AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00472_hpyl_reg_100.orf -o00472_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0921 143 glyceraldehyde-3-phosphate dehydrogenase (gap) #4 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #5 HP1350 209 protease Motif number 1 AAGTAACGCTAAATCAATATAAT 1 1 1 AATAGCTAAA 0.820408 -257 TAAAGATAGTCATAGCGTCTTAAAACAAACACC 1 74 1 CAACTCTTAA 0.660911 -184 AACAAACACCCATTACTCTTAAATCATGCCAAT 1 97 1 CATCCTTAAA 0.906791 -161 TGAAAATAATAACACAACTTAAAAAAAACTACC 1 153 1 AAAACTTAAA 0.931553 -105 ACTTAAAAAAAACTACCCTTAAAAAAATCAATC 1 169 1 AATCCTTAAA 0.961358 -89 ACCCTTAAAAAAATCAATCTAAAATTCTTAAAT 1 183 1 AATATCTAAA 0.886206 -75 AAAAACTGCTCCTAAAAACTCAAAAT 2 4 1 AATCCCTAAA 0.988445 -211 TAAAAACTCAAAATTAACCTAAAATCGCTTGAC 2 23 1 AATACCTAAA 0.979077 -192 TTGACGCAAAAACACTGCCTTAATTCTACTACA 2 51 1 AAATCCTTAA 0.745942 -164 TTTTCTTATAAACAAAACCTAAATTGAGAAAAA 2 95 1 AAAACCTAAA 0.979077 -120 TATTATATCTAATAGCGTTTAAAAAATGTAAAT 2 156 0 AAACTTTAAA 0.805464 -59 AAATAATTTTAATTAACCCTACAGCTAGGTCCA 3 37 1 AATACCTACA 0.855792 -107 AATACCAAACAAAACCCCCTAAAATTGAAATTG 3 94 1 AAACCCTAAA 0.988445 -50 CTTAATGAGACAGAACCCCTTAAGAATGCCTTT 4 17 1 CAACCCTTAA 0.921331 -72 ATTCTATCACAAATGCTCTTAAATAAAGGCATT 4 41 0 AATCCTTAAA 0.961358 -48 GCAAAAATTGAATAAAACCTTAAAGGTGATTCT 5 169 1 AAAACCTTAA 0.942476 -41 ** * * ****** Masking position 10 Map Score: 24.7829 Number of sites scoring better than the average of aligned sites = 1453 Number in coding regions = 1225 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 AGACTTGAAATTTGAAAATAATAACACAACT 1 141 1 TTTGAAATAA 0.701572 -117 TTCTACTACATTTGAAATAATTTTTCTTATA 2 74 1 TTTGAAAAAT 0.976876 -141 ATAATTTTTCTTATAAACAAAACCTAAATTG 2 90 1 TTATAAAAAA 0.831179 -125 AAACCTAAATTGAGAAAAAATTCAATTCAAA 2 109 1 TGAGAAAAAT 0.950669 -106 AAAATGTAAATTTTAAACAATAGCCCCTTTG 2 136 0 TTTTAAAAAT 0.912604 -79 TTAAACGCTATTAGATATAATAAGGGATAGT 2 167 1 TTAGATAAAT 0.967325 -48 TAAGAGCATTTGTGATAGAATGGTGATTTTT 4 53 1 TGTGATAAAT 0.905318 -36 GAATGGTGATTTTTAAATAAAGGGAAAAC 4 70 1 TTTTAAAAAA 0.806401 -19 TATCTAAAATTTAGATAACATGCCCATTCAT 5 130 0 TTAGATACAT 0.860609 -80 TATCTAAATTTTAGATAGAATAAACGCAAAA 5 144 1 TTAGATAAAT 0.967325 -66 ATTTTTGAGATTAGAAAGAATCACCTTTAAG 5 187 0 TTAGAAAAAT 0.980473 -23 ******* *** Masking position 5 Map Score: 11.5244 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 603 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 AAGTAACGCTAAATCAATATAAT 1 4 1 TAACGCTAAA 0.903636 -254 AATATAATTCAAACCCTAAACCCAAACCTT 1 26 1 AAACCCTAAA 0.8437 -232 CTGCTCCTAAAAACTCAAAATTAACCTAAA 2 16 1 AAACTCAAAA 0.973728 -199 TAAAATCGCTTGACGCAAAAACACTGCCTT 2 42 1 TGACGCAAAA 0.956553 -173 TCCAATATAATAGCGCAAAATGTAGTAAAA 3 66 1 TAGCGCAAAA 0.958464 -78 TTGAAATTGAAGTCTGAAAATAGGATAATA 3 118 1 