IGEM:Harvard/2006/Container Design 5: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
|||
Line 21: | Line 21: | ||
</div> | </div> | ||
<br style = "clear:both"> | <br style = "clear:both"> | ||
<div class="tabs-blue"> | |||
<ul> | |||
<li id="current">[[IGEM:Harvard/2006/Container_Design_5|Design 4 Overview]]</li> | |||
<li>[[IGEM:Harvard/2006/Container_Design_5/Schematics|Schematics]]</li> | |||
<li>[[IGEM:Harvard/2006/Container_Design_5/Scaffold Sequences|Scaffold]]</li> | |||
<li>[[IGEM:Harvard/2006/Container_Design_5/Python Code|Code]]</li> | |||
<li>[[IGEM:Harvard/2006/Container_Design_5/Latch Sequences|Latches]]</li> | |||
<li>[[IGEM:Harvard/2006/Container_Design_5/Oligos|Final Oligo List]]</li> | |||
</ul> | |||
</div> | |||
<br style="clear:both"> | |||
==Latches (4-oligo design, ie. staple oligos)== | ==Latches (4-oligo design, ie. staple oligos)== |
Revision as of 06:43, 27 July 2006
Latches (4-oligo design, ie. staple oligos)
partial oligo list (7/24)
c5.0.1: core barrel oligos | ||
oligo 0 | c5.0.1.1 | TAAAGTATAGCATT |
oligo 1 | c5.0.1.2 | AAGTCAGAGGGTAATTGAGCGAAACCGAGGAAACGCTGGCAT |
oligo 2 | c5.0.1.3 | GATTAAGTCTACTAATAGTAGCGGTGTCTGGAAGTATGCTGT |
oligo 3 | c5.0.1.4 | AGCTCAAAAAGACTTCAAATAAGCAAAGCGGATTGGTAATAG |
oligo 4 | c5.0.1.5 | TAAAATGAGGCAAGTCCGCTACGTATAAGGCGCTCACAATTC |
oligo 5 | c5.0.1.6 | CACACAAGCCAGCTGCATTAAGGTAGAAAGATTCATACCAGT |
oligo 6 | c5.0.1.7 | CAGGACGTTGGGAAGAAAAATACAAAGCTGCTCATATCCCTT |
oligo 8 | c5.0.1.8 | ACTAAATGTGGCGAGAAAGGAAGGCCGATTAAAGGGAGGCCA |
oligo 9 | c5.0.1.9 | CCGAGTATCCAGAACAATATTCTCAATCGTCTGAAACAGACA |
oligo 10 | c5.0.1.10 | ATATTTTAAAAATACCGAACGAACCACCAGCAGAAAAGCATC |
oligo 11 | c5.0.1.11 | ACCTTGCCTTGATACCGATAGTTTTTCACGTTGAAAATCTCC |
oligo 12 | c5.0.1.12 | AAAAAAATCCAGACGTTAGTACCACCAGAAGGAGCCTGATTG |
oligo 13 | c5.0.1.13 | TTTGGATTATACTTCTGAATACGTCAGATGAATATCCGCCAC |
oligo 14 | c5.0.1.14 | CCTCAGACCAGGCGGATAAGTTGCCTATTTCGGAATACATGG |
oligo 15 | c5.0.1.15 | CTTTTGATCAGACGATTGGCCCCCTCAGAACCGCCTCGGTCA |
oligo 16 | c5.0.1.16 | TAGCCCCGGCTTATCCGGTATCCAGTTACAAAATAAACAGCC |
oligo 17 | c5.0.1.17 | ATATTATGCAGCCTTTACAGAACCGTCACCGACTTTTTTGTC |
oligo 18 | c5.0.1.18 | ACAATCAATAGAAAATTCATAAGTATGTTAGCAAACAGATAG |
oligo 19 | c5.0.1.19 | CCGAACAGCAATAAAGCCTCAGAGCATAAAGCTAATATTTCA |
oligo 20 | c5.0.1.20 | ACGCAAGTGATATTCAACCGTTAGCATGTCAATCATAAATCA |
oligo 21 | c5.0.1.21 | GCTCATTCAGCTTTCATCAACTCTGCCAGTTTGAGACCGCTT |
oligo 22 | c5.0.1.22 | CTGGTGCCAAGGCGATTAAGTTGGGTAACGCCAGGCGACGGC |
oligo 23 | c5.0.1.23 | CAGTGCCATTCATTGAATCCCATAGTAAGAGCAACACTATCA |
oligo 24 | c5.0.1.24 | TAACCCTGGAATACCACATTCCCCGCTTTCCAGTCAGCTGAT |
oligo 25 | c5.0.1.25 | TGCCCTTCACCGCCTGGCCCTCTGGTTTGCCCCAGTAGTAAA |
oligo 26 | c5.0.1.26 | TTGGGCTCAGATGAACGGTGTCAATCATAAGGGAAAAAAGAA |
oligo 27 | c5.0.1.27 | TACACTATAATGCCACTACGACTGAGGCTTGCAGGACAACAA |
oligo 28 | c5.0.1.28 | CCATCGCTGAGAGCCAGCAGCGACAACTCGTATTAAATCCTT |
oligo 29 | c5.0.1.29 | TACTTTTGCGGGAGAAGCCTTATCGGTTGTACCAATACCGAA |
oligo 31 | c5.0.1.30 | AATCCAACCCAATAGCAAGCAGCAAGCCGTTTTTACGCCTGT |
oligo 32 | c5.0.1.31 | TTATCAACAATAGATAAGTCCAGTAATTCTGTCCACCTCAGA |
oligo 34 | c5.0.1.32 | TTACCGTTACTAGAAAAAGCCATAGGTCTGTCCAATCGCAAG |
oligo 35 | c5.0.1.33 | ACAAAGAGCGATAGCTTAGATGGTTTTGCTCAGTAACCGCCA |
oligo 36 | c5.0.1.34 | CCCTCAGAACACTGAGTTTCGATGGGATTTTGCTATTGCGAA |
oligo 37 | c5.0.1.35 | TAATAATTTGCGCCGACAATGGAGTTAAAGGCCGCTTGGCAG |
oligo 38 | c5.0.1.36 | ATTCACCACTCAAACTATCGGCCTTGCTGGTAATAAAAGAGT |
oligo 39 | c5.0.1.37 | CTGTCCAGACCCCCAGCGATTTACTTAGCCGGAACGAGGCGC |
oligo 40 | c5.0.1.38 | AGACGGTACAGACCAGGCGCAAAGGAGCGGGCGCTAAATCAA |
