Markers + reference

Allium

227 species · Amaryllidaceae · Asparagales

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Species 227
Genome length 150–155 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 564 0.0486 0.98 76.2 yes View details
rps16-trnQ_UUG LSC 1454 0.0429 0.79 74.4 yes View details
trnS_GCU-trnG_UCC LSC 1178 0.0464 0.94 75.7 yes View details
trnC_GCA-petN LSC 990 0.0400 0.96 76.4 yes View details
trnT_GGU-psbD LSC 1058 0.0426 1.00 76.0 yes View details
trnT_UGU-trnL_UAA LSC 1023 0.0405 0.97 77.2 yes View details
petA-psbJ LSC 1157 0.0445 0.98 77.3 yes View details
ycf1 IRb 1237 0.0147 0.98 57.8 no View details
ndhF SSC 2217 0.0256 0.99 67.7 yes View details
ndhF-rpl32 SSC 382 0.0560 0.97 77.2 yes View details
rpl32-trnL_UAG SSC 700 0.0727 0.99 81.4 yes View details
rps15-ycf1 SSC 362 0.0572 0.91 69.0 yes View details
ycf1 SSC 5223 0.0330 0.99 67.8 yes View details
psbM-trnD_GUC LSC 1079 0.0341 0.99 79.8 yes View details
psbE-petL LSC 987 0.0295 0.98 76.4 yes View details
ndhC-trnV_UAC LSC 445 0.0408 0.98 75.3 yes View details
rpoB-trnC_GCA LSC 1251 0.0358 0.96 74.6 yes View details
petN-psbM LSC 848 0.0358 0.99 73.5 yes View details
trnG_UCC-trnR_UCU LSC 131 0.0541 0.99 72.6 yes View details
atpH-atpI LSC 490 0.0246 0.98 72.6 yes View details
ccsA-ndhD SSC 218 0.0595 0.99 71.5 yes View details
rps16 LSC 1089 0.0352 1.00 71.3 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG ATTGATGTTCGATCCCGACG 752–923 0.938 88.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT ATTGATGTTCGATCCCGACG 748–919 0.938 87.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT ATTGATGTTCGATCCCGACG 749–920 0.938 87.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 ATCGCACTTAAAAGCCGAGT ATTGATGTTCGATCCCGACG 667–838 0.938 87.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GGTGCTCAACCTACAGGAAC 665–809 0.841 84.0
rps16_p1 rps16 CCTTTCAGGATCAGTCGTGG CCATAGGATAGAGGGGCGAA 1351–2048 0.863 85.9
rps16_p2 rps16 TCAGGATCAGTCGTGGTCTT CCATAGGATAGAGGGGCGAA 1347–2044 0.863 85.4
rps16_p3 rps16 TTCAGGATCAGTCGTGGTCT CCATAGGATAGAGGGGCGAA 1348–2045 0.863 85.4
rps16_p4 rps16 CCTTTCAGGATCAGTCGTGG AGCAACAGCAGCTCTTTGAT 2151–2540 0.445 68.9
rps16_p5 rps16 CCTTTCAGGATCAGTCGTGG ATTTCAGCAACAGCAGCTCT 2156–2545 0.401 67.2
rps16-trnQ_UUG_p1 rps16-trnQ_UUG TATGTCCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 351–1600 0.921 88.1
rps16-trnQ_UUG_p2 rps16-trnQ_UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 341–1590 0.943 88.0
rps16-trnQ_UUG_p3 rps16-trnQ_UUG TGGCGGATGTAAGAATCCAC GAGGTTCGAATCCTTCCGTC 577–1627 0.894 84.6
rps16-trnQ_UUG_p4 rps16-trnQ_UUG GGCGGATGTAAGAATCCACA GAGGTTCGAATCCTTCCGTC 576–1626 0.890 84.4
rps16-trnQ_UUG_p5 rps16-trnQ_UUG TATGTCCTTCAAGTCGCACG TTCGGAGGTTCGAATCCTTC 355–1604 0.921 83.4
trnS_GCU-trnG_UCC_p1 trnS_GCU-trnG_UCC GCTTTAGTCCACTCAGCCAT TGAACGAATCACACTTTTACCAC 754–1351 1.000 61.4
trnS_GCU-trnG_UCC_p2 trnS_GCU-trnG_UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 751–1348 1.000 60.4
trnS_GCU-trnG_UCC_p3 trnS_GCU-trnG_UCC AGTCCACTCAGCCATCTCTC TGAACGAATCACACTTTTACCAC 749–1346 0.996 60.4
trnS_GCU-trnG_UCC_p4 trnS_GCU-trnG_UCC GCTTTAGTCCACTCAGCCAT GAACGAATCACACTTTTACCACT 753–1350 1.000 59.4
trnS_GCU-trnG_UCC_p5 trnS_GCU-trnG_UCC AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 746–1343 0.996 59.4
