Langkah-Langkah Melakukan (Blast basic local alignment search tool) Primer
Nama Mahasiswa : Chairunnisa Lalusu
NIM : PO714203221011
Kelas : D4 A Tingkat II
Mata Kuliah : Biologi Sel dan Molekuler II
Dosen Pengampu : Alvin Resya Virgiawan, S.St, M.Si
Rafika, S.Si, M.Kes
1. Mencari primer dari spesies organisme yang akan dicari sekuennya pada website National Center for Biotechnology Information. Dalam
langkah-langkah berikut yang primer yang digunakan adalah primer universal dari trichophyton. Primer Forward yang didapatkan
adalah TCCGTAGGTG AACCTGCGG sedangkah primer Reverse yang didapatkan adalah TCCTCCGCTTATTGATATGC.
2. Setelah primer ditemukan selanjutnya Membuka website National Center for Biotechnology Information. Gambaran websitenya seperti
pada gambar di bawah ini.
3. Selanjutnya menekan menu bagian “BLAST”
4. Jika telah muncul tampilan menu seperti di bawah ini, selanjutnya salin primer forward yang telah didapatkan pada langkah pertama dan
tempel atau paste pada menu bagian “Enter Query Sequence”
5. Setelah itu pada halaman website yang sama, scroll kebawah sampai menu “Organisms”. Kemudian ketikkan tujuan primer yang telah di
salin sebelumnya. Dalam hal ini primer yang merujuk pada Dermatophytes. Perhatian untuk berhati-hati pada pengisian sebab jika salah
maka tidak akan terbaca oleh sistem website. Pastikan nama yang akan dicari terdapat pada pilihan nama yang telah disiapkan oleh
website. Pastikan juga terdapat kode setelah nama organisme yang akan dicari. Contohnya seperti pada gambar di bawah ini. Setelah itu
tekan menu “BLAST”.
6. Tunggu beberapa saat, jika telah muncul tampilan seperti pada gambar di bawah ini maka scroll kebawah untuk mencari descriptions
yang sesuai dengan primer yang digunakan sebelumnya pada langkah pertama.
Sequences producing significant alignments:
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Select seq Trichophyton verrucosum isolate 4 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete
OR708515.1
Select seq Trichophyton rubrum isolate sms 24 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and in
OR673592.1
Select seq Trichophyton rubrum strain JYP21284b internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR661480.1
Select seq Trichophyton rubrum strain JYP21058a internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR661435.1
Select seq Trichophyton rubrum strain JYP20042 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcr
OR661380.1
Select seq Trichophyton verrucosum strain JYP18154 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal tra
OR661344.1
Select seq Trichophyton violaceum strain JYP18125 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal tran
OR661341.1
Select seq Trichophyton rubrum strain JYP18112 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcr
OR661335.1
Select seq Trichophyton rubrum strain JYP18028 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcr
OR661301.1
Select seq Trichophyton rubrum strain JYP21028 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcr
OR661417.1
Select seq Trichophyton rubrum strain JYP18001 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcr
OR661292.1
Select seq Trichophyton erinacei isolate 392XXX2 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR428163.1
Select seq Trichophyton rubrum isolate FMB-TR internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcri
OR374017.1
Select seq Trichophyton verrucosum strain AAADVM6 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene
OR362821.1
sequence
Select seq Trichophyton rubrum isolate CV55 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete
OR249962.1
Select seq Trichophyton rubrum isolate chc strain small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and
OR244361.1
sequence
Select seq Trichophyton soudanense isolate CV15 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR206381.1
Select seq Trichophyton soudanense isolate CV8 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, compl
OR206379.1
Select seq Trichophyton soudanense isolate CV60 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR206380.1
Select seq Trichophyton soudanense isolate CV58 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR186345.1
Select seq Trichophyton soudanense isolate CV52 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR185607.1
Select seq Trichophyton soudanense isolate CV50 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR185603.1
Select seq Trichophyton soudanense isolate CV47 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR185602.1
Select seq Trichophyton soudanense isolate CV45 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR185601.1
Select seq Trichophyton soudanense isolate CV42 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR185600.1
Select seq Trichophyton soudanense isolate CV30 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR185599.1
Select seq Trichophyton soudanense isolate CV24 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR185598.1
Select seq Trichophyton soudanense isolate CV20 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR185597.1
Select seq Trichophyton soudanense isolate CV12 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR185567.1
Select seq Trichophyton soudanense isolate CV10 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR185566.1
Select seq Trichophyton soudanense isolate CV11 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR185565.1
Select seq Trichophyton soudanense isolate CV4 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, compl
OR185564.1
Select seq Trichophyton soudanense isolate CV3 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transc
OR168629.1
Select seq Trichophyton rubrum isolate URM 6212 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088198.1
Select seq Trichophyton rubrum isolate URM 4727 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088197.1
Select seq Trichophyton rubrum isolate URM 719 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transc
OR088195.1
Select seq Trichophyton concentricum isolate URM 699 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal
OR088194.1
Select seq Trichophyton rubrum isolate URM 4738 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088193.1
Select seq Trichophyton rubrum isolate URM 4159 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088191.1
Select seq Trichophyton rubrum isolate URM 4195 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088190.1
Select seq Trichophyton rubrum isolate URM 4257 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088189.1
Select seq Trichophyton rubrum isolate URM 4569 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088187.1
Select seq Trichophyton rubrum isolate URM 4735 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088186.1
Select seq Trichophyton rubrum isolate URM 5505 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088185.1
Select seq Trichophyton rubrum isolate URM 4258 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088175.1
