Supplementary Materials
Primer Sequences
Primer sequences for TEs belonging to the hAT superfamily (Figure 1B) were generated from
consensus sequences corresponding to each element ID found on TEfam
(http://tefam.biochem.vt.edu/tefam/) or REPbase (http://www.girinst.org/repbase/index.html) and
can be found in Supplementary Table 1. Adapter length was 10 bps, primer mismatch value was
5 and the restriction enzyme used was MseI, which has a recognition site of TTAA.
The primer sequences for mPing in different varieties of O. sativa (Figure 1C) were the
same as those described in Jiang et al. (2002). The length of the adaptor was 19 bp, primer
mismatch value was 0 and the restriction enzyme was MseI.
For the TF000720 element (Figure 1D), the pre-amplification primer sequence was 5’
GGCAAGCTGAAGTTATCTTG 3’ and the selective amplification primer sequence was 5’
TTTCGTGTGTAGTATCT 3’. The adapter length was 21 bps and the restriction enzyme used
was MseI.
Sources for Genomic Sequence Databases
The genomic sequence of A. aegypti was downloaded from Vectorbase (www.vectorbase.org), A.
thaliana from TAIR (www.arabidopsis.org) and C. elegans from Wormbase
(www.wormbase.org). The genome sequences for O. sativa var. indica and var. japonica was
obtained from Genomics (ftp://ftp.genomics.org.cn/; release: 23/04/2008).
Supplementary Table 1: Primer sequences and genomes used to generate output for hAT elements.
Element ID
Pre-Amplification Primer
Sequence
Selective Amplification Primer
Sequence
SIMPLEHAT2 CCCTAAACTCATTTGATTAT
GTTGAGTTGGGTTACCCATT
HATN1_CE
ATTTGGATCGCGGCGTGAG
GAGCGGCGTTTGAGCGACGC
CRATA
TGGTGGAGTAACCTCCGACG
TCCCCGTTGCCATCTCTA
TF000700
TTGTATGGTTGTTTACATTTT
GCAATAAAGAGCCGCCAGTT
HOBO
TTTATCGGGTGGACGTAGAG
GGGCTGCAGTTCTCTG
Genome
Arabidopsis thaliana
Caenorhabditis
elegans
Oryza sativa var.
japonica
Aedes aegypti
Drosophila
melanogaster
Supplementary Table 2: An Example of Text Output from TE Displayer
Lane 2:
Database: C:\Users\Becci\Desktop\TE Displayer\aaegypti.fa
Enzyme: MseI, TTAA
A total of 248 hits of pre_primer sequence.
Accession
TE_pos Enz_pos Size Sel_base Mismatch
AAGE02021692
9106
9231 146
0
AAGE02019341
82445
83329 905
0
AAGE02015032
36361
36631 291
0
AAGE02001634 168360 169044 705
0
AAGE02035910
4355
4551 217
1
AAGE02035655
3094
3152
79
1
AAGE02035583
3669
3773 125
1
AAGE02035169
3977
4088 132
1
AAGE02034801
3075
3291 237
1
AAGE02033496
2122
2358 257
1
AAGE02033409
2038
2112
95
1
AAGE02030860
29081
29152
92
1
AAGE02030445
13517
13732 236
1
AAGE02028058
6008
6162 175
1
AAGE02028020
5019
5129 131
1
AAGE02028003
21522
21597
96
1
AAGE02027559
16053
16100
68
1
AAGE02027227
33794
33869
96
1
AAGE02027010
76660
76721
82
1
AAGE02026563
10170
10293 144
1
AAGE02025719 173385 173460
96
1
AAGE02025668
6938
7176 259
1
AAGE02025638
65632
65866 255
1
AAGE02025458
56334
56439 126
1
AAGE02025430
18464
18518
75
1
AAGE02025241 157097 157155
79
1
AAGE02025058
17789
18186 418
1
AAGE02025002
23434
23595 182
1
AAGE02024088
64381
64501 141
1
AAGE02023582
25461
25534
94
1
AAGE02023311
57119
57452 354
1
AAGE02022738
93274
93795 542
1
AAGE02022381
10020
10276 277
1
AAGE02021989
80090
80157
88
1
Supplementary Figure 1: Screen shot of TE Displayer.