SEQUENCE_ID=thermod_default
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_SELF_ANY_TH=47.0
PRIMER_MAX_SELF_END_TH=47.0
PRIMER_MAX_HAIRPIN_TH=47.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=47.0
PRIMER_PAIR_MAX_COMPL_END_TH=47.0
PRIMER_PAIR_MAX_HAIRPIN_TH=47.0
PRIMER_INTERNAL_MAX_SELF_ANY_TH=47.0
PRIMER_INTERNAL_MAX_SELF_END_TH=47.0
PRIMER_INTERNAL_MAX_HAIRPIN_TH=47.0
PRIMER_MAX_TEMPLATE_MISPRIMING_TH=47.0
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=47.0
PRIMER_WT_SELF_ANY_TH=0.0
PRIMER_WT_SELF_END_TH=0.0
PRIMER_WT_HAIRPIN_TH=0.0
PRIMER_WT_TEMPLATE_MISPRIMING_TH=0.0
PRIMER_INTERNAL_WT_SELF_ANY_TH=0.0
PRIMER_INTERNAL_WT_SELF_END_TH=0.0
PRIMER_INTERNAL_WT_HAIRPIN_TH=0.0
PRIMER_PAIR_WT_COMPL_ANY_TH=0.0
PRIMER_PAIR_WT_COMPL_END_TH=0.0
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING_TH=0.0
P3_COMMENT=default values of parameters using thermodynamic approach
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTCGGGCCTCTCCCTCAACTCACCATGATGACCGTCAGGCTGAGGAGGCAGGCGGACTGAGGCGTGGTCCGCGGGGCTCAGGGAGGTGGCTCCTGCGCCGG
PRIMER_LEFT_EXPLAIN=considered 1290, GC content failed 10, low tm 60, high tm 1039, ok 181
PRIMER_RIGHT_EXPLAIN=considered 1290, GC content failed 32, low tm 38, high tm 1096, ok 124
PRIMER_INTERNAL_EXPLAIN=considered 1565, GC content failed 32, low tm 60, high tm 1290, ok 183
PRIMER_PAIR_EXPLAIN=considered 25, unacceptable product size 20, ok 5
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=0.340791
PRIMER_LEFT_0_PENALTY=0.302821
PRIMER_RIGHT_0_PENALTY=0.037969
PRIMER_INTERNAL_0_PENALTY=0.712692
PRIMER_LEFT_0_SEQUENCE=GACTTCACTTTCCGACCCTG
PRIMER_RIGHT_0_SEQUENCE=TGACGGTCATCATGGTGAGT
PRIMER_INTERNAL_0_SEQUENCE=CACCCACGAGTGAAGACTCC
PRIMER_LEFT_0=11,20
PRIMER_RIGHT_0=113,20
PRIMER_INTERNAL_0=44,20
PRIMER_LEFT_0_TM=59.697
PRIMER_RIGHT_0_TM=59.962
PRIMER_INTERNAL_0_TM=60.713
PRIMER_LEFT_0_GC_PERCENT=55.000
PRIMER_RIGHT_0_GC_PERCENT=50.000
PRIMER_INTERNAL_0_GC_PERCENT=60.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=9.59
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=40.53
PRIMER_LEFT_0_END_STABILITY=9.7000
PRIMER_RIGHT_0_END_STABILITY=6.4000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=5.1715
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.4242
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=103
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=5.17
PRIMER_PAIR_1_PENALTY=0.340791
PRIMER_LEFT_1_PENALTY=0.302821
PRIMER_RIGHT_1_PENALTY=0.037969
PRIMER_INTERNAL_1_PENALTY=0.712692
PRIMER_LEFT_1_SEQUENCE=TGACTTCACTTTCCGACCCT
PRIMER_RIGHT_1_SEQUENCE=TGACGGTCATCATGGTGAGT
PRIMER_INTERNAL_1_SEQUENCE=CACCCACGAGTGAAGACTCC
PRIMER_LEFT_1=10,20
PRIMER_RIGHT_1=113,20
PRIMER_INTERNAL_1=44,20
PRIMER_LEFT_1_TM=59.697
PRIMER_RIGHT_1_TM=59.962
PRIMER_INTERNAL_1_TM=60.713
PRIMER_LEFT_1_GC_PERCENT=50.000
PRIMER_RIGHT_1_GC_PERCENT=50.000
PRIMER_INTERNAL_1_GC_PERCENT=60.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=9.59
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=40.53
PRIMER_LEFT_1_END_STABILITY=9.1000
PRIMER_RIGHT_1_END_STABILITY=6.4000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=1.7312
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=3.4242
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=104
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=3.42
PRIMER_PAIR_2_PENALTY=0.415766
PRIMER_LEFT_2_PENALTY=0.302821
PRIMER_RIGHT_2_PENALTY=0.112944
PRIMER_INTERNAL_2_PENALTY=0.712692
PRIMER_LEFT_2_SEQUENCE=GACTTCACTTTCCGACCCTG
PRIMER_RIGHT_2_SEQUENCE=CTGACGGTCATCATGGTGAG
PRIMER_INTERNAL_2_SEQUENCE=CACCCACGAGTGAAGACTCC
PRIMER_LEFT_2=11,20
PRIMER_RIGHT_2=114,20
PRIMER_INTERNAL_2=44,20
PRIMER_LEFT_2_TM=59.697
PRIMER_RIGHT_2_TM=60.113
PRIMER_INTERNAL_2_TM=60.713
PRIMER_LEFT_2_GC_PERCENT=55.000
PRIMER_RIGHT_2_GC_PERCENT=55.000
PRIMER_INTERNAL_2_GC_PERCENT=60.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=9.19
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=0.00
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=40.53
PRIMER_LEFT_2_END_STABILITY=9.7000
PRIMER_RIGHT_2_END_STABILITY=6.4000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=5.1715
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=19.1668
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=104
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=19.17
PRIMER_PAIR_3_PENALTY=0.415766
PRIMER_LEFT_3_PENALTY=0.302821
PRIMER_RIGHT_3_PENALTY=0.112944
PRIMER_INTERNAL_3_PENALTY=0.712692
PRIMER_LEFT_3_SEQUENCE=TGACTTCACTTTCCGACCCT
PRIMER_RIGHT_3_SEQUENCE=CTGACGGTCATCATGGTGAG
PRIMER_INTERNAL_3_SEQUENCE=CACCCACGAGTGAAGACTCC
PRIMER_LEFT_3=10,20
PRIMER_RIGHT_3=114,20
PRIMER_INTERNAL_3=44,20
PRIMER_LEFT_3_TM=59.697
PRIMER_RIGHT_3_TM=60.113
PRIMER_INTERNAL_3_TM=60.713
PRIMER_LEFT_3_GC_PERCENT=50.000
PRIMER_RIGHT_3_GC_PERCENT=55.000
PRIMER_INTERNAL_3_GC_PERCENT=60.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=9.19
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=40.53
PRIMER_LEFT_3_END_STABILITY=9.1000
PRIMER_RIGHT_3_END_STABILITY=6.4000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=1.7312
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=19.1668
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=105
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=19.17
PRIMER_PAIR_4_PENALTY=0.749760
PRIMER_LEFT_4_PENALTY=0.711791
PRIMER_RIGHT_4_PENALTY=0.037969
PRIMER_INTERNAL_4_PENALTY=0.712692
PRIMER_LEFT_4_SEQUENCE=GCCGAGGATGACTTCACTTT
PRIMER_RIGHT_4_SEQUENCE=TGACGGTCATCATGGTGAGT
PRIMER_INTERNAL_4_SEQUENCE=CACCCACGAGTGAAGACTCC
PRIMER_LEFT_4=2,20
PRIMER_RIGHT_4=113,20
PRIMER_INTERNAL_4=44,20
PRIMER_LEFT_4_TM=59.288
PRIMER_RIGHT_4_TM=59.962
PRIMER_INTERNAL_4_TM=60.713
PRIMER_LEFT_4_GC_PERCENT=50.000
PRIMER_RIGHT_4_GC_PERCENT=50.000
PRIMER_INTERNAL_4_GC_PERCENT=60.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=9.59
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=40.53
PRIMER_LEFT_4_END_STABILITY=6.7000
