Markers + reference

Ampelocera

4 species · Ulmaceae · Rosales

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Species 4
Genome length 160–162 kb
Candidate markers 270
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 2075 0.0185 0.89 65.1 yes View details
rps16-trnQ-UUG LSC 1080 0.0306 0.91 73.6 yes View details
trnS-GCU-trnG-GCC LSC 750 0.0328 0.89 68.7 yes View details
trnT-GGU-psbD LSC 1329 0.0254 0.93 71.8 yes View details
trnT-UGU-trnL-UAA LSC 1703 0.0313 0.83 71.2 yes View details
rbcL-accD LSC 828 0.0298 0.98 70.4 yes View details
ndhA SSC 2596 0.0146 0.98 62.4 yes View details
rps15-ycf1 SSC 421 0.0515 0.90 79.7 yes View details
trnL-UAA SSC 39 0.0470 1.00 70.4 yes View details
psbK-psbI LSC 502 0.0242 0.94 70.2 yes View details
trnC-GCA-petN LSC 772 0.0233 0.96 69.2 yes View details
rpl32-trnL-UAG SSC 1303 0.0211 0.97 69.1 yes View details
psbZ-trnG-GCC LSC 596 0.0175 0.99 67.0 yes View details
atpH-atpI LSC 1274 0.0086 1.00 66.1 yes View details
trnG-GCC-trnfM-CAU LSC 174 0.0289 0.98 65.6 yes View details
atpF-atpH LSC 453 0.0044 1.00 64.6 yes View details
atpB-rbcL LSC 795 0.0108 0.99 63.5 yes View details
trnL-UAA LSC 37 0.0000 1.00 20.1 no 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 GCGGGTATAGGAAGTCATGT TTCCTTGAAAAAGGCGCTCA 2005–2348 1.000 74.0
matK-rps16_p2 matK-rps16 AGCGGGTATAGGAAGTCATGT TTCCTTGAAAAAGGCGCTCA 2006–2349 1.000 73.1
matK-rps16_p3 matK-rps16 GCGGGTATAGGAAGTCATGT GCTCAGCCTACAAGAACTGT 1990–2333 1.000 72.8
matK-rps16_p4 matK-rps16 GCGGGTATAGGAAGTCATGT TCAAAGAAGGCAGGGGTTTT 1960–2303 1.000 72.8
matK-rps16_p5 matK-rps16 GCGGGTATAGGAAGTCATGT TTCAAAGAAGGCAGGGGTTT 1961–2304 1.000 72.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1087–1224 1.000 86.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1070–1207 1.000 86.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TAAGGCATCGGGTTTTGGTC 1117–1254 1.000 85.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1088–1225 1.000 85.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 1100–1237 1.000 85.1
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT AGGATTACGACCCGGATCAT 543–633 1.000 86.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGATTACGACCCGGATCAT 538–628 1.000 86.2
psbK-psbI_p3 psbK-psbI GCCAAATTACCCGAGGCTTA AGGATTACGACCCGGATCAT 625–715 1.000 85.9
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGATTACGACCCGGATCAT 535–625 1.000 84.2
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGATTACGACCCGGATCAT 536–626 1.000 84.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CATCGTTAGCTTGGAAGGCT 1455–1534 1.000 86.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CATCGTTAGCTTGGAAGGCT 1454–1533 1.000 86.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGTTAGCTTGGAAGGCTAGG 1452–1531 1.000 86.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGTTAGCTTGGAAGGCTAGG 1451–1530 1.000 86.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATGATCCGGGTCGTAATCCT CATCGTTAGCTTGGAAGGCT 1676–1755 1.000 85.9
atpF-atpH_p1 atpF-atpH ATTTAACCCGAAACTCCCGG TGGTTGTGGCATTAGCACTT 562–650 1.000 82.8
atpF-atpH_p2 atpF-atpH GCCAAAAACCCAAGGAAAGG TGGTTGTGGCATTAGCACTT 536–624 1.000 81.9
atpF-atpH_p3 atpF-atpH GGCCAAAAACCCAAGGAAAG TGGTTGTGGCATTAGCACTT 537–625 1.000 81.9
atpF-atpH_p4 atpF-atpH ATTTAACCCGAAACTCCCGG TGGACTGGTTGTGGCATTAG 567–655 1.000 81.2
atpF-atpH_p5 atpF-atpH GCCAAAAACCCAAGGAAAGG TGGACTGGTTGTGGCATTAG 541–629 1.000 80.3
atpH-atpI_p1 atpH-atpI CGCAATCCCTTCTACAGCTT ATTTTTGCAACCTTAGCCGC 1434–1451 1.000 81.2
atpH-atpI_p2 atpH-atpI CGCAATCCCTTCTACAGCTT TAGCCGCCGCTTATATAGGA 1421–1438 1.000 80.8
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG ATTTTTGCAACCTTAGCCGC 1354–1371 1.000 80.2
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG TAGCCGCCGCTTATATAGGA 1341–1358 1.000 79.8
atpH-atpI_p5 atpH-atpI AATCCCTTCTACAGCTTGGC ATTTTTGCAACCTTAGCCGC 1431–1448 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Ampelocera edentula NC_063834.1 161886 View on NCBI ↗
Ampelocera hottlei MT165903.1 160662 View on NCBI ↗
Ampelocera longissima MT165904.1 160005 View on NCBI ↗
Ampelocera macrocarpa MT165905.1 161821 View on NCBI ↗