AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mixed6_pyro_reg_300.orf -o321_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RPH01107 45 Pyrococcus_OT3 #2 RPH01557 59 Pyrococcus_OT3 #3 RPH01559 70 Pyrococcus_OT3 #4 RPH01560 55 Pyrococcus_OT3 #5 RPH01561 233 Pyrococcus_OT3 #6 RPH01563 186 Pyrococcus_OT3 #7 RPH01564 300 Pyrococcus_OT3 Motif number 1 CTTTATAAGATATTAAATTTTTGTAAAAAGGAA 2 13 0 TATAATTTTG 0.979348 -47 TTCCAGGAATTATAAATCTTTTGCGGAGAAATA 3 29 0 TATAACTTTG 0.989178 -42 AATGGATGCTTATGAACCTTTACAATAAAGAAC 5 72 1 TATAACTTTC 0.979606 -162 GGAAAAACTATATAAATTTTTCGGATTTCTCAT 5 171 0 TATAATTTTG 0.979348 -63 CAACACCTCCTATCAGTCTTTTCATTTCAAAAT 5 208 0 TATAGCTTTC 0.975369 -26 ATCAAAATAATATAAAGTTTTTGATAAA 6 6 0 TATAATTTTG 0.979108 -181 AAAGGAGGATTATTAGGTTTTGCTCTCTTCCTA 6 68 1 TATAGTTTTC 0.952755 -119 GGCTTAACATTATTAGGCCTTGGATTCCTTAGT 6 128 1 TATAGCCTTG 0.947266 -59 GAAAATTATGTAATAACCTTTTGGTGATGCACG 7 278 1 TAAAACTTTG 0.936084 -23 *** ** **** * Masking position 5 Map Score: 13.7287 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 36 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 GTTGAAAGATTAAAAGTTGCAAATT 1 5 1 AAAGATAAAA 0.844391 -41 AAATTTTTGTAAAAAGGAAAA 2 1 0 AAAAAGAAAA 0.873594 -59 ATCTTATAAAGGTAATAAAAACTCTGGGAGT 2 35 1 GGTAATAAAA 0.790841 -25 ATACTAAAAAAGAAAGAAACA 4 1 0 AGAAAGAACA 0.915612 -55 ACTTAAAAATAATACTAAAAAAGAAAGAAAC 4 12 0 AATACTAAAA 0.548696 -44 CCGCCCATTTTGAAATGAAAAGACTGATAGG 5 202 1 TGAAATAAAA 0.860859 -32 CAGTAATAGTAGAAATCAAAATAATATAAAG 6 22 0 AGAAATAAAA 0.977763 -165 ACAAGTAGGAAGAGAGCAAAACCTAATAATC 6 75 0 AGAGAGAAAA 0.945952 -112 AACCAAAAACAGAACTTAAAAAGGCTTATTA 7 28 0 AGAACTAAAA 0.960909 -273 AACTTAAATGAGAAACCAAAAACAGAACTTA 7 41 0 AGAAACAAAA 0.955541 -260 ACATTCTTGTAGAACCCAACAGGAGGTGTAA 7 196 0 AGAACCAACA 0.80636 -105 GTTTAATCATGGAGATTAAAACCTTATTACT 7 228 1 GGAGATAAAA 0.904162 -73 ****** **** Masking position 8 Map Score: 9.44908 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 444 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 TTTTCCTTTTTACAAAAATTTAATATCT 2 9 1 TTTACAAAAA 0.643933 -51 CAGTCTTTTCATTTCAAAATGGGCGGAAAA 5 198 0 ATTTCAAAAT 0.790395 -36 TCCTTTCCTCATTACTAACACCAGTAATAG 6 44 0 ATTACTAACA 0.902399 -143 TAGGCCTTGGATTCCTTAGTTTTCACCATC 6 141 1 ATTCCTTAGT 0.763909 -46 CACAGTGACAATTACATAGATGGTGAAAAC 6 159 0 ATTACATAGA 0.914312 -28 ATGTTTAATGATTCCAAACAATCTTCTCCC 7 100 1 ATTCCAAACA 0.952418 -201 CATTCCTCAAATTTCAAAAATGAGTATGGA 7 129 1 ATTTCAAAAA 0.848147 -172 TATGCTCAAAATTCCATACTCATTTTTGAA 7 141 0 ATTCCATACT 0.931833 -160 TTAAAACCTTATTACTTACATCAAAACCCT 7 243 1 ATTACTTACA 0.902384 -58 CCAAAAGGTTATTACATAATTTTCTTTAAA 7 272 0 ATTACATAAT 0.891745 -29 ********** Masking position 3 Map Score: 5.20734 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 211 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 ATTTCTTCAAGCTATTTCTCCGCAAAAGAT 3 17 1 GCTATTTCTC 0.97208 -54 ATTTCCATGAGCTATTCTTCG 4 45 1 GCTATTCTTC 0.8944 -11 GGCAAATTCTTCCATTTCTCTTCTTACCTG 5 22 1 TCCATTTCTC 0.978602 -212 CTAATAATCCTCCTTTCCTCATTACTAACA 6 54 0 TCCTTTCCTC 0.97471 -133 TGCCTCTTCTCATAATTTAAT 7 2 1 GCCTCTTCTC 0.952815 -299 ACAATCTTCTCCCATTCCTCAAATTTCAAA 7 117 1 CCCATTCCTC 0.983725 -184 ********** Masking position 6 Map Score: 3.86519 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 212 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 CGTGGAGTTGATAGTTCCAGGAATTATAAATCTTTTGC 3 38 0 AAGTAGATTA 0.780504 -33 CGAAGAATAGCTCATGGAAATCTACTTAAAAATA 4 32 0 AAGTTGAATA 0.986184 -24 