Markers + reference

Axonopus

3 species · Poaceae · Poales

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Species 3
Genome length 139–140 kb
Candidate markers 284
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 284 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0044 1.00 49.0 yes View details
trnS-GCU-psbD LSC 978 0.0102 1.00 66.0 yes View details
petN-trnC-GCA LSC 938 0.0085 1.00 60.7 yes View details
trnC-GCA-rpoB LSC 1145 0.0082 1.00 59.0 yes View details
trnR-UCU-trnfM-CAU LSC 169 0.0316 1.00 60.0 yes View details
ndhC-trnV-UAC LSC 938 0.0078 1.00 64.0 yes View details
petA-psbJ LSC 699 0.0105 1.00 52.2 yes View details
rpl16 LSC 1495 0.0065 0.99 50.6 yes View details
rpl32-trnL-UAG SSC 511 0.0157 1.00 66.1 yes View details
rps4-trnT-UGU LSC 301 0.0166 1.00 63.3 yes View details
trnG-UCC-trnT-GGU LSC 1658 0.0068 1.00 62.8 yes View details
atpI-atpH LSC 803 0.0054 1.00 62.4 yes View details
atpF LSC 1381 0.0044 1.00 61.9 yes View details
ndhF-rpl32 SSC 848 0.0055 1.00 61.2 yes View details
ycf3-trnS-GGA LSC 582 0.0034 1.00 60.9 yes View details
clpP-psbB LSC 531 0.0038 0.99 60.9 yes View details
ycf15-trnL-CAA IRb 776 0.0026 1.00 60.4 yes View details
trnL-CAA-ycf15 IRa 776 0.0026 1.00 60.4 yes View details
psbK-psbI LSC 394 0.0076 1.00 59.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ATTCCTATATGTTAGAGAAAAACC AATACGTGTGCTTGGGAGTC 1136 1.000 40.5
psbA_p2 psbA AATTCCTATATGTTAGAGAAAAACC AATACGTGTGCTTGGGAGTC 1137 1.000 40.5
psbA_p3 psbA AAATTCCTATATGTTAGAGAAAAACC AATACGTGTGCTTGGGAGTC 1138 1.000 40.5
psbA_p4 psbA ATTCCTATATGTTAGAGAAAAACC TGGGAGTCCTTGCAATTTGA 1124 1.000 40.5
psbA_p5 psbA ATTCCTATATGTTAGAGAAAAACC GCTTGGGAGTCCTTGCAATT 1127 1.000 40.5
trnK-UUU_p1 trnK-UUU GACTCCCAAGCACACGTATT CATTGTAATTGGCTCCCCCT 2936–2940 0.667 62.7
trnK-UUU_p2 trnK-UUU GACTCCCAAGCACACGTATT CCATTGTAATTGGCTCCCCC 2937–2941 0.667 61.7
trnK-UUU_p3 trnK-UUU CCCCAACGATTCGATTTCCA CATTGTAATTGGCTCCCCCT 2836–2840 0.667 61.4
trnK-UUU_p4 trnK-UUU CCCCAACGATTCGATTTCCA CCATTGTAATTGGCTCCCCC 2837–2841 0.667 60.4
trnK-UUU_p5 trnK-UUU CCCCAACGATTCGATTTCCA CGCTCAAATGATAGGGTTGC 2939–2943 0.667 59.0
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TTTTTACTCCTCACGCCCAG 585–588 1.000 79.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCAGCTGTAAG TTTTTACTCCTCACGCCCAG 536–539 1.000 79.0
psbK-psbI_p3 psbK-psbI ACCCGAAGCTTATGCCATTT TTTTTACTCCTCACGCCCAG 615–618 1.000 78.2
psbK-psbI_p4 psbK-psbI TTAGCGTTTGTTTGGCAAGC TTTTTACTCCTCACGCCCAG 545–548 1.000 78.2
psbK-psbI_p5 psbK-psbI TGGCAAGCAGCTGTAAGTTT TTTTTACTCCTCACGCCCAG 533–536 1.000 77.0
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1122–1145 1.000 79.8
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1109–1132 1.000 79.2
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1108–1131 1.000 76.9
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1101–1124 1.000 76.7
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1095–1118 1.000 76.3
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 1778–1780 1.000 41.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1748–1750 1.000 41.5
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1744–1746 1.000 40.8
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1745–1747 1.000 40.8
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 1780–1782 1.000 40.8
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CTGCAAATCCTTTACCCCCA 979–1025 1.000 79.9
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TGCAAATCCTTTACCCCCAG 978–1024 1.000 79.9
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA ACTGCAAATCCTTTACCCCC 980–1026 1.000 79.9
petN-trnC-GCA_p4 petN-trnC-GCA AGCCCAAGCGAGACTTACTA GCAAATCCTTTACCCCCAGT 977–1023 1.000 79.9
petN-trnC-GCA_p5 petN-trnC-GCA AGACCACCATTAAAGCAGCC TGCAAATCCTTTACCCCCAG 994–1040 1.000 79.8

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
Axonopus compressus NC_046490.1 139227 View on NCBI ↗
Axonopus fissifolius NC_030501.1 139250 View on NCBI ↗
Axonopus ramosus NC_036129.1 139596 View on NCBI ↗