Markers + reference

Xerophyta

14 species · Velloziaceae · Pandanales

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Species 14
Genome length 155–156 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

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 725 0.0342 0.98 74.2 yes View details
rps16 LSC 754 0.0252 1.00 69.3 yes View details
atpH-atpI LSC 650 0.0426 1.00 77.0 yes View details
trnT-UGU-trnL-UAA LSC 1068 0.0372 0.90 78.1 yes View details
ndhC-trnV-UAC LSC 995 0.0315 0.97 76.8 yes View details
rbcL-accD LSC 741 0.0287 0.99 70.9 yes View details
psbE-petL LSC 1310 0.0286 0.99 73.3 yes View details
ndhF SSC 2238 0.0219 0.99 64.5 yes View details
ndhF-rpl32 SSC 906 0.0323 0.99 77.7 yes View details
ycf1 SSC 5682 0.0171 1.00 56.9 yes View details
psbC-trnS-UGA LSC 149 0.0485 1.00 78.6 yes View details
ndhG-ndhI SSC 361 0.0391 1.00 73.4 yes View details
psaA-ycf3 LSC 722 0.0135 1.00 72.8 yes View details
rpoB-trnC-GCA LSC 1288 0.0258 1.00 72.5 yes View details
trnH-GUG-psbA LSC 245 0.0453 0.92 70.9 no View details
rps16-trnQ-UUG LSC 955 0.0252 0.97 69.7 yes View details
trnL-UAG-ccsA SSC 83 0.0723 0.92 69.6 yes View details
petN-psbM LSC 584 0.0258 1.00 68.9 yes View details
rpl22-rps19 LSC 125 0.0520 1.00 68.3 yes View details
ndhE-ndhG SSC 178 0.0351 0.94 67.9 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC ATTTAAAGAAAGAACTTCGAGTT 745–818 1.000 51.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTAAAGAAAGAACTTCGAGTT 759–832 1.000 51.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTAAAGAAAGAACTTCGAGTT 758–831 1.000 51.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTAAAGAAAGAACTTCGAGTTAA 756–829 1.000 51.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG ATTTAAAGAAAGAACTTCGAGTT 770–843 1.000 51.4
rps16_p1 rps16 TGACCTCGGCAAAACATTGA TGTGATTGCGTCGATCTGTT 1937–2306 1.000 89.5
rps16_p2 rps16 TGACCTCGGCAAAACATTGA TTGTGATTGCGTCGATCTGT 1938–2307 1.000 89.5
rps16_p3 rps16 TGACCTCGGCAAAACATTGA GTTTGGGAAAACTGGGACCT 1701–2089 0.929 85.4
rps16_p4 rps16 GCTTGTTGAGGATTCCCACA TGTGATTGCGTCGATCTGTT 1442–1802 0.714 75.9
rps16_p5 rps16 GCTTGTTGAGGATTCCCACA TTGTGATTGCGTCGATCTGT 1443–1803 0.714 75.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGGCGATCATGTCCTTCAA CTTACAGCAGCTTGCCAAAC 1559–1610 0.929 85.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGCGATCATGTCCTTCAAGT CTTACAGCAGCTTGCCAAAC 1557–1608 0.929 85.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAGGCGATCATGTCCTTCAA GAAATCAAAATGGGGCGTGG 1048–1104 0.714 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGCGATCATGTCCTTCAAGT GAAATCAAAATGGGGCGTGG 1046–1102 0.714 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AATCCACAGGCGATCATGTC GAAATCAAAATGGGGCGTGG 1054–1110 0.714 77.2
atpH-atpI_p1 atpH-atpI TACCTTCTACAGCTTGGCCT CTGCGCCCACGAATGATATA 1115–1147 1.000 90.2
atpH-atpI_p2 atpH-atpI CTCAAATCAGTCCTTCCCGG CTGCGCCCACGAATGATATA 1401–1433 1.000 89.4
atpH-atpI_p3 atpH-atpI CTCAAATCAGTCCTTCCCGG GTGTAGAAGTCGGCCAACAT 1731–1763 1.000 88.3
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT CTGCGCCCACGAATGATATA 1032–1064 0.786 81.4
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT GTGTAGAAGTCGGCCAACAT 1362–1394 0.786 79.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GGTATTGTGGACATTCCCCC TTGTTTATCAGGCGACACCC 1338–1463 1.000 87.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TGTGGACATTCCCCCATTTC TTGTTTATCAGGCGACACCC 1333–1458 1.000 86.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CATTCCCCCATTTCCATCCC TTGTTTATCAGGCGACACCC 1327–1452 1.000 86.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GGTATTGTGGACATTCCCCC GCGACACCCAGATTTGAACT 1327–1452 1.000 85.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCATTTCCATCCCAGAGCAT TTGTTTATCAGGCGACACCC 1320–1445 1.000 85.5
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC CGTAAAAACAGTTAGCCAAAACG 629–656 1.000 60.9
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT CGTAAAAACAGTTAGCCAAAACG 628–655 1.000 60.9
petN-psbM_p3 petN-psbM TATGGGGAAGGAGTGGACTC CGTAAAAACAGTTAGCCAAAACG 627–654 1.000 60.5
petN-psbM_p4 petN-psbM GGGGAAGGAGTGGACTCTAG CGTAAAAACAGTTAGCCAAAACG 624–651 1.000 60.2
petN-psbM_p5 petN-psbM GTATGGGGAAGGAGTGGACT AAAACAGTTAGCCAAAACGA 624–651 1.000 56.8

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
Xerophyta acuminata PV219394.1 155449 View on NCBI ↗
Xerophyta dasylirioides PV077810.1 155184 View on NCBI ↗
Xerophyta eglandulosa PV177935.1 154908 View on NCBI ↗
Xerophyta equisetoides var. setosa PV239469.1 155106 View on NCBI ↗
Xerophyta humilis PV335039.1 155532 View on NCBI ↗
Xerophyta pinifolia PV177937.1 155087 View on NCBI ↗
Xerophyta rippsteinii PV219391.1 154893 View on NCBI ↗
Xerophyta schlechteri NC_043880.1 155498 View on NCBI ↗
Xerophyta schnizleinia PV239468.1 155197 View on NCBI ↗
Xerophyta sessiliflora PV177936.1 155035 View on NCBI ↗
Xerophyta simulans PV335040.1 155215 View on NCBI ↗
Xerophyta splendens PV335044.1 155209 View on NCBI ↗
Xerophyta squarrosa PV335037.1 154985 View on NCBI ↗
Xerophyta wentzeliana PV335045.1 154819 View on NCBI ↗