AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -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 HI0124 234 inorganic pyrophosphatase (ppa) #2 HI0596 300 ornithine carbamoyltransferase (arcB) #3 HI0811 134 argininosuccinate lyase (argH) #4 HI0812 21 glucosephosphate uridylyltransferase (galU) #5 HI0813 77 carbon storage regulator (csrA) #6 HI0814 187 alanyl-tRNA synthetase (alaS) #7 HI0815 101 universal stress protein A (uspA) #8 HI0817 170 conserved hypothetical protein #9 HI0819 37 galactokinase (galK) #10 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #11 HI1723 135 conserved hypothetical protein #12 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) #13 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 ACTTCCAATTTTTTACTTAACTTCAAGGAACAC 1 12 0 TTTTTTACTT 0.771418 -223 TTTGTTTCCTTCATTTTATCAAGTTA 1 219 0 GTTTTTATTT 0.869845 -16 CGAAAATATGTTTTAGTTTATTTTTGATGAAGA 2 39 0 TTTTTTATTT 0.951594 -262 CTAAAACATATTTTCGTTTAAATTCATCTACTA 2 56 1 TTTTTTAAAT 0.898063 -245 CTTTATTGTTATTTGTTTGATTTCTAATAGTAG 2 83 0 ATTTTTATTT 0.872091 -218 GAGTTAGATTATTTTATTAAATTCTAATAATAC 2 115 1 ATTTTTAATT 0.871624 -186 ATTGCGAGATTTTTAGTATTATTAGAATTTAAT 2 130 0 TTTTTATATT 0.874089 -171 ATTTTGTCCATTTTATTTGTATTAGTGCTAT 3 9 0 TTTTTTTATT 0.927483 -126 ATTTTGTCCATTTTTGTTTTATTATTAATATAG 3 47 1 TTTTTTTATT 0.927483 -88 AATTTTTCCTTTTTGTTTTAATTAATTATTCTA 3 112 0 TTTTTTAATT 0.951591 -23 CTTAGTTTGCATTTATTAGATATCCTATCAATC 5 45 0 ATTTTAATAT 0.623692 -33 GCAAAAAGCCTTTTTATAAATTTCAAAAATATG 6 109 1 TTTTTAATTT 0.914313 -79 GCGACTTAGTTTTTATTTTTATTATGGGTAACA 6 152 1 TTTTTTTATT 0.927483 -36 GTAATGACATTTTTATTATAAATAATGGC 8 7 0 TTTTTAAAAT 0.826819 -164 AACTTTTTCCTTGTTATAATCTATAAA 10 5 1 TTTTTTTTAT 0.851462 -203 TCATAAAAAATTTTGCTTATTTTCTTATTTTGT 10 106 1 TTTTTTTTTT 0.927483 -102 ATTTACAATAATTTAGTATAAATTAATGTAATC 10 156 1 ATTTTAAAAT 0.623362 -52 CAATCCAGTTTTTTCCTAGAAATCGTGCTATAA 11 45 0 TTTTTAAAAT 0.827052 -91 AAGCCGTAGGATTTACTAAATTTCCAATAATAA 12 13 1 ATTTTAATTT 0.787272 -112 TTCAGAGGATTTTTATTTCTTTTTAAAAAATAG 12 75 1 TTTTTTTTTT 0.927483 -50 TAAAGCAAACGTTTGCTATTTTTTAAAAAGAAA 12 90 0 GTTTTATTTT 0.702383 -35 AATAGCAAACGTTTGCTTTATTTGATTTAAAA 12 103 1 GTTTTTATTT 0.869845 -22 AAATAAAGATTTTTGCTTTTAATGCACAAAACA 13 38 1 TTTTTTTAAT 0.851462 -118 **** ** **** Masking position 7 Map Score: 28.0807 Number of sites scoring better than the average of aligned sites = 1073 Number in coding regions = 708 Number in noncoding regions = 365 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 2 TGCGCTATTTTACATCATAAAAACGATAAGT 1 52 1 TAATCATAAA 0.901913 -183 TTGACCGCACTTTATCCTAAATAAAACTCAC 1 93 0 TTATCCTAAA 0.798832 -142 TGTCTATCTATACTTAATAAAA 2 2 0 TATTAATAAA 0.754811 -299 