AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifadR_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH657 96 long-chain-fatty-acid-CoA ligase #2 MTH659 216 epoxidase #3 MTH660 119 unknown #4 MTH1343 218 imidazoleglycerol-phosphate synthase (cyclase) #5 MTH1345 79 conserved protein Motif number 1 AAGCCTATACCTCCCGAGATAAGGAAGCAGCTTGAG 1 30 1 CTCGAATAAA 0.94184 -67 AATCCATTACCCCCTCAGATATTACATGGAATGGTT 2 15 1 CCCCAATTCA 0.98783 -202 ATGTTCACATCCCTGCAGAGATGCAACCATTCCATG 2 39 0 CCCCAAGTAA 0.974407 -178 CCTAAATGATCTCCGGTTATCTGAAAATATGTCAAT 2 73 0 CTCGTATTAA 0.970646 -144 TATGCTGATGCTCTGCACATTTTTAAACAGCAATTT 2 134 1 CTCCAATTAA 0.989056 -83 TTTGGATGTGCCTAACATATCTGCAATCACCAATAT 3 22 1 CCTCAATTAA 0.941106 -98 TTTTTTTATTCTCATGATATTTATAATGTTGGTAGA 3 86 0 CTCGAATTAA 0.989039 -34 GATCCGAAGTCCCACGTCATATTCCAGGCTAGACTA 4 66 1 CCCGTATTCA 0.967444 -153 *** ** ** * ** Masking position 9 Map Score: 5.61393 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 53 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 GGAAGCAGCTTGAGGAGCACCTCGTGGAGGAAGATTAA 1 52 1 TGAGAGCTTA 0.920326 -45 TGCACATTTTTAAACAGCAATTTTTTTAAACTGAGATT 2 147 1 TAAAAGTTTA 0.9825 -70 TAAAAAGCAGTTAATAAAAAAGCGGACC 4 1 1 TAAAAGTTTA 0.987398 -218 TGGTTAACTTTAAATAGAGATGTGTGTAGGGGGCCCGT 4 101 0 TAAAAGTGTA 0.95055 -118 GTTAACCATTTAAATATTTTCTCATCAACGTGTCAGCC 4 131 1 TAAAATCTTA 0.910299 -88 ATTTATTAATTAAGGGGCATTTAGTATAAAGCTGTCTG 4 191 0 TAAGGGTTTA 0.953268 -28 CTTTATATTGTAAGAAGAGATTAGTTAACACGAAACAA 5 22 0 TAAGAGTTTA 0.98714 -58 TCTTACAATATAAAGATATATTATTACATTTTTTTGTT 5 45 1 TAAAATTTTA 0.947109 -35 **** ** ** * * Masking position 3 Map Score: 3.73547 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 14 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 AGCCTATACCTCCCGAGATAAGGAAGCAGC 1 31 1 TCCCGAGATA 0.859371 -66 TTTTCAGATAACCGGAGATCATTTAGGAGA 2 82 1 ACCGGAGATC 0.964363 -135 ATATAAGGATGCCGGTAACCTACTTCCGAA 3 54 1 GCCGGTAACC 0.937812 -66 GTAACCTACTTCCGAAAATCTACCAACATT 3 68 1 TCCGAAAATC 0.95641 -52 GGACTTCGGATCCCAAGGTCGGGGGTTCAA 4 48 0 TCCCAAGGTC 0.958598 -171 GACCTTGGGATCCGAAGTCCCACGTCATAT 4 58 1 TCCGAAGTCC 0.931381 -161 TGTGTAGGGGGCCCGTAGTCTAGCCTGGAA 4 87 0 GCCCGTAGTC 0.864097 -132 CAACGTGTCAGCCGAAGACCAGACTCAGGG 4 156 1 GCCGAAGACC 0.985171 -63 ********** Masking position 3 Map Score: 4.2397 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 549 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 AAGATTAACTTATAAGGGTGGATTT 1 82 1 TATAAGGGTG 0.982715 -15 CAATCACCAATATAAGGATGCCGGTAACCT 3 45 1 TATAAGGATG 0.985399 -75 TCATGATATTTATAATGTTGGTAGATTTTC 3 81 0 TATAATGTTG 0.933589 -39 GGGCATTTAGTATAAAGCTGTCTGCTGTCC 4 185 