Markers + reference

Psathyrostachys

2 species · Poaceae · Poales

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Species 2
Genome length 137–137 kb
Candidate markers 267
Primer pairs 85

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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19 LSC 282 NA 0.00 29.6 yes View details
trnG-UCC-trnT-GGU LSC 1196 0.0151 0.99 58.5 yes View details
petN-trnC-GCA LSC 721 0.0154 0.99 62.2 yes View details
trnF-GAA-ndhJ LSC 590 0.0328 0.98 64.5 yes View details
rbcL-psaI LSC 1676 0.0133 0.94 55.9 yes View details
rps19 LSC 282 0.0000 1.00 20.4 no View details
rpl2 IRb 1398 0.0151 1.00 57.6 yes View details
ndhH IRb 252 0.0932 0.94 75.4 yes View details
ndhF SSC 2220 0.0018 1.00 43.6 yes View details
ndhH SSC 1182 0.0034 1.00 60.7 no View details
rpl2 IRa 1398 0.0151 1.00 57.6 no View details
psbT-psbN LSC 48 0.1042 1.00 87.5 yes View details
rps19-psbA LSC 130 0.0482 0.64 74.1 yes View details
ndhH-ndhF SSC 15 0.5333 1.00 72.5 yes View details
trnH-GUG LSC 75 0.0267 1.00 67.8 yes View details
trnD-GUC-psbM LSC 804 0.0067 0.92 65.1 yes View details
rpl16 LSC 1461 0.0022 0.94 64.5 yes View details
psbM-petN LSC 747 0.0068 0.99 64.1 yes View details
rps18 LSC 513 0.0117 1.00 63.7 yes View details
trnT-UGU-trnL-UAA LSC 622 0.0065 0.99 63.6 yes View details
trnH-GUG LSC 75 NA 0.00 30.1 no 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
rps19_p1 rps19 TTCTGACCTCCGTACTTCGA TCTTAATCTTTCTATTCAGAATTCAG 385 1.000 44.0
rps19_p2 rps19 TCTGACCTCCGTACTTCGAT TCTTAATCTTTCTATTCAGAATTCAG 384 1.000 44.0
rps19_p3 rps19 CCTCCGTACTTCGATCGAGA TCTTAATCTTTCTATTCAGAATTCAG 379 1.000 44.0
rps19_p4 rps19 TTCTGACCTCCGTACTTCGA CTTCTTAATCTTTCTATTCAGAATTCA 387 1.000 44.0
rps19_p5 rps19 TTCTGACCTCCGTACTTCGA TTCTTAATCTTTCTATTCAGAATTCAG 386 1.000 44.0
rps19-psbA_p1 rps19-psbA CAAATTGGGGGAATTCGTGC TGGAAGTAATGCACGAACGT 289 0.500 58.7
rps19-psbA_p2 rps19-psbA GCAAATTGGGGGAATTCGTG TGGAAGTAATGCACGAACGT 290 0.500 58.7
rps19-psbA_p3 rps19-psbA CAAATTGGGGGAATTCGTGC CAACCGTGCTAACCTTGGTA 309 0.500 58.5
rps19-psbA_p4 rps19-psbA GCAAATTGGGGGAATTCGTG CAACCGTGCTAACCTTGGTA 310 0.500 58.5
rps19-psbA_p5 rps19-psbA CAAATTGGGGGAATTCGTGC ATCAACCGTGCTAACCTTGG 311 0.500 58.5
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTAGCACGAG 1274–1275 1.000 41.5
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGACTTACGTCTTAGCACGAG 1277–1278 1.000 41.5
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGACTTACGTCTTAGCACGAG 1276–1277 1.000 41.5
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTAGCACGA 1274–1275 1.000 41.5
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU AACGAATCACACTTTTACCACT TGACTTACGTCTTAGCACGAG 1275–1276 1.000 41.5
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 855–915 1.000 62.8
trnD-GUC-psbM_p2 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 856–916 1.000 58.6
trnD-GUC-psbM_p3 trnD-GUC-psbM CGCGGGGATTGTAGTTCAA AGAATGAACAGTGCAGTAGC 869–929 1.000 57.4
trnD-GUC-psbM_p4 trnD-GUC-psbM TCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 854–914 1.000 56.8
trnD-GUC-psbM_p5 trnD-GUC-psbM GCGGGGATTGTAGTTCAATTG AGAATGAACAGTGCAGTAGC 868–928 1.000 55.2
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT AGTATGGGGAAGGAGTGGAC 841–851 1.000 69.3
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTATGGGGAAGGAGTGGACT 840–850 1.000 69.3
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 899–909 1.000 68.9
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTCT TATGGGGAAGGAGTGGACTC 839–849 1.000 68.8
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT GGGGAAGGAGTGGACTCTAG 836–846 1.000 68.5
petN-trnC-GCA_p1 petN-trnC-GCA AGTCCACTCCTTCCCCATAC AGTTCAAATCTGGGTGCCG 829–1042 1.000 72.1
petN-trnC-GCA_p2 petN-trnC-GCA GTCCACTCCTTCCCCATACT AGTTCAAATCTGGGTGCCG 828–1041 1.000 72.1
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 770–983 1.000 71.9
petN-trnC-GCA_p4 petN-trnC-GCA AGTCCACTCCTTCCCCATAC CCAGTTCAAATCTGGGTGCC 831–1044 1.000 71.6
petN-trnC-GCA_p5 petN-trnC-GCA GTCCACTCCTTCCCCATACT CCAGTTCAAATCTGGGTGCC 830–1043 1.000 71.6

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
Psathyrostachys huashanica NC_045871.1 136632 View on NCBI ↗
Psathyrostachys juncea NC_043838.1 136597 View on NCBI ↗