1The average fold change in RPKM for all members of each transposon family is shown. Most RNA-seq reads align to multiple members of a highly conserved transposon family; therefore, we cannot report fold change in RPKM for single members of a family. Gene members of the IS5/IS1031 family are all2692, all2693, alr3610, alr3611, all4399, all4400, alr4438, alr4439, all4816, all4817, alr5157, and alr5158. Gene members of the IS630 family are alr0018, alr0019, all0362, all0363, alr0552, alr0553, alr1726, alr1727, alr1853, alr1854, alr1858, alr1859, all1971, all1972, asl1992, all2066, all2067, alr2773, alr2774, alr4628, all4867, all4868, alr5227, and alr5228. Gene members of the IS982 family are asl0588, alr0590, alr0999, all2664, alr2683, alr2694, alr3384, all3624, and alr4082. Gene members of the ISL3 family are alr1609 and alr2698.