AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_hpyl_reg_100.orf -o00450_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 HP0106 24 cystathionine gamma-synthase (metB) #2 HP0107 38 cysteine synthetase (cysK) #3 HP0194 214 triosephosphate isomerase (tpi) #4 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #5 HP0417 168 methionyl-tRNA synthetase (metS) #6 HP1118 210 gamma-glutamyltranspeptidase (ggt) #7 HP1513 226 selenocystein synthase (selA) Motif number 1 GCTCCTAAAAACTCAAAATTAACCTAAAAT 3 18 1 ACTCAAAATT 0.683054 -197 AGGGGCTATTGTTTAAAATTTACATTTTTT 3 139 1 GTTTAAAATT 0.968482 -76 ATCTAATAGCGTTTAAAAAATGTAAATTTT 3 153 0 GTTTAAAAAA 0.961096 -62 TGATTGTCCTTATTAAAATAATCATTCGTA 4 45 0 TATTAAAATA 0.769517 -20 TATAATTAACGCTCAAAAAATTGAAAAAGA 5 28 0 GCTCAAAAAA 0.956608 -141 GGTGTTTTTAGCTTAAAATTCATTATAATT 5 51 0 GCTTAAAATT 0.970878 -118 TTTAACATGCTTTTAAAAATTTAGAGAATA 5 107 0 TTTTAAAAAT 0.915391 -62 TTTAAAAGCATGTTAAAATTAAGAGATTTA 5 120 1 TGTTAAAATT 0.738075 -49 AATAGATAGAGTTTAAAAAATAAGTTAAAT 6 47 0 GTTTAAAAAA 0.961096 -164 CAAAAATGAGTTTTAAAATAGATAGAGTTT 6 63 0 TTTTAAAATA 0.930373 -148 TATAAAAAAGGCTCAAAAATGAGTTTTAAA 6 76 0 GCTCAAAAAT 0.956608 -135 AATCAGTTACGCTTAAAATTTCTTTGTTAT 6 178 0 GCTTAAAATT 0.970878 -33 TTGTTTCCATGTTCAAAATTCAAAAAGAAA 7 30 0 GTTCAAAATT 0.961852 -197 CTCTTAAGGATTTTAAAAAAGTAGTTTTAT 7 134 1 TTTTAAAAAA 0.913062 -93 AAAGTAGTTTTATCAAAAATTTAGCGGGTT 7 151 1 TATCAAAAAT 0.689147 -76 AGCGGGTTTAGTTTAAAATAACGCTTATTT 7 173 1 GTTTAAAATA 0.968461 -54 TTTTTTGAGAGTTTAAAATAAGCGTTATTT 7 188 0 GTTTAAAATA 0.968461 -39 TATTTTAAACTCTCAAAAAAGGAATCAAAC 7 198 1 TCTCAAAAAA 0.906479 -29 ********** Masking position 3 Map Score: 33.2025 Number of sites scoring better than the average of aligned sites = 797 Number in coding regions = 669 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 GGTTTTTCCTTTTTTATTGAATTT 1 10 0 TTCCTTTTTT 0.926744 -15 AACAATAAAATTCAATTTTGCGATT 2 6 0 TTCAATTTTG 0.932608 -33 TAGGTTAATTTTGAGTTTTTAGGAGCAGTT 3 14 0 TTGAGTTTTT 0.778724 -201 TGAATTTTTTCTCAATTTAGGTTTTGTTTA 3 103 0 CTCAATTTAG 0.786159 -112 CCCCTTTGAATTGAATTTTTTCTCAATTTA 3 114 0 TTGAATTTTT 0.944055 -101 TGTTTAAAATTTACATTTTTTAAACGCTAT 3 148 1 TTACATTTTT 0.888461 -67 TGAACGATCCTTATTTTATAGGTGGTAAC 3 196 0 CTTATTTTAT 0.547711 -19 TGAACTCTTTTTCAATTTTTTGAGCGTTAA 5 23 1 TTCAATTTTT 0.961434 -146 AGAATAGAGGTTGCATTTATGCTTATTTGT 5 83 0 TTGCATTTAT 0.758571 -86 CCTCTATTCTCTAAATTTTTAAAAGCATGT 5 103 1 CTAAATTTTT 0.929719 -66 