AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_mthe_reg_300.orf -o00460_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 MTH700 110 conserved protein #2 MTH702 27 acetyl-CoA synthetase related protein #3 MTH1380 167 serine hydroxymethyltransferase #4 MTH1381 151 heterodisulfide reductase, subunit A #5 MTH1383 52 DNA repair protein RadA #6 MTH1385 300 replication factor A related protein #7 MTH1496 194 amidase Motif number 1 GTGGAACTTAAACATTTAAGATGAGAAACTTT 1 21 1 AAATTTAAAT 0.650363 -90 TTAAGATGAGAAACTTTATTAAGGGAAGAGAC 1 36 1 AACTTTATAA 0.968728 -75 TATCATTAATAATCATTATTAATTTTTCCTGA 1 71 1 AACATTATAA 0.813391 -40 ACACAGAATAAACATTTATTTAATATACCTGA 4 29 1 AAATTTATTA 0.9508 -123 TTTCTATCAAAAACTTTAAGTAAGGTTTATAT 4 86 0 AACTTTAATA 0.978426 -66 TTTTGATAGAAATATTTATTTAGCACTGTGGT 4 106 1 AAATTTATTA 0.9508 -46 ATCTCCCTTAAATCTTTAAATATTCATTAAGC 5 27 0 AACTTTAATA 0.978426 -26 CACTTGCTGGAACCTTTATGAACCCTTCAATT 6 31 0 AACTTTATAA 0.968728 -270 CTTTGATAATAAGATTTAAATATATAGTAATA 6 204 1 AAATTTAATA 0.950865 -97 TCAATCTACCAATCTTTAAATATTGAACATCT 7 17 1 AACTTTAATA 0.978426 -178 ** ****** ** Masking position 6 Map Score: 14.4104 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 6 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 2 ATGATAAATGTCTCTTCCCTTAATAAAGTTTC 1 45 0 TCCTTCCCTA 0.911066 -66 ATCCTTTTTCTAACTTACATAATACTCCGAGC 3 36 1 TACTTACATA 0.970729 -132 AAATTGGTGTTAACTTCCATTACCAGTTGCGA 3 119 0 TACTTCCATA 0.981435 -49 ATAGTATATAAACCTTACTTAAAGTTTTTGAT 4 81 1 AACTTACTTA 0.919081 -71 CACTGTGGTATACCTTACATCAACTGACTATC 4 129 1 TACTTACATA 0.97073 -23 TTTAATCTCCCTTAAATCTTTAAAT 5 38 0 AACTCCCTTA 0.937265 -15 CTATCCTCCTTTAGCAGAATAAT 6 2 1 TACCTCCTTA 0.931453 -299 TTTGGTCCCTCACTTGATTAATAATAT 6 284 0 TCCTCACTTA 0.935448 -17 TCAACCTTAATAGCTGCCATGACTGCCTCGAG 7 137 0 TACTGCCATA 0.942108 -58 ATCAGACTTATATCTCACTTCAACTTGAAATA 7 168 1 TACTCACTTA 0.971184 -27 ** ******* * Masking position 10 Map Score: 11.0712 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 74 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 AGAGACATTTATCATTAATAATCATTATTA 1 62 1 ATCATTAATA 0.915938 -49 AGCGTCAGGAAAAATTAATAATGATTATTA 1 77 0 AAAATTAATA 0.940865 -34 TGAGCTCCTGAAAACTAATAAGTTATTACT 6 229 0 AAAACTAATA 0.944981 -72 TTTCATTTCCAACACTAATAAATGTGAGAT 7 45 0 AACACTAATA 0.97481 -150 AAGTCTGATCAACCTTAATAGCTGCCATGA 7 147 0 AACCTTAATA 0.941688 -48 ********** Masking position 6 Map Score: 1.93046 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 5 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 TTAATTATGTGGAACTTAAACATTTAAGAT 1 13 1 GGAACTTAAA 0.885126 -98 GGAGTATTATGTAAGTTAGAAAAAGGATAA 3 34 0 GTAAGTTAGA 0.815312 -134 AACTGGTAATGGAAGTTAACACCAATTTTA 3 123 1 GGAAGTTAAC 0.893132 -45 AAAAACTGAGGAAAGTGTAATAGTATATAA 4 62 1 GAAAGTGTAA 0.756682 -90 AAGATTTAAGGGAGATTAAA 