oligo 41 | c5.0.1.39 | GTTTTTTGGGGTCGAGGTGCCACTATTAAAGAACGGTTTGAT |
oligo 42 | c5.0.1.40 | GGTGGTTGTGAGACGGGCAACGGGAAACCTGTCGTCATACGA |
oligo 44 | c5.0.1.41 | CAGGCAAAGCGCCATTCGCCAGTGTAGATGGGCGCCTATTAT |
oligo 45 | c5.0.1.42 | AGTCAGATCGCGTTTTAATTCGAGCTTCAAAGCGAATGGCTT |
oligo 46 | c5.0.1.43 | AGAGCTTCATTAAATTTTTGTTATGTACCCCGGTTGATAATC |
oligo 47 | c5.0.1.44 | AGAAAAGGCCGGAGACAGTCAAAGGTGGCATCAATACTCCTT |
oligo 48 | c5.0.1.45 | ATTACGCTGGTTTACCAGCGCGGAAATTATTCATTATCGATA |
oligo 49 | c5.0.1.46 | GCAGCACTTTCATCGGCATTTACCCTCAGAGCCACGAGAATA |
oligo 50 | c5.0.1.47 | TAAAGTATTGAGAATCGCCATATTTAACAACGCCAATACCGA |
oligo 51 | c5.0.1.48 | CCGTGTGACTGGTAATAAGTTAGTGCCCGTATAAACAGTTAA |
oligo 52 | c5.0.1.49 | TGCCCCCGCCGTCGAGAGGGTATTTTCCCTTAGAAGGAAACA |
oligo 53 | c5.0.1.50 | GTACATAAATCAATATATGTGTTTGAATACCAAGTTTTTACA |
oligo 54 | c5.0.1.51 | TCGGGAGTCATCAATATAATCGGAATTATCATCATGTTGAAA |
oligo 55 | c5.0.1.52 | GGAATAACAAACCCTCAATCAAAAACATCGCCATTTGAATGG |
oligo 56 | c5.0.1.53 | CTATTAGTCTTTAA |
oligo 57 | c5.0.1.54 | TATTTTTGATAATCGTAAAACTCTAGCTGATAAATATAACCT |
oligo 58 | c5.0.1.55 | GTTTAGCACATAAAGGTGGCAACGGAATAAGTTTAGAGCCAT |
oligo 59 | c5.0.1.56 | TTGGGAAACCATTACCATTAGCCATCTTTTCATAAACCGGAA |
oligo 61 | c5.0.1.57 | ACGCTCAACCGGAATCATAATTCCAGTAAGCGTCACCTATTA |
oligo 62 | c5.0.1.58 | TTCTGAAACATGAAAGTATTAATTAGGATTAGCGGTAAGACG |
oligo 63 | c5.0.1.59 | CTGAGAATTAATTACATTTAACAATTTCATTTGAAATTTCAA |
oligo 64 | c5.0.1.60 | TTACCTGATTTTCAGGTTTAAATGGAAGGGTTAGAAACATTA |
oligo 66 | c5.0.1.61 | CAGAGGTCTGACCTGAAAGCGTAAGAATACGTGGCATGGATT |
oligo 68 | c5.0.1.62 | AAATACGAAACACTCATCTTTTCACGCAAATTAACGTTAGAA |
oligo 69 | c5.0.1.63 | TCAGAGCGGGAGCTAAACAGGAGGGAAGAAAGCGATAGGCTG |
oligo 70 | c5.0.1.64 | GCTGACCTTGCCCTGACGAGAGAACTGGCTCATTATCAGTTG |
oligo 71 | c5.0.1.65 | AGATTTACGTTTACCAGACGACGTCCAATACTGCGGGTCTTT |
oligo 72 | c5.0.1.66 | ACCCTGAATCGTAACCGTGCAATTAAATGTGAGCGAGTAACA |
oligo 73 | c5.0.1.67 | ACCCGTCTTTGTTAAAATTCGAATTGCTGAATATATTCATTC |
oligo 74 | c5.0.1.68 | CATATAACAGTTGATTCCCAAGGGCGCGAGCTGAAAATCACC |
oligo 76 | c5.0.1.69 | AAATTAAAAGTTACCAGAAGGCTAATATCAGAGAGAACAGGG |
oligo 77 | c5.0.1.70 | AAGCGCACAGAGCCTAATTTGTCTAAGAACGCGAGAAGAACG |
oligo 79 | c5.0.1.71 | GTAATAACACCCTCAGAGCCGGCCAGCATTGACAGGAGGTTG |
oligo 80 | c5.0.1.72 | AGGCAGGTGATACAGGAGTGTATAAATAAGGCGTTTTTCAAA |
oligo 81 | c5.0.1.73 | TATATTTTAGTTAATTTCATCGTCGCTATTAATTATGATATA |
oligo 82 | c5.0.1.74 | AGTATAGAGGAGGTTTAGTACCATTCCACAGACAGAGTTTTG |
oligo 83 | c5.0.1.75 | TCGTCTTAGGCTCCAAAAGGATTGCTTTCGAGGTGAAAGACA |
oligo 85 | c5.0.1.76 | ATCATACAGGCAAGGCAAAGATTTAAATGCAATGCAAAGGGT |
oligo 87 | c5.0.1.77 | CCGTGGGGATAGGTCACGTTGTTCAGGCTGCGCAACCTCTTC |
oligo 88 | c5.0.1.78 | GCTATTACGCCAGCTGGCGAAGACCTTTGATAGCGTTTAGAC |
oligo 90 | c5.0.1.79 | TATTACATGAATCGGCCAACGGGCGCCAGGGTGGTTTTTCTT |
oligo 91 | c5.0.1.80 | TTCACCACCGAAATCGGCAAATCAGTGAATAAGGCTTCATCA |
oligo 92 | c5.0.1.81 | AGAGTAAGACCTGCTCCATGTATACCAAGCGCGAAGACTTTT |
oligo 93 | c5.0.1.82 | TCATGAGCACCCTCAGCAGCGAATTTCTTAAACAGTGAACCT |
oligo 94 | c5.0.1.82 | CAAATATTACATTTGAGGATTTAGAAGTATTAGACGCGGAAC |
oligo 96 | c5.0.1.83 | CCTGTAGCGCCACCCTCAGAAACAGTAACAGTACCTACAAAA |
oligo 97 | c5.0.1.84 | TCGCGCAGAGGCGAATTATTCTTACCTTTTTTAATTCCTTGA |
oligo 98 | c5.0.1.85 | AAACATAACGCGAGAAAACTTAAATAAGAATAAACACAGTAG |
oligo 99 | c5.0.1.86 | GGCTTAACCGACAAAAGGTAATGAACAAGAAAAATAACCAAG |
oligo 100 | c5.0.1.87 | TACCGCACTCATCGAGAACAAAATCAGATATAGAACTTATTA |
oligo 101 | c5.0.1.88 | GCGTTTGCAAGGCCGGAAACGTCACCAATGAAACCAAAGGTG |
oligo 102 | c5.0.1.89 | AATTATCGAGAATAACATAAAATAACCCACAAGAATTGAGTT |
oligo 103 | c5.0.1.90 | AAGCCCATTAAGAAAAGTAAGCGTAGAAAATACATTATATTT |
