AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_aful_reg_100.orf -o00450_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0288 300 adenylylsulfate 3-phosphotransferase (cysC) #2 AF0423 138 sulfite reductase, subunit alpha (dsrA) #3 AF0425 41 sulfite reductase, subunit gamma (dsrD) #4 AF1452 117 signal-transducing histidine kinase #5 AF1453 37 methionyl-tRNA synthetase (metS) #6 AF1667 158 sulfate adenylyltransferase (sat) #7 AF1669 48 adenylylsulfate reductase, subunit B (aprB) Motif number 1 CGCTTTCTGGTTTAAGCTTACCTAAAAATATCTGCA 2 48 0 TAAGACCAAA 0.973857 -91 TTAGGCAATATATAAGAATTTCGAAATTTGCGCTTT 2 78 0 TAAGTTCAAA 0.993786 -61 AAAAAATTGGTGGAAGTGTTTATAAAT 3 2 0 TAAGTTAAAA 0.926984 -40 CACCAATTTTTTTAAGGTGACCTAAA 3 26 1 TAAGACCAAA 0.973857 -16 CAAATACGCTTTACAGGTAACCAAAACAAAAATTAA 4 14 0 TCAGACCAAA 0.883314 -104 ATTATTCAGATGCAATCCATTCCAAAAAACTGCCGC 4 53 0 TAATTTCAAA 0.940464 -65 AAAATAAAAGGCAAAGGAGTTCAAAAAATTTTCTAC 6 11 0 GAAGTTCAAA 0.968096 -148 CCGCGCAATTTTCAAACTCTTCGAAAATAAAAGGCA 6 34 0 TAAATTCAAA 0.965341 -125 TTTCGAATTTTCAAAGACATTCAAAACCGCGCAATT 6 60 0 TAAGTTCAAA 0.993832 -99 ATTTTAATGATTAAAGGTTTTCGAATTTTCAAAGAC 6 78 0 TAAGTTCAAT 0.953431 -81 CACAGCCTTATATAAAGGTTTCGAAAAATATTTTAA 6 107 0 TAAATTCAAA 0.965341 -52 * *** *** *** Masking position 5 Map Score: 17.0893 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 103 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 2 ATGCATCCCCTATATTTTGGGAACTTCTAGTA 1 145 0 TTATTTTGGA 0.96524 -156 CTCATAACGTTATTTTTTAATACTCTATGGAA 1 246 1 TTTTTTTAAA 0.832913 -55 CGATTGCAGATATTTTTAGGTAAGCTTAAACC 2 44 1 TTTTTTAGGA 0.980302 -95 CAAGTCCCCCTCTTTTTAGGCAATATATAAGA 2 97 0 TTTTTTAGGA 0.980302 -42 TGCTGGCGGCAGTTTTTTGGAATGGATTGCAT 4 48 1 ATTTTTTGGA 0.89615 -70 GCCAAATGCTTTTATTTACAAAGATAGGCAAT 4 91 1 TTATTTACAA 0.879252 -27 TCCTTTGCCTTTTATTTTCGAAGAGTTTGAAA 6 29 1 TTATTTTCGA 0.934686 -130 ATCATTAAAATATTTTTCGAAACCTTTATATA 6 103 1 TTTTTTCGAA 0.933601 -56 CTATGATGTATTTTTTTTCACAGCCTTATATA 6 129 0 TTTTTTTCAA 0.951961 -30 TTTAATTTTTTTTTAGAAAAATGTATGAA 7 8 1 TTTTTTAGAA 0.968808 -41 * ******** * Masking position 6 Map Score: 10.7242 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 40 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 GGTTTAAATGGGTGAGATGACAAAAC 1 7 0 GGTGAGATGA 0.988428 -294 CGTAACACGCGGAGTGTTGATAGCTACTAG 1 121 1 GGAGTGTTGA 0.971269 -180 AAGAAACCGAGGTGTCATGATAACAGATAA 1 181 1 GGTGTCATGA 0.959884 -120 AAGGGGGAGTTGTGGGAAGGTTA 2 4 1 GGGGAGTTGT 0.981235 -135 CTAAAAAGAGGGGGACTTGCAATTACAGGA 2 110 1 GGGGACTTGC 0.975908 -29 AAAGGTTGGAGGTGAGTTGA 7 39 1 GGTGAGTTGA 0.993764 -10 ********** Masking position 8 Map Score: 7.03511 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 118 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 TGTTTGACTTCTAAAAACTTTTTATCTGTTATC 