diff --git a/docs/notebooks/Example_Restriction.ipynb b/docs/notebooks/Example_Restriction.ipynb index 3dd72dd9..ce4b7edd 100755 --- a/docs/notebooks/Example_Restriction.ipynb +++ b/docs/notebooks/Example_Restriction.ipynb @@ -16,26 +16,6 @@ "Source files can be found alongside this notebook, if you would like to follow along. Annotations are made alongside the code to describe key steps." ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n", - " \"Open\n", - "" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# Install pydna \n", - "%%capture\n", - "!pip install pydna" - ] - }, { "cell_type": "code", "execution_count": null, @@ -581,22 +561,23 @@ "name": "stdout", "output_type": "stream", "text": [ - "ACCATGTCGACAAGCCATATCCAACCACCAT\n", - "ATGGCGCGCCGTTTTTTTTTAGGTGTAAATAGTCTTTTAA\n" + "ACCATGTCGACATGCAAACAGTAATGATGGATG\n", + "ATGGCGCGCCTAAAAGCCTTCTTCTCCC\n" ] } ], "source": [ - "# Generating primers for the ase1 insert fragment. \n", + "#Finding the feature containing the CDS with ase1 as a type qualifier\n", + "gene = [f for f in pombe_chromosome_I.features if f.type == \"CDS\" and \n", + " \"gene\" in f.qualifiers and \n", + " \"ase1\" in f.qualifiers[\"gene\"]][0]\n", "\n", - "#todo-manu: \n", - "# 1. find the feature containing the CDS filtering the list of features\n", - "# 2. Use the coordinates of the CDS to design primers using pydna design\n", - "# 3. Append the cut site to the primers\n", - "# 4. Do the PCR\n", + "#Reading off the CDS to design primers\n", + "fwd_pompe_seq = pombe_chromosome_I[min(gene):min(gene)+22]\n", + "back_pompe_seq = pombe_chromosome_I[max(gene)-18:max(gene)]\n", "\n", - "fwd_primer_ase1 = Dseqrecord(\"ACCATGTCGAC\") + pombe_chromosome_I[1000:1020] # Adding a SalI cut site\n", - "rvs_primer_ase1_3_start = pombe_chromosome_I[3516:3546] + Dseqrecord(\"GGCGCGCCAT\") # Adding a AscI cut site\n", + "fwd_primer_ase1 = Dseqrecord(\"ACCATGTCGAC\") + fwd_pompe_seq # Adding a SalI cut site\n", + "rvs_primer_ase1_3_start = back_pompe_seq + Dseqrecord(\"GGCGCGCCAT\") # Adding a AscI cut site\n", "rvs_primer_ase1 = rvs_primer_ase1_3_start.reverse_complement()\n", "\n", "# Printing out the primers\n", @@ -614,20 +595,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "71.72846660888155\n", - "69.94587883755406\n" + "57.08651869811922\n", + "65.11883125971309\n" ] } ], "source": [ - "# Checking that the primer Tm are matching\n", + "# Checking that the primer Tm are matching for the genomic portion of the primer\n", "\n", - "#todo-manu: \n", - "# 1. Check the Tm of the primers using the part that aligns with the genome only (here you are calculating the Tm including the restriction sites, which\n", - "# will not anneal to the template during the PCR)\n", - "\n", - "print(tm_default(fwd_primer_ase1.seq)) # Modify the primer sequence above retroactively, if Tm not matching.