~ubuntu-branches/ubuntu/precise/bioperl/precise

SEQUENCE=atgNaggtgacttttatttacatcctagttattacatgttacgaaaacgacgtaaacgtttaccatattttttttcagatgtctctttggctgcctagtgaggccactgtctacttgcctcctgtcccagtatctaaNgttgtaagcacggatgaatatgttgcacgcacaaacatatattatcatgcaggaacatccagactacttgcagttggacatccctattttcctattaaaaaacctaacaataacaaaatattagttcctaaagtatcaggattacaatacagggtatttagaataNatttacctgaccccttagtgaataagtttggttttcctgacacctcattttaNaatccagatacacagcggctggtttgggcctgtgtaggtgttgaggtaggNcgtggtcagccattaggtgtgggcattagtggccatcctttattaaataaattggatgacacagaaaatgctagtgcttatgcagcaaatgcaggtgtggataatagagaatgtatatctatggattacaaacaaacacaattgtgtttaattggttgcaaaccacctataggggaacactggggcaaaggatccccatgtaNcaatgttgcagtaaNtccaggtgattgtccaccattagagttaataaacacagttattcaggatggtgatatggttgatacNggctttggtgctatggactttactacattacaggctaacaaaagtgaagttccactggatatttgtacNtctatttgcaaatatccagattatattaaaatggtgtcagaaccatatggcgacagcttatttttttatttacgaagggaacaaatgtttgttagacatttatttaatagggctggtNctgttggtgaaaatgtaccagacgatttatacattaaaggctctgggtctactgcaaatttagccagttcaaattattttcctacacctagtggttctatggttacctctgatgcccaaatattNaataaaccttattggttacaacgagcacagggccacaataatggcatttgttggggtaaccaactatttgttactgtNgtNgatactacacgcagtacaaatatgtcattatgtgctgccatatctacttcagaaNctacatataaaaaatactaactttaaNgagtacctacgacatggggaggaatatgatttacagtttatttttcaactgtgcaaaataaccttaactgcagacgttatgacatacatacattctatgaattccactattttggaggactggaattttggtNtacaacctccNccaggaggcacactagaagatacttataggtttgtaacatcccaggcaattgcttgtcaaaaacatacacctccagcacctaaagaagatgatccccttaaaaaataNactttttgggaagtaaatttaaaNgaaaagttttctgcagacctagatcagtttcctttaggacgcaaatttttactacaagcaggattNaaggccaaaccaaaatttacattaggaaaacgaaaagctacacccaccacctcatctacctctacaactgctaaacgcaaaaaacgtaagctgtaa

PRIMER_PRODUCT_SIZE_RANGE=200-1200

PRIMER_OPT_SIZE=23

PRIMER_MIN_SIZE=22

PRIMER_MAX_SIZE=25

PRIMER_NUM_NS_ACCEPTED=0

PRIMER_NUM_RETURN=10

PRIMER_MISPRIMING_LIBRARY=mispriming.fasta

PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0

PRIMER_EXPLAIN_FLAG=1

PRIMER_OPT_TM=60

PRIMER_MIN_TM=59

PRIMER_MAX_TM=61

PRIMER_LEFT_EXPLAIN=considered 4449, too many Ns 373, GC content failed 127, low tm 2109, high tm 1284, high any compl 6, high end compl 27, high repeat similarity 31, long poly-x seq 61, ok 431

PRIMER_RIGHT_EXPLAIN=considered 4370, too many Ns 400, GC content failed 120, low tm 2106, high tm 1190, high any compl 2, high end compl 6, high repeat similarity 6, long poly-x seq 58, ok 482

PRIMER_PAIR_EXPLAIN=considered 343, unacceptable product size 320, ok 23

PRIMER_PAIR_PENALTY=0.1407

PRIMER_LEFT_PENALTY=0.081493

PRIMER_RIGHT_PENALTY=0.059210

PRIMER_LEFT_SEQUENCE=tgtgctgccatatctacttcaga

PRIMER_RIGHT_SEQUENCE=taggtgctggaggtgtatgtttt

PRIMER_LEFT=1116,23

PRIMER_RIGHT=1393,23

PRIMER_LEFT_TM=59.919

PRIMER_RIGHT_TM=59.941

PRIMER_LEFT_GC_PERCENT=43.478

PRIMER_RIGHT_GC_PERCENT=43.478

PRIMER_LEFT_SELF_ANY=4.00

PRIMER_RIGHT_SELF_ANY=2.00

PRIMER_LEFT_SELF_END=3.00

PRIMER_RIGHT_SELF_END=0.00

PRIMER_LEFT_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.

