AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_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 phoY2 57 phoY2 #2 Rv0822c 165 hypothetical protein Rv0822c #3 phoS2 271 phoS2 #4 pstB 215 pstB #5 pstC 59 pstC #6 phoY1 107 phoY1 Motif number 1 TGCTGCATTGTGCGGCGCCGACTCGTGGCG 2 66 1 TGCGGCGCCG 0.987295 -100 GCCGACTCGTGGCGGTGCTGCGCGAAGGTG 2 82 1 GGCGGTGCTG 0.948684 -84 GGCGGACGCCCGCGGTGTTGGCTGCGTGTC 2 119 0 CGCGGTGTTG 0.968367 -47 GTCCTACCGGCCTCCGAGAGTCTAGG 2 150 0 CCGGCCTCCG 0.908433 -16 GCCCTCTTTTCCGGCTGTCGGCCGAAACGG 3 14 1 CCGGCTGTCG 0.982287 -258 AGGCACACCCCCAGGTTTCGGGAGCAGTCA 3 68 0 CCAGGTTTCG 0.669162 -204 TCCCCTGAGACCCGCGGTCGAACCAGCCAC 3 127 1 CCCGCGGTCG 0.995881 -145 TGATGATGGACACGTGGCTGGTTCGACCGC 3 140 0 CACGTGGCTG 0.69923 -132 GTCGCCCTTGGCCGGGGTTGACCCCTGATG 3 165 0 GCCGGGGTTG 0.950615 -107 GCGAACTTGGCGTGCCGTCGCCCTTGGCCG 3 181 0 CGTGCCGTCG 0.975587 -91 GCAAAACAGCTGGTCGGCCGTTAGGAACTG 3 250 1 TGGTCGGCCG 0.645619 -22 AACTCCTCTCGAGGGGGTCGTGGTGGCGGA 4 13 1 GAGGGGGTCG 0.909985 -203 CCACTCGCCACCGGTGGTCGCCGAGCCACC 4 44 1 CCGGTGGTCG 0.975783 -172 CGGTGGTCGCCGAGCCACCGACCCGGGGTC 4 55 1 CGAGCCACCG 0.817318 -161 GAGCCACCGACCCGGGGTCGGTATTCGAGC 4 66 1 CCCGGGGTCG 0.996612 -150 CGGTATTCGAGCCGTCACCGTTGTGCATCG 4 84 1 GCCGTCACCG 0.839069 -132 CTAGCGTTCAGGAGGGGCCGCTGATACTGA 4 137 1 GGAGGGGCCG 0.982097 -79 TTGGACAAAGCGCGCCGTCGACCCTCAGTA 4 161 0 CGCGCCGTCG 0.997186 -55 GCATGTAGTACCCTGCGCCG 4 206 1 CCCTGCGCCG 0.957937 -10 AGGTTGCTGTCGCGTGGTGGTCAACGAGG 5 10 0 CGCGTGGTGG 0.938043 -50 CAACCTCCGTCGGGCCATCGGGCTGCTTTG 5 34 1 CGGGCCATCG 0.890719 -26 GGGTATGTCGCGCGGTGCCGCCATGGTCGA 6 25 1 CGCGGTGCCG 0.996482 -83 GGTCGATGATGGCGGTGTGGATCCGCGGCA 6 49 1 GGCGGTGTGG 0.923153 -59 GTCGTCGTGTGGTGCTGCCGCGGATCCACA 6 64 0 GGTGCTGCCG 0.922114 -44 TCTCTGACCCTGAGTCGTCGTGTGGTGCTG 6 77 0 TGAGTCGTCG 0.780152 -31 ********** Masking position 10 Map Score: 44.6571 Number of sites scoring better than the average of aligned sites = 64100 Number in coding regions = 60422 Number in noncoding regions = 3678 Number of orfs with sites within 600 bp upstream = 1365 Fraction of orfs with sites within 600 bp upstream = 0.219242 Motif number 2 CCGCATTGACACGACGCTTACGGCATT 1 8 1 GACACGACGC 0.963354 -50 GTGCGGCGCCGACTCGTGGCGGTGCTGCGC 2 75 1 