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<?xml version="1.0" ?>
<multi-test>
<load-document index="doc" url="primer3/primer3_xml/sec_struct_thal/check_primers_th_2.fa" io="local_file" format="fasta"/>
<find-object-by-name index="seq" doc="doc" name="check_primers_th_2" type="OT_SEQUENCE"/>
<plugin_primer_3 sequence="seq">
<plugin_primer_3_in
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT="1"
PRIMER_FIRST_BASE_INDEX="1"
PRIMER_EXPLAIN_FLAG="1"
PRIMER_MISPRIMING_LIBRARY="humrep_and_simple.txt"
PRIMER_PRODUCT_SIZE_RANGE="75-100"
PRIMER_NUM_RETURN="1"
PRIMER_MAX_END_STABILITY="9.0"
PRIMER_MAX_LIBRARY_MISPRIMING="12.00"
PRIMER_PAIR_MAX_LIBRARY_MISPRIMING="20.00"
PRIMER_MAX_SELF_ANY_TH="47.00"
PRIMER_MAX_SELF_END_TH="47.00"
PRIMER_MAX_HAIRPIN_TH="47.0"
PRIMER_PAIR_MAX_COMPL_ANY_TH="47.00"
PRIMER_PAIR_MAX_COMPL_END_TH="47.00"
PRIMER_MAX_TEMPLATE_MISPRIMING_TH="47.00"
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH="80.00"
PRIMER_MIN_TM="57.0"
PRIMER_OPT_TM="59.0"
PRIMER_MAX_TM="63.0"
PRIMER_PAIR_MAX_DIFF_TM="5.0"
PRIMER_TM_FORMULA="1"
PRIMER_SALT_MONOVALENT="50.0"
PRIMER_SALT_CORRECTIONS="1"
PRIMER_SALT_DIVALENT="1.5"
PRIMER_DNTP_CONC="0.6"
PRIMER_DNA_CONC="50.0"
PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT="1"
PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT="1"
PRIMER_LOWERCASE_MASKING="0"
PRIMER_MIN_GC="20.0"
PRIMER_MAX_GC="80.0"
PRIMER_MAX_NS_ACCEPTED="0"
PRIMER_MAX_POLY_X="5"
PRIMER_OUTSIDE_PENALTY="0"
PRIMER_GC_CLAMP="0"
PRIMER_LIBERAL_BASE="1"
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS="0"
PRIMER_WT_TM_LT="1.0"
PRIMER_WT_TM_GT="1.0"
PRIMER_WT_SIZE_LT="1.0"
PRIMER_WT_SIZE_GT="1.0"
PRIMER_WT_GC_PERCENT_LT="0.0"
PRIMER_WT_GC_PERCENT_GT="0.0"
PRIMER_WT_SELF_ANY_TH="0.0"
PRIMER_WT_SELF_END_TH="0.0"
PRIMER_WT_HAIRPIN_TH="0.0"
PRIMER_WT_NUM_NS="0.0"
PRIMER_WT_LIBRARY_MISPRIMING="0.0"
PRIMER_WT_SEQ_QUAL="0.0"
PRIMER_WT_END_QUAL="0.0"
PRIMER_WT_POS_PENALTY="0.0"
PRIMER_WT_END_STABILITY="0.0"
PRIMER_WT_TEMPLATE_MISPRIMING_TH="0.0"
PRIMER_PAIR_WT_PRODUCT_SIZE_LT="0.0"
PRIMER_PAIR_WT_PRODUCT_SIZE_GT="0.0"
PRIMER_PAIR_WT_PRODUCT_TM_LT="0.0"
PRIMER_PAIR_WT_PRODUCT_TM_GT="0.0"
PRIMER_PAIR_WT_DIFF_TM="0.0"
PRIMER_PAIR_WT_COMPL_ANY_TH="0.0"
PRIMER_PAIR_WT_COMPL_END_TH="0.0"
PRIMER_PAIR_WT_LIBRARY_MISPRIMING="0.0"
PRIMER_PAIR_WT_PR_PENALTY="1.0"
PRIMER_PAIR_WT_IO_PENALTY="0.0"
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING="0.0"
PRIMER_PICK_ANYWAY="0"
PRIMER_TASK="check_primers"
PRIMER_OPT_SIZE="20"
PRIMER_MIN_SIZE="19"
PRIMER_MAX_SIZE="21"
PRIMER_PICK_LEFT_PRIMER="1"
PRIMER_PICK_RIGHT_PRIMER="1"
PRIMER_PICK_INTERNAL_OLIGO="0"
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE="-1"
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE="-1"
SEQUENCE_PRIMER="TGACCTGATAGAAACGCCAA"
SEQUENCE_PRIMER_REVCOMP="TGCTTTGCGTTTTGGAATAG"/>
<plugin_primer_3_out
PRIMER_LEFT_NUM_RETURNED="0"
PRIMER_RIGHT_NUM_RETURNED="0"
PRIMER_INTERNAL_NUM_RETURNED="0"
PRIMER_PAIR_NUM_RETURNED="0"/>
</plugin_primer_3>
</multi-test>
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