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TAT_mase-nuc.txt is an unused identical copy of TAT_mase_nuc.txt (which is used in test_intelligenetics.py)
This commit is contained in:
peterc
@ -1,252 +0,0 @@
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;; Modified by adf on Sat Nov 9 17:38:25 1996
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;; Modified by adf on Sat Nov 9 16:27:39 1996
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;; Modified by kam on Mon Nov 20 12:58:58 1995
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;; Modified by kxm on Sat Nov 5 01:21:01 1994
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;; Modified by kxm on Sat Nov 5 01:12:11 1994
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;; Modified by kxm on Sat Nov 5 00:44:35 1994
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;; Modified by kxm on Sat Nov 5 00:03:23 1994
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;; Modified by kxm on Fri Nov 4 23:58:34 1994
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;; Modified by kxm on Fri Nov 4 23:17:50 1994
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;; Modified by kxm on Fri Nov 4 23:12:24 1994
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;; Modified by kxm on Fri Nov 4 22:57:56 1994
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;; Modified by kxm on Fri Nov 4 12:15:17 1994
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;; Modified by kxm on Thu Nov 3 21:30:26 1994
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;; Modified by kxm on Thu Nov 3 19:40:25 1994
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;; Modified by kam on Thu Mar 18 09:56:44 1993
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;; Modified by kam on Fri Mar 12 11:51:25 1993
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; LOCUS HIVU455
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;
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; Modified by kam on Mon Jul 20 12:24:18 1992
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; Modified by kxm on Fri Nov 4 12:15:17 1994
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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A_U455
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ATGGAGCCAGTAGATCCTAACCTAGAGCCCTGGAAACACCCGGGAAGTCAGCCTACAACTGCTTGTAGCA
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ACTGTTATTGTAAAGTGTGTTGCTGGCATTGCCAACTTTGCTTTCTGAAAAAAGGCTTAGGCATTTCCTA
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TGGCAAGAAGAAGCGGAAACCCCGACGAGGACCTCCTCAAGGCAGTAAGGATCATCAAACTCTTATACCA
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AAGCAACCCTTGCCCCAATCCCAGAGGGTCTCGGCAGGCCAGGAAGAATCGAAGAAGAAGGTGGAGAGCA
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AGGCAAAGACAGATCGATTCGCT
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; LOCUS HIVHXB2R
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;
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; Modified by kam on Mon Jul 20 12:24:18 1992
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; Modified by kxm on Fri Nov 4 12:15:17 1994
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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B_HXB2R
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ATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCA
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ATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTA
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TGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCA
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AAGCAACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAG
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AGACAGAGACAGATCCATTCGATTAG
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; HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (UG268) PROVIRAL DNA
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; ENCODING ENV, TAT, VPU, REV, AND NEF GENES.
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; Modified by kxm on Thu Nov 3 16:33:55 1994
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; Modified by kxm on Thu Nov 3 17:45:53 1994
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; Modified by kxm on Thu Nov 3 17:56:16 1994
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; Modified by kxm on Thu Nov 3 18:05:51 1994
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; Modified by kxm on Thu Nov 3 18:56:08 1994
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; Modified by kxm on Fri Nov 4 12:15:17 1994
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; Modified by cxc on Mon Nov 7 11:17:23 1994
