Markers + reference

Syzygium

176 species · Myrtaceae · Myrtales

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Species 176
Genome length 158–160 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

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 460 0.0244 1.00 79.9 yes View details
trnK-UUU-rps16 LSC 569 0.0096 1.00 59.1 yes View details
trnS-GCU-trnG-UCC LSC 794 0.0098 1.00 63.9 yes View details
psbZ-trnG-GCC LSC 545 0.0188 1.00 71.8 yes View details
trnF-GAA-ndhJ LSC 754 0.0112 1.00 59.0 yes View details
rpl22 LSC 483 0.0115 1.00 50.5 yes View details
ndhF SSC 2238 0.0073 1.00 62.3 yes View details
ndhF-rpl32 SSC 938 0.0162 1.00 67.1 yes View details
rpl32-trnL-UAG SSC 735 0.0128 1.00 72.1 yes View details
ycf1 SSC 5625 0.0090 1.00 72.0 yes View details
ndhA SSC 2170 0.0059 1.00 74.2 yes View details
petA-psbJ LSC 1020 0.0095 1.00 73.5 yes View details
petN-psbM LSC 970 0.0081 1.00 73.1 yes View details
rbcL-accD LSC 712 0.0056 0.99 69.6 yes View details
psbK-psbI LSC 386 0.0082 1.00 68.8 yes View details
trnT-UGU-trnL-UAA LSC 663 0.0087 1.00 68.6 yes View details
trnD-GUC-trnY-GUA LSC 457 0.0132 0.96 68.5 yes View details
psbM-trnD-GUC LSC 1096 0.0053 1.00 68.0 yes View details
psaA-pafI LSC 764 0.0085 0.97 67.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 351–597 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 348–594 0.989 90.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 362–608 0.989 90.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 361–607 0.989 89.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 363–609 0.983 89.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 704–950 0.994 91.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 705–951 0.994 91.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 566–812 0.989 91.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCATGGAAAAGCCCTTCCC AAAAAGGCGCTCAACCTACA 853–1101 0.994 91.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGTGTATCGTGCGGGAATC 1221–1481 0.983 90.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 507–549 1.000 84.1
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 504–546 1.000 82.1
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 505–547 1.000 82.1
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 506–548 1.000 82.1
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTACG 508–550 1.000 81.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCCCACTTTTACCACT 785–948 1.000 76.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACGAATCCCACTTTTACCACT 786–949 1.000 74.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AACGGAAAGAGAGGGATTCG ACGAATCCCACTTTTACCACT 786–949 1.000 72.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCCCACTTTTACCAC 785–948 1.000 72.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC ACGAATCCCACTTTTACCACT 721–879 0.943 70.4
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTCTTCATTCT 1070–1145 1.000 76.2
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTCTTCATTCT 1076–1151 1.000 74.7
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTCTTCATTCT 1016–1091 0.994 73.2
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTCTTCATTC 1070–1145 1.000 71.8
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTCTTCATTC 1076–1151 1.000 70.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 814–1246 1.000 65.0
