AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_mthe_reg_100.orf -o00220_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH179 117 unknown #2 MTH181 49 unknown #3 MTH182 36 glutamate N-acetyltransferase #4 MTH255 269 ribosomal protein L7a #5 MTH256 49 ribosomal protein S28 #6 MTH261 24 translation initiation factor eIF-2, gamma subunit #7 MTH262 24 conserved protein #8 MTH846 170 N-acetyl-gamma-glutamyl-phosphate reductase #9 MTH894 179 conserved protein #10 MTH895 51 conserved protein #11 MTH1254 135 argininosuccinate synthase #12 MTH1337 81 N-acetylornithine aminotransferase #13 MTH1445 64 glycinamide ribonucleotide synthetase Motif number 1 AAGATATTAACTCATATAATACATATTACA 1 47 1 CTCATATAAT 0.775863 -71 TTCAATTCCCCTTAATATTATCTTGAAG 2 32 0 CCCTTAATAT 0.837092 -18 TCTCCCGTAAAAAAAGTTCGCTG 3 24 0 CCCGTAAAAA 0.913137 -13 ATTATTCCTTCCCTTTTTAATTGGCAGCAA 4 26 1 CCCTTTTTAA 0.697386 -244 AAAGCTTCATCACATATAAAGTTTTGCTGC 4 49 0 CACATATAAA 0.826576 -221 TAAATCACCTTTATTAAATTGAAATTG 5 33 0 CCTTTATTAA 0.865182 -17 GGGCCTCCCACCCATATAATGTCCATCACT 8 85 0 CCCATATAAT 0.977747 -86 CTATACCCACCTATATAATGTCCATCACT 8 152 0 CCTATATAAT 0.934068 -19 TATAACTTATCCCATATTAATATCTATAGT 11 71 1 CCCATATTAA 0.977748 -65 TATATGGGGACCTGTATTAATGTTGAACCT 12 46 0 CCTGTATTAA 0.873859 -36 AATACAGGTCCCCATATAAATTTTTGGTGA 12 58 1 CCCATATAAA 0.983736 -24 TGACATATTTCCTATAAAATATATACTTTC 13 39 1 CCTATAAAAT 0.834395 -26 ********** Masking position 9 Map Score: 12.8074 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 299 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 TCAAGATAATATTAAGGGGAATTGAA 2 34 1 ATTAAGGGGA 0.597791 -16 TGCTGCCAATTAAAAAGGGAAGGAATAATG 4 25 0 TAAAAAGGGA 0.694939 -245 GCAGCAAAACTTTATATGTGATGAAGCTTT 4 49 1 TTTATATGTG 0.678404 -221 ACCGAGAACATATAAAGGTACTCACCCACT 4 180 1 TATAAAGGTA 0.962991 -90 ATTTCAATTTAATAAAGGTGATTTA 5 35 1 AATAAAGGTG 0.844131 -15 TAAAAGCGTTTATAGGTGTAATCT 6 9 1 TTTATAGGTG 0.913763 -16 TGATGGACATTATATGGGTGGGAGGCCCCA 8 87 1 TATATGGGTG 0.943842 -84 TGATGGACATTATATAGGTGGGTATAG 8 154 1 TATATAGGTG 0.958137 -17 AATTTATGGATATAAAGGTAAATTGGGATT 9 148 0 TATAAAGGTA 0.962991 -32 TGGGATAAGTTATAAGTGTATGTCCCACCT 11 55 0 TATAAGTGTA 0.79184 -81 CTTATAAATGGAATCATTCTGA 11 124 0 TATAAATGGA 0.80995 -12 ACCAAAAATTTATATGGGGACCTGTATTAA 12 56 0 TATATGGGGA 0.931359 -26 AAGTATATATTTTATAGGAAATATGTCATT 13 37 0 TTTATAGGAA 0.621098 -28 ********** Masking position 4 Map Score: 11.7185 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 176 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 TGAGGGATGAGACCGTCCCGGCAG 1 5 0 GACCGTCCCG 0.845865 -113 TGCTCTCTCCCTGCACCTGATT 1 106 0 CTCTCTCCCT 0.75553 -12 CTCTCATCTGCATCCATTAT 4 1 1 CTCTCATCTG 0.761756 -269 CATATAAAGGTACTCACCCACTTCATGTTA 4 188 1 TACTCACCCA 0.895438 -82 TAATGTCCATCACTGACCCGGTCGTGGCCA 8 69 0 CACTGACCCG 0.985261 -102 ATGGTGGGGCCTCCCACCCATATAATGTCC 8 91 0 CTCCCACCCA 0.943474 -80 TAATGTCCATCACTGACCTGGGTACTCTGG 8 136 0 CACTGACCTG 0.98032 -35 CTATACCCACCTATATAATGTCC 8 158 0 TACCCACCTA 0.856484 -13 ATCTTCTGGCTCCTGACCTGAATTTTATTG 9 33 0 TCCTGACCTG 0.833978 -147 TCGATGAAGTCACTGACCTTCTGAAAAATT 9 93 0 CACTGACCTT 0.919311 -87 ATAAGTGTATGTCCCACCTGCCGCAGGTAT 