Markers + reference

Prunus

120 species · Rosaceae · Rosales

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Species 120
Genome length 157–159 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

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbI-trnS-GCU LSC 137 0.0290 1.00 63.0 yes View details
trnS-GCU-trnG-UCC LSC 364 0.0238 1.00 57.8 yes View details
trnR-UCU-atpA LSC 432 0.0259 1.00 67.1 yes View details
petN-psbM LSC 1215 0.0145 0.99 56.9 yes View details
ycf3 LSC 1994 0.0063 1.00 45.5 yes View details
trnL-UAA-trnF-GAA LSC 385 0.0176 1.00 56.7 yes View details
ndhC-trnV-UAC LSC 623 0.0284 0.96 65.1 yes View details
psaJ-rpl33 LSC 461 0.0127 1.00 60.6 yes View details
ndhF SSC 2244 0.0093 0.99 51.2 yes View details
ndhF-rpl32 SSC 901 0.0162 1.00 60.9 yes View details
rpl32-trnL-UAG SSC 1424 0.0217 0.99 64.3 yes View details
trnT-GGU-psbD LSC 1218 0.0119 1.00 68.5 yes View details
rpl2-trnH-GUG IRa 317 0.0376 0.85 67.2 no View details
rps16-trnQ-UUG LSC 685 0.0128 0.96 64.6 yes View details
trnT-UGU-trnL-UAA LSC 942 0.0138 0.98 63.5 yes View details
psbE-petL LSC 1281 0.0116 1.00 62.3 yes View details
rpl33-rps18 LSC 172 0.0397 1.00 61.1 yes View details
trnC-GCA-petN LSC 890 0.0095 1.00 60.8 yes View details
trnG-UCC-trnR-UCU LSC 120 0.0260 1.00 60.6 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 566–975 1.000 91.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 564–973 1.000 91.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 548–957 1.000 90.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 559–968 1.000 89.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GTGTCGACTAGAAATGGGGC 628–1037 1.000 89.0
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 228–246 1.000 83.6
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 229–247 1.000 83.5
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA CAATTGGGAGGAGAGATGGC 252–270 1.000 83.1
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA AATTGGGAGGAGAGATGGCT 251–269 1.000 82.6
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTTTTCGTACCGAGGGTTCG 191–209 1.000 82.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 424–768 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 423–767 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 427–771 1.000 62.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 426–770 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 425–769 1.000 62.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 170–304 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 173–307 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 176–310 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 179–313 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 174–308 1.000 72.9
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 383–688 0.967 75.1
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 382–687 0.967 75.1
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 322–627 0.967 74.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 357–662 0.967 71.3
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 383–688 0.967 71.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCGAGATTTACT 763–1024 1.000 91.1
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCGAGATTTACT 781–1042 1.000 88.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 823–1084 1.000 88.5
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 841–1102 1.000 86.3
trnC-GCA-petN_p5 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC CAGCCCAAGCGAGATTTACT 758–1019 1.000 85.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (120)

