Sentence examples for bases were aligned to from inspiring English sources
The first 41 bases were aligned to the rat reference genome using the Gerald program.
The average DNA coverage was 106× as ∼21 million DNA reads, with average length of 83 bases were aligned to the coding sequences.
The remaining bases were aligned to the Genbank nonredundant protein database, which resulted in 9.48% of all BESs having a hit to coding sequences.
Reads that passed quality control (more than 90%% bases had less than 1%% sequencing error; no ambiguous bases) were aligned to the mouse genome (Mus_musculus.GRCm.38.72) with corresponding gene model annotation (Mus_musculus.GRCm38.72.gtf) by TopHat 2.0.6 [ 16].
A total of 817,470,439 reads (59,643,456,282 bases) were aligned to approximately 97% of the reference genome (53,783,377,648 bases were uniquely mapped), resulting in an average of 24.7X sequence coverage of the horse's genome (Additional file 3, Table S2).
We generated 1.3 million sequences which produced 662 million bases that were aligned to the Saccharomyces cerevisiae reference genome [ 38], using GS reference mapper version 2.3.
After sorting reads by barcodes, the barcodes were stripped and 26 base pairs were aligned to the yeast genome.
50 base reads were aligned to NCBI build 36 of the human genome allowing 6 mismatches per read.
When the total length of the spacer and the following sequence was >70 bases, the reads were aligned to target sequences (spacer + target region) with bwa (version 0.6.2) using the bwasw mode for aligning long reads and the parameter setting '-b5 -q2 -r1 -z10'.
36 - 41 base single reads were aligned to the complete and annotated AS-sens reference genome sequence (AS-WTSI) [ 25] using MAQ [ 28] and SSAHA2 [ 29] mapping software packages, producing mean -fold coverage of ~ 39 (AS-sens), ~54 (AS-15MF) or ~77 (AS-30CQ).
The 16-base long reads (excluding the 4-base DpnII recognition site) were aligned to DpnII tag tables generated by Stowers Institute http://research.stowers-institute.org/microarray/tag_tables/index.html using megaBLAST with word size of 12 and low-complexity region filtering turned off.
