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EST D-Genome mapping

Cotton46 to D-Genome (Gr221) Blastn analysis:   In an effort to add value to the Cotton46 Gossypium EST assembly, member contigs were BLASTed against the G.raimondii, D-Genome, genomic sequence, available from Phytozome. The Blastn output was analyzed to quantify significant hits both in general and when filtered for hits falling within Gr221 annotated gene boundaries. The distribution of E-values for within-gene alignments (HSP) ranging between 1x10-20 and 1x10-131 is shown in the following plot. An additional 67927 HSPs with E-value = 0 are not shown.

Since the Cotton46 contigs are composed of reads transcribed from the A and D genomes of diploids and alloployploids. It’s likely that, even in the absence of chimeras, contigs that are more "A" like or from the alloployploid, will have less significant D-genome hits and contribute to the increasing HSP count vs. E-value observed for E-values above 10-130. We have further analyzed the within-gene alignments vs. log(E-value) and the results are shown in the figures listed below.
In the above list, figures 1 through 6 are for the portion of Blast HSPs that are contained in within-gene alignments, as described above. In figure 7, both in-gene and gene-overlapping HSPs are included in the analysis.

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