psbM-trnD-GUC_p2 psbM-trnD-GUC ACTAGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 817–1249 1.000 63.6
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGAACTAGAATGAAGAGTGCAG TCAATTGGTTAGAGCACCGC 821–1253 1.000 62.9
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAAGAGTGCA TCAATTGGTTAGAGCACCGC 821–1253 1.000 62.3
psbM-trnD-GUC_p5 psbM-trnD-GUC GGAACTAGAATGAAGAGTGCAGT TCAATTGGTTAGAGCACCGC 820–1252 1.000 62.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (176)

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

Species Accession Length (bp) Link
Syzygium acre PX130303.1 159143 View on NCBI ↗
Syzygium acuminatissimum NC_053640.1 159352 View on NCBI ↗
Syzygium adelphicum NC_084350.1 159050 View on NCBI ↗
Syzygium alatum NC_084380.1 158092 View on NCBI ↗
Syzygium alliiligneum PX130304.1 159004 View on NCBI ↗
Syzygium alubo PX130306.1 158706 View on NCBI ↗
Syzygium amphoraecarpus PX130307.1 158661 View on NCBI ↗
Syzygium amplum PX130305.1 159100 View on NCBI ↗
Syzygium ampullarium PX130308.1 158903 View on NCBI ↗
Syzygium angophoroides PX108616.1 158949 View on NCBI ↗
Syzygium apodophyllum PX108618.1 159982 View on NCBI ↗
Syzygium aqueum PX396002.1 159134 View on NCBI ↗
Syzygium argyropedicum PX108619.1 159023 View on NCBI ↗
Syzygium armstrongii PX108620.1 158540 View on NCBI ↗
Syzygium aromaticum NC_047249.1 159370 View on NCBI ↗
Syzygium attenuatum PX396004.1 159804 View on NCBI ↗
Syzygium australe NC_082025.1 159111 View on NCBI ↗
Syzygium austrocaledonicum PX108621.1 158662 View on NCBI ↗
Syzygium baladense PX130309.1 159030 View on NCBI ↗
Syzygium balgooyi PX396009.1 158899 View on NCBI ↗
Syzygium bamagense NC_086714.1 159175 View on NCBI ↗
Syzygium bankense PX396003.1 159510 View on NCBI ↗
Syzygium banksii PX108622.1 159034 View on NCBI ↗
Syzygium barringtonioides PX130310.1 159076 View on NCBI ↗
Syzygium batadamba PX130311.1 158642 View on NCBI ↗
Syzygium biniflorum PX396010.1 159228 View on NCBI ↗
Syzygium boonjee PX125821.1 159023 View on NCBI ↗
Syzygium branderhorstii NC_084381.1 159112 View on NCBI ↗
Syzygium buettnerianum NC_084382.1 159101 View on NCBI ↗
Syzygium bullatum PX125822.1 158652 View on NCBI ↗
Syzygium bungadinnia PX125823.1 159032 View on NCBI ↗
Syzygium buxifolium NC_084371.1 158581 View on NCBI ↗
Syzygium canicortex PX125824.1 158926 View on NCBI ↗
Syzygium caryophyllatum NC_087814.1 158829 View on NCBI ↗
Syzygium cerasiforme PX130312.1 158998 View on NCBI ↗
Syzygium chloranthum PX125825.1 158582 View on NCBI ↗
Syzygium cinereum NC_086715.1 158399 View on NCBI ↗
Syzygium cladopterum NC_084383.1 159218 View on NCBI ↗
Syzygium claviflorum NC_087811.1 158399 View on NCBI ↗
Syzygium cleistocalyx PX130313.1 158771 View on NCBI ↗
Syzygium conglomeratum PX130314.1 159184 View on NCBI ↗
Syzygium cordatum PX130315.1 158537 View on NCBI ↗
Syzygium cormiflorum PX130316.1 159041 View on NCBI ↗
Syzygium creaghii PX125826.1 158994 View on NCBI ↗
Syzygium cryptophlebium PX125827.1 159577 View on NCBI ↗
Syzygium cumini NC_053327.1 159996 View on NCBI ↗
Syzygium dansiei PX125828.1 159267 View on NCBI ↗
Syzygium dasyphyllum PX396012.1 159143 View on NCBI ↗
Syzygium divaricatum PX125829.1 159222 View on NCBI ↗
Syzygium duthieanum PX125830.1 159089 View on NCBI ↗
Syzygium dyerianum PX396013.1 159056 View on NCBI ↗
