AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_mthe_reg_100.orf -o00640_mthe_100.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 MTH187 142 conserved protein #2 MTH216 96 acetyl-CoA synthetase #3 MTH217 134 acetyl-CoA synthetase #4 MTH563 140 succinyl-CoA synthetase, alpha subunit #5 MTH700 110 conserved protein #6 MTH702 27 acetyl-CoA synthetase related protein #7 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #8 MTH1603 63 acetyl-CoA synthetase #9 MTH1851 105 unknown #10 MTH1917 189 biotin carboxylase Motif number 1 TTTCGAGGTTATTAATAAAAAATTTATAATA 3 24 1 ATTAATAAAA 0.817403 -111 GATAGATAATATTTATTATAAATTTTTTATT 3 37 0 ATTTATATAA 0.873853 -98 TTTTACTATTATTAATCATGATAGATAATAT 3 56 0 ATTAATATGA 0.98059 -79 GCCCTTCACAATTAAGGATAATATGACTCCA 4 35 0 ATTAAGATAA 0.882861 -106 AGGAGAAGTGTTTAATTATGATAGAGTTCTG 4 70 0 TTTAATATGA 0.966455 -71 GTCTGAAATATTTAATTATGCTCATGAAGAG 4 107 0 TTTAATATGC 0.901022 -34 ATTTAATTATGTGGAACTTAAA 5 2 1 TTTAATATGT 0.769445 -109 GAACTTAAACATTTAAGATGAGAAACTTTAT 5 24 1 ATTTAAATGA 0.631337 -87 AATAATGATTATTAATGATAAATGTCTCTTC 5 60 0 ATTAATATAA 0.959768 -51 GTCAGGAAAAATTAATAATGATTATTAATGA 5 73 0 ATTAATATGA 0.98059 -38 CACCCTGATAATTTATTATAATCTGAGTTCT 7 140 1 ATTTATATAA 0.873853 -90 AATTTAAATAATTAATCAAGAATAATATTAT 7 173 0 ATTAATAAGA 0.904582 -57 TGCCAACTATTTAAATCATGAATTAAAAAAA 8 27 1 TTAAATATGA 0.739309 -37 TGAACCTCTTTTTAAGCATACCACTTGAGTT 10 126 0 TTTAAGATAC 0.575925 -64 ****** **** Masking position 5 Map Score: 13.6328 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 77 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 2 TTTGTCACTGTCATCAAGGGCCTCAATGAG 1 48 0 TCATCAAGGG 0.949545 -95 GACAAATCTGTTAGGAGGGGGGCCGCAGCA 1 72 1 TTAGGAGGGG 0.876064 -71 AGCCTTTATGAGGGGTTCAACTGCT 1 128 0 TTATGAGGGG 0.97405 -15 GTCATAAAGGCTTTCCTCATA 2 2 1 TCATAAAGGC 0.731835 -95 TTCCTCATACTCAAGAAGGGTCATAAACTG 2 23 1 TCAAGAAGGG 0.948632 -74 TTATCCTTAATTGTGAAGGGCTCTTCAGAA 4 45 1 TTGTGAAGGG 0.981459 -96 TATGATAGAGTTCTGAAGAGCCCTTCACAA 4 55 0 TTCTGAAGAG 0.914624 -86 TAAACACTTCTCCTGAACGGCTCTTCATGA 4 87 1 TCCTGAACGG 0.916635 -54 TTAATTATGCTCATGAAGAGCCGTTCAGGA 4 97 0 TCATGAAGAG 0.952816 -44 ATGAGAAACTTTATTAAGGGAAGAGACATT 5 41 1 TTATTAAGGG 0.90441 -70 TGAAAACCTCTGGTGAAGGGAACACCCTGA 7 118 1 TGGTGAAGGG 0.942161 -112 ATTATTTAAATTCTGAAGGCAAAGCTAAGA 7 192 1 TTCTGAAGGC 0.94308 -38 ********** Masking position 6 Map Score: 13.1542 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 711 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 CCCCTCCTAACAGATTTGTCACTGTCATCAAGGG 1 58 0 CAGTTTTCTG 0.932949 -85 CTGGGATCTCCAATGTTACCCAGGGCTGCTGCGG 1 94 0 CAAGTTCCGG 0.944499 -49 CCCACCTCATTTTTTTCGAGGTTATTAATAA 3 8 1 CATTTTTCGG 0.98557 -127 TTCATACCGCCATCTTTTTCTTGGTTGGTAGTAG 3 109 0 CATTTTTCGG 0.985572 -26 TCTCAGGTATCTGATTTACATAGGCCCCGGAAAA 7 31 1 CTGTTTCAGG 0.856573 -199 TTCCGGTTTTCAGGTTTTCCGGGGCCTATGTAAA 7 45 0 CAGTTTCCGG 0.995513 -185 GGAATATACACATCTTTACCCCGGGACTGACAGG 7 75 1 CATTTTCCGG 0.992855 -155 *** *** ** ** Masking position 7 Map Score: 5.04052 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 85 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 TCAAGGGCCTCAATGAGCTGTTCAACAGCG 1 35 0 CAATGAGCTG 0.83485 -108 TCCAATGTTACCCAGGGCTGCTGCGGCCCC 1 90 0 CCCAGGGCTG 0.97092 -53 CATTGGAGATCCCAGAGCAGTTGAACCCCT 1 113 1 CCCAGAGCAG 0.955722 -30 CCGCCCTCATCGAAGAACTGAAAAGACACC 2 57 1 CGAAGAACTG 0.817161 -40 GACACCTTCGCCATGAACTCGGACCC 2 81 1 CCATGAACTC 0.914602 -16 GTAAACCATGAAATGGAGAATCTCA 7 6 1 CCATGAAATG 0.920152 -224 TTACATAGGCCCCGGAAAACCTGAAAACCG 7 46 1 CCCGGAAAAC 0.643708 -184 ACATCTTTACCCCGGGACTGACAGGGCATT 7 84 1 CCCGGGACTG 0.965511 -146 TATGGATGAGCCCTGAGATGCTGC 10 5 0 CCCTGAGATG 0.966832 -185 ********** Masking position 1 Map Score: 4.28669 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 941 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 AGCATAATTAAATATTTCAGACCACAAAAG 4 116 1 AATATTTCAG 0.76604 -25 CCCTTAATAAAGTTTCTCATCTTAAATGTT 5 31 0 AGTTTCTCAT 0.882871 -80 CATGAAATGGAGAATCTCAGGTATCTGATT 7 17 1 AGAATCTCAG 0.952561 -213 GTGTATATTCCGGTTTTCAGGTTTTCCGGG 7 56 0 CGGTTTTCAG 0.888824 -174 CCTTCACCAGAGGTTTTCAGCAAAATGCCC 7 107 0 AGGTTTTCAG 0.971605 -123 AGATTATAATAAATTATCAGGGTGTTCCCT 7 134 0 AAATTATCAG 0.76987 -96 TTCATTCTGAAGTTTTTCATATGAGTCAGC 9 11 0 AGTTTTTCAT 0.861913 -95 ATTGTTTAAAAGATTATCAGTTAAAATCAC 9 78 0 AGATTATCAG 0.944411 -28 GCAGCATCTCAGGGCTCATCCA 10 3 1 AGCATCTCAG 0.921742 -187 ********** Masking position 5 Map Score: 4.19107 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 373 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TCCCCTATTTCAGATAGGAGC 1 2 0 CAGATAGGAG 0.965438 -141 ACAAATCTGTTAGGAGGGGGGCCGCAGCAG 1 73 1 TAGGAGGGGG 0.835781 -70 AACCAAGAAAAAGATGGCGGTATGAAAA 3 117 1 AAGATGGCGG 0.90287 -18 AATATGACTCCACATCGGTGGAGGTCACTG 4 17 0 CACATCGGTG 0.795897 -124 TACTACCACACAGGGGACACCGCCTG 6 7 1 CACACAGGGG 0.839144 -21 TGGCAGAATATAGATGGGTGC 8 2 0 TAGATGGGTG 0.958825 -62 ATGATTTAAATAGTTGGCAGAATATAGATG 8 16 0 TAGTTGGCAG 0.752446 -48 AAAATATTAACAGAAGGGGG 8 54 1 CAGAAGGGGG 0.977166 -10 GCATTGATAGTAGATAGGAGAGAGAAGGAG 10 48 0 TAGATAGGAG 0.934395 -142 CCATGTCATCCACATGGCAGTTACTGTAAC 10 99 1 CACATGGCAG 0.943764 -91 ********** Masking position 2 Map Score: 4.17854 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 556 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 AAGAAGGGTCATAAACTGAACGCCGCCCTC 2 35 1 ATAAACTGAA 0.93646 -62 GCCCTCATCGAAGAACTGAAAAGACACCTT 2 59 1 AAGAACTGAA 0.914105 -38 CACCTTCGCCATGAACTCGGACCC 2 83 1 ATGAACTCGG 0.880622 -14 ATAACCTCGAAAAAAATGAGGTGGG 