AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i001_Purine_Biosynthesis_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aldA 201 aldA #2 Rv0769 30 hypothetical protein Rv0769 #3 Rv0770 97 hypothetical protein Rv0770 #4 purC 50 purC #5 purQ 300 purQ #6 purL 191 purL #7 Rv0807 300 hypothetical protein Rv0807 #8 purF 86 purF #9 purM 30 purM #10 purN 115 purN Motif number 1 ACTGGCTTGCCTCCTGCCGCGACCATCCGA 1 23 0 CTCCTGCCGC 0.853282 -179 GGGGCCACGTCGCGTCGCGGACAGTCCCAT 1 73 0 CGCGTCGCGG 0.634528 -129 ACCGATGCACCAGGGGCCACGTCGCGTCGC 1 85 0 CAGGGGCCAC 0.81737 -117 GACCGTATCCGCAAGGCCGCTACACCGTCC 1 117 0 GCAAGGCCGC 0.840419 -85 CTAGCGGGTTGACAGCGCAGAAAGGAAGCC 2 11 1 GACAGCGCAG 0.681177 -20 CCGGCGCCGGCGCCGATGCAGAG 3 4 1 GCGCCGGCGC 0.499754 -94 GGCGCCGATGCAGAGCGGGGCGATGAGGTG 3 19 1 CAGAGCGGGG 0.89984 -79 GCGGGGCGATGAGGTGGGGGCACGCCCCCA 3 33 1 GAGGTGGGGG 0.922507 -65 GTACCCCCATCCGCTGGCGGGGGAGAGCGG 3 73 1 CCGCTGGCGG 0.795945 -25 GAGATACCAGCACAGGGCGCCGTCGTGCGG 4 15 1 CACAGGGCGC 0.9403 -36 ACAGGGCGCCGTCGTGCGGCGGATAGGCTG 4 26 1 GTCGTGCGGC 0.616716 -25 CAGCGGCCGCCAGGAGCCGGGCAATG 5 7 0 CAGGAGCCGG 0.890445 -294 CGCCCGGCGACAGCGGCCGCCAGGAGCCGG 5 17 0 CAGCGGCCGC 0.895224 -284 GATCTGCCCGCCGCGCCCGGCGACAGCGGC 5 30 0 CCGCGCCCGG 0.501575 -271 ACCACCCTGGCCACCGGCGCTCCTCCTCAG 5 59 0 CCACCGGCGC 0.602773 -242 GCATGTGATGCCCAAGGCGGAGATTCTTGA 5 92 1 CCCAAGGCGG 0.874583 -209 CAATCGCCTGGCCCTGCGGGTCAAGAATCT 5 112 0 GCCCTGCGGG 0.91639 -189 GATTGTCGGTGCGCTGGGGCGGCTTGGGCA 5 137 1 GCGCTGGGGC 0.857533 -164 CACGCTTGCCGAGATCGCAGAATCACTGTT 5 236 1 GAGATCGCAG 0.739343 -65 TGCGGGTCCCGGCTGATCGTCC 5 289 0 CGGGTCCCGG 0.770985 -12 CCACCATCCTGAGCGCCCGCCCCGATGTCA 6 27 1 GAGCGCCCGC 0.80231 -165 GGTGGCATCAGCCGTCGGGCTGACATCGGG 6 47 0 GCCGTCGGGC 0.743224 -145 GACGGCTGATGCCACCGGGGTTCTTGCCGC 6 61 1 GCCACCGGGG 0.661716 -131 CCCCATCGCGCTGCGGCCGCGTTGACACGG 6 115 0 CTGCGGCCGC 0.556172 -77 CGGCCGCAGCGCGATGGGGCCTAGCTAGAC 6 126 1 GCGATGGGGC 0.942112 -66 CGGGGTCCGGGCGAGCGGAGACATCACGGA 6 160 0 GCGAGCGGAG 0.710677 -32 CGCTCGCCCGGACCCCGCGCAAAACGTCG 6 173 1 GACCCCGCGC 0.723511 -19 TCCCTGAGTTCCCAAGGCGGTGA 7 4 0 CCCAAGGCGG 0.874583 -297 AAGAATCTCACAGATCGCGGGTCGGCGCAG 7 53 1 CAGATCGCGG 0.940278 -248 CAGATCGCGGGTCGGCGCAGGTTGACCGCG 7 63 1 