Markers + reference

Aeonium

11 species · Crassulaceae · Saxifragales

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Species 11
Genome length 151–151 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0002 1.00 30.1 yes View details
rpoB-trnC-GCA LSC 1093 0.0056 0.99 65.5 yes View details
trnC-GCA-petN LSC 795 0.0066 1.00 56.3 yes View details
petL-petG LSC 174 0.0138 1.00 44.3 yes View details
ycf1 IRb 1140 0.0024 1.00 35.5 no View details
ndhF-rpl32 SSC 576 0.0094 0.97 55.3 yes View details
rpl32-trnL-UAG SSC 481 0.0106 1.00 49.4 yes View details
ndhI SSC 504 0.0025 1.00 28.7 yes View details
rps15 SSC 279 0.0064 1.00 29.7 yes View details
ycf1 SSC 5160 0.0071 1.00 44.1 yes View details
trnH-GUG-psbA LSC 252 0.0229 1.00 64.3 yes View details
trnG-GCC-trnR-UCU LSC 201 0.0167 1.00 62.6 yes View details
psaA-ycf3 LSC 649 0.0072 1.00 62.5 yes View details
ndhG-ndhI SSC 258 0.0168 1.00 60.4 yes View details
psbC LSC 1422 0.0043 1.00 57.5 yes View details
trnK-UUU-rps16 LSC 639 0.0037 1.00 57.4 yes View details
psaJ-rpl33 LSC 393 0.0069 1.00 54.8 yes View details
ndhA SSC 2095 0.0037 1.00 54.7 yes View details
trnE-UUC-trnT-GGU LSC 753 0.0041 1.00 53.5 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 GTAACGCTCACAACTTCCCT 329–344 1.000 83.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GTAACGCTCACAACTTCCCT 343–358 1.000 83.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GTAACGCTCACAACTTCCCT 342–357 1.000 83.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GTAACGCTCACAACTTCCCT 344–359 1.000 83.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGAACGTAACGCTCACAACT 334–349 1.000 82.9
psbA_p1 psbA ACTCATATAGACTAATACCGAAGT GCTTGGGAGTCCCTGATGAT 1128 1.000 40.1
psbA_p2 psbA ACTCATATAGACTAATACCGAAGT TTGCTTGGGAGTCCCTGAT 1130 1.000 40.1
psbA_p3 psbA ACTCATATAGACTAATACCGAAGT CTTGGGAGTCCCTGATGATT 1127 1.000 40.1
psbA_p4 psbA AACTCATATAGACTAATACCGAAGT GCTTGGGAGTCCCTGATGAT 1129 1.000 40.1
psbA_p5 psbA ACTCATATAGACTAATACCGAAGTT GCTTGGGAGTCCCTGATGAT 1128 1.000 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTCGTCCAAACTCTACCGAC TTGAAAAGGGGGCTAAACCG 835–855 1.000 80.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA TTGAAAAGGGGGCTAAACCG 807–827 1.000 80.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC TTGAAAAGGGGGCTAAACCG 808–828 1.000 80.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGGTACAGACGAATCCCTTG TTGAAAAGGGGGCTAAACCG 816–836 1.000 80.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGACGAATCCCTTGCTTCA TTGAAAAGGGGGCTAAACCG 811–831 1.000 80.4
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGGTTTAGAAGACCTATGTCCT 281–303 1.000 49.8
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA AGGTTTAGAAGACCTATGTCCT 308–330 1.000 49.7
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA AGAAGACCTATGTCCTATCCA 302–324 1.000 49.6
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGAAGACCTATGTCCTATCCA 275–297 1.000 49.6
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA ACCAAAGGTTTAGAAGACCTATGT 313–335 1.000 49.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTGGACCTTCCCTCATTTCC ATCGGGCGAACATAATACGG 1143–1252 1.000 83.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTGGACCTTCCCTCATTTCC CCGGATTTGAACTGGGGAAA 1092–1201 1.000 83.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG ATCGGGCGAACATAATACGG 1215–1324 1.000 83.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG CCGGATTTGAACTGGGGAAA 1164–1273 1.000 83.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCTTCCGTCAAGCCATGA ATCGGGCGAACATAATACGG 1214–1323 1.000 83.0
trnC-GCA-petN_p1 trnC-GCA-petN GTTTCTCTCATTTTGGCGGC TTAAAGCAGCCCAAGCAAGA 893–922 1.000 83.8
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 837–866 1.000 83.6
trnC-GCA-petN_p3 trnC-GCA-petN TTCTCTCATTTTGGCGGCAT TTAAAGCAGCCCAAGCAAGA 891–920 1.000 82.7
trnC-GCA-petN_p4 trnC-GCA-petN GTTTCTCTCATTTTGGCGGC CAGCCCAAGCAAGACTTACT 913–916 0.909 76.4
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 857–860 0.909 75.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Aeonium arboreum NC_053947.1 150986 View on NCBI ↗
Aeonium aureum NC_085684.1 150949 View on NCBI ↗
Aeonium balsamiferum OM993519.1 150963 View on NCBI ↗
Aeonium decorum OM993520.1 150990 View on NCBI ↗
Aeonium diplocyclum OM993521.1 150783 View on NCBI ↗
Aeonium dodrantale OM993522.1 150984 View on NCBI ↗
Aeonium hybrid cultivar NC_085680.1 151034 View on NCBI ↗
Aeonium nobile OM993523.1 151030 View on NCBI ↗
Aeonium saundersii OM993524.1 150883 View on NCBI ↗
Aeonium tabuliforme OM993525.1 150896 View on NCBI ↗
Aeonium undulatum OM993526.1 150918 View on NCBI ↗