Permanent demo

Example: Salvia plastome candidate markers

This worked example uses the bundled Salvia GenBank files and displays the main MarkerSeek outputs directly on this page.

Job ID
MSK-EXAMPLE-DEMO
Samples
18
Reference
Salvia_chinensis.gb
Input folder
test_data/

Demo dataset and analysis design

The demonstration compares annotated plastomes from 18 Salvia samples. The reference file defines coordinates, feature names, and plastome regions; all candidate labels and detail pages are projected onto that reference coordinate system.

Input set

The demo uses GenBank files from test_data/. The selected coordinate reference is Salvia_chinensis.gb.

Output scope

MarkerSeek writes sliding-window Pi results, candidate-marker features, haplotypes, summary figures, primer outputs, and interactive feature payloads for the selected candidates.

Parameters used

hotspot_window
600 bp
hotspot_step
200 bp
hotspot_mode
top-percent
hotspot_value
3.0
similarity_window
200 bp
similarity_step
60 bp
primer_design
true
mafft_threads
4

Genome-wide result overview

The static figures summarize diversity and pairwise similarity across the aligned plastome. The downloadable PDF versions use the same data for publication-oriented export.

Example nucleotide diversity plot
Sliding-window nucleotide diversity with candidate hotspots.
Example pairwise similarity plot
Pairwise similarity tracks relative to the reference plastome.

Candidate markers

These candidates include the hotspot labels from the Pi plot plus the highest-scoring remaining MarkerSeek regions.

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 969 0.0366 0.57 62.0 yes View details
psbK-psbI LSC 396 0.0383 0.98 62.9 yes View details
psaA-ycf3 LSC 783 0.0342 0.97 70.1 yes View details
ndhF SSC 2217 0.0215 1.00 52.4 yes View details
rpl32-trnL-UAG SSC 703 0.0510 0.98 74.6 yes View details
ccsA-ndhD SSC 230 0.0754 0.97 65.7 yes View details
rps15-ycf1 SSC 425 0.0460 0.93 65.1 yes View details
ycf1 SSC 5508 0.0306 1.00 58.0 yes View details
trnE-UUC-trnT-GGU LSC 538 0.0340 1.00 74.3 yes View details
atpH-atpI LSC 969 0.0311 0.99 73.0 yes View details
trnK-UUU-rps16 LSC 569 0.0325 0.97 71.3 yes View details
rps4-trnT-UGU LSC 373 0.0302 0.94 71.1 yes View details
ndhC-trnV-UAC LSC 948 0.0264 0.99 70.4 yes View details
petN-psbM LSC 967 0.0305 0.99 70.2 yes View details
trnH-GUG-psbA LSC 307 0.0524 0.96 69.2 yes View details
ndhG-ndhI SSC 376 0.0465 0.98 69.0 yes View details
petA-psbJ LSC 1058 0.0333 0.96 67.4 yes View details
ndhF-rpl32 SSC 451 0.0410 0.98 67.4 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.

Feature detail example: rpl32-trnL-UAG

The selected marker preview combines summary metadata, the local Pi curve, haplotype network, species separation, and aligned bases.

label_name
rpl32-trnL-UAG
feature_type
igs
region
SSC
length_bp
703
variable_sites
106
pi
0.051
unique_haplotype_count
14
primer_available
yes
alignment_reliability
0.98
markerseek_score
74.60

