PRIMER PICKING RESULTS FOR NM_006162_10p4 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 1399 24 57.25 33.33 6.00 3.00 12.00 AGTGATTGTAAATAACATGCAACC RIGHT PRIMER 1890 21 57.83 42.86 2.00 1.00 11.00 AGGTTGTTTCTTTCCGTGAGT SEQUENCE SIZE: 2395 INCLUDED REGION SIZE: 2395 PRODUCT SIZE: 492, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00 TARGETS (start, len)*: 1469,400 EXCLUDED REGIONS (start, len)*: 0,1169 2169,226 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 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 780 AAACTGCAAACACATTTCATTGTGAGGTTTTACCCTCTGTATGAATGAAGAGAACGCTGG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 840 AAGGCTGCGAGAGGACTCTAGTATGAGTCTCCAACATTTGGAACGTTTCCTGGGCTGTCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 900 CGTACACTCCTGCTGCCTTACACAGTGCATTTTAGAATCTTCCAGTCTGTCATCTCAGCT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 960 CTTTTGTAACATGCTTCCCTTGTCTGCGCGGTTGAAACCGTAGGCTTGTTCATAGTCGCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1020 TGCTCGCATCTTTGTTTTTAATCTGGCTTCGAACATAGCACAAGTAACTTGAATAGCACA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1080 TCAATAGGTTACTGGACAAAAGCAGAAAAACCTGTTACAGGATAGCCTGCATTTGCATGT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1140 GTGTACATATCTAGGCATCTATTTATGTATAAATAATAACAGAGCCGACGTGTCCTCGCC XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1200 CAGGAGGGCTTCCCTGTCAGCAATAACCGGCATCCGTTTTGGAACCTGCGTCTGGGGCTC 1260 CAGTCGCTGCTCTTGCTGGCGTCCATCGCCGCCTCGGACGGCCGTGCATTTTCTCGTCTC 1320 ACGCAGTTCGAGGAGGACCCTAGAAAGCCAGGAGCTGTGATTGACAGTAGCTGTAGGTTA 1380 CCAGACGGCAACATTAGAAAGTGATTGTAAATAACATGCAACCTAAGTGTAATATATTTG >>>>>>>>>>>>>>>>>>>>>>>> 1440 TTCAGTTATAAGATGATTGTTTCACAGAAGCCTTACCACTCTCTGCTTCATCTAAGAAAA ******************************* 1500 CCAATACCAAAAACGCCACTTTAATGCTCAGCCCTGCGTTGTGTGTTTTCAGATGAGTTA ************************************************************ 1560 CTGTTAACAGGTAGGTTTGTGTAGGCCTTGCTGGGCACTCTGTACAATTAGTTGCTTATT ************************************************************ 1620 ACGTATGATTACTCACAGCGATCTATTGTTCCATATAACCAAAAAGCATGGTTTATTCAT ************************************************************ 1680 TGAAACACGGTTGACCTGAACTCGTGCCTTAGGAATTAATGCCCCCTTATGGAACCTGCC ************************************************************ 1740 TGAATTGCACCTGCGGGTGGAGGCTCCGGCTGTGAAGTCACTGAACAGAACGTCGCTGAT ************************************************************ 1800 GGAGAAAGGGCTCCCGCAGAAGGAACGGCCTGTACCGTGCGCTCCGGCACAATCGCGTCT ************************************************************ 1860 CTTGTGTCTCACTCACGGAAAGAAACAACCTGAAGGCCATCCCGTCGGTCTGCACGTAAC ********* <<<<<<<<<<<<<<<<<<<<< 1920 CGTGAAGACGTGTGGCCGCGTCCCACCTGCGGCTGGGTACCCTGCACCCGGCACTGTAGG 1980 AGTCACGTGCAGCCTTTCTCAGGGGACTGTCATTGAAAAGGAAACGTTTGATGTCTGTGT 2040 CAGCTGTCTTTGTAGTTAGGAAATAGATCCAATAAAGCCGTATTTTTTTGCTGGacaggc 2100 gtagtctgcgagtggttcatgatacgcgtggaagatgccgctttgttctcagagtgtgtt 2160 ttcagtggcgtgtacttggatcgtctgtgaaatgaacctcgtgttgggaaggctgtgtag XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 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 1400 23 56.24 34.78 6.00 3.00 12.00 GTGATTGTAAATAACATGCAACC RIGHT PRIMER 1890 21 57.83 42.86 2.00 1.00 11.00 AGGTTGTTTCTTTCCGTGAGT PRODUCT SIZE: 491, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00 2 LEFT PRIMER 1399 24 57.25 33.33 6.00 3.00 12.00 AGTGATTGTAAATAACATGCAACC RIGHT PRIMER 1891 20 58.75 45.00 2.00 2.00 11.00 CAGGTTGTTTCTTTCCGTGA PRODUCT SIZE: 493, PAIR ANY COMPL: 6.00, PAIR 3' COMPL: 0.00 3 LEFT PRIMER 1404 25 57.53 32.00 5.00 2.00 12.00 TTGTAAATAACATGCAACCTAAGTG RIGHT PRIMER 1890 21 57.83 42.86 2.00 1.00 11.00 AGGTTGTTTCTTTCCGTGAGT PRODUCT SIZE: 487, PAIR ANY COMPL: 6.00, PAIR 3' COMPL: 0.00 4 LEFT PRIMER 1404 25 57.53 32.00 5.00 2.00 12.00 TTGTAAATAACATGCAACCTAAGTG RIGHT PRIMER 1891 20 58.75 45.00 2.00 2.00 11.00 CAGGTTGTTTCTTTCCGTGA PRODUCT SIZE: 488, PAIR ANY COMPL: 6.00, 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 2937 0 0 1171 862 0 0 0 0 228 51 0 51 574 Right 1803 0 0 233 460 0 0 0 3 417 51 19 53 567 Pair Stats: considered 55751, unacceptable product size 54977, tm diff too large 766, high end compl 1, ok 7 primer3 release 1.0