AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00562_ecoli_reg_100.orf -o00562_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 appA 184 phosphoanhydride phosphorylase; pH 2.5 acid phosphatase; periplasmic #2 gatZ 28 putative tagatose 6-phosphate kinase 1 #3 gatY 197 tagatose-bisphosphate aldolase 1 #4 agaZ 248 putative tagatose 6-phosphate kinase 2 Motif number 1 CGCGTCTGAAAAGTTAACGAACGTAGGCCTGAT 1 99 1 AATAACGACG 0.970648 -86 GATAACGATCACAAAAACGACAATATGAAAATT 3 116 0 ACAAACGAAA 0.936556 -82 TCGATTTCAAAATATAATGAAATTATTTGTTTT 3 159 0 AATAATGAAT 0.814341 -39 TTGAAATCGAAAACAAACGACAGGAT 3 182 1 AAAAACGAAG 0.997153 -16 GGCAAAACGAAATGAAACGAAAGTTTTACGAAA 4 20 0 AAAAACGAAG 0.997153 -229 CCTTTCTATTAAGCAAATGCAAGCCCACCTTGC 4 61 1 AAAAATGCAG 0.953718 -188 AATGAAAGTCACTGAAACGAGAGTAGCTTGCGT 4 100 0 ACAAACGAAG 0.993403 -149 TCACAAAAGAAACATAATGAAAGTCACTGAAAC 4 115 0 AATAATGAAG 0.978138 -134 GTGAGATAAAAATAAAACGAAAGATAATGGTTT 4 159 0 AAAAACGAAG 0.997153 -90 TATCAACTGAAACAAAACGAAAGATTAATATCG 4 202 1 AAAAACGAAG 0.997153 -47 ** ****** ** Masking position 7 Map Score: 22.0596 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 83 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 ACGAACGTAGGCCTGATGCGGCGCATTAGC 1 115 1 GCCTGATGCG 0.997208 -70 CCTGATGCGATGCTAATGCGCCGCATCAGG 1 126 0 TGCTAATGCG 0.868629 -59 ATTATTGATTGCCTGATGCGATGCTAATGC 1 137 0 GCCTGATGCG 0.997208 -48 CTTGTTAAATGGCAGGTGCG 2 1 0 GGCAGGTGCG 0.993395 -28 GTGTTTTTATGCCGGATGCGGTGTAAACAT 3 26 0 GCCGGATGCG 0.993824 -172 GGAAGCCGTAGCAAAGTGCGCGTGTTTTTA 3 47 0 GCAAAGTGCG 0.974941 -151 GCGTCAATGGGCAAGGTGGGCTTGCATTTG 4 74 0 GCAAGGTGGG 0.970326 -175 TGATACTGCGTCATGGTGAGATAAAAATAA 4 177 0 TCATGGTGAG 0.867923 -72 ********** Masking position 7 Map Score: 13.1642 Number of sites scoring better than the average of aligned sites = 2022 Number in coding regions = 1485 Number in noncoding regions = 537 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 3 AAATACCACATTGTTTCTGCTCC 1 3 0 TTGTTTCGCT 0.991603 -182 CATTTTGTTGATGTGTTCGCTCTCCACCCTT 1 49 1 ATGTGTTGCT 0.942495 -136 CACCCTTGTGTTGGTATGGCTGGACCCGCGT 1 73 1 TTGGTATGCT 0.899053 -112 CGATATGTTTCCGCTTTTCATATCT 1 170 0 ATGTTTCGCT 0.981642 -15 CACGCGCACTTTGCTACGGCTTCCCTATCGG 3 53 1 TTGCTACGCT 0.963151 -145 ATTGTCGTTTTTGTGATCGTTATCTCGATAT 3 125 1 TTGTGATGTT 0.843058 -73 ATCCTGTCGTTTGTTTTCGATTTCAAAATAT 3 177 0 TTGTTTTGAT 0.905708 -21 CAAGGTGGGCTTGCATTTGCTTAATAGAAAG 4 62 0 TTGCATTGCT 0.866432 -187 GACTTTCATTATGTTTCTTTTGTGAATCAGA 4 123 1 ATGTTTCTTT 0.604919 -126 ATCTTTCGTTTTGTTTCAGTTGATACTGCGT 4 196 0 TTGTTTCGTT 0.974813 -53 ******* *** Masking position 2 Map Score: 8.82965 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 724 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 GGAGCAGAAACAATGTGGTA 1 1 1 GGAGCAGAAA 0.970995 -184 ACAAGGGTGGAGAGCGAACACATCAACAAA 1 52 0 AGAGCGAACA 0.940127 -133 TCAGATATGAAAAGCGGAAACATATCG 1 168 1 AAAGCGGAAA 0.983366 -17 GCCATTTAACAAGGAAAAAAC 2 