oligo 105 | c5.0.1.91 | CGGAAGCTAAATCAAAAATCAGAATCGTCATAAATAAGCTTG |
oligo 106 | c5.0.1.92 | CATGCCTGCATAAAGTGTAAAGCCTGGGGTGCCTACGTTGCG |
oligo 107 | c5.0.1.93 | CTCACTGAACTAATGCAGATACATTGTGAATTACCTTATGCG |
oligo 109 | c5.0.1.94 | CAACGTCAAAGGGCGAAAAACGTGAACCATCACCCAGGGCGC |
oligo 110 | c5.0.1.95 | TGGCAAGCCACACCCGCCGTCCGTTGTAGCAATACGCCTGAG |
oligo 111 | c5.0.1.96 | TAGAAGAAGTCACACGACCAGGAGATAGAACCCTTGAGGCGG |
oligo 112 | c5.0.1.97 | TCAGTATTAACACC |
oligo 113 | c5.0.1.98 | ATGGTCATAATGCC |
oligo 114 | c5.0.1.99 | CGCGTCTGGCCTTCCTGTAGCTTTTAACCAATAGGTCCTTTT |
oligo 115 | c5.0.1.100 | GATAAGAAGATTTAGTTTGACCATTAGA |
oligo 116 | c5.0.1.101 | AAGCCCGCATGTTT |
oligo 117 | c5.0.1.102 | TAATTGCAACGCCA |
oligo 118 | c5.0.1.103 | CACTCCAGCCAGCTTTCCGGCGGGACGACGACAGTAACGAGA |
oligo 119 | c5.0.1.104 | ATGACCAAAACTCCAACAGGTCAGGATT |
oligo 120 | c5.0.1.105 | AGAGGGGCATCAAA |
oligo 121 | c5.0.1.106 | TTCAGAAATCGGCC |
oligo 122 | c5.0.1.107 | ACGAGGCCCTCAAA |
oligo 123 | c5.0.1.108 | TAACGGATTGCAAA |
oligo 124 | c5.0.1.109 | CTTTAATCATAACG |
oligo 125 | c5.0.1.110 | CAACGTACTACGTT |
oligo 126 | c5.0.1.111 | AAGAGGATGAGATG |
oligo 127 | c5.0.1.112 | TGACGGGGGATATT |
oligo 128 | c5.0.1.113 | ATAAATTGTGTCGAAATCCGCTCTTGACAAGAACCGAAAGCC |
oligo 129 | c5.0.1.114 | GGCGAACCGGAACCCTAAAGGGAGCCCC |
oligo 130 | c5.0.1.115 | AAGAGGCCCGAACT |
oligo 131 | c5.0.1.116 | AGAAGTGAGATTTG |
oligo 132 | c5.0.1.117 | ACAGAGGCTTTGAGGACTAAAACAAAGTACAACGGTTTTTAT |
oligo 133 | c5.0.1.118 | AATCAGTGATTTTAGACAGGAACGGTAC |
oligo 134 | c5.0.1.119 | TCGGTCGAGGCACC |
oligo 135 | c5.0.1.120 | GGAAATAAACGAGG |
oligo 136 | c5.0.1.121 | TATCAGCGCCTTTA |
oligo 137 | c5.0.1.122 | GCCACGCCCACGCA |
oligo 138 | c5.0.1.123 | AGAAAGGAACAACTAAAGGAAAACAACTTTCAACATTAAAAG |
oligo 140 | c5.0.1.124 | GATCTAACCCTCAT |
oligo 141 | c5.0.1.125 | ATTAATTGTTTCAG |
oligo 142 | c5.0.1.126 | CAATAGGAACCCATGTACCGTAGCCACCACCCTCAAAGAAAT |
oligo 143 | c5.0.1.127 | TGCGTAGAGCAAAAGAAGATGATGAAAC |
oligo 144 | c5.0.1.128 | CGTACTCCCCGGAA |
oligo 145 | c5.0.1.129 | AGAAATATTTTCAG |
oligo 146 | c5.0.1.130 | GAGAAGGAGAGGCT |
oligo 147 | c5.0.1.131 | GAGTAACTTAACGG |
oligo 148 | c5.0.1.132 | CGCAGTCTTAAAGC |
oligo 149 | c5.0.1.133 | AGCCGCCCCACCAG |
oligo 150 | c5.0.1.134 | AGCCACCTCAAAAT |
oligo 151 | c5.0.1.135 | TAGCGTCCTCCCGA |
oligo 152 | c5.0.1.136 | GCTGTCTTTCCTTATCATTCCGCGTTTTAGCGAACAGACTGT |
oligo 153 | c5.0.1.137 | AGCGCGTCGTAATCAGTAGCGACAGAAT |
oligo 154 | c5.0.1.138 | CAGTAGCTTAGAGC |
oligo 155 | c5.0.1.139 | GGAGGGATAACTGA |
oligo 156 | c5.0.1.140 | TTTGAAGCCTTAGCGTCTTTCTTAGACGGGAGAATAGGTAAA |
oligo 157 | c5.0.1.141 | TATTGACCAAAGACAAAAGGGCGACATT |
oligo 158 | c5.0.1.142 | AGACACCACATATA |
oligo 159 | c5.0.1.143 | AAAAGAACAATAAT |
oligo 160 | c5.0.1.144 | GCTATCTAAACATT |
oligo 161 | c5.0.1.145 | TTAACGTAAACAAT |
oligo 162 | c5.0.1.146 | TACCGCGATAAGAA |
oligo 163 | c5.0.1.147 | CAGAACGTTTTCAT |
oligo 164 | c5.0.1.148 | GCATTTTAGAAACC |
oligo 165 | c5.0.1.149 | TATACAAACAACAT |
oligo 166 | c5.0.1.150 | GTTTGAAACATGTA |
oligo 167 | c5.0.1.151 | CAAAATCTGTTTAG |
oligo 168 | c5.0.1.152 | GTAAATCTTCTGAC |
oligo 169 | c5.0.1.153 | AACAAAAGAGTCAA |
oligo 170 | c5.0.1.154 | TGATTGCAGTGAAT |
oligo 171 | c5.0.1.155 | TGGCAATAAACAAT |
oligo 172 | c5.0.1.156 | ATCAACAATTCCTG |
oligo 173 | c5.0.1.157 | TAGCCCTATATCTG |
oligo 174 | c5.0.1.158 | GCCAACATAATAAA |
oligo 175 | c5.0.1.159 | ATCACTTTTCTTTG |
oligo 176 | c5.0.1.160 | GTAACCATGTAGCG |
oligo 177 | c5.0.1.161 | CCACTACCGTCTAT |
oligo 178 | c5.0.1.162 | GGGTTGAAAAAGAA |
oligo 179 | c5.0.1.163 | GTCCACGGAGAGAG |
oligo 180 | c5.0.1.164 | CGTATTGCGCGGGG |
