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Table 1 Abundance and Starting Nucleotide Preference for homopolymer and dimer loci in D. pulex

From: Simple sequence repeat variation in the Daphnia pulex genome

Dimers
Motif Type Count (obs) End (exp) p-value Starting Pref. Motif Type Count (obs) End (exp) p-value Starting Pref.
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   
Trimers
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   
  1. 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.
  2. Preferential starting base is determined by the highest frequency SSR for the motif grouping. * indicate highly used codons, + indicate rarely used codons.