Markers + reference

Trichosanthes

14 species · Cucurbitaceae · Cucurbitales

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Species 14
Genome length 132–158 kb
Candidate markers 258
Primer pairs 100

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 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 937 0.0238 0.99 68.2 yes View details
rps16-trnQ LSC 1323 0.0202 1.00 76.0 yes View details
psbK-psbI LSC 375 0.0234 1.00 62.1 yes View details
trnR-atpA LSC 524 0.0312 1.00 79.1 yes View details
trnC-petN LSC 901 0.0203 0.99 74.9 yes View details
trnT-psbD LSC 1082 0.0164 0.99 69.7 yes View details
psbZ-trnG LSC 538 0.0256 0.93 71.5 yes View details
trnT-trnL LSC 976 0.0189 0.86 64.5 yes View details
ycf1 IRb 1191 0.0027 1.00 35.9 no View details
ndhF-rpl32 SSC 667 0.0263 0.98 75.5 yes View details
rpl32-trnL SSC 1076 0.0327 0.99 76.1 yes View details
rps15-ycf1 SSC 398 0.0303 0.97 71.3 yes View details
ycf1 SSC 5538 0.0120 1.00 49.9 yes View details
psbI-trnS LSC 107 0.0378 0.98 73.1 yes View details
trnE-trnT LSC 934 0.0188 0.98 72.4 yes View details
trnF-ndhJ LSC 696 0.0190 0.99 70.5 yes View details
trnG-trnR LSC 222 0.0229 0.95 67.2 yes View details
ycf3-trnS LSC 616 0.0136 1.00 65.6 yes View details
atpF-atpH LSC 328 0.0077 1.00 64.8 yes View details
rpl2-trnH IRa 104 0.0232 0.93 63.9 no View details
psaA-ycf3 LSC 743 0.0123 0.97 63.0 yes View details
psbE-petL LSC 1230 0.0154 1.00 63.0 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-rps16_p1 trnK-rps16 AGTCGCGGTCTTACAAACTC CCCAATGAGCCGTTTATCGA 1250–1315 1.000 88.0
trnK-rps16_p2 trnK-rps16 GTCGCGGTCTTACAAACTCT CCCAATGAGCCGTTTATCGA 1249–1314 1.000 88.0
trnK-rps16_p3 trnK-rps16 GTCGCGGTCTTACAAACTCT TCCCAATGAGCCGTTTATCG 1250–1315 1.000 88.0
trnK-rps16_p4 trnK-rps16 ACCCGACTTGACTTGCTTTT CCCAATGAGCCGTTTATCGA 1410 0.071 42.0
trnK-rps16_p5 trnK-rps16 ACCCGACTTGACTTGCTTTT TCCCAATGAGCCGTTTATCG 1411 0.071 42.0
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1332–1430 1.000 88.7
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1343–1441 1.000 88.1
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA GACGACCAACCACTACCAAT 1428–1526 1.000 85.2
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC GACGACCAACCACTACCAAT 1439–1537 1.000 84.7
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1336–1434 1.000 83.9
psbK-psbI_p1 psbK-psbI GCTGCCGTAAGCTTTCGATA TTACGTCCCGGGTCATTAGA 487–491 1.000 80.0
psbK-psbI_p2 psbK-psbI GCTGCCGTAAGCTTTCGATA CCCGGGTCATTAGAGAGGAA 481–485 1.000 79.5
psbK-psbI_p3 psbK-psbI GCTGCCGTAAGCTTTCGATA TTCTTCACGTCCCGGATTAC 503–507 1.000 75.7
psbK-psbI_p4 psbK-psbI GCTGCCGTAAGCTTTCGATA TACGTCCCGGGTCATTAGAG 487 0.071 36.9
psbK-psbI_p5 psbK-psbI GCTGCCGTAAGCTTTCGATA GTCCCGGGTCATTAGAGAGG 484 0.071 31.7
psbI-trnS_p1 psbI-trnS TTCCTCTCTAATGACCCGGG TGGACTAAAGCGTCGGATTG 216–225 1.000 87.3
psbI-trnS_p2 psbI-trnS TTCCTCTCTAATGACCCGGG GTGGACTAAAGCGTCGGATT 217–226 1.000 87.3
psbI-trnS_p3 psbI-trnS TTCCTCTCTAATGACCCGGG GACTAAAGCGTCGGATTGCT 214–223 1.000 84.5
psbI-trnS_p4 psbI-trnS TTCCTCTCTAATGACCCGGG CTGAGTGGACTAAAGCGTCG 221–230 1.000 84.2
psbI-trnS_p5 psbI-trnS TTCCTCTCTAATGACCCGGG ATTTGGGGAGAGATGGCTGA 237–246 1.000 83.6
trnG-trnR_p1 trnG-trnR AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 302–380 1.000 72.6
trnG-trnR_p2 trnG-trnR CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 305–383 1.000 72.3
trnG-trnR_p3 trnG-trnR AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 308–386 1.000 71.8
trnG-trnR_p4 trnG-trnR CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 311–389 1.000 71.5
trnG-trnR_p5 trnG-trnR ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 372–450 1.000 69.8
trnR-atpA_p1 trnR-atpA TGGAATGAAAAGCGTCCATTG TCCACCAAGACATTCACCAA 700–754 1.000 67.9
trnR-atpA_p2 trnR-atpA TGGAATGAAAAGCGTCCATTG TTCCACCAAGACATTCACCA 701–755 1.000 67.9
trnR-atpA_p3 trnR-atpA GGAATGAAAAGCGTCCATTGT TCCACCAAGACATTCACCAA 699–753 1.000 67.9
trnR-atpA_p4 trnR-atpA GGAATGAAAAGCGTCCATTGT TTCCACCAAGACATTCACCA 700–754 1.000 67.9
trnR-atpA_p5 trnR-atpA TGGAATGAAAAGCGTCCATTG CTTCCACCAAGACATTCACCA 702–756 1.000 67.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Trichosanthes baviensis NC_046864.1 156413 View on NCBI ↗
Trichosanthes cucumeroides NC_080536.1 156714 View on NCBI ↗
Trichosanthes kirilowii NC_041088.1 157481 View on NCBI ↗
Trichosanthes kirilowii var. japonica MT211648.1 157155 View on NCBI ↗
Trichosanthes nervifolia NC_046883.1 157550 View on NCBI ↗
Trichosanthes pubera subsp. rubriflos NC_072514.1 132385 View on NCBI ↗
Trichosanthes quinquangulata NC_080537.1 157493 View on NCBI ↗
Trichosanthes reticulinervis NC_072512.1 157462 View on NCBI ↗
Trichosanthes rosthornii NC_080912.1 157077 View on NCBI ↗
Trichosanthes subrosea NC_072508.1 157298 View on NCBI ↗
Trichosanthes tetragonosperma NC_072513.1 156887 View on NCBI ↗
Trichosanthes tricuspidata NC_046866.1 157459 View on NCBI ↗
Trichosanthes tridentata NC_072507.1 157213 View on NCBI ↗
Trichosanthes truncata NC_046875.1 156686 View on NCBI ↗