t/data/bug2862.pmr

   1 SEQUENCE=atgNaggtgacttttatttacatcctagttattacatgttacgaaaacgacgtaaacgtttaccatattttttttcagatgtctctttggctgcctagtgaggccactgtctacttgcctcctgtcccagtatctaaNgttgtaagcacggatgaatatgttgcacgcacaaacatatattatcatgcaggaacatccagactacttgcagttggacatccctattttcctattaaaaaacctaacaataacaaaatattagttcctaaagtatcaggattacaatacagggtatttagaataNatttacctgaccccttagtgaataagtttggttttcctgacacctcattttaNaatccagatacacagcggctggtttgggcctgtgtaggtgttgaggtaggNcgtggtcagccattaggtgtgggcattagtggccatcctttattaaataaattggatgacacagaaaatgctagtgcttatgcagcaaatgcaggtgtggataatagagaatgtatatctatggattacaaacaaacacaattgtgtttaattggttgcaaaccacctataggggaacactggggcaaaggatccccatgtaNcaatgttgcagtaaNtccaggtgattgtccaccattagagttaataaacacagttattcaggatggtgatatggttgatacNggctttggtgctatggactttactacattacaggctaacaaaagtgaagttccactggatatttgtacNtctatttgcaaatatccagattatattaaaatggtgtcagaaccatatggcgacagcttatttttttatttacgaagggaacaaatgtttgttagacatttatttaatagggctggtNctgttggtgaaaatgtaccagacgatttatacattaaaggctctgggtctactgcaaatttagccagttcaaattattttcctacacctagtggttctatggttacctctgatgcccaaatattNaataaaccttattggttacaacgagcacagggccacaataatggcatttgttggggtaaccaactatttgttactgtNgtNgatactacacgcagtacaaatatgtcattatgtgctgccatatctacttcagaaNctacatataaaaaatactaactttaaNgagtacctacgacatggggaggaatatgatttacagtttatttttcaactgtgcaaaataaccttaactgcagacgttatgacatacatacattctatgaattccactattttggaggactggaattttggtNtacaacctccNccaggaggcacactagaagatacttataggtttgtaacatcccaggcaattgcttgtcaaaaacatacacctccagcacctaaagaagatgatccccttaaaaaataNactttttgggaagtaaatttaaaNgaaaagttttctgcagacctagatcagtttcctttaggacgcaaatttttactacaagcaggattNaaggccaaaccaaaatttacattaggaaaacgaaaagctacacccaccacctcatctacctctacaactgctaaacgcaaaaaacgtaagctgtaa
