AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_bsub_mtub_300.orf -o180_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ydiG 125 similar to molybdopterin precursor biosynthesis #2 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #3 moeB 50 molybdopterin biosynthesis protein #4 narQ 245 alternate gene name: narAA #5 ywmE 93 ywmE #6 ywmD 300 similar to hypothetical proteins from B. subtilis #7 Rv3108 98 hypothetical protein Rv3108 #8 moaA 148 moaA #9 moaB 50 moaB #10 Rv3113 122 hypothetical protein Rv3113 #11 Rv3115 161 hypothetical protein Rv3115 #12 moeB 77 moeB #13 cysA3 28 cysA3 Motif number 1 CGAACGCGGGGTTTGTCGACACGCTGAGACACCTCTGT 4 21 0 GTGGCAGTGG 0.985596 -225 GATGACGGCGGTGTTTAGGCAGGACGCCTAAGCATTTA 4 105 0 GGTGCAGCGC 0.99463 -141 TCTATATAAAGGGCTTTTACAGGATGTGATGACGGCGG 4 132 0 GGTTCAGTGG 0.97637 -114 CATTTCAAGCGATTTTGGACAGATCGTGAAAGCAGCAC 6 172 1 GTTGCAACGG 0.942391 -129 AATGCAAAAAGATATAGGACATGCTGCCTTTTGTGCTG 6 204 0 GTTGCAGTGC 0.976974 -97 GCAGGCTCATGCGCTGCGCCACGATGCGCCGATGCATT 8 26 1 GGTGCAGTGG 0.99563 -123 GCGACGATGAGAGCGCATTCACGGCCGGTCATCCCCTT 10 13 0 GGGTCAGCCG 0.9158 -110 CATCGTCGCCGCTGTTCGGCAACGTGGGAGTTCCAGTG 10 42 1 GTTGCACTGG 0.952822 -81 GCGAATTTCGGTCGTTCTGCACGCCGGCACTGGAACTC 10 69 0 GCTTCAGCGC 0.685318 -54 GGGTCAGTGAGGTAGTCGGCAAGCCGAG 11 1 0 GTGGCAGCGG 0.993421 -161 CCCAGGAGGAGAGTTACGTCCAGGGGTGTGGTGTACGG 11 36 1 GGTGCCGGGG 0.957227 -126 GCCCACTACTGGGCTACGACACGCCCACCGGCCTTACC 11 77 0 GGTGCAGCCC 0.973783 -85 TAGCCCAGTAGTGGGCGGTCATCGCGTGATCCTTCGAA 11 99 1 GGGGCACCGG 0.98493 -63 CCACGTCCCTGGCCTTGGCCAGGAGGAGAGCAATC 12 53 1 GCTGCAGGGG 0.979042 -25 * * * * ** * ** * Masking position 10 Map Score: 21.8035 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 284 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 ATTAAAACGCTCCTTAAACAGATCATACACTATTT 1 101 0 GCCAACAACA 0.838521 -25 GCACCAATGTGCATTGACAACGAACGCGGGGTTTGTC 4 42 0 GCTCACGAGC 0.917384 -204 TGCCTAAACACCGCCGTCATCACATCCTGTAAAAGCC 4 122 1 CCCCACAACC 0.983606 -124 AGCCATTTCCGCCCAGAAAGCATAAACAGCTTGTGTG 6 123 0 GCCAACAAAC 0.903726 -178 TCGTCCTCAAACGCTGACACCATCAGC 7 1 0 ACCCACACGC 0.972402 -98 CCGCCGACGACCACCAGCACCAGGGCCGCGACGATAG 7 46 1 CCCCACAGCC 0.971408 -53 CGCGACGATAGCCCATCCAGCACCGGCTAGCCACCAC 7 72 1 GCCCACACGC 0.994412 -27 CAACGCGCCATAAACGCAGGCTCATGCGCTG 8 5 1 GCCAACGAGC 0.980358 -144 CTCTCTTGAGGCGCTCTAACCGACTGCGTCCAAAGTG 8 98 1 GCCAACGCGC 0.981832 -51 GGCCGTGAATGCGCTCTCATCGTCGCCGCTGTTCGGC 10 25 1 GCCCACGCCC 0.995022 -98 GGCCTTACCTGCCCGTACACCACACCCCTGGACGTAA 11 49 0 GCCCACAACC 0.995562 -113 AGGAACCTTCACTCGTACACCACGTCCCTGGCCTTGG 12 34 1 ACCCACAGCC 0.956454 -44 ** * ** ** * ** Masking position 9 Map Score: 17.9513 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 420 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 CTCAGCGTGTCGACAAACCCCGCGTTCGTTGTCAAT 4 31 1 CGCCCCGCGT 0.97289 -215 TAAACACCGCCGTCATCACATCCTGTAAAAGCCCTT 4 126 1 CGCACACCTT 0.750142 -120 GGAACCTAAAGATCAGGCGCTCCCCCAGGCG 5 6 1 CTATCAGCGT 0.877914 -88 TAAAAATGAACGGCATTTCAAGCGATTTTGGACAGA 