Markers + reference

Milicia

2 species · Moraceae · Rosales

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Species 2
Genome length 160–160 kb
Candidate markers 267
Primer pairs 95

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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1030 0.0010 1.00 59.8 yes View details
trnE-UUC-trnT-GGU LSC 681 0.0059 1.00 62.1 yes View details
psbZ-trnG-GCC LSC 1000 0.0041 0.97 63.9 yes View details
psaI-ycf4 LSC 424 0.0047 1.00 57.8 yes View details
trnP-UGG-psaJ LSC 447 0.0023 0.98 58.4 yes View details
rpoA LSC 972 0.0031 1.00 60.5 yes View details
ycf1 IRb 1009 0.0010 1.00 59.3 no View details
rpl32-trnL-UAG SSC 1606 0.0012 1.00 59.2 yes View details
ccsA SSC 966 0.0000 1.00 32.4 yes View details
ccsA-ndhD SSC 285 0.0351 1.00 72.7 yes View details
ycf1 SSC 5643 0.0007 1.00 52.9 yes View details
psbT-psbN LSC 68 0.0147 1.00 61.0 yes View details
ycf4-cemA LSC 936 0.0000 0.99 60.0 yes View details
trnT-UGU-trnL-UAA LSC 1139 0.0000 0.99 59.8 yes View details
ndhF-rpl32 SSC 1378 0.0015 1.00 59.7 yes View details
atpB-rbcL LSC 726 0.0000 0.99 59.6 yes View details
rpl20-rps12 LSC 809 0.0012 1.00 59.6 yes View details
matK LSC 1512 0.0013 1.00 59.5 yes View details
atpF LSC 1338 0.0000 0.99 59.3 yes View details
trnC-GCA-petN LSC 1016 0.0010 1.00 59.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK AGTTGATCAACCCTTACTGCA AGCCCATCCTATTTTCGGTTC 1661 1.000 57.2
matK_p2 matK AGTTGATCAACCCTTACTGCA AAGCCCATCCTATTTTCGGT 1662 1.000 56.8
matK_p3 matK AGTTGATCAACCCTTACTGCA AGCCCATCCTATTTTCGGTT 1661 1.000 56.8
matK_p4 matK AGTTGATCAACCCTTACTGCA AACCCAATAAAGCCCATCCT 1671 1.000 55.8
matK_p5 matK AGTTGATCAACCCTTACTGCA GCCCATCCTATTTTCGGTTCA 1660 1.000 55.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC TATTTCAAAGAAGGCGGGGG 1206–1211 1.000 78.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT TATTTCAAAGAAGGCGGGGG 1205–1210 1.000 78.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC AGAAGGCGGGGGTTTTTATG 1198–1203 1.000 78.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT AGAAGGCGGGGGTTTTTATG 1197–1202 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCAAAGAAGGCGGGGG 1122–1127 1.000 78.0
atpF_p1 atpF TTTCATCGGCTCGAATGGTT AGACTAAGAAAGAGGAGATCA 1438–1445 1.000 40.4
atpF_p2 atpF TTTCATCGGCTCGAATGGTT AAGACTAAGAAAGAGGAGATCA 1439–1446 1.000 40.4
atpF_p3 atpF TCATCGGCTCGAATGGTTAC AGACTAAGAAAGAGGAGATCA 1436–1443 1.000 40.4
atpF_p4 atpF TCATCGGCTCGAATGGTTAC AAGACTAAGAAAGAGGAGATCA 1437–1444 1.000 40.4
atpF_p5 atpF GGCTCGAATGGTTACCATGA AGACTAAGAAAGAGGAGATCA 1431–1438 1.000 40.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1082–1107 1.000 78.2
trnC-GCA-petN_p2 trnC-GCA-petN GGGTGTCGCCTAATCAACAA AGCCCAAGCGAGACTTACTA 1064–1089 1.000 77.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1143–1168 1.000 76.6
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1100–1125 1.000 76.0
trnC-GCA-petN_p5 trnC-GCA-petN GGGTGTCGCCTAATCAACAA AGAGTCCACTTCTTCCCCAT 1125–1150 1.000 75.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 768–773 1.000 79.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 766–771 1.000 79.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 822–827 1.000 79.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 747–752 1.000 78.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 745–750 1.000 78.8
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG AATCGAACCCGCATCTTCTC 1137–1165 1.000 81.7
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG GAATCGAACCCGCATCTTCT 1138–1166 1.000 81.7
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG AATCGAACCCGCATCTTCTC 1140–1168 1.000 80.2
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG GAATCGAACCCGCATCTTCT 1141–1169 1.000 80.2
psbZ-trnG-GCC_p5 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC AATCGAACCCGCATCTTCTC 1138–1166 1.000 79.8

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
Milicia excelsa MZ274132.1 160136 View on NCBI ↗
Milicia regia MZ274133.1 160232 View on NCBI ↗