AAGAGAAATGGAAGAATTTGCCAATTTATGGTC 5 6 0 GAGATGAATA 0.931209 -228 TTTAACCAGTAAAGATGCTATCCAGGTAAGAAGAGAAA 5 36 0 AAGTTACATA 0.920596 -198 CCTTTACAATAAAGAACATGCTCAAATACTCCAATTAT 5 88 1 AAGATGCATA 0.979504 -146 ATGCCTGCATAGAGATTATGGCCAAATAAGGATTCAAT 5 135 0 AAGTTGCATA 0.983299 -99 AACACCAGTAATAGTAGAAATCAAAATAATATAAAGTT 6 20 0 AAGAAAAATA 0.782856 -167 TGACAATTACATAGATGGTGAAAACTAAGGAATCCAAG 6 146 0 AAGTTGAAAA 0.918368 -41 GTAGAACCCAACAGGAGGTGTAAAATTAATTTCTTAGC 7 181 0 AAGATGAATA 0.983033 -120 * ** * ** ** ** Masking position 3 Map Score: 3.98229 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 139 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TCAATCACCAAAACTAATTTAAT 1 33 0 ATCACCAAAA 0.938134 -13 AATAAAGAACATGCTCAAATACTCCAATTA 5 95 1 ATGCTCAAAT 0.966147 -139 CATAGAGATTATGGCCAAATAAGGATTCAA 5 136 0 ATGGCCAAAT 0.959448 -98 AATTACATAGATGGTGAAAACTAAGGAATC 6 150 0 ATGGTGAAAA 0.830643 -37 TCTTCTCCCATTCCTCAAATTTCAAAAATG 7 121 1 TTCCTCAAAT 0.818544 -180 GAAGAAATATATGCTCAAAATTCCATACTC 7 150 0 ATGCTCAAAA 0.973796 -151 CGTGCATCACCAAAAGGTTATTACA 7 286 0 ATCACCAAAA 0.938134 -15 ********** Masking position 7 Map Score: 2.68065 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 118 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 GAAAGATTAAAAGTTGCAAATTAAATTAGTTT 1 14 1 AATTGCAATT 0.729204 -32 TCTCCGCAAAAGATTTATAATTCCTGGAACTA 3 33 1 AGTTTAAATT 0.593018 -38 GACCATAAATTGGCAAATTCTTCCATTTC 5 8 1 AATGGCAATT 0.533854 -226 AATTATAAATAATTGGAGTATTTGAGCATGTT 5 102 0 AATGGATATT 0.903899 -132 TAATGAGGAAAGGAGGATTATTAGGTTTTGCT 6 60 1 AGAGGATATT 0.941135 -127 TCCAACTATAAATAGGACAAGTAGGAAGAGAG 6 90 0 AAAGGAAAGT 0.74817 -97 TCCTATTTATAGTTGGATTAGTAGGCTTAACA 6 105 1 AGTGGATAGT 0.937023 -82 ACAGAACTTAAAAAGGCTTATTAAATTATGAG 7 19 0 AAAGGCTATT 0.903091 -282 ACCCAACAGGAGGTGTAAAATTAATTTCTTAG 7 182 0 AGTGTAAATT 0.8796 -119 ** **** **** Masking position 10 Map Score: 2.27643 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 410 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 TTTGACGTGGAGTTGATAGTTCCA 3 57 0 ACGTGGAGTT 0.917434 -14 GAAGAATAGCTCATGGAAATCTACTTAAAA 4 35 0 TCATGGAAAT 0.939581 -21 TCTCATGCCTGCATAGAGATTATGGCCAAA 5 147 0 GCATAGAGAT 0.928931 -87 GAATCATTAAACATGGGGATAAAGTTCAAC 7 84 0 ACATGGGGAT 0.973375 -217 TGTTGTTTAATCATGGAGATTAAAACCTTA 7 224 1 TCATGGAGAT 0.987828 -77 ********** Masking position 4 Map Score: 0.706954 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 68 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ********** No masking Map Score: -1.16996e-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 10 AAGTTGCAAATTAAATTAGTTTTGGTGATTGA 1 24 1 TTAATAGTTT 0.907764 -22 GAGAAATAGCTTGAAGAAATTTCAAC 3 5 0 TTAAGAATTT 0.958329 -66 TAGTATTATTTTTAAGTAGATTTCCATGAGCT 4 26 1 TTAAGAGATT 0.939303 -30 CAAATAAGGATTCAATGAATTATAAATAATTG 5 119 0 TTAATAATTA 0.723833 -115 GGGGATAAAGTTCAACGAAATTTGTAACAACT 7 68 0 TTAACAAATT 0.940435 -233 ACAGGAGGTGTAAAATTAATTTCTTAGCTGAA 7 177 0 TAAATAATTT 0.723833 -124 ATCTCCATGATTAAACAACATTCTTGTAGAAC 7 212 0 TTAACACATT 0.852354 -89 TCAAAACCCTTTAAAGAAAATTATGTAATAAC 7 263 1 TTAAGAAATT 0.958329 -38 ** *** ***** Masking position 5 Map Score: 0.781596 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 128 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 ********** No masking Map Score: -1.16996e-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: -1.16996e-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: -1.16996e-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