Markers + reference

Gymnocladus

2 species · Fabaceae · Fabales

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Species 2
Genome length 157–165 kb
Candidate markers 257
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 9 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5484 0.3896 0.89 75.9 yes View details
ndhH SSC 1182 0.4581 0.69 76.2 yes View details
ndhA SSC 2480 0.4493 0.62 73.3 yes View details
ndhG-ndhE SSC 248 0.4348 0.56 67.0 yes View details
ndhD SSC 1494 0.4877 0.79 79.1 yes View details
ndhD-ccsA SSC 276 0.5436 0.54 66.8 yes View details
ccsA SSC 972 0.4621 0.65 75.2 yes View details
ndhF SSC 2238 0.4622 0.85 79.3 yes View details
rpl33-rps18 LSC 247 0.1267 0.89 86.1 yes View details
trnQ-UUG-psbK LSC 667 0.0713 0.84 84.2 yes View details
trnG-GCC-trnM-CAU LSC 190 0.0703 0.97 82.5 yes View details
ndhF-trnN-GUU IRa 1916 0.1739 0.95 82.5 yes View details
trnL-UAG-rpl32 SSC 1056 0.4223 0.87 81.2 yes View details
rpl32-ndhF SSC 1015 0.4297 0.86 80.9 yes View details
ndhG SSC 531 0.4563 0.86 79.8 yes View details
ndhI-ndhG SSC 911 0.3535 0.80 79.3 yes View details
trnR-UCU-atpA LSC 348 0.0818 0.95 78.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG AGGCTTCAGGTAATTTCGCG 736–835 1.000 79.5
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG GGCTTCAGGTAATTTCGCGA 735–834 1.000 79.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGCTTCAGGTAATTTCGCG 694–793 1.000 77.8
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGCTTCAGGTAATTTCGCGA 693–792 1.000 77.8
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AATGGATATGCTCTGGGACG AGGCTTCAGGTAATTTCGCG 740–839 1.000 76.2
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACTCGGGAAGCAGAA 462–556 1.000 72.7
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACTCGGGAAGC 466–560 1.000 72.7
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 452–546 1.000 70.6
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATTCACTCGGGAAGCAGAAG 461–555 1.000 70.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCAAGACATTCACTCGGGAA 468–562 1.000 69.7
trnG-GCC-trnM-CAU_p1 trnG-GCC-trnM-CAU AAGGACGATCAAAATGCGGA CTTGAGGTCACGGGTTCAAA 310–334 1.000 83.3
trnG-GCC-trnM-CAU_p2 trnG-GCC-trnM-CAU CAAGGACGATCAAAATGCGG CTTGAGGTCACGGGTTCAAA 311–335 1.000 82.7
trnG-GCC-trnM-CAU_p3 trnG-GCC-trnM-CAU AAGGACGATCAAAATGCGGA TGAGGTCACGGGTTCAAATC 308–332 1.000 82.2
trnG-GCC-trnM-CAU_p4 trnG-GCC-trnM-CAU AAGGACGATCAAAATGCGGA GTAGCTCGCAAGGCTCATAA 331–355 1.000 81.5
trnG-GCC-trnM-CAU_p5 trnG-GCC-trnM-CAU AAGGACGATCAAAATGCGGA TAGCTCGCAAGGCTCATAAC 330–354 1.000 81.5
rpl33-rps18_p1 rpl33-rps18 TCTGTCCCTGTTGTTGCAAA TCAATTCGATCCCCCGATTG 362–383 1.000 86.9
rpl33-rps18_p2 rpl33-rps18 TTCTGTCCCTGTTGTTGCAA TCAATTCGATCCCCCGATTG 363–384 1.000 86.9
rpl33-rps18_p3 rpl33-rps18 ATTCTGTCCCTGTTGTTGCA TCAATTCGATCCCCCGATTG 364–385 1.000 85.0
rpl33-rps18_p4 rpl33-rps18 TCTGTCCCTGTTGTTGCAAA ATTCGATCCCCCGATTGGAT 359–380 1.000 83.9
rpl33-rps18_p5 rpl33-rps18 TTCTGTCCCTGTTGTTGCAA ATTCGATCCCCCGATTGGAT 360–381 1.000 83.9
ycf1_p1 ycf1 TGAACTGCCGTGATTGCTTA CGAAACGGCTGCCATTATTG 684 0.500 57.2
ycf1_p2 ycf1 TGAACTGCCGTGATTGCTTA GAAACGGCTGCCATTATTGG 683 0.500 56.9
ycf1_p3 ycf1 AATTGAACTGCCGTGATTGC CGAAACGGCTGCCATTATTG 687 0.500 55.8
ycf1_p4 ycf1 AATTGAACTGCCGTGATTGC GAAACGGCTGCCATTATTGG 686 0.500 55.5
ycf1_p5 ycf1 TGAACTGCCGTGATTGCTTA AACGGCTGCCATTATTGGTA 681 0.500 55.2
ndhH_p1 ndhH GAAAACCCCGGATCGATTGA TCAGGTCCAATACGCTGTTG 1705 0.500 59.0
ndhH_p2 ndhH AGAAAACCCCGGATCGATTG TCAGGTCCAATACGCTGTTG 1706 0.500 58.9
ndhH_p3 ndhH GAAAACCCCGGATCGATTGA CGAACAGAAAGGAGCATGGA 2110 0.500 58.9
ndhH_p4 ndhH AGAAAACCCCGGATCGATTG CGAACAGAAAGGAGCATGGA 2111 0.500 58.9
ndhH_p5 ndhH GCACACACGCATTGTCTTAC TCAGGTCCAATACGCTGTTG 2071 0.500 58.9

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
Gymnocladus chinensis NC_056137.1 165315 View on NCBI ↗
Gymnocladus dioicus NC_070141.1 157472 View on NCBI ↗