\n", - "print(tm_default(rvs_primer_ase1.seq))" + "print(tm_default(fwd_primer_ase1.seq[-22:])) # Modify the primer sequence above retroactively here, if Tm not matching.\n", + "print(tm_default(rvs_primer_ase1.seq[:18]))" ] }, { @@ -639,10 +616,10 @@ "name": "stdout", "output_type": "stream", "text": [ - "LOCUS 2567bp_PCR_prod 2567 bp DNA linear UNK 01-JAN-1980\n", + "LOCUS 2263bp_PCR_prod 2263 bp DNA linear UNK 01-JAN-1980\n", "DEFINITION pcr_product_description_description_rc.\n", - "ACCESSION 2567bp\n", - "VERSION 2567bp\n", + "ACCESSION 2263bp\n", + "VERSION 2263bp\n", "DBLINK BioProject: PRJNA13836\n", " BioSample: SAMEA3138176\n", "KEYWORDS .\n", @@ -650,91 +627,57 @@ " ORGANISM .\n", " .\n", "FEATURES Location/Qualifiers\n", - " gene 2..2539\n", - " /gene=\"ase1\"\n", - " /locus_tag=\"SPOM_SPAPB1A10.09\"\n", - " 5'UTR 2..174\n", - " /gene=\"ase1\"\n", - " /locus_tag=\"SPOM_SPAPB1A10.09\"\n", - " CDS join(175..598,646..2417)\n", - " /gene=\"ase1\"\n", - " /locus_tag=\"SPOM_SPAPB1A10.09\"\n", - " /codon_start=1\n", - " /product=\"antiparallel microtubule cross-linking factor\n", - " Ase1\"\n", - " /protein_id=\"CAC21482.1\"\n", - " /translation=\"MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIE\n", - " RLHQVLGTDGDNSSLFELFTTAMNAQLHEMEQCQKKLEDDCQQRIDSIRFLVSSLKLTD\n", - " DTSSLKIESPLIQCLNRLSMVEGQYMAQYDQKLSTIKEMYHKLESYCNRLGSPFVLPDF\n", - " ENSFLSDVSDAFTESLRGRINEAEKEIDARLEVINSFEEEILGLWSELGVEPADVPQYE\n", - " QLLESHTNRPNDVYVTQELIDQLCKQKEVFSAEKEKRSDHLKSIQSEVSNLWNKLQVSP\n", - " NEQSQFGDSSNINQENISLWETELEKLHQLKKEHLPIFLEDCRQQILQLWDSLFYSEEQ\n", - " RKSFTPMYEDIITEQVLTAHENYIKQLEAEVSANKSFLSLINRYASLIEGKKELEASSN\n", - " DASRLTQRGRRDPGLLLREEKIRKRLSRELPKVQSLLIPEITAWEERNGRTFLFYDEPL\n", - " LKICQEATQPKSLYRSASAAANRPKTATTTDSVNRTPSQRGRVAVPSTPSVRSASRAMT\n", - " SPRTPLPRVKNTQNPSRSISAEPPSATSTANRRHPTANRIDINARLNSASRSRSANMIR\n", - " QGANGSDSNMSSSPVSGNSNTPFNKFPNSVSRNTHFESKSPHPNYSRTPHETYSKASSK\n", - " NVPLSPPKQRVVNEHALNIMSEKLQRTNLKEQTPEMDIENSSQNLPFSPMKISPIRASP\n", - " VKTIPSSPSPTTNIFSAPLNNITNCTPMEDEWGEEGF\"\n", - " 3'UTR 2418..2539\n", - " /gene=\"ase1\"\n", - " /locus_tag=\"SPOM_SPAPB1A10.09\"\n", - " primer_bind 1..21\n", + " primer_bind 1..22\n", " /label=\"name\"\n", " /PCR_conditions=\"primer\n", - " sequence:ACCATGTCGACAAGCCATATCCAACCACCAT\"\n", + " sequence:ACCATGTCGACATGCAAACAGTAATGATGGATG\"\n", " /ApEinfo_fwdcolor=\"#baffa3\"\n", " /ApEinfo_revcolor=\"#ffbaba\"\n", - " primer_bind