This section can be used to find out frequencies of 5 to 15 letter nucleotide sequences in non-coding segments of the Arabidopsis genome. Following non-coding segments are queried:
5'UTR3'UTRIntronCore promoterProximal promoterDistal promoterWhole genome
Core, proximal and distal promoter regions make up 3000 bp upstream region of a gene.
This section can be used to compare word frequencies between user's sequence and pre-calculated non-coding Arabidopsis genome segments (currently we support only word length 8 for frequency calculations in this section).
User can paste 1) raw sequence, 2) AGI numbers or 3) genomic coordinates
In case of AGI numbers, the segment from which sequences are to be extracted is selected (e.g. all 5'UTR segments from selected genes). In case of genomic coordinates, Arabidopsis genome release should be selected (default is TAIR9).
At the bottom of the form, a non-coding segment should be selected to compare word frequencies against.