GACTCGTGGC 0.794416 -91 GTGCGCGTAGGACACGCAGCCAACACCGCG 2 109 1 GACACGCAGC 0.807707 -57 ACGCAGCCAACACCGCGGGCGTCCGCCACC 2 122 1 CACCGCGGGC 0.991188 -44 CGTTTCGGCCGACAGCCGGAAAAGAGGGCG 3 13 0 GACAGCCGGA 0.938842 -259 CGGGAGCAGTCACAGGAAGCTGCAGCAAGC 3 50 0 CACAGGAAGC 0.876464 -222 GCCGTGCATACACAGCAGGCACACCCCCAG 3 84 0 CACAGCAGGC 0.984906 -188 TGGCTGGTTCGACCGCGGGTCTCAGGGGAA 3 126 0 GACCGCGGGT 0.96479 -146 CCTGATGATGGACACGTGGCTGGTTCGACC 3 142 0 GACACGTGGC 0.964023 -130 ATCAGGGGTCAACCCCGGCCAAGGGCGACG 3 166 1 AACCCCGGCC 0.742994 -106 GGCCAAGGGCGACGGCACGCCAAGTTCGCC 3 182 1 GACGGCACGC 0.973137 -90 CTGCGAGCAAAACAGCTGGTCGGCCGTTAG 3 244 1 AACAGCTGGT 0.643029 -28 GCTCGGCGACCACCGGTGGCGAGTGGATCC 4 40 0 CACCGGTGGC 0.966757 -176 CTCGAATACCGACCCCGGGTCGGTGGCTCG 4 65 0 GACCCCGGGT 0.951908 -151 GCACAACGGTGACGGCTCGAATACCGACCC 4 80 0 GACGGCTCGA 0.890619 -136 ACTGAGGGTCGACGGCGCGCTTTGTCCAAG 4 162 1 GACGGCGCGC 0.985287 -54 ACCACCACGCGACAGCAACCTCCGTCGGGC 5 19 1 GACAGCAACC 0.789859 -41 ACCATGGCGGCACCGCGCGACATACCCGCT 6 22 0 CACCGCGCGA 0.957317 -86 GCCGCGGATCCACACCGCCATCATCGACCA 6 48 0 CACACCGCCA 0.740573 -60 GCGGCAGCACCACACGACGACTCAGGGTCA 6 73 1 CACACGACGA 0.818524 -35 ********** Masking position 2 Map Score: 27.2027 Number of sites scoring better than the average of aligned sites = 18171 Number in coding regions = 16837 Number in noncoding regions = 1334 Number of orfs with sites within 600 bp upstream = 837 Fraction of orfs with sites within 600 bp upstream = 0.134436 Motif number 3 GCACAATGCAGCAAGGCCCACATCGTACTGA 2 48 0 GCAGGCCCAC 0.935297 -118 CCACGAGTCGGCGCCGCACAATGCAGCAAGG 2 63 0 GCCCGCACAA 0.768277 -103 CCTTCGCGCAGCACCGCCACGAGTCGGCGCC 2 79 0 GCCCGCCACG 0.996331 -87 ACACCGCGGGCGTCCGCCACCTAGACTCTCG 2 131 1 CGCCGCCACC 0.967982 -35 ATACACAGCAGGCACACCCCCAGGTTTCGGG 3 76 0 GGACACCCCC 0.86368 -196 TGCTGTGTATGCACGGCATACGGACATCCTT 3 97 1 GCCGGCATAC 0.876439 -175 CAGGGGTCAACCCCGGCCAAGGGCGACGGCA 3 168 1 CCCGGCCAAG 0.935143 -104 CAAGGGCGACGGCACGCCAAGTTCGCCGACC 3 185 1 GGACGCCAAG 0.950253 -87 AGTTCCTAACGGCCGACCAGCTGTTTTGCTC 3 248 0 GGCGACCAGC 0.807836 -24 GTGGCGAGTGGATCCGCCACCACGACCCCCT 4 24 0 GACCGCCACC 0.987117 -192 CGGGTCGGTGGCTCGGCGACCACCGGTGGCG 4 49 0 GCCGGCGACC 0.929682 -167 GTCGGTATTCGAGCCGTCACCGTTGTGCATC 4 82 1 GACCGTCACC 