[BioPython] primer3 parser
Sebastian Bassi
sbassi at asalup.org
Wed Jun 25 20:41:53 EDT 2003
I was trying to use primer3 on Biopython. I'm running Win2000, but I
have primer3 compiled (using GCC under CYGWIN, under Win2000). So
primer3 runs as a DOS program. I know it's not a DOS program, but it
runs in a console as a DOS program.
I couldn't run the Primer3Commandline.
Here is my code:
from Bio.Emboss.Applications import Primer3Commandline
from Bio.Emboss.Primer import Primer3Parser
from Bio.Application import generic_run
primercl=Primer3Commandline(cmd="primer3.exe")
primercl.set_parameter("-sequence", "in.pr3")
primercl.set_parameter("-outfile", "out.pr3")
primercl.set_parameter("-productsizerange", "30,10000")
primercl.set_parameter("-target", "100,200")
result, r, e = generic_run(primercl)
parser=Primer3Parser()
print parser.parse(open("out.pr3","r"))
When I run this, I get a error stating "out.pr3" doesn't exist, this is
because the program (primer3) didn't run. I put cmd="primer3.exe" on the
Primer3Commandline function since this is how I named the program. the
path is also fine.
Then, I tried another thing: I run primer3 "by hand" and then I tried to
parse the resulted file. To try the parse it, I did this code:
from Bio.Emboss.Applications import Primer3Commandline
from Bio.Emboss.Primer import Primer3Parser
from Bio.Application import generic_run
parser=Primer3Parser()
print parser.parse(open("data\\salida.txt","r"))
# salida.txt is the output file from primer3.
When I run this, I got this error:
>>>
Traceback (most recent call last):
File "C:\Program Files\Python22\primer3test.py", line 13, in ?
x=parser.parse(open("data\\salida.txt","r"))
File "C:\PROGRA~1\Python22\Lib\site-packages\Bio\Emboss\Primer.py",
line 154, in parse
self._scanner.feed(handle, self._consumer)
File "C:\PROGRA~1\Python22\Lib\site-packages\Bio\Emboss\Primer.py",
line 236, in feed
self._parser.parseFile(handle)
File "C:\PROGRA~1\Python22\Lib\site-packages\Martel\Parser.py", line
338, in parseFile
self.parseString(fileobj.read())
File "C:\PROGRA~1\Python22\Lib\site-packages\Martel\Parser.py", line
366, in parseString
self._err_handler.fatalError(result)
File
"C:\PROGRA~1\Python22\Lib\site-packages\_xmlplus\sax\handler.py", line
38, in fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
So there are 2 different problems:
1) primer3 doesn't run from biopython.
2) I can't parse the file product of manually ran primer3.
--
Best regards,
//=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\
\=// IT Manager Advanta Seeds - Balcarce Research Center - \=//
//=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\
\=// E-mail: sbassi at genesdigitales.com - ICQ UIN: 3356556 - \=//
http://Bioinformatica.info
