AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_ecoli_bsub_300.orf -o250_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 yabB 300 orf, hypothetical protein #2 murC 53 L-alanine adding enzyme, UDP-N-acetyl-muramate:alanine ligase #3 ftsZ 60 cell division; forms circumferential ring; tubulin-like GTP-binding protein and GTPase #4 ddlA 300 D-alanine-D-alanine ligase A #5 murB 300 UDP-N-acetylenolpyruvoylglucosamine reductase #6 ddlA 174 D-alanyl-D-alanine ligase A #7 murF 71 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase #8 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #9 yllA 70 yllA #10 yllB 125 similar to hypothetical proteins #11 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #12 ftsL 39 cell-division protein #13 spoVD 116 penicillin-binding protein #14 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #15 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #16 spoVE 60 spoVE #17 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #18 murB 26 UDP-N-acetylenolpyruvoylglucosamine reductase #19 divIB 130 cell-division initiation protein #20 ylxX 22 similar to hypothetical proteins #21 ftsA 173 cell-division protein #22 ftsZ 35 cell-division initiation protein #23 murC 249 UDP-N-acetyl muramate-alanine ligase #24 ytpS 159 ytpS #25 ytpP 234 similar to thioredoxin H1 Motif number 1 CGTCGCAAACTGACACTTTATATTTGCTGTGGA 1 40 1 TGACCTTATT 0.889003 -261 CGTTTTAAAATGACTCACTATTTTCCACAGCAA 1 63 0 TGACCCTATT 0.958633 -238 GTGACTGGCTTGACAAGCTTTTCCTCAGCTCCG 1 221 1 TGACACTTTC 0.468128 -80 ATTCCCACTTTGCCCCACAATTTCCCACTGAAA 1 262 0 TGCCCCAATT 0.840022 -39 GCCAGCCTCACCCCTTATTCCCACTTTGCC 1 281 0 TCACCTTATC 0.827453 -20 ATCTTTGAGATAACGCACTTTCTTCACCAGTAC 4 168 1 TAACCCTTTT 0.771043 -133 AGGCCGCGAATCCCCCGTTTTGTCGTGGTAATG 4 243 1 TCCCCTTTTT 0.935358 -58 GTAAGGTCCCTCTCTTTCTTTTGTATATA 7 53 0 TCCCCCTTTT 0.976672 -19 ACAAATCTCCCCCTTTGTTGTTTCTACA 8 6 1 TCTCCCTTTT 0.844493 -154 GATGTCACACCCAATTTAGCATTTACG 8 143 0 TCACCCAATT 0.89821 -17 TCATTTCGGATCACTAACTATTTATTGGAGAAA 9 34 1 TCACACTATT 0.780498 -37 GATCTCTTGCCCCACTTTCTCTCCTTAACT 10 106 0 TGCCCCTTTT 0.962168 -20 ATTGTGTTGGTCCCACCTTTTATCAGGATGAAT 11 47 0 TCCCCTTTTT 0.935358 -23 GAGACCGTTCACTCCTTATTTAGGCTTGTTT 13 96 0 TCACCTTATT 0.929503 -21 TCTATTTCACCCGCTTTTTCAG 20 4 0 TCACCCTTTT 0.977138 -19 CCCCAGTATATGACGCTCATTTCAATTTGCGAC 23 197 0 TGACCCATTC 0.685953 -53 AATAAAAATCCCTCCTTATGTATATCCATCT 25 9 1 TCCCCTTATT 0.928139 -226 **** * **** * Masking position 