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  • CG T TT GC C C GG CC G: Aagcttacgcctcacctc

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    Anonymous h0GSec9LT
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    The document contains sequences from 5 gene accessions. It performs an alignment of the sequences and calculates the percentage differences between each pair. It then clusters the accessions based on the distances between them. Primer sequences are proposed for the forward and reverse strands that could be used to amplify different lengths of DNA from each accession in PCR.

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    alignment

    Original Title

    Alignment Jadi

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    The document contains sequences from 5 gene accessions. It performs an alignment of the sequences and calculates the percentage differences between each pair. It then clusters the accessions based on the distances between them. Primer sequences are proposed for the forward and reverse strands that could be used to amplify different lengths of DNA from each accession in PCR.

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    © All Rights Reserved
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    9 views2 pages

    CG T TT GC C C GG CC G: Aagcttacgcctcacctc

    Uploaded by

    Anonymous h0GSec9LT
    The document contains sequences from 5 gene accessions. It performs an alignment of the sequences and calculates the percentage differences between each pair. It then clusters the accessions based on the distances between them. Primer sequences are proposed for the forward and reverse strands that could be used to amplify different lengths of DNA from each accession in PCR.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    of 2

    Jawaban no.

    1
    >gi| Aksesi 1: A A G C T T A C G C C T C A C C T C C C G G G C T C G A C G A A T T C G G A T C C G T C G A

    AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

    >gi| Aksesi 2: A A G C T T A C G C C T C A C C T C C C G G G C T C G A T T A A T T C G G A T C C G T C G A C C C A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A
    >gi| Aksesi 3: A A G C T T A C G C C T C A C C T C C C G G G C T C G A G C A A T T C G G A T C C G T C G A C C C A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A

    G G G C A G C T G C C T A G G C T T A A G G A G C T C T G G G G A G G T A C G G C A T T C G A A (129 bp)
    G C T G C C T A G G C T T A A G G A G C T C G G G G G A G G T A C G G C A T T C G A A (129 bp)
    G G G C A G C T G C C T A G C C T T A A G G A G C T C C G G G G A G G T A C G G C A T T C G A A (130 bp)

    >gi| Aksesi 4: A A G C T T A C G C C T C A C C T C C C G G G C T C G A G G A A T T C G G A T C C G T C G A C C C A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G A G G G C A G C T G C C T A G G C T T A A G G A G C T C G G G G G A G G T A C G G C A T T C G A A (136 bp)


    >gi| Aksesi 5: A A G C T T A C G C C T C A C C T C C C G G G C T C G A C C A A T T C G G A T C C G T C G A C C C A G A G A G A G A G A G A G A G A G A G A G A G A G A G A

    G G G C A G C T G C C T A G G G T T A A G G A G C T C G G G G G A G G T A C G G C A T T C G A A (126 bp)

    Jawaban no. 2:
    Gap pinalty masing-masing aksesi:
    Aks 1. gap pinalty = gap open + gap extntion= (2*-4)+(7*-1)= -15
    Aks 2. gap pinalty = gap open + gap extntion= (1*-4)+(7*-1)= -11
    Aks 3. gap pinalty = gap open + gap extntion= (1*-4)+(6*-1)= -10
    Aks 5. gap pinalty = gap open + gap extntion= (1*-4)+(10*-1)= -14

    Versi 2
    Aksesi 1
    Aksesi 2
    Aksesi 3
    Aksesi 4
    Aksesi 5

    Aksesi 1
    9,56%
    6,62%
    8,09%
    8,82%

    Aksesi 2

    Aksesi 3

    Aksesi 4

    Aksesi 5

    9,56%
    6,62%
    9,56%

    6,62%
    5,88%

    9,56%

    Aksesi 1
    9,56%
    6,62%
    8,09%
    8,82%

    Aksesi 2

    Aksesi 3

    Aksesi 4

    Aksesi 5

    9,56%
    6,62%
    9,56%

    6,62%
    5,88%

    9,56%

    Jawaban no.3:

    Jawaban no.4:
    Hitungan 1

    Versi 2
    Aksesi 1
    Aksesi 2
    Aksesi 3
    Aksesi 4
    Aksesi 5

    5
    ,
    8
    8

    Jarak 5-3 dg:


    Aks 1 6,62+8,82/2=7,72%
    35

    Aks 2 9,56+9,56/2=9,56%

    Aks 4 6,62+9,56/2=8,09%
    Versi 2

    Aksesi 1

    Aksesi 2

    Aksesi 4

    Aksesi 1
    Aksesi 2
    Aksesi 4
    Aksesi 5-3

    9,56
    8,09
    7,72

    6,62
    9,56

    8,09

    Versi 2
    Aksesi 1
    Aksesi 4-2
    Aksesi 5-3

    25
    3
    4

    Jarak 4-2:
    Aks 1

    Aksesi
    5-3

    6,62
    5,88

    :9,56+8,09/2=8,82

    Aksesi 1
    8,82
    7,72

    Aksesi 4-2
    8,82

    Aksesi 5-3

    Aks 5-3

    : 9,56+8,09/2=8,82

    7,72
    6,62

    5
    ,
    8
    8

    25
    3
    4

    8
    ,
    8
    2

    Jawaban no.5:
    5'A(HindIII)AG(AluI)CTTACGCCTCACCTC(prim F)CC(SmaI)GGGC(XhoI)T(TaqI)CGAGG(EcoRI)AATTCG(BamHI)GATCCG(SalI)T(TaqI)CGACCCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGCAG(AluI)CTGCCTAGGCTT(MseI)AAGG(SacI)AG(AluI)CTCGGGGGAGGTACGGCATT(TaqI)CGAA'3
    Jawaban no. 6-7:
    -)Primer Forward:
    5AAGCTTACGCCTCACCTC3
    A/T ratio = 8/18 * 100 = 44,4%
    G/T ratio = 10/18 *100 = 55,6%
    Ukuran yang dihasilkan pada masing2 aksesi:
    1. (129-18) = 111 bp
    2. (129-18) = 111 bp
    3. (130-18) = 112 bp
    4. (136-18) = 118 bp
    5. (126-18) = 108 bp
    -)Primer Reverse:
    3CCTCCATGCCGTAAGCTT5
    A/T ratio = 8/18 * 100 = 44,4%
    G/T ratio = 10/18 *100 = 55,6%
    Ukuran yang dihasilkan pada masing2 aksesi:
    1. (129-18) = 111 bp
    2. (129-18) = 111 bp
    3. (130-18) = 112 bp
    4. (136-18) = 118 bp
    5. (126-18) = 108 bp
    Jawaban no.8:
    Enzim MseI

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