File: primer_sec_struct_dpal_input

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PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
SEQUENCE_ID=Pick Primers as a reference
SEQUENCE_TEMPLATE=acaatattgtattggtgagatcatataagatttgatgtcaacatcttcgtaaaggtctcagattcgattctccccggtatcaatttaagtgagctaatttagcttcttaaaaaataaaatcaaacaacttttacataaactcagtgaaaacttggatataaagtatccttatactactctttagtcttgattagtctctgcaaagatatttatatgtactttgtattatcataagaacattcattgacattttaagttaatgaattactaacatgtcaactcttattctagccaacagttactttgttccctccacattctctttgaaatagtcaaacgtatccaatcatgcatgtctgttctgatcataacagcaaaagcatgtgtatagaaaattgatagttgaattagagtcattttccataaaaaaatattcaataagtgtgacattatttttcgtatgaattaatccattttttgctgatttgagattctttctttctttgcttcttgctttccttcatcagccattttttttgttttctctttctctctctcttcttgattcaatgaatctcaaaaatggattactattgttcattctgtttctggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatgtagctttagcttcctactatattataccatcaattcaactcagaaatatatcaaactttatgcaatcaaagattgttcttaccaattcctttgatgttataatgagctacaatagagacgtagtattcgataaatctggtcttatttcctatactagaatcaacgttccgttcccatgtgaatgtattggaggtgaatttctaggacatgtgtttgaatatacaacaaaagaaggagacgattatgatttaattgcaaatacttattacgcaagtttgacaactgttgagttattgaaaaagttcaacagctatgatccaaatcatatacctgttaaggctaag
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_NUM_RETURN=25
PRIMER_TASK=generic
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=1
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=1
=
SEQUENCE_ID=Must obtain same result as test before
SEQUENCE_TEMPLATE=acaatattgtattggtgagatcatataagatttgatgtcaacatcttcgtaaaggtctcagattcgattctccccggtatcaatttaagtgagctaatttagcttcttaaaaaataaaatcaaacaacttttacataaactcagtgaaaacttggatataaagtatccttatactactctttagtcttgattagtctctgcaaagatatttatatgtactttgtattatcataagaacattcattgacattttaagttaatgaattactaacatgtcaactcttattctagccaacagttactttgttccctccacattctctttgaaatagtcaaacgtatccaatcatgcatgtctgttctgatcataacagcaaaagcatgtgtatagaaaattgatagttgaattagagtcattttccataaaaaaatattcaataagtgtgacattatttttcgtatgaattaatccattttttgctgatttgagattctttctttctttgcttcttgctttccttcatcagccattttttttgttttctctttctctctctcttcttgattcaatgaatctcaaaaatggattactattgttcattctgtttctggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatgtagctttagcttcctactatattataccatcaattcaactcagaaatatatcaaactttatgcaatcaaagattgttcttaccaattcctttgatgttataatgagctacaatagagacgtagtattcgataaatctggtcttatttcctatactagaatcaacgttccgttcccatgtgaatgtattggaggtgaatttctaggacatgtgtttgaatatacaacaaaagaaggagacgattatgatttaattgcaaatacttattacgcaagtttgacaactgttgagttattgaaaaagttcaacagctatgatccaaatcatatacctgttaaggctaag
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_NUM_RETURN=25
PRIMER_TASK=generic
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=1
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=1
PRIMER_MUST_MATCH_THREE_PRIME=nnnnn
PRIMER_MUST_MATCH_FIVE_PRIME=nnnnn
PRIMER_INTERNAL_MUST_MATCH_THREE_PRIME=nnnnn
PRIMER_INTERNAL_MUST_MATCH_FIVE_PRIME=nnnnn
=
SEQUENCE_ID=Pick probes without G at the 3 and 5 prime end
SEQUENCE_TEMPLATE=acaatattgtattggtgagatcatataagatttgatgtcaacatcttcgtaaaggtctcagattcgattctccccggtatcaatttaagtgagctaatttagcttcttaaaaaataaaatcaaacaacttttacataaactcagtgaaaacttggatataaagtatccttatactactctttagtcttgattagtctctgcaaagatatttatatgtactttgtattatcataagaacattcattgacattttaagttaatgaattactaacatgtcaactcttattctagccaacagttactttgttccctccacattctctttgaaatagtcaaacgtatccaatcatgcatgtctgttctgatcataacagcaaaagcatgtgtatagaaaattgatagttgaattagagtcattttccataaaaaaatattcaataagtgtgacattatttttcgtatgaattaatccattttttgctgatttgagattctttctttctttgcttcttgctttccttcatcagccattttttttgttttctctttctctctctcttcttgattcaatgaatctcaaaaatggattactattgttcattctgtttctggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatgtagctttagcttcctactatattataccatcaattcaactcagaaatatatcaaactttatgcaatcaaagattgttcttaccaattcctttgatgttataatgagctacaatagagacgtagtattcgataaatctggtcttatttcctatactagaatcaacgttccgttcccatgtgaatgtattggaggtgaatttctaggacatgtgtttgaatatacaacaaaagaaggagacgattatgatttaattgcaaatacttattacgcaagtttgacaactgttgagttattgaaaaagttcaacagctatgatccaaatcatatacctgttaaggctaag