PRIMER_RIGHT_4_END_STABILITY=6.4000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=6.6985
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.4242
PRIMER_PAIR_4_COMPL_ANY_TH=8.76
PRIMER_PAIR_4_COMPL_END_TH=2.04
PRIMER_PAIR_4_PRODUCT_SIZE=112
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=10.12
=
SEQUENCE_ID=any_1
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_SELF_ANY_TH=10.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=47.0
PRIMER_INTERNAL_MAX_SELF_ANY_TH=47.0
PRIMER_WT_SELF_ANY_TH=0.0
PRIMER_INTERNAL_WT_SELF_ANY_TH=0.0
PRIMER_PAIR_WT_COMPL_ANY_TH=0.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3397, low tm 897, high tm 1543, long poly-x seq 22, ok 935
PRIMER_RIGHT_EXPLAIN=considered 3397, low tm 839, high tm 1673, high hairpin stability 1, long poly-x seq 22, ok 862
PRIMER_INTERNAL_EXPLAIN=considered 3672, low tm 953, high tm 1734, high hairpin stability 14, long poly-x seq 22, ok 949
PRIMER_PAIR_EXPLAIN=considered 58, unacceptable product size 51, ok 7
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=0.030625
PRIMER_LEFT_0_PENALTY=0.011300
PRIMER_RIGHT_0_PENALTY=0.019325
PRIMER_INTERNAL_0_PENALTY=1.584087
PRIMER_LEFT_0_SEQUENCE=CAAGCAATACGACCTGCTGA
PRIMER_RIGHT_0_SEQUENCE=ATCGCAAGTGAGGATGAGCT
PRIMER_INTERNAL_0_SEQUENCE=CGTGTGCAAAACATTTTCACA
PRIMER_LEFT_0=17,20
PRIMER_RIGHT_0=168,20
PRIMER_INTERNAL_0=116,21
PRIMER_LEFT_0_TM=60.011
PRIMER_RIGHT_0_TM=59.981
PRIMER_INTERNAL_0_TM=60.584
PRIMER_LEFT_0_GC_PERCENT=50.000
PRIMER_RIGHT_0_GC_PERCENT=50.000
PRIMER_INTERNAL_0_GC_PERCENT=38.095
PRIMER_INTERNAL_0_SELF_ANY_TH=12.25
PRIMER_LEFT_0_SELF_ANY_TH=2.42
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=10.49
PRIMER_LEFT_0_SELF_END_TH=0.00
PRIMER_RIGHT_0_SELF_END_TH=0.00
PRIMER_LEFT_0_HAIRPIN_TH=42.83
PRIMER_RIGHT_0_HAIRPIN_TH=39.48
PRIMER_INTERNAL_0_HAIRPIN_TH=37.82
PRIMER_LEFT_0_END_STABILITY=8.2000
PRIMER_RIGHT_0_END_STABILITY=7.9000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=9.4845
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=21.4669
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=152
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=21.47
PRIMER_PAIR_1_PENALTY=0.074511
PRIMER_LEFT_1_PENALTY=0.011300
PRIMER_RIGHT_1_PENALTY=0.063211
PRIMER_INTERNAL_1_PENALTY=0.019325
PRIMER_LEFT_1_SEQUENCE=CAAGCAATACGACCTGCTGA
PRIMER_RIGHT_1_SEQUENCE=CAAAAGATTTTGGCGGGTAA
PRIMER_INTERNAL_1_SEQUENCE=AGCTCATCCTCACTTGCGAT
PRIMER_LEFT_1=17,20
PRIMER_RIGHT_1=191,20
PRIMER_INTERNAL_1=149,20
PRIMER_LEFT_1_TM=60.011
PRIMER_RIGHT_1_TM=59.937
PRIMER_INTERNAL_1_TM=59.981
PRIMER_LEFT_1_GC_PERCENT=50.000
PRIMER_RIGHT_1_GC_PERCENT=40.000
PRIMER_INTERNAL_1_GC_PERCENT=50.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=2.42
PRIMER_RIGHT_1_SELF_ANY_TH=5.65
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=42.83
PRIMER_RIGHT_1_HAIRPIN_TH=39.80
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.2000
PRIMER_RIGHT_1_END_STABILITY=7.2000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=9.4845
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=0.9269
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=175
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.41
PRIMER_PAIR_2_PENALTY=0.258931
PRIMER_LEFT_2_PENALTY=0.011300
PRIMER_RIGHT_2_PENALTY=0.247631
PRIMER_INTERNAL_2_PENALTY=0.019325
PRIMER_LEFT_2_SEQUENCE=CAAGCAATACGACCTGCTGA
PRIMER_RIGHT_2_SEQUENCE=CCGTACGCACTATAGGAGCC
PRIMER_INTERNAL_2_SEQUENCE=AGCTCATCCTCACTTGCGAT
PRIMER_LEFT_2=17,20
PRIMER_RIGHT_2=368,20
PRIMER_INTERNAL_2=149,20
PRIMER_LEFT_2_TM=60.011
PRIMER_RIGHT_2_TM=59.752
PRIMER_INTERNAL_2_TM=59.981
PRIMER_LEFT_2_GC_PERCENT=50.000
PRIMER_RIGHT_2_GC_PERCENT=60.000
PRIMER_INTERNAL_2_GC_PERCENT=50.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=2.42
PRIMER_RIGHT_2_SELF_ANY_TH=8.58
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=42.83
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=8.2000
PRIMER_RIGHT_2_END_STABILITY=9.4000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=9.4845
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=17.2899
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=352
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=25.59
PRIMER_PAIR_3_PENALTY=0.266957
PRIMER_LEFT_3_PENALTY=0.019325
PRIMER_RIGHT_3_PENALTY=0.247631
PRIMER_INTERNAL_3_PENALTY=0.063211
PRIMER_LEFT_3_SEQUENCE=AGCTCATCCTCACTTGCGAT
PRIMER_RIGHT_3_SEQUENCE=CCGTACGCACTATAGGAGCC
PRIMER_INTERNAL_3_SEQUENCE=TTACCCGCCAAAATCTTTTG
PRIMER_LEFT_3=149,20
PRIMER_RIGHT_3=368,20
PRIMER_INTERNAL_3=172,20
PRIMER_LEFT_3_TM=59.981
PRIMER_RIGHT_3_TM=59.752
PRIMER_INTERNAL_3_TM=59.937
PRIMER_LEFT_3_GC_PERCENT=50.000
PRIMER_RIGHT_3_GC_PERCENT=60.000
PRIMER_INTERNAL_3_GC_PERCENT=40.000
PRIMER_INTERNAL_3_SELF_ANY_TH=4.21
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=8.58
PRIMER_INTERNAL_3_SELF_END_TH=4.21
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=43.62
PRIMER_LEFT_3_END_STABILITY=9.8000
PRIMER_RIGHT_3_END_STABILITY=9.4000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=9.8864
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=17.2899
PRIMER_PAIR_3_COMPL_ANY_TH=7.44
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=220
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=27.18
PRIMER_PAIR_4_PENALTY=0.309424
PRIMER_LEFT_4_PENALTY=0.011300
PRIMER_RIGHT_4_PENALTY=0.298125
PRIMER_INTERNAL_4_PENALTY=0.019325
PRIMER_LEFT_4_SEQUENCE=CAAGCAATACGACCTGCTGA
PRIMER_RIGHT_4_SEQUENCE=CACTAAAGCGGGATTTGAGG
PRIMER_INTERNAL_4_SEQUENCE=AGCTCATCCTCACTTGCGAT
PRIMER_LEFT_4=17,20
PRIMER_RIGHT_4=232,20
PRIMER_INTERNAL_4=149,20
PRIMER_LEFT_4_TM=60.011
PRIMER_RIGHT_4_TM=59.702
PRIMER_INTERNAL_4_TM=59.981
PRIMER_LEFT_4_GC_PERCENT=50.000
PRIMER_RIGHT_4_GC_PERCENT=50.000
PRIMER_INTERNAL_4_GC_PERCENT=50.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=2.42
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=42.83
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=8.2000
PRIMER_RIGHT_4_END_STABILITY=8.2000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=9.4845
