AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_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 b1625 300 orf, hypothetical protein #2 b1626 61 orf, hypothetical protein #3 b1627 76 orf, hypothetical protein Motif number 1 ATCCGACAAGTGAAAACATGCACCCGGACGGGCAGCAT 1 60 0 TAAAAACCCA 0.975175 -241 ACATCGAACAAGATAATAAATTCCTGGTTTAATATCCG 1 93 0 AATAAACCTT 0.943705 -208 AAAACTGCTCTGAAAAGAGTAACGCGCTTTACTATCCC 1 146 0 TAAAAACGCT 0.945735 -155 GTTATTACAATAATAAGAATGCGCTGATGGCAAATATT 1 193 0 TATAAAGCTT 0.948369 -108 CTTATTATTGTAATAACACAAGCGTTCACTTTTGGTGA 1 214 1 TATAAACGTA 0.963971 -87 TTATTAGTGATGATAAAATTTCACCAAAAGTGAACGCT 1 234 0 TATAAAACCA 0.940406 -67 TTATCATCACTAATAATACCTACCCCTTTGGTATTAAT 1 256 1 TATAAACCCT 0.992973 -45 TATAAGGCTTTTATAACCGATCGCTACTTTCT 2 5 0 TATAACGCTT 0.79299 -57 TATAAAAGCCTTATAATAACGCCCCTAAAATTAGATTT 2 28 1 TATAAACCCA 0.992973 -34 TTTCGGCCTGAAATAAAAAAGCCGCCTATTATCCGTTA 3 48 0 AATAAACGCA 0.945735 -29 * **** * *** * Masking position 6 Map Score: 9.34511 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 296 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 GCATGTCGCTCCACAAGTGCAGAGCTTACTT 1 33 0 CCAAAGTGCA 0.996599 -268 AAACATGCACCCGGACGGGCAGCATGTCGCT 1 54 0 CCGACGGGCA 0.981172 -247 GTTTAATATCCGACAAGTGAAAACATGCACC 1 74 0 CGAAAGTGAA 0.967558 -227 TGAATATTTGCCATCAGCGCATTCTTATTAT 1 191 1 CCACAGCGCA 0.98434 -110 TAAAATTTCACCAAAAGTGAACGCTTGTGTT 1 228 0 CCAAAGTGAA 0.992371 -73 ATAATTAATACCAAAGGGGTAGGTATTATTA 1 266 0 CCAAGGGGTA 0.972879 -35 *** ******* Masking position 11 Map Score: 4.63206 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 374 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 ATTCCTGGTTTAATATCCGACAAGTGAAAACA 1 80 0 TATATCCGAA 0.948455 -221 TAACGCGCTTTACTATCCCTGACAATCACCAA 1 133 0 TATATCCCTA 0.993043 -168 CAGAGCAGTTTTTCATCCCTGAATATTTGCCA 1 172 1 TTCATCCCTA 0.982258 -129 GGTGAAATTTTATCATCACTAATAATACCTAC 1 247 1 TACATCACTA 0.972005 -54 AGCCTTATAATAACGCCCCTAAAATTAGATTT 2 34 1 TACGCCCCTA 0.966659 -28 AAAAGCCGCCTATTATCCGTTAATCCAGAGCA 3 38 0 TATATCCGTA 0.986714 -39 ** ******* * Masking position 1 Map Score: 4.09759 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 63 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 AGTGCAGAGCTTACTTGTGTTGTACCGAAG 1 19 0 TTACTTGTGT 0.962886 -282 AGTAAGCTCTGCACTTGTGGAGCGACATGC 1 34 1 GCACTTGTGG 0.988732 -267 GTGCATGTTTTCACTTGTCGGATATTAAAC 1 75 1 TCACTTGTCG 0.988669 -226 CCAAAAGTGAACGCTTGTGTTATTACAATA 1 219 0 ACGCTTGTGT 0.951055 -82 ACACAAGCGTTCACTTTTGGTGAAATTTTA 1 229 1 TCACTTTTGG 0.983475 -72 ********** Masking position 5 Map Score: 4.61994 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 114 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 5 ACAAGATAATAAATTCCTGGTTTAATATCC 1 94 0 AAATTCCTGG 0.905554 -207 GTTGTTGGTGATTGTCAGGGATAGTAAAGC 1 129 1 ATTGTCAGGG 0.965958 -172 CTGATGGCAAATATTCAGGGATGAAAAACT 1 178 0 ATATTCAGGG 0.976522 -123 TGGTATTAATTATTTTATGGACCTTTT 1 284 1 TATTTTATGG 0.898586 -17 AGGCAAATCTAATTTTAGGGGCGTTATTAT 2 40 0 AATTTTAGGG 0.97997 -22 GCGGCTTTTTTATTTCAGGCCGAAAA 3 61 1 TATTTCAGGC 0.94679 -16 ********** Masking position 5 Map Score: 1.81921 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 597 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 6 CAACACAAGTAAGCTCTGCACTTGTGGAGC 1 27 1 AAGCTCTGCA 0.972771 -274 GGATGAAAAACTGCTCTGAAAAGAGTAACG 1 160 0 CTGCTCTGAA 0.99494 -141 AGCAGTTTTTCATCCCTGAATATTTGCCAT 1 175 1 CATCCCTGAA 0.939116 -126 AATAATAAGAATGCGCTGATGGCAAATATT 1 193 0 ATGCGCTGAT 0.939559 -108 CTGTTGTCGCCTGCTCTGGATTAACGGATA 3 27 1 CTGCTCTGGA 0.991405 -50 ********** Masking position 7 Map Score: 2.24751 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 452 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 ********** No masking Map Score: -3.88366e-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 8 ********** No masking Map Score: -3.88366e-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 9 ********** No masking Map Score: -3.88366e-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