AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i053_Altronate_Metabolism_ecoli_hinf_reg_300.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 uxaB 226 altronate oxidoreductase #2 b1522 111 orf, hypothetical protein #3 yneH 63 putative glutaminase #4 b1525 76 putative aldehyde dehydrogenase #5 uxaC 300 uronate isomerase Motif number 1 AATTGGTACGACAGGTTAGCAAACTTTAATA 1 169 0 ACAGGTAGCA 0.97048 -58 GCGGAAAACGACAAAATAGCATTCCCAGGGT 2 16 1 ACAAATAGCA 0.908633 -96 AATAGCATTCCCAGGGTACCTTTATTTGCCG 2 30 1 CCAGGTACCT 0.951121 -82 ACTGACCGAACCAAGATAGCATGTTCGCTGA 2 67 0 CCAAGTAGCA 0.989315 -45 GGCCAGAAATCCAGACTATCAATACTGACCG 2 90 0 CCAGATATCA 0.962314 -22 AAAAGACCTGCGAGTATATCAGAGCTGAATA 3 18 0 CGAGTTATCA 0.754793 -46 AAGTTGTATGACAAGTTATCTTTCTGCCGTC 5 46 0 ACAAGTATCT 0.941515 -255 ATCTAACTCACGAAAATATCTTCGGACTCTG 5 208 1 CGAAATATCT 0.830468 -93 GCGATGCTGACAAAGTTATCACACCAATTTC 5 239 0 CAAAGTATCA 0.889266 -62 CGCACCATAAGCAAGCTAGCTCACTCGTTGA 5 267 1 GCAAGTAGCT 0.923998 -34 ***** ***** Masking position 7 Map Score: 7.34509 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 557 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 CTGGATCATAAAGTGGTAGAACACATTGCATT 1 37 0 AAGTGTAAAC 0.989458 -190 AACCTGTTTGAATTGGTACGACAGGTTAGCAA 1 178 0 AATTGTAGAC 0.975918 -49 CAATTCAAACAGGTTGTATGACTAATCAGAAG 1 195 1 AGGTGTAGAC 0.989612 -32 TCACCTTTTAAAGTTGTATGACAAGTTATCTT 5 55 0 AAGTGTAGAC 0.995294 -246 ATTACTCTCAAAGTGGTAAATCTCGCTGCAGG 5 156 0 AAGTGTAATC 0.966135 -145 **** *** *** Masking position 7 Map Score: 4.75626 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 14 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TTAAACCATGATCCGCGCCACACTTTTCTC 1 89 1 ATCCGCGCCA 0.957981 -138 GTTCGCTGACAGCGGCGGCAAATAAAGGTA 2 46 0 AGCGGCGGCA 0.972533 -66 TATCAATACTGACCGAACCAAGATAGCATG 2 75 0 GACCGAACCA 0.887565 -37 CAAATCATAAGTCGACGGAATGCAAATTGC 5 15 0 GTCGACGGAA 0.918386 -286 TATGATTTGCGACGGCAGAAAGATAACTTG 5 36 1 GACGGCAGAA 0.966247 -265 GACATTACCTGACGACAGCAAGGCCAGTAC 5 118 1 GACGACAGCA 0.966264 -183 TCTCGCTGCAGGCCGCGCCAGTACTGGCCT 5 138 0 GGCCGCGCCA 0.985531 -163 ********** Masking position 10 Map Score: 3.45476 Number of sites scoring better than the average of aligned sites = 3377 Number in coding regions = 3253 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 4 AAAAGTGTGGCGCGGATCATGGTTTAATCG 1 86 0 CGCGGATCAT 0.980085 -141 CTGATATACTCGCAGGTCTTTTCAGACCTG 3 27 1 CGCAGGTCTT 0.994117 -37 ACTCCTGGACCGCAGGTCTGAAAAGACCTG 3 39 0 CGCAGGTCTG 0.99001 -25 TATGAAGATACGCAGATTTACTCTTGCTTT 4 55 0 CGCAGATTTA 0.92231 -22 TTTCTGCCGTCGCAAATCATAAGTCGACGG 5 27 0 CGCAAATCAT 0.954409 -274 ********** Masking position 7 Map Score: 2.52363 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 