   2 PRIMER_PRODUCT_SIZE_RANGE=200-1200
   3 PRIMER_OPT_SIZE=23
   4 PRIMER_MIN_SIZE=22
   5 PRIMER_MAX_SIZE=25
   6 PRIMER_NUM_NS_ACCEPTED=0
   7 PRIMER_NUM_RETURN=10
   8 PRIMER_MISPRIMING_LIBRARY=mispriming.fasta
   9 PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
  10 PRIMER_EXPLAIN_FLAG=1
  11 PRIMER_OPT_TM=60
  12 PRIMER_MIN_TM=59
  13 PRIMER_MAX_TM=61
  14 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
  15 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
  16 PRIMER_PAIR_EXPLAIN=considered 343, unacceptable product size 320, ok 23
  17 PRIMER_PAIR_PENALTY=0.1407
  18 PRIMER_LEFT_PENALTY=0.081493
  19 PRIMER_RIGHT_PENALTY=0.059210
  20 PRIMER_LEFT_SEQUENCE=tgtgctgccatatctacttcaga
  21 PRIMER_RIGHT_SEQUENCE=taggtgctggaggtgtatgtttt
  22 PRIMER_LEFT=1116,23
  23 PRIMER_RIGHT=1393,23
  24 PRIMER_LEFT_TM=59.919
  25 PRIMER_RIGHT_TM=59.941
  26 PRIMER_LEFT_GC_PERCENT=43.478
  27 PRIMER_RIGHT_GC_PERCENT=43.478
  28 PRIMER_LEFT_SELF_ANY=4.00
  29 PRIMER_RIGHT_SELF_ANY=2.00
  30 PRIMER_LEFT_SELF_END=3.00
  31 PRIMER_RIGHT_SELF_END=0.00
  32 PRIMER_LEFT_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
  33 PRIMER_RIGHT_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
  34 PRIMER_PAIR_MISPRIMING_SCORE=20.00, reverse EF177179 Human papillomavirus type 56 clone Qv22608, complete genome.
  35 PRIMER_LEFT_END_STABILITY=6.7000
  36 PRIMER_RIGHT_END_STABILITY=7.0000
  37 PRIMER_PAIR_COMPL_ANY=5.00
  38 PRIMER_PAIR_COMPL_END=1.00
  39 PRIMER_PRODUCT_SIZE=278
  40 PRIMER_PAIR_PENALTY_1=0.1407
  41 PRIMER_LEFT_1_PENALTY=0.081493
  42 PRIMER_RIGHT_1_PENALTY=0.059210
  43 PRIMER_LEFT_1_SEQUENCE=tgtgctgccatatctacttcaga
  44 PRIMER_RIGHT_1_SEQUENCE=ttaggtgctggaggtgtatgttt
  45 PRIMER_LEFT_1=1116,23
  46 PRIMER_RIGHT_1=1394,23
  47 PRIMER_LEFT_1_TM=59.919
  48 PRIMER_RIGHT_1_TM=59.941
  49 PRIMER_LEFT_1_GC_PERCENT=43.478
  50 PRIMER_RIGHT_1_GC_PERCENT=43.478
  51 PRIMER_LEFT_1_SELF_ANY=4.00
  52 PRIMER_RIGHT_1_SELF_ANY=2.00
  53 PRIMER_LEFT_1_SELF_END=3.00
  54 PRIMER_RIGHT_1_SELF_END=0.00
  55 PRIMER_LEFT_1_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
