AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -imalT_pyro_opreg_300.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 PH0194 60 375aa long hypothetical multiple sugar-binding transport ATP-binding protein #4 PH0206 132 544aa long hypothetical protein #5 PH0207 206 428aa long hypothetical protein #6 PH0209 300 131aa long hypothetical protein #7 PH1337 300 197aa long hypothetical protein #8 PH1338 26 202aa long hypothetical protein #9 PH1340 58 120aa long hypothetical protein Motif number 1 GCCCTCCCAGATAAAAAAGAAATAGAGAAA 1 2 0 AAAAAAGAAA 0.965308 -35 TTTACATTAAAAACAGATAACAAAGCTAACATAATAGAT 2 58 0 AAAAAAGCAA 0.826891 -112 TTTTGTTTTCAAAGGCAAAAACAGAAAAATAAATAAAGA 2 108 1 AAGAACAAAA 0.775807 -62 TGAGAAGACTAAAAACATTTCCTGGAAAAACATTGCT 3 9 0 AAAATCGAAA 0.968425 -52 CTCTTCTTAAAAATAAAATTGCATGAGAAGACTAAAAAC 3 32 0 AAAATCGAAA 0.968425 -29 TTCTCTCAGAATAGGTAAAATAATGAAAA 4 1 0 AAGAAAGAAA 0.939597 -132 GATGCCTCAAATGTAAAATATCTAGAAAAGATGCGGGGG 5 95 0 AGAAACGAAA 0.942016 -112 CTACAACTTTACAAAAGTAAACATGAAAATCAGGAAATG 5 143 1 AAAGACGAAA 0.967636 -64 AGGTTCTAATACTTGCACTACCAGGAGAAAGGGTTGGAG 6 211 1 ATGAACGAAA 0.859706 -90 GAGTAAAAGCATAGAGAATATCGTGATAACTGCAAAGAG 7 168 1 AAAAACGAAA 0.988541 -133 TGATAACTGCAAAGAGATATGCGAGAGAATTTATGAAAG 7 191 1 AAAATCGAAA 0.968425 -110 AGGAAGAGGGAGAAATGAAAAAGAGAGAATTACTTAAAG 7 233 1 AAAGAAGAAA 0.906045 -68 * * * * * * ** ** Masking position 18 Map Score: 11.775 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 184 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 TTCACCAAAGATCCCTTATGCCCTAAATCTTTATTTATTTTT 2 132 0 ATCCCACTTT 0.996313 -38 CATTTGAGGCATCATTTGTAACCTACAACTTTACAAAAGTAA 5 121 1 ATCCCCCTTT 0.986261 -86 AAACATGAAAATCAGGAAATGCCGAAACATTTATATTTAATT 5 161 1 ATCCCAATTT 0.976642 -46 CTAAAATTATATCTCCAACTGCTGTAACTTTTTCGTAAGGAA 6 250 0 ATCCTATTTT 0.944022 -51 TTCACGGGCCTCCCGAGGTTTTAAAGGCTAAG 7 1 1 TTCCCATTTT 0.929642 -300 CACTTAGTGCATCGAATATCTCCTTAGCCTTTAAAACCTCGG 7 23 0 ATCCCACTTT 0.996314 -278 TCCCCTGAATATCTGCTTTCCCCTAATCCTTTGGGATAGCTC 7 64 0 ATCCCACTTT 0.996314 -237 CTTTGCAGTTATCACGATATTCTCTATGCTTTTACTCTCGTA 7 163 0 ATCCTACTTT 0.984081 -138 *** ** * **** Masking position 20 Map Score: 9.8394 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 21 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 3 GGATGGTTCACCAAAGATCCCT 2 158 0 GATGGTTCCC 0.90239 -12 TGGTATGTTTCGTCAATTAAATAT 5 193 0 GATGTTTCTC 0.88734 -14 ATTTTTATAAGCAAGGCTCCTTAAATAGCCCC 6 16 0 GAAGGCTCTT 0.926821 -285 TTAGTGCATCGAATATCTCCTTAGCCTTTAAA 7 30 0 GATATCTCTT 0.970295 -271 TAATCCTTTGGGATAGCTCACTTAGTGCATCG 7 51 0 GATAGCTCCT 0.974562 -250 AGAATCCCCTGAATATCTGCTTTCCCCTAATC 7 78 0 GATATCTGTT 0.897273 -223 AAATTCTCTCGCATATCTCTTTGCAGTTATCA 7 191 0 GATATCTCTT 0.970295 -110 AAACCTTTAAGTAATTCTCTCTTTTTCATTTC 7 244 0 GAATTCTCCT 0.708195 -57 GCTCTTCTATGGATGTCTGTCCCCTT 9 5 0 GATGTCTGCC 0.929551 -54 TTATCAGAATGAATAGCTCTTCTATGGATGTC 9 20 0 GATAGCTCTC 0.94428 -39 * ******* ** Masking position 8 Map Score: 6.97645 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 259 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 TTTCTTTTTTATCTGGGAGGGCGTTAAA 1 19 1 ATCTGGGAGG 0.890818 -18 CTTTCACCCCCCTTAGAGGACGAATTAAG 4 114 0 CCCTTAGAGG 0.914184 -19 ATTTATGAAGCCCGGGGAGCACCGCCGAAG 5 35 1 CCCGGGGAGC 0.988582 -172 ATTGACTCCGCCTTCGGCGGTGCTCCCCGG 5 46 0 CCTTCGGCGG 0.903663 -161 GAGTCAATGAACTTGGGCGGGTTATTACCC 5 68 1 ACTTGGGCGG 0.930218 -139 TAGTCCAAGCCCCAGAGAGGAA 6 289 1 CCCAGAGAGG 0.959611 -12 GCCTTTAAAACCTCGGGAGGCCCGTGAA 7 9 0 CCTCGGGAGG 0.814601 -292 ACTTCCCTTTCCCTGGGATCGGGGTAGAAT 7 105 0 CCCTGGGATC 0.926581 -196 GGATATATATCCCGGTGAGGTAG 7 288 1 CCCGGTGAGG 0.973573 -13 ********** Masking position 7 Map Score: 5.91442 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 479 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 AAAAATGTATCTTCCTAAAATTCAAATCTAT 2 33 1 CTCCTAAAAT 0.778642 -137 AAGATCCCTTATGCCCTAAATCTTTATTTAT 2 136 0 ATCCCTAAAT 0.983021 -34 CACTTTTTAAATACCCCGAATAACTTACATT 4 58 1 ATCCCCGAAT 0.972422 -75 GTTACAAATGATGCCTCAAATGTAAAATATC 5 112 0 ATCCTCAAAT 0.934626 -95 TTAGTTCACCATTCCCTAACTATGAACTAGT 6 71 0 ATCCCTAACT 0.938947 -230 TCGGGGTAGAATCCCCTGAATATCTGCTTTC 7 86 0 ATCCCTGAAT 0.969764 -215 CGGGATATATATCCTCAAAATCTGGTAAACC 7 271 0 ATCTCAAAAT 0.865462 -30 ATATATTCATACCCAAGATTCCCCTA 8 9 1 ATCCCAAGAT 0.938939 -18 ** ******** Masking position 2 Map Score: 4.65629 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 106 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 GCCCTCCCAGATAAAAAAGAAATAGAGAAA 1 9 0 ATAAAAAGAA 0.797862 -28 TTAGTTTTGTTTTCAAAGGCAAAAACAGAAAA 2 104 1 TTTAAAGGAA 0.754199 -66 ATTTTACCTATTCTGAGAGAAATTAATATCTA 4 19 1 TTCGAGAGAA 0.896872 -114 AGAGGACGAATTAAGAAAGTACACTAAAATTG 4 97 0 TTAGAAAGAC 0.932011 -36 ATAAATTATTTCAAGAAAGGAAATATAAAT 5 9 0 TCAGAAAGAA 0.932011 -198 ACCTACAACTTTACAAAAGTAAACATGAAAAT 5 141 1 TTAAAAAGAA 0.964907 -66 AGTAGCAAATTTTTATAAGCAAGGCTCCTTAA 6 24 0 TTTATAAGAA 0.803539 -277 