AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i055_Arginine_Metabolism_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 argF 300 ornithine carbamoyltransferase 2, chain F #2 ackA 300 acetate kinase #3 pta 74 phosphotransacetylase #4 yfcC 168 putative S-transferase #5 argI 161 ornithine carbamoyltransferase 1 Motif number 1 TCGCCATGTTCTCCGCCATTTTAGAAGCATA 1 40 1 CTCCGCCATT 0.978945 -261 TAATCGTATCTGCCTCCGATTCTCTGCAGAA 1 152 0 TGCCTCCGTT 0.929825 -149 CGGACGGGTTTGCCTCCACCTTTGTAAGAAA 1 193 1 TGCCTCCACT 0.970918 -108 TATTCATTTGCAACCCCATTTCACAATTCTT 1 222 0 CAACCCCATT 0.881559 -79 CTCGCATGGCGAACGCCACTTATTGAATTAA 1 274 0 GAACGCCATT 0.898755 -27 CGCATGATGACACCGACATTTATGATTAACA 2 223 0 CACCGACATT 0.951371 -78 TTTCACACCGCCAGCTCAGCTGGCGG 3 6 1 CACCGCCACT 0.995862 -69 TACAAAACAGCACCGCCAGCTGAGCTGGCGG 3 18 0 CACCGCCACT 0.995862 -57 CCTCTTTCGTTACCGCCGATTTGGCGGGTTA 3 47 0 TACCGCCGTT 0.979956 -28 CCACTGACATTGCCTCCACCTTTGTGACAAA 5 56 1 TGCCTCCACT 0.970918 -106 ******** ** Masking position 11 Map Score: 13.4371 Number of sites scoring better than the average of aligned sites = 1748 Number in coding regions = 1674 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 TCGCCATGTTCTCCGCCATTTTAGAAGCAT 1 40 1 CTCCGCCATT 0.991949 -261 TATTCATTTGCAACCCCATTTCACAATTCT 1 223 0 CAACCCCATT 0.896067 -78 TTCATATACATTATGCCATTGGCTGAAAAT 2 129 1 TTATGCCATT 0.756585 -172 TATCTTGAGTCTATGCCATTTTGCGTAATT 2 156 0 CTATGCCATT 0.940422 -145 CGCATGATGACACCGACATTTATGATTAAC 2 224 0 CACCGACATT 0.967629 -77 TTTCACACCGCCAGCTCAGCTGGCG 3 6 1 CACCGCCAGC 0.983924 -69 TACAAAACAGCACCGCCAGCTGAGCTGGCG 3 19 0 CACCGCCAGC 0.983924 -56 CATCAATGAATTGCGCCATCCCACTTTGCA 4 131 1 TTGCGCCATC 0.821064 -38 TGTCACACACCACTGACATTGCCTCCACCT 5 47 1 CACTGACATT 0.907378 -115 ********** Masking position 8 Map Score: 9.01483 Number of sites scoring better than the average of aligned sites = 3599 Number in coding regions = 3444 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 3 GAAATGGGGTTGCAAATGAATAATTACACA 1 231 1 TGCAAATGAA 0.941666 -70 ACTTATTGAATTAAAATTCACTTTATATGT 1 258 0 TTAAAATTCA 0.893595 -43 TGTGCAAATTCACAACTCAGCG 2 3 1 TGCAAATTCA 0.965542 -298 TCATTGAGTCGTCAAATTCATATACATTAT 2 113 1 GTCAAATTCA 0.875897 -188 TGCCATTGGCTGAAAATTACGCAAAATGGC 2 142 1 TGAAAATTAC 0.817634 -159 AAAGGATTAATGCAAATTAAGAGAATAAAA 4 76 0 TGCAAATTAA 0.969739 -93 GCTTTAGACTTGCAAATGAATAATCATCCA 5 94 1 TGCAAATGAA 0.941666 -68 CCTCAATGAATTAAAATTCAATTTATATGG 5 121 0 TTAAAATTCA 0.893595 -41 ********** Masking position 5 Map Score: 8.20042 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 199 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 TAATGAAGTAAGGCAGCAAGCCTCGCCATG 1 18 1 AGGCAGCAAG 0.880935 -283 TAATCCTTAAAATCATAAAGAAGGCCAATC 1 69 1 AATCATAAAG 0.946185 -232 AACCAGGTCGAGTCAGAAATGAGAATGATT 1 95 0 AGTCAGAAAT 0.953201 -206 TTCTCTGCAGAAGCAGAAAGACATTGGATC 1 134 0 AAGCAGAAAG 0.984799 -167 GCATGATGTTAATCATAAATGTCGGTGTCA 