11 Map Score: 17.3772 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 298 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 GACTGAGCCTTTCGTTTTATTTG 5 4 0 TTCGTTTTAT 0.955095 -297 GACTGGGCCTTTCGTTTTATCTGTTGTTTG 5 38 1 TTCGTTTTAT 0.955095 -263 TGTATGTAATTCCTTTTTATTTTATATTAA 6 38 0 TCCTTTTTAT 0.89822 -137 AGTTCAGGGTTTCTTTTTATGGGTAAACAG 10 36 1 TTCTTTTTAT 0.954281 -90 GCTCCACAACTTCATTTTACACTGTTTACC 10 57 0 TTCATTTTAC 0.710412 -69 GCTGATGACCTCCTTTTAATTTTGCGTTCG 12 18 0 TCCTTTTAAT 0.770802 -22 TATGCAGGCTTTCTTTTTTTATGCCTTCAG 13 26 1 TTCTTTTTTT 0.914895 -91 TTAGGCTTGTTTCATTTTATGCCTGAATTT 13 78 0 TTCATTTTAT 0.852988 -39 GGGCTGCCTATTCTTTTATTGCAGAAAAAA 14 14 1 TTCTTTTATT 0.803792 -162 GCTGGATGTATCCTTTTATTTACGCTAAAA 14 65 1 TCCTTTTATT 0.633979 -111 TTCTAATTCGTTCTTTTTATCATTGAAGTC 14 137 0 TTCTTTTTAT 0.954281 -39 TTCTTTTTTCCCCCAGTCTA 17 113 0 TTCTTTTTTC 0.819664 -10 ATTGAAAATATTCGTTATATCCTATGTATA 21 18 0 TTCGTTATAT 0.660681 -156 TTTCACATGATTCGTTTTTTTTGGCGGATT 24 20 0 TTCGTTTTTT 0.916349 -140 TCAAGCTCGTTTCGTTTAACATCGTGTACA 25 58 0 TTCGTTTAAC 0.774111 -177 ********** Masking position 5 Map Score: 15.5486 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 132 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 AGTGGGAAATTGTGGGGCAAAGTGGGAATA 1 266 1 TGTGGGGCAA 0.967004 -35 TTACCGTATCTGTGGGGGGATGGCTTGTAG 5 249 0 TGTGGGGGGA 0.986838 -52 GATGAATTGTAGTGGGGGGAGTATCCATTG 6 137 1 AGTGGGGGGA 0.986838 -38 AAAATGAAGTTGTGGAGCGAAGTGGTGAAT 10 69 1 TGTGGAGCGA 0.944899 -57 AAGGAGAGAAAGTGGGGCAAGAGATC 10 110 1 AGTGGGGCAA 0.967004 -16 AGAAACTTAGACTGGGGGAAAAAAGAA 17 106 1 ACTGGGGGAA 0.947405 -17 CTTAATCTTTTCTGGGCCGACCAGCAGTGG 24 92 1 TCTGGGCCGA 0.884078 -68 AACATAAACAACTGGAGGGATATGAA 25 219 1 ACTGGAGGGA 0.913347 -16 ********** Masking position 10 Map Score: 8.98188 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 94 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 ATGTCCTAAAATGCCGCTCGCGTCGCAAAC 1 20 1 ATGCCGCTCG 0.895866 -281 TTACCTCGGTATGCCTTGTGACTGGCTTGA 1 204 1 ATGCCTTGTG 0.886631 -97 TTGTAGCGATGCCTTTTGCATCGTATGA 2 9 1 ATGCCTTTTG 0.974027 -45 CTCCTTTTCAATGCCATTTTAATATAAAAT 6 20 1 ATGCCATTTT 0.880732 -155 TTTGTATGTAATTCCTTTTTATTTTATATT 6 40 0 ATTCCTTTTT 0.646541 -135 ATAACTACGTATGTCGTTTGAAAGAAACAG 15 78 1 ATGTCGTTTG 0.893411 -35 GTAACCTCGCATTCCATTTGCTTTT 18 6 0 ATTCCATTTG 0.818981 -21 GCATACTATGATGCCGTTTGTTCGTTTGCT 19 50 0 ATGCCGTTTG 0.989684 -81 GCATCATAGTATGCCGTTTGTTTTGGAATA 19 66 1 ATGCCGTTTG 0.989684 -65 