Markers + reference

Anabasis

6 species · Amaranthaceae · Caryophyllales

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Species 6
Genome length 150–151 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 749 0.0255 0.95 66.6 yes View details
trnS-GCU-trnG-GCC LSC 813 0.0341 0.89 73.0 yes View details
rpoB-trnC-GCA LSC 1106 0.0152 0.98 60.5 yes View details
rps4-trnT-UGU LSC 417 0.0250 1.00 66.6 yes View details
trnT-UGU-trnL-UAA LSC 681 0.0172 0.99 60.7 yes View details
trnL-UAA-trnF-GAA LSC 376 0.0326 0.99 63.9 yes View details
accD-psaI LSC 675 0.0228 0.98 65.4 yes View details
petA-psbJ LSC 943 0.0164 0.99 62.9 yes View details
rpl16 LSC 1360 0.0137 0.98 57.4 yes View details
rpl22 LSC 615 0.0210 1.00 62.8 yes View details
trnN-GUU-ndhF IRb 681 0.0278 0.98 73.3 yes View details
rpl32-trnL-UAG SSC 940 0.0162 1.00 64.8 yes View details
trnF-GAA-ndhJ LSC 687 0.0174 0.98 69.4 yes View details
rps16-trnQ-UUG LSC 537 0.0166 0.99 68.0 yes View details
ccsA-ndhD SSC 193 0.0311 0.98 66.3 yes View details
trnH-GUG-psbA LSC 233 0.0300 0.97 64.9 yes View details
trnG-GCC-trnR-UCU LSC 115 0.0267 1.00 64.2 yes View details
psaA-ycf3 LSC 763 0.0171 0.98 64.1 yes View details
ycf15-trnL-CAA IRb 576 0.0046 1.00 63.9 yes View details
trnL-CAA-ycf15 IRa 576 0.0046 1.00 63.9 yes View details
psaJ-rpl33 LSC 249 0.0254 0.98 62.7 yes View details
ndhF-rpl32 SSC 1103 0.0136 0.97 62.7 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 ATTTCAGGCTGAGCACAACA 756–766 1.000 82.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTTCAGGCTGAGCACAACAT 755–765 1.000 82.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ATTTCAGGCTGAGCACAACA 770–780 1.000 82.3
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTTCAGGCTGAGCACAACAT 769–779 1.000 82.3
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTTCAGGCTGAGCACAACAT 768–778 1.000 82.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTATCCCAATGAGCCGTCT 1025–1086 1.000 86.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGCCGTCTATCGAATCGTTG 1013–1074 1.000 86.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT TCTATCCCAATGAGCCGTCT 1021–1082 1.000 86.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT TCTATCCCAATGAGCCGTCT 1022–1083 1.000 86.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGGGTAAATTCATCAGCGGA TCTATCCCAATGAGCCGTCT 1530–1594 0.667 71.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 427–629 1.000 85.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 438–640 1.000 84.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 457–659 1.000 84.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 468–670 1.000 83.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCGAGTCAAGAGCATCCT GAGGTTCGAATCCTTCCGTC 495–697 1.000 82.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA ACGAATCACACTTTTACCACT 813–906 1.000 58.4
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA AGAACGAATCACACTTTTACCAC 816–909 1.000 57.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA GAACGAATCACACTTTTACCACT 815–908 1.000 57.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA AACGAATCACACTTTTACCACT 814–907 1.000 56.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CTTTCGTCCACTCAGCCATC ACGAATCACACTTTTACCACT 779–872 1.000 55.6
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG CCCCTCTCACGGTAGAAGAA 569–577 1.000 82.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG GACCAGCGATTAATGTGGGT 785–793 1.000 82.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG GACCAGCGATTAATGTGGGT 788–796 1.000 82.2
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG TTGGCGCAATTTGCAGAATT 690–698 1.000 81.8
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TCGTTCCCACCTTCGATTTC GACCAGCGATTAATGTGGGT 923–931 1.000 81.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1664–1693 1.000 83.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ACCCTCATTTCCATCCCGTA GGAATGGAGAGGTCTCGGTA 1386–1419 0.833 77.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TACCCTCATTTCCATCCCGT GGAATGGAGAGGTCTCGGTA 1387–1420 0.833 77.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GGAATGGAGAGGTCTCGGTA 1874–1907 0.833 77.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCTCATTTCCATCCCGTAGC GGAATGGAGAGGTCTCGGTA 1384–1417 0.667 70.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Anabasis brevifolia ON929846.1 150961 View on NCBI ↗
Anabasis elatior ON929849.1 151145 View on NCBI ↗
Anabasis eriopoda ON929847.1 150250 View on NCBI ↗
Anabasis pelliotii ON929850.1 150499 View on NCBI ↗
Anabasis salsa ON929848.1 151277 View on NCBI ↗
Anabasis truncata ON929851.1 151338 View on NCBI ↗