AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00920_aful_reg_100.orf -o00920_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 AF1667 158 sulfate adenylyltransferase (sat) #5 AF1669 48 adenylylsulfate reductase, subunit B (aprB) Motif number 1 AGTGTTTGACTTCTAAAAACTTTTTATCTGTTATCA 1 198 0 TTCAAATTTA 0.977328 -103 AATATCTGCAATCGAGAAGTTTTTTAACCTTCCCAC 2 22 0 ATCGAATTTA 0.770002 -117 TGCAGATATTTTTAGGTAAGCTTAAACCAGAAAGCG 2 48 1 TTTGTACTTA 0.801571 -91 AAAGCGCAAATTTCGAAATTCTTATATATTGCCTAA 2 78 1 TTTAAACTTA 0.990021 -61 ATTTATAAACACTTCCACCAATTTTTT 3 2 1 TTTAAACTTA 0.990224 -40 GGCAAAGGAGTTCAAAAAATTTTCTAC 4 2 0 TTCAAATTTA 0.972874 -157 AACCGCGCAATTTTCAAACTCTTCGAAAATAAAAGG 4 36 0 TTTAAACTTA 0.990225 -123 AATTGCGCGGTTTTGAATGTCTTTGAAAATTCGAAA 4 60 1 TTTAATCTTA 0.921468 -99 GTCTTTGAAAATTCGAAAACCTTTAATCATTAAAAT 4 78 1 ATTAAACTTA 0.957802 -81 ATATAAAGGTTTCGAAAAATATTTTAATGATTAAAG 4 98 0 TTCAAAATTA 0.929097 -61 GATGTATTTTTTTTCACAGCCTTATATAAAGGTTTC 4 121 0 TTTACACTTA 0.974925 -38 CTCCAACCTTTTCATACATTTTTCTAAAAAAAAATT 5 14 0 TTCACATTTA 0.942069 -35 *** *** *** * Masking position 16 Map Score: 15.9677 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 156 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 2 ACCTCGGTTTCTTAGGAATGCATCCCCTATATT 1 161 0 CTTGGAACAT 0.833905 -140 TAGTGTTTGACTTCTAAAAACTTTTTATCTGTT 1 202 0 CTTTAAACTT 0.912091 -99 TGCAGATATTTTTAGGTAAGCTTAAACCAGAAA 2 48 1 TTTGGTACTT 0.965544 -91 AAAGCGCAAATTTCGAAATTCTTATATATTGCC 2 78 1 TTTGAAACTT 0.992769 -61 ATTTATAAACACTTCCACCAATTT 3 2 1 TTTTAAACTT 0.964328 -40 TTTAGGTCACCTTAAAAAAATTG 3 29 0 TTTGGTCCTT 0.91493 -13 GTAGAAAATTTTTTGAACTCCTTTGCCTTTTAT 4 11 1 TTTGAACCTT 0.981375 -148 AACCGCGCAATTTTCAAACTCTTCGAAAATAAA 4 39 0 TTTCAAACTT 0.983848 -120 AATTGCGCGGTTTTGAATGTCTTTGAAAATTCG 4 60 1 TTTGAATCTT 0.950781 -99 GTCTTTGAAAATTCGAAAACCTTTAATCATTAA 4 78 1 ATTGAAACTT 0.950781 -81 ATTAAAATATTTTTCGAAACCTTTATATAAGGC 4 106 1 TTTCGAACTT 0.980434 -53 GATGTATTTTTTTTCACAGCCTTATATAAAGGT 4 124 0 TTTCACACTT 0.927021 -35 *** **** *** Masking position 3 Map Score: 16.8003 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 216 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 GTTTTGTCATCTCACCCATTTAAACC 1 7 1 TCATCTCACC 0.990107 -294 CTAGTAGCTATCAACACTCCGCGTGTTACG 1 121 0 TCAACACTCC 0.975376 -180 TTATCTGTTATCATGACACCTCGGTTTCTT 1 181 0 TCATGACACC 0.965562 -120 TAACCTTCCCACAACTCCCCCTT 2 4 0 ACAACTCCCC 0.983941 -135 TCCTGTAATTGCAAGTCCCCCTCTTTTTAG 2 110 0 GCAAGTCCCC 0.979366 -29 TCAACTCACCTCCAACCTTT 5 39 0 TCAACTCACC 0.994674 -10 ********** Masking position 3 Map Score: 8.20569 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 CCTGAAATAAAGAGAGGTTTAAATGGGTGAG 1 21 0 AAGAGGTTTA 0.928943 -280 TCAGCTTGCGACAGAGTGGGCGAACGCCAAA 1 76 0 AAGAGTGGGC 0.943424 -225 TTCCCAAAATATAGGGGATGCATTCCTAAGA 1 154 1 AAGGGGATGC 0.927666 -147 ATAATTCTCCATAGTGTTTGACTTCTAAAAA 1 215 0 AAGTGTTTGA 0.875241 -86 TTCTGGTTCCATAGAGTATTAAAAAATAACG 1 253 0 AAGAGTATTA 0.822814 -48 AGCGTAATCGAAAGAAGGTGATGTAG 1 285 1 AAGAAGGTGA 0.964287 -16 TATTGCCTAAAAAGAGGGGGACTTGCAATTA 2 104 1 AAGAGGGGGA 0.9853 -35 ACTTGCAATTACAGGAGGTGAACGA 2 124 1 AAGGAGGTGA 0.938612 -15 TTTTATTTTCGAAGAGTTTGAAAATTGCGCG 4 38 1 GAGAGTTTGA 0.887575 -121 * ********* Masking position 3 Map Score: 4.24331 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 5 CTCTCTTTATTTCAGGTTTCTTTAGCTGCC 1 36 1 TTCAGGTTTC 0.97374 -265 GCTTTCTGGTTTAAGCTTACCTAAAAATAT 2 53 0 TTAAGCTTAC 0.905209 -86 ACCAATTTTTTTAAGGTGACCTAAA 3 27 1 TTAAGGTGAC 0.962787 -15 TTTTAATGATTAAAGGTTTTCGAATTTTCA 4 83 0 TAAAGGTTTT 0.91672 -76 CAGCCTTATATAAAGGTTTCGAAAAATATT 4 111 0 TAAAGGTTTC 0.981634 -48 ********** Masking position 4 Map Score: 1.68427 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 84 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TAACAGATAAAAAGTTTTTAGAAGTCAAAC 1 201 1 AAAGTTTTTA 0.933253 -100 CTGCAATCGAGAAGTTTTTTAACCTTCCCA 2 23 0 GAAGTTTTTT 0.956788 -116 CTCGATTGCAGATATTTTTAGGTAAGCTTA 2 42 1 GATATTTTTA 0.876462 -97 AAAATTGGTGGAAGTGTTTATAAAT 3 6 0 GAAGTGTTTA 0.847443 -36 CACTTCCACCAATTTTTTTAAGGTGACCTA 3 20 1 AATTTTTTTA 0.793647 -22 GTAGAAAATTTTTTGAACTCCTTT 4 5 1 AAAATTTTTT 0.818327 -154 TTTAATCATTAAAATATTTTTCGAAACCTT 4 99 1 AAAATATTTT 0.469703 -60 CCTAACCTATGATGTATTTTTTTTCACAGC 4 137 0 GATGTATTTT 0.868413 -22 TTTAATTTTTTTTTAGAAAAATG 5 4 1 AATTTTTTTT 0.825648 -45 ********** Masking position 5 Map Score: 6.08656 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 161 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 7 ********** No masking Map Score: -1.46782e-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: -1.46782e-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: -1.46782e-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