Contoh soal bioinformatika dan penyelesaiannya

 1. Primer Design

Untuk penelitian gen ice nucleation active, saya mendapatkan referensi pasangan primer dari sebuah jurnal (Nejad et al., 2006) yang dapat digunakan untuk mengamplifikasi gen inaX (Zhao dan Orser, 1990) dari Xanthomonas campesris pv. translusens. Primer forward (5´GCA AGG GCA GCG ATG TCA C 3´); dan primer reverse (5´ TCT GCG TGC TGC CGT AAC C 3´). Seandainya saya menggunakan pasangan primer tersebut; menurut anda apakah pasangan primer ini dapat digunakan untuk mengamplifikasi gen inaX dari isolat-isolat Xanthomonas campesris yang bersifat ice nucleation active yang saya punya?

a)      Buktikan bahwa primer ini cukup baik! Jika cukup bagus berapa produk PCRnya?

·         FastPCR In silico primer Output

<-ccaatgccgtcgtgcgtct-5

  || ||||||||||||||||

cgggctacggcagcacgcagacctc

Position: 3062<-3080 97%   Tm = 56,0°C

<-ccaatgccgtcgtgcgtct-5

  |||||||||||:|||||||

ccggttacggcagtacgcagaccgc

Position: 3158<-3176 95%   Tm = 56,6°C

<-ccaatgccgtcgtgcgtct-5

  || ||||||||||||||||

cgggctacggcagcacgcagacgtc

Position: 3206<-3224 100%   Tm = 60,5°C

<-ccaatgccgtcgtgcgtct-5

  |||||||||||||||||||

ccggttacggcagcacgcagaccgc

Position: 3254<-3272 85%   Tm = 44,4°C

<-ccaatgccgtcgtgcgtct-5

  |||||||||||||| :: |

ccggttacggcagcaccggcacggc

Position: 3302<-3320 89%   Tm = 52,3°C

<-ccaatgccgtcgtgcgtct-5

  || |||||||||||||| |

ccggctacggcagcacgcaaacggc

Position: 3446<-3464 89%   Tm = 52,3°C

<-ccaatgccgtcgtgcgtct-5

  || |||||||||||||| |

ccggctacggcagcacgcaaacggc

Position: 3638<-3656 100%   Tm = 60,5°C

<-ccaatgccgtcgtgcgtct-5

  |||||||||||||||||||

ccggttacggcagcacgcagacggc

Position: 3686<-3704 82%   Tm = 43,3°C

<-ccaatgccgtcgtgcgtct-5

  || ||||||||||||:  |

ctggctacggcagcacgtccaccgc

Position: 4142<-4160 88%   Tm = 44,4°C

<-ccaatgccgtcgtgcgtct-5

  ||||||| :||||||| ||

ccggttacgagagcacgctgaccgc

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 2438<-2456

 5'-tctgcgtgctgccgtaacc

PCR product size: 90bp  Ta=65°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 2582<-2600

 5'-tctgcgtgctgccgtaacc

PCR product size: 234bp  Ta=66°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 2774<-2792

 5'-tctgcgtgctgccgtaacc

PCR product size: 426bp  Ta=67°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 2822<-2840

 5'-tctgcgtgctgccgtaacc

PCR product size: 474bp  Ta=67°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 2870<-2888

 5'-tctgcgtgctgccgtaacc

PCR product size: 522bp  Ta=67°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3014<-3032

 5'-tctgcgtgctgccgtaacc

PCR product size: 666bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3062<-3080

 5'-tctgcgtgctgccgtaacc

PCR product size: 714bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3158<-3176

 5'-tctgcgtgctgccgtaacc

PCR product size: 810bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3206<-3224

 5'-tctgcgtgctgccgtaacc

PCR product size: 858bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3254<-3272

 5'-tctgcgtgctgccgtaacc

PCR product size: 906bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3302<-3320

 5'-tctgcgtgctgccgtaacc

PCR product size: 954bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3446<-3464

 5'-tctgcgtgctgccgtaacc

PCR product size: 1098bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3638<-3656

 5'-tctgcgtgctgccgtaacc

PCR product size: 1290bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 3686<-3704

 5'-tctgcgtgctgccgtaacc

PCR product size: 1338bp  Ta=68°C

>primer forward 2367->2385

 5'-gcaagggcagcgatgtcac

>primer reverse 4142<-4160

 5'-tctgcgtgctgccgtaacc

PCR product size: 1794bp  Ta=68°C

·         FastPCR sequences Output

>gaattctattcgattctcaatctgtgagattgccggattcgacgctgcgagtcgtttccacaaagcaagtcggagcgatcggtcgaagtggcggcatgccgtggcctagcttttgttgcatgtaaagtttggtttatacggcttgaatgcctgtttcgtggacacgcaggaggggcttggccaggcgcgtctggcgatggcccaggctggtttttttgccgccagaacggatgcgacgcagcgcggtttcccggcgtgtggcctgggaaatactccgatttttcttgtcgtatttatagtgaggtagtgtgatgatcgttgaaaagattttggcattgcgtacgtgcgccaataacatggccgaccactgcgggttgatctggccgatggccggtcccgtggaatgcaaattctggaaaccgtcgggactgcacgaaaatggtcttaccgggctgttgtggggcaagggcgtcggggcgcatctgagtgcgcacgccgatgcgcgctgggtcgtgtgcgaagtcgccgtcgacgagatgctgcagttggccgaagaggggatgatcaagttcccgcgcgcaactgtgcttttcgtcggaaatcgcagccaggcgctggactatattgcagccaacatgccgctctacggcgccgctctacagctggcggcacccgctgcgccggcgcatgtccacatgcccgcagcggagccgtccgcgccggcaacgcaggcgacctctgcaaccctgccgaccccagccaccccttccacccaggccaccccttccactcagtcaactcagtcaactcagtcaaccgaagcgacccagtcaaccgaggcgaccccggttgccacggtcgccgcagcgccgcctcctccgggacagcagcatgacgtgatggcgaagaagaccgaaaccggtgtctatggcagcacactcacaggcgccgaccagagccggctcgtcgcaggctacggcagtaccgaaaccgcaggcgatcacagcgatctgatcgccggctatggcagcaccgggaccgccggatccgacagttccatcctggcagggtatggcagcacgcagactgccgcgggcaggagcacgctcaccgccggctatggcagcacgcagacggcgcaggaaggcagccgtctcacctccGGTTACGGCAGCACTGCGAccagcggttctgacagcgcggtgatctccGGCTACGGCAGCACGCAAAcggccggtagcgagagttccttgaccgctGGCTACGGCAGCACGCAGAccgcgcgcaagggcagcgacatcaccgccggctatggcagtaccggtacggccgggtcggacagcgcgttgatcgccggctacggcagcacccagaccgccggcagcgagagttccttgaccgccGGCTACGGCAGCACGCAGAccgcacgcaagggcagcgacgtcaccgccggctacggcagtaccggcacggcgggtgccgacagcaccttgatcgcgggctatggcagcacgcagaccgctggcggcgaaagctctctcaccgccGGCTACGGCAGCACGCAGActgcgcggcaaggcagcgacatcaccgccggttacggcagtaccggcactgccggtgcggacagcacgctgatcgccGGTTACGGCAGCACGCAAAcctcgggcagcgacagctcgctgacagccggttatggcagcacgcagaccgcgcgcaagggcagcgacatcactgccggctacggcagcaccggcaccgccggatccgacagttcgttgatcgccGGCTACGGCAGCACGCAGAccgctggcagcgaaagttcgctgacggccGGCTACGGCAGCACGCAGAccgcccagcaagacagctcgctcaccaccggctacggcagtacctcgacggcgggtcacgacagttcgctgatcgccggctatggcagcacccagaccgccggctacgatagcaccctgaccgccggctacggcagtacgcagaccgcccaacaagacagttcgctcaccaccggttacggcagtacctccaccgccggtgccgacagtacgctgatcgccggctacggcagtacgcagaccgctggcagcgacagttcgctgacggccGGTTACGGCAGCACACAGAccgcacgcgaaggcagcgacgtcaccgccggctacggcagcaccggcaccgcgggtgcggacagtaccttgatcgccGGCTACGGCAGCACGCAGAcctccggtagcgacagttcgctgacggccggctacggcagtacgcagaccgcgcgcaagggcagcgacgtcaccgccggctatggcagcaccggcacggcgggtgcggacagcacgctgatcgccGGCTACGGCAGCACGCAGAcctccggtagcgacagttcgctgacggccggctacggcagtacgcagaccgcgcGCAAGGGCAGCGATGTCACcgccggctacggcagcaccggcacggcgggtgcggacagcacgctgatcgccGGCTACGGCAGCACGCAGAcctcgggtagcgacagttcgctgacggccggctacggcagtacgcagaccgcgcgcaagggcagcgacgtcaccgccggctacggcagcaccggcacggcgggtgcggacagcacgctgatcgcaGGTTACGGCAGCACGCAAAcctcgggcagcgacagttcgctgacggccggttatggcagtacgcagaccgcgcgcaagggcagcgacattaccgccggctacggcagcaccggcaccgcgggcgcggacagcaccttgatcgcgggctatggcagcacgcagacctccggcagcgacagttcgctgaccgccGGTTACGGCAGCACGCAGAccgcacgcgaaggcagcgacgtcaccgccGGTTACGGCAGCACCGGCAcggcgggcgcggacagcaccctgatctccGGCTACGGCAGCACGCAAAcggccggcagcgacagttcgctgaccgccggctacggcagtacgcagactgcgcgcaagggcagcgacgtcaccgccggttacggcagtaccggcaccgcgggtgcggacagcaccttgatcgcgGGCTACGGCAGCACGCAGAcctccggcagcgacagttcgctgaccgccGGTTACGGCAGTACGCAGAccgcgcgcaagggcagcgacatgaccgccggctacggcagtaccggcaccgctggcgcggatagcaccttgatcgcgGGCTACGGCAGCACGCAGAcgtccggcagcgacagctcgctgacggccGGTTACGGCAGCACGCAGAccgcacgcgaaggcagcgacgtcaccgccGGTTACGGCAGCACCGGCAcggcgggcgcggacagcaccctgatcgccGGCTACGGCAGCACGCAAAcggccggcagcgacagttcgctgaccgccggctatggcagcacgcagacggcacggcagggcagcgacgtcaccgccggctacggcagtacaggtaccgcgggcgcggacagcaccctgatcgccGGCTACGGCAGCACGCAAAcggccggcagcgacagttcgctgaccgccggctatggcagcacgcagacggcacggcagggcagcgacatcaccgccggctatggcagtaccgggaccgcgggcgccgacagttcgttgatcgccggctatggcagcacccagaccgccggctacgacagcaacctcactgccGGTTACGGCAGCACGCAGAcggcgcgcgaggacagctcgctcactgctGGCTACGGCAGCACGTCCAccgccggtcatgacagttcgctgatcgccggctatggcagtacccagaccgctggctacaacagcatcctgaccaccggctatggcagtacccagactgcacaggagagcagttctctcactgccggctacggcagcacctccacggccggctacgacagcaccttgaccgccggctatggcagtacccaaaccgccggctacaaaagcacgctgaccgcgggttatggcagcaactcgaccgccggccacgagagctcgttgatcgccggctacggtagcacccagatcgctggatacgagagcaccttgaccgcgggctacggcagttcgctgaccacgcagcagaacagttcgctgactgccggctacggcagcaccgagatcgccggctatgccagtacgctgatggccggctacggcagttcccagaccgccGGTTACGAGAGCACGCTGAccgccggctatggcagcacccagatggccgagcacagcagttcgctcactgccggttatggaagcaccggcatcgcggggcaggacagttcgctgatcgccggctacggcagcagtctgaccagcggggtacgcagctttctgaccgccggctacggcagcaacatgatcgccagctacggaagctcgctgatcgccggccatgagtgcacccagatcgccggccacaaaagcatgctgatcgcgggcaagggcagtttccagaccgcgggggctcgcagcacgctcattggcggtgccgccagcgtgcagaccgccggcgaccgcagcaagctgatcgcgggcgccgacagcacccagaccgccggcgaccgcagcaaactgttggccggacgcaacagctatctcaccgccggcgacaggagcaagctgaccgccggcgacgacagtacgttgatggctggcgatcgcagcaagctgaccgccggcaagaacagcgtgctgaccgccggcgccaacagcaggctcatcggcagtctgggttcgacgctgagcggcggggagaattcgacgctcattttccgttgctgggacggcgagcgctacaccaatctcgtggtcaggacaggggagcagggcgtggaatcggacatcccctatcaggtcgacgacgaaggaaatctggtaggaaaagcggatgacgatctggtgctggattacgaccctggcatgatcctggatgggcagtgcagtcccggcactggcgaggaactgcgcgatgtctgagcggcgcggtggccgcgcaatcggcgctcgccgcaggacgtggggcgcatcggtgacgatatggctgcgccgatagagttcggctagcgcgttgccgtggcttctggatgtgctcgtgcgcgtcgcgcatgggcacatccgcaggccgttgcggccatgctcgtggcgtcgcttgtgcggcgtcgcgcgtgttgcatggctggcgcggtatcggcggtgttgcattgccggcaatcgagatcccacgcacgcaatggcgcatgggcgctttcgcgtgtgggcaactgtgcgaagcatgcgccacacatgctgggccgatctgccagaattggctggtttcccgcc

