AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -iargR_hinf_opreg_300.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0596 300 ornithine carbamoyltransferase (arcB) #2 HI0811 134 argininosuccinate lyase (argH) #3 HI0812 21 glucosephosphate uridylyltransferase (galU) #4 HI0813 77 carbon storage regulator (csrA) #5 HI0814 187 alanyl-tRNA synthetase (alaS) #6 HI0815 101 universal stress protein A (uspA) #7 HI0817 170 conserved hypothetical protein #8 HI0819 37 galactokinase (galK) #9 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #10 HI1209 206 arginine repressor (argR) #11 HI1723 135 conserved hypothetical protein #12 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) #13 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 GAAAATATGTTTTAGTTTATTTTTGATGAAGAGGAAT 1 34 0 TTTTATTTAT 0.986467 -267 TTTATTGTTATTTGTTTGATTTCTAATAGTAGATGAA 1 78 0 TTTTATTTAT 0.986467 -223 AGTTAGATTATTTTATTAAATTCTAATAATACTAAAA 1 116 1 TTTTAATTAT 0.973924 -185 AAATCTTTCATTTTGTCCATTTTATTTGTATTAGTGC 2 14 0 TTTTATTTTT 0.956437 -121 AAATGAAAGATTTTGTCCATTTTTGTTTTATTATTAA 2 38 1 TTTTATTTTT 0.956437 -97 ATTTTTCCTTTTTGTTTTAATTAATTATTCTATTATT 2 107 0 TTTTAATTTA 0.708719 -28 TTAGTTTGCATTTATTAGATATCCTATCAATCAAGGA 4 40 0 TTTTATATAT 0.846547 -38 GCGGTTAAAATTTAAGTTATTTCAGATTATTCAAAAA 5 26 0 TTTGATTTAT 0.891024 -162 CAAAAAGCCTTTTTATAAATTTCAAAAATATGCAAAA 5 110 1 TTTTATTTAA 0.939364 -78 CATAAAAAATTTTGCTTATTTTCTTATTTTGTGACAA 9 107 1 TTTTTTTTAT 0.940333 -101 ATAGAATGATATTTCTCTATTTGTAATTGTAAGATGA 10 61 0 ATTTATTTAT 0.911688 -146 TTTTCTTCTCTTTGTTCTTATTCATATTTCAGTTGAT 10 126 1 TTTTTATTAT 0.889848 -81 GAAAGTGAATTTTTATGCAATTCTTATGCAAATTTTG 10 163 1 TTTTAATTAT 0.973935 -44 TATTTCCTACTTTCCTAAAATTTCAATCCCGCCATTA 11 106 0 TTTTAATTAT 0.973792 -30 AGCCGTAGGATTTACTAAATTTCCAATAATAAACATT 12 14 1 TTTTATTTAT 0.986323 -111 AAAGCAAACGTTTGCTATTTTTTAAAAAGAAATAAAA 12 85 0 TTTTTTTTAA 0.771219 -40 ATAGCAAACGTTTGCTTTATTTGATTTAAAA 12 104 1 TTTTATTTTT 0.956437 -21 AAAATCGATTATTTATTCAATTCTAATTATTAGTAAG 13 121 1 ATTTAATTAT 0.84107 -35 *** * **** ** Masking position 12 Map Score: 25.792 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 134 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 AAATCAAACAAATAACAATAAAGAGTTAGATT 1 93 1 AATAAATAAA 0.830316 -208 ATTAAATTCTAATAATACTAAAAATCTCGCAA 1 130 1 AATAACTAAA 0.730202 -171 AATATTCTATATTAATAATAAAACAAAAATGG 2 54 0 ATTAAATAAA 0.931081 -81 AGAATATTGCTTTATGAATAAATATGCACAAT 2 78 1 TTTTAATAAA 0.510624 -57 AGAATAATTAATTAAAACAAAAAGGAAAAATT 2 113 1 ATTAACAAAA 0.840453 -22 GTTATTTCAGATTATTCAAAAAACAATTTCTT 5 16 0 ATTTCAAAAA 0.747778 -172 ATAAAAAGGCTTTTTGCCAAAACTCCAAAATA 5 94 0 TTTTCCAAAA 0.60705 -94 AAATTTCAAAAATATGCAAAAATAGGGCGACT 