Markers + reference

Coccinia

2 species · Cucurbitaceae · Cucurbitales

Back to catalogue

Species 2
Genome length 122–157 kb
Candidate markers 206
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 206 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl2 IRb 1490 NA 0.00 36.0 yes View details
trnK-rps16 LSC 747 0.0110 0.97 67.9 yes View details
rpoB-trnC LSC 946 0.0161 0.98 62.4 yes View details
trnE-trnT LSC 968 0.0104 1.00 64.3 yes View details
psaA-ycf3 LSC 706 0.0170 1.00 55.7 yes View details
ycf3-trnS LSC 612 0.0114 1.00 57.8 yes View details
trnS-rps4 LSC 293 0.0239 1.00 65.6 yes View details
rps4 LSC 606 0.0016 1.00 44.9 yes View details
rps4-trnT LSC 323 0.0377 0.98 62.7 yes View details
psaI-ycf4 LSC 403 0.0149 1.00 56.0 yes View details
rpl2 IRa 1490 0.0000 1.00 40.0 no View details
petD-rpoA LSC 201 0.0200 1.00 64.5 yes View details
petA-psbJ LSC 1004 0.0080 0.99 64.3 yes View details
rps16-trnQ LSC 1337 0.0068 0.99 63.7 yes View details
rps7-rps12 SSC 53 0.0189 1.00 63.3 yes View details
rpl20-rps12 LSC 791 0.0063 1.00 62.4 yes View details
rbcL-accD LSC 681 0.0059 1.00 62.3 yes View details
psbM-trnD LSC 1096 0.0055 1.00 62.0 yes View details
trnC-petN LSC 892 0.0045 1.00 61.7 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl2_p1 rpl2 CGCTTCAACCGGGTTATTCT TGTTTGTAAAGACGAAGAAAGA 1596 1.000 44.0
rpl2_p2 rpl2 ATCATTACGCTTCAACCGGG TGTTTGTAAAGACGAAGAAAGA 1603 1.000 44.0
rpl2_p3 rpl2 CGCTTCAACCGGGTTATTCT TGTTTGTAAAGACGAAGAAAGAA 1596 1.000 44.0
rpl2_p4 rpl2 CGCTTCAACCGGGTTATTCT TTGTTTGTAAAGACGAAGAAAGA 1597 1.000 44.0
rpl2_p5 rpl2 ATCATTACGCTTCAACCGGG TGTTTGTAAAGACGAAGAAAGAA 1603 1.000 44.0
trnK_p1 trnK CGAATTAGACTTGATAGATTATTTCGA TGATTCCGATTGTATCTACACAGA 2678 1.000 40.3
trnK_p2 trnK TCGAATTAGACTTGATAGATTATTTCG TGATTCCGATTGTATCTACACAGA 2679 1.000 40.3
trnK_p3 trnK CGAATTAGACTTGATAGATTATTTCG TGATTCCGATTGTATCTACACAGA 2678 1.000 40.3
trnK_p4 trnK CGAATTAGACTTGATAGATTATTTCGA TGGAATATTTTGATTACGTCGTGT 2724 1.000 40.3
trnK_p5 trnK TCGAATTAGACTTGATAGATTATTTCG TGGAATATTTTGATTACGTCGTGT 2725 1.000 40.3
trnK-rps16_p1 trnK-rps16 AGTCGCGGTCTTACAAACTC GGTGCTCAACCTACAGGAAC 922–942 1.000 80.6
trnK-rps16_p2 trnK-rps16 GTCGCGGTCTTACAAACTCT GGTGCTCAACCTACAGGAAC 921–941 1.000 80.6
trnK-rps16_p3 trnK-rps16 GTCGCGGTCTTACAAACTCT AAGGCAGGTGTTTTTACGGA 882–902 1.000 79.4
trnK-rps16_p4 trnK-rps16 GTCGCGGTCTTACAAACTCT AGGCAGGTGTTTTTACGGAA 881–901 1.000 79.4
trnK-rps16_p5 trnK-rps16 CAGTCGCGGTCTTACAAACT GGTGCTCAACCTACAGGAAC 923–943 1.000 79.3
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1405–1410 1.000 79.6
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1416–1421 1.000 79.1
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA GACGACCAACCACTACCAAT 1501–1506 1.000 76.4
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC GACGACCAACCACTACCAAT 1512–1517 1.000 75.8
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1409–1414 1.000 74.8
rpoB-trnC_p1 rpoB-trnC CTCTCATTTCCACCCCCAAG TGTTTGTTGATGAGGCGACA 1038–1050 1.000 80.9
rpoB-trnC_p2 rpoB-trnC CTCTCATTTCCACCCCCAAG CCGGATTTGAACTGGGGAAA 1017–1029 1.000 80.6
rpoB-trnC_p3 rpoB-trnC CTCTCATTTCCACCCCCAAG TGGGGAAAAAGGGATTTGCA 1005–1017 1.000 80.4
rpoB-trnC_p4 rpoB-trnC TCTCTCATTTCCACCCCCAA TGTTTGTTGATGAGGCGACA 1039–1051 1.000 80.0
rpoB-trnC_p5 rpoB-trnC TTCTCTCATTTCCACCCCCA TGTTTGTTGATGAGGCGACA 1040–1052 1.000 80.0
trnC-petN_p1 trnC-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 1066–1069 1.000 77.3
trnC-petN_p2 trnC-petN TTTTGTATCGTTTTGGCGGC TCTTCCCCATACTACGAGGG 1056–1059 1.000 77.1
trnC-petN_p3 trnC-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1009–1012 1.000 77.1
trnC-petN_p4 trnC-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACGAGGG 999–1002 1.000 76.9
trnC-petN_p5 trnC-petN TGCAAATCCCTTTTTCCCCA AGAGTCCACTTCTTCCCCAT 1021–1024 1.000 76.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Coccinia grandiflora PQ423863.1 122276 View on NCBI ↗
Coccinia grandis NC_031834.1 157035 View on NCBI ↗