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

Species Accession Length (bp) Link
Prunus apetala NC_053693.1 157987 View on NCBI ↗
Prunus arborea var. montana PP595882.1 159289 View on NCBI ↗
Prunus armeniaca NC_043901.1 158071 View on NCBI ↗
Prunus armeniaca var. armeniaca PP595825.1 157770 View on NCBI ↗
Prunus avium NC_044701.1 157886 View on NCBI ↗
Prunus brachypoda NC_068700.1 158884 View on NCBI ↗
Prunus campanulata NC_044123.1 157938 View on NCBI ↗
Prunus caroliniana PP595840.1 158778 View on NCBI ↗
Prunus caudata OR687395.1 157959 View on NCBI ↗
Prunus cerasifera NC_068605.1 157952 View on NCBI ↗
Prunus cerasifera var. divaricata PV138221.1 157886 View on NCBI ↗
Prunus cerasoides NC_035891.1 157685 View on NCBI ↗
Prunus cerasoides var. rubea OR885319.1 157556 View on NCBI ↗
Prunus cerasus NC_066420.1 158116 View on NCBI ↗
Prunus cerasus x Prunus canescens MW477433.1 158192 View on NCBI ↗
Prunus clarofolia NC_066415.1 157798 View on NCBI ↗
Prunus conadenia NC_072946.1 158058 View on NCBI ↗
Prunus conradinae NC_066417.1 157751 View on NCBI ↗
Prunus crataegifolia NC_066416.1 157692 View on NCBI ↗
Prunus cyclamina PP595829.1 157867 View on NCBI ↗
Prunus davidiana NC_039735.1 158055 View on NCBI ↗
Prunus davidiana var. potaninii MT019558.1 158361 View on NCBI ↗
Prunus dictyoneura NC_051894.1 158084 View on NCBI ↗
Prunus discadenia NC_056362.1 157915 View on NCBI ↗
Prunus discoidea NC_066413.1 157827 View on NCBI ↗
Prunus dolichadenia NC_066424.1 157788 View on NCBI ↗
Prunus domestica NC_050959.1 157395 View on NCBI ↗
Prunus duclouxii NC_064107.1 157914 View on NCBI ↗
Prunus dulcis NC_034696.1 157723 View on NCBI ↗
Prunus emarginata OR687386.1 158028 View on NCBI ↗
Prunus fasciculata NC_054253.1 157986 View on NCBI ↗
Prunus ferganensis PP595847.1 157790 View on NCBI ↗
Prunus fruticosa NC_054254.1 158217 View on NCBI ↗
Prunus fujianensis NC_059022.1 158972 View on NCBI ↗
Prunus glandulosa PP595831.1 158079 View on NCBI ↗
Prunus gongshanensis NC_059024.1 158564 View on NCBI ↗
Prunus grisea PP595870.1 156648 View on NCBI ↗
Prunus henryi OR687420.1 157958 View on NCBI ↗
Prunus himalaica NC_059025.1 158524 View on NCBI ↗
Prunus himalayana PP595856.1 158841 View on NCBI ↗
Prunus humilis NC_035880.1 158012 View on NCBI ↗
Prunus hypoleuca NC_059027.1 158873 View on NCBI ↗
Prunus hypoxantha NC_053881.1 158740 View on NCBI ↗
Prunus incisa OR687429.1 157943 View on NCBI ↗
Prunus incisoserrata NC_059023.1 158768 View on NCBI ↗
Prunus itosakura AP041288.1 157813 View on NCBI ↗
Prunus jamasakura AP041397.1 157897 View on NCBI ↗
Prunus japonica NC_053703.1 158080 View on NCBI ↗
Prunus japonica var. nakaii PP595868.1 158078 View on NCBI ↗
Prunus jenkinsii NC_068604.1 158407 View on NCBI ↗
Prunus jingningensis NC_053689.1 157913 View on NCBI ↗
Prunus kansuensis NC_023956.1 157736 View on NCBI ↗
Prunus lannesiana MT576877.1 157780 View on NCBI ↗
Prunus laurocerasus NC_068706.1 158620 View on NCBI ↗
Prunus leveilleana OR687431.1 157917 View on NCBI ↗
Prunus maackii NC_064105.1 158015 View on NCBI ↗
Prunus mahaleb NC_066421.1 157493 View on NCBI ↗
Prunus mahaleb var. mahaleb PP541872.1 157759 View on NCBI ↗
Prunus mandshurica NC_068703.1 158089 View on NCBI ↗
