PRIMER PICKING RESULTS FOR NM_006162_10p2 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 639 18 61.17 61.11 4.00 0.00 12.00 CCCACACGCAGTTTGACC RIGHT PRIMER 1097 24 59.95 41.67 3.00 2.00 12.00 TGTCCAGTAACCTATTGATGTGCT SEQUENCE SIZE: 2395 INCLUDED REGION SIZE: 2395 PRODUCT SIZE: 459, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 1.00 TARGETS (start, len)*: 669,400 EXCLUDED REGIONS (start, len)*: 0,369 1369,1026 0 cagcatcttcccagcatcgcggccggcacctggcacctgcactttggccgtcagagacgt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 60 gctggtaccgtgctacggacgagggcggtcactctggcgaccccagctctctgccgaggc XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 agccaggcactggctcacgacactcatggaccagggtgggaccgaggaggaaatgtgggt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 180 tcctggggagatgccttgtcacaggcgtgagcgtcactgatggagaagcagggctggggg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 240 cgttgctttgatgtttatggtatttctctaatactttctcaatttttcttttcttacagT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 AAATGAAATAATACGAAATGACCTCTCCAGCACGAGCACCCACTCCTAGTTGCCACATTG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 360 GAGCACTCAGTTCAGCAGGGGTATGCTGACTTCAGCAGACAAAGACTTTTGAATAAATAA XXXXXXXXX 420 ACTGAACTCACACCTGGTACCACTCAGAACCTCCAACTGACTGAATGCCAGGAGCTGAAC 480 ATTAATATGTGCAAAGATTGGCTCTCCAACAAGAAGGAAAGCAGGGAGGAAGGGAGACCA 540 CTGTGTCACCTGGAGGAGAAGTCATCTCATGACAACAGAAGGGAGGTGGCCGGGCTGAGC 600 ACGGGAGACCCACCGTGCAGGGGCCTTTCATGGGAACGGCCCACACGCAGTTTGACCCCA >>>>>>>>>>>>>>>>>> 660 CGCCCAGCCCTTCTGGCACCCCTGGGGTTCAATACTGGAAGTGCCTTATTTAACCAGACC *************************************************** 720 ATCAGGGCATCATAGAATTGAGCATTGAATTTGCTACTGTAGGAGTATTTTTAGGAGCAG ************************************************************ 780 AAACTGCAAACACATTTCATTGTGAGGTTTTACCCTCTGTATGAATGAAGAGAACGCTGG ************************************************************ 840 AAGGCTGCGAGAGGACTCTAGTATGAGTCTCCAACATTTGGAACGTTTCCTGGGCTGTCA ************************************************************ 900 CGTACACTCCTGCTGCCTTACACAGTGCATTTTAGAATCTTCCAGTCTGTCATCTCAGCT ************************************************************ 960 CTTTTGTAACATGCTTCCCTTGTCTGCGCGGTTGAAACCGTAGGCTTGTTCATAGTCGCA ************************************************************ 1020 TGCTCGCATCTTTGTTTTTAATCTGGCTTCGAACATAGCACAAGTAACTTGAATAGCACA ************************************************* <<<<<< 1080 TCAATAGGTTACTGGACAAAAGCAGAAAAACCTGTTACAGGATAGCCTGCATTTGCATGT <<<<<<<<<<<<<<<<<< 1140 GTGTACATATCTAGGCATCTATTTATGTATAAATAATAACAGAGCCGACGTGTCCTCGCC 1200 CAGGAGGGCTTCCCTGTCAGCAATAACCGGCATCCGTTTTGGAACCTGCGTCTGGGGCTC 1260 CAGTCGCTGCTCTTGCTGGCGTCCATCGCCGCCTCGGACGGCCGTGCATTTTCTCGTCTC 1320 ACGCAGTTCGAGGAGGACCCTAGAAAGCCAGGAGCTGTGATTGACAGTAGCTGTAGGTTA XXXXXXXXXXX 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 638 18 61.34 61.11 4.00 1.00 11.00 GCCCACACGCAGTTTGAC RIGHT PRIMER 1097 24 59.95 41.67 3.00 2.00 12.00 TGTCCAGTAACCTATTGATGTGCT PRODUCT SIZE: 460, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 2.00 2 LEFT PRIMER 639 18 61.17 61.11 4.00 0.00 12.00 CCCACACGCAGTTTGACC RIGHT PRIMER 1118 24 59.30 33.33 5.00 0.00 12.00 TGTAACAGGTTTTTCTGCTTTTGT PRODUCT SIZE: 480, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 3.00 3 LEFT PRIMER 638 18 61.34 61.11 4.00 1.00 11.00 GCCCACACGCAGTTTGAC RIGHT PRIMER 1119 24 59.42 37.50 7.00 0.00 12.00 CTGTAACAGGTTTTTCTGCTTTTG PRODUCT SIZE: 482, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 3.00 4 LEFT PRIMER 639 18 61.17 61.11 4.00 0.00 12.00 CCCACACGCAGTTTGACC RIGHT PRIMER 1098 25 61.12 40.00 3.00 2.00 12.00 TTGTCCAGTAACCTATTGATGTGCT PRODUCT SIZE: 460, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 1.00 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 1953 0 0 376 528 0 0 0 7 405 65 0 53 519 Right 2648 0 0 1029 641 0 0 0 13 320 52 0 56 537 Pair Stats: considered 98786, unacceptable product size 97602, tm diff too large 1178, high end compl 1, ok 5 primer3 release 1.0