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PRIMER_SEQUENCE_ID=seq49-int
SEQUENCE=CTTATATACTACAGTAATTAATAACATATTAGATGTGATTCAATTTTTAATACAAGCTGAAAAATCCTAGAATTGACGGGTTTAGATCGATATTAATACAAGATGATATACTACATGTGAAACTCTTAAATTAACAATCAAACTACAAGTGTATAATCTTAAACACTAAACAATATAGATAATATCAACAAAATATATACAACTCACAGATTACTATACATTTAAAATCAAATAAAATAATATCATATATATTTAAATCATCTTTACAATAAAAGTTTTTAGTTTAACTAAAGTATAAGCCTACCTGCGGTATACTGCAGGTTAATAACTAGATTATAGGGCTTATTGGATCTAAAGACGGGTCATCAAAGATTTCCTAAACTGAAGCAAAATATACTGAATATTCAAATATCTATCTGTTACCAAATTA
INCLUDED_REGION=150,130
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-430
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 402, GC content failed 221, low tm 181, ok 0
PRIMER_RIGHT_EXPLAIN=considered 402, GC content failed 321, low tm 81, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq54-int
SEQUENCE=CTCTTCTCTCGTCTCTCGTCAGCATATGCGTAAGAGCATCTCCATTGGTGAGATACTCCATGAGTACCTCATAATATATTATTAATATTTTAATTTAAGTAGAGAAACTTATACTAAAATTGTGCTTCCATTGGTGAAATACTCTTATGAGTATCTCATTAACATTAACATATTATTATATGTTTTTTATATTAAATTTAAAATCTCTACAATATTTTCAAACATATCAATTATTATTTTTACAATTATATTATTAAATAGTTTTATTATTTTTAAAACCATAATTAAACATAATTAAACATAATTAAACATTACTTTACATATAAAATCATAATAAAAAATATATCAATTAAACATAAAATTCCATATAAAACCATGATAACATAAATTAAATAGAAAAAATATATAAATTACACAGAAATTACATATAAAACCATGATAACATAAATCAAAACTAACTATATTATCTATTATGGTTTTACTCTTCATTTGATAATGCACCAAACTTTTGTCATATATGCTCAACTAGGTCATCTTTTAGTTGTTGGTGCATATCTCTATCACGAAGTCGAATTCGATTGCCAAAAATGTTGTAAAATAAAAATAGAAAATTTTAAATGTTTGTTTTC
INCLUDED_REGION=150,329
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-629
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 1596, GC content failed 1406, low tm 190, ok 0
PRIMER_RIGHT_EXPLAIN=considered 1596, GC content failed 1311, low tm 285, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq61-int
SEQUENCE=GACTATGACATCTCTAAGATAAGCAATACTCATGACTCTCGCTTGAGAAGTGCATTCTCATATTGACTACACCATTAGGCAATATGTTTCCTAACGTTTAACCATACAAGTTTGTCCCCCTCTTTCCCTTTGCAATACTAATTAGTATAACAAATTTCATTAGAGAATGTTTAATTTCATAAATATCTCAATATTTTGATATCTTATCCTATCTTCCATATTTTCTTTGCATTTTTTGTAAATAACTACATATTATTATCTTCAAAAATGAATTTCACATTTCAACAAAATAAAATATTTTCATGTTTCTACATGCATGCTAGTTTATTCTCTTAATAGTTGATACAATATTCCTAATACTCTTTAAGACGTGCATAAACTTTTTAAAATTGAATGATAATTAATTTAATTCACATCGACTTTAGACTACGTTCCAAGTAAACTTCC
INCLUDED_REGION=150,147
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-447
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 464, GC content failed 232, low tm 219, long poly-x seq 13, ok 0
PRIMER_RIGHT_EXPLAIN=considered 464, GC content failed 225, low tm 226, long poly-x seq 13, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq63-int
