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10.test
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10.test
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Michigan State University: RDP Primer Design
--------------------------------------------
Program User Settings
--------------------------------------------
Fasta file: /work/gunturus/netbeans/PrimerDesignTestFiles/10.fasta
Sliding Scale - t or f? true
Tree Weighted - t or f? false
Henikoff Weighted - t or f? false
Product Min Length: 50
Product Max Length: 280
Filters: T end: false, No Poly3GC: true, Poly Run: 4, GC Content:0.35 - 0.7
Oligo Min Size: 17
Oligo Max Size: 23
Max Number Mismatches: 0
Melting Temp Min: 50.0
Melting Temp Max: 55.0
Homodimer Max: 35.0
Hairpin Max: 35.0
Sodium Conc: 50.0
Magnesium Conc: 1.5
Max Degeneracy for each primer: 1
Max Num of Assays: 5
Sequence Length: 2556
--------------------------------------------
1 Primer Pair: DegeneratePair{fwdOligo=[Oligo{seq=GGTGATGCTCTATGTCG}{ Tm:51.104295068781255}{EndPos:1308}
] revOligo=[Oligo{seq=CGCTGATAGTCGTCGTT}{ Tm:53.57712353986443}{EndPos:1407}
]}
Sequences hit
AYVM01000020_proteinid_ESW64469
CP000463_proteinid_ABJ08452
AYWP01000015_proteinid_ESY65944
--------------------------------------------
uniform weighted coverage: 0.30000000000000004
uniform Seq coverage: 0.3
--------------------------------------------
1 Primer Pair: DegeneratePair{fwdOligo=[Oligo{seq=GTTGGAGAAGTTCATCGA}{ Tm:51.13460444762893}{EndPos:1681}
] revOligo=[Oligo{seq=CCGTCATAGCCGTGATA}{ Tm:52.40930449187209}{EndPos:1791}
]}
Sequences hit
AQPH01000002_proteinid_EPY03426
GQ167279_proteinid_ACT67911
--------------------------------------------
uniform weighted coverage: 0.5
uniform Seq coverage: 0.5
--------------------------------------------
1 Primer Pair: DegeneratePair{fwdOligo=[Oligo{seq=ATCAAGGACATGATCCACAT}{ Tm:53.629645470139906}{EndPos:384}
] revOligo=[Oligo{seq=AAGTCCGACGTGAACTG}{ Tm:53.56006666264665}{EndPos:487}
]}
Sequences hit
FQ859181_proteinid_CCB66896
MPOK01000095_proteinid_OOH75520
--------------------------------------------
uniform weighted coverage: 0.7
uniform Seq coverage: 0.7
--------------------------------------------
1 Primer Pair: DegeneratePair{fwdOligo=[Oligo{seq=ATTAGAGGATGTGCTTATGC}{ Tm:52.40305046105556}{EndPos:336}
] revOligo=[Oligo{seq=AAGACAATGTCTCTTTCCTG}{ Tm:52.40305046105556}{EndPos:505}
]}
Sequences hit
CAHT01000076_proteinid_CCG92393
--------------------------------------------
uniform weighted coverage: 0.7999999999999999
uniform Seq coverage: 0.8
--------------------------------------------
1 Primer Pair: DegeneratePair{fwdOligo=[Oligo{seq=TCGAGAAGAGCCTGAGAG}{ Tm:54.57113905062039}{EndPos:1166}
] revOligo=[Oligo{seq=GCTGGTAGTCGTCGTTG}{ Tm:54.57078506199167}{EndPos:1406}
]}
Sequences hit
JGVW01000086_proteinid_KDB07443
--------------------------------------------
uniform weighted coverage: 0.8999999999999999
uniform Seq coverage: 0.9
--------------------------------------------
Total Runtime: 69 seconds
Finished at: 2018/11/19 03:45:25