GTCGGCGCAG 0.367762 -238 CAGGTTGACCGCGCTGGCGCGGGGTCCATA 7 80 1 GCGCTGGCGC 0.795945 -221 GATCTAAGAACATCGGCCGGAAACCTGGTT 7 159 1 CATCGGCCGG 0.678032 -142 ACTTGACATGGCGCGGCCGCAACAACCAGG 7 182 0 GCGCGGCCGC 0.512777 -119 CGGGTTGTATGCGAGCCCAGTTCCGAACTG 7 213 0 GCGAGCCCAG 0.826019 -88 CGCATACAACCCGATCCCAGTCTCAGCAGC 7 230 1 CCGATCCCAG 0.794489 -71 ATCCCAGTCTCAGCAGCGGCGCTTGGCCGC 7 243 1 CAGCAGCGGC 0.803697 -58 TGGATCCATCCAGATGGCGGCCAAGCGCCG 7 259 0 CAGATGGCGG 0.962234 -42 CCGGCGTGCTGAGCTGCGGCTATGGTGTGT 8 13 1 GAGCTGCGGC 0.937974 -74 GTGTGTGAGGGTGGCGCCGGGGTGCCCGAC 8 37 1 GTGGCGCCGG 0.51627 -50 CAAAACGCACGCGCGGTAGCCTTTAT 9 7 1 GCACGCGCGG 0.689121 -24 TCTGCGGTTGGTGAGGCCGCAACTGTCTGA 10 11 1 GTGAGGCCGC 0.917113 -105 CACACGCTTTGAGGAGCCAGACTAGGCTCG 10 92 1 GAGGAGCCAG 0.596033 -24 ********** Masking position 9 Map Score: 60.9396 Number of sites scoring better than the average of aligned sites = 122667 Number in coding regions = 114742 Number in noncoding regions = 7925 Number of orfs with sites within 600 bp upstream = 1743 Fraction of orfs with sites within 600 bp upstream = 0.279955 Motif number 2 CCTCCTGCCGCGACCATCCGATAGCTTGGA 1 14 0 CGACCATCCG 0.920699 -188 GACTGGCTTGCCTCCTGCCGCGACCATCCG 1 24 0 CCTCCTGCCG 0.637029 -178 ATGGGACTGTCCGCGACGCGACGTGGCCCC 1 73 1 CCGCGACGCG 0.947449 -129 CCTGACCGATGCACCAGGGGCCACGTCGCG 1 89 0 GCACCAGGGG 0.935045 -113 GACGGTGTAGCGGCCTTGCGGATACGGTCT 1 118 1 CGGCCTTGCG 0.737119 -84 CCACTTGTGGGGGCGTGCCCCCACCTCATC 3 40 0 GGGCGTGCCC 0.42669 -58 CCGCTCTCCCCCGCCAGCGGATGGGGGTAC 3 73 0 CCGCCAGCGG 0.979159 -25 CCGCTGGCGGGGGAGAGCGGCGCTC 3 83 1 GGGAGAGCGG 0.703356 -15 AGCCTATCCGCCGCACGACGGCGCCCTGTG 4 25 0 CCGCACGACG 0.496864 -26 CGCGCCAGCCTATCCGCCGCA 4 40 0 GCGCCAGCCT 0.974849 -11 GCGACAGCGGCCGCCAGGAGCCGGGCAATG 5 11 0 CCGCCAGGAG 0.73946 -290 GCCGCGCCCGGCGACAGCGGCCGCCAGGAG 5 21 0 GCGACAGCGG 0.786193 -280 CGCTGTCGCCGGGCGCGGCGGGCAGATCTG 5 32 1 GGGCGCGGCG 0.681169 -269 CCCTGGCCACCGGCGCTCCTCCTCAGATCT 5 55 0 CGGCGCTCCT 0.617365 -246 ATCACATGCACGACCACCCTGGCCACCGGC 5 71 0 CGACCACCCT 0.764777 -230 TGCATGTGATGCCCAAGGCGGAGATTCTTG 5 91 1 GCCCAAGGCG 0.847997 -210 TTGACCCGCAGGGCCAGGCGATTGTCGGTG 5 118 1 GGGCCAGGCG 0.991278 -183 ATTCCGAGATGCCCAAGCCGCCCCAGCGCA 5 146 0 GCCCAAGCCG 0.913322 -155 ATGTGCGTCAGGGCAAGAGGTTTGAGCTGG 5 181 1 GGGCAAGAGG 0.68075 -120 AGCTGGAGGTCGACGATACGGTTGATGACA 5 205 1 CGACGATACG 0.382164 -96 TCTGCGATCTCGGCAAGCGTGGTGTCATCA 5 227 0 CGGCAAGCGT 0.790371 -74 GAGGACTGGACGATCAGCCGGGACCCGCA 5 282 1 CGATCAGCCG 0.716086 -19 ATTTTGCGCACCACCATCCTGAGCGCCCGC 6 17 1 CCACCATCCT 0.658194 -175 CATCCTGAGCGCCCGCCCCGATGTCAGCCC 6 31 1 GCCCGCCCCG 0.76313 -161 AACCCCGGTGGCATCAGCCGTCGGGCTGAC 6 53 0 GCATCAGCCG 0.736335 -139 GCGTTGACACGGACAAGCCGACGGATAGGT 6 97 0 GGACAAGCCG 0.95077 -95 CGCGGCCGCAGCGCGATGGGGCCTAGCTAG 6 124 1 GCGCGATGGG 0.844122 -68 CGCGGGGTCCGGGCGAGCGGAGACATCACG 6 162 0 GGGCGAGCGG 0.932249 -30 CCGCTCGCCCGGACCCCGCGCAAAACGTCG 6 172 1 GGACCCCGCG 0.819256 -20 TCACCGCCTTGGGAACTCAGGGA 7 4 1 CCGCCTTGGG 0.526374 -297 GGTCAACCTGCGCCGACCCGCGATCTGTGA 7 60 0 CGCCGACCCG 0.875413 -241 TATGGACCCCGCGCCAGCGCGGTCAACCTG 7 80 0 GCGCCAGCGC 0.872138 -221 AGAATTGTGCGGTCAAGGCGATAACTCTTG 7 111 1 GGTCAAGGCG 0.665867 -190 ATCCAGATGGCGGCCAAGCGCCGCTGCTGA 7 252 0 CGGCCAAGCG 0.770336 -49 GGGCACCCCGGCGCCACCCTCACACACCAT 8 34 0 GCGCCACCCT 0.920152 -53 CTTACGTGTCGGGCACCCCGGCGCCACCCT 8 44 0 GGGCACCCCG 0.87745 -43 CAAAACGCACGCGCGGTAGCCTTTAT 9 7 1 GCACGCGCGG 0.872146 -24 CGTGTGAGCACCACCAGCCTGCATCCCAGT 10 68 0 CCACCAGCCT 0.912255 -48 ACGGCGAGCCTAGTCTGGCTC 10 105 0 CGGCGAGCCT 0.948888 -11 ********** Masking position 4 Map Score: 57.1341 Number of sites scoring better than the average of aligned sites = 59505 Number in coding regions = 55087 Number in noncoding regions = 4418 Number of orfs with sites within 600 bp upstream = 1502 Fraction of orfs with sites within 600 bp upstream = 0.241246 Motif number 3 GCCGGCGCCGATGCAGAGCGGGGCGATGAG 3 16 1 ATGCAGAGCG 0.754501 -82 TCTCCCCCGCCAGCGGATGGGGGTACCTCC 3 69 0 CAGCGGATGG 0.836417 -29 CCAGAGATACCAGCACAGGGCGCCGTCGTG 4 12 1 CAGCACAGGG 0.919287 -39 TGCCCGGCTCCTGGCGGCCGCTGTCGCCGG 5 14 1 CTGGCGGCCG 0.90418 -287 CTCCTCAGATCTGCCCGCCGCGCCCGGCGA 5 37 0 CTGCCCGCCG 0.829593 -264 CACGACCACCCTGGCCACCGGCGCTCCTCC 5 63 0 CTGGCCACCG 0.94408 -238 CGTGCATGTGATGCCCAAGGCGGAGATTCT 5 89 1 ATGCCCAAGG 0.54733 -212 CAAGCCGCCCCAGCGCACCGACAATCGCCT 5 133 0 CAGCGCACCG 0.929475 -168 GAGGTTTGAGCTGGAGGTCGACGATACGGT 5 197 1 CTGGAGGTCG 0.730931 -104 CCGGTGGCATCAGCCGTCGGGCTGACATCG 