Syzygium effusum NC_084386.1 159064 View on NCBI ↗
Syzygium endophloium PX170161.1 158917 View on NCBI ↗
Syzygium erythrocalyx PX170162.1 159060 View on NCBI ↗
Syzygium erythrodoxum PX130317.1 159081 View on NCBI ↗
Syzygium eucalyptoides PX130318.1 158923 View on NCBI ↗
Syzygium fibrosum PX170163.1 159135 View on NCBI ↗
Syzygium filiforme PX396015.1 158794 View on NCBI ↗
Syzygium floribundum PX170165.1 159149 View on NCBI ↗
Syzygium fluviatile NC_082026.1 158550 View on NCBI ↗
Syzygium forrestii NC_044106.1 159996 View on NCBI ↗
Syzygium forte PX396005.1 159123 View on NCBI ↗
Syzygium fratris PX130320.1 158675 View on NCBI ↗
Syzygium fullagarii PX170166.1 159068 View on NCBI ↗
Syzygium garcinioides NC_084387.1 158825 View on NCBI ↗
Syzygium gilletii PX130321.1 158430 View on NCBI ↗
Syzygium glaucum PX130322.1 159141 View on NCBI ↗
Syzygium glenum PX170167.1 157830 View on NCBI ↗
Syzygium glomeratum PX130323.1 158469 View on NCBI ↗
Syzygium grande PX130324.1 159070 View on NCBI ↗
Syzygium graveolens PX170168.1 158786 View on NCBI ↗
Syzygium griffithii PX396016.1 159034 View on NCBI ↗
Syzygium grijsii NC_065156.1 158591 View on NCBI ↗
Syzygium guehoi PX130325.1 158412 View on NCBI ↗
Syzygium guillauminii PX130326.1 159161 View on NCBI ↗
Syzygium guineense PX130327.1 158530 View on NCBI ↗
Syzygium gustavioides PX170169.1 158831 View on NCBI ↗
Syzygium hedraiophyllum PX170170.1 159203 View on NCBI ↗
Syzygium hemilamprum PX170171.1 157985 View on NCBI ↗
Syzygium hirtum PX130328.1 159102 View on NCBI ↗
Syzygium houttuynii PX130329.1 158861 View on NCBI ↗
Syzygium imperiale PX130330.1 159376 View on NCBI ↗
Syzygium incarnatum PX130331.1 159057 View on NCBI ↗
Syzygium jambos NC_052728.1 158541 View on NCBI ↗
Syzygium jiewhoei NC_084388.1 159271 View on NCBI ↗
Syzygium johnsonii PX125900.1 159211 View on NCBI ↗
Syzygium kalahiense PX130332.1 159062 View on NCBI ↗
Syzygium kanneliyense PX130333.1 158630 View on NCBI ↗
Syzygium kunstleri PX130334.1 158964 View on NCBI ↗
Syzygium kuranda PX125901.1 158744 View on NCBI ↗
Syzygium latifolium PX125902.1 158503 View on NCBI ↗
Syzygium leptostemon PX130335.1 158964 View on NCBI ↗
Syzygium linocieroideum PX130336.1 158937 View on NCBI ↗
Syzygium longiflorum PX396017.1 158227 View on NCBI ↗
Syzygium longipes PX125903.1 159129 View on NCBI ↗
Syzygium lunduense PX396018.1 158873 View on NCBI ↗
Syzygium macilwraithianum PX125904.1 159184 View on NCBI ↗
Syzygium mackinnonianum PX125905.1 159221 View on NCBI ↗
Syzygium malaccense NC_052867.1 158954 View on NCBI ↗
Syzygium mamillatum PX130338.1 158326 View on NCBI ↗
Syzygium maraca PX130339.1 158999 View on NCBI ↗
Syzygium mauritianum PX130340.1 158380 View on NCBI ↗
Syzygium medium PX130341.1 158996 View on NCBI ↗
Syzygium megacarpum NC_082027.1 158956 View on NCBI ↗
Syzygium monospermum PX130342.1 159081 View on NCBI ↗
Syzygium montis-adam PX130343.1 159246 View on NCBI ↗
Syzygium mouanum PX130344.1 159046 View on NCBI ↗
Syzygium mulgraveanum PX125906.1 159041 View on NCBI ↗
Syzygium multibracteolatum PX130345.1 159473 View on NCBI ↗
Syzygium neesianum PX130346.1 158323 View on NCBI ↗
Syzygium neocaledonicum PX130347.1 159119 View on NCBI ↗
Syzygium neolaurifolium PX130348.1 158553 View on NCBI ↗
Syzygium nervosum NC_053907.1 158979 View on NCBI ↗
Syzygium ngadimanianum PX125907.1 157956 View on NCBI ↗