0.791672 -134 CCTCGTTGACCACCACGCGACAGCAAC 5 7 1 TGCCACCACG 0.698512 -53 GCTCCGCAAAGCAGCCCGATG 5 49 0 GCCCGCAAAG 0.980048 -11 AGGCTACGCCAAGCGGGTATGTC 6 3 1 GCACGCCAAG 0.971284 -105 TGGCGGCACCGCGCGACATACCCGCTTGGCG 6 17 0 GCCGACATAC 0.654428 -91 TGCTGCCGCGGATCCACACCGCCATCATCGA 6 51 0 GACCACACCG 0.737794 -57 ** ******** Masking position 7 Map Score: 18.5312 Number of sites scoring better than the average of aligned sites = 32919 Number in coding regions = 30671 Number in noncoding regions = 2248 Number of orfs with sites within 600 bp upstream = 1142 Fraction of orfs with sites within 600 bp upstream = 0.183424 Motif number 4 TTGACACGACGCTTACGGCATTTTCCAAGG 1 16 1 GCTTACGGCA 0.966707 -42 ACGATGTGGGCCTTGCTGCATTGTGCGGCG 2 53 1 CCTTGCTGCA 0.979882 -113 ACGGTAACAAGCTTGCTGCAGCTTCCTGTG 3 40 1 GCTTGCTGCA 0.975197 -232 AGCAAATGAAGCTAACAGCACTAGGTTAAC 3 216 0 GCTAACAGCA 0.969049 -56 CAGCTGTTTTGCTCGCAGCAAATGAAGCTA 3 232 0 GCTCGCAGCA 0.987529 -40 TTCAGTTCCTAACGGCCGACCAGCTGT 3 255 0 CCTAACGGCC 0.916263 -17 CGCGCTTTGTCCAAGGAGCATCCCAAGGAG 4 177 1 CCAAGGAGCA 0.949766 -39 AAGGAGCATCCCAAGGAGCATGTAGTACCC 4 189 1 CCAAGGAGCA 0.949766 -27 TCGTTGACCACCACGCGACAGCAACCTCCG 5 13 1 CCACGCGACA 0.858999 -47 ********** Masking position 2 Map Score: 8.5446 Number of sites scoring better than the average of aligned sites = 2947 Number in coding regions = 2705 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 5 ATCGAGACCCTGTCGAAATCGCGTC 2 6 1 GACCCTGTCG 0.968998 -160 TGCATTGTGCGGCGCCGACTCGTGGCGGTG 2 69 1 GGCGCCGACT 0.895944 -97 CTAGGTGGCGGACGCCCGCGGTGTTGGCTG 2 125 0 GACGCCCGCG 0.996088 -41 GGCGCCCTCTTTTCCGGCTG 3 1 1 GGCGCCCTCT 0.970223 -271 TCCTTCCCCTGAGACCCGCGGTCGAACCAG 3 123 1 GAGACCCGCG 0.821834 -149 TTGGCGTGCCGTCGCCCTTGGCCGGGGTTG 3 175 0 GTCGCCCTTG 0.745368 -97 CCGCCACCACGACCCCCTCGAGAGGAGTTG 4 12 0 GACCCCCTCG 0.996455 -204 CGTGGTGGCGGATCCACTCGCCACCGGTGG 4 31 1 GATCCACTCG 0.659273 -185 CTCGAATACCGACCCCGGGTCGGTGGCTCG 4 65 0 GACCCCGGGT 0.850001 -151 TTGGACAAAGCGCGCCGTCGACCCTCAGTA 4 161 0 CGCGCCGTCG 0.918767 -55 CCTCGTTGACCACCACGCGACAGCAAC 5 8 1 GACCACCACG 0.934622 -52 CGCCATCATCGACCATGGCGGCACCGCGCG 6 33 0 GACCATGGCG 0.824298 -75 ********** Masking position 1 Map Score: 10.7857 Number of sites scoring better than the average of