Markers + reference

Phippsiomeles

2 species · Rosaceae · Rosales

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Species 2
Genome length 160–160 kb
Candidate markers 270
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 278 0.0433 1.00 69.3 yes View details
trnR-UCU-atpA LSC 620 0.0169 0.95 72.9 yes View details
atpH-atpI LSC 1171 0.0190 0.99 70.6 yes View details
trnT-GGU-psbD LSC 1449 0.0056 0.98 60.0 yes View details
psbC-trnS-UGA LSC 255 0.0000 1.00 33.8 yes View details
trnS-UGA-psbZ LSC 314 0.0446 1.00 78.4 yes View details
trnT-UGU-trnL-UAA LSC 1282 0.0119 0.92 69.4 yes View details
ndhC-trnV-UAC LSC 586 0.0172 0.89 71.3 yes View details
psbE-petL LSC 1266 0.0095 1.00 64.2 yes View details
petB LSC 1452 0.0048 1.00 56.5 yes View details
rpl32-trnL SSC 1398 0.0087 0.99 64.6 yes View details
atpF-atpH LSC 471 0.0089 0.96 65.2 yes View details
rbcL-accD LSC 568 0.0089 0.99 63.9 yes View details
accD-psaI LSC 852 0.0036 0.97 63.4 yes View details
rpoB-trnC-GCA LSC 1217 0.0058 1.00 62.1 yes View details
rps11-rpl336 LSC 166 0.0301 1.00 61.9 yes View details
rpl20-rps12 LSC 764 0.0052 1.00 61.8 yes View details
psbM-trnD-GUC LSC 1241 0.0016 0.98 61.6 yes View details
petN-psbM LSC 1247 0.0065 0.98 61.2 yes View details
petA-psbJ LSC 1008 0.0040 1.00 61.1 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 403 1.000 81.5
trnH-GUG-psbA_p2 trnH-GUG-psbA ATATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 453 1.000 81.4
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 406 1.000 81.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 406 1.000 81.2
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 405 1.000 81.2
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 798–806 1.000 68.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 797–805 1.000 68.3
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 737–745 1.000 67.7
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 772–780 1.000 64.6
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 798–806 1.000 64.3
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CTGGTTGTCGCATTAGCTCT 568–585 1.000 82.3
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGACTGGTTGTCGCATTAG 572–589 1.000 81.6
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG ACTGGTTGTCGCATTAGCTC 569–586 1.000 80.2
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GACTGGTTGTCGCATTAGCT 570–587 1.000 80.2
atpF-atpH_p5 atpF-atpH GATGGCCAATAACCCAAGGA CTGGTTGTCGCATTAGCTCT 546–563 1.000 79.7
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1263–1295 1.000 81.7
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1229–1261 1.000 81.7
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1293–1325 1.000 80.8
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1259–1291 1.000 80.8
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1230–1262 1.000 80.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TAAGCCCTGCTCAATGAACC CCGGATTTGAACTGGGGAAA 1372–1383 1.000 78.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TAAGCCCTGCTCAATGAACC AAAAGGATTTGCAGTCCCCC 1354–1365 1.000 76.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1306–1317 1.000 76.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCTGTTAAGCCCTGCTCAA CCGGATTTGAACTGGGGAAA 1378–1389 1.000 76.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCCTCTGTTAAGCCCTGC CCGGATTTGAACTGGGGAAA 1382–1393 1.000 75.5
petN-psbM_p1 petN-psbM AGTAAATCTCGCTTGGGCTG AAAACAGTCAGCCAAGGTGA 1332–1353 1.000 78.0
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC AAAACAGTCAGCCAAGGTGA 1275–1296 1.000 77.4
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT AAAACAGTCAGCCAAGGTGA 1274–1295 1.000 77.4
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC AAAACAGTCAGCCAAGGTGA 1273–1294 1.000 76.9
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG AAAACAGTCAGCCAAGGTGA 1270–1291 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
Phippsiomeles matudae NC_045421.1 159668 View on NCBI ↗
Phippsiomeles microcarpa subsp. hintonii MN062001.1 159633 View on NCBI ↗