CCTTATTTAACTTATTTTTTAAACTCTATC 6 43 1 CTTATTTTTT 0.829633 -168 TATTTTAAAACTCATTTTTGAGCCTTTTTT 6 73 1 CTCATTTTTG 0.922008 -138 GGATTTCTTTTTGAATTTTGAACATGGAAA 7 27 1 TTGAATTTTG 0.903554 -200 TTTGATAAAACTACTTTTTTAAAATCCTTA 7 138 0 CTACTTTTTT 0.871839 -89 ACTAAACCCGCTAAATTTTTGATAAAACTA 7 155 0 CTAAATTTTT 0.929719 -72 GTGCGTTTGATTCCTTTTTTGAGAGTTTAA 7 202 0 TTCCTTTTTT 0.926744 -25 ********** Masking position 6 Map Score: 18.8636 Number of sites scoring better than the average of aligned sites = 1046 Number in coding regions = 848 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 3 CGCTATTAGATATAATAAGGGATAGTTACC 3 172 1 TATAATAAGG 0.940927 -43 TTACCACCTATAAAATAAGGATCGTTCA 3 197 1 TAAAATAAGG 0.982848 -18 AGAATGAAATAAGCTATAATAAGC 4 5 1 TGAAATAAGC 0.971602 -60 TGAAATAAGCTATAATAAGCCCATTTTGAA 4 15 1 TATAATAAGC 0.968659 -50 TTGTCCTTATTAAAATAATCATTCGTATTC 4 42 0 TAAAATAATC 0.906669 -23 AAAACACCCCACAAATAAGCATAAATGCAA 5 73 1 ACAAATAAGC 0.962254 -96 AGCGTTTTGATCAAATAAGCCTTATTTAAC 6 24 1 TCAAATAAGC 0.989214 -187 ATAGAGTTTAAAAAATAAGTTAAATAAGGC 6 42 0 AAAAATAAGT 0.800366 -169 TTTGAGAGTTTAAAATAAGCGTTATTTTAA 7 185 0 TAAAATAAGC 0.991087 -42 TTTTAAACTCTCAAAAAAGGAATCAAACGC 7 200 1 TCAAAAAAGG 0.869293 -27 ********** Masking position 5 Map Score: 16.0063 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 147 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AAAAACTGCTCCTAAAAACTCAAAA 3 3 1 AAACTCCTAA 0.976561 -212 CTAAAAACTCAAAATTAACCTAAAATCGCTTGA 3 22 1 AAAATCCTAA 0.963325 -193 CTTGACGCAAAAACACTGCCTTAATTCTACTAC 3 50 1 AAACACCTTA 0.976557 -165 TTTTTCTTATAAACAAAACCTAAATTGAGAAAA 3 94 1 AAACACCTAA 0.971278 -121 TTATAGGTGGTAACTATCCCTTATTATATCTAA 3 177 0 TAACTCCTTA 0.914122 -38 CATTCGTATTCAAAATGGGCTTATTATAGCTTA 4 20 0 CAAAAGCTTA 0.819182 -45 GCGTTTTGATCAAATAAGCCTTATTTAACTTAT 6 25 1 CAAATCCTTA 0.948251 -186 CAAAATTCAAAAAGAAATCCTAAGATTCCTTTC 7 14 0 AAAGACCTAA 0.905694 -213 GGTTTAGTTTAAAATAACGCTTATTTTAAACTC 7 177 1 AAAATGCTTA 0.90789 -50 ***** ***** Masking position 3 Map Score: 6.50705 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 381 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 AGGTTAATTTTGAGTTTTTAGGAGCAGTTTT 3 12 0 TGAGTTTTAG 0.84153 -203 TTTTGCGTCAAGCGATTTTAGGTTAATTTTG 3 31 0 AGCGTTTTAG 0.903268 -184 ATTATATCTAATAGCGTTTAAAAAATGTAAA 3 157 0 ATAGGTTTAA 0.952664 -58 TTTTCTACCCATAGCGTTTTGATCAAATAAG 6 12 1 ATAGGTTTTG 0.945249 -199 TTTAAAATAGATAGAGTTTAAAAAATAAGTT 6 51 0 ATAGGTTTAA 0.952659 -160 