AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_hpyl_reg_100.orf -o00910_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 HP0004 121 carbonic anhydrase (icfA) #2 HP0380 65 glutamate dehydrogenase (gdhA) #3 HP0382 182 zinc-metallo protease (YJR117W) #4 HP0512 290 glutamine synthetase (glnA) #5 HP0643 164 glutamyl-tRNA synthetase (gltX) #6 HP0649 57 aspartate ammonia-lyase (aspA) #7 HP0723 128 L-asparaginase II (ansB) #8 HP0943 21 D-amino acid dehydrogenase (dadA) #9 HP0944 300 translation initiation inhibitor, putative Motif number 1 ATTAAAACTTAATTACCCTTTTAG 2 1 1 ATAACTAATT 0.74586 -65 GTGTTACAATAAAAACACTTAAAACAATAAAGGA 2 34 1 AAAACTAAAA 0.977154 -32 TTTTAGGATTAAAAACGCTCAAAAATAGTCTCTT 3 51 1 AAAACCAAAA 0.959601 -132 AAAATTTACCATAAAACCATAAAATTAAATAAAT 3 96 0 ATAACTAAAA 0.85092 -87 GATTTTCTTCAAAAAATCCTAATAGTGTGGTTGC 4 118 1 AAAACTAATA 0.974762 -173 CATGCATCTTAATAAAACTTGATACAGATTCTAC 4 196 1 AAAACTGATA 0.810353 -95 CACCCCTATCAATCAAACTCAATTCATAACAATT 4 256 1 AACACCAATT 0.802366 -35 TAACCACCTTTAATTGTTATGAATT 4 276 0 AACATTAATT 0.682127 -15 GCTTTTTGATAACCAACCATAAAAAGCTTGGCGT 5 22 1 AACACTAAAA 0.931736 -143 ATTATACCTAAAGAATACTTAATTGTGTTGTGGT 5 112 0 AAAACTAATT 0.958072 -53 AAAAACCCTTTATTTAAAAATAGT 5 151 0 AAAACTTATT 0.634212 -14 ACATCGTTAAAATAAATTTAAAAAGGGTTA 7 7 0 AAAATAAAAA 0.771278 -122 TAAAAGAATCAACAATTTCAAAAATATTCTCATT 7 84 0 AAAATAAAAA 0.771278 -45 GAGTGTCTGTAAAAATGCTCAAAAGCATTTTCTA 9 45 1 AAAACCAAAA 0.959601 -256 CATTTTCTATAATAAGCCATAATAAAAGGGCTTG 9 70 1 AAAACTAATA 0.974755 -231 AATTGATGACAACAAAGCCTAAAACTCAAACAAA 9 124 1 AAAACTAAAA 0.977153 -177 AAACCCGTTTAAGAATTTCTAAATATGGGTAAAA 9 156 1 AAAATTAAAT 0.881616 -145 AATATGGGTAAAAAATATACAATACCTTATAATA 9 177 1 AAAATCAATA 0.862809 -124 AATACCTTATAATAAGATGAAAATTCATGGCGTT 9 197 1 AAAATAAAAT 0.666925 -104 ** ** * ***** Masking position 5 Map Score: 21.3764 Number of sites scoring better than the average of aligned sites = 1058 Number in coding regions = 867 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 2 TTCTTGCATTTCTTTTTGTTATAATGGCGT 1 35 0 TCTTTTTGTT 0.783189 -87 ACTTAATTACCCTTTTAGTGTTACAATAAA 2 17 1 CCTTTTAGTG 0.976015 -49 GAGCGGCATCCTTTATTGTTTTAAGTGT 2 48 0 TCCTTTATTG 0.920331 -18 GACAAACCTTTTTGTTTATAGCGGGT 3 7 1 CCTTTTTGTT 0.872944 -176 TAATTCCTACACTTTTATTGGTAAATTTAA 3 143 1 ACTTTTATTG 0.908716 -40 TACAGATTCTACTTTTTTTGCCCCATAAAT 4 218 1 ACTTTTTTTG 0.761676 -73 TAACCACCTTTAATTGTTATGAATTG 4 275 0 CCTTTAATTG 0.822419 -16 AAAAACCCTTTATTTAAAAATAGTT 5 150 0 CCCTTTATTT 0.920331 -15 TACTATAAAATCTTTTAATTTCAAAAGGTG 7 48 1 TCTTTTAATT 0.791751 -81 AATTGTTGATTCTTTTATTTTGTTTGAAGG 7 101 1 TCTTTTATTT 0.923261 -28 GCTGATAGTCCCTTTAATAAA 8 3 0 CCCTTTAATA 0.6136 -19 GGCTTTGCCCTCTTTTAGTGGCAATGAGTG 9 20 1 TCTTTTAGTG 0.955357 -281 GCTTGCAAGCCCTTTTATTATGGCTTATTA 9 79 0 CCTTTTATTA 0.908716 -222 ********** Masking position 5 Map Score: 12.9322 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 436 