Markers + reference

Gagnebina

2 species · Fabaceae · Fabales

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Species 2
Genome length 160–160 kb
Candidate markers 268
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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1055 0.0068 0.56 54.3 yes View details
rps16-trnQ-UUG LSC 623 0.0082 0.98 65.3 yes View details
trnR-UCU-atpA LSC 373 0.0164 0.98 60.7 yes View details
atpH-atpI LSC 1537 0.0052 0.99 62.2 yes View details
rpoB-trnC-GCA LSC 1216 0.0033 0.99 53.3 yes View details
psbC LSC 1422 0.0000 1.00 32.2 yes View details
psbC-trnS-UGA LSC 243 0.0422 0.98 79.0 yes View details
psbZ-trnG-GCC LSC 589 0.0052 0.99 54.2 yes View details
trnM-CAU-atpE LSC 275 0.0218 1.00 52.4 yes View details
accD-psaI LSC 691 0.0094 0.92 68.1 yes View details
rps3-rps19 LSC 411 0.0438 1.00 77.7 yes View details
ndhE SSC 306 0.0033 1.00 39.7 yes View details
psaA-ycf3 LSC 784 0.0000 0.93 63.1 yes View details
ndhD-ccsA SSC 557 0.0055 0.98 62.9 yes View details
trnT-UGU-trnL-UAA LSC 1065 0.0057 0.99 62.6 yes View details
psbE-petL LSC 1381 0.0029 0.98 62.1 yes View details
rbcL-accD LSC 906 0.0035 0.96 62.0 yes View details
atpF LSC 1280 0.0024 0.98 61.9 yes View details
petA-psbJ LSC 878 0.0046 1.00 61.8 yes View details
rps11-rpl36 LSC 164 0.0124 0.98 61.4 yes View details
trnY-GUA-trnE-UUC LSC 66 0.0152 1.00 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
trnK-UUU_p1 trnK-UUU TGACTTGATACATATGACTTGGA TGCGGTTGTATCTACACATCT 2692–2698 1.000 40.2
trnK-UUU_p2 trnK-UUU TGACTTGATACATATGACTTGGA TGATTGCGGTTGTATCTACACA 2696–2702 1.000 40.2
trnK-UUU_p3 trnK-UUU TGACTTGATACATATGACTTGGA TGCGGTTGTATCTACACATCTT 2692–2698 1.000 40.2
trnK-UUU_p4 trnK-UUU TGACTTGATACATATGACTTGGA TTGCGGTTGTATCTACACATCT 2693–2699 1.000 40.2
trnK-UUU_p5 trnK-UUU TGACTTGATACATATGACTTGGAT TGCGGTTGTATCTACACATCT 2692–2698 1.000 40.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAAGGCGCTCAACCTACA 840–1262 1.000 83.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CCTTGAAAAAGGCGCTCAAC 845–1267 1.000 81.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CTTGAAAAAGGCGCTCAACC 844–1266 1.000 81.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TGAAAAAGGCGCTCAACCTA 842–1264 1.000 81.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGGCGGGTGTTTTTATGGAA 795–1217 1.000 81.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TCGAATAGAAATGGGGCGTG 751–762 1.000 81.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 692–703 1.000 81.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT TCGAATAGAAATGGGGCGTG 753–764 1.000 80.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 694–705 1.000 80.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA TCGAATAGAAATGGGGCGTG 739–750 1.000 79.8
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACTCGGGAAGC 483–491 1.000 68.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCAAGACATTCACTCGGGAA 485–493 1.000 65.0
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AAGACATTCACTCGGGAAGC 518–526 1.000 64.9
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACCAAGACATTCACTCGGGA 486–494 1.000 63.5
trnR-UCU-atpA_p5 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA AAGACATTCACTCGGGAAGC 482–490 1.000 62.3
atpF_p1 atpF TTCATCTGCGCGAATGGTTA AGTCTATCTATAAGAGGAGATGA 1388–1397 1.000 41.6
atpF_p2 atpF CGCGAATGGTTACCATGAGT AGTCTATCTATAAGAGGAGATGA 1380–1389 1.000 41.6
atpF_p3 atpF TTCATCTGCGCGAATGGTTA AGTCTATCTATAAGAGGAGATGAT 1388–1397 1.000 41.6
atpF_p4 atpF AATTTCATCTGCGCGAATGG AGTCTATCTATAAGAGGAGATGA 1391–1400 1.000 41.5
atpF_p5 atpF ATTTCATCTGCGCGAATGGT AGTCTATCTATAAGAGGAGATGA 1390–1399 1.000 41.5
atpH-atpI_p1 atpH-atpI AGCGGCAGAAATCAATGGAT AGTGGTTCCGATACCTGTCA 1676–1684 1.000 79.7
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCTGCGG 1616–1624 1.000 79.2
atpH-atpI_p3 atpH-atpI AAGCGGCAGAAATCAATGGA AGTGGTTCCGATACCTGTCA 1677–1685 1.000 78.9
atpH-atpI_p4 atpH-atpI CGAAGCGGCAGAAATCAATG AGTGGTTCCGATACCTGTCA 1679–1687 1.000 78.8
atpH-atpI_p5 atpH-atpI GAAGCGGCAGAAATCAATGG AGTGGTTCCGATACCTGTCA 1678–1686 1.000 78.6

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
Gagnebina commersoniana PV870688.1 160196 View on NCBI ↗
Gagnebina pterocarpa PV870696.1 160040 View on NCBI ↗