Markers + reference

Melampyrum

5 species · Orobanchaceae · Lamiales

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Species 5
Genome length 144–144 kb
Candidate markers 259
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 473 0.0486 0.73 65.8 yes View details
rps16-trnQ-UUG LSC 713 0.0534 0.94 84.2 yes View details
trnS-GCU-trnG-UCC LSC 698 0.0384 0.96 82.3 yes View details
ycf3-trnS-GGA LSC 864 0.0213 0.99 65.1 yes View details
trnT-UGU-trnL-UAA LSC 732 0.0295 1.00 70.8 yes View details
rps8 LSC 405 0.0064 1.00 37.4 yes View details
ndhD-psaC SSC 1216 0.0320 0.99 70.8 yes View details
psaC-rps15 SSC 856 0.0331 0.96 72.9 yes View details
trnL-UAG-ccsA SSC 110 0.0691 0.96 77.0 yes View details
trnF-GAA-ndhJ LSC 591 0.0255 1.00 69.7 yes View details
atpI-rps2 LSC 237 0.0346 1.00 68.4 yes View details
petN-psbM LSC 953 0.0172 0.99 67.1 yes View details
rbcL-accD LSC 575 0.0255 0.98 67.0 yes View details
rpl22-rps19 LSC 69 0.0357 0.93 66.0 yes View details
trnE-UUC-trnT-GGU LSC 585 0.0139 0.96 65.5 yes View details
accD-psaI LSC 635 0.0181 1.00 65.1 yes View details
rpl32-trnL-UAG SSC 735 0.0242 0.97 65.1 yes View details
trnT-GGU-psbD LSC 1293 0.0143 0.98 63.4 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 90 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 CCTCTAGACCTGGCTGCTAT 401–536 1.000 89.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTGGCTGCTAT 415–550 1.000 89.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTGGCTGCTAT 414–549 1.000 89.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTGGCTGCTAT 416–551 1.000 89.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC CCTCTAGACCTGGCTGCTAT 406–541 1.000 85.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGTTCGAACCCTTCCGTC 779–819 1.000 71.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTCGAACCCTTCCGTCC 778–818 1.000 71.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GGTTCGAACCCTTCCGTC 771–811 1.000 66.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GTTCGAACCCTTCCGTCC 770–810 1.000 66.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGAACCCTTCCGTCCC 777–817 1.000 65.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCCTTAACT 807–825 1.000 75.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 806–824 1.000 75.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCCTTAACT 861–879 1.000 73.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAACCGAAAGACCCCTTAACT 808–826 1.000 73.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAACCGAAAGACCCCTTAACT 807–825 1.000 73.6
atpI-rps2_p1 atpI-rps2 CCTACCTCCACACCGGATAT GGCTTTGCGAGAGTGTATCA 480–517 1.000 84.8
atpI-rps2_p2 atpI-rps2 CCTACCTCCACACCGGATAT TGGCTTTGCGAGAGTGTATC 481–518 1.000 84.8
atpI-rps2_p3 atpI-rps2 CCTACCTCCACACCGGATAT CCTAAAAGAGATGCGGCTGT 605–642 1.000 83.8
atpI-rps2_p4 atpI-rps2 ACGTGAGTAAAGCCAAAGCA GGCTTTGCGAGAGTGTATCA 845–882 1.000 82.9
atpI-rps2_p5 atpI-rps2 ACGTGAGTAAAGCCAAAGCA TGGCTTTGCGAGAGTGTATC 846–883 1.000 82.8
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TGCTACTGCACTATTCATTCT 1059–1094 1.000 49.7
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TGCTACTGCACTATTCATTCT 1057–1092 1.000 49.7
petN-psbM_p3 petN-psbM CGTAGTGTGGGGAAGAAGTG TGCTACTGCACTATTCATTCT 1056–1091 1.000 49.1
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTATTCATTCT 1111–1146 1.000 48.3
petN-psbM_p5 petN-psbM TCGTAGTGTGGGGAAGAAGT TGCTACTGCACTATTCATTCTAGT 1057–1092 1.000 48.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CTCCGATCACCTTCCTTTCG GAACCGATGACTTACGCCTT 733–747 1.000 83.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GATCACCTTCCTTTCGCAGT GAACCGATGACTTACGCCTT 729–743 1.000 83.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CTCCGATCACCTTCCTTTCG CCGATGACTTACGCCTTACC 730–744 1.000 82.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 680–694 1.000 82.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATCACCTTCCTTTCGCAGT CCGATGACTTACGCCTTACC 726–740 1.000 82.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Melampyrum cristatum PP484617.1 144004 View on NCBI ↗
Melampyrum koreanum NC_057523.1 143865 View on NCBI ↗
Melampyrum roseum NC_053791.1 143896 View on NCBI ↗
Melampyrum setaceum var. nakaianum OL999306.1 143512 View on NCBI ↗
Melampyrum sylvaticum PP484619.1 143891 View on NCBI ↗