AGTCTGAAAA 0.716168 -26 AGGCTCTAAAGTAAGCCCCA 5 1 1 AGGCTCTAAA 0.931189 -209 TTCACATGCAAATCGCAAAGCATGCCCGTT 5 47 0 AATCGCAAAG 0.874029 -163 TGTATCGTTTAGGCTCAAAATGAGTGAATG 5 103 1 AGGCTCAAAA 0.971408 -107 TAGATAGAATAAACGCAAAAATTGAATAAA 5 155 1 AAACGCAAAA 0.983362 -55 GATTCTTTCTAATCTCAAAAATGG 5 196 1 AATCTCAAAA 0.958512 -14 ********** Masking position 8 Map Score: 12.8661 Number of sites scoring better than the average of aligned sites = 937 Number in coding regions = 837 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 AGCGTCTTAAAACAAACACCCATTACTCTTA 1 87 1 AACAAACCCC 0.983485 -171 GAAATTTGAAAATAATAACACAACTTAAAAA 1 147 1 AATAATACAC 0.745917 -111 CACAACTTAAAAAAAACTACCCTTAAAAAAA 1 165 1 AAAAAACACC 0.673444 -93 AACTACCCTTAAAAAAATCAATCTAAAATTC 1 179 1 AAAAAAACAA 0.913426 -79 AATACACTAAAACAATCTCAAGGTTTCAAAA 1 230 1 AACAATCCAA 0.936985 -28 AAACTGCTCCTAAAAACTCAAAATTAACCTA 2 13 1 TAAAAACCAA 0.642486 -202 TTTTCTTATAAACAAAACCTAAATTGAGAAA 2 95 1 AACAAAACTA 0.806432 -120 CTAAATTGAGAAAAAATTCAATTCAAAGGGG 2 113 1 AAAAAATCAA 0.686563 -102 GTAAATTTTAAACAATAGCCCCTTTGAATTG 2 131 0 AACAATACCC 0.945129 -84 TAAAATACCAAACAAAACCCCCTAAAATTGA 3 91 1 AACAAAACCC 0.973827 -53 CCCTTTATTTAAAAATCACCATTCTATCACA 4 63 0 AAAAATCCCA 0.912978 -26 TAAACGATACAACAAAAACGCGTAACTCCCC 5 83 0 AACAAAACGC 0.895079 -127 TTTTAGATAGAATAAACGCAAAAATTGAATA 5 152 1 AATAAACCAA 0.880188 -58 ******* *** Masking position 5 Map Score: 9.80786 Number of sites scoring better than the average of aligned sites = 1504 Number in coding regions = 1327 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 5 ACTCTTAAATCATGCCAATTCACACTCTTT 1 111 1 CATGCCAATT 0.991479 -147 AATCGCAAAGCATGCCCGTTACAAAAACAT 5 37 0 CATGCCCGTT 0.990572 -173 GATCCATTCACATGCAAATCGCAAAGCATG 5 53 0 CATGCAAATC 0.945482 -157 ATTTAGATAACATGCCCATTCATTCACTCA 5 123 0 CATGCCCATT 0.992468 -87 ********** Masking position 3 Map Score: 2.87496 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 50 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 GCTAAATCAATATAATTCAAACCCTAAACC 1 18 1 TATAATTCAA 0.857173 -240 ATAGCTATATTTTAATTTAAGAATTTTAGA 1 200 0 TTTAATTTAA 0.814924 -58 TGAGAAAAAATTCAATTCAAAGGGGCTATT 2 119 1 TTCAATTCAA 0.649909 -96 GTTTTACTCCTTGAATTCAACTCAATAAAT 3 11 1 TTGAATTCAA 0.499122 -133 ATTTTCAGACTTCAATTTCAATTTTAGGGG 3 109 0 TTCAATTTCA 0.830747 -35 ACCTTTAAGGTTTTATTCAATTTTTGCGTT 5 166 0 TTTTATTCAA 0.864134 -44 ********** Masking position 5 Map Score: 2.14893 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 118 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 ********** No masking Map Score: 1.37435e-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: 1.37435e-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: 1.37435e-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