6 49 0 CAGCCGTCGG 0.945796 -143 ACGGATAGGTATGCCCGCGGCAAGAACCCC 6 77 0 ATGCCCGCGG 0.95682 -115 TGACACGGACAAGCCGACGGATAGGTATGC 6 93 0 AAGCCGACGG 0.882113 -99 GCGCGGGGTCCGGGCGAGCGGAGACATCAC 6 163 0 CGGGCGAGCG 0.776849 -29 CGACGTTTTGCGCGGGGTCCGGGCGAG 6 175 0 TTGCGCGGGG 0.686289 -17 GTTGACCGCGCTGGCGCGGGGTCCATACAG 7 83 1 CTGGCGCGGG 0.775036 -218 GTCTCAGCAGCGGCGCTTGGCCGCCATCTG 7 249 1 CGGCGCTTGG 0.587331 -52 AGCCGCAGCTCAGCACGCCGGAA 8 4 0 CAGCACGCCG 0.933432 -83 ACGTGTCGGGCACCCCGGCGCCACCCTCAC 8 41 0 CACCCCGGCG 0.671104 -46 TCTGCGGTTGGTGAGGCCGCA 10 2 1 CTGCGGTTGG 0.81706 -114 GGTACTGAGTCTGCACTGGGATGCAGGCTG 10 54 1 CTGCACTGGG 0.908657 -62 CTGCACTGGGATGCAGGCTGGTGGTGCTCA 10 64 1 ATGCAGGCTG 0.355558 -52 ********** Masking position 10 Map Score: 18.0196 Number of sites scoring better than the average of aligned sites = 36365 Number in coding regions = 33997 Number in noncoding regions = 2368 Number of orfs with sites within 600 bp upstream = 1110 Fraction of orfs with sites within 600 bp upstream = 0.178285 Motif number 4 CGTCGCGTCGCGGACAGTCCCATGTTAGCT 1 66 0 CGGACAGTCC 0.73764 -136 GCCGCTACACCGTCCTGACCGATGCACCAG 1 102 0 CGTCCTGACC 0.97746 -100 GATATTGCCTCATCGAGACCGTATCCGCAA 1 133 0 CATCGAGACC 0.78288 -69 CGCCGGCGCCGATGCAGAGCGGGGCGATGA 3 15 1 GATGCAGAGC 0.728594 -83 ATCCGCTGGCGGGGGAGAGCGGCGCTC 3 81 1 GGGGGAGAGC 0.686619 -17 CGCACGACGGCGCCCTGTGCTGGTATCTCT 4 14 0 CGCCCTGTGC 0.777451 -37 CCGGGCGCGGCGGGCAGATCTGAGGAGGAG 5 40 1 CGGGCAGATC 0.945121 -261 CCCGGCTGATCGTCCAGTCCTCGATCACGG 5 274 0 CGTCCAGTCC 0.951812 -27 TGCGCACCACCATCCTGAGCGCCCGCCCCG 6 21 1 CATCCTGAGC 0.903622 -171 CATCAGCCGTCGGGCTGACATCGGGGCGGG 6 42 0 CGGGCTGACA 0.846353 -150 GTTCTTGCCGCGGGCATACCTATCCGTCGG 6 80 1 CGGGCATACC 0.86761 -112 TGTCTCCGCTCGCCCGGACCCCGCGCAAAA 6 167 1 CGCCCGGACC 0.875467 -25 CGGGTCGGCGCAGGTTGACCGCGCTGGCGC 7 70 1 CAGGTTGACC 0.595245 -231 TCGGTGGATCCATCCAGATGGCGGCCAAGC 7 263 0 CATCCAGATG 0.332649 -38 TTCCGGCGTGCTGAGCTGCGGCTATG 8 7 1 CGTGCTGAGC 0.972308 -80 CGAATTCGGCGGTGCAGACGTC 8 75 1 GGTGCAGACG 0.701508 -12 CAGACAGTTGCGGCCTCACCAACCGCAGA 10 10 0 CGGCCTCACC 0.883918 -106 ********** Masking position 8 Map Score: 11.945 Number of sites scoring better than the average of aligned sites = 18233 Number