AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_ecoli_reg_100.orf -o00510_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 yabB 300 orf, hypothetical protein #2 dsbC 24 protein disulfide isomerase II #3 xerD 111 site-specific recombinase #4 ispB 258 octaprenyl diphosphate synthase #5 rfaS 36 lipopolysaccharide core biosynthesis #6 rfaQ 300 lipopolysaccharide core biosynthesis #7 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #8 yifM_2 241 orf, conceptual translation in SwissProt is fused with b4404 #9 ubiC 111 chorismate lyase Motif number 1 TGCGACGCGAGCGGCATTTTAGGACATATC 1 17 0 GCGGCATTTT 0.944436 -284 CCGTAAACATCGGGTTTTTTACCTCGGTAT 1 186 1 CGGGTTTTTT 0.74093 -115 CGATTCTGCTGTGGCTTTTGCGGCTAGTGT 3 24 1 GTGGCTTTTG 0.899924 -88 GTGCGCGGAAGCGGAGTTTTAT 4 3 0 GCGGAGTTTT 0.931793 -256 TTGTCAAAGGCGTGCGTTTTGCGTAATATT 4 82 0 CGTGCGTTTT 0.953669 -177 TACCGTACAAGTTGTGTTTTTTTTCTTCGT 4 128 0 GTTGTGTTTT 0.798172 -131 GGCGAAAAGCCCGGCTTTTGCG 4 247 1 CCGGCTTTTG 0.889565 -12 GGGGCGGTAGCGTGCTTTTTTCTGCTTAAC 6 214 1 CGTGCTTTTT 0.869096 -87 ACGTAAACACGTGGCGTTTTTGGCATAAGA 7 16 0 GTGGCGTTTT 0.988795 -224 ACGTGTTTACGTGGCGTTTTGCTTTTATAT 7 34 1 GTGGCGTTTT 0.988795 -206 CCGTCAGCAGCGTTTTTTCTTCCACG 8 7 1 GCAGCGTTTT 0.944436 -235 TTTGCCACCCGCGGCGATTTGAGCTTTTTT 8 204 1 GCGGCGATTT 0.948588 -38 CTTTGGGTGCGTTTTGGCAAAAAAG 8 227 0 GGTGCGTTTT 0.97833 -15 ********** Masking position 8 Map Score: 16.2321 Number of sites scoring better than the average of aligned sites = 1792 Number in coding regions = 1576 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 TGTCCTAAAATGCCGCTCGCGTCGCAAACT 1 21 1 TGCCGCTCGC 0.930931 -280 CGGTATGCCTTGTGACTGGCTTGACAAGCT 1 210 1 TGTGACTGGC 0.891262 -91 GAATAAGGGGTGAGGCTGGC 1 291 1 TGAGGCTGGC 0.966721 -10 AGCACGCTACCGCCCCAGGCTCAACAGCTA 6 200 0 CGCCCCAGGC 0.960261 -101 AATCTTAATGCCGCGCTGGCGATGTTAGGA 7 68 1 CCGCGCTGGC 0.956654 -172 GAAGAAAAAACGCTGCTGACGG 8 3 0 CGCTGCTGAC 0.916665 -239 AATCCCACACTGTGGCTGGCTCTGCTGAGT 8 45 1 TGTGGCTGGC 0.986559 -197 GACTCGCTTTTGCGCCAGGCGACGTAGTGG 8 165 0 TGCGCCAGGC 0.953854 -77 CTCAAATCGCCGCGGGTGGCAAATACACAG 8 197 0 CGCGGGTGGC 0.976585 -45 AAAACATCACCGTTCCTGGCATCCTGGACG 9 18 1 CGTTCCTGGC 0.960335 -94 TTACCGATGCCCGTGCTGGCGAGGGCAACC 9 61 0 CCGTGCTGGC 0.933457 -51 ********** Masking position 10 Map Score: 10.5074 Number of sites scoring better than the average of aligned sites = 4281 Number in coding regions = 4090 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 3 GGGGAAGATATGTCCTAAAATGC 1 3 1 GGAAATATGT 0.732498 -298 TATTTGCTGTGGAAAATAGTGAGTCATTTTA 1 60 1 GGAAATAGTG 0.834769 -241 AAAACGGTGATGACGATGAGGGATTTTTTCT 