  56 PRIMER_RIGHT_1_MISPRIMING_SCORE=11.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.
  57 PRIMER_PAIR_1_MISPRIMING_SCORE=20.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.
  58 PRIMER_LEFT_1_END_STABILITY=6.7000
  59 PRIMER_RIGHT_1_END_STABILITY=7.0000
  60 PRIMER_PAIR_1_COMPL_ANY=5.00
  61 PRIMER_PAIR_1_COMPL_END=1.00
  62 PRIMER_PRODUCT_SIZE_1=279
  63 PRIMER_PAIR_PENALTY_2=0.1407
  64 PRIMER_LEFT_2_PENALTY=0.081493
  65 PRIMER_RIGHT_2_PENALTY=0.059210
  66 PRIMER_LEFT_2_SEQUENCE=tgtgctgccatatctacttcaga
  67 PRIMER_RIGHT_2_SEQUENCE=tttaggtgctggaggtgtatgtt
  68 PRIMER_LEFT_2=1116,23
  69 PRIMER_RIGHT_2=1395,23
  70 PRIMER_LEFT_2_TM=59.919
  71 PRIMER_RIGHT_2_TM=59.941
  72 PRIMER_LEFT_2_GC_PERCENT=43.478
  73 PRIMER_RIGHT_2_GC_PERCENT=43.478
  74 PRIMER_LEFT_2_SELF_ANY=4.00
  75 PRIMER_RIGHT_2_SELF_ANY=2.00
  76 PRIMER_LEFT_2_SELF_END=3.00
  77 PRIMER_RIGHT_2_SELF_END=0.00
  78 PRIMER_LEFT_2_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
  79 PRIMER_RIGHT_2_MISPRIMING_SCORE=11.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
  80 PRIMER_PAIR_2_MISPRIMING_SCORE=20.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
  81 PRIMER_LEFT_2_END_STABILITY=6.7000
  82 PRIMER_RIGHT_2_END_STABILITY=6.6000
  83 PRIMER_PAIR_2_COMPL_ANY=5.00
  84 PRIMER_PAIR_2_COMPL_END=2.00
  85 PRIMER_PRODUCT_SIZE_2=280
  86 PRIMER_PAIR_PENALTY_3=0.2276
  87 PRIMER_LEFT_3_PENALTY=0.081493
  88 PRIMER_RIGHT_3_PENALTY=0.146140
  89 PRIMER_LEFT_3_SEQUENCE=tgtgctgccatatctacttcaga
  90 PRIMER_RIGHT_3_SEQUENCE=aaggggatcatcttctttaggtg
  91 PRIMER_LEFT_3=1116,23
  92 PRIMER_RIGHT_3=1410,23
  93 PRIMER_LEFT_3_TM=59.919
  94 PRIMER_RIGHT_3_TM=59.854
  95 PRIMER_LEFT_3_GC_PERCENT=43.478
  96 PRIMER_RIGHT_3_GC_PERCENT=43.478
  97 PRIMER_LEFT_3_SELF_ANY=4.00
  98 PRIMER_RIGHT_3_SELF_ANY=7.00
  99 PRIMER_LEFT_3_SELF_END=3.00
 100 PRIMER_RIGHT_3_SELF_END=1.00
 101 PRIMER_LEFT_3_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
 102 PRIMER_RIGHT_3_MISPRIMING_SCORE=11.00, X74481 Human papillomavirus type 52 genomic DNA.
 103 PRIMER_PAIR_3_MISPRIMING_SCORE=20.00, DQ057317 Human papillomavirus type 52 isolate HK1151 L1 protein (L1) gene, partial cds.