5 126 1 AATTCAAAAA 0.645483 -62 TGTTACCCATAATAAAAATAAAAACTAAGTCG 5 153 0 AATAAATAAA 0.830316 -35 GCCATTATTTATAATAAAAATGTCATTA 7 7 1 ATTAAATAAA 0.931965 -164 AGTGTAAACCTTTGTAAATAAAAAAGCCATCG 7 121 0 TTTTAATAAA 0.900631 -50 AATCTTATATTTTGATCATAAATAATTTACGA 9 36 1 TTTACATAAA 0.836416 -172 GTATGAACTAAATCATAAAAAATTTTGCTTAT 9 94 1 AATAAAAAAA 0.76762 -114 AACCGTGATCTTTGTCACAAAATAAGAAAATA 9 123 0 TTTTACAAAA 0.7804 -85 ATACTAAATTATTGTAAATAAACCGTGATCTT 9 143 0 ATTTAATAAA 0.933744 -65 GATTACATTAATTTATACTAAATTATTGTAAA 9 157 0 ATTAACTAAA 0.886355 -51 AATCGTTTACATTGATAAAAAACAGGAGTCAA 9 185 1 ATTAAAAAAA 0.904914 -23 TTATCTCACTTTTTTGAAAAAACTTTACGAGA 11 13 1 TTTTAAAAAA 0.510254 -123 TTTATTTAGCTTTGTGCATAAAAAATCCTAAT 13 13 0 TTTTCATAAA 0.754059 -143 ATAATCGATTTTTGTGAATAAAAATTCTATAG 13 101 0 TTTTAATAAA 0.811134 -55 *** * ****** Masking position 3 Map Score: 22.4533 Number of sites scoring better than the average of aligned sites = 705 Number in coding regions = 445 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 3 AACAAATAACAATAAAGAGTTAGATTATTTT 1 99 1 AATAAAAGTT 0.777934 -202 TACATTGGGGAATAAACATACATCATTCGAG 1 256 0 AATAAAATAC 0.742202 -45 TTGCTTTATGAATAAATATGCACAATAATAG 2 84 1 AATAAAATGC 0.937595 -51 ACAATAATAGAATAATTAATTAAAACAAAAA 2 105 1 AATAATAATT 0.515567 -30 CAGATTATTCAAAAAACAATTTCTTGTTAA 5 10 0 AAAAAAAATT 0.666761 -178 TTATAAATTTCAAAAATATGCAAAAATAGGG 5 122 1 CAAAAAATGC 0.56055 -66 CATTTTGAGCAATAAAAAACTGTGTACTAGA 6 31 0 AATAAAAACT 0.813158 -71 CATTATTTATAATAAAAATGTCATTACAAGA 7 13 1 AATAAAATGT 0.911744 -158 AACCTTTGTAAATAAAAAAGCCATCGCTTGA 7 116 0 AATAAAAAGC 0.923721 -55 ATATTTTGATCATAAATAATTTACGATAAAT 9 42 1 CATAAAAATT 0.905107 -166 TGAACTAAATCATAAAAAATTTTGCTTATTT 9 97 1 CATAAAAATT 0.905114 -111 ACATTTCTGAGATAAATATTTTCTTCTCTTT 10 108 1 GATAAAATTT 0.730678 -99 ATAAGAATTGCATAAAAATTCACTTTCATCA 10 159 0 CATAAAATTC 0.945091 -48 AATTTCCAATAATAAACATTTTCCCCCTATA 12 31 1 AATAAAATTT 0.948985 -94 TTTAAAAAGAAATAAAAATCCTCTGAAATGT 12 71 0 AATAAAATCC 0.887041 -54 TAGCTTTGTGCATAAAAAATCCTAATTT 13 8 0 CATAAAAATC 0.932764 -148 CACAAAGCTAAATAAAGATTTTTGCTTTTAA 13 29 1 AATAAAATTT 0.948985 -127 GATTTTTGTGAATAAAAATTCTATAGAGTAT 13 96 0 AATAAAATTC 0.964354 -60 ATTAGAATTGAATAAATAATCGATTTTTGTG 13 117 0 AATAAAAATC 0.956113 -39 ****** **** Masking position 5 Map Score: 21.8672 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 277 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 4 CTTCATCAAAAATAAACTAAAACATATTTTC 1 40 1 AAAAACTAAA 0.747265 -261 TTGCATTATAAGAGAGGTAAAATGAAATTTG 1 203 0 AGGAGGTAAA 0.92969 -98 ATACAAATAAAATGGACAAAATGAAAGATTT 2 20 1 AAGGACAAAA 0.86106 -115 ATAAAACAAAAATGGACAAAATCTTTCATTT 2 38 0 AAGGACAAAA 0.86106 -97 