Markers + reference

Glyceria

30 species · Poaceae · Poales

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Species 30
Genome length 135–137 kb
Candidate markers 255
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 9 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 546 0.0282 1.00 68.4 yes View details
trnG-trnfM LSC 465 0.0358 1.00 70.5 yes View details
trnG-trnT LSC 1639 0.0246 0.98 74.5 yes View details
ycf3-rps4 LSC 980 0.0219 0.99 68.4 yes View details
trnT-trnL LSC 778 0.0246 0.97 75.0 yes View details
ndhF SSC 2220 0.0144 1.00 52.7 yes View details
ndhF-rpl32 SSC 822 0.0268 0.95 74.8 yes View details
rpl32-trnL SSC 642 0.0291 0.99 73.7 yes View details
rbcL-psaI LSC 1433 0.0150 0.97 78.0 yes View details
ndhC-trnV LSC 860 0.0184 1.00 75.9 yes View details
rps16-trnQ LSC 1071 0.0188 0.99 72.8 yes View details
trnL-trnF LSC 364 0.0203 0.97 70.0 yes View details
trnS-psbD LSC 957 0.0169 1.00 68.7 yes View details
trnF-ndhJ LSC 488 0.0189 1.00 66.8 yes View details
trnC-rpoB LSC 1114 0.0119 0.99 66.0 yes View details
psbK-psbI LSC 399 0.0233 1.00 65.3 yes View details
psbE-petL LSC 1203 0.0155 1.00 64.9 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
trnK_p1 trnK AACTCAGATTGCTCTTTTCT TCGATCGTATCTAAGATCCT 2594–2642 0.900 41.4
trnK_p2 trnK AACTCAGATTGCTCTTTTCT TTCGATCGTATCTAAGATCCT 2595–2643 0.900 41.4
trnK_p3 trnK AAACTCAGATTGCTCTTTTCT TCGATCGTATCTAAGATCCT 2595–2643 0.900 41.4
trnK_p4 trnK AAACTCAGATTGCTCTTTTCT TTCGATCGTATCTAAGATCCT 2596–2644 0.900 41.4
trnK_p5 trnK AACTCAGATTGCTCTTTTCT TTTCGATCGTATCTAAGATCCT 2596–2644 0.900 41.4
trnK-rps16_p1 trnK-rps16 TGAGGATCAGTCGTGGTCTT TCGAGCCGTATGAGGAGAAA 940–990 1.000 86.9
trnK-rps16_p2 trnK-rps16 TGAGGATCAGTCGTGGTCTT TTTCTCGAGCCGTATGAGGA 944–994 1.000 86.9
trnK-rps16_p3 trnK-rps16 ACGTCTAATTAGAGCGGGGA TCGAGCCGTATGAGGAGAAA 1127–1176 1.000 86.7
trnK-rps16_p4 trnK-rps16 ACGTCTAATTAGAGCGGGGA TTTCTCGAGCCGTATGAGGA 1131–1180 1.000 86.7
trnK-rps16_p5 trnK-rps16 ACGTCTAATTAGAGCGGGGA CCTTTGAAGTCTGTCAGGCA 1259–1308 1.000 85.9
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA AGTGTCGCATAAAACCCGAA 838–1247 0.967 85.9
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC AGTGTCGCATAAAACCCGAA 849–1258 0.967 85.3
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAGGCAGCGGGTTTTGATC 799–1208 1.000 84.8
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC TAAGGCAGCGGGTTTTGATC 810–1219 1.000 84.3
rps16-trnQ_p5 rps16-trnQ ATCATGTCCTTCAAGTCGCA AGTGTCGCATAAAACCCGAA 850–1259 0.967 80.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGTCCTGGGTCATTGGATA 484–525 1.000 89.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGTCCTGGGTCATTGGAT 485–526 1.000 89.4
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCACGCCCAG 508–549 1.000 88.7
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGTCCTGGGTCATTGGA 486–527 1.000 87.6
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGTCCTGGGTCATTGGATA 481–522 1.000 87.4
trnS-psbD_p1 trnS-psbD ATTAGCAATCCGCCGCTTTA GACAAAAACGAAACGGTCCC 1042–1115 1.000 87.6
trnS-psbD_p2 trnS-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1041–1114 1.000 86.6
trnS-psbD_p3 trnS-psbD ATTAGCAATCCGCCGCTTTA CCGACAAAAACGAAACGGTC 1044–1117 1.000 86.4
trnS-psbD_p4 trnS-psbD ATTAGCAATCCGCCGCTTTA CGACAAAAACGAAACGGTCC 1043–1116 1.000 86.4
trnS-psbD_p5 trnS-psbD GAGCGGAAAGAGAGGGATTC GACAAAAACGAAACGGTCCC 1093–1166 1.000 85.9
trnG-trnfM_p1 trnG-trnfM AGGAGAAGATACGGGTTCGA CGAGGCTCATAACCTTGAGG 539–768 1.000 84.1
trnG-trnfM_p2 trnG-trnfM AGGAGAAGATACGGGTTCGA TTCCACCTTTTTCGTCCACC 602–832 1.000 83.8
trnG-trnfM_p3 trnG-trnfM AGGAGAAGATACGGGTTCGA CACCTTTTTCGTCCACCAGT 599–829 1.000 83.8
trnG-trnfM_p4 trnG-trnfM AGGAGAAGATACGGGTTCGA CAGTTTGGTAGCTCACGAGG 554–783 1.000 83.5
trnG-trnfM_p5 trnG-trnfM AGGAGAAGATACGGGTTCGA TTTTTCGTCCACCAGTTCCC 595–825 0.900 79.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (30)