 104 PRIMER_LEFT_3_END_STABILITY=6.7000
 105 PRIMER_RIGHT_3_END_STABILITY=7.9000
 106 PRIMER_PAIR_3_COMPL_ANY=4.00
 107 PRIMER_PAIR_3_COMPL_END=2.00
 108 PRIMER_PRODUCT_SIZE_3=295
 109 PRIMER_PAIR_PENALTY_4=0.2322
 110 PRIMER_LEFT_4_PENALTY=0.173020
 111 PRIMER_RIGHT_4_PENALTY=0.059210
 112 PRIMER_LEFT_4_SEQUENCE=actgcaaatttagccagttcaaa
 113 PRIMER_RIGHT_4_SEQUENCE=tttaggtgctggaggtgtatgtt
 114 PRIMER_LEFT_4=930,23
 115 PRIMER_RIGHT_4=1395,23
 116 PRIMER_LEFT_4_TM=60.173
 117 PRIMER_RIGHT_4_TM=59.941
 118 PRIMER_LEFT_4_GC_PERCENT=34.783
 119 PRIMER_RIGHT_4_GC_PERCENT=43.478
 120 PRIMER_LEFT_4_SELF_ANY=8.00
 121 PRIMER_RIGHT_4_SELF_ANY=2.00
 122 PRIMER_LEFT_4_SELF_END=2.00
 123 PRIMER_RIGHT_4_SELF_END=0.00
 124 PRIMER_LEFT_4_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
 125 PRIMER_RIGHT_4_MISPRIMING_SCORE=11.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
 126 PRIMER_PAIR_4_MISPRIMING_SCORE=19.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
 127 PRIMER_LEFT_4_END_STABILITY=7.3000
 128 PRIMER_RIGHT_4_END_STABILITY=6.6000
 129 PRIMER_PAIR_4_COMPL_ANY=4.00
 130 PRIMER_PAIR_4_COMPL_END=2.00
 131 PRIMER_PRODUCT_SIZE_4=466
 132 PRIMER_PAIR_PENALTY_5=0.2322
 133 PRIMER_LEFT_5_PENALTY=0.173020
 134 PRIMER_RIGHT_5_PENALTY=0.059210
 135 PRIMER_LEFT_5_SEQUENCE=actgcaaatttagccagttcaaa
 136 PRIMER_RIGHT_5_SEQUENCE=taggtgctggaggtgtatgtttt
 137 PRIMER_LEFT_5=930,23
 138 PRIMER_RIGHT_5=1393,23
 139 PRIMER_LEFT_5_TM=60.173
 140 PRIMER_RIGHT_5_TM=59.941
 141 PRIMER_LEFT_5_GC_PERCENT=34.783
 142 PRIMER_RIGHT_5_GC_PERCENT=43.478
 143 PRIMER_LEFT_5_SELF_ANY=8.00
 144 PRIMER_RIGHT_5_SELF_ANY=2.00
 145 PRIMER_LEFT_5_SELF_END=2.00
 146 PRIMER_RIGHT_5_SELF_END=0.00
 147 PRIMER_LEFT_5_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
 148 PRIMER_RIGHT_5_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
 149 PRIMER_PAIR_5_MISPRIMING_SCORE=21.00, reverse PPHT39 Human papillomavirus ORFs.
 150 PRIMER_LEFT_5_END_STABILITY=7.3000
 151 PRIMER_RIGHT_5_END_STABILITY=7.0000
 152 PRIMER_PAIR_5_COMPL_ANY=4.00
 153 PRIMER_PAIR_5_COMPL_END=3.00
 154 PRIMER_PRODUCT_SIZE_5=464
 155 PRIMER_PAIR_PENALTY_6=0.2322
 156 PRIMER_LEFT_6_PENALTY=0.173020
 157 PRIMER_RIGHT_6_PENALTY=0.059210
 158 PRIMER_LEFT_6_SEQUENCE=actgcaaatttagccagttcaaa
 159 PRIMER_RIGHT_6_SEQUENCE=ttaggtgctggaggtgtatgttt
 160 PRIMER_LEFT_6=930,23
 161 PRIMER_RIGHT_6=1394,23
 162 PRIMER_LEFT_6_TM=60.173
 163 PRIMER_RIGHT_6_TM=59.941
 164 PRIMER_LEFT_6_GC_PERCENT=34.783
 165 PRIMER_RIGHT_6_GC_PERCENT=43.478
 166 PRIMER_LEFT_6_SELF_ANY=8.00
 167 PRIMER_RIGHT_6_SELF_ANY=2.00
 168 PRIMER_LEFT_6_SELF_END=2.00
 169 PRIMER_RIGHT_6_SELF_END=0.00
 170 PRIMER_LEFT_6_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
 171 PRIMER_RIGHT_6_MISPRIMING_SCORE=11.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.
 172 PRIMER_PAIR_6_MISPRIMING_SCORE=20.00, reverse PPHT39 Human papillomavirus ORFs.
 173 PRIMER_LEFT_6_END_STABILITY=7.3000
 174 PRIMER_RIGHT_6_END_STABILITY=7.0000
 175 PRIMER_PAIR_6_COMPL_ANY=4.00
 176 PRIMER_PAIR_6_COMPL_END=3.00
 177 PRIMER_PRODUCT_SIZE_6=465
 178 PRIMER_PAIR_PENALTY_7=0.2545
 179 PRIMER_LEFT_7_PENALTY=0.173020
 180 PRIMER_RIGHT_7_PENALTY=0.081493
 181 PRIMER_LEFT_7_SEQUENCE=actgcaaatttagccagttcaaa
 182 PRIMER_RIGHT_7_SEQUENCE=tctgaagtagatatggcagcaca
 183 PRIMER_LEFT_7=930,23
 184 PRIMER_RIGHT_7=1138,23
 185 PRIMER_LEFT_7_TM=60.173
 186 PRIMER_RIGHT_7_TM=59.919
 187 PRIMER_LEFT_7_GC_PERCENT=34.783
 188 PRIMER_RIGHT_7_GC_PERCENT=43.478
 189 PRIMER_LEFT_7_SELF_ANY=8.00
 190 PRIMER_RIGHT_7_SELF_ANY=4.00
 191 PRIMER_LEFT_7_SELF_END=2.00
 192 PRIMER_RIGHT_7_SELF_END=3.00
 193 PRIMER_LEFT_7_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
 194 PRIMER_RIGHT_7_MISPRIMING_SCORE=12.00, reverse FJ385268 Human papillomavirus type 58 isolate HPV58sc78, complete genome.