CACATTCCTCTTCATCAAAAATAAACTAAAA 2 31 1 TTATCAAAAA 0.944891 -270 ATATTCTATATTAATAATAAAACAAAAATGG 3 54 0 TTATAATAAA 0.928857 -81 TTGTGCATATTTATTCATAAAGCAATATTCT 3 78 0 TTTTCATAAA 0.955025 -57 TTATTTCAGATTATTCAAAAAACAATTTCTT 6 16 0 TTTTCAAAAA 0.930914 -172 TAAAAAGGCTTTTTGCCAAAACTCCAAAATA 6 94 0 TTTGCCAAAA 0.592645 -94 GCCATTATTTATAATAAAAATGTCATTA 8 8 1 TTATAATAAA 0.69478 -163 TAAACCTTTGTAAATAAAAAAGCCATCGCTT 8 118 0 TAATAAAAAA 0.713302 -53 ATCTTATATTTTGATCATAAATAATTTACGA 10 37 1 TTATCATAAA 0.961837 -171 CCGCTTTCAATTTATCGTAAATTATTTATGA 10 51 0 TTATCGTAAA 0.79745 -157 AAGTATGAACTAAATCATAAAAAATTTTGCT 10 92 1 TAATCATAAA 0.901913 -116 ATTACATTAATTTATACTAAATTATTGTAAA 10 157 0 TTATACTAAA 0.72851 -51 ATCGTTTACATTGATAAAAAACAGGAGTCAA 10 186 1 TTATAAAAAA 0.89258 -22 CTCGTAAAGTTTTTTCAAAAAAGTGAGATAA 11 13 0 TTTTCAAAAA 0.783711 -123 TTTTTATTTCTTTTTAAAAAATAGCAAACGT 12 84 1 TTTTAAAAAA 0.728615 -41 TTATTTAGCTTTGTGCATAAAAAATCCTAAT 13 13 0 TTTGCATAAA 0.883067 -143 TAATCGATTTTTGTGAATAAAAATTCTATAG 13 101 0 TTTGAATAAA 0.775931 -55 ** ******** Masking position 1 Map Score: 26.0884 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 386 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 AAGTTAAGTAAAAAATTGGAAGTAATAAGGTGCG 1 22 1 AAAAAGAATA 0.952119 -213 TTTACATCATAAAAACGATAAGTAAACGTTTGCG 1 60 1 AAAAAAAATA 0.787316 -175 ATTTGTAGAGAAAATCAGCAAATAGATCCATCTC 1 140 0 AAAATGAATA 0.888057 -95 TTATCAAGTTAAAAAACGCAACAAGTATAGCAG 1 196 0 AAAAAGAAAA 0.96852 -39 TAGAAATCAAACAAATAACAATAAAGAGTTAGAT 2 90 1 ACAAAAAAAA 0.588498 -211 TTACCAGTTGAAAAACGACAACAAATTTCATTTT 2 182 1 AAAAAAAAAA 0.851355 -119 CTAATACAAATAAAATGGACAAAATGAAAGATTT 3 17 1 TAAAAGCAAA 0.771184 -118 ATAATAAAACAAAAATGGACAAAATCTTTCATTT 3 38 0 AAAAAGCAAA 0.917966 -97 ATTAATTAAAACAAAAAGGAAAAATT 3 119 1 ACAAAGAAAA 0.884822 -16 TGTTTTTTGAATAATCTGAAATAACTTAAATTTT 6 23 1 ATAATGAAAA 0.664582 -165 ATAAATTTCAAAAATATGCAAAAATAGGGCGACT 6 124 1 AAAATGAAAA 0.924665 -64 TACCCATAATAAAAATAAAAACTAAGTCGCCCTA 6 148 0 AAAAAAAATA 0.787316 -40 GGAGCCAGTTAAAAACCGAACCAATCAGTTAAGG 7 70 1 AAAAAGACAA 0.775326 -32 TTATTTATAATAAAAATGTCATTACAAGATCTAT 8 15 1 TAAAAGCATA 0.68537 -156 ATTTCCTGAGTAAATTTGAAATTAGTGTAAACCT 8 142 0 TAAATGAATA 0.704864 -29 TCTTTGTCACAAAATAAGAAAATAAGCAAAATTT 10 113 0 AAAATGAATA 0.888057 -95 AGTTTTTTCAAAAAAGTGAGATAAAA 11 3 0 AAAAAGGAAA 0.806739 -133 TTGCTATTTTTTAAAAAGAAATAAAAATCCTCTG 12 77 0 TTAAAGAAAA 0.599332 -48 ***** * ** ** Masking position 4 Map Score: 15.7049 Number of sites scoring better than the average of aligned sites = 942 Number in coding regions = 716 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 TATTACTTCCAATTTTTTACTTAACTTCAAG 1 18 0 AATTTTTACT 0.649803 -217 AAAATAATCTAACTCTTTATTGTTATTTGTT 