SEQUENCE=TTATTCTCCAATTTGGATTTTCTTTCTCGAAAGTGAAAGGAATGATGAATGGTAAAGAAATTGGACACCTTTTCCCATGGATACTATGGTATGTATAGAAGGCTCAAAATAGCTTTATACAGTAGAAACTCTATAAATTAGTAATGTTGGGATCATGAAATTTTATTAATTTATAATGATATTAATTTATCCTATAAATTAATATTTATTAACTTATACGATAAGTTAATAAATATTAATTTATAGAAATATTTACATAAAATACAATATTATATTCTTTTTAAAATGTTTCTTAATTTAAGTTTTTATATGTTTTGTTGTTTGCATATATAATTATGTTAGTTTTAGTTTTTTTTTTACTTCTTTAATTTATTTTTCAGCAAGATATTGTGTCTATATATCTACGCCATTAACGTCAATGTAAACGTAAACATGAAGCTTAATCCAATTTCTCTTTACTCAAATCTTAGCAATGCTTTCTCAAAAAGATTTTACAAAATCAACTATGACGGATCAAATA
INCLUDED_REGION=150,220
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-520
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 942, GC content failed 900, low tm 42, ok 0
PRIMER_RIGHT_EXPLAIN=considered 942, GC content failed 843, low tm 99, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq100-int
SEQUENCE=ACCAAAGTTCAGAAATTTGAATTAGAGACATTAAAATATAAAAATATCATTCTACTTCCACTAAAACCCTCTTCCAAGCTAACGATGCGGGTTTAATTCCCAAGACTTGCGCAAAAAGCATGCCCAATATTGCTTTATCCAACCTCCGATGACCGTCTCTATCTTCTTCTCCTTTTCTCGTTCTTTTGATTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTGATTCTGATACTTAATCTTCTGTCTTCACATATGGAGCATAGATACTTGACTCGAGTAGCTTTGGATCGTTAACATCAAGATCCTCAACATGGTCTGCGAAGACGTAAACTACTCTACTACGATAGTAGTCATATTCATGCTGA
INCLUDED_REGION=150,121
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-421
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 348, low tm 344, ok 4
PRIMER_RIGHT_EXPLAIN=considered 348, low tm 348, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq164-int
SEQUENCE=ACTTGAAAAACCATCATAAACAATTTTAATCTCGATAAAACTACATGTACTTTCGGATTTGTTCTTAAAACTACGCCTCCAATTGAACCGACCAGTTAACCGATAATTATACATCCGGTTTGACTTACCCATAATTTAACCAAAACTAATCCGATTTTGACTCTATTTTAACCCAATTTATACCCAAAAAATATATTCTCTAGAAGAAAAATACTTTTTATTTATTTTCATTTATTTTTGATAAAAAAATAAAAATAAATTAATTAATTTTACCAAAATAATAAAATAACAAAATATACCGCAAAATAATATAACAAAATAGACAACAAATTCTTTTTATAAATACAATGGTGTTATATATATAAATGTATTTGGTATATACTCTAAATTTAATAATTCAAAAGCCATTTTCTTTTTACAAACACCATAATCATATATAAATATATATATATATATATACATATATAACTCATCTTGAATATATAAAAAGAAAACTGAATCTATAAAGAAAAATAAATTTATAAATACCATAAGATATACTTTGATTGTGGTGTTTACGGATATTTATAAAAATAAATTTGGCATATATTTTGAATTTCATTACATATATAGAGTTCAAAGGTCATATATTATGATTTCAAGAAAAATGAATATTTTTGTTTAAAAAAAGACAT
INCLUDED_REGION=150,374
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-674
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 1830, GC content failed 1143, low tm 674, long poly-x seq 13, ok 0
PRIMER_RIGHT_EXPLAIN=considered 1866, GC content failed 1253, low tm 613, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq179-int
SEQUENCE=CAGAGAGATTTGACAGCGAAGCTCCACCATGTTTTAGATCATATATAGCCGTTTGAAGAAAAAAACTGAAAATGTCGTCCACATTGTGCTACACTCTGTCCCTATAGGACCTACGCAACTTTTCTATAAGCCATATTTCAAATATTTCCGGTTATTTTTGACATCTTAATATATATATGACAGTTAAAAACAAGCAGATTAAAAATATTTATTTTTAAAAAGTTCAACCAATCATAATAAAGACTACAGAATATAAATATTAAATAAAATATTAAAATAATATATAATTTTTGGGAAAAATGTTATTTAATACCTCAACTAACAAAAAATGGCCAAATTAACCGTGAACTCGTGAAATGGCCGTTTTAACTCTCAACAAAAAGTTGACTTCTGTTTTAACCTTTAAGTTTGCGTTGACTCGGCCTAATTAACCACCGTTAAAAATCCTTCTAACAGCGTAATTGACAGCCGTTA