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=2.8328
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=216
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=12.32
=
SEQUENCE_ID=any_salt
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_SALT_CORRECTIONS=1
PRIMER_SALT_MONOVALENT=50.0
PRIMER_SALT_DIVALENT=2.5
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_SELF_ANY_TH=60.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=47.0
PRIMER_INTERNAL_MAX_SELF_ANY_TH=47.0
PRIMER_WT_SELF_ANY_TH=0.0
PRIMER_INTERNAL_WT_SELF_ANY_TH=0.0
PRIMER_PAIR_WT_COMPL_ANY_TH=0.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3397, low tm 52, high tm 3139, long poly-x seq 22, ok 184
PRIMER_RIGHT_EXPLAIN=considered 3397, low tm 59, high tm 3137, long poly-x seq 22, ok 179
PRIMER_INTERNAL_EXPLAIN=considered 3672, low tm 432, high tm 2545, high hairpin stability 10, long poly-x seq 22, ok 663
PRIMER_PAIR_EXPLAIN=considered 16, unacceptable product size 11, ok 5
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.177993
PRIMER_LEFT_0_PENALTY=0.842396
PRIMER_RIGHT_0_PENALTY=0.335596
PRIMER_INTERNAL_0_PENALTY=0.132562
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.227701
PRIMER_LEFT_1_PENALTY=0.842396
PRIMER_RIGHT_1_PENALTY=0.385305
PRIMER_INTERNAL_1_PENALTY=0.132562
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.369023
PRIMER_LEFT_2_PENALTY=0.335596
PRIMER_RIGHT_2_PENALTY=1.033427
PRIMER_INTERNAL_2_PENALTY=0.172991
PRIMER_LEFT_2_SEQUENCE=GTAGTGAGCTATTACAGGTC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=235,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=59.664
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=46.51
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=7.6000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=9.4090
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=167
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=22.74
PRIMER_PAIR_3_PENALTY=1.418732
PRIMER_LEFT_3_PENALTY=0.385305
PRIMER_RIGHT_3_PENALTY=1.033427
PRIMER_INTERNAL_3_PENALTY=0.172991
PRIMER_LEFT_3_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_3_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_3_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_3=224,20
PRIMER_RIGHT_3=401,20
PRIMER_INTERNAL_3=340,20
PRIMER_LEFT_3_TM=60.385
PRIMER_RIGHT_3_TM=61.033
PRIMER_INTERNAL_3_TM=59.827
PRIMER_LEFT_3_GC_PERCENT=45.000
PRIMER_RIGHT_3_GC_PERCENT=40.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.2000
PRIMER_RIGHT_3_END_STABILITY=9.9000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=178
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_4_PENALTY=1.422920
PRIMER_LEFT_4_PENALTY=1.087323
PRIMER_RIGHT_4_PENALTY=0.335596
PRIMER_INTERNAL_4_PENALTY=0.132562
PRIMER_LEFT_4_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=99,20
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=61.087
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=30.000
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=8.1000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=156
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=any_weight
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_SALT_CORRECTIONS=1
PRIMER_SALT_MONOVALENT=50.0
PRIMER_SALT_DIVALENT=2.5
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_SELF_ANY_TH=47.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=47.0
PRIMER_INTERNAL_MAX_SELF_ANY_TH=47.0
PRIMER_WT_SELF_ANY_TH=1.0
PRIMER_INTERNAL_WT_SELF_ANY_TH=0.1
PRIMER_PAIR_WT_COMPL_ANY_TH=0.7
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3397, low tm 52, high tm 3139, high hairpin stability 2, long poly-x seq 22, ok 182
PRIMER_RIGHT_EXPLAIN=considered 3397, low tm 59, high tm 3137, long poly-x seq 22, ok 179
PRIMER_INTERNAL_EXPLAIN=considered 3672, low tm 432, high tm 2545, high hairpin stability 37, long poly-x seq 22, ok 636
PRIMER_PAIR_EXPLAIN=considered 18, unacceptable product size 11, ok 7
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.226125
PRIMER_LEFT_0_PENALTY=0.859989
PRIMER_RIGHT_0_PENALTY=0.353561
PRIMER_INTERNAL_0_PENALTY=0.134205
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.275443
PRIMER_LEFT_1_PENALTY=0.859989
PRIMER_RIGHT_1_PENALTY=0.403040
PRIMER_INTERNAL_1_PENALTY=0.134205
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.417097
PRIMER_LEFT_2_PENALTY=0.353561
PRIMER_RIGHT_2_PENALTY=1.050960
PRIMER_INTERNAL_2_PENALTY=0.174635
PRIMER_LEFT_2_SEQUENCE=GTAGTGAGCTATTACAGGTC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=235,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=59.664
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=46.51
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=7.6000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=9.4090
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=167
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=22.74
PRIMER_PAIR_3_PENALTY=1.466415
PRIMER_LEFT_3_PENALTY=0.403040
PRIMER_RIGHT_3_PENALTY=1.050960
PRIMER_INTERNAL_3_PENALTY=0.174635
PRIMER_LEFT_3_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_3_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_3_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_3=224,20
PRIMER_RIGHT_3=401,20
PRIMER_INTERNAL_3=340,20
PRIMER_LEFT_3_TM=60.385
PRIMER_RIGHT_3_TM=61.033
PRIMER_INTERNAL_3_TM=59.827
PRIMER_LEFT_3_GC_PERCENT=45.000
PRIMER_RIGHT_3_GC_PERCENT=40.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.2000
PRIMER_RIGHT_3_END_STABILITY=9.9000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=178
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_4_PENALTY=1.470977
PRIMER_LEFT_4_PENALTY=1.104840
PRIMER_RIGHT_4_PENALTY=0.353561
PRIMER_INTERNAL_4_PENALTY=0.134205
PRIMER_LEFT_4_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=99,20
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=61.087
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=30.000