·           Primer forward (5´GCA AGG GCA GCG ATG TCA C 3´)

Minimum base pairs required for single primer self-dimerization: 5.
Minimum base pairs required for a hairpin: 4.

Potential hairpin formation :

 None !

3' Complementarity:
 None !
 

All potential self-annealing sites are marked in red (allowing 1 mis-match):

 None !

·           primer reverse (5´ TCT GCG TGC TGC CGT AAC C 3´).

Minimum base pairs required for single primer self-dimerization: 5.
Minimum base pairs required for a hairpin: 4.

Potential hairpin formation :

 None !

3' Complementarity:
 None !
 

All potential self-annealing sites are marked in red (allowing 1 mis-match):

 None !

Primer dari jurnal jurnal Nejad et al., (2006) dengan kemungkinan produk PCRnya yaitu 90-1794 bp dan telah diperiksa kelayakan menggunakan DNA calculator diketahui bahwa primer tersebut tidak memiliki potensi terjadi hairpin, Complementary dan self annealing. Dari hasil tersebut dapat disimpulkan bahwa desain primer tersebut sudah sesuai dengan ketentuan syarat  pembuatan primer yang baik. Selain itu, jika dilihat dari output sekuens pada proses fastPCR in silico tersebut, diketahui bahwa terdapat banyak tanda merah pada sekuens yang menandakan bahwa primer tersebut memiliki banyak Reverse Complement pada sekuens sehingga primer dapat mengamplifikasi dibanyak lokasi pada sekuens.

b)      Buat/disain primer sendiri, jika produk PCR yang diinginkan lebih dari 1000 bp! (Xanthomonas campesris ice nucleation gene inaX, dapat diakses melalui GenBank: X52970.1)

·         Primer 3 Output

No mispriming library specified

Using 1-based sequence positions

OLIGO            start  len      tm     gc%   any    3' seq

LEFT PRIMER       3687   20   60.06   55.00  3.00  2.00 TACGACAGCAACCTCACTGC

RIGHT PRIMER      4855   20   59.97   55.00  4.00  2.00 GTCCTGACCACGAGATTGGT

SEQUENCE SIZE: 5360

INCLUDED REGION SIZE: 5360

PRODUCT SIZE: 1169, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 3.00

    1 GAATTCTATTCGATTCTCAATCTGTGAGATTGCCGGATTCGACGCTGCGAGTCGTTTCCA

                                                                 

   61 CAAAGCAAGTCGGAGCGATCGGTCGAAGTGGCGGCATGCCGTGGCCTAGCTTTTGTTGCA

                                                                 

  121 TGTAAAGTTTGGTTTATACGGCTTGAATGCCTGTTTCGTGGACACGCAGGAGGGGCTTGG

                                                                 

  181 CCAGGCGCGTCTGGCGATGGCCCAGGCTGGTTTTTTTGCCGCCAGAACGGATGCGACGCA

                                                                 

  241 GCGCGGTTTCCCGGCGTGTGGCCTGGGAAATACTCCGATTTTTCTTGTCGTATTTATAGT

                                                                 

  301 GAGGTAGTGTGATGATCGTTGAAAAGATTTTGGCATTGCGTACGTGCGCCAATAACATGG

                                                                 

  361 CCGACCACTGCGGGTTGATCTGGCCGATGGCCGGTCCCGTGGAATGCAAATTCTGGAAAC

                                                                 

  421 CGTCGGGACTGCACGAAAATGGTCTTACCGGGCTGTTGTGGGGCAAGGGCGTCGGGGCGC

                                                                 

  481 ATCTGAGTGCGCACGCCGATGCGCGCTGGGTCGTGTGCGAAGTCGCCGTCGACGAGATGC

                                                                 

  541 TGCAGTTGGCCGAAGAGGGGATGATCAAGTTCCCGCGCGCAACTGTGCTTTTCGTCGGAA

                                                                 

  601 ATCGCAGCCAGGCGCTGGACTATATTGCAGCCAACATGCCGCTCTACGGCGCCGCTCTAC

                                                                 

  661 AGCTGGCGGCACCCGCTGCGCCGGCGCATGTCCACATGCCCGCAGCGGAGCCGTCCGCGC

                                                                 

  721 CGGCAACGCAGGCGACCTCTGCAACCCTGCCGACCCCAGCCACCCCTTCCACCCAGGCCA

                                                                 

  781 CCCCTTCCACTCAGTCAACTCAGTCAACTCAGTCAACCGAAGCGACCCAGTCAACCGAGG

                                                                 

  841 CGACCCCGGTTGCCACGGTCGCCGCAGCGCCGCCTCCTCCGGGACAGCAGCATGACGTGA

                                                                 

  901 TGGCGAAGAAGACCGAAACCGGTGTCTATGGCAGCACACTCACAGGCGCCGACCAGAGCC

                                                                 

  961 GGCTCGTCGCAGGCTACGGCAGTACCGAAACCGCAGGCGATCACAGCGATCTGATCGCCG

                                                                 

 1021 GCTATGGCAGCACCGGGACCGCCGGATCCGACAGTTCCATCCTGGCAGGGTATGGCAGCA

                                                                 

 1081 CGCAGACTGCCGCGGGCAGGAGCACGCTCACCGCCGGCTATGGCAGCACGCAGACGGCGC

                                                                 

 1141 AGGAAGGCAGCCGTCTCACCTCCGGTTACGGCAGCACTGCGACCAGCGGTTCTGACAGCG

                                                                 

 1201 CGGTGATCTCCGGCTACGGCAGCACGCAAACGGCCGGTAGCGAGAGTTCCTTGACCGCTG

                                                                 

 1261 GCTACGGCAGCACGCAGACCGCGCGCAAGGGCAGCGACATCACCGCCGGCTATGGCAGTA

                                                                 

 1321 CCGGTACGGCCGGGTCGGACAGCGCGTTGATCGCCGGCTACGGCAGCACCCAGACCGCCG

                                                                 

 1381 GCAGCGAGAGTTCCTTGACCGCCGGCTACGGCAGCACGCAGACCGCACGCAAGGGCAGCG

                                                                  

 1441 ACGTCACCGCCGGCTACGGCAGTACCGGCACGGCGGGTGCCGACAGCACCTTGATCGCGG

                                                                 

 1501 GCTATGGCAGCACGCAGACCGCTGGCGGCGAAAGCTCTCTCACCGCCGGCTACGGCAGCA

                                                                  

 1561 CGCAGACTGCGCGGCAAGGCAGCGACATCACCGCCGGTTACGGCAGTACCGGCACTGCCG

                                                                 

 1621 GTGCGGACAGCACGCTGATCGCCGGTTACGGCAGCACGCAAACCTCGGGCAGCGACAGCT

                                                                  

 1681 CGCTGACAGCCGGTTATGGCAGCACGCAGACCGCGCGCAAGGGCAGCGACATCACTGCCG

                                                                 

 1741 GCTACGGCAGCACCGGCACCGCCGGATCCGACAGTTCGTTGATCGCCGGCTACGGCAGCA

                                                                  

 1801 CGCAGACCGCTGGCAGCGAAAGTTCGCTGACGGCCGGCTACGGCAGCACGCAGACCGCCC

                                                                 

 1861 AGCAAGACAGCTCGCTCACCACCGGCTACGGCAGTACCTCGACGGCGGGTCACGACAGTT

                                                                 

 1921 CGCTGATCGCCGGCTATGGCAGCACCCAGACCGCCGGCTACGATAGCACCCTGACCGCCG

                                                                 

 1981 GCTACGGCAGTACGCAGACCGCCCAACAAGACAGTTCGCTCACCACCGGTTACGGCAGTA

                                                                 

 2041 CCTCCACCGCCGGTGCCGACAGTACGCTGATCGCCGGCTACGGCAGTACGCAGACCGCTG

                                                                 

 2101 GCAGCGACAGTTCGCTGACGGCCGGTTACGGCAGCACACAGACCGCACGCGAAGGCAGCG

                                                                 

 2161 ACGTCACCGCCGGCTACGGCAGCACCGGCACCGCGGGTGCGGACAGTACCTTGATCGCCG

                                                                 

 2221 GCTACGGCAGCACGCAGACCTCCGGTAGCGACAGTTCGCTGACGGCCGGCTACGGCAGTA

                                                                 

 2281 CGCAGACCGCGCGCAAGGGCAGCGACGTCACCGCCGGCTATGGCAGCACCGGCACGGCGG

                                                                 

 2341 GTGCGGACAGCACGCTGATCGCCGGCTACGGCAGCACGCAGACCTCCGGTAGCGACAGTT

                                                                 

 2401 CGCTGACGGCCGGCTACGGCAGTACGCAGACCGCGCGCAAGGGCAGCGATGTCACCGCCG

                                                                 

