AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifruR_mjan_opreg_100.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0107 167 dihydropteroate synthase #2 MJ0542 127 phosphoenolpyruvate synthase #3 MJ0641 166 phosphoglycerate kinase (pgk) #4 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #5 MJ1596 226 3-isopropylmalate dehydrogenase 2 (leuB2) Motif number 1 TAATTAAATTAAAACATAATTTATACTTAGCT 1 15 0 AAAATAATTT 0.809245 -153 CTTAAAATGAAAACTATAAATGTAATTAAATT 1 37 0 AAAATAAATG 0.742006 -131 TAATACTGCGAAAGTCTTAAAATGAAAACTAT 1 52 0 AAACTTAAAA 0.65232 -116 CCTTAAGCATAAATTTTCTTTAAAAAATTTAT 1 107 1 AAATTCTTTA 0.81006 -61 ATTTTCTTTAAAAAATTTATTTCTACGAAAGT 1 119 1 AAATTTATTT 0.851272 -49 CGAAAGTCCTAAATCTTATATTGACTATGAAA 1 144 1 AAATTATATT 0.724128 -24 TTATGAAACTTTTTTTAATTTTTTATA 2 6 1 AAATTTTTTA 0.944863 -122 TTACAAGTGAAAATGTTATAAAAAATTAAAAA 2 22 0 AAATTATAAA 0.811043 -106 ATTATCATTCAAATATTTAAATTTATTTTAAA 2 78 1 AAATTTAAAT 0.646799 -50 ATTTTAAAATAAAAGCTATATATAATCCCCTA 2 102 1 AAACTATATA 0.728953 -26 AAGAAATCTTAAATAATTATTAAGTTAATTTT 3 21 0 AAAATTATTA 0.909973 -146 GTTTTTGCAGAAAGAATAAATATAAAGAAATC 3 45 0 AAAATAAATA 0.949337 -122 CTTTCTGCAAAAACCTTAAAAACTTTAAAATG 3 63 1 AAATTAAAAA 0.889369 -104 AAAAACTTTAAAATGATAATTAGGAAATATCT 3 80 1 AAAATAATTA 0.950235 -87 TCATTTGTAGAAACTTTTCTTAGATATTTCCT 3 101 0 AAATTTCTTA 0.763462 -66 AAAACTTCTAAAAACATAAAAATCTTAGAGGG 3 145 1 AAAATAAAAA 0.874826 -22 TTAATCACCAAAATGATTTTAAAATTAAAAAT 4 11 1 AAAATTTTAA 0.847194 -184 ACTTCCCTTAAAAGTTTTATTTTTAATTTTAA 4 29 0 AAATTTATTT 0.874032 -166 AAAACAACACAAAATATAAATACTTATAATGC 4 64 0 AAAATAAATA 0.949064 -131 ACCATATCAAAAATGATTAAAATACTCAACAA 4 96 0 AAAATTAAAA 0.874824 -99 AGTCACCAACAAAACATTTTTATGTGAAAGTA 4 131 1 AAAATTTTTA 0.936407 -64 TTTTTATGTGAAAGTATTTTTATTAATATTGC 4 147 1 AAAATTTTTA 0.931065 -48 TTATCACCAAAAAGATTAATTATAGCAATATT 4 171 0 AAATTAATTA 0.969726 -24 TATTTCTATTAAACGTTAATAAGAGGGATAAA 5 12 0 AAATTAATAA 0.922824 -215 ATAGAAATAGAAACAATAAATATACCGTATTA 5 35 1 AAAATAAATA 0.949391 -192 TTAATACTTAAAAATATCTTTAAACTATACTG 5 64 1 AAAATCTTTA 0.762802 -163 ATTTATTAATAAACTTTAATTAATTTTGAAGA 5 96 0 AAATTAATTA 0.96978 -131 ATTTATTGTCAAATATTTATTAATAAACTTTA 5 110 0 AAATTTATTA 0.969146 -117 GAAGGCATTTAAATATTTATTGTCAAATATTT 5 124 0 AAATTTATTG 0.830554 -103 GACAGCACCAAAAACTTTTTTATATAGTGTCT 5 204 0 AAATTTTTTA 0.944866 -23 *** ******* Masking position 7 Map Score: 46.3144 Number of sites scoring better than the average of aligned sites = 2235 Number in coding regions = 1403 Number in noncoding regions = 832 Number of orfs with sites within 600 bp upstream = 567 Fraction of orfs with sites within 600 bp upstream = 0.0910697 Motif number 2 TAAATGCCTTTTAATATATAATACTGCGAAA 1 71 0 TTAATATTAA 0.686366 -97 TTAAAGAAAATTTATGCTTAAGGGCATCTAA 1 99 0 TTTATGCTAA 0.785 -69 AAGCATAAATTTTCTTTAAAAAATTTATTTC 1 111 1 TTTCTTTAAA 0.969141 -57 AAAAAATTTATTTCTACGAAAGTCCTAAATC 1 128 1 TTTCTACAAA 0.943296 -40 AATCTTATATTGACTATGAAAGT 1 155 1 TGACTATAAA 0.788578 -13 ACTCTACTATTTTATTTATAATATTATCATT 2 56 1 TTTATTTTAA 0.862937 -72 