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=8.1000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=156
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=any_2
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_SALT_CORRECTIONS=1
PRIMER_SALT_MONOVALENT=50.0
PRIMER_SALT_DIVALENT=2.5
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_SELF_ANY_TH=5.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=5.0
PRIMER_INTERNAL_MAX_SELF_ANY_TH=5.0
PRIMER_WT_SELF_ANY_TH=1.0
PRIMER_INTERNAL_WT_SELF_ANY_TH=1.0
PRIMER_PAIR_WT_COMPL_ANY_TH=1.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3213, low tm 52, high tm 2974, high any compl 25, high hairpin stability 2, long poly-x seq 22, ok 138
PRIMER_RIGHT_EXPLAIN=considered 3293, low tm 59, high tm 3043, high any compl 14, long poly-x seq 19, ok 158
PRIMER_INTERNAL_EXPLAIN=considered 3185, low tm 432, high tm 2188, high any compl 82, high hairpin stability 34, long poly-x seq 22, ok 427
PRIMER_PAIR_EXPLAIN=considered 20, unacceptable product size 12, ok 8
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.231515
PRIMER_LEFT_0_PENALTY=0.859989
PRIMER_RIGHT_0_PENALTY=0.353561
PRIMER_INTERNAL_0_PENALTY=0.148991
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.280764
PRIMER_LEFT_1_PENALTY=0.859989
PRIMER_RIGHT_1_PENALTY=0.403040
PRIMER_INTERNAL_1_PENALTY=0.148991
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.422487
PRIMER_LEFT_2_PENALTY=0.353561
PRIMER_RIGHT_2_PENALTY=1.050960
PRIMER_INTERNAL_2_PENALTY=0.189431
PRIMER_LEFT_2_SEQUENCE=GTAGTGAGCTATTACAGGTC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=235,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=59.664
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=46.51
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=7.6000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=9.4090
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=167
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=22.74
PRIMER_PAIR_3_PENALTY=1.471735
PRIMER_LEFT_3_PENALTY=0.403040
PRIMER_RIGHT_3_PENALTY=1.050960
PRIMER_INTERNAL_3_PENALTY=0.189431
PRIMER_LEFT_3_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_3_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_3_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_3=224,20
PRIMER_RIGHT_3=401,20
PRIMER_INTERNAL_3=340,20
PRIMER_LEFT_3_TM=60.385
PRIMER_RIGHT_3_TM=61.033
PRIMER_INTERNAL_3_TM=59.827
PRIMER_LEFT_3_GC_PERCENT=45.000
PRIMER_RIGHT_3_GC_PERCENT=40.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.2000
PRIMER_RIGHT_3_END_STABILITY=9.9000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=178
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_4_PENALTY=1.476366
PRIMER_LEFT_4_PENALTY=1.104840
PRIMER_RIGHT_4_PENALTY=0.353561
PRIMER_INTERNAL_4_PENALTY=0.148991
PRIMER_LEFT_4_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=99,20
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=61.087
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=30.000
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=8.1000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=156
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=any_no_effect
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_SALT_CORRECTIONS=1
PRIMER_SALT_MONOVALENT=50.0
PRIMER_SALT_DIVALENT=2.5
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_SELF_ANY_TH=0.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=0.0
PRIMER_INTERNAL_MAX_SELF_ANY_TH=0.0
PRIMER_WT_SELF_ANY_TH=0.0
PRIMER_INTERNAL_WT_SELF_ANY_TH=0.0
PRIMER_PAIR_WT_COMPL_ANY_TH=0.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3397, low tm 52, high tm 3139, long poly-x seq 22, ok 184
PRIMER_RIGHT_EXPLAIN=considered 3397, low tm 59, high tm 3137, long poly-x seq 22, ok 179
PRIMER_INTERNAL_EXPLAIN=considered 3672, low tm 432, high tm 2545, high any compl 11, high hairpin stability 4, long poly-x seq 22, ok 658
PRIMER_PAIR_EXPLAIN=considered 16, unacceptable product size 11, ok 5
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.177993
PRIMER_LEFT_0_PENALTY=0.842396
PRIMER_RIGHT_0_PENALTY=0.335596
PRIMER_INTERNAL_0_PENALTY=0.132562
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.227701
PRIMER_LEFT_1_PENALTY=0.842396
PRIMER_RIGHT_1_PENALTY=0.385305
PRIMER_INTERNAL_1_PENALTY=0.132562
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.369023
PRIMER_LEFT_2_PENALTY=0.335596
PRIMER_RIGHT_2_PENALTY=1.033427
PRIMER_INTERNAL_2_PENALTY=0.172991
PRIMER_LEFT_2_SEQUENCE=GTAGTGAGCTATTACAGGTC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=235,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=59.664
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=46.51
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=7.6000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=9.4090
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=167
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=22.74
PRIMER_PAIR_3_PENALTY=1.418732
PRIMER_LEFT_3_PENALTY=0.385305
PRIMER_RIGHT_3_PENALTY=1.033427
PRIMER_INTERNAL_3_PENALTY=0.172991
PRIMER_LEFT_3_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_3_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_3_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_3=224,20
PRIMER_RIGHT_3=401,20
PRIMER_INTERNAL_3=340,20
PRIMER_LEFT_3_TM=60.385
PRIMER_RIGHT_3_TM=61.033
PRIMER_INTERNAL_3_TM=59.827
PRIMER_LEFT_3_GC_PERCENT=45.000
PRIMER_RIGHT_3_GC_PERCENT=40.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.2000
PRIMER_RIGHT_3_END_STABILITY=9.9000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=178
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_4_PENALTY=1.422920
PRIMER_LEFT_4_PENALTY=1.087323
PRIMER_RIGHT_4_PENALTY=0.335596
PRIMER_INTERNAL_4_PENALTY=0.132562
PRIMER_LEFT_4_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=99,20
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=61.087
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=30.000
