AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i081_ecoli_bsub_300.orf -o081_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 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #2 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #3 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #4 osmE 201 activator of ntrL gene #5 licB 127 phosphotransferase system (PTS) lichenan-specific enzyme IIB component #6 licR 162 transcriptional regulator (antiterminator) #7 yxzF 28 yxzF #8 yxlJ 128 similar to DNA-3-methyladenine glycosidase Motif number 1 CCGGCGCAATGGCCGGTTTCCGTTGTTACT 3 31 0 GGCCGGTTTC 0.935241 -268 CCGGCCATTGCGCCGGTTTTTTTTGGCCTG 3 45 1 CGCCGGTTTT 0.977045 -254 TCGTCGATGAGGGCAGTTTT 3 289 1 GGGCAGTTTT 0.990997 -10 GTTAGCTTTAAGGAAGTTTTGTCTTTTCTG 4 25 0 AGGAAGTTTT 0.855349 -177 GGAATACATTGGGCGCTTTTTCAAGCCCGT 4 144 0 GGGCGCTTTT 0.983817 -58 CAAACTCTAGGGGGTCTTTTAC 5 116 1 GGGGTCTTTT 0.829694 -12 TCCCGGCTGTTTTTTTATAGGTC 6 4 1 CGGCTGTTTT 0.985435 -159 TTTTTTTATAGGTCAGTTTTCCCTCTAGTC 6 20 1 GGTCAGTTTT 0.92477 -143 TCTACTAGTTAGGAGGTTTTTCTC 6 149 1 AGGAGGTTTT 0.924316 -14 TCAAAAAAAACGGCTGTTTTAAAATCTTTC 8 55 0 CGGCTGTTTT 0.985435 -74 ********** Masking position 7 Map Score: 12.8398 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 789 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 2 TCAATTCGTCTGAAAGCTTGAGTAACA 3 8 1 GTCTGAAAGC 0.977916 -291 CTTTTTTTGTGGCTGAAAGGAGTATACGGT 3 186 0 GGCTGAAAGG 0.986826 -113 GTTACCCAGAGCATGGAAGCAGGTTAAGGC 3 233 1 GCATGGAAGC 0.864344 -66 TGTCTTTTCTGTCTGGAGGGGTTCA 4 6 0 GTCTGGAGGG 0.838177 -196 AGACAAAACTTCCTTAAAGCTAACCCGTTG 4 31 1 TCCTTAAAGC 0.663231 -171 AGCGACAGCGGGCTGAATGGTGGTTAAAAC 4 75 1 GGCTGAATGG 0.967479 -127 TACAGGAATCCTCTGAAAGCGGAGCCGTTT 4 109 1 CTCTGAAAGC 0.958036 -93 CCCTGAGTGTTTATGAAAGCGATTTCATAA 5 49 1 TTATGAAAGC 0.844625 -79 TTTCATAATATGATGATAGCAACAGCAGGA 5 71 1 TGATGATAGC 0.685671 -57 GCAGAAAGGATGATGAAGGGATGCGAAATG 6 99 0 TGATGAAGGG 0.798119 -64 TCAGTGAATAGGCAGAAAGGATGATGAAGG 6 110 0 GGCAGAAAGG 0.888599 -53 TCCCCTGATTGCCTCTTCCTTA 7 17 0 CCCTGATTGC 0.74557 -12 TAACAATATTCCCTGAATGGAAAGATTTTA 8 36 1 CCCTGAATGG 0.919146 -93 ********** Masking position 9 Map Score: 10.3213 Number of sites scoring better than the average of aligned sites = 3120 Number in coding regions = 2912 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 3 ATCGTTCCTCTCTTTTCTTACCGGCACGATTAC 1 26 0 TCTTTTTCCG 0.939791 -25 TTGCGCCGGTTTTTTTTGGCCTGAGTTCTTAAT 3 52 1 TTTTTGGCTG 0.974797 -247 ATAAATTGTTTCTCCTTGACCTGTGGTTATGAC 3 121 0 TCTCTGACTG 0.92775 -178 CAACATGACTTTTTTTGTGGCTGAAAGGAGTAT 3 191 0 TTTTTTGCTG 0.972752 -108 GGAAGTTTTGTCTTTTCTGTCTGGAGGGGTTCA 4 11 0 TCTTTTGCTG 0.982738 -191 ATTCCGTCCTCTTGTTTATCAGCGTGTTAGAT 4 180 0 TCTTTTACAG 0.909837 -22 TATATACCTTTTTTCCGTTGCTGCGGAAAAACC 5 18 1 TTTTCTTCTG 0.782833 -110 CCGGCTGTTTTTTTATAGGTCAGTTTTCCCTCT 6 13 1 TTTTTGGCAG 0.934033 -150 AAACAGCCGTTTTTTTTGATCTGCTTCGGGAAT 8 66 1 TTTTTGACTG 0.949307 -63 GAATCGACCTCTCCTTTTACCGATTTTTGTAC 8 107 0 TCTCTTTCCG 0.870325 -22 **** * ** *** Masking position 3 Map Score: 7.37067 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 268 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 TACGGGTAATCGTGCCGGTAAGAAAAGAGAG 1 21 1 CGTGCGGTAA 0.864974 -30 GAAATAACTCTTTGACGGGAAAATTTAAAAT 2 14 0 TTTGCGGGAA 0.919585 -71 TCAATTCGTCTGAAAGCTTGAGTAA 3 5 1 TTCGCTGAAA 0.941246 -294 TCGCGAATTATTTGCCCGAAATGTGAAGAGG 3 90 1 TTTGCCGAAA 0.924299 -209 TGACTTTTTTTGTGGCTGAAAGGAGTATACG 3 188 0 TGTGCTGAAA 0.981273 -111 GCTAACCCGTTGCTACTGAAACGACAAGCGA 4 49 1 TGCTCTGAAA 0.960367 -153 TTTTCAAGCCCGTGAACGAAACGGCTCCGCT 4 126 0 CGTGACGAAA 0.763584 -76 TTTTTTCCGTTGCTGCGGAAAAACCCTGAGT 5 26 1 TGCTCGGAAA 0.974641 -102 AAACCCTGAGTGTTTATGAAAGCGATTTCAT 5 46 1 TGTTATGAAA 0.794519 -82 TTTTTTGATCTGCTTCGGGAATGGTACAATG 8 77 1 TGCTCGGGAA 0.949465 -52 **** ****** Masking position 10 Map Score: 6.59683 Number of sites scoring better than the average of aligned sites = 1626 Number in coding regions = 1524 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 TTTAAATTTTCCCGTCAAAGAGTTATTTCA 2 16 1 CCCGTCAAAG 0.926689 -69 ACAACGGAAACCGGCCATTGCGCCGGTTTT 3 35 1 CCGGCCATTG 0.766411 -264 ATTAAGAACTCAGGCCAAAAAAAACCGGCG 3 55 0 CAGGCCAAAA 0.957303 -244 GTCATAACCACAGGTCAAGGAGAAACAATT 3 121 1 CAGGTCAAGG 0.987984 -178 AACAATTTATAAGGTCAAAGAAATACTATT 3 144 1 AAGGTCAAAG 0.914347 -155 TACTATTGCTCAGGTCTATACCGTATACTC 3 167 1 CAGGTCTATA 0.820582 -132 AGCATGGAAGCAGGTTAAGGCTTGCGGAGT 3 242 1 CAGGTTAAGG 0.877801 -57 GAGAGAATGGCAAGTCAATGAACATCCGGA 6 51 0 CAAGTCAATG 0.881891 -112 AATATTGTTACCGTTCAAAAAAGGAGGGCC 8 16 0 CCGTTCAAAA 0.784467 -113 ATTCCCGAAGCAGATCAAAAAAAACGGCTG 8 69 0 CAGATCAAAA 0.836384 -60 ********** Masking position 7 Map Score: 4.18995 Number of sites scoring better than the average of aligned sites = 1622 Number in coding regions = 1511 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 TGGCCGGTTTCCGTTGTTACTCAAGCTTTC 3 22 0 CCGTTGTTAC 0.989015 -277 TAAAGCTAACCCGTTGCTACTGAAACGACA 4 45 1 CCGTTGCTAC 0.989816 -157 ACCATTCAGCCCGCTGTCGCTTGTCGTTTC 4 66 0 CCGCTGTCGC 0.989963 -136 TACCTTTTTTCCGTTGCTGCGGAAAAACCC 5 22 1 CCGTTGCTGC 0.995454 -106 TTGTAATGTCCTGCTGTTGCTATCATCATA 5 79 0 CTGCTGTTGC 0.976724 -49 ********** Masking position 5 Map Score: 6.66856 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 327 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AATTGCGGTTTTTAAGGGTATTTTTCT 2 68 1 TTTAAGGGAT 0.870829 -17 TTCGCAAGTTACCCAGAGCATGGAAGCAGGT 3 226 1 ACCCAGAGAT 0.916148 -73 ACGGCTCCGCTTTCAGAGGATTCCTGTATGA 4 106 0 TTTCAGAGAT 0.950313 -96 TTTCATAAACACTCAGGGTTTTTCCGCAGCA 5 36 0 ACTCAGGGTT 0.943272 -92 AGATGCAGGGATTCAGTGAATAGGCAGAAAG 6 121 0 ATTCAGTGAT 0.691542 -42 AAATCTTTCCATTCAGGGAATATTGTTACCG 8 33 0 ATTCAGGGAT 0.959147 -96 ******** ** Masking position 5 Map Score: 0.772344 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 210 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 ATTAAGAACTCAGGCCAAAAAAAACCGGCG 3 55 0 CAGGCCAAAA 0.927078 -244 ATACTCCTTTCAGCCACAAAAAAAGTCATG 3 191 1 CAGCCACAAA 0.976651 -108 GATTATCTGTCAGCCAGACACTCCGCAAGC 3 261 0 CAGCCAGACA 0.980587 -38 TGAACCCCTCCAGACAGAAAAGACAAAACT 4 11 1 CAGACAGAAA 0.976252 -191 ATTCAGTGAATAGGCAGAAAGGATGATGAA 6 112 0 TAGGCAGAAA 0.955528 -51 ********** Masking position 8 Map Score: 0.658625 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 306 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 ********** No masking Map Score: 1.73616e-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: 1.73616e-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: 1.73616e-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