SEQUENCE_ID=Details of SEQUENCE_OVERLAP_JUNCTION_LIST and PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION TEST 01 -- OVERLAP
P3_COMMENT=The 50th nt is uppercase
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PRODUCT_SIZE_RANGE=40-100
PRIMER_MIN_GC=0
PRIMER_MIN_TM=0
PRIMER_PICK_ANYWAY=0
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION=2
PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION=2
SEQUENCE_OVERLAP_JUNCTION_LIST=50
PRIMER_TASK=pick_detection_primers
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_MAX_POLY_X=100
PRIMER_MAX_SELF_ANY=100
PRIMER_MAX_SELF_END=100
PRIMER_FIRST_BASE_INDEX=1
PRIMER_MIN_SIZE=16
SEQUENCE_PRIMER=cttgattcaatgaatctcaa
SEQUENCE_PRIMER_REVCOMP=aaaaaaacacaatccAga
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=22.403937
PRIMER_LEFT_0_PENALTY=8.942519
PRIMER_RIGHT_0_PENALTY=13.461417
PRIMER_LEFT_0_SEQUENCE=cttgattcaatgaatctcaa
PRIMER_RIGHT_0_SEQUENCE=aaaaaaacacaatccAga
PRIMER_LEFT_0=1,20
PRIMER_RIGHT_0=65,18
PRIMER_LEFT_0_TM=51.057
PRIMER_RIGHT_0_TM=48.539
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=27.778
PRIMER_LEFT_0_SELF_ANY=11.00
PRIMER_RIGHT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=5.00
PRIMER_RIGHT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=7.0000
PRIMER_RIGHT_0_END_STABILITY=8.2000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_END=2.00
PRIMER_PAIR_0_PRODUCT_SIZE=65
PRIMER_PAIR_0_PRODUCT_TM=62.0
=
SEQUENCE_ID=Details of SEQUENCE_OVERLAP_JUNCTION_LIST and PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION TEST 02 -- OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
SEQUENCE_PRIMER=cttgattcaatgaatctcaa
SEQUENCE_PRIMER_REVCOMP=aaaaaaacacaatccAg
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=25.992387
PRIMER_LEFT_0_PENALTY=8.942519
PRIMER_RIGHT_0_PENALTY=17.049867
PRIMER_LEFT_0_SEQUENCE=cttgattcaatgaatctcaa
PRIMER_RIGHT_0_SEQUENCE=aaaaaaacacaatccAg
PRIMER_LEFT_0=1,20
PRIMER_RIGHT_0=65,17
PRIMER_LEFT_0_TM=51.057
PRIMER_RIGHT_0_TM=45.950
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=29.412
PRIMER_LEFT_0_SELF_ANY=11.00
PRIMER_RIGHT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=5.00
PRIMER_RIGHT_0_SELF_END=1.00
PRIMER_LEFT_0_END_STABILITY=7.0000
PRIMER_RIGHT_0_END_STABILITY=8.2000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_END=1.00
PRIMER_PAIR_0_PRODUCT_SIZE=65
PRIMER_PAIR_0_PRODUCT_TM=62.0
=
SEQUENCE_ID=Details of SEQUENCE_OVERLAP_JUNCTION_LIST and PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION TEST 03 -- NO OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
SEQUENCE_PRIMER=cttgattcaatgaatctcaa
SEQUENCE_PRIMER_REVCOMP=aaaaaaacacaatccA
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no overlap of required point 1, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
SEQUENCE_ID=Details of SEQUENCE_OVERLAP_JUNCTION_LIST and PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION TEST 08 -- OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
SEQUENCE_PRIMER=ttgttcattctgtttcTgg
SEQUENCE_PRIMER_REVCOMP=catcacacccttttacacatt
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=15.138591
PRIMER_LEFT_0_PENALTY=9.157204
PRIMER_RIGHT_0_PENALTY=5.981388
PRIMER_LEFT_0_SEQUENCE=ttgttcattctgtttcTgg
PRIMER_RIGHT_0_SEQUENCE=catcacacccttttacacatt
PRIMER_LEFT_0=34,19
PRIMER_RIGHT_0=100,21
PRIMER_LEFT_0_TM=51.843
PRIMER_RIGHT_0_TM=55.019
PRIMER_LEFT_0_GC_PERCENT=36.842
PRIMER_RIGHT_0_GC_PERCENT=38.095
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_RIGHT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=0.00