18 1 AAGGAAAAAA 0.752688 -11 CGAGGAGTGAAAGGCAAAAAAACGGCCTCC 3 83 0 AAGGCAAAAA 0.930101 -115 TTATATTTTGAAATCGAAAACAAACGACAG 3 175 1 AAATCGAAAA 0.895013 -23 TTTGTGAATCAGATCAGAAAACCATTATCT 4 141 1 AGATCAGAAA 0.931138 -108 AATCTGAACTGGAGAGGAAA 4 239 1 GGAGAGGAAA 0.923927 -10 ********** Masking position 8 Map Score: 4.03566 Number of sites scoring better than the average of aligned sites = 1777 Number in coding regions = 1589 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 5 ATCAACAAAATGCCGACGAACCAAAGTAAAT 1 30 0 TGCCACGAAC 0.98735 -155 CGCACCTGCCATTTAACAAGGAAAAAA 2 7 1 TGCCTTTAAC 0.98899 -22 CATTTCGTTTTGCCTATTAACGCCTTTCTAT 4 39 1 TGCCATTAAC 0.995614 -210 AAGCCCACCTTGCCCATTGACGCAAGCTACT 4 81 1 TGCCATTGAC 0.992544 -168 **** ****** Masking position 10 Map Score: 2.6762 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 51 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GGATGCGGTGTAAACATACGTGGCAGTGCT 3 13 0 TAAACATACG 0.949664 -185 GACAATATGAAAATTATTCGAGGAGTGAAA 3 101 0 AAATTATTCG 0.844851 -97 TTTGAAATCGAAAACAAACGACAGGAT 3 181 1 AAAACAAACG 0.823147 -17 GTCCTTTCGTAAAACTTTCGTTTCATTTCG 4 16 1 AAAACTTTCG 0.972376 -233 CAGAAAACCATTATCTTTCGTTTTATTTTT 4 155 1 TTATCTTTCG 0.896739 -94 ACTGCGATATTAATCTTTCGTTTTGTTTCA 4 209 0 TAATCTTTCG 0.972376 -40 ********** Masking position 3 Map Score: 1.88241 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 369 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 TTGGTTCGTCGGCATTTTGTTGATGTGTTC 1 37 1 GGCATTTTGT 0.900132 -148 TCGAATAATTTTCATATTGTCGTTTTTGTG 3 110 1 TTCATATTGT 0.883789 -88 AGTAAGTCCTTTCGTAAAACTTTCG 4 6 1 GTCCTTTCGT 0.979083 -243 AAACTTTCGTTTCATTTCGTTTTGCCTATT 4 27 1 TTCATTTCGT 0.977894 -222 TTTCATTATGTTTCTTTTGTGAATCAGATC 4 126 1 TTTCTTTTGT 0.940167 -123 AGAAAACCATTATCTTTCGTTTTATTTTTA 4 156 1 TATCTTTCGT 0.823984 -93 ATATTAATCTTTCGTTTTGTTTCAGTTGAT 4 203 0 TTCGTTTTGT 0.955531 -46 ********** Masking position 5 Map Score: 4.26621 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 166 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 ATTAGCATCGCATCAGGCAATCAATAATGT 1 139 1 CATCAGGCAA 0.94464 -46 AACGGCCTCCCGATAGGGAAGCCGTAGCAA 3 63 0 CGATAGGGAA 0.943024 -135 ATTCGAGGAGTGAAAGGCAAAAAAACGGCC 3 86 0 TGAAAGGCAA 0.896078 -112 ACAAAAACGACAATATGAAAATTATTCGAG 3 109 0 CAATATGAAA 0.719681 -89 AGAAAGGCGTTAATAGGCAAAACGAAATGA 4 38 0 TAATAGGCAA 0.981111 -211 AACGCCTTTCTATTAAGCAAATGCAAGCCC 4 57 1 TATTAAGCAA 0.777558 -192 TAGCTTGCGTCAATGGGCAAGGTGGGCTTG 4 80 0 CAATGGGCAA 0.970595 -169 ********** Masking position 9 Map Score: 1.32928 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 479 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 9 ********** No masking Map Score: 1.69352e-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 10 ********** No masking Map Score: 1.69352e-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 11 ********** No masking Map Score: 1.69352e-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