Markers + reference

Cynometra

4 species · Fabaceae · Fabales

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Species 4
Genome length 158–160 kb
Candidate markers 258
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 856 0.0132 0.96 60.7 yes View details
atpF-atpH LSC 611 0.0147 0.96 63.1 yes View details
trnC-GCA-petN LSC 1082 0.0037 1.00 44.0 yes View details
psbZ-trnG-GCC LSC 687 0.0152 0.98 64.4 yes View details
accD-psaI LSC 577 0.0148 1.00 65.3 yes View details
petA-psbJ LSC 828 0.0111 1.00 64.6 yes View details
ndhF-rpl32 SSC 1041 0.0111 0.99 69.9 yes View details
rpl32-trnL-UAG SSC 1218 0.0111 0.99 62.8 yes View details
ccsA-psaC SSC 1925 0.0070 0.99 48.7 yes View details
ndhG-ndhI SSC 455 0.0136 1.00 46.3 yes View details
rps15-ycf1 SSC 431 0.0171 0.98 45.5 yes View details
trnT-UGU-trnL-UAA LSC 746 0.0074 1.00 66.4 yes View details
petN-psbM LSC 1259 0.0074 1.00 64.5 yes View details
trnH-GUG-psbA LSC 253 0.0270 0.98 64.0 yes View details
trnF-GAA-ndhJ LSC 696 0.0034 0.99 62.0 yes View details
rps8-rpl14 LSC 209 0.0048 1.00 61.6 yes View details
atpH-atpI LSC 1203 0.0036 1.00 61.2 yes View details
rpl20-rps12 LSC 769 0.0030 1.00 60.5 yes View details
rps3-rps19 LSC 627 0.0048 0.96 60.0 yes View details
rpoC1 LSC 2866 0.0018 0.99 58.3 yes View details
trnE-UUC-trnT-GGU LSC 910 0.0053 0.97 57.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCCAT 319–437 1.000 82.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCCAT 333–451 1.000 82.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCCAT 332–450 1.000 82.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCCAT 334–452 1.000 82.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GCTATGTTATGGGCGAACGA CCTCTAGACCTAGCTGCCAT 383–501 1.000 82.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATGAATCAAACGAGGGACCC 945–989 1.000 80.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATGAATCAAACGAGGGACCC 944–988 1.000 80.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATGAATCAAACGAGGGACCC 999–1043 1.000 79.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC ATGAATCAAACGAGGGACCC 947–991 1.000 77.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGACGCTTTAGTCCACTCAG ATGAATCAAACGAGGGACCC 940–984 1.000 77.8
atpF-atpH_p1 atpF-atpH TAAACCCGAAACTCTCAGCG AGGCAGAGGGAAAAATACGG 769–794 1.000 80.2
atpF-atpH_p2 atpF-atpH CGTATGGCCAGTAACCCAAA AGGCAGAGGGAAAAATACGG 751–776 1.000 80.0
atpF-atpH_p3 atpF-atpH TAAACCCGAAACTCTCAGCG CCTGAGGCAGAGGGAAAAAT 773–798 1.000 79.4
atpF-atpH_p4 atpF-atpH CGTATGGCCAGTAACCCAAA CCTGAGGCAGAGGGAAAAAT 755–780 1.000 79.2
atpF-atpH_p5 atpF-atpH TAAACCCGAAACTCTCAGCG GCAGAGGGAAAAATACGGGG 767–792 1.000 78.7
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1324–1325 1.000 79.2
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1290–1291 1.000 79.1
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TCCCTGTCATGTTCCTTGGA 1373–1374 1.000 78.2
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCCTGTCATGTTCCTTGGA 1339–1340 1.000 78.1
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1291–1292 1.000 78.0
rpoC1_p1 rpoC1 GAGAGACCCGAATTCACACC TCCAGATTCATAGGAAGGAAGC 2943–2979 1.000 59.6
rpoC1_p2 rpoC1 GGAGAGACCCGAATTCACAC TCCAGATTCATAGGAAGGAAGC 2944–2980 1.000 59.6
rpoC1_p3 rpoC1 GAGAGACCCGAATTCACACC CCAGATTCATAGGAAGGAAGCT 2942–2978 1.000 59.5
rpoC1_p4 rpoC1 GGAGAGACCCGAATTCACAC CCAGATTCATAGGAAGGAAGCT 2943–2979 1.000 59.5
rpoC1_p5 rpoC1 GATCCTAGTTGACCCGGAGA TCCAGATTCATAGGAAGGAAGC 2959–2995 1.000 59.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1138–1161 1.000 79.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACGAGGG 1189–1212 1.000 77.6
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1156–1179 1.000 77.2
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TCTTCCCCATACTACGAGGG 1207–1230 1.000 75.4
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCCCCATACTACGAGGGAAA 1186–1209 1.000 73.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Cynometra cebuensis PQ790067.1 158474 View on NCBI ↗
Cynometra iripa NC_047314.1 159685 View on NCBI ↗
Cynometra lenticellata NC_047333.1 159443 View on NCBI ↗
Cynometra ramiflora NC_047332.1 159812 View on NCBI ↗