Markers + reference

Arachis

16 species · Fabaceae · Fabales

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Species 16
Genome length 156–156 kb
Candidate markers 259
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-UAA-trnT-UGU LSC 903 0.0110 1.00 54.1 yes View details
trnS-UGA-psbC LSC 262 0.0295 1.00 66.3 yes View details
rpoC2 LSC 4140 0.0046 1.00 42.8 yes View details
atpI-atpH LSC 1374 0.0078 1.00 49.8 yes View details
trnR-UCU-trnS-GCU LSC 1782 0.0071 1.00 54.3 yes View details
psbE-petL LSC 1355 0.0087 1.00 49.5 yes View details
rpl32-trnL-UAG SSC 856 0.0197 0.84 67.2 yes View details
ycf1 SSC 5268 0.0065 1.00 42.0 yes View details
trnK-UUU-rbcL LSC 752 0.0062 0.99 60.7 yes View details
psbD-trnT-GGU LSC 1534 0.0083 0.99 59.3 yes View details
rpl16-rps3 LSC 1218 0.0050 1.00 59.3 yes View details
ycf3-psaA LSC 956 0.0062 0.98 58.2 yes View details
psbM-petN LSC 1104 0.0069 0.99 53.5 yes View details
trnC-GCA-rpoB LSC 1203 0.0077 1.00 53.4 yes View details
trnQ-UUG-accD LSC 1386 0.0073 0.99 52.8 yes View details
rpl2-trnH-GUG LSC 124 0.0220 1.00 52.2 no View details
rps11-rpl36 LSC 574 0.0072 1.00 51.6 yes View details
trnP-UGG-psaJ LSC 435 0.0057 1.00 51.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rbcL_p1 trnK-UUU-rbcL ACCCTACCGAGGTTATGGAC AGTCCTGAATTAGCTGCTGC 917–935 1.000 82.4
trnK-UUU-rbcL_p2 trnK-UUU-rbcL ACCCTACCGAGGTTATGGAC CGAGCAAATGGAGTCCTGAA 928–946 1.000 81.8
trnK-UUU-rbcL_p3 trnK-UUU-rbcL CCTACCGAGGTTATGGACGA AGTCCTGAATTAGCTGCTGC 915–933 1.000 81.6
trnK-UUU-rbcL_p4 trnK-UUU-rbcL CCGAGGTTATGGACGAAACA AGTCCTGAATTAGCTGCTGC 911–929 1.000 81.2
trnK-UUU-rbcL_p5 trnK-UUU-rbcL ACCGAGGTTATGGACGAAAC AGTCCTGAATTAGCTGCTGC 912–930 1.000 81.1
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC AAGAGAAAAGCCGGCTATCG 1010–1036 1.000 82.5
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 959–985 1.000 82.1
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT AAGAGAAAAGCCGGCTATCG 1016–1042 1.000 81.1
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 991–1017 1.000 81.1
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 965–991 1.000 80.7
ycf3-psaA_p1 ycf3-psaA ATTGCTGAGGCTTGGTTTGA TGCCCATTCCTCGAAAGAAG 1104–1151 1.000 84.8
ycf3-psaA_p2 ycf3-psaA TTGCTGAGGCTTGGTTTGAT TGCCCATTCCTCGAAAGAAG 1103–1150 1.000 84.8
ycf3-psaA_p3 ycf3-psaA ATTGCTGAGGCTTGGTTTGA GCCCATTCCTCGAAAGAAGT 1103–1150 1.000 84.8
ycf3-psaA_p4 ycf3-psaA TTGCTGAGGCTTGGTTTGAT GCCCATTCCTCGAAAGAAGT 1102–1149 1.000 84.8
ycf3-psaA_p5 ycf3-psaA TTGGTTGAAGATCACAGGGC TGCCCATTCCTCGAAAGAAG 1018–1065 1.000 84.2
trnS-UGA-psbC_p1 trnS-UGA-psbC GTTGGAGAGATGGCTGAGTG TAGGTCATTTATGGCACGCG 458–464 1.000 81.1
trnS-UGA-psbC_p2 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG TAGGTCATTTATGGCACGCG 454–460 1.000 81.0
trnS-UGA-psbC_p3 trnS-UGA-psbC ATAGCCCCGGTCTTGAAAAC TAGGTCATTTATGGCACGCG 434–440 1.000 80.4
trnS-UGA-psbC_p4 trnS-UGA-psbC GGGTTCGAATCCCTCTCTCT TAGGTCATTTATGGCACGCG 386–392 1.000 80.2
trnS-UGA-psbC_p5 trnS-UGA-psbC TTTGGTTGGAGAGATGGCTG TAGGTCATTTATGGCACGCG 462–468 1.000 79.6
psbD-trnT-GGU_p1 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GGCGTAAGTCATCGGTTCAA 1519–1672 1.000 82.9
psbD-trnT-GGU_p2 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GGCGTAAGTCATCGGTTCAA 1520–1673 1.000 82.8
psbD-trnT-GGU_p3 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GGCGTAAGTCATCGGTTCAA 1521–1674 1.000 82.8
psbD-trnT-GGU_p4 psbD-trnT-GGU ACAAAAACGAAACGGTCCCT GGCGTAAGTCATCGGTTCAA 1518–1671 1.000 82.2
psbD-trnT-GGU_p5 psbD-trnT-GGU AACCCACAAAAACGAAACGG GGCGTAAGTCATCGGTTCAA 1523–1676 1.000 82.0
psbM-petN_p1 psbM-petN TCATTCTAGTTCCCACTGCC TCTTGCTTGGGCTGCTTTAA 1234–1250 1.000 75.2
psbM-petN_p2 psbM-petN CATTCTAGTTCCCACTGCCT TCTTGCTTGGGCTGCTTTAA 1233–1249 1.000 75.1
psbM-petN_p3 psbM-petN TCATTCTAGTTCCCACTGCC ATCTTGCTTGGGCTGCTTTA 1235–1251 1.000 73.5
psbM-petN_p4 psbM-petN TCATTCTAGTTCCCACTGCC TAAATCTTGCTTGGGCTGCT 1238–1254 1.000 73.4
psbM-petN_p5 psbM-petN CATTCTAGTTCCCACTGCCT ATCTTGCTTGGGCTGCTTTA 1234–1250 1.000 73.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (16)

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

Species Accession Length (bp) Link
Arachis batizocoi NC_063737.1 156346 View on NCBI ↗
Arachis cardenasii MK144824.1 156413 View on NCBI ↗
Arachis correntina MK144828.1 156287 View on NCBI ↗
Arachis diogoi MK144821.1 156384 View on NCBI ↗
Arachis duranensis NC_047337.1 156318 View on NCBI ↗
Arachis helodes MK144826.1 156491 View on NCBI ↗
Arachis hoehnei MK144827.1 156437 View on NCBI ↗
Arachis ipaensis MK144829.1 156453 View on NCBI ↗
Arachis lutescens NC_085210.1 156398 View on NCBI ↗
Arachis monticola MK144818.1 156395 View on NCBI ↗
Arachis paraguariensis MK144823.1 156437 View on NCBI ↗
Arachis pintoi MW561116.1 156185 View on NCBI ↗
Arachis porphyrocalyx PQ463259.1 156391 View on NCBI ↗
Arachis praecox PQ463258.1 156295 View on NCBI ↗
Arachis stenosperma MK144819.1 156405 View on NCBI ↗
Arachis villosa MK144825.1 156447 View on NCBI ↗