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

Species Accession Length (bp) Link
Glyceria acutiflora PZ098586.1 136103 View on NCBI ↗
Glyceria alnasteretum PZ098606.1 136346 View on NCBI ↗
Glyceria arkansana NC_050406.1 136143 View on NCBI ↗
Glyceria australis PZ098320.1 136036 View on NCBI ↗
Glyceria borealis PZ098588.1 135317 View on NCBI ↗
Glyceria canadensis PZ098590.1 136264 View on NCBI ↗
Glyceria declinata PZ098381.1 135808 View on NCBI ↗
Glyceria depauperata PZ098318.1 135921 View on NCBI ↗
Glyceria drummondii PZ098380.1 136027 View on NCBI ↗
Glyceria elata PZ098592.1 136416 View on NCBI ↗
Glyceria fluitans PZ098604.1 135910 View on NCBI ↗
Glyceria grandis PZ098593.1 136385 View on NCBI ↗
Glyceria insularis PZ098402.1 135835 View on NCBI ↗
Glyceria ischyroneura PZ098319.1 136442 View on NCBI ↗
Glyceria leptolepis PZ098321.1 135742 View on NCBI ↗
Glyceria leptostachya PZ098374.1 135984 View on NCBI ↗
Glyceria lithuanica PZ098278.1 136488 View on NCBI ↗
Glyceria maxima PZ098384.1 136316 View on NCBI ↗
Glyceria melicaria PZ098595.1 136637 View on NCBI ↗
Glyceria multiflora PZ098603.1 135879 View on NCBI ↗
Glyceria nemoralis PZ098322.1 136115 View on NCBI ↗
Glyceria notata PZ098281.1 135827 View on NCBI ↗
Glyceria nubigena PZ098316.1 136641 View on NCBI ↗
Glyceria obtusa PZ098597.1 136688 View on NCBI ↗
Glyceria pulchella PZ098317.1 136504 View on NCBI ↗
Glyceria septentrionalis NC_050405.1 136159 View on NCBI ↗
Glyceria spiculosa PZ098385.1 136293 View on NCBI ↗
Glyceria striata PZ098601.1 135935 View on NCBI ↗
Glyceria tonglensis PZ098323.1 136110 View on NCBI ↗
Glyceria triflora PZ098279.1 136377 View on NCBI ↗