trnG_UCC-trnR_UCU_p1 trnG_UCC-trnR_UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 183–246 1.000 75.3
trnG_UCC-trnR_UCU_p2 trnG_UCC-trnR_UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 186–249 1.000 75.1
trnG_UCC-trnR_UCU_p3 trnG_UCC-trnR_UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 189–252 1.000 74.7
trnG_UCC-trnR_UCU_p4 trnG_UCC-trnR_UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 192–255 1.000 74.5
trnG_UCC-trnR_UCU_p5 trnG_UCC-trnR_UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 187–250 1.000 72.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 351–603 0.982 90.5
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT ATAGGGGAATCCATGGAGGG 439–691 0.974 89.9
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 352–604 0.982 89.3
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 407–659 0.969 89.3
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 411–663 0.978 89.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (227)

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

Species Accession Length (bp) Link
Allium akaka subsp. bozgushense PQ305991.1 153238 View on NCBI ↗
Allium aladaghense PQ306013.1 152375 View on NCBI ↗
Allium alaicum PQ306043.1 152217 View on NCBI ↗
Allium alamutense PQ305992.1 153274 View on NCBI ↗
Allium alekii PQ306003.1 153418 View on NCBI ↗
Allium alexeianum PQ306027.1 152606 View on NCBI ↗
Allium altaicum NC_040972.1 153129 View on NCBI ↗
Allium altissimum PQ306039.1 151870 View on NCBI ↗
Allium amphibolum NC_084231.1 153248 View on NCBI ↗
Allium angulosum NC_077652.1 153473 View on NCBI ↗
Allium anisopodium NC_068830.1 153407 View on NCBI ↗
Allium arkitense PQ306044.1 152208 View on NCBI ↗
Allium aroides PQ306037.1 152052 View on NCBI ↗
Allium assadii PQ306017.1 152431 View on NCBI ↗
Allium atropurpureum PQ306006.1 153220 View on NCBI ↗
Allium atrosanguineum PZ015912.1 153521 View on NCBI ↗
Allium austrosibiricum NC_077653.1 153493 View on NCBI ↗
Allium backhousianum PQ306046.1 152256 View on NCBI ↗
Allium bakhtiaricum PQ306041.1 152207 View on NCBI ↗
Allium bidentatum NC_068829.1 153443 View on NCBI ↗
Allium bisotunense PQ305998.1 153208 View on NCBI ↗
Allium brachyscapum PQ306021.1 152598 View on NCBI ↗
Allium breviscapum PQ305994.1 153173 View on NCBI ↗
Allium bucharicum PQ306031.1 152644 View on NCBI ↗
Allium caeruleum NC_049099.1 153267 View on NCBI ↗
Allium caesium NC_068787.1 151533 View on NCBI ↗
Allium caespitosum NC_068828.1 153667 View on NCBI ↗
Allium cardiostemon PQ306004.1 153910 View on NCBI ↗
Allium caricoides NC_062825.1 153075 View on NCBI ↗
Allium caspium subsp. baissunense PQ306032.1 152522 View on NCBI ↗
Allium cepa NC_024813.1 153538 View on NCBI ↗
Allium cepa var. aggregatum OR605568.1 153736 View on NCBI ↗
Allium cernuum NC_057572.1 153750 View on NCBI ↗
Allium changduense NC_058218.1 153659 View on NCBI ↗
Allium chienchuanense NC_065779.1 153549 View on NCBI ↗
Allium chitralicum PQ306023.1 152555 View on NCBI ↗
Allium chlorotepalum PQ305995.1 153103 View on NCBI ↗
Allium chrysantherum PQ306008.1 153444 View on NCBI ↗
Allium chrysanthum NC_042154.1 153621 View on NCBI ↗
Allium chrysocephalum NC_042155.1 153710 View on NCBI ↗
Allium condensatum NC_068831.1 154124 View on NCBI ↗
