Markers + reference

Australopyrum

2 species · Poaceae · Poales

Back to catalogue

Species 2
Genome length 135–135 kb
Candidate markers 276
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19 IRb 282 NA 0.00 29.4 no View details
rps19 IRa 282 NA 0.00 30.4 yes View details
psbK-psbI LSC 405 0.0296 1.00 65.5 yes View details
rpl23-psaI LSC 1062 0.0295 0.51 67.2 yes View details
psbE-petL LSC 1168 0.0126 0.61 51.1 yes View details
trnF-GAA-ndhJ LSC 581 0.0189 1.00 69.2 yes View details
trnT-UGU-trnL-UAA LSC 615 0.0132 0.98 68.1 yes View details
trnR-UCU-rps14 LSC 379 0.0211 1.00 66.3 yes View details
ndhK-ndhC LSC 50 0.0400 1.00 63.9 yes View details
petN-trnC-GCA LSC 490 0.0103 0.99 62.9 yes View details
psaJ-rpl33 LSC 443 0.0113 1.00 62.4 yes View details
trnC-GCA-rpoB LSC 1159 0.0104 1.00 61.6 yes View details
psaA-ycf3 LSC 690 0.0015 0.96 61.4 yes View details
matK-trnK-UUU LSC 681 0.0044 1.00 61.3 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps19_p1 rps19 TTCTGACCTCCGTACTTCGA AGATATTGGGTATTTCTGTTACT 430 0.500 20.0
rps19_p2 rps19 TTCTGACCTCCGTACTTCGA AAGATATTGGGTATTTCTGTTACT 431 0.500 20.0
rps19_p3 rps19 TTCTGACCTCCGTACTTCGA AGATATTGGGTATTTCTGTTACTT 430 0.500 20.0
rps19_p4 rps19 TCTGACCTCCGTACTTCGAT AGATATTGGGTATTTCTGTTACT 429 0.500 20.0
rps19_p5 rps19 CCTCCGTACTTCGATCGAGA AGATATTGGGTATTTCTGTTACT 424 0.500 20.0
trnK-UUU_p1 trnK-UUU CACAAGCTTGTACTTTCGCG AATGTTTTGACAGAAGCGCG 2898–2906 1.000 80.3
trnK-UUU_p2 trnK-UUU GACTCCCAAGCACACGTATT AATGTTTTGACAGAAGCGCG 2827–2835 1.000 80.0
trnK-UUU_p3 trnK-UUU GACTCCCAAGCACACGTATT TTTGGCCATCGTGATTAGGG 2952–2960 1.000 79.9
trnK-UUU_p4 trnK-UUU TGCGGTCAATAAGGTAGGGA AATGTTTTGACAGAAGCGCG 2989–2997 1.000 79.7
trnK-UUU_p5 trnK-UUU AAGCTTGTACTTTCGCGTCT AATGTTTTGACAGAAGCGCG 2895–2903 1.000 79.6
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT AATGTTTTGACAGAAGCGCG 875 1.000 69.5
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG AATGTTTTGACAGAAGCGCG 875 1.000 67.7
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT AATGTTTTGACAGAAGCGCG 874 1.000 67.7
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAAGAGAAGTGGGTAGA AATGTTTTGACAGAAGCGCG 873 1.000 63.0
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA AATGTTTTGACAGAAGCGCG 875 1.000 62.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCGCGTCCAG 549–554 1.000 80.7
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCCGTCCTGGGTCATTAGA 527–532 1.000 79.4
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTACTCCTCGCGTCCAG 546–551 1.000 78.7
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTTTTACTCCTCGCGTCCAG 547–552 1.000 78.7
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTTTTACTCCTCGCGTCCAG 548–553 1.000 78.7
trnS-CGA_p1 trnS-CGA CCTCGTGAGCTACCAAACTG GGCTCAGTGTCATGAACCTT 978–987 1.000 77.3
trnS-CGA_p2 trnS-CGA CAAACTGCTCTACTCCGCTC GGCTCAGTGTCATGAACCTT 965–974 1.000 76.7
trnS-CGA_p3 trnS-CGA CCTCGTGAGCTACCAAACTG AGCCTTCTTGTCAAATGGCT 931–940 1.000 76.5
trnS-CGA_p4 trnS-CGA AAACTGCTCTACTCCGCTCT GGCTCAGTGTCATGAACCTT 964–973 1.000 76.0
trnS-CGA_p5 trnS-CGA CAAACTGCTCTACTCCGCTC AGCCTTCTTGTCAAATGGCT 918–927 1.000 75.9
petN-trnC-GCA_p1 petN-trnC-GCA AGTCCACTCCTTCCCCATAC AGTTCAAATCTGGGTGCCG 598–1063 1.000 71.4
petN-trnC-GCA_p2 petN-trnC-GCA GTCCACTCCTTCCCCATACT AGTTCAAATCTGGGTGCCG 597–1062 1.000 71.4
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 539–1004 1.000 71.2
petN-trnC-GCA_p4 petN-trnC-GCA AGTCCACTCCTTCCCCATAC CCAGTTCAAATCTGGGTGCC 600–1065 1.000 70.9
petN-trnC-GCA_p5 petN-trnC-GCA GTCCACTCCTTCCCCATACT CCAGTTCAAATCTGGGTGCC 599–1064 1.000 70.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Australopyrum pectinatum MW309815.1 135041 View on NCBI ↗
Australopyrum retrofractum NC_043840.1 135417 View on NCBI ↗