5 43 1 GGAGATTAAA 0.903407 -10 GGCAGTCTGTGAAAATTAGAGCCTCTTTAA 6 71 1 GAAAATTAGA 0.826398 -230 GGGGACATCAGAAGGTTAAAGAGGCTCTAA 6 86 0 GAAGGTTAAA 0.935587 -215 TTTTCAGTATGAAGGCGAAAGACAGTTATC 6 128 0 GAAGGCGAAA 0.766452 -173 TATTAGTGTTGGAAATGAAATTAAAACCAC 7 55 1 GGAAATGAAA 0.934346 -140 TATTTCAAGTTGAAGTGAGATATAAGTCTG 7 170 0 TGAAGTGAGA 0.729813 -25 ********** Masking position 3 Map Score: 1.77089 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 430 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 ACTACCACACAGGGGACACCGCCTGG 2 12 1 AGGGGACACC 0.9743 -16 GCGTTTTTTATGTTGACATCGCAACTGGTA 3 101 1 TGTTGACATC 0.946423 -67 TGGTAATGGAAGTTAACACCAATTTTATAT 3 126 1 AGTTAACACC 0.945561 -42 AGTGAACATATGGGGACATCAGAAGGTTAA 6 97 0 TGGGGACATC 0.960858 -204 ACAGTTATCCAGTGAACATATGGGGACATC 6 107 0 AGTGAACATA 0.873458 -194 ACTCGTCTGAATTTTACATCTATATTTTCA 6 158 1 ATTTTACATC 0.736024 -143 ATCTTTAAATATTGAACATCTCACATTTAT 7 28 1 ATTGAACATC 0.935691 -167 ********** Masking position 6 Map Score: 1.43008 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 322 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GATTATTAATGATAAATGTCTCTTCCCTTAA 1 54 0 GATAAAGTCT 0.989286 -57 TTAGAAAAAGGATAAAGGATTTGATGGGGTT 3 18 0 GATAAAGATT 0.943573 -150 AGGTATATTAAATAAATGTTTATTCTGTGTG 4 28 0 AATAAAGTTT 0.856695 -124 ATGTTCACTGGATAACTGTCTTTCGCCTTCA 6 118 1 GATAACGTCT 0.971233 -183 ACGCCCCGTCTATAAAAGACTTGGTGAGCTC 6 252 0 TATAAAGACT 0.904609 -49 GTTGAAGTGAGATATAAGTCTGATCAACCTT 7 161 0 GATATAGTCT 0.957947 -34 ****** **** Masking position 4 Map Score: 2.34834 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 25 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 ACACAGGGGACACCGCCTGG 2 18 1 CACCGCCTGG 0.967567 -10 TTCCGAATCCGATTGCTCGGAGTATTATGT 3 52 0 GATTGCTCGG 0.955155 -116 AACGCGTGTTGATAGCTGGGGGGATTCCGA 3 76 0 GATAGCTGGG 0.893914 -92 AATTTTCACAGACTGCCCCATGGACCACTT 6 58 0 GACTGCCCCA 0.937825 -243 CCGGTCCATGGACCGCCGGGACAGCCATGA 7 97 0 GACCGCCGGG 0.995044 -98 TAGCTGCCATGACTGCCTCGAGGGTGGAGT 7 129 0 GACTGCCTCG 0.984382 -66 ********** Masking position 2 Map Score: 1.12826 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 293 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 TATTCATTAAGCATGGATCGTCGGTAAA 5 9 0 GCATGGATCG 0.983523 -44 ACAGACTGCCCCATGGACCACTTGCTGGAA 6 51 0 CCATGGACCA 0.991033 -250 AGTTTCCGGTCCATGGACCGCCGGGACAGC 7 102 0 CCATGGACCG 0.996568 -93 ********** Masking position 7 Map Score: 0.860194 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 ********** No masking Map Score: -2.41341e-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 ********** No masking Map Score: -2.41341e-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 11 ********** No masking Map Score: -2.41341e-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