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; Modified by kam on Mon Nov 20 12:19:08 1995
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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; Modified by adf on Sat Nov 9 17:38:25 1996
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C_UG268A
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%CAGGAAGTCAGCCTAAAACTCCTTGTACTAAGTGTTTTGGTAAAAAATGTAGTTATCATTGTCAAGTTT
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GCTTTCTGAACAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAACGCTCCTCC
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AAGCAGTGAGGATCATCAAAATCTTATATCAAAGCAACCCTTACCCCAACCCCGAGGGGACCCGACAGGC
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CCGGAGAAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGAGATTAA
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; LOCUS HIVELI
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;
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; Modified by kam on Mon Jul 20 12:24:18 1992
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; Modified by kxm on Fri Nov 4 12:15:17 1994
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; Modified by kxm on Fri Nov 4 23:17:50 1994
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; Modified by kam on Mon Nov 20 12:19:08 1995
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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D_ELI
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ATGGATCCAGTAGATCCTAACCTAGAGCCCTGGAACCATCCAGGAAGTCAGCCTAGGACTCCTTGTAACA
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AGTGTCATTGTAAAAAGTGTTGCTATCATTGCCCAGTTTGCTTCTTAAACAAAGGCTTAGGCATCTCCTA
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TGGCAGGAAGAAGCGGAGACAGCGACGAGGACCTCCTCAAGGCGGTCAGGCTCATCAAGTTCCTATACCA
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AAGCAACCCTCCTCCCAGCCCCGAGGGGACCCGACAGGCCCGAAGGAACAGAAGAAGAAGGTGGAGAGCG
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AGGCAGAGACAGATCCGTGAGATTGCTGA
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; Region 70 to 290 stored
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;
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; Region 70 to 290, from file bz163a.mase-nuc
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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F_BZ163A
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ATGGAGCTAGTAGATCCTAACTTAGATCCCTGGAACCATCCAGGAAGCCAGCCTACAACTCCTTGTACAA
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AATGCTATTGTAAACGATGTTGCTTTCATTGTCAATGGTGCTTTACAACGAAGGGCTTAGGCATCTCCTA
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TGGCAGGAAGAAGCGGAAACAGCGGCACCGAACTCCTCAGAGCAGCCAGATACATCAAGATCTTGTACCA
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AAGCAACCCATATCCCAAGCCCGAGGGAACCCGACAGGCCCGAAGAAATCGAAGAAGGAGGTGGAGAGCA
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AGGCAGAGACAGATCCGTGAGATTAGTAG
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; Modified by kam on Mon Jul 20 12:10:15 1992
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; Modified by kxm on Fri Nov 4 12:15:17 1994
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; Modified by kxm on Sat Nov 5 00:44:35 1994
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; Modified by kam on Mon Nov 20 12:19:08 1995
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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O_ANT70
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ATGGATCCAGTAGATCCTGAGGTGCCCCCTTGGCACCACCCTGGAAGTCAGCCCCAGATCCCTTGTAATA
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ATTGCTATTGCAAAAGATGCTGCTATCATTGCTATGTTTGTTTCGTAAGAAAGGGTTTGGGAATCTCCTA
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TGGCAGGAAGAAGCGAGGACGACCAGCTGCTGCAAGCCATCCAGATCATAAAGATCCTGTACCAAAGCAA
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TCCCCAACCATCACCAAGAGGAAGCAGGAACGCCAGGAAGAACAGGAGGAGGAGGTGGAGAAGAAGGCAG
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GCCCAGGTGGATACCCTCGCCGCAAGGGTTCTTGCCACTGTTGTACACGGACCTCAGAACAA
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;
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; Modified by rkl on Wed Jun 30 09:36:11 1993
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; Modified by kxm on Fri Nov 4 12:15:17 1994
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; Modified by kxm on Sat Nov 5 00:44:35 1994
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; Modified by kam on Mon Nov 20 12:19:08 1995
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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O_MVP5180
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ATGGATCCAGTAGATCCTGAGATGCCCCCTTGGCATCACCCTGGGAGCAAGCCCCAAACCCCTTGTAATA
