AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icytR_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 MTH816 43 sporulation protein IVFB related protein #2 MTH817 56 conserved protein #3 MTH1591 30 phosphonopyruvate decarboxylase #4 MTH1592 21 conserved protein #5 MTH1593 205 ribosomal protein S3a #6 MTH1594 72 conserved protein #7 MTH1598 300 conserved protein Motif number 1 ATGATTTATTCATAGCACCCCATATAATAGAA 1 21 1 CAAGCCCCCA 0.997387 -23 GAGGGGTCCCGATCCATTTGA 4 10 0 GAGGGCCCGA 0.981083 -12 TTCATGACCACACAGCACCCCAAACCACCATG 5 33 1 CAAGCCCCCA 0.997387 -173 TCCATTTCGGGAGGGCCTCCCAGTTCCTT 6 54 1 GAGGCTCCCA 0.983492 -19 CTGATAACGCCCCACAGGAGGGCC 7 3 1 GAAACCCCCA 0.989376 -298 CAATGGTTCTCATGGCCCTCCTGTGGGGCGTT 7 16 0 CAGGCCTCCT 0.938376 -285 ACCACAACGGCAAGGTGCCCGAGACGTCTCCA 7 74 1 CAGGTCCCGA 0.965765 -227 AAAAGAGATAGAGAGCGCCTGAGAAGTAAAGA 7 179 1 GAAGCCCTGA 0.959738 -122 ATACCGGATAGAGAACCCCCCTCAATAACTCA 7 220 1 GAAACCCCCT 0.967135 -81 ** *** ***** Masking position 2 Map Score: 13.9517 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 307 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 ATAGCACTGGCCTCCTCCAGGGGGAGGAGGTTG 6 18 1 CCTCCAGGGG 0.97435 -55 AGGAGGTTGACCTCCATTTCGGGAGGGCCTCCC 6 42 1 CCTCCTCGGG 0.992362 -31 TTCTCATGGCCCTCCTGTGGGGCGTTATCAG 7 9 0 CCTCCGGGGC 0.979086 -292 GACCTCACATCCACCACAACGGCAAGGTGCCCG 7 62 1 CCACCACGGC 0.985853 -239 TGTTTGATTTCCTCAGACTGTGCATAATAATCC 7 111 1 CCTCATGTGC 0.955826 -190 GGTCTCCCTCCCGGTGTGCAGCAGGTGAT 7 282 0 CCTCCTGTGC 0.983842 -19 ***** ***** Masking position 4 Map Score: 7.17085 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 212 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 TGTGTGGTCATGAATATGAACAGCCAGTTAT 5 16 0 TAATATGAAC 0.962579 -190 GTTAACCAGTTAAATATGAATTTTTTGAATT 5 137 1 TAATATGAAT 0.835124 -69 ACAGCTGGATTTAACATAAATTCAAAAAATT 5 155 0 TAACATAAAT 0.835124 -51 ATCTCAATGGTTCTCATGGCCCTCCTGTGGG 7 21 0 TCTCATGGCC 0.836269 -280 TTGAGATGATTAAACATGACCTCACATCCAC 7 45 1 TAACATGACC 0.974596 -256 GTGGAGTGGATTATTATGCACAGTCTGAGGA 7 120 0 TATTATGCAC 0.88427 -181 TTAAATAATCTCCACATGAACATGGTAGTGG 7 147 0 TCACATGAAC 0.984788 -154 AAACTTAAGATGCACATACACTGAGTTATTG 7 242 0 TCACATACAC 0.923163 -59 CAGGTGATATTGATCATAAACTTAAGATGCA 7 259 0 TATCATAAAC 0.931002 -42 * ********* Masking position 6 Map Score: 5.23725 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 440 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 GTTCTATTATATGGGGTGCTATGAATAAAT 1 24 0 TTGGGGTGCT 0.995658 -20 GACATGGTGGTTTGGGGTGCTGTGTGGTCAT 5 36 0 TTGGGGTGCT 0.995658 -170 ATGGCCCTCCTGTGGGGCGTTATCAG 7 6 0 TTGGGGCGTT 0.994304 -295 TATGGAGACGTCTCGGGCACCTTGCCGTTGT 7 77 0 TTCGGGCACC 0.93856 -224 ACTCTTTACTTCTCAGGCGCTCTCTATCTCT 7 182 0 TTCAGGCGCT 0.976624 -119 ACTGAGTTATTGAGGGGGGTTCTCTATCCGG 7 223 0 TAGGGGGGTT 0.941409 -78 * ********* Masking position 1 Map Score: 4.77564 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 93 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 GATTTATTCATAGCACCCCATATAATAGAA 1 23 1 TAGCACCCCA 0.987123 -21 GATTAACCCACCTTCCTAGATTT 3 18 0 TAACCCACCT 0.929572 -13 CATGACCACACAGCACCCCAAACCACCATG 5 35 1 CAGCACCCCA 0.972155 -171 CATTTCGGGAGGGCCTCCCAGTTCCTT 6 56 1 GGGCCTCCCA 0.943087 -17 CTGATAACGCCCCACAGGAGGGCC 7 5 1 TAACGCCCCA 0.969251 -296 ATGGTTCTCATGGCCCTCCTGTGGGGCGTT 7 16 0 TGGCCCTCCT 0.948215 -285 ACCGGATAGAGAACCCCCCTCAATAACTCA 7 222 1 GAACCCCCCT 0.986059 -79 ********** Masking position 4 Map Score: 5.35235 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 402 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CATTCTGTACATCATATCCATTCGGTTTTT 2 36 0 ATCATATCCA 0.968283 -21 TAACTGGCTGTTCATATTCATGACCACACA 5 17 1 TTCATATTCA 0.60674 -189 ACCCCAAACCACCATGTCAAGATTTAAATA 5 49 1 ACCATGTCAA 0.909206 -157 TATATCACCTTAATCTTTAACAC 5 193 0 ATCACCTTAA 0.885803 -13 GTCATGTTTAATCATCTCAATGGTTCTCAT 7 35 0 ATCATCTCAA 0.970871 -266 TAAACATGACCTCACATCCACCACAACGGC 7 55 1 CTCACATCCA 0.924863 -246 GTGCATAATAATCCACTCCACTACCATGTT 7 130 1 ATCCACTCCA 0.874564 -171 CCACTCCACTACCATGTTCATGTGGAGATT 7 142 1 ACCATGTTCA 0.868784 -159 CTTTTCTTAAATAATCTCCACATGAACATG 7 154 0 ATAATCTCCA 0.872184 -147 GGATAGAGAACCCCCCTCAATAACTCAGTG 7 225 1 CCCCCCTCAA 0.804469 -76 ********** Masking position 7 Map Score: 3.4649 Number of sites scoring better than the average of aligned sites = 1562 Number in coding regions = 1453 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 7 CCAGGATCAAAAAACTCGAGCGATG 2 5 1 GATCAAAAAC 0.988413 -52 AAACTCGAGCGATGAAAAACCGAATGGATAT 2 22 1 GATGAAAAAC 0.983414 -35 AGATCATAAATCTAGGAAGGTG 3 2 1 GATCATAAAC 0.986826 -29 GAACCATTGAGATGATTAAACATGACCTCAC 7 39 1 GATGATTAAC 0.958487 -262 AGGTGATATTGATCATAAACTTAAGATGCAC 7 258 0 GATCATAAAT 0.960599 -43 ********* * Masking position 5 Map Score: 4.5593 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 31 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: 1.57984e-12 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: 1.57984e-12 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: 1.57984e-12 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