Pi Curve

Haplotype Network

Species Separation

Alignment Viewer

                         1                                                                                                   
Salvia_aethiopis_1       GTTATTAAGAAATAAAGCGG-AAACCTTAGAAC---------CGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_amarissima_2      GTTATTAAGAAATAAAGCGGAAAACCTTACAACAATATAAATCGACCTGACTCAAAAATGGAATCCTTCCATTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_chinensis_3       GTTATTAAGAAATAAAGCGGAAAACCTTAGAACAATATAAATCGACCTGACTCAAAAATGGAACGCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_dorrii_4          GTTATTAAGAAATAAAGCGGAAAACCTTAGAAGAATATAAATCGACCTGACTCAAAAATTGAACCCTTCCATTTC-AAAAAAAATTCCCCAATTCCATTT
Salvia_eremostachya_5    GTTATTAAGAAATAAAGCGGAAAACCTTAGAACAATATAAATCGACCTGACTCAAAAATTGAACCCTTCCATTTC-AAAAAAAATTCCCCAATTCCATTT
Salvia_fruticosa_6       GTTATTAAGAAATAAAGCGG-AAACCTTAGAACAATATAAATCGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_huberi_7          GTTATTAAGAAATAAAGCGG-AAACCTTAGAACAATATAAATCGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_kronenburgii_8    GTTATTAAGAAATAAAGCGG-AAACCTTAGAACAATATAAATCGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_limbata_9         GTTATTAAGAAATAAAGCGG-AAACCCTAGAAC---------CGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_mohavensis_10     GTTATTAAGAAATAAAGCGGAAAACCTTAGAACAATATAAATCGACCTGACTCAAAAATTGAACCCTTCCATTTC-AAAAAAAATTCCCCAATTCCATTT
Salvia_officinalis_subsp GTTATTAAGAAATAAAGCGG-AAACCTTAGAACAATATAAATCGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_pachyphylla_12    GTTATTAAGAAATAAAGCGGAAAACCTTAGAACAATATAAATCGACCTGACTCAAAAATGGAACCCTTCCATTTC-AAAAAAAATTCCCCAATTCCATTT
Salvia_pratensis_13      GTTATTAAGAAATAAAGCGG-AAACCCTAGAAC---------CGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_saccardiana_14    GTTATTAAGAAATAAAGCGG-AAACCCTAGAAC---------CGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_sonomensis_15     GTTATTAAGAAATAAAGCGGAAAACCTTAGAACAATATAAATCGACCTGACTCAAAAATGGAACCCTTCCATTTC-AAAAAAAATTCCCCAATTCCATTT
Salvia_spathacea_16      GTTATTAAGAAATAAAGCGGAAAACCTTAGAAGAATATAAATCGACCTGACTCAAAAATTGAACCCTTCCATTTC-AAAAAAAATTCCCCAATTCCATTT
Salvia_verbenaca_17      GTTATTAAGAAATAAAGCGG-AAACCCTAGAAC---------CGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
Salvia_xanthocheila_18   GTTATTAAGAAATAAAGCGG-AAACCCTAGAAC---------CGACCTGATTCAAAAATGGAACCCTTCCGTTTCAAAAAAAAATTCCCCAATTCCATTT
                         101                                                                                                 
Salvia_aethiopis_1       CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCAAATTTAAACAAAGTTTTATCAATACAAAAAAATACAAGATACTAGATTTA
Salvia_amarissima_2      CCTATTGATTAATTCACCAGGAAATGGAATTCTTCTGTTTACTTTGACCGAATTCAAACAAAGTTTTTTTAAC-AAAAAAAACACAAGATACTCGATTTC
Salvia_chinensis_3       CCTGGTAAATTAATCAATGGGAAATGGAATTCTTCTGGTTACTTTGACCGAATTCAAACAAAGTTTTTTTAACAAAAAAAAACACAAGATACTTGATTTA
Salvia_dorrii_4          CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACTGAATTCAAACAAAGTTTTTTTTAACAAAAAAAACACAAGATACTCAATTTA
Salvia_eremostachya_5    CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACTGAATTCAAACAAAGTTTTTTTAACAAAAAAAAACACAAGATACTCAATTTA
Salvia_fruticosa_6       CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCTAATTTAAACAAAGTTTTTTT---ACAAAAAAATACAAGATACTCGATTTA
Salvia_huberi_7          CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCTAATTTAAACAAAGTTTTTTT---ACAAAAAAATACAAGATACTCGATTTA
Salvia_kronenburgii_8    CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCTAATTTAAACAAAGTTTTTTT---ACAAAAAAATACAAGATACTCGATTTA
