Markers + reference

Tradescantia

2 species · Commelinaceae · Commelinales

Back to catalogue

Species 2
Genome length 164–165 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1137 0.0044 1.00 61.3 yes View details
rps16-trnQ-UUG LSC 2280 0.0142 0.99 65.3 yes View details
trnS-GCU-trnG-UCC LSC 689 0.0120 0.97 69.0 yes View details
rbcL-accD LSC 1088 0.0038 0.96 64.9 yes View details
accD-psaI LSC 600 0.0083 1.00 63.5 yes View details
petA-psbJ LSC 880 0.0114 1.00 65.5 yes View details
clpP LSC 2473 0.0020 1.00 57.9 yes View details
rps3-rpl22 LSC 599 0.0067 0.99 62.3 yes View details
ndhF SSC 2217 0.0014 1.00 53.1 yes View details
rps15-ycf1 SSC 705 0.0072 0.99 64.2 yes View details
trnE-UUC-trnT-GGU LSC 915 0.0023 0.96 64.2 yes View details
rps4-trnT-UGU LSC 670 0.0016 0.96 63.5 yes View details
matK-trnK-UUU LSC 1150 0.0044 0.99 62.5 yes View details
ndhF-rpl32 SSC 522 0.0058 0.98 62.1 yes View details
rps8-rpl14 LSC 538 0.0000 0.93 61.8 yes View details
petN-psbM LSC 1247 0.0048 1.00 61.5 yes View details
psbM-trnD-GUC LSC 1164 0.0017 0.98 61.4 yes View details
trnT-GGU-psbD LSC 970 0.0011 0.98 61.0 yes View details
atpH-atpI LSC 1326 0.0000 0.97 60.8 yes View details
rpl20-rps12 LSC 970 0.0000 0.98 60.3 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
matK-trnK-UUU_p1 matK-trnK-UUU AGAAGATGCTGTTGCCAAGA TCGGGGTTGCTAACTCAATG 1239–1246 1.000 75.8
matK-trnK-UUU_p2 matK-trnK-UUU AGAAGATGCTGTTGCCAAGA GGGGTTGCTAACTCAATGGT 1237–1244 1.000 75.0
matK-trnK-UUU_p3 matK-trnK-UUU AGAAGATGCTGTTGCCAAGAT TCGGGGTTGCTAACTCAATG 1239–1246 1.000 71.8
matK-trnK-UUU_p4 matK-trnK-UUU AGAAGATGCTGTTGCCAAGAT GGGGTTGCTAACTCAATGGT 1237–1244 1.000 70.9
matK-trnK-UUU_p5 matK-trnK-UUU AGAAGATGCTGTTGCCAAGA CGGGGTTGCTAACTCAATGG 1238–1245 1.000 69.5
rps16_p1 rps16 AGGTACTATAATTACATTACCTTCT ATATCCCGAATTCCCATCGC 1318 1.000 40.3
rps16_p2 rps16 AGGTACTATAATTACATTACCTTCTT ATATCCCGAATTCCCATCGC 1318 1.000 40.3
rps16_p3 rps16 AGGTACTATAATTACATTACCTTCT CGCGTTGAGCCAATGACTAT 1301 1.000 40.3
rps16_p4 rps16 AGGTACTATAATTACATTACCTTCTTT ATATCCCGAATTCCCATCGC 1318 1.000 40.3
rps16_p5 rps16 AGGTACTATAATTACATTACCTTCTT CGCGTTGAGCCAATGACTAT 1301 1.000 40.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 2345–2349 1.000 78.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGGACACAAAATCCACAGCT GAGGTTCGAATCCTTCCGTC 2383–2387 1.000 78.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 2371–2375 1.000 77.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 2372–2376 1.000 77.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA TTTAAACAGTGATGGGGCGT 2405–2409 1.000 76.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAGAAGTCTCGGGTAGTTGC ACGAATCACACTTTTACCACT 826–837 1.000 54.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GAAGTCTCGGGTAGTTGCAG ACGAATCACACTTTTACCACT 824–835 1.000 54.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 752–763 1.000 54.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCGGGTAGTTGCAGTAAACG ACGAATCACACTTTTACCACT 818–829 1.000 54.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GAAGTCTCGGGTAGTTGCAG GAACGAATCACACTTTTACCACT 826–837 1.000 53.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCAGCGGAAAT ATTTTTGCAACGTTAGCCGC 1415–1419 1.000 77.3
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGTCCC ATTTTTGCAACGTTAGCCGC 1498–1502 1.000 76.3
atpH-atpI_p3 atpH-atpI AATAACGGAAGCAGCGGAAA ATTTTTGCAACGTTAGCCGC 1416–1420 1.000 76.1
atpH-atpI_p4 atpH-atpI ATAACGGAAGCAGCGGAAAT CCGCGGCTTATATAGGTGAA 1399–1403 1.000 76.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC ATTTTTGCAACGTTAGCCGC 1430–1434 1.000 75.8
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTTATCT 1351–1354 1.000 50.6
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTTATCT 1350–1353 1.000 50.6
petN-psbM_p3 petN-psbM TCCCTCTCGCTCGTAGTATG TGCTACTGCACTGTTTATCT 1365–1368 1.000 50.5
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTTATCT 1409–1412 1.000 50.3
petN-psbM_p5 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTTATCT 1349–1352 1.000 50.1

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
Tradescantia ohiensis MZ203134.1 164140 View on NCBI ↗
Tradescantia virginiana MW617994.1 164925 View on NCBI ↗