INCLUDED_REGION=150,174
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-474
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 666, GC content failed 392, low tm 274, ok 0
PRIMER_RIGHT_EXPLAIN=considered 666, GC content failed 404, low tm 262, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq270-int
SEQUENCE=TGGAGAAAAAATCTCTGTTGAAAATCTTAAGAGTCCATGGGAAGCATGATGAGTGTCAGCTGCATGAAAGTGTGTAGCTTTCGTTTTCCATGCATCAAAGTTAAGCTTATTATATGTCATTGTTTTGATTAAATTACATAAAAGTAACGATTAAAGTAGACTGTAATTATTAAAAACATCAACTTAATTTGCTTTTAAAACTCCAACTAATTATCCAACAACAAATTCAAAACAATAAAAATTAGATACATATAAATGTCAATAAAATAAATTCCTCACCTTTACCTATAACTACTTTTTCTATCCACTAAATATTTTGTAATGCTTTGTGTTACCAATCAATCAAATCCTTAGTAGTAAACCGCTTACCAAATACGACCAATATATCATTGAGTTTGAGACATTGACTAGTGCAGAGGATTGCTAGATTTCCTATGGGAACGAGGGAGCTACAAATTCGGAAAGT
INCLUDED_REGION=150,166
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-466
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 618, GC content failed 323, low tm 293, ok 2
PRIMER_RIGHT_EXPLAIN=considered 618, GC content failed 227, low tm 389, ok 2
PRIMER_PAIR_EXPLAIN=considered 1, unacceptable product size 1, ok 0
=
PRIMER_SEQUENCE_ID=seq286-int
SEQUENCE=TGAGAACGTCGTTAAAGGAGTAATATTTGATAAACATCGATCAATAAGAAAACTTACGTTTGGTCAAAGAGGAGAATCGAGCAAGGTACGAATTTATCGACCGGACGAAGGAGTTTGGAGATCGGAGCGAAGACGAAACATCAAGCAAGCCACGATCCTATTTTCTTCAAATTAATTACCTTTTTCAGAAAATATACTTTTTTATTCTTTTTGATAAATACCATATTTTATGGATTTTACATTAATTTGGAACAATTATTTTAATGATACATGTATAATTATTTTTTTTTAAACTATGGGTTATTTTTTTCAAAAAAATAATGTGTGGATGTTTCAAAAAAAATCAAATTTCATAATGAAACAAACAAAAATTCGAAGAAGATAATACACATTGTGTTGAGAACAAACAATTATTACACATTGTCGGATTAACCATATAAATACCGAACTTTGCCTTTTGATTTGGCCAAAACCTTAAAGTTAAGGTAAAACCTTCATAGCTGTCCAACAATGTTAATAA
INCLUDED_REGION=150,220
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-520
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 884, GC content failed 644, low tm 225, long poly-x seq 15, ok 0
PRIMER_RIGHT_EXPLAIN=considered 831, GC content failed 606, low tm 195, long poly-x seq 30, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq399-int
SEQUENCE=ACGATGTAAGTAGTCGAAATTTGCTAATGTAGTTTCATTAGCTAATATTGATTTTATTACTAATTTAGTTAGTTGACTGATCAATAGGGATTTGAGACAAATTCAAGACCGGTTCAAGACTCAAAGGGAAGATCAGTTTGGTTCTATGATCCAAATGTTTGATATATTTACTTCTATTATTTTGTAATTTATACCCTTTTAACAAAATTATCATTTTGTAATATTTGAGATTTTTTTCAAACTTTAATAAAGAAAACAATTGATGAGTATTTTTTTTTAATATACCATTAGTATTCCACTATAATAATCATCATCGGAAAAAAAAAAACACGCCTGATTACATCAACGTTGCTAAAACAGTATGTCCTATAAAAGCTAGGCAAGCAGTGTTAGCTACTAAATCCAACTCTAATCAAGCAGTATAAAAACTTGAAACAACAAATAAAC
INCLUDED_REGION=150,147
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-447
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 485, GC content failed 383, low tm 97, long poly-x seq 5, ok 0