oligo 181 | c5.0.1.165 | TTAATTGATGAGTG |
oligo 182 | c5.0.1.166 | TAGTACCGCGACCG |
oligo 183 | c5.0.1.167 | TGTAAAAGTTTTCC |
oligo 184 | c5.0.1.168 | GTGCGGGCTGTTGG |
oligo 185 | c5.0.1.169 | GTAATGGAACAAAC |
oligo 186 | c5.0.1.170 | TTAAATTAGATTGT |
oligo 187 | c5.0.1.171 | AGATTCACTGAGTA |
c5.0.2: top lid oligos | ||
oligo 0 | c5.0.2.1 | CCCTGCCAGGGATC |
oligo 1 | c5.0.2.2 | GCCGCCACCAGAACCACCACCCGGAAGTTGGAAGCATCTGTA |
oligo 2 | c5.0.2.3 | AGCAACTCCCTGGAGTGACTCCAGTGCCAAGCTTTCGCCAGG |
oligo 3 | c5.0.2.4 | GTTTTCCTTCCGGCACCGCTTCGACAGTATCGGCCCTGTAGC |
oligo 4 | c5.0.2.5 | CAGCTTTCAATAGGAACGCCAGTAAAACTAGCATGGAGAGTC |
oligo 5 | c5.0.2.6 | TGGAGCAAGTAATGTGTAGGTAAATTTTTAGAACCCATTAAC |
oligo 6 | c5.0.2.7 | ATCCAATCGAGCTGAAAAGGTGTTTTAAATATGCATTAGAGC |
oligo 7 | c5.0.2.8 | TTAATTGCAAAAAGATTAAGAGGAAGCCCGAAAGACAAAAAT |
oligo 8 | c5.0.2.9 | CAGGTCTCCAGAGGGGGTAATAGTAAAATGTTTAGAAGAGCA |
oligo 9 | c5.0.2.10 | ACACTATTCTGGAAGTTTCATCTGTTTAGCTATATTTTCATT |
oligo 10 | c5.0.2.11 | TGGGGCGAAATCATACAGGCACGATTTTAAGAACTATCAACG |
oligo 11 | c5.0.2.12 | TAACAAAGCTGCTCATTCAGTGAACGGTGTACAGAGTGAGAA |
oligo 12 | c5.0.2.13 | AGGCCGGATCTACAAAGGCTATCAGGTCATTGCCTTCAATCA |
oligo 13 | c5.0.2.14 | TATGTACCTCATCTTTGACCCCTACAGAGGCTTTGAGGACTA |
oligo 14 | c5.0.2.15 | AAGACTTGCTTGCAGGGAGTTGTGAGCGAGTAACACCGTGCA |
oligo 15 | c5.0.2.16 | TCTGCCAGTTTGAGGGGACGACTGGTGCCGGAAACAATAATA |
oligo 16 | c5.0.2.17 | ATTTTTTACGATCTAAAGTTTTGTCGTCTTTCCAGATGTACC |
oligo 17 | c5.0.2.18 | GTAACACGGGTGGATGTTCTTAACCCCGCTTCTAATCTATTT |
oligo 18 | c5.0.2.19 | ACGCTCGCGTCGGTGGGCACGTGCTCAGTACCAGGTTGAGTA |
oligo 19 | c5.0.2.20 | ACAGTGCCCGTATAAACAGTTATTTACCGTTCCAGCATTGAC |
oligo 20 | c5.0.2.21 | AGGAGGTTGAGGCAGGTCAGAAACAGGGCTTAAGCGAATCGG |
oligo 21 | c5.0.2.22 | CTGACGCTGTCCCGCCAAAATCTAAGTGGTTGTGATGGCGAA |
oligo 22 | c5.0.2.23 | AGGGGGATTCGCCATTCAGGCTGGGCGCATCGTAAACCCGTC |
oligo 23 | c5.0.2.24 | GGATTCTAAATTCGCATTAAAAGAAAAGCCCCAAAGCTATTT |
oligo 24 | c5.0.2.25 | TTGAGAGAGACAGTCAAATCAAATACTTTTGCGGGCAAAATT |
oligo 25 | c5.0.2.26 | AAGCAATAAATGGTCAATAACTCCATATAACAGTTTTTAATT |
oligo 26 | c5.0.2.27 | GCTCCTTTTTTAATTCGAGCTTCAAAGCGAACCAGCAAATGC |
oligo 27 | c5.0.2.28 | TTTAAACAATACTGCGGAATCGTCATAA |
oligo 28 | c5.0.2.29 | TCCTGGTTGGTGTAATGAGTACGATTGGCCTTGATAAGCCAG |
oligo 29 | c5.0.2.30 | AATGGAAAGCGCAGTCTCTGAAATGCCCCCTGCCTAAGAGAA |
oligo 30 | c5.0.2.31 | GGATTAGCCCTCAGAACCGCCCCCAATAGGAACCCACGTTAG |
oligo 31 | c5.0.2.32 | TAAATGAATAGAAAGGAACAACTTAAACAGCTTGAATTCGGT |
oligo 32 | c5.0.2.33 | CGCTGAGTTTCATGAGGAAGTGAAAGAGGCAAAAGGCTCCAT |
oligo 33 | c5.0.2.34 | GTTACTTGAAAGAGGACAGATGAATAAGGCTTGCCAACTTTA |
oligo 34 | c5.0.2.35 | ATCATTGAAAGATTCATCAGTTTACGAGGCATAGTACTGGAT |
oligo 35 | c5.0.2.36 | AGCGTCCAGTTCAGAAAACGAGAATGACCATAAATCTTCAAA |
oligo 36 | c5.0.2.37 | TATCGCGTTGATAAGAGGTCATTTTTGCGGATGGCACTAAAG |
oligo 37 | c5.0.2.38 | TACGGTGCATAACCCTCGTTTACTAACGGAACAACATTATTA |
oligo 38 | c5.0.2.39 | CAGGTAGTGAATTACCTTATGAGGCAAAGAATTAGAGAAGCC |
oligo 39 | c5.0.2.40 | TTTATTTCAACGCAAGGATAAAAAGATTCAAAAGGCCAGGCG |
oligo 40 | c5.0.2.41 | CATAGGCTGATAAATTGTGTCGAAATCCGCGACCTAATACAC |
oligo 41 | c5.0.2.42 | TAAAACACCCGGTTGATAATCTTTTTGTTAAATCAGCTCATT |
oligo 42 | c5.0.2.43 | TTTTAACCATCAACATTAAATAAAGGCCGCTTTTGTTTATCA |
oligo 43 | c5.0.2.44 | GCTTGCTTTCGAGGTGAATTTCTAAAGGAATTGCGCAGGCAA |
oligo 44 | c5.0.2.45 | AGCGCCATGTGCTGCAAGGCGATTAAGTTGGGTAACTCAGGA |
oligo 45 | c5.0.2.46 | GAAGCCATGAGTTTCGTCACCACCGTACTCAGGAGGTTTAGT |
oligo 46 | c5.0.2.47 | ACCGCCAGATTAGCGGGGTTTAATATAGGGGCCTTTACGTGG |
oligo 47 | c5.0.2.48 | TGCTTGTTACCTCGATAAAGAAGAGCCGCCGCCAGTAAGCGT |
oligo 48 | c5.0.2.49 | CATACATGGCTTTTGATGATAACGGGGTCAGTGCCCGGATAA |
