AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_aquae_reg_300.orf -o00950_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 fabZ 23 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase #2 aq_260 300 hypothetical protein #3 aspC4 80 aminotransferase (AspC family) #4 aspC3 31 aminotransferase (AspC family) #5 mtfB 300 mannosyltransferase B #6 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #7 aq_1510 113 putative protein #8 aspC1 260 aspartate aminotransferase #9 pepA_carB2 26 pepA: leucine aminopeptidase, carB2: carbamoyl-phosphate synthase large subunit Motif number 1 ATGAGTTTTCCACAATTCTCCAC 2 3 0 CCAATTCTCC 0.670585 -298 TATAACGACACAATCTACTCAAAAGAAAACC 2 44 1 CATCTACTCA 0.804234 -257 CTTTCTCCTCCTTTATTTAAG 3 1 1 CTTCTCCTCC 0.989358 -80 TCCGCTACCTCCTTTAAAGTTTTTA 3 66 0 CACCTCCTTT 0.9442 -15 CCATACACCACTTTCTCCTTCCAC 5 4 0 CTTCTCCTTC 0.97244 -297 CTTTTGCTCACTACATACTCTCCAAACCATC 5 76 0 CACATACTCT 0.735253 -225 TATCCGATATCATGCTCCTTTGGGACTTGGA 6 12 1 CTGCTCCTTT 0.820958 -52 CGCTCTCCTCCGAAAGTAGAG 7 1 1 CCTCTCCTCC 0.991714 -113 AATAAAATTACACTCTACTTTCGGAGGAGAG 7 13 0 CCTCTACTTT 0.89055 -101 ATTAACTTGACACACTTCTTCAAAATGAATA 7 40 0 CCACTTCTTC 0.780954 -74 ATACCCTTCTCTATCTCCTCGAGCTTCTTTG 8 112 1 CATCTCCTCG 0.954919 -149 ATAGCCTTAGCGAACTCCTCCAAGGACATTC 8 154 1 CAACTCCTCC 0.978496 -107 GGACATTCCCCTTTCTTCTCTGATCTTCCTT 8 177 1 CTTCTTCTCT 0.927476 -84 CTCTGATCTTCCTTATCCTCTCTCCCACTCC 8 194 1 CTTATCCTCT 0.926221 -67 AATCATGGCTCCACCTCCTCCCTTTTTAATT 8 225 1 CACCTCCTCC 0.986216 -36 ACTGTTTATACTATATACTTTAA 9 3 0 CATATACTTT 0.653427 -24 * ********* Masking position 6 Map Score: 19.6833 Number of sites scoring better than the average of aligned sites = 1084 Number in coding regions = 989 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 AACTTATGAGTTTTCCACAATTCTCCAC 2 9 0 TTTTCCACAA 0.988084 -292 TTTTCCACATTTATCCACATTTTTAACGTA 2 92 0 TTATCCACAT 0.965401 -209 ACTTAAGAAGTTTTCCACATTTATCCACAT 2 102 0 TTTTCCACAT 0.991128 -199 TTTCCACAACTTTTCCACATGAACAACTTA 2 186 0 TTTTCCACAT 0.991128 -115 TCCCGAAAAACTTTCCACAACTTTTCCACA 2 197 0 CTTTCCACAA 0.969545 -104 GATTATTTTCTCGTCCACATCAACTCCACC 5 192 0 TCGTCCACAT 0.927207 -109 GGCTATAGGCATTTCCACAAAGAAGCTCGA 8 130 0 ATTTCCACAA 0.954862 -131 ********** Masking position 7 Map Score: 12.0661 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 24 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 GTGTCGTTATATGAACAACTTATGAGTTTTC 2 24 0 ATGAACACTT 0.991972 -277 ACCACGGTGTATAAACTACTTACGTTAAAAA 2 72 1 ATAAACACTT 0.987436 -229 GTTTCGTAGTATGAATAACTTAAGAAGTTTT 2 118 0 ATGAATACTT 0.976613 -183 CTTACGAATTATAAATAACTTAAGTTGTTCA 2 166 1 ATAAATACTT 0.963714 -135 ACTTTTCCACATGAACAACTTAAGTTATTTA 2 177 0 ATGAACACTT 0.991972 -124 ATCTGTTGCCATACACCACTTTCTCCTTCCA 5 12 0 ATACACACTT 0.966375 -289 ****** **** Masking position 5 Map Score: 8.80726 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 = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 CATTTATCCACATTTTTAACGTAAGTAGTT 2 85 0 CATTTTTAAC 0.865609 -216 ACAATCCGGTGACTTAAAACTTACGAATTA 2 147 1 GACTTAAAAC 0.938719 -154 TCATTATCCCAACTTTAAACACATGCTCAT 