Markers + reference

Melia

2 species · Meliaceae · Sapindales

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Species 2
Genome length 160–172 kb
Candidate markers 273
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 460 0.0470 0.65 76.3 yes View details
petN-psbM LSC 1319 0.0147 0.83 65.7 yes View details
psbM-trnD-GUC LSC 525 0.0210 1.00 59.9 yes View details
trnT-GGU-psbD LSC 1252 0.0185 0.99 63.1 yes View details
trnS-UGA-psbZ LSC 366 0.0083 0.98 45.5 yes View details
psbZ-trnG-GCC LSC 522 0.0823 0.95 85.3 yes View details
rps4-trnT-UGU LSC 350 0.0260 0.99 54.9 yes View details
petB LSC 1471 0.0088 1.00 55.7 yes View details
rpl16 LSC 1443 0.0112 0.99 52.1 yes View details
ycf1 IRb 1086 0.0018 1.00 46.1 no View details
ndhF-rpl32 SSC 1039 0.0215 0.94 67.0 yes View details
rpl32-trnL-UAG SSC 1119 0.0171 0.99 57.3 yes View details
ycf1 SSC 5466 0.0135 1.00 45.4 yes View details
psbT-psbN LSC 65 0.0615 1.00 82.7 yes View details
psbC-trnS-UGA LSC 247 0.0366 1.00 73.9 yes View details
rps11-rpl36 LSC 121 0.0342 0.97 72.3 yes View details
petA-psbJ LSC 494 0.0173 0.94 70.7 yes View details
ndhI-ndhA SSC 82 0.0494 0.99 70.4 yes View details
atpH-atpI LSC 1219 0.0159 0.98 69.9 yes View details
rbcL-accD LSC 590 0.0191 0.98 67.3 yes View details
petD-rpoA LSC 260 0.0231 1.00 65.8 yes View details
trnE-UUC-trnT-GGU LSC 823 0.0147 0.99 65.4 yes View details
ycf3-trnS-GGA LSC 879 0.0122 0.93 65.0 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 386–529 1.000 84.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 400–543 1.000 84.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 399–542 1.000 84.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 401–544 1.000 84.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 435–578 1.000 82.5
trnG-UCC_p1 trnG-UCC TTGTTCGACAAAAGTCCCGA TTAATGTGCCGCTGAATTGA 879–890 1.000 64.6
trnG-UCC_p2 trnG-UCC TTGTTCGACAAAAGTCCCGA TTCATTAATGTGCCGCTGAA 883–894 1.000 64.6
trnG-UCC_p3 trnG-UCC TTGTTCGACAAAAGTCCCGA TTTCATTAATGTGCCGCTGA 884–895 1.000 64.6
trnG-UCC_p4 trnG-UCC TTGTTCGACAAAAGTCCCGA CATTAATGTGCCGCTGAATTGA 881–892 1.000 64.1
trnG-UCC_p5 trnG-UCC TTGTTCGACAAAAGTCCCGA TCATTAATGTGCCGCTGAATTG 882–893 1.000 64.1
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TACAAGCGGGATTCAAGCTC 1351–1364 1.000 82.2
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TACAAGCGGGATTCAAGCTC 1315–1328 1.000 81.7
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 1373–1386 1.000 81.5
atpH-atpI_p4 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1327–1340 1.000 81.4
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 1377–1390 1.000 80.9
petN-psbM_p1 petN-psbM CTTGGGCCGCTTTAATGGTA TGCTACTGCACTGTTCATTCT 1299–1469 1.000 71.7
petN-psbM_p2 petN-psbM TTGGGCCGCTTTAATGGTAG TGCTACTGCACTGTTCATTCT 1298–1468 1.000 71.7
petN-psbM_p3 petN-psbM GGCCGCTTTAATGGTAGTCT TGCTACTGCACTGTTCATTCT 1295–1465 1.000 71.1
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1250–1420 1.000 70.9
petN-psbM_p5 petN-psbM GGGCCGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTCT 1296–1466 1.000 68.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 636–640 1.000 59.7
psbM-trnD-GUC_p2 psbM-trnD-GUC TTGACTGACCGTTTTTACGT TTCAATTGGTCAGAGCACCG 685–689 1.000 58.0
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTTTGACTGACCGTTTTTACG TTCAATTGGTCAGAGCACCG 688–692 1.000 57.3
psbM-trnD-GUC_p4 psbM-trnD-GUC CTTTGACTGACCGTTTTTACGT TTCAATTGGTCAGAGCACCG 687–691 1.000 57.3
psbM-trnD-GUC_p5 psbM-trnD-GUC TCACTTTGACTGACCGTTTT TTCAATTGGTCAGAGCACCG 690–694 1.000 57.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 903–910 1.000 80.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 901–908 1.000 80.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 957–964 1.000 80.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 882–889 1.000 80.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 880–887 1.000 80.0

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
Melia azedarach NC_050650.1 160393 View on NCBI ↗
Melia dubia BK059531.1 171956 View on NCBI ↗