oligo 49 | c5.0.2.50 | GTGCCGTGGAATAGGTGTATCAGTACAAACTACAATCATAGT |
oligo 50 | c5.0.2.51 | TAGCGTACACGTTGAAAATCTTTTAATTGTATCGGCGGGATC |
oligo 51 | c5.0.2.52 | GTCACCCGAGGGTAGCAACGGCCAGCGATTATACCTTTGTAT |
oligo 52 | c5.0.2.53 | CATCGCCTGGCTGACCTTCATTATTCATTACCCAAGGCTCAT |
oligo 53 | c5.0.2.54 | TATACCACGTTAATAAAACGAACCAGACGACGATACAAAAGA |
oligo 54 | c5.0.2.55 | AGTTTTGTTACCCTGACTATTATAGTCA |
oligo 55 | c5.0.2.56 | GAATTGTCAACCTTATGACAAATTTCACATAAATCGGCTGAG |
oligo 56 | c5.0.2.57 | ACTCCTCATTTCGGAACCTATTATTCTG |
oligo 57 | c5.0.2.58 | ATTAAGAATTTCTC |
oligo 58 | c5.0.2.59 | CGACGGCTATGATA |
oligo 59 | c5.0.2.60 | CCTCTTCGCTATTACGCCAGCATTCATGCGCACGATCAGGGA |
oligo 60 | c5.0.2.61 | TAGCAAGACCCTCAGAACCGCCACCCTC |
oligo 61 | c5.0.2.62 | CTCATTTCTTAAGT |
oligo 62 | c5.0.2.63 | GCCAGCTCAGTCAC |
oligo 63 | c5.0.2.64 | GATAGGTCACGTTGGTGTAGATGCGCAACTGTTGGTCAGCGG |
oligo 64 | c5.0.2.65 | AGTGAGAATTTTCTGTATGGGATTTTGC |
oligo 65 | c5.0.2.66 | AACAGTTGAAGGGC |
oligo 66 | c5.0.2.67 | GGCCTTCTCAGGAA |
oligo 67 | c5.0.2.68 | GTAAACGTTAATATTTTGTTACCGTGGGAACAAACCGCATAA |
oligo 68 | c5.0.2.69 | CCGATATTACCGATAGTTGCGCCGACAA |
oligo 69 | c5.0.2.70 | TCGCCCAGGCGGAT |
oligo 70 | c5.0.2.71 | GGTAATCTCAAAAA |
oligo 71 | c5.0.2.72 | AAATTAATGCCGGAGAGGGTAAACAGGAAGATTGTCACCAAC |
oligo 72 | c5.0.2.73 | CTAAAACTTCCATTAAACGGGTAAAATA |
oligo 73 | c5.0.2.74 | ACGAAGGATAAGCA |
oligo 74 | c5.0.2.75 | ATGCCTGAACAAGA |
oligo 75 | c5.0.2.76 | CCAAAAACATTATGACCCTGTCCATCAATATGATAAACTGAC |
oligo 76 | c5.0.2.77 | CAACTTTAGCCGGAACGAGGCGCAGACG |
oligo 77 | c5.0.2.78 | GGAACCGTTCAACC |
oligo 78 | c5.0.2.79 | GTAGTAGCTCATAT |
oligo 79 | c5.0.2.80 | TGACCATTAGATACATTTCGCAAAGCCTCAGAGCAGATGGTT |
oligo 80 | c5.0.2.81 | TAATTTCCTGACGAGAAACACCAGAACG |
oligo 81 | c5.0.2.82 | GGCTTGATAAAGCT |
oligo 82 | c5.0.2.83 | TCAACATGGCATCA |
oligo 83 | c5.0.2.84 | AGGTCAGGATTAGAGAGTACCGATTCCCAATTCTGAACGCCA |
oligo 84 | c5.0.2.85 | AAAGGAATGAGATTTAGGAATACCACAT |
oligo 85 | c5.0.2.86 | GATACATCGAACGA |
oligo 86 | c5.0.2.87 | ATTGCATCTGAATA |
oligo 87 | c5.0.2.88 | TCCCCCTACCGGAA |
oligo 88 | c5.0.2.89 | GCTTTTGAAAACCA |
oligo 89 | c5.0.2.90 | AAATCTAGTCAGGA |
oligo 90 | c5.0.2.91 | AACCGGACAAGAGT |
oligo 91 | c5.0.2.92 | ACGGAGAAAGCGCG |
oligo 92 | c5.0.2.93 | TCGGAACTCAGCAG |
oligo 93 | c5.0.2.94 | AGGAGCCCCAAAAA |
oligo 94 | c5.0.2.95 | ACAGCCCCGCCTGT |
oligo 95 | c5.0.2.96 | ATAGCCCCGAGAGG |
oligo 96 | c5.0.2.97 | AGTTTTACAGGAGT |
oligo 97 | c5.0.2.98 | CTCATTAATTCACA |
c5.0.3: bottom lid oligos | ||
oligo 0 | c5.0.3.1 | CATTAAAGTAGCGC |
oligo 1 | c5.0.3.2 | CGTTGCGCTCACTGCCCGCTTTTTAGCGTCAGACTGGTGAAT |
oligo 2 | c5.0.3.3 | TATCACCAGGGAGGGAAGGTAATGTTAGCAAACGTCCAAAAG |
oligo 3 | c5.0.3.4 | AACTGGCACCCACAAGAATTGCAAAGTCAGAGGGTGTTACAA |
oligo 4 | c5.0.3.5 | AATAAACACCAACGCTAACGACCAATAGCAAGCAACAAGCCG |
oligo 5 | c5.0.3.6 | TTTTTATGCCTGTTTATCAACACGACGACAATAAATTCTTAC |
oligo 6 | c5.0.3.7 | CAGTATAACTAGAAAAAGCCTGATGCAAATCCAATCTCCGGC |
oligo 7 | c5.0.3.8 | TTAGGTTGTGAGTGAATAACCTTGCTTCTGTAAATACAATTT |
oligo 8 | c5.0.3.9 | CATTTGAGATTCGCCTGATTGCTTTGAATACCAAGAAAGAAA |
oligo 9 | c5.0.3.10 | TTGCGTACGCGAGAAAACTTTAATAAGAATAAACACCGGAAT |
oligo 10 | c5.0.3.11 | CATAATTAAGCCAACGCTCAATAACATTATCATTTACTAATA |
oligo 11 | c5.0.3.12 | GATTAGAGCCGTCAATAGATAAATCAATATCTGGTGAACAAG |
oligo 12 | c5.0.3.13 | AAAAATAACCAAGTACCGCACTCATCGAGAACAAGATCAGAT |
oligo 13 | c5.0.3.14 | ATAGAAGCGCGAACTGATAGCTCACCAGTCACACGACCAGTA |
oligo 14 | c5.0.3.15 | ATAAAAGCATTGCAACAGGAATCCCAATCCAAATAGACGGGA |
oligo 15 | c5.0.3.16 | GAATTAACTGAACACCCTGAAAGTTAAGCCCAATACAGAATC |
oligo 16 | c5.0.3.17 | CTGAGAACGCCGCTACAGGGCGCGTACTATGGTTGAAAGCGA |