0 TATAAAGCTG 0.973514 -34 CTTCTTACAATATAAAGATATATTATTACA 5 43 1 TATAAAGATA 0.892867 -37 ********** Masking position 5 Map Score: 2.90432 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 40 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 TAACTTATAAGGGTGGATTT 1 87 1 GGGTGGATTT 0.985793 -10 CATCCTTATATTGGTGATTGCAGATATGTT 3 35 0 TTGGTGATTG 0.899687 -85 TTTATAATGTTGGTAGATTTTCGGAAGTAG 3 73 0 TGGTAGATTT 0.959293 -47 AAGCGGACCCGGGGGGATTTGAACCCCCGA 4 30 1 GGGGGGATTT 0.986826 -189 TTACATTTTTTTGTTGATTTAA 5 68 1 TTGTTGATTT 0.948568 -12 ********** Masking position 7 Map Score: 1.31381 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 66 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 CAGATAACCGGAGATCATTTAGGAGATTACT 2 86 1 GAGATCATTA 0.983854 -131 GATCATTTAGGAGATTACTTAACAGTTCGTC 2 98 1 GAGATTATTA 0.990772 -119 ACGTTGATGAGAAAATATTTAAATGGTTAAC 4 131 0 GAAAATATTA 0.914309 -88 ATTGTAAGAAGAGATTAGTTAACACGAAACA 5 23 0 GAGATTATTA 0.990772 -57 ******* *** Masking position 7 Map Score: 1.64498 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 AAGCCTATACCTCCCGAGATAAGGAAGCAG 1 30 1 CTCCCGAGAT 0.956814 -67 AATCCATTACCCCCTCAGATATTACATGGA 2 15 1 CCCCTCAGAT 0.959477 -202 GGTTCAAATCCCCCCGGGTCCGCTTTTTTA 4 25 0 CCCCCGGGTC 0.984326 -194 GGGATTTGAACCCCCGACCTTGGGATCCGA 4 43 1 CCCCCGACCT 0.981409 -176 AGACTACGGGCCCCCTACACACATCTCTAT 4 96 1 CCCCCTACAC 0.973491 -123 TGTCTGCTGTCCCCTGAGTCTGGTCTTCGG 4 167 0 CCCCTGAGTC 0.990164 -52 ATACTAAATGCCCCTTAATTAATAAAT 4 202 1 CCCCTTAATT 0.843704 -17 ********** Masking position 4 Map Score: 4.97609 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 361 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 AGGCTTCTTTCTCTGCTCTATGAAG 1 6 0 CTCTGCTCTA 0.943785 -91 CCTAAATGATCTCCGGTTATCTGAAAATAT 2 79 0 CTCCGGTTAT 0.818078 -138 TATGCTGATGCTCTGCACATTTTTAAACAG 2 134 1 CTCTGCACAT 0.823345 -83 ATCACTCTCCTTTTGGATGTGCCT 3 5 1 CTCTCCTTTT 0.940544 -115 CTCTCTACTTTTTTTATTCTCA 3 108 0 CTCTACTTTT 0.914335 -12 CTTTTTTATTAACTGCTTTTTA 4 3 0 AACTGCTTTT 0.699703 -216 ATCCCCCCGGGTCCGCTTTTTTATTAACTG 4 18 0 GTCCGCTTTT 0.966346 -201 TGTCCCCTGAGTCTGGTCTTCGGCTGACAC 4 160 0 GTCTGGTCTT 0.946059 -59 GTATAAAGCTGTCTGCTGTCCCCTGAGTCT 4 176 0 GTCTGCTGTC 0.849257 -43 ********** Masking position 3 Map Score: 1.42424 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 342 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 ********** No masking Map Score: 9.90086e-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: 9.90086e-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 11 ********** No masking Map Score: 9.90086e-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