PRIMER PICKING RESULTS FOR NM_006162_1p2 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 609 19 59.60 57.89 4.00 3.00 12.00 CCCCTCGATGACTTTCCTC RIGHT PRIMER 1101 21 59.30 52.38 5.00 1.00 11.00 gaggagacacctattggcaga SEQUENCE SIZE: 1180 INCLUDED REGION SIZE: 1180 PRODUCT SIZE: 493, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 3.00 TARGETS (start, len)*: 669,400 EXCLUDED REGIONS (start, len)*: 0,369 1180,0 0 gttcgcccccgtttcccccgccagccccagcgcccccctgcccggcccccggattccccg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 60 ttcccgcccctacgcccccatcccctccccgtgcgcccctccccgtgcgcccccctcccc XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 gtgcgccccccctccccgtgcgcccccctccccgtgcgccccccctccccgggcgccccc XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 180 ctccccgggcgccccccctccccgtgcgcccccccctccccgtgcgccccccctccccgt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 240 gcgcgccccgcctcttgcgcccctgcccccaggcgagcggctgccgcggcgcggggaggG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 GCGGGCGCTCGGCGACTCGTCCCCGGGGCCCCGCGCGGGCCCGGGCAGCAGGGGCGTGAT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 360 GTCACGGCAGGGAGGGGGCGCGGGAGCCGCCGGGCCGGCGGGGAGGCGGGGGAGGTGTTT XXXXXXXXX 420 TCCAGCTTTAAAAAGGCAGGAGGCAGAGCGCGGCCCTGCGTCAGAGCGAGACTCAGAGGC 480 TCCGAACTCGCCGGCGGAGTCGCCGCGCCAGATCCCAGCAGCAGGGCGCGGGCACCGGGG 540 CGCGGGCAGGGCTCGGAGCCACCGCGCAGGTCCTAGGGCCGCGGCCGGGCCCCGCCACGC 600 GCGCACACGCCCCTCGATGACTTTCCTCCGGGGCGCGCGGCGCTGAGCCCGGGGCGAGGG >>>>>>>>>>>>>>>>>>> 660 CTGTCTTCCCGGAGACCCGACCCCGGCAGCGCGGGGCGGCCGCTTCTCCTGTGCCTCCGC *************************************************** 720 CCGCCGCTCCACTCCCCGCCGCCGCCGCGCGGATGCCAAGCACCAGCTTTCCAGTCCCTT ************************************************************ 780 CCAAGTTTCCACTTGGCCCTGCGGCTGCGGTCTTCGGGAGAGGAGAAACTTTGGGGCCCG ************************************************************ 840 CGCCGCGCGCCGGCGGCACCATGAAGTCAGCGGAGGAAGgtaagccccgcgcggcctccg ************************************************************ 900 cccccggacccctgcgccccccacggcccgggccgcgccccccgaccccgcccccgtcgc ************************************************************ 960 ccgcacggaggggtccgggccagagaacgaggtcggccgggtctgtgcgcccagggaggg ************************************************************ 1020 gcgcggcgcggaccgggaacggcgtcccccagctcccagcagcccggttccgagcgcgcc ************************************************* 1080 ttctgccaataggtgtctcctctgccccagcgctgagggcgcgaggcgaggccgccgcgg <<<<<<<<<<<<<<<<<<<<< 1140 gtcccgccgaggaagcggctcgcaggccggcgatttgggg 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 609 19 59.60 57.89 4.00 3.00 12.00 CCCCTCGATGACTTTCCTC RIGHT PRIMER 1106 21 61.02 57.14 5.00 3.00 11.00 gggcagaggagacacctattg PRODUCT SIZE: 498, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 2.00 2 LEFT PRIMER 609 19 59.60 57.89 4.00 3.00 12.00 CCCCTCGATGACTTTCCTC RIGHT PRIMER 1100 21 58.80 47.62 5.00 1.00 11.00 aggagacacctattggcagaa PRODUCT SIZE: 492, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 2.00 3 LEFT PRIMER 609 19 59.60 57.89 4.00 3.00 12.00 CCCCTCGATGACTTTCCTC RIGHT PRIMER 1099 21 58.80 52.38 4.00 3.00 11.00 ggagacacctattggcagaag PRODUCT SIZE: 491, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 2.00 4 LEFT PRIMER 609 19 59.60 57.89 4.00 3.00 12.00 CCCCTCGATGACTTTCCTC RIGHT PRIMER 1100 22 59.77 50.00 5.00 3.00 11.00 aggagacacctattggcagaag PRODUCT SIZE: 492, 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 2347 0 0 376 1755 0 0 0 1 75 15 0 32 93 Right 647 0 0 0 563 0 0 0 0 26 0 0 12 46 Pair Stats: considered 154, unacceptable product size 113, tm diff too large 32, ok 9 primer3 release 1.0