Table 3

Complex repeats. Transposons identified by RepeatMasker are assigned to three classes. Each class has a number of families (e.g., tourist-like MITEs), and each family has a number of different subfamilies. The number of subfamilies is listed, as well as their total and mean size. Repeat content for each family is given as a percentage by length, normalized with respect to the data set (assembled contigs, fully masked reads, or cDNAs) or with respect to all identified transposons.

NumberTotal (bp)Mean (bp)93-11assembled contigs93-11 fully masked readsFull-length cDNAs
% of data set% of repeats% of data set% of repeats% of data set% of repeats
Class ILINEs518,9973,7991.19057.430.13180.220.02572.51
Subtotal 6.7254 41.99 57.6766 97.33 0.2631 25.65
Class IIAc/DsTEs31,5675220.10990.690.01450.020.00000.00
Subtotal 2.8190 17.60 0.9293 1.57 0.1807 17.62
Class IIIStowaway-like7016,1122302.237013.970.12470.210.191018.62
Unknown MITEs21,3416710.49503.090.20800.350.04584.46
Subtotal 6.4725 40.41 0.6556 1.11 0.5818 56.73
Grand Total 213 231,327 1,086 16.0169 100.00 59.2615 100.00 1.0255 100.00