TTTAACAGCTATGCCGCTTTACAGCAGCTG 23 58 1 ATGCCGCTTT 0.920883 -192 ********** Masking position 2 Map Score: 9.74345 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 298 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TTGCGACGCGAGCGGCATTTTAGGACATAT 1 18 0 AGCGGCATTT 0.771722 -283 ATCCGCTCCCGGCGGATTTGTCCTACTCAG 5 83 0 GGCGGATTTG 0.982455 -218 ATCCGCCGGGAGCGGATTTGAACGTTGCGA 5 96 1 AGCGGATTTG 0.959834 -205 ATGTTAGACAGGAGGCTTGGAAATACATTC 17 12 0 GGAGGCTTGG 0.915497 -111 CGGCAGATTAGGAGGATTTAGC 22 24 1 GGAGGATTTA 0.842241 -12 CTCCCTTAGCGGCGTATTTTATATGTTTTG 23 150 0 GGCGTATTTT 0.755163 -100 CGCCGCTAAGGGAGGCTTTTCAGCCGCCGC 23 166 1 GGAGGCTTTT 0.940776 -84 CGTTTTTTTTGGCGGATTTATGGGAGT 24 8 0 GGCGGATTTA 0.949803 -152 ACAAGGGCTTAGCGGCTTTTCACATGATTC 24 37 0 AGCGGCTTTT 0.960041 -123 GCCCTTGTTTAGCGGCTTGGTTTCTGCTGA 24 59 1 AGCGGCTTGG 0.942482 -101 ********** Masking position 8 Map Score: 8.27318 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 795 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 AGCTGTAAGAAAAAATCCCTCATCGTCATCA 1 97 0 AAAAATCCTC 0.950278 -204 CAAATTAAGCAGAAGGCCATCCTGACGGATG 5 179 1 AGAAGGCCTC 0.982924 -122 TAGAAACGCAAAAAGGCCATCCGTCAGGATG 5 196 0 AAAAGGCCTC 0.979452 -105 AAAGAAAGCCGTCGTTATGCAGG 13 3 1 AGAAAGCCTC 0.979452 -114 GCATAAAAAAAGAAAGCCTGCATAACGACGG 13 19 0 AGAAAGCCGC 0.936172 -98 AACAGCTGTTAAAAGTCTGTCTATTCCAAAA 19 86 0 AAAAGTCTTC 0.749589 -45 AATAAAAATCCCTCCTTATGTATA 25 4 1 AAAAATCCTC 0.950278 -231 ******** ** Masking position 4 Map Score: 3.80706 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 66 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 TAAAAAACCCGATGTTTACGGCTAATATCAGC 1 175 0 GATGTTAGGC 0.976231 -126 AAATTCATACGATGCAAAAGGCATCGCTACAA 2 11 0 GATGCAAGGC 0.890783 -43 ATGAATTTAAGAAGTTAATGGCGTAAAGA 2 35 1 GAAGTTAGGC 0.97141 -19 TGAGGCCGACGATGATTACGGCCTCAGGCGAC 3 17 1 GATGATAGGC 0.948689 -44 CGCTTTGTCAGCAGAAGATTGCAACAATCTTT 4 207 1 GCAGAAATGC 0.767428 -94 TTGATGCCTGGCAGTTTATGGCGGGCGTCCTG 5 150 0 GCAGTTAGGC 0.955392 -151 TGGGCATGCTGATGTTGAATGCATTTGTATGT 6 61 0 GATGTTATGC 0.955816 -114 TGAAGAAGGACACTGCCGGTAAAAGG 7 5 1 GAAGGAATGC 0.770765 -67 AAGCGGCATAGCTGTTAAATGCTCTAAACACT 23 45 0 GCTGTTATGC 0.927417 -205 ****** * *** Masking position 8 Map Score: 4.28935 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 393 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 AAATTAGCTTCCCGTTCATCATTTTTGTGA 4 128 1 CCCGTTCATC 0.900724 -173 AAAAACCTATCCCGTCTAACACAAAGTGCA 4 278 0 CCCGTCTAAC 