AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_mjan_reg_300.orf -o294_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 Purged sequences: RMJ04875 26 M_jannaschii_chromosome Input sequences: #1 RMJ07097 300 M_jannaschii_chromosome #2 RMJ01352 82 M_jannaschii_chromosome #3 RMJ07952 220 M_jannaschii_chromosome #4 RMJ10405 122 M_jannaschii_chromosome #5 RMJ01297 29 M_jannaschii_chromosome #6 RMJ15032 300 M_jannaschii_chromosome #7 RMJ02393 89 M_jannaschii_chromosome #8 RMJ01220 226 M_jannaschii_chromosome #9 RMJ11540 84 M_jannaschii_chromosome Motif number 1 TTCAATAATATAATATATACATTAA 1 5 0 TAATATAACA 0.848208 -296 AGGTATTTTTTAATAGAGATATTTGCAGAGG 1 36 1 TAATAGAATA 0.835975 -265 TGCAAAACATTTATAGAATAAAAAGGCAATC 1 160 0 TTATAGATAA 0.409072 -141 GATAAATTTTTTATATAAAAACAGTAGTTAT 1 202 1 TTATATAAAA 0.786538 -99 AAAACAGTAGTTATATAAATACAAATACTTT 1 219 1 TTATATAATA 0.797655 -82 TGAAGGTGATATATATTAAAACAAAAGATGT 1 255 1 ATATATTAAA 0.692367 -46 ATAATAATAAAAAAATAATAACATCTTTTGT 1 275 0 AAAAATATAA 0.77881 -26 AAAAAATAATAATAAAAAAATA 1 289 0 AAAAATATAA 0.77881 -12 CAAAAATATTTAGGAATATCTC 2 2 1 AAAAATATTA 0.790225 -81 TATCTCCGAAAAATATATATACTCCCATAAT 2 27 1 AAATATAATA 0.927779 -56 TCCCATAATAAAAAATTGAAAATGTAAGATT 2 49 1 AAAAATTAAA 0.8195 -34 AATATGCACAAAAAATAAAAAGGTGTAGTGA 3 37 0 AAAAATAAAA 0.853141 -184 TTGTGCATATTAATAGAAATATTTGAATATT 3 57 1 TAATAGAATA 0.835968 -164 ATTTAGTTCTAAATATTCAAATATTTCTATT 3 68 0 AAATATTAAA 0.9037 -153 AAAACATTATTAAGATAAATAAGGCACACAA 3 120 1 TAAGATAATA 0.599614 -101 TAGGGCGTTCAAATATTCATATTTAATTTAT 3 164 1 AAATATTATA 0.909419 -57 AACACAAATTTTATATAATTAGGTAATTTAA 4 48 0 TTATATATTA 0.704404 -75 TTTGATAGTATAATATTTTCATTAAAAATTT 4 96 1 TAATATTTCA 0.725436 -27 TTTAATAAATTTTTAATGAAAATAT 4 108 0 ATAAATTTTA 0.413708 -15 AATTAATAAAAAATATATAAAATTATT 6 7 0 AAATATAAAA 0.92312 -294 ATAAGTAATATAATATACATAATAACCTACA 6 40 0 TAATATAATA 0.942651 -261 CATGCCAAAATAATATATAAATCTTACGATT 6 80 1 TAATATAAAA 0.938888 -221 ATTTTTTAAAAAATATTATTACTCAAATATT 6 108 1 AAATATTTTA 0.858135 -193 TTATTTGTTTAAAAATTAATATTTGAGTAAT 6 125 0 AAAAATTATA 0.82927 -176 AGATATTTTAAAATATTTTAAAGTTTTCTTT 6 163 1 AAATATTTAA 0.850391 -138 AAGTTTTCTTTAATATTGTTAGGAAAATAGA 6 183 1 TAATATTTTA 0.88505 -118 ATATCACATTTAATATTTAAAGTTTAACAGC 6 250 0 TAATATTAAA 0.923029 -51 TTGAATGAGATAAAAGAAACACAAATAAAAA 7 24 1 TAAAAGAACA 0.456009 -66 CAATTTTCTCTAATATTTTTAGCATTTTTAT 7 48 0 TAATATTTTA 0.851453 -42 TTAAAATTTAAAGCTTTTGTTC 7 78 0 TAAAATTAAA 0.853057 -12 ATCGATAAAATAAAATTAAAATAAATCTTCT 9 33 0 TAAAATTAAA 0.852968 -52 AAAAAGTTTTTAATAGATTTATCGATAAAAT 9 53 0 TAATAGATTA 0.755138 -32 ******* *** Masking position 5 Map Score: 34.1631 Number of sites scoring better than the average of aligned sites = 2547 Number in coding regions = 1611 Number in noncoding regions = 936 Number of orfs with sites within 600 bp upstream = 574 Fraction of orfs with sites