Markers + reference

Solanum

197 species · Solanaceae · Solanales

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Species 197
Genome length 154–156 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

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 447 0.0397 1.00 74.8 yes View details
rps16-trnQ-UUG LSC 1019 0.0378 1.00 82.6 yes View details
trnF-GAA-ndhJ LSC 637 0.0280 0.97 62.5 yes View details
cemA LSC 690 0.0478 1.00 64.2 yes View details
petA-psbJ LSC 1091 0.0341 0.98 70.2 yes View details
rps12-psbB LSC 2591 0.0257 1.00 69.9 yes View details
ndhF-rpl32 SSC 785 0.0349 1.00 76.4 yes View details
rpl32-trnL-UAG SSC 921 0.0328 1.00 70.6 yes View details
ycf1 SSC 5664 0.0262 1.00 67.1 yes View details
ndhA SSC 2250 0.0171 1.00 70.3 yes View details
trnK-UUU-rps16 LSC 662 0.0312 1.00 70.1 yes View details
psbE-petL LSC 988 0.0167 1.00 68.7 yes View details
rpoB-trnC-GCA LSC 1314 0.0172 1.00 68.6 yes View details
ndhC-trnV-UAC LSC 1102 0.0205 0.99 66.8 yes View details
accD-psaI LSC 746 0.0269 0.99 66.4 yes View details
trnS-GCU-trnG-UCC LSC 642 0.0232 0.99 66.2 yes View details
atpB-rbcL LSC 812 0.0209 1.00 65.9 yes View details
atpF-atpH LSC 401 0.0189 1.00 65.8 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 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 TTCCCTCTAGACCTAGCTGC 442–909 0.995 90.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 456–923 0.995 90.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 455–922 0.995 90.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 457–924 0.995 90.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 494–961 0.995 89.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGGTATGTTGCTGCCA 1268–1432 0.995 90.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGGTATGTTGCTGCCA 1267–1431 0.995 90.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGTACGAGGAGAAAGCTTCC 857–1018 0.980 89.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCTATCCCAATGAGCCGTCT 804–965 0.964 88.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCTATCCCAATGAGCCGTCT 803–964 0.964 88.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 697–1639 1.000 90.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 680–1622 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTCGAGCTAAGAGCACCTTC GAGGTTCGAATCCTTCCGTC 751–1693 0.990 90.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 698–1640 1.000 89.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 694–1636 1.000 88.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 676–734 0.995 63.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 725–783 0.995 62.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 679–737 0.995 62.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 678–736 0.995 62.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 677–735 0.995 61.3
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CCTGAGGCAGAGGGAAAAAT 580–615 1.000 86.9
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG CCTGAGGCAGAGGGAAAAAT 550–585 1.000 86.8
atpF-atpH_p3 atpF-atpH AGTGGCCCAAAGAAACGAAA CCTGAGGCAGAGGGAAAAAT 551–586 1.000 86.0
atpF-atpH_p4 atpF-atpH TGGCCCAAAGAAACGAAAGA CCTGAGGCAGAGGGAAAAAT 549–584 0.954 85.5
atpF-atpH_p5 atpF-atpH TGGCCCAAAGAAACGAAAGA GCAGAGGGAAAAATACGAGGT 543–578 0.949 81.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1166–1430 0.995 83.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1165–1429 1.000 82.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1171–1435 0.980 81.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC AGTCCTCTGCCTTACCACTC 1135–1399 0.995 80.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1164–1428 1.000 79.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (197)

