Markers + reference

Micractinium

2 species · Chlorellaceae · Chlorellales

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Species 2
Genome length 124–140 kb
Candidate markers 227
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 227 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnD-GUC-trnG-GCC Genome 732 0.2312 0.82 79.8 yes View details
psbB-clpP Genome 991 0.1690 0.81 81.3 yes View details
petD-trnC-GCA Genome 1550 0.1992 0.83 81.9 yes View details
psbA-ycf1 Genome 1004 0.2500 0.73 78.2 yes View details
trnH-GUG-trnL-CAA Genome 710 0.2443 0.93 83.1 yes View details
trnT-GGU-cysA Genome 859 0.3154 0.69 77.5 yes View details
rrn16-trnL-GAG Genome 955 0.1429 0.97 84.2 yes View details
trnL-GAG-trnS-GGA Genome 458 0.3952 1.00 78.0 yes View details
atpE-atpB Genome 692 0.2404 0.64 75.0 yes View details
trnS-UGA-psbM Genome 565 0.1686 0.93 87.8 yes View details
trnI-UAU-psaB Genome 709 0.1843 0.83 86.7 yes View details
rpoA-rps11 Genome 687 0.1724 0.85 86.5 yes View details
psbZ-trnG-UCC Genome 621 0.0945 0.97 86.3 yes View details
psbD-petG Genome 812 0.1149 0.93 85.1 yes View details
rps11-rpl36 Genome 764 0.1621 0.91 84.3 yes View details
rps2-trnT-UGU Genome 383 0.1203 0.91 84.0 yes View details
infA-rps8 Genome 607 0.1460 0.76 84.0 yes View details
rpl23-cemA Genome 818 0.1230 0.84 83.6 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
trnD-GUC-trnG-GCC_p1 trnD-GUC-trnG-GCC TTCAATTGGTCAGAGCACCG ACGCGGATTGTCACTAGTTC 925 0.500 56.1
trnD-GUC-trnG-GCC_p2 trnD-GUC-trnG-GCC TTCAATTGGTCAGAGCACCG TTTGGGACCGGTACCTTTTG 1162 0.500 56.1
trnD-GUC-trnG-GCC_p3 trnD-GUC-trnG-GCC TTCAATTGGTCAGAGCACCG GAGATTTTGGGACCGGTACC 1167 0.500 55.9
trnD-GUC-trnG-GCC_p4 trnD-GUC-trnG-GCC TTCAATTGGTCAGAGCACCG GGCAAACCGGGTAATACCAT 1247 0.500 55.7
trnD-GUC-trnG-GCC_p5 trnD-GUC-trnG-GCC TTCAATTGGTCAGAGCACCG CGAATCTAGTAGCAGGCACC 906 0.500 55.0
rps2-trnT-UGU_p1 rps2-trnT-UGU GCGGATTCCATTCACGAGTA TTCGACTCCGATAGAAGGCT 467–482 1.000 88.9
rps2-trnT-UGU_p2 rps2-trnT-UGU GCGGATTCCATTCACGAGTA GTTCGACTCCGATAGAAGGC 468–483 1.000 88.3
rps2-trnT-UGU_p3 rps2-trnT-UGU ATGCCCAAAATGCATTCCAC TTCGACTCCGATAGAAGGCT 445–460 1.000 87.7
rps2-trnT-UGU_p4 rps2-trnT-UGU ATGCCCAAAATGCATTCCAC GTTCGACTCCGATAGAAGGC 446–461 1.000 87.2
rps2-trnT-UGU_p5 rps2-trnT-UGU GCCCAAAATGCATTCCACTT TTCGACTCCGATAGAAGGCT 443–458 1.000 87.2
psbD-petG_p1 psbD-petG GAAAACGAAACGGTCACGAC CGTCGTGGAGATCAGCTTAA 926 0.500 55.5
psbD-petG_p2 psbD-petG CGACGAAGCCAGTCATCTAC CGTCGTGGAGATCAGCTTAA 910 0.500 54.1
psbD-petG_p3 psbD-petG ACCAGCCACGTTTTTCTTGA CGTCGTGGAGATCAGCTTAA 882 0.500 53.6
psbD-petG_p4 psbD-petG TGAAAACGAAACGGTCACGA CGTCGTGGAGATCAGCTTAA 927 0.500 52.6
psbD-petG_p5 psbD-petG CCAGCCACGTTTTTCTTGAG CGTCGTGGAGATCAGCTTAA 881 0.500 52.3
rpoA-rps11_p1 rpoA-rps11 ACCTTGCTCTTGAATTCGTGA CGAGACATTACTCCGATCCC 768–807 1.000 77.3
rpoA-rps11_p2 rpoA-rps11 ACCTTGCTCTTGAATTCGTGA CATTACTCCGATCCCACACA 763–802 1.000 75.2
rpoA-rps11_p3 rpoA-rps11 ACCTTGCTCTTGAATTCGTGA TACTCCGATCCCACACAATG 760–799 1.000 75.2
rpoA-rps11_p4 rpoA-rps11 ACCTTGCTCTTGAATTCGTGA ACATTACTCCGATCCCACAC 764–803 1.000 75.1
rpoA-rps11_p5 rpoA-rps11 TCGTGAATCCACACAAGAGA CGAGACATTACTCCGATCCC 753–792 1.000 74.4
rps11-rpl36_p1 rps11-rpl36 ACCCTGATTTCTCGCATTCC TAGTTTTGCCTGTGTGTCCC 1444–1480 1.000 91.5
rps11-rpl36_p2 rps11-rpl36 ACAAGTTTGCGCTGCATTTT TAGTTTTGCCTGTGTGTCCC 1415–1451 1.000 91.3
rps11-rpl36_p3 rps11-rpl36 ACCCTGATTTCTCGCATTCC GGAAGGCGTCGTAACTCAAT 1649–1685 1.000 90.8
rps11-rpl36_p4 rps11-rpl36 ACAAGTTTGCGCTGCATTTT GGAAGGCGTCGTAACTCAAT 1620–1656 1.000 90.8
rps11-rpl36_p5 rps11-rpl36 ACGTTCACCCTGATTTCTCG GGAAGGCGTCGTAACTCAAT 1655–1691 1.000 90.6
infA-rps8_p1 infA-rps8 ATTGAGTTACGACGCCTTCC CGTCTTGGCGGAGAAATTCT 665–666 1.000 89.8
infA-rps8_p2 infA-rps8 ATTGAGTTACGACGCCTTCC CTCGTCTTGGCGGAGAAATT 667–668 1.000 89.8
infA-rps8_p3 infA-rps8 ATTGAGTTACGACGCCTTCC AAAATCTCGTCTTGGCGGAG 672–673 1.000 89.7
infA-rps8_p4 infA-rps8 ATTGAGTTACGACGCCTTCC AGAAAATCTCGTCTTGGCGG 674–675 1.000 89.7
infA-rps8_p5 infA-rps8 ATTGAGTTACGACGCCTTCC TCGTCTTGGCGGAGAAATTC 666–667 1.000 89.7

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
Micractinium simplicissimum NC_071969.1 123552 View on NCBI ↗
Micractinium singularis MN894287.1 139597 View on NCBI ↗