2 217 1 AATCATAAAT 0.931758 -84 CGGATATCTGAACCGGAAATAATCACTATT 4 39 1 AACCGGAAAT 0.944091 -130 GAGAATAAAAAACCGGAAATAGTGATTATT 4 56 0 AACCGGAAAT 0.944091 -113 TAAGCAAGATAATCAGAAAGGATTAATGCA 4 92 0 AATCAGAAAG 0.981701 -77 TGCAAGTCTAAAGCATAAATCTTTGTCACA 5 78 0 AAGCATAAAT 0.94283 -84 ********** Masking position 8 Map Score: 10.6552 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 270 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 AGCCTCGCCATGTTCTCCGCCATTTTAGAAG 1 36 1 TGTTTCCGCC 0.961268 -265 GTGAAAATAATCGTATCTGCCTCCGATTCTC 1 159 0 TCGTTCTGCC 0.736267 -142 ACGGACGGGTTTGCCTCCACCTTTGTAAGAA 1 192 1 TTGCTCCACC 0.955291 -109 TATCCTCGCATGGCGAACGCCACTTATTGAA 1 278 0 TGGCAACGCC 0.982034 -23 TTTCACACCGCCAGCTCAGCTG 3 2 1 TTCAACCGCC 0.798848 -73 GGTGCTGTTTTGTAACCCGCCAAATCGGCGG 3 35 1 TGTACCCGCC 0.934893 -40 TTATCCTCTTTCGTTACCGCCGATTTGGCGG 3 51 0 TCGTACCGCC 0.969655 -24 ATACTCTTATTGTCACACACCACTGACATTG 5 37 1 TGTCCACACC 0.807345 -125 ACCACTGACATTGCCTCCACCTTTGTGACAA 5 55 1 TTGCTCCACC 0.955291 -107 ATCCCTCCTGTGGCTAACGCCTCAATGAATT 5 139 0 TGGCAACGCC 0.982034 -23 **** ****** Masking position 1 Map Score: 7.00774 Number of sites scoring better than the average of aligned sites = 2506 Number in coding regions = 2398 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 6 ATGCTTCTAAAATGGCGGAGAACATGGCGAGG 1 38 0 AATGCGGGAA 0.679022 -263 GCCTCCGATTCTCTGCAGAAGCAGAAAGACAT 1 140 0 CTCGCAGAGC 0.879746 -161 TCTGCAGAGAATCGGAGGCAGATACGATTATT 1 153 1 ATCGAGGAGA 0.862864 -148 AAATTCACAACTCAGCGGGACAACGTTCAAAA 2 16 1 CTCGCGGACA 0.968168 -285 TGCAAAAAAAATTTGCAGTGCATGATGTTAAT 2 198 1 ATTGCAGGCA 0.945367 -103 CGGGTTACAAAACAGCACCGCCAGCTGAGCTG 3 22 0 AACGCACGCC 0.916065 -53 AACCCGCCAAATCGGCGGTAACGAAAGAGGAT 3 48 1 ATCGCGGAAC 0.919009 -27 CGGTTCAGATATCCGCAGCGCAAAGCTGCGGA 4 22 0 ATCGCAGGCA 0.991175 -147 CGCTGCGGATATCTGAACCGGAAATAATCACT 4 34 1 ATCGAACGGA 0.776457 -135 TATCTTGCTTAACTGCGCTGCATCAATGAATT 4 111 1 AACGCGCGCA 0.958911 -58 CAATAAGAGTATCGGCAGGACATTAAGAGGAA 5 17 0 ATCGCAGACA 0.983349 -145 *** **** *** Masking position 5 Map Score: 6.70975 Number of sites scoring better than the average of aligned sites = 3707 Number in coding regions = 3538 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 7 TTTATGATTTTAAGGATTATGCTTCTAAAAT 1 57 0 TAGGATTATG 0.812557 -244 GAGTCAGAAATGAGAATGATTGGCCTTCTTT 1 85 0 TGGAATGATT 0.85061 -216 TTTTCAGCCAATGGCATAATGTATATGAATT 2 127 0 ATGCATAATG 0.780186 -174 GCAAATTTTTTTTGCATGATGGAAGAAATAT 2 183 0 TTGCATGATG 0.977727 -118 AAAAATTTGCAGTGCATGATGTTAATCATAA 2 204 1 AGGCATGATG 0.987802 -97 CATAGAGCGTAGCGCATGATGACACCGACAT 2 235 0 AGGCATGATG 0.987802 -66 AGCGCAAAGCTGCGGATGATGACGAGA 4 7 0 TGGGATGATG 0.989991 -162 ATTCAATTTATATGGATGATTATTCATTTGC 5 105 0 TAGGATGATT 0.884314 -57 ** ******** Masking position 6 Map Score: 6.43061 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 569 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 