AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_mthe_reg_300.orf -o294_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH01701 256 M.thermo #2 RTH00023 76 M.thermo #3 RTH00986 172 M.thermo #4 RTH01292 101 M.thermo #5 RTH00823 153 M.thermo Motif number 1 TCCTTCAGTGATTTTTTTAATGTGTGTCTTT 1 21 1 ATTTTTTAAT 0.937503 -236 ATAAACATGAAATTTTTTAATTAGTGATCCT 1 65 0 AATTTTTAAT 0.968486 -192 ACGGCGAATAAATATATAAATGTCTTCTGCA 1 126 0 AATTATAAAT 0.862873 -131 TATAAGATTCAGCTTTTTAATAGATGACGGC 1 152 0 AGCTTTTAAT 0.894168 -105 TAAAAAGCTGAATCTTATAATACTCATGACC 1 164 1 AATTTATAAT 0.862736 -93 TACTCATGACCATATATTAATCTTGCTGCCT 1 184 1 CATTATTAAT 0.863098 -73 AGGACCGTTAATCGTATTAATTAAATTAATA 2 12 1 ATCTATTAAT 0.936097 -65 GTGAACTCAAAATATTTAAATGAACATCCAT 3 57 0 AATTTTAAAT 0.907886 -116 GGTGCTTATGATTCTTTTGATGTCACACTGA 3 108 0 ATTTTTTGAT 0.794079 -65 TCAAAAGTTTCTCTTATTAATTCTGTAGGTG 3 139 0 CTCTATTAAT 0.823476 -34 AGTTTATTTTATCATTTTCATGAGGAGTGAT 5 16 0 ATCTTTTCAT 0.798443 -138 CCCTCCAGTAAACTTTATAATCACCCCGCCC 5 60 0 AACTTATAAT 0.863442 -94 GTGGGAGAAAAATGTATAAATGGATTCCACC 5 90 1 AATTATAAAT 0.864971 -64 *** ******* Masking position 10 Map Score: 10.9496 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 48 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 TAATGTGTGTCAGCAGGATCACTAATTAAAA 1 51 1 CAGCAGGACA 0.960161 -206 ATCTTATAATACTCATGACCATATATTAATC 1 175 1 ACTCATGACA 0.967321 -82 ACGGCGCAGGCAGCAAGATTAATATATGGTC 1 191 0 CAGCAAGATA 0.737607 -66 TATTAACTGACCGGATGAACAAAAATTATGA 2 41 1 CCGGATGACA 0.941989 -36 GATGAACAAAAATTATGATCAGGTAGATTTG 2 54 1 AATTATGACA 0.825271 -23 ACATCAAAAGAATCATAAGCACCCACCTACA 3 116 1 AATCATAACA 0.808033 -57 CAGTTAGCTTCAGCATGAACT 4 1 0 CAGCATGACT 0.929112 -101 TCTTTAATCCCCTCATGAGCAGTTAGCTTCA 4 20 0 CCTCATGACA 0.991701 -82 TATCTCCGCACATCAAGATAAATAGATCCAC 4 51 1 CATCAAGAAA 0.84128 -51 ATGAATCACTCCTCATGAAAATGATAAAATA 5 12 1 CCTCATGAAA 0.953828 -142 CTCCAGTAAACTTTATAATCACCCCGCCCCA 5 58 0 CTTTATAACA 0.378826 -96 ******** ** Masking position 5 Map Score: 7.06301 Number of sites scoring better than the average of aligned sites = 906 Number in coding regions = 850 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 ACATTAAAAAAATCACTGAAGGAAGGTAGAACC 1 4 0 ATAGGGTAGA 0.938923 -253 CTTCTGCATAAGAAAATTTAGGTTAACGGAAAAATAATAT 1 94 0 ATAGGACGGA 0.984709 -163 ACTCTCTAAGACCTGATCATGGAATATGGAGATAAGCCTG 1 223 1 ATTGGATGGA 0.992393 -34 CCATAAATGAACTGATTACTGGTATATGGATGTTCATTTA 3 32 1 ATTGGATGGA 0.992392 -141 TAATAAGAGAAACTTTTGAAGGCTGATGGGAA 3 151 1 ATAGGATGGG 0.995149 -22 ATAGATCCACAGAAGTTACAGGTTTAATGAGAGTGATTTT 4 72 1 ATAGGAATGA 0.849308 -30 ATGATAAAATAAACTGTAAATGTATATGGGGCGGGGTGAT 5 32 1 ATATGATGGG 