Markers + reference

Synura

3 species · Mallomonadaceae · Synurales

Back to catalogue

Species 3
Genome length 129–133 kb
Candidate markers 336
Primer pairs 85

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 336 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tatC LSC 747 0.4462 0.99 84.1 yes View details
acpP-trnP LSC 1202 0.3814 0.17 66.7 yes View details
psbD-rns IRb 2080 0.4152 0.62 73.0 yes View details
rnl-psaC IRb 840 0.3507 0.69 75.0 yes View details
ccs1-trnN IRa 606 0.4223 0.46 72.1 yes View details
psaC-rnl IRa 840 0.3507 0.69 75.0 yes View details
rns-psbD IRa 2080 0.4062 0.63 73.1 yes View details
ccs1 IRb 1371 0.2183 0.96 83.5 yes View details
ccs1 IRa 1371 0.2176 0.96 83.5 yes View details
trnH(GUG)-rpl19 LSC 1315 0.3606 0.97 83.1 yes View details
rps2 LSC 753 0.1680 0.97 83.1 yes View details
dnaB LSC 1773 0.2672 0.97 83.0 yes View details
rpl4 LSC 645 0.2748 0.94 82.9 yes View details
psbW-clpC LSC 635 0.3434 0.99 82.7 yes View details
secA-rpl27 IRb 932 0.3266 0.96 82.7 yes View details
rpl27-secA IRa 932 0.3251 0.96 82.7 yes View details
ycf54 SSC 744 0.3582 0.99 82.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tatC_p1 tatC TAAACTTGACCACGACCACG ACCACAAAGTACAGAAACTGCT 1680 0.333 35.3
tatC_p2 tatC TAAACTTGACCACGACCACG CCACAAAGTACAGAAACTGCTG 1679 0.333 34.5
tatC_p3 tatC TAAACTTGACCACGACCACG ACCACAAAGTACAGAAACTGC 1680 0.333 33.5
tatC_p4 tatC AACAGATGTTGGGGCTTCAA ACCACAAAGTACAGAAACTGCT 1318 0.333 33.4
tatC_p5 tatC ACAGATGTTGGGGCTTCAAA ACCACAAAGTACAGAAACTGCT 1317 0.333 33.4
trnH(GUG)-rpl19_p1 trnH(GUG)-rpl19 GCACTTGGAATTGTTGGAGC AACCCAGTCGGATGCATTTT 2224 0.333 52.2
trnH(GUG)-rpl19_p2 trnH(GUG)-rpl19 GCACTTGGAATTGTTGGAGC ACCCAGTCGGATGCATTTTT 2223 0.333 52.2
trnH(GUG)-rpl19_p3 trnH(GUG)-rpl19 TGGCACTTGGAATTGTTGGA AACCCAGTCGGATGCATTTT 2226 0.333 52.1
trnH(GUG)-rpl19_p4 trnH(GUG)-rpl19 TGGCACTTGGAATTGTTGGA ACCCAGTCGGATGCATTTTT 2225 0.333 52.1
trnH(GUG)-rpl19_p5 trnH(GUG)-rpl19 TAAGATTCAGGCGAACGACG ACCCAGTCGGATGCATTTTT 1787 0.333 52.0
rps2_p1 rps2 GACTAATCCCAGCAGGTTCG CGTTTGTTGGAGCAGCAAAT 1415 0.333 51.8
rps2_p2 rps2 GACTAATCCCAGCAGGTTCG GGAATTAAAGCTCCTGCCCA 1365 0.333 51.7
rps2_p3 rps2 GACTAATCCCAGCAGGTTCG AGCTCCTGCCCAATTACAAC 1357 0.333 51.6
rps2_p4 rps2 GACTAATCCCAGCAGGTTCG GTCCCATTTGAGTGATGGCA 1280 0.333 51.6
rps2_p5 rps2 GACTAATCCCAGCAGGTTCG TATCGTTTGTTGGAGCAGCA 1418 0.333 51.4
psbW-clpC_p1 psbW-clpC AATTGGGGTGTAGCCAAGTG CGCCAATTGTAAAGCACCAG 1789 0.333 52.6
psbW-clpC_p2 psbW-clpC TAGGTTCGAATCCTCCCTCC CGCCAATTGTAAAGCACCAG 1738 0.333 52.5
psbW-clpC_p3 psbW-clpC AATTGGGGTGTAGCCAAGTG GAACCAGCAACAATTCGAGC 1422 0.333 52.5
psbW-clpC_p4 psbW-clpC TAGGTTCGAATCCTCCCTCC GAACCAGCAACAATTCGAGC 1371 0.333 52.4
psbW-clpC_p5 psbW-clpC CCCTCCTCGCCCATTTATTC CGCCAATTGTAAAGCACCAG 1844 0.333 52.4
dnaB_p1 dnaB CCTCTTGAGATTAAGACAGGCC CCTGCGTTCTACCAACTGAA 2183 0.333 34.4
dnaB_p2 dnaB CCTCTTGAGATTAAGACAGGCC ACCAACTGAACTAAGGACGC 2173 0.333 34.4
dnaB_p3 dnaB CCTCTTGAGATTAAGACAGGCC AAAAGAACGGATGCAGGAGG 2518 0.333 34.4
dnaB_p4 dnaB CCTCTTGAGATTAAGACAGGCC ACCCTCGACACCAGATTTTG 2207 0.333 34.3
dnaB_p5 dnaB CCTCTTGAGATTAAGACAGGCC CAGATTTTGGAGACCTGCGT 2196 0.333 34.3
acpP-trnP_p1 acpP-trnP GGAACAACTGTACGCGTAGT AAAGCAGACACGCTACCAAA 494–1479 0.667 77.9
acpP-trnP_p2 acpP-trnP TGTAGGAACAACTGTACGCG AAAGCAGACACGCTACCAAA 1483 0.333 52.6
acpP-trnP_p3 acpP-trnP GTAGGAACAACTGTACGCGT AAAGCAGACACGCTACCAAA 1482 0.333 52.6
acpP-trnP_p4 acpP-trnP TGTAGGAACAACTGTACGCG GGGATGACAGGATTCGAACC 1520 0.333 52.5
acpP-trnP_p5 acpP-trnP GGAACAACTGTACGCGTAGT GGGATGACAGGATTCGAACC 1516 0.333 52.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Synura petersenii MH795128.1 133059 View on NCBI ↗
Synura sphagnicola MH795129.1 128699 View on NCBI ↗
Synura uvella NC_040134.1 133257 View on NCBI ↗