in coding regions = 17163 Number in noncoding regions = 1070 Number of orfs with sites within 600 bp upstream = 704 Fraction of orfs with sites within 600 bp upstream = 0.113074 Motif number 5 TCTCGATGAGGCAATATCGGACAAGTGTCC 1 145 1 GCAATATCGG 0.850388 -57 GGGCGGCTTGGGCATCTCGGAATATCAGAT 5 153 1 GGCATCTCGG 0.965489 -148 CAGTGATTCTGCGATCTCGGCAAGCGTGGT 5 234 0 GCGATCTCGG 0.994763 -67 CGTCCAGTCCTCGATCACGGTGTTGGCCAA 5 264 0 TCGATCACGG 0.946737 -37 GGCGAGCGGAGACATCACGGAGGCAGTCTA 6 151 0 GACATCACGG 0.892764 -41 TCACCGCCTTGGGAACTCAGGGAGAAATGA 7 11 1 GGGAACTCAG 0.710532 -290 ACAGAATTGTGCGGTCAAGGCGATAACTCT 7 109 1 GCGGTCAAGG 0.932848 -192 ACCAGATCTAGCGATCTAAGAACATCGGCC 7 147 1 GCGATCTAAG 0.935166 -154 CGCGATAAAGGCTACCGCGCG 9 20 0 GCGATAAAGG 0.921285 -11 ********** Masking position 10 Map Score: 5.67079 Number of sites scoring better than the average of aligned sites = 4846 Number in coding regions = 4561 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 6 TGTCCAAGCTATCGGATGGTCGCGGCAGGA 1 12 1 ATCGGATGGT 0.609349 -190 GTCCCATGTTAGCTGCATGTTTAGCAGACT 1 50 0 AGCTGCATGT 0.818619 -152 CTAGCGGGTTGACAGCGCAGAA 2 3 1 AGCGGGTTGA 0.959605 -28 GCCGATGCAGAGCGGGGCGATGAGGTGGGG 3 22 1 AGCGGGGCGA 0.80937 -76 CGCCCCCACAAGTGGGAGGTACCCCCATCC 3 55 1 AGTGGGAGGT 0.851506 -43 AAGAGGTTTGAGCTGGAGGTCGACGATACG 5 195 1 AGCTGGAGGT 0.972016 -106 GATCTCGGCAAGCGTGGTGTCATCAACCGT 5 222 0 AGCGTGGTGT 0.819202 -79 ACGCGGCCGCAGCGCGATGGGGCCTAGCTA 6 123 1 AGCGCGATGG 0.811005 -69 TCGGCCGGAAACCTGGTTGTTGCGGCCGCG 7 171 1 ACCTGGTTGT 0.848892 -130 TGAGACTGGGATCGGGTTGTATGCGAGCCC 7 225 0 ATCGGGTTGT 0.95489 -76 CTTGGCCGCCATCTGGATGGATCCACCGAT 7 264 1 ATCTGGATGG 0.804686 -37 CTGGGATGCAGGCTGGTGGTGCTCACACGC 10 69 1 GGCTGGTGGT 0.861305 -47 ********** Masking position 9 Map Score: 3.66743 Number of sites scoring better than the average of aligned sites = 4128 Number in coding regions = 3796 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 7 ********** No masking Map Score: -1.94446e-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 8 ********** No masking Map Score: -1.94446e-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 9 ********** No masking Map Score: -1.94446e-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