AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i008_bsub_mtub_300.orf -o008_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 ileS 300 isoleucyl-tRNA synthetase #2 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #3 lsp 102 signal peptidase II #4 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #5 pyrP 171 uracil permease #6 upp 134 uracil phosphoribosyltransferase #7 glyA 206 serine hydroxymethyltransferase #8 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #9 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #10 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #11 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #12 ywlB 66 alternate gene name: ipc-28d #13 spoIIR 140 alternate gene name: ipc-27d, csfX #14 upp 104 upp Motif number 1 GGTACCACCCTTTTAGAAAAAGCAAGCATACACTTTTT 1 195 0 TAAAGCAAGA 0.56881 -106 CTGCATTTTTTCAGAAAATAAAAAAAGCCCTCTCATCC 1 260 0 TAAAAAAAAC 0.976055 -41 AGGATGTCACTCTTGGCACAAAAAAAGCCCGGCTTTTA 2 28 0 TAAAAAAAAC 0.976055 -50 GCTTCGTTTATTATTTCAGAAAAGAAACCCTCTGTCAA 4 98 0 TAAAAAGAAC 0.968274 -176 CACCTCACAGTTCATATAGAAGAAAAAACCCCTCCTGC 4 239 0 TAAAGAAAAA 0.891503 -35 TATGCCTCTTTGCGTAAAAAAGCAAAGAGGTTTTTTTA 5 91 1 TAAAGCAAAA 0.849675 -81 GATGACTCAATGACTGTATAAAAAAACCTCTTTGCTTT 5 109 0 TAAAAAAAAC 0.976055 -63 ACACTTCTATTGATTCTACAAAAAAAGACATTGAGTTT 6 65 0 TAAAAAAAAA 0.957612 -70 TAATTGTTGATGGGACAATAAAAAAGGAGCTGAAACAC 6 104 1 TAAAAAAAGA 0.840576 -31 TATTTCACTATCTTAAAATAAAAGAAAAGACTGGCTAT 7 20 0 TAAAAAGAAA 0.944179 -187 TCTAAATTTTTATTGGTAAAAACGAATATTAATAACTT 7 82 0 TAAAACGAAA 0.920793 -125 TGTACAATAGTGATGGTAAAAACAAAGAACAGGATACG 7 159 1 TAAAACAAAA 0.939541 -48 TATACCAATAAAAGAAACGAAGTCGCCG 9 1 1 TAAAAAGAAC 0.968274 -75 CTCTATTATATATGAAGAAAAAAGAAACGGCGACTTCG 9 28 0 TAAAAAGAAC 0.968274 -48 ATAAAAGATGTCCTGTAATAAAACAAGCGTTATCCACA 11 63 0 TAAAAACAAC 0.874965 -94 GGGATAAACGTGCAGGGTGAAAAAAATCTAGCAAGCTG 13 53 0 TTAAAAAAAC 0.76603 -88 TTGTCCATAATAGGGCTAGAAACAAAGCACGGAGAGGA 13 100 1 TAAAACAAAC 0.965565 -41 * * ******* * Masking position 10 Map Score: 23.0067 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 479 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 2 TCAGAAAATAAAAAAAGCCCTCTCATCCCATA 1 256 0 AAAAAGCCTC 0.975539 -45 TATTTTCTGAAAAAATGCAGTGGAGGAATGAA 1 278 1 AAAATGCGTG 0.784992 -23 TGCAAAAGAGCCCGGCGTAAAAGCC 2 4 1 AAAGAGCCGG 0.939003 -74 TCTTGGCACAAAAAAAGCCCGGCTTTTACGCC 2 24 0 AAAAAGCCGG 0.991829 -54 ATTTTATCAATAAAAAGCACTGGAGTAAAGAA 3 41 0 TAAAAGCCTG 0.932799 -62 CATATAGAAGAAAAAACCCCTCCTGCCAGAGC 4 233 0 AAAAACCCTC 0.757541 -41 CAAAGAGGCATACAAAGACCTGCCGAATACTT 5 71 0 TAAAAGACTG 0.871253 -101 