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

Species Accession Length (bp) Link
Solanum abancayense NC_041586.1 155492 View on NCBI ↗
Solanum acaule NC_041551.1 155570 View on NCBI ↗
Solanum achacachense NC_041587.1 155510 View on NCBI ↗
Solanum acroglossum NC_041588.1 155270 View on NCBI ↗
Solanum acroscopicum NC_041589.1 155477 View on NCBI ↗
Solanum actaeibotrys NC_062865.1 154726 View on NCBI ↗
Solanum aculeatissimum NC_061388.1 155820 View on NCBI ↗
Solanum aethiopicum NC_039608.1 155608 View on NCBI ↗
Solanum aethiopicum x Solanum melongena MN218092.1 155606 View on NCBI ↗
Solanum agnewiorum NC_039416.1 155586 View on NCBI ↗
Solanum ahanhuiri NC_050205.1 155486 View on NCBI ↗
Solanum albidum NC_062866.1 154715 View on NCBI ↗
Solanum albornozii NC_041590.1 155604 View on NCBI ↗
Solanum aligerum NC_062867.1 155852 View on NCBI ↗
Solanum alphonsei NC_062514.1 155557 View on NCBI ↗
Solanum ambosinum NC_041591.1 155489 View on NCBI ↗
Solanum americanum NC_062693.1 155266 View on NCBI ↗
Solanum anamatophilum NC_086523.1 155525 View on NCBI ↗
Solanum andreanum NC_041592.1 155536 View on NCBI ↗
Solanum anguivi NC_039611.1 155577 View on NCBI ↗
Solanum angustifidum NC_062517.1 155233 View on NCBI ↗
Solanum annuum NC_062873.1 155413 View on NCBI ↗
Solanum anomalostemon NC_062874.1 156138 View on NCBI ↗
Solanum arcanum NC_062078.1 155516 View on NCBI ↗
Solanum aridum NC_062419.1 155112 View on NCBI ↗
Solanum augustii NC_086525.1 155503 View on NCBI ↗
Solanum aureitomentosum NC_039412.1 155303 View on NCBI ↗
Solanum avilesii NC_041593.1 155555 View on NCBI ↗
Solanum berthaultii NC_034951.1 155533 View on NCBI ↗
Solanum betaceum NC_086868.1 155937 View on NCBI ↗
Solanum brachyantherum NC_062871.1 155905 View on NCBI ↗
Solanum bradei NC_062872.1 155949 View on NCBI ↗
Solanum brevicaule NC_041597.1 155522 View on NCBI ↗
Solanum bukasovii NC_041598.1 155518 View on NCBI ↗
Solanum bukasovii f. multidissectum NC_041621.1 155523 View on NCBI ↗
Solanum cajamarquense NC_041599.1 155525 View on NCBI ↗
Solanum campylacanthum NC_039609.1 155017 View on NCBI ↗
Solanum canasense NC_041600.1 155506 View on NCBI ↗
Solanum cardiophyllum NC_041601.1 155456 View on NCBI ↗
Solanum carolinense PX547999.2 155315 View on NCBI ↗
Solanum cerasiferum NC_039599.1 155413 View on NCBI ↗
Solanum chacoense NC_041602.1 155518 View on NCBI ↗
Solanum chaucha NC_050209.1 155518 View on NCBI ↗
Solanum cheesmaniae NC_026876.1 155520 View on NCBI ↗
Solanum chenopodioides NC_062510.1 155410 View on NCBI ↗
Solanum chilense NC_026877.1 155528 View on NCBI ↗
Solanum chiquidenum NC_069597.1 155413 View on NCBI ↗
Solanum chmielewskii NC_062079.1 155504 View on NCBI ↗
Solanum chomatophilum NC_041603.1 155427 View on NCBI ↗
Solanum chrysotrichum NC_062507.1 154898 View on NCBI ↗
Solanum clivorum NC_062513.1 155531 View on NCBI ↗
Solanum commersonii NC_028069.2 155525 View on NCBI ↗
Solanum commersonii x Solanum andigenum NC_069598.1 155564 View on NCBI ↗
Solanum corneliomulleri NC_062080.1 155544 View on NCBI ↗
Solanum crotonoides NC_062497.1 153797 View on NCBI ↗
Solanum cucullatum NC_062498.1 155490 View on NCBI ↗
Solanum dasyphyllum NC_039607.1 155716 View on NCBI ↗
Solanum deflexicarpum NC_062864.1 155706 View on NCBI ↗
Solanum demissum NC_041552.1 155558 View on NCBI ↗
Solanum dimorphandrum NC_062496.1 156084 View on NCBI ↗
Solanum doddsii PZ094980.1 155512 View on NCBI ↗
Solanum dolichocremastrum NC_086526.1 155525 View on NCBI ↗
Solanum dulcamara NC_035724.1 155580 View on NCBI ↗
