AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iompR_ecoli_hinf_300.orf -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 ompF 300 outer membrane protein 1a (Ia;b;F) #2 ompC 300 outer membrane protein 1b (Ib;c) #3 fadL 300 transport of long-chain fatty acids; sensitivity to phage T2 #4 HI0138 60 ribonuclease H (rnh) #5 HI0139 251 outer membrane protein P2 (ompP2) #6 HI0401 206 long-chain fatty acid transport protein (fadL) Motif number 1 CAAAGTTCCTTAAATTTTACTTTTGGTTACATAT 1 86 1 TAATTTTTTT 0.963962 -215 TTTTGGTTACATATTTTTTCTTTTTGAAACCAAA 1 106 1 AATTTTTTTT 0.964076 -195 AATAGTTCCGTAAATTTTTATTGACAGAACTTAT 1 229 1 TAATTTTTTA 0.823093 -72 AATCAATAACTTATTCTTAAGTATTTGACAGCAC 2 21 0 TATTCTTGTT 0.764551 -280 TTGTTTTAGATCATTTTTAAGTGTGATTTCGGTC 3 54 0 TATTTTTGTT 0.959886 -247 TGGATTCGGGTGAATTTTGTTTTAGATCATTTTT 3 70 0 TAATTTTTTA 0.823227 -231 AACCTCAATGATTTATTTTTATACAAACTATG 3 279 0 TATTTATTTT 0.783771 -22 TAAGTATTAAATATTTTTAGGTATCGAAAAATAT 5 29 0 AATTTTTGTT 0.941932 -223 ATGAATTTGATTATTTTTTATTCTGTTTTAGGTT 5 63 0 TATTTTTTTT 0.975364 -189 TCAATACTCCAAAATTTTAATTTTCTTGAAATCT 5 118 0 AAATTTTTTT 0.917999 -134 ATTGACATCAAAAATTTTTTTTGTAAAGATGCAG 5 147 1 AAATTTTTTT 0.947873 -105 CCTTATATGAATATTTTTGTGCATTTTATCATTT 6 19 1 AATTTTTGCT 0.81325 -188 GTGCATTTTATCATTTTTCTTTTTCCCCATAAAT 6 37 1 TATTTTTTTT 0.975367 -170 ATTGTTTTGTTGAATTTTTGTCATTTATGGGGAA 6 59 0 TAATTTTTCT 0.878116 -148 ATAATTGCCCAGATTTTTATTTATAACAAAGGGT 6 178 1 AATTTTTTTT 0.964058 -29 * ****** ** * Masking position 3 Map Score: 17.4468 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 121 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 GTTCCTTAAATTTTACTTTTGGTTACATAT 1 90 1 TTTTACTTTT 0.910214 -211 GGTTACATATTTTTTCTTTTTGAAACCAAA 1 110 1 TTTTTCTTTT 0.949786 -191 GTTCCCTTGCATTTACATTTTGAAACATCT 2 121 1 ATTTACATTT 0.804904 -180 ACTTTTAAGATGTTTCATTTATCGCTATAG 2 149 0 TGTTTCATTT 0.8524 -152 TGTTGGATTATTCTGCATTTTTGGGGAGAA 2 195 1 TTCTGCATTT 0.911209 -106 ATATGCCTTTATTTGCTTTTTTATGCCACT 2 264 0 ATTTGCTTTT 0.892931 -37 ATGAATATTTTTGTGCATTTTATCATTTTT 6 25 1 TTGTGCATTT 0.911209 -182 CATTTTATCATTTTTCTTTTTCCCCATAAA 6 40 1 TTTTTCTTTT 0.949786 -167 TTGTTGAATTTTTGTCATTTATGGGGAAAA 6 57 0 TTTGTCATTT 0.8524 -150 AGCAGGAGCTTTTTGCATTTAATGGATTGT 6 88 0 TTTTGCATTT 0.97774 -119 ********** Masking position 8 Map Score: 8.7582 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 276 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TATTTCCATAGAGACGTGATGATATTTACAGCAATTTTAA 1 34 0 GAATGATACA 0.986084 -267 CGTCTCTATGGAAATATGACGGTGTTCACAAAGTTCCTTA 1 58 1 GAATGACACA 0.994514 -243 AGTTTGAATGGAAAGATGCCTGCAGACACATAAAGACACC 1 178 1 GAATGCCACA 0.994403 -123 TTTTTTTTATGACACCTGCCACTGCCGTCAATAAGTTCTG 1 253 0 GAATGCCTCA 0.969551 -48 TGCAAAATCGGATAAGTGACCGAAATCACACTTAAAAATG 3 37 1 GAATGACACA 0.994514 -264 TTTCCATTAAAATACTTGCCATTCTACACAACAACCTTTT 4 27 1 AAATGCCACA 0.95202 -34 TAATTTTCTTGAAATCTGATCGAGATCACATTTTTTAAAT 5 95 0 GAATGATACA 0.986084 -157 TGGGGAAAAAGAAAAATGATAAAATGCACAAAAATATTCA 6 26 0 GAATGATACA 0.986084 -181 ** * **** *** Masking position 4 Map Score: 11.9932 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 