Elements.gil

sequence Neonothopanus_Luc
{
    from Unoptimized
    {
        ATGAATCTTCCGTCTTTCGTCCAACGTCTCTCCACAGCAAGCAGTCGCAGTATAGCGATTACTTGCGTAGTTGTCCTTGCCTCTGCAATCGCCTTTCCCTTCATCCGCAGAGACTACCAGACCTTCCTGGAAGTGGGACCCTCGTACGCCCCGCAGAACTTTAGAGGATACATCATCGTCTGTGTCCTCTCGTTGTTCCGCCAAGAACAAAAAGGACTCGAAATCTACGATCGGCTCCCAGAGAAACGAAGGTGGTTGTCCGACCTTCCCTTTCGTGACGGGCCCAGACCCAGCATCACAAGCCATATCATTCAACGACAGCGTACCCAACTAGTTGATCCGGACTTCGCTACCCAGGAGCTCATAGGCAAAGTCATCCCTCGTGTGCAAGCACGACACACCGACAAAACATTCCTCAGCACCTCCAAATTCGAATTTCACGCAAAAGCCATATTCCTCCTGCCTTCCATCCCAATCAACGACCCTCTGAACGTTCCAAGCCACGACACTGTCCGACGAACGAAGCGCGAGATCGCGCATATGCATGATTATCATGATTGCACTCTTCACATCGCTCTCGCTGCTCAGGACGGAAAGGAGGTTTTGAAGAAGGGATGGGGGCAACGACACCCACTCGCTGGACCTGGAGTGCCCGGCCCACCGACGGAGTGGACGTTTCTCTATGCGCCTCGAAACGAAGAAGAGGTTCGAGTTGTGGAGATGATTATTGAGGCTGCCATAGGTTACATGACGAATGATCCGGCAGGAAAAGTTGTAGAAGCCACTGGAAAG
    }
}

sequence Neonothopanus_CPH
{
    from Unoptimized
    {
        ATGGCGCCGATTTTGACAGTGAGTTCCAGTTCAATGGTGCTGAATAGCTCAAAACAGGCTATATTGAATATTTCTGAATATCACCAGCCCTGGACTCGTCTCATTCGATTTGTAGCCGTTGAGACGTCACTCGTGCATATTGGTGAACCCATCGAGGTGACTTTGGACGTCGGGCAGGCAAAATGTGAAGGCAAGACGATCAAAGCGTACGAGATTATTGGATCAGGGTCGGCCTTGGACCTCTCAGCTCAGGTATCGAAGAATGTGCTAACCGTAAAGGAACTCTTGATGCCGCTTTCGAGAGAAGAGGTCAAGACTGTGCGGTGCTTGGGACTGAACTATTTTACTCATGCTTCCACCGGGCGCCCGCTGTCGACTAGATTACCGACTTTGTTCTATAAGCCAGTGACTTCACTCATCGGACCTGAGGCGTTCATTAATATTCCTTCCGCTGTTCAACCACCGAAGGAGCATCAGTCCGATTATGAAGCGGAGTTGGTAATTATTATTGGGAGAGCGGCGAAGGATGTACCGGAAGAGGAGGCTTTGAATTATGTTTTGGGATACACCGCCGCCAACGACATTTCATTTAGGAAATATCAATTTGCAGTTTCCCAGTGGTGTTTTTCGAAAGGTTTCGATAATACAAACCCAATCGGTCCGTGCATCGTTTCCGCATCTTCCATTCCGAACCCGCAAGACATCCAGATCCAATGCAAACTGAACGGGAATGTCGTTCAGAATGGAAACACCAGTGATCAAATTTTTAATATCAAGAAAACAGTCGCTTTTTTGTCGCAAGGAACAACACTTGAGTCAGGATCAATCATCCTGACCGGTACGCCTGGCGGAGTGGGATTTGTGCGCGATCCACCGCTTTACCTTAAAGATGGAGATGAAGTAGTGACTTGGATTGGAAGTGGGGTTGGAAGTTTAGTCAACGTAGTAAAAGAAGAGAAGACT
    }
}

