Markers + reference

Synarthrophyton

2 species · Hapalidiaceae · Hapalidiales

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Species 2
Genome length 179–182 kb
Candidate markers 460
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 9 remaining regions by MarkerSeek score (out of 460 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf21 Genome 525 0.2500 0.05 69.5 yes View details
ycf56 Genome 690 0.2406 1.00 78.8 yes View details
ycf37 Genome 504 0.2843 0.97 79.9 yes View details
ycf37-chlN Genome 584 0.3096 0.96 82.1 yes View details
orf160 Genome 498 0.3052 1.00 76.6 yes View details
syfB Genome 1995 0.3010 0.99 78.7 yes View details
chlB Genome 3552 0.2372 0.99 75.6 yes View details
acsF-petN Genome 452 0.3032 0.96 80.7 yes View details
rps5 Genome 552 0.1639 0.97 80.4 yes View details
ycf60 Genome 618 0.1363 0.99 80.2 yes View details
ccdA Genome 732 0.2617 0.99 79.7 yes View details
upp Genome 600 0.2778 0.99 79.7 yes View details
orf456 Genome 1365 0.3193 0.99 79.7 yes View details
ycf29 Genome 651 0.2365 0.99 79.6 yes View details
accB-ycf45 Genome 408 0.2786 0.94 79.6 yes View details
hisS Genome 1260 0.2222 0.99 79.4 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf21_p1 ycf21 ACCCAATGACATGAATGGTA CGTCAGATAAGAATTGAATTTTCT 740 0.500 20.0
ycf21_p2 ycf21 TACCCAATGACATGAATGGT CGTCAGATAAGAATTGAATTTTCT 741 0.500 20.0
ycf21_p3 ycf21 ACCCAATGACATGAATGGTA CGTCAGATAAGAATTGAATTTTCTTCT 740 0.500 20.0
ycf21_p4 ycf21 TACCCAATGACATGAATGGT CGTCAGATAAGAATTGAATTTTCTTCT 741 0.500 20.0
ycf21_p5 ycf21 ACCCAATGACATGAATGGTA CGTCAGATAAGAATTGAATTTTCTTC 740 0.500 20.0
ycf60_p1 ycf60 GCAGCTCCTAAACGAATTGC TGCCACTGATTGAGCTCTTC 1589 0.500 57.7
ycf60_p2 ycf60 GCAGCTCCTAAACGAATTGC GCAGCGCAACCAATATCTTC 1906 0.500 57.7
ycf60_p3 ycf60 GCAGCTCCTAAACGAATTGC TAACAGCAGCGCAACCAATA 1911 0.500 57.1
ycf60_p4 ycf60 GCAGCTCCTAAACGAATTGC AGCAGCGCAACCAATATCTT 1907 0.500 56.6
ycf60_p5 ycf60 GCAGCTCCTAAACGAATTGC TCAGCATTTTTGCATCCAGC 1675 0.500 55.6
ccdA_p1 ccdA AAATTTCCACTGACGTGCAC AGGATAGGCGAGGGTACTTC 1669–1941 1.000 82.2
ccdA_p2 ccdA AAATTTCCACTGACGTGCAC GGTTCAAATCCTTCCTGGGG 1150–1153 1.000 81.0
ccdA_p3 ccdA AAATTTCCACTGACGTGCAC TACCAATTTCACCACGTCCG 1486–1758 1.000 80.6
ccdA_p4 ccdA AAATTTCCACTGACGTGCAC ACGCCAAACCATCCAATGTA 1788–2062 1.000 80.5
ccdA_p5 ccdA AAATTTCCACTGACGTGCAC TACGCCAAACCATCCAATGT 1789–2063 1.000 80.5
ycf56_p1 ycf56 ATAGTTTCTCCTGGCTGTGC CAGCTGGTTCATGGGCTTTA 1315 0.500 55.4
ycf56_p2 ycf56 ATAGTTTCTCCTGGCTGTGC GTTTTGGCAGCTGGTTCATG 1322 0.500 55.0
ycf56_p3 ycf56 CCTGGCTGTGCATGTACTTT CAGCTGGTTCATGGGCTTTA 1306 0.500 55.0
ycf56_p4 ycf56 CCTGGCTGTGCATGTACTTT GTTTTGGCAGCTGGTTCATG 1313 0.500 54.6
ycf56_p5 ycf56 ACCAACATTCATGCCTGGAT CAGCTGGTTCATGGGCTTTA 1690 0.500 54.4
ycf37_p1 ycf37 TCGGGATATAGCGCAGTTTG AATCCTCTTGAAGCTCGTGG 1306–1466 1.000 85.8
ycf37_p2 ycf37 GTCGGGATATAGCGCAGTTT AATCCTCTTGAAGCTCGTGG 1307 0.500 55.7
ycf37_p3 ycf37 TACTGTCGGTTGGGTACGTA AATCCTCTTGAAGCTCGTGG 1715 0.500 55.3
ycf37_p4 ycf37 TCGGGATATAGCGCAGTTTG ATCCTCTTGAAGCTCGTGGA 1305 0.500 55.3
ycf37_p5 ycf37 GTCGGGATATAGCGCAGTTT ATCCTCTTGAAGCTCGTGGA 1306 0.500 55.3
ycf37-chlN_p1 ycf37-chlN TCGGGATATAGCGCAGTTTG TGATGCGCAGGAGAAAAACT 1746 0.500 58.0
ycf37-chlN_p2 ycf37-chlN GTCGGGATATAGCGCAGTTT TGATGCGCAGGAGAAAAACT 1747 0.500 58.0
ycf37-chlN_p3 ycf37-chlN TCGGGATATAGCGCAGTTTG TACAACATTGATGCGCAGGA 1754 0.500 58.0
ycf37-chlN_p4 ycf37-chlN GTCGGGATATAGCGCAGTTT TACAACATTGATGCGCAGGA 1755 0.500 57.9
ycf37-chlN_p5 ycf37-chlN TCGGGATATAGCGCAGTTTG ACATTGATGCGCAGGAGAAA 1750 0.500 57.4

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
Synarthrophyton chejuense NC_039977.1 179264 View on NCBI ↗
Synarthrophyton patena NC_066049.1 181685 View on NCBI ↗