AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mjan_pyro_300.orf -o321_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ00843 201 M_jannaschii_chromosome #2 RMJ04712 278 M_jannaschii_chromosome #3 RPH01107 45 Pyrococcus_OT3 #4 RPH01557 59 Pyrococcus_OT3 #5 RPH01559 70 Pyrococcus_OT3 #6 RPH01560 55 Pyrococcus_OT3 #7 RPH01561 233 Pyrococcus_OT3 #8 RPH01563 186 Pyrococcus_OT3 #9 RPH01564 300 Pyrococcus_OT3 Motif number 1 CATCACCAACTTATTAGGAATTTATAATGATT 1 14 1 TTATTAGATT 0.778999 -188 AGATTTATCATTATTAATCATTATAAATTCCT 1 29 0 TTATTAAATT 0.782531 -173 AACCTCACTTTAATAAAGATTTGAGAGCATAT 1 143 1 TAATAAATTT 0.935356 -59 TTTTTATACCATATAAGGAATTTTGATGCCAA 2 43 1 ATATAAGATT 0.821102 -236 ACTTTCACAGAAATAAAATTTTATGATTGAAT 2 85 0 AAATAAATTT 0.824103 -194 TAAAAAAGATTTATAAAAATTTTGGAGAAAAT 2 193 0 TTATAAATTT 0.971051 -86 TTTTCCTTTTTACAAAAATTTAATATCTTAT 4 10 1 TTACAAATTT 0.799726 -50 TTTATTACCTTTATAAGATATTAAATTTTTGT 4 22 0 TTATAAGATT 0.934098 -38 GTTCCAGGAATTATAAATCTTTTGCGGAGAAA 5 31 0 TTATAAATTT 0.971052 -40 AAATGGATGCTTATGAACCTTTACAATAAAGA 7 71 1 TTATGAATTT 0.830313 -163 ATTCAATGAATTATAAATAATTGGAGTATTTG 7 110 0 TTATAAAATT 0.935357 -124 CGGAAAAACTATATAAATTTTTCGGATTTCTC 7 173 0 ATATAAATTT 0.915697 -61 AATCAAAATAATATAAAGTTTTTGATAAA 8 8 0 ATATAAATTT 0.915698 -179 GAAAGGAGGATTATTAGGTTTTGCTCTCTTCC 8 67 1 TTATTAGTTT 0.890968 -120 TCTCATAATTTAATAAGCCTTTTTAAGTTCTG 9 18 1 TAATAAGTTT 0.934098 -283 TTGATGTAAGTAATAAGGTTTTAATCTCCATG 9 235 0 TAATAAGTTT 0.934098 -66 GAAAATTATGTAATAACCTTTTGGTGATGCAC 9 278 1 TAATAACTTT 0.731536 -23 ******* *** Masking position 6 Map Score: 21.5874 Number of sites scoring better than the average of aligned sites = 873 Number in coding regions = 563 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 2 TATAAGCCTATTATCACCAAAAGTTATAAA 1 63 0 TTATCACCAA 0.929082 -139 CCAATAGGGGTTTTCCCCATGGCAATATAA 1 88 0 TTTTCCCCAT 0.980492 -114 ACACACAATATTTTCTCCAAAATTTTTATA 2 184 1 TTTTCTCCAA 0.921271 -95 TGCTTCATAATTATCCCTATTAAAGCATAT 2 249 0 TTATCCCTAT 0.948566 -30 TATTTGGCCATAATCTCTATGCAGGCATGA 7 145 1 TAATCTCTAT 0.811096 -89 GATTCCTTAGTTTTCACCATCTATGTAATT 8 150 1 TTTTCACCAT 0.957096 -37 TCGTTGAACTTTATCCCCATGTTTAATGAT 9 82 1 TTATCCCCAT 0.98775 -219 AATAAGGTTTTAATCTCCATGATTAAACAA 9 226 0 TAATCTCCAT 0.949424 -75 ********** Masking position 9 Map Score: 8.76834 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 258 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GTGATACCCTAACACCTCCTCGCTATGCCC 2 120 1 AACACCTCCT 0.994844 -159 TTTGCTAATTTACACCTCCGGGCATAGCGA 2 139 0 TACACCTCCG 0.992036 -140 TACCAACACCTCCTATCAGTCTTT 7 220 0 AACACCTCCT 0.994844 -14 CAAAACCTAATAATCCTCCTTTCCTCATTA 8 60 0 TAATCCTCCT 0.941539 -127 AAATTAATTTTACACCTCCTGTTGGGTTCT 9 187 1 TACACCTCCT 0.996397 -114 ********** Masking position 7 Map Score: 8.07124 