1 90 1 TGACATGAGG 0.862578 -211 CCTTTCAGTGGGAAATTGTGGGGCAAAGTGG 1 260 1 GGAATTGTGG 0.764475 -41 GGGCAAAGTGGGAATAAGGGGTGAGGCTGGC 1 280 1 GGAAAAGGGG 0.947596 -21 TTTAGTCACGGCACAATAAGGCATAATGGAT 3 65 1 GCACATAAGG 0.832636 -47 ATCAAATGAGTGACCATAAGGGGCGCAA 3 94 1 TGACATAAGG 0.895267 -18 CTATAAATATTCACAATAGGGCGCGAATATT 4 57 1 TCACATAGGG 0.904617 -202 GTGATTGTACTGAAAAAATGGCACAGATAAA 4 161 0 TGAAAAATGG 0.788913 -98 TTTATGGTTAGGAATATAGGGTGATTGTACT 4 181 0 GGAAATAGGG 0.987131 -78 GTGAACAAAGGCAACTTAGGGTTTATGGTTA 4 202 0 GCAATTAGGG 0.830633 -57 TATGTAGATTTGAAAATGGGGCCGAGTTTCA 6 19 0 TGAAATGGGG 0.968047 -282 CTTTCCCTTCTGAATAAAGGTCTTCGTGGTT 7 182 1 TGAAAAAGGT 0.626295 -58 **** ****** Masking position 3 Map Score: 7.88989 Number of sites scoring better than the average of aligned sites = 713 Number in coding regions = 628 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 CAAGGCATACCGAGGTAAAAAACCCGATGTTTA 1 189 0 CAGGAAAAAC 0.723303 -112 TCTGATACACTAGCCGCAAAAGCCACAGCAGAA 3 27 0 TGCCAAAAGC 0.885723 -85 CCTTATTGTGCCGTGACTAAAGCGATTCTGATA 3 53 0 CGTGTAAAGC 0.839697 -59 GTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTG 4 234 1 CGGGAAAAGC 0.995378 -25 GCTACCGCCCCAGGCTCAACAGCTACCTGAATA 6 192 0 CGGCAACAGC 0.975935 -109 AAAAGAGTCGCTAGTGGAAAAGCCATTTCGAAA 6 262 1 CAGTAAAAGC 0.941394 -39 ATTAAGATTACAGATATAAAAGCAAAACGCCAC 7 44 0 CGATAAAAGC 0.910887 -196 GAAAAACTGGCTGGGCTTAATGCCACCACTCAG 8 69 0 CGGGTAATGC 0.871616 -173 GGCGACGTAGTGGGTAAAAAAGCTTATATCTCA 8 145 0 TGGTAAAAGC 0.962725 -97 ACTACGTCGCCTGGCGCAAAAGCGAGTCGGCTG 8 167 1 CGGCAAAAGC 0.995378 -75 TGGGTGCGTTTTGGCAAAAAAGCTCAAATCGCC 8 216 0 TGGCAAAAGC 0.981598 -26 * *** ****** Masking position 9 Map Score: 10.3734 Number of sites scoring better than the average of aligned sites = 1026 Number in coding regions = 949 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 GTCATTTTAAAACGGTGATGACGATGAGGG 1 82 1 AACGGTGATG 0.994384 -219 TAAAATAAACAACGCTGATATTAGCCGTAA 1 162 1 AACGCTGATA 0.949506 -139 TGGAAGAAAAAACGCTGCTGACGG 8 5 0 AACGCTGCTG 0.982065 -237 GGATGCCAGGAACGGTGATGTTTTCCTTTA 9 12 0 AACGGTGATG 0.994384 -100 TGGCATCCTGGACGGTGATGCCCCTACGGT 9 34 1 GACGGTGATG 0.984789 -78 GAAGTGGTAAAACGATGTTGAACCTTACGC 9 92 0 AACGATGTTG 0.931248 -20 ********** Masking position 6 Map Score: 7.99379 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 160 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 CAAATATAAAGTGTCAGTTTGCGACGCGAGC 1 35 0 GTGTCAGTTG 0.943924 -266 TGGGAATAAGGGGTGAGGCTGGC 1 288 1 GGGTGAGCTG 0.962052 -13 AAAATCATTCGGGTCGGATTGCTGCGAAAGA 6 123 1 GGGTCGGTTG 0.987394 -178 AGCGACTCTTTTGTGTGATTGTCTGGTTAAG 6 243 0 TTGTGTGTTG 