AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_mthe_reg_300.orf -o199_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 Purged sequences: RTH00858 16 M.thermo RTH01019 18 M.thermo RTH00618 16 M.thermo RTH01420 17 M.thermo RTH00961 18 M.thermo RTH01010 21 M.thermo RTH01561 41 M.thermo Input sequences: #1 RTH01790 170 M.thermo #2 RTH00571 19 M.thermo #3 RTH02039 22 M.thermo #4 RTH00851 46 M.thermo #5 RTH00189 109 M.thermo #6 RTH01001 16 M.thermo #7 RTH01648 30 M.thermo #8 RTH00952 236 M.thermo #9 RTH00723 62 M.thermo #10 RTH01329 300 M.thermo #11 RTH01081 40 M.thermo #12 RTH00257 22 M.thermo #13 RTH00964 38 M.thermo #14 RTH00179 113 M.thermo #15 RTH00330 34 M.thermo #16 RTH01858 70 M.thermo #17 RTH00707 98 M.thermo #18 RTH01259 73 M.thermo #19 RTH01854 151 M.thermo #20 RTH01592 235 M.thermo #21 RTH00422 120 M.thermo #22 RTH00483 26 M.thermo #23 RTH01562 52 M.thermo #24 RTH00987 33 M.thermo #25 RTH00617 300 M.thermo Motif number 1 GTTTTACTTGCCCAGTCTGCATTGTGGAAAT 1 118 1 CCCAGTCTCA 0.823565 -53 ATATGCCCCTTCCAGTCCTCC 5 1 0 TCCAGTCCCC 0.989879 -109 GGGCATATTTTCCAGTCCAGCGAAAAAACTT 5 24 1 TCCAGTCCGC 0.996019 -86 CCACAAGATTTCCAGTCTTGCGCCTTACCTG 8 88 0 TCCAGTCTGC 0.985753 -149 GGGTTCAAATCCCAGTCCCGGCGTCGGTTAA 8 134 1 CCCAGTCCGG 0.985736 -103 ATTCGCAAACCCCCGTCCCGCGAATTCACTC 8 199 1 CCCCGTCCGC 0.995455 -38 CGGGTTCAATTCCCGGCCAGGGCGTTTCCTG 10 163 1 TCCCGGCCGG 0.936102 -138 GGGCCCGTAGCTCAGTCTGGCAGAGCGCTTG 10 195 1 CTCAGTCTGC 0.910139 -106 CGGGTTCAATTCCCGTCGGGCCCGCTATCTA 10 245 1 TCCCGTCGGC 0.964607 -56 AATTCAGTCCTCCAGATAAAAAG 10 288 0 TTCAGTCCCC 0.937767 -13 TGATGGGGGGTCCCGCCCAGATTCATGATAT 20 29 1 TCCCGCCCGA 0.904941 -207 ******** ** Masking position 7 Map Score: 14.1911 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 129 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 TATTTATAAATATTTCCACAATGCAGACTG 1 130 0 TATTTCCACA 0.870931 -41 TTAACTTTACCTCCTTACA 2 3 0 TACCTCCTTA 0.918747 -17 AAATTTCAGGTATCCCCTTAAAAAGTTTTT 5 47 0 TATCCCCTTA 0.948652 -63 TAAATCACCTCAGTAACTTTTA 7 19 0 AATCACCTCA 0.831153 -12 AGGTTTCTCTTATCTCCACACCAGGTGATC 9 41 1 TATCTCCACA 0.954807 -22 TCCTTTTTGTTATTCCCTTAAATCCATTA 13 10 0 TATTCCCTTA 0.855084 -29 GAATATAGGAAATTACCTTAGACAAACAGC 14 37 1 AATTACCTTA 0.462382 -77 AATATACCTCCATATATGATGGTT 14 100 0 TACCTCCATA 0.884576 -14 AAGCCTATATATCTCATCAATAAATTTCT 16 10 1 TATCTCATCA 0.838392 -61 ACTGTATATATAACTCCTTATTTAAATAAA 18 38 1 TAACTCCTTA 0.684218 -36 AAATATGTCTTATCACAATAACATATTTCA 20 194 1 TATCACAATA 0.618104 -42 TTACTACCCCCACACTTATCTATG 20 222 0 TACCCCCACA 0.938186 -14 AAGGATAGATTACTCCATCACTCATCCCAA 21 57 1 TACTCCATCA 0.54344 -64 ATGATCACCTCAAATTTTATTT 23 41 0 GATCACCTCA 0.805351 -12 CAGGGTGCGATATTACCACAATATAAGGGA 25 187 1 TATTACCACA 0.850263 -114 ********** Masking