within 600 bp upstream = 0.092194 Motif number 2 TTTTAATAGAGATATTTGCAGAGGCTCTGCAA 1 43 1 GTTTTGCAGA 0.991424 -258 TACTTTGGATGGTATTTGCAGAGCCTCTGCAA 1 58 0 GTTTTGCAGA 0.991424 -243 TCCAAAGTATGTTCTTTGCAAAGTTATTTAAA 1 81 1 GTTTTGCAAA 0.995126 -220 TTATCTTATAGTTCTTTGCAAAACATTTATAG 1 175 0 GTTTTGCAAA 0.995126 -126 AATTAAAATAGTTTTTTGCAAAACATTATTAA 3 101 1 GTTTTGCAAA 0.995126 -120 CCTATTTATAGTTTTTTGCAAAAGGTATAAAT 3 189 0 GTTTTGCAAA 0.995126 -32 TAAATCTTACGATTTTTTAAAAAATATTATTA 6 97 1 GTTTTTAAAA 0.914386 -204 AATGATAAAAGATATTTTAAAATATTTTAAAG 6 154 1 GTTTTTAAAA 0.914386 -147 * * ******** Masking position 10 Map Score: 18.2292 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 27 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 TATTATATTATTGAAAGGTATTTTTTAATAGAGA 1 21 1 TTGAAAGTTT 0.936635 -280 AAGGTATTTTTTAATAGAGATATTTGCAGAGGCT 1 35 1 TTAATAGTTT 0.856826 -266 AATCAATATAATGAACTCCTTCTTAGAGGGAGTT 1 130 0 ATGAACTTTT 0.344335 -171 GTTTTTATATAAAAAATTTATCTTATAGTTCTTT 1 190 0 AAAAAATTTT 0.691406 -111 GCACAAAAAATAAAAAGGTGTAGTGATATTATAC 3 29 0 TAAAAAGTGT 0.582553 -192 TTTGTGCATATTAATAGAAATATTTGAATATTTA 3 56 1 TTAATAGTTT 0.856829 -165 CTAAATGGAATTAAAATAGTTTTTTGCAAAACAT 3 93 1 TTAAAATTTT 0.962214 -128 ATATGAATATTTGAACGCCCTATTTGGGACGTTC 3 152 0 TTGAACGTTT 0.732289 -69 CAAAAAACTATAAATAGGGCTATTTTGT 3 203 1 TAAATAGTTT 0.725194 -18 ACCTAATTATATAAAATTTGTGTTAAACAAAATT 4 55 1 ATAAAATTTT 0.864123 -68 TAATATTTTCATTAAAAATTTATTAAA 4 106 1 ATTAAAATTT 0.234045 -17 TACGATTTTTTAAAAAATATTATTACTCAAATAT 6 104 1 TAAAAAATTT 0.783336 -197 ATTATTTGTTTAAAAATTAATATTTGAGTAATAA 6 123 0 TAAAAATTTT 0.918449 -178 TTAAAATATTTTAAAATATCTTTTATCATTATTT 6 150 0 TTAAAATTTT 0.962315 -151 TTTAAAATATTTTAAAGTTTTCTTTAATATTGTT 6 169 1 TTTAAAGTTT 0.83312 -132 ATATCAATCATCAAAATTTCTGTTAAAAG 6 282 1 TCAAAATTTT 0.776067 -19 ATAATTTAAAAGTGGTATTATGGAATTAA 8 6 1 TTAAAAGTTT 0.970679 -221 CCTCTATGCTTTGAAATACTTCTTCCTTTTAATT 8 34 0 TTGAAATTTT 0.919386 -193 AAATAAAAATCATTCTTTTATTAGAAG 9 4 1 TAAAAATTTT 0.918106 -81 TAAAATAAAATTAAAATAAATCTTCTAATAAAAG 9 25 0 TTAAAATTTT 0.962324 -60 GATAAATCTATTAAAAACTTTTTTGGTGATAATT 9 61 1 TTAAAAATTT 0.890591 -24 ******* * ** Masking position 11 Map Score: 23.9578 Number of sites scoring better than the average of aligned sites = 1059 Number in coding regions = 863 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 4 ATACCTTTCAATAATATAATATATACATTA 1 12 0 ATAATATAAT 0.846619 -289 TCATCCTTAGTTAATTTAAATAACTTTGCA 1 97 0 TTAATTTAAA 0.751487 -204 CAAAACATTTATAGAATAAAAAGGCAATCA 1 159 0 ATAGAATAAA 0.543031 -142 GCAAAGAACTATAAGATAAATTTTTTATAT 1 188 1 ATAAGATAAA 0.820686 -113 AGATAAATTTTTTATATAAAAACAGTAGTT 1 201 1 TTTATATAAA 0.414811 -100 AAAAACAGTAGTTATATAAATACAAATACT 1 218 1 GTTATATAAA 0.493822 -83 ATCTTTTGTTTTAATATATATCACCTTCAA 1 254 0 TTAATATATA 0.48736 -47 TAATAAAAAAATAATAACATCTTTTGTTTT 1 272 0 ATAATAACAT 0.143936 -29 