Markers + reference

Callerya

3 species · Fabaceae · Fabales

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Species 3
Genome length 130–132 kb
Candidate markers 225
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 225 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpF Genome 652 0.0077 1.00 63.1 yes View details
trnG-UCC-trnS-GCU Genome 897 0.0213 1.00 70.9 yes View details
ycf4 Genome 639 0.0000 1.00 32.9 yes View details
petL-petG Genome 163 0.0082 1.00 44.7 yes View details
ndhB-rps7 Genome 367 0.0054 1.00 43.6 yes View details
ycf1 Genome 5247 0.0009 1.00 53.1 yes View details
trnL-UAG-rpl32 Genome 653 0.0041 1.00 60.8 yes View details
ndhJ-trnF-GAA Genome 739 0.0027 1.00 60.3 yes View details
petN-trnC-GCA Genome 1129 0.0027 1.00 60.3 yes View details
clpP-psbB Genome 875 0.0023 1.00 60.3 yes View details
ycf3-psaA Genome 963 0.0021 1.00 59.9 yes View details
atpI-atpH Genome 1434 0.0021 1.00 59.9 yes View details
ndhK Genome 684 0.0015 1.00 59.6 yes View details
rbcL-atpB Genome 748 0.0013 1.00 59.5 yes View details
atpB Genome 1497 0.0013 1.00 59.5 yes View details
trnG-UCC-psbZ Genome 812 0.0012 1.00 59.5 yes View details
trnT-GGU-trnE-UUC Genome 809 0.0012 1.00 59.4 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
rbcL-atpB_p1 rbcL-atpB AACACCAGCTTTGAACCCAA AGCTACATCTAGGACCGGAC 900–903 1.000 82.8
rbcL-atpB_p2 rbcL-atpB AACACCAGCTTTGAACCCAA CCTGGGGGAAAAGCTACATC 911–914 1.000 82.5
rbcL-atpB_p3 rbcL-atpB AACACCAGCTTTGAACCCAA CGGACCGATTATTTGGACGA 885–888 1.000 81.3
rbcL-atpB_p4 rbcL-atpB GCTTTGAACCCAACACTTGC AGCTACATCTAGGACCGGAC 893–896 1.000 80.5
rbcL-atpB_p5 rbcL-atpB AACACCAGCTTTGAACCCAA ACCGGACCGATTATTTGGAC 887–890 1.000 80.4
atpB_p1 atpB AACCGATCAACTTGCTTTGT ACAATTCGATTGGGGGTCAG 1611 1.000 68.4
atpB_p2 atpB AACCGATCAACTTGCTTTGT CAATTCGATTGGGGGTCAGT 1610 1.000 68.4
atpB_p3 atpB ACCGATCAACTTGCTTTGTT ACAATTCGATTGGGGGTCAG 1610 1.000 68.4
atpB_p4 atpB ACCGATCAACTTGCTTTGTT CAATTCGATTGGGGGTCAGT 1609 1.000 68.4
atpB_p5 atpB ACCGATCAACTTGCTTTGTT TGGGGGTCAGTACACAAAGA 1600 1.000 67.9
ndhK_p1 ndhK ATGGCGAAAGGGAGCATTAG TTTGTACAAAAGGATCCTGT 777 1.000 44.1
ndhK_p2 ndhK GGCGAAAGGGAGCATTAGAA TTTGTACAAAAGGATCCTGT 775 1.000 44.1
ndhK_p3 ndhK ATGGCGAAAGGGAGCATTAG TTTTGTACAAAAGGATCCTGT 778 1.000 44.1
ndhK_p4 ndhK GGCGAAAGGGAGCATTAGAA TTTTGTACAAAAGGATCCTGT 776 1.000 44.1
ndhK_p5 ndhK TTTATGCATGGCGAAAGGGA TTTGTACAAAAGGATCCTGT 784 1.000 44.1
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC GGGATAGCTCAGCTGGTAGA 879 1.000 83.6
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CCTCGTGTCACCAGTTCAAA 843 1.000 83.2
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC AGAATGGTCGGGATAGCTCA 888 1.000 82.9
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CTGGTAGAGCAGAGGACTGA 867 1.000 82.5
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC AGTTCAAATCTGGTTCCCGG 831 1.000 82.0
ycf3-psaA_p1 ycf3-psaA AGCCCTTACCCCTGGTAATT TGCCCATTCCTCGAAAGAAG 1109–1111 1.000 83.2
ycf3-psaA_p2 ycf3-psaA AGCCCTTACCCCTGGTAATT GCCCATTCCTCGAAAGAAGT 1108–1110 1.000 83.2
ycf3-psaA_p3 ycf3-psaA AGCTATAGCCCTTACCCCTG TGCCCATTCCTCGAAAGAAG 1115–1117 1.000 83.0
ycf3-psaA_p4 ycf3-psaA AGCTATAGCCCTTACCCCTG GCCCATTCCTCGAAAGAAGT 1114–1116 1.000 83.0
ycf3-psaA_p5 ycf3-psaA TTGGTTGAAGATCACAGGGC TGCCCATTCCTCGAAAGAAG 1073–1075 1.000 82.5
trnG-UCC-psbZ_p1 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGATGGTTGGTCG 948–1008 1.000 82.6
trnG-UCC-psbZ_p2 trnG-UCC-psbZ TACATAAAAAGGCAGGGGCG CTTCTCCTGATGGTTGGTCG 988–1048 1.000 82.0
trnG-UCC-psbZ_p3 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA TTGCTTCTCCTGATGGTTGG 951–1011 1.000 81.1
trnG-UCC-psbZ_p4 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA TCCTGATGGTTGGTCGAGTA 944–1004 1.000 80.9
trnG-UCC-psbZ_p5 trnG-UCC-psbZ CGTCTTCTCCTTGGCAAAGA GCTTCTCCTGATGGTTGGTC 949–1009 1.000 80.7

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
Callerya dielsiana NC_062690.1 130435 View on NCBI ↗
Callerya nitida NC_063901.1 132442 View on NCBI ↗
Callerya nitida var. hirsutissima NC_061358.1 132361 View on NCBI ↗