Markers + reference

Echinothamnion

2 species · Rhodomelaceae · Ceramiales

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Species 2
Genome length 168–168 kb
Candidate markers 455
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 455 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf37 Genome 471 0.1253 1.00 76.4 yes View details
trpA Genome 810 0.1099 1.00 79.1 yes View details
psaC-ycf22 Genome 925 0.1583 0.99 80.1 yes View details
ycf58 Genome 414 0.1401 1.00 75.2 yes View details
QQP88_pgp117 Genome 798 0.1584 0.99 80.2 yes View details
dnaB Genome 1758 0.1109 1.00 78.2 yes View details
syfB Genome 2019 0.1294 1.00 78.2 yes View details
ompR-rns Genome 390 0.1585 1.00 81.8 no View details
rps1 Genome 816 0.0994 1.00 80.1 yes View details
moeB Genome 1062 0.1026 1.00 79.1 yes View details
trnS.2-trnM.3 Genome 22 0.2273 1.00 78.6 yes View details
ycf53 Genome 723 0.0941 1.00 78.5 yes View details
rnz Genome 675 0.0800 1.00 78.3 yes View details
dsbD Genome 738 0.0962 1.00 78.3 yes View details
ycf22 Genome 672 0.0952 1.00 78.2 yes View details
pbsA-bas1 Genome 145 0.1481 0.93 78.2 yes View details
trnP-ycf52 Genome 152 0.2482 0.93 77.8 yes View details
ccs1 Genome 1329 0.0828 1.00 77.8 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
ycf37_p1 ycf37 ACCGCTTTTTGTTTTCATACGA CGGCTTCATGATAGATCCGG 954 0.500 39.5
ycf37_p2 ycf37 ACCGCTTTTTGTTTTCATACGA ACTCAGTCGGTTGGGTAAGA 1255 0.500 39.5
ycf37_p3 ycf37 ACCGCTTTTTGTTTTCATACGA TTTGTGACTCAGTCGGTTGG 1261 0.500 39.1
ycf37_p4 ycf37 ACCGCTTTTTGTTTTCATACGA GTCGGTTGGGTAAGAAGACC 1250 0.500 38.8
ycf37_p5 ycf37 ACCGCTTTTTGTTTTCATACGA TTCAAGGACAAGGCTTAGGC 1075 0.500 38.0
trnP-ycf52_p1 trnP-ycf52 GCTACCAAGCTGCGCTATAT CGGCTTCATGATAGATCCGG 231 0.500 59.3
trnP-ycf52_p2 trnP-ycf52 GCTACCAAGCTGCGCTATAT ACTCAGTCGGTTGGGTAAGA 532 0.500 59.3
trnP-ycf52_p3 trnP-ycf52 GCTACCAAGCTGCGCTATAT TTTGTGACTCAGTCGGTTGG 538 0.500 58.9
trnP-ycf52_p4 trnP-ycf52 GCTACCAAGCTGCGCTATAT GTCGGTTGGGTAAGAAGACC 527 0.500 58.6
trnP-ycf52_p5 trnP-ycf52 GCTACCAAGCTGCGCTATAT TTCAAGGACAAGGCTTAGGC 352 0.500 57.7
ycf53_p1 ycf53 TCATCCAGAGGCTAGTCCAG GCGAACGACAAAAAGTATGGA 1175 0.500 45.0
ycf53_p2 ycf53 TCATCCAGAGGCTAGTCCAG AGCGAACGACAAAAAGTATGG 1176 0.500 44.9
ycf53_p3 ycf53 TCAAAATCACGGTTTTGCGG GCGAACGACAAAAAGTATGGA 1319 0.500 44.6
ycf53_p4 ycf53 TCAAAATCACGGTTTTGCGG AGCGAACGACAAAAAGTATGG 1320 0.500 44.5
ycf53_p5 ycf53 CAAAATCACGGTTTTGCGGT GCGAACGACAAAAAGTATGGA 1318 0.500 44.4
rnz_p1 rnz AATAGCTGCTGGTTCTTGGG AGAGTTTGAATCACGGCCAT 1597–1598 1.000 79.8
rnz_p2 rnz CTGCTGGTTCTTGGGCAATA AGAGTTTGAATCACGGCCAT 1592–1593 1.000 79.6
rnz_p3 rnz AATAGCTGCTGGTTCTTGGG CCACCAACATCAATCACTGC 1213–1214 1.000 78.9
rnz_p4 rnz CTGCTGGTTCTTGGGCAATA CCACCAACATCAATCACTGC 1208–1209 1.000 78.7
rnz_p5 rnz TGCTGGTTCTTGGGCAATAT AGAGTTTGAATCACGGCCAT 1591–1592 1.000 76.7
dsbD_p1 dsbD AATTGCGGACGGAGAGATTC CACCCTTAGGAACAATCTCCTG 1700 0.500 42.6
dsbD_p2 dsbD GAATTGCGGACGGAGAGATT CACCCTTAGGAACAATCTCCTG 1701 0.500 42.6
dsbD_p3 dsbD AATCCTTCCTGGGGAGTTCA CACCCTTAGGAACAATCTCCTG 1431 0.500 42.6
dsbD_p4 dsbD ATCCTTCCTGGGGAGTTCAA CACCCTTAGGAACAATCTCCTG 1430 0.500 42.6
dsbD_p5 dsbD TCAAATCCTTCCTGGGGAGT CACCCTTAGGAACAATCTCCTG 1434 0.500 42.6
ccs1_p1 ccs1 TCGTTCTGTTTACCTAAGCCA CCGACACCTATGCATGGAAA 1977 0.500 43.4
ccs1_p2 ccs1 TCGTTCTGTTTACCTAAGCCA AATATCACCAGGACCGGGAA 2122 0.500 42.8
ccs1_p3 ccs1 TCGTTCTGTTTACCTAAGCCA CTACCGACACCTATGCATGG 1980 0.500 42.5
ccs1_p4 ccs1 TCGTTCTGTTTACCTAAGCCA TACCGACACCTATGCATGGA 1979 0.500 42.0
ccs1_p5 ccs1 TCGTTCTGTTTACCTAAGCCA CCGGGAAGACCTGAAGAATC 2109 0.500 41.2

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
Echinothamnion hookeri NC_079646.1 168059 View on NCBI ↗
Echinothamnion hystrix NC_079647.1 168117 View on NCBI ↗