aligned sites = 21218 Number in coding regions = 20112 Number in noncoding regions = 1106 Number of orfs with sites within 600 bp upstream = 733 Fraction of orfs with sites within 600 bp upstream = 0.117732 Motif number 6 GGCGCCCTCTTTTCCGGCTGTCGGCCG 3 5 1 CCCTCTTCGG 0.983185 -267 AGCCACGTGTCCATCATCAGGGGTCAACCCCGG 3 151 1 CCATCCAGGG 0.978076 -121 CGTGCCGTCGCCCTTGGCCGGGGTTGACCCCTG 3 168 0 CCCTTCCGGG 0.70921 -104 CACCACGACCCCCTCGAGAGGAGTTGC 4 5 0 CCCTCGAGAG 0.983142 -211 GTGGCGGATCCACTCGCCACCGGTGGTCGCCGA 4 35 1 CACTCCACGG 0.98567 -181 TATCAGCGGCCCCTCCTGAACGCTAGGATTTCA 4 130 0 CCCTCGACGC 0.984366 -86 GCGCCGTCGACCCTCAGTATCAGCGGCCCCTCC 4 147 0 CCCTCTACAG 0.984765 -69 ***** ** *** Masking position 4 Map Score: 2.27635 Number of sites scoring better than the average of aligned sites = 935 Number in coding regions = 854 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 GTGCTAAAGCCTACGTTCCCGACCTTGGA 1 39 0 CCTACGTTCC 0.882695 -19 ACGATGTGGGCCTTGCTGCATTGTGCGGCG 2 53 1 CCTTGCTGCA 0.78967 -113 CCTACGCGCACCTTCGCGCAGCACCGCCAC 2 90 0 CCTTCGCGCA 0.923562 -76 GGCTGCGTGTCCTACGCGCACCTTCGCGCA 2 100 0 CCTACGCGCA 0.971416 -66 GTCCTACCGGCCTCCGAGAGTC 2 154 0 CCTACCGGCC 0.993232 -12 GCCAAGTTCGCCGACCGTTAACCTAGTGCT 3 200 1 CCGACCGTTA 0.861896 -72 TTCAGTTCCTAACGGCCGACCAGCTGT 3 255 0 CCTAACGGCC 0.942489 -17 CCGGTGGTCGCCGAGCCACCGACCCGGGGT 4 54 1 CCGAGCCACC 0.917101 -162 GGGTCGGTATTCGAGCCGTCACCGTTGTGC 4 80 1 TCGAGCCGTC 0.752386 -136 TCATTGAAATCCTAGCGTTCAGGAGGGGCC 4 126 1 CCTAGCGTTC 0.873994 -90 AAGCGCGCCGTCGACCCTCAGTATCAGCGG 4 154 0 TCGACCCTCA 0.797079 -62 ACAGCAACCTCCGTCGGGCCATCGGGCTGC 5 30 1 CCGTCGGGCC 0.968673 -30 ********** Masking position 2 Map Score: 10.6373 Number of sites scoring better than the average of aligned sites = 13971 Number in coding regions = 12868 Number in noncoding regions = 1103 Number of orfs with sites within 600 bp upstream = 772 Fraction of orfs with sites within 600 bp upstream = 0.123996 Motif number 8 ********** No masking Map Score: -3.30951e-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 9 ********** No masking Map Score: -3.30951e-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 10 ********** No masking Map Score: -3.30951e-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