0.860556 -58 TGCACAGGACTGGTGGGTTTGGAACGGACTT 7 154 1 TGGTGGGTTG 0.980636 -86 GCCAGCCACAGTGTGGGATTGAACTGACCGT 8 34 0 GTGTGGGTTG 0.988997 -208 CTTTGGGTGCGTTTTGGCAAAAAAG 8 227 0 GGGTGCGTTT 0.899824 -15 ******* *** Masking position 4 Map Score: 3.61713 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 163 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 CTGTGGAAAATAGTGAGTCATTTTAAAACG 1 66 1 TAGTGAGTCA 0.912431 -235 CAGTGGGAAATTGTGGGGCAAAGTGGGAAT 1 265 1 TTGTGGGGCA 0.85965 -36 CTTTTGCGGCTAGTGTATCAGAATCGCTTT 3 38 1 TAGTGTATCA 0.964105 -74 CAATAAGGCATAATGGATCAAATGAGTGAC 3 78 1 TAATGGATCA 0.861002 -34 AAAGTATATTTTGTGTATAAAAATCATTCG 6 104 1 TTGTGTATAA 0.793506 -197 TTTGACGTGCTAGTGTATCATTTCTTTCGC 6 146 0 TAGTGTATCA 0.964105 -155 AAAGAGTCGCTAGTGGAAAAGCCATTTCGA 6 263 1 TAGTGGAAAA 0.818242 -38 CCAGGCGACGTAGTGGGTAAAAAAGCTTAT 8 151 0 TAGTGGGTAA 0.955065 -91 ********** Masking position 10 Map Score: 3.52526 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 122 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 ATTTTAAAACGGTGATGACGATGAGGGATT 1 85 1 GGTGATGACG 0.850662 -216 TAAAAAACCCGATGTTTACGGCTAATATCA 1 177 0 GATGTTTACG 0.962069 -124 CCCACTGAAAGGAGTTTACGGAGCTGAGGA 1 242 0 GGAGTTTACG 0.984741 -59 GCAGAATCGAGAAGCTTACGTT 3 3 0 GAAGCTTACG 0.971209 -109 AATAGGGCGCGAATATTACGCAAAACGCAC 4 71 1 GAATATTACG 0.856095 -188 TTTATGACCAGGATTTTTCGAAATGGCTTT 6 280 0 GGATTTTTCG 0.759331 -21 AAAAACGCCACGTGTTTACGTGGCGTTTTG 7 25 1 CGTGTTTACG 0.869246 -215 AAACGATGTTGAACCTTACGCTTTACCGAT 9 83 0 GAACCTTACG 0.885511 -29 ********** Masking position 6 Map Score: 2.4236 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 414 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 CTAGCCGCAAAAGCCACAGCAGAATCGAGA 3 21 0 AAGCCACAGC 0.691623 -91 CATTTCGATAATGTCAGTACGGCCTATGTA 6 44 0 ATGTCAGTAC 0.822769 -257 ATTTGTCTTATGCCAAAAACGCCACGTGT 7 10 1 ATGCCAAAAA 0.788525 -230 ATTGCATAACATGCCAGCAAATTCCAGGAA 7 101 0 ATGCCAGCAA 0.962936 -139 GCTGGGCTTAATGCCACCACTCAGCAGAGC 8 63 0 ATGCCACCAC 0.969154 -179 CCCCCCAGATATGCCAGAAAAACTGGCTGG 8 88 0 ATGCCAGAAA 0.960162 -154 ACCGTCCAGGATGCCAGGAACGGTGATGTT 9 20 0 ATGCCAGGAA 0.93394 -92 CTGGACGGTGATGCCCCTACGGTTGCCCTC 9 41 1 ATGCCCCTAC 0.934328 -71 CGCTTTACCGATGCCCGTGCTGGCGAGGGC 9 65 0 ATGCCCGTGC 0.918794 -47 ********** Masking position 1 Map Score: 4.63606 Number of sites scoring better than the average of aligned sites = 780 Number in coding regions = 733 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 ACACTTTATATTTGCTGTGGAAAATAGTGA 1 52 1 TTTGCTGTGG 0.972618 -249 GCTTCTCGATTCTGCTGTGGCTTTTGCGGC 3 18 1 TCTGCTGTGG 0.992964 -94 TGTGGCTGGCTCTGCTGAGTGGTGGCATTA 