position 2 Map Score: 7.57623 Number of sites scoring better than the average of aligned sites = 1005 Number in coding regions = 906 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 GTCCAGCGAAAAAACTTTTTAAGGGGATACCTGAAA 5 38 1 AAATTTGGGG 0.948772 -72 TTTTTAATTATATAAGTTTAATGGGG 14 1 0 TAATTTGGGG 0.941131 -113 AATCCTCCTGTAAAAAAGGGAAGAGGTGGGT 15 6 0 TAAAGGGAGG 0.660374 -29 CAGCTTCTTGTTTACATTTATGGGGGATCATTAATT 17 61 0 TTATTTGGGG 0.836935 -38 TACAGTAGATAATACTATGCAAGGGGGCAGTAT 18 8 0 AAAATGGGGG 0.947985 -66 GTTGGGGCAAAATAAAATTATTGATGGTCCACGTGG 20 66 0 AAAATTGATG 0.677213 -170 ACATATTTCATAGATAAGTGTGGGGGTAGTAA 20 214 1 TAAAGTGGGG 0.95538 -22 GTTTTTTAACTATATAAATAGCGGGGATAAACC 21 98 1 TAAAATGGGG 0.952003 -23 ACCCATAAAAAATAAAATTTGAGGTGATCAT 23 32 1 AAAATTGGTG 0.879502 -21 TCACCAGAAAAAAATTAATTGGGAGGA 24 2 0 AAAAATGAGG 0.868505 -32 ATGGACCTTTTTAATAAATGGTGGGGATGTGCCAGA 25 90 1 TTAAATGGGG 0.864274 -211 GAGCGGAGGGATGACCATTGCCGGGGGTCTCAGGGT 25 152 0 ATAATTGGGG 0.948772 -149 TTGGAATTAAAAAAAGATTAAGGAGGCGAATAGC 25 277 1 AAAATTGAGG 0.943123 -24 ** * *** **** Masking position 4 Map Score: 9.09691 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 188 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 GGTACTAAAAATTGTATGGTATCCATATTTAAACTTTCCGCTG 1 17 0 ATTTGTATTA 0.971522 -154 CCTTTCTATTATTCACTGATATGAATCTGTCCATATATA 4 7 0 ATATGTATTA 0.923833 -40 ATATAACTGTATATTATGACATCTATTTAAGTATTGCTGCCGT 8 17 0 ATTTGTATTA 0.971523 -220 TATGACATGCATGCTATGAGTTACATTTTTCTAGTATTT 10 7 0 ATTTGTATTA 0.971523 -294 CTAGAGAACAATGGAATGCTCTCATTCTAGAGACTTGCCCTGG 10 79 1 ATATGTTTTA 0.731008 -222 TGATGAAATGATCCTGCAGTGTTGATCTTAAAAA 11 2 0 ATTCATATTA 0.726099 -39 TCCATATATGATGGTTTAGCCTGATTTTTTAGATCCAGCAAAT 14 73 0 ATTTATTTTA 0.775779 -41 TTCAGCCATGATCCTCTACTGTGCATTTGAGTATATG 17 5 0 ATTTATATTA 0.939181 -94 CTTGCATAGTATTATCTACTGTATATATAACTCCTTATTTAAA 18 21 1 ATTTATATTC 0.726099 -53 TGATCCTGTTCTGCTATTTATTTAAATAAGGAGTTATA 18 46 0 CTTTGTATTA 0.854155 -28 CGGGATCCATATTAATTAGGATTCATATGTTTACTACCTTTAT 19 41 1 ATATATATTA 0.845921 -111 GATGTTTTTAATTTTATGGAATCTATATATAAACTTTGTGCAT 25 26 1 ATTTGTATTA 0.971522 -275 ** * ** * ** * * Masking position 12 Map Score: 7.29546 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 14 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TTAACTTTACCTCCTTACA 2 1 0 CCTCCTTACA 0.97869 -19 ATTTCAGGTATCCCCTTAAAAAGTTTTTTC 5 45 0 TCCCCTTAAA 0.803229 -65 TCAAGAAACCTCCTTGTATTCAGCATTT 5 92 0 CCTCCTTGTA 0.963227 -18 TCTCTAGTTACCTGCTTATATACTTTTCCA 10 56 0 CCTGCTTATA 0.898349 -245 AATTCAGTCCTCCAGATAAAAAGTCACC 10 283 0 CCTCCAGATA 0.836588 -18 CCCCATTAAACTTATATAAT 14 1 1 CCCCATTAAA 0.803229 -113 AATATACCTCCATATATGATGGTTTA 14 98 0 CCTCCATATA 0.96452 -16 AATTAATGATCCCCCATAAATGTAAACAAG 17 61 1 CCCCCATAAA 0.95378 -38 ATACTGCCCCCTTGCATAGTATTATC 18 7 1 CCCCCTTGCA 0.942806 -67 GAAAACACCACCTACTTATATATACCTGAT 19 132 0 CCTACTTATA 0.85638 -20 GCTATTCGCCTCCTTAATCTTTTTTTAA 25 283 0 CCTCCTTAAT 0.875603 -18 ********** Masking position 2 Map Score: 7.02152 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 423 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 CCGAATATCCTCCTGGTTATTT 3 6 0 TCCTCCTGGT 0.854944 -17 GTTATATGATACATCCTGTGCCGGGATAGC 8 53 1 ACATCCTGTG 0.782135 -184 GGAGCTTTGCTCCTCCTGGGTTCAAATCCC 8 117 1 TCCTCCTGGG 0.960764 -120 TCATTAACCTCCAGTAAGAGTGAATT 8 221 0 ACCTCCAGTA 0.911965 -16 AGGATCACCTGGTGTGGAGATAAGAG 9 47 0 ACCTGGTGTG 0.824812 -16 TAGCCCCTACACCACCAGGGCAAGTCTCTA 10 106 0 ACCACCAGGG 0.759988 -195 AATTCAGTCCTCCAGATAAAAAGTCAC 10 284 0 TCCTCCAGAT 0.731271 -17 GATGAAATGATCCTGCAGTGTTGATCTTAA 11 14 0 TCCTGCAGTG 0.95834 -27 TTAAATCCTCCTGTAAAAAAGGGAA 15 20 0 TCCTCCTGTA 0.901799 -15 ACCTTCAGTTCATCAGCACA 16 61 0 ACCTTCAGTT 0.866158 -10 GTAAACAAGAAGCTGCAGTGTGATAGG 17 82 1 AGCTGCAGTG 0.732085 -17 AACATCACCTTCTGTTTGAGTCAGAA 19 7 1 ACCTTCTGTT 0.849492 -145 ATAAAGGTTTTCCTTGAGTGGGGGTGTGTG 21 19 0 TCCTTGAGTG 0.750555 -102 ********** Masking position 8 Map Score: 6.97853 Number of sites scoring better than the average of aligned sites = 1648 Number in coding regions = 1544 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 7 TTCAATCCCTTTCTATTATT 4 37 0 TTCAATCCCT 0.804951 -10 AATATGCCCCTTCCAGTCCTCC 5 3 0 TTCCAGTCCT 0.966409 -107 GGGGCATATTTTCCAGTCCAGCGAAAAAAC 5 23 1 TTCCAGTCCA 0.897379 -87 TCCTCCTGGGTTCAAATCCCAGTCCCGGCG 8 127 1 TTCAAATCCC 0.955588 -110 TTATATACTTTTCCATTCCTATATGACATG 10 41 0 TTCCATTCCT 0.971991 -260 GCGACTCGGGTTCAATTCCCGGCCAGGGCG 10 157 1 TTCAATTCCC 0.965537 -144 TGGTCGCGGGTTCAATTCCCGTCGGGCCCG 10 239 1 TTCAATTCCC 0.965537 -62 CCATCACTCATCCCAATCCTAGCCCTTGTT 21 71 1 TCCCAATCCT 0.861629 -50 CTTTTTTTAATTCCAATCACTATATCAAAC 25 263 0 TTCCAATCAC 0.805607 -38 ********** Masking position 5 Map Score: 8.1987 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 103 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TTGTGGAAATATTTATAAATAAATCCGGACAG 1 139 1 ATTATAAAAA 0.92286 -32 AAACTTATATAATTAAAAAGAATATAGGAAAT 14 18 1 ATTAAAAAAA 0.896807 -96 TATAAATAATAATTATAGAGAAATTTATTGAT 16 26 0 ATTATAGAAA 0.672542 -45 CATCAGCACACCTTATAAATAATAATTATAGA 16 39 0 CTTATAAAAA 0.907768 -32 TGTTTACTACCTTTATAAAAATTTTTCCTATA 19 68 1 CTTATAAAAT 0.79523 -84 TCACATTCAAAATTAAAAATCAATTTCTGTGA 20 124 0 ATTAAAAACA 0.877291 -112 CAAGGAAAACCTTTATAAATCTTGAAGGATAG 21 33 1 CTTATAAACT 0.763281 -88 CTATTTATATAGTTAAAAAACAAGGGCTAGGA 21 87 0 ATTAAAAACA 0.877281 -34 TTAAAAACATCATTATAAATCATTAA 25 5 0 CTTATAAACA 0.890071 -296 GATTCCATAAAATTAAAAACATCATTATAAAT 25 17 0 ATTAAAAAAT 0.775864 -284 CATCCCCACCATTTATTAAAAAGGTCCATGTC 25 