Table 1 |
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|
Abundance and Starting Nucleotide Preference for homopolymer and dimer loci in D. pulex |
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|
Dimers |
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|
|
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|
Motif Type |
Count (obs) |
End (exp) |
p-value |
Starting Pref. |
Motif Type |
Count (obs) |
End (exp) |
p-value |
Starting Pref. |
|
|
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|
TA |
48814 |
42186 |
0 |
T |
GC |
8444 |
7623 |
1E-39 |
G |
|
AT |
35558 |
42186 |
CG |
6802 |
7623 |
||||
|
GA |
33951 |
31919 |
0 |
G/T |
AC |
33773 |
29999 |
0 |
A/T |
|
AG |
30185 |
31919 |
CA |
26535 |
29999 |
||||
|
TC |
40029 |
31919 |
TG |
35249 |
29999 |
||||
|
CT |
23511 |
31919 |
GT |
24437 |
29999 |
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|
|
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|
Trimers |
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|
|
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|
AAC+ |
2728 |
2821 |
1E-78 |
T/C |
ACT |
598 |
695 |
7E-15 |
G/T |
|
ACA* |
2431 |
2821 |
CTA+ |
734 |
695 |
||||
|
CAA* |
3380 |
2821 |
TAC+ |
791 |
695 |
||||
|
GTT* |
2339 |
2821 |
AGT |
665 |
695 |
||||
|
TGT* |
2657 |
2821 |
TAG+ |
564 |
695 |
||||
|
TTG* |
3390 |
2821 |
GTA+ |
815 |
695 |
||||
|
AAG |
5734 |
4486 |
0 |
T/A |
AGC+ |
1839 |
2823 |
1E-226 |
C/G |
|
AGA* |
3657 |
4486 |
GCA* |
2363 |
2823 |
||||
|
GAA* |
4278 |
4486 |
CAG+ |
4131 |
2823 |
||||
|
CTT |
3393 |
4486 |
GCT |
3115 |
2823 |
||||
|
TCT |
3692 |
4486 |
TGC+ |
2725 |
2823 |
||||
|
TTC+ |
6161 |
4486 |
CTG |
2767 |
2823 |
||||
|
AAT* |
4099 |
2937 |
5E-216 |
A |
AGG+ |
971 |
1039 |
2E-18 |
G/T |
|
ATA+ |
2260 |
2937 |
GGA* |
1222 |
1039 |
||||
|
TAA* |
2406 |
2937 |
GAG+ |
988 |
1039 |
||||
|
ATT* |
3533 |
2937 |
CCT |
905 |
1039 |
||||
|
TAT* |
2233 |
2937 |
TCC |
1207 |
1039 |
||||
|
TTA |
3093 |
2937 |
CTC |
940 |
1039 |
||||
|
ACC+ |
855 |
1089 |
4E-40 |
C/T |
ATC |
1153 |
1404 |
8E-46 |
T |
|
CAC+ |
1057 |
1089 |
TCA* |
1703 |
1404 |
||||
|
CCA* |
1383 |
1089 |
CAT* |
1342 |
1404 |
||||
|
GGT |
1034 |
1089 |
GAT* |
1452 |
1404 |
||||
|
GTG |
921 |
1089 |
TGA |
1661 |
1404 |
||||
|
TGG* |
1285 |
1089 |
ATG* |
1111 |
1404 |
||||
|
ACG |
1229 |
1373 |
8E-11 |
G |
CCG |
703 |
742 |
1E-47 |
G |
|
CGA |
1406 |
1373 |
CGC+ |
519 |
742 |
||||
|
GAC+ |
1561 |
1373 |
GGC |
916 |
742 |
||||
|
CGT |
1325 |
1373 |
CGG |
731 |
742 |
||||
|
TCG |
1267 |
1373 |
GCG+ |
585 |
742 |
||||
|
GTC |
1452 |
1373 |
GCC |
995 |
742 |
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|
|
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|
This table shows nonrandom starting nucleotides in both dimers and trimers. Motif type indicates largest possible repeat identified for each staggered SSR set. P-value calculated using Pearson's chi-square test for random expectation based upon observed and expected frequencies. Preferential starting base is determined by the highest frequency SSR for the motif grouping. * indicate highly used codons, + indicate rarely used codons. |
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|
Sung et al. BMC Genomics 2010 11:691 doi:10.1186/1471-2164-11-691 |
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