Markers + reference

Croomia

3 species · Stemonaceae · Pandanales

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Species 3
Genome length 154–155 kb
Candidate markers 274
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1086 0.0184 0.98 67.6 yes View details
trnS-GCU-trnG-UCC LSC 819 0.0220 1.00 68.3 yes View details
trnS-UGA-lhbA LSC 348 0.0192 1.00 61.2 yes View details
rps3 LSC 654 0.0061 1.00 50.7 yes View details
ndhD SSC 1506 0.0062 1.00 48.1 yes View details
rpl32-ndhF SSC 958 0.0250 0.99 64.9 yes View details
ndhD-ccsA SSC 205 0.0423 1.00 75.8 yes View details
ndhE-psaC SSC 385 0.0202 0.99 69.6 yes View details
rpl22-psbA LSC 115 0.0236 0.98 69.1 no View details
atpH-atpI LSC 561 0.0126 0.99 67.8 yes View details
accD-psaI LSC 678 0.0074 1.00 66.9 yes View details
psbM-trnD-GUC LSC 797 0.0067 1.00 66.7 yes View details
atpF-atpH LSC 178 0.0187 1.00 65.1 yes View details
ndhC-trnV-UAC LSC 542 0.0088 0.98 65.0 yes View details
rpl16-rps3 LSC 169 0.0377 0.99 64.6 yes View details
trnF-GAA-ndhJ LSC 703 0.0109 1.00 63.1 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_p1 trnK-UUU ATTTTCCGGATGGGTTGCC TCGATCATATCTACATATCATATTTTC 2684–2692 1.000 41.8
trnK-UUU_p2 trnK-UUU ATTTTCCGGATGGGTTGCC CGATCATATCTACATATCATATTTTC 2683–2691 1.000 41.8
trnK-UUU_p3 trnK-UUU TTTTCCGGATGGGTTGCC TCGATCATATCTACATATCATATTTTC 2683–2691 1.000 41.8
trnK-UUU_p4 trnK-UUU TTTTCCGGATGGGTTGCC CGATCATATCTACATATCATATTTTC 2682–2690 1.000 41.8
trnK-UUU_p5 trnK-UUU ATTTTCCGGATGGGTTGCCC TCGATCATATCTACATATCATATTTTC 2684–2692 1.000 41.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1017–1177 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1015–1175 1.000 85.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1023–1183 1.000 85.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1024–1184 1.000 85.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 999–1159 1.000 84.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 884–918 1.000 56.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCGAACCCTCGGTACCAATA ACGAATCACACTTTTACCACT 917–951 1.000 55.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 887–921 1.000 55.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 886–920 1.000 55.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GTCTTAAGCGATCGAAGGGG ACGAATCACACTTTTACCACT 953–987 1.000 55.6
atpF-atpH_p1 atpF-atpH TTAAACCCGAAACTCCCAGC CGGACTAGTCGTGGCATTAG 295–603 1.000 79.2
atpF-atpH_p2 atpF-atpH TTAAACCCGAAACTCCCAGC GGACTAGTCGTGGCATTAGC 294–602 1.000 79.0
atpF-atpH_p3 atpF-atpH TTAAACCCGAAACTCCCAGC GCGGAGGGTAAAATACGAGG 360–668 1.000 78.9
atpF-atpH_p4 atpF-atpH TTAAACCCGAAACTCCCAGC AGTCGTGGCATTAGCACTTT 289–597 1.000 78.7
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTCCCAGC ACTAGTCGTGGCATTAGCAC 292–600 1.000 77.8
atpH-atpI_p1 atpH-atpI TCCGATAGAAGCAAGCCCTA TTTTTGCAACTTTAGCCGCG 679–686 1.000 77.7
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 640–647 1.000 77.6
atpH-atpI_p3 atpH-atpI TCCGATAGAAGCAAGCCCTA TAGGTGAATCCATGGAGGGT 652–659 1.000 77.2
atpH-atpI_p4 atpH-atpI TACCCTCTACAGCTTGACCC TTTTTGCAACTTTAGCCGCG 725–732 1.000 77.1
atpH-atpI_p5 atpH-atpI GATAGAAGCAAGCCCTACGG TTTTTGCAACTTTAGCCGCG 676–683 1.000 77.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCCGTAGC TGCCATATGTCTCACTGGGA 820–937 1.000 81.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCCGTAGC TTCAATTGGTCAGAGCACCG 794–911 1.000 78.7
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCCGTAGC ATGCCATATGTCTCACTGGG 821–938 1.000 75.0
psbM-trnD-GUC_p4 psbM-trnD-GUC TAGAATGAACAGTGCCGTAGC TGCCATATGTCTCACTGGGA 821–938 1.000 74.8
psbM-trnD-GUC_p5 psbM-trnD-GUC ACTAGAATGAACAGTGCCGT TGCCATATGTCTCACTGGGA 823–940 1.000 74.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Croomia heterosepala NC_039673.1 154407 View on NCBI ↗
Croomia japonica NC_039672.1 154672 View on NCBI ↗
Croomia pauciflora NC_039674.1 155261 View on NCBI ↗