AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00750_bsub_reg_100.orf -o00750_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yclB 89 similar to phenylacrylic acid decarboxylase #2 serC 146 phosphoserine aminotransferase #3 yjmC 104 similar to malate dehydrogenase #4 yugK 103 similar to NADH-dependent butanol dehydrogenase #5 yugJ 229 similar to NADH-dependent butanol dehydrogenase #6 hom 200 homoserine dehydrogenase Motif number 1 TTGCGAAATGTTCACAAAATAAAATAACCTCAT 2 12 0 TTCAAAAAAA 0.97377 -135 AAAATTAGAATTATCAAAAGAAATTGACGGATG 2 46 0 TTCAAAAAAA 0.973769 -101 TTCTAATTTTTTATCAAAAAACTGAATTTTTGT 2 69 1 TTCAAAAACT 0.952828 -78 TACAATTATCCTATCACAAAAATTCAGTTTTTT 2 84 0 CTCACAAAAT 0.858687 -63 GCTTGGAGAGTGCCCAAAAAACTGAAAAGGAAG 3 71 1 TGCAAAAACT 0.7611 -34 GTAACATAAGTTGACAAAAAAGAAAAAGGGAAG 4 37 0 TTCAAAAAGA 0.919504 -67 CCAAATGATGCTGGTAAAAAACAGATTTTCCAT 4 71 0 CTTAAAAACA 0.857521 -33 TTCCCAGCACCTTGCAAAATAAAACCATCTGGT 5 129 1 CTCAAAAAAA 0.978317 -101 GGAGAAAATCTGACAAAAATAATTAGAAAATA 6 10 1 CTCAAAATAA 0.894365 -191 AGCGTTTACATTCGCAAAATTCAGCCTAATGAT 6 69 1 TTCAAAATCA 0.928322 -132 CCCGCTCCTGTTTTGACAAGACATCATTAGGCT 6 91 0 TTGACAAACA 0.861419 -110 AAGACAATTGTTAACTCAACACAGACATATAAG 6 142 0 TTCTCAAACA 0.757632 -59 TGATTGTCCTCTTGGAAAAGACAATTGTTAACT 6 159 0 CTGAAAAACA 0.942582 -42 TCCAAGAGGACAATCAAAAGAAAGGTGGAGTTT 6 176 1 CACAAAAAAA 0.827627 -25 ** ***** *** Masking position 8 Map Score: 13.4036 Number of sites scoring better than the average of aligned sites = 1224 Number in coding regions = 1000 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 2 AAGAAAGCGCCTCCTTATCATACCTT 1 3 1 GACGCCTCTT 0.982968 -87 TATGATCTCTCCCTGTTTTCCACGTTA 2 130 0 GACTCCCTTT 0.977368 -17 GCAAGTGCCTCCTTCCTTTTCAGT 3 91 0 GCTGCCTCTT 0.974501 -14 CAGCCAAACGGCTATTTCCCCTTTTT 4 3 0 GCTTCCCCTT 0.988652 -101 TAGCCGTTTGGCTGCTTCCCTTTTTCTTTTTTGT 4 23 1 GCTTCCCTTT 0.966163 -81 GTTTTGCAACCTCCTCCATGAATTATTAA 5 6 1 GCCTCCTCAT 0.977937 -224 ATCTATACATGCATTCTCCATATGAGGGAAGCTG 5 69 1 GCCTCCATTG 0.903537 -161 GACATCTCCTCCTTAGATTTTTTA 5 216 0 GACTCCTCTT 0.992616 -14 CATTATATAAGCCCGCTCCTGTTTTGACAAGACA 6 101 0 GCCTCCTGTT 0.983756 -100 AAAAACTCCACCTTTCTTTTGATT 6 187 0 AACTCCACTT 0.836307 -14 ** ****** ** Masking position 8 Map Score: 10.5301 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 515 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 GATTTAATAGATATTTTTCATATGGATATA 1 53 1 ATATTTTTCA 0.853022 -37 ATTATTTTAAATATTCTTTATATTATATTG 3 11 0 ATATTCTTTA 0.90377 -94 GGTAAAAAACAGATTTTCCATTGTAACATA 4 62 0 AGATTTTCCA 0.961347 -42 