Markers + reference

Abies

17 species · Pinaceae · Pinales

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Species 17
Genome length 120–122 kb
Candidate markers 232
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 232 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
cemA-ycf4 Genome 444 0.0079 0.99 60.5 yes View details
trnV-UAC-trnE-UUC Genome 4290 0.0059 0.88 58.0 yes View details
atpH-atpF Genome 343 0.0101 0.73 36.7 yes View details
rpl32-trnV-GAC Genome 799 0.0063 0.98 62.8 yes View details
ycf2-trnH-GUG Genome 324 0.0075 1.00 50.1 yes View details
trnI-CAU-psbA Genome 153 0.0036 0.99 72.4 no View details
trnL-CAA-ycf2 Genome 731 0.0024 1.00 56.4 yes View details
ycf1 Genome 5898 0.0015 1.00 55.1 yes View details
psbD-trnT-GGU Genome 1314 0.0015 1.00 53.6 yes View details
petL-psbE Genome 1265 0.0023 1.00 53.4 yes View details
rpl14-rpl16 Genome 118 0.0099 0.98 52.2 yes View details
rps15-psaC Genome 1256 0.0025 1.00 50.3 yes View details
rps12-rps7 Genome 52 0.0181 1.00 50.2 yes View details
rps7-trnL-CAA Genome 1463 0.0017 1.00 50.0 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU ATCCAGAACCGGAACAAGTG TCACATTCCACTTCGATCGT 2698–2708 1.000 71.4
trnK-UUU_p2 trnK-UUU GGATCCAGAACCGGAACAAG TCACATTCCACTTCGATCGT 2700–2710 1.000 70.8
trnK-UUU_p3 trnK-UUU ATCCAGAACCGGAACAAGTG CTCACATTCCACTTCGATCGT 2699–2709 1.000 70.7
trnK-UUU_p4 trnK-UUU GGACAGAGGTACCTATCGCA TCACATTCCACTTCGATCGT 2679–2689 1.000 70.4
trnK-UUU_p5 trnK-UUU TGGACAGAGGTACCTATCGC TCACATTCCACTTCGATCGT 2680–2690 1.000 70.4
petL-psbE_p1 petL-psbE AGTAGACGTGGAAGGACTGA TTCTCCCGTATTCCCAGACA 1327–1336 1.000 75.0
petL-psbE_p2 petL-psbE AGTAGACGTGGAAGGACTGA AATGTCAGCAAAGGAGCGTT 1345–1354 1.000 73.8
petL-psbE_p3 petL-psbE GACGTGGAAGGACTGAATGA TTCTCCCGTATTCCCAGACA 1323–1332 1.000 73.7
petL-psbE_p4 petL-psbE AGACGTGGAAGGACTGAATG TTCTCCCGTATTCCCAGACA 1324–1333 1.000 73.6
petL-psbE_p5 petL-psbE AGTAGACGTGGAAGGACTGA TCTCCCGTATTCCCAGACAT 1326–1335 1.000 73.1
cemA-ycf4_p1 cemA-ycf4 CACTTCCAATTCGCGAATCG AACAGAAAGCTGCCGAATCA 594–616 1.000 81.8
cemA-ycf4_p2 cemA-ycf4 CACTTCCAATTCGCGAATCG TATCGAACAGAAAGCTGCCG 599–621 1.000 79.7
cemA-ycf4_p3 cemA-ycf4 CTCGTCAGTTCTGTCCGAAA AACAGAAAGCTGCCGAATCA 557–579 1.000 79.3
cemA-ycf4_p4 cemA-ycf4 CACTTCCAATTCGCGAATCG AAGGGCCTACAAAACATCCC 660 0.059 39.9
cemA-ycf4_p5 cemA-ycf4 CACTTCCAATTCGCGAATCG GGGCCTACAAAACATCCCTT 658 0.059 39.9