PRIMER_PAIR_MISPRIMING_SCORE=20.00, reverse EF177179 Human papillomavirus type 56 clone Qv22608, complete genome.

PRIMER_LEFT_END_STABILITY=6.7000

PRIMER_RIGHT_END_STABILITY=7.0000

PRIMER_PAIR_COMPL_ANY=5.00

PRIMER_PAIR_COMPL_END=1.00

PRIMER_PRODUCT_SIZE=278

PRIMER_PAIR_PENALTY_1=0.1407

PRIMER_LEFT_1_PENALTY=0.081493

PRIMER_RIGHT_1_PENALTY=0.059210

PRIMER_LEFT_1_SEQUENCE=tgtgctgccatatctacttcaga

PRIMER_RIGHT_1_SEQUENCE=ttaggtgctggaggtgtatgttt

PRIMER_LEFT_1=1116,23

PRIMER_RIGHT_1=1394,23

PRIMER_LEFT_1_TM=59.919

PRIMER_RIGHT_1_TM=59.941

PRIMER_LEFT_1_GC_PERCENT=43.478

PRIMER_RIGHT_1_GC_PERCENT=43.478

PRIMER_LEFT_1_SELF_ANY=4.00

PRIMER_RIGHT_1_SELF_ANY=2.00

PRIMER_LEFT_1_SELF_END=3.00

PRIMER_RIGHT_1_SELF_END=0.00

PRIMER_LEFT_1_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_1_MISPRIMING_SCORE=11.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.

PRIMER_PAIR_1_MISPRIMING_SCORE=20.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.

PRIMER_LEFT_1_END_STABILITY=6.7000

PRIMER_RIGHT_1_END_STABILITY=7.0000

PRIMER_PAIR_1_COMPL_ANY=5.00

PRIMER_PAIR_1_COMPL_END=1.00

PRIMER_PRODUCT_SIZE_1=279

PRIMER_PAIR_PENALTY_2=0.1407

PRIMER_LEFT_2_PENALTY=0.081493

PRIMER_RIGHT_2_PENALTY=0.059210

PRIMER_LEFT_2_SEQUENCE=tgtgctgccatatctacttcaga

PRIMER_RIGHT_2_SEQUENCE=tttaggtgctggaggtgtatgtt

PRIMER_LEFT_2=1116,23

PRIMER_RIGHT_2=1395,23

PRIMER_LEFT_2_TM=59.919

PRIMER_RIGHT_2_TM=59.941

PRIMER_LEFT_2_GC_PERCENT=43.478

PRIMER_RIGHT_2_GC_PERCENT=43.478

PRIMER_LEFT_2_SELF_ANY=4.00

PRIMER_RIGHT_2_SELF_ANY=2.00

PRIMER_LEFT_2_SELF_END=3.00

PRIMER_RIGHT_2_SELF_END=0.00

PRIMER_LEFT_2_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_2_MISPRIMING_SCORE=11.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.

PRIMER_PAIR_2_MISPRIMING_SCORE=20.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_LEFT_2_END_STABILITY=6.7000

PRIMER_RIGHT_2_END_STABILITY=6.6000

PRIMER_PAIR_2_COMPL_ANY=5.00

PRIMER_PAIR_2_COMPL_END=2.00

PRIMER_PRODUCT_SIZE_2=280

PRIMER_PAIR_PENALTY_3=0.2276

PRIMER_LEFT_3_PENALTY=0.081493

PRIMER_RIGHT_3_PENALTY=0.146140

PRIMER_LEFT_3_SEQUENCE=tgtgctgccatatctacttcaga

PRIMER_RIGHT_3_SEQUENCE=aaggggatcatcttctttaggtg

PRIMER_LEFT_3=1116,23

PRIMER_RIGHT_3=1410,23

PRIMER_LEFT_3_TM=59.919

PRIMER_RIGHT_3_TM=59.854

PRIMER_LEFT_3_GC_PERCENT=43.478

PRIMER_RIGHT_3_GC_PERCENT=43.478

PRIMER_LEFT_3_SELF_ANY=4.00

PRIMER_RIGHT_3_SELF_ANY=7.00

PRIMER_LEFT_3_SELF_END=3.00

PRIMER_RIGHT_3_SELF_END=1.00

PRIMER_LEFT_3_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_3_MISPRIMING_SCORE=11.00, X74481 Human papillomavirus type 52 genomic DNA.

PRIMER_PAIR_3_MISPRIMING_SCORE=20.00, DQ057317 Human papillomavirus type 52 isolate HK1151 L1 protein (L1) gene, partial cds.