sequence Neonothopanus_HISPS
{
    from Unoptimized
    {
        ATGAATTCCAAAGTGAATCTTCCCTCCACTTTGCTTGATGTTTTCCTCGAGATCGCTGGCGAGCCATCTACCGCTTCGCGTGATGTTTTGGAATGTGGCGAGCACAGATGGACTTACCAGCAGCTTGACGTTGTTTCATCTGCTTTAGCCCAGCATCTCAAGTACACTGTCGGTCTATCTCCTACAGTCGCAGTGATCAGCGAAAATCATCCTTATGTTTTTGCCTTGATCCTGGCTGTGTGGAAAGTTGGGGGCATTTTCGCGCCCCTCGACGCACATGCTCCTGCTGAGTTGGTAGCTGGCATGTTAAGCATAATCTCTCCTTCGTGCTTAGTACTTCAGAGCACAGATGTAGCTAATCAAACTCTTGCGTGTGATCTCGATATTCCTGTTGAGGTATTCCACTCGCGTCAATCCACTATTCCTGAACTAAACAAGAAATATCTCACCGATTCTGGGTTACCGGCGGGTTTTCCGCTCTCAGATTCAAACAAACCGGCTCTGTATCTCTTCACCTCGTCTGCCACTTCTCGGAGCAATCTTAAATGCGTGCCTCTCACTCACGCTTTCATCCTGAGCAATAGCCTCTCGAAACGCGCATGGTGCCAACGTATGCGGCCAGAGACAGACTTCGATGGCATACGCGTTCTTGGATGGGCTCCATGGTCTCATGTCTTGGCGCACATGCAGGACATCGGGCCCGTCACTTTACTCAATGCTGGATGCTACGTCTTTGCTACTATCCCTTCCTCGTACCCCACGGATGTGCAGAGTGACAGCAATTTGATATCTCATGTCGCAAATGCTATCATACACAAGGGTGTAAAATCGTTTGCTTGTCTCCCTTTTGTACTCGGAGGGCTGAAAGCATTATGCGAGTCCAAGCCATCCGTCAAAGCAGATCTACAGGTCGAAGAGCAAGCTCAGCTTTTGATCTCTCTAAGGCGCATGGAAATTCTTGAATGCGGAGGTGCGATGCTCGAAGCGAATGTTGCGTCTTGGGCTATCGAGAATCATATTCCGGTCTCTATTGGTATCGGTATGACAGAAACTGGTGGCGCGCTTTTCGCTGGACCTGTTCAGGATATCCGGACCGGTTTTTCTGCGGACAATAAATTCATCAAGGACGCTACCTACTTCCTAGTTGCAAATGGAGATGAATCTGGGAACGATGTAACTGAAGGGGAGCTAGTTGTGAAAAGTAAAATGCTCCCGCGAGGCTATCTTGGCTACAATGATTCTTCCTTTTCCGTTGACGATGACGGATTGGTTACGTTCAAGACAGGCGACAGATACAGTGTTACACGCGACGGAAGATTCTCTTGGCTAGGCAGGAATACTGATTTCATTCAGATGACTAGTGGAGAGACATTAGATCCCCGACCTGTCGAGAGTTCGCTCTGCCAAAGTCCTCTCATCTCTCAAGCATGCGTTATTGGAGACAAGTTTCTCAACGGGCCTGCCACTGCTGTTTGCGCGATCGTTGAGCTTGAGCCGACAATGGTAGAAACGGGAGAGGCTAACTCGCGGGACATAGTCCAAGTCTTTGCACCCATCAACCGAGACCTGCCTCCTCCTTTAAGGATAGCATGGTCGCACATTTTAATTCTCAAGCATTCCGAGAAGATACCGATGACGAAGAAGGGAACGATTTTCCGTAAGAAGATTGAGCAGATGTTTGGCGCTGCATTGGGCATTGCTTCCATCCCTACAAACAGTGTCAATGGATCCGTTGGCTCCGGAGAAGAGCCTCAAGCTACTGCAGATGAGACTGTTCTACAAGATGAACTATCAAATACCGTGAAGAAAATAATCAGCCGTGTTCTAGGAGTAACTGATGAGGAATTGCTTTGGACACTGTCATTCGCAGAGCTGGGAATGACCTCAACACTGGCTATTCGTATCGTAAACGAGCTGAACGAAACTCTCGTTGGGGGCGATCTCCCTATCAATGCTTGCTACATTTATGTCGACCTTTCCTCTCTGAGCAAGGCTGTGTATGCGAAACTGGCTCATCTCGAGCTGTCAGATCATGTTCCTGAGCTCAAACAAGCTCCCTTCAAGTCTTCTGGCGGGAAAGAGATTGTCATTGTCGGCCAAGCGTTTCGTCTACCCGGCTCAATCAATGACGTTGCCTCTCTTCGGGATGCATTCCTAGCAAGACAGACATCGTCCATCATCGCTGGAATACCTTCCGATCGCTGGGACCATGCCAGCTTCTATCCCAAGGACATATGTTTCGACAAGGCTGGTCTTGTGGATATAGCTCATTATGATCATAGCTTCTTCGGAATCACAGCAACGGAAGCGCTCCATCTGTCTCCAACCATGCGTCTTGCACTGGAAGTTTCGTTTGAGGCGCTTGAGAATGCTAATATCCCAACGTCGCGATTGAAAGGCTCGCAGACGGCAGTTTATGTTGCAACAACAGATGACGGATTTGAGACCCTGTTGAATGCTGAGGCTGGCTATGAAGCTTATACACGGTTTTATGGTACTGGTCGGGCAGCAAGTACGGCGAGTGGGCGCATAAGCTATCTTCTTGATATACATGGACCCTCCGTCACTATTGACACGGCATGCAGTGGTGGAGTTGTTTGTATCGATCAAGCAATCAACTATTTACAATCGTCGAGTTCAGCGGACACCGCTATCGTGTTCCTTTCTGCTCAAGGGATGGTCTCCCCGAGGGGACGATGTGCGACATTTACGGCTGATGCTGACGGCTATGTCCCTTCTGAGGGTGCAGTTGCTTTCGTATTGAAAACTCGCGAAGCCGCTATACGCGACAAAGACAACATTCTCGCTACAATCAAAGCGACACAGATTTCGCACAACGGCCGCTCACAAGGACTTGTAGCACCGAACGTAAACTCGCAAGTTGACCTTCATCGTTCGTTGCTCGAGAAAGCTCGTCTTAGTCCTGCTGATGTCCAATTCATTGAAGCTCATGGGACAGGAACGTCATTGGGAGATCTCTCAGAGATTCAAGCTATAAACGCTGCTTACACTTCCTCTCAGCCACGTACGACCGGCCCACTCATAGTCAGCGCTTCCAAGACTGTCGTTGGCCATACCGAACCAGCTGGTCCTTTGGTTGGTATGTTGTCGGTCTTGCTGTCTTTCCAGGAAGGCGCAGTCCCTGGTCTCGCTCATCTTACCACACGTAACCTCAATCCTACGTTGGACTATTCTTCAGTGCCGCTTCTCATTCCCTCTGAACCTGTTCGTCTACAAACACCAAAGCCTTATAGAGCTGCCGTAATGTCCTACGGCTTTTCGGGTACCCTGGCCGGCCTCGTTCTAGAGAGCCCTGACGAACGTAGCTCAGAAGAAGAGCCGCCTGATGACAAGCCGATGCTGTTCGTCGTTAGCGCAAAGACACACACGGCACTAATTGAATACCTGCAACGGTATCTCGAGTTCCTCTTACATGCGAATCCCCGCGATTTCTGTGATATCTGCTACACAAGCTGTGTCGGGAGGGAACACTATAGATATCGGTTTGCTTGTGTTGCAAATGACATGGAAGACCTCATTGGCCAACTTCAAAGACGTTTGTCTAGCAAGTTACCATCGAAGCCGCTATACAAACGCGGTGCTCTGGCCTTTGCGTTTTCTGGACAGGGGACACAGTTTCAAGGAATGGCGACAGATCTTGCGAAGAGGTACTCTGGCTTCCGAAAAATCGTTTCCGGACTCGCAAAGAGTGCTGGCGAGCTCTCGGGTTACGCTATTGACCGTTATCTTCTCGCGTATGACGTTGGTAGCAGTATTGCTACTCCTAATAGTGAGGTGGACCAGATCTGCATTTTCGTATACCAATGCTCTGTCCTTCGCTGGTTGGGGAGTATTGGAATTAAACCAAACGTGGTAATCGGCCATAGCCTTGGAGAGATTTCGGCTTCTGTGGCGGCAGGGGCACTTTCTCTTGACATTGCTCTGGATCTTGTCATCTCACGAGCTGGGTTGTTGCGCCCCTCGACAGATGTTCCTGCGGGAATGGCTGCTGTGGCCGCTTCACAACAGGAGGTCATTGAGTTGATTGATGCGCTGGACCCCGACAAGGCAAATTCGCTCAGTGTTTCGGTTATAAATGGACCTCAAAATATCGTTGTGTCAGGCGCTTCAGCAGCTATTGAGAGAATGGTCGCTTCTGCGAAGGAGAAGAAGATCAAAGCTTCTGTTCTGAATATTAGCCAAGCTTTTCACAGTTCGTATGTTGACAGTGCCATTACGGGTCTTCGAGCTTGGTCAGAAAAACATATTTCCTCAGCGATACCACTGCAGATTCCGCTGTATTCGACATTGCTGGGAGCTCGGATATCAAAGGGCCAAAAACTGAACCCAGACCACTGGGTCGACCACGCACGGAAGCCCGTACAGTTCGCACAAGCAGCTACGGCGATGAAAGAAACCTTCACCGGAGTCATCATGGATATCGGACCCCAAGCAGTAGCATGGTCACTTCTGCTTGCAAACGGACTCACATCCGTAACCGCGCTTGCTGCGAAGAGAGGGAGGAGTCAGCAGGTGGCTTTCTTGAGCGCCTTGGCGGAGTTGTATCAGGATTATGGCATTGTTCCTGATTTTGTGGCGCTTTATGCTCAGGAGGAGGAAATAGACAAGTTGAGGAAGACGGATATTTTGACATATCCGTTTCAGCGTGTTAGGAGGTATCCGAGTTTTATACCTTCAAGGCGTGTGAGAGGTGGAGAAATTCCTTCGAGCCATCCCAGCGAGTCTGCGACGTTGGAGAACACGAATGAGGGTACGGCTTTGCGTGCTGAGTCGAGGGTGTTGTGCAGGGAGGATCTGCATGATAGCATCGTTACCTCTGTGAAGGATGTTCTAGAGCTCAAACCAAATGAAGATCTAGATTTGTCTGAAAGCCTGAACGCGCTTGGTGTGGACTCTATAATGTTTGCTCAGTTAAGGAAACGTATTGGGGAGGGACTCGGGTTGAGTATCCCGACAGTGTTCCTTTCGGATGCCTTTTCTATTAATGAGATGGTTAATAATCTTATGGAACAGGCGGAGACGCCTGGTGAAGAGGGCGTAATGCAGGAGAAT
    }
}

