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The aligned core is comprised of alignment columns that contain all input genomes and no gaps.
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These alignments formed the lamprey CNE set (comprised of alignments of CNEs from human, fugu, zebrafish and lamprey) and the gnathostome CNE set (containing alignments of CNEs from human, fugu and zebrafish).
Our final dataset was comprised of 7890 alignments totalling 4,952,907 bp of sequence and these were used for all subsequent analyses.
This was carried out with the construction of a RNAseq analysis pipeline comprised of GSNAP for alignment and genome construction, and Cufflinks to determine if differential expression and changes in transcript abundance were statistically significant.
The sequence alignment was comprised of 393 unambiguously alignable positions (including 7 positions with gaps), of which 80 were variable and 45 were parsimony informative.
The top left corner has the score distribution for the predicted novel miRNA, the top right corner has the predicted hairpin structure for the novel pre-miRNA and the major part comprises of the alignment of the reads to the mature (red), loop (yellow) and the star regions (purple) of the precursor miRNA.
The sequence alignment of cytochrome b was comprised of 539 unambiguously alignable positions, of which 197 were variable and 150 were parsimony informative.
The subsequent mask comprising of the structures to be fabricated also comprised of a dimensionally similar hexagon (alignment feature) which was formed after etching.
The ORF A alignment was comprised of 298 bp.
The amino acids alignment was comprised of 179 amino acids.
The optional module utilizes a multiple sequence alignment (MSA) comprised of available reference genomes for the target.
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