Hotspot

rps16-trnQ-UUG

LSC · 5947-6915 · 969 bp

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Pi 0.0366
MarkerSeek score 62.00
Primer available yes
Label rps16-trnQ-UUG

Feature Metadata

label_name
rps16-trnQ-UUG
feature_type
igs
region
LSC
length_bp
969
variable_sites
97
pi
0.0366
unique_haplotype_count
14
primer_available
yes
alignment_reliability
0.57
markerseek_score
62.00

Pi Curve

Alignment Viewer

                         1                                                                                                   
Salvia_aethiopis_1       AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGCCCATAGACATCACAATCTACAC-TTT
Salvia_amarissima_2      AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTACGGAATCATGAATAGTCATCGGTTCAGCTGTCCATAGACATCGCAATCTCCACTTTT
Salvia_chinensis_3       AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTACGGAATCATGAATAGTCATCGGTTCAGCTGTCCATAGACATCGCAATCTACACTTTT
Salvia_dorrii_4          AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTACGGAATCATGAATAGTCATCGGTTCAGCTGTCCATAGACATCGCAATCTCCACTTTT
Salvia_eremostachya_5    AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTACGGAATCATGAATAGTCATCGGTTCAGCTGTCCATAGACATCGCAATCTCCACTTTT
Salvia_fruticosa_6       AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGTCCATAGACATCACAATCTACAC-TTT
Salvia_huberi_7          AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGTCCATAGACATCACAATCTACAC-TTT
Salvia_kronenburgii_8    AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGTCCATAGACATCACAATCTACAC-TTT
Salvia_limbata_9         AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGTCCATAGACATCACAATCTACAC-TTT
Salvia_mohavensis_10     AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTACGGAATCATGAATAGTCATCGGTTCAGCTGTCCATAGACATCGCAATCTCCACTTTT
Salvia_officinalis_subsp AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGTCCATAGACATCACAATCTACAC-TTT
Salvia_pachyphylla_12    AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTACGGAATCATGAATAGTCATCGGTTCAGCTGTCCATAGACATCGCAATCTCCACTTTT
Salvia_pratensis_13      AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGTCCATAGACATCACAATCTACAC-TTT
Salvia_saccardiana_14    AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGTCCATAGACATCACAATCTACAC-TTT
Salvia_sonomensis_15     AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTACGGAATCATGAATAGTCATCGGTTCAGCTGTCCATAGACATCGCAATCTCCACTTTT
Salvia_spathacea_16      AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTACGGAATCATGAATAGTCATCGGTTCAGCTGTCCATAGACATCGCAATCTCCACTTTT
Salvia_verbenaca_17      AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCGTCCATAGACATCACAATCTACAC-TTT
Salvia_xanthocheila_18   AACATTCCTCTAATTTGGAACCGGTATGGAATTGATTCAATTATGGAATCATGAATAGTCATCGGTTCAGCCATCCATAGACATCACAATCTACAC-TTT
                         101                                                                                                 
Salvia_aethiopis_1       TCTTCTAT--------ATATGATACATTAAACAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACAAAGTTAACAGACTA-----------
Salvia_amarissima_2      TCTTCTATATATGAATATATAATACATGAAACAATATTTTTCTGAAAAAATCCTAGCAAGACAAC-----------------------------------
Salvia_chinensis_3       TCTTCTATATATGAATATATAATACATGAAACAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATATTTAACAGACTATATAGAATATA
Salvia_dorrii_4          TCTTCTATATATGAATATATAATACATGAAAGAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATATTTAACAGACTA-----------
