Markers + reference

Centrolobium

2 species · Fabaceae · Fabales

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Species 2
Genome length 159–159 kb
Candidate markers 264
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-UAA-trnT-UGU LSC 1147 0.0044 1.00 61.5 yes View details
psbZ-trnS-UGA LSC 354 0.0000 1.00 30.4 yes View details
trnS-UGA-psbC LSC 242 0.0455 1.00 78.6 yes View details
trnY-GUA-trnD-GUC LSC 518 0.0106 0.91 58.1 yes View details
rpoC2 LSC 4203 0.0019 1.00 54.8 yes View details
atpF LSC 1317 0.0008 1.00 51.2 yes View details
petA-psbJ LSC 1103 0.0054 1.00 62.0 yes View details
psbE-petL LSC 1369 0.0059 0.99 48.1 yes View details
trnP-UGG-psaJ LSC 636 0.0079 1.00 63.6 yes View details
ndhF-rpl32 SSC 757 0.0106 1.00 59.4 yes View details
rpl32-trnL-UAG SSC 833 0.0072 1.00 54.7 yes View details
ndhG SSC 531 0.0075 1.00 57.2 yes View details
trnL-UAG-ccsA SSC 120 0.0345 0.97 75.4 yes View details
atpH-atpF LSC 467 0.0091 0.95 65.9 yes View details
psbM-petN LSC 1306 0.0034 0.90 64.2 yes View details
ycf3-psaA LSC 872 0.0035 0.97 63.6 yes View details
rps11-rpl36 LSC 532 0.0020 0.93 62.8 yes View details
rpl16-rps3 LSC 167 0.0180 1.00 62.8 yes View details
trnQ-UUG-rps16 LSC 607 0.0066 1.00 62.5 yes View details
trnK-UUU-rbcL LSC 724 0.0055 1.00 62.2 yes View details
psbA-trnK-UUU LSC 324 0.0066 0.94 61.2 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU AACACCAAACCATCCGATGT CGGCTTGGGGAGAGATTTTT 518–538 1.000 79.8
psbA-trnK-UUU_p2 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA CGGCTTGGGGAGAGATTTTT 494–514 1.000 79.5
psbA-trnK-UUU_p3 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA CGGCTTGGGGAGAGATTTTT 443–463 1.000 78.2
psbA-trnK-UUU_p4 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CGGCTTGGGGAGAGATTTTT 468–488 1.000 77.7
psbA-trnK-UUU_p5 psbA-trnK-UUU CCATCCGATGTAAAGACGGT CGGCTTGGGGAGAGATTTTT 509–529 1.000 77.3
trnK-UUU_p1 trnK-UUU CTCCCAAGCACACGAATTCT TAGACAAAGGGGTGGTCCAT 2984–2992 1.000 79.0
trnK-UUU_p2 trnK-UUU ACTCCCAAGCACACGAATTC TAGACAAAGGGGTGGTCCAT 2985–2993 1.000 76.7
trnK-UUU_p3 trnK-UUU GACTCCCAAGCACACGAATT TAGACAAAGGGGTGGTCCAT 2986–2994 1.000 76.7
trnK-UUU_p4 trnK-UUU CTCCCAAGCACACGAATTCT TCTAGACAAAGGGGTGGTCC 2986–2994 1.000 76.6
trnK-UUU_p5 trnK-UUU CTCCCAAGCACACGAATTCT ACTCTAGACAAAGGGGTGGT 2988–2996 1.000 76.1
trnK-UUU-rbcL_p1 trnK-UUU-rbcL TACCGAGGGTATGGACGAAA AGTCCTGAATTAGCTGCTGC 895–939 1.000 79.2
trnK-UUU-rbcL_p2 trnK-UUU-rbcL TACCGAGGGTATGGACGAAA GAGGCTAGCAAATGGAGTCC 910–954 1.000 79.1
trnK-UUU-rbcL_p3 trnK-UUU-rbcL CTACCGAGGGTATGGACGAA AGTCCTGAATTAGCTGCTGC 896–940 1.000 77.8
trnK-UUU-rbcL_p4 trnK-UUU-rbcL CTACCGAGGGTATGGACGAA GAGGCTAGCAAATGGAGTCC 911–955 1.000 77.8
trnK-UUU-rbcL_p5 trnK-UUU-rbcL CGAGGGTATGGACGAAACAA AGTCCTGAATTAGCTGCTGC 892–936 1.000 77.3
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1205–1211 1.000 78.9
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU CCCATTGTTAATTCCGGGGT GCGATGCTCTAACCTCTGAG 1290–1296 1.000 78.2
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1237–1243 1.000 78.0
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 1211–1217 1.000 77.5
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU CCCATTGTTAATTCCGGGGT GGAATCGAACCGATGACCAT 1322–1328 1.000 77.3
ycf3-psaA_p1 ycf3-psaA AGCCCTTACCCCTGGTAATT TGCCCATTCCTCGAAAGAAG 1001–1020 1.000 81.3
ycf3-psaA_p2 ycf3-psaA AGCCCTTACCCCTGGTAATT GCCCATTCCTCGAAAGAAGT 1000–1019 1.000 81.3
ycf3-psaA_p3 ycf3-psaA AGCTATAGCCCTTACCCCTG TGCCCATTCCTCGAAAGAAG 1007–1026 1.000 81.0
ycf3-psaA_p4 ycf3-psaA AGCTATAGCCCTTACCCCTG GCCCATTCCTCGAAAGAAGT 1006–1025 1.000 81.0
ycf3-psaA_p5 ycf3-psaA TTGGTTGAAGATCACAGGGC TGCCCATTCCTCGAAAGAAG 965–984 1.000 80.7
psbZ-trnS-UGA_p1 psbZ-trnS-UGA CGACCAACCATCAGGAGAAG CAACCACTCAGCCATCTCTC 477 1.000 79.7
psbZ-trnS-UGA_p2 psbZ-trnS-UGA CGACCAACCATCAGGAGAAG GAGCTATCAACCACTCAGCC 484 1.000 79.4
psbZ-trnS-UGA_p3 psbZ-trnS-UGA CGACCAACCATCAGGAGAAG GGAGCTATCAACCACTCAGC 485 1.000 79.4
psbZ-trnS-UGA_p4 psbZ-trnS-UGA CGACCAACCATCAGGAGAAG CAAGACCGGAGCTATCAACC 492 1.000 79.4
psbZ-trnS-UGA_p5 psbZ-trnS-UGA CCAACCATCAGGAGAAGCAA CAACCACTCAGCCATCTCTC 474 1.000 78.2

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
Centrolobium microchaete MW628956.1 158908 View on NCBI ↗
Centrolobium tomentosum NC_067527.1 158971 View on NCBI ↗