AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i343_ecoli_bsub_100.orf -o343_ecoli_bsub_100.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 yiaY 189 putative oxidoreductase #2 gbsA 198 glycine betaine aldehyde dehydrogenase #3 ywiA 133 similar to hypothetical proteins Motif number 1 GGAAATGATTAATTAAGTTTTAAAATAA 1 8 1 ATTATTAAGT 0.900476 -182 TTTGTATTAATTTATTTTAAAACTTAATTAA 1 19 0 TTTATTTAAA 0.919571 -171 AACAATGTGCTTTTTTTAAATTCATAAGAAT 1 50 0 TTTTTTAAAT 0.687663 -140 TTTTTATTAGATTAATTTTGATAATCAATAA 1 98 1 ATTATTTTGA 0.763113 -92 CTGACCCTCTTTTCCTTTAGAAAATTAAATT 2 12 1 TTTCTTTAGA 0.977155 -187 AGAAAATTAAATTCGTTAAGTTATTTCTTTA 2 30 1 ATTCTTAAGT 0.926047 -169 CGTTAAGTTATTTCTTTATGTTCTTTATCTT 2 43 1 TTTCTTATGT 0.938318 -156 TTTCCTCATGTTTCGTTAAGATAAAGAACAT 2 60 0 TTTCTTAAGA 0.986844 -139 CATTTTGATTTTTCTTTTTGACTTTTCCTCA 2 83 0 TTTCTTTTGA 0.938318 -116 ACATTAAATTTTTATTTAACAAACTTTATTT 2 161 1 TTTATTAACA 0.887489 -38 TTTAACAAACTTTATTTACGTCAAGGAGGCT 2 175 1 TTTATTACGT 0.865927 -24 AAAATTGTAATTTACTTAAAAAGGGCATAGT 3 39 0 TTTATTAAAA 0.95472 -95 AGAGGTAGATTTTAGTTAAAAATTGTAATTT 3 57 0 TTTATTAAAA 0.95472 -77 CACAACCGTTTTTCATTTGAATCATATGTAT 3 100 1 TTTCTTTGAA 0.779758 -34 **** ****** Masking position 6 Map Score: 15.9921 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 302 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 2 ATGAATTTAAAAAAAGCACATTGTTTAATGAATA 1 56 1 AAAACATTGT 0.91069 -134 TTAATCTAATAAAAAGCACATTGTATTCATTAAA 1 79 0 AAAACATTGT 0.91069 -111 AATCAATAATACTGATCATATTTTCGAATGAAAA 1 120 1 ACTACATTTT 0.964033 -70 ACTGACCCTCTTTTCCTTTAGAAA 2 1 1 ACTACCTTTT 0.983396 -198 TTTCTTTTTGACTTTTCCTCATGTTTCGTTAAGA 2 70 0 ACTTCCATGT 0.84948 -129 TTAAACTGTCAAAGTCCCATTTTGATTTTTCTTT 2 97 0 AAATCCTTTG 0.953881 -102 TTGACAGTTTAAAAACCATATGTTAGATTAAGGT 2 119 1 AAAACATGTT 0.741417 -80 TAGTAGAATGACTATGCCCTTTTGGGAGATCC 3 9 0 ACTTCCTTTG 0.970677 -125 TAGTCATTCTACTATGCCCTTTTTAAGTAAATTA 3 29 1 ACTTCCTTTT 0.983059 -105 CTTTTTAAGTAAATTACAATTTTTAACTAAAATC 3 47 1 AAATCATTTT 0.942003 -87 TTTTAACTAAAATCTACCTCTTGGATATACATAC 3 67 1 AATTCCTTGG 0.944504 -67 GGATATACATACACAACCGTTTTTCATTTGAATC 3 89 1 ACAACCTTTT 0.983059 -45 *** * ** **** Masking position 1 Map Score: 14.3916 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 374 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 TCATTAAACAATGTGCTTTTTTTAAATTCA 1 57 0 ATGTGCTTTT 0.973848 -133 AATGAATACAATGTGCTTTTTATTAGATTA 1 82 1 ATGTGCTTTT 0.973848 -108 AGTAAGCTGCCCGCCCTTTTTTACACTTTC 1 159 1 CCGCCCTTTT 0.964805 -31 ACTGACCCTCTTTTCCTTTAGAAA 2 5 1 ACCCTCTTTT 0.92503 -194 TTATTTCTTTATGTTCTTTATCTTAACGAA 2 50 1 ATGTTCTTTA 0.898095 -149 TAGAATGACTATGCCCTTTTGGGAGATCC 3 10 0 ATGCCCTTTT 0.994543 -124 TCATTCTACTATGCCCTTTTTAAGTAAATT 3 32 1 ATGCCCTTTT 0.994543 -102 AATACCATCCCCTATACATATGATTC 3 118 0 ATCCCCTATA 0.808814 -16 ********** Masking position 7 Map Score: 11.1579 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 292 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 GGAAATGATTAATTAAGTTTTAAAATAAATT 1 11 1 AATTAGTTTT 0.958579 -179 TTTTTAAATTCATAAGAATTTTGTATTAATT 1 38 0 CATAAAATTT 0.899777 -152 TAACTTAACGAATTTAATTTTCTAAAGGAAA 2 22 0 AATTTATTTT 0.896621 -177 GTCAAAGTCCCATTTTGATTTTTCTTTTTGA 2 93 0 CATTTGATTT 0.934348 -106 CTTAATCTAACATATGGTTTTTAAACTGTCA 2 120 0 CATATGTTTT 0.934348 -79 TTGTTAAAAACATTAAATTTTTATTTAACAA 2 152 1 CATTAATTTT 0.95852 -47 CCTTGACGTAAATAAAGTTTGTTAAATAAAA 2 170 0 AATAAGTTTG 0.793091 -29 TTTTTAAGTAAATTACAATTTTTAACTAAAA 3 48 1 AATTAAATTT 0.900499 -86 ***** ***** Masking position 2 Map Score: 5.33953 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 271 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 ********** No masking Map Score: -9.78117e-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 6 ********** No masking Map Score: -9.78117e-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 7 ********** No masking Map Score: -9.78117e-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