oligo 17 | c5.0.3.18 | AAGGAGCTAAAGGTGGCAACAAGACAAAAGGGCGACATTCAA |
oligo 18 | c5.0.3.19 | CCGATTGGTCACCGACTTGAGCAACGTCAAAGGGCAAATCCT |
oligo 19 | c5.0.3.20 | GTTTGATGGTGGTTCCGAAATGGGCAACAGCTGATCTGTCGT |
oligo 20 | c5.0.3.21 | GCCAGCTGCATTAATGAATCGGATAGCAGCACCGTGAGCCAG |
oligo 21 | c5.0.3.22 | CAAAATCTTTACCAGCGCCAATATAAAAGAAACGCTTACCAG |
oligo 22 | c5.0.3.23 | AAGGAAACAATGAAATAGCAAAGGGAAGCGCATTAAGAAACG |
oligo 23 | c5.0.3.24 | ATTTTTTAGTTGCTATTTTGCCTAAGAACGCGAGGAGAACGG |
oligo 24 | c5.0.3.25 | GTATTAAATATCCCATCCTAAAGAATATAAAGTACTGAGAAT |
oligo 25 | c5.0.3.26 | CGCCATATAAATAAGGCGTTATTCAAATATATTTTGAATTTA |
oligo 26 | c5.0.3.27 | TCAAAATAATTTTCCCTTAGAATCCTTGAAAACATATGATGA |
oligo 27 | c5.0.3.28 | AACAAACAGAGGCGAATTATTCATTTCA |
oligo 28 | c5.0.3.29 | AACGTCACCAATGAAACCATCGCCAACGCGCGGGGGGGTGGT |
oligo 29 | c5.0.3.30 | TTTTCTTTTCACCAGTGAGACCGGCAAAATCCCTTAGAGTCC |
oligo 30 | c5.0.3.31 | ACTATTAACTAAATCGGAACCGAAAGGAAGGGAAGCTTTGAC |
oligo 31 | c5.0.3.32 | GAGCACGAAAGGGATTTTAGATAGTAATAACATCAATATTAC |
oligo 32 | c5.0.3.33 | CGCCAGCGGACATTCTGGCCAATTTTTGAATGGCTCTGCAAC |
oligo 33 | c5.0.3.34 | AGTGCCAAATATCAAACCCTCATACATTTGAGGATCGAACGT |
oligo 34 | c5.0.3.35 | TATTAATCCTGATTGTTTGGACGTAAAACAGAAATTTACAAA |
oligo 35 | c5.0.3.36 | ATCGCGCATCAAGAAAACAAAATTAATTACATTTACGTCGCT |
oligo 36 | c5.0.3.37 | ATTAATTCATAGGTCTGAGAGACTACCTTTTTAACCGCAAGA |
oligo 37 | c5.0.3.38 | CAAAGAAGATTTTCAGGTTTATCAGATGATGGCAATTCATCA |
oligo 38 | c5.0.3.39 | ATATAATTTTAAAAGTTTGAGCAGTAGGGCTTAATCGACAAA |
oligo 39 | c5.0.3.40 | AGGTAAAGTAATTCTGTCCAGAATAGATAAGTCCTCAGTTGG |
oligo 40 | c5.0.3.41 | CAAATCAGAGGTGAGGCGGTCAGTATTAACACCGCATTAGTC |
oligo 41 | c5.0.3.42 | TTTAATGGCTTATCCGGTATTACCCAGCTACAATTTTATCCT |
oligo 42 | c5.0.3.43 | GAATCTTAGCCATATTATTTAAAACGCTCATGGAATTAACCG |
oligo 43 | c5.0.3.44 | TTGTAGCAATACTTCTTTGATCAGGAACGGTACGCATAAGAG |
oligo 44 | c5.0.3.45 | CAAGAAACCGAGGAAACGCAATAATAACGGAATACAGAAAAT |
oligo 45 | c5.0.3.46 | ACATACAGGGCGCTAGGGCGCGTTTTTTGGGGTCGAGGTGCC |
oligo 46 | c5.0.3.47 | GTAAAGCAAGAACGTGGACTCCCATTTGGGAATTAAATCAGT |
oligo 47 | c5.0.3.48 | AGCGACAGAATCAAGTTTGCCTCCAGTCGGGAAACTGCCCTT |
oligo 48 | c5.0.3.49 | CACCGCCTGGCCCTGAGAGAGGCCCCAGCAGGCGAGAAAAAC |
oligo 49 | c5.0.3.50 | CGTCTATATCACCCAAATCAATGGCAAGTGTAGCGCGCCGCG |
oligo 50 | c5.0.3.51 | CTTAATGGTGTTTTTATAATCGTCCATCACGCAAAATACCTA |
oligo 51 | c5.0.3.52 | CATTTTGTTACATTGGCAGATCCTAAAACATCGCCCAGAAGA |
oligo 52 | c5.0.3.53 | TAAAACAACAGTTGAAAGGAATAGGAGCACTAACATGCGGAA |
oligo 53 | c5.0.3.54 | CAAAGAACATATTCCTGATTAACGTCAGATGAATAGAGAAAC |
oligo 54 | c5.0.3.55 | AATAACGATTACCTTTTTTAATGGAAAC |
oligo 55 | c5.0.3.56 | ATCAATAGAAAATTCATATGGACCAGTAGCACCATTCCAGTT |
oligo 56 | c5.0.3.57 | TGGAACAATAAATCAAAAGAATAGCCCG |
oligo 57 | c5.0.3.58 | GTGTTGTTACCATT |
oligo 58 | c5.0.3.59 | ACGCAGTAATATTG |
oligo 59 | c5.0.3.60 | TAAGCAGATAGCCGAACAAAGAAAGACACCACGGAGGCGAAC |
oligo 60 | c5.0.3.61 | GTGGCGACTAAAGGGAGCCCCCGATTTA |
oligo 61 | c5.0.3.62 | GAAAGCCATAAGTT |
oligo 62 | c5.0.3.63 | AGAGATAATGATTA |
oligo 63 | c5.0.3.64 | CAGAGAGAATAACATAAAAACTAGCTATCTTACCGACAGGAG |
oligo 64 | c5.0.3.65 | GCCGATTTATAACGTGCTTTCCTCGTTA |
oligo 65 | c5.0.3.66 | GAGCTAAAAGCCCT |
oligo 66 | c5.0.3.67 | TTTGCCAAATTGAG |
oligo 67 | c5.0.3.68 | TTGAAGCCTTAAATCAAGATTGTTTAACGTCAAAATAATATC |
oligo 68 | c5.0.3.69 | CAGAACACTTGCCTGAGTAGAAGAACTC |
oligo 69 | c5.0.3.70 | TTGCTGGATGAAAA |
oligo 70 | c5.0.3.71 | ACCGCGCGCGTCTT |
oligo 71 | c5.0.3.72 | CTGTCTTTCCTTATCATTCCACGTTTTAGCGAACCGTGGCAC |
oligo 72 | c5.0.3.73 | AGACAATACAGAGATAGAACCCTTCTGA |
oligo 73 | c5.0.3.74 | AGAATACTCCCGAC |
oligo 74 | c5.0.3.75 | AGAACGCTTTCATC |
