are exclusive - you cannot sort by both groups together. If you click on a column header of them, the selected column will be put to the left on their group, and disabled for further selection.

The first group is sorted "lexicographic", meaning by letters. Just the coordinate is a bit different, It sorts first it sort by species, then chromosome and then the start coodinate. The latter is sorted numerically. The secord group (species) sorts by symbols and the order of the symbols is "+", "-" and then "N".

In addition to manual selection by clicking in the checkbox symbol - here you can select the rows by a starting and ending number. Selections are active till the whole table is deselected again, meaning you can selected several ranges/areas of rows.

Display the selected ranges of columns.

Export the selected rows to Excel (or Libre/Open-Office)

Download the selected rows as a text file.

Displays the fasta data for the selected rows in a separate window.

Like "Display Fasta" - but has the opportunity to write into a local file.

Displays Muscle data of the selected rows in a separate window.

Optimizes symbols for the selected rows by using muscle and samtools. Note, that the maximum of selectable rows is 1000!

Displays perfect rows of all the underlaying data

Prints the visible page

Resets the display and displays all original data again.