Markers + reference

Croton

6 species · Euphorbiaceae · Malpighiales

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Species 6
Genome length 150–177 kb
Candidate markers 282
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 282 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 582 0.0813 0.97 83.1 yes View details
trnG-UCC-trnR-UCU LSC 887 0.1064 0.85 84.3 yes View details
psbM-trnD-GUC LSC 1424 0.0534 0.83 80.6 yes View details
trnE-UUC-trnT-GGU LSC 1621 0.0555 0.80 78.3 yes View details
psbZ-trnG-GCC LSC 744 0.0604 0.92 81.2 yes View details
ndhC-trnV-UAC LSC 762 0.0726 0.87 80.8 yes View details
accD-psaI LSC 505 0.0907 0.93 80.3 yes View details
ndhF-trnL-UAG SSC 1622 0.0706 0.91 83.0 yes View details
rpoA-trnH-GUG LSC 3427 0.2144 0.24 67.6 no View details
trnK-UUU-rps16 LSC 706 0.0538 0.98 85.2 yes View details
atpF-atpH LSC 618 0.0532 0.80 83.4 yes View details
trnD-GUC-trnY-GUA LSC 474 0.0495 0.96 82.2 yes View details
trnG-GCC-trnfM-CAU LSC 257 0.0836 0.79 77.7 yes View details
rpl33-rps18 LSC 419 0.0579 0.82 77.7 yes View details
trnF-GAA-ndhJ LSC 820 0.0361 0.97 77.5 yes View details
trnH-GUG-psbA LSC 413 0.0628 0.85 77.4 yes View details
rps15-ycf1 SSC 376 0.0731 0.91 77.4 yes View details
trnR-UCU-atpA LSC 397 0.0687 0.91 76.6 yes View details
psaA-ycf3 LSC 610 0.0324 0.97 75.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CTGTCGAAGCTCCATCTATCA 387–498 1.000 74.9
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CTGTCGAAGCTCCATCTATCA 388–499 1.000 74.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG CTGTCGAAGCTCCATCTATCA 380–491 1.000 73.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGTCGAAGCTCCATCTATCA 386–497 1.000 73.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGTCGAAGCTCCATCTATCA 387–498 1.000 72.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTTAGCCGCACTTAAAAGCC TTCGCCTTAATCAAACACAA 661–1157 1.000 55.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTCGCCTTAATCAAACACAA 656–1152 1.000 55.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 GTTAGCCGCACTTAAAAGCC TCGCCTTAATCAAACACAAT 660–1156 1.000 53.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TCGCCTTAATCAAACACAAT 655–1151 1.000 53.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTTAGCCGCACTTAAAAGCC TCGCCTTAATCAAACACAATT 660–1156 1.000 52.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TAGCAATCCGACGCTTTAGG ACCACTAAACTATACCCGCT 392–858 1.000 71.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGG ACCACTAAACTATACCCGCT 391–857 1.000 64.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GACGCTTTAGGCCACTCAG ACCACTAAACTATACCCGCT 383–849 1.000 63.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TAGCAATCCGACGCTTTAGG TACCACTAAACTATACCCGCT 393–859 1.000 63.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACTCGTACAACGGATTAGCA ACCACTAAACTATACCCGCT 407–873 1.000 62.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 751–968 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGAAGACCTCTGTCCTATCCA 757–974 1.000 75.3
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 757–974 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTCTGTCCT 763–980 1.000 74.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT AGAAGACCTCTGTCCTATCCA 740–957 1.000 72.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGCTTTCTTCTTCAGGAACA 252–449 1.000 62.5
trnR-UCU-atpA_p2 trnR-UCU-atpA ACAAGAAAAGCGTCCATTGTC CGCTTTCTTCTTCAGGAACA 505 0.167 17.7
trnR-UCU-atpA_p3 trnR-UCU-atpA GACAAGAAAAGCGTCCATTGT CGCTTTCTTCTTCAGGAACA 506 0.167 17.7
trnR-UCU-atpA_p4 trnR-UCU-atpA ACAAGAAAAGCGTCCATTGTC CGCTTTCTTCTTCAGGAACAAG 505 0.167 16.5
trnR-UCU-atpA_p5 trnR-UCU-atpA GACAAGAAAAGCGTCCATTGT CGCTTTCTTCTTCAGGAACAAG 506 0.167 16.5
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GGCTGGTTGTAGCATTAGCA 549–774 1.000 89.1
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGGCTGGTTGTAGCATTAG 551–776 1.000 87.7
atpF-atpH_p3 atpF-atpH CAAGGAAACGAACGCGAAAG GGCTGGTTGTAGCATTAGCA 704 0.167 41.9
atpF-atpH_p4 atpF-atpH AAGGAAACGAACGCGAAAGA GGCTGGTTGTAGCATTAGCA 703 0.167 41.3
atpF-atpH_p5 atpF-atpH AGGAAACGAACGCGAAAGAA GGCTGGTTGTAGCATTAGCA 702 0.167 41.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Croton bonplandianus PX697006.1 177025 View on NCBI ↗
Croton kongensis PV200213.1 170323 View on NCBI ↗
Croton laevigatus MN713923.1 162515 View on NCBI ↗
Croton setiger PX316409.1 159415 View on NCBI ↗
Croton tiglium NC_040113.1 150021 View on NCBI ↗
Croton yunnanensis NC_068637.1 161127 View on NCBI ↗