Markers + reference

Alstonia

3 species · Apocynaceae · Gentianales

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Species 3
Genome length 155–178 kb
Candidate markers 269
Primer pairs 75

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps12-psbB LSC 2450 0.2367 0.87 81.5 yes View details
ycf15-trnL-CAA IRb 7806 0.0628 0.05 53.8 yes View details
trnN-GUU-rps15 IRb 7062 0.0675 0.17 56.5 yes View details
rps15-trnN-GUU IRa 7062 0.1355 0.84 74.0 yes View details
trnL-CAA-ycf15 IRa 7806 0.0628 0.05 53.8 yes View details
trnT-UGU-trnL-UAA LSC 767 0.0945 0.98 89.4 yes View details
ycf3-trnS-GGA LSC 498 0.0650 0.99 87.1 yes View details
rpoB-trnC-GCA LSC 1281 0.0781 0.96 86.4 yes View details
psbM-trnD-GUC LSC 838 0.0730 0.97 86.4 yes View details
atpH-atpI LSC 1052 0.0718 0.99 84.8 yes View details
trnC-GCA-petN LSC 875 0.0865 0.98 84.8 yes View details
petN-psbM LSC 1062 0.0875 0.97 84.2 yes View details
ndhF-rpl32 SSC 648 0.1203 0.99 84.2 yes View details
ndhC-trnV-UAC LSC 675 0.1096 0.96 84.0 yes View details
trnS-GCU-trnG-UCC LSC 521 0.0912 0.95 83.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 566–601 1.000 63.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 567–602 1.000 61.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 552–587 1.000 60.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TACCACTAAACTATACCCGC 552–587 1.000 59.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 547–582 1.000 59.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TGCTTTGGCTTTACTCACGT 1415–1467 1.000 88.7
atpH-atpI_p2 atpH-atpI ATAAACAACCCGCACACACT TGCTTTGGCTTTACTCACGT 2122–2168 1.000 88.6
atpH-atpI_p3 atpH-atpI ATAAACAACCCGCACACACT GAATACGGTCCTTGGGTTCC 2268–2314 1.000 88.2
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT GAATACGGTCCTTGGGTTCC 1561–1613 1.000 88.1
atpH-atpI_p5 atpH-atpI ATAAACAACCCGCACACACT TTCGGAACCCACAAACCATT 2363–2409 1.000 87.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CTTACCACTCGGCCATGC 1277–1324 1.000 66.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CTTACCACTCGGCCATGC 1282–1329 1.000 65.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CTTACCACTCGGCCATGC 1276–1323 1.000 65.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACATTCCCTCATTTCCATCCC CTTACCACTCGGCCATGC 1284–1331 1.000 64.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CCTTACCACTCGGCCATG 1278–1325 1.000 63.6
trnC-GCA-petN_p1 trnC-GCA-petN CGCAGTCAGCAGTCAATAGT ACTTCTTCCCCACACTACGA 1295–1317 1.000 91.9
trnC-GCA-petN_p2 trnC-GCA-petN CGCAGTCAGCAGTCAATAGT TTCTTCCCCACACTACGAGT 1302–1315 0.667 76.5
trnC-GCA-petN_p3 trnC-GCA-petN ATACTAGACGGGGATGGGTG ACTTCTTCCCCACACTACGA 1203 0.333 53.2
trnC-GCA-petN_p4 trnC-GCA-petN ATACTAGACGGGGATGGGTG TTCTTCCCCACACTACGAGT 1201 0.333 53.2
trnC-GCA-petN_p5 trnC-GCA-petN GGATGGGTGTGGATCCAATC TTCTTCCCCACACTACGAGT 1190 0.333 53.2
petN-psbM_p1 petN-psbM TAGGTTGGAGAGCCCGATAG TTCAAAACCAGCGGGATTCA 1982 0.333 53.2
petN-psbM_p2 petN-psbM ACTCGTAGTGTGGGGAAGAA TTCAAAACCAGCGGGATTCA 1312 0.333 53.2
petN-psbM_p3 petN-psbM TCGTAGTGTGGGGAAGAAGT TTCAAAACCAGCGGGATTCA 1310 0.333 53.2
petN-psbM_p4 petN-psbM AGTGTCTAATGGCTGGACCT TTCAAAACCAGCGGGATTCA 2007 0.333 52.9
petN-psbM_p5 petN-psbM GAATTAGGTTGGAGAGCCCG TTCAAAACCAGCGGGATTCA 1986 0.333 52.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 926–946 1.000 51.3
psbM-trnD-GUC_p2 psbM-trnD-GUC AATGCAAGAATATTTACTTCCAT TTCAATTGGTCAGAGCACCG 925–945 1.000 51.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCAT TTCAATTGGTCAGAGCACCG 926–946 1.000 51.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCA GTTCAATTGGTCAGAGCACC 927–947 1.000 51.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AATGCAAGAATATTTACTTCCAT GTTCAATTGGTCAGAGCACC 926–946 1.000 51.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Alstonia mairei MW770447.1 178195 View on NCBI ↗
Alstonia scholaris NC_057091.1 154699 View on NCBI ↗
Alstonia yunnanensis NC_068670.1 155591 View on NCBI ↗