AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00920_aful_reg_300.orf -o00920_aful_300.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 AF1665 147 ornithine cyclodeaminase (arcB) #5 AF1667 158 sulfate adenylyltransferase (sat) #6 AF1669 48 adenylylsulfate reductase, subunit B (aprB) Motif number 1 TCTCACCCATTTAAACCTCTCTTTATTTCAGGTTT 1 20 1 TTAATCTCTA 0.919573 -281 CCTCTCTTTATTTCAGGTTTCTTTAGCTGCCATTG 1 35 1 TTCATTTCTA 0.789152 -266 TGATAACAGATAAAAAGTTTTTAGAAGTCAAACAC 1 198 1 TAAATTTTTA 0.810325 -103 GTGGGAAGGTTAAAAAACTTCTCGATTGCAGATAT 2 22 1 TAAACTTCTA 0.825616 -117 CGCTTTCTGGTTTAAGCTTACCTAAAAATATCTGC 2 49 0 TTAATTACCA 0.741831 -90 TTAGGCAATATATAAGAATTTCGAAATTTGCGCTT 2 79 0 TAAAATTTCA 0.683267 -60 AATTTTTCTATTCAATTTTTCCTTCAATAGATGCT 4 59 0 TTAATTTCCC 0.809842 -89 AAATTGAATAGAAAAATTTTTCTTACAGCATCTCA 4 76 1 GAAATTTTCA 0.851167 -72 TAAAGTTAATGTCAAGTTTTCTTGAGATGCTGTAA 4 98 0 GTAATTTCTA 0.880068 -50 TGACATTAACTTTAATACTTTTCAAGAAGACAGGA 4 119 1 TTAACTTTTA 0.849174 -29 GTAGAAAATTTTTTGAACTCCTTTGC 5 2 1 TAAATTTTTA 0.696936 -157 CCGCGCAATTTTCAAACTCTTCGAAAATAAAAGGC 5 35 0 TTAATCTTCA 0.934542 -124 TTGCGCGGTTTTGAATGTCTTTGAAAATTCGAAAA 5 62 1 TTAATCTTTA 0.854522 -97 ATTTTAATGATTAAAGGTTTTCGAATTTTCAAAGA 5 79 0 TTAATTTTCA 0.975235 -80 CTTTAATCATTAAAATATTTTTCGAAACCTTTATA 5 98 1 TAAATTTTTA 0.913288 -61 TTTAATTTTTTTTTAGAAAAATGTA 6 1 1 TTAATTTTTA 0.969069 -48 TCAACTCACCTCCAACCTTTTCATACATTTTTCTA 6 24 0 TCAATTTTCA 0.882955 -25 ** ** ***** * Masking position 5 Map Score: 19.1803 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 198 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 CCATAGAGTATTAAAAAATAACGTTATGAG 1 246 0 TTAAAAAATA 0.748559 -55 TGTGGGAAGGTTAAAAAACTTCTCGATTGC 2 21 1 TTAAAAAACT 0.814375 -118 ATATAAGAATTTCGAAATTTGCGCTTTCTG 2 75 0 TTCGAAATTT 0.842328 -64 TTAGGTCACCTTAAAAAAATTGGTGGAAGT 3 21 0 TTAAAAAAAT 0.923068 -21 TGAGATGCTGTAAGAAAAATTTTTCTATTC 4 81 0 TAAGAAAAAT 0.805808 -67 GGCAAAGGAGTTCAAAAAATTTTCTAC 5 8 0 TTCAAAAAAT 0.9392 -151 TTTCAAACTCTTCGAAAATAAAAGGCAAAG 5 31 0 TTCGAAAATA 0.912528 -128 TTTCGAAGAGTTTGAAAATTGCGCGGTTTT 5 44 1 TTTGAAAATT 0.934241 -115 TTTGAATGTCTTTGAAAATTCGAAAACCTT 5 71 1 TTTGAAAATT 0.934241 -88 ATATAAAGGTTTCGAAAAATATTTTAATGA 5 104 0 TTCGAAAAAT 0.976769 -55 TAATTTTTTTTTAGAAAAATGTATGAAAAG 6 13 1 TTAGAAAAAT 0.970289 -36 ********** Masking position 5 Map Score: 13.8628 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 142 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 GGTTTAAATGGGTGAGATGACAAAAC 1 7 0 GGTGAGATGA 0.987263 -294 CGTAACACGCGGAGTGTTGATAGCTACTAG 1 121 1 GGAGTGTTGA 0.968432 -180 AAGAAACCGAGGTGTCATGATAACAGATAA 1 181 1 GGTGTCATGA 0.955975 -120 AAGGGGGAGTTGTGGGAAGGTTA 2 4 1 GGGGAGTTGT 0.979362 -135 CTAAAAAGAGGGGGACTTGCAATTACAGGA 2 110 1 GGGGACTTGC 0.973517 -29 AAAGGTTGGAGGTGAGTTGA 6 39 1 GGTGAGTTGA 0.993133 -10 ********** Masking position 8 Map Score: 7.0195 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 TTTAAATGGGTGAGATGACAAAAC 1 3 0 TGAGATGAAA 0.424411 -298 AATTGAGTCAATGGCAGCTAAAGAAACCTGAA 1 46 0 ATGGCAGAAA 0.982384 -255 AGGTGTCATGATAACAGATAAAAAGTTTTTAG 1 190 1 ATAACAGAAA 0.912498 -111 TAAAAAGTTTTTAGAAGTCAAACACTATGGAG 1 208 1 TTAGAAGAAA 0.839616 -93 TATGGTAGATAAGAAAGATAAAACAATTTTGC 4 15 1 AAGAAAGAAA 0.888997 -133 ATGCTCTCGAAGGGCAGGCAAAATTGTTTTAT 4 32 0 AGGGCAGAAA 0.969305 -116 GAGAGCATCTATTGAAGGAAAAATTGAATAGA 4 56 1 ATTGAAGAAA 0.918924 -92 TGAAGGAAAAATTGAATAGAAAAATTTTTCTT 4 68 1 ATTGAATAAA 0.635881 -80 CTCTTCGAAAATAAAAGGCAAAGGAGTTCAAA 5 22 0 ATAAAAGAAA 0.885973 -137 CGAATTTTCAAAGACATTCAAAACCGCGCAAT 5 61 0 AAGACATAAA 0.623455 -98 ACCTTTATATAAGGCTGTGAAAAAAAATACAT 5 124 1 AAGGCTGAAA 0.878909 -35 ******* *** Masking position 10 Map Score: 3.89673 Number of sites scoring better than the average of aligned sites = 883 Number in coding regions = 790 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 AACCTGAAATAAAGAGAGGTTTAAATGGGT 1 24 0 AAAGAGAGGT 0.885481 -277 TCAGCTTGCGACAGAGTGGGCGAACGCCAA 1 77 0 ACAGAGTGGG 0.977558 -224 AGCGTAATCGAAAGAAGGTGATGTAG 1 285 1 AAAGAAGGTG 0.969306 -16 TATTGCCTAAAAAGAGGGGGACTTGCAATT 2 104 1 AAAGAGGGGG 0.993801 -35 ACTTGCAATTACAGGAGGTGAACGA 2 124 1 ACAGGAGGTG 0.938864 -15 ********** Masking position 3 Map Score: 0.744676 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 393 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 ********** No masking Map Score: -9.49695e-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 7 ********** No masking Map Score: -9.49695e-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 8 ********** No masking Map Score: -9.49695e-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