TTCTCATTTCTGACTCGACCTGGTTGTAGA 1 100 1 TGACTCGACC 0.963335 -201 TAATCGTATCTGCCTCCGATTCTCTGCAGA 1 153 0 TGCCTCCGAT 0.936753 -148 CGGACGGGTTTGCCTCCACCTTTGTAAGAA 1 193 1 TGCCTCCACC 0.99448 -108 TAGCGCATGATGACACCGACATTTATGATT 2 227 0 TGACACCGAC 0.970267 -74 TTTCACACCGCCAGCTCAGCTG 3 3 1 TCACACCGCC 0.956791 -72 CCACTGACATTGCCTCCACCTTTGTGACAA 5 56 1 TGCCTCCACC 0.99448 -106 ********** Masking position 1 Map Score: 6.03997 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 446 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 GCTGCCTTACTTCATTACTTCAGC 1 4 0 TTCATTACTC 0.944811 -297 GTAGTACATATTCATTGAGTCGTCAAATTCA 2 102 1 TTCATTGAGC 0.989297 -199 TCTCTTAATTTGCATTAATCCTTTCTGATTA 4 82 1 TGCATTAATC 0.944811 -87 GATGGCGCAATTCATTGATGCAGCGCAGTTA 4 120 0 TTCATTGATC 0.988456 -49 TGAATTTTAATTCATTGAGGCGTTAGCCACA 5 131 1 TTCATTGAGC 0.989297 -31 ********* * Masking position 6 Map Score: 3.1404 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 14 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 TTCACACACGGACGGGTTTGCCTCCACCTTTG 1 185 1 GACGGTTGCC 0.991329 -116 AATTCAATAAGTGGCGTTCGCCATGCGAGGAT 1 276 1 GTGGGTTGCC 0.995557 -25 AGGACATTAAGAGGAATGAGCC 5 1 0 GAGGATGGCC 0.988035 -161 GGCAATGTCAGTGGTGTGTGACAATAAGAGTA 5 38 0 GTGGGTGGAC 0.983098 -124 TTAATTCATTGAGGCGTTAGCCACAGGAGGGA 5 137 1 GAGGGTTGCC 0.997519 -25 **** *** *** Masking position 7 Map Score: 5.42982 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 71 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 11 GTTCGCCATGCGAGGATAAA 1 291 1 CGAGGATAAA 0.983659 -10 ATAATTGATACGTGGCTAAAAAAACGTCAG 2 271 0 CGTGGCTAAA 0.844483 -30 CGGTAACGAAAGAGGATAAACC 3 63 1 AGAGGATAAA 0.986415 -12 ATGCAAATTAAGAGAATAAAAAACCGGAAA 4 67 0 AGAGAATAAA 0.932949 -102 AGATAATCAGAAAGGATTAATGCAAATTAA 4 86 0 AAAGGATTAA 0.858216 -83 TTGCAAGTCTAAAGCATAAATCTTTGTCAC 5 79 0 AAAGCATAAA 0.874502 -83 ********** Masking position 7 Map Score: 1.92514 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 177 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 12 AATTAAAATTCACTTTATATGTGTAATTAT 1 250 0 CACTTTATAT 0.921586 -51 ACGTTCAAAACATTTTGTCTTCCATACCCA 2 38 1 CATTTTGTCT 0.895983 -263 GAGTCTATGCCATTTTGCGTAATTTTCAGC 2 150 0 CATTTTGCGT 0.912296 -151 TTTATTCTCTTAATTTGCATTAATCCTTTC 4 77 1 TAATTTGCAT 0.749694 -92 TGCGCCATCCCACTTTGCATACTTACCACT 4 142 1 CACTTTGCAT 0.981142 -27 GCATACTTACCACTTTGTTTT 4 158 1 CACTTTGTTT 0.929052 -11 AATTAAAATTCAATTTATATGGATGATTAT 5 113 0 CAATTTATAT 0.83913 -49 ********** Masking position 2 Map Score: 1.54601 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 275 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 13 ********** No masking Map Score: 2.11274e-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 14 ********** No masking Map Score: 2.11274e-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 15 ********** No masking Map Score: 2.11274e-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