AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -ifnr_bbur_opreg_100.orf -g0.282 -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 = 0.282 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 BB0729 76 glutamate transporter (gltP) #2 BB0732 263 penicillin-binding protein (pbp-3) Motif number 1 AGTGCATTCTTTTTTAAACTTAAGGGGGTA 1 36 0 TTTTTAAACT 0.918968 -41 GCTTCAAATTGTTTTAAACAGTTTTACACA 2 12 1 GTTTTAAACA 0.985418 -252 GTTTTAAACAGTTTTACACAAATAAAAAAG 2 22 1 GTTTTACACA 0.993853 -242 TAGCTTAATTGTTTTAAACTTTTTTATTTG 2 40 0 GTTTTAAACT 0.985613 -224 TATTGTTATAATTTTACACTATGTAAACAG 2 172 0 ATTTTACACT 0.986444 -92 TATAACAATAATTTTACACTATAACAATCA 2 192 1 ATTTTACACT 0.986444 -72 ********** Masking position 5 Map Score: 14.5327 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 11 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 AACAAGATTAATTAATTTTTGAATATA 1 5 1 AGTTATTATT 0.988658 -72 CTCTTATATAAGCTTAGTGCATTCTTTTTTAAA 1 48 0 AGTTATGATT 0.978214 -29 AATTGTTTTAAACTTTTTTATTTGTGTAAAACT 2 31 0 AATTTTTTTT 0.931366 -233 GCGTGTTTATAGCTTAATTGTTTTAAACTTTTT 2 46 0 AGTTATTTTT 0.979668 -218 TTTTAAGGGTAGATTTATTGATTTTTGGCTAAG 2 78 0 AGTTTTTATT 0.991241 -186 GGATGATGGTATGTTTTTGATTTTAAGGGTAGA 2 98 0 ATTTTTGTTT 0.790104 -166 GCATTTTGTAAGTTTTGTTAATTGAAAGATGCT 2 140 0 AGTTTTTATT 0.991206 -124 ATCAACCCATAACATTATTAATTCTTATGCACT 2 218 1 AAATTTTATT 0.891031 -46 ATGCACTTATAGTATACTTTAGTAAAAAGT 2 244 1 AGATATTAGT 0.87147 -20 ** *** ** *** Masking position 8 Map Score: 11.2314 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 336 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 ATTTTTGAATATACCCCCTTAAGTTTAAAAA 1 25 1 ATACCCCTTA 0.965574 -52 ATTACCTCTTATATAAGCTTAGTGCATTCTT 1 55 0 ATAAAGCTTA 0.977844 -22 TTACACAAATAAAAAAGTTTAAAACAATTAA 2 35 1 AAAAAGTTTA 0.814684 -229 ATTAAGCTATAAACACGCTTAGCCAAAAATC 2 61 1 AAAACGCTTA 0.985913 -203 AAATCAATAAATCTACCCTTAAAATCAAAAA 2 87 1 ATCACCCTTA 0.990997 -177 TCTTTCAATTAACAAAACTTACAAAATGCTG 2 144 1 AACAAACTTA 0.911521 -120 CACTATAACAATCAACCCATAACATTATTAA 2 208 1 ATCACCCATA 0.958076 -56 *** ******* Masking position 1 Map Score: 4.9125 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 139 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AACAAGATTAATTAATTTTT 1 1 1 AACAAGATTA 0.864049 -76 TTTTTGAATATACCCCCTTAAGTTTAAAAA 1 26 1 TACCCCCTTA 0.928011 -51 TTACCTCTTATATAAGCTTAGTGCATTCTT 1 55 0 TATAAGCTTA 0.950435 -22 TTAAGCTATAAACACGCTTAGCCAAAAATC 2 62 1 AACACGCTTA 0.941137 -202 AATCAATAAATCTACCCTTAAAATCAAAAA 2 88 1 TCTACCCTTA 0.929342 -176 AAATCAAAAACATACCATCATCCACCTCTC 2 108 1 CATACCATCA 0.873011 -156 AGTGTAAAATTATAACAATAATTTTACACT 2 182 1 TATAACAATA 0.779098 -82 ACAATCAACCCATAACATTATTAATTCTTA 2 215 1 CATAACATTA 0.942257 -49 ********** Masking position 10 Map Score: 2.11458 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 256 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 ATTGTTTTAAACAGTTTTACACAAATAAAAA 2 19 1 ACATTTTACA 0.781453 -245 CACAAATAAAAAAGTTTAAAACAATTAAGCT 2 38 1 AAATTTAAAA 0.905768 -226 CTTAAAATCAAAAACATACCATCATCCACCT 2 104 1 AAACATACCA 0.981919 -160 TTCAATTAACAAAACTTACAAAATGCTGTTT 2 147 1 AAACTTACAA 0.902294 -117 ACATAGTGTAAAATTATAACAATAATTTTAC 2 178 1 AAATATAACA 0.982617 -86 CAATAATTTTACACTATAACAATCAACCCAT 2 197 1 ACATATAACA 0.969705 -67 TATAACAATCAACCCATAACATTATTAATTC 2 211 1 AACCATAACA 0.936371 -53 ACTTTTTACTAAAGTATACTATAAGTGCATA 2 243 0 AAATATACTA 0.895521 -21 *** ******* Masking position 1 Map Score: 6.27628 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 261 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 ********** No masking Map Score: -8.99385e-14 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: -8.99385e-14 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: -8.99385e-14 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