Allium confragosum NC_068788.1 153119 View on NCBI ↗
Allium costatovaginatum PQ306047.1 151831 View on NCBI ↗
Allium cretaceum PZ015913.1 153076 View on NCBI ↗
Allium cristophii PQ306014.1 152318 View on NCBI ↗
Allium cupuliferum subsp. cupuliferum PQ306033.1 152360 View on NCBI ↗
Allium cyaneum NC_058219.1 152230 View on NCBI ↗
Allium cyathophorum NC_045912.1 154174 View on NCBI ↗
Allium cyathophorum var. farreri NC_045843.1 153111 View on NCBI ↗
Allium cyrilli PQ306007.1 153608 View on NCBI ↗
Allium darwasicum PQ306024.1 152586 View on NCBI ↗
Allium decoratum PQ306028.1 152577 View on NCBI ↗
Allium delicatulum MN648631.1 152984 View on NCBI ↗
Allium deneliae PQ306009.1 153423 View on NCBI ↗
Allium derderianum PQ305996.1 153164 View on NCBI ↗
Allium dodecadontum PQ306045.1 152257 View on NCBI ↗
Allium dumebuchum NC_077654.1 153507 View on NCBI ↗
Allium eduardii NC_068827.1 153497 View on NCBI ↗
Allium efeae PQ306010.1 153525 View on NCBI ↗
Allium egorovae PQ306001.1 153233 View on NCBI ↗
Allium elburzense PQ306019.1 152557 View on NCBI ↗
Allium ellisii PQ306016.1 152535 View on NCBI ↗
Allium esfahanicum PQ306018.1 152432 View on NCBI ↗
Allium fasciculatum NC_045845.1 152931 View on NCBI ↗
Allium ferganicum NC_057975.1 153126 View on NCBI ↗
Allium fetisowii NC_049100.1 154018 View on NCBI ↗
Allium filidens NC_068789.1 153150 View on NCBI ↗
Allium fistulosum NC_040222.1 153164 View on NCBI ↗
Allium flavescens NC_077655.1 153428 View on NCBI ↗
Allium forrestii NC_049101.1 153186 View on NCBI ↗
Allium funckiifolium PV817864.1 153582 View on NCBI ↗
Allium fuscoviolaceum NC_084232.1 153451 View on NCBI ↗
Allium galanthum NC_050981.1 153222 View on NCBI ↗
Allium giganteum PQ306042.1 152598 View on NCBI ↗
Allium glaciale NC_084233.1 153409 View on NCBI ↗
Allium glomeratum NC_068790.1 153406 View on NCBI ↗
Allium graveolens PQ305993.1 153262 View on NCBI ↗
Allium guanxianense NC_088574.1 152480 View on NCBI ↗
Allium gypsaceum PQ306038.1 152314 View on NCBI ↗
Allium haemanthoides PQ305999.1 153109 View on NCBI ↗
Allium hamedanense PQ306000.1 153168 View on NCBI ↗
Allium haneltii NC_068791.1 152344 View on NCBI ↗
Allium herderianum NC_042156.1 153605 View on NCBI ↗
Allium hindukuschense PQ306022.1 153032 View on NCBI ↗
Allium hissaricum PQ306026.1 152295 View on NCBI ↗
Allium hookeri NC_065781.1 153682 View on NCBI ↗
Allium hookeri var. hookeri OK055713.1 153592 View on NCBI ↗
Allium hymenorrhizum NC_084234.1 153289 View on NCBI ↗
Allium inconspicuum PZ015914.1 152127 View on NCBI ↗
Allium inderiense PZ015915.1 152029 View on NCBI ↗
Allium insufficiens PQ306025.1 152507 View on NCBI ↗
Allium iranshahrii PQ306002.1 153065 View on NCBI ↗
Allium isakulii PQ306035.1 152572 View on NCBI ↗
Allium jesdianum subsp. angustitepalum PQ306029.1 152625 View on NCBI ↗
Allium jesdianum subsp. jesdianum PQ306030.1 152626 View on NCBI ↗
Allium jodanthum NC_067034.1 152121 View on NCBI ↗
Allium karamanoglui PQ306012.1 153269 View on NCBI ↗
Allium karataviense NC_057573.1 151808 View on NCBI ↗
Allium kazerouni PQ308285.1 152238 View on NCBI ↗
Allium keusgenii PQ308307.1 153125 View on NCBI ↗
Allium kharputense PQ308318.1 153368 View on NCBI ↗
Allium kingdonii NC_046030.1 153559 View on NCBI ↗
