PRIMER PICKING RESULTS FOR NM_006162_2p2 Using mispriming library /data/utswmc/elxr/ELXR-main/repbase/humrep_and_simple.fa Using 0-based sequence positions OLIGO start len tm gc% any 3' rep seq LEFT PRIMER 601 20 61.14 60.00 4.00 2.00 11.00 GTCCTCCCTAGCTCCAAACG RIGHT PRIMER 1100 20 60.03 60.00 4.00 0.00 11.00 GAGCTGGTGTACTGGGTGGT SEQUENCE SIZE: 1699 INCLUDED REGION SIZE: 1699 PRODUCT SIZE: 500, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00 TARGETS (start, len)*: 669,400 EXCLUDED REGIONS (start, len)*: 0,369 1369,330 0 gtgaggacccggccgcctctccctgggaaggacgttcgggggcttgtgctgctgttaggg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 60 gaggaggggaggtgggcagtgaggggctcacgggagccttgttggccaggtgggactggg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 gctgtcactccaagtcgcccggagctgtccggcagcgtggtctcagggacgtttgctgag XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 180 gcccgctccttggggtccgttggtcgaggccgggggttgctggccggccctgagttcatg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 240 ggtttctgctttgtgatgcccagcccctcatgctcccatctgcttctttttctctctagA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 ACACTATGGCTATGCATCCTCCAACGTCAGCCCCGCCCTGCCGCTCCCCACGGCGCACTC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 360 CACCCTGCCGGCCCCGTGCCACAACCTTCAGACCTCCACACCGGGCATCATCCCGCCGGC XXXXXXXXX 420 GGATCACCCCTCGGGGTACGGAGCAGCTTTGGACGGTGGGCCCGCGGGCTACTTCCTCTC 480 CTCCGGCCACACCAGGCCTGATGGGGCCCCTGCCCTGGAGAGTCCTCGCATCGAGATAAC 540 CTCGTGCTTGGGCCTGTACCACAACAATAACCAGTTTTTCCACGATGTGGAGGTGGAAGA 600 CGTCCTCCCTAGCTCCAAACGGTCCCCCTCCACGGCCACGCTGAGTCTGCCCAGCCTGGA >>>>>>>>>>>>>>>>>>>> 660 GGCCTACAGAGACCCCTCGTGCCTGAGCCCGGCCAGCAGCCTGTCCTCCCGGAGCTGCAA *************************************************** 720 CTCAGAGGCCTCCTCCTACGAGTCCAACTACTCGTACCCGTACGCGTCCCCCCAGACGTC ************************************************************ 780 GCCATGGCAGTCTCCCTGCGTGTCTCCCAAGACCACGGACCCCGAGGAGGGCTTTCCCCG ************************************************************ 840 CGGGCTGGGGGCCTGCACACTGCTGGGTTCCCCGCGGCACTCCCCCTCCACCTCGCCCCG ************************************************************ 900 CGCCAGCGTCACTGAGGAGAGCTGGCTGGGTGCCCGCTCCTCCAGACCCGCGTCCCCTTG ************************************************************ 960 CAACAAGAGGAAGTACAGCCTCAACGGCCGGCAGCCGCCCTACTCACCCCACCACTCGCC ************************************************************ 1020 CACGCCGTCCCCGCACGGCTCCCCGCGGGTCAGCGTGACCGACGACTCGTGGTTGGGCAA ************************************************* 1080 CACCACCCAGTACACCAGCTCGGCCATCGTGGCCGCCATCAACGCGCTGACCACCGACAG <<<<<<<<<<<<<<<<<<<< 1140 CAGCCTGGACCTGGGAGATGGCGTCCCTGTCAAGTCCCGCAAGACCACCCTGGAGCAGCC 1200 GCCCTCAGTGGCGCTCAAGGTGGAGCCCGTCGGGGAGGACCTGGGCAGCCCCCCGCCCCC 1260 GGCCGACTTCGCGCCCGAAGACTACTCCTCTTTCCAGCACATCAGGAAGGGCGGCTTCTG 1320 CGACCAGTACCTGGCGGTGCCGCAGCACCCCTACCAGTGGGCGAAGCCCAAGCCCCTGTC XXXXXXXXXXX 1380 CCCTACGTCCTACATGAGgtgagccggcagcgcggggcgggacggggaggcgaggggagg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1440 cgcggggcggggcggaacgcggggagcgggacggggggcggcgcggggcggccgtgtctg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1500 gggacgagagtcaggacctgggtgggcaggtgggctcctcgtggagctgggaggcagagt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1560 ctgtccccatgtctgcctcctcatgcagacttttccttgtgcgcctcgcctctgcctccg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1620 tctgcgcgtttcccatctgaagtctccagatcctctcgggccctgctgatggcctcgtgt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1680 tcgctcagtctctgcaaac XXXXXXXXXXXXXXXXXXX KEYS (in order of precedence): XXXXXX excluded region ****** target >>>>>> left primer <<<<<< right primer ADDITIONAL OLIGOS start len tm gc% any 3' rep seq 1 LEFT PRIMER 599 21 61.89 57.14 4.00 0.00 11.00 ACGTCCTCCCTAGCTCCAAAC RIGHT PRIMER 1097 21 61.32 57.14 4.00 0.00 11.00 CTGGTGTACTGGGTGGTGTTG PRODUCT SIZE: 499, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 3.00 2 LEFT PRIMER 599 21 61.89 57.14 4.00 0.00 11.00 ACGTCCTCCCTAGCTCCAAAC RIGHT PRIMER 1096 20 60.32 55.00 4.00 0.00 11.00 TGGTGTACTGGGTGGTGTTG PRODUCT SIZE: 498, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 3.00 3 LEFT PRIMER 602 19 60.34 57.89 4.00 2.00 11.00 TCCTCCCTAGCTCCAAACG RIGHT PRIMER 1100 20 60.03 60.00 4.00 0.00 11.00 GAGCTGGTGTACTGGGTGGT PRODUCT SIZE: 499, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00 4 LEFT PRIMER 599 20 61.14 55.00 4.00 0.00 11.00 ACGTCCTCCCTAGCTCCAAA RIGHT PRIMER 1097 21 61.32 57.14 4.00 0.00 11.00 CTGGTGTACTGGGTGGTGTTG PRODUCT SIZE: 499, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 2.00 Statistics con too in in no tm tm high high high high sid many tar excl bad GC too too any 3' lib poly end ered Ns get reg GC% clamp low high compl compl sim X stab ok Left 2136 0 0 375 1075 0 0 0 12 175 28 0 52 419 Right 2124 0 0 335 1332 0 0 1 4 121 42 0 51 238 Pair Stats: considered 1554, unacceptable product size 1533, tm diff too large 13, ok 8 primer3 release 1.0