Additional file 4: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

Table S2. Statistics and designation of B1 subfamilies and families. “Ory” stands for O. palustris and “Sig” stands for S. hispidus. “Peak” indicates the peak of the B1 divergence distribution of the subfamily or family identified by kernel smoothing. Copy numbers are normalized as copies per three Gbp of MiSeq sequence used for the search. Designation of families is only shown after the first subfamily that belongs to it; all subsequent subfamilies belong to this family until the demarcation of the next family. Characters in family names: “OS” represents families shared by O. palustris and S. hispidus and “OSP” for families shared by O. palustris, S. hispidus and P. maniculatus. Numbers in the family names reflect their divergence within the family group with “1” being the youngest. Copy numbers of families are rounded sums of subfamily copy numbers per three Gbp of sequences.and S. hispidus genome. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (XLSX 13 kb)