Markers + reference

Gomphogyne

2 species · Cucurbitaceae · Cucurbitales

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Species 2
Genome length 157–157 kb
Candidate markers 271
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 7 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 1061 0.0641 0.87 90.7 yes View details
rpoB-trnC-GCA LSC 1215 0.0133 0.99 67.0 yes View details
trnT-GGU-psbD LSC 1179 0.0180 0.94 73.6 yes View details
psaA-ycf3 LSC 741 0.0096 0.98 65.8 yes View details
ndhC LSC 363 0.0000 1.00 24.3 yes View details
ndhC-trnV-UAC LSC 708 0.0539 0.92 91.3 yes View details
petA-psbJ LSC 988 0.0274 1.00 74.6 yes View details
psbE-petL LSC 1281 0.0080 0.97 65.8 yes View details
psbB LSC 1527 0.0007 1.00 49.3 yes View details
psbB-psbT LSC 192 0.0426 0.98 67.4 yes View details
rpl32-trnL-UAG SSC 927 0.0504 0.88 89.6 yes View details
trnS-GCU-trnG-UCC LSC 788 0.0053 0.96 66.0 yes View details
trnR-ACG-trnN-GUU SSC 623 0.0064 1.00 62.4 yes View details
trnN-GUU-trnR-ACG SSC 623 0.0064 1.00 62.4 yes View details
trnE-UUC-trnT-GGU LSC 916 0.0000 0.89 61.9 yes View details
atpF LSC 1350 0.0052 1.00 61.8 yes View details
ndhJ LSC 540 0.0021 0.88 61.6 yes View details
ndhF-rpl32 SSC 641 0.0031 1.00 60.7 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
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CATCGTTAGCTTGGAAGGCT 1540–1578 1.000 83.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CACTTCGCTGCATTTCTTGG CATCGTTAGCTTGGAAGGCT 1897–1935 1.000 82.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTCGCTGCATTTCTTGGTG CATCGTTAGCTTGGAAGGCT 1895–1933 1.000 82.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CACTTCGCTGCATTTCTTGG CGTTAGCTTGGAAGGCTAGG 1894–1932 1.000 82.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CTTCGCTGCATTTCTTGGTG CGTTAGCTTGGAAGGCTAGG 1892–1930 1.000 82.5
trnG-UCC_p1 trnG-UCC ATTAGCAATCCGCCGCTTTA CCCCTCTCACGGTAGAAGAA 2642–2802 1.000 82.6
trnG-UCC_p2 trnG-UCC CCGTAATCCTGGACGTGAAG CCCCTCTCACGGTAGAAGAA 2826–2986 1.000 82.3
trnG-UCC_p3 trnG-UCC ACGGAAAGAGAGGGATTCGA CCCCTCTCACGGTAGAAGAA 2691–2851 1.000 81.7
trnG-UCC_p4 trnG-UCC ATTAGCAATCCGCCGCTTTA AATTGGCAAGAGGTCAACGA 2693–2853 1.000 81.7
trnG-UCC_p5 trnG-UCC ATTAGCAATCCGCCGCTTTA TTGGCAAGAGGTCAACGATT 2691–2851 1.000 81.7
atpF_p1 atpF TTGCTCAATACGTTCACGGA ACTCTATTTCGAAACTAAATAGGA 1571–1623 1.000 40.4
atpF_p2 atpF TGCTCAATACGTTCACGGAT ACTCTATTTCGAAACTAAATAGGA 1570–1622 1.000 40.4
atpF_p3 atpF TTGCTCAATACGTTCACGGA ACTCTATTTCGAAACTAAATAGGAA 1571–1623 1.000 40.4
atpF_p4 atpF TGCTCAATACGTTCACGGAT ACTCTATTTCGAAACTAAATAGGAA 1570–1622 1.000 40.4
atpF_p5 atpF TTGCTCAATACGTTCACGGA ACTCTATTTCGAAACTAAATAGGAAA 1571–1623 1.000 40.4
atpH-atpI_p1 atpH-atpI GATCCCTTCTACAGCTTGGC TTTTGCAACTTTAGCTGCCG 1121–1233 1.000 86.6
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC CGAATCCATGGAGGGTCATC 1091–1203 1.000 86.4
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTGCAACTTTAGCTGCCG 1044–1156 1.000 85.9
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG CGAATCCATGGAGGGTCATC 1014–1126 1.000 85.6
atpH-atpI_p5 atpH-atpI CGATCCCTTCTACAGCTTGG TTTTGCAACTTTAGCTGCCG 1122–1234 1.000 85.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCTCATTTCCACCCCCAAG GCGTCTTTTGTTGATGAGGC 1321–1325 1.000 80.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCTCATTTCCACCCCCAAG CCGGATTTGAACTGGGGAAA 1296–1300 1.000 79.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCTCTCATTTCCACCCCCAA GCGTCTTTTGTTGATGAGGC 1322–1326 1.000 79.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCTCTCATTTCCACCCCCA GCGTCTTTTGTTGATGAGGC 1323–1327 1.000 79.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCTCTCATTTCCACCCCCAA CCGGATTTGAACTGGGGAAA 1297–1301 1.000 78.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 919–1019 1.000 81.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 898–998 1.000 81.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 898–998 1.000 81.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 877–977 1.000 81.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 895–995 1.000 81.2

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
Gomphogyne cissiformis var. cissiformis MH256801.1 157334 View on NCBI ↗
Gomphogyne cissiformis var. villosa MF784515.1 156585 View on NCBI ↗