AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ilexA_mthe_opreg_100.orf -g0.495 -x5 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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH34 236 ribosomal protein S18 (E.coli S13) #2 MTH40 58 DNA-dependent RNA polymerase, subunit N #3 MTH442 195 excinuclease ABC subunit B #4 MTH443 41 excinuclease ABC subunit A #5 MTH472 140 DNA helicase II #6 MTH511 240 DNA helicase II #7 MTH543 107 unknown #8 MTH1208 220 DNA-dependent DNA polymerase family B (PolB1) #9 MTH1692 113 conserved protein Motif number 1 TACCTGGCTAGGCTATCCCGGCACAGGATGT 1 63 0 GGTATCCCGG 0.969509 -174 CCAGTCTTGCGCCTTACCTGGCTAGGCTATC 1 77 0 GCTTACCTGG 0.961132 -160 ACTCAACTTTATGTATCCTGGCAAAGGTATA 3 115 1 ATTATCCTGG 0.809014 -81 ACATTTTCTGGTAATGAGAAT 4 1 1 ACTTTTCTGG 0.878328 -41 AATAGTTTGTGGTTTTTCTGGTGAAGGGCCT 7 50 0 GGTTTTCTGG 0.986807 -58 ATAGTGTTTAGGATTTCCTGGGGGTGTTGGA 8 95 0 GGTTTCCTGG 0.996951 -126 TAGGTGTGCCGGTTTTCGTGGTGTGGTGGTT 9 24 1 GGTTTCGTGG 0.991431 -90 TCACCCTGCCGGTTTTCGTGGTTGTAGTGGT 9 75 1 GGTTTCGTGG 0.991431 -39 ** ******** Masking position 4 Map Score: 9.28654 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 271 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 TTTTTATTTTATAAACTAAAGAGTAGAATGATTCAGT 2 32 1 AATAAGATAT 0.97963 -27 TATGTTTAAAACAAGTTCAGTGGGGGTATCATCACAGGATTA 3 34 1 AATAGGATAT 0.920763 -162 ATAACCAAACAAAACATTAATATTCCCATCAATCAAATCTAT 5 79 1 AATAATATAA 0.952547 -62 TAGTCTGAGTATGACATAATAATGTACATTAAAATTATTGAA 6 47 1 AATAATATAA 0.952566 -194 AGTTATTATGAAGAATTTAATAGGCTGATGAATTCAATAAAA 6 98 0 AATAAGATAA 0.983942 -143 GATTATTGAAAATACATTAACATTAAAATTAAAGTTATTATG 6 130 0 AATAATATAA 0.952418 -111 AGTTGCTGGCATGAAATGAACAGTTTAATCCTGTGATCAGTA 8 35 0 AATAAGATCT 0.916911 -186 ATTTCATGCCAGCAACTAAGAAGGCTTATTATAAGTCCAACA 8 60 1 AATAAGATAT 0.98029 -161 TAGCAGAATAAACACTTAAGTAGCACTATTAAGATATAGTGT 8 119 0 AATAAGATAA 0.983943 -102 * * * * ** ** ** Masking position 9 Map Score: 7.01728 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 14 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 GGGACTGGGATTTGAACCCAGGAGGAGCAAAGCT 1 119 0 TTAACAGGAG 0.894172 -118 CTTGTTTTAAACATAAATCAGAGGATGGTAATGA 3 15 0 AAAACAGAGG 0.850136 -181 TCAGTGGGGGTATCATCACAGGATTATGGAACAC 3 50 1 TTATCAGGAT 0.925211 -146 CTGGAGTCTCATATCTGACAGGGTATCCCACGTG 3 81 0 AACTCAGGGT 0.954615 -115 TATTGTGGGATTATATTTCAGGGTCAACTTATAT 3 145 0 TAATCAGGGT 0.964702 -51 TGGTAATGAGAATTAAGGCAGGATTAAAGAGTT 4 19 1 ATAACAGGAT 0.90943 -23 TCGCACTGATATATCATTCAGGGGTTCATC 