Solanum ehrenbergii NC_086550.1 155594 View on NCBI ↗
Solanum elaeagnifolium KX792501.2 155049 View on NCBI ↗
Solanum emulans NC_062499.1 155417 View on NCBI ↗
Solanum ensifolium PP744563.1 155295 View on NCBI ↗
Solanum etuberosum NC_041604.1 155302 View on NCBI ↗
Solanum ferocissimum PZ094979.1 154550 View on NCBI ↗
Solanum galapagense NC_026878.1 155474 View on NCBI ↗
Solanum gandarillasii NC_069603.1 155507 View on NCBI ↗
Solanum glabratum NC_039603.1 155368 View on NCBI ↗
Solanum gourlayi NC_041606.1 155448 View on NCBI ↗
Solanum gracilifrons NC_069599.1 155511 View on NCBI ↗
Solanum habrochaites NC_026879.1 155465 View on NCBI ↗
Solanum hieronymi NC_062501.1 155579 View on NCBI ↗
Solanum hirtulum PZ183444.1 155580 View on NCBI ↗
Solanum hjertingii MK690623.1 155545 View on NCBI ↗
Solanum hondelmannii NC_041608.1 155541 View on NCBI ↗
Solanum hougasii MF471372.1 155549 View on NCBI ↗
Solanum huancabambense NC_086521.1 155587 View on NCBI ↗
Solanum huaylasense NC_062081.1 155571 View on NCBI ↗
Solanum hybrid cultivar NC_069605.1 155564 View on NCBI ↗
Solanum hypacrarthrum NC_041611.1 155484 View on NCBI ↗
Solanum iltisii NC_062503.1 156073 View on NCBI ↗
Solanum incamayoense NC_041612.1 155462 View on NCBI ↗
Solanum incanum NC_039605.1 155657 View on NCBI ↗
Solanum infundibuliforme NC_069600.1 155536 View on NCBI ↗
Solanum insanum MW384851.1 155534 View on NCBI ↗
Solanum iopetalum NC_062717.1 155625 View on NCBI ↗
Solanum jamesii NC_041613.1 155592 View on NCBI ↗
Solanum japonense NC_054186.1 155451 View on NCBI ↗
Solanum kurtzianum NC_041614.1 155506 View on NCBI ↗
Solanum laciniatum NC_062424.1 156018 View on NCBI ↗
Solanum lanzae NC_039417.1 155269 View on NCBI ↗
Solanum lasiocarpum NC_086861.1 155671 View on NCBI ↗
Solanum laxissimum NC_041615.1 155540 View on NCBI ↗
Solanum leptophyes NC_041616.1 155470 View on NCBI ↗
Solanum lesteri NC_086547.1 155344 View on NCBI ↗
Solanum lichtensteinii NC_039598.1 155574 View on NCBI ↗
Solanum lignicaule NC_069601.1 155467 View on NCBI ↗
Solanum limbaniense NC_041617.1 155508 View on NCBI ↗
Solanum linnaeanum NC_039600.1 155574 View on NCBI ↗
Solanum lycopersicum NC_007898.3 155461 View on NCBI ↗
Solanum lyratum PX395653.1 155828 View on NCBI ↗
Solanum macrocarpon NC_039606.1 155820 View on NCBI ↗
Solanum marinasense NC_041610.1 155492 View on NCBI ↗
Solanum medians NC_041618.1 155530 View on NCBI ↗
Solanum megistacrolobum NC_041619.1 155559 View on NCBI ↗
Solanum melongena NC_030207.1 154289 View on NCBI ↗
Solanum melongena x Solanum aethiopicum MN218085.1 155581 View on NCBI ↗
Solanum melongena x Solanum torvum MN218093.1 155583 View on NCBI ↗
Solanum microdontum NC_041594.1 155513 View on NCBI ↗
Solanum mochiquense NC_062718.1 155547 View on NCBI ↗
Solanum morelliforme NC_086548.1 155658 View on NCBI ↗
Solanum mortonii NC_062426.1 154731 View on NCBI ↗
Solanum multiinterruptum NC_041620.1 155514 View on NCBI ↗
Solanum multispinum NC_062427.1 155145 View on NCBI ↗
Solanum muricatum NC_083980.1 155733 View on NCBI ↗
Solanum neocardenasii NC_086544.1 155539 View on NCBI ↗
Solanum neorickii NC_026880.1 155513 View on NCBI ↗
Solanum neorossii NC_086546.1 155259 View on NCBI ↗
Solanum nigrum NC_028070.2 155432 View on NCBI ↗
Solanum nitidum NC_062486.1 155748 View on NCBI ↗
Solanum okadae NC_065381.1 155515 View on NCBI ↗
Solanum opacum NC_062487.1 155408 View on NCBI ↗
Solanum oplocense x Solanum tuberosum NC_069596.1 155296 View on NCBI ↗
Solanum pachyandrum NC_062488.1 155844 View on NCBI ↗
Solanum palustre NC_041622.1 155301 View on NCBI ↗
Solanum pampasense NC_041623.1 155519 View on NCBI ↗
Solanum paposanum NC_062489.1 155847 View on NCBI ↗