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 1 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 CACCAAAAGTTATAAATAAGATTTATCATT 1 49 0 TATAAATAAG 0.941996 -153 TTTGAGAGCATATCAATAGGAGCAAAACCC 1 162 1 TATCAATAGG 0.948559 -40 TAAAGTCCTTTGTCAATAGGGTTTTCCC 2 9 0 TGTCAATAGG 0.929224 -270 CCTTATATGGTATAAAAAGCTGTAAAGTCC 2 31 0 TATAAAAAGC 0.843458 -248 TGCCCGGAGGTGTAAATTAGCAAATTATTA 2 145 1 TGTAAATTAG 0.61934 -134 ATAGAGTATTTATAAAAAAGATTTATAAAA 2 207 0 TATAAAAAAG 0.917305 -72 ATTAAATTTTTGTAAAAAGGAAAA 4 5 0 TGTAAAAAGG 0.926444 -55 TTCAATGAATTATAAATAATTGGAGTATTT 7 111 0 TATAAATAAT 0.644574 -123 TTTATCAAAAACTTTATATTAT 8 3 1 TATCAAAAAC 0.706371 -184 CTAATCCAACTATAAATAGGACAAGTAGGA 8 96 0 TATAAATAGG 0.962823 -91 ********** Masking position 5 Map Score: 7.92651 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 229 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 TATTGCCATGGGGAAAACCCCTATTGGGAT 1 91 1 GGGAAAACCC 0.979821 -111 TATCAATAGGAGCAAAACCCTTGGATGTAT 1 172 1 AGCAAAACCC 0.968129 -30 GGGAAAACCCTATTGACAAA 2 1 1 GGGAAAACCC 0.979821 -278 TGCCTTTGGCATCAAAATTCCTTATATGGT 2 50 0 ATCAAAATTC 0.694784 -229 TTTTATTTCTGTGAAAGTCCTGTGATACCC 2 99 1 GTGAAAGTCC 0.691179 -180 TAAATACTCTATCAAACCTCATATATATGC 2 225 1 ATCAAACCTC 0.773591 -54 TATAAAGGTAATAAAAACTCTGGGAGTTAC 4 39 1 ATAAAAACTC 0.817165 -21 CAAAATGGGCGGAAAAACTATATAAATTTT 7 184 0 GGAAAAACTA 0.560755 -50 GTAGGAAGAGAGCAAAACCTAATAATCCTC 8 72 0 AGCAAAACCT 0.726322 -115 TACATAGATGGTGAAAACTAAGGAATCCAA 8 147 0 GTGAAAACTA 0.801584 -40 AATTGTCACTGTGAAAGCTCG 8 176 1 GTGAAAGCTC 0.90962 -11 TATTACTTACATCAAAACCCTTTAAAGAAA 9 252 1 ATCAAAACCC 0.963266 -49 ********** Masking position 5 Map Score: 8.00778 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 245 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 TGGAGAAAATATTGTGTGTCTTTCAAGATAATAAT 2 168 0 ATTGCTTTCA 0.837791 -111 TTAATTTGCAACTTTTAATCTTTCAAC 3 3 0 ATTTCTTTCA 0.956721 -43 TAAATTGGCAAATTCTTCCATTTCTCTTCTTACCT 7 16 1 ATCTATTTCT 0.944105 -218 AAATACTCCAATTATTTATAATTCATTGAATCCTT 7 111 1 ATTTAATTCA 0.860215 -123 AACTATATAAATTTTTCGGATTTCTCATGCCTGCA 7 164 0 ATTTATTTCT 0.95344 -70 ACCTCCTATCAGTCTTTTCATTTCAAAATGGGCGG 7 202 0 ATTTATTTCA 0.975023 -32 AAAACTTTATATTATTTTGATTTCTACTATTACTG 8 18 1 ATTTATTTCT 0.953437 -169 TAGGCCTTGGATTCCTTAGTTTTCACCATCTATGT 8 141 1 ATCTTTTTCA 0.869875 -46 ATCTTCTCCCATTCCTCAAATTTCAAAAATGAGTA 9 120 1 ATCTATTTCA 0.969879 -181 * * ** ****** Masking position 12 Map Score: 5.66175 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 183 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 GGTGATAATAGGCTTATATTGCCATGGGGA 1 75 1 GGCTTATATT 0.72678 -127 AAGATTTGAGAGCATATCAATAGGAGCAAA 1 158 1 AGCATATCAA 0.731021 -44 AGATGCCTTTGGCATCAAAATTCCTTATAT 2 53 0 GGCATCAAAA 0.706369 -226 TGATGCCAAAGGCATCTTTATTCAATCATA 2 66 1 GGCATCTTTA 0.921381 -213 