Our sequence assembly measurements benefited from another metric for evaluating the consistency of producing separated sets of sequence clusters. The external consistency index provides insight into whether assemblers have produced well-separated sequence clusters. Although the ECI may depend on the rate of evolution of gene families and paralogization in natural species, biased indices can indicate erroneous clustering procedures. Previous works have shown that values higher than 75 may signify overlapping sequence clusters that are clustered incorrectly by algorithms. All of the software used in this study computed a satisfactory average ECI distance between consensus pairs. Therefore, CAP3 presented the best results for internal consistency, whereas Celera produced the best values for external consistency. However, the general ECI average for cluster comparison was adequate in CAP3, and because internal consistency helps ensure better consensus quality, we chose the CAP3 clusters and consensus to analyze further. Folinic acid calcium salt pentahydrate Hereafter, all references to clusters or unigenes will be referred as the CAP3-generated data. The NCBI Unigene database contains a “set of LOUREIRIN-B transcript sequences that appear to come from the same transcription locus.” We compared the number of unigenes found for organisms of phylum Arthropoda to the number obtained for the spiders we analyzed. Fifteen arthropods and a single arachnid, the blacklegged tick, were found in the Unigene database. The three arthropod organisms with the highest number of unigenes in the Unigene database are the black-legged tick Ixodes scapularis, the mosquito Aedes aegypti and the fruit fly Drosophila melanogaster. Therefore, an arachnid displayed the highest number of unigenes among organisms from the Arthropoda clade. The high number of unigenes found here for both groups of spider was in accordance with the available Unigene data and provided evidence that the Chelicerata clade presents a richer repertoire of genes than the Arthropoda clade. These numbers provide further evidence of the broader use of antisense transcripts in Araneomorphae compared with spiders from the infraorder Mygalomorphae, suggesting that the first clade is represented by more complex organisms not only in terms of anatomical and behavioral characteristics, but also regarding molecular regulatory mechanisms. These numbers are also in accordance with the evidence found in previous works that complexification of animal behavior may account for RNA-based regulatory networks. We also investigated the relative proportions of sense and antisense transcripts. When the genome of the spiders under analysis is not known, it is difficult to predict the correct sense of transcripts. Therefore, transcripts were considered antisense if they differed in strand from the majority of other transcripts in the same cluster. The CAP3 assembler provided the information on the reads’ strands for each cluster. The consensus sequence of each family of spidroins shown in Table 4 was chosen to be multiple aligned against silk proteins from a number of other spiders’ species. To avoid an overestimation of deletion events in the evolution of these sequences, they were aligned using Prankster software. The Prankster multiple alignment of spidroin sequences was exported and converted into a minimum evolution phylogenetic analysis using MEGA software. Because we have only partial sequences from a number of spidroins, the phylogeny analysis was performed using the C-terminus of the translated nucleotide sequences.