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Searching The By sequence option uses a string search tool to return all positions in the set of genomic regions that match the given stringsstring(s). The string match is case insensitive, meaning if you search for ATCG, you may get atcG as a match. Nucleotides that are lower case have been "repeat masked", meaning they are located in a repetitive region of the genome. Your search string may contain any of the characters from the IUPAC nucleotide code . For example, if you search for WAAA, you  may get back AAAA or TAAA (or any variation of upper and lower cases), because W represents A or T.

 By database

The By database option uses an alignment matrix to match sequences against a motif database. We distribute the JASPAR database, but you can add any custom or public motif database. 

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Let h be the maximum of L_A. The quality score of a sequence is calculated as Q_A(S) =L_A(S)/h.  A quality score of 1 corresponds to a sequence with the most likely base at each position of the alignment matrix. The user will specify a threshold Q_A.   all All sequences that have a score T_A>Q_A *h will be reported.

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