Markers + reference

Indigofera

23 species · Fabaceae · Fabales

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Species 23
Genome length 134–160 kb
Candidate markers 267
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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 1392 0.0494 0.91 84.1 yes View details
trnL-UAA-trnT-UGU LSC 1080 0.0632 0.86 79.7 yes View details
psbK-trnQ-UUG LSC 810 0.0738 0.94 89.1 yes View details
accD-psaI LSC 592 0.0612 0.87 76.5 yes View details
trnP-UGG-psaJ LSC 928 0.0530 0.84 81.1 yes View details
ndhF-rpl32 SSC 799 0.0629 0.91 81.2 yes View details
rpl32-trnL-UAG SSC 958 0.0706 0.71 75.3 yes View details
ndhG-ndhI SSC 612 0.0496 0.88 86.1 yes View details
atpH-atpF LSC 592 0.0437 0.99 95.4 yes View details
petA-psbJ LSC 1210 0.0269 0.98 86.9 yes View details
trnG-GCC-psbZ LSC 762 0.0454 0.85 81.9 yes View details
psbD-trnT-GGU LSC 1453 0.0227 0.98 79.7 yes View details
trnQ-UUG-rps16 LSC 495 0.0385 0.98 79.1 yes View details
trnR-UCU-trnG-UCC LSC 291 0.0376 0.97 78.5 yes View details
rps16-accD LSC 677 0.0393 0.96 77.8 yes View details
ndhJ-trnF-GAA LSC 804 0.0299 0.98 77.5 yes View details
trnC-GCA-rpoB LSC 1230 0.0199 0.99 77.4 yes View details
rps3-rps19 LSC 521 0.0403 0.94 76.2 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
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA AGTCCTGAATTAGCTGCTGC 1401–1784 1.000 83.6
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA CCGTGAAGCTAGCAAATGGA 1420–1803 1.000 81.8
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA TCCGTGAAGCTAGCAAATGG 1421–1804 1.000 81.8
trnK-UUU-rbcL_p4 trnK-UUU-rbcL GCCGAGTACTCTACCATTGAG AGTCCTGAATTAGCTGCTGC 1400–1783 1.000 80.9
trnK-UUU-rbcL_p5 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA GCTGCTGCTTGTGAAGTATG 1389–1772 1.000 79.6
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA GATGGCCTCTGCGTAAAGAT CCTCGTGTCACCAGTTCAAA 876–950 1.000 89.6
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA ATAGGATGGCCTCTGCGTAA CCTCGTGTCACCAGTTCAAA 880–954 1.000 89.3
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA ATGCCCGAAAGTTGGATAGG CCTCGTGTCACCAGTTCAAA 895–969 1.000 88.8
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA AGTTGGATAGGATGGCCTCT CCTCGTGTCACCAGTTCAAA 886–960 1.000 87.6
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA TAGGATGGCCTCTGCGTAAA CCTCGTGTCACCAGTTCAAA 879–953 1.000 87.5
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC CCGGTTGACCCTTTAGCTTT 1354–1867 1.000 91.2
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC AGCGCGATTGGTTTCTAAGT 1227–1740 1.000 91.2
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 769–1280 1.000 90.9
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC CTGACCGGTTGACCCTTTAG 1358–1871 0.957 89.5
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGGGCTTGAGGAATAGTAG 1439–1952 0.957 89.0
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTTCCGGTACATCCTTATGG 696–879 0.913 59.4
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CATAAAAAGGAAGGGGCGGA TTTCCGGTACATCCTTATGG 734–915 0.783 54.4
trnG-GCC-psbZ_p3 trnG-GCC-psbZ ACATAAAAAGGAAGGGGCGG TTTCCGGTACATCCTTATGG 735–916 0.783 54.3
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CATAAAAAGGAAGGGGCGGA TTTTCCGGTACATCCTTATGG 735–916 0.783 53.2
trnG-GCC-psbZ_p5 trnG-GCC-psbZ ACATAAAAAGGAAGGGGCGG TTTTCCGGTACATCCTTATGG 736–917 0.783 53.0
psbD-trnT-GGU_p1 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GTGGTAGAGTAACGCCATGG 1443–1676 1.000 90.1
psbD-trnT-GGU_p2 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GTGGTAGAGTAACGCCATGG 1444–1677 1.000 90.1
psbD-trnT-GGU_p3 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GTGGTAGAGTAACGCCATGG 1445–1678 1.000 90.1
psbD-trnT-GGU_p4 psbD-trnT-GGU CACAAAAACGAAACGGTCCC TCAGTGGTAGAGTAACGCCA 1446–1679 1.000 90.0
psbD-trnT-GGU_p5 psbD-trnT-GGU CCACAAAAACGAAACGGTCC TCAGTGGTAGAGTAACGCCA 1447–1680 1.000 90.0
trnC-GCA-rpoB_p1 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA CTGATTCAACCCGGGTAGTG 1337–1414 1.000 89.6
trnC-GCA-rpoB_p2 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA TCTGATTCAACCCGGGTAGT 1338–1415 1.000 89.3
trnC-GCA-rpoB_p3 trnC-GCA-rpoB ATTCTCTTGTCGATCAGGCG CTGATTCAACCCGGGTAGTG 1361–1438 1.000 88.4
trnC-GCA-rpoB_p4 trnC-GCA-rpoB ATTCTCTTGTCGATCAGGCG TCTGATTCAACCCGGGTAGT 1362–1439 1.000 88.1
trnC-GCA-rpoB_p5 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA CCTCATTTCTACCCCCAAGC 1308–1385 0.913 85.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Indigofera amblyantha NC_079826.1 159686 View on NCBI ↗
Indigofera argentea NC_070249.1 158639 View on NCBI ↗
Indigofera atropurpurea NC_079829.1 158847 View on NCBI ↗
Indigofera bracteata OR491707.1 158539 View on NCBI ↗
Indigofera bungeana NC_079830.1 159777 View on NCBI ↗
Indigofera carlesii NC_079831.1 159172 View on NCBI ↗
Indigofera cassioides NC_079832.1 158679 View on NCBI ↗
Indigofera caudata NC_079841.1 158586 View on NCBI ↗
Indigofera decora NC_079833.1 159164 View on NCBI ↗
Indigofera franchetii NC_079828.1 158531 View on NCBI ↗
Indigofera hebepetala var. glabra OQ147482.1 158457 View on NCBI ↗
Indigofera hirsuta NC_079834.1 159873 View on NCBI ↗
Indigofera kirilowii NC_079835.1 159615 View on NCBI ↗
Indigofera koreana NC_086646.1 159517 View on NCBI ↗
Indigofera linifolia NC_047353.1 160040 View on NCBI ↗
Indigofera linnaei NC_079836.1 159455 View on NCBI ↗
Indigofera litoralis PP092931.1 134363 View on NCBI ↗
Indigofera miniata MW628948.1 159935 View on NCBI ↗
Indigofera pendula NC_079837.1 159034 View on NCBI ↗
Indigofera scabrida NC_079838.1 157918 View on NCBI ↗
Indigofera suffruticosa NC_079839.1 158517 View on NCBI ↗
Indigofera tinctoria NC_026680.1 158367 View on NCBI ↗
Indigofera wightii NC_079840.1 159787 View on NCBI ↗