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
SINEs71,2541790.08880.550.00470.010.02682.61
gypsy-like19105,6145,5593.728523.2841.689470.350.123812.07
copia-like535,1517,0301.717510.7215.850626.750.08698.47
Subtotal 6.7254 41.99 57.6766 97.33 0.2631 25.65
Class IIAc/DsTEs31,5675220.10990.690.01450.020.00000.00
En/SpmTEs35,5581,8530.25901.620.27700.470.00000.00
MULEs2225,8001,1732.450015.300.63781.080.180717.62
Subtotal 2.8190 17.60 0.9293 1.57 0.1807 17.62
Class IIIStowaway-like7016,1122302.237013.970.12470.210.191018.62
tourist-like7719,9332593.740523.350.32280.540.345133.65
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