TCCCTATTAAAGCATATATATGAGGTTTGA 2 236 0 AGCATATATA 0.928218 -43 ATAATTATGAAGCATCTAATATCA 2 265 1 AGCATCTAAT 0.905846 -14 TTACCTGGATAGCATCTTTACTGGTTAAAT 7 45 1 AGCATCTTTA 0.915378 -189 AAGGTTCATAAGCATCCATTTAACCAGTAA 7 62 0 AGCATCCATT 0.766951 -172 AACTTAAAAAGGCTTATTAAATTATGAGAA 9 17 0 GGCTTATTAA 0.582527 -284 TGGAATTTTGAGCATATATTTCTTCAGCTA 9 155 1 AGCATATATT 0.89829 -146 ********** Masking position 5 Map Score: 1.85217 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 461 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 8 ATTAGCAAATTATTATCTTGAAAGACACACA 2 160 1 TATTACTTGA 0.923249 -119 TTGCAAATTAAATTAGTTTTGGTGATTGA 3 27 1 AATTATTTTG 0.765296 -19 CCAGAGTTTTTATTACCTTTATAAGATATTA 4 31 0 TATTACTTTA 0.93582 -29 TTTTGCGGAGAAATAGCTTGAAGAAATTTCA 5 13 0 AAATACTTGA 0.700265 -58 TCTTTTTTAGTATTATTTTTAAGTAGATTTC 6 19 1 TATTATTTTA 0.918595 -37 CAAATACTCCAATTATTTATAATTCATTGAA 7 110 1 AATTATTATA 0.687452 -124 AAAAACTTTATATTATTTTGATTTCTACTAT 8 17 1 TATTATTTGA 0.903312 -170 TCAGCTAAGAAATTAATTTTACACCTCCTGT 9 178 1 AATTATTTTA 0.933126 -123 GTTATTACATAATTTTCTTTAAAGGGTTTTG 9 264 0 AATTTCTTTA 0.739067 -37 ***** ***** Masking position 4 Map Score: 2.12329 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 217 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 9 CTAATAAGTTGGTGATGCTT 1 1 0 GGTGATGCTT 0.858447 -201 TATAACTTTTGGTGATAATAGGCTTATATT 1 65 1 GGTGATAATA 0.94374 -137 TATGCCCGGAGGTGTAAATTAGCAAATTAT 2 143 1 GGTGTAAATT 0.866988 -136 TAAAAATTTTGGAGAAAATATTGTGTGTCT 2 182 0 GGAGAAAATA 0.866988 -97 TTTGACGTGGAGTTGATAGTTCCAGGAA 5 53 0 GGAGTTGATA 0.943136 -18 ACTGATAGGAGGTGTTGGTA 7 224 1 GGTGTTGGTA 0.947102 -10 TACTATTACTGGTGTTAGTAATGAGGAAAG 8 42 1 GGTGTTAGTA 0.918619 -145 TTGAGGAATGGGAGAAGATTGTTTGGAATC 9 109 0 GGAGAAGATT 0.865676 -192 ********** Masking position 9 Map Score: 3.5185 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 235 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 TCCTAATAAGTTGGTGATGCTT 1 3 0 TTGGTGATGC 0.970273 -199 TTTATAACTTTTGGTGATAATAGGCTTATA 1 63 1 TTGGTGATAA 0.649271 -139 GAAATAAAATTTTATGATTGAATAAAGATG 2 78 0 TTTATGATTG 0.862025 -201 TAAATTAGTTTTGGTGATTGA 3 35 1 TTGGTGATTG 0.953417 -11 CCGCAAAAGATTTATAATTCCTGGAACTAT 5 36 1 TTTATAATTC 0.77203 -35 ACTCCAATTATTTATAATTCATTGAATCCT 7 115 1 TTTATAATTC 0.77203 -119 ATCCCCATGTTTAATGATTCCAAACAATCT 9 94 1 TTAATGATTC 0.854224 -207 TAATAACCTTTTGGTGATGCACG 9 288 1 TTGGTGATGC 0.970273 -13 ********** Masking position 7 Map Score: 1.70792 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 240 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 11 ********** No masking Map Score: -1.29076e-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: -1.29076e-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: -1.29076e-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