complement(2518..2548)\n", + " primer_bind complement(2225..2242)\n", " /label=\"name_rc\"\n", " /PCR_conditions=\"primer\n", - " sequence:ATGGCGCGCCGTTTTTTTTTAGGTGTAAATAGTCTTTTAA\"\n", + " sequence:ATGGCGCGCCTAAAAGCCTTCTTCTCCC\"\n", " /ApEinfo_fwdcolor=\"#baffa3\"\n", " /ApEinfo_revcolor=\"#ffbaba\"\n", "ORIGIN\n", - " 1 accatgtcga caagccatat ccaaccacca tttttgtgcc aagcttttat gcaaggttaa\n", - " 61 ttccttgtac tgcttgttat gttataatat atcaacatct taacagtttt catatcttcc\n", - " 121 tttatattct attaattgaa tttcaaacat cgttttattg agctcattta catcaaccgg\n", - " 181 ttcaatgcaa acagtaatga tggatgacat tcaaagcact gattctattg ctgaaaaaga\n", - " 241 taatcactct aataatgaat ctaactttac ttggaaagcg tttcgtgaac aagtggaaaa\n", - " 301 gcatttttct aaaattgaaa ggcttcacca agtccttgga acagatggag acaattcatc\n", - " 361 attatttgag ttgtttacaa cggcaatgaa tgcccagctt catgaaatgg aacagtgcca\n", - " 421 gaaaaaactt gaagatgact gtcagcaaag aattgattca atcagatttt tggtttcctc\n", - " 481 attaaagtta acggatgata cttctagtct caaaattgag tctcctttaa ttcagtgttt\n", - " 541 gaatcgtttg tcaatggtag aaggacaata tatggcacag tatgatcaaa agttaagtac\n", - " 601 gattaaaggt atgtaatcgt ctttaattta gacttgtgtt ttaactgatg tatagaaatg\n", - " 661 tatcacaaat tggagtcata ttgtaaccgc ttaggaagtc cgttcgtttt acctgatttt\n", - " 721 gagaattcat ttttatctga tgtatccgat gcttttactg aatctttgag aggacgcatc\n", - " 781 aacgaagccg aaaaggagat tgatgcgaga ttagaggtta ttaattcctt tgaagaagaa\n", - " 841 attttgggtt tgtggtctga actcggtgtt gagcccgctg atgttccaca atacgaacaa\n", - " 901 ttgcttgaat cccatactaa tcgaccaaat gatgtttatg ttactcaaga acttatcgac\n", - " 961 caactttgca agcaaaaaga agttttttcc gctgaaaaag aaaagagaag tgatcattta\n", - " 1021 aaaagtatac aatcagaagt tagcaacttg tggaataagc ttcaagtttc tcccaatgaa\n", - " 1081 caaagtcaat ttggcgattc atcaaacatt aatcaagaaa atatttcatt atgggaaact\n", - " 1141 gaacttgaaa aacttcatca gttaaaaaag gagcatttac ccattttttt agaagactgt\n", - " 1201 cgtcaacaaa ttcttcagct ttgggattct ctgttttatt cagaagaaca aagaaagtcc\n", - " 1261 tttacaccta tgtatgaaga cattattaca gagcaggttc ttacggccca tgaaaactat\n", - " 1321 ataaagcaac tagaggccga agtttctgct aataagtcct ttttaagctt aattaatcgc\n", - " 1381 tatgcctctt taatagaagg aaagaaagag cttgaagcta gttctaatga tgcctctcgt\n", - " 1441 ctaacacaac ggggacgccg ggacccaggt ttacttctac gtgaagagaa aatccgtaag\n", - " 1501 cgactttcta gagaacttcc taaggttcag tcgctgctta taccagagat tacagcatgg\n", - " 1561 gaagaaagaa atggaaggac gttccttttt tatgatgaac cacttctcaa gatttgccaa\n", - " 1621 gaggccactc aaccaaaatc attatataga agtgcaagtg ctgccgcaaa ccgcccgaaa\n", - " 1681 acagcaacta