trnV-UAC-trnE-UUC_p1 trnV-UAC-trnE-UUC ACGGGAAAAGCGGGTAATTT TAAAACGCCACATGTCCGAT 172–214 0.529 68.9
trnV-UAC-trnE-UUC_p2 trnV-UAC-trnE-UUC ACGGGAAAAGCGGGTAATTT GCAAAGGGATTGAACGAACG 242–284 0.529 67.1
trnV-UAC-trnE-UUC_p3 trnV-UAC-trnE-UUC ACGGGAAAAGCGGGTAATTT GGGATTGAACGAACGGAAGA 237–279 0.529 66.9
trnV-UAC-trnE-UUC_p4 trnV-UAC-trnE-UUC ACGGGAAAAGCGGGTAATTT AGGGATTGAACGAACGGAAG 238–280 0.529 66.8
trnV-UAC-trnE-UUC_p5 trnV-UAC-trnE-UUC AAGCGGGTAATTTGTCACGA GCAAAGGGATTGAACGAACG 235–277 0.529 66.6
atpH-atpF_p1 atpH-atpF TGTGGCCCTAGCACTTCTAT CCAGCAGAAGGCCAATAACT 338–436 1.000 83.3
atpH-atpF_p2 atpH-atpF ATGGACTAGTTGTGGCCCTA CCAGCAGAAGGCCAATAACT 348–446 1.000 82.1
atpH-atpF_p3 atpH-atpF TATGGACTAGTTGTGGCCCT CCAGCAGAAGGCCAATAACT 349–447 1.000 82.1
atpH-atpF_p4 atpH-atpF AGCGGAAGGTAAAATACGGG CCAGCAGAAGGCCAATAACT 413–511 1.000 81.5
atpH-atpF_p5 atpH-atpF TTGTGGCCCTAGCACTTCTA CCAGCAGAAGGCCAATAACT 339–437 1.000 81.5
rpl14-rpl16_p1 rpl14-rpl16 ATTTTTCGGGCTCCACTGTT GTCATCAGACCAGGTCGAAT 275–294 1.000 77.0
rpl14-rpl16_p2 rpl14-rpl16 ATTTTTCGGGCTCCACTGTT GAAACCGTCGCTAGAGCAG 230–249 1.000 74.2
rpl14-rpl16_p3 rpl14-rpl16 TTTCGGGCTCCACTGTTATC GTCATCAGACCAGGTCGAAT 272–291 1.000 73.9
rpl14-rpl16_p4 rpl14-rpl16 ATTTTTCGGGCTCCACTGTT ACTTTATGAAATGGGCGGAGT 255–274 1.000 73.9
rpl14-rpl16_p5 rpl14-rpl16 TTTTTCGGGCTCCACTGTTA GTCATCAGACCAGGTCGAAT 274–293 1.000 71.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Abies alba NC_042410.1 121243 View on NCBI ↗
Abies balsamea NC_042778.1 121574 View on NCBI ↗
Abies beshanzuensis NC_045884.1 121399 View on NCBI ↗
Abies beshanzuensis var. ziyuanensis MH706705.1 121274 View on NCBI ↗
Abies delavayi NC_057313.1 120141 View on NCBI ↗
Abies delavayi subsp. fansipanensis MH706720.1 120093 View on NCBI ↗
Abies ernestii MH706707.1 121841 View on NCBI ↗
Abies fabri NC_057314.1 120027 View on NCBI ↗
Abies fanjingshanensis NC_042777.1 120057 View on NCBI ↗
Abies fargesii NC_042775.1 121799 View on NCBI ↗
Abies ferreana NC_062889.1 120049 View on NCBI ↗
Abies forrestii MH706715.1 120022 View on NCBI ↗
Abies kawakamii NC_042776.1 121290 View on NCBI ↗
Abies koreana NC_026892.1 121373 View on NCBI ↗
Abies nukiangensis NC_057315.1 120017 View on NCBI ↗
Abies recurvata MH706712.1 120063 View on NCBI ↗
Abies yuanbaoshanensis NC_050849.1 121795 View on NCBI ↗