 195 PRIMER_PAIR_7_MISPRIMING_SCORE=19.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
 196 PRIMER_LEFT_7_END_STABILITY=7.3000
 197 PRIMER_RIGHT_7_END_STABILITY=8.2000
 198 PRIMER_PAIR_7_COMPL_ANY=5.00
 199 PRIMER_PAIR_7_COMPL_END=2.00
 200 PRIMER_PRODUCT_SIZE_7=209
 201 PRIMER_PAIR_PENALTY_8=0.3192
 202 PRIMER_LEFT_8_PENALTY=0.173020
 203 PRIMER_RIGHT_8_PENALTY=0.146140
 204 PRIMER_LEFT_8_SEQUENCE=actgcaaatttagccagttcaaa
 205 PRIMER_RIGHT_8_SEQUENCE=aaggggatcatcttctttaggtg
 206 PRIMER_LEFT_8=930,23
 207 PRIMER_RIGHT_8=1410,23
 208 PRIMER_LEFT_8_TM=60.173
 209 PRIMER_RIGHT_8_TM=59.854
 210 PRIMER_LEFT_8_GC_PERCENT=34.783
 211 PRIMER_RIGHT_8_GC_PERCENT=43.478
 212 PRIMER_LEFT_8_SELF_ANY=8.00
 213 PRIMER_RIGHT_8_SELF_ANY=7.00
 214 PRIMER_LEFT_8_SELF_END=2.00
 215 PRIMER_RIGHT_8_SELF_END=1.00
 216 PRIMER_LEFT_8_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
 217 PRIMER_RIGHT_8_MISPRIMING_SCORE=11.00, X74481 Human papillomavirus type 52 genomic DNA.
 218 PRIMER_PAIR_8_MISPRIMING_SCORE=19.00, X74481 Human papillomavirus type 52 genomic DNA.
 219 PRIMER_LEFT_8_END_STABILITY=7.3000
 220 PRIMER_RIGHT_8_END_STABILITY=7.9000
 221 PRIMER_PAIR_8_COMPL_ANY=3.00
 222 PRIMER_PAIR_8_COMPL_END=2.00
 223 PRIMER_PRODUCT_SIZE_8=481
 224 PRIMER_PAIR_PENALTY_9=0.3690
 225 PRIMER_LEFT_9_PENALTY=0.309788
 226 PRIMER_RIGHT_9_PENALTY=0.059210
 227 PRIMER_LEFT_9_SEQUENCE=atgctagtgcttatgcagcaaat
 228 PRIMER_RIGHT_9_SEQUENCE=taggtgctggaggtgtatgtttt
 229 PRIMER_LEFT_9=475,23
 230 PRIMER_RIGHT_9=1393,23
 231 PRIMER_LEFT_9_TM=60.310
 232 PRIMER_RIGHT_9_TM=59.941
 233 PRIMER_LEFT_9_GC_PERCENT=39.130
 234 PRIMER_RIGHT_9_GC_PERCENT=43.478
 235 PRIMER_LEFT_9_SELF_ANY=6.00
 236 PRIMER_RIGHT_9_SELF_ANY=2.00
 237 PRIMER_LEFT_9_SELF_END=3.00
 238 PRIMER_RIGHT_9_SELF_END=0.00
 239 PRIMER_LEFT_9_MISPRIMING_SCORE=12.00, EU918766 Human papillomavirus type 33 isolate LZcc12-33, complete genome.
 240 PRIMER_RIGHT_9_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
 241 PRIMER_PAIR_9_MISPRIMING_SCORE=22.00, reverse PPHT39 Human papillomavirus ORFs.
 242 PRIMER_LEFT_9_END_STABILITY=7.2000
 243 PRIMER_RIGHT_9_END_STABILITY=7.0000
 244 PRIMER_PAIR_9_COMPL_ANY=5.00
 245 PRIMER_PAIR_9_COMPL_END=2.00
 246 PRIMER_PRODUCT_SIZE_9=919
 247 =