Editing Inverted repeat (section)

==Understanding inverted repeats==

===Example of an inverted repeat===
[[File:Inverted-Repeat.gif|thumb|500px|left|The 5 base-pair sequence on the left is "repeated" and "inverted" to form sequence on the right.]]

Beginning with this initial sequence:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; {{color|blue|5'-TTACG-3'}}

The complement created by base pairing is:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; {{color|green|3'-AATGC-5'}}

The reverse complement is:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; {{color|green|5'-CGTAA-3'}}

And, the inverted repeat sequence is:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; {{color|blue|5'---TTACGnnnnnn}}{{color|green|CGTAA---3'}}

"nnnnnn" represents any number of intervening nucleotides.
{{Clear}}
<!--
===Direct repeat vs. inverted repeat===
A well-defined direct repeat is that which has a duplicated sequence as follows:<ref name=Bissler>{{cite journal|last=Bissler|first=JJ|title=DNA inverted repeats and human disease.|journal=Frontiers in Bioscience|date=Mar 27, 1998|volume=3|pages=d408-18|pmid=9516381|doi=10.2741/a284}}</ref> 
:::{{color|blue|5´ '''ACATACA'''ACATACA 3´}}
:::{{color|green|3´ '''TGTATGT'''TGTATGT 5´}}
The nucleotide sequence written in bold characters signifies the repeated sequence.<ref name=Bissler>{{cite journal}}</ref> Linguistically, a typical direct repeat is comparable to saying "bye-bye".<ref name=Bissler>{{cite journal}}</ref> There is similarity between direct and inverted repeat, or else a palindrome, with the exception of the second half of the inverted repeat positioned in the complementary strand as follows:<ref name=Bissler>{{cite journal}}</ref> 
:::{{color|blue|5´ '''ACATACG'''CGTATGT 3´}}
:::{{color|green|3´ TGTATGC'''GCATACA''' 5´}}
The last repeats suggest that palindromes can be related linguistically to a string of characters that reads the same in both directions, such as "level". In all, repeated sequence without the [[complementarity (molecular biology)|reverse complement]] and without inversion, is a [[direct repeat]].<ref name=Ussery2008 /> Based on the same initial sequence discussed above in the section titled "understanding inverted repeats", a direct repeat would be: {{color|blue|5' TTACGnnnnnnTTACG 3'}}
-->

===Vs. direct repeat===
A direct repeat occurs when a sequence is repeated with the same pattern downstream.<ref name=Ussery2008 />  There is no inversion and no reverse complement associated with a direct repeat. The nucleotide sequence written in bold characters signifies the repeated sequence. It may or may not have intervening nucleotides.
:::{{color|blue |5´ '''TTACG'''nnnnnnTTACG 3´}}
:::{{color|green|3´ '''AATGC'''nnnnnnAATGC 5´}}
Linguistically, a typical direct repeat is comparable to rhyming, as in "t'''ime''' on a d'''ime'''".

===Vs. tandem repeat===
A direct repeat with ''no'' intervening nucleotides between the initial sequence and its downstream copy is a [[Tandem repeat]]. The nucleotide sequence written in bold characters signifies the repeated sequence.
:::{{color|blue |5´ '''TTACG'''TTACG 3´}}
:::{{color|green|3´ '''AATGC'''AATGC 5´}}
Linguistically, a typical tandem repeat is comparable to stuttering, or deliberately repeated words, as in "bye-bye".

===Vs. palindrome===
{{main|Palindromic sequence}}
An inverted repeat sequence with ''no'' intervening nucleotides between the initial sequence and its downstream [[complementarity (molecular biology)|reverse complement]] is a [[palindromic sequence|palindrome]].<ref name=Ussery2008 /> <br />&nbsp; &nbsp; EXAMPLE:<br />
&nbsp; &nbsp; &nbsp; &nbsp; Step 1: start with an inverted repeat: {{color|blue|5' TTACGnnnnnnCGTAA 3'}}<br />
&nbsp; &nbsp; &nbsp; &nbsp; Step 2: remove intervening nucleotides: {{color|blue|5' TTACGCGTAA 3'}}<br />
&nbsp; &nbsp; &nbsp; &nbsp; This resulting sequence is palindromic because it is the reverse complement of itself.<ref name=Ussery2008 />
:::{{color|blue|5' TTACGCGTAA 3'}} &nbsp; test sequence (from Step 2 with intervening nucleotides removed)
:::{{color|green|3' AATGCGCATT 5'}} &nbsp; complement of test sequence
:::{{color|blue|5' TTACGCGTAA 3'}} &nbsp; reverse complement &nbsp; &nbsp; This is the same as the test sequence above, and thus, it is a palindrome.