PRIMER_RIGHT_EXPLAIN=considered 480, GC content failed 400, low tm 73, long poly-x seq 7, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq414-int
SEQUENCE=GGAAGAGGCACCACCAGCCTTCTCATTCTCCTCTTCATCAGCCATCGACAAAGTTATTAGGAGTGGAATAGTATCCCGCGCCAATCATGCACTACCGGCAACAACAACGAGCTCTTCTTAAGATCAACATGTGCGTCATAAGAATGGGCTGATCAACATGTTTGTTTTTGCTCTGTTTTTATAATGAAAGTTTAAGTTCATTTGTTTTTCTTTTTTCCATAACTAATCTTTTCTTTTTTGTTGATCAAATAAATATCAAATTTCAACCCAAAAAAAAAAAAAATCCTGCAAGATATTGGAATAAGAGATTTATTTGGAAAAAAATTATATATAACACGAACGGTGTTATGTAAACTCAACATAATTCGATCGTAAGAGAGTTTCTCAATATATTTGGAAAAGGTAAAACCAAACGAAACTAAAATTAC
INCLUDED_REGION=150,128
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-428
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 332, GC content failed 99, low tm 215, long poly-x seq 15, ok 3
PRIMER_RIGHT_EXPLAIN=considered 265, GC content failed 139, low tm 88, long poly-x seq 38, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq427-int
SEQUENCE=ATTATATACTACAATAGTTAATAACATATTAGATGTGATTCAATTTTTAATACAAGCTGGAAAATCTTAGAATTGACGGGTTTAGATCGATATTAATACAAGATGGTATGCTACATGTGAAACTCTTAAATTAACAATCAAACTACAAGTGTATAATCTTAAACACTAAACAATATAGATAATATCAACAAAACATATACAACTCACAGTTTACTATACATTTAAAATCAAATAAAATAATATCATATATTTTTAAATCATCTTTATAATAAAAGTTTTTAGTTTAACTAAAATATAAGCCTACCTGCGGTATACTGCAGATTAATCTCTAGATTATAGGGCTTATTGGAACTAAAGACGGGTCATCAAAGATTTCCTAAACTGAAGCAAAATATACTGAATATTCAAATATTTATATGTTACCAAATTATAAACAA
INCLUDED_REGION=150,137
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-437
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 444, GC content failed 233, low tm 211, ok 0
PRIMER_RIGHT_EXPLAIN=considered 444, GC content failed 373, low tm 71, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq464-int
SEQUENCE=CCAGCTGGCGAAGAAGTAAAAAAGCAAATAGATTAGCCAAAATACGACAACACCCTCTACCTACAAGCCATAGATACCATGACTCATAAGGGCAACACCGACATTTGTCATCATTTGATAAATCTAACCAACCCTGAAGGGCATATTCGTCTTTCCAAATAGTTATAAAGAGACAGAGACGAAGAAGGAGAGAGAGAAAGAGACAAGATTAGAGAAGAGGATAAGAGAGAGAAAGATATAGAGAATTTGTTGTCTTTTTTTCTTTTTCTTTTGTGGGGTATTTGTTTTTTTTTTTCTCCTTAAAAAGTTTTTTTTTTTGTGTGTATGAAAAAAAAAGCTTTGAAATTCTCTCTCGACAATGGTGTCGGACCAGGATCTAGCGAAAGGAGTCGAGACTTTGCTTCGACAATCCGACCCTAGCTCTCTCACATCGTTAAGCAGTATTGTTCAGCAGCTTGAAGCTAAGTTAGGGTTAGACCT
INCLUDED_REGION=150,180
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-480
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 649, GC content failed 32, low tm 581, long poly-x seq 16, ok 20
PRIMER_RIGHT_EXPLAIN=considered 557, GC content failed 131, low tm 367, long poly-x seq 48, ok 11
PRIMER_PAIR_EXPLAIN=considered 36, unacceptable product size 28, ok 8
PRIMER_PAIR_QUALITY=8.4784
PRIMER_LEFT_SEQUENCE=CAGAGACGAAGAAGGAGAGAGA
PRIMER_RIGHT_SEQUENCE=CCCCACAAAAGAAAAAGAAAAA
PRIMER_LEFT=173,22
PRIMER_RIGHT=277,22
PRIMER_LEFT_TM=58.011
