AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00410_ecoli_reg_100.orf -o00410_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 speE 105 spermidine synthase = putrescine aminopropyltransferase #2 panD 273 aspartate 1-decarboxylase #3 panB 113 3-methyl-2-oxobutanoate hydroxymethyltransferase #4 pepD 260 aminoacyl-histidine dipeptidase (peptidase D) #5 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #6 goaG 37 4-aminobutyrate aminotransferase #7 tynA 247 copper amine oxidase (tyramine oxidase) #8 ydbO 284 orf, hypothetical protein #9 gadB 300 glutamate decarboxylase isozyme #10 b2659 230 orf, hypothetical protein #11 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #12 gadA 210 glutamate decarboxylase isozyme #13 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase Motif number 1 AATATTTCTACAAAAAGGTATCAGGGA 1 5 0 CAAAAGGTCA 0.905392 -101 AACACCCGTAAAAAAAGGGCGCAACATAATAGC 1 63 0 AAAAAGGGCA 0.976639 -43 GGGTGTTAACAAAGGAGGTATCAACCC 1 89 1 AAAGAGGTCA 0.976639 -17 GAATTTCCTCAAAGCAGGCATCGCCTGCTTCGT 2 224 1 AAAGAGGTCG 0.971745 -50 GTTCGAGGGGAAAATAGGTTGCGCGAGATTATA 4 50 1 AAAAAGGGCG 0.971745 -211 TGATAGACGTGAAACAGGAGTCATA 5 260 1 GAAAAGGTCA 0.905392 -15 ATGATTTATAAAAATAGGGTGCGAAATCCGTCA 8 148 1 AAAAAGGGCG 0.971745 -137 GAATTAATTAAAAACACGAATCACATTGTTTTA 8 233 0 AAAAACGTCA 0.843852 -52 TTAATTCACGAAAACTGGAATCGTAAAGGTGAT 8 259 1 AAAATGGTCG 0.828832 -26 TCGCATTAAAAAAGTAGGATTTATCGATAAAGT 9 254 0 AAAGAGGTTA 0.902235 -47 CCTTTGAAAACAGGATGTAGCG 11 7 1 AAAAAGGGTA 0.902236 -16 AGGCAATAAAAAAGTAGGATTTATCCGCAATGG 12 164 0 AAAGAGGTTA 0.902235 -47 **** *** *** Masking position 3 Map Score: 12.6086 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 87 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 CGCAAAGCCACACGGAAGACAGGGAAG 2 7 0 CACGGAAGAA 0.644971 -267 CAATTCGTTACAGGCGATACATGGCACGCTT 2 115 1 CAGGCGATAA 0.731393 -159 TCGTTAACGACAGGGTAGAAAGGTAGAAGTT 2 253 1 CAGGGTAGAA 0.91499 -21 CAGAAGGTGACAGTGCTGCTACGTTA 3 6 0 CAGTGCTGCA 0.839719 -108 CACCTTCTGGCAGTGCTGCTACGGATAAATC 3 28 1 CAGTGCTGCA 0.839719 -86 CTCTCCCTGACGCGGGATAAAGTGGTATTCT 4 142 1 CGCGGGATAA 0.744295 -119 CAACACAAGACAGGCTTGCGAGATATGTTTG 4 173 0 CAGGCTTGCA 0.79148 -88 TACTGTTTTGCGGGTGATCGACAAGGAGACT 4 236 1 CGGGTGATCA 0.800488 -25 GTAAGTGATTCGGGGGAGCGAACGCAGCCAA 5 121 1 CGGGGGAGCA 0.990912 -154 CATCTATTTTCAGGGCATCCACTGTATGAAA 7 94 1 CAGGGCATCA 0.954753 -154 GGTTGTTTGGCAGGTGTGCCAGCTTTTCATA 7 118 0 CAGGTGTGCA 0.837137 -130 GCCCACAGAGCGCGGTTGCTAACAAGAACAC 7 207 1 CGCGGTTGCA 0.802276 -41 CCCGTTTTATCGGGGCAGATATAACATTAAA 10 11 0 CGGGGCAGAA 0.971986 -220 CCCGATAAAACGGGGCAGATAATATGTTTAG 10 28 1 CGGGGCAGAA 0.971986 -203 GGTCATTTTGCAGTGAAGCCATTTACTGTTT 10 68 1 CAGTGAAGCA 0.752726 -163 CATTGCTGTTCGGGCGATCAAATTAA 12 6 0 CGGGCGATCA 0.9004 -205 ********* * Masking position 11 Map Score: 11.6409 Number of sites scoring better than the average of aligned sites = 1946 Number in coding regions = 1788 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 3 TGGCTTTGCGTGAAGGCAGTATCCAGTCAA 2 28 1 TGAAGGCAGT 0.743248 -246 ATCAATTCGTTACAGGCGATACATGGCACG 2 113 1 TACAGGCGAT 0.875062 -161 CTAAACAAAAATCGGGCAATACTGCGTGAG 2 195 1 ATCGGGCAAT 0.814057 -79 TCGTTAACGAAGCAGGCGATGCCTGCTTTG 2 233 0 AGCAGGCGAT 0.939616 -41 GTCACATTGGTGGGGGCAATGATTTATCCG 3 49 0 TGGGGGCAAT 0.923417 -65 AATACTGTTTTGCGGGTGATCGACAAGGAG 4 234 1 TGCGGGTGAT 0.90384 -27 ACCTGGCAGGTGCAGGCAATCCCCTTTGCA 7 146 1 TGCAGGCAAT 0.970568 -102 AACCGCGCTCTGTGGGCGGTTTAGTCAGGT 7 194 0 TGTGGGCGGT 0.912831 -54 AACATTGCTGTTCGGGCGATCAAATTAA 12 9 0 TTCGGGCGAT 0.971084 -202 AACAGCAATGTTTGGGCGATTTTTATTACG 12 27 1 TTTGGGCGAT 0.88501 -184 TAAATTTATTTGAAGGCAATAAAAAAGTAG 12 180 0 TGAAGGCAAT 0.882939 -31 ********** Masking position 10 Map Score: 9.32929 Number of sites scoring better than the average of aligned sites = 1469 Number in coding regions = 1406 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 TCTGGCGCACTAAAAACCAGTATTTCACATGA 4 87 1 TAAAAACCAA 0.878875 -174 CGTGAATTAATTAAAAACACGAATCACATTGT 8 237 0 TTAAAAACAA 0.830383 -48 ATCAGACCTTAAAATATCACTATTAGTACTTG 9 41 0 AAAATATCAA 0.689129 -260 AATGCGCATAAAAATAACAGCATAAAACACCT 9 100 1 AAAATAACAA 0.933608 -201 ATTTTTTCATTGAAAAACAATACAATATGAAA 9 148 0 TGAAAAACAA 0.878875 -153 TATCTCACGATAAATAACATTAGGATTTTGTT 9 193 1 TAAATAACAA 0.968804 -108 GACTCGTGTTTAAATAACAAAATCCTAATGTT 9 208 0 TAAATAACAA 0.968804 -93 ATCTGGTCGATAAAAAACAGTAAATGGCTTCA 10 81 0 TAAAAAACAA 0.968804 -150 AGGCTTAATTTAAATAACAAAATCCTAAGCAG 12 118 0 TAAATAACAA 0.968804 -93 ACTTAAGGTCAAAAAAACAGAAGGGTAAAAA 13 10 0 AAAAAAACAA 0.933608 -180 ********* * Masking position 6 Map Score: 7.8098 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 37 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 GCAGTATCCAGTCAAGGCGCGCTATCGTCA 2 43 1 GTCAAGGCGC 0.883216 -231 TTTATCCCGCGTCAGGGAGAGGCAGTGCGT 4 133 0 GTCAGGGAGA 0.958084 -128 CAGGTAAGTGATTCGGGGGAGCGAACGCAG 5 118 1 ATTCGGGGGA 0.93958 -157 GTTTGTGAACGTCAGGGCGCAGAGATCCCC 5 220 0 GTCAGGGCGC 0.958464 -55 TTACGTGATAATTCAGGAGACACAGAATGC 9 75 1 ATTCAGGAGA 0.825214 -226 AAAGCAACAGGTTAGGGGGAGTTAACATTA 10 124 0 GTTAGGGGGA 0.967653 -107 AAACATTGCTGTTCGGGCGATCAAATTAA 12 10 0 GTTCGGGCGA 0.989105 -201 GAACAGCAATGTTTGGGCGATTTTTATTAC 12 26 1 GTTTGGGCGA 0.94564 -185 CACCTTGCGGATTCAGGAGACTGAC 13 175 1 ATTCAGGAGA 0.825214 -15 ********** Masking position 2 Map Score: 6.23294 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 431 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 AAACTGCTGACGCAAATGCCGTCAGATGAG 2 159 1 CGCAAATGCC 0.825546 -115 TCGGGATTCGCTCACTTGCCGCCTTGATGC 5 78 0 CTCACTTGCC 0.92508 -197 TCCTTCAAGCCGCCTCTGCCTTGGCTGCGT 5 142 0 CGCCTCTGCC 0.921137 -133 GGCAACTATTCGCCGTTGCCCTTCATTCAC 7 14 0 CGCCGTTGCC 0.97891 -234 GAAAAGCTGGCACACCTGCCAAACAACCTG 7 121 1 CACACCTGCC 0.923624 -127 GGGGATTGCCTGCACCTGCCAGGTTGTTTG 7 140 0 TGCACCTGCC 0.951474 -108 GCCCACAGAGCGCGGTTGCTAACAAGAACA 7 207 1 CGCGGTTGCT 0.894145 -41 TAATGTTTTCCGCAGTTGCTATACAGATCG 8 103 0 CGCAGTTGCT 0.949311 -182 ACGAGTCCTTTGCACTTGCTTACTTTATCG 9 233 1 TGCACTTGCT 0.87624 -68 ********** Masking position 7 Map Score: 4.91587 Number of sites scoring better than the average of aligned sites = 1350 Number in coding regions = 1296 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 GACGGCATTTGCGTCAGCAGTTTGCGTACCG 2 151 0 GCGTCAGCAT 0.829106 -123 GACGCAAATGCCGTCAGATGAGTAGACACTA 2 167 1 CCGTCAGATA 0.622467 -107 GGGCAATACTGCGTGAGAATTTCCTCAAAGC 2 208 1 GCGTGAGAAT 0.87298 -66 AAAATAGGTTGCGCGAGATTATAGAGATCTG 4 60 1 GCGCGAGATA 0.886248 -201 GGTTTTTAGTGCGCCAGATCTCTATAATCTC 4 74 0 GCGCCAGATT 0.984789 -187 CAAGACAGGCTTGCGAGATATGTTTGAGAAT 4 168 0 TTGCGAGATT 0.709128 -93 ATAAAGAATGTCGCCAGAAATAAACGGGCAT 5 182 1 TCGCCAGAAT 0.963934 -93 TTTGGCAGGTGTGCCAGCTTTTCATACAGTG 7 113 0 GTGCCAGCTT 0.703941 -135 TATTAACCTCGTCAGATGTTGTGTTCTTG 7 229 0 TCGTCAGATT 0.954975 -19 CGCTACTCTCCAGATGTTTCACATTTC 8 7 1 TCTCCAGATT 0.740428 -278 ATGTTATTTATCGTGAGATATTACGCGAATA 9 182 0 TCGTGAGATT 0.897138 -119 CCGTTTTATCGGGGCAGATATAACATTAAA 10 10 0 GGGGCAGATT 0.677119 -221 TTAATTTGATCGCCCGAACAGCAATGTTTG 12 10 1 TCGCCCGAAA 0.532934 -201 CTGATCACGCTCGGCAGAAATCACGCTCTGG 13 67 0 TCGGCAGAAT 0.8906 -123 ********* * Masking position 7 Map Score: 5.72635 Number of sites scoring better than the average of aligned sites = 2528 Number in coding regions = 2410 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 8 AGTATCCAGTCAAGGCGCGCTATCGTCAGCC 2 45 1 CAAGGCGCGT 0.928008 -229 CAGGGAGAGGCAGTGCGTAAAAAGACGCGGA 4 120 0 CAGTGCGTAA 0.816958 -141 GTATAGATTGCCGGGCGCATTGCGCTTACCC 5 30 0 CCGGGCGCAT 0.976309 -245 