Table 4 Comparison of various repeat class in common unaligned sequences with GRCm38
Repeat ClassNumber of bp in common unaligned sequences (6,128,602 bp)GRCm38 (number of bp in complete genome) excluding “alt loci” (2,559,396,830 bp excl N/X-runs)
Satellites3,671,543 (59.91%)3,302,550 (0.13%)
LINE1300,944 (4.91%)488,443,086 (18.86%)
ERVL-MaLRs17,196 (0.28%)113,630,025 (4.31%)
B2-B432,901 (0.54%)111,079,403 (4.22%)
ERVL16,550 (0.27%)29,593,691 (1.12%)
hAT-Charlie413 (0.01%)16,625,654 (0.63%)
ERV_classI20,863 (0.34%)24,057,863 (0.91%)
Unclassified:1,080 (0.02%)8,303,004 (0.32%)
Alu/B1101,229 (1.65%)62,434,516 (2.37%)
TcMar-Tigger502 (0.01%)4,546,701 (0.17%)
ERV_classII252,653 (4.12%)121,444,463 (4.61%)
LTR307,262 (5.01%)289,477,645 (10.99%)
Simple repeats311,973 (5.09%)69,151,432 (2.63%)
Low complexity25,984 (0.42%)9,687,916 (0.37%)