TQiSoft's Webgenetics(sm)

Dyad Repeats of a DNA Sequence

This program searches a DNA sequence for dyad repeats (stem-loops). There are no mismatches allowed in the stems. The results are ordered according to the stem sizes, from long to short, then the sequences of the stems, alphabetically.

Example output:

repeat  gap  sites      sequences       sites

  12   2072   1935  5' CCGTTCCGCATT 3'  1946
              4030  3' GGCAAGGCGTAA 5'  4019

  11   1589    752  5' ACAACTGGTGG 3'  762
              2362  3' TGTTGACCACC 5'  2352

  11    846   3697  5' GACGTGCCTCG 3'  3707
              4564  3' CTGCACGGAGC 5'  4554

  11   4974   1331  5' TGCAATCGAGA 3'  1341
              6326  3' ACGTTAGCTCT 5'  6316

  10    299   1147  5' ACTTACACAT 3'  1156
              1465  3' TGAATGTGTA 5'  1456

 ...

The first and second columns are the sizes of repeats and gaps respectively.