Markers + reference

Gelasia

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 268
Primer pairs 110

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnC-GCA LSC 768 0.0026 1.00 53.3 yes View details
trnY-GUA-rpoB LSC 1091 0.0028 0.99 61.4 yes View details
atpH LSC 246 0.0041 1.00 41.3 yes View details
pafII-cemA LSC 894 0.0023 0.99 60.7 yes View details
clpP1-psbB LSC 450 0.0067 1.00 59.5 yes View details
psbB-psbT LSC 196 0.0054 0.94 59.5 yes View details
ndhF SSC 2226 0.0018 1.00 43.7 yes View details
ndhF-rpl32 SSC 1111 0.0045 1.00 61.3 yes View details
rpl32-trnL-UAG SSC 910 0.0045 0.97 62.9 yes View details
ndhD SSC 1530 0.0000 1.00 26.2 yes View details
ndhG SSC 531 0.0038 1.00 54.8 yes View details
ndhH SSC 1182 0.0025 1.00 60.2 yes View details
ndhD-psaC SSC 91 0.0549 1.00 81.9 yes View details
rpl22-rps19 LSC 72 0.0161 0.86 63.8 yes View details
rps16-trnQ-UUG LSC 978 0.0021 0.98 61.5 yes View details
trnF-GAA-ndhJ LSC 690 0.0029 1.00 60.4 yes View details
trnR-ACG IRb 74 0.0135 1.00 60.3 yes View details
trnR-ACG IRa 74 0.0135 1.00 60.3 yes View details
trnK-UUU-rps16 LSC 841 0.0024 1.00 60.1 yes View details
petA LSC 963 0.0021 1.00 59.9 yes View details
psbE-petL LSC 1229 0.0016 1.00 59.8 yes View details
psbM-trnD-GUC LSC 662 0.0015 1.00 59.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1029–1036 1.000 77.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 1028–1035 1.000 77.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 968–975 1.000 76.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 967–974 1.000 76.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 983–990 1.000 75.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1035–1051 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1050–1066 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1049–1065 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1106–1122 1.000 76.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1039–1055 1.000 75.0
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA GCTTCGTTTGTTGATGAGGC 944–950 1.000 78.7
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 919–925 1.000 78.3
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CTTCGTTTGTTGATGAGGCG 943–949 1.000 77.1
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 901–907 1.000 76.1
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC GCTTCGTTTGTTGATGAGGC 880–886 1.000 74.8
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 779 1.000 50.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 773 1.000 50.0
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 776 1.000 49.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCAG TTCAATAGGCAAGAGCACCG 780 1.000 48.4
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCA TTCAATAGGCAAGAGCACCG 780 1.000 47.5
trnY-GUA-rpoB_p1 trnY-GUA-rpoB CGAATTTACAGTCCGTCCCC AGTTCTTCTGTCAAACCCTGA 1202–1214 1.000 60.5
trnY-GUA-rpoB_p2 trnY-GUA-rpoB ACGAATTTACAGTCCGTCCC AGTTCTTCTGTCAAACCCTGA 1203–1215 1.000 60.3
trnY-GUA-rpoB_p3 trnY-GUA-rpoB CGAATTTACAGTCCGTCCCC TCAAACCCTGATCAATGAACCT 1192–1204 1.000 59.1
trnY-GUA-rpoB_p4 trnY-GUA-rpoB ACGAATTTACAGTCCGTCCC TCAAACCCTGATCAATGAACCT 1193–1205 1.000 58.9
trnY-GUA-rpoB_p5 trnY-GUA-rpoB CGAATTTACAGTCCGTCCCC TCTTCTGTCAAACCCTGATCA 1199–1211 1.000 58.8
atpH_p1 atpH CGGCCCAATCCATTTATCCA AAGTCCTACGAACACGAACG 1068 1.000 79.9
atpH_p2 atpH TTTCTATGCAAGGAGTCGGC AAGTCCTACGAACACGAACG 1084 1.000 79.8
atpH_p3 atpH CGGCCCAATCCATTTATCCA TGGCCCAAAGAAACGAAAGA 1288 1.000 79.7
atpH_p4 atpH TTTCTATGCAAGGAGTCGGC TGGCCCAAAGAAACGAAAGA 1304 1.000 79.6
atpH_p5 atpH TAGAGGCGAGGTCGAACTAG AAGTCCTACGAACACGAACG 961 1.000 79.6

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
Gelasia circumflexa PX370051.1 152917 View on NCBI ↗
Gelasia sericeolanata PX924390.1 152973 View on NCBI ↗