Sequences were removed if regions near the microsatellite contained other perfect microsatellites, single base pair repeats longer than five base pairs, or long, imperfect microsatellites.
Also, a 143 base pair repeat sequence occurring at two positions was named waka/jwka.
In Bb lp28-2, the 60 base pair repeat sequence overlaps the 3' end of BB_G01 by 3 bp.
All of these regions contain genetic stutters called short tandem repeats, in which a pattern of base pairs repeats itself over and over.
For these four data sets total number of base pairs, non-conserved base pairs, conserved base pairs, repeat base pairs, conserved repeat base pairs, non-conserved repeat base pairs, conserved non-repeat base pairs, non-conserved non-repeat base pairs, conserved pTRRs, and non-conserved pTRR and appropriate pTRR densities were calculated as above (Additional file 1 Table 5).
The total number of base pairs, non-conserved base pairs, conserved base pairs, repeat base pairs, conserved repeat base pairs, non-conserved repeat base pairs, conserved non-repeat base pairs, non-conserved non-repeat base pairs, conserved pTRRs, and non-conserved pTRRs were calculated for both the gene desert intergenic distal and intergenic proximal regions as described above.
Microsatellites are short tandem (1 6 base pairs) repeated DNA sequences with high susceptibility for replication errors.
The transferred DNA (T-DNA) is delimited by 23 base-pair repeats on the tumor-inducing (Ti) plasmid.
CCMP452 orf97 (Heak452_Cp014), which overlaps chlI, contains a perfect 24 base pair tandem repeat.
Additionally, conserved secondary structures are predicted among Helitrons from Lepidoptera and Diptera, which form two inverted repeats [a 5′-inverted repeat (5′-IR), and base pairing between subterminal inverted repeats (SIRs)] that may be required for replication, mobilization, or integration [ 4, 13, 18].