Allium koelzii PQ308317.1 153129 View on NCBI ↗
Allium koksuense PQ308336.1 152911 View on NCBI ↗
Allium komarowii PQ308293.1 152427 View on NCBI ↗
Allium koreanum NC_057579.1 153162 View on NCBI ↗
Allium korolkowii PZ015923.1 153271 View on NCBI ↗
Allium kujukense PQ308337.1 149653 View on NCBI ↗
Allium ledebourianum PV684023.1 152930 View on NCBI ↗
Allium lineare PZ015916.1 153478 View on NCBI ↗
Allium lipskyanum PQ308292.1 152459 View on NCBI ↗
Allium lusitanicum OR884983.1 153482 View on NCBI ↗
Allium lycaonicum PQ308321.1 153685 View on NCBI ↗
Allium macleanii PQ308305.1 152350 View on NCBI ↗
Allium macranthum NC_049102.1 152876 View on NCBI ↗
Allium macrostemon NC_077656.1 153126 View on NCBI ↗
Allium mahneshanense PQ308316.1 153100 View on NCBI ↗
Allium mairei NC_045913.1 152913 View on NCBI ↗
Allium majus PQ308298.1 152624 View on NCBI ↗
Allium maowenense NC_042157.1 153608 View on NCBI ↗
Allium materculae PQ308313.1 153178 View on NCBI ↗
Allium michaelis NC_068792.1 153134 View on NCBI ↗
Allium microdictyon NC_077657.1 153561 View on NCBI ↗
Allium minus NC_077658.1 153499 View on NCBI ↗
Allium minutiflorum PQ308310.1 153083 View on NCBI ↗
Allium mirum PQ308306.1 152670 View on NCBI ↗
Allium moderense PQ308312.1 153095 View on NCBI ↗
Allium moly MZ019477.1 153793 View on NCBI ↗
Allium monanthum NC_042726.1 154804 View on NCBI ↗
Allium mongolicum NC_062084.1 153609 View on NCBI ↗
Allium monophyllum PQ308324.1 152838 View on NCBI ↗
Allium montanostepposum PZ015917.1 152938 View on NCBI ↗
Allium mozaffarianii PQ308322.1 153494 View on NCBI ↗
Allium muliense ON184008.1 153113 View on NCBI ↗
Allium nanodes NC_045520.1 154032 View on NCBI ↗
Allium neriniflorum NC_049103.1 154280 View on NCBI ↗
Allium nerinifolium NC_057574.1 154129 View on NCBI ↗
Allium nevskianum PQ308301.1 152560 View on NCBI ↗
Allium nigrum NC_057585.1 152241 View on NCBI ↗
Allium nikolaii NC_068793.1 152485 View on NCBI ↗
Allium nuratavicum PQ306034.1 152319 View on NCBI ↗
Allium nutans PZ015918.1 153513 View on NCBI ↗
Allium obliquum NC_037199.1 152387 View on NCBI ↗
Allium ochotense NC_057581.1 154048 View on NCBI ↗
Allium oleraceum subsp. oleraceum OR884984.1 152189 View on NCBI ↗
Allium omeiense NC_065780.1 153592 View on NCBI ↗
Allium ophiophyllum PZ269957.1 152642 View on NCBI ↗
Allium oreophilum PQ308338.1 152357 View on NCBI ↗
Allium orientale PQ306011.1 153323 View on NCBI ↗
Allium oschaninii NC_044470.1 153580 View on NCBI ↗
Allium ovalifolium NC_062881.1 153706 View on NCBI ↗
Allium ovalifolium var. cordifolium PV817884.1 153705 View on NCBI ↗
Allium ovalifolium var. leuconeurum PV817892.1 153699 View on NCBI ↗
Allium pallasii NC_068794.1 151465 View on NCBI ↗
Allium pangasicum PQ308328.1 151737 View on NCBI ↗
Allium plurifoliatum NC_058220.1 153234 View on NCBI ↗
Allium polyrhizum NC_049104.1 153086 View on NCBI ↗
Allium praemixtum NC_044412.1 153226 View on NCBI ↗
Allium prattii NC_037432.1 154482 View on NCBI ↗
Allium prostratum NC_077659.1 153597 View on NCBI ↗
Allium protensum PQ308299.1 152575 View on NCBI ↗
Allium pseudohollandicum PQ308288.1 152610 View on NCBI ↗
Allium pseudowinklerianum PQ308333.1 151535 View on NCBI ↗
Allium pskemense NC_044411.1 153788 View on NCBI ↗
Allium ramosum NC_084235.1 153494 View on NCBI ↗
