Markers + reference

Cercis

3 species · Fabaceae · Fabales

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Species 3
Genome length 159–159 kb
Candidate markers 261
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnR-UCU LSC 1898 0.0112 0.97 68.9 yes View details
atpF-atpH LSC 652 0.0190 0.94 73.9 yes View details
rpoB-trnC-GCA LSC 1179 0.0097 0.99 52.2 yes View details
trnT-GGU-psbD LSC 1735 0.0143 0.97 70.0 yes View details
accD-psaI LSC 897 0.0169 0.97 73.2 yes View details
trnN-GUU-ndhF IRb 1296 0.0401 0.88 77.7 yes View details
ndhG-ndhI SSC 475 0.0228 0.99 72.4 yes View details
ndhD-psaC SSC 252 0.0265 1.00 69.4 yes View details
petN-psbM LSC 856 0.0081 0.97 66.8 yes View details
trnT-UGU-trnL-UAA LSC 1465 0.0048 0.95 66.2 yes View details
rps3-rps19 LSC 630 0.0116 1.00 66.2 yes View details
psbZ-trnG-GCC LSC 508 0.0095 0.97 64.9 yes View details
ndhF-rpl32 SSC 1032 0.0045 1.00 64.2 yes View details
rps11-rpl36 LSC 325 0.0343 0.42 63.9 yes View details
trnK-UUU-rps16 LSC 756 0.0053 0.99 63.0 yes View details
atpH-atpI LSC 988 0.0021 0.98 62.3 yes View details
trnR-UCU-atpA LSC 363 0.0068 0.94 61.7 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AAAAAGGCGCTCAACCTACA 899–914 1.000 76.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA AAAAAGGCGCTCAACCTACA 900–915 1.000 76.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 897–912 1.000 75.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CCTTGAAAAAGGCGCTCAAC 904–919 1.000 74.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CTTGAAAAAGGCGCTCAACC 903–918 1.000 74.7
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1937–1969 1.000 67.9
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1936–1968 1.000 67.9
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1943–1975 1.000 67.2
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1942–1974 1.000 67.2
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 1991–2023 1.000 66.6
trnR-UCU-atpA_p1 trnR-UCU-atpA AGAGAAAAGCGTCCATTGTCT TGAAGCAGAAGCCCTTTTGA 509–525 1.000 70.3
trnR-UCU-atpA_p2 trnR-UCU-atpA AGAGAAAAGCGTCCATTGTCT GTGAAGCAGAAGCCCTTTTG 510–526 1.000 69.8
trnR-UCU-atpA_p3 trnR-UCU-atpA AGAGAAAAGCGTCCATTGTCT TACCAAGACATTCACGGGTG 527–543 1.000 69.5
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGAAGCAGAAGCCCTTTTGA 451–467 1.000 68.1
trnR-UCU-atpA_p5 trnR-UCU-atpA AGAGAAAAGCGTCCATTGTCT GGTGAAGCAGAAGCCCTTTT 511–527 1.000 67.8
atpF-atpH_p1 atpF-atpH CGGATGTCCAGTAACCCAAG AGGCAGAGGGAAAAATACGG 778–817 1.000 82.0
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AGGCAGAGGGAAAAATACGG 798–837 1.000 81.2
atpF-atpH_p3 atpF-atpH CGGATGTCCAGTAACCCAAG GCAGAGGGAAAAATACGGGG 776–815 1.000 80.4
atpF-atpH_p4 atpF-atpH CGGATGTCCAGTAACCCAAG GGCAGAGGGAAAAATACGGG 777–816 1.000 80.4
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG GCAGAGGGAAAAATACGGGG 796–835 1.000 79.6
atpH-atpI_p1 atpH-atpI GCCAATCCAGCAGCAATAAC TTTGCAACTTTAGCTGCAGC 1067–1089 1.000 79.2
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC CGAATCCATGGAGGGTCATC 1038–1060 1.000 78.9
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG TTTGCAACTTTAGCTGCAGC 1062–1084 1.000 78.8
atpH-atpI_p4 atpH-atpI CCTTCTACAGCTTGACCTGC TTTGCAACTTTAGCTGCAGC 1133–1155 1.000 78.6
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG CGAATCCATGGAGGGTCATC 1033–1055 1.000 78.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG AGACCCAGTCAGTAAACGGA 2209–2227 1.000 81.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AGACCCAGTCAGTAAACGGA 2017–2035 1.000 81.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CCGACCTATCCCTACCCAAT 2237–2255 1.000 80.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGACCTATCCCTACCCAAT 2045–2063 1.000 80.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGACATTCCCTCATTTCCGC AGACCCAGTCAGTAAACGGA 1535–1553 0.667 67.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Cercis canadensis NC_046396.1 158960 View on NCBI ↗
Cercis chinensis MZ128523.1 158999 View on NCBI ↗
Cercis glabra NC_036762.1 159181 View on NCBI ↗