PRIMER_RIGHT_TM=59.511
PRIMER_LEFT_SELF_ANY=2.00
PRIMER_RIGHT_SELF_ANY=1.00
PRIMER_LEFT_SELF_END=0.00
PRIMER_RIGHT_SELF_END=0.00
PRIMER_LEFT_END_STABILITY=6.4000
PRIMER_RIGHT_END_STABILITY=7.6000
PRIMER_PAIR_COMPL_ANY=2.00
PRIMER_PAIR_COMPL_END=0.00
PRIMER_PRODUCT_SIZE=105
PRIMER_PAIR_QUALITY_1=8.6305
PRIMER_LEFT_1_SEQUENCE=GACAGAGACGAAGAAGGAGAGA
PRIMER_RIGHT_1_SEQUENCE=CCCCACAAAAGAAAAAGAAAAA
PRIMER_LEFT_1=171,22
PRIMER_RIGHT_1=277,22
PRIMER_LEFT_1_TM=57.859
PRIMER_RIGHT_1_TM=59.511
PRIMER_LEFT_1_SELF_ANY=2.00
PRIMER_RIGHT_1_SELF_ANY=1.00
PRIMER_LEFT_1_SELF_END=0.00
PRIMER_RIGHT_1_SELF_END=0.00
PRIMER_LEFT_1_END_STABILITY=6.4000
PRIMER_RIGHT_1_END_STABILITY=7.6000
PRIMER_PAIR_1_COMPL_ANY=2.00
PRIMER_PAIR_1_COMPL_END=0.00
PRIMER_PRODUCT_SIZE_1=107
PRIMER_PAIR_QUALITY_2=8.6305
PRIMER_LEFT_2_SEQUENCE=GAGACAGAGACGAAGAAGGAGA
PRIMER_RIGHT_2_SEQUENCE=CCCCACAAAAGAAAAAGAAAAA
PRIMER_LEFT_2=169,22
PRIMER_RIGHT_2=277,22
PRIMER_LEFT_2_TM=57.859
PRIMER_RIGHT_2_TM=59.511
PRIMER_LEFT_2_SELF_ANY=2.00
PRIMER_RIGHT_2_SELF_ANY=1.00
PRIMER_LEFT_2_SELF_END=0.00
PRIMER_RIGHT_2_SELF_END=0.00
PRIMER_LEFT_2_END_STABILITY=7.9000
PRIMER_RIGHT_2_END_STABILITY=7.6000
PRIMER_PAIR_2_COMPL_ANY=2.00
PRIMER_PAIR_2_COMPL_END=0.00
PRIMER_PRODUCT_SIZE_2=109
PRIMER_PAIR_QUALITY_3=8.7278
PRIMER_LEFT_3_SEQUENCE=CAGAGACGAAGAAGGAGAGAGA
PRIMER_RIGHT_3_SEQUENCE=CCCCACAAAAGAAAAAGAAAA
PRIMER_LEFT_3=173,22
PRIMER_RIGHT_3=277,21
PRIMER_LEFT_3_TM=58.011
PRIMER_RIGHT_3_TM=58.262
PRIMER_LEFT_3_SELF_ANY=2.00
PRIMER_RIGHT_3_SELF_ANY=1.00
PRIMER_LEFT_3_SELF_END=0.00
PRIMER_RIGHT_3_SELF_END=0.00
PRIMER_LEFT_3_END_STABILITY=6.4000
PRIMER_RIGHT_3_END_STABILITY=7.3000
PRIMER_PAIR_3_COMPL_ANY=2.00
PRIMER_PAIR_3_COMPL_END=0.00
PRIMER_PRODUCT_SIZE_3=105
PRIMER_PAIR_QUALITY_4=8.8799
PRIMER_LEFT_4_SEQUENCE=GACAGAGACGAAGAAGGAGAGA
PRIMER_RIGHT_4_SEQUENCE=CCCCACAAAAGAAAAAGAAAA
PRIMER_LEFT_4=171,22
PRIMER_RIGHT_4=277,21
PRIMER_LEFT_4_TM=57.859
PRIMER_RIGHT_4_TM=58.262
PRIMER_LEFT_4_SELF_ANY=2.00
PRIMER_RIGHT_4_SELF_ANY=1.00
PRIMER_LEFT_4_SELF_END=0.00
PRIMER_RIGHT_4_SELF_END=0.00
PRIMER_LEFT_4_END_STABILITY=6.4000
PRIMER_RIGHT_4_END_STABILITY=7.3000
PRIMER_PAIR_4_COMPL_ANY=2.00
PRIMER_PAIR_4_COMPL_END=0.00
PRIMER_PRODUCT_SIZE_4=107
=
PRIMER_SEQUENCE_ID=seq518-int
SEQUENCE=ATACTCTCATATTTGAAACATAAGTCTCCTCAAAAAAGCATTTGTGAAATGGTTTATACGACCTTGCGTGATGATGTAAGGTTTGTCTCCATGATATGCCCTTGTATATTAACCCAAGATATGAGAGACGTCGAGAAACATACAAATAATGCACTATAATTTATAACAGTAAAGTTTTAAAATAATGTTTCCTAAGATAAAAAATTTAAAATAATGTTATAATAGGTATCATTAATTGGAATTTATATTCAAAATGAAAATAGACAAGTCTTAAGAAAATAAATAATAACAAAAACTAAGAAGGAGAAAAGGTTTCCTCTTTGATTAGAATGCAATATATGGGGTTATTTTCCACTGTTCTCAATTAAAATATTCTTCTGAAAATCCACATTATTCCCTCATTTTCATGTATATAATTCTCTTACATGGCCAGTTGCAACTACAATC
INCLUDED_REGION=150,147