AAAAAATAATAATAAAAAAATAATAACA 1 283 0 ATAATAAAAA 0.833264 -18 ATATACTCCCATAATAAAAAATTGAAAATG 2 43 1 ATAATAAAAA 0.833264 -40 TAATATGCACAAAAAATAAAAAGGTGTAGT 3 39 0 AAAAAATAAA 0.424551 -182 TTTGTGCATATTAATAGAAATATTTGAATA 3 56 1 TTAATAGAAA 0.636484 -165 CAAAACATTATTAAGATAAATAAGGCACAC 3 119 1 TTAAGATAAA 0.658936 -102 TGCAAAAGGTATAAATTAAATATGAATATT 3 175 0 ATAAATTAAA 0.705084 -46 ATATAATTAGGTAATTTAATTACCTTAAAA 4 37 0 GTAATTTAAT 0.343898 -86 AAATTACCTAATTATATAAAATTTGTGTTA 4 50 1 ATTATATAAA 0.624233 -73 ATGACATTTGATAGTATAATATTTTCATTA 4 90 1 ATAGTATAAT 0.463905 -33 CCTACACAAATTAATAAAAAATATATAAAA 6 16 0 TTAATAAAAA 0.678158 -285 TACTGCATAAGTAATATAATATACATAATA 6 47 0 GTAATATAAT 0.63871 -254 TCATGCCAAAATAATATATAAATCTTACGA 6 79 1 ATAATATATA 0.692819 -222 AAACTTTAAAATATTTTAAAATATCTTTTA 6 159 0 ATATTTTAAA 0.282972 -142 TAAATGTGATATAATATCAATCATCAAAAT 6 269 1 ATAATATCAA 0.777131 -32 ATTGAATGAGATAAAAGAAACACAAATAAA 7 23 1 ATAAAAGAAA 0.575485 -67 TTAAAATTTAAAGCTTTTGTTC 7 78 0 AAAATTTAAA 0.400668 -12 ATAATTTAAAAGTGGTATTA 8 1 1 ATAATTTAAA 0.87871 -226 TAAAATAAAATTAAAATAAATCTTCTAATA 9 29 0 TTAAAATAAA 0.769522 -56 AGATTTATCGATAAAATAAAATTAAAATAA 9 40 0 ATAAAATAAA 0.88884 -45 ********** Masking position 2 Map Score: 16.9562 Number of sites scoring better than the average of aligned sites = 2209 Number in coding regions = 1552 Number in noncoding regions = 657 Number of orfs with sites within 600 bp upstream = 480 Fraction of orfs with sites within 600 bp upstream = 0.077096 Motif number 5 AGATATTTGCAGAGGCTCTGCAAATACCATCC 1 52 1 AGGGTCTGCA 0.970337 -249 TTTATTCTATAAATGTTTTGCAAAGAACTATA 1 169 1 AATGTTTGCA 0.823889 -132 GTATAGCAATAGAGGCTTTGCCTCTATGCTTT 8 56 0 AGGGTTTGCC 0.996238 -171 TATACTCCAGAGCGGGGTTGCCAGAGGCAACC 8 83 1 AGGGGTTGCC 0.995466 -144 CCAGATAGAAAGTGGGGTTGCCTCTGGCAACC 8 98 0 AGGGGTTGCC 0.995466 -129 CTCACTATAGAAGGGCTTTGCCCCTCTATTGG 8 138 0 AAGGTTTGCC 0.98895 -89 ** ** ****** Masking position 9 Map Score: 6.47724 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 21 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TATTGATTGCCTTTTTATTCTATAAATGTT 1 156 1 CTTTTTATTC 0.910217 -145 ACCATAAAGTATTTGTATTTATATAACTAC 1 225 0 ATTTGTATTT 0.746711 -76 TTATTTTTTTATTATTATTTTTT 1 288 1 ATTATTATTT 0.644535 -13 ATCACTACACCTTTTTATTTTTTGTGCATA 3 36 1 CTTTTTATTT 0.947737 -185 GCAAAAAACTATTTTAATTCCATTTAGTTC 3 90 0 ATTTTAATTC 0.897448 -131 TATTACTCAAATATTAATTTTTAAACAAAT 6 124 1 ATATTAATTT 0.643796 -177 TATTTTTAGCATTTTTATTTGTGTTTCTTT 7 36 0 ATTTTTATTT 0.939941 -54 TGAACAAAAGCTTTAAATTTTAA 7 77 1 CTTTAAATTT 0.697348 -13 CATAATACCACTTTTAAATTAT 8 3 0 CTTTTAAATT 0.677438 -224 ATACTTCTTCCTTTTAATTCCATAATACCA 8 23 0 CTTTTAATTC 0.910216 -204 TAAAAGAATGATTTTTATTT 9 1 0 ATTTTTATTT 0.939941 -84 TAGAAGATTTATTTTAATTTTATTTTATCG 9 32 1 ATTTTAATTT 0.939831 -53 ********** Masking position 7 Map Score: 13.0094 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 