1 199 0 CAAACTTTTT 0.947146 -102 TATCTGCAATCGAGAAGTTTTTTAACCTTCCCA 2 23 0 CAAGTTTTTT 0.924816 -116 ATAAACACTTCCACCAATTTTTTTAAGGTGACC 3 15 1 CCAATTTTTT 0.983328 -27 GTATTTGCTGGCGGCAGTTTTTTGGAATGGATT 4 43 1 GCAGTTTTTT 0.788724 -75 TTATTTACCCCTCGCAACCTTTTCCCTCC 5 19 1 CCAACCTTTT 0.953547 -19 CAAAGGAGTTCAAAAAATTTTCTAC 6 3 0 CAAATTTTCT 0.944227 -156 CATTCAAAACCGCGCAATTTTCAAACTCTTCGA 6 46 0 CCAATTTTCA 0.85526 -113 ATAAAGGTTTCGAAAAATATTTTAATGATTAAA 6 99 0 CAAATATTTT 0.818403 -60 CCAACCTTTTCATACATTTTTCTAAAAAAAAAT 7 15 0 CCATTTTTCT 0.882687 -34 TCAACTCACCTCCAACCTTTTCATACATTTT 7 28 0 CCAACCTTTT 0.953547 -21 * ********* Masking position 6 Map Score: 5.90704 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 324 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 CTCTCTTTATTTCAGGTTTCTTTAGCTGCC 1 36 1 TTCAGGTTTC 0.981707 -265 GATTACGCTCTTCTGGTTCCATAGAGTATT 1 264 0 TTCTGGTTCC 0.984764 -37 AATTTGCGCTTTCTGGTTTAAGCTTACCTA 2 60 0 TTCTGGTTTA 0.936451 -79 TTTAGGTCACCTTAAAAAAA 3 32 0 TTTAGGTCAC 0.914746 -10 TTAATTTTTGTTTTGGTTACCTGTAAAGCG 4 14 1 TTTTGGTTAC 0.971534 -104 ********** Masking position 7 Map Score: 1.69668 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 95 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 CCTGAAATAAAGAGAGGTTTAAATGGGTGAG 1 21 0 AAGAGGTTTA 0.911547 -280 TCAGCTTGCGACAGAGTGGGCGAACGCCAAA 1 76 0 AAGAGTGGGC 0.929303 -225 TTCCCAAAATATAGGGGATGCATTCCTAAGA 1 154 1 AAGGGGATGC 0.909988 -147 ATAATTCTCCATAGTGTTTGACTTCTAAAAA 1 215 0 AAGTGTTTGA 0.846864 -86 TTCTGGTTCCATAGAGTATTAAAAAATAACG 1 253 0 AAGAGTATTA 0.785436 -48 AGCGTAATCGAAAGAAGGTGATGTAG 1 285 1 AAGAAGGTGA 0.955126 -16 TATTGCCTAAAAAGAGGGGGACTTGCAATTA 2 104 1 AAGAGGGGGA 0.981425 -35 ACTTGCAATTACAGGAGGTGAACGA 2 124 1 AAGGAGGTGA 0.923388 -15 TTTTATTTTCGAAGAGTTTGAAAATTGCGCG 6 38 1 GAGAGTTTGA 0.861563 -121 * ********* Masking position 3 Map Score: 2.4976 Number of sites scoring better than the average of aligned sites = 1296 Number in coding regions = 1214 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 ATCTCACCCATTTAAACCTCTCTTTATTTC 1 19 1 TTTAAACCTC 0.946222 -282 CGAGAAGTTTTTTAACCTTCCCACAACTCC 2 16 0 TTTAACCTTC 0.973492 -123 TAAAACGTTATTTACCCCTCGCAACCTTTT 5 12 1 TTTACCCCTC 0.977167 -26 CCTCGCAACCTTTTCCCTCC 5 28 1 TTTTCCCTCC 0.94425 -10 TAGAAAATTTTTTGAACTCCTTTGCCTTTT 6 12 1 TTTGAACTCC 0.911667 -147 ********** Masking position 3 Map Score: 0.308187 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 178 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 ********** No masking Map Score: -3.03101e-13 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 9 ********** No masking Map Score: -3.03101e-13 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: -3.03101e-13 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