Salvia_limbata_9         CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCAAATTTAAACAAAGTTTTATCAATACAAAAAAATACAAGATACTAGATTTA
Salvia_mohavensis_10     CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACTGAATTCAAACAAAGTTTTTTTTAACAAAAAAAACACAAGATACTCAATTTA
Salvia_officinalis_subsp CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCTAATTTAAACAAAGTTTTTTT---ACAAAAAAATACAAGATACTCGATTTA
Salvia_pachyphylla_12    CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACTGAATTCAAACAAAGTTTTTTTTAACAAAAAAAACACAAGATACTCAATTTA
Salvia_pratensis_13      CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCAAATTTAAACAAAGTTTTATCAATACAAAAAAATACAAGATACTAGATTTA
Salvia_saccardiana_14    CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCAAATTTAAACAAAGTTTTATCAATACAAAAAAATACAAGATACTAGATTTA
Salvia_sonomensis_15     CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACTGAATTCAAACAAAGTTTTTTTTAACAAAAAAAACACAAGATACTCAATTTA
Salvia_spathacea_16      CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACTGAATTCAAACAAAGTTTTTTTTAACAAAAAAAACACAAGATACTCAATTTA
Salvia_verbenaca_17      CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCAAATTTAAACAAAGTTTTATCAATACAAAAAA-------ATACTAGATTTA
Salvia_xanthocheila_18   CCTGGTGAATTAATCAATAGGAAATGGAATTCTTCTGTTTACTTTGACCAAATTTAAACAAAGTTTTATCAATACAAAAAAATACAAGATACTAGATTTA
                         201                                                                                                 
Salvia_aethiopis_1       TATTTTAGTATATTTTGTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTAATATA--TCTTTTTTGTACAACTTGCTTACTTTTGGATTTT
Salvia_amarissima_2      AATTTTCGTATATTTTATTTCCAGGACGGGAGTCTTTTTTTCCCATCAACCTATTTGTACTATAAATATTTTTTGTACAACTTTCTTACTTTTGAATTTC
Salvia_chinensis_3       AATTTTCGTATATTTTCTTGCCAGGACGGGAGTCTTTTTTTCCCATCAATCTATTTGTACTATAAATATTTTTTGCACAACTTTCTTACTTTTTAATTTC
Salvia_dorrii_4          AATTTGAGTATATTTTCTTTCCAGGACGGGAGTCTTTTTTTCCCATCAACCTATTTGTACTATAAATATTTTTTGTACAACTTTCTTACTTTTGAATTTC
Salvia_eremostachya_5    AATTTGAGTATATTTTCTTTCCAGGACGAGAGTCTTTTTTTCCCATCAACCTATTTGTACTATAAATATTTTTTGTACAACTTTCTGACTTTTGAATTTC
Salvia_fruticosa_6       TATTTTAGTATATTTTCTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTACTATA--CCTTT-TTGTACAACTTGCTTACTTTTGGATTTT
Salvia_huberi_7          TATTTTAGTATATTTTCTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTACTATA--CCTTT-TTGGACAACTTGCTTACTTTTGGATTTT
Salvia_kronenburgii_8    TATTTTAGTATATTTTCTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTACTATA--CCTTT-TTGGACAACTTGCTTACTTTTGGATTTT
Salvia_limbata_9         TATTTTAGTATATTTTGTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTAATAGA--TCTTTTTTGTACAACTTGCTTACTTTTGGATTTT
Salvia_mohavensis_10     AATTTTAGTATATTTTCTTTCCAGGACGGGAGTCTTTTTTTCCCATCAACCTATTTGTACTATAAATATTTTTTGTACAACTTTCTTACTTTTGAATTTC
Salvia_officinalis_subsp TATTTTAGTATATTTTCTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTACTATA--CCTTT-TTGTACAACTTGCTTACTTTTGGATTTT
Salvia_pachyphylla_12    AATTTTAGTATATTTTCTTTCCAGGACGGGAGTCTTTTTTTCCCATCAACCTATTTGTACTA--------------------------------------
Salvia_pratensis_13      TATTTTAGTATATTTTGTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTAATATA--TCTTTTTTGTACAACTTGCTTACTTTTGGATTT-
Salvia_saccardiana_14    TATTTTAGTATATTTTGTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTAATATA--TCTTTTTTGTACAACTTGCTTACTTTTGGATTT-
Salvia_sonomensis_15     AATTTTAGTATATTTTCTTTCCAGGACGGGAGTCTTTTTTTCCCATCAACCTATTTGTACTA--------------------------------------
