AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_mjan_reg_300.orf -o174_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ08819 34 M_jannaschii_chromosome #2 RMJ07487 255 M_jannaschii_chromosome #3 RMJ14506 155 M_jannaschii_chromosome Motif number 1 AGTGTAGTATTGATTGAAATGATATATATG 2 27 0 TGATTGAAAT 0.980947 -229 GAGATAAAATTGAGTTTAAATTAATTAATA 2 86 0 TGAGTTTAAA 0.913156 -170 CATCAAAAATTGATTAAGAAAATTTAAGAT 2 120 0 TGATTAAGAA 0.946732 -136 GGGGTAACTATGATTGAAATTATAAGACTA 2 151 1 TGATTGAAAT 0.980947 -105 ATATTTATTTTGATTTAAAAAAGGCACAGC 2 221 0 TGATTTAAAA 0.983256 -35 AATTCAGAATTGAGTAAAATTACTTTGGTG 3 17 0 TGAGTAAAAT 0.972351 -139 TACTCAATTCTGAATTAAATCGATAAGTAT 3 31 1 TGAATTAAAT 0.908272 -125 AAAATACTAATGATTATAAATTATAATAGA 3 105 0 TGATTATAAA 0.960222 -51 AAAAACCCCCTTATTAAAAATACTAATGAT 3 121 0 TTATTAAAAA 0.874305 -35 ********** Masking position 5 Map Score: 12.7725 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 363 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 2 CTTTTTTTGTGATATTTTGGTGATATTT 1 17 1 GATATTTTGG 0.960752 -18 ATATATATGCTTTACTTAGGTTCTA 2 6 0 TTTACTTAGG 0.715993 -250 TGATTGAAATGATATATATGCTTTACTTAG 2 17 0 GATATATATG 0.696963 -239 AACAAGGATAGAGATTTTTGTATTAATTAA 2 66 1 GAGATTTTTG 0.944626 -190 AAGAAAATTTAAGATTTAGGAGATAAAATT 2 105 0 AAGATTTAGG 0.965223 -151 TTGAAATTATAAGACTATGGCTAACCAAAT 2 164 1 AAGACTATGG 0.911807 -92 AATCAAAATAAATATTTGTGAGGGATAGCT 2 236 1 AATATTTGTG 0.889939 -20 ATTGAGTAAAATTACTTTGGTGCTAACT 3 9 0 ATTACTTTGG 0.873201 -147 ATCCATGATAAATATTTATGGCAATAAAAT 3 67 0 AATATTTATG 0.956643 -89 TAAATTATAATAGATTATTGACATCCATGA 3 89 0 TAGATTATTG 0.750982 -67 CCTTATTAAAAATACTAATGATTATAAATT 3 113 0 AATACTAATG 0.89175 -43 ********** Masking position 4 Map Score: 8.36979 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 804 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 ACTTCTCTTTTTTTGTGATATTTTGGTGAT 1 10 1 TTTTTGGATA 0.92564 -25 TTTTGTGATATTTTGGTGATATTT 1 21 1 TTTTGGGATA 0.991099 -14 ATATGCTTTACTTAGGTTCTA 2 1 0 CTTAGGTCTA 0.940282 -255 CAATACTACACTACGGCTATAAACAAGGATA 2 45 1 CTACGGTATA 0.893799 -211 AAATTTAAGATTTAGGAGATAAAATTGAGTT 2 100 0 TTTAGGGATA 0.97975 -156 AGTAAAATTACTTTGGTGCTAACT 3 4 0 CTTTGGGCTA 0.990751 -152 TGATAAATATTTATGGCAATAAAATAAATAT 3 61 0 TTATGGAATA 0.959088 -95 AAGGGGGTTTTTATGGAACTAACGGTT 3 139 1 TTATGGACTA 0.958364 -17 ****** **** Masking position 11 Map Score: 8.24661 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 486 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 TCACCAAAATATCACAAAAAAAGAGAAGT 1 10 0 ATCACAAAAA 0.962006 -25 AAATATCACCAAAATATCACAAAA 1 21 0 ATCACCAAAA 0.991048 -14 TAGAACCTAAGTAAAGCATAT 2 2 1 AGAACCTAAG 0.779353 -254 ACTCAATTTTATCTCCTAAATCTTAAATTT 2 101 1 ATCTCCTAAA 0.878972 -155 ATAGTTACCCCTCATCAAAAATTGATTAAG 2 132 0 CTCATCAAAA 0.923762 -124 AAGACTATGGCTAACCAAATAACGGAACTG 2 174 1 CTAACCAAAT 0.859603 -82 AGCTATCCCTCACAAATATTTATTTTGA 2 238 0 CTCACAAATA 0.816435 -18 AGTTAGCACCAAAGTAATTTTACT 3 5 1 AGCACCAAAG 0.976843 -151 ********** Masking position 8 Map Score: 4.96972 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 554 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 5 ATCCTTGTTTATAGCCGTAGTGTAGTATTG 2 45 0 ATAGCCGTAG 0.976052 -211 CGTTATTTGGTTAGCCATAGTCTTATAATT 2 168 0 TTAGCCATAG 0.864739 -88 ACGGCAATGCAGTTCCGTTATTTGGTTAGC 2 183 0 AGTTCCGTTA 0.913625 -73 ACGGAACTGCATTGCCGTTTTATTTGGCTG 2 195 1 ATTGCCGTTT 0.937279 -61 TATTTATTTTATTGCCATAAATATTTATCA 3 62 1 ATTGCCATAA 0.978164 -94 AACCGTTAGTTCCATAAAAACCCCCTT 3 139 0 AGTTCCATAA 0.926202 -17 ********** Masking position 8 Map Score: 1.4385 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 241 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 ********** No masking Map Score: -2.24942e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: -2.24942e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: -2.24942e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0