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ATTGCTATTGCAAAAGATGCTGCTATCATTGCTATGTTTGTTTCACAAAGAAGGGTTTGGGAATCTCCCA
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TGGCAGGAAGAAGCGAAGAAGACCAGCAGCTGCTGCAAGCTATCCAGATAATAAAGATCCTGTACCAGAG
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CAATCCCTGTCCCACACCGGCAGGAAGCAGAAACGCCAGGAAGAACAGGAGAAGAAGGTGGAGAAGGAGA
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CAGGCCCAAGTGGACAGCCTTGCCACCAGGATTCTTGCAACAGTTGTACACGGATCTCAGGACAATAA
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; LOCUS SIVCPZ
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;
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; Modified by kam on Fri Jul 17 11:13:21 1992
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; Modified by kxm on Fri Nov 4 12:15:17 1994
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; Modified by kxm on Fri Nov 4 23:12:24 1994
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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CPZGAB
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ATGGATCCAATAGATCCTGACCTGGAGCCCTGGAAACACCCAGGCAGTCAGCCAAGAACAGTTTGTAATA
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ATTGCTATTGCAAAGCTTGTTGTTATCACTGTATATATTGCTTCACAAAAAAAGGCTTAGGAATCTCCTA
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TGGCAGGAAGAAGCGAACCACAAGACGACGCACGGCTCCTGCAGGCAGTAAAAATAATCAAGATTCTATA
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CCAAAGCAACCCTTATCCCAGTCCAGAGGGAACAAGGAAGGCTCGGAGAAATCGACGAAGGAGGTGGCGA
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GCAAGACAGAAGCAGATCAGTGAGATTAG
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;
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; Modified by kxm on Fri Nov 4 12:15:17 1994
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; Modified by kxm on Fri Nov 4 23:12:24 1994
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; Modified by kxm on Fri Nov 4 23:58:34 1994
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; Modified by acs on Mon Nov 27 10:24:48 1995
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; Modified by kam on Thu Nov 30 09:43:33 1995
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; Modified by bwb on Fri Dec 1 09:03:00 1995
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; Written from MASE, from file "HIV1TAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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CPZANT
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ATGGACCCCGTAGACGCTGAAACACCTCCATGGTTACACCCTCCTGCTACACCAGCAACGCCATGCAATA
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ACTGTTACTGTAAATGCTGTTGTTACCATTGCCCTCTCTGCTTCACAAAAAAAGGCTTGGGGATTTCCTA
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TGGCAGGAAGAGAAGAGCTCGAAGGAACAGACGAACAACTGCTGAAAGCAGTGAAAATAATCAAGATCCT
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GTATCAAAATCCCTACCCAAAACCAGCAGGATCCAGAGCAGCCAGAAGAAATAAGAGAAGAAGGTGGAAG
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AAAAGACAGGATCAGGTGGAGGGCCTTGC
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;; Modified by cxc on Thu Oct 20 14:56:54 1994
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; LOCUS HIV2ROD.nuc
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;
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; Modified by kam on Thu Jul 29 11:47:29 1993
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; Modified by cxc on Fri Oct 28 14:37:09 1994
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; Written from MASE, from file "HIV2SIVTAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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A_ROD
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ATGGAGACACCCTTGAAGGCGCCAGAGAGCTCATTAAAGTCCTGCAACGAGCCCTTTTCACGCACTTCAG
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AGCAGGATGTGGCCACTCAAGAATTGGCCAGACAAGGGGAGGAAATCCTCTCTCAGCTATACCGACCCCT
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AGAAACATGCAATAACTCATGCTATTGTAAGCGATGCTGCTACCATTGTCAGATGTGTTTTCTAAACAAG
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GGGCTCGGGATATGTTATGAACGAAAGGGCAGACGAAGAAGGACTCCAAAGAAAACTAAGACTCATCCGT
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CTCCTACACCAGACAAATCCATATCCACAAGGACCGGGGACAGCCAGCCAACGAAGAAACAGAAGAAGAC
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GGTGGAAGCAACGGTGGAGACAGATACTGGCCCTGGCCGA
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;; Modified by bwb on Wed Sep 14 11:35:17 1994
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; HIV2 (ISOLATE EHO) PROVIRUS NUCLEOCAPSID CORE PROTEIN (GAG)
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; GENE, 3' END THROUGH THE 3' LTR.