5 124 0 AACTTTAAAC 0.890063 -177 CAGAGCATGGAATTTATAACCCTCTGGGTG 5 253 1 AATTTATAAC 0.958071 -48 CCCTCTGGGTGATTTTTAACTGAATACCTA 5 272 1 GATTTTTAAC 0.945204 -29 GTGTCAAGTTAATTTAAAACACTTTTTGAT 7 58 1 AATTTAAAAC 0.954136 -56 TACCTCTAGAGATTTATAACAAAAATCAAA 7 82 0 GATTTATAAC 0.963772 -32 CTCCCTTTTTAATTTAAAATTTTAAGGAA 8 242 1 AATTTAAAAT 0.716671 -19 ********** Masking position 8 Map Score: 6.24488 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 100 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 GTGTATGGCAACAGATGGCTTATTGAGAGC 5 27 1 ACAGATGGCT 0.989988 -274 TCAACCTTCGAGCGATGGTTTGGAGAGTAT 5 63 1 AGCGATGGTT 0.931221 -238 AGGTGGTATGAGAGATGGCTGTGGTGGAGT 5 170 1 AGAGATGGCT 0.991774 -131 TAAAAATCACCCAGAGGGTTATAAATTCCA 5 260 0 CCAGAGGGTT 0.897003 -41 TGGCACTGGGAGAGAGGGCAAAAGAGCCCG 8 17 0 AGAGAGGGCA 0.958054 -244 AACGTGGATTACAGGTGGCTGGCACTGGGA 8 36 0 ACAGGTGGCT 0.968822 -225 TCGAGGAGATAGAGAAGGGTATCTCCAGAC 8 104 0 AGAGAAGGGT 0.919691 -157 ********** Masking position 4 Map Score: 4.43202 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 65 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ATCTCTCATACCACCTGACCTCATCATCAT 5 156 0 CCACCTGACC 0.96056 -145 CACATCAACTCCACCACAGCCATCTCTCAT 5 177 0 CCACCACAGC 0.978468 -124 CTGTTATGATCTCCCTGACCTGATTATTTT 5 213 0 CTCCCTGACC 0.960561 -88 TAGATCAGTTACACCACTGCAAGTCCAAGT 6 36 0 ACACCACTGC 0.875465 -28 TTTGCCCTCTCTCCCAGTGCCAGCCACCTG 8 25 1 CTCCCAGTGC 0.978468 -236 CTTATCCTCTCTCCCACTCCAATCATGGCT 8 205 1 CTCCCACTCC 0.978468 -56 ********** Masking position 5 Map Score: 2.42022 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 107 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 CGGTGTATAAACTACTTACGTTAAAAATGTGG 2 76 1 ACTTTACGTT 0.884925 -225 AATGTGGAAAACTTCTTAAGTTATTCATACTA 2 111 1 ACTTTAAGTT 0.961526 -190 TTCCACATGAACAACTTAAGTTATTTATAATT 2 172 0 ACATTAAGTT 0.817474 -129 AAATTTCAAAACCCATTGATTTTCAAGCTTTT 2 226 0 ACCTTGATTT 0.820051 -75 ACTATTTATTTTGTATTAATAA 2 289 0 ACTTTATTTT 0.917301 -12 CTTTCTCCTCCTTTATTTAAGATAAGTG 3 7 1 CCTTTTATTT 0.83841 -74 ATCTCCCTGACCTGATTATTTTCTCGTCCACA 5 203 0 CCTTTATTTT 0.90147 -98 AATTTAAAACACTTTTTGATTTTTGTTATAAA 7 68 1 ACTTTGATTT 0.944926 -46 CCACCTCCTCCCTTTTTAATTTAAAATTTTAA 8 235 1 CCTTTAATTT 0.961526 -26 *** ******* Masking position 6 Map Score: 3.49852 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 79 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 8 GGCTTATTGAGAGCTTCTTTTCAACCTTCG 5 43 1 GAGCTTCTTT 0.983928 -258 AATCTGTTATGATCTCCCTGACCTGATTAT 5 216 0 GATCTCCCTG 0.95468 -85 CTATCTCCTCGAGCTTCTTTGTGGAAATGC 8 122 1 GAGCTTCTTT 0.983928 -139 TTTCTTCTCTGATCTTCCTTATCCTCTCTC 8 188 1 GATCTTCCTT 0.983928 -73 ********** Masking position 5 Map Score: 0.851797 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 52 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ********** No masking Map Score: -7.50743e-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: -7.50743e-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 11 ********** No masking Map Score: -7.50743e-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