AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_ecoli_bsub_300.orf -o334_ecoli_bsub_300.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 ywlB 66 alternate gene name: ipc-28d #8 spoIIR 140 alternate gene name: ipc-27d, csfX #9 prfA 125 peptide chain release factor 1 Motif number 1 AATTACTCCAAAAGGGGGCGCTCTCTTTTA 1 125 1 AAAGGGGGCG 0.908041 -89 CTTGCATCATACAGGATGCGTAAGATCAAT 1 154 0 ACAGGATGCG 0.93473 -60 TTCTTTTTTTACAGGGTGCATTTACGCCT 2 23 1 ACAGGGTGCA 0.984943 -19 TCAGCACTGTTCACGGTGCGTAATA 3 48 1 TCACGGTGCG 0.893768 -15 GGTTAATAAAACAAGGTGCGATTCTT 4 38 1 ACAAGGTGCG 0.971834 -16 GCTGTCAATCAGAGGGGGATTTGTCTAGAA 5 57 0 AGAGGGGGAT 0.84651 -73 GCTGCTTATGGCAGGGAGATAAGG 5 116 1 GCAGGGAGAT 0.9459 -14 GAACGCAAAAACGGGGTGAACGG 7 54 1 ACGGGGTGAA 0.87525 -13 GGATAAACGTGCAGGGTGAAAAAAATCTAG 8 60 0 GCAGGGTGAA 0.962402 -81 CCTATTATGGACAAGGAGAGCCTGGGATAA 8 84 0 ACAAGGAGAG 0.936405 -57 TAGAAACAAAGCACGGAGAGGAACGGTGGG 8 116 1 GCACGGAGAG 0.934491 -25 CCAGTATAGCAGAGGGAGCTTTTCCAGCTG 9 27 1 AGAGGGAGCT 0.914144 -99 ********** Masking position 5 Map Score: 13.5628 Number of sites scoring better than the average of aligned sites = 1164 Number in coding regions = 1022 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 2 GCGTAAGATCAATAAAAGAGAGCGCCCCCT 1 137 0 AATAAAAGAG 0.945499 -77 TGCACCCTGTAAAAAAAGAAAATGATGTAC 2 13 0 AAAAAAAGAA 0.92129 -29 ACTTATGCTGAATTAAAGAAATGA 3 5 0 AATTAAAGAA 0.92129 -58 CTCACTGGTTAATAAAACAAGGTGCGATTC 4 32 1 AATAAAACAA 0.977234 -22 ATTTGTCTAGAATAGAAGAAATAATCTTTC 5 39 0 AATAGAAGAA 0.945499 -91 GATGTCCTGTAATAAAACAAGCGTTATCCA 6 65 0 AATAAAACAA 0.977234 -92 TATTCACAACAATAAAACGATTGTTTTACG 6 121 0 AATAAAACGA 0.929616 -36 ********** Masking position 6 Map Score: 7.27248 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 32 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 3 GTGGATAAGTATGTGTATAAACTGCAC 6 8 0 ATGTGTATAA 0.911049 -149 GCTAATAAAGAAGTGGATAAGTATGTGTAT 6 20 0 AAGTGGATAA 0.930118 -137 TATCCACAAATTGTGGACAACGCTAATAAA 6 41 0 TTGTGGACAA 0.895082 -116 TGTCCACAATTTGTGGATAACGCTTGTTTT 6 52 1 TTGTGGATAA 0.972987 -105 CGTTTTATTGTTGTGAATAAGGAGTTTGGT 6 132 1 TTGTGAATAA 0.934255 -25 TCTAGCCCTATTATGGACAAGGAGAGCCTG 8 90 0 TTATGGACAA 0.827379 -51 ********** Masking position 4 Map Score: 5.57862 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 42 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 ATAACCCTTAATGCTAGCGTTACCGTCCGCTA 1 44 1 ATGCTACGTA 0.819683 -170 GCGTTACCGTCCGCTATCGTCTATGTTCAAGT 1 60 1 CCGCTACGCT 0.953347 -154 CAGAATCTAACGGCTTTCGGCAATTACTCCAA 1 104 1 CGGCTTCGCA 0.99082 -110 TAGGGTTAGTCTGCTTGCATCATACAGGATGC 1 165 0 CTGCTTCACA 0.974558 -49 GTGAACAGTGCTGATTTCGCCATAACAACTTA 3 30 0 CTGATTCGCA 0.974558 -33 ATTGCTAAGGCTGCTTATGGCAGGGAGATAAG 5 107 1 CTGCTTTGCA 0.987739 -23 TGGGATTGAAATGCTTTTGACTGGGGTTAATC 9 55 1 ATGCTTTGCT 0.9053 -71 ****** ** ** Masking position 5 Map Score: 1.85237 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 953 