Salvia_eremostachya_5    TCTTCTATATATGAATATATAATACATGAAAGAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATATTTAACAGACTA-----------
Salvia_fruticosa_6       TCTTCTATATATGAATATATGATACATGAAACAAGATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATAGTTAACAGACTA-----------
Salvia_huberi_7          TCTTCTATATATGAATATATGATACATGAAACAAGATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATAGTTAACAGACTA-----------
Salvia_kronenburgii_8    TCTTCTATATATGAATATATGATACATGAAACAAGATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATAGTTAACAGACTA-----------
Salvia_limbata_9         TCTTCTAT--------ATATGATACATTAAACAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACAAAGTTAACAGACTA-----------
Salvia_mohavensis_10     TCTTCTATATATGAATATATAATACATGAAAGAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATATTTAACAGACTA-----------
Salvia_officinalis_subsp TCTTCTATATATGAATATATGATACATGAAACAAGATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATAGTTAACAGACTA-----------
Salvia_pachyphylla_12    TCTTCTATATATGAATATATAATACATGAAAGAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATATTTAACAGACTA-----------
Salvia_pratensis_13      TCTTCTATAC---AATATATGATACATTAAACAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACAAAGTTAACAGACTA-----------
Salvia_saccardiana_14    TCTTCTATAC---AATATATGATACATTAAACAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACAAAGTTAACAGACTA-----------
Salvia_sonomensis_15     TCTTCTATATATGAATATATAATACATGAAAGAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATATTTAACAGACTA-----------
Salvia_spathacea_16      TCTTCTATATATGAATATATAATACATGAAAGAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACATATTTAACAGACTA-----------
Salvia_verbenaca_17      TCTTCTATA------TATATGATACATTAAACAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACAAAGTTAACAGACTA-----------
Salvia_xanthocheila_18   TCTTCTAT--------ATATGATACATTAAACAATATTTTTCTGAAAAAATCCTAGCAAGACAACATTTTTAACAAAGTTAACAGACTA-----------
                         201                                                                                                 
Salvia_aethiopis_1       ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_amarissima_2      ----------------------------------------------------------------------------------------------------
Salvia_chinensis_3       TATAAACTAATAGAATATATATAAAATAGATAATAGAAAGAAAAAAGAAATCTATATCTATAATATATAGATATATATGGAAATAATATATAAACGAATA
Salvia_dorrii_4          -ATAGAATTATAGAATATATATATAAAATATAATAGAAAGAAAAAAGAAATCTATAATATATATATATAGA-ATATATATAAATAATATATAAACGAATA
Salvia_eremostachya_5    -ATAGAATTATAGAATATATATAAAATATATAATAGAAAGAAAAAAGAAATCTATATCTATAATATATAGA-ATATATTTAAATAATATATAAACGAATA
Salvia_fruticosa_6       ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_huberi_7          ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_kronenburgii_8    ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_limbata_9         ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_mohavensis_10     -ATAGAATTATAGAATATATATAAA-----------------------------------------------------ATAAATAATATATAAACGAATA
Salvia_officinalis_subsp ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_pachyphylla_12    -ATAGAATTATAGAATATATATAAAATATATAATAGAAAGAAAAAAGAAATC-------------------------TATAAATAATATATAAACGAATA
Salvia_pratensis_13      ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_saccardiana_14    ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_sonomensis_15     -ATAGAATTATAGAATATATATAAAATATAT-----------------------------------------------ATAAATAATATATAAACGAATA