TGGGACAATAAAAAAGGAGCTGAAACACAGT 6 114 1 AAAAGGACTG 0.850476 -21 TGATGGTAAAAACAAAGAACAGGATACGGATA 7 169 1 AAAAAGACAG 0.868569 -38 TATGGTGTGAATCAAAGAGCGGACAGGCTGCG 8 85 1 ATAAAGACGG 0.905241 -72 CTGCGCGGTCAATAAAGCGGGCGGGCCGCATC 8 112 1 AAAAAGCGGC 0.963117 -45 CGCATAGGCTAAAAAAGCGGGGCGTGTCCAAG 10 43 1 AAAAAGCGGG 0.982548 -36 GGACAACGCTAATAAAGAAGTGGATAAGTATG 11 25 0 AAAAAGAGTG 0.951085 -132 TTTTGAAAGTATAAAAGATGTCCTGTAATAAA 11 79 0 ATAAAGAGTC 0.59279 -78 CATAGATTGGAAGAAAGAACGCAAAAACGGGG 12 38 1 AAAAAGACGC 0.964848 -29 TAGGGCTAGAAACAAAGCACGGAGAGGAACGG 13 110 1 AAAAAGCCGG 0.991829 -31 ** ***** *** Masking position 4 Map Score: 19.8192 Number of sites scoring better than the average of aligned sites = 1096 Number in coding regions = 943 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 3 GTGAGAGTCCGGGATGGCCGGAATCATGTA 1 93 1 GGGATGGCCG 0.988195 -208 GCATCGTAACGTGATGAACGTCCTAACCTA 1 157 0 GTGATGAACG 0.935264 -144 AAAAATGCAGTGGAGGAATGAAA 1 288 1 TGGAGGAATG 0.764157 -13 AACCGTAAACTGGAGGAACGTTT 3 90 1 TGGAGGAACG 0.965395 -13 AGAAGGATAACGGATAGACGGGATGCGTGT 4 170 1 CGGATAGACG 0.655943 -104 TCAATAAAGCGGGCGGGCCGCATCACACAC 8 120 1 GGGCGGGCCG 0.959633 -37 AGAAAAATAAGGGGTGACTGAC 9 64 1 GGGGTGACTG 0.923515 -12 ACGCAAAAACGGGGTGAACGG 12 56 1 GGGGTGAACG 0.988445 -11 AGGAGAGCCTGGGATAAACGTGCAGGGTGA 13 71 0 GGGATAAACG 0.923527 -70 ACAAAGCACGGAGAGGAACGGTGGGGACCG 13 121 1 GAGAGGAACG 0.946116 -20 GAGAGGAACGGTGGGGACCG 13 131 1 GTGGGGACCG 0.946107 -10 TATATGGACGGGGTTGACCGGTCGCGCGGA 14 19 1 GGGTTGACCG 0.951941 -86 ACCGGTCGCGCGGATGGACGCACCCGTATC 14 35 1 CGGATGGACG 0.942618 -70 AGCCCCCTTTTAGGGGACCGAGCCACGATT 14 65 1 TAGGGGACCG 0.794886 -40 ********** Masking position 3 Map Score: 17.061 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 480 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 TTAAAACAGTCCAGAGAGGCTGAGAAGGAT 4 148 1 CCAGAGAGGC 0.959407 -126 TCCTGCCAGAGCATAGAGGGGTTTTAGGAC 4 215 0 GCATAGAGGG 0.919231 -59 CTATGCTCTGGCAGGAGGGGTTTTTTCTTC 4 229 1 GCAGGAGGGG 0.799501 -45 TTTAAGCAATCCAGAGAGGTTGCAAAGAGG 5 22 1 CCAGAGAGGT 0.976601 -150 CAGAGAGGTTGCAAAGAGGTGCACAACAAA 5 33 1 GCAAAGAGGT 0.985216 -139 GCTTTTTTACGCAAAGAGGCATACAAAGAC 5 84 0 GCAAAGAGGC 0.974184 -88 GCGTAAAAAAGCAAAGAGGTTTTTTTATAC 5 102 1 GCAAAGAGGT 0.985216 -70 GGGCATAAGCCCAAGCGGGTTTTAGGATC 6 10 0 CCAAGCGGGT 0.863828 -125 CAGAAAATCTGCAAACAGGTCATTTGCAAA 8 16 1 GCAAACAGGT 0.953046 -141 CTATGCGTGTCCAAAAAGGGTTAGAACATC 10 20 0 CCAAAAAGGG 0.953207 -59 CGGGGCGTGTCCAAGGGGGTTATTTATGT 10 60 1 CCAAGGGGGT 0.954185 -19 GGCTCGGTCCCCTAAAAGGGGGCTGATACG 14 59 0 CCTAAAAGGG 0.702337 -46 ********** Masking position 2 Map