 2461 GCTACGGCAGCACCGGCACGGCGGGTGCGGACAGCACGCTGATCGCCGGCTACGGCAGCA

                                                                  

 2521 CGCAGACCTCGGGTAGCGACAGTTCGCTGACGGCCGGCTACGGCAGTACGCAGACCGCGC

                                                                 

 2581 GCAAGGGCAGCGACGTCACCGCCGGCTACGGCAGCACCGGCACGGCGGGTGCGGACAGCA

                                                                  

 2641 CGCTGATCGCAGGTTACGGCAGCACGCAAACCTCGGGCAGCGACAGTTCGCTGACGGCCG

                                                                 

 2701 GTTATGGCAGTACGCAGACCGCGCGCAAGGGCAGCGACATTACCGCCGGCTACGGCAGCA

                                                                  

 2761 CCGGCACCGCGGGCGCGGACAGCACCTTGATCGCGGGCTATGGCAGCACGCAGACCTCCG

                                                                 

 2821 GCAGCGACAGTTCGCTGACCGCCGGTTACGGCAGCACGCAGACCGCACGCGAAGGCAGCG

                                                                 

 2881 ACGTCACCGCCGGTTACGGCAGCACCGGCACGGCGGGCGCGGACAGCACCCTGATCTCCG

                                                                 

 2941 GCTACGGCAGCACGCAAACGGCCGGCAGCGACAGTTCGCTGACCGCCGGCTACGGCAGTA

                                                                 

 3001 CGCAGACTGCGCGCAAGGGCAGCGACGTCACCGCCGGTTACGGCAGTACCGGCACCGCGG

                                                                 

 3061 GTGCGGACAGCACCTTGATCGCGGGCTACGGCAGCACGCAGACCTCCGGCAGCGACAGTT

                                                                 

 3121 CGCTGACCGCCGGTTACGGCAGTACGCAGACCGCGCGCAAGGGCAGCGACATGACCGCCG

                                                                 

 3181 GCTACGGCAGTACCGGCACCGCTGGCGCGGATAGCACCTTGATCGCGGGCTACGGCAGCA

                                                                 

 3241 CGCAGACGTCCGGCAGCGACAGCTCGCTGACGGCCGGTTACGGCAGCACGCAGACCGCAC                                                               

 3301 GCGAAGGCAGCGACGTCACCGCCGGTTACGGCAGCACCGGCACGGCGGGCGCGGACAGCA

                                                                 

 3361 CCCTGATCGCCGGCTACGGCAGCACGCAAACGGCCGGCAGCGACAGTTCGCTGACCGCCG

                                                                 

 3421 GCTATGGCAGCACGCAGACGGCACGGCAGGGCAGCGACGTCACCGCCGGCTACGGCAGTA

                                                                 

 3481 CAGGTACCGCGGGCGCGGACAGCACCCTGATCGCCGGCTACGGCAGCACGCAAACGGCCG

                                                                 

 3541 GCAGCGACAGTTCGCTGACCGCCGGCTATGGCAGCACGCAGACGGCACGGCAGGGCAGCG

                                                                 

 3601 ACATCACCGCCGGCTATGGCAGTACCGGGACCGCGGGCGCCGACAGTTCGTTGATCGCCG

                                                                 

 3661 GCTATGGCAGCACCCAGACCGCCGGCTACGACAGCAACCTCACTGCCGGTTACGGCAGCA

                                >>>>>>>>>>>>>>>>>>>>             

 3721 CGCAGACGGCGCGCGAGGACAGCTCGCTCACTGCTGGCTACGGCAGCACGTCCACCGCCG

                                                                 

 3781 GTCATGACAGTTCGCTGATCGCCGGCTATGGCAGTACCCAGACCGCTGGCTACAACAGCA

                                                                 

 3841 TCCTGACCACCGGCTATGGCAGTACCCAGACTGCACAGGAGAGCAGTTCTCTCACTGCCG

                                                                 

 3901 GCTACGGCAGCACCTCCACGGCCGGCTACGACAGCACCTTGACCGCCGGCTATGGCAGTA

                                                                 

 3961 CCCAAACCGCCGGCTACAAAAGCACGCTGACCGCGGGTTATGGCAGCAACTCGACCGCCG

                                                                 

 4021 GCCACGAGAGCTCGTTGATCGCCGGCTACGGTAGCACCCAGATCGCTGGATACGAGAGCA

                                                                 

 4081 CCTTGACCGCGGGCTACGGCAGTTCGCTGACCACGCAGCAGAACAGTTCGCTGACTGCCG

                                                                 

 4141 GCTACGGCAGCACCGAGATCGCCGGCTATGCCAGTACGCTGATGGCCGGCTACGGCAGTT

                                                                 

 4201 CCCAGACCGCCGGTTACGAGAGCACGCTGACCGCCGGCTATGGCAGCACCCAGATGGCCG

                                                                 

 4261 AGCACAGCAGTTCGCTCACTGCCGGTTATGGAAGCACCGGCATCGCGGGGCAGGACAGTT

                                                                 

 4321 CGCTGATCGCCGGCTACGGCAGCAGTCTGACCAGCGGGGTACGCAGCTTTCTGACCGCCG

                                                                 

 4381 GCTACGGCAGCAACATGATCGCCAGCTACGGAAGCTCGCTGATCGCCGGCCATGAGTGCA

                                                                 

 4441 CCCAGATCGCCGGCCACAAAAGCATGCTGATCGCGGGCAAGGGCAGTTTCCAGACCGCGG

                                                                  

 4501 GGGCTCGCAGCACGCTCATTGGCGGTGCCGCCAGCGTGCAGACCGCCGGCGACCGCAGCA                                                             

 4561 AGCTGATCGCGGGCGCCGACAGCACCCAGACCGCCGGCGACCGCAGCAAACTGTTGGCCG

                                                                  

 4621 GACGCAACAGCTATCTCACCGCCGGCGACAGGAGCAAGCTGACCGCCGGCGACGACAGTA

                                                                 

 4681 CGTTGATGGCTGGCGATCGCAGCAAGCTGACCGCCGGCAAGAACAGCGTGCTGACCGCCG

                                                                  

 4741 GCGCCAACAGCAGGCTCATCGGCAGTCTGGGTTCGACGCTGAGCGGCGGGGAGAATTCGA

                                                                 

 4801 CGCTCATTTTCCGTTGCTGGGACGGCGAGCGCTACACCAATCTCGTGGTCAGGACAGGGG

                                         <<<<<<<<<<<<<<<<<<<<    

 4861 AGCAGGGCGTGGAATCGGACATCCCCTATCAGGTCGACGACGAAGGAAATCTGGTAGGAA

                                                                 

 4921 AAGCGGATGACGATCTGGTGCTGGATTACGACCCTGGCATGATCCTGGATGGGCAGTGCA

                                                                 

 4981 GTCCCGGCACTGGCGAGGAACTGCGCGATGTCTGAGCGGCGCGGTGGCCGCGCAATCGGC

                                                                 

 5041 GCTCGCCGCAGGACGTGGGGCGCATCGGTGACGATATGGCTGCGCCGATAGAGTTCGGCT

                                                                 

 5101 AGCGCGTTGCCGTGGCTTCTGGATGTGCTCGTGCGCGTCGCGCATGGGCACATCCGCAGG

                                                                 

 5161 CCGTTGCGGCCATGCTCGTGGCGTCGCTTGTGCGGCGTCGCGCGTGTTGCATGGCTGGCG

                                                                 

 5221 CGGTATCGGCGGTGTTGCATTGCCGGCAATCGAGATCCCACGCACGCAATGGCGCATGGG

                                                                 

 5281 CGCTTTCGCGTGTGGGCAACTGTGCGAAGCATGCGCCACACATGCTGGGCCGATCTGCCA

                                                                 

 5341 GAATTGGCTGGTTTCCCGCC

                         

KEYS (in order of precedence):

>>>>>> left primer

<<<<<< right primer

ADDITIONAL OLIGOS

                    start  len      tm     gc%   any    3' seq

 1 LEFT PRIMER       3687   20   60.06   55.00  3.00  2.00 TACGACAGCAACCTCACTGC

   RIGHT PRIMER      4931   20   60.07   50.00  2.00  0.00 GTCATCCGCTTTTCCTACCA

   PRODUCT SIZE: 1245, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 1.00

 2 LEFT PRIMER        426   20   60.12   50.00  4.00  0.00 GGACTGCACGAAAATGGTCT

   RIGHT PRIMER      4855   20   59.97   55.00  4.00  2.00 GTCCTGACCACGAGATTGGT

   PRODUCT SIZE: 4430, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00

 3 LEFT PRIMER       3687   20   60.06   55.00  3.00  2.00 TACGACAGCAACCTCACTGC

   RIGHT PRIMER      4858   20   60.11   55.00  4.00  1.00 CCTGTCCTGACCACGAGATT

   PRODUCT SIZE: 1172, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 2.00

 4 LEFT PRIMER       3687   20   60.06   55.00  3.00  2.00 TACGACAGCAACCTCACTGC

   RIGHT PRIMER      4897   20   59.89   55.00  4.00  2.00 TCGACCTGATAGGGGATGTC

   PRODUCT SIZE: 1211, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 2.00

Statistics

         con   too    in    in          no    tm    tm  high  high        high     

         sid  many   tar  excl   bad    GC   too   too   any    3'  poly   end     

        ered    Ns   get   reg   GC% clamp   low  high compl compl     X  stab    ok

Left   40157     0     0     0  1431     0  1070 35483     1     8    23   374  1758

Right  39961     0     0     0  1280     0   402 36520     0     1     0   412  1344

Pair Stats:

considered 41, unacceptable product size 30, ok 11

primer3 release 1.1.4

(primer3_results.cgi release 0.4.0)

