JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.
authorFábio Madeira <fmmarquesmadeira@dundee.ac.uk>
Mon, 10 Apr 2017 09:49:33 +0000 (10:49 +0100)
committerFábio Madeira <fmmarquesmadeira@dundee.ac.uk>
Mon, 10 Apr 2017 09:54:42 +0000 (10:54 +0100)
commitd2505558e66c02edaa597a08ae8c2eb54c4c0476
tree98ddb6d2e3add2099755eaafd39dc1c1fe035be1
parente38d8820d388eb2737e1badbfdb49dba3bde7923
JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.
472 files changed:
binaries/src/compilebin.sh
binaries/src/tcoffee/bin/binaries/linux/t_coffee
binaries/src/tcoffee/example/1D4V-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1D4V-2.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1D4V-3.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1EXT-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1EXT-2.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1EXT-3.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1EXT-4.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1JMA-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1JMA-2.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1OQE-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1SG1-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1SG1-2.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1SG1-3.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1SG1-4.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1XU1-2.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/1XU2-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/2HEY-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/2HEY-2.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/2HEY-4.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/2RPJ-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/2UWI-1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/2UWI-2.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/2UWI-3.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/2seqs.fas [new file with mode: 0644]
binaries/src/tcoffee/example/3d.aln [new file with mode: 0644]
binaries/src/tcoffee/example/3d.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/3d.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/3d_sample2.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/3d_sample3.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/3d_sample4.aln [new file with mode: 0644]
binaries/src/tcoffee/example/3d_sample5.aln [new file with mode: 0644]
binaries/src/tcoffee/example/3d_sample5.template_list [new file with mode: 0644]
binaries/src/tcoffee/example/b30.aln [new file with mode: 0644]
binaries/src/tcoffee/example/block1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/block2.aln [new file with mode: 0644]
binaries/src/tcoffee/example/cache [new file with mode: 0644]
binaries/src/tcoffee/example/charge_relay_lib.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/combined_aln.aln [new file with mode: 0644]
binaries/src/tcoffee/example/combined_aln.aln.aln [new file with mode: 0644]
binaries/src/tcoffee/example/command_line.txt [new file with mode: 0644]
binaries/src/tcoffee/example/error_report.T-COFFEE [new file with mode: 0644]
binaries/src/tcoffee/example/g0.aln [new file with mode: 0644]
binaries/src/tcoffee/example/g10.aln [new file with mode: 0644]
binaries/src/tcoffee/example/g15.aln [new file with mode: 0644]
binaries/src/tcoffee/example/g5.aln [new file with mode: 0644]
binaries/src/tcoffee/example/kinases.aln [new file with mode: 0644]
binaries/src/tcoffee/example/marna.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/new_profile1_pdb1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/newprf.aln [new file with mode: 0644]
binaries/src/tcoffee/example/p120.aln [new file with mode: 0644]
binaries/src/tcoffee/example/p250 [new file with mode: 0644]
binaries/src/tcoffee/example/p350.aln [new file with mode: 0644]
binaries/src/tcoffee/example/prf1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/prf1.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/prf1.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/prf2.aln [new file with mode: 0644]
binaries/src/tcoffee/example/prf2.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/prf2.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/prf3.aln [new file with mode: 0644]
binaries/src/tcoffee/example/prf3.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/profile1_pdb1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/profile1_pdb1.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/profile1_pdb1_1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/profile2_pdb2.aln [new file with mode: 0644]
binaries/src/tcoffee/example/profile2_pdb2.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/profile2_pdb2.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample1.score_ascii [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln1.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln1.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln1.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln1_1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln1_2.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln2.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln2.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln2.msf [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln3.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln4.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln5.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln6.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln6.cache [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln7.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_aln7.cache_aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_dnaseq1.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_lib1.mocca_lib [new file with mode: 0644]
binaries/src/tcoffee/example/sample_lib1.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/sample_lib2.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/sample_lib3.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/sample_lib4.tc_lib02 [new file with mode: 0644]
binaries/src/tcoffee/example/sample_lib5.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/sample_list1.lib_list [new file with mode: 0644]
binaries/src/tcoffee/example/sample_param_file.param [new file with mode: 0644]
binaries/src/tcoffee/example/sample_profile1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_profile2.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq1.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.alifold [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.cons.stk [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.cw.stk [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.cw_aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.stk [new file with mode: 0644]
binaries/src/tcoffee/example/sample_rnaseq2.tcoffee.stk [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq1.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq1.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq1.score_ascii [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq1.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq2.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq3.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq4.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq5.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq6.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq7.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sample_seq8.seq [new file with mode: 0644]
