[EMBOSS] Eprimer3 alternative output formats

Stefanie Lück lueck at ipk-gatersleben.de
Wed Mar 25 13:54:44 UTC 2009


Hi!

Is there an argument in the eprimer 3 to get an alternative output format?

Something like this, which I got once from primer3 running on a server:

PRIMER_SEQUENCE_ID=HF15E08r
SEQUENCE=GCATGTAATAATGCCAAAGCTCACAGCTGCAGTTGAATCTTGGGACCCGCGGAGCGAGAATGTACCAATCCATGTATGGGTACACCCATGGCTGCCAACTCTAGGGCAAAGGATAGATACACTGTGCCACTCTATCCGGTACAAGCTGAGTAGTGTCCTCCAATTATGGCAAGCTCACGATTCATCAGCTTATGCTGTGCTATCTCCATGGAAGGGTGTATTTGATCCAGCAAGTTGGGAAGACTTGATAGTGCGTTATATCATTCCTAAACTGAAAATGGCACTCCAGGAGTTCCAGATTAACCCAGCAAGCCAAAAGTTTGACCAGTTTAACTGGGTTATGATCTGGGCTTCTGCTGTCCCGGTACACCATATGGTCCATATGTTGGAAGTTGATTTCTTTAGCAAGTGGCAGCTGGTTTTGTACCATTGGCTGAGCTCACCAAATCCTGATTTCAATGAGATAATGAATTGGTAT
PRIMER_PRODUCT_SIZE_RANGE=500-1000 450-500 400-450 350-400 300-350 250-300 200-250 150-200
PRIMER_OPT_TM=60.0
PRIMER_MIN_TM=58.0
PRIMER_MAX_TM=65.0
PRIMER_MAX_DIFF_TM=3.0
PRIMER_DNA_CONC=420
PRIMER_NUM_RETURN=1
PRIMER_PAIR_PENALTY=0.8691
PRIMER_LEFT_PENALTY=0.708329
PRIMER_RIGHT_PENALTY=0.160746
PRIMER_LEFT_SEQUENCE=GCATGTAATAATGCCAAAGC
PRIMER_RIGHT_SEQUENCE=TTGAAATCAGGATTTGGTGA
PRIMER_LEFT=0,20
PRIMER_RIGHT=458,20
PRIMER_LEFT_TM=59.292
PRIMER_RIGHT_TM=60.161
PRIMER_LEFT_GC_PERCENT=40.000
PRIMER_RIGHT_GC_PERCENT=35.000
PRIMER_LEFT_SELF_ANY=7.00
PRIMER_RIGHT_SELF_ANY=8.00
PRIMER_LEFT_SELF_END=2.00
PRIMER_RIGHT_SELF_END=2.00
PRIMER_LEFT_END_STABILITY=8.5000
PRIMER_RIGHT_END_STABILITY=7.9000
PRIMER_PAIR_COMPL_ANY=5.00
PRIMER_PAIR_COMPL_END=3.00
PRIMER_PRODUCT_SIZE=459

Thanks in advance!
Stefanie



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