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 TCTCATTTTGATTAAAATTCGTTTGTTTTTAA 1 85 0 ATAAAATTGT 0.924732 -37 ATTAAAAACGCTCAAAAATAGTCTCTTTTTTC 3 58 1 CTAAAAATGT 0.924432 -125 TGGTAAATTTTTGAAAAATTGTTATAATTCCT 3 119 1 TTAAAAATGT 0.978749 -64 GGATGATATTATAAAAATTGGTGGGAATGATA 4 13 0 ATAAAATTGT 0.924732 -278 AAACCCTTTATTTAAAAATAGTTTTTGATTAT 5 141 0 TTAAAAATGT 0.978749 -24 TATGTAATAATTGAAAAATATTCTAGCTATTG 6 26 0 TTAAAAATTT 0.937869 -32 TTAAAATAAATTTAAAAAGGGTTA 7 3 0 TTAAAAAGGT 0.896626 -126 CCTTTTGAAATTAAAAGATTTTATAGTATAGT 7 44 0 TTAAAGATTT 0.739765 -85 AATCAACAATTTCAAAAATATTCTCATTATGG 7 80 0 TTAAAAATTT 0.937869 -49 GAGTGGTAGCTTTAAAATTGATGACAACAAAG 9 109 1 TTAAAATTAT 0.861272 -192 TTATAATAAGATGAAAATTCATGGCGTTTTGC 9 203 1 ATAAAATTAT 0.736001 -98 ** ****** ** Masking position 6 Map Score: 10.0176 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 253 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 4 GGCATCCTTTATTGTTTTAAGTGTTTTTATTG 2 40 0 ATTGTTTAAT 0.91712 -26 TTTTTGAAAAATTGTTATAATTCCTACACTTT 3 126 1 ATTGTTTAAT 0.916888 -57 TATTATAAAAATTGGTGGGAATGATAAG 4 7 0 ATTGGTGGAT 0.957919 -284 TCATCCCATAATTGTTCGCATTATTCCTTTTT 4 39 1 ATTGTTGCAT 0.922899 -252 ACAACCTCTGATAGATAGGAATGACAAATTGA 4 79 1 ATAGATGGAT 0.859172 -212 TGACAAATTGATTGTTTTGATTTTCTTCAAAA 4 100 1 ATTGTTTGAT 0.979742 -191 ATTGAGTTTGATTGATAGGGGTGATTATAGCA 4 247 0 ATTGATGGGT 0.900705 -44 ACCACCTTTAATTGTTATGAATTGAGTTTGAT 4 267 0 ATTGTTTGAT 0.972177 -24 TTATTTCTTTATTAATTTGATTGCATAATAAT 9 244 1 ATTAATTGAT 0.747253 -57 ****** *** * Masking position 6 Map Score: 4.7236 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 85 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 GAAAGCCCTTTAAAGTGTAAAA 1 2 1 AAAGCCTTTA 0.961686 -120 AAAAGAAATGCAAGAATTTTAGCTATGATAA 1 49 1 CAAGATTTTA 0.850467 -73 TTAGCTATGATAAGCGTTTTAAAAACAAACG 1 67 1 TAAGCTTTTA 0.84144 -55 GTTGGATAACACAGCTTTTTAGGATTAAAAA 3 35 1 ACAGCTTTTA 0.882552 -148 GATTTTACCGCATGCATCTTAATAAAACTTG 4 186 1 CATGCTCTTA 0.891253 -105 TGGCTAACGCCAAGCTTTTTATGGTTGGTTA 5 31 0 CAAGCTTTTA 0.97628 -134 AAAAACCCTTTATTTAAAAATA 5 153 0 AAAACCTTTA 0.643111 -12 AAAAGCTCCTTATGTAATAATT 6 46 0 AAAGCCCTTA 0.933172 -12 AACCTGCCCCTTCAAACAAAATA 7 116 0 CCTGCCCTTC 0.673321 -13 AAAATGCTCAAAAGCATTTTCTATAATAAGC 9 56 1 AAAGCTTTTC 0.931372 -245 CACTCGCTTGCAAGCCCTTTTATTATGGCTT 9 83 0 CAAGCCTTTT 0.882758 -218 CGCAAAACGCCATGAATTTTCATCTTATTAT 9 205 0 CATGATTTTC 0.560617 -96 ***** ***** Masking position 9 Map Score: 6.90525 Number of sites scoring better than the average of aligned sites = 1530 Number in coding regions = 1350 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 6 GTAAAATAACGCCATTATAACAAAAAGAAA 1 27 1 GCCATTATAA 0.951495 -95 AAGAATTTTAGCTATGATAAGCGTTTTAAA 1 60 1 GCTATGATAA 0.954701 -62 TATCCAACCCGCTATAAACAAAAAGGTTTG 3 13 0 GCTATAAACA 0.688882 -170 TAAAAGTGTAGGAATTATAACAATTTTTCA 3 130 0 GGAATTATAA 0.751374 -53 AAAATTGGTGGGAATGATAAG 4 2 0 GGAATGATAA 0.670359 -289 ATTATGGGATGATATTATAAAAATTGGTGG 