Prunus matuurae NC_045230.1 157928 View on NCBI ↗
Prunus maximowiczii NC_026981.1 157852 View on NCBI ↗
Prunus mira NC_040125.1 158153 View on NCBI ↗
Prunus mongolica NC_037849.1 158039 View on NCBI ↗
Prunus mugus NC_072947.1 157926 View on NCBI ↗
Prunus mume NC_023798.1 157712 View on NCBI ↗
Prunus mume var. cernua MK881169.1 158168 View on NCBI ↗
Prunus napaulensis NC_068702.1 158864 View on NCBI ↗
Prunus nipponica OR687404.1 157919 View on NCBI ↗
Prunus obtusata NC_068701.1 158882 View on NCBI ↗
Prunus padus NC_026982.1 158955 View on NCBI ↗
Prunus patentipila OR687398.1 158004 View on NCBI ↗
Prunus pedunculata NC_037850.1 157851 View on NCBI ↗
Prunus pensylvanica OR687388.1 157973 View on NCBI ↗
Prunus persica NC_014697.1 157790 View on NCBI ↗
Prunus phaeosticta NC_065751.1 158752 View on NCBI ↗
Prunus pleiocerasus NC_066411.1 157754 View on NCBI ↗
Prunus polytricha NC_072948.1 157989 View on NCBI ↗
Prunus pseudocerasus NC_030599.1 157834 View on NCBI ↗
Prunus pusilliflora NC_066414.1 157599 View on NCBI ↗
Prunus rufa NC_048528.1 157723 View on NCBI ↗
Prunus salicina NC_047442.1 157916 View on NCBI ↗
Prunus salicina x Prunus armeniaca NC_060490.1 157916 View on NCBI ↗
Prunus sargentii OR687432.1 157872 View on NCBI ↗
Prunus sargentii var. verecunda NC_053694.1 157917 View on NCBI ↗
Prunus schneideriana NC_064106.1 157923 View on NCBI ↗
Prunus serotina NC_036133.1 158778 View on NCBI ↗
Prunus serrula NC_072949.1 157973 View on NCBI ↗
Prunus serrulata NC_066418.1 157816 View on NCBI ↗
Prunus setulosa OR687394.1 157821 View on NCBI ↗
Prunus sibirica NC_068704.1 158172 View on NCBI ↗
Prunus simonii MW406463.1 157924 View on NCBI ↗
Prunus speciosa NC_043921.1 157916 View on NCBI ↗
Prunus spinosa subsp. spinosa PP541873.1 157583 View on NCBI ↗
Prunus stipulacea NC_068705.1 157914 View on NCBI ↗
Prunus subhirtella PP595835.1 157866 View on NCBI ↗
Prunus subhirtella var. ascendens OR687415.1 157932 View on NCBI ↗
Prunus subhirtella var. pendula OR687416.1 157830 View on NCBI ↗
Prunus subhirtella var. subhirtella KP760074.1 157817 View on NCBI ↗
Prunus szechuanica NC_066423.1 157773 View on NCBI ↗
Prunus takasagomontana NC_061417.1 157946 View on NCBI ↗
Prunus takesimensis NC_039379.1 157948 View on NCBI ↗
Prunus tangutica MZ145044.1 158131 View on NCBI ↗
Prunus tatsienensis NC_066422.1 157721 View on NCBI ↗
Prunus tianshanica NC_066419.1 157577 View on NCBI ↗
Prunus tomentosa NC_036394.1 158356 View on NCBI ↗
Prunus tongmuensis ON422320.1 157926 View on NCBI ↗
Prunus topengii NC_068683.1 159289 View on NCBI ↗
Prunus transarisanensis OR687433.1 158006 View on NCBI ↗
Prunus trichantha NC_064108.1 157758 View on NCBI ↗
Prunus trichostoma NC_066412.1 157743 View on NCBI ↗
Prunus triloba NC_046742.1 158455 View on NCBI ↗
Prunus ussuriensis NC_065730.1 157785 View on NCBI ↗
Prunus virginiana NC_068699.1 158972 View on NCBI ↗
Prunus wilsonii NC_059026.1 158720 View on NCBI ↗
Prunus x cistena NC_081501.1 157935 View on NCBI ↗
Prunus yedoensis NC_026980.1 157859 View on NCBI ↗
Prunus yunnanensis NC_072950.1 157928 View on NCBI ↗
Prunus zhengheensis NC_062793.1 158106 View on NCBI ↗
Prunus zhuxiensis PV208095.1 157828 View on NCBI ↗
Prunus zippeliana NC_043926.1 158940 View on NCBI ↗