AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_mixed5_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aspS 276 aspartate tRNA synthetase #2 hisS 110 histidine tRNA synthetase #3 gcpE 26 orf, hypothetical protein #4 yfgA 284 putative membrane protein #5 yfgB 149 orf, hypothetical protein #6 ndk 148 nucleoside diphosphate kinase #7 b2520 47 orf, hypothetical protein Motif number 1 CCGCGCTGGAACGCCTCGTTACCACTTTAT 1 118 0 ACGCCTCGTT 0.980412 -159 CCGTAAGAGCCTGGCCCGCGCTGGAACGCC 1 133 0 CTGGCCCGCG 0.895848 -144 CTGCCGGCGGATGCCCCCTGCTGCGCAGGT 1 238 0 ATGCCCCCTG 0.980787 -39 GTGATGGGAAGCGCCTCGCTTCCCGTGTAT 2 15 1 GCGCCTCGCT 0.905376 -96 TTGAACCCGCATGGCTCCCGAAACATTGAG 2 47 1 ATGGCTCCCG 0.845339 -64 TAGCCATTACGCCACGGTTACTTTATGT 4 9 1 ACGCCACGGT 0.985718 -276 ATAAAACATTACGCCACGGTACATAAAGTA 4 29 0 ACGCCACGGT 0.985718 -256 GTCAGCAAAAACGCACCGTTAATATTGACC 4 86 0 ACGCACCGTT 0.914396 -199 AATTTCGTAAATGCCGCGTGCAAACGTGGC 5 12 1 ATGCCGCGTG 0.973301 -138 TGGCGCACGGATGCCACGTTTGCACGCGGC 5 24 0 ATGCCACGTT 0.968877 -126 GTACAATGCAGCGCCCCCGGACGAGCAGCC 5 60 1 GCGCCCCCGG 0.968187 -90 GAAAAAAGAAACGCCCCGGTGAGCGGCTGC 5 84 0 ACGCCCCGGT 0.996402 -66 ATTACACGTTATGGCCCCTGGAGGGTTGAA 5 111 0 ATGGCCCCTG 0.968738 -39 TCAATAGTCAACGGCCCTGTTGCTCATTAT 6 70 1 ACGGCCCTGT 0.921774 -79 AGCGTACGAGATGGCGCGGATTATAATGAG 6 92 0 ATGGCGCGGA 0.798618 -57 CCCTGCCACAATGGCCCGTTAGCAACGTCG 7 21 0 ATGGCCCGTT 0.987069 -27 ********** Masking position 7 Map Score: 26.7462 Number of sites scoring better than the average of aligned sites = 1772 Number in coding regions = 1635 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 2 GATTAGCCGATGGCGGAACGACAAATTTTGTT 1 21 1 TGGCGGAAGC 0.975968 -256 TACGCCAGTTTGCTATAAAGGTGTTGCCCGAA 1 65 0 TGCTATAAGT 0.658118 -212 TATAGCAAACTGGCGTAGAGTCTGATTTCAGG 1 80 1 TGGCGTAGGC 0.975967 -197 CTGGAAATTCTGCCGCACCGTAAGAGCCTGGC 1 148 0 TGCCGCACGA 0.931403 -129 CATTCAGTTGTGACATACAGCTAACGCTGCGA 1 199 1 TGACATACGT 0.721739 -78 AAAGTAACCGTGGCGTAATGGCTA 4 3 0 TGGCGTAAGC 0.99248 -282 TTATGTACCGTGGCGTAATGTTTTATGAATGA 4 33 1 TGGCGTAAGT 0.982555 -252 CGTTACATACTGCCTTAAAGTCAGCAAAAACG 4 103 0 TGCCTTAAGC 0.953164 -182 GTGAGCATGATGGTTCACCGGCATCTCAATTC 4 240 1 TGGTTCACGC 0.845175 -45 GTACAAATTCTGGCGCACGGATGCCACGTTTG 5 32 0 TGGCGCACGT 0.985097 -118 TTTTCATCCCTGCCACAATGGCCCGTTAGCAA 7 26 0 TGCCACAAGC 0.96944 -22 ******** * * Masking position 7 Map Score: 10.5681 Number of sites scoring better than the average of aligned sites = 2007 Number in coding regions = 1916 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 ATCGGCTAATCGCATTAAGGT 1 2 0 CGCATTAAGG 0.959142 -275 