Markers + reference

Gleditsia

6 species · Fabaceae · Fabales

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Species 6
Genome length 162–171 kb
Candidate markers 266
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1667 0.1615 0.78 86.4 yes View details
trnR-UCU-atpA LSC 549 0.0988 0.85 80.2 yes View details
trnC-GCA-petN LSC 1309 0.0530 0.95 95.6 yes View details
psbZ-trnG-GCC LSC 1020 0.0983 0.88 85.0 yes View details
trnT-UGU-trnL-UAA LSC 1946 0.0984 0.93 84.5 yes View details
ndhC-trnV-UAC LSC 981 0.0996 0.74 79.4 yes View details
accD-psaI LSC 674 0.1178 0.86 83.2 yes View details
ndhG-ndhI SSC 534 0.1057 0.81 80.6 yes View details
rps8-rpl14 LSC 468 0.0747 0.91 93.1 yes View details
rpl33-rps18 LSC 311 0.0611 0.98 92.0 yes View details
rps11-rpl36 LSC 397 0.0914 0.94 91.5 yes View details
rps3-rps19 LSC 629 0.0354 0.95 81.9 yes View details
rbcL-accD LSC 1170 0.0490 0.90 80.0 yes View details
trnG-UCC-trnR-UCU LSC 442 0.0557 0.91 78.9 yes View details
rps19-trnH-GUG IRa 118 0.0887 0.80 75.9 no View details
petA-psbJ LSC 1359 0.0322 0.98 73.7 yes View details
rpl32-trnL-UAG SSC 805 0.0240 0.99 72.9 yes View details
ndhF-rpl32 SSC 961 0.0135 0.97 70.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 817–1926 0.833 84.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 819–1928 0.833 83.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 805–1914 0.833 83.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 820–1929 0.833 83.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 818–1927 0.833 81.9
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT TGTCCTATCCATTAGACAATG 499–525 1.000 50.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGTCCTATCCATTAGACAATG 510–536 1.000 49.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGTCCTATCCATTAGACAATG 513–539 1.000 49.8
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGTCCTATCCATTAGACAATG 514–540 1.000 49.8
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT TGTCCTATCCATTAGACAATG 580–606 1.000 49.2
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAACTCTTTTTACTTCAGGAACA 483–1180 1.000 52.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACTCTTTTTACTTCAGGAAC 484–1181 1.000 52.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACTCTTTTTACTTCAGGA 484–1181 1.000 52.0
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACTCTTTTTACTTCAGGAA 484–1181 1.000 52.0
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAACTCTTTTTACTTCAGGAACAA 483–1180 1.000 52.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1242–1425 1.000 90.1
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1303–1486 1.000 88.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1260–1443 1.000 87.9
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 1321–1504 1.000 86.3
trnC-GCA-petN_p5 trnC-GCA-petN GTATAGTTTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 1294–1477 1.000 84.6
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CCGGTACATCATTATGGATTGGA GCGTCTTCTCTTTGGCAAAG 679–1602 1.000 64.7
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TCCGGTACATCATTATGGATTGG GCGTCTTCTCTTTGGCAAAG 680–1603 1.000 64.7
psbZ-trnG-GCC_p3 psbZ-trnG-GCC CCGGTACATCATTATGGATTGG GCGTCTTCTCTTTGGCAAAG 679–1602 1.000 63.0
psbZ-trnG-GCC_p4 psbZ-trnG-GCC CCGGTACATCATTATGGATTGGA AACCCGCGTCTTCTCTTTG 684–1607 1.000 58.6
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TCCGGTACATCATTATGGATTGG AACCCGCGTCTTCTCTTTG 685–1608 1.000 58.6
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1330–2690 1.000 90.9
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1338–2698 1.000 90.4
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1362–2722 1.000 90.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1370–2730 1.000 89.5
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 1344–2704 1.000 89.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Gleditsia fera NC_070140.1 165027 View on NCBI ↗
Gleditsia japonica NC_047281.1 162391 View on NCBI ↗
Gleditsia japonica var. delavayi NC_070139.1 170796 View on NCBI ↗
Gleditsia japonica var. velutina PV998909.1 166424 View on NCBI ↗
Gleditsia microphylla NC_047369.1 162544 View on NCBI ↗
Gleditsia sinensis NC_047282.1 163175 View on NCBI ↗