349 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 CATCTTTATTCATTACGCGCGAT 1 4 1 CTTTATTCAT 0.960009 -223 CCGCGCCACACTTTTCTCATAAAACTGCTC 1 101 1 CTTTTCTCAT 0.821569 -126 TAAAACTGCTCATTAATCATCAGGAGTTGA 1 120 1 CATTAATCAT 0.879466 -107 CGCCGAACCCCTGTTTTGATCAACTCCTGA 1 139 0 CTGTTTTGAT 0.832476 -88 GTTCCCTTCTGATTAGTCATACAACCTGTT 1 202 0 GATTAGTCAT 0.87564 -25 TTGGTTCGGTCAGTATTGATAGTCTGGATT 2 84 1 CAGTATTGAT 0.921081 -28 AGTGGCTTAATATTATTCATTTTAAAGCAA 4 32 1 TATTATTCAT 0.793228 -45 AATATTCCCACATTTGTGATGGCTCTCACC 5 82 0 CATTTGTGAT 0.893935 -219 TTTTAACTACGTTTATTGATCTAACTCACG 5 190 1 GTTTATTGAT 0.87272 -111 ********** Masking position 4 Map Score: 3.37339 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 473 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 6 CCACTTTATGATCCAGGAAAAGGCGTTTTT 1 53 1 ATCCAGGAAA 0.979956 -174 TCATGGTTTAATCGAGGAAAAACGCCTTTT 1 70 0 ATCGAGGAAA 0.95814 -157 GAATTGCGGAAAACGACAAAAT 2 3 1 ATTGCGGAAA 0.891104 -109 AAATAAAGGTACCCTGGGAATGCTATTTTG 2 27 0 ACCCTGGGAA 0.915279 -85 TAAGCCACTTATTCACGAATCGAGAATGCT 4 11 0 ATTCACGAAT 0.778995 -66 TATTGATCTAACTCACGAAAATATCTTCGG 5 203 1 ACTCACGAAA 0.958149 -98 ATATCTTCGGACTCTGGAAATTGGTGTGAT 5 223 1 ACTCTGGAAA 0.966521 -78 ********** Masking position 9 Map Score: 3.41049 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 533 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 ATCTTTATTCATTACGCGCGATTTGAATGCA 1 12 1 ATTACGCCGA 0.974471 -215 TATTAAGCCACTTATTCACGAATCGAGAATG 4 13 0 CTTATTCCGA 0.973393 -64 AGTTAAAAAAATTACTCTCAAAGTGGTAAAT 5 167 0 ATTACTCCAA 0.974098 -134 GTTTATTGATCTAACTCACGAAAATATCTTC 5 200 1 CTAACTCCGA 0.983059 -101 TTTCGTCTTCCTCTCAACGAGTGAGCT 5 284 0 CTTCCTCCAA 0.974471 -17 ******* *** Masking position 2 Map Score: 0.969239 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 89 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 AGCATGTTCGCTGACAGCGGCGGCAAATAAA 2 50 0 CTGACGCGGC 0.992707 -62 ACTATCAATACTGACCGAACCAAGATAGCAT 2 76 0 CTGACGAACC 0.942379 -36 TTTCTACTCCTGGACCGCAGGTCTGAAAAGA 3 43 0 TGGACGCAGG 0.959854 -21 GGGACATTACCTGACGACAGCAAGGCCAGTA 5 116 1 CTGACACAGC 0.982932 -185 AGTACTGGCGCGGCCTGCAGCGAGATTTACC 5 143 1 CGGCCGCAGC 0.992858 -158 TGTGATAACTTTGTCAGCATCGCACCATAAG 5 247 1 TTGTCGCATC 0.879894 -54 ***** ***** Masking position 5 Map Score: 0.536751 Number of sites scoring better than the average of aligned sites = 1611 Number in coding regions = 1552 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 ********** No masking Map Score: 8.47978e-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 10 ********** No masking Map Score: 8.47978e-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: 8.47978e-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