Score: 13.8998 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 157 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 CATCCCGGACTCTCACCATCTCCGGGTCGCTA 1 77 0 TCTCCCTCTC 0.944554 -224 CGAATTTGAAGCGCCGCTTCCCGAGGATATGG 4 35 1 GCGCGCTCCC 0.983483 -239 CCGTTATCCTTCTCAGCCTCTCTGGACTGTTT 4 151 0 TCTCGCTCTC 0.957219 -123 GTGTATAGGCGCGCACCTTGTCCTAAAACCCC 4 196 1 GCGCCCTGTC 0.996783 -78 TTTATTGACCGCGCAGCCTGTCCGCTCTTTGA 8 96 0 GCGCGCTGTC 0.997487 -61 GGCTAAAAAAGCGGGGCGTGTCCAAGGGGGTT 10 49 1 GCGGGCTGTC 0.985369 -30 TTTATCCCAGGCTCTCCTTGTCCATAATAGGG 13 83 1 GCTCCCTGTC 0.991815 -58 GCGTCCATCCGCGCGACCGGTCAACCCCGTCC 14 24 0 GCGCACGGTC 0.953916 -81 **** ** **** Masking position 7 Map Score: 9.03572 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 183 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TTCAGATGAAAAAACGGTTGAAAGGGACAG 1 25 1 AAAACGGTTG 0.984461 -276 TGCTTTTTCTAAAAGGGTGGTACCGCGAGA 1 209 1 AAAAGGGTGG 0.965006 -92 AACCTCAGAAAAAACGGTTGACAGAGGGTT 4 81 1 AAAACGGTTG 0.984461 -193 TGGATTGCTTAAAAAGGTGATCTA 5 5 0 AAAAAGGTGA 0.813983 -167 TTTATTGGTAAAAACGAATATTAATAACTT 7 82 0 AAAACGAATA 0.738549 -125 TGCGTGTCCAAAAAGGGTTAGAACATCTGA 10 17 0 AAAAGGGTTA 0.968453 -62 TTATACTTTCAAAAGGATTACACGCGTAAA 11 97 1 AAAAGGATTA 0.92308 -60 TCACAACAATAAAACGATTGTTTTACGCGT 11 118 0 AAAACGATTG 0.961401 -39 ********** Masking position 4 Map Score: 6.68493 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 200 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AAAATAAAAAAAGCCCTCTCATCCCATAAG 1 254 0 AAGCCCTCTC 0.872008 -47 GAATTAATCGAAAACCTCAGAAAAAACGGT 4 69 1 AAAACCTCAG 0.790095 -205 TTCAGAAAAGAAACCCTCTGTCAACCGTTT 4 92 0 AAACCCTCTG 0.977003 -182 ACCTTGTCCTAAAACCCCTCTATGCTCTGG 4 210 1 AAAACCCCTC 0.875752 -64 TAGAAGAAAAAACCCCTCCTGCCAGAGCAT 4 231 0 AACCCCTCCT 0.893085 -43 ACTGTATAAAAAAACCTCTTTGCTTTTTTA 5 105 0 AAAACCTCTT 0.948685 -67 GATCCTAAAACCCGCTTGGGCTTATGC 6 8 1 AAACCCGCTT 0.960817 -127 CATCGTCAAAAAACCCGCCGGGCATAAGCC 6 29 0 AAACCCGCCG 0.952024 -106 ACATAAATAACCCCCTTGGACACGCCC 10 62 0 TAACCCCCTT 0.872169 -17 CTTAAACCTCCTAAAACACTAT 13 3 1 TAAACCTCCT 0.809205 -138 ********** Masking position 2 Map Score: 5.00379 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 227 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 8 CCACGAACAGGAGAATATGTCGAATTTGAA 4 15 1 GAGAATATGT 0.535208 -259 GCCGCTTCCCGAGGATATGGCAGAATTAAT 4 47 1 GAGGATATGG 0.970979 -227 AGAGGCTGAGAAGGATAACGGATAGACGGG 4 162 1 AAGGATAACG 0.891724 -112 AGAGGGGTTTTAGGACAAGGTGCGCGCCTA 4 201 0 TAGGACAAGG 0.787897 -73 ATTGAGTTTCAAGAACATCGTCAAAAAACC 6 44 0 AAGAACATCG 0.549362 -91 ACGGATAGGAGAGGATCTCGCTG 7 