AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i055_Arginine_Metabolism_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 argF 300 ornithine carbamoyltransferase 2, chain F #2 yfcC 168 putative S-transferase #3 argI 161 ornithine carbamoyltransferase 1 #4 HI0594 104 conserved hypothetical transmembrane protein #5 HI0596 300 ornithine carbamoyltransferase (arcB) Motif number 1 GAAGGCCAATCATTCTCATTTCTGACTCGACCTGG 1 88 1 CATTCCATTA 0.982439 -213 GACGGGTTTGCCTCCACCTTTGTAAGAAAGAATTG 1 195 1 CCTCCCCTTA 0.987568 -106 TATTCATTTGCAACCCCATTTCACAATTCTTTCTT 1 218 0 CAACCCATTA 0.993062 -83 ATGAATTGCGCCATCCCACTTTGCATACTTACCAC 2 136 1 CCATCCATTA 0.982091 -33 ACTGACATTGCCTCCACCTTTGTGACAAAGATTTA 3 58 1 CCTCCCCTTA 0.987568 -104 TTGGTTAAACCAACCGCACTTTTTACCTTGAGAAT 4 35 0 CAACCCATTA 0.993062 -70 AATGTTTTACCAACCGCACTTTAAACGTTAAACAT 4 68 1 CAACCCATTA 0.993062 -37 TACATACTGGCATTACCAGTTGAAAAACGACAACA 5 170 1 CATTACATTA 0.862019 -131 ***** ** ** * Masking position 15 Map Score: 10.9504 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 47 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 GTCGAGTCAGAAATGAGAATGATTGGCCTTC 1 88 0 AAATGGAATG 0.947521 -213 TCTTTCTTACAAAGGTGGAGGCAAACCCGTC 1 195 0 AAAGGGGAGG 0.981747 -106 AAGAATTGTGAAATGGGGTTGCAAATGAATA 1 222 1 AAATGGGTTG 0.988529 -79 TAAGTATGCAAAGTGGGATGGCGCAATTCAT 2 136 0 AAGTGGATGG 0.971659 -33 TCTTTGTCACAAAGGTGGAGGCAATGTCAGT 3 58 0 AAAGGGGAGG 0.981747 -104 TCAAGGTAAAAAGTGCGGTTGGTTTAACCAA 4 39 1 AAGTGGGTTG 0.990483 -66 TTAACGTTTAAAGTGCGGTTGGTAAAACATT 4 68 0 AAGTGGGTTG 0.990483 -37 ***** ***** Masking position 2 Map Score: 10.3773 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 86 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 TGATTGGCCTTCTTTATGATTTTAAGGATTAT 1 68 0 TCTTTTGTTT 0.970647 -233 CGATCCAATGTCTTTCTGCTTCTGCAGAGAAT 1 133 1 TCTTTTGTTC 0.97557 -168 ATCATCCGCAGCTTTGCGCTGCGGATATCTGA 2 18 1 GCTTTCGTGC 0.813767 -151 AAATAGTGATTATTTCCGGTTCAGATATCCGC 2 38 0 TATTTCGTTC 0.936987 -131 AAATAATCACTATTTCCGGTTTTTTATTCTCT 2 55 1 TATTTCGTTT 0.924889 -114 TTGCATTAATCCTTTCTGATTATCTTGCTTAA 2 91 1 CCTTTTGTTA 0.894695 -78 TTGTGACAAAGATTTATGCTTTAGACTTGCAA 3 77 1 GATTTTGTTT 0.851735 -85 AGCGAGCTCCTTATGTTTAACGTTTAAAG 4 86 0 TCCTTTGTTA 0.93386 -19 TGTTTTAGTTTATTTTTGATGAAGAGGAATGT 5 32 0 TATTTTGTGA 0.864701 -269 AACTAAAACATATTTTCGTTTAAATTCATCTA 5 54 1 TATTTCGTTA 0.938159 -247 ATAATCTAACTCTTTATTGTTATTTGTTTGAT 5 95 0 TCTTTTTTTA 0.745105 -206 AATAATCTCCTTGTGTTTTGACTATACAT 5 282 0 TCCTTTGTTT 0.919746 -19 ***** ** *** Masking position 5 Map Score: 9.40023 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 456 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 4 CAAAGGTGGAGGCAAACCCGTCCGTGTGTGAA 1 185 0 GGCAACCGTC 0.987383 -116 ATCCTCGCATGGCGAACGCCACTTATTGAATT 1 276 0 GGCAACCCAC 0.993724 -25 GGCTCATTCCTCTTAATGTCCT 3 1 1 GGCCATCCTC 0.994196 -161 TACTCTTATTGTCACACACCACTGACATTGCC 3 38 1 GTCCACCCAC 0.982241 -124 TCCCTCCTGTGGCTAACGCCTCAATGAATTAA 3 137 0 GGCAACCCTC 0.997064 -25 AGTATAGATAGACACATTCCTCTTCATCAAAA 5 19 1 GACCATCCTC 0.967525 -282 *** *** **** Masking position 6 Map Score: 8.09425 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 88 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TCACTTTATATGTGTAATTATTCATTTGCAACC 1 238 0 TGTATTATTC 0.980558 -63 ACATATAAAGTGAATTTTAATTCAATAAGTGGC 1 258 1 TGTTTAATTC 0.980558 -43 