Salvia_spathacea_16      -ATAGAATTATAGAATATATATATAAAATATAATAGAAAGAAAAAAGAAATCTATAATATATATATATAGA-ATATATATAAATAATATATAAACGAATA
Salvia_verbenaca_17      ---------ATAGAATATATA-------------------------------------------------------------------------------
Salvia_xanthocheila_18   ---------ATAGAATATATA-------------------------------------------------------------------------------
                         301                                                                                                 
Salvia_aethiopis_1       ----------------------------------------------------------------------------------------------------
Salvia_amarissima_2      --------------------------------------------------------CTTTTTCAAAGATCCCACGTACAGGGAATCGTTAAAAATCTTTT
Salvia_chinensis_3       AGTTTTGAAATCTGCATCTTCAAGTGACTTAATAAGATAAATTAAACGATTTCCTACTTTTTCAAAGATTCCACGTATAGGGAATCATTAAAAATATTTC
Salvia_dorrii_4          AGTTTTGGAATCTGCATCTTCAAGTGACTTAATAAGATAAATTAAACGATTTCCTACTTTTTCAAAGATTCCACGTACAGGGAATCATTAAAAATATTTT
Salvia_eremostachya_5    AGTTTTGGAATCTGCATCTTCAAGTGACTTAATAAGATAAATTAAACGATTTCCTACTTTTTCAAAGATTCCACGTACAGGGAATCATTAAAAATATTTT
Salvia_fruticosa_6       ----------------------------------------------------------------------------------------------------
Salvia_huberi_7          ----------------------------------------------------------------------------------------------------
Salvia_kronenburgii_8    ----------------------------------------------------------------------------------------------------
Salvia_limbata_9         ----------------------------------------------------------------------------------------------------
Salvia_mohavensis_10     AGTTTTGGAATCTGCATCTTCAAGTGACTTAATAAGATAAATTAAACGATTTCCTACTTTTTCAAAGATTCCACGTACAGGGAATCATTAAAAATATTTT
Salvia_officinalis_subsp ----------------------------------------------------------------------------------------------------
Salvia_pachyphylla_12    AGTTTTGGAATCTGCATCTTCAAGTGACTTAATAAGATAAATTAAACGATTTCCTACTTTTTCAAAGATTCCACGTACAGGGAATCATTAAAAATATTTT
Salvia_pratensis_13      ----------------------------------------------------------------------------------------------------
Salvia_saccardiana_14    ----------------------------------------------------------------------------------------------------
Salvia_sonomensis_15     AGTTTTGGAATCTGCATCTTCAAGTGACTTAATAAGATAAATTAAACGATTTCCTACTTTTTCAAAGATTCCACGTACAGGGAATCATTAAAAATATTTT
Salvia_spathacea_16      AGTTTTGGAATCTGCATCTTCAAGTGACTTAATAAGATAAATTAAACGATTTCCTACTTTTTCAAAGATTCCACGTACAGGGAATCATTAAAAATATTTT
Salvia_verbenaca_17      ----------------------------------------------------------------------------------------------------
Salvia_xanthocheila_18   ----------------------------------------------------------------------------------------------------
                         401                                                                                                 
Salvia_aethiopis_1       ----------------------------------------------------------------------------------------------------
Salvia_amarissima_2      TTTATT---------------------TCTAAATTAAATTAAACATCATTTTTTAATTTACTTTAGTTTGATTGGGTTGGGTTTGAAGAAAATTGGACAA
Salvia_chinensis_3       TATATTTCTAAATGAAATTAACTATAATTAAAATTAAATTAAACATCATTTTTGAATTTATTTTAGTTTGATTGGGTTGGGTTTGAAGAAAATTGGACAA