6 159 1 CGCTCAGCGT 0.996373 -142 GCGCCATAAACGCAGGCTCATGCGCTGCGCCACGAT 8 15 1 CGATCAGCGT 0.990923 -134 GCCGAACGAACAGTCGATTGATCAACGA 9 3 1 CGAACATCGT 0.93345 -48 GATTGATCAACGACTCCACAGTTGAGGAAGGAACC 9 26 1 CGCACATTGG 0.766318 -25 AGCGCATTCACGGCCGGTCATCCCCTTGT 10 4 0 CGCTCACCCT 0.940437 -119 CTATGCGACCCGACTATTCGGGTGCGGCGAATTTCG 10 97 0 CGCTCGGTGG 0.841852 -26 ACACGCCCACCGGCCTTACCTGCCCGTACACCACAC 11 61 0 CGCACCGCCG 0.926309 -101 CTGGTCGTTTCGAAGGATCACGCGATGACCGCCCAC 11 109 0 CGATCAGCGT 0.990924 -53 TGCGTCATTTCCTTCGATTGACTTTTGC 11 144 0 CGCTCCTCGT 0.974389 -18 ACTGCCACCCGAAGGATCACGCGAGGAACCTTCAC 12 10 1 CGATCAGCGG 0.98768 -68 ** * *** *** * Masking position 9 Map Score: 13.0347 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 659 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 AAAGCATAGCAAAAGCAAAGGCTCAACGCTAC 2 91 0 AAAGAAAGGC 0.989536 -46 AAGATGACATAAAAGATAAGGAGAACAGGTTT 3 28 1 AAAGTAAGGA 0.881196 -23 CACGTGTTATAAAAGGAACGGCGGCTAAATGC 4 80 1 AAAGAACGGC 0.985366 -166 AACGGCGGCTAAATGCTTAGGCGTCCTGCCTA 4 96 1 AAAGTTAGGC 0.922499 -150 GAGTGTGAAAAAATATAAAGGCAGGAACATTG 4 208 1 AAAAAAAGGC 0.979647 -38 TTTTTAAACCAATAAAAAAGGCGCCTGGGGGA 5 31 0 AATAAAAGGC 0.871345 -63 GAAATGGCTAAAAATGAACGGCATTTCAAGCG 6 151 1 AAATAACGGC 0.912407 -150 GAAAATGCAAAAAGATATAGGACATGCTGCCT 6 213 0 AAAAATAGGA 0.860131 -88 GGAAAATATGAAAAAGAAAGGAAGTAATCAT 6 280 1 AAAAAAAGGA 0.931418 -21 ATCGTTACCGAAATGCATCGGCGCATCGTGGC 8 43 0 AAAGATCGGC 0.968242 -106 *** * ****** Masking position 2 Map Score: 11.2577 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 614 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 TGTTTATTAAAGAGGAATAGCTGTTCAGTA 2 53 0 AGAGGAATAG 0.772019 -84 ATAAAAGATAAGGAGAACAGGTTTG 3 36 1 AGGAGAACAG 0.947838 -15 AACATTGCGGAGGGGAAGAGACA 4 233 1 AGGGGAAGAG 0.987222 -13 AAAAGGCGCCTGGGGGAGCGCCTGATCTTT 5 18 0 TGGGGGAGCG 0.979041 -76 GCGTCCAAAGTGGAGGATCGAAAAGATGAT 8 123 1 TGGAGGATCG 0.928931 -26 TCACTGACCCAGGAGGAGAGTTACGTCCAG 11 29 1 AGGAGGAGAG 0.992489 -133 GGCCTTGGCCAGGAGGAGAGCAATC 12 63 1 AGGAGGAGAG 0.992489 -15 ********** Masking position 7 Map Score: 6.69968 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 154 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 CCTAAGCATTTAGCCGCCGTTCCTTTTATA 4 87 0 TAGCCGCCGT 0.837777 -159 CTGGTGGTCGTCGGCGGAGCCATGATCGTC 7 33 0 TCGGCGGAGC 0.977768 -66 GGATGGGCTATCGTCGCGGCCCTGGTGCTG 7 60 0 TCGTCGCGGC 0.987949 -39 GTGGTGGCTAGCCGGTGCTGGATGGGCT 7 81 0 TAGCCGGTGC 0.919066 -18 CCGAAATGCATCGGCGCATCGTGGCGCAGC 8 38 0 TCGGCGCATC 0.956693 -111 TGCGCTCTCATCGTCGCCGCTGTTCGGCAA 10 34 1 TCGTCGCCGC 0.984868 -89 CGACCGAAATTCGCCGCACCCGAATAGTCG 10 93 1 TCGCCGCACC 0.964932 -30 CGCACCCGAATAGTCGGGTCGCATAG 10 107 1 TAGTCGGGTC 0.843905 -16 ********** Masking position 1 Map Score: 5.44242 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 557 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 GTTATAAAAGGAACGGCGGCTAAATGCTTA 4 85 1 GAACGGCGGC 0.991743 -161 CGTCCTGCCTAAACACCGCCGTCATCACAT 4 117 1 AAACACCGCC 0.95165 -129 