Solanum paucissectum NC_041624.1 155369 View on NCBI ↗
Solanum pennellii NC_035742.1 155254 View on NCBI ↗
Solanum peruvianum NC_026881.1 155561 View on NCBI ↗
Solanum phureja NC_041625.1 155492 View on NCBI ↗
Solanum pimpinellifolium NC_026882.1 155442 View on NCBI ↗
Solanum pinnatum NC_062490.1 155820 View on NCBI ↗
Solanum pittosporifolium NC_086862.1 155926 View on NCBI ↗
Solanum piurae NC_069602.1 155337 View on NCBI ↗
Solanum plowmanii NC_062491.1 155554 View on NCBI ↗
Solanum polhillii NC_039414.1 155422 View on NCBI ↗
Solanum polyadenium NC_041627.1 155257 View on NCBI ↗
Solanum pruinosum PV802126.1 155419 View on NCBI ↗
Solanum pygmaeum NC_062493.1 155300 View on NCBI ↗
Solanum raphanifolium NC_068253.1 155556 View on NCBI ↗
Solanum remyanum NC_062477.1 155893 View on NCBI ↗
Solanum richardii NC_039610.1 155187 View on NCBI ↗
Solanum rostratum NC_057245.1 155559 View on NCBI ↗
Solanum salicifolium NC_062481.1 155464 View on NCBI ↗
Solanum sanchez-vegae NC_062482.1 155804 View on NCBI ↗
Solanum scabrum NC_062483.1 155482 View on NCBI ↗
Solanum septemlobum NC_056313.1 155465 View on NCBI ↗
Solanum sisymbriifolium NC_061213.1 155771 View on NCBI ↗
Solanum sogarandinum NC_041628.1 155562 View on NCBI ↗
Solanum sparsipilum NC_041629.1 155469 View on NCBI ↗
Solanum spegazzinii NC_041630.1 155519 View on NCBI ↗
Solanum stenophyllidium NC_041596.1 155578 View on NCBI ↗
Solanum stenotomum NC_041607.1 155492 View on NCBI ↗
Solanum stenotomum subsp. goniocalyx NC_050204.1 155492 View on NCBI ↗
Solanum stenotomum subsp. stenotomum NC_050206.1 155492 View on NCBI ↗
Solanum stipuloideum NC_086522.1 155529 View on NCBI ↗
Solanum stoloniferum MF471373.1 155567 View on NCBI ↗
Solanum supinum NC_039601.1 155769 View on NCBI ↗
Solanum tacnaense NC_069606.1 155486 View on NCBI ↗
Solanum talarense NC_062484.1 155289 View on NCBI ↗
Solanum tarapatanum NC_069607.1 155495 View on NCBI ↗
Solanum tarderemotum PV802113.1 155537 View on NCBI ↗
Solanum tarijense NC_041631.1 155546 View on NCBI ↗
Solanum tarnii NC_086549.1 155590 View on NCBI ↗
Solanum tarnii x Solanum tuberosum NC_069604.1 155590 View on NCBI ↗
Solanum torvum NC_085711.1 154942 View on NCBI ↗
Solanum trachycyphum NC_062468.1 155510 View on NCBI ↗
Solanum trifidum NC_086545.1 155593 View on NCBI ↗
Solanum triflorum PV802111.1 155262 View on NCBI ↗
Solanum trilobatum NC_039602.1 155289 View on NCBI ↗
Solanum trisectum NC_062469.1 155852 View on NCBI ↗
Solanum tuberosum NC_008096.2 155296 View on NCBI ↗
Solanum tuberosum subsp. andigenum NC_050207.1 155530 View on NCBI ↗
Solanum tuberosum x Solanum microdontum NC_069595.1 155493 View on NCBI ↗
Solanum tweedianum NC_062471.1 155449 View on NCBI ↗
Solanum umalilaense NC_062472.1 155492 View on NCBI ↗
Solanum umtuma NC_039413.1 155541 View on NCBI ↗
Solanum usambarense NC_039415.1 155411 View on NCBI ↗
Solanum valdiviense NC_062474.1 155426 View on NCBI ↗
Solanum venturii NC_041609.1 155477 View on NCBI ↗
Solanum vernei NC_041633.1 155590 View on NCBI ↗
Solanum verrucosum NC_041632.1 155479 View on NCBI ↗
Solanum viarum PV866731.1 156209 View on NCBI ↗
Solanum villosum NC_062476.1 155399 View on NCBI ↗
Solanum violaceimarmoratum NC_041634.1 155505 View on NCBI ↗
Solanum violaceum NC_039604.1 155748 View on NCBI ↗
Solanum virginianum NC_073005.1 154497 View on NCBI ↗
Solanum wittmackii NC_086524.1 155490 View on NCBI ↗
Solanum wrightii MN218084.1 155506 View on NCBI ↗
Solanum x blanco-galdosii NC_041595.1 155553 View on NCBI ↗
Solanum x curtilobum NC_050210.1 155492 View on NCBI ↗
Solanum x juzepczukii NC_050208.1 155532 View on NCBI ↗