TAATTAAAACAAAAAGGAAAAATT 2 121 1 AAAAGGAAAA 0.926194 -14 AATGCAAACTAAGGAGATAAAAG 4 65 1 AAGAGATAAA 0.864443 -13 TATAGATTATAACAAGGAAAAAGTT 9 5 0 AAAAGGAAAA 0.926194 -203 CTTTCATAAGTATGAACTAAATCATAAAAAA 9 85 1 TAGAACTAAA 0.664297 -123 AAAATAAGAAAATAAGCAAAATTTTTTATGA 9 106 0 AAAAGCAAAA 0.904621 -102 ATAAGAACAAAGAGAAGAAAATATTTATCTC 10 116 0 AGGAAGAAAA 0.891301 -91 TTTTCAAAAAAGTGAGATAAAA 11 2 0 AGGAGATAAA 0.766101 -134 ATTGCACTTGAATGGAGTAAAGGGTTATTAG 11 74 1 AAGGAGTAAA 0.853238 -62 AGGGGAAGTATAGGGGGAAAATGTTTATTAT 12 39 0 TAGGGGAAAA 0.811808 -86 TATTTTTTAAAAAGAAATAAAAATCCTCTGA 12 76 0 AAGAAATAAA 0.737106 -49 TTTTGTGCATTAAAAGCAAAAATCTTTATTT 13 38 0 TAAAGCAAAA 0.686897 -118 AACACTAGACAAAGAGGAAAAGTGCGGTTAT 13 67 1 AAGAGGAAAA 0.973197 -89 TCTAATTATTAGTAAGGAAAATAT 13 142 1 AGAAGGAAAA 0.86569 -14 ** ******** Masking position 9 Map Score: 14.0461 Number of sites scoring better than the average of aligned sites = 922 Number in coding regions = 725 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 5 GCTATTTGAGAAGTGCGGTTAAAATTTAAG 5 47 0 AAGTGCGGTT 0.991062 -141 TAGCGTCGTGAAGTGCGGTTTTATTTTGGA 5 73 1 AAGTGCGGTT 0.991062 -115 CAAAGAGGAAAAGTGCGGTTATACTCTATA 13 76 1 AAGTGCGGTT 0.991062 -80 ********** Masking position 2 Map Score: 4.6738 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 280 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 6 TGGTTGGTGGAATGCCAACCGTTCCTTGATTGA 4 18 1 AATGCACCTT 0.976145 -60 AACTGGCTCCAATGCTAACATTTTGAGCAATAA 6 47 0 AATGCACATT 0.937839 -55 TGTAAATAAAAAAGCCATCGCTTGACCAATTAA 7 108 0 AAAGCACGTT 0.983738 -63 ATTTGAAATTAGTGTAAACCTTTGTAAATAAAA 7 130 0 AGTGTACCTT 0.85979 -41 CATACTTATGAAAGTAACCGCTTTCAATTTATC 9 66 0 AAAGTACGTT 0.966989 -142 GTTTTTTATCAATGTAAACGATTACATTAATTT 9 175 0 AATGTACGTT 0.974402 -33 TAAATCAAATAAAGCAAACGTTTGCTATTTTTT 12 99 0 AAAGCACGTT 0.9837 -26 ***** * ** ** Masking position 7 Map Score: 3.90087 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 61 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 AACTTAAATTTTAACCGCACTTCTCAAATA 5 45 1 TTAACCGCAC 0.980335 -143 ACTCCAAAATAAAACCGCACTTCACGACGC 5 75 0 AAAACCGCAC 0.992124 -113 GAGCCAGTTAAAAACCGAACCAATCAGTTA 6 71 1 AAAACCGAAC 0.969422 -31 TCTATAGAGTATAACCGCACTTTTCCTCTT 13 78 0 ATAACCGCAC 0.992124 -78 ********** Masking position 4 Map Score: 3.32797 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 35 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 AATAATCTAACTCTTTATTGTTATTTGTTT 1 98 0 CTCTTTATTG 0.812783 -203 AATAATCTCCTTGTGTTTTGACTATA 1 285 0 CTCCTTGTGT 0.922378 -16 CTTTTATCTCCTTAGTTTGCATTTATT 4 61 0 CTCCTTAGTT 0.907749 -17 AATCGACTCCTTAACTGATTGGTTCG 6 86 0 CTCCTTAACT 0.85124 -16 CACCACCAGCCTCTTAATCTAATTTAATTG 7 85 1 