Markers + reference

Astelia

2 species · Asteliaceae · Asparagales

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Species 2
Genome length 158–158 kb
Candidate markers 265
Primer pairs 90

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 697 0.0253 0.96 74.7 yes View details
rps16-trnQ LSC 1679 0.0181 0.99 65.9 yes View details
trnS-trnG LSC 857 0.0264 0.97 69.6 yes View details
trnD-trnY LSC 294 0.0386 0.97 65.3 yes View details
trnT-trnL LSC 959 0.0184 0.96 66.1 yes View details
ndhC-trnV LSC 1660 0.0226 0.98 68.1 yes View details
ndhF SSC 2205 0.0132 1.00 50.1 yes View details
ndhF-rpl32 SSC 965 0.0271 0.95 65.8 yes View details
psaC-ndhE SSC 333 0.0370 0.97 64.7 yes View details
psbC-trnS LSC 137 0.0730 1.00 82.5 yes View details
rps19-psbA LSC 155 0.0403 0.96 79.2 no View details
trnH-rpl2 IRb 43 0.1163 1.00 74.4 yes View details
rpl2-trnH IRa 43 0.1163 1.00 74.4 yes View details
psbE-petL LSC 1336 0.0169 0.89 71.3 yes View details
psbT-psbN LSC 59 0.0678 1.00 70.9 yes View details
rps3-rps19 LSC 490 0.0168 0.97 69.0 yes View details
ndhJ-ndhK LSC 81 0.0247 1.00 66.7 yes View details
rps8-rpl14 LSC 202 0.0248 1.00 66.7 yes View details
trnR-atpA LSC 119 0.0254 0.99 66.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-rps16_p1 trnK-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 797–811 1.000 82.6
trnK-rps16_p2 trnK-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 796–810 1.000 82.6
trnK-rps16_p3 trnK-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAAGGCGCTCAACC 801–815 1.000 81.0
trnK-rps16_p4 trnK-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 801–815 1.000 81.0
trnK-rps16_p5 trnK-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 800–814 1.000 81.0
rps16-trnQ_p1 rps16-trnQ CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1770–1777 1.000 81.4
rps16-trnQ_p2 rps16-trnQ GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1768–1775 1.000 81.4
rps16-trnQ_p3 rps16-trnQ AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1776–1783 1.000 81.3
rps16-trnQ_p4 rps16-trnQ GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1777–1784 1.000 81.3
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1752–1759 1.000 80.5
trnS-trnG_p1 trnS-trnG AATCTGCCGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 940–963 1.000 68.8
trnS-trnG_p2 trnS-trnG CAATCTGCCGCTTTAGTCCA AACCGAAAGACCCCTTAACT 941–964 1.000 68.8
trnS-trnG_p3 trnS-trnG CGGAGAGAGAGGGATTCGAA AACCGAAAGACCCCTTAACT 994–1017 1.000 68.1
trnS-trnG_p4 trnS-trnG GCTTTAGTCCACTCAGCCAT AACCGAAAGACCCCTTAACT 932–955 1.000 67.6
trnS-trnG_p5 trnS-trnG AATCTGCCGCTTTAGTCCAC AAACCGAAAGACCCCTTAACT 941–964 1.000 66.9
trnR-atpA_p1 trnR-atpA GGAATGAAAAGCGTCCATTGT TGCTACCAAGACATTCACCG 294–295 1.000 68.3
trnR-atpA_p2 trnR-atpA GGTTCAAATCCTATTGGACGC TGCTACCAAGACATTCACCG 234–235 1.000 67.1
trnR-atpA_p3 trnR-atpA GGAATGAAAAGCGTCCATTGT GCTACCAAGACATTCACCGA 293–294 1.000 66.0
trnR-atpA_p4 trnR-atpA GGAATGAAAAGCGTCCATTGT TACCAAGACATTCACCGAGC 291–292 1.000 66.0
trnR-atpA_p5 trnR-atpA AGGAATGAAAAGCGTCCATTG TGCTACCAAGACATTCACCG 296 0.500 44.4
trnD-trnY_p1 trnD-trnY GTGCTCTGACCGATTGAACT CTGGTTCAAATCCAGCTCGG 337–346 1.000 76.7
trnD-trnY_p2 trnD-trnY GGATCCTAGTTCGGGACTGA CTGGTTCAAATCCAGCTCGG 394–403 1.000 76.2
trnD-trnY_p3 trnD-trnY GTGCTCTGACCGATTGAACT TCTACGCTGGTTCAAATCCA 343–352 1.000 74.8
trnD-trnY_p4 trnD-trnY GGATCCTAGTTCGGGACTGA TCTACGCTGGTTCAAATCCA 400–409 1.000 74.3
trnD-trnY_p5 trnD-trnY ATCGGATCCTAGTTCGGGAC CTGGTTCAAATCCAGCTCGG 397–406 1.000 73.7
psbC-trnS_p1 psbC-trnS TCGATCGTGATTTGGAACCC GAGAGATGGCTGAGTGGTTG 276 1.000 82.6
psbC-trnS_p2 psbC-trnS TCGATCGTGATTTGGAACCC GGCTGAGTGGTTGATAGCTC 269 1.000 82.4
psbC-trnS_p3 psbC-trnS AACCCGTTCTTTCCATGACC GAGAGATGGCTGAGTGGTTG 261 1.000 82.1
psbC-trnS_p4 psbC-trnS TGGAACCCGTTCTTTCCATG GAGAGATGGCTGAGTGGTTG 264 1.000 82.1
psbC-trnS_p5 psbC-trnS TCGATCGTGATTTGGAACCC AGCTCTGGTCTTGAAAACCG 254 1.000 82.1

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
Astelia alpina PV409670.1 158401 View on NCBI ↗
Astelia pumila MH752980.1 158219 View on NCBI ↗