Salvia_dorrii_4          TTTATTTCGAAATGAAATTAACTATAATTTAAATGAAATTAAACATCATTTTTGAATTTACTTTAGTTTGATTGGGTTGGGTTTGAAGAAAATTGGACAA
Salvia_eremostachya_5    TTTATTTCGAAATGAAATTAACTATAATTTAAATGAAATTAAACATCATTTTTGAATTTACTTTAGTTTGATTGGGTTGGGTTTGAAGAAAATTGGACAA
Salvia_fruticosa_6       ----------------------------------------------------------------------------------------------------
Salvia_huberi_7          ----------------------------------------------------------------------------------------------------
Salvia_kronenburgii_8    ----------------------------------------------------------------------------------------------------
Salvia_limbata_9         ----------------------------------------------------------------------------------------------------
Salvia_mohavensis_10     TTTATTTCGAAATGAAATTAACTATAATTTAAATGAAATTAAACATCATTTTTGAATTTACTTTAGTTTGATTGGGTTGGGTTTGAAGAAAATTGGACAA
Salvia_officinalis_subsp ----------------------------------------------------------------------------------------------------
Salvia_pachyphylla_12    TTTATTTCGAAATGAAATTAACTATAATTTAAATGAAATTAAACATCATTTTTGAATTTACTTTAGTTTGATTGGGTTGGGTTTGAAGAAAATTGGACAA
Salvia_pratensis_13      ----------------------------------------------------------------------------------------------------
Salvia_saccardiana_14    ----------------------------------------------------------------------------------------------------
Salvia_sonomensis_15     TTTATTTCGAAATGAAATTAACTATAATTTAAATGAAATTAAACATCATTTTTGAATTTACTTTAGTTTGATTGGGTTGGGTTTGAAGAAAATTGGACAA
Salvia_spathacea_16      TTTATTTCGAAATGAAATTAACTATAATTTAAATGAAATTAAACATCATTTTTGAATTTACTTTAGTTTGATTGGGTTGGGTTTGAAGAAAATTGGACAA
Salvia_verbenaca_17      ----------------------------------------------------------------------------------------------------
Salvia_xanthocheila_18   ----------------------------------------------------------------------------------------------------
                         501                                                                                                 
Salvia_aethiopis_1       -----------------------------------------------------------------------------TTAAAATAGAT------------
Salvia_amarissima_2      TAAGCACCGACTTTGATCTTTATAGGAGGATCGGTCTTTCTTTTTGAATTGACTCATCACTAATTTCAAATAAATATTTGAAATAAATCAAAGAAACGAA
Salvia_chinensis_3       TAAGCACCGCCTTTGATCTTTATAGGCGGATCGGTCTTTCTTTTTGAAGTGACTCATCACTAATTTCAAATAAAGATTTGAAATAGATCAAAGAAACGAA
Salvia_dorrii_4          TAAGCACCGCCTTTGATCTTTATAGGAGGATCAGTCTTTCTTTTTGAATTGACTCATCACTAATTTCAAATAAAGATTTGAAATAGATCAAAGAAACGAA
Salvia_eremostachya_5    TAAGCACCGCCTTTGATCTTTATAGGAGGATCAGTCTTTCTTTTTGAATTGACTCATCACTAATTTCAAATAAAGATTTGAAATAGATCAAAGAAACGAA
Salvia_fruticosa_6       -----------------------------------------------------------------------------TTAAAATATAT------------
Salvia_huberi_7          -----------------------------------------------------------------------------TTAAAATATAT------------
Salvia_kronenburgii_8    -----------------------------------------------------------------------------TTAAAATATAT------------
Salvia_limbata_9         -----------------------------------------------------------------------------TTAAAATAGAT------------
Salvia_mohavensis_10     TAAGCACCGCCTTTGATCTTTATAGGAGGATCAGTCTTTCTTTTTGAATTGACTCATCACTAATTTCAAATAAAGATTTGAAATAGATCAAAGAAACGAA
Salvia_officinalis_subsp -----------------------------------------------------------------------------TTAAAATATAT------------