PRIMER_RIGHT_0_SELF_END=1.00
PRIMER_LEFT_0_END_STABILITY=8.2000
PRIMER_RIGHT_0_END_STABILITY=6.6000
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=1.00
PRIMER_PAIR_0_PRODUCT_SIZE=67
PRIMER_PAIR_0_PRODUCT_TM=64.4
=
SEQUENCE_ID=Details of SEQUENCE_OVERLAP_JUNCTION_LIST and PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION TEST 09 -- NO OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
SEQUENCE_PRIMER=ttgttcattctgtttcTg
SEQUENCE_PRIMER_REVCOMP=catcacacccttttacacatt
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no overlap of required point 1, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
SEQUENCE_ID=Test for 5' overlap on reverse primer -- OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION=3
SEQUENCE_PRIMER=cttgattcaatgaatctcaa
SEQUENCE_PRIMER_REVCOMP=tccAgaaacagaatgaacaatag
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=15.822707
PRIMER_LEFT_0_PENALTY=8.942519
PRIMER_RIGHT_0_PENALTY=6.880188
PRIMER_LEFT_0_SEQUENCE=cttgattcaatgaatctcaa
PRIMER_RIGHT_0_SEQUENCE=tccAgaaacagaatgaacaatag
PRIMER_LEFT_0=1,20
PRIMER_RIGHT_0=53,23
PRIMER_LEFT_0_TM=51.057
PRIMER_RIGHT_0_TM=56.120
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=34.783
PRIMER_LEFT_0_SELF_ANY=11.00
PRIMER_RIGHT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=5.00
PRIMER_RIGHT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=7.0000
PRIMER_RIGHT_0_END_STABILITY=5.9000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_END=1.00
PRIMER_PAIR_0_PRODUCT_SIZE=53
PRIMER_PAIR_0_PRODUCT_TM=61.0
=
SEQUENCE_ID=Test for 5' overlap on reverse primer -- NO OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
SEQUENCE_PRIMER=cttgattcaatgaatctcaa
SEQUENCE_PRIMER_REVCOMP=ccAgaaacagaatgaacaatag
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no overlap of required point 1, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
SEQUENCE_ID=Test for 5' overlap on reverse primer  -- NO OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
SEQUENCE_PRIMER=cttgattcaatgaatctcaa
SEQUENCE_PRIMER_REVCOMP=cAgaaacagaatgaacaatag
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no overlap of required point 1, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
SEQUENCE_ID=Test for 5' overlap on forward primer  -- OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
SEQUENCE_PRIMER=tcTggattgtgtttttttc
SEQUENCE_PRIMER_REVCOMP=catcacacccttttacacatt
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=16.029050
PRIMER_LEFT_0_PENALTY=10.047662
PRIMER_RIGHT_0_PENALTY=5.981388
PRIMER_LEFT_0_SEQUENCE=tcTggattgtgtttttttc
PRIMER_RIGHT_0_SEQUENCE=catcacacccttttacacatt
PRIMER_LEFT_0=48,19
PRIMER_RIGHT_0=100,21
PRIMER_LEFT_0_TM=50.952
PRIMER_RIGHT_0_TM=55.019
PRIMER_LEFT_0_GC_PERCENT=31.579
PRIMER_RIGHT_0_GC_PERCENT=38.095
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_RIGHT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=0.00
PRIMER_RIGHT_0_SELF_END=1.00
PRIMER_LEFT_0_END_STABILITY=7.3000
PRIMER_RIGHT_0_END_STABILITY=6.6000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=53
PRIMER_PAIR_0_PRODUCT_TM=62.5
=
SEQUENCE_ID=Test for 5' overlap on forward primer -- NO OVERLAP
SEQUENCE_TEMPLATE=cttgattcaatgaatctcaaaaatggattactattgttcattctgtttcTggattgtgtttttttcaaagttgaatccaaatgtgtaaaagggtgtgatg
SEQUENCE_OVERLAP_JUNCTION_LIST=50
SEQUENCE_PRIMER=cTggattgtgtttttttc
SEQUENCE_PRIMER_REVCOMP=catcacacccttttacacatt
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no overlap of required point 1, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