3 6 0 AAAAAATGAG 0.671054 -129 TTTTTTATTAATAACCTCGAAAAAAATGAG 3 16 0 ATAACCTCGA 0.778848 -119 GTAAACCATGAAATGGAGAATCTCAGG 7 8 1 ATGAAATGGA 0.87782 -222 TAGGCCCCGGAAAACCTGAAAACCGGAATA 7 51 1 AAAACCTGAA 0.846261 -179 ATAATTTATTATAATCTGAGTTCTGAATAA 7 147 1 ATAATCTGAG 0.768246 -83 AAACTTCAGAATGAACTGAATTTTAATTGT 9 26 1 ATGAACTGAA 0.959188 -80 TGCCATGTGGATGACATGGGGACTTACGGT 10 88 0 ATGACATGGG 0.865237 -102 ********** Masking position 4 Map Score: 4.54515 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 625 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 8 CTGTTCAACAGCGGGTTCCCCTATTTCAGATA 1 16 0 GGGTTCCCCT 0.963674 -127 ACCCAGGGCTGCTGCGGCCCCCCTCCTAACAG 1 79 0 GTGGGCCCCC 0.909828 -64 AGCCTTTATGAGGGGTTCAACTGCTCTGGGA 1 122 0 GGGGTTCAAC 0.942232 -21 TTCGATGAGGGCGGCGTTCAGTTTATGACCCT 2 39 0 GGGGTTCAGT 0.978741 -58 CTCCACATCGGTGGAGGTCACTGAAAAAA 4 8 0 GGGGGTCACT 0.983643 -133 CCAGGCGGTGTCCCCTGTGTGGTAGT 6 12 0 GGGGTCCCCT 0.99346 -16 CCCTTCACCAGAGGTTTTCAGCAAAATGCCCT 7 106 0 GGGTTTCAGC 0.911914 -124 ATAAATTATCAGGGTGTTCCCTTCACCAGAGG 7 124 0 AGGGTTCCCT 0.949355 -106 * ** ******* Masking position 4 Map Score: 4.97935 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 572 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 GGGGGGCCGCAGCAGCCCTGGGTAACATTG 1 88 1 AGCAGCCCTG 0.980286 -55 TGAGGGGTTCAACTGCTCTGGGATCTCCAA 1 115 0 AACTGCTCTG 0.97307 -28 TAGAGTTCTGAAGAGCCCTTCACAATTAAG 4 50 0 AAGAGCCCTT 0.550045 -91 ACTTCTCCTGAACGGCTCTTCATGAGCATA 4 92 1 AACGGCTCTT 0.633318 -49 GTTTTCAGCAAAATGCCCTGTCAGTCCCGG 7 95 0 AAATGCCCTG 0.962831 -135 GGGGATATGGATGAGCCCTGAGATGCTGC 10 10 0 ATGAGCCCTG 0.941231 -180 GAGTTACAGTAACTGCCATGTGGATGACAT 10 101 0 AACTGCCATG 0.946752 -89 ********** Masking position 1 Map Score: 4.18658 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 388 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 TTTTTTCAGTGACCTCCACCGAT 4 3 1 TTTTCATGAC 0.848939 -138 AAGTTTCTCATCTTAAATGTTTAAGTTCCAC 5 21 0 TCTTAATGTT 0.784165 -90 GTTAATATTTTTTTAATTCATGATTTAAATA 8 34 0 TTTTAATCAT 0.860806 -30 ATGAACTGAATTTTAATTGTTTATCAACACA 9 36 1 TTTTAATGTT 0.931875 -70 AGGTTTGTGATTTTAACTGATAATCTTTTAA 9 72 1 TTTTAATGAT 0.973935 -34 TGTCTGTATTGTTTAAAAGATTATCAGTTAA 9 84 0 GTTTAAAGAT 0.784165 -22 GGTAACCGGGTTTGCATTGATAGTAGATAGG 10 60 0 TTTGCATGAT 0.84894 -130 CACCTTGAAGTTTTAACAGATATATAGTATA 10 162 0 TTTTAAAGAT 0.931875 -28 ****** **** Masking position 6 Map Score: 0.55859 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 63 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 11 ********** No masking Map Score: -1.52523e-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: -1.52523e-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: -1.52523e-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