·         FastPCR In silico primer Output

In silico Primer(s) search for: 1

primer forward  5'-tacgacagcaacctcactgc

Position: 3687->3706 100%   Tm = 57,3°C

5-tacgacagcaacctcactgc->

  ||||||||||||||||||||

gctacgacagcaacctcactgccggt

primer reverse   5'-gtcctgaccacgagattggt

Position: 4836<-4855 100%   Tm = 56,3°C

<-tggttagagcaccagtcctg-5

  ||||||||||||||||||||

acaccaatctcgtggtcaggacaggg

>primer forward 3687->3706

 5'-tacgacagcaacctcactgc

>primer reverse  4836<-4855

 5'-gtcctgaccacgagattggt

PCR product size: 1169bp  Ta=64°C

·         FastPCR sequences Output

>1gaattctattcgattctcaatctgtgagattgccggattcgacgctgcgagtcgtttccacaaagcaagtcggagcgatcggtcgaagtggcggcatgccgtggcctagcttttgttgcatgtaaagtttggtttatacggcttgaatgcctgtttcgtggacacgcaggaggggcttggccaggcgcgtctggcgatggcccaggctggtttttttgccgccagaacggatgcgacgcagcgcggtttcccggcgtgtggcctgggaaatactccgatttttcttgtcgtatttatagtgaggtagtgtgatgatcgttgaaaagattttggcattgcgtacgtgcgccaataacatggccgaccactgcgggttgatctggccgatggccggtcccgtggaatgcaaattctggaaaccgtcgggactgcacgaaaatggtcttaccgggctgttgtggggcaagggcgtcggggcgcatctgagtgcgcacgccgatgcgcgctgggtcgtgtgcgaagtcgccgtcgacgagatgctgcagttggccgaagaggggatgatcaagttcccgcgcgcaactgtgcttttcgtcggaaatcgcagccaggcgctggactatattgcagccaacatgccgctctacggcgccgctctacagctggcggcacccgctgcgccggcgcatgtccacatgcccgcagcggagccgtccgcgccggcaacgcaggcgacctctgcaaccctgccgaccccagccaccccttccacccaggccaccccttccactcagtcaactcagtcaactcagtcaaccgaagcgacccagtcaaccgaggcgaccccggttgccacggtcgccgcagcgccgcctcctccgggacagcagcatgacgtgatggcgaagaagaccgaaaccggtgtctatggcagcacactcacaggcgccgaccagagccggctcgtcgcaggctacggcagtaccgaaaccgcaggcgatcacagcgatctgatcgccggctatggcagcaccgggaccgccggatccgacagttccatcctggcagggtatggcagcacgcagactgccgcgggcaggagcacgctcaccgccggctatggcagcacgcagacggcgcaggaaggcagccgtctcacctccggttacggcagcactgcgaccagcggttctgacagcgcggtgatctccggctacggcagcacgcaaacggccggtagcgagagttccttgaccgctggctacggcagcacgcagaccgcgcgcaagggcagcgacatcaccgccggctatggcagtaccggtacggccgggtcggacagcgcgttgatcgccggctacggcagcacccagaccgccggcagcgagagttccttgaccgccggctacggcagcacgcagaccgcacgcaagggcagcgacgtcaccgccggctacggcagtaccggcacggcgggtgccgacagcaccttgatcgcgggctatggcagcacgcagaccgctggcggcgaaagctctctcaccgccggctacggcagcacgcagactgcgcggcaaggcagcgacatcaccgccggttacggcagtaccggcactgccggtgcggacagcacgctgatcgccggttacggcagcacgcaaacctcgggcagcgacagctcgctgacagccggttatggcagcacgcagaccgcgcgcaagggcagcgacatcactgccggctacggcagcaccggcaccgccggatccgacagttcgttgatcgccggctacggcagcacgcagaccgctggcagcgaaagttcgctgacggccggctacggcagcacgcagaccgcccagcaagacagctcgctcaccaccggctacggcagtacctcgacggcgggtcacgacagttcgctgatcgccggctatggcagcacccagaccgccggctacgatagcaccctgaccgccggctacggcagtacgcagaccgcccaacaagacagttcgctcaccaccggttacggcagtacctccaccgccggtgccgacagtacgctgatcgccggctacggcagtacgcagaccgctggcagcgacagttcgctgacggccggttacggcagcacacagaccgcacgcgaaggcagcgacgtcaccgccggctacggcagcaccggcaccgcgggtgcggacagtaccttgatcgccggctacggcagcacgcagacctccggtagcgacagttcgctgacggccggctacggcagtacgcagaccgcgcgcaagggcagcgacgtcaccgccggctatggcagcaccggcacggcgggtgcggacagcacgctgatcgccggctacggcagcacgcagacctccggtagcgacagttcgctgacggccggctacggcagtacgcagaccgcgcgcaagggcagcgatgtcaccgccggctacggcagcaccggcacggcgggtgcggacagcacgctgatcgccggctacggcagcacgcagacctcgggtagcgacagttcgctgacggccggctacggcagtacgcagaccgcgcgcaagggcagcgacgtcaccgccggctacggcagcaccggcacggcgggtgcggacagcacgctgatcgcaggttacggcagcacgcaaacctcgggcagcgacagttcgctgacggccggttatggcagtacgcagaccgcgcgcaagggcagcgacattaccgccggctacggcagcaccggcaccgcgggcgcggacagcaccttgatcgcgggctatggcagcacgcagacctccggcagcgacagttcgctgaccgccggttacggcagcacgcagaccgcacgcgaaggcagcgacgtcaccgccggttacggcagcaccggcacggcgggcgcggacagcaccctgatctccggctacggcagcacgcaaacggccggcagcgacagttcgctgaccgccggctacggcagtacgcagactgcgcgcaagggcagcgacgtcaccgccggttacggcagtaccggcaccgcgggtgcggacagcaccttgatcgcgggctacggcagcacgcagacctccggcagcgacagttcgctgaccgccggttacggcagtacgcagaccgcgcgcaagggcagcgacatgaccgccggctacggcagtaccggcaccgctggcgcggatagcaccttgatcgcgggctacggcagcacgcagacgtccggcagcgacagctcgctgacggccggttacggcagcacgcagaccgcacgcgaaggcagcgacgtcaccgccggttacggcagcaccggcacggcgggcgcggacagcaccctgatcgccggctacggcagcacgcaaacggccggcagcgacagttcgctgaccgccggctatggcagcacgcagacggcacggcagggcagcgacgtcaccgccggctacggcagtacaggtaccgcgggcgcggacagcaccctgatcgccggctacggcagcacgcaaacggccggcagcgacagttcgctgaccgccggctatggcagcacgcagacggcacggcagggcagcgacatcaccgccggctatggcagtaccgggaccgcgggcgccgacagttcgttgatcgccggctatggcagcacccagaccgccggcTACGACAGCAACCTCACTGCcggttacggcagcacgcagacggcgcgcgaggacagctcgctcactgctggctacggcagcacgtccaccgccggtcatgacagttcgctgatcgccggctatggcagtacccagaccgctggctacaacagcatcctgaccaccggctatggcagtacccagactgcacaggagagcagttctctcactgccggctacggcagcacctccacggccggctacgacagcaccttgaccgccggctatggcagtacccaaaccgccggctacaaaagcacgctgaccgcgggttatggcagcaactcgaccgccggccacgagagctcgttgatcgccggctacggtagcacccagatcgctggatacgagagcaccttgaccgcgggctacggcagttcgctgaccacgcagcagaacagttcgctgactgccggctacggcagcaccgagatcgccggctatgccagtacgctgatggccggctacggcagttcccagaccgccggttacgagagcacgctgaccgccggctatggcagcacccagatggccgagcacagcagttcgctcactgccggttatggaagcaccggcatcgcggggcaggacagttcgctgatcgccggctacggcagcagtctgaccagcggggtacgcagctttctgaccgccggctacggcagcaacatgatcgccagctacggaagctcgctgatcgccggccatgagtgcacccagatcgccggccacaaaagcatgctgatcgcgggcaagggcagtttccagaccgcgggggctcgcagcacgctcattggcggtgccgccagcgtgcagaccgccggcgaccgcagcaagctgatcgcgggcgccgacagcacccagaccgccggcgaccgcagcaaactgttggccggacgcaacagctatctcaccgccggcgacaggagcaagctgaccgccggcgacgacagtacgttgatggctggcgatcgcagcaagctgaccgccggcaagaacagcgtgctgaccgccggcgccaacagcaggctcatcggcagtctgggttcgacgctgagcggcggggagaattcgacgctcattttccgttgctgggacggcgagcgctacACCAATCTCGTGGTCAGGACaggggagcagggcgtggaatcggacatcccctatcaggtcgacgacgaaggaaatctggtaggaaaagcggatgacgatctggtgctggattacgaccctggcatgatcctggatgggcagtgcagtcccggcactggcgaggaactgcgcgatgtctgagcggcgcggtggccgcgcaatcggcgctcgccgcaggacgtggggcgcatcggtgacgatatggctgcgccgatagagttcggctagcgcgttgccgtggcttctggatgtgctcgtgcgcgtcgcgcatgggcacatccgcaggccgttgcggccatgctcgtggcgtcgcttgtgcggcgtcgcgcgtgttgcatggctggcgcggtatcggcggtgttgcattgccggcaatcgagatcccacgcacgcaatggcgcatgggcgctttcgcgtgtgggcaactgtgcgaagcatgcgccacacatgctgggccgatctgccagaattggctggtttcccgcc

·         DNA calculator

primer forward  5'-tacgacagcaacctcactgc-3’

Minimum base pairs required for single primer self-dimerization: 5.
Minimum base pairs required for a hairpin: 4.

Potential hairpin formation :

 None !

3' Complementarity:
 None !
 

All potential self-annealing sites are marked in red (allowing 1 mis-match):

 None !

primer reverse   5'-gtcctgaccacgagattggt-3’

Minimum base pairs required for single primer self-dimerization: 5.
Minimum base pairs required for a hairpin: 4.

Potential hairpin formation :

 None !

3' Complementarity:
 None !
 

All potential self-annealing sites are marked in red (allowing 1 mis-match):

 None !

Pada percobaan ini, disain primer yang dibuat secara mandiri dari sekuens ice nucleation gene inaX bakteri  Xanthomonas campesris dengan produk PCR yaitu 1169 bp atau lebih dari 1000 bp yang telah diuji potensialnya dengan menggunakan DNA calculator diketahui bahwa primer tersebut tidak berpotensi terjadi hairpin, Complementary dan self annealing. Dari hasil tersebut dapat disimpulkan bahwa desain primer tersebut sudah sesuai dengan ketentuan syarat  pembuatan primer yang baik. Sehingga dapat digunakan untuk suatu penelitian

2.      Gene and Promoter Prediction

Prediksikan gen dan promoter (jika ada) dari sekuen nukleotida di bawah ini. Sebutkan nama gen, produk gen dan organismenya! Kelompokkan organisme tersebut sebagai prokariot atau eukariot! 

Sekuens Nucleotida 1.

Nama gen              : TAP1

Produk Gen           : Peroxidase

Nama Spesies        : Solanum lycopersicum (Eukaryota)

GENSCAN  sekuen Nucleotida 1.

GENSCAN 1.0    Date run: 26-Dec-114   Time: 11:25:41

Sequence /tmp/12_26_14-11:25:41.fasta : 2907 bp : 34.67% C+G : Isochore 1 ( 0 - 43 C+G%)

Parameter matrix: HumanIso.smat

Predicted genes/exons:

Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..

----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 1.00 Prom +    336    375   40                              -2.25

 1.01 Init +    428    772  345  1  0   50  -35   231 0.456   4.30

 1.02 Intr +   1635   1832  198  2  0   -3  106   203 0.997  11.63

 1.03 Term +   2115   2666  552  2  0   78   48   397 0.998  28.02

 1.04 PlyA +   2725   2730    6                               1.05

Suboptimal exons with probability > 1.000

Exnum Type S .Begin ...End .Len Fr Ph B/Ac Do/T CodRg P.... Tscr..

