Sentence examples for loci sequences were from inspiring English sources

Then, the loci sequences were used as a BLAST database to add other 21-nt sequences that were not identified originally as phased (in order to by-pass the genome divergence), in two pass: first we select only new sequences with 100%% of identity on 85%% of their length (minimum HSP length of 16), then we change the threshold to 85%% of identity on 85%% of their length (min HSP length of 16).

Thus, when the two new loci sequences were concatenated to the original ST sequences we observed the complete discrimination of the strains, although our adapted scheme remains limited to L. interrogans and L. kirschneri.

CRISPR loci sequences were independently confirmed by Sanger sequencing of PCR amplicons.

To assess relationships among alleles at identified loci, sequences were first aligned in ClustalX (Larkin et al. 2007).

The candidate loci sequences were obtained from the strains L. interrogans Fiocruz L1-130 and L. interrogans Lai 56601 strains from the Leptolist server.

PCR reaction volumes and cycling conditions were as above, except the extension time for initial long-PCRs to generate the entire locus (∼8 10 kb) was 10 min. PCR products were then Sanger-sequenced as above and complete mating-type loci sequences were deposited in GenBank: KF961042 KF961047.

IFN sub-loci sequences were then analyzed in RepeatMasker version 3.1.9 run in default mode with blastp version 2.0MP-WashU [ 54] to determine the percentage of repetitive elements.

To ensure the targeted species locus sequences were obtained, the edited sequences were validated using sequence similarity searches (GenBank BLASTn).

These markers included 696 SNPs, 51 EST-SSRs, 94 gSSRs, 51 ITPs and 25 ESTPs for which locus sequences were available.

The contigs containing capsule locus sequences were compared with the N. meningitidis complete reference genome sequences by using blastn (http://blast.ncbi.nlm.nih.gov) to identify orthologous sequences and determine their levels of similarity.

Simple scans for loci of unusually low diversity would incorrectly suggest selection at many of the loci surveyed: in the Canadian population, for example, nearly half of the loci sequenced are devoid of variation (Table S2).