PRIMER PICKING RESULTS FOR NM_006162_10p1 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 237 18 59.65 50.00 2.00 0.00 12.00 gggcgttgctttgatgtt RIGHT PRIMER 736 21 59.91 47.62 3.00 1.00 12.00 TTCTATGATGCCCTGATGGTC SEQUENCE SIZE: 2395 INCLUDED REGION SIZE: 2395 PRODUCT SIZE: 500, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 0.00 TARGETS (start, len)*: 269,400 EXCLUDED REGIONS (start, len)*: 0,0 969,1426 0 cagcatcttcccagcatcgcggccggcacctggcacctgcactttggccgtcagagacgt 60 gctggtaccgtgctacggacgagggcggtcactctggcgaccccagctctctgccgaggc 120 agccaggcactggctcacgacactcatggaccagggtgggaccgaggaggaaatgtgggt 180 tcctggggagatgccttgtcacaggcgtgagcgtcactgatggagaagcagggctggggg >>> 240 cgttgctttgatgtttatggtatttctctaatactttctcaatttttcttttcttacagT >>>>>>>>>>>>>>> ******************************* 300 AAATGAAATAATACGAAATGACCTCTCCAGCACGAGCACCCACTCCTAGTTGCCACATTG ************************************************************ 360 GAGCACTCAGTTCAGCAGGGGTATGCTGACTTCAGCAGACAAAGACTTTTGAATAAATAA ************************************************************ 420 ACTGAACTCACACCTGGTACCACTCAGAACCTCCAACTGACTGAATGCCAGGAGCTGAAC ************************************************************ 480 ATTAATATGTGCAAAGATTGGCTCTCCAACAAGAAGGAAAGCAGGGAGGAAGGGAGACCA ************************************************************ 540 CTGTGTCACCTGGAGGAGAAGTCATCTCATGACAACAGAAGGGAGGTGGCCGGGCTGAGC ************************************************************ 600 ACGGGAGACCCACCGTGCAGGGGCCTTTCATGGGAACGGCCCACACGCAGTTTGACCCCA ************************************************************ 660 CGCCCAGCCCTTCTGGCACCCCTGGGGTTCAATACTGGAAGTGCCTTATTTAACCAGACC ********* <<<< 720 ATCAGGGCATCATAGAATTGAGCATTGAATTTGCTACTGTAGGAGTATTTTTAGGAGCAG <<<<<<<<<<<<<<<<< 780 AAACTGCAAACACATTTCATTGTGAGGTTTTACCCTCTGTATGAATGAAGAGAACGCTGG 840 AAGGCTGCGAGAGGACTCTAGTATGAGTCTCCAACATTTGGAACGTTTCCTGGGCTGTCA 900 CGTACACTCCTGCTGCCTTACACAGTGCATTTTAGAATCTTCCAGTCTGTCATCTCAGCT 960 CTTTTGTAACATGCTTCCCTTGTCTGCGCGGTTGAAACCGTAGGCTTGTTCATAGTCGCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1020 TGCTCGCATCTTTGTTTTTAATCTGGCTTCGAACATAGCACAAGTAACTTGAATAGCACA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1080 TCAATAGGTTACTGGACAAAAGCAGAAAAACCTGTTACAGGATAGCCTGCATTTGCATGT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1140 GTGTACATATCTAGGCATCTATTTATGTATAAATAATAACAGAGCCGACGTGTCCTCGCC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1200 CAGGAGGGCTTCCCTGTCAGCAATAACCGGCATCCGTTTTGGAACCTGCGTCTGGGGCTC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1260 CAGTCGCTGCTCTTGCTGGCGTCCATCGCCGCCTCGGACGGCCGTGCATTTTCTCGTCTC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1320 ACGCAGTTCGAGGAGGACCCTAGAAAGCCAGGAGCTGTGATTGACAGTAGCTGTAGGTTA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1380 CCAGACGGCAACATTAGAAAGTGATTGTAAATAACATGCAACCTAAGTGTAATATATTTG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1440 TTCAGTTATAAGATGATTGTTTCACAGAAGCCTTACCACTCTCTGCTTCATCTAAGAAAA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1500 CCAATACCAAAAACGCCACTTTAATGCTCAGCCCTGCGTTGTGTGTTTTCAGATGAGTTA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1560 CTGTTAACAGGTAGGTTTGTGTAGGCCTTGCTGGGCACTCTGTACAATTAGTTGCTTATT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1620 ACGTATGATTACTCACAGCGATCTATTGTTCCATATAACCAAAAAGCATGGTTTATTCAT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1680 TGAAACACGGTTGACCTGAACTCGTGCCTTAGGAATTAATGCCCCCTTATGGAACCTGCC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1740 TGAATTGCACCTGCGGGTGGAGGCTCCGGCTGTGAAGTCACTGAACAGAACGTCGCTGAT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1800 GGAGAAAGGGCTCCCGCAGAAGGAACGGCCTGTACCGTGCGCTCCGGCACAATCGCGTCT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1860 CTTGTGTCTCACTCACGGAAAGAAACAACCTGAAGGCCATCCCGTCGGTCTGCACGTAAC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1920 CGTGAAGACGTGTGGCCGCGTCCCACCTGCGGCTGGGTACCCTGCACCCGGCACTGTAGG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1980 AGTCACGTGCAGCCTTTCTCAGGGGACTGTCATTGAAAAGGAAACGTTTGATGTCTGTGT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2040 CAGCTGTCTTTGTAGTTAGGAAATAGATCCAATAAAGCCGTATTTTTTTGCTGGacaggc XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2100 gtagtctgcgagtggttcatgatacgcgtggaagatgccgctttgttctcagagtgtgtt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2160 ttcagtggcgtgtacttggatcgtctgtgaaatgaacctcgtgttgggaaggctgtgtag XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2220 acgcggccattcgccgttggaagggcatcttgccagtagagctgttccctttcttctatg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2280 tttaggtaaaaacctgccgtagaaatttgcgagacgccggatagttcccaggccctgtaa XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2340 ctgaagcagctcagaaatgttcatccgggcgaggtggagaaggaactcctgctag XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 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 237 18 59.65 50.00 2.00 0.00 12.00 gggcgttgctttgatgtt RIGHT PRIMER 735 21 59.52 47.62 3.00 1.00 12.00 TCTATGATGCCCTGATGGTCT PRODUCT SIZE: 499, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 0.00 2 LEFT PRIMER 237 18 59.65 50.00 2.00 0.00 12.00 gggcgttgctttgatgtt RIGHT PRIMER 734 21 60.49 52.38 3.00 1.00 12.00 CTATGATGCCCTGATGGTCTG PRODUCT SIZE: 498, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 0.00 3 LEFT PRIMER 237 18 59.65 50.00 2.00 0.00 12.00 gggcgttgctttgatgtt RIGHT PRIMER 733 20 59.48 50.00 3.00 1.00 12.00 TATGATGCCCTGATGGTCTG PRODUCT SIZE: 497, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 0.00 4 LEFT PRIMER 237 18 59.65 50.00 2.00 0.00 12.00 gggcgttgctttgatgtt RIGHT PRIMER 736 22 60.85 45.45 3.00 1.00 12.00 TTCTATGATGCCCTGATGGTCT PRODUCT SIZE: 500, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 0.00 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 1389 0 0 0 810 0 0 0 2 181 51 0 61 284 Right 2927 0 0 1433 73 0 0 0 10 535 90 0 44 742 Pair Stats: considered 5798, unacceptable product size 5768, tm diff too large 24, ok 6 primer3 release 1.0