Alignment+with+whole+plasmid+070512

code reverse_primer pcomb              AGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTG 60 reverse forward

reverse_primer pcomb              GCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTA 120 reverse forward

reverse_primer pcomb              GCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGG 180 reverse forward

reverse_primer pcomb              AATTGTGAGCGGATAACAATTGAATTCAGGAGGAATTTAAAATGAAAAAGACAGCTATCG 240 reverse forward

reverse_primer pcomb              CGATTGCAGTGGCACTGGCTGGTTTCGCTACCGTGGCCCAGGCGGCCGAGCTCGCCATGG 300 reverse forward

reverse_primer pcomb              CTGGTTGGGCAGCGAGTAATAACAATCCAGCGGCTGCCGTAGGCAATAGGTATTTCATTA 360 reverse forward

reverse_primer pcomb              TGACTGTCTCCTTGGCGACTAGCTAGTTTAGAATTCGTAATCATGGTCATAGCTGTTTCC 420 reverse forward

reverse_primer pcomb              TGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTG 480 reverse forward

reverse_primer pcomb              TAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCC 540 reverse forward

reverse_primer pcomb              CGCTTTCCAGTCGGGAAACCTGTCGTGTTACTAATGATGGTGATGGTGATGGCTAGTTTT 600 reverse forward

reverse_primer pcomb              GTCACAAGATTTGGGCTCAACTTTCTTGTCCACCTTGGTGTTGCTGGGCTTGTGATTCAC 660 reverse forward

reverse_primer pcomb              GTTGCAGATGTAGGTCTGGGTGCCCAAGCTGCTGGAGGGCACGGTCACCACGCTGCTGAG 720 reverse forward

reverse_primer pcomb              GGAGTAGAGTCCTGAGGACTGTAGGACAGCCGGGAAGGTGTGCACGCCGCTGGTCAGGGC 780 reverse forward

reverse_primer pcomb              GCCTGAGTTCCACGACACCGTCGCCGGTTCGGGGAAGTAGTCCTTGACCAGGCAGCCCAG 840 reverse forward

reverse_primer pcomb              GGCCGCTGTGCCCCCAGAGGTGCTCTTGGAGGAGGGTGCCAGGGGGAAGACCGATGGGCC 900 reverse forward

reverse_primer pcomb              CTTGGTGGAGGCTGCGGAGACGGTGACCGTGGTACCAGCAGAAACCTGGCCAGGCTCCCA 960 reverse forward

reverse_primer pcomb              GGCTCCTCATCTATGGTACATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCA 1020 reverse forward

reverse_primer pcomb              GTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAG 1080 reverse forward

reverse_primer pcomb              TGTACTACTGTCAGCAGTATGGTGGCTCACCGTGGTTCGGCCAAGGGACCAAGGTGGAAC 1140 reverse forward

reverse_primer pcomb              TCAAACGAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTTGA 1200 reverse forward

reverse_primer pcomb              AATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAAAG 1260 reverse forward

reverse_primer pcomb              TACAGTGGAAGGTGGATAACGCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGC 1320 reverse forward

reverse_primer pcomb              AGGACAGCAAGGACAGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGACT 1380 reverse forward

reverse_primer pcomb              ACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGGCCTGAGCTTGCCCGTCA 1440 reverse forward

reverse_primer pcomb              CAAAGAGCTTCAACAGGGGAGAGTGTTAGTTCTAGATAATTAATTAGGAGGAATTTAAAA 1500 reverse forward

reverse_primer pcomb              TGAAATACCTATTGCCTACGGCAGCCGCTGGATTGTTATTACTCGCTGCCCAACCAGCCA 1560 reverse forward

reverse_primer pcomb              TGGCCGAGGTGCAGCTGCTCGAGATGAGCGATAAAATTATTCACCTGACTGACGACAGTT 1620 reverse forward

reverse_primer pcomb              TTGACACGGATGTACTCAAAGCGGACGGGGCGATCCTCGTCGATTTCTGGGCAGAGTGGT 1680 reverse forward

reverse_primer pcomb              GCGGTCCGTGCAAAATGATCGCCCCGATTCTGGATGAAATCGCTGACGAATATCAGGGCA 1740 reverse forward

reverse_primer pcomb              AACTGACCGTTGCAAAACTGAACATCGATCAAAACCCTGGCACTGCGCCGAAATATGGCA 1800 reverse forward

reverse_primer pcomb              TCCGTGGTATCCCGACTCTGCTGCTGTTCAAAAACGGTGAAGTGGCGGCAACCAAAGTGG 1860 reverse forward            ---NNNNNNNNG 9

reverse_primer pcomb              GTGCACTGTCTAAAGGTCAGTTGAAAGAGTTCCTCGACGCTAACCTGGCGTACCCGTACG 1920 reverse forward            NNGNNNTGNCTAN-GGNCAGTTGAA-GAGTTCCTCGACGCTAACCTGGCGTACCCGTACG 67

reverse_primer pcomb              ACGTTCCGGACTACGGTTCTACTAG-TGGCCAG--GCCGGCCAGCACCATCACCAT 1973 reverse            ---NNTTNNTAGCACCNTCACCAT 21 forward            ACGTTCCGGACTACGGTTCTACTAGGCGGCCGCTTTTTTTTTTTTTAGCACCATCACCAT 127

reverse_primer pcomb              CACCATGGC-GCATACCCGTACGACGTTCCGGACTACGCTTCTTAGGAGGGTGGTGGCTC 2032 reverse            CANCATGGNCGCATACCCGTACGACGTTCCGGACTACGCTTCTTAGGAGGGTGGTGGCTC 81 forward            CACCATGGC-GCATACCCGTACGACGTTCCGGACTACGCTTCTTAGGAGGGTGGTGGCTC 186

