Markers + reference

Chorilaena

2 species · Rutaceae · Sapindales

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Species 2
Genome length 157–157 kb
Candidate markers 268
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 378 0.0372 0.99 62.4 yes View details
trnK-UUU-rps16 LSC 571 0.0233 0.98 59.6 yes View details
trnR-UCU-atpA LSC 240 0.0278 0.90 63.1 yes View details
atpH-atpI LSC 1174 0.0225 0.98 62.5 yes View details
petN-psbM LSC 1257 0.0176 1.00 62.2 yes View details
psbZ-trnG-GCC LSC 512 0.0373 1.00 70.9 yes View details
trnF-GAA-ndhJ LSC 408 0.0319 1.00 58.5 yes View details
rps3-rpl22 LSC 368 0.0387 0.84 68.0 yes View details
ccsA-ndhD SSC 320 0.0635 0.93 78.8 yes View details
ndhD SSC 1476 0.0061 1.00 51.2 yes View details
ndhA SSC 2238 0.0117 0.99 50.5 yes View details
rpl22-trnH-GUG IRa 143 0.1043 0.80 78.2 no View details
trnG-UCC-trnR-UCU LSC 187 0.0802 1.00 77.5 yes View details
psbC-trnS-UGA LSC 249 0.0406 0.99 76.0 yes View details
ndhD-psaC SSC 185 0.0337 0.96 73.7 yes View details
trnW-CCA-trnP-UGG LSC 208 0.0476 0.61 69.0 yes View details
rps4-trnT-UGU LSC 366 0.0286 0.86 68.6 yes View details
psbE-petL LSC 1432 0.0102 0.96 68.6 yes View details
trnT-UGU-trnL-UAA LSC 869 0.0207 0.94 68.3 yes View details
trnC-GCA-petN LSC 621 0.0180 0.98 63.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATTTCAGGCAGAGCACAACA 906–908 1.000 80.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTTCAGGCAGAGCACAACAT 905–907 1.000 80.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ATTTCAGGCAGAGCACAACA 920–922 1.000 80.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTTCAGGCAGAGCACAACAT 919–921 1.000 80.4
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTTCAGGCAGAGCACAACAT 918–920 1.000 80.4
trnK-UUU_p1 trnK-UUU CGAGAGAATTGAGGGCTTGT TTGATCGTGGAGAAACGGAC 2996 0.500 56.3
trnK-UUU_p2 trnK-UUU CGAGAGAATTGAGGGCTTGT CGTGGAGAAACGGACTCATT 2991 0.500 56.2
trnK-UUU_p3 trnK-UUU CGAGAGAATTGAGGGCTTGT GATCGTGGAGAAACGGACTC 2994 0.500 56.1
trnK-UUU_p4 trnK-UUU TCGAGAGAATTGAGGGCTTG TTGATCGTGGAGAAACGGAC 2997 0.500 54.0
trnK-UUU_p5 trnK-UUU TCGAGAGAATTGAGGGCTTG CGTGGAGAAACGGACTCATT 2992 0.500 53.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG ATTTCAAAGAAAGCGGGGGT 676–681 1.000 83.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG CCCAATGAGCCGTTTATCGA 849–854 1.000 82.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TCCCAATGAGCCGTTTATCG 850–855 1.000 82.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AATTGGAACCCTAGGGCTCT ATTTCAAAGAAAGCGGGGGT 924–929 1.000 82.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGCGCCAAGAATTCAAACTT ATTTCAAAGAAAGCGGGGGT 857–862 1.000 82.0
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAATCAATTGCGTCCAA 314 1.000 69.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAATCAATTGCGTCCAA 317 1.000 69.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ATGGAAATCAATTGCGTCCA 315 1.000 67.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG ATGGAAATCAATTGCGTCCA 318 1.000 67.2
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGGAAATCAATTGCGTCCAA 318 1.000 66.9
trnR-UCU-atpA_p1 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT CGAGGAAGCAGAAACCCTTT 371–395 1.000 82.9
trnR-UCU-atpA_p2 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT TTCACCGAGGAAGCAGAAAC 376–400 1.000 82.8
trnR-UCU-atpA_p3 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT GGAAGCAGAAACCCTTTTGC 368–392 1.000 82.5
trnR-UCU-atpA_p4 trnR-UCU-atpA ACTGAAAGGCGTCCATTGTC CGAGGAAGCAGAAACCCTTT 372–396 1.000 80.6
trnR-UCU-atpA_p5 trnR-UCU-atpA GACTGAAAGGCGTCCATTGT CGAGGAAGCAGAAACCCTTT 373–397 1.000 80.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1261–1271 1.000 81.4
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1262–1272 1.000 80.2
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGCGAATCTATGGAGGGAC 1234–1244 1.000 77.3
atpH-atpI_p4 atpH-atpI TAACGGAAGCGGCAGAAATC TTTTGCAACTTTAGCTGCGG 1260–1270 1.000 76.6
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT ACAAGCGGTATTCAAGCTCT 1284–1294 1.000 76.3

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
Chorilaena euphemiae NC_081902.1 157091 View on NCBI ↗
Chorilaena quercifolia NC_081869.1 156892 View on NCBI ↗