Markers + reference

Arundinaria

3 species · Poaceae · Poales

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Species 3
Genome length 139–140 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnD-psbM LSC 990 0.0088 1.00 52.3 yes View details
rpoC2 LSC 4554 0.0026 1.00 45.2 yes View details
atpF LSC 1395 0.0096 1.00 51.3 yes View details
ycf3-trnS LSC 591 0.0169 1.00 65.3 yes View details
petD LSC 1232 0.0011 1.00 36.0 yes View details
ndhF-rpl32 SSC 823 0.0147 0.99 63.8 yes View details
rpl32-trnL SSC 703 0.0114 1.00 42.3 yes View details
ndhG-ndhI SSC 246 0.0271 1.00 57.3 yes View details
psaA-ycf3 LSC 626 0.0075 1.00 65.9 yes View details
trnT-trnL LSC 826 0.0056 1.00 63.9 yes View details
trnR-trnfM LSC 153 0.0132 0.99 62.1 yes View details
rps16-trnQ LSC 1550 0.0017 0.99 61.5 yes View details
psbE-petL LSC 1228 0.0033 1.00 60.8 yes View details
petB LSC 1462 0.0032 1.00 60.8 yes View details
petD-rpoA LSC 213 0.0313 1.00 60.0 yes View details
petN-trnC LSC 910 0.0015 1.00 59.8 yes View details
trnF-ndhJ LSC 583 0.0046 1.00 58.2 yes View details
ycf4 LSC 558 0.0024 1.00 56.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1607–1624 1.000 79.7
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1618–1635 1.000 79.2
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1611–1628 1.000 78.6
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1622–1639 1.000 78.1
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1667–1684 1.000 77.9
trnD-psbM_p1 trnD-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1074–1075 1.000 49.3
trnD-psbM_p2 trnD-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1106–1107 1.000 47.8
trnD-psbM_p3 trnD-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1075–1076 1.000 46.2
trnD-psbM_p4 trnD-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1074–1075 1.000 46.2
trnD-psbM_p5 trnD-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1075–1076 1.000 45.1
petN-trnC_p1 petN-trnC AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 958–959 1.000 70.6
petN-trnC_p2 petN-trnC AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 960–961 1.000 70.2
petN-trnC_p3 petN-trnC CCACTCCTCCCCCATACTAC AGTTCAAATCTGGGTGCCG 1014–1015 1.000 69.6
petN-trnC_p4 petN-trnC CCACTCCTCCCCCATACTAC CCAGTTCAAATCTGGGTGCC 1016–1017 1.000 69.1
petN-trnC_p5 petN-trnC TCCACTCCTCCCCCATACTA AGTTCAAATCTGGGTGCCG 1015–1016 1.000 68.8
rpoC2_p1 rpoC2 GGGGCATTCTGATTTCGCTA GAAAACTCTGTTGTTCCGCG 406 1.000 82.3
rpoC2_p2 rpoC2 CTATTTGCGTACCGACCCAA GAAAACTCTGTTGTTCCGCG 914 1.000 81.1
rpoC2_p3 rpoC2 TATTTGCGTACCGACCCAAG GAAAACTCTGTTGTTCCGCG 913 1.000 81.1
rpoC2_p4 rpoC2 CTATTTGCGTACCGACCCAA TGAGATGCATTTCCTCTGGC 1098 1.000 80.7
rpoC2_p5 rpoC2 TATTTGCGTACCGACCCAAG TGAGATGCATTTCCTCTGGC 1097 1.000 80.7
atpF_p1 atpF AGAGGATATGCTCGCCTTCT CATCAACCCATCGCCCATTA 2001–2003 1.000 80.9
atpF_p2 atpF AGAGGATATGCTCGCCTTCT TTTTGCCAGTCTGTCTGTCC 2284–2286 1.000 80.8
atpF_p3 atpF GTATTGCGAGACAGCCAGAA CATCAACCCATCGCCCATTA 2319–2321 1.000 80.7
atpF_p4 atpF GTATTGCGAGACAGCCAGAA TTTTGCCAGTCTGTCTGTCC 2602–2604 1.000 80.6
atpF_p5 atpF AGAGGATATGCTCGCCTTCT CAATTTCGCCTCTCCCATCA 2123–2124 0.667 66.9
trnR-trnfM_p1 trnR-trnfM AGAAGACCTCTGTCCTATCCA GTTTGGTAGCTCACAAGGCT 237–239 1.000 64.5
trnR-trnfM_p2 trnR-trnfM AGAAGACCTCTGTCCTATCCA TTTGGTAGCTCACAAGGCTC 236–238 1.000 63.8
trnR-trnfM_p3 trnR-trnfM AGAAGACCTCTGTCCTATCCA TTATCCACTAGTTCCCCGCT 280–282 1.000 63.7
trnR-trnfM_p4 trnR-trnfM AGGTTTAGAAGACCTCTGTCCT GTTTGGTAGCTCACAAGGCT 243–245 1.000 63.7
trnR-trnfM_p5 trnR-trnfM AGGTTTAGAAGACCTCTGTCCT TTATCCACTAGTTCCCCGCT 286–288 1.000 63.0

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
Arundinaria appalachiana NC_023934.1 139547 View on NCBI ↗
Arundinaria fargesii NC_024712.1 139696 View on NCBI ↗
Arundinaria tecta NC_023935.1 139499 View on NCBI ↗