PRIMER_LEFT_3_END_STABILITY=6.7000

PRIMER_RIGHT_3_END_STABILITY=7.9000

PRIMER_PAIR_3_COMPL_ANY=4.00

PRIMER_PAIR_3_COMPL_END=2.00

PRIMER_PRODUCT_SIZE_3=295

PRIMER_PAIR_PENALTY_4=0.2322

PRIMER_LEFT_4_PENALTY=0.173020

PRIMER_RIGHT_4_PENALTY=0.059210

PRIMER_LEFT_4_SEQUENCE=actgcaaatttagccagttcaaa

PRIMER_RIGHT_4_SEQUENCE=tttaggtgctggaggtgtatgtt

PRIMER_LEFT_4=930,23

PRIMER_RIGHT_4=1395,23

PRIMER_LEFT_4_TM=60.173

PRIMER_RIGHT_4_TM=59.941

PRIMER_LEFT_4_GC_PERCENT=34.783

PRIMER_RIGHT_4_GC_PERCENT=43.478

PRIMER_LEFT_4_SELF_ANY=8.00

PRIMER_RIGHT_4_SELF_ANY=2.00

PRIMER_LEFT_4_SELF_END=2.00

PRIMER_RIGHT_4_SELF_END=0.00

PRIMER_LEFT_4_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_4_MISPRIMING_SCORE=11.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.

PRIMER_PAIR_4_MISPRIMING_SCORE=19.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_LEFT_4_END_STABILITY=7.3000

PRIMER_RIGHT_4_END_STABILITY=6.6000

PRIMER_PAIR_4_COMPL_ANY=4.00

PRIMER_PAIR_4_COMPL_END=2.00

PRIMER_PRODUCT_SIZE_4=466

PRIMER_PAIR_PENALTY_5=0.2322

PRIMER_LEFT_5_PENALTY=0.173020

PRIMER_RIGHT_5_PENALTY=0.059210

PRIMER_LEFT_5_SEQUENCE=actgcaaatttagccagttcaaa

PRIMER_RIGHT_5_SEQUENCE=taggtgctggaggtgtatgtttt

PRIMER_LEFT_5=930,23

PRIMER_RIGHT_5=1393,23

PRIMER_LEFT_5_TM=60.173

PRIMER_RIGHT_5_TM=59.941

PRIMER_LEFT_5_GC_PERCENT=34.783

PRIMER_RIGHT_5_GC_PERCENT=43.478

PRIMER_LEFT_5_SELF_ANY=8.00

PRIMER_RIGHT_5_SELF_ANY=2.00

PRIMER_LEFT_5_SELF_END=2.00

PRIMER_RIGHT_5_SELF_END=0.00

PRIMER_LEFT_5_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_5_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.

PRIMER_PAIR_5_MISPRIMING_SCORE=21.00, reverse PPHT39 Human papillomavirus ORFs.

PRIMER_LEFT_5_END_STABILITY=7.3000

PRIMER_RIGHT_5_END_STABILITY=7.0000

PRIMER_PAIR_5_COMPL_ANY=4.00

PRIMER_PAIR_5_COMPL_END=3.00

PRIMER_PRODUCT_SIZE_5=464

PRIMER_PAIR_PENALTY_6=0.2322

PRIMER_LEFT_6_PENALTY=0.173020

PRIMER_RIGHT_6_PENALTY=0.059210

PRIMER_LEFT_6_SEQUENCE=actgcaaatttagccagttcaaa

PRIMER_RIGHT_6_SEQUENCE=ttaggtgctggaggtgtatgttt

PRIMER_LEFT_6=930,23

PRIMER_RIGHT_6=1394,23

PRIMER_LEFT_6_TM=60.173

PRIMER_RIGHT_6_TM=59.941

PRIMER_LEFT_6_GC_PERCENT=34.783

PRIMER_RIGHT_6_GC_PERCENT=43.478

PRIMER_LEFT_6_SELF_ANY=8.00

PRIMER_RIGHT_6_SELF_ANY=2.00

PRIMER_LEFT_6_SELF_END=2.00

PRIMER_RIGHT_6_SELF_END=0.00

PRIMER_LEFT_6_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_6_MISPRIMING_SCORE=11.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.

PRIMER_PAIR_6_MISPRIMING_SCORE=20.00, reverse PPHT39 Human papillomavirus ORFs.