oligo 75 | c5.0.3.76 | CATTTTCGAGCCAGTAATAAGTTTACGAGCATGTACTTGCTG |
oligo 76 | c5.0.3.77 | AACCTCACGCTGAGAGCCAGCAGCAAAT |
oligo 77 | c5.0.3.78 | GCATCACGAAACCA |
oligo 78 | c5.0.3.79 | ATACAAACAACATG |
oligo 79 | c5.0.3.80 | TTTGAAATACCGACCGTGTGATTTAACAACGCCAATTAAATC |
oligo 80 | c5.0.3.81 | CTTTGCCTTAGAAGTATTAGACTTTACA |
oligo 81 | c5.0.3.82 | ACTCGTACATGTAA |
oligo 82 | c5.0.3.83 | AAATGCTGTTTAGT |
oligo 83 | c5.0.3.84 | ACGCTGAGAAGAGTCAATAGTAGTTAATTTCATCTCAAAATT |
oligo 84 | c5.0.3.85 | ATTTGCATTATACTTCTGAATAATGGAA |
oligo 85 | c5.0.3.86 | ACCATATTCTGACC |
oligo 86 | c5.0.3.87 | AATATATGGGTTAT |
oligo 87 | c5.0.3.88 | AAAGAAGAGCGATA |
oligo 88 | c5.0.3.89 | ACATCGGTACAGTA |
oligo 89 | c5.0.3.90 | TTATCATACCACCA |
oligo 90 | c5.0.3.91 | ATATCTTTTGAGGA |
oligo 91 | c5.0.3.92 | CCACCAGATTAAAA |
oligo 92 | c5.0.3.93 | GGATTATACGCTCA |
oligo 93 | c5.0.3.94 | AGAGTCTAGTGAGG |
oligo 94 | c5.0.3.95 | CCACACCGTCACGC |
oligo 95 | c5.0.3.96 | GTGAACCCAGGGCG |
oligo 96 | c5.0.3.97 | CTGGTTTTTGCAGC |
oligo 97 | c5.0.3.98 | GGCGCCAAGAGGCG |
c5.0.4: barrel oligos @ outside aptamers -aptamers | ||
oligo 7 | c5.0.4.1 | ATAAATCGTGTTGTTCCAGTTTGGAACAAGAGTCCGTAAAGC |
oligo 43 | c5.0.4.2 | GCCGGAAGCAGGTCGACTCTAAGGGGGATGTGCTGCGGAAAC |
oligo 65 | c5.0.4.3 | TCATTTTTTTACAAACAATTCAAATGAAAAATCTAGATAAAA |
oligo 75 | c5.0.4.4 | ATCAATAGATAAAAATTTTTAGAACCCTCATATATATTAGCA |
oligo 78 | c5.0.4.5 | GGTATTAAATATCCCATCCTAATTTACGAGCATGTCGAGCCA |
c5.0.5: barrel oligos @ inside aptamers -aptamers | ||
oligo 33 | c5.0.5.1 | GCCGCCATTGATATTCACAAACAAATAAATCCTCATCTGAAT |
oligo 67 | c5.0.5.2 | ATTTACATTTTGCGGGATCGTGAAGTTTCCATTAAACGGGTA |
oligo 89 | c5.0.5.3 | TGGATAGCGATAAAAACCAAAATAGCGAGAGGCTTACAACAT |
oligo 95 | c5.0.5.4 | AAAGAAAAATGAATTTTCTGTTCACCAGTACAAACTACAACG |
oligo 104 | c5.0.5.5 | TCATTTGTTCTGCGAACGAGTGGTCATTTTTGCGGACCAGAC |
c5.0.6: barrel oligos @ top latches -latches | ||
oligo 60 | c5.0.6.1 | CCGCCTCGACGACGACAATAAATTCTTACCAGTATAAAGCCA |
oligo 84 | c5.0.6.2 | GCATCGGCCTACATTTTGACGACCGCCAGCCATTGCAACAGG |
oligo 86 | c5.0.6.3 | GAGAAAGCCCCAAAAACAGGAGTAAACGTTAATATGGATTCT |
c5.0.7: barrel oligos @ bottom latches -latches | ||
oligo 30 | c5.0.7.1 | GCCCTTTATAATAAGAGCAAGCAAAAATGAAAATATTATCCC |
oligo 108 | c5.0.7.2 | ATTTTAAAACACCAGAACGAGCAGGCGAAAATCCTTGGACTC |
oligo 139 | c5.0.7.3 | TTTGAGTACCTACCATATCAAAATTATT |
c5.0.8: barrel outward biotinylated oligos | ||
oligo 7 | c5.0.8.1 | ATAAATCGTGTTGTTCCAGTTTGGAACAAGAGTCCGTAAAGCTTT-biotin |
oligo 43 | c5.0.8.2 | GCCGGAAGCAGGTCGACTCTAAGGGGGATGTGCTGCGGAAACTTT-biotin |
oligo 65 | c5.0.8.3 | TCATTTTTTTACAAACAATTCAAATGAAAAATCTAGATAAAATTT-biotin |
oligo 75 | c5.0.8.4 | ATCAATAGATAAAAATTTTTAGAACCCTCATATATATTAGCATTT-biotin |
oligo 78 | c5.0.8.5 | GGTATTAAATATCCCATCCTAATTTACGAGCATGTCGAGCCATTT-biotin |
c5.0.9: barrel inward biotinylated oligos | ||
oligo 33 | c5.0.9.1 | GCCGCCATTGATATTCACAAACAAATAAATCCTCATCTGAATTTT-biotin |
oligo 67 | c5.0.9.2 | ATTTACATTTTGCGGGATCGTGAAGTTTCCATTAAACGGGTATTT-biotin |
oligo 89 | c5.0.9.3 | TGGATAGCGATAAAAACCAAAATAGCGAGAGGCTTACAACATTTT-biotin |
oligo 95 | c5.0.9.4 | AAAGAAAAATGAATTTTCTGTTCACCAGTACAAACTACAACGTTT-biotin |
oligo 104 | c5.0.9.5 | TCATTTGTTCTGCGAACGAGTGGTCATTTTTGCGGACCAGACTTT-biotin |
lids oligo list
lid1
lid1 oligo sequence list
lid2
lid2 oligo sequence list
barrel oligo list
oligo path
Schematics and .AI Files
-
Double-Ply Barrel Schematic
(ai file) -
Double-Ply Lid 2D Schematic, Plus "Up" & "Down" Points
(ai file) -
Double-Ply Barrel and Lid In-Out Schematic
(ai file) -
Double-Ply Barrel 2D Schematic, Plus "In" & "Out" Points & Latch Points & *NUMBERING!*
