It will find inverted repeats that include a proportion of mismatches and gaps (bulges in the stem loop).
It works by finding all possible inverted matches satisfying the specified conditions of minimum and maximum length of palindrome, maximum gap between repeated regions and number of mismatches allowed.
Secondary structures like inverted repeats in genomic sequences may be implicated in initiation of DNA replication.
% palindrome Input sequence: embl:hsts1 Enter minimum length of palindrome : 15 Enter maximum length of palindrome : Enter maximum gap between repeated regions : Number of mismatches allowed : Output file [hsts1.pal]: Report overlapping matches [Y]:
Mandatory qualifiers: [-insequence] sequence Sequence USA -minpallen integer Enter minimum length of palindrome -maxpallen integer Enter maximum length of palindrome -gaplimit integer Enter maximum gap between repeated regions -nummismatches integer Number of mismatches allowed [-outfile] outfile Output file name -[no]overlap bool Report overlapping matches Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose
|Mandatory qualifiers||Allowed values||Default|
|Sequence USA||Readable sequence||Required|
|-minpallen||Enter minimum length of palindrome||Integer 1 or more||10|
|-maxpallen||Enter maximum length of palindrome||Any integer value||100|
|-gaplimit||Enter maximum gap between repeated regions||Integer 0 or more||100|
|-nummismatches||Number of mismatches allowed||Positive integer||0|
|Output file name||Output file||<sequence>.palindrome|
|-[no]overlap||Report overlapping matches||Yes/No||Yes|
|Optional qualifiers||Allowed values||Default|
|Advanced qualifiers||Allowed values||Default|
Palindromes of: HSTS1 Sequence length is: 18596 Start at position: 1 End at position: 18596 Minimum length of Palindromes is: 15 Maximum length of Palindromes is: 100 Maximum gap between elements is: 100 Number of mismatches allowed in Palindrome: 0 Palindromes: 126 caaaaaaaaaaaaaaaa 142 ||||||||||||||||| 217 gtttttttttttttttt 201 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 215 tttttttttttttttt 200 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 214 tttttttttttttttt 199 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 213 tttttttttttttttt 198 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 212 tttttttttttttttt 197 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 211 tttttttttttttttt 196 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 210 tttttttttttttttt 195 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 209 tttttttttttttttt 194 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 208 tttttttttttttttt 193 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 207 tttttttttttttttt 192 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 206 tttttttttttttttt 191 127 aaaaaaaaaaaaaaaa 142 |||||||||||||||| 205 tttttttttttttttt 190 127 aaaaaaaaaaaaaaaagaccgccagggct 155 ||||||||||||||||||||||||||||| 204 ttttttttttttttttctggcggtcccga 176
Several examples can be seen in the sample output above.
|einverted||Finds DNA inverted repeats|
|equicktandem||Finds tandem repeats|
|etandem||Looks for tandem repeats in a nucleotide sequence|
einverted also looks for inverted repeats but is much slower and more sensitive, as it finds low-quality (very mismatched) repeats and repeats with gaps.