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_NUM_RETURN=25
PRIMER_TASK=generic
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=1
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=1
PRIMER_MUST_MATCH_THREE_PRIME=nnnnn
PRIMER_MUST_MATCH_FIVE_PRIME=nnnnn
PRIMER_INTERNAL_MUST_MATCH_THREE_PRIME=nnnnh
PRIMER_INTERNAL_MUST_MATCH_FIVE_PRIME=hnnnn
=
SEQUENCE_ID=Pick probes without G at 5 nucleotides the 3 and 5 prime end
SEQUENCE_TEMPLATE=acaatattgtattggtgagatcatataagatttgatgtcaacatcttcgtaaaggtctcagattcgattctccccggtatcaatttaagtgagctaatttagcttcttaaaaaataaaatcaaacaacttttacataaactcagtgaaaacttggatataaagtatccttatactactctttagtcttgattagtctctgcaaagatatttatatgtactttgtattatcataagaacattcattgacattttaagttaatgaattactaacatgtcaactcttattctagccaacagttactttgttccctccacattctctttgaaatagtcaaacgtatccaatcatgcatgtctgttctgatcataacagcaaaagcatgtgtatagaaaattgatagttgaattagagtcattttccataaaaaaatattcaataagtgtgacattatttttcgtatgaattaatccattttttgctgatttgagattctttctttctttgcttcttgctttccttcatcagccattttttttgttttctctttctctctctcttcttgattcaatgaatctcaaaaatggattactattgttcattctgtttctggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatgtagctttagcttcctactatattataccatcaattcaactcagaaatatatcaaactttatgcaatcaaagattgttcttaccaattcctttgatgttataatgagctacaatagagacgtagtattcgataaatctggtcttatttcctatactagaatcaacgttccgttcccatgtgaatgtattggaggtgaatttctaggacatgtgtttgaatatacaacaaaagaaggagacgattatgatttaattgcaaatacttattacgcaagtttgacaactgttgagttattgaaaaagttcaacagctatgatccaaatcatatacctgttaaggctaag
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_NUM_RETURN=25
PRIMER_TASK=generic
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=1
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=1
PRIMER_MUST_MATCH_THREE_PRIME=nnnnn
PRIMER_MUST_MATCH_FIVE_PRIME=nnnnn
PRIMER_INTERNAL_MUST_MATCH_THREE_PRIME=hhhhh
PRIMER_INTERNAL_MUST_MATCH_FIVE_PRIME=hhhhh
=
SEQUENCE_ID=Primers must end in AG
SEQUENCE_TEMPLATE=acaatattgtattggtgagatcatataagatttgatgtcaacatcttcgtaaaggtctcagattcgattctccccggtatcaatttaagtgagctaatttagcttcttaaaaaataaaatcaaacaacttttacataaactcagtgaaaacttggatataaagtatccttatactactctttagtcttgattagtctctgcaaagatatttatatgtactttgtattatcataagaacattcattgacattttaagttaatgaattactaacatgtcaactcttattctagccaacagttactttgttccctccacattctctttgaaatagtcaaacgtatccaatcatgcatgtctgttctgatcataacagcaaaagcatgtgtatagaaaattgatagttgaattagagtcattttccataaaaaaatattcaataagtgtgacattatttttcgtatgaattaatccattttttgctgatttgagattctttctttctttgcttcttgctttccttcatcagccattttttttgttttctctttctctctctcttcttgattcaatgaatctcaaaaatggattactattgttcattctgtttctggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatgtagctttagcttcctactatattataccatcaattcaactcagaaatatatcaaactttatgcaatcaaagattgttcttaccaattcctttgatgttataatgagctacaatagagacgtagtattcgataaatctggtcttatttcctatactagaatcaacgttccgttcccatgtgaatgtattggaggtgaatttctaggacatgtgtttgaatatacaacaaaagaaggagacgattatgatttaattgcaaatacttattacgcaagtttgacaactgttgagttattgaaaaagttcaacagctatgatccaaatcatatacctgttaaggctaag
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_NUM_RETURN=25
PRIMER_TASK=generic
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=1
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=1
PRIMER_MUST_MATCH_THREE_PRIME=nnnAG
PRIMER_MUST_MATCH_FIVE_PRIME=nnnnn
=