Markers + reference

Aster

12 species · Asteraceae · Asterales

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Species 12
Genome length 152–153 kb
Candidate markers 265
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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG_ucc-trnT_ggu LSC 259 0.0714 0.77 68.7 yes View details
trnT_ugu-trnL_uaa LSC 748 0.0344 0.88 70.8 yes View details
ndhC-trnV_uac LSC 892 0.0142 0.90 70.5 yes View details
accD-psaI LSC 957 0.0361 0.91 73.0 yes View details
ycf4-cemA LSC 891 0.0145 0.99 66.0 yes View details
petD LSC 1244 0.0125 0.99 60.2 yes View details
ycf1 IRb 618 0.0021 1.00 36.8 no View details
rpl32-trnL_uag SSC 807 0.0150 0.98 65.6 yes View details
ndhA SSC 2173 0.0087 0.98 61.0 yes View details
ycf1 SSC 5094 0.0079 1.00 45.9 yes View details
ycf1 IRa 618 0.0016 1.00 34.0 no View details
psbC-trnS_uga LSC 229 0.0190 1.00 69.2 yes View details
ycf3-trnS_gga LSC 870 0.0096 0.98 65.0 yes View details
trnS_gcu-trnC_gca LSC 797 0.0116 1.00 64.8 yes View details
trnK_uuu-rps16 LSC 817 0.0093 0.99 62.9 yes View details
trnG_gcc-trnfM_cau LSC 211 0.0165 1.00 62.2 yes View details
petA-psbJ LSC 714 0.0082 0.99 62.0 yes View details
ndhE-ndhG SSC 228 0.0102 0.98 61.7 yes View details
psaA-ycf3 LSC 766 0.0057 1.00 61.3 yes View details
trnR_ucu-trnG_ucc LSC 260 0.0154 0.92 60.4 yes View details
psbZ-trnG_gcc LSC 327 0.0083 0.98 60.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK_uuu-rps16_p1 trnK_uuu-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 947–1005 1.000 81.7
trnK_uuu-rps16_p2 trnK_uuu-rps16 CCGCACTTAAAAGCCGAGTA TTCCTTGAAAAAGGCGCTCA 941–999 1.000 81.6
trnK_uuu-rps16_p3 trnK_uuu-rps16 TCGCGGTCTTCCAAACTTTA TTCCTTGAAAAAGGCGCTCA 1013–1071 1.000 79.4
trnK_uuu-rps16_p4 trnK_uuu-rps16 CGCGGTCTTCCAAACTTTAC TTCCTTGAAAAAGGCGCTCA 1012–1070 1.000 79.0
trnK_uuu-rps16_p5 trnK_uuu-rps16 TCCTAGCCGCACTTAAAAGC TCCTTGAAAAAGGCGCTCAG 946–1004 1.000 78.1
trnS_gcu-trnC_gca_p1 trnS_gcu-trnC_gca ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 928–957 1.000 83.7
trnS_gcu-trnC_gca_p2 trnS_gcu-trnC_gca ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 910–939 1.000 81.6
trnS_gcu-trnC_gca_p3 trnS_gcu-trnC_gca CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 864–893 1.000 80.2
trnS_gcu-trnC_gca_p4 trnS_gcu-trnC_gca AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 929–958 1.000 79.5
trnS_gcu-trnC_gca_p5 trnS_gcu-trnC_gca CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 846–875 1.000 78.2
trnR_ucu-trnG_ucc_p1 trnR_ucu-trnG_ucc AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 309–340 1.000 70.5
trnR_ucu-trnG_ucc_p2 trnR_ucu-trnG_ucc AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 312–343 1.000 70.3
trnR_ucu-trnG_ucc_p3 trnR_ucu-trnG_ucc AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 315–346 1.000 69.8
trnR_ucu-trnG_ucc_p4 trnR_ucu-trnG_ucc AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 318–349 1.000 69.6
trnR_ucu-trnG_ucc_p5 trnR_ucu-trnG_ucc AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 313–344 1.000 68.1
trnG_ucc-trnT_ggu_p1 trnG_ucc-trnT_ggu ATGAAACCGAAAGACCCCTT ACTGAGTTAAAAGGAAAGGGCT 359–525 0.500 42.8
trnG_ucc-trnT_ggu_p2 trnG_ucc-trnT_ggu AATGAAACCGAAAGACCCCT ACTGAGTTAAAAGGAAAGGGCT 360–526 0.500 42.7
trnG_ucc-trnT_ggu_p3 trnG_ucc-trnT_ggu AATGAAACCGAAAGACCCCT CACTGAGTTAAAAGGAAAGGGC 361–527 0.500 42.3
trnG_ucc-trnT_ggu_p4 trnG_ucc-trnT_ggu ATGAAACCGAAAGACCCCTT CACTGAGTTAAAAGGAAAGGGC 360–526 0.500 42.3
trnG_ucc-trnT_ggu_p5 trnG_ucc-trnT_ggu GAATGAAACCGAAAGACCCCT ACTGAGTTAAAAGGAAAGGGCT 361–527 0.500 40.8
psbC-trnS_uga_p1 psbC-trnS_uga CTGTTCTTTCCATGACCCCC GAGAGATGGCTGAGTGGTTG 334–355 1.000 84.9
psbC-trnS_uga_p2 psbC-trnS_uga TCTTCGTAGGGCATTTGTGG AAGTCCCGGTCTTGAAAACC 397–418 1.000 84.3
psbC-trnS_uga_p3 psbC-trnS_uga TCTTCGTAGGGCATTTGTGG GAGAGATGGCTGAGTGGTTG 418–439 1.000 84.1
psbC-trnS_uga_p4 psbC-trnS_uga TCTTCGTAGGGCATTTGTGG TGGCTGAGTGGTTGAAAGTC 412–433 1.000 84.0
psbC-trnS_uga_p5 psbC-trnS_uga TCTTCGTAGGGCATTTGTGG GTCTTTCGGAGAGATGGCTG 426–447 1.000 83.6
psbZ-trnG_gcc_p1 psbZ-trnG_gcc TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 471–502 1.000 81.3
psbZ-trnG_gcc_p2 psbZ-trnG_gcc GCTTCTCCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 469–500 1.000 80.9
psbZ-trnG_gcc_p3 psbZ-trnG_gcc CTCCTGATGGTTGGTCAAGT CGTCTTCTCCTTGGCAAAGA 465–496 1.000 76.1
psbZ-trnG_gcc_p4 psbZ-trnG_gcc TGCTTCTCCTGATGGTTGGT CGTCTTCTCCTTGGCAAAGA 470–501 1.000 75.5
psbZ-trnG_gcc_p5 psbZ-trnG_gcc TCTCCTGATGGTTGGTCAAG CGTCTTCTCCTTGGCAAAGA 466–497 1.000 73.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Aster ageratoides NC_058273.1 153071 View on NCBI ↗
Aster altaicus NC_072176.1 152473 View on NCBI ↗
Aster altaicus var. uchiyamae NC_049875.1 152457 View on NCBI ↗
Aster amellus OR896874.1 152906 View on NCBI ↗
Aster bellidiastrum OR896897.1 152726 View on NCBI ↗
Aster boweri PP234528.1 152713 View on NCBI ↗
Aster danyangensis PX645512.1 152451 View on NCBI ↗
Aster pekinensis NC_056301.1 152815 View on NCBI ↗
Aster prainii PP234575.1 152522 View on NCBI ↗
Aster scaber PQ178990.1 152778 View on NCBI ↗
Aster semiprostratus PP234574.1 152687 View on NCBI ↗
Aster tataricus NC_042913.1 152992 View on NCBI ↗