194 1 GAGGATCTCG 0.805674 -13 TAATAAAGAAGTGGATAAGTATGTGTATAA 11 18 0 GTGGATAAGT 0.822967 -139 TCCACAAATTGTGGACAACGCTAATAAAGA 11 39 0 GTGGACAACG 0.95208 -118 TCCACAATTTGTGGATAACGCTTGTTTTAT 11 54 1 GTGGATAACG 0.96024 -103 TTTTATTGTTGTGAATAAGGAGTTTGGTCA 11 134 1 GTGAATAAGG 0.892331 -23 TAGCCCTATTATGGACAAGGAGAGCCTGGG 13 88 0 ATGGACAAGG 0.87209 -53 GCCGGGAGTATATGGACGGGGTTGA 14 6 1 GAGTATATGG 0.766357 -99 ********** Masking position 5 Map Score: 6.30216 Number of sites scoring better than the average of aligned sites = 974 Number in coding regions = 847 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 9 TGAGTTCAGCAAGGAAACTAAAGGGCTGAT 1 124 0 AAGGAAACTA 0.859133 -177 GGACTGTTTTAAAGAATCTATTCAGCTTCG 4 130 0 AAAGAATCTA 0.925124 -144 TCTTAAAATAAAAGAAAAGACTGGCTATGC 7 18 0 AAAGAAAAGA 0.778309 -189 GATTATTTTTAAAAAATCTAAATTTTTATT 7 106 0 AAAAAATCTA 0.828462 -101 TATACCAATAAAAGAAACGAAGTCGCCGTT 9 11 1 AAAGAAACGA 0.969173 -65 TATGAAGAAAAAAGAAACGGCGACTTCGTT 9 26 0 AAAGAAACGG 0.893053 -50 TATTCACAACAATAAAACGATTGTTTTACG 11 121 0 AATAAAACGA 0.718415 -36 TGCAGGGTGAAAAAAATCTAGCAAGCTGTT 13 51 0 AAAAAATCTA 0.828462 -90 ********** Masking position 5 Map Score: 1.73697 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 534 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 10 CCCGGCTTTTACGCCGGGCTCTTTTGCA 2 9 0 ACGCCGGGCT 0.994079 -69 CCCGGCGTAAAAGCCGGGCTTTTTTTGTGC 2 21 1 AAGCCGGGCT 0.995009 -57 TATCCTCGGGAAGCGGCGCTTCAAATTCGA 4 34 0 AAGCGGCGCT 0.963362 -240 GTCAAAAAACCCGCCGGGCATAAGCCCAAG 6 25 0 CCGCCGGGCA 0.952854 -110 AATAAAAGAAAAGACTGGCTATGCAGTCCT 7 12 0 AAGACTGGCT 0.840028 -195 TAGGCTAAAAAAGCGGGGCGTGTCCAAGGG 10 47 1 AAGCGGGGCG 0.981005 -32 ********** Masking position 3 Map Score: 3.67324 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 148 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 ACATGACTGTCCCTTTCAACCGTTTTTTCAT 1 30 0 CCCTTCAACC 0.995021 -271 ATAAAAAAAGCCCTCTCATCCCATAAGGGAC 1 250 0 CCCTTCATCC 0.987514 -51 AAAAGAAACCCTCTGTCAACCGTTTTTTCTG 4 86 0 CTCTTCAACC 0.968664 -188 TATCCGTTATCCTTCTCAGCCTCTCTGGACT 4 155 0 CCTTTCAGCC 0.97638 -119 CATCCGCGCGACCGGTCAACCCCGTCCATAT 14 20 0 ACCGTCAACC 0.918725 -85 ATGGACGCACCCGTATCAGCCCCCTTTTAGG 14 48 1 CCGTTCAGCC 0.98394 -57 **** ****** Masking position 6 Map Score: 3.88756 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 58 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 ********** No masking Map Score: -2.69052e-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: -2.69052e-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: -2.69052e-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