5 121 1 AACACAGGGG 0.934921 -20 GCTGTGCATCTATAATTTCAGAGGTGATGTT 6 8 0 TTATCAGAGG 0.874826 -233 ATGTATTTTCAATAATCTCAGGGGAGGCTACCGG 6 155 1 ATATCAGGGG 0.97757 -86 GTGTATTAATACTGATCACAGGATTAAACTGTTC 8 26 1 ATATCAGGAT 0.944538 -195 TTTATTAATCTCACATAACAGAATAGGTAC 8 201 1 TAATCAGAAT 0.731969 -20 TACAACCACGAAAACCGGCAGGGTGATCATTGCA 9 67 0 AACCCAGGGT 0.848179 -47 * * ** ****** Masking position 10 Map Score: 7.21833 Number of sites scoring better than the average of aligned sites = 830 Number in coding regions = 776 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 4 ATGATACATCCTGTGCCGGGATAGCCTAGCCA 1 58 1 CTGCCGGGAT 0.976324 -179 TTGCTTTAACCGACGCCGGGACTGGGATTTGA 1 138 0 CCGCCGGGAC 0.987969 -99 TCGCAAACCCCCGTCCCGCGAATTCACTCTTA 1 201 1 CTCCCGCGAA 0.962311 -36 TTATATATACCTTTGCCAGGATACATAAAGTT 3 119 0 CTGCCAGGAT 0.976782 -77 CCTTAATTCTCATTACCAGAAAATGT 4 5 0 CTACCAGAAA 0.902156 -37 GAGACCATGGCAGTGCCCCGACTGAGGCCCTT 7 26 1 CTGCCCCGAC 0.9246 -82 GACTGAGGCCCTTCACCAGAAAAACCACAAAC 7 45 1 CCACCAGAAA 0.922304 -63 ATAAGTCCAACACCCCCAGGAAATCCTAAACA 8 90 1 CCCCCAGGAA 0.984866 -131 ATGTCAACCACCACACCACGAAAACCGGCACA 9 28 0 CCACCACGAA 0.968815 -86 * ********* Masking position 11 Map Score: 6.10562 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 362 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 CAATACTTAAATAGATGTCATAATATACAGT 1 24 1 ATAGATGTAT 0.961141 -213 TTAATCCGGTACAGATTTAATAACCAAACAA 5 60 1 ACAGATTTAT 0.871329 -81 ATCAGTGCGAATAGATTTGATTGATGGGAAT 5 100 0 ATAGATTTAT 0.960977 -41 TTTATATTCAATAATTTTAATGTACATTATT 6 64 0 ATAATTTTAT 0.842035 -177 ATTATTGAATATAAATTTTTTTATTGAATTC 6 80 1 ATAAATTTTT 0.792362 -161 ATTCTTCATAATAACTTTAATTTTAATGTTA 6 124 1 ATAACTTTAT 0.859635 -117 CCCATAAATGTTATTCTATGGTTT 6 227 0 ATAAATGTAT 0.783646 -14 TGAATAGAAAATAAATGTTATAAATAGTTTG 7 72 0 ATAAATGTAT 0.783646 -36 ******** ** Masking position 3 Map Score: 4.6771 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 20 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 AACAAGTTCAGTGGGGGTATCATCACAGGA 3 43 1 GTGGGGGTAT 0.965353 -153 ATTAATACACGGGGAGGTAGAGGGT 8 6 0 GGGGAGGTAG 0.982919 -215 AGGATTTCCTGGGGGTGTTGGACTTATAAT 8 87 0 GGGGGTGTTG 0.979846 -134 TTTTCGTGGTGTGGTGGTTGACATAAAGGT 9 36 1 GTGGTGGTTG 0.984985 -78 GCCGGTTTTCGTGGTTGTAGTGGTTGATGT 9 82 1 GTGGTTGTAG 0.976592 -32 ********** Masking position 8 Map Score: 2.56305 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 145 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TAGGCTATCCCGGCACAGGATGTATCATAT 1 56 0 