sequence Neonothopanus_NNH3H
{
    from Unoptimized
    {
        ATGGCACTATCTGAGAGTCCTTTGAACGTCTTGATAGTAGGAGCGGGGCTCGGGGGGCTTGCTGCTGCCATAGCACTACGTCGTCAAGGGCATATCGTGAAAATATTCGATTCCTCCAGTTTCAAAACCGAACTTGGTGCAGGACTTGCTGTCCCGCCTAATACCCTGCGTAGTCTGCAGGAACTCGGGTGCAGTGTCGAGAACCTCAATGCTGTGGATAATCTTTGCTTCACTGCGATGGGGTATGACGGGAGTGTAGGAATGATGAACAATATGACCGACTATCGAGAGGCGTACGGTCATCCTTGGGTCATGGTTCACCGTGTCGACTTGCATAATGAGCTGAAGCGCGTGGCGCTTGATCCAGACGGCCTCGGACCTCCTGCAACTTTGCATCTCAACCATCGTGTCACATTCTGCGACATCGACTCTTGCACTGTCACGTTCGCTAATGGGACTTCTAAATCGGCAGATCTTATCGTAGGCGCAGACGGTATACGCTCTACCATTCGCAAGTTCATTCTTGGAGAAGACGTCGTTATACCCGCGTCAGGAATAGCAGGGTTTCGATGGCTTGTGCAAGCTGACGCGCTGGATCCGTATCCTGAACTCGACTGGATCGTGAAGAACCCTCCTCTAGGAGCCCGACTGATTTCCGCTCCTAGGAATCAACAGTCTACTGATAGGCGCACTATCATCATCTATGCGTGTCGTAGCGGCACCATGGTCAACGTACTCGCAGTACATGATGATGATCGTGACCAGAACGCCGTAGATTGGAGTGCACCAGCTTCCAAAGATGATTTATTCCACATCTTCCACGACTACCACCCACGATTCCAGCGGCTTCTGGAGCTGGCGCAAGATATCAATCTCTGGCAAATGCGTGTTGTTCCTGTTCTGAAACAATGGGTTAACAAACGTGTTTGCTTGTTAGGAGATGCGGCACACGCTTCTTTACCTACATTAGGGCAGGGATTTGGTATGGGTCTAGAAGATGCCGTAGCACTGGGTACGCTTCTTCCAAAGGGGGCCACAGTATCTCAGATCGAGAGCCGACTCGCGGTGTATGAAATTCTGCGCAAGGAGCGTGCTGAATTTGTTTCGGCTGAGTCATATGAAGAGCAGTACGTTCCAGAAAAACGCGGGCTTTACTTAAGATCGAAGGAATTGCGCGACAGTGTCATGGGTTACGATATTAAAATGGAGAGCGAGAAGGTTCTCGTGGCATTACTTAGCGGTTCTTCA
    }
}

