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- ARB: a Short Introduction
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# Search

- OCCURRENCE
- DESCRIPTION
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## OCCURRENCE

### ARB_EDIT4/Edit/Search

## DESCRIPTION

### Search

### Search patterns

In the text field you can enter multiple search patterns. Different patterns are separated by newlines or commas.
'?' is treated as single letter wildcard
'#' is an end-of-line comment
Text written behind # will not be used for search. Instead this text will be displayed in the message window when you position your cursor on a found pattern.

### Mark species with matches

Marks all species which match one of the current search patterns. Does not unmark rest on species.

### Last/Next

Jumps to the last/next occurrence of any of the given patterns. You can repeat your last search by pressing CTRL-S.

### Show ?

If checked, the found parts are shown in different background colors (defined at Properties/Data Search)
If the different search patterns overlap, they are shown in the following order:
User (shown above all others) Probe Primer (shown below all other)

### Open folded?

If checked, the Last/Next-Button will open folded groups, to jump to the next occurrence. Otherwise search will jump over folded groups.

### Auto jump?

If checked, the cursor will automatically jump to the nearest occurrence, if you change the search pattern or other search parameters.

### Ignore gaps in sequence?

If checked, gaps in sequence will be ignored. (ACGU will find A-CG-U, AC---GU, ...)

### Ignore gaps in pattern?

If checked, gaps in the search pattern will be ignored. (A-CG-U, AC---GU, ... will find ACGU)

### Treat T and U as match?

If checked, T and U will be treated as equal. (ACGU will find ACGT and vice versa)

### Ignore case?

If checked, a and A, c and C, ... are treated as equal (aCGu will find ACGU, AcgU, acgu, ...)

### Search for complement?

If checked, search will go as well for complemented patterns.

### Search for reverse?

If checked, search will go as well for reversed patterns.

### Exact!

If checked, search will only go for the given combination of 'complement' and 'reverse'.

    Example: If 'Exact', 'complement' and 'reverse' are checked,
             search will go only for complemented AND reversed
             patterns.

### Allowed mismatches

Defines the minimum and maximum allowed number of non-matching base characters.

## NOTES

### Found patterns hide possibly activated column statistics.

## EXAMPLES

### None

## WARNINGS

### None

## BUGS

### No bugs known