AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_ecoli_reg_100.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 0.976588 -241 ACATCGAACAAGATAATAAATTCCTGGTTTAATATCCG 1 93 0 AATAAACCTT 0.946812 -208 AAAACTGCTCTGAAAAGAGTAACGCGCTTTACTATCCC 1 146 0 TAAAAACGCT 0.948736 -155 GTTATTACAATAATAAGAATGCGCTGATGGCAAATATT 1 193 0 TATAAAGCTT 0.951233 -108 CTTATTATTGTAATAACACAAGCGTTCACTTTTGGTGA 1 214 1 TATAAACGTA 0.966 -87 TTATTAGTGATGATAAAATTTCACCAAAAGTGAACGCT 1 234 0 TATAAAACCA 0.943684 -67 TTATCATCACTAATAATACCTACCCCTTTGGTATTAAT 1 256 1 TATAAACCCT 0.99338 -45 TATAAGGCTTTTATAACCGATCGCTACTTTCT 2 5 0 TATAACGCTT 0.802677 -57 TATAAAAGCCTTATAATAACGCCCCTAAAATTAGATTT 2 28 1 TATAAACCCA 0.99338 -34 TTTCGGCCTGAAATAAAAAAGCCGCCTATTATCCGTTA 3 48 0 AATAAACGCA 0.948736 -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 0.996451 -268 AAACATGCACCCGGACGGGCAGCATGTCGCT 1 54 0 CCGACGGGCA 0.980365 -247 GTTTAATATCCGACAAGTGAAAACATGCACC 1 74 0 CGAAAGTGAA 0.966187 -227 TGAATATTTGCCATCAGCGCATTCTTATTAT 1 191 1 CCACAGCGCA 0.983667 -110 TAAAATTTCACCAAAAGTGAACGCTTGTGTT 1 228 0 CCAAAGTGAA 0.99204 -73 ATAATTAATACCAAAGGGGTAGGTATTATTA 1 266 0 CCAAGGGGTA 0.971726 -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 TGTTTTCACTTGTCGGATATTAAACCAGGAAT 1 80 1 TTCGGATATA 0.946496 -221 TTGGTGATTGTCAGGGATAGTAAAGCGCGTTA 1 133 1 TAGGGATATA 0.992765 -168 TGGCAAATATTCAGGGATGAAAAACTGCTCTG 1 172 0 TAGGGATGAA 0.981559 -129 GTAGGTATTATTAGTGATGATAAAATTTCACC 1 247 0 TAGTGATGTA 0.970913 -54 AAATCTAATTTTAGGGGCGTTATTATAAGGCT 2 34 0 TAGGGGCGTA 0.965451 -28 TGCTCTGGATTAACGGATAATAGGCGGCTTTT 3 38 1 TACGGATATA 0.986192 -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 TGCAGAGCTTACTTGTGTTGTACCGAAGCA 1 17 0 ACTTGTGTTG 0.99425 -284 TAAGCTCTGCACTTGTGGAGCGACATGCTG 1 36 1 ACTTGTGGAG 0.990641 -265 AAAAGTGAACGCTTGTGTTATTACAATAAT 1 217 0 GCTTGTGTTA 0.962303 -84 ACAAGCGTTCACTTTTGGTGAAATTTTATC 1 231 1 ACTTTTGGTG 0.985362 -70 ********** Masking position 6 Map Score: 3.08947 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 41 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 ATTCCTGGTTTAATATCCGACAAGTGAAAA 1 82 0 TAATATCCGA 0.887338 -219 TAACGCGCTTTACTATCCCTGACAATCACC 1 135 0 TACTATCCCT 0.982439 -166 CAGAGCAGTTTTTCATCCCTGAATATTTGC 1 172 1 TTTCATCCCT 0.969033 -129 GGTGAAATTTTATCATCACTAATAATACCT 1 247 1 TATCATCACT 0.951753 -54 AAAAGCCGCCTATTATCCGTTAATCCAGAG 3 40 0 TATTATCCGT 0.984956 -37 ********** Masking position 5 Map Score: 1.91537 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 77 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 GCTCCACAAGTGCAGAGCTTACTTGTGTTG 1 27 0 TGCAGAGCTT 0.9699 -274 CGTTACTCTTTTCAGAGCAGTTTTTCATCC 1 160 1 TTCAGAGCAG 0.994393 -141 ATGGCAAATATTCAGGGATGAAAAACTGCT 1 175 0 TTCAGGGATG 0.932942 -126 AATATTTGCCATCAGCGCATTCTTATTATT 1 193 1 ATCAGCGCAT 0.933437 -108 TATCCGTTAATCCAGAGCAGGCGACAACAG 3 27 0 TCCAGAGCAG 0.990479 -50 ********** Masking position 4 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