AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_ecoli_bsub_100.orf -o334_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #2 prfA 41 peptide chain release factor RF-1 #3 yrdD 62 putative DNA topoisomerase #4 smf_2 53 orf, fragment 2 #5 smf_1 129 orf, fragment 1 #6 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #7 prfA 125 peptide chain release factor 1 Motif number 1 AAGGGGGCGCTCTCTTTTATTGATCTTACG 1 136 1 TCTCTTTTAT 0.957828 -78 AGTACATCATTTTCTTTTTTTACAGGGTGC 2 12 1 TTTCTTTTTT 0.925752 -30 TCATTTCTTTAATTCAGCATAAG 3 4 1 TTTCTTTAAT 0.884451 -59 AGAATCGCACCTTGTTTTATTAACCAGTGA 4 33 0 CTTGTTTTAT 0.945216 -21 AGAAAGATTATTTCTTCTATTCTAGACAAA 5 38 1 TTTCTTCTAT 0.922118 -92 TACTTATCCACTTCTTTATTAGCGTTGTCC 6 27 1 CTTCTTTATT 0.89037 -130 GTGGATAACGCTTGTTTTATTACAGGACAT 6 64 1 CTTGTTTTAT 0.945216 -93 TATTACAGGACATCTTTTATACTTTCAAAA 6 81 1 CATCTTTTAT 0.930534 -76 GGAAAAGCTCCCTCTGCTATACTGGAATTC 7 22 0 CCTCTGCTAT 0.907748 -104 GGTCTTCACCTCTGTTTTCCTGTGCGTA 7 108 0 CCTCTGTTTT 0.911989 -18 ********** Masking position 5 Map Score: 10.2515 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 383 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 TATCTCAAGGACTTGTCATCACT 1 4 0 ACTTGTCATC 0.717082 -210 TTAATGCTAGCGTTACCGTCCGCTATCGTC 1 51 1 CGTTACCGTC 0.884834 -163 CGTTACCGTCCGCTATCGTCTATGTTCAAG 1 61 1 CGCTATCGTC 0.941431 -153 AGCAGACTAACCCTATCAACGTTGGTATTA 1 182 1 CCCTATCAAC 0.953808 -32 CCTTATCTCCCTGCCATAAG 5 120 0 CCTTATCTCC 0.897537 -10 TTATACACATACTTATCCACTTCTTTATTA 6 18 1 ACTTATCCAC 0.960965 -139 TCTTTATTAGCGTTGTCCACAATTTGTGGA 6 39 1 CGTTGTCCAC 0.980133 -118 ATAAAACAAGCGTTATCCACAAATTGTGGA 6 54 0 CGTTATCCAC 0.990189 -103 TGACCAAACTCCTTATTCACAACAATAAAA 6 134 0 CCTTATTCAC 0.924563 -23 ********** Masking position 4 Map Score: 5.97915 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 861 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 TTACTCCAAAAGGGGGCGCTCTCTTTTATT 1 127 1 AGGGGGCGCT 0.968246 -87 TGCATCATACAGGATGCGTAAGATCAATAA 1 152 0 AGGATGCGTA 0.93041 -62 CTTTTTTTACAGGGTGCATTTACGCCT 2 25 1 AGGGTGCATT 0.965825 -17 AGCACTGTTCACGGTGCGTAATA 3 50 1 ACGGTGCGTA 0.95196 -13 TTAATAAAACAAGGTGCGATTCTT 4 40 1 AAGGTGCGAT 0.857752 -14 TGTCAATCAGAGGGGGATTTGTCTAGAATA 5 55 0 AGGGGGATTT 0.924939 -75 AAGATTGCTAAGGCTGCTTATGGCAGGGAG 5 104 1 AGGCTGCTTA 0.925888 -26 TGCTTATGGCAGGGAGATAAGG 5 118 1 AGGGAGATAA 0.703013 -12 AGTATAGCAGAGGGAGCTTTTCCAGCTGGG 7 29 1 AGGGAGCTTT 0.975873 -97 ********** Masking position 1 Map Score: 6.04441 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 511 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 CAGTTATAACCCTTAATGCTAGCGTTACCG 