PRIMER_LEFT_6_END_STABILITY=7.3000

PRIMER_RIGHT_6_END_STABILITY=7.0000

PRIMER_PAIR_6_COMPL_ANY=4.00

PRIMER_PAIR_6_COMPL_END=3.00

PRIMER_PRODUCT_SIZE_6=465

PRIMER_PAIR_PENALTY_7=0.2545

PRIMER_LEFT_7_PENALTY=0.173020

PRIMER_RIGHT_7_PENALTY=0.081493

PRIMER_LEFT_7_SEQUENCE=actgcaaatttagccagttcaaa

PRIMER_RIGHT_7_SEQUENCE=tctgaagtagatatggcagcaca

PRIMER_LEFT_7=930,23

PRIMER_RIGHT_7=1138,23

PRIMER_LEFT_7_TM=60.173

PRIMER_RIGHT_7_TM=59.919

PRIMER_LEFT_7_GC_PERCENT=34.783

PRIMER_RIGHT_7_GC_PERCENT=43.478

PRIMER_LEFT_7_SELF_ANY=8.00

PRIMER_RIGHT_7_SELF_ANY=4.00

PRIMER_LEFT_7_SELF_END=2.00

PRIMER_RIGHT_7_SELF_END=3.00

PRIMER_LEFT_7_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_7_MISPRIMING_SCORE=12.00, reverse FJ385268 Human papillomavirus type 58 isolate HPV58sc78, complete genome.

PRIMER_PAIR_7_MISPRIMING_SCORE=19.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_LEFT_7_END_STABILITY=7.3000

PRIMER_RIGHT_7_END_STABILITY=8.2000

PRIMER_PAIR_7_COMPL_ANY=5.00

PRIMER_PAIR_7_COMPL_END=2.00

PRIMER_PRODUCT_SIZE_7=209

PRIMER_PAIR_PENALTY_8=0.3192

PRIMER_LEFT_8_PENALTY=0.173020

PRIMER_RIGHT_8_PENALTY=0.146140

PRIMER_LEFT_8_SEQUENCE=actgcaaatttagccagttcaaa

PRIMER_RIGHT_8_SEQUENCE=aaggggatcatcttctttaggtg

PRIMER_LEFT_8=930,23

PRIMER_RIGHT_8=1410,23

PRIMER_LEFT_8_TM=60.173

PRIMER_RIGHT_8_TM=59.854

PRIMER_LEFT_8_GC_PERCENT=34.783

PRIMER_RIGHT_8_GC_PERCENT=43.478

PRIMER_LEFT_8_SELF_ANY=8.00

PRIMER_RIGHT_8_SELF_ANY=7.00

PRIMER_LEFT_8_SELF_END=2.00

PRIMER_RIGHT_8_SELF_END=1.00

PRIMER_LEFT_8_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.

PRIMER_RIGHT_8_MISPRIMING_SCORE=11.00, X74481 Human papillomavirus type 52 genomic DNA.

PRIMER_PAIR_8_MISPRIMING_SCORE=19.00, X74481 Human papillomavirus type 52 genomic DNA.

PRIMER_LEFT_8_END_STABILITY=7.3000

PRIMER_RIGHT_8_END_STABILITY=7.9000

PRIMER_PAIR_8_COMPL_ANY=3.00

PRIMER_PAIR_8_COMPL_END=2.00

PRIMER_PRODUCT_SIZE_8=481

PRIMER_PAIR_PENALTY_9=0.3690

PRIMER_LEFT_9_PENALTY=0.309788

PRIMER_RIGHT_9_PENALTY=0.059210

PRIMER_LEFT_9_SEQUENCE=atgctagtgcttatgcagcaaat

PRIMER_RIGHT_9_SEQUENCE=taggtgctggaggtgtatgtttt

PRIMER_LEFT_9=475,23

PRIMER_RIGHT_9=1393,23

PRIMER_LEFT_9_TM=60.310

PRIMER_RIGHT_9_TM=59.941

PRIMER_LEFT_9_GC_PERCENT=39.130

PRIMER_RIGHT_9_GC_PERCENT=43.478

PRIMER_LEFT_9_SELF_ANY=6.00

PRIMER_RIGHT_9_SELF_ANY=2.00

PRIMER_LEFT_9_SELF_END=3.00

PRIMER_RIGHT_9_SELF_END=0.00

PRIMER_LEFT_9_MISPRIMING_SCORE=12.00, EU918766 Human papillomavirus type 33 isolate LZcc12-33, complete genome.

PRIMER_RIGHT_9_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.

PRIMER_PAIR_9_MISPRIMING_SCORE=22.00, reverse PPHT39 Human papillomavirus ORFs.

PRIMER_LEFT_9_END_STABILITY=7.2000

PRIMER_RIGHT_9_END_STABILITY=7.0000

PRIMER_PAIR_9_COMPL_ANY=5.00

PRIMER_PAIR_9_COMPL_END=2.00

PRIMER_PRODUCT_SIZE_9=919

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