TTGTGAACGTCAGGGCGCAGAGATCCCCGGG 5 217 0 CAGGGCGCAA 0.978432 -58 AAACCGCCCACAGAGCGCGGTTGCTAACAAG 7 202 1 CAGAGCGCGT 0.989647 -46 AGTTGCTATACAGATCGCATAGTTAACATTT 8 89 0 CAGATCGCAA 0.807508 -196 ATCGTTCATCCAGAGCGTGATTTCTGCCGAG 13 58 1 CAGAGCGTGT 0.973935 -132 GTGATTTCTGCCGAGCGTGATCAGATCGGCA 13 74 1 CCGAGCGTGT 0.954871 -116 ********* * Masking position 6 Map Score: 4.27582 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 864 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ATTGACCGCGGATGCACGGTCAATATTTCTAC 1 27 0 GATGCCGGCA 0.978651 -79 TTCTCTGAACGCTGCTCGGTAAACAATAAAGA 2 79 0 GCTGCCGGAA 0.988542 -195 TAACGTAGCAGCACTGTCACCTTCTGGCA 3 8 1 GCAGCCTGCA 0.988727 -106 TTTATCCGTAGCAGCACTGCCAGAAGGTGACA 3 25 0 GCAGCCTGCA 0.988727 -89 TCATACAGTGGATGCCCTGAAAATAGATGTAC 7 91 0 GATGCCTGAA 0.972349 -157 ACAGTAAATGGCTTCACTGCAAAATGACCGTT 10 65 0 GCTTCCTGAA 0.94152 -166 ***** *** ** Masking position 12 Map Score: 3.22602 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 324 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 TGGGGGCAATGATTTATCCGTAGCAGCACT 3 39 0 GATTTATCCG 0.945205 -75 GCTGTCTGGCATTTTATCAGTCACATTGGT 3 68 0 ATTTTATCAG 0.739064 -46 GCACAACATCAATTTATCAGGATACGTT 3 96 1 AATTTATCAG 0.843736 -18 TATAAATCATTATTTATCAGTGCATTAATG 8 128 0 TATTTATCAG 0.885542 -157 ATCCTAATGTTATTTATCGTGAGATATTAC 9 189 0 TATTTATCGT 0.674551 -112 AAAAAAGTAGGATTTATCGATAAAGTAAGC 9 250 0 GATTTATCGA 0.883022 -51 TATCTGCCCCGTTTTATCGGGGCAGATATA 10 19 0 GTTTTATCGG 0.945392 -212 CATTTACTGTTTTTTATCGACCAGATAATC 10 87 1 TTTTTATCGA 0.657207 -144 AAAAAAGTAGGATTTATCCGCAATGGAAGC 12 160 0 GATTTATCCG 0.945205 -51 ********** Masking position 5 Map Score: 3.62746 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 368 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 11 ATTGACCGCGGATGCACGGTCAATATTTCT 1 29 0 GATGCACGGT 0.943374 -77 TTCTCTGAACGCTGCTCGGTAAACAATAAA 2 81 0 GCTGCTCGGT 0.928833 -193 TAACGTAGCAGCACTGTCACCTTCTGG 3 8 1 GCAGCACTGT 0.964937 -106 TTTATCCGTAGCAGCACTGCCAGAAGGTGA 3 27 0 GCAGCACTGC 0.938453 -87 CATTCAAGTTGCATCAAGGCGGCAAGTGAG 5 68 1 GCATCAAGGC 0.911472 -207 ACCTTTTGACTCTTCACGGTTAATCGGAAA 6 11 0 TCTTCACGGT 0.760729 -27 ACAGTAAATGGCTTCACTGCAAAATGACCG 10 67 0 GCTTCACTGC 0.945489 -164 ATCCGCAATGGAAGCAAGGCATTACAGGCT 12 145 0 GAAGCAAGGC 0.85801 -66 ********** Masking position 5 Map Score: 3.17228 Number of sites scoring better than the average of aligned sites = 1504 Number in coding regions = 1449 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 12 AACAATAAAGAGGTGGCTGACGATAGCGCG 