2 99 0 AACTTTTATT 0.764744 -202 CTCGAATGATGTATGTTTATTCCCCAATGTA 2 256 1 GTATTTTATT 0.617293 -45 CTATTATTGTGCATATTTATTCATAAAGCAA 3 84 0 GCATTTTATT 0.865019 -51 TTTTTGTTTTAATTAATTATTCTATTATTGT 3 105 0 AATTATTATT 0.5532 -30 TTAACAAGAAATTGTTTTTTGAATAATCTG 6 10 1 AATTTTTTTT 0.555938 -178 TCTAGTACACAGTTTTTTATTGCTCAAAATG 7 31 1 AGTTTTTATT 0.831208 -71 TCTTGTAATGACATTTTTATTATAAATAATG 8 13 0 ACATTTTATT 0.84922 -158 TCAAGCGATGGCTTTTTTATTTACAAAGGTT 8 116 1 GCTTTTTATT 0.890851 -55 ATTTATCGTAAATTATTTATGATCAAAATAT 10 42 0 AATTTTTATG 0.850049 -166 AAATAAGCAAAATTTTTTATGATTTAGTTCA 10 97 0 AATTTTTATG 0.850059 -111 TATAGGGGGAAAATGTTTATTATTGGAAATT 12 31 0 AAATTTTATT 0.924464 -94 ACATTTCAGAGGATTTTTATTTCTTTTTAAA 12 71 1 GGATTTTATT 0.814799 -54 AAATTAGGATTTTTTATGCACAAAGCTA 13 8 1 GATTTTTATG 0.865785 -148 TTAAAAGCAAAAATCTTTATTTAGCTTTGTG 13 29 0 AAATTTTATT 0.924464 -127 ATACTCTATAGAATTTTTATTCACAAAAATC 13 96 1 GAATTTTATT 0.933001 -60 CACAAAAATCGATTATTTATTCAATTCTAAT 13 117 1 GATTTTTATT 0.946618 -39 **** ****** Masking position 7 Map Score: 17.6576 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 227 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 5 TTAGGATAAAGTGCGGTCAAAATTATGAATA 1 104 1 GTGCGGTAAA 0.992984 -131 TGCATTATAAGAGAGGTAAAATGAAATTTGT 2 202 0 GAGAGGTAAA 0.922182 -99 TATTTGAGAAGTGCGGTTAAAATTTAAGTTA 6 44 0 GTGCGGTAAA 0.992984 -144 GCGTCGTGAAGTGCGGTTTTATTTTGGAGTT 6 75 1 GTGCGGTTTA 0.90277 -113 CTAACATTTTGAGCAATAAAAAACTGTGTAC 7 35 0 GAGCAATAAA 0.763748 -67 TTTCAAAAAAGTGAGATAAAA 11 1 0 GTGAGATAAA 0.898277 -135 CTAGTGTTTTGTGCATTAAAAGCAAAAATCT 13 44 0 GTGCATTAAA 0.833551 -112 AAGAGGAAAAGTGCGGTTATACTCTATAGAA 13 78 1 GTGCGGTATA 0.981065 -78 ******* *** Masking position 11 Map Score: 6.79658 Number of sites scoring better than the average of aligned sites = 1098 Number in coding regions = 735 Number in noncoding regions = 363 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 6 ATTTAGGATAAAGTGCGGTCAAAATTATGA 1 102 1 AAGTGCGGTC 0.994019 -133 GCTATTTGAGAAGTGCGGTTAAAATTTAAG 6 47 0 AAGTGCGGTT 0.994634 -141 TAGCGTCGTGAAGTGCGGTTTTATTTTGGA 6 73 1 AAGTGCGGTT 0.994634 -115 CAAAGAGGAAAAGTGCGGTTATACTCTATA 13 76 1 AAGTGCGGTT 0.994634 -80 ********** Masking position 4 Map Score: 9.01979 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 7 TCCCCAATGTATAGTCAAAACACAAGGAGA 2 276 1 ATAGTCAAAA 0.683486 -25 TACAAATAAAATGGACAAAATGAAAGATTT 3 21 1 ATGGACAAAA 0.979857 -114 TAAAACAAAAATGGACAAAATCTTTCATTT 3 38 0 ATGGACAAAA 0.979857 -97 ATGAATAAATATGCACAATAATAGAATAAT 3 91 1 ATGCACAATA 0.917603 -44 CAGTTTTTTATTGCTCAAAATGTTAGCATT 7 40 1 TTGCTCAAAA 0.834509 -62 TAAATTATTTATGATCAAAATATAAGATTT 10 35 0 ATGATCAAAA 0.907203 -173 TTTCATAAGTATGAACTAAATCATAAAAAA 