TCTGAGACACAAAAAGAGCCCTCTATATAA 4 161 0 AAAAAGAGCC 0.864336 -85 AAACCAATAAAAAAGGCGCCTGGGGGAGCG 5 28 0 AAAAGGCGCC 0.974485 -66 TGTTACATACAAAAAGAGGCT 6 2 0 AAAAAGAGGC 0.925165 -299 AAAGCAGCACAAAAGGCAGCATGTCCTATA 6 200 1 AAAAGGCAGC 0.879015 -101 AACGCGCCATAAACGCAGGCTCATGCGCTG 8 12 1 AAACGCAGGC 0.960927 -137 CCACGTTGCCGAACAGCGGCGACGATGAGA 10 39 0 GAACAGCGGC 0.983905 -84 CGGTCGTTCTGCACGCCGGCACTGGAACTC 10 69 0 GCACGCCGGC 0.935311 -54 ********** Masking position 3 Map Score: 8.99899 Number of sites scoring better than the average of aligned sites = 1198 Number in coding regions = 1096 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 8 AAAATATAAAGGCAGGAACATTGCGGAGGG 4 217 1 GGCAGGAACA 0.780526 -29 AAACAGTTTGGGCGGGAATGATACCCTAAA 5 60 1 GGCGGGAATG 0.988849 -34 ATGCTTTCTGGGCGGAAATGGCTAAAAATG 6 137 1 GGCGGAAATG 0.960303 -164 GGTGGTCGTCGGCGGAGCCATGATCGTCCT 7 31 0 GGCGGAGCCA 0.825082 -68 CCAGCACCAGGGCCGCGACGATAGCCCATC 7 59 1 GGCCGCGACG 0.934457 -40 GTGGTGGCTAGCCGGTGCTGGATGGGCTAT 7 79 0 GCCGGTGCTG 0.870459 -20 GGGATGACCGGCCGTGAATGCGCTCTCATC 10 16 1 GCCGTGAATG 0.802833 -107 GTTGCCGAACAGCGGCGACGATGAGAGCGC 10 35 0 AGCGGCGACG 0.885509 -88 CGTTCTGCACGCCGGCACTGGAACTCCCAC 10 65 0 GCCGGCACTG 0.95214 -58 CCTGGCCAAGGCCAGGGACGTGGTGTACGA 12 46 0 GCCAGGGACG 0.941481 -32 GGCGGGAATCCTTTCGCATA 13 19 0 GGCGGGAATC 0.927979 -10 ********** Masking position 3 Map Score: 6.21704 Number of sites scoring better than the average of aligned sites = 2056 Number in coding regions = 1961 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 9 ATTAAAACGCTCCTTAAACAGATC 1 112 0 AAACGCTCCT 0.826481 -14 TCGAACCATCTCCCTCATGATGTTA 2 6 1 CCATCTCCCT 0.758402 -131 AGCAAAGGCTCAACGCTACTGCTTGTCTGT 2 80 0 CAACGCTACT 0.809334 -57 TTATATTTTTTCACACTCCTCGGATTTTGT 4 196 0 TCACACTCCT 0.718533 -50 TTCCCCTCCGCAATGTTCCTGCCTTTATAT 4 220 0 CAATGTTCCT 0.758193 -26 AGGCGCTCCCCCAGGCGCCTTTTTTATTGG 5 25 1 CCAGGCGCCT 0.957903 -69 CAACGCGCCATAAACGCAGG 8 1 1 CAACGCGCCA 0.891957 -148 TGCCCGTACACCACACCCCTGGACGTAACT 11 47 0 CCACACCCCT 0.969179 -115 TACGACACGCCCACCGGCCTTACCTGCCCG 11 71 0 CCACCGGCCT 0.903391 -91 CACTCGTACACCACGTCCCTGGCCTTGGCC 12 43 1 CCACGTCCCT 0.978289 -35 ********** Masking position 3 Map Score: 1.63452 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 336 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 AGTCCTTTATACAGAGGTGT 4 1 1 AGTCCTTTAT 0.966409 -245 ATCCTGTAAAAGCCCTTTATATAGAGGGCT 4 145 1 AGCCCTTTAT 0.984807 -101 ACACAAAAAGAGCCCTCTATATAAAGGGCT 4 155 0 AGCCCTCTAT 0.966889 -91 TGATCACACAAGCTGTTTATGCTTTCTGGG 6 119 1 AGCTGTTTAT 0.895041 -182 TCAACTGTGGAGTCGTTGATCAATCGACTG 9 21 0 AGTCGTTGAT 0.898964 -30 ********** Masking position 6 Map Score: 0.73591 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 70 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 ********** No masking Map Score: -4.67335e-15 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: -4.67335e-15 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: -4.67335e-15 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