caacggactc tgttaataga acaccttctc aacgagggcg tgtagctgta\n", - " 1741 ccttcaacac caagtgttag gtccgcttct cgagctatga cgagtccaag gacaccgctt\n", - " 1801 cctagagtaa aaaacactca aaatccaagt cgttccatta gtgcagaacc gccatcagca\n", - " 1861 accagtaccg ccaatagaag acaccccact gctaatcgaa ttgatataaa cgctagatta\n", - " 1921 aacagtgcta gtcggtctcg aagcgcgaac atgataagac aaggggcaaa tggtagtgac\n", - " 1981 agcaatatgt cttcttcacc cgtttctgga aattccaata ccccttttaa caagtttcca\n", - " 2041 aattctgtat ctcgcaatac acattttgaa tccaagtcac cgcacccaaa ttactctcga\n", - " 2101 actcctcatg aaacgtattc aaaggcttca tctaagaacg tcccattaag tcctccaaag\n", - " 2161 cagcgtgtag ttaatgaaca cgctttaaat attatgtcgg aaaaattgca aagaactaat\n", - " 2221 ctgaaagaac aaacacccga gatggacatt gaaaacagct cgcagaacct tcctttttct\n", - " 2281 cctatgaaga tatcccccat aagagcatca cccgtaaaga caattccatc atcaccgtcc\n", - " 2341 cccactacca acattttttc tgctccactc aacaatatta caaattgtac accgatggag\n", - " 2401 gatgaatggg gagaagaagg cttttaagct tcttatttac ctaatcgatc aaatttaaat\n", - " 2461 atacatattt ttgcatatga atacagcata tagataattc ataaaagttt attaactgag\n", - " 2521 gtcataatta aaagactatt tacacctaaa aaaaaacggc gcgccat\n", + " 1 accatgtcga catgcaaaca gtaatgatgg atgacattca aagcactgat tctattgctg\n", + " 61 aaaaagataa tcactctaat aatgaatcta actttacttg gaaagcgttt cgtgaacaag\n", + " 121 tggaaaagca tttttctaaa attgaaaggc ttcaccaagt ccttggaaca gatggagaca\n", + " 181 attcatcatt atttgagttg tttacaacgg caatgaatgc ccagcttcat gaaatggaac\n", + " 241 agtgccagaa aaaacttgaa gatgactgtc agcaaagaat tgattcaatc agatttttgg\n", + " 301 tttcctcatt aaagttaacg gatgatactt ctagtctcaa aattgagtct cctttaattc\n", + " 361 agtgtttgaa tcgtttgtca atggtagaag gacaatatat ggcacagtat gatcaaaagt\n", + " 421 taagtacgat taaaggtatg taatcgtctt taatttagac ttgtgtttta actgatgtat\n", + " 481 agaaatgtat cacaaattgg agtcatattg taaccgctta ggaagtccgt tcgttttacc\n", + " 541 tgattttgag aattcatttt tatctgatgt atccgatgct tttactgaat ctttgagagg\n", + " 601 acgcatcaac gaagccgaaa aggagattga tgcgagatta gaggttatta attcctttga\n", + " 661 agaagaaatt ttgggtttgt ggtctgaact cggtgttgag cccgctgatg ttccacaata\n", + " 721 cgaacaattg cttgaatccc atactaatcg accaaatgat gtttatgtta ctcaagaact\n", + " 781 tatcgaccaa ctttgcaagc aaaaagaagt tttttccgct gaaaaagaaa agagaagtga\n", + " 841 tcatttaaaa agtatacaat cagaagttag caacttgtgg aataagcttc aagtttctcc\n", + " 901 caatgaacaa agtcaatttg gcgattcatc aaacattaat caagaaaata tttcattatg\n", + " 961 ggaaactgaa cttgaaaaac ttcatcagtt aaaaaaggag catttaccca tttttttaga\n", + " 1021 agactgtcgt caacaaattc ttcagctttg ggattctctg ttttattcag aagaacaaag\n", + " 1081 aaagtccttt acacctatgt atgaagacat