AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imetR_mthe_opreg_300.orf -g0.495 -x5 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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH124 126 conserved protein #2 MTH777 48 conserved protein #3 MTH778 68 unknown #4 MTH779 300 conserved protein #5 MTH1380 167 serine hydroxymethyltransferase #6 MTH1381 151 heterodisulfide reductase, subunit A #7 MTH1383 52 DNA repair protein RadA #8 MTH1385 300 replication factor A related protein Motif number 1 GCATCAAGCCCCCTCCAAATAGTATTTAAGATGAA 1 47 0 CCCTCAATTT 0.989363 -80 CTGTAAACCTCCCTACAACTGCATTCCTGTCCATT 1 89 0 CCCTCAATAT 0.915062 -38 CTCATCAAGATCTCTGTAAACCTCC 1 112 0 CTCACAAATT 0.799087 -15 GATTATCTCCCCATTATGGGTTCTTGATCATTCA 2 25 0 CCCATATGTT 0.79411 -24 CCCTCAATATATGATCTAGTTGCAACC 3 3 1 CTCATATTTT 0.68929 -66 GTTTTTATTGTCCTGCATTTATTTTTACTGATTAA 4 112 0 TCCTCATTTT 0.821255 -189 AGCTACCAGCCCCAACAAAGTATACATTAAGCCTT 4 230 1 CCCACAAGTC 0.944542 -71 ATGGGTTAACCCCATCAAATCCTTTATCCTTTTTC 5 11 1 CCCACAATTT 0.992251 -157 CCTTTATGAACCCTTCAATTATTCTGCTAAAGGAG 8 16 0 CCCTCAATTT 0.989363 -285 TCATAAAGGTTCCAGCAAGTGGTCCATGGGGCAGT 8 42 1 TCCACAATTC 0.860447 -259 TTTCACCCGGCCCTATAAATACTTTGATAATAAGA 8 183 1 CCCTTAATTT 0.953559 -118 TTTTCAGGAGCTCACCAAGTCTTTTATAGACGGGG 8 245 1 CTCACAATTT 0.965831 -56 **** *** * * * Masking position 7 Map Score: 11.6308 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 204 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 GAGATTTATCATTTTCACAGGAGATC 1 7 0 ATTTTCACAG 0.980265 -120 AGTTGTAGGGAGGTTTACAGAGATCTTGAT 1 104 1 AGGTTTACAG 0.965667 -23 GATTAAATGAAGTTTTTCAGGTTTCCTTAT 4 88 0 AGTTTTTCAG 0.968716 -213 TCCTGCATTTATTTTTACTGATTAAATGAA 4 107 0 ATTTTTACTG 0.948857 -194 CTTTCCTCAGTTTTTTTCAGGTATATTAAA 6 47 0 TTTTTTTCAG 0.849879 -105 AGAGGCTCTAATTTTCACAGACTGCCCCAT 8 67 0 ATTTTCACAG 0.980265 -234 ATGTCCCCATATGTTCACTGGATAACTGTC 8 108 1 ATGTTCACTG 0.911483 -193 AATTCAGACGAGTTTTTCAGTATGAAGGCG 8 141 0 AGTTTTTCAG 0.968716 -160 ********** Masking position 5 Map Score: 8.68597 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 80 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 GAAACCTGAAAAACTTCATTTAATCAGTAAAA 4 93 1 AACTTCATTA 0.894914 -208 TTAATAAGGTTAACTTTAAATATTAAAAGGCT 4 259 0 TACTTTAATA 0.876214 -42 TTATCCGTCGAAGATTTAATAAGGTTAACTTT 4 274 0 AAATTTAAAA 0.878393 -27 ACACAGAATAAACATTTATTTAATATACCTGA 6 29 1 AAATTTATTA 0.948743 -123 TTTCTATCAAAAACTTTAAGTAAGGTTTATAT 6 86 0 AACTTTAATA 0.978217 -66 TTTTGATAGAAATATTTATTTAGCACTGTGGT 6 106 1 AAATTTATTA 0.948743 -46 ATCTCCCTTAAATCTTTAAATATTCATTAAGC 7 27 0 AACTTTAATA 0.978217 -26 CACTTGCTGGAACCTTTATGAACCCTTCAATT 8 31 0 AACTTTATAA 0.920121 -270 CTTTGATAATAAGATTTAAATATATAGTAATA 8 204 1 AAATTTAATA 0.958077 -97 ** ****** ** Masking position 6 Map Score: 9.30103 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 4 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 ATACTATTTGGAGGGGGCTTGATGCGAACTG 1 57 1 GAGGGGGCTG 0.957505 -70 TCATTCACCAGCTGGGACCGC 2 1 0 GCTGGGACGC 0.952763 -48 TGGGCACTTCCCTGTGGCCTGGAATGATTTT 4 48 1 CCTGTGGCTG 0.960764 -253 GAGTGGACTGGCCGGGATTTGAACCCGGGGC 4 165 1 GCCGGGATTG 0.890601 -136 GGGATTTGAACCCGGGGCCTCCGCCATGCCA 4 178 1 CCCGGGGCTC 0.974687 -123 GTAGAGCGTCGCCTTGGCATGGCGGAGGCCC 4 192 0 GCCTTGGCTG 0.845869 -109 TGTATACTTTGTTGGGGCTGGTAGCTCAGGT 4 225 0 GTTGGGGCGG 0.947792 -76 TGTGTATTTTGCTGTGACTTT 6 1 0 GCTGTGACTT 0.885582 -151 TGGACCACTTGCTGGAACCTTTATGAACCCT 8 37 0 GCTGGAACTT 0.711196 -264 GCAAGTGGTCCATGGGGCAGTCTGTGAAAAT 8 56 1 CATGGGGCGT 0.854076 -245 GTCTTTTATAGACGGGGCGTGATATTATTAA 8 263 1 GACGGGGCTG 0.987431 -38 ******** ** Masking position 6 Map Score: 5.56564 Number of sites scoring better than the average of aligned sites = 1074 Number in coding regions = 1002 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 CCCATATCTCTGGTTTCAGGGTCCGGATTT 3 37 1 TGGTTTCAGG 0.863959 -32 ATGATTTTTAAGTTTAAAGGGAGTCACCGG 4 18 0 AGTTTAAAGG 0.966537 -283 AGTTAGAAAAAGGATAAAGGATTTGATGGG 5 21 0 AGGATAAAGG 0.951868 -147 GAATATTTAAAGATTTAAGGGAGATTAAA 7 34 1 AGATTTAAGG 0.919626 -19 GGACATCAGAAGGTTAAAGAGGCTCTAATT 8 84 0 AGGTTAAAGA 0.854995 -217 CGAGTTTTTCAGTATGAAGGCGAAAGACAG 8 133 0 AGTATGAAGG 0.88063 -168 ATAACTTATTAGTTTTCAGGAGCTCACCAA 8 233 1 AGTTTTCAGG 0.95111 -68 ********** Masking position 8 Map Score: 2.75869 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 211 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 ATGAAGTTTTTCAGGTTTCCTTATTAAAAT 4 82 0 TCAGGTTTCC 0.939901 -219 TTAAAAGGCTTAATGTATACTTTGTTGGGG 4 239 0 TAATGTATAC 0.888658 -62 GAAGATTTAATAAGGTTAACTTTAAATATT 4 267 0 TAAGGTTAAC 0.927156 -34 TCAGTTTTTTTCAGGTATATTAAATAAATG 6 41 0 TCAGGTATAT 0.935286 -111 AAACTTTAAGTAAGGTTTATATACTATTAC 6 78 0 TAAGGTTTAT 0.945749 -74 TCAGTTGATGTAAGGTATACCACAGTGCTA 6 126 0 TAAGGTATAC 0.980986 -26 ********** Masking position 6 Map Score: 2.41557 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 94 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 CTTTAAACTTAAAAATCATTGGGCACTTCC 4 29 1 AAAAATCATT 0.900436 -272 ATTAAAATAAAAAAATCATTCCAGGCCACA 4 60 0 AAAAATCATT 0.900436 -241 TTTAATCAGTAAAAATAAATGCAGGACAAT 4 111 1 AAAAATAAAT 0.738047 -190 GCAGGACAATAAAAACAGTTTAAAAAACAG 4 131 1 AAAAACAGTT 0.971298 -170 AAACAGTTTAAAAAACAGTTTTGAGTGGAC 4 143 1 AAAAACAGTT 0.971298 -158 TAGGAAAATAGTTGCAATGACAA 5 155 0 GAAAATAGTT 0.896096 -13 TATGAAGGCGAAAGACAGTTATCCAGTGAA 8 121 0 AAAGACAGTT 0.912329 -180 ********** Masking position 5 Map Score: 2.60522 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 32 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 ********** No masking Map Score: -8.50219e-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 9 ********** No masking Map Score: -8.50219e-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 10 TCTCTTATCTTGGTTTCATCTTAAATACTA 1 33 1 TGGTTTCATC 0.894575 -94 AAGGATTTGATGGGGTTAACCCAT 5 5 0 TGGGGTTAAC 0.95279 -163 AAAAAACGCGTGTTGATAGCTGGGGGGATT 5 80 0 TGTTGATAGC 0.87364 -88 GCGTTTTTTATGTTGACATCGCAACTGGTA 5 101 1 TGTTGACATC 0.948807 -67 AATATAAAATTGGTGTTAACTTCCATTACC 5 127 0 TGGTGTTAAC 0.960543 -41 AGTGAACATATGGGGACATCAGAAGGTTAA 8 97 0 TGGGGACATC 0.978482 -204 ********** Masking position 8 Map Score: 0.345892 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 259 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ********** No masking Map Score: -8.50219e-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 12 ********** No masking Map Score: -8.50219e-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: -8.50219e-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