AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i185_4_6_1_10_mjan_reg_300.orf -o185_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 RMJ04550 300 M_jannaschii_chromosome #2 RMJ11031 105 M_jannaschii_chromosome #3 RMJ00227 80 M_jannaschii_chromosome #4 RMJ05430 300 M_jannaschii_chromosome #5 RMJ07035 147 M_jannaschii_chromosome Motif number 1 AATATTGGGATAAACAAGTAATTT 1 1 1 AATATGTAAA 0.968078 -300 TAAATATAAAAATTTAATTATAAAAGTCCATAAA 1 32 0 AATTTATAAA 0.964144 -269 TATACGCTATAATATAATTATAAATATAAAAATT 1 52 0 AATATATAAA 0.965343 -249 TATTATAGCGTATAATGTCATAAAACAATTAATA 1 72 1 TATAAGTAAA 0.708662 -229 CACATTAGTTTATTTAAAGTTAATAAGATTGGGG 1 106 0 TATTTATAAT 0.910667 -195 ATGTGGAAATAATATGGAAATAAAAGAAAATATC 1 135 1 AATATGTAAA 0.968078 -166 GAAAAATTTATATTTTACACTAAAATAATTTTAA 1 184 1 TATTTATAAA 0.951578 -117 TTTAATAAATAATATCATAGTAATAATAATTTAA 1 213 1 AATATATAAT 0.950468 -88 ATTTTTATATTTTAATTTAAATTGAATATAC 2 8 1 TATTTATAAA 0.951585 -98 GAATCTTTGGAATTTTGCTGTAATAAAAAAAGGT 3 26 0 AATTTGTAAT 0.920283 -55 ATTTAATTTTAATATAATTTTAAAAG 3 65 1 AATATATAAA 0.972855 -16 TAATTTCAAGTATATAAAACTAATGTTTGTCTCG 4 115 0 TATATATAAT 0.933462 -186 ***** * **** Masking position 12 Map Score: 16.6333 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 375 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 GACTTTTATAATTAAATTTTTATATTTATAA 1 38 1 ATTAATTTTT 0.918851 -263 TATATTTATAATTATATTATAGCGTATAATG 1 58 1 ATTAATTATA 0.968865 -243 TAATTGTTTTATGACATTATACGCTATAATA 1 72 0 ATGAATTATA 0.915692 -229 TTATTTCCACATTAGTTTATTTAAAGTTAAT 1 116 0 ATTATTTATT 0.879338 -185 GATAGAAAAATTTATATTTTACACTAAAATA 1 180 1 TTTAATTTTA 0.839176 -121 ATATTATTTATTAAAATTATTTTAGTGTAAA 1 197 0 TTAAATTATT 0.701706 -104 TATTATTACTATGATATTATTTATTAAAATT 1 210 0 ATGAATTATT 0.92637 -91 TACGAATTTCGTTAAATTATTATTACTATGA 1 227 0 GTTAATTATT 0.893855 -74 ATTTTTATATTTTAATTTAAATTG 2 4 1 TTTAATTTTA 0.839176 -102 TTATATTAAAATTAAATAATTGGAATCTTTG 3 51 0 ATTAATAATT 0.794063 -30 CTTTTAAAATTATATTAAAATTAAATAAT 3 62 0 ATTAATTAAA 0.762159 -19 AGTTGTAGGGATTAGATTATAGATTCTAAGA 5 103 1 ATTAATTATA 0.968865 -45 GAGGCTTATTTTTAGTTTATTTTTAG 5 132 1 TTTATTTATT 0.792224 -16 **** ****** Masking position 4 Map Score: 11.9582 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 461 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 ATAATTTAACGAAATTCGTAAAATAGGGGG 1 238 1 GAAATTCGTA 0.968762 -63 TTATTACAGCAAAATTCCAAAGATTCCAAT 3 34 1 AAAATTCCAA 0.948753 -47 TGTTGCTAAGGAAGCTCCAAGCTTTAGCTC 4 15 1 GAAGCTCCAA 0.924093 -286 GAGAGTTAATGAAATTCGAAGGATTTCATC 4 57 0 GAAATTCGAA 0.980296 -244 TTATATACTTGAAATTAGTATAATGCTTTA 4 132 1 GAAATTAGTA 0.775941 -169 CTAAAGGGTGGAGGTTCCAACACGGAACAC 4 234 0 GAGGTTCCAA 0.933789 -67 AAGATCAGTTAAAATTCCTAAATACTCCCG 4 272 1 AAAATTCCTA 0.920258 -29 GTGCATCCCGGATATTCCAATAGGGCAGAG 5 45 1 GATATTCCAA 0.943833 -103 ********** Masking position 2 Map Score: 6.43975 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 255 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 AATATTGGGATAAACAAGTAA 1 1 1 AAATTGGGAT 0.958685 -300 TAAAGTTAATAAGATTGGGGTATTAATTGTT 1 95 0 AAATTGGGGT 0.985647 -206 CGAAATTCGTAAAATAGGGGGATTAAAATCG 1 247 1 AAATAGGGGG 0.990903 -54 ATATTGCTAAAACCTTGGGGGAGGGGGTGAA 1 279 1 AACTTGGGGG 0.986719 -22 TCAATCAAATTGCATTGGGGGATGGAA 2 89 1 TGATTGGGGG 0.948275 -17 GCTACGCTCGAAGATAGGGAGGCGGCGAGAC 4 90 1 AAATAGGGAG 0.973549 -211 ** ******** Masking position 5 Map Score: 5.69692 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 88 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 TGGTGTCATCGGGCAGAGTCAGAGCTACCC 4 166 0 GGGCAGAGTC 0.99157 -135 CGCTAACGCTTGGCAGTGCCTCTTAAACC 5 10 0 TGGCAGTGCC 0.994193 -138 AGCGTTAGCGAGGCAGTGCATCCCGGATAT 