AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iphoB_pyro_opreg_100.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0024 36 284aa long hypothetical sugar transport membrane protein #2 PH0025 169 426aa long hypothetical protein #3 PH0164 300 160aa long hypothetical protein #4 PH0194 60 375aa long hypothetical multiple sugar-binding transport ATP-binding protein #5 PH0206 132 544aa long hypothetical protein #6 PH1037 129 142aa long hypothetical protein #7 PH1214 267 441aa long hypothetical cytoplasmic protein #8 PH1238 73 231aa long hypothetical protein #9 PH1239 59 237aa long hypothetical protein #10 PH1241 48 167aa long hypothetical protein #11 PH1605 300 425aa long hypothetical protein #12 PH1606 43 447aa long hypothetical protein #13 PH1607 25 249aa long hypothetical PHNP protein #14 PH1815 24 284aa long hypothetical cobalt transport ATP-binding protein Motif number 1 AGGAAGATACATTTTTAATTGGTAAATTTA 2 19 0 ATTTTTAATT 0.946349 -151 ATGCAATTTTATTTTTAAGAAGAG 4 47 1 ATTTTTAAGA 0.810169 -14 AACCGAAACACTTTTTAAATACCCCGAATA 5 50 1 CTTTTTAAAT 0.781691 -83 AGCCCGCTTAATTTATAATTCCCCATACCC 7 21 0 ATTTATAATT 0.718553 -247 AGATACAGACATTTTTAAATGACACTATGG 7 114 1 ATTTTTAAAT 0.885029 -154 ATGAGGAGACATTTATCATATGATGTCACC 7 142 0 ATTTATCATA 0.545031 -126 TGTTAGACTGATTTTTAATACTTAAAGTTT 7 225 0 ATTTTTAATA 0.93272 -43 GCTTTTAACAATTTTTAAAAGTTTTAGTTT 8 23 0 ATTTTTAAAA 0.939217 -51 GCTTTTAGGAGTTTTTAAAATAAAAGGTTA 9 15 0 GTTTTTAAAA 0.835393 -45 GCCCTTTTCTATTTTTCAAAGATCGTC 9 43 1 ATTTTTCAAA 0.880857 -17 TTAACACTTGATTTTTAAAT 10 1 0 ATTTTTAAAT 0.885029 -48 GGGTTCTATCGTTTTTCATTTTTTCAAGAA 11 41 1 GTTTTTCATT 0.726507 -260 TTTACACAAAATTTTTACTTTACCAAGTAA 11 239 1 ATTTTTACTT 0.727142 -62 TTTCCATTATATTTTTAAATCGAAATCGCT 12 13 1 ATTTTTAAAT 0.885029 -31 ********** Masking position 6 Map Score: 14.8072 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 59 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 CCCTTATGCCCTAAATCTTTATTTATTTTT 2 132 0 CTAAATCTTT 0.78347 -38 GGATATCGGTGAAAAAATTTACAGTAACGG 3 23 1 GAAAAAATTT 0.92369 -278 ACATTTCCTGGAAAAACATTGCT 4 4 0 GAAAAACATT 0.861284 -57 ATATCTAACCGAAACACTTTTTAAATACCC 5 44 1 GAAACACTTT 0.949379 -89 CTCATAACTCCCAAAACTTTGACAAATTTA 7 167 1 CCAAAACTTT 0.912376 -101 GAGATTCTAACAAAAACTTTAAGTATTAAA 7 212 1 CAAAAACTTT 0.966075 -56 AAGTTGAAAACTAAAACTTTTAAAAATTGT 8 16 1 CTAAAACTTT 0.966075 -58 GTTAAAAGCTGTAACACTTTTTCTGAAATT 8 44 1 GTAACACTTT 0.949379 -30 CAGATTGATCGAAAAAATTTACACAAAATT 11 222 1 GAAAAAATTT 0.92369 -79 ACTTGGTAAAGTAAAAATTTTGTGTAAATT 11 237 0 GTAAAAATTT 0.92369 -64 ATATATAATTGTAAAACTGTCAATTACTTG 11 262 0 GTAAAACTGT 0.901984 -39 ********** Masking position 4 Map Score: 11.5421 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 64 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 GGATGGTTCACCAAAGATCCCTTATGCCCTA 2 149 0 CACCAATCCC 0.962303 -21 TCCCTGAACTCCTCCCTAAGCCCGTTACTGTAA 3 41 0 CCTCCAGCCC 0.986063 -260 ATAGAGAAGTCCCTTCTTATCCCTGAACTCCTC 3 60 0 CCCTCATCCC 0.887653 -241 TTAGAATAACCTTCAAAACGCCATCAATCCAAT 3 256 0 CTTCACGCCA 0.729675 -45 ATTGGAATAGCCTGGCTAATCCCGTTCATGGGA 6 60 1 CCTGCATCCC 0.959003 -70 TTACCGATGCCATCAATACTCCCATGAACGGGA 6 79 0 CATCACTCCC 0.962303 -51 ATGAAGCGGTCCCCCAGGAGCCCGCTTAATTTA 7 36 0 CCCCAAGCCC 0.988718 -232 AGGGATGAATCATGTCATCGCCCAGCTAATTCT 7 81 1 CATGCCGCCC 0.942748 -187 ATAAATGTCTCCTCATAACTCCCAAAACTTTGA 7 156 1 CCTCTCTCCC 0.93131 -112 ATTTTAAAAACTCCTAAAAGCCCTTTTCTATTT 9 24 1 CTCCAAGCCC 0.971637 -36 CTCGCAACCTCCCGAGATTTATT 10 36 0 CTCGACTCCC 0.938268 -13 **** * ***** Masking position 11 Map Score: 9.84615 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 339 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TTTCTCTATTTCTTTTTTATCTGGGAGG 1 8 1 ATTTCTTTTT 0.813132 -29 GTTAGCTTTGTTATCTGTTTTTAATGTAAAT 2 67 1 TTATCTTTTT 0.907169 -103 CTTTATTTATTTTTCTGTTTTTGCCTTTGAA 2 115 0 TTTTCTTTTT 0.968676 -55 TTTTCATTATTTTACCTATTC 5 1 1 TTTTCATATT 0.864325 -132 TACATTGGACTTTTCAATTTTAGTGTACTTT 5 83 1 TTTTCATTTT 0.97839 -50 AAAGTTTTAGTTTTCAACTTTAGGT 8 5 0 TTTTCACTTT 0.904232 -69 GTTACAGCTTTTAACAATTTTTAAAAGTTTT 8 28 0 TTAACATTTT 0.799078 -46 CTAAAAGCCCTTTTCTATTTTTCAAAGATCG 9 37 1 TTTTCTTTTT 0.968676 -23 GTTCTATCGTTTTTCATTTTTTCAAGAAGTA 11 43 1 TTTTCATTTT 0.97839 -258 TACCAAGTAATTGACAGTTTTACAATTATAT 11 259 1 TTGACATTTT 0.769731 -42 ****** **** Masking position 2 Map Score: 10.1056 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 71 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TTTAACGCCCTCCCAGATAAAAAAGAAATAGA 1 15 0 CCCTAGATAA 0.915892 -22 GAAGGGACTTCTCTATAAGATGCTAGAAATACGGG 3 77 1 CTCTAGATGA 0.771375 -224 CAAGCTCATGCCTACTAAGATGATACGCCAGGAGA 3 152 0 CCTAAGATGA 0.942793 -149 ACGTTGAGGCCCTTGAAAGAGGGGAACCTCAGCCG 3 217 1 CCTTAGAGGA 0.983167 -84 AACTAACCACCCCTAACAGCGGTTAGAATAACCTT 3 276 0 CCCTAGCGGA 0.966151 -25 CATTATTTTACCTATTCTGAGAGAAATTAATATCT 5 15 1 CCTATGAGAA 0.698654 -118 CTTTCACCCCCCTTAGAGGACGAATTAAGAAA 5 111 0 CCCCAGAGGG 0.978811 -22 TCGGTAAGGCCCTATGAAGAGATCGTGAGCGGCTG 6 105 1 CCTAAGAGAG 0.876335 -25 AATGGTGGTTCCCCTAAAGAGGATAGATAAGATTC 11 137 0 CCCCAGAGGA 0.991264 -164 GATGCTCCCAAGGAGAGGGGAGTA 14 7 1 CCCAAGAGGA 0.992743 -18 **** ***** * Masking position 1 Map Score: 6.13969 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 266 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TTCTTATCCCTGAACTCCTCCCTAAGCCCGTT 3 48 0 TGACCCTCCC 0.964941 -253 AAGAGAGTCCTAAACTTCTCCTCAAGCTCATG 3 177 0 TAACTCTCCT 0.95884 -124 CGGTTAGATATTAATTTCTCTCAGAATAGGTA 5 23 0 TTATTCTCTC 0.589351 -110 GTGTACTTTCTTAATTCGTCCTCTAAGGGGGG 5 105 1 TTATCGTCCT 0.797818 -28 AGTTAGGAACTAGATACCTCCTAATTTTCATC 6 14 0 TAATCCTCCT 0.981049 -116 GATGACATGATTCATCCCTCCTGAACCGATGA 7 68 0 TTATCCTCCT 0.964486 -200 CATCATATGATAAATGTCTCCTCATAACTCCC 7 147 1 TAATTCTCCT 0.93593 -121 TGTTAGTCGCCTCCCTACATTTATG 7 253 0 TATCCCTCCC 0.961336 -15 