Salvia_spathacea_16      AATTTGAGTATATTTTCTTTCCAGGACGGGAGTCTTTTTTTCCCATCAACCTATTTGTACTATAAATATTTTTTGTACAACTTTCTTACTTTTGAATTTC
Salvia_verbenaca_17      TATTTTAGTATGTTTTGTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTAATATA--TCTTTTTTGTACAACTTGCTTACTTTTGGATTTT
Salvia_xanthocheila_18   TATTTTAGTATATTTTGTTTCCAGGATGGGAGTCTTTTTTTCCCATCAATCTATTTGTAATATA--TCTTTTTTGTACAACTTGCTTACTTTTGGATTTT
                         301                                                                                                 
Salvia_aethiopis_1       TATATATTCTTATATAGAGCCCCTATAGCTCTCACCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_amarissima_2      TATAAATTCTTATATAGAGCCGATATATCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTTGAATAAT
Salvia_chinensis_3       TATAAATTCTTATATAGAGCCCATATATCTCTCCCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATGGGTGTGAATTTTGAATAAT
Salvia_dorrii_4          TATAAATTCTTATATAGAGCCTATATATCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTTGAATAAT
Salvia_eremostachya_5    TATAAATTCTTATATAGAGCCCATATATCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTTGAATAAT
Salvia_fruticosa_6       TATAAATTCTTATATAGAGCCCATATAGCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_huberi_7          TATAAATTCTTATATAGAGCCCATATAGCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_kronenburgii_8    TATAAATTCTTATATAGAGCCCATATAGCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_limbata_9         TATATATTCTTATATAGAGCCCCTATAGCTCTCACCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_mohavensis_10     TATAAATTCTTATATAGAGCCTATATATCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTTGAATAAT
Salvia_officinalis_subsp TATAAATTCTTATATAGAGCCCATATAGCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_pachyphylla_12    ----------------------------------------------------------------------------------------------------
Salvia_pratensis_13      TATATATTCTTATATAGAGCCCCTATAGCTCTCACCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_saccardiana_14    TATATATTCTTATATAGAGCCCCTATAGCTCTCACCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_sonomensis_15     ----------------------------------------------------------------------------------------------------
Salvia_spathacea_16      TATAAATTCTTATATAGAGCCTATATATCTCTCGCCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTTGAATAAT
Salvia_verbenaca_17      TATATATTCTTATATAGAGCCCCTATAGCTCTCACCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
Salvia_xanthocheila_18   TATATATTCTTATATAGAGCCCCTATAGCTCTCACCATCAATTCACGCAAAAACACTTAATGAAAATATTCTGGATAAATATGTGTGAATTTGGAAAAAT
                         401                                                                                                 
Salvia_aethiopis_1       CTAAAATATTTTTTTGTTTATTGATAAAACTTATTTTTGGGTTGTACTTTTTAAAATGAAAATCAAATAAATCAAAAACGGTAAATTAAAA---------
Salvia_amarissima_2      CTAAAATATTTTTTTT------------------------------------------------------------------------------------
Salvia_chinensis_3       CTAAAATCTTTTTTGGTTCATTCATAAAACAGATTTTTGGGTTGTACTTTTTGAAATTAAAATCAAATAACTCAAAAACGGTAAATTTTAAAAAATGTTT
Salvia_dorrii_4          CTAAAATATTTTTTTGTTCATTTATAAAACTCATTTTGGGGTTGTACTTTTTAAAATTAAAATCAAATAACTTAAAAACGGTAAATAAAAAAATGTTTTT
Salvia_eremostachya_5    CTAAAATATTTTTTTGTTCATTCATAAAACTCATTTTGGGGTTGTACTTTTTAAAATGAAAATCAAATAACTCAAAAACGGTAAATAAAAAAATGTTTTT
Salvia_fruticosa_6       CTAAAATATTTTTTTGTTCATTGATAAAACTTATTTTTGGGTTGTACTTTTTTAAATGAAAATCAAATAAATCAAAAACGGTAAATAAAAA---------
Salvia_huberi_7          CTAAAATATTTTTTTGTTCATTGATAAAACTTATTTTGGGGTTGTACTTTTTTAAATGAAAATCAAATAAATCAAAAACGGTAAATAAAAA---------
