Searching and Analyzing for a Different Lengths of Microsatellite Repeats in the Completed Genome of Phoenix Dactylifera Chloroplast, by Using Regular Expression Builder-Language

Variations of Simple Sequence Repeats (SSRs) or microsatellites is mainly caused by slipped-strand impairing and resulting errors during DNA replication and recombination. In this study, A new tool called Repeater Finder Regular Expression (RFRE) was programmed by using visual basic language to detect different lengths of sequence repeats in the chloroplast of the completed genome of date palm (Phoenix dactylifera). The user could write many different probabilities of combined operator to retrieve more than one patterns and very specific patterns of repeats. Not only searching automatically for fixed di, tri, tetra penta or hexa repeats but finding the perfect repeat and imperfect repeat. The most abundant founding pattern was (AAAA) {2}. Three long repeats (40 nt) were detected, 2 repeats were located in the noncoding region, however, the 3rd repeat was partially located in the rp3 gene. The program was validated by designing specific primers to target the repeat (8675-8715). The genomic DNA was isolated from date palm, and the repeat 8675-8715 was amplified by PCR. The PCR product was sequenced and the repeat was submitted to DDBJ as microsatellite EPDCO. In a comparison to date palm isolate and palm isolates from EPDCO was clusterd with date palm isolates, EPDCO sequence was clustered to date palm isolates. The microsatellite EPDCO is a unique marker for Date Palm. This study focused on analyzing the tandem repeats in date palm chloroplast genome by using the core power of the Regex. Engine.