----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

NO EXONS FOUND AT GIVEN PROBABILITY CUTOFF

Predicted peptide sequence(s):

>/tmp/12_26_14-11:25:41.fasta|GENSCAN_predicted_peptide_1|364_aa

MGFRLSHLSLALSFVALALAGVAIYRNTYEAIIMKNGSLLKNVSPDFDSLESGVASILTL

NNNKKRNSDKYLRQQLTPEACVFSAVRAVVDSAIDAETRMGASLIRLHFHDCFVDGCDGG

ILLDDINGTFTGEQNSPPNANSARGYEVIAQAKQSVINTCPNVSVSCADILAIAARDSVA

KLGGQTYSVALGRSDARTANFSGAINQLPAPFDNLTVQIQKFSDKNFTLREMVALAGAHT

VGFARCSTVCTSGNVNPAAQLQCNCSATLTDSDLQQLDTTPTMFDKVYYDNLNSNQGIMF

SDQVLTGDATTAGFVTDYSNDVNVFLGDFAAAMIKMGDLPPSAGAQLEIRDVCSRVNPTS

VASM

ORIGIN     

        1 gcagggatcg ttaataatta tactcaagta ttaacgtcaa ttaagaacta atatctttgc

       61 accaaatgag aaaagaaaca taaatctatc ctcgaaatta tctttccttc ttaaaatcga

      121 tattgtgact acaacatgaa agaaaattat tgacatttga cataattatc ggataaatat

      181 agctaagaaa acatcacacg ttacacagct agaactttag aaaagaaaga aaagtcactt

      241 tcacatgaaa catcaattct cagtttgtaa ttacacgata attcaaagat gaattaataa

      301 taacagtaat attgacaagt aattataagt cttcacctgc ctatataaat agaggcataa

      361 ataaaagcaa aatcatccct atcgaaagcc tttaatttgt ttcctcgata gacatttaaa

      421 ttaagtgatg ggttttcgtt tgagtcattt gagtcttgca ttgagttttg tggcacttgc

      481 acttgcaggt gttgctattt atagaaatac ttatgaagcc atcatcatga aaaacggttc

      541 actcctcaaa aatgtttctc cagatttcga ttcgttggaa tcaggcgtag ccagtatttt

      601 aaccttaaat aataataaga agagaaattc agacaagtac ttgagacagc aactaactcc

      661 ggaggcatgc gttttctcag ctgtacgagc agttgtggac agtgctattg atgcagaaac

      721 tcgcatggga gcttctctca ttcgtctcca ctttcatgac tgcttcgttg atgtaaatat

      781 atatttcctt cgctcttttt ttatcgtatt tgattatgca caaaatttta tttgaagtca

      841 cttaaatatt ttatgcttgt tcaaacaaat ttgaaaattc tttcagtttt tcctgaactc

      901 acaatgcatg cagtcaatta ctttactagg gaaaatgcac aagtacattc tcaacctatg

      961 tccgaaatta cagagacaca cttatattat actaaggttc tattactccc ctgaacttat

     1021 tttataagta atattctacc tagcttgaaa aaaaagtcaa cctgcgtaag gccaacaaga

     1081 tagtgtcacg taggccgaaa aaaagtaaaa aattattaat aaaataagtt aagtaaaata

     1141 ataggacctt agtatagtat aagcgtgtct ctaaaatttc gggtataggt taaagggact

     1201 acttaaattg aaatgaaaag agtagaggga tatcattttt taagacaggc taaaaagagt

     1261 acaatgttag gtgtagcata ttaattgaat ccgagtcctt ttcctcttat taattaaacc

     1321 tggccgtatg atcatatttt tctttcataa ataaataaat tgttgaaaga tctgaggcta

     1381 cgaactccaa attaaaatta taatgccata cttgttgttt taaatcgcaa atatttaaaa

     1441 aaaaaatact ttttcttttg aactccccgt caagtaaaat atcttcgcac acattttgct

     1501 tctacatgaa ctccaaaaac tttgaaaagt ctagtctgct ttccagtttt attttatttt

     1561 agatcttctg cagttgattt atgtatttga ctaattatac ctctctcgtt ttctttttta

     1621 ttacgaaaaa taagggttgt gatggaggta ttctgctaga tgatattaat ggaacattta

     1681 caggggaaca aaactcacca cccaacgcca actcagccag aggttatgaa gtaatagcac

     1741 aagctaaaca aagtgtcata aacacatgcc ccaacgtatc tgtatcttgt gccgacatat

     1801 tagctattgc tgctcgtgat tctgttgcta aagtaagtct atcattcatt ttacagtttg

     1861 ataatttcta ccaaaattaa ttacgaatag taacaaatgg atatttaatc aaactctaaa

     1921 gtcatcgtgg aagttgagaa atgttcaaag agatgaccaa attccacatc cacaatcaat

     1981 gtggaaattg tgacacctcg cctgtgggcg tctaacattt aatagatgaa gcattgtatt

     2041 tatttaggtt atgatgatat gacaaagaaa ttgacttggg ctaactcaaa ctctgtttta

     2101 ttggtatttg acagttagga ggacaaactt atagcgttgc attagggaga agcgatgcta

     2161 gaactgccaa ctttagtggt gctataaatc aacttccagc tccattcgac aacctaacag

     2221 tccaaataca gaaattcagc gacaaaaatt tcaccctccg tgaaatggtt gcactagctg

     2281 gtgcacacac ggtaggtttc gccaggtgtt ccacagtttg caccagcggt aacgttaatc

     2341 ctgccgcaca actccaatgc aactgctccg ccacgctaac tgattctgat ttgcaacaat

     2401 tggatactac tcctactatg ttcgacaaag tttactacga taacttaaac agcaaccaag

     2461 gcataatgtt ttcagatcaa gttttgaccg gggatgctac aactgctggt tttgtaacgg

     2521 attatagcaa cgatgtgaac gttttccttg gagattttgc tgctgccatg atcaagatgg

     2581 gagacttgcc cccctccgcc ggcgctcaat tggaaattcg tgatgtttgt agcagggtta

     2641 atcccacttc agtggcttct atgtgaaaaa ttcggaaatt ttaattaact tatctcgcga

     2701 ctagttgctt catgttttct tcaaaataaa agaatcactg gctccagaat gtggtttggt

     2761 tttggtattt gttttgtaat ccatcctatt ttatatgaat attgttttcc ttgtgtgcta

     2821 atgttggagc tgatcagaat agttcaattc gttattaaaa atttaataat ctgcaaaata

     2881 aaaataggac tcaaatagcc ttatgaa

//

Sekuens Nucleotida 2.

Nama gen              : GH1

Produk Gen           : Growth hormone

Nama Spesies        : Bos taurus (Eukaryota)

GENSCAN sekuen Nucleotida 2.

GENSCAN 1.0    Date run: 26-Dec-114   Time: 11:26:26

Sequence /tmp/12_26_14-11:26:26.fasta : 2856 bp : 58.44% C+G : Isochore 4 (57 - 100 C+G%)

Parameter matrix: HumanIso.smat

Predicted genes/exons:

Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..

----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- -----

 1.01 Init +    630    723   94  2  1   76  115    68 0.967   8.94

 1.02 Intr +    971   1131  161  0  2  100   52   170 0.997  15.50

 1.03 Intr +   1359   1475  117  2  0   74   70   121 0.999  10.73

 1.04 Intr +   1703   1864  162  1  0   34   39   306 0.670  21.67

 1.05 Term +   2138   2338  201  1  0  125   33   367 0.997  33.26

 1.06 PlyA +   2416   2421    6                               1.05

Suboptimal exons with probability > 1.000

Exnum Type S .Begin ...End .Len Fr Ph B/Ac Do/T CodRg P.... Tscr..

----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

NO EXONS FOUND AT GIVEN PROBABILITY CUTOFF

Predicted peptide sequence(s):