0.967586 -23 CATCGTTCTACCTGTCCAAATTCAGGCATA 13 61 1 CCTGTCCAAA 0.942807 -56 TTCCAAGCCTCCTGTCTAACATGAAGCTTG 17 20 1 CCTGTCTAAC 0.972978 -103 ATGCGATAACCCTGTCCAACAAAACAGGGT 17 60 1 CCTGTCCAAC 0.990702 -63 TGCCTGTTCACCTCATTCAAAT 19 119 0 CCTGTTCACC 0.941928 -12 ********** Masking position 5 Map Score: 2.63997 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 106 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 9 ATGTCACATCTCCTTTTCAATGCCATTTTA 6 11 1 TCCTTTTCAA 0.936598 -164 TACTATCTTATCATTTTCACCGGAAAATGA 6 105 0 TCATTTTCAC 0.956186 -70 ATATGAAAAATCTTTTTCAAGCTCCATTAT 15 28 0 TCTTTTTCAA 0.833099 -85 TGTCCTTTTCTCCTCCTGTTTC 15 101 0 TCCTTTTCTC 0.920472 -12 TCTATTTCACCCGCTTTTTC 20 13 0 TCTATTTCAC 0.796372 -10 TATTTTTATGTGCTTTTCACATTTTATGTT 21 49 0 TGCTTTTCAC 0.958071 -125 TATGGGTTCATTTTCACACCAAACATG 23 8 1 TCATTTTCAC 0.956186 -242 AGGGCTTAGCGGCTTTTCACATGATTCGTT 24 34 0 GGCTTTTCAC 0.85854 -126 ********** Masking position 5 Map Score: 3.12206 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 224 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 TTCTCTCCGATTTGTGCCTGTCGCCTGAGG 3 38 0 TTTGTGCCTG 0.957644 -23 GGGAAGCTAATTTATTCCTGGCTTAAATGG 4 111 0 TTTATTCCTG 0.905042 -190 TCTGCTTAATTTGATGCCTGGCAGTTTATG 5 162 0 TTGATGCCTG 0.957644 -139 GCTTTCTTTTTTTATGCCTTCAGAGGAGCA 13 33 1 TTTATGCCTT 0.905042 -84 CTTGTTTCATTTTATGCCTGAATTTGGACA 13 73 0 TTTATGCCTG 0.986573 -44 TCACTCCTTATTTAGGCTTGTTTCATTTTA 13 89 0 TTTAGGCTTG 0.879942 -28 CCCTAATGACTTTAAGCTTGGGGTGTCGAT 16 37 1 TTTAAGCTTG 0.831795 -24 ********** Masking position 2 Map Score: 3.0953 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 228 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 11 AAAAAACTCACCGCATGGCCATTTAAGCCA 4 93 1 CCGCATGGCC 0.983788 -208 GGGTGGCGGGCAGGACGCCCGCCATAAACT 5 140 1 CAGGACGCCC 0.978997 -161 GGCCATCCGTCAGGATGGCCTTCTGCTTAA 5 183 0 CAGGATGGCC 0.990789 -118 GGCCATCCTGACGGATGGCCTTTTTGCGTT 5 193 1 ACGGATGGCC 0.94727 -108 CATTCAACATCAGCATGCCCAAAAATAATT 6 72 1 CAGCATGCCC 0.967 -103 TATACCACTGCTGGTCGGCCCAGAAAAGAT 24 96 0 CTGGTCGGCC 0.896987 -64 ********** Masking position 7 Map Score: 2.26299 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 190 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 CGGCCTCAGGCGACAGGCACAAATCGGAGAG 3 35 1 CGACAGGCCA 0.983435 -26 CAAATAAAACGAAAGGCTCAGTCGAAAGAC 5 10 1 CGAAAGGCCA 0.986227 -291 ACAGATAAAACGAAAGGCCCAGTCTTTCGAC 5 31 0 CGAAAGGCCA 0.986228 -270 AAGAGTTTGTAGAAACGCAAAAAGGCCATCC 5 205 0 AGAAACGCAA 