Markers + reference

Tulipa

87 species · Liliaceae · Liliales

Back to catalogue

Species 87
Genome length 151–153 kb
Candidate markers 277
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0023 1.00 31.4 yes View details
rps16-trnQ-UUG LSC 858 0.0142 0.96 60.6 yes View details
trnS-GCU-trnG-GCC LSC 745 0.0144 0.99 65.3 yes View details
trnE-UUC-trnT-GGU LSC 937 0.0219 0.92 69.7 yes View details
petA-psbJ LSC 578 0.0215 0.97 72.8 yes View details
psaJ-rpl33 LSC 613 0.0188 0.97 64.1 yes View details
ycf1 IRb 1656 0.0033 1.00 35.2 no View details
ndhF-rpl32 SSC 705 0.0151 0.97 68.4 yes View details
rpl32-trnL-UAG SSC 752 0.0256 0.99 68.1 yes View details
ndhD SSC 1506 0.0053 1.00 41.5 yes View details
rps15-ycf1 SSC 420 0.0206 1.00 59.6 yes View details
ycf1 SSC 5307 0.0098 1.00 49.3 yes View details
ycf4-cemA LSC 547 0.0152 0.99 76.0 yes View details
rpl14-rpl16 LSC 131 0.0373 0.95 69.7 yes View details
accD-psaI LSC 813 0.0131 0.98 67.6 yes View details
trnT-GGU-psbD LSC 1146 0.0102 1.00 65.8 yes View details
psbE-petL LSC 1165 0.0107 1.00 65.6 yes View details
rpoB-trnC-GCA LSC 879 0.0107 0.96 65.5 yes View details
ccsA-ndhD SSC 182 0.0534 1.00 64.7 yes View details
ycf3-trnS-GGA LSC 570 0.0100 1.00 64.3 yes View details
trnK-UUU-rps16 LSC 682 0.0113 0.99 63.8 yes View details
rps8-rpl14 LSC 191 0.0262 1.00 63.4 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
psbA_p1 psbA TTGCTCTGTCAACGATTCGT GCGTGCTCTTTTGCAAAGAT 1817–1880 1.000 84.1
psbA_p2 psbA TGGGTATTGCTCTGTCAACG GCGTGCTCTTTTGCAAAGAT 1823–1886 0.977 83.3
psbA_p3 psbA TTGCTCTGTCAACGATTCGT GTGCTTGGGAGTCCTTGAAA 1143–1180 1.000 81.3
psbA_p4 psbA TGGGTATTGCTCTGTCAACG GTGCTTGGGAGTCCTTGAAA 1149–1186 0.977 80.6
psbA_p5 psbA TGGGTATTGCTCTGTCAACG AAATGCAAGCACGATTTGGG 1437–1474 0.977 80.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACATCTATCCCGATGAGCCA 913–960 0.977 89.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACCTATACCCCGGAGACCTA TTCTCGAGCCGTATGAGGAT 1625–1672 0.977 87.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACCTATACCCCGGAGACCTA ACATCTATCCCGATGAGCCA 1565–1612 0.954 86.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CTCGCGGAAAACCCTTTTTC TTCTCGAGCCGTATGAGGAT 1355–1402 0.598 72.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CTCGCGGAAAACCCTTTTTC ACATCTATCCCGATGAGCCA 1295–1342 0.586 72.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 749–1055 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 760–1066 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 753–1059 1.000 89.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 764–1070 1.000 88.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 755–1061 1.000 87.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC TGATGAGGGATAGCGGAGAG ACGAATCACACTTTTACCACT 676–1000 1.000 63.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC GAGGGATAGCGGAGAGAGAG ACGAATCACACTTTTACCACT 672–996 1.000 62.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GATGAGGGATAGCGGAGAGA ACGAATCACACTTTTACCACT 675–999 1.000 62.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATGAGGGATAGCGGAGAGAG ACGAATCACACTTTTACCACT 674–998 1.000 62.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TGATGAGGGATAGCGGAGAG GAACGAATCACACTTTTACCACT 678–1002 1.000 62.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG GCGACACCCAGATTTGAACT 1024–1108 0.920 82.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 999–1083 0.920 82.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG CCTTACCACTTGGCCATGTC 978–1062 0.897 81.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTTGTCAATCAGGCGACACC 1036–1120 0.920 80.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT GCGACACCCAGATTTGAACT 1025–1109 0.920 79.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 498–1041 1.000 90.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 496–1039 1.000 90.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 552–1095 1.000 90.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 477–1020 1.000 90.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 475–1018 1.000 90.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (87)