Syzygium ngoyense PX125908.1 158992 View on NCBI ↗
Syzygium oblanceolatum PX130349.1 158860 View on NCBI ↗
Syzygium odoratum NC_059005.1 159352 View on NCBI ↗
Syzygium oleosum PX130350.1 158980 View on NCBI ↗
Syzygium owariense PX130351.1 158537 View on NCBI ↗
Syzygium pachycladum NC_084389.1 158853 View on NCBI ↗
Syzygium pachyphyllum PX396007.1 159032 View on NCBI ↗
Syzygium paniculatum NC_087812.1 159121 View on NCBI ↗
Syzygium paniense PX130352.1 159226 View on NCBI ↗
Syzygium papyraceum PX125909.1 158724 View on NCBI ↗
Syzygium paradoxum PX130353.1 158994 View on NCBI ↗
Syzygium pendens PX125910.1 158263 View on NCBI ↗
Syzygium perspicuinervium PX130354.1 159076 View on NCBI ↗
Syzygium polypetaloideum PX130356.1 158420 View on NCBI ↗
Syzygium pringlei PX130357.1 159152 View on NCBI ↗
Syzygium pseudofastigiatum PX125911.1 159140 View on NCBI ↗
Syzygium pseudoformosum PX130358.1 158994 View on NCBI ↗
Syzygium puberulum NC_087813.1 159098 View on NCBI ↗
Syzygium pustulatum PX125912.1 158996 View on NCBI ↗
Syzygium pycnanthum PX108613.1 158955 View on NCBI ↗
Syzygium pyrifolium PX130360.1 158173 View on NCBI ↗
Syzygium racemosum PX130361.1 159109 View on NCBI ↗
Syzygium rejangense PX130362.1 158860 View on NCBI ↗
Syzygium resa PX125913.1 157999 View on NCBI ↗
Syzygium ridleyi PX125914.1 158250 View on NCBI ↗
Syzygium roemeri NC_084390.1 159035 View on NCBI ↗
Syzygium rotundifolium PX130364.1 158671 View on NCBI ↗
Syzygium rubrimolle PX125915.1 158745 View on NCBI ↗
Syzygium rugosum PX130365.1 159591 View on NCBI ↗
Syzygium saliciforme NC_084391.1 159139 View on NCBI ↗
Syzygium samarangense NC_060657.1 159109 View on NCBI ↗
Syzygium sarmentosum PX130367.1 159106 View on NCBI ↗
Syzygium sayeri NC_084392.1 158834 View on NCBI ↗
Syzygium scortechinii PX396019.1 159035 View on NCBI ↗
Syzygium sharoniae PX130369.1 159069 View on NCBI ↗
Syzygium smithii PX108614.1 158462 View on NCBI ↗
Syzygium subcrenatum PX130371.1 158114 View on NCBI ↗
Syzygium subdecussatum PX125916.1 158168 View on NCBI ↗
Syzygium suberosum NC_084393.1 159308 View on NCBI ↗
Syzygium suborbiculare PX125917.1 158888 View on NCBI ↗
Syzygium syzygioides PX396020.1 158106 View on NCBI ↗
Syzygium taeniatum NC_084394.1 158939 View on NCBI ↗
Syzygium tawahense PX130372.1 159017 View on NCBI ↗
Syzygium tetragonum PX396021.1 159035 View on NCBI ↗
Syzygium tierneyanum NC_084395.1 159117 View on NCBI ↗
Syzygium toninense PX130374.1 159070 View on NCBI ↗
Syzygium trachyanthum PX130375.1 159152 View on NCBI ↗
Syzygium trachyphloium PX125918.1 159153 View on NCBI ↗
Syzygium tripetalum PX130376.1 158927 View on NCBI ↗
Syzygium tsoongii NC_082028.1 159371 View on NCBI ↗
Syzygium tympananthum NC_084396.1 159134 View on NCBI ↗
Syzygium unipunctatum PX396024.1 159199 View on NCBI ↗
Syzygium urceolatum PX125919.1 159199 View on NCBI ↗
Syzygium velarum PX130299.1 158952 View on NCBI ↗
Syzygium venosum PX130300.1 158414 View on NCBI ↗
Syzygium versteegii NC_084397.1 158948 View on NCBI ↗
Syzygium viriosum PX130378.1 158531 View on NCBI ↗
Syzygium wagapense PX130379.1 158584 View on NCBI ↗
Syzygium wesa PX130301.1 158393 View on NCBI ↗
Syzygium wilsonii PX396023.1 159002 View on NCBI ↗
Syzygium xerampelinum PX130302.1 159127 View on NCBI ↗
Syzygium zeylanicum PX130380.1 159473 View on NCBI ↗