0.875705 -96 CGAAACGCGAACGCAAAATTA 12 1 1 CGAAACGCAA 0.978514 -39 AGCAATCGACACCCCAAGCTTAAAGTC 16 44 0 CGACACCCAA 0.896447 -17 ******** ** Masking position 5 Map Score: 1.8618 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 88 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 13 AGTGTCAGTTTGCGACGCGAGCGGCATTTTAGGA 1 23 0 TCGACCAGCG 0.982726 -278 ATTTGTGCCTGTCGCCTGAGGCCGTAATCATCGT 3 25 0 GCGCCGGGCG 0.9792 -36 GTAGGACAAATCCGCCGGGAGCGGATTTGAACGT 5 87 1 TCGCCGAGCG 0.993235 -214 TTGTAGATATGACGACAGGAAGAGTTTGTAGAAA 5 221 0 GCGACGAAGG 0.809208 -80 TTCAAGTTCTGACTGAAGCTGTTCATATGAC 19 8 1 TTGACGAGCG 0.954894 -123 ACATATAAAATACGCCGCTAAGGGAGGCTTTTCA 23 154 1 TCGCCCAAGG 0.879548 -96 CATTTCAATTTGCGACCGCGGCGGCTGAAAAGCC 23 179 0 TCGACGGGCG 0.981278 -71 TATAAGTGGTTTTGCCTCAAGCAGTTTGGTATGA 25 150 1 TTGCCCAGCG 0.953787 -85 * **** * *** * Masking position 6 Map Score: 1.71186 Number of sites scoring better than the average of aligned sites = 1278 Number in coding regions = 1219 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 14 TTTCGACTGAGCCTTTCGTTTTATTTG 5 8 0 GCCTTTCGTT 0.953892 -293 GAAAGACTGGGCCTTTCGTTTTATCTGTTG 5 34 1 GCCTTTCGTT 0.953892 -267 CACCCTCCGGGCCGTTGCTTCGCAACGTTC 5 115 0 GCCGTTGCTT 0.887922 -186 ATACTATGATGCCGTTTGTTCGTTTGCTTA 19 48 0 GCCGTTTGTT 0.989186 -83 ATCATAGTATGCCGTTTGTTTTGGAATAGA 19 68 1 GCCGTTTGTT 0.989186 -63 GGAACAGATAGACGTTTGTTGGAGGTACAA 23 228 1 GACGTTTGTT 0.922273 -22 TTTGCCTCAAGCAGTTTGGTATGATCCAAA 25 160 1 GCAGTTTGGT 0.784995 -75 ********** Masking position 5 Map Score: 4.50817 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 121 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ACGGCTAATATCAGCGTTGTTTATTTTACGT 1 159 0 TCAGCTTGTT 0.832739 -142 GCCGTAAACATCGGGTTTTTTACCTCGGTAT 1 185 1 TCGGGTTTTT 0.909225 -116 AGCTTCCCGTTCATCATTTTTGTGATCTTGC 4 133 1 TCATCTTTTT 0.857396 -168 CCTGAACTAGTCAGGGTTCTTTAAAACTTTA 10 13 0 TCAGGTTCTT 0.918177 -113 CCTGACTAGTTCAGGGTTTCTTTTTATGGGT 10 29 1 TCAGGTTTCT 0.953814 -97 CCGTCGTTATGCAGGCTTTCTTTTTTTATGC 13 19 1 GCAGGTTTCT 0.828328 -98 TTGAAAGATATCAGCATTTTTTCTGCAATAA 14 29 0 TCAGCTTTTT 0.955175 -147 GTTATCATATTCATGATTTTTTTCCATATGA 15 52 0 TCATGTTTTT 0.931279 -61 ATGTTTAGTATCAGGTTATTTCTTTCCGATT 23 117 0 TCAGGTATTT 0.871101 -133 TTATGTTCTTACATGTTTTTTATCGATACTC 25 195 0 ACATGTTTTT 0.681152 -40 ***** ***** Masking position 7 Map Score: 2.29469 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 311 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041