operation Opticin
{
    ctcccccgggcaccactgtctaacccaagccccagttcagacagcctcc

    $InnerCode

    ACCAGAGTCCC
}

operation OpticinWithNearby
{
    ggcgctctaggtgagggtgaagtgcctcatttccacctatttttatctttggattctggctatgaagctgaagccttgtcactctctggctggagaaagaagctgcaaagacaagctctatctctccatatcccccgactccagccttctctgaggactcagaatctgagggatggggccccttccttgcaggggatggcactccctgttcctcaaagatgtggccttatcaggagagtggacaaggaaaagaaagaaggagctgacagagtaagaggagagagagcaggagctggaggtggggggtgaagcggaaggtggggggagaattctcttttgtcaaatacaggaatggggcaggggaccccctgaggaaagaggaggggaaacagctggacatcagaaggaatgagaagtctgattggtcgcaggcctggccaactccttgccctcccccgggcaccactgtctaacccaagccccagttcagacagcctcc

    $InnerCode

    ACCAGAGTCCCCACCTTTCTGGAAGCTGCAGGGCTCTCCATCCAGGATCCAGAAGCATTGAAGGGGTAAGGCTCAAGGTTGAGGCCTCTGGCCATCGGTGC
}

//Detects Per1 and cuts TRAP2's AA
sequence TRAPzyme1
{
    TCCTCTCAGGCAGAAGACGAACAAAAAGGGGAAAGCTCAAAAGTGAGAGGAGTCGGAGGG
}

//PolyA sequence that shouldn't bind to anything
sequence PolyA40
{
    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
}

//Antiattenuator sequence for TRAPzyme 2
sequence TRAPzyme2_AA
{
    GGGGAGGGAGGGCCGGAGTA
}

sequence TRAPzyme2
{
    TACTCCGGCCCTCCCTCCCCTTGCAAAGCCGGAAAGCCGGAGTAGTCAGGCAA
}

operation RaxPromoter
{
    gagggccagttggctccccgcctttagcgccgagagccccagctacccc
    $InnerCode
    GAGCCCGAACT
}

//Produced using RAX
sequence TRAPzyme3_AA
{
    GGGGAGGGAGGGAAAAAGTA
}

sequence TRAPzyme3
{
    TACTTTTTCCCTCCCTCCCCTTGCAAAGTTTTCCCTAAAAAGTAGTCAGGCAA
}

sequence DetectRAX
{
    Elements: .RaxPromoter
    {
        Elements: TRAPzyme3_AA
    }
}

operation Per1Promoter
{
    gtgcccggcattatgcaacccgcctccccgcccgcccggtggagcttcc
    $InnerCode
    ACTCGGCTGCG
}

sequence DetectPer1
{
    Elements: .Per1Promoter
    {
        TTTTTGTTCGTCTTCTGCCTGAAGAGGA
    }
}