1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
|
<?xml version="1.0" ?>
<multi-test>
<load-document index="doc" url="primer3/primer3_xml/sec_struct_thal/pick_detection_primers_th_1.fa" io="local_file" format="fasta"/>
<find-object-by-name index="seq" doc="doc" name="pick_detection_primers_th_1" 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="75-200"
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="generic"
PRIMER_OPT_SIZE="20"
PRIMER_MIN_SIZE="19"
PRIMER_MAX_SIZE="21"
SEQUENCE_INTERNAL_EXCLUDED_REGION="37,21"
SEQUENCE_TARGET="37,21"/>
<plugin_primer_3_out
PRIMER_LEFT_NUM_RETURNED="1"
PRIMER_RIGHT_NUM_RETURNED="1"
PRIMER_INTERNAL_NUM_RETURNED="0"
PRIMER_PAIR_NUM_RETURNED="1"
PRIMER_PAIR_0_PENALTY="1.608735"
PRIMER_LEFT_0_PENALTY="1.001812"
PRIMER_RIGHT_0_PENALTY="0.606923"
PRIMER_LEFT_0_SEQUENCE="AGACATGACACTGACGATGC"
PRIMER_RIGHT_0_SEQUENCE="AGCTATCGATTTGGGTCGGG"
PRIMER_LEFT_0="10,20"
PRIMER_RIGHT_0="97,20"
PRIMER_LEFT_0_TM="57.998"
PRIMER_RIGHT_0_TM="59.607"
PRIMER_LEFT_0_GC_PERCENT="50.000"
PRIMER_RIGHT_0_GC_PERCENT="55.000"
PRIMER_LEFT_0_SELF_ANY_TH="0.00"
PRIMER_RIGHT_0_SELF_ANY_TH="1.71"
PRIMER_RIGHT_0_SELF_ANY_STUCT="Tm: 1.7&deg;C dG: -5464 cal/mol dH: -44800 cal/mol dS: -127 cal/mol*K\n 5' AGCTATCGATTTGGGTCGGG 3'\n ||||||\n3' GGGCTGGGTTTAGCTATCGA 5'\n"
PRIMER_LEFT_0_SELF_END_TH="0.00"
PRIMER_RIGHT_0_SELF_END_TH="0.00"
PRIMER_LEFT_0_HAIRPIN_TH="0.00"
PRIMER_RIGHT_0_HAIRPIN_TH="41.74"
PRIMER_RIGHT_0_HAIRPIN_STUCT="Tm: 41.7&deg;C dG: -421 cal/mol dH: -28000 cal/mol dS: -89 cal/mol*K\n5' AGCTATCGATTTU+2510\n ||| U+2502\n 3' GGGCTGGGU+2518\n"
PRIMER_LEFT_0_LIBRARY_MISPRIMING="11.00, MER25 Older LINE1 5' end region - a consensus"
PRIMER_RIGHT_0_LIBRARY_MISPRIMING="11.00, THE1b consensus sequence"
PRIMER_PAIR_0_LIBRARY_MISPRIMING="20.00, MER25 Older LINE1 5' end region - a consensus"
PRIMER_LEFT_0_END_STABILITY="3.9100"
PRIMER_RIGHT_0_END_STABILITY="5.1400"
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH="9.4379"
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH="1.9633"
PRIMER_PAIR_0_COMPL_ANY_TH="0.00"
PRIMER_PAIR_0_COMPL_END_TH="1.96"
PRIMER_PAIR_0_COMPL_END_STUCT="Tm: 2.0&deg;C dG: -1409 cal/mol dH: -77000 cal/mol dS: -244 cal/mol*K\n5' AGCTATCGATTTGGGTCGGG 3'\n |||| | ||| |\n 3' CGTAGCAGT-CACAGTACAGA 5'\n"
PRIMER_PAIR_0_PRODUCT_SIZE="88"
PRIMER_PAIR_0_PRODUCT_TM="82.1"
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH="11.40"/>
</plugin_primer_3>
</multi-test>
|
