Van Oudenaarden Lab:Y39A3CR.6

Progress:

Probes designed: (03-04-2010 - Christoph Engert)

Probes coupled:

Probes purified:

Probes tested:

Dyes available:

- >Y39A3CR.6 (spliced + UTR - 1038) ATGTCCGACT CCCCGCAGAG CTGCAAAAAG CCGCGAACTC GGAAAGAAAC TATTCAAAAG CGAGAAACAC GAAGTAAGCA TGAAAAACGA CGAAGGGAAG AGATGAATGA AGTGATTTGT GAAATGTCGA CACTTTTGCC CGAAGATATT CGGGCTCATA AGCTGCGAAG AGTGGATCAG AAGCCTCGTC AGCTGGACAA ATGCTTTATC ATTGGGAGTA CTGTTGATAT TATTCGGAAT AGTGATTATA AACCACCGCT GCTCTCCGAC CCGCTCGTCC AGGATATTTT CAGCCTGACC AACTGTTTTA TGGTTTTTCT GAACAATTTT ATTGTCGTGG ATATTAAGGG AGACCATCAG GCAGTTTTTG ATATTGAAAA AAAACGTATG ATTGGAAAAG ATATCCGATG TTTTCTGGAC TACGATTCAA CGTCCAAACT GTCATTTCTC ACTTCCAAAG AAATGCTCAA TGAGCTCCAA CTCAAAAGCT TCATGGCGAA GTCAATGACG TGCAGAATAA AGGAATCGGC GGAGAAACCC ACGGAAACAG TTTTAGTCTG TGTGCCTGAT GAGCTTCCAG CTCTCCCGGT TACTGTACCC AAGGCTCCGC CCATTTTAGC TTCGCCCCTT CAGAAGACAC CGCCCCCGCC GTCGAGTTTG GAGGTGAAAA GCCCGATTTT GGCGGCACTT TTGAGGCGAA AAGAGGATAA TTGTGTGAAA GTGAGCTCCC CAAGCTCCTT CCTCTCGCCG GGCTCCTCCA CCTCGTCTAC AGTACCCAAT GTGAAACCTA CAGTAACCCG CCGACCTACA GTACCCACAA AACGGAAGAG ACTACGATCG ATGAATGTTA TAGTGGAAAG TTATCCGTTG GATGATGAGA AGTCGGATGG AAATTCACAA AAATCGGCGA AAATTGGGAA AAAGAGGTTT TTTCTAACAA AAAAAAACGT TAAAACCTAC AGTAATCTAC TCCAAAATCC ATGCGAGACC CTTAAAACTG AAAATTTCAA ATTTAGCTCA ACAAGACCTT TCAAATGA - Name of probe set: hlh-33 Probes designed on Wed, 03 Mar 10 23:24:13 -0700 42 probes designed for target of length 1038

Probe (5'->3'), Probe name, Probe number, Probe position, Percent GC

tttttgcagctctgcgggga, hlh-33_1, 1, 10, 55 tagtttctttccgagttcgc, hlh-33_2, 2, 33, 45 cttcgtgtttctcgcttttg, hlh-33_3, 3, 55, 45 ccttcgtcgtttttcatgct, hlh-33_4, 4, 77, 45 caaatcacttcattcatctc, hlh-33_5, 5, 100, 35 gggcaaaagtgtcgacattt, hlh-33_6, 6, 122, 45 gcttatgagcccgaatatct, hlh-33_7, 7, 144, 45 ggcttctgatccactcttcg, hlh-33_8, 8, 166, 55 aaagcatttgtccagctgac, hlh-33_9, 9, 188, 45 tatcaacagtactcccaatg, hlh-33_10, 10, 210, 40 cagcggtggtttataatcac, hlh-33_11, 11, 242, 45 aaaatatcctggacgagcgg, hlh-33_12, 12, 271, 50 cataaaacagttggtcaggc, hlh-33_13, 13, 293, 45 cccttaatatccacgacaat, hlh-33_14, 14, 331, 40 atcaaaaactgcctgatggt, hlh-33_15, 15, 353, 40 ccaatcatacgttttttttc, hlh-33_16, 16, 376, 30 ccagaaaacatcggatatct, hlh-33_17, 17, 399, 40 agtttggacgttgaatcgta, hlh-33_18, 18, 421, 40 ttctttggaagtgagaaatg, hlh-33_19, 19, 443, 35 tgagttggagctcattgagc, hlh-33_20, 20, 465, 50 attgacttcgccatgaagct, hlh-33_21, 21, 487, 45 cgattcctttattctgcacg, hlh-33_22, 22, 509, 45 ctgtttccgtgggtttctcc, hlh-33_23, 23, 531, 55 tcatcaggcacacagactaa, hlh-33_24, 24, 553, 45 agtaaccgggagagctggaa, hlh-33_25, 25, 575, 55 taaaatgggcggagccttgg, hlh-33_26, 26, 599, 55 gtgtcttctgaaggggcgaa, hlh-33_27, 27, 621, 55 ttttcacctccaaactcgac, hlh-33_28, 28, 651, 45 aaaagtgccgccaaaatcgg, hlh-33_29, 29, 673, 50 acaattatcctcttttcgcc, hlh-33_30, 30, 695, 40 agcttggggagctcactttc, hlh-33_31, 31, 717, 55 ttgggtactgtagacgaggt, hlh-33_32, 32, 760, 50 gcgggttactgtaggtttca, hlh-33_33, 33, 782, 50 gttttgtgggtactgtaggt, hlh-33_34, 34, 804, 45 cattcatcgatcgtagtctc, hlh-33_35, 35, 828, 45 aacggataactttccactat, hlh-33_36, 36, 850, 35 tccatccgacttctcatcat, hlh-33_37, 37, 872, 45 ttttcgccgatttttgtgaa, hlh-33_38, 38, 894, 35 agaaaaaacctctttttccc, hlh-33_39, 39, 916, 35 ggagtagattactgtaggtt, hlh-33_40, 40, 954, 40 ttaagggtctcgcatggatt, hlh-33_41, 41, 976, 45 gaaaggtcttgttgagctaa, hlh-33_42, 42, 1013, 40 -- Input sequence with probe locations:

atgtccgactccccgcagagctgcaaaaagccgcgaactcggaaagaaactattcaaaagcgagaaacac aggggcgtctcgacgttttt  cgcttgagcctttctttgat  gttttcgctctttgtg Probe # 1, 55% GC     Probe # 2, 45% GC     Probe # 3, 45% G

gaagtaagcatgaaaaacgacgaagggaagagatgaatgaagtgatttgtgaaatgtcgacacttttgcc cttc tcgtactttttgctgcttcc   ctctacttacttcactaaac  tttacagctgtgaaaacgg C    Probe # 4, 45% GC      Probe # 5, 35% GC     Probe # 6, 45% GC

cgaagatattcgggctcataagctgcgaagagtggatcagaagcctcgtcagctggacaaatgctttatc g tctataagcccgagtattcg  gcttctcacctagtcttcgg  cagtcgacctgtttacgaaa  g   Probe # 7, 45% GC     Probe # 8, 55% GC     Probe # 9, 45% GC     P

attgggagtactgttgatattattcggaatagtgattataaaccaccgctgctctccgacccgctcgtcc taaccctcatgacaactat           cactaatatttggtggcgac         ggcgagcagg robe # 10, 40% GC             Probe # 11, 45% GC           Probe # 12

aggatattttcagcctgaccaactgttttatggtttttctgaacaattttattgtcgtggatattaaggg tcctataaaa cggactggttgacaaaatac                  taacagcacctataattccc , 50% GC   Probe # 13, 45% GC                    Probe # 14, 40% GC

agaccatcaggcagtttttgatattgaaaaaaaacgtatgattggaaaagatatccgatgttttctggac tggtagtccgtcaaaaacta  cttttttttgcatactaacc   tctataggctacaaaagacc Probe # 15, 40% GC    Probe # 16, 30% GC     Probe # 17, 40% GC

tacgattcaacgtccaaactgtcatttctcacttccaaagaaatgctcaatgagctccaactcaaaagct atgctaagttgcaggtttga gtaaagagtgaaggtttctt  cgagttactcgaggttgagt  tcga Probe # 18, 40% GC   Probe # 19, 35% GC    Probe # 20, 50% GC    Prob

tcatggcgaagtcaatgacgtgcagaataaaggaatcggcggagaaacccacggaaacagttttagtctg agtaccgcttcagtta gcacgtcttatttccttagc  cctctttgggtgcctttgtc  aatcagac e # 21, 45% GC   Probe # 22, 45% GC    Probe # 23, 55% GC    Probe #

tgtgcctgatgagcttccagctctcccggttactgtacccaaggctccgcccattttagcttcgcccctt acacggactact aaggtcgagagggccaatga    ggttccgaggcgggtaaaat  aagcggggaa 24, 45% GC   Probe # 25, 55% GC      Probe # 26, 55% GC    Probe # 27

cagaagacaccgcccccgccgtcgagtttggaggtgaaaagcccgattttggcggcacttttgaggcgaa gtcttctgtg         cagctcaaacctccactttt  ggctaaaaccgccgtgaaaa  ccgctt , 55% GC           Probe # 28, 45% GC    Probe # 29, 50% GC    Probe

aagaggataattgtgtgaaagtgagctccccaagctccttcctctcgccgggctcctccacctcgtctac ttctcctattaaca ctttcactcgaggggttcga                       tggagcagatg
 * 30, 40% GC   Probe # 31, 55% GC                         Probe # 32,

agtacccaatgtgaaacctacagtaacccgccgacctacagtacccacaaaacggaagagactacgatcg tcatgggtt actttggatgtcattgggcg  tggatgtcatgggtgttttg    ctctgatgctagc 50% GC   Probe # 33, 50% GC    Probe # 34, 45% GC      Probe # 35, 4

atgaatgttatagtggaaagttatccgttggatgatgagaagtcggatggaaattcacaaaaatcggcga tacttac tatcacctttcaataggcaa  tactactcttcagcctacct  aagtgtttttagccgct 5% GC   Probe # 36, 35% GC    Probe # 37, 45% GC    Probe # 38, 35% G

aaattgggaaaaagaggttttttctaacaaaaaaaaacgttaaaacctacagtaatctactccaaaatcc ttt ccctttttctccaaaaaaga                  ttggatgtcattagatgagg  ttagg C   Probe # 39, 35% GC                    Probe # 40, 40% GC    Probe

atgcgagacccttaaaactgaaaatttcaaatttagctcaacaagacctttcaaatga tacgctctgggaatt                aatcgagttgttctggaaag # 41, 45% GC                  Probe # 42, 40% GC