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=8.1000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=156
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=end_th1
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_SELF_END_TH=10.0
PRIMER_PAIR_MAX_COMPL_END_TH=10.0
PRIMER_INTERNAL_MAX_SELF_END_TH=10.0
PRIMER_WT_SELF_END_TH=0.0
PRIMER_INTERNAL_WT_SELF_END_TH=0.0
PRIMER_PAIR_WT_COMPL_END_TH=0.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3397, low tm 52, high tm 3139, long poly-x seq 22, ok 184
PRIMER_RIGHT_EXPLAIN=considered 3397, low tm 59, high tm 3137, long poly-x seq 22, ok 179
PRIMER_INTERNAL_EXPLAIN=considered 3672, low tm 432, high tm 2545, high any compl 11, high hairpin stability 4, long poly-x seq 22, ok 658
PRIMER_PAIR_EXPLAIN=considered 16, unacceptable product size 11, ok 5
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.177993
PRIMER_LEFT_0_PENALTY=0.842396
PRIMER_RIGHT_0_PENALTY=0.335596
PRIMER_INTERNAL_0_PENALTY=0.132562
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.227701
PRIMER_LEFT_1_PENALTY=0.842396
PRIMER_RIGHT_1_PENALTY=0.385305
PRIMER_INTERNAL_1_PENALTY=0.132562
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.369023
PRIMER_LEFT_2_PENALTY=0.335596
PRIMER_RIGHT_2_PENALTY=1.033427
PRIMER_INTERNAL_2_PENALTY=0.172991
PRIMER_LEFT_2_SEQUENCE=GTAGTGAGCTATTACAGGTC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=235,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=59.664
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=46.51
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=7.6000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=9.4090
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=167
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=22.74
PRIMER_PAIR_3_PENALTY=1.418732
PRIMER_LEFT_3_PENALTY=0.385305
PRIMER_RIGHT_3_PENALTY=1.033427
PRIMER_INTERNAL_3_PENALTY=0.172991
PRIMER_LEFT_3_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_3_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_3_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_3=224,20
PRIMER_RIGHT_3=401,20
PRIMER_INTERNAL_3=340,20
PRIMER_LEFT_3_TM=60.385
PRIMER_RIGHT_3_TM=61.033
PRIMER_INTERNAL_3_TM=59.827
PRIMER_LEFT_3_GC_PERCENT=45.000
PRIMER_RIGHT_3_GC_PERCENT=40.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.2000
PRIMER_RIGHT_3_END_STABILITY=9.9000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=178
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_4_PENALTY=1.422920
PRIMER_LEFT_4_PENALTY=1.087323
PRIMER_RIGHT_4_PENALTY=0.335596
PRIMER_INTERNAL_4_PENALTY=0.132562
PRIMER_LEFT_4_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=99,20
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=61.087
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=30.000
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=8.1000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=156
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=end_th2
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_SELF_END_TH=47.0
PRIMER_PAIR_MAX_COMPL_END_TH=47.0
PRIMER_INTERNAL_MAX_SELF_END_TH=47.0
PRIMER_WT_SELF_END_TH=0.1
PRIMER_INTERNAL_WT_SELF_END_TH=0.01
PRIMER_PAIR_WT_COMPL_END_TH=1.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3155, low tm 52, high tm 2924, high any compl 32, high hairpin stability 2, long poly-x seq 22, ok 123
PRIMER_RIGHT_EXPLAIN=considered 3213, low tm 59, high tm 2968, high any compl 23, long poly-x seq 19, ok 144
PRIMER_INTERNAL_EXPLAIN=considered 2916, low tm 432, high tm 1999, high any compl 116, high hairpin stability 22, long poly-x seq 22, ok 325
PRIMER_PAIR_EXPLAIN=considered 20, unacceptable product size 12, ok 8
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.199513
PRIMER_LEFT_0_PENALTY=0.844155
PRIMER_RIGHT_0_PENALTY=0.337393
PRIMER_INTERNAL_0_PENALTY=0.132726
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.248969
PRIMER_LEFT_1_PENALTY=0.844155
PRIMER_RIGHT_1_PENALTY=0.387078
PRIMER_INTERNAL_1_PENALTY=0.132726
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.390538
PRIMER_LEFT_2_PENALTY=0.337393
PRIMER_RIGHT_2_PENALTY=1.035180
PRIMER_INTERNAL_2_PENALTY=0.173155
PRIMER_LEFT_2_SEQUENCE=GTAGTGAGCTATTACAGGTC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=235,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=59.664
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=46.51
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=7.6000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=9.4090
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=167
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=22.74
PRIMER_PAIR_3_PENALTY=1.439994
PRIMER_LEFT_3_PENALTY=0.387078
PRIMER_RIGHT_3_PENALTY=1.035180
PRIMER_INTERNAL_3_PENALTY=0.173155
PRIMER_LEFT_3_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_3_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_3_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_3=224,20
PRIMER_RIGHT_3=401,20
PRIMER_INTERNAL_3=340,20
PRIMER_LEFT_3_TM=60.385
PRIMER_RIGHT_3_TM=61.033
PRIMER_INTERNAL_3_TM=59.827
PRIMER_LEFT_3_GC_PERCENT=45.000
PRIMER_RIGHT_3_GC_PERCENT=40.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.2000
PRIMER_RIGHT_3_END_STABILITY=9.9000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=178
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_4_PENALTY=1.444433
PRIMER_LEFT_4_PENALTY=1.089075
PRIMER_RIGHT_4_PENALTY=0.337393
PRIMER_INTERNAL_4_PENALTY=0.132726
PRIMER_LEFT_4_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=99,20
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=61.087
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=30.000
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=8.1000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=156
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=hairpin1
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_HAIRPIN_TH=50.0
PRIMER_PAIR_MAX_HAIRPIN_TH=50.0
PRIMER_INTERNAL_MAX_HAIRPIN_TH=50.0
PRIMER_WT_HAIRPIN_TH=1.0
