Markers + reference

Cycas

53 species · Cycadaceae · Cycadales

Back to catalogue

Species 53
Genome length 162–162 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 492 0.0074 0.97 55.7 yes View details
psbK-psbI LSC 757 0.0047 1.00 46.9 yes View details
rpoC2 LSC 4098 0.0018 1.00 34.8 yes View details
accD-psaI LSC 456 0.0048 1.00 34.9 yes View details
rps19 LSC 279 0.0029 1.00 24.9 yes View details
ndhF SSC 2241 0.0031 0.99 43.0 yes View details
ndhF-rpl32 SSC 1153 0.0064 0.99 59.3 yes View details
rpl32-trnP-GGG SSC 1122 0.0048 0.99 52.1 yes View details
ycf1 SSC 5328 0.0033 1.00 48.0 yes View details
ycf1-chlN SSC 314 0.0064 1.00 40.3 yes View details
chlL-trnN-GUU IRa 1428 0.0026 1.00 41.2 yes View details
trnH-GUG-psbA IRa 467 0.0096 1.00 79.0 no View details
rps19-rpl2 LSC 64 0.0471 0.98 70.3 yes View details
rps16 LSC 1126 0.0037 1.00 60.8 yes View details
ycf3-trnS-GGA LSC 765 0.0048 1.00 58.9 yes View details
petA-psbJ LSC 1104 0.0042 1.00 57.7 yes View details
trnS-GCU-ycf12 LSC 689 0.0042 1.00 57.6 yes View details
atpH-atpI LSC 612 0.0045 0.99 56.8 yes View details
trnE-UUC-psbD LSC 1445 0.0023 1.00 55.9 yes View details
atpE-atpB LSC 8 0.0142 1.00 53.7 yes View details
atpB-rbcL LSC 697 0.0044 0.99 53.1 yes View details
psbM-trnD-GUC LSC 1112 0.0033 1.00 51.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU AAAACACCGAACCATCCGAT CACGGTTTGGGGAGAGATTT 664–705 1.000 83.7
psbA-trnK-UUU_p2 psbA-trnK-UUU AGTAATCCAGTCGCAGAAGC CACGGTTTGGGGAGAGATTT 623–664 1.000 83.3
psbA-trnK-UUU_p3 psbA-trnK-UUU AAAACACCGAACCATCCGAT GAAAGCCGTGTGCAATGAAA 692–733 0.943 81.7
psbA-trnK-UUU_p4 psbA-trnK-UUU AGTAATCCAGTCGCAGAAGC GAAAGCCGTGTGCAATGAAA 651–692 0.943 81.2
psbA-trnK-UUU_p5 psbA-trnK-UUU CACCGAACCATCCGATGTAA GAAAGCCGTGTGCAATGAAA 688–729 0.943 80.8
rps16_p1 rps16 TGGGAACAGGAATGACTAAATGA TCGATCCCTGTTCCTATCGT 1292–1328 1.000 54.5
rps16_p2 rps16 TGGGAACAGGAATGACTAAATGA TCGAATTCGATCCCTGTTCC 1298–1334 1.000 52.6
rps16_p3 rps16 TGGGAACAGGAATGACTAAATGA CGAATTCGATCCCTGTTCCT 1297–1333 1.000 52.6
rps16_p4 rps16 TGGGAACAGGAATGACTAAATG TCGATCCCTGTTCCTATCGT 1292–1328 1.000 51.0
rps16_p5 rps16 TCTTCATATAAGATCGCATGGGA TCGATCCCTGTTCCTATCGT 1310–1346 1.000 50.6
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CGTCCAGGATCGTTCGATAG 876–898 1.000 79.9
psbK-psbI_p2 psbK-psbI GCCAAATTACCCGAGGCTTA CGTCCAGGATCGTTCGATAG 963–985 1.000 79.8
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGTCCAGGATCGTTCGATA 877–899 1.000 79.8
psbK-psbI_p4 psbK-psbI GCCAAATTACCCGAGGCTTA ACGTCCAGGATCGTTCGATA 964–986 1.000 79.7
psbK-psbI_p5 psbK-psbI GCCAAATTACCCGAGGCTTA TACGTCCAGGATCGTTCGAT 965–987 1.000 79.7
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 CGGAGAGAGAGGGATTCGAA AGTTACCTTTGCGAACTGCT 867–892 1.000 79.8
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 ATTGAACGGAGAGAGAGGGA AGTTACCTTTGCGAACTGCT 873–898 1.000 78.0
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 TGAACGGAGAGAGAGGGATT AGTTACCTTTGCGAACTGCT 871–896 1.000 78.0
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 TTGAACGGAGAGAGAGGGAT AGTTACCTTTGCGAACTGCT 872–897 1.000 78.0
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 AACGGAGAGAGAGGGATTCG AGTTACCTTTGCGAACTGCT 869–894 1.000 77.5
atpH-atpI_p1 atpH-atpI TAACGGAAGCAGCAGGAATC CTTTGCAACTTTAGCCGCAG 698–718 1.000 81.4
atpH-atpI_p2 atpH-atpI GCAGCAGGAATCAAGGGATT CTTTGCAACTTTAGCCGCAG 690–710 1.000 79.8
atpH-atpI_p3 atpH-atpI CAATAACGGAAGCAGCAGGA CTTTGCAACTTTAGCCGCAG 701–721 1.000 79.5
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG CTTTGCAACTTTAGCCGCAG 709–729 1.000 79.4
atpH-atpI_p5 atpH-atpI CAATACCCTCTACGGCTTGG CTTTGCAACTTTAGCCGCAG 785–805 1.000 79.2
rpoC2_p1 rpoC2 CGGAGAGTATTTTCGGAATTGC CCATCCGATTGTTCCCGAAT 233 1.000 65.3
rpoC2_p2 rpoC2 CGGAGAGTATTTTCGGAATTGC TGTCACCATCCGATTGTTCC 238 1.000 64.6
rpoC2_p3 rpoC2 CCATTTTGGTACTCGGAGAG CCATCCGATTGTTCCCGAAT 246 1.000 63.5
rpoC2_p4 rpoC2 CCATTTTGGTACTCGGAGAG TGTCACCATCCGATTGTTCC 251 1.000 62.8
rpoC2_p5 rpoC2 GGAGAGTATTTTCGGAATTGCC CCATCCGATTGTTCCCGAAT 232 1.000 62.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (53)

