Markers + reference

Siraitia

2 species · Cucurbitaceae · Cucurbitales

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Species 2
Genome length 159–159 kb
Candidate markers 268
Primer pairs 95

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 299 0.0337 0.99 62.4 yes View details
trnG-UCC-trnR-UCU LSC 275 0.0229 0.95 61.1 yes View details
trnT-GGU-psbD LSC 1075 0.0103 0.99 65.2 yes View details
ndhC-trnV LSC 790 0.0228 1.00 58.0 yes View details
trnM-CAU-atpE LSC 174 0.0462 0.99 74.4 yes View details
ndhF-rpl32 SSC 660 0.0092 0.99 61.4 yes View details
rpl32-trnL-TAG SSC 1376 0.0082 0.98 65.8 yes View details
ccsA SSC 972 0.0051 1.00 61.6 yes View details
ycf1 SSC 5550 0.0043 1.00 44.2 yes View details
psbZ-trnG-GCC LSC 600 0.0070 0.95 67.6 yes View details
ndhH-rps15 SSC 103 0.0194 1.00 63.7 yes View details
psbK-psbI LSC 391 0.0106 0.97 63.4 yes View details
trnK-UUU-rps16 LSC 824 0.0049 0.99 62.9 yes View details
ndhJ-ndhK LSC 113 0.0177 1.00 62.7 yes View details
rpoB-trnC-GCA LSC 939 0.0064 1.00 62.5 yes View details
accD-psaI LSC 749 0.0054 0.99 62.5 yes View details
trnR-ACG-trnN-GUU IRb 619 0.0065 1.00 62.5 yes View details
trnN-GUU-trnR-ACG IRa 619 0.0065 1.00 62.5 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
psbA-trnK-UUU_p1 psbA-trnK-UUU AAACGACCCCATAGGCTTTC ACTCCATCCGACTAGTTCCG 389–391 1.000 76.6
psbA-trnK-UUU_p2 psbA-trnK-UUU GAAACGACCCCATAGGCTTT ACTCCATCCGACTAGTTCCG 390–392 1.000 76.6
psbA-trnK-UUU_p3 psbA-trnK-UUU CCAGTTACAGAAACGACCCC ACTCCATCCGACTAGTTCCG 399–401 1.000 76.0
psbA-trnK-UUU_p4 psbA-trnK-UUU AAACGACCCCATAGGCTTTC ACTAGTTCCGGGTTCGAGTC 379–381 1.000 74.9
psbA-trnK-UUU_p5 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA ACTCCATCCGACTAGTTCCG 420–422 1.000 74.7
trnK-UUU_p1 trnK-UUU TGAAGGGCTTGTTATTCAACAG TCCGTTTCATGACCTTTGCT 2987–2995 1.000 53.6
trnK-UUU_p2 trnK-UUU GAAGGGCTTGTTATTCAACAGT TCCGTTTCATGACCTTTGCT 2986–2994 1.000 53.6
trnK-UUU_p3 trnK-UUU AGGGCTTGTTATTCAACAGT TCCGTTTCATGACCTTTGCT 2984–2992 1.000 53.3
trnK-UUU_p4 trnK-UUU GGACTCCCAAGCACATGAAT ACTCACATGATGGTCTCATTGT 3000 0.500 38.4
trnK-UUU_p5 trnK-UUU GGACTCCCAAGCACATGAAT CTCACATGATGGTCTCATTGT 2999 0.500 32.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC AGAAGGCAGGGGTTTTTACG 982–1147 1.000 79.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT AGAAGGCAGGGGTTTTTACG 981–1146 1.000 79.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT AGAAGGCAGGGGTTTTTACG 983–1148 1.000 78.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAC AGAAGGCAGGGGTTTTTACG 984–1149 1.000 78.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGAAGGCAGGGGTTTTTACG 908–1073 1.000 78.2
psbK-psbI_p1 psbK-psbI CTGCCGTAAGCTTTCGATGA TTACGTCCCGGGTCATTAGA 502–503 1.000 78.5
psbK-psbI_p2 psbK-psbI CTGCCGTAAGCTTTCGATGA ACGTCCCGGGTCATTAGATA 500–501 1.000 76.7
psbK-psbI_p3 psbK-psbI CTGCCGTAAGCTTTCGATGA TACGTCCCGGGTCATTAGAT 501–502 1.000 76.7
psbK-psbI_p4 psbK-psbI CTGCCGTAAGCTTTCGATGA TTCTTCACGTCCCGGATTAC 518–519 1.000 74.3
psbK-psbI_p5 psbK-psbI CTGCCGTAAGCTTTCGATGA CGTCCCGGGTCATTAGATAG 499–500 1.000 71.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 342–355 1.000 67.9
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 345–358 1.000 67.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 348–361 1.000 67.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 351–364 1.000 66.9
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 412–425 1.000 65.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCTCATTTCCACCCCCAAG CCGGATTTGAACTGGGGAAA 1025–1239 1.000 78.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCTCATTTCCACCCCCAAG TGGGGAAAAAGGGATTTGCA 1013–1227 1.000 78.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCTCTCATTTCCACCCCCAA CCGGATTTGAACTGGGGAAA 1026–1240 1.000 77.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCTCTCATTTCCACCCCCA CCGGATTTGAACTGGGGAAA 1027–1241 1.000 77.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCTCTCATTTCCACCCCCAA TGGGGAAAAAGGGATTTGCA 1014–1228 1.000 77.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Siraitia grosvenorii NC_043881.1 158755 View on NCBI ↗
Siraitia siamensis NC_046482.1 159190 View on NCBI ↗