AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icytR_hpyl_opreg_300.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP1108 259 pyruvate ferredoxin oxidoreductase, gamma subunit #2 HP1112 109 adenylosuccinate lyase (purB) #3 HP1113 65 outer membrane protein (omp24) #4 HP1180 300 pyrimidine nucleoside transport protein (nupC) Motif number 1 AATCACACCTTAAATAATAACAAAGTTTAAA 1 36 1 TAAAAATAAC 0.82064 -224 AATAACAAAGTTTAAAATAAATATTAGTGGT 1 51 1 TTTAAATAAA 0.955872 -209 ACAAGCGTTCTTAATAAAAACCACTAATATT 1 70 0 TTAAAAAAAC 0.865806 -190 CGCTTGTCTTTTTAGAATAAATGGCCATAAA 1 94 1 TTTAAATAAA 0.955872 -166 TTTAGGAATTTTTATAGGAAAATGGGGGCAT 1 146 0 TTTAAGGAAA 0.85832 -114 AGCCTAGAATTATACAAGAAAAACTATTAAT 1 197 0 TATAAAGAAA 0.929115 -63 CTTAATATCGTATAAAATAAATTGAATTCAG 1 226 0 TATAAATAAA 0.948194 -34 TTTAAACCCCTTTAAAGTAACATAAATCCCA 2 68 1 TTTAAGTAAC 0.92078 -42 TAGTTTTGTTTTTATAAAAACGCGCC 3 6 0 TTTAAAAAAC 0.967932 -60 AAAACAAAACTATAAAATAAGCGCTAAAAAA 3 25 1 TATAAATAAG 0.811554 -41 GGAAGTAGGATTGATAATAAAAGTTTAATGT 4 41 1 TTGAAATAAA 0.90478 -260 TTTTAATGGATTTTTAAGAAAGGTTTTTGTA 4 74 1 TTTTAAGAAA 0.691655 -227 AGAATGAGATTATACAAAAACCTTTCTTAAA 4 86 0 TATAAAAAAC 0.942099 -215 CTGAGCTACCTTGACAAAAAAATAAAAGAAT 4 112 0 TTGAAAAAAA 0.891119 -189 TAATCTTTTTTTTAGCAAAACTAAACTACAA 4 239 1 TTTACAAAAC 0.810828 -62 **** ****** Masking position 9 Map Score: 17.7481 Number of sites scoring better than the average of aligned sites = 777 Number in coding regions = 610 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 AATCAAATCACACCTTAAATAATAACAAAG 1 31 1 CACCTTAAAT 0.967091 -229 TGTTATAAGACACATTAATAGTTTTTCTTG 1 184 1 CACATTAATA 0.835467 -76 GGTAATATGTCTCCTTAATATCGTATAAAA 1 240 0 CTCCTTAATA 0.947359 -20 CCCTTTAATTAAATCAAGGG 2 1 1 CCCTTTAATT 0.941192 -109 CGCAAAAAAGCCCCTTGATTTAATTAAAGG 2 12 0 CCCCTTGATT 0.992932 -98 TGCGATTTTTCCCCTTGATTCTTTAAACCC 2 47 1 CCCCTTGATT 0.992932 -63 ATTCTTTAAACCCCTTTAAAGTAACATAAA 2 64 1 CCCCTTTAAA 0.937712 -46 AAAACCCCTTAAAACTTCAATTTT 3 52 0 CCCCTTAAAA 0.983877 -14 CCCCTCTTGACACCATGATTTTGATTTAAA 4 191 1 CACCATGATT 0.896435 -110 ********** Masking position 6 Map Score: 12.8337 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 315 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 CCATACAGACTAAAATCAAATCACACCTTAA 1 18 1 TAAAATAAAT 0.953994 -242 AAATCACACCTTAAATAATAACAAAGTTTAA 1 35 1 TTAAATATAA 0.632983 -225 ATAACAAAGTTTAAAATAAATATTAGTGGTT 1 52 1 TTAAAAAAAT 0.874232 -208 CCATTTATTCTAAAAAGACAAGCGTTCTTAA 1 87 0 TAAAAAACAA 0.921767 -173 TAAAAATTCCTAAAAAGATATTGTTATAAGA 1 163 1 TAAAAAATAT 0.819035 -97 TAATATCGTATAAAATAAATTGAATTCAGCC 1 224 0 TAAAATAATT 0.688152 -36 TAAACCCCTTTAAAGTAACATAAATCCCATT 2 70 1 TAAAGTACAT 0.673835 -40 CGACAATCCTTAAAATCAAAATGGGATTTAT 2 89 0 TAAAATAAAA 0.948027 -21 CGCGTTTTTATAAAAACAAAACTATAAAATA 3 13 1 TAAAAAAAAA 0.941334 -53 AAAAATCCATTAAAATTACATTAAACTTTTA 4 58 0 TAAAATACAT 0.938372 -243 AAACCTTTCTTAAAAATCCATTAAAATTACA 4 69 0 TAAAAACCAT 0.645054 -232 TACCTTGACAAAAAAATAAAAGAATGAGATT 4 106 0 AAAAAAAAAA 0.594961 -195 TAAATGAAGTTTAAATCAAAATCATGGTGTC 4 199 0 TTAAATAAAA 0.874231 -102 TAAACGGATATTAAATGAAGTTTAAATCAAA 4 210 0 TTAAATAAGT 0.696391 -91 TTAGTTTTGCTAAAAAAAAGATTAAACGGAT 4 232 0 TAAAAAAAGA 0.823244 -69 ****** **** Masking position 4 Map Score: 15.0036 Number of sites scoring better than the average of aligned sites = 931 Number in coding regions = 699 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 4 TTTTCCTATAAAAATTCCTAAAAAGATATT 1 155 1 AAAATTCCTA 0.886553 -105 ACAAGGCGCAAAAAAGCCCCTTGATTTAAT 2 18 0 AAAAAGCCCC 0.977494 -92 AATCAAGGGGAAAAATCGCACAAGGCGCAA 2 37 0 AAAAATCGCA 0.957544 -73 TTAAAGTAACATAAATCCCATTTTGATTTT 2 79 1 ATAAATCCCA 0.958766 -31 TGTTTTTATAAAAACGCGCC 3 1 0 AAAACGCGCC 0.891963 -65 GAAAATGCCCAACTTTTGTCA 4 2 1 AAAATGCCCA 0.971905 -299 AACTTTTATTATCAATCCTACTTCCTCAAA 4 36 0 ATCAATCCTA 0.661216 -265 ********** Masking position 4 Map Score: 2.1425 Number of sites scoring better than the average of aligned sites = 1175 Number in coding regions = 1080 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 CCCCTTGATTCTTTAAACCCCTTTAAAGTA 2 57 1 CTTTAAACCC 0.982362 -53 CGACAATCCTTAAAATCAAAATGGGATT 2 92 0 CTTAAAATCA 0.848639 -18 GAGACCAGCGCTCTAAACCAGCTGAGCTAC 4 134 0 CTCTAAACCA 0.95875 -167 AAGAGGGGGACTTGAACCCCCGACCTCCGG 4 169 0 CTTGAACCCC 0.974881 -132 AAGTCCCCCTCTTGACACCATGATTTTGAT 4 186 1 CTTGACACCA 0.972938 -115 ********** Masking position 5 Map Score: 0.491947 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 156 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ATATTTATTTTAAACTTTGTTATTATTTAA 1 45 0 TAAACTTTGT 0.811949 -215 TTATACAAGAAAAACTATTAATGTGTCTTA 1 189 0 AAAACTATTA 0.874482 -71 TTATAAAAACAAAACTATAAAATAAGCGCT 3 20 1 AAAACTATAA 0.928686 -46 AAAACCCCTTAAAACTTCAATTTTTTAGCG 3 46 0 AAAACTTCAA 0.953435 -20 AAAATTACATTAAACTTTTATTATCAATCC 4 48 0 TAAACTTTTA 0.910191 -253 GATTTTGATTTAAACTTCATTTAATATCCG 4 207 1 TAAACTTCAT 0.920624 -94 TTAGCAAAACTAAACTACAATAGCCTTGCA 4 250 1 TAAACTACAA 0.953444 -51 ********** Masking position 4 Map Score: 4.04716 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 157 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 ********** No masking Map Score: 1.20325e-12 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: 1.20325e-12 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: 1.20325e-12 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