Markers + reference

Alternanthera

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 152–152 kb
Candidate markers 255
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 688 0.0336 1.00 71.7 yes View details
trnC-petN LSC 505 0.0376 1.00 71.7 yes View details
petN-psbM LSC 977 0.0351 0.99 74.4 yes View details
psbE-petL LSC 1302 0.0301 0.99 66.2 yes View details
rpl16 LSC 1457 0.0172 1.00 55.0 yes View details
rps3-rps19 LSC 684 0.0322 1.00 67.9 yes View details
ycf2 IRb 6873 0.0084 1.00 51.7 no View details
ndhF SSC 2238 0.0179 1.00 53.5 yes View details
ndhF-rpl32 SSC 806 0.0390 0.96 73.1 yes View details
rpl32-trnL SSC 672 0.0402 1.00 68.0 yes View details
ycf1 SSC 5463 0.0196 1.00 53.0 yes View details
ycf2 IRa 6873 0.0084 1.00 51.7 yes View details
psbI-trnS LSC 199 0.0556 0.90 78.3 yes View details
psaJ-rpl33 LSC 439 0.0349 0.98 75.6 yes View details
rps19-trnH LSC 17 0.0909 0.65 74.3 no View details
ndhC-trnV LSC 478 0.0318 0.99 71.8 yes View details
rpoC2-rpoC1 LSC 186 0.0552 0.97 71.5 yes View details
atpF-atpH LSC 449 0.0227 0.98 70.6 yes View details
rpl16-rps3 LSC 150 0.0467 1.00 68.4 yes View details
psbC-trnS LSC 271 0.0406 1.00 68.3 yes View details
rps16-trnQ LSC 615 0.0309 1.00 68.0 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
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 688–701 1.000 80.5
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 699–712 1.000 79.9
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 718–731 1.000 79.6
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 729–742 1.000 79.1
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA AGAAATCTAAGTGGGGCGTG 747–760 1.000 77.7
psbI-trnS_p1 psbI-trnS GTAATCCTGGACGCGAAGAA GTCATTCGTACCGAGGGTTC 240–259 1.000 84.2
psbI-trnS_p2 psbI-trnS GTAATCCTGGACGCGAAGAA AGTCATTCGTACCGAGGGTT 241–260 1.000 81.3
psbI-trnS_p3 psbI-trnS GTAATCCTGGACGCGAAGAA TTTTCAACGGGGAGAGATGG 301–320 1.000 80.3
psbI-trnS_p4 psbI-trnS GTAATCCTGGACGCGAAGAA GATGGCTGAGTGGACGAAAG 286–305 1.000 79.3
psbI-trnS_p5 psbI-trnS GTAATCCTGGACGCGAAGAA GAGTCATTCGTACCGAGGGT 242–261 1.000 77.7
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAGAAAACGA GCAGAGGGAAAAATACGAGGT 605–613 1.000 74.1
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GCAGAGGGAAAAATACGAGGT 632–640 1.000 73.3
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAGAAAACGA AGCAGAGGGAAAAATACGAGG 606–614 1.000 72.0
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG AGCAGAGGGAAAAATACGAGG 633–641 1.000 71.3
atpF-atpH_p5 atpF-atpH ACACCAAGCACTACACTGAG GCAGAGGGAAAAATACGAGGT 682–690 1.000 69.8
atpH-atpI_p1 atpH-atpI TACCTTGACCAACTCCAGGT GCGAATCCATGGAAGGTCAT 802–811 1.000 81.5
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCCTGTCCC GCGAATCCATGGAAGGTCAT 829–838 1.000 81.2
atpH-atpI_p3 atpH-atpI GCAGTACCTTGACCAACTCC GCGAATCCATGGAAGGTCAT 806–815 1.000 80.8
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 831–840 1.000 80.5
atpH-atpI_p5 atpH-atpI TACCTTCTACAGCCTGTCCC TTTTGCAACTTTAGCCGCAG 858–867 1.000 80.2
rpoC2-rpoC1_p1 rpoC2-rpoC1 GGCAGTTCCATCTATCGCTT AGGATTTTGTCAAGCCTGCT 260–265 1.000 80.2
rpoC2-rpoC1_p2 rpoC2-rpoC1 GTGAAAGACCAAATTGGCCC AGGATTTTGTCAAGCCTGCT 236–241 1.000 79.0
rpoC2-rpoC1_p3 rpoC2-rpoC1 AGTCGTTTCATGGCAGTTCC AGGATTTTGTCAAGCCTGCT 271–276 1.000 78.2
rpoC2-rpoC1_p4 rpoC2-rpoC1 AAAGACCAAATTGGCCCGTT AGGATTTTGTCAAGCCTGCT 233–238 1.000 78.1
rpoC2-rpoC1_p5 rpoC2-rpoC1 GGCAGTTCCATCTATCGCTT GGATTTTGTCAAGCCTGCTC 259–264 1.000 77.5
trnC-petN_p1 trnC-petN TGTTCCCCAGTTCAAATCCG AGAGTCCACTTCTTCCCCAT 623–638 1.000 78.8
trnC-petN_p2 trnC-petN TGTTCCCCAGTTCAAATCCG TACCATTAAAGCAGCCCAGG 574–589 1.000 78.4
trnC-petN_p3 trnC-petN ACTGCAAATCCTTGTTCCCC AGAGTCCACTTCTTCCCCAT 635–650 1.000 76.6
trnC-petN_p4 trnC-petN GCAAATCCTTGTTCCCCAGT AGAGTCCACTTCTTCCCCAT 632–647 1.000 76.6
trnC-petN_p5 trnC-petN TGCAAATCCTTGTTCCCCAG AGAGTCCACTTCTTCCCCAT 633–648 1.000 76.6

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
Alternanthera philoxeroides NC_042798.1 152255 View on NCBI ↗
Alternanthera sessilis PP239384.1 151935 View on NCBI ↗