1 39 1 CCTTAATGCT 0.754582 -175 ATTGCCAGAATCTAACGGCTTTCGGCAATT 1 99 1 TCTAACGGCT 0.978168 -115 CTTTTATTGATCTTACGCATCCTGTATGAT 1 149 1 TCTTACGCAT 0.925347 -65 AAATAATCTTTCTAACTCCTGAACACATCT 5 21 0 TCTAACTCCT 0.966094 -109 TTTTATACTTTCAAAAGGATTACACGCGTA 6 95 1 TCAAAAGGAT 0.889702 -62 TTCTGACCAAACTCCTTATTCACAAC 6 141 0 CCAAACTCCT 0.936406 -16 TTAACCCCAGTCAAAAGCATTTCAATCCCA 7 55 0 TCAAAAGCAT 0.913755 -71 ********** Masking position 5 Map Score: 1.93816 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 460 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 AGCATTAAGGGTTATAACTGCAACGTATCTCA 1 27 0 GTATAATGCA 0.975198 -187 TGTTCAAGTTGTCTTAATTGCCAGAATCTAAC 1 83 1 GTTTAATGCC 0.986716 -131 GCCCCCTTTTGGAGTAATTGCCGAAAGCCGTT 1 112 0 GGGTAATGCC 0.991962 -102 AGGCGTAAATGCACCCTGTAAAA 2 29 0 GGGTAATGCA 0.991106 -13 ATAAGTATGTGTATAAACTGCAC 6 2 0 GTTAAATGCA 0.954698 -155 ** **** **** Masking position 6 Map Score: 1.84121 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 83 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TTGTTATGGCGAAATCAGCACTGTTCACGGTGC 3 34 1 GACAGCACTG 0.987626 -29 CCGGGAAGCGAAGGGCCTCACTGGTTAATAAAA 4 16 1 AACCTCACTG 0.974428 -38 TCTAACTCCTGAACACATCTCTGGAGATTT 5 8 0 GACATCTCTG 0.992709 -122 TATTCTAGACAAATCCCCCTCTGATTGACAGCA 5 55 1 AACCCCTCTG 0.976287 -75 CCCTCTGATTGACAGCATCACTGACCAATCGCA 5 71 1 GACATCACTG 0.992701 -59 GGTCTTCACCTCTGTTTTCCTGTG 7 112 0 GTCACCTCTG 0.97316 -14 ** ******** Masking position 12 Map Score: 4.87097 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 117 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ********** No masking Map Score: 3.64809e-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 8 TGGCAATTAAGACAACTTGAACATAGACGAT 1 75 0 GCAACTTGAA 0.915624 -139 GATAGGGTTAGTCTGCTTGCATCATACAGGA 1 168 0 GCTGCTTGCA 0.912435 -46 GTCTGCGGGAAATAATACCAA 1 203 0 GCTGCGGGAA 0.987565 -11 TATTACGCACCGTGAACAGTGCTGAT 3 47 0 CCACCGTGAA 0.959713 -16 GGAATCCGGGAAGCGAAGGGCC 4 2 1 GATCCGGGAA 0.947824 -52 CATCCCTCCTCGAATTCCAGTATA 7 4 1 CCTCCTCGAA 0.958355 -122 GCTCCCTCTGCTATACTGGAATTCGAGGAGG 7 15 0 CATACTGGAA 0.891605 -111 GCATTTCAATCCCAGCTGGAAAAGCTCCCTC 7 38 0 CCAGCTGGAA 0.980586 -88 * ********* Masking position 11 Map Score: 3.96754 Number of sites scoring better than the average of aligned sites = 1370 Number in coding regions = 1310 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 9 ********** No masking Map Score: 3.64809e-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: 3.64809e-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: 3.64809e-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