TATAAGCGAGAGAGTGTTTTGTAAAGCTTGT 6 141 1 AGAGGTTTTG 0.975878 -70 AACTTTTTCCATAGAGTTTGGCGGTTTCTAT 7 75 0 ATAGGTTTGG 0.963905 -152 TCAAAAATTTAGCGGGTTTAGTTTAAAATAA 7 163 1 AGCGGTTTAG 0.981824 -64 ATTCCTTTTTTGAGAGTTTAAAATAAGCGTT 7 192 0 TGAGGTTTAA 0.929122 -35 GATGAGTGCGTTTGATTCCTTTTTT 7 212 0 AGTGGTTTGA 0.827161 -15 **** ****** Masking position 7 Map Score: 12.0062 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 573 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 GGTTTTTCCTTTTTTATTGAATTT 1 9 0 TCCTTTTTTA 0.9203 -16 CAAAAACACTGCCTTAATTCTACTACATTT 3 57 1 GCCTTAATTC 0.915254 -158 TGAACGATCCTTATTTTATAGGTGGTA 3 198 0 TCCTTATTTT 0.932073 -17 TGATTGTCCTTATTAAAATAATCATT 4 49 0 TCCTTATTAA 0.849682 -16 AATTTTTTGAGCGTTAATTATAATGAATTT 5 36 1 GCGTTAATTA 0.91267 -133 GATCAAATAAGCCTTATTTAACTTATTTTT 6 32 1 GCCTTATTTA 0.987759 -179 TCATTTTTGAGCCTTTTTTATAGCTAGCGC 6 84 1 GCCTTTTTTA 0.967257 -127 TTTAAAATAAGCGTTATTTTAAACTAAACC 7 177 0 GCGTTATTTT 0.925482 -50 ********** Masking position 5 Map Score: 8.73113 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 271 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AAAAACTGCTCCTAAAAACTCAAAA 3 6 1 CTGCTCCTAA 0.928613 -209 TGCAACCTCTATTCTCTAAATTTTTAAAAG 5 98 1 ATTCTCTAAA 0.890239 -71 TAATTTTAACATGCTTTTAAAAATTTAGAG 5 111 0 ATGCTTTTAA 0.949094 -58 AATTTGTTTAAATCTCTTAATTTTAACATG 5 128 0 AATCTCTTAA 0.890239 -41 AACTTACATGATGCTATTAATGGTTTGAGC 6 112 0 ATGCTATTAA 0.949094 -99 GCTCATTAAGATGCTCTTAAGGATTTTAAA 7 121 1 ATGCTCTTAA 0.989827 -106 ********** Masking position 5 Map Score: 3.23012 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 211 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 TAGGTGGTAACTATCCCTTATTATATCTAA 3 177 0 CTATCCCTTA 0.935957 -38 TTCATTATAATTAACGCTCAAAAAATTGAA 5 33 0 TTAACGCTCA 0.923673 -136 TTTTTTATAGCTAGCGCTCAAACCATTAAT 6 97 1 CTAGCGCTCA 0.971704 -114 ACAAAACACTCTCTCGCTTATAACTTACAT 6 133 0 CTCTCGCTTA 0.981425 -78 GAAAAAGTTCCGCTCGCTCAATAAGCTCAT 7 97 1 CGCTCGCTCA 0.96784 -130 TTAGTTTAAAATAACGCTTATTTTAAACTC 7 180 1 ATAACGCTTA 0.894951 -47 ********** Masking position 8 Map Score: 2.01523 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 276 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 ********** No masking Map Score: -1.66734e-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: -1.66734e-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 11 ********** No masking Map Score: -1.66734e-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