10 86 1 ATGAACTAAA 0.75235 -122 AGGATTTTTTATGCACAAAGCTAAATAAAG 13 16 1 ATGCACAAAG 0.942875 -140 TTTGCTTTTAATGCACAAAACACTAGACAA 13 49 1 ATGCACAAAA 0.987523 -107 TAGAATTTTTATTCACAAAAATCGATTATT 13 104 1 ATTCACAAAA 0.885831 -52 ********** Masking position 8 Map Score: 9.95724 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 153 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 TAAAACTCACGCAAACGTTTACTTATCGTTTT 1 71 0 GCAAACGTTC 0.499817 -164 TTGGTGGAATGCCAACCGTTCCTTGATTGATA 5 21 1 GCCAACCTTC 0.928595 -57 TGAAATTAGTGTAAACCTTTGTAAATAAAAAA 8 128 0 GTAAACCTTT 0.682054 -43 ACTTATGAAAGTAACCGCTTTCAATTTATCGT 10 64 0 GTAACCGTTC 0.839081 -144 TTTTATCAATGTAAACGATTACATTAATTTAT 10 173 0 GTAAACGTTC 0.560049 -35 CCATTATCTAATAACCCTTTACTCCATTCAAG 11 80 0 ATAACCCTTC 0.758882 -56 ATTTCCAATAATAAACATTTTCCCCCTATACT 12 32 1 ATAAACATTC 0.739727 -93 TTAAAAAATAGCAAACGTTTGCTTTATTTGAT 12 97 1 GCAAACGTTC 0.499889 -28 ******* ** * Masking position 4 Map Score: 4.27133 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 57 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 CTGATTTTCTCTACAAATGAGACTGCGAGT 1 156 1 CTACAAATGA 0.857323 -79 TCATCTACTATTAGAAATCAAACAAATAAC 2 79 1 TTAGAAATCA 0.835638 -222 TCTAATAATACTAAAAATCTCGCAATAAAA 2 137 1 CTAAAAATCT 0.832918 -164 ATTAGATATCCTATCAATCAAGGAACGGTT 5 34 0 CTATCAATCA 0.884929 -44 ATTACAAGATCTATAAATCAGGTTCATTTC 8 35 1 CTATAAATCA 0.966614 -136 GCTTTTAACGCTAGAAATGAACCTGATTTA 8 48 0 CTAGAAATGA 0.941547 -123 TTGTTATAATCTATAAATCTTATATTTTGA 10 21 1 CTATAAATCT 0.926448 -187 CAGTTTTTTCCTAGAAATCGTGCTATAATC 11 43 0 CTAGAAATCG 0.943333 -93 ********** Masking position 6 Map Score: 3.04902 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 28 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 AAATTCATCTACTATTAGAAATCAAACAAAT 2 75 1 ACTATAGAAA 0.852518 -226 GATTTTTAGTATTATTAGAATTTAATAAAAT 2 125 0 ATTATAGAAT 0.781993 -176 GAACAGTTGCATTATAAGAGAGGTAAAATGA 2 209 0 ATTATAGAGA 0.852518 -92 TTTTATTTTTATTATGGGTAACAAGGATTCT 6 162 1 ATTATGGTAA 0.926755 -26 TTTATACTAAATTATTGTAAATAAACCGTGA 10 147 0 ATTATGTAAA 0.793741 -61 CGGGATTGAAATTTTAGGAAAGTAGGAAATA 11 112 1 ATTTTGGAAA 0.860988 -24 GAAAATGTTTATTATTGGAAATTTAGTAAAT 12 23 0 ATTATGGAAA 0.971856 -102 TTCAATTCTAATTATTAGTAAGGAAAATAT 13 136 1 ATTATAGTAA 0.888583 -20 ***** ***** Masking position 1 Map Score: 1.58838 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 97 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 ********** No masking Map Score: 1.89958e-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 12 ********** No masking Map Score: 1.89958e-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: 1.89958e-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