Markers + reference

Pharus

2 species · Poaceae · Poales

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Species 2
Genome length 142–142 kb
Candidate markers 290
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 290 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbZ-trnfM LSC 677 0.0859 0.91 80.0 yes View details
trnG-trnT LSC 1353 0.0363 1.00 67.4 yes View details
psbM-petN LSC 1170 0.0257 1.00 65.4 yes View details
atpI-atpH LSC 812 0.0296 1.00 75.7 yes View details
atpH LSC 246 0.0000 1.00 21.1 yes View details
rbcL LSC 1443 0.0139 1.00 54.6 yes View details
psaJ-rpl33 LSC 325 0.0502 0.98 68.5 yes View details
trnfM-trnG LSC 95 0.1124 0.94 78.0 yes View details
infA-rps8 LSC 78 0.0385 1.00 73.9 yes View details
ndhH-ndhF SSC 35 0.0323 0.89 73.6 yes View details
trnfM LSC 72 0.1111 1.00 72.6 yes View details
psbF-psbE LSC 10 0.5000 1.00 72.5 yes View details
psaJ LSC 129 0.0698 1.00 69.6 yes View details
psbA LSC 1062 0.0132 1.00 66.3 yes View details
ndhF-rpl32 SSC 829 0.0145 1.00 66.0 yes View details
rps3-rpl22 LSC 57 0.0182 0.96 64.5 yes View details
trnfM LSC 60 0.0167 1.00 49.1 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1179–1180 1.000 69.5
psbA_p2 psbA TTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1180–1181 1.000 69.5
psbA_p3 psbA TCTGGCTTTCCTTCCTTCAAA AATACGTGTGCTTGGGAGTC 1179–1180 1.000 67.5
psbA_p4 psbA TTCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1180–1181 1.000 67.5
psbA_p5 psbA TTTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1181–1182 1.000 67.5
psbZ-trnfM_p1 psbZ-trnfM CAACCACTCAGCCATCTCTC AGCCTTCCAAGCTAACGATG 1436–1446 1.000 87.9
psbZ-trnfM_p2 psbZ-trnfM CAACCACTCAGCCATCTCTC CCTAGCCTTCCAAGCTAACG 1439–1449 1.000 87.7
psbZ-trnfM_p3 psbZ-trnfM GAGCTATCAACCACTCAGCC AGCCTTCCAAGCTAACGATG 1443–1453 1.000 87.6
psbZ-trnfM_p4 psbZ-trnfM GGAGCTATCAACCACTCAGC AGCCTTCCAAGCTAACGATG 1444–1454 1.000 87.6
psbZ-trnfM_p5 psbZ-trnfM CAACCACTCAGCCATCTCTC TTGTTTCAGCTCGGTGGAAA 1717–1727 1.000 86.4
trnfM_p1 trnfM TTTCTAGGGCCGGGAACTAA AGCCTTCCAAGCTAACGATG 300–306 1.000 87.9
trnfM_p2 trnfM AATTCAGCTTTCTAGGGCCG AGCCTTCCAAGCTAACGATG 308–314 1.000 87.6
trnfM_p3 trnfM AATTCAGCTTTCTAGGGCCG TTGTTTCAGCTCGGTGGAAA 589–595 1.000 83.6
trnfM_p4 trnfM AGAAGATGCGGGTTCGATTC AGCCTTCCAAGCTAACGATG 547 0.500 59.3
trnfM_p5 trnfM GAGAAGATGCGGGTTCGATT AGCCTTCCAAGCTAACGATG 548 0.500 59.3
trnfM-trnG_p1 trnfM-trnG TTTCTAGGGCCGGGAACTAA AGCCTTCCAAGCTAACGATG 300–306 1.000 87.9
trnfM-trnG_p2 trnfM-trnG AATTCAGCTTTCTAGGGCCG AGCCTTCCAAGCTAACGATG 308–314 1.000 87.6
trnfM-trnG_p3 trnfM-trnG AATTCAGCTTTCTAGGGCCG TTGTTTCAGCTCGGTGGAAA 589–595 1.000 83.6
trnfM-trnG_p4 trnfM-trnG AGAAGATGCGGGTTCGATTC AGCCTTCCAAGCTAACGATG 547 0.500 59.3
trnfM-trnG_p5 trnfM-trnG GAGAAGATGCGGGTTCGATT AGCCTTCCAAGCTAACGATG 548 0.500 59.3
trnG-trnT_p1 trnG-trnT ACGAATCACACTTTTACCACT TTGAACCGATGACTTACGCC 1444–1450 1.000 52.3
trnG-trnT_p2 trnG-trnT AACGAATCACACTTTTACCACT TTGAACCGATGACTTACGCC 1445–1451 1.000 50.3
trnG-trnT_p3 trnG-trnT ACGAATCACACTTTTACCACT CGATGACTTACGCCTTACCA 1438–1444 1.000 50.0
trnG-trnT_p4 trnG-trnT ACGAATCACACTTTTACCACT TGACTTACGCCTTACCATGG 1435–1441 1.000 49.1
trnG-trnT_p5 trnG-trnT ACGAATCACACTTTTACCACT GACTTACGCCTTACCATGGC 1434–1440 1.000 48.9
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 1332–1339 1.000 69.4
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTAGTATGGGGGAGGAGTGG 1276–1283 1.000 68.5
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTATGGGGGAGGAGTGGA 1275–1282 1.000 67.8
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTC TAGTAAGTCTCGCTTGGGCT 1332–1339 1.000 65.3
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT AGTAGTATGGGGGAGGAGTG 1277–1284 1.000 64.5

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
Pharus lappulaceus NC_023245.1 141928 View on NCBI ↗
Pharus latifolius NC_021372.1 142077 View on NCBI ↗