TAACGTGATGGGAAGCGCCTC 2 2 1 AACGTGATGG 0.944547 -109 TGGCTCCCGAAACATTGAGGGAAGCGTTGA 2 58 1 AACATTGAGG 0.919134 -53 CATTGAGGGAAGCGTTGAGGGTTCATTTTT 2 70 1 AGCGTTGAGG 0.979792 -41 ACGGATGTTTCGCGGTGTGGGTGAGCATGA 4 220 1 CGCGGTGTGG 0.959114 -65 GGTGTGGGTGAGCATGATGGTTCACCGGCA 4 233 1 AGCATGATGG 0.944547 -52 CTCGTTATTACACGTTATGGCCCCTGGAGG 5 117 0 CACGTTATGG 0.968322 -33 ********** Masking position 3 Map Score: 4.76522 Number of sites scoring better than the average of aligned sites = 670 Number in coding regions = 631 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 TATGAGTTCGGGCAACACCTTTATAGCAAA 1 59 1 GGCAACACCT 0.915916 -218 TGGCCCGCGCTGGAACGCCTCGTTACCACT 1 122 0 TGGAACGCCT 0.930038 -155 CTGCCGCACCGTAAGAGCCTGGCCCGCGCT 1 141 0 GTAAGAGCCT 0.842175 -136 TAACGTGATGGGAAGCGCCTCGCTTCCCGT 2 11 1 GGAAGCGCCT 0.985529 -100 GTGTGCTCGTGACAAAGCCCACATTCACTA 4 155 0 GACAAAGCCC 0.813495 -130 ATTTGTACAATGCAGCGCCCCCGGACGAGC 5 56 1 TGCAGCGCCC 0.97583 -94 AAACGCCCCGGTGAGCGGCTGCTCGTCCGG 5 76 0 GTGAGCGGCT 0.898752 -74 GGTTGAAAAAAGAAACGCCCCGGTGAGCGG 5 88 0 AGAAACGCCC 0.899887 -62 TTCATCAATAGTCAACGGCCCTGTTGCTCA 6 66 1 GTCAACGGCC 0.944568 -83 ********** Masking position 4 Map Score: 4.72947 Number of sites scoring better than the average of aligned sites = 3084 Number in coding regions = 2759 Number in noncoding regions = 325 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 5 ACCTTTATAGCAAACTGGCGTAGAGTCTGA 1 75 1 CAAACTGGCG 0.914917 -202 ATCCCTTAACTTAGCTGCCGGCGGATGCCC 1 252 0 TTAGCTGCCG 0.979446 -25 AAATGAGAATTGAGATGCCGGTGAACCATC 4 248 0 TGAGATGCCG 0.985551 -37 TAATTTCGTAAATGCCGCGTGCAAACG 5 8 1 GTAAATGCCG 0.895906 -142 CGCCCCCGGACGAGCAGCCGCTCACCGGGG 5 71 1 CGAGCAGCCG 0.983517 -79 TACCAGCGTACGAGATGGCGCGGATTATAA 6 96 0 CGAGATGGCG 0.987246 -53 ********** Masking position 3 Map Score: 2.67929 Number of sites scoring better than the average of aligned sites = 821 Number in coding regions = 792 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 AAAAATTAACAAAATTTGTCGTTCCGCCATC 1 29 0 AAAATTTGCG 0.969057 -248 ATTATACTGGAAATTCTGCCGCACCGTAAGA 1 155 0 AAATTCTGCG 0.992027 -122 GAAAAATCTCCCGCGTTACCCGT 3 14 0 AAAATCTCCG 0.97891 -13 TGCATTGTACAAATTCTGGCGCACGGATGCC 5 39 0 AAATTCTGCG 0.992027 -111 ******** ** Masking position 5 Map Score: 1.74188 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 58 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 GTGTATGATTGAACCCGCATGGCTCCCGAA 2 39 1 GAACCCGCAT 0.987777 -72 ATATAAAAATGAACCCTCAACGCTTCCCTC 2 74 0 GAACCCTCAA 0.939834 -37 AGATGCCGGTGAACCATCATGCTCACCCAC 4 236 0 GAACCATCAT 0.970782 -49 TCATTTAAACGTACCTGCAGCGA 4 272 1 