Allium regelii PQ308325.1 152587 View on NCBI ↗
Allium remediorum PQ308289.1 152285 View on NCBI ↗
Allium rosenorum PQ308300.1 152857 View on NCBI ↗
Allium roylei NC_084236.1 153588 View on NCBI ↗
Allium rude NC_042158.1 153697 View on NCBI ↗
Allium sabulosum NC_068795.1 151627 View on NCBI ↗
Allium sahandicum PQ308315.1 153236 View on NCBI ↗
Allium saralicum PQ308319.1 153239 View on NCBI ↗
Allium sarawschanicum PQ308302.1 152879 View on NCBI ↗
Allium sativum NC_031829.1 153172 View on NCBI ↗
Allium schachimardanicum PQ308304.1 153094 View on NCBI ↗
Allium schisticola PQ308320.1 153046 View on NCBI ↗
Allium schoenoprasoides NC_049105.1 153583 View on NCBI ↗
Allium schoenoprasum NC_057575.1 152852 View on NCBI ↗
Allium scotostemon PQ308327.1 152285 View on NCBI ↗
Allium senescens NC_057580.1 153542 View on NCBI ↗
Allium severtzovioides PQ308329.1 151791 View on NCBI ↗
Allium sewerzowii PQ308330.1 151790 View on NCBI ↗
Allium siculum NC_057584.1 154225 View on NCBI ↗
Allium sikkimense NC_058221.1 152549 View on NCBI ↗
Allium songpanicum MN648634.1 153247 View on NCBI ↗
Allium spicatum NC_045911.1 153187 View on NCBI ↗
Allium spirale NC_068826.1 153549 View on NCBI ↗
Allium splendens NC_084237.1 153416 View on NCBI ↗
Allium spurium NC_077660.1 153529 View on NCBI ↗
Allium stipitatum PQ308290.1 152191 View on NCBI ↗
Allium strictum NC_049106.1 152962 View on NCBI ↗
Allium subakaka PQ308314.1 153158 View on NCBI ↗
Allium suworowii PQ308326.1 152572 View on NCBI ↗
Allium taeniopetalum PQ308295.1 151931 View on NCBI ↗
Allium tanguticum NC_068796.1 152980 View on NCBI ↗
Allium tenuissimum NC_068825.1 153459 View on NCBI ↗
Allium teretifolium NC_080287.1 153353 View on NCBI ↗
Allium tetraploideum NC_061763.1 152906 View on NCBI ↗
Allium thunbergii var. deltoides OQ701006.1 152457 View on NCBI ↗
Allium thunbergii var. teretifolium OQ701013.1 153353 View on NCBI ↗
Allium tianschanicum PZ015921.1 153315 View on NCBI ↗
Allium trautvetterianum PQ308303.1 152322 View on NCBI ↗
Allium tricoccum NC_057583.1 153565 View on NCBI ↗
Allium trifurcatum NC_045844.1 153456 View on NCBI ↗
Allium tripedale PV409669.1 154225 View on NCBI ↗
Allium triquetrum NC_064123.1 153249 View on NCBI ↗
Allium tschimganicum PQ308331.1 151823 View on NCBI ↗
Allium tuberosum NC_044709.1 154056 View on NCBI ↗
Allium turkestanicum PZ015922.1 152759 View on NCBI ↗
Allium ubipetrense PQ308308.1 153174 View on NCBI ↗
Allium ulleungense NC_077661.1 154049 View on NCBI ↗
Allium ursinum MH157875.2 153252 View on NCBI ↗
Allium vavilovii NC_084238.1 153573 View on NCBI ↗
Allium victorialis NC_037240.1 154074 View on NCBI ↗
Allium victoris PQ308332.1 151808 View on NCBI ↗
Allium viridiflorum PQ308296.1 152148 View on NCBI ↗
Allium wallichii NC_065777.1 152615 View on NCBI ↗
Allium wallichii var. platyphyllum ON184004.1 152926 View on NCBI ↗
Allium winklerianum PQ308297.1 152295 View on NCBI ↗
Allium x cepiforme NC_062794.1 153152 View on NCBI ↗
Allium xiangchengense NC_065778.1 152294 View on NCBI ↗
Allium xichuanense NC_042159.1 153673 View on NCBI ↗
Allium yingshanense PP056265.1 152183 View on NCBI ↗
Allium zagricum PQ308309.1 153167 View on NCBI ↗
Allium zebdanense MZ019480.1 153147 View on NCBI ↗
Allium zergericum PQ308335.1 152276 View on NCBI ↗