AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_ecoli_reg_100.orf -o00460_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #2 ansA 166 cytoplasmic L-asparaginase I #3 bglX 195 beta-D-glucoside glucohydrolase, periplasmic #4 glyA 300 serine hydroxymethyltransferase #5 ansB 175 periplasmic L-asparaginase II #6 ggt 119 gamma-glutamyltranspeptidase #7 asnA 151 asparagine synthetase A Motif number 1 CGCCAAACTTTACGGCCTGTCTCATTCTTACGAT 1 27 1 TACCCTGCCA 0.986626 -78 ACAATAATAACACGGCCTGCCGCAATCGTAAGAA 1 51 0 CACCCTGCCA 0.994828 -54 GATACTCTTCCTGTCAAAATATAAGAAA 1 87 0 CTCCCTGCAA 0.970289 -18 ATCAGGTGCGCTCCCCCTGCCTCACGTATATACT 2 111 1 CTCCCTGCCA 0.994005 -56 AAAAGAAATCCGTTTCCGGTTGCAAGCTCTTTAT 4 119 1 CGTCCGGTCA 0.854954 -182 CCGCATCTCCTGACTCAGCTAACAATA 4 284 0 CATCCTGCCA 0.987332 -17 TTCTTCGTTTTGTTACCTGCCTCTAACTTTGTAG 5 54 1 TGTCCTGCCT 0.94335 -122 TAAGTTTACTCGCTTCCCGACAAAACGATGATTA 6 38 1 CGCCCCGCAA 0.962426 -82 TTTATACTCCTGCGTCCTGTTGCTTATGATTAAG 7 126 0 TGCCCTGTCT 0.845104 -26 *** **** * ** Masking position 7 Map Score: 8.16345 Number of sites scoring better than the average of aligned sites = 903 Number in coding regions = 851 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 CGTAAAGTTTGGCGAACAAAAGATGGAACG 1 11 0 GGCGAACAAA 0.95503 -94 AGGATTCGTCGACGTAAAAAATAATGTGGC 2 41 0 GACGTAAAAA 0.835006 -126 AATGATATCGAAAGAGCAAAAGTATATACG 2 135 0 AAAGAGCAAA 0.50858 -32 GCCACCACAAGGAGTGGAAA 3 1 0 GGAGTGGAAA 0.89342 -195 TCCTTGTGGTGGCGAAAAAATATCACAAAC 3 18 1 GGCGAAAAAA 0.969288 -178 AGCATGATGGAGAGAGAAAAAGAATGCTCA 3 109 0 AGAGAGAAAA 0.874482 -87 AGAATGTGATGAAGTGAAAAATTTGCATCA 4 81 1 GAAGTGAAAA 0.835006 -220 GCAAGGCTTTGGAGAATAAAGAGCTTGCAA 4 138 0 GGAGAATAAA 0.956736 -163 AGAATTAAACGGCATAAAAAAGTATTATGC 5 28 0 GGCATAAAAA 0.62192 -148 TTTGTCGGGAAGCGAGTAAACTTAAAGGAT 6 32 0 AGCGAGTAAA 0.867561 -88 CTTAATCTCTGGAGAATAACG 6 109 1 GGAGAATAAC 0.791505 -11 ACAGGACGCAGGAGTATAAAAA 7 140 1 GGAGTATAAA 0.941396 -12 ********** Masking position 8 Map Score: 8.08045 Number of sites scoring better than the average of aligned sites = 2027 Number in coding regions = 1802 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 3 GCCGTAAAGTTTGGCGAACAAAAGATGGAA 1 13 0 TTGGCGAACA 0.906429 -92 CTTGTACTGAGTGGCCGACAGATCGTCGGC 2 13 1 GTGGCCGACA 0.986486 -154 AAAAAATAATGTGGCCGACGATCTGTCGGC 2 26 0 GTGGCCGACG 0.991437 -141 GGGAAGAGGATTCGTCGACGTAAAAAATAA 2 47 0 TTCGTCGACG 0.942201 -120 GTGATATTTTTTCGCCACCACAAGGAGTGG 3 14 0 TTCGCCACCA 0.946057 -182 TTGCACCATTTTCGCTGCCACGTCGGGCAA 3 157 1 TTCGCTGCCA 0.853366 -39 TCTTCCTTTGTTGCCCGACGTGGCAGCGAA 3 167 0 TTGCCCGACG 0.971298 -29 GGCGGTCCTGTTGGACAACGGCGAACAGTA 4 236 0 TTGGACAACG 0.912026 -65 ********** Masking position 2 Map Score: 4.30604 Number of sites scoring better than the average of aligned sites = 1199 Number in coding regions = 1148 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 CGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCG 2 84 1 TTCTTGTAGT 0.974127 -83 TTTCAAAATATTCACTCGCTGAATTGTTATACAAGGC 3 57 0 TTACTGTTGT 0.929257 -139 GAATGCTCAGTTTATTGTCTGAATTTTCAAAATATTC 3 81 0 TTATTGTTTT 0.948513 -115 AAGAACCATTTACATTGCAGGGCTATTTTTTATAAGA 4 29 0 TAATTGTATT 0.702232 -272 CGGAAACGGATTTCTTTTCAGGTTTGTGATGCAAATT 4 100 0 TTCTTGTTGT 0.978897 -201 GGCCAAAAATTTTATTGTTAGCTGAGTCAGGAGATGC 4 272 1 TTATTGGAGT 0.914273 -29 TTTATGCCGTTTAATTCTTCGTTTTGTTACCTGCCTC 5 40 1 TTATTGTTGT 0.982528 -136 AGGATTTTCTTATGCGGATTGATGATTCATTC 7 6 1 TTCTTGTTGA 0.879697 -146 AGTTAGGCTTTTTATTGAATGATTATTGCATGTGTGT 7 77 1 TTATTGTATT 0.937343 -75 ** *** * **** Masking position 6 Map Score: 2.36602 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 70 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TATTGTCTGAATTTTCAAAATATTCACTCG 3 76 0 ATTTTCAAAA 0.777887 -120 TTCTTTGGTGTTTTTCAGAAAGAATGTGAT 4 61 1 TTTTTCAGAA 0.823084 -240 AAGCTCTTTATTCTCCAAAGCCTTGCGTAG 4 142 1 TTCTCCAAAG 0.961169 -159 AACTTTGTAGATCTCCAAAATATATTCACG 5 78 1 ATCTCCAAAA 0.941021 -98 CTTAAAGGATATCTTCAGAGGAGGATACGC 6 12 0 ATCTTCAGAG 0.962201 -108 CGTTATTCTCCAGAGATTAAGGGGC 6 105 0 TTCTCCAGAG 0.971623 -15 ********** Masking position 4 Map Score: 2.11036 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 137 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 ACTCTTCCTGTCAAAATATAAGAAACGACA 1 82 0 TCAAAATATA 0.914599 -23 ATTCGTCGACGTAAAAAATAATGTGGCCGA 2 38 0 GTAAAAAATA 0.799803 -129 CTTGTGGTGGCGAAAAAATATCACAAACTA 3 20 1 CGAAAAAATA 0.796578 -176 GTCTGAATTTTCAAAATATTCACTCGCTGA 3 72 0 TCAAAATATT 0.628012 -124 AATGCATCTTATAAAAAATAGCCCTGCAAT 4 23 1 ATAAAAAATA 0.729401 -278 TTATGCCGTCTTAAAATAGAGGA 5 4 0 TTAAAATAGA 0.900122 -172 TTGTAGATCTCCAAAATATATTCACGTTGT 5 82 1 CCAAAATATA 0.928227 -94 AAAAAGAAGGCTAAAATAGAATGAATCATC 7 31 0 CTAAAATAGA 0.915847 -121 TTTTGATTCATTAAAAAAGAAGGCTAAAAT 7 44 0 TTAAAAAAGA 0.879736 -108 ********** Masking position 5 Map Score: 2.09934 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 143 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 7 TGCAAATTTTTCACTTCATCACATTCTTTCT 4 77 0 TACTTCATCA 0.889735 -224 GCGAACAGTATAACCGAATCATTGTGCGATA 4 215 0 TACCGAATCA 0.943372 -86 ATTTTATTGTTAGCTGAGTCAGGAGATGCGG 4 280 1 TGCTGAGTCA 0.917383 -21 TATATAACTCTGAATTAATCATCGTTTTGTC 6 56 0 TAATTAATCA 0.922002 -64 AGGCTAAAATAGAATGAATCATCAATCCGCA 7 23 0 AAATGAATCA 0.84468 -129 GCCTTCTTTTTTAATGAATCAAAAGTGAGTT 7 50 1 TAATGAATCA 0.963143 -102 TCGGTTTTTGTTGCTTAATCATAAGCAACAG 7 113 1 TGCTTAATCA 0.946354 -39 * ********* Masking position 11 Map Score: 0.527944 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 250 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 ********** No masking Map Score: -4.73632e-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: -4.73632e-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 10 ********** No masking Map Score: -4.73632e-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