Salvia_kronenburgii_8    CTAAAATATTTTTTTGTTCATTGATAAAACTTATTTTTGGGTTGTACTTTTTTAAATGAAAATCAAATAAATCAAAAACGGTAAATAAAAA---------
Salvia_limbata_9         CTAAAATATTTTTTTGTTTATTGATAAAACTTATTTTTGGGTTGTACTTTTTAAAATGAAAATCAAATAAATCAAAAACGGTAAATTAAAA---------
Salvia_mohavensis_10     CTAAAATATTTTTTTGTTCATTTATAAAACTCATTTTGGGGTTGTACTTTTTAAAATTAAAATCAAATAACTTAAAAACGGTAAATAAAAAAATGTTTTT
Salvia_officinalis_subsp CTAAAATATTTTTTTGTTCATTGATAAAACTTATTTTTGGGTTGTACTTTTTTAAATGAAAATCAAATAAATCAAAAACGGTAAATAAAAA---------
Salvia_pachyphylla_12    ----------------------------------------------------------------------------------------------------
Salvia_pratensis_13      CTAAAATATTTTTTTGTTTATTGATAAAACTTATTTTTGGGTTGTACTTTTTAAAATGAAAATCAAATAAATCAAAAACGGTAAATTAAAA---------
Salvia_saccardiana_14    CTAAAATATTTTTTTGTTTATTGATAAAACTTATTTTTGGGTTGTACTTTTTAAAATGAAAATCAAATAAATCAAAAACGGTAAATTAAAA---------
Salvia_sonomensis_15     ----------------------------------------------------------------------------------------------------
Salvia_spathacea_16      CTAAAATATTTTTTTGTTCATTTATAAAACTCATTTTGGGGTTGTACTTTTTAAAATTAAAATCAAATAACTTAAAAACGGTAAATAAAAAAATGTTTTT
Salvia_verbenaca_17      CTAAAATATTTTTTTGTTTATTGATAAAACTTATTTTTGGGTTGTACTTTTTAAAATGAAAATCAAATAAATAAAAAACGGTAAATTAAAA---------
Salvia_xanthocheila_18   CTAAAATATTTTTTTGTTTATTGATAAAACTTATTTTTGGGTTGTACTTTTTAAAATGAAAATCAAATAAATCAAAAACGGTAAATTAAAA---------
                         501                                                                                                 
Salvia_aethiopis_1       ---ATGGGGGGCTTAATTCCTAGTAAGACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAACAAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_amarissima_2      ---GGGGGAAGCTTAATTCATAGTAAAACTTGCTGGTTTTAAAAGAGTTACGAGTCTAAAATCCACAATAAAACTAAAACAATGAACCTTCAAGTACATA
Salvia_chinensis_3       TTTTGGGGGGGCTTAATGCATAGTAAAACTTGCTGCTTTTACAAGAGTTCCAAGTCTAAAACCCACAATAAAACTAAAACAATGAACCTTCAAGTACATA
Salvia_dorrii_4          TTTTGGGGGGGCTTAATTCATAGTAAAACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAATAAAACTAAAACAATGAACCTTCAAGTACATA
Salvia_eremostachya_5    TTT-TGGGGGGCTTAATTCATAGTAAAACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAATAAAACTAAAACAATGAACCTTCAAGTACATA
Salvia_fruticosa_6       ---ATGGGGGGCTTAATTCATAGTAAGACTTGCTAGTTTTACAAGAGTTCCA-----------------AAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_huberi_7          ---ATGGGGGGCTTAATTCATAGTAAGACTTGCTAGTTTTACAAGAGTTCCA-----------------AAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_kronenburgii_8    ---ATGGGGGGCTTAATTCATAGTAAGACTTGCTAGTTTTACAAGAGTTCCA-----------------AAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_limbata_9         ---ATGGGGGGCTTAATTCCTAGTAAGACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAACAAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_mohavensis_10     TTTGGGGGGGGCTTAATTCATAGTAAAACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAATAAAACTAAAACAATGAACCTTCAAGTACATA
Salvia_officinalis_subsp ---ATGGGGGGCTTAATTCATAGTAAGACTTGCTAGTTTTACAAGAGTTCCA-----------------AAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_pachyphylla_12    ----------------------------------------------------------------------------------------------------
Salvia_pratensis_13      ---ATGGGGGGCTTAATTCCTAGTAAGACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAACAAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_saccardiana_14    ---ATGGGGGGCTTAATTCCTAGTAAGACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAACAAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_sonomensis_15     ----------------------------------------------------------------------------------------------------