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; Modified by bwb on Wed Sep 14 11:35:17 1994
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; Modified by bwb on Thu Sep 15 15:12:52 1994
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; Written from MASE, from file "HIV2SIVTAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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B_EHOA
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ATGGAAATACCCTTGAAGGAGCAGGAGAGCTCATTAAACTCCTCCAGCGGGCACTCTTCCTCCACTTCAG
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AGGGGGTTGCCAACACTCAAGGATTGGACAACCGGGGGGAGGAAATCCTCTCTCAGCTATACCGCCCTCT
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TAAGGCATGCAGTAATACATGCTACTGTAAAAAATGTTCCTACCATTGCCAGCTTTGCTTTCTTAAAAAG
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GGCCTGGGGATATGTTATGAACGCTCGAGAAAGAGATCTTCAAAAAGGGCTAAGACTACTACATCTTCTG
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CACCAAACAACAGATCCCTATCCGCAAGGACCGGGGACAGCCAGCCAACGAAGAAACAGAAGAAGGAGGT
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GGAAACAACGAGGGCTACAGATCTTGGCCCTGGCAGATCGAATACATCCACTTCCCGATTCGCCAACTGA
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; LOCUS SIVMM251.nuc
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;
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; Modified by kam on Wed Sep 2 10:04:14 1992
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; Modified by cxc on Fri Oct 28 14:37:09 1994
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; Written from MASE, from file "HIV2SIVTAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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D_MM251
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ATGGAGACACCCTTGAGGGAGCAGGAGAACTCATTAGAATCCTCCAACGAGCGCTCTTCATGCATTTTAG
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AGGCGGATGCAACCACTCCAGAATCGGCCAACCTGGGGGAGGAAATCCTCTCTCAACTATACCGCCCTCT
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TGAGGCGTGCTATAACACATGCTATTGTAAAAAGTGTTGCTACCATTGCCAGTTTTGTTTTCTTAAAAAG
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GGATTGGGGATATGTTATGAGCAGTCACGAAAGAGAAGAAGAACTCCGAAAAAGGCTAAGGCTAATACAT
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CTTCTGCATCAAACAAACTCATACCCAACAGGACCCGGCACTGCCAACCAGAGAAGGCAAAGAAGGAGAC
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GGTGGAGAAGGCGGTGGCAACAGCTCCTGGCCTTGGCAGA
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; LOCUS SIVSTM.nuc
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;
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; Modified by kam on Wed Sep 2 10:04:14 1992
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; Modified by cxc on Fri Oct 28 14:37:09 1994
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; Written from MASE, from file "HIV2SIVTAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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STM_STM
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ATGGAGACACCCTTGAAGGAGCAGGAGAGCTCATTAAGATCCTCCAGCGAGCCCTCTTCATGCACTTCAG
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AGGCGGTTGCCGCCACTCCAGGATTGGCCAACCAGGAGGAGGAAATCCTTTGGCAACTATACCGCCCACT
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AGAGGAGTGTTGTAACAAGTGCTTTTGCAAAAAATGTTGCTATCACTGCCAGCTGTGTTTTGTTACAAAA
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GGTCTTGGAATAACCTATGAGCGATCAAGAAGAAGAGTTAAGAAAAAGGCTAAGACTTATCCAATTTCTG
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CATCAAACAACAGATCCCTATCCACAAGGGCCAGGAACAGCCAACCAAAGAAGGAACAGAAGAAGGAGGT
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GGAGACAGAGGTGGAATCAACTCCTGGCCTTGGCAAA
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;; Modified by rkl on Mon Apr 19 10:38:05 1993
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;; Modified by rkl on Mon Apr 19 10:30:34 1993
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; LOCUS SIVAGM3
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;
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; Modified by rkl on Mon Apr 19 10:30:34 1993
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; Modified by adf on Wed Oct 19 13:36:17 1994
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; Modified by adf on Wed Oct 19 13:40:23 1994
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; Written from MASE, from file "AGMTAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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VER_AGM3
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ATGGACAAGGGGGAGGACGAGCAGGGCGCGTACCACCAGGACTTGATTGAACAACTCAAAGCACCCCTGA