8 55 1 TCTGCTGAGT 0.97305 -187 CAAAAGCGAGTCGGCTGTGTATTTGCCACC 8 183 1 TCGGCTGTGT 0.981657 -59 ********** Masking position 6 Map Score: 1.83995 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 36 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 GTTAATTTGCTTCGCACGTTGGACGTAAAA 1 137 1 TTCGCACGTT 0.474113 -164 AAAAACACAACTTGTACGGTAACGTTTATC 4 137 1 CTTGTACGGT 0.865025 -122 TTCGATAATGTCAGTACGGCCTATGTAGAT 6 41 0 TCAGTACGGC 0.855116 -260 AAATGATACACTAGCACGTCAAAGTAAGTG 6 153 1 CTAGCACGTC 0.904953 -148 CCTAACATCGCCAGCGCGGCATTAAGATTA 7 67 0 CCAGCGCGGC 0.96925 -173 AGCGTTTTTTCTTCCACGGTCAGTTCAATC 8 19 1 CTTCCACGGT 0.897499 -223 GCTTTTTTACCCACTACGTCGCCTGGCGCA 8 155 1 CCACTACGTC 0.847292 -87 GTGTATTTGCCACCCGCGGCGATTTGAGCT 8 199 1 CACCCGCGGC 0.718716 -43 TTCCTGGCATCCTGGACGGTGATGCCCCTA 9 30 1 CCTGGACGGT 0.871189 -82 GACGGTGATGCCCCTACGGTTGCCCTCGCC 9 44 1 CCCCTACGGT 0.929477 -68 GTTGCCCTCGCCAGCACGGGCATCGGTAAA 9 62 1 CCAGCACGGG 0.905671 -50 ********** Masking position 7 Map Score: 2.96544 Number of sites scoring better than the average of aligned sites = 3621 Number in coding regions = 3474 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 12 GAATCATTGAAAAGGTGTGCGCGGAAGCGG 4 19 0 AAAGGTGTGC 0.989333 -240 AGCACTTGTCAAAGGCGTGCGTTTTGCGTA 4 87 0 AAAGGCGTGC 0.98087 -172 CCTTCTGAATAAAGGTCTTCGTGGTTATAC 7 187 1 AAAGGTCTTC 0.957176 -53 GAAAGCTCATACAGGTCTGCCCCCCAGATA 8 107 0 ACAGGTCTGC 0.977426 -135 ********** Masking position 3 Map Score: 0.951123 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 75 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 ATGAGGGATTTTTTCTTACAGCTATTCATA 1 105 1 TTTTCTTACA 0.912013 -196 CTTCCCGTTCTTTTCAGACA 2 1 0 TTTTCAGACA 0.89786 -24 ACCCGAATGATTTTTATACACAAAATATAC 6 107 0 TTTTTATACA 0.448421 -194 AACACGTGGCGTTTTTGGCATAAGACAAAT 7 11 0 GTTTTTGGCA 0.858879 -229 TTCCAGGAATTTTCCTAACATCGCCAGCGC 7 80 0 TTTCCTAACA 0.667233 -160 ATTCCTGGAATTTGCTGGCATGTTATGCAA 7 100 1 TTTGCTGGCA 0.930187 -140 CAGCAGCGTTTTTTCTTCCACGGTCAGTTC 8 15 1 TTTTCTTCCA 0.89576 -227 CCCAGCCAGTTTTTCTGGCATATCTGGGGG 8 87 1 TTTTCTGGCA 0.980455 -155 CGATTTGAGCTTTTTTGCCAAAACGCACCC 8 218 1 TTTTTTGCCA 0.880925 -24 AAACATCACCGTTCCTGGCATCCTGGACGG 9 19 1 GTTCCTGGCA 0.913371 -93 ********** Masking position 3 Map Score: 4.67323 Number of sites scoring better than the average of aligned sites = 1311 Number in coding regions = 1190 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 14 ********** No masking Map Score: -7.15216e-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 15 ********** No masking Map Score: -7.15216e-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