************************************************************************ * Output from: * * * * PRIMER * * (Version 0.5) * * * * Copyright 1991, Whitehead Institute for Biomedical Research * ************************************************************************ Analyzing sequence 1 (seq1) '*' = target, 'X' = restriction site, '?' = N, number = high repeat homology +10 +20 +30 +40 TNNAGCTCGG TACCCGGGGA TCCTAATAGA ATCTCAGAAT CTGAGAATAA 1 -??------- ---------- ---------- ---------- ---------- ANNTCGAGCC ATGGGCCCCT AGGATTATCT TAGAGTCTTA GACTCTTATT +10 +20 +30 +40 CAGGNTCCAT GAAATGANTG TCAAAGAAAA AGATTCAGAG AAGAGAAAGC 51 ----?----- -------?-- ---------- ---------- ---------- GTCCNAGGTA CTTTACTNAC AGTTTCTTTT TCTAAGTCTC TTCTCTTTCG +10 +20 +30 +40 GGGTCAGCTG AGTAATAAAC ACCATGCAAA AATGAAACAA ACAAACCCCT 101 ---------- ---------- ---------- ---------- ---------- CCCAGTCGAC TCATTATTTG TGGTACGTTT TTACTTTGTT TGTTTGGGGA +10 +20 +30 +40 TGCCCCCTCA ACACACACAC ACACACACAC ACACACACAC ACACACACAC 151 ---------- -********* ********** ********** ********** ACGGGGGAGT TGTGTGTGTG TGTGTGTGTG TGTGTGTGTG TGTGTGTGTG +10 +20 +30 +40 ACACACACAC ACTTACTTCT TAAGGTCCAC ACCCGCAGCA GCAGCAGCAT 201 ********** *--------- ---------- ---------- ---------- TGTGTGTGTG TGAATGAAGA ATTCCAGGTG TGGGCGTCGT CGTCGTCGTA +10 +20 +30 +40 CACCTGGGGC TGTGTTAGAG ATATGGGCTA TAGTCTAGCT CCNGTCTCTG 251 ---------- ---------- ---------- ---------- --?------- GTGGACCCCG ACACAATCTC TATACCCGAT ATCAGATCGA GGNCAGAGAC +10 +20 +30 +40 AGGCTGAACT GTACACTCTT TCTTTTACCT GGNAACTGTA TTTCCCTGTG 301 ---------- ---------- ---------- --?------- ---------- TCCGACTTGA CATGTGAGAA AGAAAATGGA CCNTTGACAT AAAGGGACAC +10 +20 +30 +40 ATTTCACGGG NCTTTCTTAG GCATGCACGC CAGTTTTCTN ATCTTGCAAT 351 ---------- ?--------- ---------- ---------? ---------- TAAAGTGCCC NGAAAGAATC CGTACGTGCG GTCAAAAGAN TAGAACGTTA +10 +20 +30 +40 TTGGTTAAGG GTAGTAATCC TT 401 ---------- ---------- -- AACCAATTCC CATCATTAGG AA Acceptable regions for a primer: base 1 to 161 base 212 to 422 Examining 142 forward primers...38 forward primers accepted. Examining 192 reverse primers...53 reverse primers accepted. Testing pairs... Product size range 100-150... forward primer 127->147 : CAAAAATGAAACAAACAAACC Tm = 54.9 reverse primer 272->254 : ATCTCTAACACAGCCCCAG Tm = 55.2 PCR product length: 146, GC = 50% Product size range 150-250... forward primer 107->127 : GCTGAGTAATAAACACCATGC Tm = 55.0 reverse primer 278->259 : GCCCATATCTCTAACACAGC Tm = 54.9 PCR product length: 172, GC = 49% Product size range 250-400... forward primer 107->127 : GCTGAGTAATAAACACCATGC Tm = 55.0 reverse primer 401->381 : AATTGCAAGATNAGAAAACTG Tm = 55.0 PCR product length: 295, GC = 47%