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 5 GTCTGCGGGAAATAATACCAAC 1 202 0 CTGCGGGAAA 0.919784 -12 GCACTGTTCACGGTGCGTAATA 3 51 1 CGGTGCGTAA 0.883216 -12 AAAAGATGTCCTGTAATAAAACAAGCGTTA 6 69 0 CTGTAATAAA 0.705564 -88 TCATCTGGTCTAAAAATAGATTTG 7 5 1 CTGGTCTAAA 0.886135 -62 CAAGGAGAGCCTGGGATAAACGTGCAGGGT 8 73 0 CTGGGATAAA 0.974461 -68 GCTTTTCCAGCTGGGATTGAAATGCTTTTG 9 44 1 CTGGGATTGA 0.91019 -82 ATGCTTTTGACTGGGGTTAATCACTATACT 9 65 1 CTGGGGTTAA 0.976298 -61 CTCTGTTTTCCTGTGCGTAACATTCTCATT 9 97 0 CTGTGCGTAA 0.96607 -29 ********** Masking position 10 Map Score: 2.16151 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 875 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 AGCATTAAGGGTTATAACTGCAACGTATCTCA 1 27 0 GTTAACTGCA 0.986313 -187 TGTTCAAGTTGTCTTAATTGCCAGAATCTAAC 1 83 1 GTTAATTGCC 0.980437 -131 GCCCCCTTTTGGAGTAATTGCCGAAAGCCGTT 1 112 0 GGTAATTGCC 0.981847 -102 AGGCGTAAATGCACCCTGTAAAA 2 29 0 GGTAAATGCA 0.96591 -13 ATAAGTATGTGTATAAACTGCAC 6 2 0 GTAAACTGCA 0.956339 -155 ** ******** Masking position 6 Map Score: 0.664425 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 65 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 CGATAGCGGACGGTAACGCTAGCATTAAGG 1 49 0 CGGTAACGCT 0.986802 -165 CACAAATTGTGGACAACGCTAATAAAGAAG 6 37 0 GGACAACGCT 0.992785 -120 CACAATTTGTGGATAACGCTTGTTTTATTA 6 56 1 GGATAACGCT 0.993929 -101 ********** Masking position 5 Map Score: 0.185027 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 59 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 GAAGAAATAATCTTTCTAACTCCTGAACACA 5 24 0 TCTTTCTACT 0.885806 -106 AAAGATTATTTCTTCTATTCTAGACAAATCC 5 40 1 TCTTCTATCT 0.938768 -90 GGTCAGTGATGCTGTCAATCAGAGGGGGATT 5 66 0 GCTGTCAACA 0.712274 -64 TTACAGGACATCTTTTATACTTTCAAAAGGA 6 83 1 TCTTTTATCT 0.948946 -74 TTGCGTTCTTTCTTCCAATCTATGAGGCAAA 7 31 0 TCTTCCAACT 0.924228 -36 AATCTAGCAAGCTGTTAATCTTATTTATGGT 8 36 0 GCTGTTAACT 0.94125 -105 TCCTCTCCGTGCTTTGTTTCTAGCCCTATTA 8 107 0 GCTTTGTTCT 0.746234 -34 AAAAGCTCCCTCTGCTATACTGGAATTCGAG 9 19 0 TCTGCTATCT 0.95178 -107 GGTCTTCACCTCTGTTTTCCTGTGCGTAACA 9 105 0 TCTGTTTTCT 0.926214 -21 ******** ** Masking position 3 Map Score: 3.66925 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 251 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 9 AGTGATGACAAGTCCTTGAG 1 1 1 AGTGATGACA 0.871225 -213 TTTATTAACCAGTGAGGCCCTTCGCTTCCC 4 18 0 AGTGAGGCCC 0.984431 -36 AACAAAGCACGGAGAGGAACGGTGGGGACC 8 120 1 GGAGAGGAAC 0.948565 -21 GGAGAGGAACGGTGGGGACCG 8 130 1 GGTGGGGACC 0.991241 -11 GGAAAACAGAGGTGAAGACC 9 116 1 GGTGAAGACC 0.980138 -10 ********** Masking position 4 Map Score: 1.01085 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 179 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ********** No masking Map Score: 6.70342e-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: 6.70342e-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: 6.70342e-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