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-447
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 495, GC content failed 389, low tm 103, long poly-x seq 3, ok 0
PRIMER_RIGHT_EXPLAIN=considered 504, GC content failed 336, low tm 168, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq529-int
SEQUENCE=GCACATTTAAGGGGGAAAATAGTTCTTTTTAAACTAGTGGCAGCTACAAGGCCCATGACAAGTTAATGATCAATGGATCTCAAGCCCACTAATAGTATTAGATTAATAGATAATTAATGGACCGTATGAAATTTCTTAATTGCCAAGTTGATGAAACAGCTATAAATAGAAAATTCGATGATTTGGTGATTTTTTTTAAAATATAACAAACAGATTGATTAATAGAAAATTGTGTGGTTTTATGTATAATAATACTTTTCACAATCTTTTCTTTTCTTCATATAAACAAAACAGTCAAAAGAAGAATTTATGAAATTGTTAACAAATTTATAGCCATGGCCGGAAAGTTGGATTGAGCCCAAAATTTTGATTAGTCTTCGATGCAAATGTAATCACCAAGAGATATTTTCTTAGGAATTATGTTAGCTCTTTTCCAATCTTATAACATCATGTAGTGTTTTTTGG
INCLUDED_REGION=150,165
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-465
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 593, GC content failed 262, low tm 318, long poly-x seq 5, ok 8
PRIMER_RIGHT_EXPLAIN=considered 612, GC content failed 201, low tm 411, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq564-int
SEQUENCE=TGCATACTTGCAGGCATTTGACCAACGACTATACATATTGAAAGCAAAATATCCACCAGGGATGATAGGGTTAGATCCCACATTCAATATCTTTTGTCTTTGTTATTTATGAAAAACAAATATTTATCAGGAAAAAAACGTTTCTTCTCTAGTGGTATAAGATAATAACAAAATTTAATACTTAGTTAATGTATTTACTATCTTCAAACTTACCATCCTTCAACATTAATATTGATCAATTTTTATTTTTTTTACTAAACTACTTCCACTAAAAAAATGCAAAAGAAGAGATATATATTTAAGTCAAAGTAATTAAAGATGGATGGGTGATTCTTCAGCAAAACGGCGCCGTAGAGGTGTCTTATCCTACATTACAGCTGGGTTGTGGCAGACATCATAGGGCCTACGTATATTTGAGCTTTACTGTACGTAAAGCTTTAACATATCTAGTTAGTTCTCACTGTAC
INCLUDED_REGION=150,166
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-466
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 612, GC content failed 349, low tm 258, long poly-x seq 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 542, GC content failed 261, low tm 259, long poly-x seq 21, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, unacceptable product size 1, ok 0
=
PRIMER_SEQUENCE_ID=seq592-int
SEQUENCE=GTTTAAACGCAGCGGGTGCGGTTGCGGTTGCGGAAGTTTGCGGAAACGGGCGGTTGCGGTTTCAAGCGTTATCAAGTGTTTTGAACGACTGGTTGAGCGTTTGGTAATGGGTGCGTTTGCGGGAGTTTTATGACTGGTAAACCAGCGGGTGCGATAGTAATTAAATAAAAAATAACCAAAATAAATATAATATATTACTATTAAAAAAAAAAATACAATATATTATTATGATAAATTGATAATATTTGAAAAATTAAACATACTTAATAATTAAAACCATAAATAAAACTGAAAATTCAAAAATAAATAAATTTTATAAGAAAAAGCTTAATACTTTATGCATTTGGTACATCACCAAAATTGCATCAAGTAGTGTGATAAACTGTAAATAACGTTGAACTCGCGGGTTTTCCGGATTGCCTCTATACATATGATAAAGTTTCTTCAAGATATCCAAACGATTTTTAACAC
INCLUDED_REGION=150,171
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-471
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 648, GC content failed 644, low tm 4, ok 0
PRIMER_RIGHT_EXPLAIN=considered 648, GC content failed 628, low tm 20, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq607-int
