Markers + reference

Gamochaeta

2 species · Asteraceae · Asterales

Back to catalogue

Species 2
Genome length 151–152 kb
Candidate markers 271
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 369 0.0326 1.00 67.6 yes View details
trnK-UUU-rps16 LSC 804 0.0087 1.00 63.3 yes View details
rps16-trnQ-UUG LSC 993 0.0070 1.00 52.1 yes View details
psbK-psbI LSC 415 0.0072 1.00 59.1 yes View details
trnS-GCU-trnC-GCA LSC 723 0.0071 0.97 54.7 yes View details
atpI-atpH LSC 1124 0.0053 1.00 62.0 yes View details
atpF LSC 1267 0.0063 1.00 62.5 yes View details
psbZ-trnG-GCC LSC 303 0.0429 1.00 69.4 yes View details
trnG-GCC-trnfM-CAU LSC 223 0.0314 1.00 70.5 yes View details
petA-psbJ LSC 771 0.0156 1.00 67.7 yes View details
psbE-petL LSC 1277 0.0063 1.00 59.9 yes View details
ndhD SSC 1530 0.0020 1.00 46.4 yes View details
ndhD-ccsA SSC 265 0.0340 1.00 72.0 yes View details
trnL-UAG-rpl32 SSC 660 0.0093 0.98 65.8 yes View details
psaC-ndhD SSC 90 0.0333 1.00 71.7 yes View details
trnF-GAA-ndhJ LSC 574 0.0089 0.98 65.3 yes View details
petN-psbM LSC 557 0.0037 0.96 63.5 yes View details
trnT-GGU-psbD LSC 1296 0.0054 0.99 62.4 yes View details
rbcL LSC 1458 0.0055 1.00 61.9 yes View details
accD-psaI LSC 797 0.0050 1.00 61.6 yes View details
rpl16 LSC 1378 0.0044 1.00 61.5 yes View details
trnI-GAU-trnA-UGC IRb 64 0.0156 1.00 61.5 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 488–499 1.000 78.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 502–513 1.000 78.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 501–512 1.000 78.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 503–514 1.000 78.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 489–500 1.000 77.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1001–1004 1.000 77.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 1000–1003 1.000 77.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 940–943 1.000 76.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 939–942 1.000 76.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1025–1028 1.000 76.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1066–1080 1.000 78.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1070–1084 1.000 74.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1096–1110 1.000 74.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1058–1072 1.000 73.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1065–1079 1.000 73.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 552 1.000 72.5
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 549 1.000 70.5
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 550 1.000 70.5
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 551 1.000 70.5
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTACG 553 1.000 70.2
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 787–810 1.000 77.1
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 769–792 1.000 74.9
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA TTTCGTCCACTCAGCCATCT CCGGATTTGAACTGGGGAAA 786–809 1.000 74.0
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA TCCACTCAGCCATCTCTCC CCGGATTTGAACTGGGGAAA 781–804 1.000 73.4
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA ATTAGCAATCCGCCGCTTT CCGGATTTGAACTGGGGAAA 802–825 1.000 72.4
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 703–719 1.000 61.9
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 703–719 1.000 60.2
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 704–720 1.000 55.9
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 695–711 1.000 55.9
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 689–705 1.000 55.1

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
Gamochaeta erythractis OR783471.1 151447 View on NCBI ↗
Gamochaeta pensylvanica NC_072076.1 151574 View on NCBI ↗