binaries/src/tcoffee/example/sample_tree.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sample_tree2.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sample_tree3.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/seq.fas [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases.small [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases.small.blosum62mt.sim_file [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases1_small.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases1_small.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases1_small.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases2_small.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases2_small.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases2_small.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_chain.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_large.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_large.code_name [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_large.coded.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_large.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_large.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_large.muscle [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_large_muscle_trim.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_oneseq.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_pair.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.b62_aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.cw_aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.expresso [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.g0.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.g0.cw_aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.g10.cw_aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.g10.score_ascii [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.g15.cw_aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.mafft [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.mcoffee [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.muscle [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.ph [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.probcons [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.score_ascii [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.score_html [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.tc_aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.tc_aln.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small.template_file [new file with mode: 0644]
binaries/src/tcoffee/example/sproteases_small_dna.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/struc1.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/struc2.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/struc3.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/struc4.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/struc5.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/struc6.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/struc7.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/struc8.pdb [new file with mode: 0644]
binaries/src/tcoffee/example/sv.aln [new file with mode: 0644]
binaries/src/tcoffee/example/sv.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/sv.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/sv.maln [new file with mode: 0644]
binaries/src/tcoffee/example/t_coffee.log [new file with mode: 0644]
binaries/src/tcoffee/example/template_file.template [new file with mode: 0644]
binaries/src/tcoffee/example/template_file6.template [new file with mode: 0644]
binaries/src/tcoffee/example/template_file7.template [new file with mode: 0644]
binaries/src/tcoffee/example/test.lib [new file with mode: 0644]
binaries/src/tcoffee/example/test.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/test_lib.tc_lib [new file with mode: 0644]
binaries/src/tcoffee/example/three_cdna.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/three_pdb.aln [new file with mode: 0644]
binaries/src/tcoffee/example/three_pdb.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/three_pdb.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/three_pdb_two_seq.aln [new file with mode: 0644]
binaries/src/tcoffee/example/three_pdb_two_seq.dnd [new file with mode: 0644]
binaries/src/tcoffee/example/three_pdb_two_seq.fasta [new file with mode: 0644]
binaries/src/tcoffee/example/tlara_tRNA_aln10.output [new file with mode: 0644]
binaries/src/tcoffee/example/tlara_tRNA_aln50.output [new file with mode: 0644]
binaries/src/tcoffee/example/tlara_tRNA_aln51.output [new file with mode: 0644]
binaries/src/tcoffee/example/two_profiles.template_file [new file with mode: 0644]
binaries/src/tcoffee/example/x [new file with mode: 0644]
binaries/src/tcoffee/install
binaries/src/tcoffee/license.txt
binaries/src/tcoffee/mcoffee/BLOSUM.diag_prob_t10 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/BLOSUM.scr [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/BLOSUM75.diag_prob_t2 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/BLOSUM75.scr [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/BLOSUM90.scr [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/New_KS.267.obs [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/New_KS.267.seq [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/blosum80.mat [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/blosum80_trunc.mat [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/dna_diag_prob_100_exp_110000 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/dna_diag_prob_100_exp_220000 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/dna_diag_prob_100_exp_330000 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/dna_diag_prob_100_exp_550000 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/dna_diag_prob_150_exp_110000 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/dna_diag_prob_200_exp_110000 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/dna_diag_prob_250_exp_110000 [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/dna_matrix.scr [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/hmmtop.arch [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/hmmtop.psv [new file with mode: 0644]
binaries/src/tcoffee/mcoffee/mix80.mod [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/coffee_defines.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/data_headers/perl_header_lib.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/data_headers/programmes_define.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/define_header.h
binaries/src/tcoffee/t_coffee_source/dev1_lib_header.h
binaries/src/tcoffee/t_coffee_source/dev_lib/dev1.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dev_lib/dev1.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dev_lib/dev1.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dev_lib/dev1.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/CUSTOM_evaluate_for_struc.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/CUSTOM_evaluate_for_struc.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/CUSTOM_evaluate_for_struc.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/CUSTOM_evaluate_for_struc.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_dirichlet.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_dirichlet.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_dirichlet.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_dirichlet.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_domain.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_domain.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_domain.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_domain.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_struc.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_struc.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_struc.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/evaluate_for_struc.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/fasta_dp.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/fsa_dp.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/fsa_dp.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/fsa_dp.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/fsa_dp.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/pavie.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/pavie_dp.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/pavie_dp.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/pavie_dp.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/pavie_dp.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/showpair.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/showpair.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/showpair.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/showpair.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/util_domain_dp.c [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/util_domain_dp.deps [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/util_domain_dp.h [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/util_domain_dp.o [new file with mode: 0644]
binaries/src/tcoffee/t_coffee_source/dp_lib/util_domain_dp_drivers.c [new file with mode: 0644]
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