Salvia_spathacea_16      TTTTGGGGGGGCTTAATTCATAGTAAAACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAATAAAACTAAAACAATGAACCTTCAAGTACATA
Salvia_verbenaca_17      ---ATGGGGGTCTTAATTCCTAGTAAGACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAACAAAACTAAAATAATGAACCTTCAAGTACATA
Salvia_xanthocheila_18   ---ATGGGGGGCTTAATTCCTAGTAAGACTTGCTGGTTTTACAAGAGTTCCAAGTCTAAAATCCACAACAAAACTAAAATAATGAACCTTCAAGTACATA
                         601                                                                                                 
Salvia_aethiopis_1       TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_amarissima_2      TTTGAAGAAATTGGTATTCATCGATTTGAATCTTTCCTGCAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATAAAGTCAAGA
Salvia_chinensis_3       TTTGAAGAAATTTGTATTCATCAATTTGAATCTTTCCAACAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATAGGGTCAAGA
Salvia_dorrii_4          TTTGAACAAATATGTATTCATCGATTTGAATCTTTCCTGCAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATAAAGTCAAGA
Salvia_eremostachya_5    TTTGAACAAATTGGTATTCATCGATTTGAATCTTTCCTGCAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATAAAGTCAAGA
Salvia_fruticosa_6       TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAA---TGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_huberi_7          TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAA---TGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_kronenburgii_8    TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAA---TGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_limbata_9         TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_mohavensis_10     TTTGAACAAATATGTATTCATCGATTTGAATCTTTCCTGCAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATAAAGTCAAGA
Salvia_officinalis_subsp TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAA---TGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_pachyphylla_12    -------------------------------------------------------------TAGACGATTTCTTATTCATAGGCTATTATAAAGTCAAGA
Salvia_pratensis_13      TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_saccardiana_14    TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_sonomensis_15     -------------------------------------------------------------TAGACGATTTCTTATTCATAGGCTATTATAAAGTCAAGA
Salvia_spathacea_16      TTTGAACAAATATGTATTCATCGATTTGAATCTTTCCTGCAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATAAAGTCAAGA
Salvia_verbenaca_17      TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
Salvia_xanthocheila_18   TTTGAACAAATTTTTATTCATCGATTTGAATCTTTTCTAGAAAATATTGCATTCTTAAATCTAGACGATTTCTTATTCATAGGCTATTATGGGGTCAAGA
                         701
Salvia_aethiopis_1       CAA
Salvia_amarissima_2      CAG
Salvia_chinensis_3       CAA
Salvia_dorrii_4          CAA
Salvia_eremostachya_5    CAA
Salvia_fruticosa_6       CAA
Salvia_huberi_7          CAA
Salvia_kronenburgii_8    CAA
Salvia_limbata_9         CAA
Salvia_mohavensis_10     CAA
Salvia_officinalis_subsp CAA
Salvia_pachyphylla_12    CAA
Salvia_pratensis_13      CAA
Salvia_saccardiana_14    CAA
Salvia_sonomensis_15     CAA
Salvia_spathacea_16      CAA
Salvia_verbenaca_17      CAA
Salvia_xanthocheila_18   CAA

Downloadable output files

The same files are available here for checking column names, figure exports, primer results, and reusable FASTA/TSV outputs.

Download all results candidate_marker_features.tsv haplotype_assignments.tsv pi_plot.pdf pi_windows.tsv primers.tsv sample_metadata.tsv similarity_plot.pdf