449 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 7 TACAAATACTTTATGGTTGAAGGTGATATA 1 238 1 TTATGGTTGA 0.966107 -63 TTAAAAATGATTAAGATTGATTAGGGATAG 4 13 0 TTAAGATTGA 0.950279 -110 ACAGAAATTTTGATGATTGATATTATATCA 6 275 0 TGATGATTGA 0.966107 -26 GTAAATTTTCTTATGATTGAGGGATTATT 8 208 1 TTATGATTGA 0.979827 -19 ********** Masking position 7 Map Score: 1.45264 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 11 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 8 ATATTTTTCGGAGATATTCCTAAATATTTT 2 13 0 GAGATATTCC 0.914378 -70 CCGAAAAATATATATACTCCCATAATAAAA 2 32 1 TATATACTCC 0.929147 -51 ATTTTGGCATGATATACTGCATAAGTAATA 6 61 0 GATATACTGC 0.959101 -240 TCTATGCTTTGAAATACTTCTTCCTTTTAA 8 36 0 GAAATACTTC 0.827169 -191 AGCCTCTATTGCTATACTCCAGAGCGGGGT 8 71 1 GCTATACTCC 0.972935 -156 CCCCTCTATTGGGATACTCCCCAGATAGAA 8 120 0 GGGATACTCC 0.970877 -107 ********** Masking position 5 Map Score: 0.994261 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 19 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 CAGAGCCTCTGCAAATATCTCTATTAAAAA 1 42 0 GCAAATATCT 0.917665 -259 CAGAGGCTCTGCAAATACCATCCAAAGTAT 1 61 1 GCAAATACCA 0.929702 -240 AAATAACTTTGCAAAGAACATACTTTGGAT 1 80 0 GCAAAGAACA 0.972931 -221 TAAATGTTTTGCAAAGAACTATAAGATAAA 1 178 1 GCAAAGAACT 0.988041 -123 ATAATGTTTTGCAAAAAACTATTTTAATTC 3 100 0 GCAAAAAACT 0.973453 -121 TATACCTTTTGCAAAAAACTATAAATAGGG 3 192 1 GCAAAAAACT 0.973453 -29 CAATAGAGGGGCAAAGCCCTTCTATAGTGA 8 139 1 GCAAAGCCCT 0.954703 -88 ********** Masking position 5 Map Score: 9.14696 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 52 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 CCCATAATAAAAAATTGAAAATGTAAGATT 2 50 1 AAAATTGAAA 0.750661 -33 CTTTTGCAAAAAACTATAAATAGGGCTATT 3 197 1 AAACTATAAA 0.746002 -24 TGTTTAACACAAATTTTATATAATTAGGTA 4 54 0 AAATTTTATA 0.670106 -69 TTTAATAAATTTTTAATGAAAATATT 4 107 0 AAATTTTTAA 0.649329 -16 CTCAAATATTAATTTTTAAACAAATAATGA 6 129 1 AATTTTTAAA 0.670106 -172 ATGATAAAAGATATTTTAAAATATTTTAAA 6 155 1 ATATTTTAAA 0.781749 -146 ATATTAAAGAAAACTTTAAAATATTTTAAA 6 169 0 AAACTTTAAA 0.96206 -132 AACTGCTGTTAAACTTTAAATATTAAATGT 6 246 1 AAACTTTAAA 0.96206 -55 AATTGAACAAAAGCTTTAAATTTTAA 7 74 1 AAGCTTTAAA 0.826848 -16 ATAATTTAAAAGTGGTATTA 8 1 1 ATAATTTAAA 0.781749 -226 CAATCATAAGAAAATTTACACCTCCGAGCG 8 197 0 AAAATTTACA 0.750661 -30 TCGATAAAATAAAATTAAAATAAATCTTCT 9 33 0 AAAATTAAAA 0.670106 -52 ********** Masking position 1 Map Score: 5.88143 Number of sites scoring better than the average of aligned sites = 837 Number in coding regions = 587 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 11 ********** No masking Map Score: 1.12509e-12 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 12 ********** No masking Map Score: 1.12509e-12 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: 1.12509e-12 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