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AGCGGTGTACAAACAAGTGCTATTGTAAATGTTGCTGTTATCACTGTCAGCTTTGCTTTTTACAAAAGGG
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ATTAGGTGTTACCTATCATGCCCCTAGGATCAGAAGAAAGAAGATTGCTCCGCTTGATCGCTTTCCTGAA
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CAAAAACAATCCATATCCACCCGTGGAAGGGACAGCCAGACAACGCAGAAGGGCCAGGAGAAGGTGGAGA
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CAAGCGCAAGAACAGCTCCGAGCCTTGGCAGAAAGAATCTGGCACAGCAGAGTGGAAGAGCAACTGGTGC
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AAGC
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;
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; LOCUS SIVAGM677
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;
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; Modified by rkl on Mon Apr 19 10:30:34 1993
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; Modified by rkl on Mon Apr 19 10:38:05 1993
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; Modified by adf on Wed Oct 19 13:36:17 1994
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; Modified by adf on Wed Oct 19 13:40:23 1994
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; Written from MASE, from file "AGMTAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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GRI_AGM677
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ATGGACAAGGAGGAGGAGCCCCACCCCCTCCTCCAGGACTTGCATAGGCCATTACAACCATGTACTAATA
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AATGCTATTGCAAAAAATGCTGTTATCACTGTGAGCTTTGCTTCCTGCAGAAGGGCTTAGGAGTGCGTTA
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TCATGTCTCTAGGAAAAGAAGAAAAACAAGCACTCAAGATAATCAAGACCCTATACGGCAGCAATCCATA
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TCCACAGTTCAGCGGAACGGCCAGACAACGGAGGAGGGCAAGACAGAGGTGGAG
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;
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; LOCUS SIVAGMSAB
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;
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; Modified by rkl on Mon Apr 19 10:30:34 1993
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; Modified by rkl on Mon Apr 19 10:38:05 1993
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; Modified by adf on Wed Oct 19 13:36:17 1994
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; Modified by adf on Wed Oct 19 13:40:23 1994
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; Written from MASE, from file "AGMTAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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SAB_SAB1C
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ATGGACCAGGAGCAGGAGGCCCGCCCCCAGGTCTGGGAGGAGCTTCAGGAGGAGCTGCATCGGCCGCTCC
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AGGCCTGTGATAATACTTGCTTCTGCAAAGTTTGCTGCTTTCATTGTATTCTCTGCTTCCATAAAAAGGC
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CCTAGGCATTCGCTATTATGTCCCTAGGCCAAGAAGAGCTTCTAAGAAGATTTCGCATAATCAAGTTTCT
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CTACACAAC
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;
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; LOCUS SIVSYK
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;
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; Modified by rkl on Mon Apr 19 10:30:34 1993
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; Modified by rkl on Mon Apr 19 10:38:05 1993
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; Modified by adf on Wed Oct 19 13:36:17 1994
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; Modified by adf on Wed Oct 19 13:40:23 1994
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; Modified by kam on Mon Feb 5 11:31:14 1996
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; Written from MASE, from file "AGMTAT.mase-nuc"
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; Modified by adf on Sat Nov 9 16:27:39 1996
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SYK_SYK
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ATGTCCTCAACGGACCAGATATGCCAGACACAGAGGGTACCCCCATCCTTCTTAGAAGGAACATTCCTAG
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AGAAAGGACCACCAACACCATGTAATAAATGCTTTTGCAAAAACTGTTGCTATCATTGCCAGCTTTGTTT
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CCTTCAAAAGGGATTGGGAATCACTTATGCCAGACCAAGGAAGCGAGCAGCTCGCAGTATTTCTGAGGAT
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GATAGCGCACCTACAGGAACCCTACCCAGGGCCGGAAGGACCCAGGCAAACCCGCAGACGAAGAAGAAGG
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CAGTGGAGACAGAGAAGGACTCAACGTCTCTACCTTCAGCAGAGAATCTT
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