AATATTTAAATTTATTTTAAAATAAAAGCTA 2 89 1 TTTATTTAAA 0.935825 -39 AATTATTAAGTTAATTTTAATAACTGAT 3 8 0 TTAATTTAAT 0.636358 -159 TTATTTAAGATTTCTTTATATTTATTCTTTC 3 37 1 TTTCTTTTAT 0.731555 -130 ATATTTATTCTTTCTGCAAAAACCTTAAAAA 3 54 1 TTTCTGCAAA 0.948234 -113 CTAAGAAAAGTTTCTACAAATGACGATAATC 3 110 1 TTTCTACAAT 0.827645 -57 AGTTTTATTTTTAATTTTAAAATCATTTTGG 4 18 0 TTAATTTAAA 0.888293 -177 ACAAAACATTTTTATGTGAAAGTATTTTTAT 4 139 1 TTTATGTAAA 0.897818 -56 ATTGTTTCTATTTCTATTAAACGTTAATAAG 5 21 0 TTTCTATAAA 0.948488 -206 ATATACCGTATTAATACTTAAAAATATCTTT 5 54 1 TTAATACTAA 0.693182 -173 TAAACTATACTGTCTTCAAAATTAATTAAAG 5 84 1 TGTCTTCAAA 0.917631 -143 AAGCTACTGGTTACTTCAAAATGTTTTTGAA 5 173 1 TTACTTCAAA 0.943746 -54 TTTTATATAGTGTCTTTCAAAAACATTTTGA 5 188 0 TGTCTTTAAA 0.914826 -39 ******* *** Masking position 5 Map Score: 22.5342 Number of sites scoring better than the average of aligned sites = 1463 Number in coding regions = 1210 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 3 ATTTATTCTTTCTGCAAAAACCTTAAAAAC 3 56 1 TCTGCAAAAA 0.899407 -111 TTAATCACCAAAATGATTTTAAAA 4 5 1 TCACCAAAAT 0.984787 -190 ATTAAAATACTCAACAAAAAACAACACAAA 4 83 0 TCAACAAAAA 0.971151 -112 ATGGTTTAAGTCACCAACAAAACATTTTTA 4 123 1 TCACCAACAA 0.983692 -72 AAAAATACTTTCACATAAAAATGTTTTGTT 4 138 0 TCACATAAAA 0.792984 -57 ACTTATCACCAAAAAGATTAATTAT 4 180 0 TCACCAAAAA 0.991961 -15 AACTATACTGTCTTCAAAATTAATTAAAGT 5 86 1 TCTTCAAAAT 0.759875 -141 ATAGTGTCTTTCAAAAACATTTTGAAGTAA 5 183 0 TCAAAAACAT 0.629582 -44 AGACAGCACCAAAAACTTTTTTATA 5 212 0 GCACCAAAAA 0.966479 -15 ********** Masking position 7 Map Score: 8.59096 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 432 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 4 ATAAATTATGTTTTAATTTAATTACATTTATA 1 23 1 TTTTAATAAT 0.922916 -145 ATAGTTTTCATTTTAAGACTTTCGCAGTATTA 1 52 1 TTTTAAGTTT 0.864946 -116 TCTAAATGCCTTTTAATATATAATACTGCGAA 1 72 0 TTTTAATATA 0.852202 -96 ATGAAACTTTTTTTAATTTTTTATAACATTTT 2 13 1 TTTTAATTTT 0.975943 -115 ACTATTTTATTTATAATATTATCATTCAAATA 2 61 1 TTATAATTAT 0.760969 -67 CATTCAAATATTTAAATTTATTTTAAAATAAA 2 83 1 TTTAAATATT 0.752056 -45 CTAATTATCATTTTAAAGTTTTTAAGGTTTTT 3 71 0 TTTTAAATTT 0.81207 -96 TTTTTAGAAGTTTTAATAGATTATCGTCATTT 3 127 0 TTTTAATATT 0.968583 -40 CCCTCTAAGATTTTTATGTTTTTAGAAGTTTT 3 145 0 TTTTTATTTT 0.799859 -22 AAAGTTTTATTTTTAATTTTAAAATCATTTTG 4 19 0 TTTTAATTAA 0.730258 -176 ATATAAATACTTATAATGCATTACTTCCCTTA 4 51 0 TTATAATATT 0.852634 -144 TTGTTGAGTATTTTAATCATTTTTGATATGGT 4 96 1 TTTTAATTTT 0.975959 -99 GTGAAAGTATTTTTATTAATATTGCTATAATT 4 154 1 TTTTATTTAT 0.625496 -41 TATTAATAAACTTTAATTAATTTTGAAGACAG 5 93 0 CTTTAATATT 0.817972 -134 ******* *** Masking position 2 Map Score: 15.4254 Number of sites scoring better than the average of aligned sites = 1195 Number in coding regions = 859 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 5 ********** No masking Map Score: 3.79592e-14 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: 3.79592e-14 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: 3.79592e-14 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