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As we observed, the high homologous proteins (id > 45%) can be successfully aligned, using a matrices designed for large evolutionary distances.
After genotypes procedure, the markers of aa xx bb style were 3598 and all of them could be successfully aligned with reference including 3580 unique markers.
These spindles appeared to be highly disorganized, and although a bipolar structure could be formed in an "outwards-in" manner, chromosomes could not be successfully aligned.
A single Apodanthaceae nad1 B/C sequence could not be successfully aligned with the 70-taxon nad1 B/C data set of Won and Renner [ 20] nor with newly generated Cucurbitales nad1 B/C sequences.
This behavior was not observed for the intermediate edit distance (option –n 0.03), as >95% of Helicos reads that could be successfully aligned to the chicken genome consisted of reads shorter than 27 nucleotides.
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The majority of known UCEs (all 481 elements from the human-mouse-rat alignment [ 1], 23,695 out of 23,699 elements from the D. melanogaster Drosophila pseudoobscura alignment, and all 126 elements from the D. melanogaster Anopheles gambiae alignment [ 3]) were successfully aligned.
In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database.
Alignment of the unmapped contigs with each other revealed that there were five alignment pairs that were present in both strains; in total, 81.5kb were successfully aligned (Additional file 8).
Although some material have been successfully aligned [24], it is very difficult to manipulate CNTs to form arrays, which makes it difficult to be economical and practical.
Within the amplified region of mtDNA, 579 bp of the COI gene sequences from 22 specimens were successfully aligned, containing nine variable sites and defining a total of six haplotypes.
About 80% of 236,004 available A. gambiae ESTs were successfully aligned to A. gambiae reference genomes.
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