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The Tandem Repeats Finder (TRF 4.04) [42] that uses conservative approach, detected 71 repeats, the e-tandem identified 30 regions and the TandemSWAN [43], designed to identify imperfect or "fuzzy" repeats generated more than 600 hits.
Precision is defined as the fraction of the number of true tandem duplications (true positives) among all tandem duplications identified by our algorithm (true positives and false positives).
Two novel microsatellites were found: MAML3_MS1, a (CA)n tandem repeat located in the promoter region and MAML3_MS2, a (CGG n tandem repeat identified in exon 1.
Then, repeated elements arrayed in tandem were identified with ETANDEM from the EMBOSS package whereas dispersed repeated elements were located with REPuter 2.74 [29].
The tandem MS/MS identified more than 300 peptides using MASCOT and SeqQuest algorithms and non-redundant NCBI and SwissProt databases (see Methods for details).
In addition, several blocks of tandem repeats identified as HemolysinCabind domains were also found.
Tandem repeats identified in the pea genome included microsatellites, three variants of telomeric minisatellites, and exceptional diversity of satellite repeats.
There were 7,789 tandem repeats identified with dinucleotide "AT" having the most abundant repeats dispersed in the N. apis genome.
Spoligotyping and pattern of variable number of tandem repeats identified 10 molecular groups; two found by conventional methods were subdivided.
For VNTRfinder, flanking regions of each tandem repeat identified in the reference sequence(s) are then aligned to the related regions of target sequence(s).
In the case of the tandem duplications identified here, it is not clear what the basis of the membrane localization and activation is.
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