9 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 ACGTGATGATATTTACAGCAATTTTAATCT 1 31 0 ATTTACAGCA 0.968575 -270 GTCAATAAAAATTTACGGAACTATTGATGA 1 224 0 ATTTACGGAA 0.890195 -77 GTAAATTTTTATTGACAGAACTTATTGACG 1 238 1 ATTGACAGAA 0.968575 -63 GACAGAACTTATTGACGGCAGTGGCAGGTG 1 251 1 ATTGACGGCA 0.981502 -50 TTCTTAAGTATTTGACAGCACTGAATGTCA 2 12 0 TTTGACAGCA 0.966516 -289 AAATCGGATAAGTGACCGAAATCACACTTA 3 41 1 AGTGACCGAA 0.86453 -260 TTCGCGCTCCTGTTACAGCACGTAACATAG 3 254 1 TGTTACAGCA 0.864666 -47 ATTTTGGAGTATTGACATCAAAAATTTTTT 5 137 1 ATTGACATCA 0.898013 -115 ********** Masking position 5 Map Score: 6.98631 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 237 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 GTTACATATTTTTTCTTTTTGAAACCAAAT 1 111 1 TTTTCTTTTT 0.848133 -190 AACCAAATCTTTATCTTTGTAGCACTTTCA 1 133 1 TTATCTTTGT 0.895777 -168 ACCCTCATGGTTTTTTTTATGACACCTGCC 1 273 0 TTTTTTTTAT 0.939627 -28 CCTCAATGATTTATTTTTATACAAACTATG 3 279 0 TTATTTTTAT 0.91402 -22 TGAATTTGATTATTTTTTATTCTGTTTTAG 5 66 0 TATTTTTTAT 0.686516 -186 ACATCAAAAATTTTTTTTGTAAAGATGCAG 5 151 1 TTTTTTTTGT 0.938481 -101 CCTTATATGAATATTTTTGTGCATTTTATC 6 19 1 ATATTTTTGT 0.594515 -188 ATTTTATCATTTTTCTTTTTCCCCATAAAT 6 41 1 TTTTCTTTTT 0.848133 -166 ACTCTATTCCTTATTTTTATTAGAGCTACG 6 125 0 TTATTTTTAT 0.91402 -82 TTGCCCAGATTTTTATTTATAACAAAGGGT 6 182 1 TTTTATTTAT 0.763657 -25 ********** Masking position 6 Map Score: 7.81962 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 171 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 6 GAAAGATGCCTGCAGACACATAAAGACACCAAAC 1 188 1 TGCAGAATAA 0.975076 -113 TATTGCGGAATGGCGAAATAAGCACCTAACATCA 2 77 0 TGGCGAAACA 0.946143 -224 GAAACATCTATAGCGATAAATGAAACATCTTAAA 2 142 1 TAGCGAATAA 0.799455 -159 TCCCCAAAAATGCAGAATAATCCAACACGAATAT 2 188 0 TGCAGAATCA 0.966476 -113 AGAATGGACTTGCCGACTGATTAATGAGGGTTAA 2 221 1 TGCCGAATAA 0.980533 -80 TTAATCAGTATGCAGTGGCATAAAAAAGCAAATA 2 251 1 TGCAGTATAA 0.860478 -50 TATCCGATTTTGCAGAATTAACAACTGGAGCAGC 3 17 0 TGCAGAAAAA 0.953507 -284 TCGTCCGTTTTGGCGATTGGACAATTCTATTGGA 5 182 1 TGGCGAGAAA 0.912484 -70 ACAATTCTATTGGAGAAAAGTTCAATCATAGATA 5 202 1 TGGAGAGTCA 0.927039 -50 ****** ** ** Masking position 1 Map Score: 3.86076 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 289 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 GTGCTGTCAAATACTTAAGAATAAGTTATTG 2 21 1 AACTTAAGAA 0.806419 -280 CATTCCGCAATAATCTTAAAAAGTTCCCTTG 2 99 1 TATCTTAAAA 0.855483 -202 GATAAATGAAACATCTTAAAAGTTTTAGTAT 2 156 1 AATCTTAAAA 0.89655 -145 GACCGAAATCACACTTAAAAATGATCTAAAA 3 54 1 AACTTAAAAA 0.854032 -247 CACTTAAAAATGATCTAAAACAAAATTCACC 3 65 1 TATCTAAAAC 0.848971 -236 TTTTCAAATATGATCTAAGAAACGCGATCCA 3 133 0 TATCTAAGAA 0.902989 -168 GGTCTGAGGTACATCTTAGAAATCAGACCAG 3 217 0 AATCTTAGAA 0.860541 -84 ATATTTTTCGATACCTAAAAATATTTAATAC 5 29 1 AACCTAAAAA 0.953993 -223 TTTAATACTTAAACCTAAAACAGAATAAAAA 5 52 1 AACCTAAAAC 0.899154 -200 ATAATCAAATTCATTTAAAAAATGTGATCTC 5 83 1 TATTTAAAAA 0.786717 -169 * ********* Masking position 6 Map Score: 4.72601 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 57 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 