(ai file) -
Double-Ply Barrel 2D Schematic, Plus Latches, Loops, & Aptamers
(ai file)
Automated schematic
Here's a link to a python file that automatically creates a schematic. Call maked(inf,outf) where inf is a token list and outf is the file you'd like to output to (should be .bmp). It uses a nifty module called pygame. I haven't tried it out on Macs yet. Still, it gives fairly colorful results.
-
Design 5 barrel
ASCII Diagrams
- Double-Ply Barrel (42-helix outer barrel)
... ... 070 068 066 064 ... ... ... 071 069 067 065 063 ... ... 030 000 002 004 062 ... ... 031 029 001 003 005 061 ... ... 032 028 ... ... 006 060 ... 033 027 ... ... ... 007 059 034 026 ... ... ... 008 058 035 025 ... ... ... ... 009 057 036 024 ... ... ... ... 010 056 037 023 ... ... ... 011 055 038 022 ... ... ... 012 054 ... 039 021 ... ... 013 053 ... ... 040 020 018 016 014 052 ... ... 041 019 017 015 051 ... ... 042 044 046 048 050 ... ... ... 043 045 047 049 ... ...
- Double-Ply Lid (19 helices long)
... 000 002 004 006 008 010 012 014 016 ... 037 001 003 005 007 009 011 013 015 017 ... 036 034 032 030 028 026 024 022 020 018 ... ... 035 033 031 029 027 025 023 021 019 ...
scaffold splitting
Barrel
!/usr/bin/python import string import sys import fileinput def nowhite(s): return ''.join([c for c in s if c in string.letters]) seq = '' # read in sequence for line in fileinput.input("-"): seq = seq + nowhite(line) box_1 = 96 * 32 + 72 loop = 66 box_2 = 11 + 12 + 96 * 6 + 68 box_3 = 16 + 12 + 6 * 96 + 65 box_4 = 19 + 12 + 6 * 96 + 65 box_5 = 19 + 12 + 6 * 96 + 68 box_6 = 16 + 12 + 6 * 96 + 72 box_7 = 12 + 12 + 3 * 96 box_1_seq = seq[:box_1] seq = seq[box_1:] loop_1_seq = seq[:loop] seq = seq[loop:] box_2_seq = seq[:box_2] seq = seq[box_2:] loop_2_seq = seq[:loop] seq = seq[loop:] box_3_seq = seq[:box_3] seq = seq[box_3:] loop_3_seq = seq[:loop] seq = seq[loop:] box_4_seq = seq[:box_4] seq = seq[box_4:] loop_4_seq = seq[:loop] seq = seq[loop:] box_5_seq = seq[:box_5] seq = seq[box_5:] loop_5_seq = seq[:loop] seq = seq[loop:] box_6_seq = seq[:box_6] seq = seq[box_6:] loop_6_seq = seq[:loop] seq = seq[loop:] box_7_seq = seq[:box_7] seq = seq[box_7:] extra_scaffold = seq barrel = box_1_seq + box_2_seq + box_3_seq + box_4_seq + box_5_seq + box_6_seq + box_7_seq #print out the length of each segment and its sequence barrel_file = file('barrel_scaffold.txt', 'w') print len(barrel) print barrel barrel_file.write(barrel)
Lids
#!/usr/bin/python import string import sys import fileinput def nowhite(s): return ''.join([c for c in s if c in string.letters]) seq = '' # read in sequence for line in fileinput.input("-"): seq = seq + nowhite(line) scaffold_len = 7572 lid_1 = 96 * 38 lid_2 = 96 * 38 linker_len = scaffold_len - lid_1 - lid_2 linker_1 = linker_len / 2 #store first segment up to end of lid 1 lid_1_seq = seq[:lid_1] #reset sequence to start at end of lid 1 seq = seq[lid_1:] linker_1_seq = seq[:linker_1] seq = seq[linker_1:] lid_2_seq = seq[:lid_2] seq = seq[lid_2:] #linker 2 is the rest of the scaffold linker_2_seq = seq # check to make sure linker 1 and linker 2 are the same length if(len(linker_1_seq) != len(linker_2_seq)): print 'Error: linker 1 is not the same length as linker 2' #print out the length of each segment and its sequence lid_1_file = file('lid_1_scaffold.txt', 'w') lid_2_file = file('lid_2_scaffold.txt', 'w') print len(lid_1_seq) print lid_1_seq lid_1_file.write(lid_1_seq) print len(linker_1_seq) print linker_1_seq print len(lid_2_seq) print lid_2_seq lid_2_file.write(lid_2_seq) print len(linker_2_seq) print linker_2_seq