tattacagag caggttctta cggcccatga\n", + " 1141 aaactatata aagcaactag aggccgaagt ttctgctaat aagtcctttt taagcttaat\n", + " 1201 taatcgctat gcctctttaa tagaaggaaa gaaagagctt gaagctagtt ctaatgatgc\n", + " 1261 ctctcgtcta acacaacggg gacgccggga cccaggttta cttctacgtg aagagaaaat\n", + " 1321 ccgtaagcga ctttctagag aacttcctaa ggttcagtcg ctgcttatac cagagattac\n", + " 1381 agcatgggaa gaaagaaatg gaaggacgtt ccttttttat gatgaaccac ttctcaagat\n", + " 1441 ttgccaagag gccactcaac caaaatcatt atatagaagt gcaagtgctg ccgcaaaccg\n", + " 1501 cccgaaaaca gcaactacaa cggactctgt taatagaaca ccttctcaac gagggcgtgt\n", + " 1561 agctgtacct tcaacaccaa gtgttaggtc cgcttctcga gctatgacga gtccaaggac\n", + " 1621 accgcttcct agagtaaaaa acactcaaaa tccaagtcgt tccattagtg cagaaccgcc\n", + " 1681 atcagcaacc agtaccgcca atagaagaca ccccactgct aatcgaattg atataaacgc\n", + " 1741 tagattaaac agtgctagtc ggtctcgaag cgcgaacatg ataagacaag gggcaaatgg\n", + " 1801 tagtgacagc aatatgtctt cttcacccgt ttctggaaat tccaataccc cttttaacaa\n", + " 1861 gtttccaaat tctgtatctc gcaatacaca ttttgaatcc aagtcaccgc acccaaatta\n", + " 1921 ctctcgaact cctcatgaaa cgtattcaaa ggcttcatct aagaacgtcc cattaagtcc\n", + " 1981 tccaaagcag cgtgtagtta atgaacacgc tttaaatatt atgtcggaaa aattgcaaag\n", + " 2041 aactaatctg aaagaacaaa cacccgagat ggacattgaa aacagctcgc agaaccttcc\n", + " 2101 tttttctcct atgaagatat cccccataag agcatcaccc gtaaagacaa ttccatcatc\n", + " 2161 accgtccccc actaccaaca ttttttctgc tccactcaac aatattacaa attgtacacc\n", + " 2221 gatggaggat gaatggggag aagaaggctt ttaggcgcgc cat\n", "//\n" ] } @@ -759,7 +702,7 @@ "output_type": "stream", "text": [ "(Dseqrecord(-30), Dseqrecord(-3916))\n", - "(Dseqrecord(-10), Dseqrecord(-2557), Dseqrecord(-8))\n" + "(Dseqrecord(-10), Dseqrecord(-2253), Dseqrecord(-8))\n" ] } ], @@ -786,7 +729,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "LOCUS name 6465 bp DNA circular UNK 01-JAN-1980\n", + "LOCUS name 6161 bp DNA circular UNK 01-JAN-1980\n", "DEFINITION description.\n", "ACCESSION id\n", "VERSION id\n", @@ -872,33 +815,10 @@ " primer_bind 3859..3876\n", " /label=\"SP6\"\n", " /note=\"SP6 promoter, forward primer\"\n", - " CDS join(4081..4504,4552..6323)\n", - " /gene=\"ase1\"\n", - " /locus_tag=\"SPOM_SPAPB1A10.09\"\n", - " /codon_start=1\n", - " /product=\"antiparallel microtubule cross-linking