Markers + reference

Melica

60 species · Poaceae · Poales

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Species 60
Genome length 134–135 kb
Candidate markers 255
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ LSC 988 0.0083 1.00 62.2 yes View details
trnG-trnfM LSC 466 0.0112 1.00 67.4 yes View details
trnG-trnT LSC 1573 0.0098 0.99 79.1 yes View details
psbM-trnC LSC 1705 0.0086 1.00 74.0 yes View details
rbcL-psaI LSC 984 0.0105 0.99 79.9 yes View details
petA-psbJ LSC 825 0.0095 1.00 62.6 yes View details
rpl16 LSC 1450 0.0070 0.98 61.7 yes View details
ndhF SSC 2220 0.0041 1.00 47.0 yes View details
ndhF-trnL SSC 1691 0.0131 1.00 78.1 yes View details
trnT-tRNA-Leu LSC 766 0.0075 1.00 73.2 yes View details
psaA-ycf3 LSC 653 0.0086 0.97 70.6 yes View details
ndhC-trnV LSC 853 0.0070 1.00 70.3 yes View details
trnS-psbD LSC 953 0.0059 0.99 70.2 yes View details
trnD-psbM LSC 693 0.0066 1.00 69.4 yes View details
psaC-ndhE SSC 465 0.0084 1.00 69.2 yes View details
trnC-rpoB LSC 1106 0.0056 1.00 68.1 yes View details
trnR-rps14 LSC 378 0.0109 0.98 66.6 yes View details
atpI-atpH LSC 603 0.0054 0.99 64.5 yes View details
psbT-psbN LSC 48 0.0372 1.00 63.6 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
trnK_p1 trnK AACTCAGATTGCTCTTTTCT TCGATCGTATCTAAGATCCCT 2619–2655 1.000 46.0
trnK_p2 trnK AAACTCAGATTGCTCTTTTCT TCGATCGTATCTAAGATCCCT 2620–2656 1.000 46.0
trnK_p3 trnK AAAACTCAGATTGCTCTTTTCT TCGATCGTATCTAAGATCCCT 2621–2657 1.000 46.0
trnK_p4 trnK AACTCAGATTGCTCTTTTCT TTCGATCGTATCTAAGATCCCT 2620–2656 1.000 46.0
trnK_p5 trnK AAACTCAGATTGCTCTTTTCT TTCGATCGTATCTAAGATCCCT 2621–2657 1.000 46.0
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA AGCAGCTTGCCAAACAAAAG 1390–1649 1.000 88.7
rps16-trnQ_p2 rps16-trnQ AAGTCGCACGTTGCTTTCTA CTTACAGCAGCTTGCCAAAC 1395–1654 1.000 88.6
rps16-trnQ_p3 rps16-trnQ GACTATGTCGAGCCAAGAGC AGCAGCTTGCCAAACAAAAG 1467–1726 1.000 88.3
rps16-trnQ_p4 rps16-trnQ GACTATGTCGAGCCAAGAGC CTTACAGCAGCTTGCCAAAC 1472–1731 1.000 88.3
rps16-trnQ_p5 rps16-trnQ TCATGTCCTTCAAGTCGCAC AGCAGCTTGCCAAACAAAAG 1401–1660 1.000 88.1
trnS-psbD_p1 trnS-psbD ATTAGCAATCCGCCGCTTTA GACAAAAACGAAACGGTCCC 1074–1156 1.000 88.3
trnS-psbD_p2 trnS-psbD ATTAGCAATCCGCCGCTTTA GAGCAATAGGCCAGACCATC 1095–1177 1.000 88.2
trnS-psbD_p3 trnS-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1073–1155 1.000 87.2
trnS-psbD_p4 trnS-psbD ATTAGCAATCCGCCGCTTTA CCGACAAAAACGAAACGGTC 1076–1158 1.000 87.0
trnS-psbD_p5 trnS-psbD ATTAGCAATCCGCCGCTTTA CGACAAAAACGAAACGGTCC 1075–1157 1.000 87.0
trnG-trnfM_p1 trnG-trnfM GCGAGCGTAGTTCAATGGTA ACCAGTTCCCGGTATACTCC 527–658 0.983 88.1
trnG-trnfM_p2 trnG-trnfM GCGAGCGTAGTTCAATGGTA CCAGTTCCCGGTATACTCCA 526–657 0.983 88.1
trnG-trnfM_p3 trnG-trnfM GTCGACCCAAGCGGATATAC CGAGGCTCATAACCTTGAGG 518–649 0.967 87.7
trnG-trnfM_p4 trnG-trnfM GTCGACCCAAGCGGATATAC ACCAGTTCCCGGTATACTCC 567–698 0.950 86.5
trnG-trnfM_p5 trnG-trnfM GTCGACCCAAGCGGATATAC CCAGTTCCCGGTATACTCCA 566–697 0.950 86.5
trnG-trnT_p1 trnG-trnT ACGAATCACACTTTTACCACT TACGTCTTACCACGGCAGTA 1362–1738 0.983 61.3
trnG-trnT_p2 trnG-trnT ACGAATCACACTTTTACCACT TACCACGGCAGTACTCTACC 1355–1731 0.983 61.1
trnG-trnT_p3 trnG-trnT GAACGAATCACACTTTTACCACT TACGTCTTACCACGGCAGTA 1364–1740 0.983 60.3
trnG-trnT_p4 trnG-trnT ACGAATCACACTTTTACCACT TCTTACCACGGCAGTACTCT 1358–1734 0.933 59.4
trnG-trnT_p5 trnG-trnT ACGAATCACACTTTTACCACT GTCTTACCACGGCAGTACTC 1359–1735 0.933 58.8
trnD-psbM_p1 trnD-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 736–829 1.000 68.3
trnD-psbM_p2 trnD-psbM TAGGTATGCCATACACCCCG AGAATGAACAGTGCAGTAGC 768–861 0.983 65.8
trnD-psbM_p3 trnD-psbM TTCAATTGGTCAGAGCACCG AGGAACTAGAATGAACAGTGCA 743–836 1.000 65.0
trnD-psbM_p4 trnD-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 737–830 1.000 64.1
trnD-psbM_p5 trnD-psbM TAGGTATGCCATACACCCCG AGGAACTAGAATGAACAGTGCA 775–868 0.983 62.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (60)

