AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -inarP_mthe_opreg_100.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 MTH170 141 phosphoribosylaminoimidazolesuccinocarboxamide synthase #2 MTH420 300 conserved protein #3 MTH1354 124 NADH oxidase Motif number 1 AGTGTGTCCCCTCTGATACGGGGATTGCCGGTGCT 2 47 0 CCTGTCGGAT 0.99771 -254 TTATCTGTCAGTCTGCAGCCCGGAGTGTGTCCCCT 2 70 0 GCTGACGGAG 0.98618 -231 ATTTCGGTGTCCCTGTATCATGGATTTATCTGTCA 2 95 0 CCTGACGGAT 0.998244 -206 GCTCACAGAACACTGCAGCACTGATATGAGTAAAG 2 155 1 CCTGACTGAT 0.98873 -146 TACCATAGATCTCTGGTCCCGGGTTAATATGCTTT 2 195 0 CCTGTCGGTT 0.989085 -106 TCCTTACCTTCCCTTTACCATAGATCTCTGGTCCC 2 210 0 CCTTACAGAT 0.95999 -91 CTATCCCCTTCTCCTAGGAGTTATCGGTTA 3 105 0 CCTTTCGGAG 0.987616 -20 * *** * * **** Masking position 4 Map Score: 10.3745 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 153 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 TGCGAAATCAGATTCATGCTTCTTAGGGTGAA 1 14 0 GATCTGCTTC 0.881343 -128 ATGAAATCCTGATCAACTCTCCAATACTTATA 1 95 0 GATACTCTCC 0.963385 -47 AGTTTTTGTGGTTGATTTCTCCGGGTGCAGCA 2 19 1 GTTATTCTCC 0.943845 -282 CTGATACGGGGATTGCCGGTGCTGCACCCGGA 2 38 0 GATGCGGTGC 0.980459 -263 TAGATTTTTGGTTAAATGCTGCATATTTCGGT 2 122 0 GTTATGCTGC 0.97963 -179 CCTTTACTCATATCAGTGCTGCAGTGTTCTGT 2 159 0 TATATGCTGC 0.902718 -142 CTTTACCATAGATCTCTGGTCCCGGGTTAATA 2 201 0 GATTTGGTCC 0.956465 -100 GTAAGGATGTGATTATCTGTCCTTCAGTATCA 2 238 1 GATACTGTCC 0.947064 -63 TCAGGGAATGGATTGCTGGCGCAGACAGAAGG 2 267 1 GATGTGGCGC 0.936291 -34 GTTTGATGCTCCCTTATAACTA 3 1 1 GTTGTGCTCC 0.983162 -124 *** * ****** Masking position 3 Map Score: 9.34057 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 317 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 ATATTGCGATTCAGTTATATAATCTTGCGA 1 41 0 TCAGTTATAT 0.952493 -101 AATTCTATTATGAGTTATATTGCGATTCAG 1 57 0 TGAGTTATAT 0.938519 -85 CTGCAGACTGACAGATAAATCCATGATACA 2 87 1 ACAGATAAAT 0.925566 -214 ACCCGGGACCAGAGATCTATGGTAAAGGGA 2 206 1 AGAGATCTAT 0.875353 -95 TAACTACCACACAGATCTATTGATGTATCC 3 27 1 ACAGATCTAT 0.879037 -98 TATAAATAATTCAGATATATTTATAAATTT 3 57 0 TCAGATATAT 0.978614 -68 AAAATGAAGAAGAGACCTATAACCGATAAC 3 86 1 AGAGACCTAT 0.936824 -39 ********** Masking position 3 Map Score: 9.01649 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 31 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 AGATTCATGCTTCTTAGGGTGAAATA 1 4 0 TTCTGGGTGA 0.995965 -138 TCTCCAATACTTATATAGGTGTAAATTCTATTA 1 77 0 TTATAGGTGA 0.983031 -65 TGTGGTTGATTTCTCCGGGTGCAGCACCGGCAA 2 25 1 TTCTGGGTGA 0.957359 -276 TGTGTGGTAGTTATAAGGGAGCATCAAAC 3 7 0 TTATGGGAGA 0.989089 -118 **** ***** * Masking position 4 Map Score: 2.13407 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 20 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 GCAAGATTATATAACTGAATCGCAATATAAC 1 43 1 ATAACTGATC 0.922111 -99 AGACTGACAGATAAATCCATGATACAGGGAC 2 91 1 ATAAATCATG 0.96889 -210 GCATTTAACCAAAAATCTATGCTCACAGAAC 2 135 1 AAAAATCATG 0.884837 -166 ATTTGGATACATCAATAGATCTGTGTGGTAG 3 30 0 ATCAATAATC 0.952792 -95 ATCCAAATTTATAAATATATCTGAATTATTT 3 53 1 ATAAATAATC 0.982206 -72 TCTTCATTTTATAAATAATTCAGATATATTT 3 65 0 ATAAATATTC 0.931589 -60 ******* *** Masking position 6 Map Score: 0.431902 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 21 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 TGGTTGATTTCTCCGGGTGCAGCACCGGCA 2 27 1 CTCCGGGTGC 0.969826 -274 GGGGACACACTCCGGGCTGCAGACTGACAG 2 71 1 TCCGGGCTGC 0.961677 -230 TGCTGCATATTTCGGTGTCCCTGTATCATG 2 108 0 TTCGGTGTCC 0.973201 -193 TGCTGCAGTGTTCTGTGAGCATAGATTTTT 2 145 0 TTCTGTGAGC 0.973115 -156 AAAACAGCCCTTCTGTCTGCGCCAGCAATC 2 277 0 TTCTGTCTGC 0.987127 -24 ACATCAATAGATCTGTGTGGTAGTTATAAG 3 23 0 ATCTGTGTGG 0.910911 -102 ********** Masking position 5 Map Score: 1.39173 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 198 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ********** No masking Map Score: 1.72962e-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: 1.72962e-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: 1.72962e-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