Markers + reference

Caroxylon

3 species · Amaranthaceae · Caryophyllales

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Species 3
Genome length 151–151 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 885 0.0324 1.00 65.0 yes View details
trnC-GCA-petN LSC 480 0.0299 1.00 67.7 yes View details
psbM-trnD-GUC LSC 1279 0.0214 1.00 67.4 yes View details
trnT-GGU-psbD LSC 1328 0.0232 1.00 67.2 yes View details
trnT-UGU-trnL-UAA LSC 704 0.0256 1.00 63.3 yes View details
rbcL-accD LSC 686 0.0267 1.00 65.9 yes View details
trnN-GUU-ndhF IRb 1643 0.0165 1.00 57.0 yes View details
ndhF-rpl32 SSC 1111 0.0255 1.00 69.0 yes View details
rps15-ycf1 SSC 297 0.0393 1.00 68.3 yes View details
ycf1 SSC 5481 0.0162 1.00 48.1 yes View details
ndhC-trnV-UAC LSC 786 0.0187 1.00 72.1 yes View details
petN-psbM LSC 702 0.0247 1.00 71.3 yes View details
psaA-ycf3 LSC 730 0.0192 1.00 69.9 yes View details
trnS-GGA-rps4 LSC 339 0.0295 1.00 68.3 yes View details
atpH-atpI LSC 702 0.0199 1.00 67.5 yes View details
trnR-ACG-trnN-GUU IRb 377 0.0283 1.00 65.9 yes View details
trnN-GUU-trnR-ACG IRa 377 0.0283 1.00 65.9 yes View details
trnP-UGG-psaJ LSC 418 0.0099 0.97 65.4 yes View details
rpoA-rps11 LSC 71 0.0329 1.00 64.8 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC GAATGGCTCGTACAACGGAT CATCGTTAGCTTGGAAGGCT 1687–1705 1.000 82.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA CATCGTTAGCTTGGAAGGCT 1682–1700 1.000 81.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GAATGGCTCGTACAACGGAT CGTTAGCTTGGAAGGCTAGG 1684–1702 1.000 81.8
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC GAATGGCTCGTACAACGGAT GTAATCAAACCCGGAGACCC 1021 0.667 66.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA GTAATCAAACCCGGAGACCC 1016 0.667 65.9
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCCGCAG 787–792 1.000 80.8
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 845–850 1.000 80.6
atpH-atpI_p3 atpH-atpI AACGGAAGCAGCAGAAATCA CGAATCCATGGAGGGTCATC 757–762 1.000 80.6
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 805–810 1.000 80.4
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 815–820 1.000 80.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC GCCCAAGCGAGACTTACAAT 590–594 1.000 80.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACAAT 534–538 1.000 80.5
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 652–656 1.000 79.5
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 596–600 1.000 79.5
trnC-GCA-petN_p5 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC ATTAAAGCAGCCCAAGCGAG 599–603 1.000 75.3
petN-psbM_p1 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAACGGTCAGCCAAAATGA 807–810 1.000 68.6
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AAAACGGTCAGCCAAAATGA 745–748 1.000 68.2
petN-psbM_p3 petN-psbM ATTGTAAGTCTCGCTTGGGC AAACGGTCAGCCAAAATGAT 806–809 1.000 66.8
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC AACGGTCAGCCAAAATGATT 805–808 1.000 66.8
petN-psbM_p5 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAAACGGTCAGCCAAAATGA 808–811 1.000 66.6
psbM-trnD-GUC_p1 psbM-trnD-GUC TCATTTTGGCTGACCGTTTT TCAATTGGTTAGAGCACCGC 1430–1443 1.000 67.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AATCATTTTGGCTGACCGTT TCAATTGGTTAGAGCACCGC 1432–1445 1.000 65.3
psbM-trnD-GUC_p3 psbM-trnD-GUC ATCATTTTGGCTGACCGTTT TCAATTGGTTAGAGCACCGC 1431–1444 1.000 65.3
psbM-trnD-GUC_p4 psbM-trnD-GUC TCATTTTGGCTGACCGTTTTT TCAATTGGTTAGAGCACCGC 1430–1443 1.000 65.1
psbM-trnD-GUC_p5 psbM-trnD-GUC TTTGGCTGACCGTTTTTACA TCAATTGGTTAGAGCACCGC 1426–1439 1.000 64.4
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1482–1509 1.000 80.8
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1485–1512 1.000 80.6
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CAAAAACGAAACGGTCCCTC 1481–1508 1.000 79.6
trnT-GGU-psbD_p4 trnT-GGU-psbD TCCGATAAGGGGCTTTTTGG ACAAAAACGAAACGGTCCCT 1438–1444 0.667 64.3
trnT-GGU-psbD_p5 trnT-GGU-psbD CGATAAGGGGCTTTTTGGGT ACAAAAACGAAACGGTCCCT 1436–1442 0.667 64.1

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
Caroxylon dzhungaricum ON929853.1 151109 View on NCBI ↗
Caroxylon laricinum PP503424.1 151115 View on NCBI ↗
Caroxylon nitrarium NC_084117.1 150777 View on NCBI ↗