4 21 0 GATATTATAA 0.732359 -270 TGCGTCTGCTTCCATAATAACACTCCTTGA 4 149 1 TCCATAATAA 0.746795 -142 CCCCATAAATGCTATAATCACCCCTATCAA 4 238 1 GCTATAATCA 0.954143 -53 GTATTCTTTAGGTATAATCAAAAACTATTT 5 128 1 GGTATAATCA 0.878381 -37 AAATATTCTAGCTATTGTAACCAAATCTTG 6 13 0 GCTATTGTAA 0.831648 -45 AAAAGCATTTTCTATAATAAGCCATAATAA 9 65 1 TCTATAATAA 0.824839 -236 TCTATAATAAGCCATAATAAAAGGGCTTGC 9 75 1 GCCATAATAA 0.958866 -226 TGTTATGTCAGCTATTATTATGCAATCAAA 9 259 0 GCTATTATTA 0.815055 -42 ********** Masking position 4 Map Score: 10.1774 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 224 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 TCTTTAACCCTTAAATCTCATTTTGA 1 106 0 TTTCCCTTAT 0.978337 -16 TAGTCTCTTTTTTCTACCATATTTATTTAATTTT 3 76 1 TTTACCATAT 0.943101 -107 TCCAAACTCCTTTCTCCATTAAATTTACCAATAA 3 157 0 TTTCCATTAT 0.834556 -26 TTTAGCGGATTTTACCGCATGCATCTTAATAAAA 4 179 1 TTTCGCATGT 0.931997 -112 TTCTACTTTTTTTGCCCCATAAATGCTATAATCA 4 224 1 TTTCCCATAT 0.986388 -67 TAGAAAATGCTTTTGAGCATTTTTACAGACACTC 9 45 0 TTTAGCATTT 0.678975 -256 ATTGTATATTTTTTACCCATATTTAGAAATTCTT 9 166 0 TTTCCCATAT 0.986388 -135 ATTCATGGCGTTTTGCGCTCATTTTTTATTTCTT 9 219 1 TTTCGCTCAT 0.880589 -82 *** ****** * Masking position 3 Map Score: 2.06173 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 176 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 AATTTTTCAAAAATTTACCATAAAACCATA 3 109 0 AAATTTACCA 0.952478 -74 TTTCTCCATTAAATTTACCAATAAAAGTGT 3 151 0 AAATTTACCA 0.952478 -32 TGGTTATCAAAAAGCTAACAGCGTTT 5 7 0 AAAGCTAACA 0.930487 -158 TGATAAAAACAGAACTACCACAACACAATT 5 96 1 AGAACTACCA 0.920235 -69 CATCAATTTTAAAGCTACCACTCGCTTGCA 9 102 0 AAAGCTACCA 0.985886 -199 ********** Masking position 6 Map Score: 1.51275 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 28 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 TCTTTAACCCTTAAATCTCATTTTGAT 1 105 0 CCCTTAAATC 0.944099 -17 TACCATAAAACCATAAAATTAAATAAATAT 3 94 0 CCATAAAATT 0.793408 -89 ATTAAATTTACCAATAAAAGTGTAGGAATT 3 144 0 CCAATAAAAG 0.82315 -39 ACTCCTTTCTCCATTAAATTTACCAATAAA 3 156 0 CCATTAAATT 0.894495 -27 ATAATATCATCCCATAATTGTTCGCATTAT 4 33 1 CCCATAATTG 0.857298 -258 CTTTTTTTGCCCCATAAATGCTATAATCAC 4 229 1 CCCATAAATG 0.955778 -62 TAACCACCTTTAATTGTTATGAATTG 4 275 0 CCTTTAATTG 0.696364 -16 TGATAACCAACCATAAAAAGCTTGGCGTTA 5 28 1 CCATAAAAAG 0.82315 -137 AAGTGCTAATCTCTTAAATGATGCCTATTC 5 61 1 CTCTTAAATG 0.889973 -104 TTTTACTATACTATAAAATCTTTTAATTTC 7 40 1 CTATAAAATC 0.506642 -89 ********** Masking position 6 Map Score: 3.85955 Number of sites scoring better than the average of aligned sites = 706 Number in coding regions = 625 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 ********** No masking Map Score: -1.88842e-14 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: -1.88842e-14 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 12 ********** No masking Map Score: -1.88842e-14 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