GTACCTGCAG 0.959241 -13 TAAAAAAATGTTACCTTCATCAATAGTCAA 6 51 1 TTACCTTCAT 0.837133 -98 GTTGTTGTCTGTACCAGCGTACGAGATGGC 6 107 0 GTACCAGCGT 0.950256 -42 ********** Masking position 3 Map Score: 1.38986 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 377 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 GCGCTGGAACGCCTCGTTACCACTTTATAT 1 116 0 GCCTCGTTAC 0.993343 -161 AAATTCTGCCGCACCGTAAGAGCCTGGCCC 1 146 0 GCACCGTAAG 0.871929 -131 TGACCAAGTCGCAGCGTTAGCTGTATGTCA 1 209 0 GCAGCGTTAG 0.973108 -68 GATGGGAAGCGCCTCGCTTCCCGTGTATGA 2 17 1 GCCTCGCTTC 0.885592 -94 GAAAAATCTCCCGCGTTACCCGTCTG 3 8 0 CCCGCGTTAC 0.935341 -19 AAAACATTACGCCACGGTACATAAAGTAAC 4 27 0 GCCACGGTAC 0.942415 -258 CAGCAAAAACGCACCGTTAATATTGACCAG 4 84 0 GCACCGTTAA 0.911205 -201 ACTTACTGTTGCATCGTTACATACTGCCTT 4 119 0 GCATCGTTAC 0.981537 -166 GCGCACGGATGCCACGTTTGCACGCGGCAT 5 22 0 GCCACGTTTG 0.941338 -128 TGCTATTCCGGCCTCGTTATTACACGTTAT 5 129 0 GCCTCGTTAT 0.958588 -21 CTGCCACAATGGCCCGTTAGCAACGTCGAA 7 19 0 GGCCCGTTAG 0.944542 -29 ********** Masking position 5 Map Score: 15.0719 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 572 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 TAGAGTCTGATTTCAGGCCCGATATAAAGTG 1 95 1 TTTCAGCCCG 0.926585 -182 GCGTTTCTTTTTTCAACCCTCCAGGGGCCAT 5 100 1 TTTCACCCTC 0.971845 -50 TATTACACGTTATGGCCCCTGGAGGGTTGAA 5 111 0 TATGGCCCTG 0.919881 -39 TCTGTTTTGTCCCTGATTGTTGCTA 6 5 1 TTTTGCCCTG 0.982267 -144 TTTTACCTCTGTAAATTGTTC 6 138 0 TTTTACTCTG 0.911788 -11 TTTTCATCCCTGCCACAATGGC 7 36 0 TTTCACCCTG 0.993401 -12 ***** ***** Masking position 3 Map Score: 0.571665 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 267 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 10 GCAGAATTTCCAGTATAATAGCCGCCTTTT 1 167 1 CAGTATAATA 0.852398 -110 TATGTCACAACTGAATGAAAAAAGGCGGCT 1 186 0 CTGAATGAAA 0.923035 -91 GCAGCGTTAGCTGTATGTCACAACTGAATG 1 199 0 CTGTATGTCA 0.954662 -78 TATTCTCTTTCTGAATATAAAAATGAACCC 2 88 0 CTGAATATAA 0.809885 -23 GACTTTAAGGCAGTATGTAACGATGCAACA 4 113 1 CAGTATGTAA 0.964995 -172 AACGATGCAACAGTAAGTTAGCCTTAGTGA 4 131 1 CAGTAAGTTA 0.851265 -154 CGGTCTTATACTGTATGATAACGGTTAACT 4 188 1 CTGTATGATA 0.964995 -97 ********** Masking position 5 Map Score: 2.50289 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 185 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 ********** No masking Map Score: 1.48036e-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 12 ********** No masking Map Score: 1.48036e-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 13 ********** No masking Map Score: 1.48036e-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