Select seq Trichophyton rubrum isolate URM 5413 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088174.1
Select seq Trichophyton rubrum isolate URM 4726 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088173.1
Select seq Trichophyton rubrum isolate URM 5908 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal trans
OR088172.1
Select seq Trichophyton rubrum isolate URM 6213 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, an
OR088170.1
sequence
Select seq Trichophyton rubrum isolate URM 5145 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088169.1
Select seq Trichophyton rubrum isolate URM 5544 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088166.1
Select seq Trichophyton rubrum isolate URM 5904 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088165.1
Select seq Trichophyton rubrum isolate URM 5558 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088160.1
Select seq Trichophyton rubrum isolate URM 3239 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088159.1
Select seq Trichophyton rubrum isolate URM 6753 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088154.1
Select seq Trichophyton rubrum isolate URM 5907 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088153.1
Select seq Trichophyton rubrum isolate URM 471 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, compl
OR088152.1
Select seq Trichophyton rubrum isolate URM 5906 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088151.1
Select seq Trichophyton rubrum isolate URM 5307 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088150.1
Select seq Trichophyton rubrum isolate URM 5905 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088149.1
Select seq Trichophyton rubrum isolate URM 5543 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088148.1
Select seq Trichophyton rubrum isolate URM 5144 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088147.1
Select seq Trichophyton rubrum isolate URM 5143 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088146.1
Select seq Trichophyton rubrum isolate URM 6206 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088145.1
Select seq Trichophyton rubrum isolate URM 4730 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088144.1
Select seq Trichophyton rubrum isolate URM 4194 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088143.1
Select seq Trichophyton rubrum isolate URM 2875 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR088142.1
Select seq Trichophyton rubrum culture NFCCI:5520 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal tran
OR083328.1
Select seq Trichophyton verrucosum isolate CH-21 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, com
OR058573.1
Select seq Trichophyton verrucosum isolate KJ-7 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comple
OR058571.1
Select seq Trichophyton verrucosum isolate CH-30 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, an
OR058568.1
sequence
Select seq Trichophyton verrucosum isolate CH-45 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, an
OR058567.1
sequence
Select seq Trichophyton verrucosum isolate CH-46 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, com
OR058566.1
Select seq Trichophyton verrucosum isolate HW-12 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, an
OR058565.1
sequence
Select seq Trichophyton verrucosum isolate KJ-3-2 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, com
OR058564.1
Select seq Trichophyton verrucosum isolate KJ-14 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR058562.1
Select seq Trichophyton verrucosum isolate KJ-15 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR058561.1
Select seq Trichophyton verrucosum isolate NN-3 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR058559.1
Select seq Trichophyton verrucosum isolate NN-7 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and
OR058558.1
sequence
Select seq Trichophyton verrucosum isolate SJ-6 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comple
OR058556.1
Select seq Trichophyton verrucosum isolate CH-15 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, com
OR058554.1
Select seq Trichophyton verrucosum isolate SJ-15 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR058551.1
Select seq Trichophyton verrucosum isolate SJ-16 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comp
OR058550.1
Select seq Trichophyton verrucosum breed genomic DNA sequence contains 18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2, 28S rRNA gene. small subunit ribosoma
OR056436.1
transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
Select seq Trichophyton verrucosum breed genomic DNA sequence contains 18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2, 28S rRNA gene. internal transcribed spa
OR056370.1
and large subunit ribosomal RNA gene, partial sequence
Select seq Trichophyton rubrum isolate clinic small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and inter
OQ714118.1
Select seq Trichophyton rubrum isolate clinic internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete s
OQ709158.1
Select seq Trichophyton rubrum isolate clinic internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete s
OQ621414.1
Select seq Trichophyton mentagrophytes isolate clinic small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA ge
OQ619051.1
Select seq Trichophyton rubrum isolate clinic internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete s
OQ619050.1
Select seq Trichophyton rubrum isolate clinic small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and inter
OQ619049.1
Select seq Trichophyton rubrum isolate clinic small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and inter
OQ619047.1
Select seq Trichophyton benhamiae isolate clinic internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, comple
OQ618207.1
Select seq Trichophyton rubrum isolate clinic small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, com
OQ618204.1
Select seq Trichophyton rubrum isolate clinic internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete s
OQ618183.1
Select seq Trichophyton rubrum isolate clinic small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, com
OQ617954.1
Select seq Trichophyton rubrum isolate clinic internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete s
OQ617939.1
Select seq Trichophyton rubrum isolate clinic small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and inter
OQ617934.1
Select seq Trichophyton violaceum isolate clinic small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, co
OQ617924.1
Select seq Trichophyton benhamiae isolate T.ben_NB20 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal
OQ600605.1
Sequences producing significant alignments
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Berikut cara menemukan primer yang akan digunakan pada metode PCR dan cara menggunakan website National Center for
Biotechnology Information sebagai alat untuk mencari primer yang sesuai.