>/tmp/12_26_14-11:26:26.fasta|GENSCAN_predicted_peptide_1|244_aa

MAQQGPIPGSQDPVHQTTQGPVDSSPAMMAAGPRTSLLLAFALLCLPWTQVVGAFPAMSL

SGLFANAVLRAQHLHQLAADTFKEFERTYIPEGQRYSIQNTQVAFCFSETIPAPTGKNEA

QQKSDLELLRISLLLIQSWLGPLQFLSRVFTNSLVFGTSDRVYEKLKDLEEGILALMREL

EDGTPRAGQILKQTYDKFDTNMRSDDALLKNYGLLSCFRKDLHKTETYLRVMKCRRFGEA

ORIGIN     

        1 gtactggggt gggttgcctt tctcttctcc aggggattta tctgacccag ggattgaacc

       61 tgagtctcct gcatttgcag ctagattctt tacggctgag ccacctggga agcccattcg

      121 cttctgctgc tgctgctgct gctaagttgc ttcagtcgtg tccgacctgt gcgacgccat

      181 agacagcagc ccaccaggtc cccgtccctg ggattctcca ggcaagaaca ttggagtggg

      241 ttgccatttc ctcctccaat gcatgaaagt gaaaagtgaa agtgaagtca ctcagttgtg

      301 tccgaccctc agcgacccca tggactgcag ccttccagaa tggggtgcca ttgccttctc

      361 ctcgcttctg ctacctcccc tttaaaaaga aaacctatgg ggtgggctct caagctgaga

      421 ccctgtgtgc acagccctct ggctggtggc agtggagacg ggatgatgac aagcctgggg

      481 gacatgaccc cagagaagga acgggaacag gatgagtgag aggaggttct aaattatcca

      541 ttagcacagg ctgccagtgg tccttgcata aatgtataga gcacacaggt ggggggaaag

      601 ggagagagag aagaagccag ggtataaaaa tggcccagca gggaccaatt ccaggatccc

      661 aggacccagt tcaccagacg actcagggtc ctgtggacag ctcaccagct atgatggctg

      721 caggtaagct cgctaaaatc ccctccattc gcgtgtccta aaggggtaat gcggggggcc

      781 ctgccgatgg atgtgttcag agctttgggc tttagggctt ccgaatgtga acataggtat

      841 ctacacccag acatttggcc aagtttgaaa tgttctcagt ccctggaggg aagggtaggt

      901 ggggctggca ggagatcagg cgtctagctc cctggggccc tccgtcgcgg ccctcctggt

      961 ctctccctag gcccccggac ctccctgctc ctggctttcg ccctgctctg cctgccctgg

     1021 actcaggtgg tgggcgcctt cccagccatg tccttgtccg gcctgtttgc caacgctgtg

     1081 ctccgggctc agcacctgca tcagctggct gctgacacct tcaaagagtt tgtaagctcc

     1141 cgagggatgc gtcctagggg tggggaggca ggaaggggtg aatccacacc ccctccacac

     1201 agtgggagga aactgaggag ttcagccgta ttttatccaa gtagggatgt ggttagggga

     1261 gcagaaacgg gggtgtgtgg ggtggggagg gttccgaata aggcggggag gggaaccgcg

     1321 caccagctta gacctgggtg ggtgtgttct tcccccagga gcgcacctac atcccggagg

     1381 gacagagata ctccatccag aacacccagg ttgccttctg cttctctgaa accatcccgg

     1441 cccccacggg caagaatgag gcccagcaga aatcagtgag tggcaacctc ggaccgagga

     1501 gcaggggacc tccttcatcc taagtaggct gccccagctc ccgcaccggc ctggggcggc

     1561 cttctccccg aggtggcgga ggttgttgga tggcagtgga ggatgatggt gggcggtggt

     1621 ggcaggaggt cctcgggcag aggccgacct tgcagggctg ccccagaccc gcggcaccca

     1681 ccgaccaccc acctgccagc aggacttgga gctgcttcgc atctcactgc tcctcatcca

     1741 gtcgtggctt gggcccctgc agttcctcag cagagtcttc accaacagct tggtgtttgg

     1801 cacctcggac cgtgtctatg agaagctgaa ggacctggag gaaggcatcc tggccctgat

     1861 gcgggtgggg atggcgttgt gggtcccttc catgtggggg ccatgcccgc cctctcctgg

     1921 cttagccagg agaatgcacg tgggcttggg gagacagatc cctgctctct ccctctttct

     1981 agcagtccag ccttgaccca ggggaaacct tttccccttt tgaaacctcc ttcctcgccc

     2041 ttctccaagc ctgtagggga gggtggaaaa tggagcgggc aggagggagc tgctcctgag

     2101 ggcccttcgg cctctctgtc tctccctccc ttggcaggag ctggaagatg gcaccccccg

     2161 ggctgggcag atcctcaagc agacctatga caaatttgac acaaacatgc gcagtgacga

     2221 cgcgctgctc aagaactacg gtctgctctc ctgcttccgg aaggacctgc ataagacgga

     2281 gacgtacctg agggtcatga agtgccgccg cttcggggag gccagctgtg ccttctagtt

     2341 gccagccatc tgttgtttgc ccctcccccg tgccttcctt gaccctggaa ggtgccactc

     2401 ccactgtcct ttcctaataa aatgaggaaa ttgcatcgca ttgtctgagt aggtgtcatt

     2461 ctattctggg gggtggggtg gggcaggaca gcaaggggga ggattgggaa gacaatagca

     2521 ggcatgctgg ggatgcggtg ggctctatgg gtacccaggt gctgaagaat tgacccggtt

     2581 cctcctgggc cagaaagaag caggcacatc cccttctctg tgacacaccc tgtccacgcc

     2641 cctggttctt agttccagcc ccactcatag gacactcata gctcaggagg gctccgcctt

     2701 caatcccacc cgctaaagta cttggagcgg tctctccctc cctcatcagc ccaccaaacc

     2761 aaacctagcc tccaagagtg ggaagaaatt aaagcaagat aggctattaa gtgcagaggg

     2821 agagaaaatg cctccaacat gtgaggaagt aatgag

//

Sekuens Nucleotida 3.

Nama gen              : Gene for chitinase

Produk Gen           : Chitinase

Nama Spesies        : Aeromonas caviae (Prokaryota)

GenMark sekuen Nucleotida 3.

GeneMark.hmm PROKARYOTIC (Version 3.25)

Date: Tue Dec 30 03:30:50 2014

Sequence file name: seq.fna

Model file name: GeneMark_hmm_heuristic.mod

RBS: false

Model information: Heuristic_model_for_genetic_code_11_and_GC_62

FASTA definition line: empty-fasta-def-line

Predicted genes

   Gene    Strand    LeftEnd    RightEnd       Gene     Class

    #                                         Length

    1        +         155        2752         2598        1

ORIGIN     

        1 ccggtctaag ggtctgcgta cctaggatag cggggccacc acaggttgta tcgtccatgg

       61 gccaagccat ggctgcgatg ttgtctgcgt tacctggcag gttgcgttgc ctttttcgtt

      121 gttaattcca ataacgaaat aaggaagttc aaatatgtta agtccaaaac tttccctgct

      181 ggcgcttctg gtcggggggc tttgcactac ctccgccttc gccgctgccc cgggcaaacc

      241 caccattggc tccggcccca ccaagtttgc catcgttgaa gtcaatcagg ccgcttcggc

      301 ctacaaccag ttggtgaccg tccacaagga tggcgctccc gtcagcgtga cctggaacct

      361 ctggtccggt gacgtcggac agaccgccaa ggtactgctc gacggcaagg aggtgtggtc

      421 aggcccggcc ttcgccgcgg gtaccgccaa cttcaaggtc accaaggggg ggcgttacca

      481 gatgcaggtg gccctgtgca acgcccatgg ctgcaccctc tccgacaaga aggagctgat

      541 ggtcgccgat accgacggca gccacctggc gccgctcaat gcgcccctca aggagaacaa

      601 caagccttac gccaacaagt ccggcaaggt ggtgggggcc tactacgtgg agtggggggt

      661 ctatggtcgc aagttcaccg tggacaagat cccggcccag aacctgaccc atatcctcta

      721 cggcttcacc cccatctgcg gtggcaacgg catcaacgac agcctcaaag agatctccgg

      781 cagcttcgag gcgttgcagc gctcctgtgc gggccgcgaa gacttcaagg tctccatcca

      841 tgatccctgg gcggcgatcc agatgtccca gggcaacctc agcgcctggg atgagcccta

      901 caagggcaac ttcggcaacc tgatggcgct caaacaggcc catccggacc tcaagatcct

      961 gccgtctgtc ggcggatgga ccctctcaga tcccttctat ttcctgggtg acaagaccaa

     1021 gcgcgatacc ttcgtcgcct cggtcaaaga gttcctgcag acctggaaat tcttcgacgg

     1081 cgtggacatc gactgggagt tcccgggcgg acagggggcc aaccccagcc tgggcggccc

     1141 gaatgacggc gccacctatg tggtgctgat gaaggagctg cgagccatgc tcgatgaact

     1201 ggaagccgag accggccgcc agtatgagct gacctcggcc atcagcgccg gcggtgacaa

     1261 gattgccaag gtggattatc aggcggctca gcagtacatg gaccacatct tcctgatgag

     1321 ctacgacttc agcggcgcct tcgacctgac gaatctgccc caccagacca acctctttgc

     1381 ctccagctgg gatccggcca ccaagtacac cgccgacaag ggcgtcaagg cgctgctggg

     1441 tcagggggtg acaccgggca agattgtggt gggggcggcc atgtatggcc gtggcatgac

     1501 cggagtgaag aactaccagg ccggcaaccc ctgcaccggc accgccaccg gaccggtgag

     1561 cggtacctgg gaaaatggcg tggtggatta ccgcgacatc gtcaacaacc gcatgggcgc

     1621 aggctgggag cagggctatg acgagtcggc cgaggccccc tatgtcttca aggccagcag

     1681 tggtgacctc atcaccttcg acaacgaccg ctcggtcaag gccaaggggc agtacgtgct

     1741 ggcgaaccag ctcggcggtc tgttcgcctg ggaaattgat gcggacaacg gcgacatcct

     1801 caacgccatg cacgaggggc tgggccacgg cgagggtacg ctgccgccgg tcaacaagcc

     1861 gccggttgcc aatgccggca gcgatctgag tgccaccggc ccggccgagg tgaccctcaa

     1921 gggcagtgcc tcccacgatc cggaaaacgg ggcgctgacc tacagctgga aacaggtctc

     1981 cggaccccag gccagcctgc tggatgccac ccaggccaag gcccgtgtgg tactggatgc

     2041 cgtcagcagc gacatcaatc tggtgttcga gctgaccgtg accgacgatc aggggctctc

     2101 ggccaaggat caggtggtgg tcaccaacaa ggcgccgcag ccgaacctgc cccccgtggt

     2161 cagcgtaccg gccagtgcga ccgtcgaggc cggcaagcag gtgagcatca aggccaccgc

     2221 ttccgacccc aatggtgatg ccctgagcta tcagtggaca gtgccggccg ggctcagcgc

     2281 caccggtctg gacagcgcga ccctggtggt cacgggctcg aacgtgacca gtgacacggc

     2341 ctacgatctg accctggtgg tcaccgacgg ggcgctggat gccacagccg ttacccgcct

     2401 gaccgtcaag ccggccagta caggtggtgg ctgtgaggcc tgcgatccgg atgcggccaa

     2461 ccacccggcc tggagtgcag gtaccgtcta caacaccaat gacaaggtga gccacaacca

     2521 gctggtgtgg caggccaagt attggaccca gggcaacgag ccgagccgca ccgccgatca

     2581 gtggaaactg gtgagccagg tgcaactggg ttgggatgcc ggagtggtct acaacggtgg

     2641 tgatgtcacc agccacaacg gccgtaagtg gaaggcccag tactggtcca agggcgatga

     2701 gcccggcaag gccgccgtct gggtcgatca gggcgcggcg agctgcaact gatctgccgt

     2761 gatgaaaaat ggggccgagg ggatttttgt cttgcgtggt cgggtgtgtg ttccctgtca

     2821 ggggaaaggc gcactcgctt tgtcaaaaag gcccgtcagg gccttttttc atggtatgtc

     2881 accggttcac agcggttttt gccacaggct gagcagcaga tcctg

//

Lampiran

·         FASTA Xanthomonas campesris ice nucleation gene inaX (NCBI)

