TABLE 2

List of indels >1 kb in the two strains of D. virilis

StrainStrain difference IDRepeat lengthBest hit to SuperlibraryRepeat classLTR length% terminal repeat identities
GEPgep_contig9_1558396811dvir.2.37.centroidLTR412100.0
GEPgep_contig9_3145796809dvir.2.37.centroidLTR412100.0
GEPgep_contig4_2596016437dvir.35.83.centroidLTR427100.0
GEPgep_contig5_830745409dvir.5.67.centroidLTR227100.0
GEPgep_contig5_1867882539dvir.16.2.centroidDNANANA
GEPgep_contig4_406742489dvir.16.2.centroidDNANANA
GEPgep_contig5_1393571704dvir.35.83.centroidLTRNANA
GEPgep_contig4_1669601616Helitron-1N1_DVirDNA/HelitronNANA
GEPgep_contig5_1367541422dvir.35.83.centroidLTRNANA
GEPgep_contig8_1559191343dvir.3.94.centroidLTRNANA
GEPgep_contig5_1354171329dvir.35.83.centroidLTRNANA
GEPgep_contig5_1381821167dvir.35.83.centroidLTRNANA
CAF1caf_contig8_17723010,606Ulysses_ILTR/Gypsy212099.7
CAF1caf_contig5_1810626394dvir.2.53.centroidLTR412100.0
CAF1caf_contig8_533822123dvir.21.15.centroidLTRNANA
  • Analysis of indels >1 kb in the two strains (GEP and CAF1) of D. virilis shows that most of the large indels have sequence similarity to LTR retrotransposons and DNA transposons. All of the indels >3 kb are classified as LTR retroelements in the Superlibrary; five of the six terminal repeats that can be identified have perfect sequence identity.