PRIMER_INTERNAL_WT_HAIRPIN_TH=1.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3155, low tm 52, high tm 2924, high any compl 32, long poly-x seq 22, ok 125
PRIMER_RIGHT_EXPLAIN=considered 3213, low tm 59, high tm 2968, high any compl 23, long poly-x seq 19, ok 144
PRIMER_INTERNAL_EXPLAIN=considered 2916, low tm 432, high tm 1999, high any compl 116, high hairpin stability 4, long poly-x seq 22, ok 343
PRIMER_PAIR_EXPLAIN=considered 15, unacceptable product size 10, ok 5
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.235070
PRIMER_LEFT_0_PENALTY=0.861748
PRIMER_RIGHT_0_PENALTY=0.355358
PRIMER_INTERNAL_0_PENALTY=0.149156
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.284296
PRIMER_LEFT_1_PENALTY=0.861748
PRIMER_RIGHT_1_PENALTY=0.404813
PRIMER_INTERNAL_1_PENALTY=0.149156
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.475262
PRIMER_LEFT_2_PENALTY=0.404813
PRIMER_RIGHT_2_PENALTY=1.052714
PRIMER_INTERNAL_2_PENALTY=0.189595
PRIMER_LEFT_2_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=224,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=60.385
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=0.00
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=8.2000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=178
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_3_PENALTY=1.479914
PRIMER_LEFT_3_PENALTY=1.106592
PRIMER_RIGHT_3_PENALTY=0.355358
PRIMER_INTERNAL_3_PENALTY=0.149156
PRIMER_LEFT_3_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_3_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_3_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_3=99,20
PRIMER_RIGHT_3=254,20
PRIMER_INTERNAL_3=145,20
PRIMER_LEFT_3_TM=61.087
PRIMER_RIGHT_3_TM=59.664
PRIMER_INTERNAL_3_TM=59.867
PRIMER_LEFT_3_GC_PERCENT=30.000
PRIMER_RIGHT_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.1000
PRIMER_RIGHT_3_END_STABILITY=5.1000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=156
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=3.56
PRIMER_PAIR_4_PENALTY=1.495033
PRIMER_LEFT_4_PENALTY=1.121710
PRIMER_RIGHT_4_PENALTY=0.355358
PRIMER_INTERNAL_4_PENALTY=0.149156
PRIMER_LEFT_4_SEQUENCE=TCTATCTGTACAACGTGTG
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=103,19
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=59.898
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=42.105
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=6.4000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=0.0000
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=152
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=hairpin2
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_HAIRPIN_TH=40.0
PRIMER_PAIR_MAX_HAIRPIN_TH=40.0
PRIMER_INTERNAL_MAX_HAIRPIN_TH=40.0
PRIMER_WT_HAIRPIN_TH=0.0
PRIMER_INTERNAL_WT_HAIRPIN_TH=0.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3155, low tm 52, high tm 2924, high any compl 32, high hairpin stability 9, long poly-x seq 22, ok 116
PRIMER_RIGHT_EXPLAIN=considered 3213, low tm 59, high tm 2968, high any compl 23, high hairpin stability 12, long poly-x seq 19, ok 132
PRIMER_INTERNAL_EXPLAIN=considered 2916, low tm 432, high tm 1999, high any compl 116, high hairpin stability 26, long poly-x seq 22, ok 321
PRIMER_PAIR_EXPLAIN=considered 11, unacceptable product size 6, ok 5
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.199513
PRIMER_LEFT_0_PENALTY=0.844155
PRIMER_RIGHT_0_PENALTY=0.337393
PRIMER_INTERNAL_0_PENALTY=0.132726
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.248969
PRIMER_LEFT_1_PENALTY=0.844155
PRIMER_RIGHT_1_PENALTY=0.387078
PRIMER_INTERNAL_1_PENALTY=0.132726
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.439994
PRIMER_LEFT_2_PENALTY=0.387078
PRIMER_RIGHT_2_PENALTY=1.035180
PRIMER_INTERNAL_2_PENALTY=0.173155
PRIMER_LEFT_2_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=224,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=60.385
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=0.00
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=8.2000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=178
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_3_PENALTY=1.444433
PRIMER_LEFT_3_PENALTY=1.089075
PRIMER_RIGHT_3_PENALTY=0.337393
PRIMER_INTERNAL_3_PENALTY=0.132726
PRIMER_LEFT_3_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_3_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_3_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_3=99,20
PRIMER_RIGHT_3=254,20
PRIMER_INTERNAL_3=145,20
PRIMER_LEFT_3_TM=61.087
PRIMER_RIGHT_3_TM=59.664
PRIMER_INTERNAL_3_TM=59.867
PRIMER_LEFT_3_GC_PERCENT=30.000
PRIMER_RIGHT_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.1000
PRIMER_RIGHT_3_END_STABILITY=5.1000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=156
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=3.56
PRIMER_PAIR_4_PENALTY=1.459178
PRIMER_LEFT_4_PENALTY=1.103821
PRIMER_RIGHT_4_PENALTY=0.337393
PRIMER_INTERNAL_4_PENALTY=0.132726
PRIMER_LEFT_4_SEQUENCE=TCTATCTGTACAACGTGTG
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=103,19
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=59.898
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=42.105
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=6.4000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=0.0000
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=152
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=hairpin3
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_HAIRPIN_TH=0.0
PRIMER_PAIR_MAX_HAIRPIN_TH=25.0
PRIMER_INTERNAL_MAX_HAIRPIN_TH=47.0
PRIMER_PICK_ANYWAY=1
PRIMER_WT_HAIRPIN_TH=0.0
PRIMER_INTERNAL_WT_HAIRPIN_TH=1.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3155, low tm 52, high tm 2924, high any compl 32, high hairpin stability 36, long poly-x seq 22, ok 89
PRIMER_RIGHT_EXPLAIN=considered 3213, low tm 59, high tm 2968, high any compl 23, high hairpin stability 32, long poly-x seq 19, ok 112