GenBank: X52970.1

GenBank Graphics

>gi|48531|emb|X52970.1| Xanthomonas campesris ice nucleation gene inaX

GAATTCTATTCGATTCTCAATCTGTGAGATTGCCGGATTCGACGCTGCGAGTCGTTTCCACAAAGCAAGT

CGGAGCGATCGGTCGAAGTGGCGGCATGCCGTGGCCTAGCTTTTGTTGCATGTAAAGTTTGGTTTATACG

GCTTGAATGCCTGTTTCGTGGACACGCAGGAGGGGCTTGGCCAGGCGCGTCTGGCGATGGCCCAGGCTGG

TTTTTTTGCCGCCAGAACGGATGCGACGCAGCGCGGTTTCCCGGCGTGTGGCCTGGGAAATACTCCGATT

TTTCTTGTCGTATTTATAGTGAGGTAGTGTGATGATCGTTGAAAAGATTTTGGCATTGCGTACGTGCGCC

AATAACATGGCCGACCACTGCGGGTTGATCTGGCCGATGGCCGGTCCCGTGGAATGCAAATTCTGGAAAC

CGTCGGGACTGCACGAAAATGGTCTTACCGGGCTGTTGTGGGGCAAGGGCGTCGGGGCGCATCTGAGTGC

GCACGCCGATGCGCGCTGGGTCGTGTGCGAAGTCGCCGTCGACGAGATGCTGCAGTTGGCCGAAGAGGGG

ATGATCAAGTTCCCGCGCGCAACTGTGCTTTTCGTCGGAAATCGCAGCCAGGCGCTGGACTATATTGCAG

CCAACATGCCGCTCTACGGCGCCGCTCTACAGCTGGCGGCACCCGCTGCGCCGGCGCATGTCCACATGCC

CGCAGCGGAGCCGTCCGCGCCGGCAACGCAGGCGACCTCTGCAACCCTGCCGACCCCAGCCACCCCTTCC

ACCCAGGCCACCCCTTCCACTCAGTCAACTCAGTCAACTCAGTCAACCGAAGCGACCCAGTCAACCGAGG

CGACCCCGGTTGCCACGGTCGCCGCAGCGCCGCCTCCTCCGGGACAGCAGCATGACGTGATGGCGAAGAA

GACCGAAACCGGTGTCTATGGCAGCACACTCACAGGCGCCGACCAGAGCCGGCTCGTCGCAGGCTACGGC

AGTACCGAAACCGCAGGCGATCACAGCGATCTGATCGCCGGCTATGGCAGCACCGGGACCGCCGGATCCG

ACAGTTCCATCCTGGCAGGGTATGGCAGCACGCAGACTGCCGCGGGCAGGAGCACGCTCACCGCCGGCTA

TGGCAGCACGCAGACGGCGCAGGAAGGCAGCCGTCTCACCTCCGGTTACGGCAGCACTGCGACCAGCGGT

TCTGACAGCGCGGTGATCTCCGGCTACGGCAGCACGCAAACGGCCGGTAGCGAGAGTTCCTTGACCGCTG

GCTACGGCAGCACGCAGACCGCGCGCAAGGGCAGCGACATCACCGCCGGCTATGGCAGTACCGGTACGGC

CGGGTCGGACAGCGCGTTGATCGCCGGCTACGGCAGCACCCAGACCGCCGGCAGCGAGAGTTCCTTGACC

GCCGGCTACGGCAGCACGCAGACCGCACGCAAGGGCAGCGACGTCACCGCCGGCTACGGCAGTACCGGCA

CGGCGGGTGCCGACAGCACCTTGATCGCGGGCTATGGCAGCACGCAGACCGCTGGCGGCGAAAGCTCTCT

CACCGCCGGCTACGGCAGCACGCAGACTGCGCGGCAAGGCAGCGACATCACCGCCGGTTACGGCAGTACC

GGCACTGCCGGTGCGGACAGCACGCTGATCGCCGGTTACGGCAGCACGCAAACCTCGGGCAGCGACAGCT

CGCTGACAGCCGGTTATGGCAGCACGCAGACCGCGCGCAAGGGCAGCGACATCACTGCCGGCTACGGCAG

CACCGGCACCGCCGGATCCGACAGTTCGTTGATCGCCGGCTACGGCAGCACGCAGACCGCTGGCAGCGAA

AGTTCGCTGACGGCCGGCTACGGCAGCACGCAGACCGCCCAGCAAGACAGCTCGCTCACCACCGGCTACG

GCAGTACCTCGACGGCGGGTCACGACAGTTCGCTGATCGCCGGCTATGGCAGCACCCAGACCGCCGGCTA

CGATAGCACCCTGACCGCCGGCTACGGCAGTACGCAGACCGCCCAACAAGACAGTTCGCTCACCACCGGT

TACGGCAGTACCTCCACCGCCGGTGCCGACAGTACGCTGATCGCCGGCTACGGCAGTACGCAGACCGCTG

GCAGCGACAGTTCGCTGACGGCCGGTTACGGCAGCACACAGACCGCACGCGAAGGCAGCGACGTCACCGC

CGGCTACGGCAGCACCGGCACCGCGGGTGCGGACAGTACCTTGATCGCCGGCTACGGCAGCACGCAGACC

TCCGGTAGCGACAGTTCGCTGACGGCCGGCTACGGCAGTACGCAGACCGCGCGCAAGGGCAGCGACGTCA

CCGCCGGCTATGGCAGCACCGGCACGGCGGGTGCGGACAGCACGCTGATCGCCGGCTACGGCAGCACGCA

GACCTCCGGTAGCGACAGTTCGCTGACGGCCGGCTACGGCAGTACGCAGACCGCGCGCAAGGGCAGCGAT

GTCACCGCCGGCTACGGCAGCACCGGCACGGCGGGTGCGGACAGCACGCTGATCGCCGGCTACGGCAGCA

CGCAGACCTCGGGTAGCGACAGTTCGCTGACGGCCGGCTACGGCAGTACGCAGACCGCGCGCAAGGGCAG

CGACGTCACCGCCGGCTACGGCAGCACCGGCACGGCGGGTGCGGACAGCACGCTGATCGCAGGTTACGGC

AGCACGCAAACCTCGGGCAGCGACAGTTCGCTGACGGCCGGTTATGGCAGTACGCAGACCGCGCGCAAGG

GCAGCGACATTACCGCCGGCTACGGCAGCACCGGCACCGCGGGCGCGGACAGCACCTTGATCGCGGGCTA

TGGCAGCACGCAGACCTCCGGCAGCGACAGTTCGCTGACCGCCGGTTACGGCAGCACGCAGACCGCACGC

GAAGGCAGCGACGTCACCGCCGGTTACGGCAGCACCGGCACGGCGGGCGCGGACAGCACCCTGATCTCCG

GCTACGGCAGCACGCAAACGGCCGGCAGCGACAGTTCGCTGACCGCCGGCTACGGCAGTACGCAGACTGC

GCGCAAGGGCAGCGACGTCACCGCCGGTTACGGCAGTACCGGCACCGCGGGTGCGGACAGCACCTTGATC

GCGGGCTACGGCAGCACGCAGACCTCCGGCAGCGACAGTTCGCTGACCGCCGGTTACGGCAGTACGCAGA

CCGCGCGCAAGGGCAGCGACATGACCGCCGGCTACGGCAGTACCGGCACCGCTGGCGCGGATAGCACCTT

GATCGCGGGCTACGGCAGCACGCAGACGTCCGGCAGCGACAGCTCGCTGACGGCCGGTTACGGCAGCACG

CAGACCGCACGCGAAGGCAGCGACGTCACCGCCGGTTACGGCAGCACCGGCACGGCGGGCGCGGACAGCA

CCCTGATCGCCGGCTACGGCAGCACGCAAACGGCCGGCAGCGACAGTTCGCTGACCGCCGGCTATGGCAG

CACGCAGACGGCACGGCAGGGCAGCGACGTCACCGCCGGCTACGGCAGTACAGGTACCGCGGGCGCGGAC

AGCACCCTGATCGCCGGCTACGGCAGCACGCAAACGGCCGGCAGCGACAGTTCGCTGACCGCCGGCTATG

GCAGCACGCAGACGGCACGGCAGGGCAGCGACATCACCGCCGGCTATGGCAGTACCGGGACCGCGGGCGC

CGACAGTTCGTTGATCGCCGGCTATGGCAGCACCCAGACCGCCGGCTACGACAGCAACCTCACTGCCGGT

TACGGCAGCACGCAGACGGCGCGCGAGGACAGCTCGCTCACTGCTGGCTACGGCAGCACGTCCACCGCCG

GTCATGACAGTTCGCTGATCGCCGGCTATGGCAGTACCCAGACCGCTGGCTACAACAGCATCCTGACCAC

CGGCTATGGCAGTACCCAGACTGCACAGGAGAGCAGTTCTCTCACTGCCGGCTACGGCAGCACCTCCACG

GCCGGCTACGACAGCACCTTGACCGCCGGCTATGGCAGTACCCAAACCGCCGGCTACAAAAGCACGCTGA

CCGCGGGTTATGGCAGCAACTCGACCGCCGGCCACGAGAGCTCGTTGATCGCCGGCTACGGTAGCACCCA

GATCGCTGGATACGAGAGCACCTTGACCGCGGGCTACGGCAGTTCGCTGACCACGCAGCAGAACAGTTCG

CTGACTGCCGGCTACGGCAGCACCGAGATCGCCGGCTATGCCAGTACGCTGATGGCCGGCTACGGCAGTT

CCCAGACCGCCGGTTACGAGAGCACGCTGACCGCCGGCTATGGCAGCACCCAGATGGCCGAGCACAGCAG

TTCGCTCACTGCCGGTTATGGAAGCACCGGCATCGCGGGGCAGGACAGTTCGCTGATCGCCGGCTACGGC

AGCAGTCTGACCAGCGGGGTACGCAGCTTTCTGACCGCCGGCTACGGCAGCAACATGATCGCCAGCTACG

GAAGCTCGCTGATCGCCGGCCATGAGTGCACCCAGATCGCCGGCCACAAAAGCATGCTGATCGCGGGCAA

GGGCAGTTTCCAGACCGCGGGGGCTCGCAGCACGCTCATTGGCGGTGCCGCCAGCGTGCAGACCGCCGGC

GACCGCAGCAAGCTGATCGCGGGCGCCGACAGCACCCAGACCGCCGGCGACCGCAGCAAACTGTTGGCCG

GACGCAACAGCTATCTCACCGCCGGCGACAGGAGCAAGCTGACCGCCGGCGACGACAGTACGTTGATGGC

TGGCGATCGCAGCAAGCTGACCGCCGGCAAGAACAGCGTGCTGACCGCCGGCGCCAACAGCAGGCTCATC

GGCAGTCTGGGTTCGACGCTGAGCGGCGGGGAGAATTCGACGCTCATTTTCCGTTGCTGGGACGGCGAGC

GCTACACCAATCTCGTGGTCAGGACAGGGGAGCAGGGCGTGGAATCGGACATCCCCTATCAGGTCGACGA

CGAAGGAAATCTGGTAGGAAAAGCGGATGACGATCTGGTGCTGGATTACGACCCTGGCATGATCCTGGAT

GGGCAGTGCAGTCCCGGCACTGGCGAGGAACTGCGCGATGTCTGAGCGGCGCGGTGGCCGCGCAATCGGC

GCTCGCCGCAGGACGTGGGGCGCATCGGTGACGATATGGCTGCGCCGATAGAGTTCGGCTAGCGCGTTGC

CGTGGCTTCTGGATGTGCTCGTGCGCGTCGCGCATGGGCACATCCGCAGGCCGTTGCGGCCATGCTCGTG

GCGTCGCTTGTGCGGCGTCGCGCGTGTTGCATGGCTGGCGCGGTATCGGCGGTGTTGCATTGCCGGCAAT

CGAGATCCCACGCACGCAATGGCGCATGGGCGCTTTCGCGTGTGGGCAACTGTGCGAAGCATGCGCCACA

CATGCTGGGCCGATCTGCCAGAATTGGCTGGTTTCCCGCC

·         Pencarian nama gen, produk gen, organismenya, dan kelompok organismenya dilakukan dengan menggunakan BLASTn

Sekuens nucleotide 1

Tomato TAP1 gene for anionic peroxidase

GenBank: X15853.1

FASTA Graphics

LOCUS       X15853                  2907 bp    DNA     linear   PLN 14-NOV-2006

DEFINITION  Tomato TAP1 gene for anionic peroxidase.

ACCESSION   X15853

VERSION     X15853.1  GI:19359

KEYWORDS    anionic peroxidase; glycoprotein; peroxidase.

SOURCE      Solanum lycopersicum (Lycopersicon esculentum)

  ORGANISM  Solanum lycopersicum

            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;

            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;

            Pentapetalae; asterids; lamiids; Solanales; Solanaceae;

            Solanoideae; Solaneae; Solanum; Lycopersicon.

