Markers + reference

Orbea

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 161–162 kb
Candidate markers 274
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 342 0.0449 0.91 75.6 yes View details
accD LSC 1554 0.0171 0.94 61.8 yes View details
clpP1 LSC 2072 0.0454 0.97 73.6 yes View details
trnN-GUU-ycf1 IRb 1032 0.0270 0.29 49.3 yes View details
ycf1 IRb 5571 0.0146 0.99 46.6 yes View details
ycf1 IRa 5571 0.0146 0.99 46.6 no View details
ycf1-trnN-GUU IRa 1032 0.0270 0.29 49.3 yes View details
trnfM-CAU LSC 74 0.0405 1.00 75.8 yes View details
rps19-rpl2 IRb 24 0.0417 1.00 71.7 yes View details
rps12-clpP1 LSC 111 0.0901 1.00 71.6 yes View details
trnG-GCC LSC 71 0.0282 1.00 67.7 yes View details
rps11-rpl36 LSC 111 0.0270 1.00 67.2 yes View details
psbE-petL LSC 1135 0.0071 0.99 63.8 yes View details
trnK-UUU-rps16 LSC 800 0.0077 0.97 63.5 yes View details
atpB-rbcL LSC 792 0.0000 0.96 62.2 yes View details
rps2 LSC 711 0.0056 1.00 62.0 yes View details
trnR-ACG-trnN-GUU IRb 426 0.0117 1.00 61.9 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 80 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 TTCCCTCTAGACCTAGCTGC 410–411 1.000 85.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 424–425 1.000 85.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 423–424 1.000 85.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 425–426 1.000 85.0
trnH-GUG-psbA_p5 trnH-GUG-psbA AAAACAAAAGGGCGAACGAC TTCCCTCTAGACCTAGCTGC 474 0.500 57.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TCAAAAGGGTGGGGGTTTTT 951–953 1.000 79.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCAAAAGGGTGGGGGTTTT 952–954 1.000 79.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTCAAAAGGGTGGGGGTTT 953–955 1.000 79.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTTCAAAAGGGTGGGGGTT 954–956 1.000 79.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAAGGGTGGGGGTTTTT 889–891 1.000 78.8
rps2_p1 rps2 CAAGGTCTGCCCAGTTATTT GCCAATCTACGGTAGAGCAG 927–948 1.000 62.0
rps2_p2 rps2 CAAGGTCTGCCCAGTTATTT AGCCAATCTACGGTAGAGCA 928–949 1.000 61.4
rps2_p3 rps2 CAAGGTCTGCCCAGTTATTTT GCCAATCTACGGTAGAGCAG 927–948 1.000 60.3
rps2_p4 rps2 CAAGGTCTGCCCAGTTATTTT AGCCAATCTACGGTAGAGCA 928–949 1.000 59.7
rps2_p5 rps2 CAAGGTCTGCCCAGTTATTTTT GCCAATCTACGGTAGAGCAG 927–948 1.000 58.1
trnG-GCC_p1 trnG-GCC AGGAGAGTCTTTGGTCTGGG ACTACACGATCACCGACAAC 256–274 1.000 75.1
trnG-GCC_p2 trnG-GCC GGAGAGTCTTTGGTCTGGGA ACTACACGATCACCGACAAC 255–273 1.000 75.0
trnG-GCC_p3 trnG-GCC AGGAGAGTCTTTGGTCTGGG GGGAGGCTATAGGAAAGGGA 295–312 1.000 74.7
trnG-GCC_p4 trnG-GCC AGAGTCTTTGGTCTGGGACT ACTACACGATCACCGACAAC 253–271 1.000 74.6
trnG-GCC_p5 trnG-GCC GGAGAGTCTTTGGTCTGGGA GGGAGGCTATAGGAAAGGGA 294–311 1.000 74.6
trnfM-CAU_p1 trnfM-CAU TCTCTTTGCCAGGGAGAAGA TTCATCGACGTTGTTTTGCG 609–722 1.000 84.5
trnfM-CAU_p2 trnfM-CAU GTGCCCGTTGTATTTGCTTC TTCATCGACGTTGTTTTGCG 1098–1194 1.000 84.4
trnfM-CAU_p3 trnfM-CAU ATTAGCGTGCCCGTTGTATT TTCATCGACGTTGTTTTGCG 1104–1200 1.000 84.3
trnfM-CAU_p4 trnfM-CAU GTGCCCGTTGTATTTGCTTC GCAAAGTTCCGTCATTGAGC 1179–1275 1.000 84.2
trnfM-CAU_p5 trnfM-CAU GTGCCCGTTGTATTTGCTTC CAATCCCCACCACGGAATAG 1132–1228 1.000 84.2
atpB-rbcL_p1 atpB-rbcL CTACATCTAGTACCGGGCCA AACACCGGCTTTGAATCCAA 915–943 1.000 79.9
atpB-rbcL_p2 atpB-rbcL GCGCAAAGGCTACATCTAGT AACACCGGCTTTGAATCCAA 924–952 1.000 79.5
atpB-rbcL_p3 atpB-rbcL GGAAACCCCAGAACCAGAAG AACACCGGCTTTGAATCCAA 854–882 1.000 79.5
atpB-rbcL_p4 atpB-rbcL CGATACGTCCCAGGTTGTTT AACACCGGCTTTGAATCCAA 885–913 1.000 79.4
atpB-rbcL_p5 atpB-rbcL TCTAGTACCGGGCCAATGAT AACACCGGCTTTGAATCCAA 910–938 1.000 79.2

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
Orbea sprengeri subsp. commutata PQ412530.1 162017 View on NCBI ↗
Orbea variegata NC_079601.1 161348 View on NCBI ↗