Markers + reference

Combretum

2 species · Combretaceae · Myrtales

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Species 2
Genome length 154–159 kb
Candidate markers 277
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 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 601 0.0656 0.43 63.3 yes View details
rps16-JXY33_pgt003 LSC 1279 0.2340 0.46 77.7 yes View details
JXY33_pgt008-JXY33_pgt009 LSC 441 0.0664 0.96 77.2 yes View details
JXY33_pgt011-psbD LSC 1441 0.0491 0.79 71.9 yes View details
ycf4-cemA LSC 988 0.0381 0.61 65.9 yes View details
psbE-petL LSC 1304 0.0338 0.98 68.3 yes View details
ndhF SSC 2232 0.0197 1.00 54.5 yes View details
ndhF-rpl32 SSC 639 0.2185 0.95 85.4 yes View details
ndhE SSC 306 0.0033 1.00 41.1 yes View details
ndhE-ndhG SSC 250 0.2366 0.90 77.0 yes View details
rps15-JXY33_pgp007 SSC 5113 0.0239 0.93 62.6 yes View details
JXY33_pgt021-JXY33_pgt022 LSC 202 0.0982 0.81 85.7 yes View details
rpl32-JXY33_pgt031 SSC 403 0.0578 0.99 80.2 yes View details
JXY33_pgt027-JXY33_pgt028 IRb 68 0.0441 1.00 77.9 yes View details
JXY33_pgt034-JXY33_pgt035 IRa 68 0.0441 1.00 77.9 yes View details
rpl20-rps12 LSC 774 0.0275 0.99 75.4 yes View details
JXY33_pgt004-JXY33_pgt005 LSC 701 0.0320 0.94 75.1 yes View details
petN-psbM LSC 963 0.0299 0.94 73.8 yes View details
accD-psaI LSC 633 0.0202 0.94 73.6 yes View details
psbM-JXY33_pgt008 LSC 797 0.0352 1.00 72.6 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-psbA_p1 trnH-psbA CTGCACGTGAACTAGGTGTT TCAGTGCTATGCATGGTTCC 1103 0.500 58.6
trnH-psbA_p2 trnH-psbA CTGCACGTGAACTAGGTGTT CAGTGCTATGCATGGTTCCT 1102 0.500 58.5
trnH-psbA_p3 trnH-psbA CTGCACGTGAACTAGGTGTT CCTCTAGACCTAGCTGCTGT 717 0.500 58.4
trnH-psbA_p4 trnH-psbA CTGCACGTGAACTAGGTGTT TTCCCTCTAGACCTAGCTGC 720 0.500 58.3
trnH-psbA_p5 trnH-psbA CTGCACGTGAACTAGGTGTT CGGATGGTATGCCTCTAGGA 1229 0.500 58.3
rps16-JXY33_pgt003_p1 rps16-JXY33_pgt003 CCACAGCTGATTATGTCCGT GAGGTTCGAATCCTTCCGTC 706–1373 1.000 88.9
rps16-JXY33_pgt003_p2 rps16-JXY33_pgt003 ATTATGTCCGTCAAGTCGCG GAGGTTCGAATCCTTCCGTC 697–1364 1.000 87.8
rps16-JXY33_pgt003_p3 rps16-JXY33_pgt003 GCGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 678–1345 1.000 87.2
rps16-JXY33_pgt003_p4 rps16-JXY33_pgt003 TCCACAGCTGATTATGTCCG GAGGTTCGAATCCTTCCGTC 707–1374 1.000 86.6
rps16-JXY33_pgt003_p5 rps16-JXY33_pgt003 CCACAGCTGATTATGTCCGT GGGTTTTGGTCCCGGTATTC 727–1394 1.000 85.2
JXY33_pgt004-JXY33_pgt005_p1 JXY33_pgt004-JXY33_pgt005 CAATCCGACGCTTTAGTCCA AAATCAAACCGAGGGATCCC 814–820 1.000 82.5
JXY33_pgt004-JXY33_pgt005_p2 JXY33_pgt004-JXY33_pgt005 AATCCGACGCTTTAGTCCAC AAATCAAACCGAGGGATCCC 813–819 1.000 82.5
JXY33_pgt004-JXY33_pgt005_p3 JXY33_pgt004-JXY33_pgt005 ACGGAAAGAGAGGGATTCGA AAATCAAACCGAGGGATCCC 868–874 1.000 81.2
JXY33_pgt004-JXY33_pgt005_p4 JXY33_pgt004-JXY33_pgt005 CAATCCGACGCTTTAGTCCA CGGAAAAATCAAACCGAGGG 819–825 1.000 81.0
JXY33_pgt004-JXY33_pgt005_p5 JXY33_pgt004-JXY33_pgt005 AATCCGACGCTTTAGTCCAC CGGAAAAATCAAACCGAGGG 818–824 1.000 81.0
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTCTTCATTCT 1104–1118 1.000 70.1
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTCTTCATTCT 1110–1124 1.000 68.7
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTCTTCATTCT 1050–1064 1.000 67.5
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTCTTCATTC 1104–1118 1.000 65.8
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTCTTCATTC 1110–1124 1.000 64.3
psbM-JXY33_pgt008_p1 psbM-JXY33_pgt008 AGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 908–944 1.000 56.2
psbM-JXY33_pgt008_p2 psbM-JXY33_pgt008 ACTAGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 911–947 1.000 54.7
psbM-JXY33_pgt008_p3 psbM-JXY33_pgt008 AGGAACTAGAATGAAGAGTGCAG TTCAATTGGTCAGAGCACCG 915–951 1.000 54.1
psbM-JXY33_pgt008_p4 psbM-JXY33_pgt008 AGGAACTAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 915–951 1.000 53.4
psbM-JXY33_pgt008_p5 psbM-JXY33_pgt008 GGAACTAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 914–950 1.000 53.4
JXY33_pgt008-JXY33_pgt009_p1 JXY33_pgt008-JXY33_pgt009 ATTTGATTCCGTCGGGACTG CTGGTTCAAATCCAGCTCGG 551–566 1.000 79.3
JXY33_pgt008-JXY33_pgt009_p2 JXY33_pgt008-JXY33_pgt009 TTGGATTTGATTCCGTCGGG CTGGTTCAAATCCAGCTCGG 555–570 1.000 77.4
JXY33_pgt008-JXY33_pgt009_p3 JXY33_pgt008-JXY33_pgt009 GATTTGATTCCGTCGGGACT CTGGTTCAAATCCAGCTCGG 552–567 1.000 77.0
JXY33_pgt008-JXY33_pgt009_p4 JXY33_pgt008-JXY33_pgt009 ATTTGATTCCGTCGGGACTG TGGTTCAAATCCAGCTCGG 550–565 1.000 76.6
JXY33_pgt008-JXY33_pgt009_p5 JXY33_pgt008-JXY33_pgt009 CGGTGCTCTGACCAATTGAA CTGGTTCAAATCCAGCTCGG 495–510 1.000 76.4

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
Combretum indicum NC_053324.1 159425 View on NCBI ↗
Combretum kraussii NC_053328.1 154018 View on NCBI ↗