PRIMER PICKING RESULTS FOR NM_006162_10p3 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 1039 21 59.86 42.86 6.00 2.00 11.00 AATCTGGCTTCGAACATAGCA RIGHT PRIMER 1529 21 59.77 38.10 4.00 3.00 12.00 TGAGCATTAAAGTGGCGTTTT SEQUENCE SIZE: 2395 INCLUDED REGION SIZE: 2395 PRODUCT SIZE: 491, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 1.00 TARGETS (start, len)*: 1069,400 EXCLUDED REGIONS (start, len)*: 0,769 1769,626 0 cagcatcttcccagcatcgcggccggcacctggcacctgcactttggccgtcagagacgt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 60 gctggtaccgtgctacggacgagggcggtcactctggcgaccccagctctctgccgaggc XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 agccaggcactggctcacgacactcatggaccagggtgggaccgaggaggaaatgtgggt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 180 tcctggggagatgccttgtcacaggcgtgagcgtcactgatggagaagcagggctggggg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 240 cgttgctttgatgtttatggtatttctctaatactttctcaatttttcttttcttacagT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 AAATGAAATAATACGAAATGACCTCTCCAGCACGAGCACCCACTCCTAGTTGCCACATTG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 360 GAGCACTCAGTTCAGCAGGGGTATGCTGACTTCAGCAGACAAAGACTTTTGAATAAATAA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 420 ACTGAACTCACACCTGGTACCACTCAGAACCTCCAACTGACTGAATGCCAGGAGCTGAAC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 480 ATTAATATGTGCAAAGATTGGCTCTCCAACAAGAAGGAAAGCAGGGAGGAAGGGAGACCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 540 CTGTGTCACCTGGAGGAGAAGTCATCTCATGACAACAGAAGGGAGGTGGCCGGGCTGAGC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 ACGGGAGACCCACCGTGCAGGGGCCTTTCATGGGAACGGCCCACACGCAGTTTGACCCCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 660 CGCCCAGCCCTTCTGGCACCCCTGGGGTTCAATACTGGAAGTGCCTTATTTAACCAGACC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 720 ATCAGGGCATCATAGAATTGAGCATTGAATTTGCTACTGTAGGAGTATTTTTAGGAGCAG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 780 AAACTGCAAACACATTTCATTGTGAGGTTTTACCCTCTGTATGAATGAAGAGAACGCTGG 840 AAGGCTGCGAGAGGACTCTAGTATGAGTCTCCAACATTTGGAACGTTTCCTGGGCTGTCA 900 CGTACACTCCTGCTGCCTTACACAGTGCATTTTAGAATCTTCCAGTCTGTCATCTCAGCT 960 CTTTTGTAACATGCTTCCCTTGTCTGCGCGGTTGAAACCGTAGGCTTGTTCATAGTCGCA 1020 TGCTCGCATCTTTGTTTTTAATCTGGCTTCGAACATAGCACAAGTAACTTGAATAGCACA >>>>>>>>>>>>>>>>>>>>> *********** 1080 TCAATAGGTTACTGGACAAAAGCAGAAAAACCTGTTACAGGATAGCCTGCATTTGCATGT ************************************************************ 1140 GTGTACATATCTAGGCATCTATTTATGTATAAATAATAACAGAGCCGACGTGTCCTCGCC ************************************************************ 1200 CAGGAGGGCTTCCCTGTCAGCAATAACCGGCATCCGTTTTGGAACCTGCGTCTGGGGCTC ************************************************************ 1260 CAGTCGCTGCTCTTGCTGGCGTCCATCGCCGCCTCGGACGGCCGTGCATTTTCTCGTCTC ************************************************************ 1320 ACGCAGTTCGAGGAGGACCCTAGAAAGCCAGGAGCTGTGATTGACAGTAGCTGTAGGTTA ************************************************************ 1380 CCAGACGGCAACATTAGAAAGTGATTGTAAATAACATGCAACCTAAGTGTAATATATTTG ************************************************************ 1440 TTCAGTTATAAGATGATTGTTTCACAGAAGCCTTACCACTCTCTGCTTCATCTAAGAAAA ***************************** 1500 CCAATACCAAAAACGCCACTTTAATGCTCAGCCCTGCGTTGTGTGTTTTCAGATGAGTTA <<<<<<<<<<<<<<<<<<<<< 1560 CTGTTAACAGGTAGGTTTGTGTAGGCCTTGCTGGGCACTCTGTACAATTAGTTGCTTATT 1620 ACGTATGATTACTCACAGCGATCTATTGTTCCATATAACCAAAAAGCATGGTTTATTCAT 1680 TGAAACACGGTTGACCTGAACTCGTGCCTTAGGAATTAATGCCCCCTTATGGAACCTGCC 1740 TGAATTGCACCTGCGGGTGGAGGCTCCGGCTGTGAAGTCACTGAACAGAACGTCGCTGAT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 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 1039 21 59.86 42.86 6.00 2.00 11.00 AATCTGGCTTCGAACATAGCA RIGHT PRIMER 1530 21 59.42 42.86 4.00 1.00 11.00 CTGAGCATTAAAGTGGCGTTT PRODUCT SIZE: 492, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 1.00 2 LEFT PRIMER 1039 21 59.86 42.86 6.00 2.00 11.00 AATCTGGCTTCGAACATAGCA RIGHT PRIMER 1519 21 60.64 42.86 2.00 0.00 12.00 AGTGGCGTTTTTGGTATTGGT PRODUCT SIZE: 481, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 3.00 3 LEFT PRIMER 1044 21 59.40 47.62 6.00 2.00 11.00 GGCTTCGAACATAGCACAAGT RIGHT PRIMER 1529 21 59.77 38.10 4.00 3.00 12.00 TGAGCATTAAAGTGGCGTTTT PRODUCT SIZE: 486, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 1.00 4 LEFT PRIMER 1039 21 59.86 42.86 6.00 2.00 11.00 AATCTGGCTTCGAACATAGCA RIGHT PRIMER 1527 21 59.31 38.10 4.00 1.00 11.00 AGCATTAAAGTGGCGTTTTTG PRODUCT SIZE: 489, PAIR ANY COMPL: 3.00, 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 2346 0 0 776 47 0 0 0 4 561 79 0 46 833 Right 2205 0 0 633 286 0 0 0 16 418 62 0 41 749 Pair Stats: considered 893, unacceptable product size 884, ok 9 primer3 release 1.0