87 0 ATTATTAAAA 0.58079 -214 TAGTGATTGGAATTAAAAAAAGATTAAGGAGG 25 271 1 ATTAAAAAAG 0.670013 -30 * ******* ** Masking position 5 Map Score: 3.95742 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 28 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 CTGATACGATGTGGTCTGTGGTTTTACTTGC 1 98 1 GTGGTCTGGG 0.992663 -73 TCGCGGGACGGGGGTTTGCGAATTCTTCATA 8 191 0 GGGGTTTGGA 0.89228 -46 ACTTGCCCTGGTGGTGTAGGGGCTATCATGC 10 111 1 GTGGTGTAGG 0.958978 -190 TTTTAACCAAGTGGTCGCGGGTTCAATTCCC 10 228 1 GTGGTCGCGG 0.971397 -73 TCCTTGAGTGGGGGTGTGTGGAAGAATA 21 8 0 GGGGTGTGGG 0.993199 -113 ACCATTGCCGGGGGTCTCAGGGTGTATAATG 25 144 0 GGGGTCTCGG 0.993199 -157 ******** ** Masking position 5 Map Score: 2.6838 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 114 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 CAGACTGGGCAAGTAAAACCACAGACCACA 1 107 0 AAGTAAAACC 0.924565 -64 AAACTTTTTAAGGGGATACCTGAAATTTTT 5 49 1 AGGGGATACC 0.937589 -61 GTGTGGAGATAAGAGAAACCTGTAGTTAGA 9 32 0 AAGAGAAACC 0.965054 -31 ACCCCCACTCAAGGAAAACCTTTATAAATC 21 24 1 AAGGAAAACC 0.979878 -97 ACCACAATATAAGGGAAACCGAAGATTAGT 25 201 1 AAGGGAAACC 0.990968 -100 ********** Masking position 6 Map Score: 1.89036 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 44 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 11 CCGTAAAATTAGATAGCGGGCCCGACGGGA 10 255 0 AGATAGCGGG 0.988446 -46 TTTGAGTCAGAAATAACGGGATCCATATTA 19 25 1 AAATAACGGG 0.893807 -127 TAACATGTCATGATGGGGGGTCCCGCCCAG 20 19 1 TGATGGGGGG 0.92315 -217 TTAACTATATAAATAGCGGGGATAAACC 21 103 1 AAATAGCGGG 0.981952 -18 CCTTTTTAATAAATGGTGGGGATGTGCCAG 25 95 1 AAATGGTGGG 0.919046 -206 GGGATGTGCCAGATAGGCGGAGGATTATTA 25 113 1 AGATAGGCGG 0.930875 -188 ********** Masking position 4 Map Score: 0.832555 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 65 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 GGAGGACTGGAAGGGGCATATTTTCCAGT 5 10 1 GAAGGGGCAT 0.921885 -100 TTTGAACCCAGGAGGAGCAAAGCTCCACAA 8 113 0 GGAGGAGCAA 0.954967 -124 CATAAGAGTCGTAGGTGCAACAGGGTTGCT 8 165 0 GTAGGTGCAA 0.934673 -72 CCCTGGTGGTGTAGGGGCTATCATGCGGGC 10 116 1 GTAGGGGCTA 0.93344 -185 CCGGCTCAAGGTTGGGGCAAAATAAAATTA 20 82 0 GTTGGGGCAA 0.977607 -154 ATCTGGCACCGATGGAGCCATGGCTCACAT 20 150 0 GATGGAGCCA 0.910327 -86 TGGGATGAGTGATGGAGTAATCTATCCTTC 21 56 0 GATGGAGTAA 0.782667 -65 ********** Masking position 5 Map Score: 1.06543 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 87 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 13 ********** No masking Map Score: -6.60562e-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 14 ********** No masking Map Score: -6.60562e-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 15 ********** No masking Map Score: -6.60562e-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