REFERENCE   1  (bases 1 to 2907)

  AUTHORS   Roberts,E. and Kolattukudy,P.E.

  TITLE     Molecular cloning, nucleotide sequence, and abscisic acid induction

            of a suberization-associated highly anionic peroxidase

  JOURNAL   Mol. Gen. Genet. 217 (2-3), 223-232 (1989)

   PUBMED   2528055

COMMENT     See <x15854> for TAP2 sequence.

FEATURES             Location/Qualifiers

     source          1..2907

                     /organism="Solanum lycopersicum"

                     /mol_type="genomic DNA"

                     /cultivar="Castlemart II"

                     /db_xref="taxon:4081"

                     /clone_lib="lambda charon 4A"

     regulatory      254..258

                     /regulatory_class="CAAT_signal"

     regulatory      344..350

                     /regulatory_class="TATA_box"

     gene            428..2666

                     /gene="TAP1"

     CDS             join(428..772,1635..1832,2115..2666)

                     /gene="TAP1"

                     /codon_start=1

                     /product="peroxidase"

                     /protein_id="CAA33852.1"

                     /db_xref="GI:295815"

                     /db_xref="GOA:P15003"

                     /db_xref="InterPro:IPR000823"

                     /db_xref="InterPro:IPR002016"

                     /db_xref="InterPro:IPR010255"

                     /db_xref="InterPro:IPR019793"

                     /db_xref="InterPro:IPR019794"

                     /db_xref="UniProtKB/Swiss-Prot:P15003"

                     /translation="MGFRLSHLSLALSFVALALAGVAIYRNTYEAIIMKNGSLLKNVS

                     PDFDSLESGVASILTLNNNKKRNSDKYLRQQLTPEACVFSAVRAVVDSAIDAETRMGA

                     SLIRLHFHDCFVDGCDGGILLDDINGTFTGEQNSPPNANSARGYEVIAQAKQSVINTC

                     PNVSVSCADILAIAARDSVAKLGGQTYSVALGRSDARTANFSGAINQLPAPFDNLTVQ

                     IQKFSDKNFTLREMVALAGAHTVGFARCSTVCTSGNVNPAAQLQCNCSATLTDSDLQQ

                     LDTTPTMFDKVYYDNLNSNQGIMFSDQVLTGDATTAGFVTDYSNDVNVFLGDFAAAMI

                     KMGDLPPSAGAQLEIRDVCSRVNPTSVASM"

     sig_peptide     428..502

                     /gene="TAP1"

     mat_peptide     join(650..772,1635..1832,2115..2663)

                     /gene="TAP1"

                     /product="peroxidase"

     exon            428..772

                     /gene="TAP1"

                     /number=1

     intron          773..1634

                     /gene="TAP1"

                     /number=1

     exon            1635..1832

                     /gene="TAP1"

                     /number=2

     intron          1833..2114

                     /gene="TAP1"

                     /number=2

     exon            2115..2820

                     /number=3

     regulatory      2798..2803

                     /regulatory_class="polyA_signal_sequence"

     polyA_site      2820

Sekuens nucleotide 2

Bovine growth hormone gene, complete cds

GenBank: M57764.1

FASTA Graphics

Go to:

LOCUS       BOVGHGH                 2856 bp    DNA     linear   MAM 27-APR-1993

DEFINITION  Bovine growth hormone gene, complete cds.

ACCESSION   M57764 M28453

VERSION     M57764.1  GI:163091

KEYWORDS    growth hormone.

SOURCE      Bos taurus (cattle)

  ORGANISM  Bos taurus

            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;

            Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia;

            Pecora; Bovidae; Bovinae; Bos.

REFERENCE   1  (bases 1 to 2856)

  AUTHORS   Gordon,D.F., Quick,D.P., Erwin,C.R., Donelson,J.E. and Maurer,R.A.

  TITLE     Nucleotide sequence of the bovine growth hormone chromosomal gene

  JOURNAL   Mol. Cell. Endocrinol. 33 (1), 81-95 (1983)

   PUBMED   6357899

COMMENT     Original source text: Bovine liver DNA.

FEATURES             Location/Qualifiers

     source          1..2856

                     /organism="Bos taurus"

                     /mol_type="genomic DNA"

                     /db_xref="taxon:9913"

                     /tissue_type="liver"

     gene            join(649..723,971..1131,1359..1475,1703..1864,2138..2439)

                     /gene="GH1"

     mRNA            join(649..723,971..1131,1359..1475,1703..1864,2138..2439)

                     /gene="GH1"

                     /product="growth hormone"

     exon            649..723

                     /gene="GH1"

                     /number=1

     CDS             join(711..723,971..1131,1359..1475,1703..1864,2138..2338)

                     /gene="GH1"

                     /codon_start=1

                     /product="growth hormone"

                     /protein_id="AAA30544.1"

                     /db_xref="GI:163092"

                     /translation="MMAAGPRTSLLLAFALLCLPWTQVVGAFPAMSLSGLFANAVLRA

                     QHLHQLAADTFKEFERTYIPEGQRYSIQNTQVAFCFSETIPAPTGKNEAQQKSDLELL

                     RISLLLIQSWLGPLQFLSRVFTNSLVFGTSDRVYEKLKDLEEGILALMRELEDGTPRA

                     GQILKQTYDKFDTNMRSDDALLKNYGLLSCFRKDLHKTETYLRVMKCRRFGEASCAF"

     intron          724..970

                     /gene="GH1"

                     /number=1

     exon            971..1131

                     /gene="GH1"

                     /number=2

     intron          1132..1358

                     /gene="GH1"

                     /number=2

     exon            1359..1475

                     /gene="GH1"

                     /number=3

     intron          1476..1702

                     /gene="GH1"

                     /number=3

     exon            1703..1864

                     /gene="GH1"

                     /number=4

     intron          1865..2137

                     /gene="GH1"

                     /number=4

     exon            2138..2439

                     /gene="GH1"

                     /number=5

Sekuens nucleotide 3

Aeromonas caviae gene for chitinase, strain WS7b

GenBank: AJ431785.1

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LOCUS       AJ431785                2925 bp    DNA     linear   ENV 15-APR-2005

DEFINITION  Aeromonas caviae gene for chitinase, strain WS7b.

ACCESSION   AJ431785

VERSION     AJ431785.1  GI:19171466

KEYWORDS    ENV; chitinase.

SOURCE      Aeromonas caviae (Aeromonas punctata)

  ORGANISM  Aeromonas caviae

            Bacteria; Proteobacteria; Gammaproteobacteria; Aeromonadales;

            Aeromonadaceae; Aeromonas.

REFERENCE   1

  AUTHORS   Malik,A.

  TITLE     Konstruksi fusi transkripsi gen kitinase dari Aeromonas caviae dan

            ekspresinya pada Pseudomonas fluorescens (Fusion transcription

            construction of Aeromonas caviae chitinase gene and its expression

            in Pseudomonas fluorescens)

  JOURNAL   Thesis (2000) Department of Biology, Bogor Agricultural University,

            Bogor, Indonesia

REFERENCE   2

  AUTHORS   Malik,A., Wenuganen,S., Suwanto,A. and Tjahjono,B.

  TITLE     Cloning, DNA sequence, and expression of Aeromonas caviae WS7b

            chitinase gene

  JOURNAL   Unpublished

REFERENCE   3  (bases 1 to 2925)

  AUTHORS   Malik,A.

  TITLE     Direct Submission

  JOURNAL   Submitted (22-FEB-2002) Malik A., Molecular Biology, Seameo

            Biotrop, Jl Raya Tajur km 6, Bogor, INDONESIA

FEATURES             Location/Qualifiers

     source          1..2925

                     /organism="Aeromonas caviae"

                     /mol_type="genomic DNA"

                     /strain="WS7b"

                     /isolation_source="soil sample"

                     /db_xref="taxon:648"

                     /environmental_sample

                     /country="Indonesia:Bangka Island"

     regulatory      142..145

                     /regulatory_class="ribosome_binding_site"

     CDS             155..2752

                     /codon_start=1

                     /transl_table=11

                     /product="chitinase"

                     /protein_id="CAD24484.1"

                     /db_xref="GI:19171467"

                     /db_xref="GOA:Q8RQE5"

                     /db_xref="HSSP:1EDQ"

                     /db_xref="InterPro:IPR001223"

                     /db_xref="InterPro:IPR001579"

                     /db_xref="InterPro:IPR002859"

                     /db_xref="InterPro:IPR003610"

                     /db_xref="InterPro:IPR011583"

                     /db_xref="InterPro:IPR013540"

                     /db_xref="InterPro:IPR013781"

                     /db_xref="InterPro:IPR013783"

                     /db_xref="InterPro:IPR014756"

                     /db_xref="InterPro:IPR017853"

                     /db_xref="InterPro:IPR022409"

                     /db_xref="UniProtKB/TrEMBL:Q8RQE5"

                     /translation="MLSPKLSLLALLVGGLCTTSAFAAAPGKPTIGSGPTKFAIVEVN

                     QAASAYNQLVTVHKDGAPVSVTWNLWSGDVGQTAKVLLDGKEVWSGPAFAAGTANFKV

                     TKGGRYQMQVALCNAHGCTLSDKKELMVADTDGSHLAPLNAPLKENNKPYANKSGKVV

                     GAYYVEWGVYGRKFTVDKIPAQNLTHILYGFTPICGGNGINDSLKEISGSFEALQRSC

                     AGREDFKVSIHDPWAAIQMSQGNLSAWDEPYKGNFGNLMALKQAHPDLKILPSVGGWT

                     LSDPFYFLGDKTKRDTFVASVKEFLQTWKFFDGVDIDWEFPGGQGANPSLGGPNDGAT

                     YVVLMKELRAMLDELEAETGRQYELTSAISAGGDKIAKVDYQAAQQYMDHIFLMSYDF

                     SGAFDLTNLPHQTNLFASSWDPATKYTADKGVKALLGQGVTPGKIVVGAAMYGRGMTG

                     VKNYQAGNPCTGTATGPVSGTWENGVVDYRDIVNNRMGAGWEQGYDESAEAPYVFKAS

                     SGDLITFDNDRSVKAKGQYVLANQLGGLFAWEIDADNGDILNAMHEGLGHGEGTLPPV

                     NKPPVANAGSDLSATGPAEVTLKGSASHDPENGALTYSWKQVSGPQASLLDATQAKAR

                     VVLDAVSSDINLVFELTVTDDQGLSAKDQVVVTNKAPQPNLPPVVSVPASATVEAGKQ

                     VSIKATASDPNGDALSYQWTVPAGLSATGLDSATLVVTGSNVTSDTAYDLTLVVTDGA

                     LDATAVTRLTVKPASTGGGCEACDPDAANHPAWSAGTVYNTNDKVSHNQLVWQAKYWT

                     QGNEPSRTADQWKLVSQVQLGWDAGVVYNGGDVTSHNGRKWKAQYWSKGDEPGKAAVW

                     VDQGAASCN"

     stem_loop       2765..2788

     stem_loop       2825..2841

     stem_loop       2845..2868