0.958174 -122 GGGTGATTATAAAGTTTACTGGAGGGTGGGAGAAAAATGT 5 65 1 ATTGGGTGGG 0.986379 -89 * * *** ***** Masking position 1 Map Score: 4.39222 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 246 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 GGTTCTACCTTCCTTCAGTGATT 1 4 1 TCTACCTTCC 0.881455 -253 CAGGCTTATCTCCATATTCCATGATCAGGT 1 233 0 TCCATATTCC 0.958299 -24 TAAATGAACATCCATATACCAGTAATCAGT 3 42 0 TCCATATACC 0.958276 -131 ATCATAAGCACCCACCTACAGAATTAATAA 3 127 1 CCCACCTACA 0.969968 -46 TTCCCATCAGCCTTCAAAAGTT 3 161 0 CCCATCAGCC 0.934159 -12 ATCACCCCGCCCCATATACATTTACAGTTT 5 42 0 CCCATATACA 0.928272 -112 ACATTTTTCTCCCACCCTCCAGTAAACTTT 5 75 0 CCCACCCTCC 0.977422 -79 ********** Masking position 4 Map Score: 3.85831 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 493 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TATATATTTATTCGCCGTCATCTATTAAAA 1 139 1 TTCGCCGTCA 0.975546 -118 TCTTGCTGCCTGCGCCGTAACTCTCTAAGA 1 204 1 TGCGCCGTAA 0.98207 -53 TTCCCATCAGCCTTCAAAAGTTTCTC 3 157 0 TCAGCCTTCA 0.917562 -16 ATAAATGGATTCCACCATAACTCGAAAGGA 5 105 1 TCCACCATAA 0.976816 -49 AACGGTCCACCATAAAATCAGTTGA 5 139 0 TCCACCATAA 0.976816 -15 ********** Masking position 8 Map Score: 1.37349 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 97 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 AGAAGACATTTATATATTTATTCGCCGTCA 1 129 1 TATATATTTA 0.812767 -128 GGTCAGTTAATATTAATTTAATTAATACGA 2 23 0 TATTAATTTA 0.790235 -54 GATGTTCATTTAAATATTTTGAGTTCACAG 3 60 1 TAAATATTTT 0.687358 -113 CCCCGCCCCATATACATTTACAGTTTATTT 5 38 0 TATACATTTA 0.950895 -116 GCGGGGTGATTATAAAGTTTACTGGAGGGT 5 62 1 TATAAAGTTT 0.84841 -92 GGAATCCATTTATACATTTTTCTCCCACCC 5 88 0 TATACATTTT 0.959053 -66 ********** Masking position 6 Map Score: 1.11921 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 15 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 ATATTATTTTTCCGTTAACCTAAATTTTCT 1 94 1 TCCGTTAACC 0.961774 -163 TAGGACCGTTAATCGTATTAATTA 2 5 1 ACCGTTAATC 0.977521 -72 ACATCCATATACCAGTAATCAGTTCATTTA 3 35 0 ACCAGTAATC 0.977879 -138 GTGCGGAGATATCTTTAATCCCCTCATGAG 4 32 0 ATCTTTAATC 0.813057 -70 CTCTCATTAAACCTGTAACTTCTGTGGATC 4 75 0 ACCTGTAACT 0.880704 -27 TCTCCCACCCTCCAGTAAACTTTATAATCA 5 68 0 TCCAGTAAAC 0.903633 -86 ********** Masking position 6 Map Score: 0.449149 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 198 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 ********** No masking Map Score: -3.31523e-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: -3.31523e-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 ********** No masking Map Score: -3.31523e-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