Markers + reference

Citropsis

3 species · Rutaceae · Sapindales

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Species 3
Genome length 159–160 kb
Candidate markers 285
Primer pairs 95

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 285 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-psbK LSC 352 0.0189 1.00 38.4 yes View details
trnR-UCU-atpA LSC 195 0.0273 1.00 51.7 yes View details
petN-psbM LSC 1276 0.0106 0.98 40.9 yes View details
petA-psbJ LSC 1095 0.0110 1.00 53.5 yes View details
rpl20 LSC 354 0.0094 1.00 34.5 yes View details
ycf1 IRb 1122 0.0042 1.00 41.0 no View details
ndhF SSC 2238 0.0069 1.00 35.1 yes View details
rpl32-trnL-UAG SSC 1080 0.0144 0.95 45.7 yes View details
ycf1 SSC 5490 0.0060 1.00 29.2 yes View details
psbC-trnS-UGA LSC 247 0.0270 1.00 57.2 yes View details
ndhE-ndhG SSC 284 0.0170 0.96 54.0 yes View details
psaA-pafI LSC 717 0.0077 0.97 53.8 yes View details
trnW-CCA-trnP-UGG LSC 171 0.0195 1.00 52.4 yes View details
psbZ-trnG-GCC LSC 547 0.0097 1.00 51.4 yes View details
atpH-atpI LSC 981 0.0061 1.00 50.1 yes View details
rpoB-trnC-GCA LSC 1203 0.0061 1.00 50.1 yes View details
trnT-GGU-psbD LSC 1251 0.0081 0.98 50.1 yes View details
psbE-petL LSC 1369 0.0054 1.00 50.1 yes View details
ndhH-rps15 SSC 101 0.0330 1.00 50.1 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
trnK-UUU_p1 trnK-UUU TCCGTGTCAACCAACAATCC TGATCATGGAGAAATGGGCC 2938–2952 1.000 75.2
trnK-UUU_p2 trnK-UUU ATCTCCGTGTCAACCAACAA TGATCATGGAGAAATGGGCC 2941–2955 1.000 73.4
trnK-UUU_p3 trnK-UUU TCTCCGTGTCAACCAACAAT TGATCATGGAGAAATGGGCC 2940–2954 1.000 73.4
trnK-UUU_p4 trnK-UUU CCGTGTCAACCAACAATCCA TGATCATGGAGAAATGGGCC 2937–2951 1.000 72.9
trnK-UUU_p5 trnK-UUU TCCGTGTCAACCAACAATCC GATCATGGAGAAATGGGCCT 2951 0.333 44.8
trnQ-UUG-psbK_p1 trnQ-UUG-psbK AAGAGGGTTGCTCAAAAGGG CTTACAGCAGCTTGCCAAAC 646 1.000 81.5
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GAGGGTTGCTCAAAAGGGAA CTTACAGCAGCTTGCCAAAC 644 1.000 81.5
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AAGAGGGTTGCTCAAAAGGG GCCTCGGGTAATTTAGCGAA 556 0.333 52.9
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAGGGTTGCTCAAAAGGGAA GCCTCGGGTAATTTAGCGAA 554 0.333 52.8
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CGGGGAACACAAATGCATTC GCCTCGGGTAATTTAGCGAA 700 0.333 52.8
trnR-UCU-atpA_p1 trnR-UCU-atpA AATGGAATGAAAGGCGTCCA GAAGCCCTTTTGCAAGAAGC 346–377 1.000 78.3
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAATGAAAGGCGTCCATT GAAGCCCTTTTGCAAGAAGC 344–375 1.000 78.3
trnR-UCU-atpA_p3 trnR-UCU-atpA AATGGAATGAAAGGCGTCCA AGCCCTTTTGCAAGAAGCTA 344–375 1.000 77.7
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAATGAAAGGCGTCCATT AGCCCTTTTGCAAGAAGCTA 342–373 1.000 77.7
trnR-UCU-atpA_p5 trnR-UCU-atpA ATGGAATGAAAGGCGTCCAT GAAGCCCTTTTGCAAGAAGC 345–376 1.000 76.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCCGTCATGTTCCTTGGATT 1115–1369 1.000 79.2
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1068–1322 1.000 79.2
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT CCCGTCATGTTCCTTGGATT 1171–1425 1.000 78.6
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCGG 1124–1378 1.000 78.6
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA CCCGTCATGTTCCTTGGATT 1153–1407 1.000 78.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC ATCGTTTGTTGATCAGGCGA 1314–1355 1.000 79.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC ACCAGCCAAGCAGAATAAGG 1347–1388 1.000 79.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC GTTTGTTGATCAGGCGACAC 1311–1352 1.000 78.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC AAAAGGATTTGCAGTCCCCC 1273–1314 1.000 77.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC CAGCCAAGCAGAATAAGGGA 1345–1386 1.000 77.1
petN-psbM_p1 petN-psbM AAGTACGCGACTCTTGACAC TTGTACAAGTAAGGCGGTCG 2467–2476 1.000 81.2
petN-psbM_p2 petN-psbM GTACGCGACTCTTGACACTT TTGTACAAGTAAGGCGGTCG 2465–2474 1.000 81.2
petN-psbM_p3 petN-psbM ACATTTTCCCTTTCGCTCGT TTGTACAAGTAAGGCGGTCG 1764–1779 1.000 81.0
petN-psbM_p4 petN-psbM AAGTACGCGACTCTTGACAC GCGGTTAGGTGGTTGTACAA 2479–2488 1.000 80.8
petN-psbM_p5 petN-psbM GTACGCGACTCTTGACACTT GCGGTTAGGTGGTTGTACAA 2477–2486 1.000 80.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Citropsis gabunensis PQ300131.1 159473 View on NCBI ↗
Citropsis gilletiana LC794888.1 159581 View on NCBI ↗
Citropsis schweinfurthii LC794889.1 159581 View on NCBI ↗