Salvia_pachyphylla_12    TAAGCACCGCCTTTGATCTTTATAGGAGGATCAGTCTTTCTTTTTGAATTGACTCATCACTAATTTCAAATAAAGATTTGAAATAGATCAAAGAAACGAA
Salvia_pratensis_13      -----------------------------------------------------------------------------TTAAAATAGAT------------
Salvia_saccardiana_14    -----------------------------------------------------------------------------TTAAAATAGAT------------
Salvia_sonomensis_15     TAAGCACCGCCTTTGATCTTTATAGGAGGATCAGTCTTTCTTTTTGAATTGACTCATCACTAATTTCAAATAAAGATTTGAAATAGATCAAAGAAACGAA
Salvia_spathacea_16      TAAGCACCGCCTTTGATCTTTATAGGAGGATCAGTCTTTCTTTTTGAATTGACTCATCACTAATTTCAAATAAAGATTTGAAATAGATCAAAGAAACGAA
Salvia_verbenaca_17      -----------------------------------------------------------------------------TTAAAATAGAT------------
Salvia_xanthocheila_18   -----------------------------------------------------------------------------TTAAAATAGAT------------
                         601                                                                                                 
Salvia_aethiopis_1       ---------------AATAGAAAGAAATCCTTT-TTTTCATGAGATTTATAAAAAAACAATGTAAGTTAATATTTGACTTTTGATTCTTTTAATCAGATT
Salvia_amarissima_2      GAAAGAAATAAGATAAGAAGAAAAAAATCCTTTTTTTTCATGAGATGTATCAAAAAATAATGTAAGTTAATATTTGAATTTTGATTCTTTTAATCAGATT
Salvia_chinensis_3       GAAAGAAATAAGATAAGAAGAAAAAAATCCTTTTTTTTCATGAGATGTATAAAAAAATAATGTAAGTTAATATTTGCATTTTGATTCTTTTAATCAGATT
Salvia_dorrii_4          GAAAGAAATAAGATAAGAAGAAAAAATCCCTTTTTTTTCATGAGATGTATAAAAAACTAATGTAAGTTAATATTTGAATTTTGATTCTTTTAATCAGATT
Salvia_eremostachya_5    GAAAGAAATAAGATAAGAAGAAAAAATCCCTTTTTTTTCATGAGATGTATAAAAAACTAATGTAAGTTAATATTTGAATTTTGATTCTTTTAATCAGATT
Salvia_fruticosa_6       ---------------AATAGAAAGAAATCCTTTTTTTTCATGAGATGTATAAAAAAATAATGTAAGTTAATATTTGAATTTTGATTTTCGTAATCTGATT
Salvia_huberi_7          ---------------AATAGAAAGAAATCCTTTTTTTTCATGAGATGTATAAAAAAATAATGTAAGTTAATATTTGAATTTTGATTTTCGTAATCTGATT
Salvia_kronenburgii_8    ---------------AATAGAAAGAAATCCTTTTTTTTCATGAGATGTATAAAAAAATAATGTAAGTTAATATTTGAATTTTGATTTTCGTAATCTGATT
Salvia_limbata_9         ---------------AATAGAAAGAAATCCTTT-TTTTCATGAGATTTATAAAAAAACAATGTAAGTTAATATTTGACTTTTGATTCTTTTAATCAGATT
Salvia_mohavensis_10     GAAAGAAATAAGATAAGAAGAAAAAATCCCTTTTTTTTCATGAGATGTATAAAAAACTAATGTAAGTTAATATTTGAATTTTGATTCTTTTAATCAGATT
Salvia_officinalis_subsp ---------------AATAGAAAGAAATCCTTTTTTTTCATGAGATGTATAAAAAAATAATGTAAGTTAATATTTGAATTTTGATTTTCGTAATCTGATT
Salvia_pachyphylla_12    GAAAGAAATAAGATAAGAAGAAAAAATCCCTTTTTTTTCATGAGATGTATAAAAAACTAATGTAAGTTAATATTTGAATTTTGATTCTTTTAATCAGATT
Salvia_pratensis_13      ---------------AATAGAAAGAAATCCTTT-TTTTCATGAGATTTATAAAAAAATAATGTAAGTTACTATTTGACTTTTGATTCTTTTAATCAGATT
Salvia_saccardiana_14    ---------------AATAGAAAGAAATCCTTT-TTTTCATGAGATTTATAAAAAAATAATGTAAGTTACTATTTGACTTTTGATTCTTTTAATCAGATT
Salvia_sonomensis_15     GAAAGAAATAAGATAAGAAGAAAAAATCCCTTTTTTTTCATGAGATGTATAAAAAACTAATGTAAGTTAATATTTGAATTTTGATTCTTTTAATCAGATT
Salvia_spathacea_16      GAAAGAAATAAGATAAGAAGAAAAAATCCCTTTTTTTTCATGAGATGTATAAAAAACTAATGTAAGTTAATATTTGAATTTTGATTCTTTTAATCAGATT
Salvia_verbenaca_17      ---------------AATAGAAAGAAATCCTTT-TTTTCATGAGATTTATAAAAAAATAATGCAAATTAATATTTGACTTTTGATTCTTTTAATCAGATT
Salvia_xanthocheila_18   ---------------AATAGAAAGAAATCCTTT-TTTTCATGAGATTTATAAAAAACCAATGTAAGTTAATATTTGACTTTTGATTCTTTTAATCAGATT
                         701                                                                                                 