reverse_primer pcomb              TGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGG 2092 reverse            TGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGG 141 forward            TGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGG 246

reverse_primer pcomb              TTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAA 2152 reverse            TTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAA 201 forward            TTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAA 306

reverse_primer pcomb              TGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGA 2212 reverse            TGCCGATGAAAACGTGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGA 261 forward            TGCCGATGAAAACGTGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGA 366

reverse_primer pcomb              TTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGG 2272 reverse            TTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGG 321 forward            TTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGG 426

reverse_primer pcomb              TGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAA 2332 reverse            TGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAA 381 forward            TGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAA 486

reverse_primer pcomb              TTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATG 2392 reverse            TTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATG 441 forward            TTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATG 546

reverse_primer pcomb              TCGCCCTTTTGTCTTTAGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAAT 2452 reverse            TCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAAT 501 forward            TCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAAT 606

reverse_primer pcomb              AAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATT 2512 reverse            AAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATT 561 forward            AAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATT 666

reverse_primer     TTGCTAACATACTGCGTAATAAGGAG-- 26 pcomb              TTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAAGCTAGCTAATTAATTTAAGC 2572 reverse            TTCTACGTTTGCTAACATACTGCGTAATAAGGAGGCC---GCAGATCTGCTCT--C 612 forward            TTCTACGTTTGCTAACATACTGCGTAATAAGGAGGCC---GCAGATCTGCTCT--C 717 **************************

reverse_primer     -GCCGCAGATCTGGGAAATTG--- 46 pcomb              GGCCGCAGATCTGGGAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTT 2632 reverse            TGAGGAGGATCTGGGAAATNGTAAGCGTTAATATTTTNTTAAAATNCGCNNNNAANNNNN 672 forward            TGANGAGGATCTGGGAAATTGTAAGCGTTAATATTTTGNTAAAATTCGCGTTAAATTTTT 777 * *  ************ *

reverse_primer pcomb              GTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAAATCCCTTATAAATCAA 2692 reverse            NNNNNN-- 678 forward            GTTAANTCAGCTCATTTTTTAACCAATNNNCCGAAATCGNNAAA-TCCCTTATAAATCAA 836

reverse_primer pcomb              AAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAA 2752 reverse forward            A-GAATANACCGANATANGGTTNAGTGTTGTNCN-GTTTGNNACNN-ANNCCACTATNNN 893

reverse_primer pcomb              AGAACGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTATCAGGGCGATGGCCCACTAC 2812 reverse forward            N-AANGTGGANTCCAANNGNNNNNNNNNNANN-CNGTCTATCNNGNNNANGGCNNNNAN- 950

reverse_primer pcomb              GTGAACCATCACCCTAATCAAGTTTTTTGGGGTCGAGGTGCCGTAAAGCACTAAATCGGA 2872 reverse forward

reverse_primer pcomb              ACCCTAAAGGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCGGCGAACGTGGCGAGAA 2932 reverse forward

reverse_primer pcomb              AGGAAGGGAAGAAAGCGAAAGGAGCGGGCGCTAGGGCGCTGGCAAGTGTAGCGGTCACGC 2992 reverse forward

reverse_primer pcomb              TGCGCGTAACCACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCGCGTCAGGTGGCA 3052 reverse forward

reverse_primer pcomb              CTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATA 3112 reverse forward

reverse_primer pcomb              TGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGA 3172 reverse forward

reverse_primer pcomb              GTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTC 3232 reverse forward

reverse_primer pcomb              CTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTG 3292 reverse forward

reverse_primer pcomb              CACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCC 3352 reverse forward

reverse_primer pcomb              CCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTAT 3412 reverse forward

reverse_primer pcomb              CCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACT 3472 reverse forward

reverse_primer pcomb              TGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAAT 3532 reverse forward

reverse_primer pcomb              TATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGA 3592 reverse forward

reverse_primer pcomb              TCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCC 3652 reverse forward

reverse_primer pcomb              TTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGA 3712 reverse forward

reverse_primer pcomb              TGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAG 3772 reverse forward

reverse_primer pcomb              CTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGC 3832 reverse forward

reverse_primer pcomb              GCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGT 3892 reverse forward

reverse_primer pcomb              CTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCT 3952 reverse forward

reverse_primer pcomb              ACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTG 4012 reverse forward

reverse_primer pcomb              CCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTG 4072 reverse forward

reverse_primer pcomb              ATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCA 4132 reverse forward

reverse_primer pcomb              TGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGA 4192 reverse forward

reverse_primer pcomb              TCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAA 4252 reverse forward

reverse_primer pcomb              AACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGA 4312 reverse forward

reverse_primer pcomb              AGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGT 4372 reverse forward

reverse_primer pcomb              TAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGT 4432 reverse forward

reverse_primer pcomb              TACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGAT 4492 reverse forward

reverse_primer pcomb              AGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCT 4552 reverse forward

reverse_primer pcomb              TGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCA 4612 reverse forward

reverse_primer pcomb              CGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAG 4672 reverse forward

reverse_primer pcomb              AGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTC 4732 reverse forward

reverse_primer pcomb              GCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGA 4792 reverse forward

reverse_primer pcomb              AAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACA 4852 reverse forward

reverse_primer pcomb              TGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAG 4912 reverse forward

reverse_primer pcomb              CTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGG 4972 reverse forward

reverse_primer     - pcomb              A 4973 reverse            - forward            - code