The window "Motif search" serves to search of motifs in a sequence. Sequences of motifs are set in the 15-letter alphabet. In heading after a mark "#" the dropping down list serves for a choice of a sequence in which there will be a search is located.
The field "from" serves for definition of number of a position with which search begins.
The field "to" serves for definition of number of a position on which search comes to an end.
The field "length" serves for definition of length of area of search.
The dropping down list "chain" serves for a choice of a direction of search:
(+/-) - search in a direct and reverse chains.
(+) - search in a direct chain.
(-) - search in a reverse chain.
The field "motif" serves to input of a sequence of motif in the 15-letter alphabet. The given field is obligatory for filling.
The field "mismatch" serves for set allowable quantity of discrepancies by search. If the field is not filled, to parameter value 0 automatically is appropriated. Restrictions on quantity of discrepancies: no more than half of length of motif, and also no more than 1000.
The field "Command summary" displays the current adjustments of a command (the chosen parameters). The given field is only information and does not serve for adjustment of parameters of command.
Notes.
Parameters "from", "to" and "length" are connected among themselves. Simultaneously can be given no more than two parameters. At recalculation of parameters there is a check that values of parameters do not contradict each other and are intelligent.
If parameters "from", "to" and "length" are not given, to parameter "from" value "BEGIN" is appropriated (the beginning of a sequence), to parameter "To" is appropriated value "END" (the end of a sequence).
If the parameter "length" is given only, to parameter "to" value "BEGIN" is appropriated (the beginning of a sequence), to parameter "to" value of parameter "length" is appropriated.
If the parameter "to" is given only, to parameter "from" value "BEGIN" (the beginning of a sequence) is appropriated.
If the parameter "from" is given only, to parameter "to" value "END" (the end of a sequence) is appropriated.
If parameters "from" and "length" are given, value "to" is calculated in view of the specified values (to=from length-1).
If parameters "to" and "length" are given, value "from" is calculated in view of the specified values (from=to-lenhgth+1).