Salvia_aethiopis_1       ACGAAAATCAAAATCG---AAAAAATAGGTAAGGTTTATCCTATCTATCAGATAGACGGAACTGTTGTCGCTGTTTGTTATTTGTTATAAATGTTTTATA
Salvia_amarissima_2      ACGAAAATCAAAATCGAA-AAAAAATAGGTAAGGTTTCTCCTATCTATCAGATAGACGGAACTGTTGTCACTATTTGTTGTTTGTTATAGATGTTTTATA
Salvia_chinensis_3       ACGAAAATCAAAATCGAACAAAAAATAGGTAAGATTTCTCCTATCTATTAGATAGACGGAACTGTTGTCACTGTTTGTTGTTTGTTATAGATGTTTTATA
Salvia_dorrii_4          ACGAAAATCAAAATCGAA-AAAAAATAGGTAAGGTTTCTCCTATCTATCAGATAGACGGAACTGTTGTCACTATTTGTTGTTTGTTATAGATGTTTTATA
Salvia_eremostachya_5    ACGAAAATCAAAATCGAA-AAAAAATAGGTAAGGTTTCTCCTATCTATCAGATAGACGGAACAGTTGTCACTATTTGTTGTTTGTTATAGATGTTTTATA
Salvia_fruticosa_6       AAAAGAATCAAAATCGA--AAAAAATAGGTAAGGTTTATCCTATCTATCAGATAGACGGAACTGTTGTCGCCGTTTGTTGTTTGTTAGAAATGTTTTATA
Salvia_huberi_7          AAAAGAATCAAAATCGA--AAAAAATAGGTAAGGTTTATCCTATCTATCAGATAGACGGAACTGTTGTCGCCGTTTGTTGTTTGTTAGAAATGTTTTATA
Salvia_kronenburgii_8    AAAAGAATCAAAATCGA--AAAAAATAGGTAAGGTTTATCCTATCTATCAGATAGACGGAACTGTTGTCGCCGTTTGTTGTTTGTTAGAAATGTTTTATA
Salvia_limbata_9         ACGAAAATAAAAATCG---AAAAAATAGGTAAGGTTTATCCTATCTATCAGATATACGGAACTGTTGTCGCTGTTTGTTATTTGTTATAAATGTTTTATA
Salvia_mohavensis_10     ACGAAAATCAAAATCGAA-AAAAAATAGGTAAGGTTTCTCCTATCTATCAGATAGACGGAACTGTTGTCACTATTTGTTGTTTGTTATAGATGTTTTATA
Salvia_officinalis_subsp AAAAGAATTAAAATCGA--AAAAAATAGGTAAGGTTTATCCTATCTATCAGATAGACGGAACTGCTGTCGCCGTTTGTTGTTTGTTAGAAATGTTTTATA
Salvia_pachyphylla_12    ACGAAAATCAAAATCGAA-AAAAAATAGGTAAGGTTTCTCCTATCTATCAGATAGACGGAACTGTTGTCACTATTTGTTGTTTGTTATAGATGTTTTATA
Salvia_pratensis_13      ATGAAAATCAAAATCG---AAAAAATAGGTAAGGTTTATCTTATCTATCAGATAGACGGAACTGTTGTCGCTGTTTGTTATTTGTTATAAATGTTTTATA
Salvia_saccardiana_14    ATGAAAATCAAAATCG---AAAAAATAGGTAAGGTTTATCTTATCTATCAGATAGACGGAACTGTTGTCGCTGTTTGTTATTTGTTATAAATGTTTTATA
Salvia_sonomensis_15     ACGAAAATCAAAATCGAA-AAAAAATAGGTAAGGTTTCTCCTATCTATCAGATAGACGGAACTGTTGTCACTATTTGTTGTTTGTTATAGATGTTTTATA
Salvia_spathacea_16      ACGAAAATCAAAATCGAA-AAAAAATAGGTAAGGTTTCTCCTATCTATCAGATAGACGGAACTGTTGTCACTATTTGTTGTTTGTTATAGATGTTTTATA
Salvia_verbenaca_17      ACGAAAATCAAAATCG---AAAAAATAGGTAAGGTTTATCCTATCTATCAGATAGACGGAACTGTTGTCGCTGTTTGTTATTTGTTATAAATGTTTTATA
Salvia_xanthocheila_18   ACGAAAATCAAAATCG---AAAAAATAGGTAAGGTTTATCCTATCTATCAGATAGACGGAACTGTTGTCGCTGTTTGTTATTTGTTATAAATGTTTTATA
                         801                                                                                                 
Salvia_aethiopis_1       TCTACT--ACTATATAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA---CCCC
Salvia_amarissima_2      TCTACTATACTATAGAATATGAGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATATTTAAAGTAATATAGATTAACTGCTACCCACCCCCCC
Salvia_chinensis_3       TCTACTATACTCTAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCACCCCCCC
Salvia_dorrii_4          TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAATAATATAGATTAACTGCTATCCACCCCCCC
Salvia_eremostachya_5    TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAATAATATAGATTAACTGCTATCCACCCCCCC
Salvia_fruticosa_6       TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA--TCCCC
Salvia_huberi_7          TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA--TCCCC
Salvia_kronenburgii_8    TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA--TCCCC
Salvia_limbata_9         TCTACT--ACTATATAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA---CCCC
Salvia_mohavensis_10     TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAATAATATAGATTAACTGCTATCCACCCCCCC
