Sentence examples for bp were identified using from inspiring English sources
The SSRs with the minimal length of 14 bp were identified using WebSat [ 14].
Direct repeats ≥ 20 bp were identified using VMATCH and then divided into distinct families with MATCHCLUSTER by allowing 15% sequence dissimilarity (-erate option set to 15).
Direct repeats longer than 10 bp were identified using the REPFIND program (Betley et al. 2002) and web-server (http://cagt.bu.edu/page/REPFIND_submit, last accessed June 14 , 2013.
ORFs longer than 150 bp were identified using ORFfinder, codon usage Table 4 (http://www.ncbi.nlm.nih.gov/projects/gorf/). ORFs were used to search the non-redundant NCBI database with BLASTP to annotate and find conserved genes.
The GC- and AT-skews, which indicate compositional differences between the two strands, were calculated according to the formulae of Perna and Kocher [ 68] Exact direct repeats longer than 10 bp were identified using the Reputer program package [ 69].
After constructing an index of repeated sequences using MKVTREE with the -dna -pl -allout and -v options, direct repeats ≥ 30 bp were identified using VMATCH (-d and -l options) and then assigned to distinct families with MATCHCLUSTER by allowing 10% sequence dissimilarity (-erate option set to 10).
Nevertheless, a section of the gel encompassing the correct product size (∼359 bp) was identified using marker ladders and excised from each negative control lane.
The wild-type Jnk1 (460 bp) and knockout Jnk1 (390 bp) alleles were identified using the amplimers 5'-CGCCAGTCCAAAATCAAGAATC-3', 5'-GCCATTCTGGTAGAGGAAGTTTCTC-3', and 5'-CCAGCTCATTCCTCCACTCATG-3'.
The wild-type Trp53 (470 bp) and knockout Trp53 (700 bp) alleles were identified using the amplimers 5'-TATACTCAGAGCCGGCCT-3', 5'-ACAGCGTGGTGGTACCTTAT-3' and 5'-CTATCAGGACATAGCGTTGG-3'.
The wild-type Jnk2 (400 bp) and knockout Jnk2 (270 bp) alleles were identified using the amplimers 5'- GGAGCCCGATAGTATCGAGTTACC-3', 5'-GTTAGACAATCCCAGAGGTTGTGTG-3', and 5'-CCAGCTCATTCCTCCACTCATG-3'.
In brief, sequences containing repetitive regions (≥30 bp, ≤15% deviation from perfect repeat structure, ≥30 bp flanking regions) were identified using RepeatMasker v3.2.9 (Smit et al. 1996) and then assembled using CAP3 to eliminate redundancy (Huang and Madan 1999).