PRIMER_INTERNAL_EXPLAIN=considered 2916, low tm 432, high tm 1999, high any compl 116, high hairpin stability 22, long poly-x seq 22, ok 325
PRIMER_PAIR_EXPLAIN=considered 9, unacceptable product size 4, ok 5
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.199513
PRIMER_LEFT_0_PENALTY=0.844155
PRIMER_RIGHT_0_PENALTY=0.337393
PRIMER_INTERNAL_0_PENALTY=0.149156
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=9.99
PRIMER_PAIR_1_PENALTY=1.248969
PRIMER_LEFT_1_PENALTY=0.844155
PRIMER_RIGHT_1_PENALTY=0.387078
PRIMER_INTERNAL_1_PENALTY=0.149156
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.07
PRIMER_PAIR_2_PENALTY=1.439994
PRIMER_LEFT_2_PENALTY=0.387078
PRIMER_RIGHT_2_PENALTY=1.035180
PRIMER_INTERNAL_2_PENALTY=0.189595
PRIMER_LEFT_2_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=224,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=60.385
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=0.00
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=8.2000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=13.3303
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=178
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=26.14
PRIMER_PAIR_3_PENALTY=1.444433
PRIMER_LEFT_3_PENALTY=1.089075
PRIMER_RIGHT_3_PENALTY=0.337393
PRIMER_INTERNAL_3_PENALTY=0.149156
PRIMER_LEFT_3_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_3_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_3_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_3=99,20
PRIMER_RIGHT_3=254,20
PRIMER_INTERNAL_3=145,20
PRIMER_LEFT_3_TM=61.087
PRIMER_RIGHT_3_TM=59.664
PRIMER_INTERNAL_3_TM=59.867
PRIMER_LEFT_3_GC_PERCENT=30.000
PRIMER_RIGHT_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.1000
PRIMER_RIGHT_3_END_STABILITY=5.1000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=156
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=3.56
PRIMER_PAIR_4_PENALTY=1.459178
PRIMER_LEFT_4_PENALTY=1.103821
PRIMER_RIGHT_4_PENALTY=0.337393
PRIMER_INTERNAL_4_PENALTY=0.149156
PRIMER_LEFT_4_SEQUENCE=TCTATCTGTACAACGTGTG
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=103,19
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=59.898
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=42.105
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=6.4000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=0.0000
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=3.5614
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=152
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=3.56
=
SEQUENCE_ID=template1
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_MAX_TEMPLATE_MISPRIMING_TH=45.0
PRIMER_WT_TEMPLATE_MISPRIMING_TH=1.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3155, low tm 52, high tm 2924, high any compl 32, high hairpin stability 36, long poly-x seq 22, ok 89
PRIMER_RIGHT_EXPLAIN=considered 3213, low tm 59, high tm 2968, high any compl 23, high hairpin stability 32, long poly-x seq 19, ok 112
PRIMER_INTERNAL_EXPLAIN=considered 2916, low tm 432, high tm 1999, high any compl 116, high hairpin stability 22, long poly-x seq 22, ok 325
PRIMER_PAIR_EXPLAIN=considered 9, unacceptable product size 4, ok 5
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.237872
PRIMER_LEFT_0_PENALTY=0.862933
PRIMER_RIGHT_0_PENALTY=0.356975
PRIMER_INTERNAL_0_PENALTY=0.149156
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=8.2452
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=11.83
PRIMER_PAIR_1_PENALTY=1.289639
PRIMER_LEFT_1_PENALTY=0.862933
PRIMER_RIGHT_1_PENALTY=0.408971
PRIMER_INTERNAL_1_PENALTY=0.149156
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.12
PRIMER_PAIR_2_PENALTY=1.481183
PRIMER_LEFT_2_PENALTY=0.410025
PRIMER_RIGHT_2_PENALTY=1.053423
PRIMER_INTERNAL_2_PENALTY=0.189595
PRIMER_LEFT_2_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=224,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=60.385
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=0.00
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=8.2000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=4.3889
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=178
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=12.84
PRIMER_PAIR_3_PENALTY=1.482689
PRIMER_LEFT_3_PENALTY=1.107749
PRIMER_RIGHT_3_PENALTY=0.356975
PRIMER_INTERNAL_3_PENALTY=0.149156
PRIMER_LEFT_3_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_3_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_3_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_3=99,20
PRIMER_RIGHT_3=254,20
PRIMER_INTERNAL_3=145,20
PRIMER_LEFT_3_TM=61.087
PRIMER_RIGHT_3_TM=59.664
PRIMER_INTERNAL_3_TM=59.867
PRIMER_LEFT_3_GC_PERCENT=30.000
PRIMER_RIGHT_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.1000
PRIMER_RIGHT_3_END_STABILITY=5.1000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=8.2452
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=156
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=10.13
PRIMER_PAIR_4_PENALTY=1.499108
PRIMER_LEFT_4_PENALTY=1.124168
PRIMER_RIGHT_4_PENALTY=0.356975
PRIMER_INTERNAL_4_PENALTY=0.149156
PRIMER_LEFT_4_SEQUENCE=TCTATCTGTACAACGTGTG
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=103,19
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=59.898
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=42.105
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=6.4000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=3.5779
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=8.2452
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=152
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=9.52
=
SEQUENCE_ID=template2
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_THERMODYNAMIC_ALIGNMENT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=5
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=50.0
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING_TH=1.0
