Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers

Table 4 Repeat elements screened from the unigenes of the H. flava transcriptome

Repeat elements	Number of elements^a	Length occupied (bp)	Percentage of sequence
SINEs	51	3006	0.01
ALUs	0	0	0.00
MIRs	0	0	0.00
LINEs	67	3979	0.01
LINE1	4	211	0.00
LINE2	11	639	0.00
L3/CR1	36	2248	0.00
LTR elements	51	10,209	0.02
ERVL	3	129	0.00
ERVL-MaLRs	0	0	0.00
ERV_class I	1	39	0.00
ERV_class II	0	0	0.00
DNA elements	311	50,419	0.09
hAT-Charlie	27	6158	0.01
TcMar-Tigger	64	5295	0.01
Unclassified	0	0	0.00
Total interspersed repeats		67,613	0.12
Small RNA	1142	84,596	0.15
Satellites	1	52	0.00
Simple repeats	7872	262,944	0.48
Low complexity	577	23,233	0.04

Total unigene sequences: 69,822; total length of 55,278,029 bp; GC(%): 53.09%; bases masked: 438,287 bp
LINE Long-interspersed nuclear elements, LTR long-terminal repeats, SINE short-interspersed nuclear elements
^aMost repeats fragmented by insertions or deletions were counted as 1 element

ISSN: 1756-3305