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

Species Accession Length (bp) Link
Melica altissima PZ098388.1 134730 View on NCBI ↗
Melica amethystina PZ098314.1 134506 View on NCBI ↗
Melica argentata PZ098300.1 134311 View on NCBI ↗
Melica argyrea PZ098626.1 134788 View on NCBI ↗
Melica aristata PZ098364.1 134771 View on NCBI ↗
Melica arzivencoi PZ098297.1 134803 View on NCBI ↗
Melica bonariensis PZ098298.1 134787 View on NCBI ↗
Melica brasiliana PZ098301.1 134688 View on NCBI ↗
Melica brevicoronata PZ098299.1 134711 View on NCBI ↗
Melica bulbosa PZ098328.1 134753 View on NCBI ↗
Melica californica PZ098356.1 134628 View on NCBI ↗
Melica chilensis PZ098303.1 134893 View on NCBI ↗
Melica ciliata PZ098294.1 134615 View on NCBI ↗
Melica dendroides PZ098271.1 134029 View on NCBI ↗
Melica eligulata PZ098376.1 134229 View on NCBI ↗
Melica eremophila PZ098264.1 134652 View on NCBI ↗
Melica frutescens PZ098357.1 134665 View on NCBI ↗
Melica fugax PZ098600.1 134577 View on NCBI ↗
Melica geyeri PZ098360.1 134790 View on NCBI ↗
Melica harfordii PZ098329.1 134712 View on NCBI ↗
Melica hyalina PZ098304.1 134660 View on NCBI ↗
Melica imperfecta PZ098370.1 134691 View on NCBI ↗
Melica longiflora PZ098367.1 134669 View on NCBI ↗
Melica macra PZ098629.1 134749 View on NCBI ↗
Melica minuta PZ098390.1 134368 View on NCBI ↗
Melica mollis PZ098368.1 134697 View on NCBI ↗
Melica montezumae PZ098283.1 135215 View on NCBI ↗
Melica mutica NC_027477.1 134710 View on NCBI ↗
Melica nitens PZ098617.1 134757 View on NCBI ↗
Melica nutans PZ098274.1 134699 View on NCBI ↗
Melica onoei PZ098308.1 134905 View on NCBI ↗
Melica paulsenii PZ098286.1 134282 View on NCBI ↗
Melica penicillaris PZ098295.1 134587 View on NCBI ↗
Melica persica PZ098296.1 134661 View on NCBI ↗
Melica picta PZ098387.1 134771 View on NCBI ↗
Melica porteri PZ098282.1 134544 View on NCBI ↗
Melica racemosa PZ098272.1 134507 View on NCBI ↗
Melica radula PZ098407.1 134777 View on NCBI ↗
Melica rectiflora PZ098315.1 134281 View on NCBI ↗
Melica rigida PZ098265.1 134682 View on NCBI ↗
Melica sarmentosa PZ098631.1 134280 View on NCBI ↗
Melica scaberrima PZ098309.1 134827 View on NCBI ↗
Melica scabra PZ098292.1 134830 View on NCBI ↗
Melica scabrosa NC_050212.1 134889 View on NCBI ↗
Melica schuetzeana PZ098406.1 134626 View on NCBI ↗
Melica secunda PZ098310.1 134703 View on NCBI ↗
Melica smithii PZ098330.1 134546 View on NCBI ↗
Melica spectabilis PZ098331.1 134657 View on NCBI ↗
Melica stricta PZ098363.1 134635 View on NCBI ↗
Melica stuckertii PZ098305.1 134697 View on NCBI ↗
Melica subulata NC_027478.1 134765 View on NCBI ↗
Melica teneriffae PZ098369.1 134809 View on NCBI ↗
Melica tenuis PZ098306.1 134696 View on NCBI ↗
Melica torreyana PZ098371.1 134729 View on NCBI ↗
Melica transsilvanica PZ098393.1 134509 View on NCBI ↗
Melica turczaninowiana PZ098277.1 134891 View on NCBI ↗
Melica uniflora PZ098266.1 134748 View on NCBI ↗
Melica violacea PZ098287.1 134817 View on NCBI ↗
Melica virgata PZ098291.1 134773 View on NCBI ↗
Melica yajiangensis PZ098404.1 134325 View on NCBI ↗