Markers + reference

Ormosia

10 species · Fabaceae · Fabales

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Species 10
Genome length 170–174 kb
Candidate markers 292
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 292 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC-trnV-UAC LSC 551 0.0523 0.85 73.4 yes View details
atpH-atpI LSC 1333 0.0241 0.60 66.7 yes View details
rpoB-trnC-GCA LSC 983 0.0646 0.75 76.9 yes View details
trnC-GCA-petN LSC 1200 0.0473 0.93 77.5 yes View details
psbZ-trnG-GCC LSC 1136 0.0541 0.83 83.0 yes View details
psaA-ycf3 LSC 909 0.0449 0.93 81.0 yes View details
psbK-trnQ-UUG LSC 977 0.0750 0.85 79.2 yes View details
clpP IRb 2073 0.0167 0.95 57.1 yes View details
rpl32-trnL-UAG SSC 1046 0.0862 0.47 76.4 yes View details
rpl14-rps8 IRa 828 0.0380 0.86 81.7 yes View details
rps12-clpP LSC 173 0.0680 0.97 80.6 yes View details
trnD-GUC-trnY-GUA LSC 463 0.0390 0.98 78.9 yes View details
atpE-trnS-GCU LSC 851 0.0349 0.97 78.6 yes View details
rps8-rpl14 IRb 828 0.0298 0.87 76.5 yes View details
rbcL-atpB LSC 788 0.0188 0.98 75.8 yes View details
trnP-UGG-psaJ LSC 649 0.0311 0.95 75.6 yes View details
trnT-UGU-trnL-UAA LSC 788 0.0340 0.96 75.4 yes View details
trnK-UUU-rbcL LSC 1333 0.0357 0.94 75.0 yes View details
rps11-rpl36 IRb 604 0.0286 0.88 71.3 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-rbcL_p1 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA TGCTTGTGAAGTCTGGAAGG 1374–1437 1.000 81.0
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA GCTGCTTGTGAAGTCTGGAA 1376–1439 1.000 79.9
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA GCTTGTGAAGTCTGGAAGGA 1373–1436 1.000 78.7
trnK-UUU-rbcL_p4 trnK-UUU-rbcL GCCGAGTACTCTACCATTGAG TGCTTGTGAAGTCTGGAAGG 1373–1436 1.000 78.3
trnK-UUU-rbcL_p5 trnK-UUU-rbcL GCCGAGTACTCTACCATTGAG GCTGCTTGTGAAGTCTGGAA 1375–1438 1.000 77.2
rbcL-atpB_p1 rbcL-atpB AACACCAGCTTTGAACCCAA GCGATACGTCCCAAGTTTCT 894–957 1.000 86.5
rbcL-atpB_p2 rbcL-atpB AACACCAGCTTTGAACCCAA AAGCTACATCCAGTACCGGA 926–989 1.000 85.1
rbcL-atpB_p3 rbcL-atpB AACACCAGCTTTGAACCCAA CTACATCCAGTACCGGACCA 923–986 1.000 84.5
rbcL-atpB_p4 rbcL-atpB AACACCAGCTTTGAACCCAA TACATCCAGTACCGGACCAA 922–985 1.000 84.5
rbcL-atpB_p5 rbcL-atpB GCTTTGAACCCAACACTTGC GCGATACGTCCCAAGTTTCT 887–950 1.000 84.2
atpE-trnS-GCU_p1 atpE-trnS-GCU CTCTCAGACGAGCTAGGACA CAATCCGACGCTTTAGTCCA 917–1082 1.000 90.2
atpE-trnS-GCU_p2 atpE-trnS-GCU CTCTCAGACGAGCTAGGACA AATCCGACGCTTTAGTCCAC 916–1081 1.000 90.2
atpE-trnS-GCU_p3 atpE-trnS-GCU CGAGCTAGGACACGAGTAGA CAATCCGACGCTTTAGTCCA 909–1074 1.000 90.0
atpE-trnS-GCU_p4 atpE-trnS-GCU CGAGCTAGGACACGAGTAGA AATCCGACGCTTTAGTCCAC 908–1073 1.000 90.0
atpE-trnS-GCU_p5 atpE-trnS-GCU TCTCAGACGAGCTAGGACAC CAATCCGACGCTTTAGTCCA 916–1081 1.000 88.4
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 556–1021 1.000 90.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 564–1029 1.000 89.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 588–1053 1.000 89.2
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 596–1061 1.000 88.6
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 570–1035 1.000 88.3
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CTTGATATTATCAGAAATGCCCA AGAAGGTCTACGGTTCGAGT 531–676 1.000 52.0
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TGATATTATCAGAAATGCCCA AGAAGGTCTACGGTTCGAGT 529–674 1.000 52.0
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CTTGATATTATCAGAAATGCCCAA AGAAGGTCTACGGTTCGAGT 531–676 1.000 52.0
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TGATATTATCAGAAATGCCCAA AGAAGGTCTACGGTTCGAGT 529–674 1.000 52.0
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TTGATATTATCAGAAATGCCCA AGAAGGTCTACGGTTCGAGT 530–675 1.000 52.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCTGCGGCTTATATAGGTGA 803–1407 1.000 82.9
atpH-atpI_p2 atpH-atpI CGCAATCCCTTCTACAGCTT GCTGCGGCTTATATAGGTGA 891–1495 1.000 82.5
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT ACAAGCGGTATTCAAGCTCT 839–1443 1.000 82.5
atpH-atpI_p4 atpH-atpI CGCAATCCCTTCTACAGCTT ACAAGCGGTATTCAAGCTCT 927–1531 1.000 82.2
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCTGCGGCTTATATAGGTGA 804–1408 1.000 81.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Ormosia bahiensis MW628939.1 174074 View on NCBI ↗
Ormosia balansae NC_081486.1 170836 View on NCBI ↗
Ormosia elliptica NC_081487.1 169797 View on NCBI ↗
Ormosia fordiana MW752862.1 173431 View on NCBI ↗
Ormosia hosiei NC_039418.1 171642 View on NCBI ↗
Ormosia microphylla NC_081489.1 172973 View on NCBI ↗
Ormosia olivacea NC_081488.1 172829 View on NCBI ↗
Ormosia pinnata NC_064393.1 171641 View on NCBI ↗
Ormosia semicastrata f. pallida OQ862760.1 173946 View on NCBI ↗
Ormosia sericeolucida LC703159.1 171088 View on NCBI ↗