factor\n", - " Ase1\"\n", - " /protein_id=\"CAC21482.1\"\n", - " /translation=\"MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIE\n", - " RLHQVLGTDGDNSSLFELFTTAMNAQLHEMEQCQKKLEDDCQQRIDSIRFLVSSLKLTD\n", - " DTSSLKIESPLIQCLNRLSMVEGQYMAQYDQKLSTIKEMYHKLESYCNRLGSPFVLPDF\n", - " ENSFLSDVSDAFTESLRGRINEAEKEIDARLEVINSFEEEILGLWSELGVEPADVPQYE\n", - " QLLESHTNRPNDVYVTQELIDQLCKQKEVFSAEKEKRSDHLKSIQSEVSNLWNKLQVSP\n", - " NEQSQFGDSSNINQENISLWETELEKLHQLKKEHLPIFLEDCRQQILQLWDSLFYSEEQ\n", - " RKSFTPMYEDIITEQVLTAHENYIKQLEAEVSANKSFLSLINRYASLIEGKKELEASSN\n", - " DASRLTQRGRRDPGLLLREEKIRKRLSRELPKVQSLLIPEITAWEERNGRTFLFYDEPL\n", - " LKICQEATQPKSLYRSASAAANRPKTATTTDSVNRTPSQRGRVAVPSTPSVRSASRAMT\n", - " SPRTPLPRVKNTQNPSRSISAEPPSATSTANRRHPTANRIDINARLNSASRSRSANMIR\n", - " QGANGSDSNMSSSPVSGNSNTPFNKFPNSVSRNTHFESKSPHPNYSRTPHETYSKASSK\n", - " NVPLSPPKQRVVNEHALNIMSEKLQRTNLKEQTPEMDIENSSQNLPFSPMKISPIRASP\n", - " VKTIPSSPSPTTNIFSAPLNNITNCTPMEDEWGEEGF\"\n", - " 3'UTR 6324..6445\n", - " /gene=\"ase1\"\n", - " /locus_tag=\"SPOM_SPAPB1A10.09\"\n", - " primer_bind complement(6424..6454)\n", + " primer_bind complement(6131..6148)\n", " /label=\"name_rc\"\n", " /PCR_conditions=\"primer\n", - " sequence:ATGGCGCGCCGTTTTTTTTTAGGTGTAAATAGTCTTTTAA\"\n", + " sequence:ATGGCGCGCCTAAAAGCCTTCTTCTCCC\"\n", " /ApEinfo_fwdcolor=\"#baffa3\"\n", " /ApEinfo_revcolor=\"#ffbaba\"\n", "ORIGIN\n", @@ -967,49 +887,44 @@ " 3721 agcgggtgtt ggcgggtgtc ggggctggct taactatgcg gcatcagagc agattgtact\n", " 3781 gagagtgcac catatggaca tattgtcgtt agaacgcggc tacaattaat acataacctt\n", " 3841 atgtatcata cacatacgat ttaggtgaca ctatagaacg cggccgccag ctgaagcttc\n", - " 3901 gtacgctgca ggtcgacaag ccatatccaa ccaccatttt tgtgccaagc ttttatgcaa\n", - " 3961 ggttaattcc ttgtactgct tgttatgtta taatatatca acatcttaac agttttcata\n", - " 4021 tcttccttta tattctatta attgaatttc aaacatcgtt ttattgagct catttacatc\n", - " 4081 aaccggttca atgcaaacag taatgatgga tgacattcaa agcactgatt ctattgctga\n", - " 4141 aaaagataat cactctaata atgaatctaa ctttacttgg aaagcgtttc gtgaacaagt\n", - " 4201 ggaaaagcat ttttctaaaa ttgaaaggct tcaccaagtc cttggaacag atggagacaa\n", - " 4261 ttcatcatta tttgagttgt ttacaacggc aatgaatgcc cagcttcatg aaatggaaca\n", - " 4321 gtgccagaaa aaacttgaag atgactgtca gcaaagaatt gattcaatca gatttttggt\n", - " 4381 ttcctcatta aagttaacgg atgatacttc tagtctcaaa attgagtctc ctttaattca\n", - " 4441 gtgtttgaat cgtttgtcaa tggtagaagg acaatatatg gcacagtatg atcaaaagtt\n", - " 4501 aagtacgatt aaaggtatgt aatcgtcttt aatttagact tgtgttttaa ctgatgtata\n", - " 4561 gaaatgtatc acaaattgga gtcatattgt aaccgcttag gaagtccgtt cgttttacct\n", - " 4621 gattttgaga attcattttt atctgatgta tccgatgctt ttactgaatc tttgagagga\n", - " 4681 cgcatcaacg aagccgaaaa ggagattgat gcgagattag aggttattaa ttcctttgaa\n", - " 4741 gaagaaattt tgggtttgtg gtctgaactc ggtgttgagc ccgctgatgt tccacaatac\n", - " 4801 gaacaattgc ttgaatccca tactaatcga ccaaatgatg tttatgttac tcaagaactt\n", - " 4861 atcgaccaac tttgcaagca