TCACTATTTCCGGTTTTTTATTCTCTTAATTTG 2 61 1 CGTTTTATTC 0.972732 -108 TCAATTTATATGGATGATTATTCATTTGCAAGT 3 101 0 TGTATTATTC 0.980558 -61 CCATATAAATTGAATTTTAATTCATTGAGGCGT 3 121 1 TGTTTAATTC 0.980558 -41 AAGAGGAATGTGTCTATCTATACTTAATAAAA 5 10 0 TGTTCTATAC 0.881036 -291 TCTCGAATGATGTATGTTTATTCCCCAATGTAT 5 255 1 TGTTTTATTC 0.991448 -46 ** * ******* Masking position 10 Map Score: 7.13353 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 35 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 GGCCTTCTTTATGATTTTAAGGATTATGCT 1 65 0 ATGATTTTAA 0.74189 -236 AGACATTGGATCGAATTCTACAACCAGGTC 1 116 0 TCGAATTCTA 0.64932 -185 CACATATAAAGTGAATTTTAATTCAATAAG 1 257 1 GTGAATTTTA 0.939271 -44 TCCATATAAATTGAATTTTAATTCATTGAG 3 120 1 TTGAATTTTA 0.894453 -42 CTAATAGTAGATGAATTTAAACGAAAATAT 5 63 0 ATGAATTTAA 0.842183 -238 TGTTATTTGTTTGATTTCTAATAGTAGATG 5 80 0 TTGATTTCTA 0.774161 -221 TTAGTATTATTAGAATTTAATAAAATAATC 5 121 0 TAGAATTTAA 0.745058 -180 ATTTTATTGCGAGATTTTTAGTATTATTAG 5 138 0 GAGATTTTTA 0.840781 -163 TGCCAGTATGTAGAATTTTATTGCGAGATT 5 152 0 TAGAATTTTA 0.829338 -149 ********** Masking position 6 Map Score: 6.19869 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 127 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 GAGTCAGAAATGAGAATGATTGGCCTTCTT 1 86 0 TGAGAATGAT 0.892079 -215 TTTCTGCTTCTGCAGAGAATCGGAGGCAGA 1 145 1 TGCAGAGAAT 0.849723 -156 CGTCCGTGTGTGAAAATAATCGTATCTGCC 1 169 0 TGAAAATAAT 0.799281 -132 GAAATGGGGTTGCAAATGAATAATTACACA 1 231 1 TGCAAATGAA 0.973852 -70 AGCGCAAAGCTGCGGATGATGACGAGA 2 8 0 TGCGGATGAT 0.953975 -161 AAAGGATTAATGCAAATTAAGAGAATAAAA 2 76 0 TGCAAATTAA 0.852423 -93 GCTTTAGACTTGCAAATGAATAATCATCCA 3 94 1 TGCAAATGAA 0.973852 -68 TTATTTTTGATGAAGAGGAATGTGTCTATC 5 25 0 TGAAGAGGAA 0.890135 -276 ********** Masking position 6 Map Score: 5.06096 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 359 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 8 AAGGCAGCAAGCCTCGCCATGTTCTCCGCC 1 27 1 GCCTCGCCAT 0.934192 -274 GGACGGGTTTGCCTCCACCTTTGTAAGAAA 1 194 1 GCCTCCACCT 0.956622 -107 TTATTCATTTGCAACCCCATTTCACAATTC 1 224 0 GCAACCCCAT 0.978971 -77 AATGAATTGCGCCATCCCACTTTGCATACT 2 135 1 GCCATCCCAC 0.937736 -34 CACTGACATTGCCTCCACCTTTGTGACAAA 3 57 1 GCCTCCACCT 0.956622 -105 ATTGGTTAAACCAACCGCACTTTTTACCTT 4 41 0 CCAACCGCAC 0.942149 -64 CAATGTTTTACCAACCGCACTTTAAACGTT 4 67 1 CCAACCGCAC 0.942149 -38 ********** Masking position 8 Map Score: 2.34937 Number of sites scoring better than the average of aligned sites = 943 Number in coding regions = 880 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 9 TGTTCTCCGCCATTTTAGAAGCATAATCCTTAAAATC 1 46 1 CATTTAATAT 0.9797 -255 AATTAAAATTCACTTTATATGTGTAATTATTCATTTG 1 243 0 CATTTAATAT 0.9797 -58 TGATGCAGCGCAGTTAAGCAAGATAATCAGAAAGGAT 2 99 0 CATTAACTAT 0.949294 -70 AATTAAAATTCAATTTATATGGATGATTATTCATTTG 3 106 0 CATTTAATAT 0.9797 -56 ACCAACCGCACTTTTTACCTTGAGAATGGCTTCCCAA 4 25 0 CTTTTACGAT 0.872537 -80 CAACAAATTTCATTTTACCTCTCTTATAATGCAACTG 5 200 1 CATTTACTAT 0.986994 -101 ** **** * * ** Masking position 7 Map Score: 0.203803 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 ********** No masking Map Score: 5.35339e-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: 5.35339e-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 12 ********** No masking Map Score: 5.35339e-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