ATGCATGTATAGATTCTCCAATATGTCACA 5 53 0 AGATTCTCCA 0.975278 -177 CGCTTATATCAGCTTCTTTCCCAGCACCTT 5 112 1 AGCTTCTTTC 0.860643 -118 TCTCCTCCTTAGATTTTTTATTATGCAGAA 5 206 0 AGATTTTTTA 0.962808 -24 TATTTTTGTCAGATTTTCTCC 6 2 0 AGATTTTCTC 0.934933 -199 TGATATGACAAGATTCTTTATTTTCTAATT 6 31 0 AGATTCTTTA 0.976225 -170 ********** Masking position 1 Map Score: 8.29737 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 168 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 ATTTAATAGATATTTTTCATATGGATATAT 1 54 1 TATTTTTCAT 0.912427 -36 TGATAATTCTAATTTTTTATCAAAAAACTG 2 63 1 AATTTTTTAT 0.788366 -84 TTATTTTAAATATTCTTTATATTATATTG 3 10 0 TATTCTTTAT 0.912427 -95 GTAAAAAACAGATTTTCCATTGTAACATAA 4 61 0 GATTTTCCAT 0.967973 -43 TGCATGTATAGATTCTCCAATATGTCACAA 5 52 0 GATTCTCCAA 0.895735 -178 TCTATACATGCATTCTCCATATGAGGGAAG 5 70 1 CATTCTCCAT 0.931577 -160 CTCCTCCTTAGATTTTTTATTATGCAGAAT 5 205 0 GATTTTTTAT 0.951076 -25 GATATGACAAGATTCTTTATTTTCTAATTA 6 30 0 GATTCTTTAT 0.968588 -171 ********** Masking position 2 Map Score: 6.42416 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 332 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 ACCTTTTAGGTATTAATTATAGATTTAATA 1 32 1 TATTAATTAT 0.881338 -58 CTTTTGATAATTCTAATTTTTTATCAAAAA 2 59 1 TTCTAATTTT 0.879228 -88 TTAAATATTCTTTATATTATATTG 3 5 0 TTTATATTAT 0.822262 -100 TACAAATTATTTTAAATATTCTTTATATTA 3 16 0 TTTAAATATT 0.628911 -89 ACATTTTATTTACAAATTATTTTAAATATT 3 26 0 TACAAATTAT 0.819431 -79 TCTATAACTGTTTTAATAATTCATGGAGGA 5 22 0 TTTTAATAAT 0.881336 -208 CTCCTTAGATTTTTTATTATGCAGAATGTC 5 202 0 TTTTTATTAT 0.881334 -28 ATTCTTTATTTTCTAATTATTTTTGTCAGA 6 19 0 TTCTAATTAT 0.952122 -182 ********** Masking position 6 Map Score: 3.10585 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 287 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 6 TTAAAATAATTTGTAAATAAAATGTGTTTG 3 31 1 TTGTAAATAA 0.826387 -74 AGATTTTCCATTGTAACATAAGTTGACAAA 4 52 0 TTGTAACATA 0.980616 -52 CAGTTATAGATTGTGACATATTGGAGAATC 5 42 1 TTGTGACATA 0.957964 -188 TCCCAGCACCTTGCAAAATAAAACCATCTG 5 130 1 TTGCAAAATA 0.910027 -100 TATATAATGTTTGTAACTTATATGTCTGTG 6 126 1 TTGTAACTTA 0.972455 -75 ********** Masking position 6 Map Score: 1.34588 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 57 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 ********** No masking Map Score: -1.70998e-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 8 ********** No masking Map Score: -1.70998e-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 9 ********** No masking Map Score: -1.70998e-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