aaaagaagtt ttttccgctg aaaaagaaaa gagaagtgat\n", - " 4921 catttaaaaa gtatacaatc agaagttagc aacttgtgga ataagcttca agtttctccc\n", - " 4981 aatgaacaaa gtcaatttgg cgattcatca aacattaatc aagaaaatat ttcattatgg\n", - " 5041 gaaactgaac ttgaaaaact tcatcagtta aaaaaggagc atttacccat ttttttagaa\n", - " 5101 gactgtcgtc aacaaattct tcagctttgg gattctctgt tttattcaga agaacaaaga\n", - " 5161 aagtccttta cacctatgta tgaagacatt attacagagc aggttcttac ggcccatgaa\n", - " 5221 aactatataa agcaactaga ggccgaagtt tctgctaata agtccttttt aagcttaatt\n", - " 5281 aatcgctatg cctctttaat agaaggaaag aaagagcttg aagctagttc taatgatgcc\n", - " 5341 tctcgtctaa cacaacgggg acgccgggac ccaggtttac ttctacgtga agagaaaatc\n", - " 5401 cgtaagcgac tttctagaga acttcctaag gttcagtcgc tgcttatacc agagattaca\n", - " 5461 gcatgggaag aaagaaatgg aaggacgttc cttttttatg atgaaccact tctcaagatt\n", - " 5521 tgccaagagg ccactcaacc aaaatcatta tatagaagtg caagtgctgc cgcaaaccgc\n", - " 5581 ccgaaaacag caactacaac ggactctgtt aatagaacac cttctcaacg agggcgtgta\n", - " 5641 gctgtacctt caacaccaag tgttaggtcc gcttctcgag ctatgacgag tccaaggaca\n", - " 5701 ccgcttccta gagtaaaaaa cactcaaaat ccaagtcgtt ccattagtgc agaaccgcca\n", - " 5761 tcagcaacca gtaccgccaa tagaagacac cccactgcta atcgaattga tataaacgct\n", - " 5821 agattaaaca gtgctagtcg gtctcgaagc gcgaacatga taagacaagg ggcaaatggt\n", - " 5881 agtgacagca atatgtcttc ttcacccgtt tctggaaatt ccaatacccc ttttaacaag\n", - " 5941 tttccaaatt ctgtatctcg caatacacat tttgaatcca agtcaccgca cccaaattac\n", - " 6001 tctcgaactc ctcatgaaac gtattcaaag gcttcatcta agaacgtccc attaagtcct\n", - " 6061 ccaaagcagc gtgtagttaa tgaacacgct ttaaatatta tgtcggaaaa attgcaaaga\n", - " 6121 actaatctga aagaacaaac acccgagatg gacattgaaa acagctcgca gaaccttcct\n", - " 6181 ttttctccta tgaagatatc ccccataaga gcatcacccg taaagacaat tccatcatca\n", - " 6241 ccgtccccca ctaccaacat tttttctgct ccactcaaca atattacaaa ttgtacaccg\n", - " 6301 atggaggatg aatggggaga agaaggcttt taagcttctt atttacctaa tcgatcaaat\n", - " 6361 ttaaatatac atatttttgc atatgaatac agcatataga taattcataa aagtttatta\n", - " 6421 actgaggtca taattaaaag actatttaca cctaaaaaaa aacgg\n", + " 3901 gtacgctgca ggtcgacatg caaacagtaa tgatggatga cattcaaagc actgattcta\n", + " 3961 ttgctgaaaa agataatcac tctaataatg aatctaactt tacttggaaa gcgtttcgtg\n", + " 4021 aacaagtgga aaagcatttt tctaaaattg aaaggcttca ccaagtcctt ggaacagatg\n", + " 4081 gagacaattc atcattattt gagttgttta caacggcaat gaatgcccag cttcatgaaa\n", + " 4141 tggaacagtg ccagaaaaaa cttgaagatg actgtcagca aagaattgat tcaatcagat\n", + " 4201 ttttggtttc ctcattaaag ttaacggatg atacttctag tctcaaaatt gagtctcctt\n", + " 4261 taattcagtg tttgaatcgt