SEQUENCE_TEMPLATE=AGTGAGCTCATTCAATACAAGCAATACGACCTGCTGATTATCGACGATATTCAGTTCATCAAAGGAAAGTGAGCTCATTAAGACCGTACGATGGAAGAATTTTTCTATCTGTACAACGTGTGCAAAACATTTTCACAATGAGAAAAAACAGCTCATCCTCACTTGCGATGTTTTACCCGCCAAAATCTTTTGCACCGAAGGTATGGACGACCGCCTCAAATCCCGCTTTAGTGTAGTAGTGAGCTATTACAGGTCGTGGGGGCTGACCGCAGTAAGCTGCGGCTTTGGAACTCGAGCCGCCCGAATTGGAAATGCGCAAAACCGTGTCTATCGCCATTTTGCAGAAAAAGGCTCCTATAGTGCGTACGGAAGCGGCGGGGTACGCACTATAGACATCAGTATCG
PRIMER_LEFT_EXPLAIN=considered 3155, low tm 52, high tm 2924, high any compl 32, high hairpin stability 36, long poly-x seq 22, ok 89
PRIMER_RIGHT_EXPLAIN=considered 3213, low tm 59, high tm 2968, high any compl 23, high hairpin stability 32, long poly-x seq 19, ok 112
PRIMER_INTERNAL_EXPLAIN=considered 2916, low tm 432, high tm 1999, high any compl 116, high hairpin stability 22, long poly-x seq 22, ok 325
PRIMER_PAIR_EXPLAIN=considered 12, unacceptable product size 5, ok 7
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=5
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=1.260686
PRIMER_LEFT_0_PENALTY=0.862933
PRIMER_RIGHT_0_PENALTY=0.356975
PRIMER_INTERNAL_0_PENALTY=0.149156
PRIMER_LEFT_0_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_0_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_0_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_0=98,20
PRIMER_RIGHT_0=254,20
PRIMER_INTERNAL_0=145,20
PRIMER_LEFT_0_TM=60.842
PRIMER_RIGHT_0_TM=59.664
PRIMER_INTERNAL_0_TM=59.867
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_INTERNAL_0_SELF_END_TH=0.00
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=0.00
PRIMER_INTERNAL_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=8.7000
PRIMER_RIGHT_0_END_STABILITY=5.1000
PRIMER_LEFT_0_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_0_TEMPLATE_MISPRIMING_TH=8.2452
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=157
PRIMER_PAIR_0_TEMPLATE_MISPRIMING_TH=11.83
PRIMER_PAIR_1_PENALTY=1.311255
PRIMER_LEFT_1_PENALTY=0.862933
PRIMER_RIGHT_1_PENALTY=0.408971
PRIMER_INTERNAL_1_PENALTY=0.149156
PRIMER_LEFT_1_SEQUENCE=ATTTTTCTATCTGTACAACG
PRIMER_RIGHT_1_SEQUENCE=GCTCACTACTACACTAAAGC
PRIMER_INTERNAL_1_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_1=98,20
PRIMER_RIGHT_1=243,20
PRIMER_INTERNAL_1=145,20
PRIMER_LEFT_1_TM=60.842
PRIMER_RIGHT_1_TM=60.385
PRIMER_INTERNAL_1_TM=59.867
PRIMER_LEFT_1_GC_PERCENT=30.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_INTERNAL_1_SELF_END_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=0.00
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_INTERNAL_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=8.7000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_1_TEMPLATE_MISPRIMING_TH=3.5867
PRIMER_RIGHT_1_TEMPLATE_MISPRIMING_TH=10.0714
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=146
PRIMER_PAIR_1_TEMPLATE_MISPRIMING_TH=10.12
PRIMER_PAIR_2_PENALTY=1.504145
PRIMER_LEFT_2_PENALTY=0.410025
PRIMER_RIGHT_2_PENALTY=1.053423
PRIMER_INTERNAL_2_PENALTY=0.189595
PRIMER_LEFT_2_SEQUENCE=GCTTTAGTGTAGTAGTGAGC
PRIMER_RIGHT_2_SEQUENCE=ATACTGATGTCTATAGTGCG
PRIMER_INTERNAL_2_SEQUENCE=GCAGAAAAAGGCTCCTATAG
PRIMER_LEFT_2=224,20
PRIMER_RIGHT_2=401,20
PRIMER_INTERNAL_2=340,20
PRIMER_LEFT_2_TM=60.385
PRIMER_RIGHT_2_TM=61.033
PRIMER_INTERNAL_2_TM=59.827
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_2_GC_PERCENT=45.000
PRIMER_INTERNAL_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_INTERNAL_2_SELF_END_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=0.00
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_INTERNAL_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=8.2000
PRIMER_RIGHT_2_END_STABILITY=9.9000
PRIMER_LEFT_2_TEMPLATE_MISPRIMING_TH=12.8055
PRIMER_RIGHT_2_TEMPLATE_MISPRIMING_TH=4.3889
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=178
PRIMER_PAIR_2_TEMPLATE_MISPRIMING_TH=12.84
PRIMER_PAIR_3_PENALTY=1.504650
PRIMER_LEFT_3_PENALTY=1.107749
PRIMER_RIGHT_3_PENALTY=0.356975
PRIMER_INTERNAL_3_PENALTY=0.149156
PRIMER_LEFT_3_SEQUENCE=TTTTTCTATCTGTACAACGT
PRIMER_RIGHT_3_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_3_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_3=99,20
PRIMER_RIGHT_3=254,20
PRIMER_INTERNAL_3=145,20
PRIMER_LEFT_3_TM=61.087
PRIMER_RIGHT_3_TM=59.664
PRIMER_INTERNAL_3_TM=59.867
PRIMER_LEFT_3_GC_PERCENT=30.000
PRIMER_RIGHT_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_GC_PERCENT=45.000
PRIMER_INTERNAL_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_INTERNAL_3_SELF_END_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=0.00
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_INTERNAL_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=8.1000
PRIMER_RIGHT_3_END_STABILITY=5.1000
PRIMER_LEFT_3_TEMPLATE_MISPRIMING_TH=1.8838
PRIMER_RIGHT_3_TEMPLATE_MISPRIMING_TH=8.2452
PRIMER_PAIR_3_COMPL_ANY_TH=0.00
PRIMER_PAIR_3_COMPL_END_TH=0.00
PRIMER_PAIR_3_PRODUCT_SIZE=156
PRIMER_PAIR_3_TEMPLATE_MISPRIMING_TH=10.13
PRIMER_PAIR_4_PENALTY=1.520779
PRIMER_LEFT_4_PENALTY=1.124168
PRIMER_RIGHT_4_PENALTY=0.356975
PRIMER_INTERNAL_4_PENALTY=0.149156
PRIMER_LEFT_4_SEQUENCE=TCTATCTGTACAACGTGTG
PRIMER_RIGHT_4_SEQUENCE=GACCTGTAATAGCTCACTAC
PRIMER_INTERNAL_4_SEQUENCE=AAACAGCTCATCCTCACTTG
PRIMER_LEFT_4=103,19
PRIMER_RIGHT_4=254,20
PRIMER_INTERNAL_4=145,20
PRIMER_LEFT_4_TM=59.898
PRIMER_RIGHT_4_TM=59.664
PRIMER_INTERNAL_4_TM=59.867
PRIMER_LEFT_4_GC_PERCENT=42.105
PRIMER_RIGHT_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_GC_PERCENT=45.000
PRIMER_INTERNAL_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_INTERNAL_4_SELF_END_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=0.00
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_INTERNAL_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=6.4000
PRIMER_RIGHT_4_END_STABILITY=5.1000
PRIMER_LEFT_4_TEMPLATE_MISPRIMING_TH=3.5779
PRIMER_RIGHT_4_TEMPLATE_MISPRIMING_TH=8.2452
PRIMER_PAIR_4_COMPL_ANY_TH=0.00
PRIMER_PAIR_4_COMPL_END_TH=0.00
PRIMER_PAIR_4_PRODUCT_SIZE=152
PRIMER_PAIR_4_TEMPLATE_MISPRIMING_TH=9.52
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