CAGAATTAACAACTGGAGCAGCACTTTC 3 9 0 AACTGGAGCA 0.918011 -292 AAATTTTGCCAGCTGGATCGCGTTTCTTAG 3 120 1 AGCTGGATCG 0.97729 -181 GCAACATTCCAGCTGGTCCGACCTATACTC 3 181 1 AGCTGGTCCG 0.984406 -120 TACGTGCTGTAACAGGAGCGCGAAGTGTAG 3 248 0 AACAGGAGCG 0.969002 -53 GTAAAGATGCAGCTCGTCCGTTTTGGCGAT 5 169 1 AGCTCGTCCG 0.93041 -83 ACGACTAGTTAGCAGGAGCTTTTTGCATTT 6 98 0 AGCAGGAGCT 0.85243 -109 ********** Masking position 1 Map Score: 2.03718 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 581 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 GACGGTGTTCACAAAGTTCCTTAAATTTTA 1 75 1 ACAAAGTTCC 0.885854 -226 CGCTACCGTGAAAGTGCTACAAAGATAAAG 1 141 0 AAAGTGCTAC 0.844643 -160 CAATAATCTTAAAAAGTTCCCTTGCATTTA 2 106 1 AAAAAGTTCC 0.955006 -195 GAAAGTGCTGCTCCAGTTGTT 3 2 1 AAAGTGCTGC 0.936825 -299 CATTAAATGCAAAAAGCTCCTGCTAACTAG 6 94 1 AAAAAGCTCC 0.96245 -113 AAAATAAGGAATAGAGTTGCACTCAATAGA 6 138 1 ATAGAGTTGC 0.84968 -69 TATTTATAACAAAGGGTTCCAA 6 195 1 AAAGGGTTCC 0.951802 -12 ********** Masking position 3 Map Score: 1.49802 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 213 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 AGACACCAAACTCTCATCAATAGTTCCGTAA 1 211 1 CTCTCATAAT 0.945462 -90 TATTTATTACCCTCATGGTTTTTTTTATGA 1 281 0 CCCTCATGTT 0.970044 -20 TACTGATTAACCCTCATTAATCAGTCGGCAA 2 230 0 CCCTCATAAT 0.97929 -71 GGAGGTGGCGCACTCATGGATTCGGGTGAAT 3 89 0 CACTCATGAT 0.985689 -212 GAGAAAAGTTCAATCATAGATAGTAAACAAC 5 214 1 CAATCATGAT 0.92957 -38 ******* *** Masking position 6 Map Score: 0.633646 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 TATAAGGAAATCATATAAATAGATTA 1 7 1 GAAATCATAT 0.893403 -294 TTTTCTTTTTGAAACCAAATCTTTATCTTT 1 121 1 GAAACCAAAT 0.923028 -180 GACACATAAAGACACCAAACTCTCATCAAT 1 202 1 GACACCAAAC 0.906929 -99 ATAAGTGACCGAAATCACACTTAAAAATGA 3 48 1 GAAATCACAC 0.965042 -253 GTACATCTTAGAAATCAGACCAGTGGCGAG 3 210 0 GAAATCAGAC 0.965042 -91 AAATCTGATCGAGATCACATTTTTTAAATG 5 94 0 GAGATCACAT 0.893148 -158 TAATTTTCTTGAAATCTGATCGAGATCACA 5 105 0 GAAATCTGAT 0.803795 -147 TTGGAGTATTGACATCAAAAATTTTTTTTG 5 140 1 GACATCAAAA 0.812425 -112 ********** Masking position 4 Map Score: 2.12165 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 177 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 GATTTTAACCTTGAATTATTATTGCTTGAT 2 51 1 TTGAATTATT 0.948761 -250 CATATTCGTGTTGGATTATTCTGCATTTTT 2 187 1 TTGGATTATT 0.967073 -114 CTGTTTTAGGTTTAAGTATTAAATATTTTT 5 45 0 TTTAAGTATT 0.778325 -207 TTTAAATGAATTTGATTATTTTTTATTCTG 5 72 0 TTTGATTATT 0.870426 -180 AATTAAAATTTTGGAGTATTGACATCAAAA 5 130 1 TTGGAGTATT 0.96055 -122 GTTTTGGCGATTGGACAATTCTATTGGAGA 5 188 1 TTGGACAATT 0.813553 -64 CTATCTATGATTGAACTTTTCTCCAATAGA 5 207 0 TTGAACTTTT 0.848936 -45 GATTGTTTTGTTGAATTTTTGTCATTTATG 6 64 0 TTGAATTTTT 0.871442 -143 ********** Masking position 5 Map Score: 5.26738 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 48 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 13 ********** No masking Map Score: 1.86405e-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: 1.86405e-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: 1.86405e-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