ttgtcaatgg tagaaggaca atatatggca cagtatgatc\n", + " 4321 aaaagttaag tacgattaaa ggtatgtaat cgtctttaat ttagacttgt gttttaactg\n", + " 4381 atgtatagaa atgtatcaca aattggagtc atattgtaac cgcttaggaa gtccgttcgt\n", + " 4441 tttacctgat tttgagaatt catttttatc tgatgtatcc gatgctttta ctgaatcttt\n", + " 4501 gagaggacgc atcaacgaag ccgaaaagga gattgatgcg agattagagg ttattaattc\n", + " 4561 ctttgaagaa gaaattttgg gtttgtggtc tgaactcggt gttgagcccg ctgatgttcc\n", + " 4621 acaatacgaa caattgcttg aatcccatac taatcgacca aatgatgttt atgttactca\n", + " 4681 agaacttatc gaccaacttt gcaagcaaaa agaagttttt tccgctgaaa aagaaaagag\n", + " 4741 aagtgatcat ttaaaaagta tacaatcaga agttagcaac ttgtggaata agcttcaagt\n", + " 4801 ttctcccaat gaacaaagtc aatttggcga ttcatcaaac attaatcaag aaaatatttc\n", + " 4861 attatgggaa actgaacttg aaaaacttca tcagttaaaa aaggagcatt tacccatttt\n", + " 4921 tttagaagac tgtcgtcaac aaattcttca gctttgggat tctctgtttt attcagaaga\n", + " 4981 acaaagaaag tcctttacac ctatgtatga agacattatt acagagcagg ttcttacggc\n", + " 5041 ccatgaaaac tatataaagc aactagaggc cgaagtttct gctaataagt cctttttaag\n", + " 5101 cttaattaat cgctatgcct ctttaataga aggaaagaaa gagcttgaag ctagttctaa\n", + " 5161 tgatgcctct cgtctaacac aacggggacg ccgggaccca ggtttacttc tacgtgaaga\n", + " 5221 gaaaatccgt aagcgacttt ctagagaact tcctaaggtt cagtcgctgc ttataccaga\n", + " 5281 gattacagca tgggaagaaa gaaatggaag gacgttcctt ttttatgatg aaccacttct\n", + " 5341 caagatttgc caagaggcca ctcaaccaaa atcattatat agaagtgcaa gtgctgccgc\n", + " 5401 aaaccgcccg aaaacagcaa ctacaacgga ctctgttaat agaacacctt ctcaacgagg\n", + " 5461 gcgtgtagct gtaccttcaa caccaagtgt taggtccgct tctcgagcta tgacgagtcc\n", + " 5521 aaggacaccg cttcctagag taaaaaacac tcaaaatcca agtcgttcca ttagtgcaga\n", + " 5581 accgccatca gcaaccagta ccgccaatag aagacacccc actgctaatc gaattgatat\n", + " 5641 aaacgctaga ttaaacagtg ctagtcggtc tcgaagcgcg aacatgataa gacaaggggc\n", + " 5701 aaatggtagt gacagcaata tgtcttcttc acccgtttct ggaaattcca ataccccttt\n", + " 5761 taacaagttt ccaaattctg tatctcgcaa tacacatttt gaatccaagt caccgcaccc\n", + " 5821 aaattactct cgaactcctc atgaaacgta ttcaaaggct tcatctaaga acgtcccatt\n", + " 5881 aagtcctcca aagcagcgtg tagttaatga acacgcttta aatattatgt cggaaaaatt\n", + " 5941 gcaaagaact aatctgaaag aacaaacacc cgagatggac attgaaaaca gctcgcagaa\n", + " 6001 ccttcctttt tctcctatga agatatcccc cataagagca tcacccgtaa agacaattcc\n", + " 6061 atcatcaccg tcccccacta ccaacatttt ttctgctcca ctcaacaata ttacaaattg\n", + " 6121 tacaccgatg gaggatgaat ggggagaaga aggcttttag g\n", "//\n" ] } @@ -1042,7 +957,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.5" + "version": "3.12.4" } }, "nbformat": 4,