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

Species Accession Length (bp) Link
Cycas aculeata MZ339196.1 162003 View on NCBI ↗
Cycas aenigma MZ339189.1 162140 View on NCBI ↗
Cycas apoa MZ339182.1 162056 View on NCBI ↗
Cycas bifida NC_065481.1 161965 View on NCBI ↗
Cycas bougainvilleana NC_064315.1 162098 View on NCBI ↗
Cycas campestris MZ339193.1 162037 View on NCBI ↗
Cycas chamaoensis MZ339184.1 162000 View on NCBI ↗
Cycas changjiangensis PV588045.1 162074 View on NCBI ↗
Cycas circinalis MT731952.1 162038 View on NCBI ↗
Cycas clivicola MZ339183.1 161999 View on NCBI ↗
Cycas collina MZ339179.1 161854 View on NCBI ↗
Cycas crassipes NC_081490.1 162050 View on NCBI ↗
Cycas debaoensis MT731949.1 162095 View on NCBI ↗
Cycas diannanensis MZ339165.1 162013 View on NCBI ↗
Cycas dolichophylla MZ339170.1 161838 View on NCBI ↗
Cycas edentata NC_064314.1 162091 View on NCBI ↗
Cycas falcata NC_064309.1 162108 View on NCBI ↗
Cycas ferruginea NC_081491.1 162043 View on NCBI ↗
Cycas glauca MZ339181.1 162099 View on NCBI ↗
Cycas guizhouensis NC_081492.1 162048 View on NCBI ↗
Cycas hainanensis MZ339171.1 162215 View on NCBI ↗
Cycas hongheensis NC_059061.1 162048 View on NCBI ↗
Cycas lindstromii MZ339185.1 162061 View on NCBI ↗
Cycas longisporophylla NC_081493.1 162045 View on NCBI ↗
Cycas longlinensis NC_081494.1 162038 View on NCBI ↗
Cycas maconochiei subsp. viridis MZ339166.1 162164 View on NCBI ↗
Cycas media subsp. media MZ339192.1 162106 View on NCBI ↗
Cycas micronesica NC_064311.1 162075 View on NCBI ↗
Cycas multipinnata MZ339174.1 162060 View on NCBI ↗
Cycas nongnoochiae MZ339169.1 162096 View on NCBI ↗
Cycas pectinata MZ339190.1 162086 View on NCBI ↗
Cycas platyphylla MZ339178.1 162051 View on NCBI ↗
Cycas riuminiana MZ339167.1 162101 View on NCBI ↗
Cycas rumphii NC_064316.1 162099 View on NCBI ↗
Cycas sainathii NC_064317.1 161757 View on NCBI ↗
Cycas schumanniana MZ339186.1 162002 View on NCBI ↗
Cycas seemannii NC_064312.1 162104 View on NCBI ↗
Cycas segmentifida MZ286582.1 162163 View on NCBI ↗
Cycas sexseminifera MZ339172.1 162107 View on NCBI ↗
Cycas shiwandashanica NC_053567.1 162020 View on NCBI ↗
Cycas siamensis MZ339177.1 162117 View on NCBI ↗
Cycas simplicipinna MZ339180.1 161961 View on NCBI ↗
Cycas sundaica NC_064318.1 162099 View on NCBI ↗
Cycas szechuanensis NC_042668.1 162083 View on NCBI ↗
Cycas taiwaniana MZ339194.1 162204 View on NCBI ↗
Cycas tanqingii MZ339173.1 162060 View on NCBI ↗
Cycas tansachana MZ339187.1 162058 View on NCBI ↗
Cycas thouarsii NC_064310.1 161770 View on NCBI ↗
Cycas vespertilio MZ339188.1 162105 View on NCBI ↗
Cycas wadei MZ339175.1 161632 View on NCBI ↗
Cycas x multifrondis MZ339191.1 161993 View on NCBI ↗
Cycas zambalensis MZ339168.1 162085 View on NCBI ↗
Cycas zeylanica NC_064313.1 161759 View on NCBI ↗