5 30 1 AGGCAGTGCA 0.977338 -118 TATTCCAATAGGGCAGAGCCCTATGGTGTG 5 57 1 GGGCAGAGCC 0.997846 -91 ********** Masking position 5 Map Score: 4.16403 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 11 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 TAATAAGATTGGGGTATTAATTGTTTTATG 1 90 0 GGGGTATTAA 0.947465 -211 ATAAACTAATGTGGAAATAATATGGAAATA 1 127 1 GTGGAAATAA 0.899843 -174 TGGAAATAATATGGAAATAAAAGAAAATAT 1 138 1 ATGGAAATAA 0.746483 -163 TCGTAAAATAGGGGGATTAAAATCGCATAT 1 253 1 GGGGGATTAA 0.975982 -48 ACCTTGGGGGAGGGGGTGAAT 1 290 1 AGGGGGTGAA 0.956662 -11 AAATTGCATTGGGGGATGGAA 2 95 1 GGGGGATGGA 0.924376 -11 AGCGTAGCAAGGAGAGTTAATGAAATTCGA 4 68 0 GGAGAGTTAA 0.809418 -233 CACCCTTTAGGTGGAGAGAAGATCAGTTAA 4 254 1 GTGGAGAGAA 0.937073 -47 GCAGAGCCCTATGGTGTGAAAATGGATTAA 5 69 1 ATGGTGTGAA 0.83296 -79 ********** Masking position 10 Map Score: 4.09776 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 344 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 AATTTCTTCTCTTTTACCTTTTTTTATTAC 3 9 1 CTCTTACCTT 0.954501 -72 CATCTGAATCCTCTCCGAGCTAAAGCTTGGAG 4 29 0 CTCTCAGCTA 0.983752 -272 ATTTCATTAACTCTCCTTGCTACGCTCGAAGA 4 72 1 CTCTCTGCTA 0.937252 -229 CACCAACCTGCCCTGTGACCTATCGGCGACGA 4 191 1 CCCTTACCTA 0.984012 -110 ACACGGAACACCCTGCTACTTATCGTCGCCGA 4 213 0 CCCTCACTTA 0.984012 -88 ATAATCTAATCCCTACAACTTTACTTAATCCA 5 91 0 CCCTCACTTT 0.970577 -57 **** * ***** Masking position 4 Map Score: 1.67556 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 57 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 ATAAAACAATTAATACCCCAATCTTATTAA 1 91 1 TAATACCCCA 0.955309 -210 TATGCGATTTTAATCCCCCTATTTTACGAA 1 252 0 TAATCCCCCT 0.971108 -49 ATTCACCCCCTCCCCCAAGGTTTTAGC 1 284 0 CCCTCCCCCA 0.99168 -17 TTCCATCCCCCAATGCAATTTG 2 94 0 CCATCCCCCA 0.995103 -12 ********** Masking position 4 Map Score: 1.5186 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 28 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 ATTACTTGTTTATCCCAATATT 1 3 0 TATCCCAATA 0.786479 -298 ATTTCCATATTATTTCCACATTAGTTTATT 1 126 0 TATTTCCACA 0.933781 -175 TATTTTCTTTTATTTCCATATTATTTCCAC 1 137 0 TATTTCCATA 0.971851 -164 AAATATCCAGTATTCACAGATAGAAAAATT 1 162 1 TATTCACAGA 0.821266 -139 GTAAGTTTCCTACTTCCATATATATATAAT 2 47 0 TACTTCCATA 0.973493 -59 GTAGGAAACTTACTTCCAGAATTATTCAAT 2 64 1 TACTTCCAGA 0.962207 -42 AATTCCTAAATACTCCCGTAGTGGAGA 4 284 1 TACTCCCGTA 0.940837 -17 GCATCCCGGATATTCCAATAGGGCAGAGCC 5 47 1 TATTCCAATA 0.918251 -101 ********** Masking position 2 Map Score: 5.88699 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 188 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 ATTGCTAAAACCTTGGGGGAGGGGGTGAAT 1 281 1 CCTTGGGGGA 0.976281 -20 GCAGGGTGTTCCGTGTTGGAACCTCCACCC 4 229 1 CCGTGTTGGA 0.991978 -72 CTAAATACTCCCGTAGTGGAGA 4 289 1 CCGTAGTGGA 0.991978 -12 TAGGGCTCTGCCCTATTGGAATATCCGGGA 5 50 0 CCCTATTGGA 0.97658 -98 ********** Masking position 4 Map Score: 1.4421 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 TAAGGAAGCTCCAAGCTTTAGCTCGGAGAGG 4 21 1 CCAAGCTTAG 0.984431 -280 AGGCGGCGAGACAAACATTAGTTTTATATAC 4 109 1 ACAAACTTAG 0.948784 -192 GTTGGAACCTCCACCCTTTAGGTGGAGAGAA 4 243 1 CCACCCTTAG 0.983876 -58 AGAGGCACTGCCAAGCGTTAGCGAGGCAGTG 5 17 1 CCAAGCTTAG 0.979469 -131 ****** **** Masking position 8 Map Score: 1.53071 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 10 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 ********** No masking Map Score: 1.58751e-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 13 ********** No masking Map Score: 1.58751e-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 14 ********** No masking Map Score: 1.58751e-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