Salvia_officinalis_subsp TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA--TCCCC
Salvia_pachyphylla_12    TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAATAATATAGATTAACTGCTATCCACCCCCCC
Salvia_pratensis_13      TCTACTATACTATATAATATGGGACTTGATTATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA---CCCC
Salvia_saccardiana_14    TCTACTATACTATATAATATGGGACTTGATTATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA---CCCC
Salvia_sonomensis_15     TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAATAATATAGATTAACTGCTATCCACCCCCCC
Salvia_spathacea_16      TCTACTATACTATAGAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAATAATATAGATTAACTGCTATCCACCCCCCC
Salvia_verbenaca_17      TCTACT--ACTATATAATATGGGACTTGATTATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA---CCCC
Salvia_xanthocheila_18   TCTACT--ACTATATAATATGGGACTTGATCATTTGTTAATGAAATTCGAACAGACACAGATGTTTAAAGTAATATAGATTAACTGCTATCCA---CCCC
                         901                                                                  
Salvia_aethiopis_1       CATTTCTTTT----------TTATATTATGATAGGGCTTATATGGAAATAATGGAGAAATGGATCCGTG
Salvia_amarissima_2      CACTTCCTTT----------TTCTATTATGATAGGGTTTATATGGGAATAATGGAGAAATGTATCCGTG
Salvia_chinensis_3       CACTTCCTTTTTAGATTATGTTATATTATGATAGGATTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_dorrii_4          CACTTCCTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_eremostachya_5    CACTTCCTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_fruticosa_6       CACTTCTTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_huberi_7          CACTTCTTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_kronenburgii_8    CACTTCTTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_limbata_9         CATTTCTTTT----------TTATATTATGATAGGGCTTATATGGAAATAATGGAGAAATGGATCCGTG
Salvia_mohavensis_10     CACTTCCTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_officinalis_subsp CACTTCTTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_pachyphylla_12    CACTTCCTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_pratensis_13      CATTTCTTTT----------TTATATTATGATAGGGCTTATATGGAAATAATGGAGAAATGGATCCGTG
Salvia_saccardiana_14    CATTTCTTTT----------TTATATTATGATAGGGCTTATATGGAAATAATGGAGAAATGGATCCGTG
Salvia_sonomensis_15     CACTTCCTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_spathacea_16      CACTTCCTTT----------TTATATTATGATAGGGTTTATATGGGAATAATGGAGAAATGGATCCGTG
Salvia_verbenaca_17      CATTTCTTTT----------TTATATTATGATAGGGCTTATATGGAAATAATGGAGAAATGGATCCGTG
Salvia_xanthocheila_18   CATTTCTTTT----------TTATATTATGATAGGGCTTATATGGAAATAATGGAGAAATGGATCCGTG

Haplotype Network

Species Separation

Primer Ranking

Primer ID fwd_seq rev_seq fwd_gc rev_gc fwd_tm rev_tm amplicon_size cross_species_success_rate primer_score
rps16-trnQ-UUG_p1 AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 45.0 55.0 58.1 58.1 616-1042 bp 1.0 90.3
rps16-trnQ-UUG_p2 CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 50.0 55.0 57.2 58.1 608-1034 bp 1.0 85.1
rps16-trnQ-UUG_p3 AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 50.0 55.0 58.9 58.1 615-1041 bp 1.0 84.5
rps16-trnQ-UUG_p4 GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 50.0 55.0 59.1 58.1 611-1037 bp 1.0 82.9
rps16-trnQ-UUG_p5 AAGTCGCACGTTGCTTTCTA GTTCGAATCCTTCCGTCCC 45.0 57.9 58.1 57.9 613-1039 bp 1.0 82.4

Downloads

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