Markers + reference

Eschenbachia

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–153 kb
Candidate markers 273
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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnC-GCA LSC 796 0.0176 1.00 63.0 yes View details
petN-psbM LSC 506 0.0264 0.97 74.4 yes View details
psbM-trnD-GUC LSC 614 0.0183 0.98 67.8 yes View details
atpI-atpH LSC 1152 0.0106 0.99 66.2 yes View details
trnG-trnT-GGU LSC 418 0.0443 0.76 75.0 yes View details
trnT-GGU-psbD LSC 1322 0.0123 0.98 57.7 yes View details
trnS-GGA-rps4 LSC 298 0.0369 1.00 66.7 yes View details
trnT-UGU-trnL-UAA LSC 693 0.0260 0.89 74.4 yes View details
petB LSC 1420 0.0113 0.99 52.6 yes View details
ndhF-rpl32 SSC 1038 0.0205 0.99 64.6 yes View details
rpl32-trnL-UAG SSC 832 0.0210 0.97 68.5 yes View details
ccsA-ndhD SSC 269 0.0335 1.00 61.0 yes View details
rps14-psaB LSC 133 0.0376 1.00 72.1 yes View details
ycf1-ndhF SSC 18 0.0556 1.00 68.8 yes View details
rpl33-rps18 LSC 185 0.0170 0.95 66.9 yes View details
trnF-GAA-ndhJ LSC 644 0.0140 1.00 66.8 yes View details
ycf4-cemA LSC 904 0.0091 0.98 66.2 yes View details
trnE-UUC-rpoB LSC 1039 0.0118 0.98 66.1 yes View details
rps19-rpl2 IRb 55 0.0189 0.96 65.9 yes View details
ycf3-trnS-GGA LSC 860 0.0176 0.99 65.5 yes View details
ndhE-ndhG SSC 229 0.0219 1.00 65.5 yes View details
ndhC-trnV-UAC LSC 810 0.0078 0.95 65.3 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
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 946–947 1.000 79.4
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 928–929 1.000 77.2
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 882–883 1.000 75.6
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 947–948 1.000 75.2
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 864–865 1.000 73.5
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 655–668 1.000 62.6
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 655–668 1.000 60.9
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 656–669 1.000 56.6
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 647–660 1.000 56.6
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 641–654 1.000 55.8
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTAGAAAGGCAGTAGGAACT TTCAATAGGCTAGAGCACCG 733–746 1.000 49.3
psbM-trnD-GUC_p2 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCTAGAGCACCG 718–731 1.000 48.1
psbM-trnD-GUC_p3 psbM-trnD-GUC AGTAGAAAGGCAGTAGGAACT CAATAGGCTAGAGCACCGC 731–744 1.000 47.7
psbM-trnD-GUC_p4 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCTAGAGCACCG 712–725 1.000 47.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGTAGAAAGGCAGTAGGAACT TTCAATAGGCTAGAGCACCG 734–747 1.000 47.4
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 1181–1182 1.000 64.3
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 1140–1141 1.000 63.7
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 1171–1172 1.000 63.5
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 1176–1177 1.000 63.5
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 1171–1172 1.000 63.0
atpI-atpH_p1 atpI-atpH AGTGGTTCCGATCCCTGTTA ATAACGGAAGCGGCAGAAAT 1288–1299 1.000 81.0
atpI-atpH_p2 atpI-atpH AGTGGTTCCGATCCCTGTTA TACCTTGACCAACTCCAGGT 1344–1355 1.000 80.3
atpI-atpH_p3 atpI-atpH AGTGGTTCCGATCCCTGTTA AGCCAATCCAGCAGCAATAA 1304–1315 1.000 80.1
atpI-atpH_p4 atpI-atpH AGTGGTTCCGATCCCTGTTA AATAACGGAAGCGGCAGAAA 1289–1300 1.000 79.8
atpI-atpH_p5 atpI-atpH AGTGGTTCCGATCCCTGTTA GCAGTACCTTGACCAACTCC 1348–1359 1.000 79.7
trnG-trnT-GGU_p1 trnG-trnT-GGU AATGAAACCGAAAGACCCCT TCCCCTATCGGATCTGAACC 509–561 1.000 78.2
trnG-trnT-GGU_p2 trnG-trnT-GGU ATGAAACCGAAAGACCCCTT TCCCCTATCGGATCTGAACC 508–560 1.000 78.2
trnG-trnT-GGU_p3 trnG-trnT-GGU AATGAAACCGAAAGACCCCT GATCTGAACCGAGGGCTTAC 499–551 1.000 76.5
trnG-trnT-GGU_p4 trnG-trnT-GGU ATGAAACCGAAAGACCCCTT GATCTGAACCGAGGGCTTAC 498–550 1.000 76.5
trnG-trnT-GGU_p5 trnG-trnT-GGU GAATGAAACCGAAAGACCCCT TCCCCTATCGGATCTGAACC 510–562 1.000 76.3

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
Eschenbachia blinii NC_037605.1 152503 View on NCBI ↗
Eschenbachia leucantha PV780506.1 152294 View on NCBI ↗