TTCATCAGCATACACCCTTCCTGGGACTCTCA 11 75 1 TAACCTTCCT 0.890037 -226 TACTCCCCTCTCCTTGGGAGCA 14 13 0 TATCCCTCTC 0.811263 -12 ** ** ****** Masking position 9 Map Score: 4.20681 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 501 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 TTATCTGTTTTTAATGTAAATTAGGCATTAG 2 77 1 TTATGTAAAT 0.977728 -93 CCTAAGCCCGTTACTGTAAATTTTTTCACCG 3 29 0 TTATGTAAAT 0.977728 -272 CTTTTCAATTTTAGTGTACTTTCTTAATTCG 5 92 1 TTATGTACTT 0.85736 -41 TTTGACAAATTTAATGTAAATCCTAGAAGAG 7 184 1 TTATGTAAAT 0.977728 -84 AAGTAAAAATTTTGTGTAAATTTTTTCGATC 11 228 0 TTTTGTAAAT 0.930278 -73 *** ******* Masking position 5 Map Score: 2.29188 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 6 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GGATGTTAAATGGGCCTATCTCCTGGCGTA 3 134 1 TGGGCCTATC 0.927343 -167 AGGAGAAGTTTAGGACTCTCTTCGGTATAG 3 187 1 TAGGACTCTC 0.955679 -114 GCCTGGTCAATTGGAATAGCCTGGCTAATC 6 51 1 TTGGAATAGC 0.870492 -79 AAAGTTTTTGTTAGAATCTCTTCTAGGATT 7 202 0 TTAGAATCTC 0.874681 -66 ACACCCTTCCTGGGACTCTCATTCTCTTAT 11 86 1 TGGGACTCTC 0.988462 -215 TTATCAAACTTTGGAATCTCCCACCGAATC 11 112 1 TTGGAATCTC 0.978316 -189 GAAAGAGTCCTGTGAATATCC 13 15 1 TGTGAATATC 0.841618 -11 ********** Masking position 7 Map Score: 2.19889 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 127 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TGTATCTTCCTAAAATTCAAATCTATTATG 2 38 1 TAAAATTCAA 0.874478 -132 TTCTTAAAAATAAAATTGCATGAGAAGACT 4 38 0 TAAAATTGCA 0.949644 -23 GAAAGTACACTAAAATTGAAAAGTCCAATG 5 85 0 TAAAATTGAA 0.95809 -48 ACCTAAAGTTGAAAACTAAAACT 8 4 1 TAAAGTTGAA 0.949674 -70 ACGATCTTTGAAAAATAGAAAAGGGCTTTT 9 39 0 AAAAATAGAA 0.654205 -21 ATTTAAAAATCAAGTGTTAATCC 10 4 1 TAAAAATCAA 0.687704 -45 AGCAAGCTACTAACGTTGCAATGCTTC 11 8 0 TAACGTTGCA 0.784334 -293 GTACTTCTTGAAAAAATGAAAAACGATAGA 11 45 0 AAAAAATGAA 0.791339 -256 CTTAACCTTTAAAAGTTGCACATTAAAGTC 11 188 0 AAAAGTTGCA 0.890891 -113 ********** Masking position 3 Map Score: 3.17452 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 216 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 10 AAAATACTGGAAGGATATCGG 3 2 1 AAATACTGGA 0.961264 -299 AAGATGCTAGAAATACGGGATCTGTACGCT 3 93 1 AAATACGGGA 0.884203 -208 ACCTCAGCCGATTTATTGGATTGATGGCGT 3 242 1 ATTTATTGGA 0.737164 -59 GACTAAAAACATTTCCTGGAAAAACATTGC 4 12 0 ATTTCCTGGA 0.946451 -49 AATTTAATGTAAATCCTAGAAGAGATTCTA 7 191 1 AAATCCTAGA 0.795378 -77 AAATCTTGTTAATTCATGGATATATAATTG 11 281 0 AATTCATGGA 0.886061 -20 CGATTTAAAAATATAATGGAAAGG 12 5 0 ATATAATGGA 0.865587 -39 ********** Masking position 1 Map Score: 0.332478 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 297 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 ********** No masking Map Score: -7.15216e-13 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: -7.15216e-13 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: -7.15216e-13 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