CGGCACAGGA 0.881001 -181 CACAGGATTATGGAACACGTGGGATACCCT 3 66 1 TGGAACACGT 0.964733 -130 TTATGTATCCTGGCAAAGGTATATATAAGT 3 123 1 TGGCAAAGGT 0.934632 -73 GAGAATTCAATGGAAAAACTATAAAAGTGG 6 193 1 TGGAAAAACT 0.769249 -48 CCACGAAAACCGGCACACCTAATCATATAT 9 15 0 CGGCACACCT 0.988963 -99 AGGGTGATCATTGCAAACCTTTATGTCAAC 9 52 0 TTGCAAACCT 0.82334 -62 CGGAACACCTTTACATCAAC 9 104 0 CGGAACACCT 0.977472 -10 ********** Masking position 5 Map Score: 1.72484 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 217 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 GAAATCTTGTGGAGCTTTGCTCCTCCTGGG 1 107 1 GGAGCTTTGC 0.982821 -130 TTCGCGGGACGGGGGTTTGCGAATTCTTCA 1 193 0 GGGGGTTTGC 0.974897 -44 TCAGACTATAAGGGCTGTGCATCTATAATT 6 25 0 AGGGCTGTGC 0.961548 -216 GGCACTGCCATGGTCTCTGCTCTAGTGGGG 7 13 0 TGGTCTCTGC 0.964815 -95 GGCCTCAGTCGGGGCACTGCCATGGTCTCT 7 25 0 GGGGCACTGC 0.989891 -83 ACCGGCAGGGTGATCATTGCAAACCTTTAT 9 58 0 TGATCATTGC 0.821437 -56 ********** Masking position 8 Map Score: 1.54186 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 255 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ACGACTCTTATGAAGAATTCGCAAACCCCC 1 183 1 TGAAGAATTC 0.980152 -54 ACTGAATCATTCTACTCTTTAG 2 47 0 TGAATCATTC 0.947836 -12 TACAGATTCTTTAATAATTCCTTGTGTTCA 5 24 1 TTAATAATTC 0.88104 -117 TTTAATAGGCTGATGAATTCAATAAAAAAA 6 95 0 TGATGAATTC 0.924131 -146 AAAGTTATTATGAAGAATTTAATAGGCTGA 6 112 0 TGAAGAATTT 0.884258 -129 CTATTCAATATTAAACATTCAC 7 96 1 TTAAACATTC 0.776886 -12 ********** Masking position 7 Map Score: 1.2194 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 150 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 AGATGTCATAATATACAGTTATATGATACA 1 36 1 ATATACAGTT 0.948809 -201 AAATAAAAATATATAAAGTTATCGATTGAT 2 11 0 ATATAAAGTT 0.823479 -48 TAAGGCAGGATTAAAGAGTT 4 32 1 TTAAAGAGTT 0.915861 -10 AATAAATGTTATAAATAGTTTGTGGTTTTT 7 64 0 ATAAATAGTT 0.882125 -44 GATCACAGGATTAAACTGTTCATTTCATGC 8 39 1 TTAAACTGTT 0.871553 -182 CACTATTAAGATATAGTGTTTAGGATTTCC 8 108 0 ATATAGTGTT 0.920342 -113 AAGTAGCAGAATAAACACTTAAGTAGCACT 8 134 0 ATAAACACTT 0.831115 -87 TGTGAGATTAATAAAGTGTTCCCGCTGCGT 8 186 0 ATAAAGTGTT 0.948809 -35 ********** Masking position 5 Map Score: 3.53413 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 22 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ********** No masking Map Score: 2.73092e-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: 2.73092e-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: 2.73092e-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