GCTGTAACTTTTTCGTAAGGAACTCCAACCCT 6 240 0 TTTGTAAGAA 0.900385 -61 TTAGCGGAATTTACGAGAGTAAAAGCATAGAG 7 152 1 TTAGAGAGAA 0.965738 -149 GCGAGAGAATTTATGAAAGCAAAGGAAGAGGG 7 211 1 TTAGAAAGAA 0.985014 -90 *** ***** ** Masking position 11 Map Score: 3.95731 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 181 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 TTAAATTTACCAATTAAAAATGTATCTTCCT 2 18 1 CAATTAAAAT 0.917018 -152 TTATTCGGGGTATTTAAAAAGTGTTTCGGTT 4 50 0 TATTTAAAAG 0.727526 -83 AAGTACACTAAAATTGAAAAGTCCAATGTAA 4 82 0 AAATTAAAAG 0.959078 -51 ATGATGCCTCAAATGTAAAATATCTAGAAAA 5 105 0 AAATGAAAAT 0.90205 -102 TATGTTTCGTCAATTAAATATAAATGTTTCG 5 183 0 CAATTAATAT 0.666435 -24 ATGAACTAGTAAATTTAAAAGTATTAGTAGC 6 50 0 AAATTAAAAG 0.959078 -251 GGGGCAAGTACATTGGAAAAGTTGATGAAAT 6 151 1 CATTGAAAAG 0.911922 -150 GAAGAGGGAGAAATGAAAAAGAGAGAATTAC 7 235 1 AAATGAAAAG 0.959259 -66 ***** ***** Masking position 7 Map Score: 3.23869 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 128 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TACTTTCTTAATTCGTCCTCTAAGGGGGGTG 4 108 1 ATTCGCCTCT 0.749866 -25 AGTTCATTGACTCCGCCTTCGGCGGTGCTCC 5 50 0 CTCCGCTTCG 0.971635 -157 AGAACCTTTCCTTCGCCCTCCTTGATGTCAA 6 187 0 CTTCGCCTCC 0.99335 -114 GGTTCTAATACTTGCACTACCAGGAGAAAGG 6 212 1 CTTGCCTACC 0.82057 -89 TTCACGGGCCTCCCGAGGTTTTA 7 3 1 CACGGCCTCC 0.940491 -298 AACGTGACAACTTCGACTTCCCTTTCCCTGG 7 119 0 CTTCGCTTCC 0.991982 -182 TTTTTCATTTCTCCCTCTTCCTTTGCTTTCA 7 224 0 CTCCCCTTCC 0.984385 -77 ***** ***** Masking position 7 Map Score: 2.54017 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 222 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 CAATGTTTTTCCAGGAAATGTTTTTAGTCT 3 13 1 CCAGGAAATG 0.962225 -48 ATAAATTATTTCAAGAAAGGAAATATAAAT 5 11 0 TCAAGAAAGG 0.915282 -196 AACATGAAAATCAGGAAATGCCGAAACATT 5 162 1 TCAGGAAATG 0.959346 -45 AGTTCATAGTTAGGGAATGGTGAACTAAAT 6 74 1 TAGGGAATGG 0.90083 -227 CAAGGAGGGCGAAGGAAAGGTTCTAATACT 6 194 1 GAAGGAAAGG 0.963034 -107 ACCCCGATCCCAGGGAAAGGGAAGTCGAAG 7 110 1 CAGGGAAAGG 0.975458 -191 ********** Masking position 6 Map Score: 1.94977 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 221 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 ********** No masking Map Score: -1.19839e-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 11 ********** No masking Map Score: -1.19839e-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: -1.19839e-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