11 44 0 GTCCCACCTG 0.930683 -92 ********** Masking position 3 Map Score: 7.67795 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 826 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 ATGAGTTAATATCTTTACCCCTCAGTTTGAGGGA 1 28 0 ATCTTACCCA 0.923335 -90 CTCTCATCTGCATCCATTATTCCTTCCCT 4 6 1 ATCTGATCCA 0.977995 -264 TAGAAATTAAAGCTTCATCACATATAAAGTTTTG 4 53 0 AGCTTATCAA 0.892711 -217 TCTCATGAAAATCTGTATCCAGCAAGTTTTATAT 4 146 1 ATCTGATCCA 0.977681 -124 CACCCACTTCATGTTAATCCATAACTTGGATTAT 4 202 1 ATGTTATCCA 0.978411 -68 AATTACACCAATCTGGATCAATAATCCAAGTTAT 4 222 0 ATCTGATCAA 0.948497 -48 CACCCATATAATGTCCATCACTGACCCGGTCGTG 8 73 0 ATGTCATCAA 0.928681 -98 CACCTATATAATGTCCATCACTGACCTGGGTACT 8 140 0 ATGTCATCAA 0.928681 -31 TCATGTTAACAGGTTCAACCTGGAATTTGAGGTG 10 26 1 AGGTTAACCA 0.86036 -26 ACCTGTATTAATGTTGAACCTAAACTGATAATAA 12 33 0 ATGTTAACCA 0.934764 -49 ***** **** * Masking position 7 Map Score: 9.0335 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 101 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 AGAACTATTCTCATGGAATCCTCATCAATGT 1 74 0 TCATGGAATC 0.897936 -44 ATACGATTTCTCATGAAAATCTGTATCCAGC 4 138 1 TCATGAAAAC 0.845469 -132 GGTGGTCATAGACACCAATTTTTT 7 6 1 TCATAGACAC 0.943483 -19 GAAGATATCCCCATGGACAGTTAAAGGTTGT 8 14 1 CCATGGACAT 0.97694 -157 TATAAGTATTTCATGGACAACCTTTAACTGT 8 30 0 TCATGGACAC 0.994162 -141 ACTGACCCGGTCGTGGCCACCAAAATTTATA 8 57 0 TCGTGGCCAC 0.902872 -114 ACCGGGTCAGTGATGGACATTATATGGGTGG 8 77 1 TGATGGACAT 0.963503 -94 CCCAGGTCAGTGATGGACATTATATAGGTGG 8 144 1 TGATGGACAT 0.963503 -27 CTTCATCGAACCATGGAAAGTTATATATACT 9 114 1 CCATGGAAAT 0.932817 -66 ********* * Masking position 4 Map Score: 8.54307 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 416 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 ATCTATTTAAGGATACTTCAAGATAATATTAAGGGG 2 17 1 GGATATATAA 0.950601 -33 AAGACGCCCAGGAAAACAAGGATTAATAGAAATTAA 4 77 0 GGAAAATTAA 0.799617 -193 GGATGATCCGGGATAATTCAGAATACGATTTCTCAT 4 116 1 GGATATATAC 0.975015 -154 ATCGAACCATGGAAAGTTATATATACTGGCAATCCC 9 118 1 GGAAATATAC 0.970725 -62 GCCCACTTCCGGAAAAATCCGTATACCTGCGGCAGG 11 22 1 GGAAATATAC 0.988234 -114 CTTATAAATGGAATCATTCTGATACGCTCATGTTT 11 111 0 GGAATTATAC 0.949733 -25 ATATTTTATAGGAAATATGTCATTAATAATAATGAC 13 25 0 GGAAATTTAA 0.950593 -40 ***** * **** Masking position 3 Map Score: 2.9332 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 23 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 ACATATAAAGTTTTGCTGCCAATTAAAAAG 4 38 0 TTTTGCTGCC 0.973976 -232 ATTGAAAGGCTTTTAGTGCCTTTCAT 5 7 0 TTTTAGTGCC 0.92672 -43 AAAAAATTGGTGTCTATGACCACC 7 11 0 AATTGGTGTC 0.880297 -14 TACTTATAAATTTTGGTGGCCACGACCGGG 8 53 1 TTTTGGTGGC 0.981987 -118 GGAAAGTTATATATACTGGCAATCCCAATT 9 128 1 ATATACTGGC 0.81964 -52 CTGAATTGCTGGCCCACTTCCGG 11 4 1 AATTGCTGGC 0.966907 -132 ********** Masking position 4 Map Score: 0.309561 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 104 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 ********** No masking Map Score: 2.95118e-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: 2.95118e-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: 2.95118e-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