SEQUENCE=AATGTAACCATGGGCGTTCGGGTATTCGGTTTGGTTCCCGTTCGGTTCTAGTTCGGTTCCGATTCTTTCTGTTCTCGATTTTAGGATCCATATAGGAACCGAAACAGTTTCAGTTCGGTTCAGGTTCGGGTTCGGTTCTGAAGTTTAGGATCCATTAGAATATTTTATTTCGAATATTTCAGATATTTTTTGTCTTTTTTTCCGGATATTTTGGTGTTTTTATATATTTTTCCTTATTTGGGTATTTTTGATTATTCAAACTAAAAATAACTAATATCTTTGGATATATAATCATATTTCGGATACGCAAAATATTTTGGTTCGGTTCGGGTTCAGTTCTAATTACTTTGGTTCTAGAATTTAGGATCTATTTGAGTAGTTTACCATTTCGGGTCGGATTCGGGTTGCTTCAGTTCGGATTCGGTTCTTTCAGTTT
INCLUDED_REGION=150,136
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-436
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 354, GC content failed 232, low tm 88, long poly-x seq 22, ok 12
PRIMER_RIGHT_EXPLAIN=considered 432, GC content failed 245, low tm 171, long poly-x seq 4, ok 12
PRIMER_PAIR_EXPLAIN=considered 1, unacceptable product size 1, ok 0
=
PRIMER_SEQUENCE_ID=seq668-int
SEQUENCE=TTGTGGGGAAACTTAAATGATTAATTGATACCAAAACAAAATGTGTTTTGATGATTAACGTGGGGACCAAAACGTGGGTCGGAGAGTGCCCGGGGCCGGGAGTGCTAGCCCTCTTAATTTACGTGACTCACTTAATTACACGCATCTACCATTTTGTCATGGTGATTTATTTATATGTATACTATAAATTTAATATTTTATTTTCAAATAAAAAAACAAAAAATTTAATTAATTATCTCATATTTCCTTTGTTCTTTAAACTTGATTTTTTTTTTAAACACACATATTAAAAAACATATTAAATATTGGTTATAAATATATTACTTTTTGTGTATTACAGTTTTCTATAACTCTAAACCAATGATAATTAACTATTTTTCTTGAAAATTACAATTCACCAATACTAACCAATAAATATTACAAAGAAAACTTAAAAAATCAATCTTTTAGAAACAATTTTTTTTCTCTATATAATCAATCATTTAATAACAGAGGGAATATCGTTTTCCTTTCTGCTAAAATATCTTAGCTTTCTAATAGGTAATTTAGCGTACCGATTCATTTGTATTAACATGAATCTAATCTTTTATTTTCTGTTTTTACTACTAGTTAAATCGTTAGTCAAC
INCLUDED_REGION=150,326
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-626
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 1562, GC content failed 1017, low tm 540, long poly-x seq 5, ok 0
PRIMER_RIGHT_EXPLAIN=considered 1549, GC content failed 1039, low tm 500, long poly-x seq 10, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=seq745-int
SEQUENCE=TTAGTGCTCAGGAGAAATAAAATGTTGATAGACGTCTTTGAACAATCAATGGAGTGGAAGGTGTGGCCGAATTAGTCAATTTGTTAACAAATGCCAAGGCCAAATATTTTGTTGGGCTTTTAGTTTGGCCCAAATTGTATACAATGCTTGATGACAAACTCGGAAAAAAAAAGCAAAAAAACAAAAAAAAACCTCTCATAATACATTAGTTTATTATATAAAATGTTCCACTAAATCACACATCTCCTCCTCACTCAACACGAAACCCTTCCAAATTCCTTCACTATCCATTTCAATTTCATCCTCCCCTTGTCCTTGATGCTCCATTGAAGCTATGTGAAGCTCATCACCATAATCAAACACACCTCCACATTGATCATCGATGTCATCACCATACTCTTCTGGCTCAGCTTTAACAAACTTTCCATTATCCTCAACACCATGGCTTGAGATCAC
INCLUDED_REGION=150,156
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-456
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 449, GC content failed 188, low tm 208, long poly-x seq 31, ok 22
PRIMER_RIGHT_EXPLAIN=considered 558, GC content failed 112, low tm 341, high tm 10, ok 95
PRIMER_PAIR_EXPLAIN=considered 1, unacceptable product size 1, ok 0
=
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