2 60 0 AGGTGGCTGA 0.942247 -214 GCCCCCACCAATGTGACTGATAAAATGCCA 3 62 1 ATGTGACTGA 0.935335 -52 GTGATCGACAAGGAGACTTAAC 4 249 1 AGGAGACTTA 0.917412 -12 TCGGTGAATGAAGGGCAACGG 7 2 1 CGGTGAATGA 0.892535 -246 TATGTTTGAACTGTGACGGATTTCGCACCC 8 164 0 CTGTGACGGA 0.843128 -121 TGCTAAGATGCGGAGACTTAAGGTCAAAAA 13 27 0 CGGAGACTTA 0.930625 -163 TTGCGGATTCAGGAGACTGAC 13 179 1 AGGAGACTGA 0.976031 -11 ********** Masking position 10 Map Score: 2.25716 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 215 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ATTATGTTGCGCCCTTTTTTTACGGGTGTT 1 66 1 GCCCTTTTTT 0.951183 -40 ACGCAGTATTGCCCGATTTTTGTTTAGTGT 2 192 0 GCCCGATTTT 0.96882 -82 AAGTGTCCCAGCCTGTTTATCTACGGCTTA 4 14 1 GCCTGTTTAT 0.963714 -247 CGGGCCGTATGCCCGTTTATTTCTGGCGAC 5 191 0 GCCCGTTTAT 0.982096 -84 GCGAATAGTTGCCCTTTTATTTCACTAAGT 7 31 1 GCCCTTTTAT 0.937358 -217 ATATTTTAAGGTCTGATTTTTACGTGATAA 9 56 1 GTCTGATTTT 0.804078 -245 CGATAATAAAGTCTGTTTTTAATATTATCA 12 55 1 GTCTGTTTTT 0.90416 -156 ********** Masking position 7 Map Score: 5.12656 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 213 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 14 GCAACATAATAGCTAACATTGACCGCGGAT 1 46 0 AGCTAACATT 0.799796 -60 AAAAACCAGTATTTCACATGAGTCCGCGTC 4 98 1 ATTTCACATG 0.880268 -163 GGTTTAGTCAGGTTCACATTATCAGTACTG 7 177 0 GGTTCACATT 0.904445 -71 CTCTCCAGATGTTTCACATTTCTGTTGCTA 8 16 1 GTTTCACATT 0.880268 -269 CAGATCGCATAGTTAACATTTCGTTAAAAG 8 80 0 AGTTAACATT 0.937659 -205 CCACCCAAGAATTTCATATTGTATTGTTTT 9 137 1 ATTTCATATT 0.595879 -164 ATCGGGGCAGATATAACATTAAA 10 4 0 ATATAACATT 0.676752 -227 GGTTAGGGGGAGTTAACATTAGAGAACAGA 10 115 0 AGTTAACATT 0.937659 -116 TAATATAAACATTTAACATGATAATATTAA 12 73 0 ATTTAACATG 0.85098 -138 ********** Masking position 6 Map Score: 2.73421 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 45 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 15 AATGCCAGACAGCACAACATCAATTTATCA 3 85 1 AGCACAACAT 0.941841 -29 CGGCAATCTATACACAAAATCATTCAAGTT 5 48 1 TACACAAAAT 0.834487 -227 ATTCTTTATATACACTTCATCCTTCAAGCC 5 161 0 TACACTTCAT 0.746627 -114 AAAATAGATGTACACATCATGCATAATGTG 7 74 0 TACACATCAT 0.934184 -174 TGCTAACAAGAACACAACATCTGACGAGGT 7 223 1 AACACAACAT 0.960105 -25 TCCGCATCTTAGCACATCGTTCATCCAGAG 13 43 1 AGCACATCGT 0.792823 -147 GCATATTTTTAACACAAAATACACACTTCG 13 124 1 AACACAAAAT 0.867813 -66 ********** Masking position 4 Map Score: 0.880371 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 118 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912