P3_COMMENT=Testing PRIMER_MAX_POLY_X
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_MAX_NS_ACCEPTED=100
PRIMER_MAX_TM=99
PRIMER_MIN_TM=50
PRIMER_TASK=check_primers
SEQUENCE_ID=primer3_poly_x_01
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_PICK_RIGHT_PRIMER=0
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=CNCNCCATTGAGTAGCAAGG
P3_COMMENT=CNCNCC - need to join disjoint N regions, fails on poly_x
PRIMER_LEFT_EXPLAIN=considered 1, long poly-x seq 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=primer3_poly_x_02
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=NNNNNCAATTGAGTAGCAAGG
P3_COMMENT=Nx5 at 5' end, fails on poly_x
PRIMER_LEFT_EXPLAIN=considered 1, long poly-x seq 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=primer3_poly_x_03
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=CCATCTGAGTAGCAGAGGNNNN
P3_COMMENT=GGNNNN at 3' end, fails on poly_x
PRIMER_LEFT_EXPLAIN=considered 1, long poly-x seq 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=primer3_poly_x_04
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=ANCNCCATTGAGTAGCAAGG
P3_COMMENT=CNCNNG disjoint N regions with different end bp where 3' end bp
P3_COMMENT=is the same as bp between Ns - returns 1 primer
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=1.677021
PRIMER_LEFT_0_SEQUENCE=ANCNCCATTGAGTAGCAAGG
PRIMER_LEFT_0=0,20
PRIMER_LEFT_0_TM=58.323
PRIMER_LEFT_0_GC_PERCENT=50.000
PRIMER_LEFT_0_SELF_ANY=3.50
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=8.5000
=
SEQUENCE_ID=primer3_poly_x_05
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=CNCNNGCATTGAGTAGCAAGG
P3_COMMENT=CNCNNG disjoint N regions with different end bp where 5' end bp
P3_COMMENT=is the same as bp between Ns - returns 1 primer
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=3.867932
PRIMER_LEFT_0_SEQUENCE=CNCNNGCATTGAGTAGCAAGG
PRIMER_LEFT_0=0,21
PRIMER_LEFT_0_TM=62.868
PRIMER_LEFT_0_GC_PERCENT=55.556
PRIMER_LEFT_0_SELF_ANY=3.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=8.5000
=
SEQUENCE_ID=primer3_poly_x_06
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=CCCNCCCACATTGAGTAGCAAGG
P3_COMMENT=CCCNCCC, fails on poly_x
PRIMER_LEFT_EXPLAIN=considered 1, long poly-x seq 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=primer3_poly_x_07
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=CNNNNGACATTGAGTAGCAAGG
P3_COMMENT=CNNNNG, returns 1 primer
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=2.222749
PRIMER_LEFT_0_SEQUENCE=CNNNNGACATTGAGTAGCAAGG
PRIMER_LEFT_0=0,22
PRIMER_LEFT_0_TM=60.223
PRIMER_LEFT_0_GC_PERCENT=50.000
PRIMER_LEFT_0_SELF_ANY=3.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=8.5000
=
SEQUENCE_ID=primer3_poly_x_08
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=CCCCCGACATTGAGTAGCAAGG
P3_COMMENT=Cx5, returns 1 primer
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=9.012183
PRIMER_LEFT_0_SEQUENCE=CCCCCGACATTGAGTAGCAAGG
PRIMER_LEFT_0=0,22
PRIMER_LEFT_0_TM=67.012
PRIMER_LEFT_0_GC_PERCENT=59.091
PRIMER_LEFT_0_SELF_ANY=3.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=8.5000
=
SEQUENCE_ID=primer3_poly_x_09
PRIMER_MAX_POLY_X=5
SEQUENCE_PRIMER=CCCCCCGACATTGAGTAGCAAGG
P3_COMMENT=Cx6, fails on poly_x
PRIMER_LEFT_EXPLAIN=considered 1, long poly-x seq 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=primer3_poly_x_10
PRIMER_MAX_POLY_X=10
SEQUENCE_PRIMER=CCCCCCGACATTGAGTAGCAAGG
P3_COMMENT=Cx6, returns 1 primer
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=12.699102
PRIMER_LEFT_0_SEQUENCE=CCCCCCGACATTGAGTAGCAAGG
PRIMER_LEFT_0=0,23
PRIMER_LEFT_0_TM=69.699
PRIMER_LEFT_0_GC_PERCENT=60.870
PRIMER_LEFT_0_SELF_ANY=3.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=8.5000
=