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

Species Accession Length (bp) Link
Tulipa aff. brachystemon OR288292.1 152090 View on NCBI ↗
Tulipa affinis OR288285.1 152119 View on NCBI ↗
Tulipa agenensis OR288341.1 152391 View on NCBI ↗
Tulipa albanica OR288316.1 152167 View on NCBI ↗
Tulipa alberti NC_083128.1 152359 View on NCBI ↗
Tulipa anadroma OR288299.1 152458 View on NCBI ↗
Tulipa anisophylla OR288443.1 152094 View on NCBI ↗
Tulipa armena OR288353.1 152488 View on NCBI ↗
Tulipa banuensis OR288509.1 152284 View on NCBI ↗
Tulipa behmiana PP933987.1 151116 View on NCBI ↗
Tulipa biflora OR288276.1 152016 View on NCBI ↗
Tulipa bifloriformis OR288305.1 152042 View on NCBI ↗
Tulipa borszczowii OR288386.1 151059 View on NCBI ↗
Tulipa brachystemon NC_086584.1 152089 View on NCBI ↗
Tulipa buhseana NC_052014.1 152062 View on NCBI ↗
Tulipa butkovii NC_088749.1 152229 View on NCBI ↗
Tulipa carinata OR288368.1 152425 View on NCBI ↗
Tulipa cinnabarina OR288350.1 152112 View on NCBI ↗
Tulipa clusiana OR288369.1 151583 View on NCBI ↗
Tulipa clusiana f. cashmeriana OR288438.1 151649 View on NCBI ↗
Tulipa cretica OR288342.1 152073 View on NCBI ↗
Tulipa dasystemon OR288284.1 152097 View on NCBI ↗
Tulipa dianaeverettiae OR288502.1 152005 View on NCBI ↗
Tulipa ferganica OR288278.1 152135 View on NCBI ↗
Tulipa foliosa OR288366.1 152429 View on NCBI ↗
Tulipa gesneriana NC_063831.1 151958 View on NCBI ↗
Tulipa hageri OR288375.1 152091 View on NCBI ↗
Tulipa harazensis OR288513.1 152350 View on NCBI ↗
Tulipa heteropetala OR288358.1 152423 View on NCBI ↗
Tulipa heterophylla NC_088750.1 151868 View on NCBI ↗
Tulipa heweri OR288336.1 152291 View on NCBI ↗
Tulipa hissarica OR288448.1 152450 View on NCBI ↗
Tulipa hoogiana OR288397.1 152313 View on NCBI ↗
Tulipa humilis OR288437.1 152054 View on NCBI ↗
Tulipa hungarica OR288387.1 152057 View on NCBI ↗
Tulipa hybrid cultivar OR288303.1 152156 View on NCBI ↗
Tulipa iliensis NC_052697.1 151744 View on NCBI ↗
Tulipa ingens OR288446.1 152427 View on NCBI ↗
Tulipa ivasczenkoae OR288496.1 152454 View on NCBI ↗
Tulipa jacquesii OR288364.1 151751 View on NCBI ↗
Tulipa julia OR288351.1 152503 View on NCBI ↗
Tulipa kolbintsevii OR288357.1 152060 View on NCBI ↗
Tulipa kolpakowskiana NC_083129.1 152088 View on NCBI ↗
Tulipa korolkowii NC_088751.1 152155 View on NCBI ↗
Tulipa kosovarica OR288319.1 152157 View on NCBI ↗
Tulipa kuschkensis OR288515.1 152419 View on NCBI ↗
Tulipa lanata OR288450.1 152420 View on NCBI ↗
Tulipa lehmanniana OR288335.1 151137 View on NCBI ↗
Tulipa lemmersii NC_086585.1 152119 View on NCBI ↗
Tulipa linifolia OR288440.1 151477 View on NCBI ↗
Tulipa luanica OR288324.1 152147 View on NCBI ↗
Tulipa maximowiczii OR288452.1 152020 View on NCBI ↗
Tulipa montana OR288348.1 151589 View on NCBI ↗
Tulipa neustruevae OR288298.1 152072 View on NCBI ↗
Tulipa orithyioides OR288374.1 152059 View on NCBI ↗
Tulipa orphanidea OR288376.1 151894 View on NCBI ↗
Tulipa ostrowskiana OR288293.1 152098 View on NCBI ↗
Tulipa patens NC_061194.1 152051 View on NCBI ↗
Tulipa platystemon OR288289.1 152114 View on NCBI ↗
Tulipa praestans OR288377.1 152211 View on NCBI ↗
Tulipa regelii OR288356.1 152105 View on NCBI ↗
Tulipa scardica OR288328.1 152101 View on NCBI ↗
Tulipa scharipovii OR288483.1 151989 View on NCBI ↗
Tulipa schrenkii NC_063594.1 152088 View on NCBI ↗
Tulipa serbica OR288330.1 152149 View on NCBI ↗
Tulipa sinkiangensis NC_063595.1 151929 View on NCBI ↗
Tulipa sosnowskyi OR288396.1 152675 View on NCBI ↗
Tulipa sprengeri OR288347.1 152362 View on NCBI ↗
Tulipa suaveolens OR288352.1 152144 View on NCBI ↗
Tulipa subquinquefolia OR288442.1 152412 View on NCBI ↗
Tulipa sylvestris OR288332.1 151924 View on NCBI ↗
Tulipa systola OR288382.1 152349 View on NCBI ↗
Tulipa talassica OR288390.1 152078 View on NCBI ↗
Tulipa tetraphylla OR288280.1 152072 View on NCBI ↗
Tulipa thianschanica NC_061964.1 152070 View on NCBI ↗
Tulipa toktogulica OR288279.1 152215 View on NCBI ↗
Tulipa turkestanica OR288281.1 152040 View on NCBI ↗
Tulipa ulophylla OR288409.1 152308 View on NCBI ↗
Tulipa undulatifolia OR288520.1 152410 View on NCBI ↗
Tulipa undulatifolia var. micheliana OR288402.1 152338 View on NCBI ↗
Tulipa uniflora OR288355.1 152297 View on NCBI ↗
Tulipa urumiensis OR288291.1 152015 View on NCBI ↗
Tulipa uzbekistanica OR288467.1 152359 View on NCBI ↗
Tulipa vvedenskyi OR288430.1 152226 View on NCBI ↗
Tulipa x tschimganica OR288383.1 152232 View on NCBI ↗
Tulipa zenaidae NC_086586.1 152021 View on NCBI ↗
Tulipa zonneveldii NC_088752.1 152395 View on NCBI ↗