Markers + reference

Pseudostaurastrum

2 species · Goniochloridaceae · Goniochloridales

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Species 2
Genome length 120–120 kb
Candidate markers 355
Primer pairs 85

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 355 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf60 LSC 1194 0.2085 1.00 80.8 yes View details
orf1_gon LSC 996 0.2437 1.00 79.3 yes View details
lysR LSC 828 0.3354 0.96 82.4 yes View details
rpoC2 LSC 4074 0.1863 1.00 74.2 yes View details
rpoC1 LSC 2334 0.1752 1.00 77.1 yes View details
ycf19 LSC 630 0.2476 1.00 78.9 yes View details
groEL LSC 1587 0.2159 0.96 82.5 yes View details
clpN SSC 522 0.2893 1.00 77.2 yes View details
rns-trnI(gat) IRb 68 0.0714 0.82 81.2 yes View details
trnI(gat)-rns IRa 68 0.0714 0.82 81.2 yes View details
atpB LSC 1482 0.1001 1.00 81.1 yes View details
rps5 SSC 630 0.1521 0.98 80.8 yes View details
ycf12-rbcS LSC 154 0.1224 0.95 80.5 yes View details
thiG IRb 810 0.0901 1.00 79.8 yes View details
thiG IRa 810 0.0901 1.00 79.8 yes View details
trnF(gaa)-trnC(gca) SSC 119 0.2936 0.92 79.7 yes View details
chlI SSC 1185 0.1502 1.00 79.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps5_p1 rps5 TCTTCTTCTGCATCTTGCCG AGATTCGTGCAATTCGTCCA 1383 0.500 57.1
rps5_p2 rps5 TCTTCTTCTGCATCTTGCCG CAATTCGTCCACCTGAACCA 1374 0.500 57.0
rps5_p3 rps5 TCTTCTTCTGCATCTTGCCG GATTCGTGCAATTCGTCCAC 1382 0.500 56.6
rps5_p4 rps5 TCTTCTTCTGCATCTTGCCG TCGTCCACCTGAACCATACA 1370 0.500 54.9
rps5_p5 rps5 TCTTCTTCTGCATCTTGCCG CGTCCACCTGAACCATACAA 1369 0.500 54.1
rns-trnI(gat)_p1 rns-trnI(gat) GACCGAGGTGAAGTCGTAAC TACCAGCTGAGCTATACCCC 215–227 1.000 85.2
rns-trnI(gat)_p2 rns-trnI(gat) GACCGAGGTGAAGTCGTAAC TGGACTTGAACCAGAGACCT 181–193 1.000 84.7
rns-trnI(gat)_p3 rns-trnI(gat) GACCGAGGTGAAGTCGTAAC GCTGGGCTATTCTGGACTTG 193–205 1.000 82.8
rns-trnI(gat)_p4 rns-trnI(gat) AAGTCGTAACAAGGTAGCCG TACCAGCTGAGCTATACCCC 205–217 1.000 82.6
rns-trnI(gat)_p5 rns-trnI(gat) TGACCGAGGTGAAGTCGTAA TACCAGCTGAGCTATACCCC 216–228 1.000 82.2
thiG_p1 thiG AATGGTTGTAAAGCTGGGCA TGACAGCAAAACTCAGTCGT 1562 0.500 57.5
thiG_p2 thiG ATGGTTGTAAAGCTGGGCAA TGACAGCAAAACTCAGTCGT 1561 0.500 57.5
thiG_p3 thiG AATGGTTGTAAAGCTGGGCA AGTGCGTCAAAGAGGAACAA 1766 0.500 57.3
thiG_p4 thiG ATGGTTGTAAAGCTGGGCAA AGTGCGTCAAAGAGGAACAA 1765 0.500 57.3
thiG_p5 thiG GGGTAGCCCTTAGGAAAAGC TGACAGCAAAACTCAGTCGT 1764 0.500 57.1
ycf60_p1 ycf60 TTGATCCAAGGCCTTCATCG ACTGGAGATCTTGATGCTTGT 2262 0.500 43.7
ycf60_p2 ycf60 ATAAAAACTCACGGCTGCCA ACTGGAGATCTTGATGCTTGT 1699 0.500 43.3
ycf60_p3 ycf60 TCTGCCACACGCTTCTAAAA ACTGGAGATCTTGATGCTTGT 2060 0.500 42.0
ycf60_p4 ycf60 AACGTGTTGGCTCAATCCAA ACTGGAGATCTTGATGCTTGT 2085 0.500 41.5
ycf60_p5 ycf60 ACGTGTTGGCTCAATCCAAA ACTGGAGATCTTGATGCTTGT 2084 0.500 41.5
orf1_gon_p1 orf1_gon TCTGCAGTTTGGATTTGTTGT CCTTCGCCGGTTTTCATTTC 1607 0.500 40.2
orf1_gon_p2 orf1_gon TCTGCAGTTTGGATTTGTTGT TGCGGTTGAATGACGTGTTA 1515 0.500 39.4
orf1_gon_p3 orf1_gon TCTGCAGTTTGGATTTGTTGT GCCGGTTTTCATTTCAGCAA 1602 0.500 39.2
orf1_gon_p4 orf1_gon TCTGCAGTTTGGATTTGTTGT TAACTGCGGTTGAATGACGT 1519 0.500 39.2
orf1_gon_p5 orf1_gon TCTGCAGTTTGGATTTGTTGT GACGAAAAACACCACCCAAC 1327 0.500 38.8
lysR_p1 lysR CAGTTGTACCGGGTTACAGA AACTGCCGGTTCCAAAATCT 1921 0.500 51.1
lysR_p2 lysR CAGTTGTACCGGGTTACAGA ACTGCCGGTTCCAAAATCTT 1920 0.500 51.1
lysR_p3 lysR TCAGTTGTACCGGGTTACAG AACTGCCGGTTCCAAAATCT 1922 0.500 51.1
lysR_p4 lysR TCAGTTGTACCGGGTTACAG ACTGCCGGTTCCAAAATCTT 1921 0.500 51.1
lysR_p5 lysR CAGTTGTACCGGGTTACAGA GTACAAAAATGGGCCGAACG 2168 0.500 50.9

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
Pseudostaurastrum enorme PX978885.1 119681 View on NCBI ↗
Pseudostaurastrum limneticum PX978886.1 119724 View on NCBI ↗