CTCTTAATCT 0.805714 -86 GTCAGTCTCCCTCTTTAGCTTTAGCAAAGA 8 15 1 CTCTTTAGCT 0.93509 -23 AAATACTCCTTATGTGTTAGTTAAT 10 6 1 CTCCTTATGT 0.943469 -201 ATATTTTCTTCTCTTTGTTCTTATTCATAT 10 123 1 CTCTTTGTTC 0.755566 -84 AAAAGCAAAAATCTTTATTTAGCTTTGTGC 13 28 0 ATCTTTATTT 0.618814 -128 CGCACTTTTCCTCTTTGTCTAGTGTTTTGT 13 63 0 CTCTTTGTCT 0.954514 -93 ********** Masking position 5 Map Score: 3.28446 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 85 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 GTTAGATTATTTTATTAAATTCTAATAATA 1 117 1 TTTATTAAAT 0.853733 -184 TTAGTTTGCATTTATTAGATATCCTATCAA 4 47 0 TTTATTAGAT 0.940782 -31 TAAAAAACTGTGTACTAGATCACAATTTAA 6 20 0 TGTACTAGAT 0.961425 -82 CTTGACCAATTAAATTAGATTAAGAGGCTG 7 91 0 TAAATTAGAT 0.698484 -80 TTCATAAGTATGAACTAAATCATAAAAAAT 9 87 1 TGAACTAAAT 0.784823 -121 TACATTAATTTATACTAAATTATTGTAAAT 9 156 0 TATACTAAAT 0.802531 -52 CTCAGAAATGTGAACTAGATCATAGAATGA 10 89 0 TGAACTAGAT 0.908487 -118 TTGAAAAAACTTTACGAGATTATAGCACGA 11 26 1 TTTACGAGAT 0.85053 -110 GGAGTAAAGGGTTATTAGATAATGGCGGGA 11 87 1 GTTATTAGAT 0.749486 -49 AGCCGTAGGATTTACTAAATTTCCAATAAT 12 14 1 TTTACTAAAT 0.917365 -111 AAACGTTTGCTTTATTTGATTTAAAA 12 109 1 TTTATTTGAT 0.66872 -16 ********** Masking position 4 Map Score: 5.24183 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 137 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 CGTTTTTCAACTGGTAATGCCAGTATGTAG 1 169 0 CTGGTAATGC 0.974335 -132 TTTTACCTCTCTTATAATGCAACTGTTCGA 1 212 1 CTTATAATGC 0.968648 -89 ATTTATAGATCTTGTAATGACATTTTTATT 7 23 0 CTTGTAATGA 0.941686 -148 TGCGTCACAGCTTTTAACGCTAGAAATGAA 7 57 0 CTTTTAACGC 0.960844 -114 AAGATTTTTGCTTTTAATGCACAAAACACT 13 43 1 CTTTTAATGC 0.981975 -113 ********** Masking position 5 Map Score: 1.68673 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 74 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 TTGTTATTTGTTTGATTTCTAATAGTAGATGA 1 79 0 TGATTTCTAA 0.743981 -222 AATTTTATTGCGAGATTTTTAGTATTATTAGA 1 137 0 CGATTTTTAG 0.953096 -164 CCAACCGTTCCTTGATTGATAGGATATCTAAT 4 32 1 CGATTGATAG 0.949625 -46 TAGAAATGAACCTGATTTATAGATCTTGTAAT 7 35 0 CGATTTATAG 0.980967 -136 GATCAAAATATAAGATTTATAGATTATAACAA 9 21 0 TGATTTATAG 0.945694 -187 GAGATTATAGCACGATTTCTAGGAAAAAACTG 11 41 1 CGATTTCTAG 0.982034 -95 * ********* Masking position 6 Map Score: 1.02126 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 9 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 ********** No masking Map Score: 5.50914e-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 13 ********** No masking Map Score: 5.50914e-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 14 ********** No masking Map Score: 5.50914e-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