Markers + reference

Arthraxon

5 species · Poaceae · Poales

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Species 5
Genome length 140–141 kb
Candidate markers 265
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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1495 0.0118 1.00 63.1 yes View details
psbK-psbI LSC 408 0.0137 1.00 54.7 yes View details
trnT-GGU-trnE-UUC LSC 879 0.0131 0.98 65.4 yes View details
trnD-GUC-psbM LSC 965 0.0090 1.00 61.1 yes View details
petN-trnC-GCA LSC 944 0.0097 0.98 58.0 yes View details
trnC-GCA-rpoB LSC 1135 0.0090 1.00 57.7 yes View details
trnT-UGU-trnL-UAA LSC 794 0.0098 0.99 58.5 yes View details
ndhC-trnV-UAC LSC 909 0.0155 1.00 64.2 yes View details
petA-psbJ LSC 910 0.0088 1.00 46.0 yes View details
ndhF SSC 2217 0.0037 1.00 45.9 yes View details
rpl32-trnL-UAG SSC 524 0.0126 1.00 61.0 yes View details
atpI-atpH LSC 823 0.0052 1.00 67.3 yes View details
trnG-GCC-trnfM-CAU LSC 446 0.0103 1.00 58.6 yes View details
trnG-UCC-trnT-GGU LSC 1647 0.0067 1.00 56.3 yes View details
ndhK LSC 762 0.0021 1.00 56.0 yes View details
trnY-GUA-trnD-GUC LSC 230 0.0148 1.00 55.5 yes View details
rpoB LSC 3228 0.0018 1.00 55.5 yes View details
psbE-petL LSC 1072 0.0076 1.00 54.9 yes View details
trnS-GCU-psbD LSC 991 0.0030 1.00 54.3 yes View details
rpoC2-rps2 LSC 317 0.0069 1.00 53.8 yes View details
ndhF-rpl32 SSC 840 0.0060 1.00 53.5 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1568–1584 1.000 81.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1579–1595 1.000 80.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1572–1588 1.000 80.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1583–1599 1.000 79.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1574–1590 1.000 78.4
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TTTTTACTCCTCACGCCCAG 599–607 1.000 80.9
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCACGCCCAG 550–558 1.000 80.9
psbK-psbI_p3 psbK-psbI TTAGCGTTTGTTTGGCAAGC TTTTTACTCCTCACGCCCAG 559–567 1.000 80.0
psbK-psbI_p4 psbK-psbI ACCCGAAGCTTATGCCATTT TTTTTACTCCTCACGCCCAG 629–637 1.000 79.8
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTACTCCTCACGCCCAG 547–555 1.000 78.9
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1115–1172 1.000 81.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1114–1171 1.000 80.9
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1111–1168 1.000 80.6
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1098–1155 1.000 80.0
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ATAAGCCGGACCATCCTACA 1101–1158 1.000 78.2
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA TTCTTTCGTCCACCGGTTTT 579–591 1.000 79.8
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA TTTCTTTCGTCCACCGGTTT 580–592 1.000 79.8
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA TTTTCTTTCGTCCACCGGTT 581–593 1.000 79.7
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA TTTTTCTTTCGTCCACCGGT 582–594 1.000 79.7
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GTAGCGAGCGTAGTTCAGTG TTCTTTCGTCCACCGGTTTT 618–630 1.000 79.3
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT AGCCCTTTTAACTCAGTGGT 1363–1759 1.000 46.1
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT AGGCATAAGTCATCGGTTCA 1326–1722 1.000 46.0
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGGTAAGGCATAAGTCATCGG 1331–1727 1.000 45.2
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GGTAAGGCATAAGTCATCGGT 1330–1726 1.000 45.2
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT AGCCCTTTTAACTCAGTGGT 1365–1761 1.000 45.2
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC ACCACTAAGTGAAAAGCCCT GCTGCCTCCTTGAAAGAGAG 960–1013 1.000 73.3
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC ACCACTAAGTGAAAAGCCCT TGTCCTGAACCACTAGACGA 939–992 1.000 73.2
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TGAACCGATGACTTATGCCT GCTGCCTCCTTGAAAGAGAG 930–983 1.000 73.2
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC TGAACCGATGACTTATGCCT TGTCCTGAACCACTAGACGA 909–962 1.000 73.1
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC CCGATGACTTATGCCTTACCA GCTGCCTCCTTGAAAGAGAG 926–979 1.000 72.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Arthraxon hispidus NC_035048.1 140507 View on NCBI ↗
Arthraxon lanceolatus NC_035017.1 140381 View on NCBI ↗
Arthraxon lancifolius MT113359.1 139976 View on NCBI ↗
Arthraxon microphyllus NC_035050.1 139858 View on NCBI ↗
Arthraxon prionodes NC_030613.1 140486 View on NCBI ↗