AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -inarL_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 PH0016 300 475aa long hypothetical protein #2 PH0514 300 352aa long hypothetical protein #3 PH0538 78 290aa long hypothetical protein #4 PH1359 300 639aa long hypothetical protein #5 PH1509 300 440aa long hypothetical NADH oxidase #6 PH1670 300 102aa long hypothetical protein Motif number 1 GGCAAGAGAGCTACTTGCCCCATTGC 1 5 1 AGGAGCTACT 0.87685 -296 GGAATCGTGAGGAGAGCTACTTCAAAAATTTA 1 133 1 GGGAGCTACT 0.9728 -168 CACCCTTCAGGGCGAGGTAGATCACTTGGAGT 1 185 1 GGGAGGTAGT 0.982464 -116 TGAGAAAAGTGGTGAGTAAATTACTAGCCCTT 2 231 0 GGGAGTAAAT 0.924202 -70 TTCCTTGAGGGGTGAGAAAAGTGGTGAGTAAA 2 243 0 GGGAGAAAAT 0.975679 -58 GATCTTGGAAAGCGAGGAAGATTTTGAAAAGG 4 248 1 AGGAGGAAGT 0.96015 -53 ATTTTGAAAAGGGGAGGTACGTTGTAAAATAT 4 268 1 GGGAGGTACT 0.985795 -33 TTAAAATGTTGGGGAGAAAATGAGGGCATTCG 5 244 0 GGGAGAAAAG 0.920913 -57 TCTCCACCCAAGAGAGAAAGGGTTAAGAGATA 5 276 0 AGGAGAAAGG 0.749033 -25 GAGATAATTAGGGGAGAAACCTCTAGAGAAAA 6 19 0 GGGAGAAACT 0.984609 -282 CAAGAATCTTTGAGAGGAACTTTATAAGTTCC 6 62 1 TGGAGGAACT 0.921946 -239 TCCAGTTAAAGGGGAGGCAAATAAGGAACTTA 6 86 0 GGGAGGCAAT 0.951466 -215 CAAACTCCAAGGAGAACAAGATTGAAGGAGTT 6 159 0 GGGAACAAGT 0.791515 -142 AAAGATATTGGGTGAGGAAAGTGCTTAAGGAA 6 228 0 GGGAGGAAAT 0.989474 -73 ** ******* * Masking position 5 Map Score: 21.069 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 329 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 ATCAGCGTAGCAAAGATTTCCAATTTTCTTTAGAAAGTTCA 1 66 0 CTTATTTTTT 0.946486 -235 TACGCTGATGGTATGTTTTTCAATATCTCTCTGGGGGAATC 1 98 1 GTTATATCTC 0.825388 -203 AGAGCTACTTCAAAAATTTATATTTTCTCTTCGAAAACATC 1 145 1 CTTATTTCTT 0.955546 -156 AAAGCTAACACTAGTATTTTGCCTTTTCTTCAAAATTTATC 1 242 1 CTTCTTTTTC 0.9404 -59 TAATCTATAGCTCGCGCTTTCAATATCCATCCTTGCGAACT 2 90 1 CTTATATCTC 0.981271 -211 ATAACTCTCTCAAGCTTTTCCATTTTTAATCTCCTCCTAAA 4 30 0 CTTATTTTTC 0.98037 -271 CAGAAGCTACCCGTAAATTCTATTATCACTTCATCATCTGA 4 126 0 CTTATATCTT 0.948862 -175 TCCAAGATCTCAACTGGTTTTATTTTTAATCCGAAATCCAA 4 216 0 CTTATTTTTC 0.98037 -85 CAACGTACCTCCCCTTTTCAAAATCTTCCTCGCTTTCCAAG 4 251 0 CTCATCTTTC 0.793832 -50 CAAATGTTGACATTTTGTTGGCCTTTCCTTCCTTATTTCGA 5 117 0 CTTCTTTCTC 0.950437 -184 AAAATGAGGGCATTCGTTCAAATTTTTCCTTCATATTTCAG 5 219 0 CTCATTTTTT 0.83697 -82 TCATTTTCTCCCCAACATTTTAATATCTCTTAACCCTTTCT 5 253 1 CTTATATCTT 0.948862 -48 AGCTTTTATGCTTATCCTTATTCTATTTTTCCAATTGTCAA 6 120 1 CTTTTATTTC 0.83315 -181 TTTGGTCTGACTATTACTTGAATTATTGTTCCATCTTTGGT 6 187 1 CTTATATTTC 0.97733 -114 * ** * **** ** Masking position 8 Map Score: 13.3741 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 121 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 ATATTTTCTCTTCGAAAACATCACCCTTCAGGGCGAGG 1 164 1 TCACTACCTT 0.977655 -137 AGTGTTAGCTTTCAATTGCTCCAAGCTTCCAGAGAGCA 1 216 0 TCACCAGCTT 0.967697 -85 TCACGACCAATCCAAAGTCGTCAAGCTTTCCTAATCTA 2 59 1 TCACTAGCTT 0.993087 -242 GCAGCCTGAAGTCTATATCCTTAAGCTTTGGATAAGCT 2 191 1 GCACTAGCTT 0.993615 -110 GTGAGTAAATTACTAGCCCTTGAAGCTTATCCAAAGCT 2 214 0 TCACTAGCTT 0.993087 -87 TAAATTCCTTGATAACTCTCTCAAGCTTTTCCATTTTT 4 44 0 GTATTAGCTT 0.725084 -257 GTGAGGCCCAGGCAAAGATATTACGCTTTTCAGATGAT 4 97 1 GCATTAGCTT 0.964162 -204 CCTTATCGAATGCTAGCTCATACTGCTTTATCCATTAT 5 70 0 TCACTCGCTT 0.967697 -231 CCCAACATTTTAATATCTCTTAACCCTTTCTCTCTTGG 5 263 1 TAACTACCTT 0.810941 -38 TTTTCCAATTGTCAACTCCTTCAATCTTGTTCTCCTTG 6 146 1 GCACTATCTT 0.94559 -155 * * * * * * **** Masking position 5 Map Score: 10.5438 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 134 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 AATATCTCTCTGGGGGAATCGTGAGGAGAGCTACTTCA 1 119 1 TGCGTGAGAG 0.979064 -182 AGCTTTCAATTGCTCCAAGCTTCCAGAGAGCACTCCAA 1 210 0 TGCTTCCGAG 0.968239 -91 TTGACGACTTTGGATTGGTCGTGAGGAGAAGTGACATG 2 45 0 TGCGTGAGAG 0.979064 -256 GAGCTATAGATTAGGAAAGCTTGACGACTTTGGATTGG 2 65 0 TTCTTGAGAC 0.858604 -236 GTACTATAGGTGGGTTCCCCTTGAGGAGATAGCAAAGT 2 128 0 TGCTTGAGAG 0.99186 -173 TCCTTAAGCTTTGGATAAGCTTCAAGGGCTAGTAATTT 2 208 1 TTCTTCAGGG 0.975999 -93 CAAAGATATTTAACGTTTCCTTGAGGGGTGAGAAAAGT 2 253 0 TACTTGAGGG 0.954975 -48 CTTGTGGGGGTGCAAGTAACTTGCAGGG 3 1 0 TGCTTGCGGG 0.985977 -78 GTTTTGGAAATGGTTTTAACTTGTGGGGGTGCAAGTAA 3 20 0 TGCTTGTGGG 0.962655 -59 TATCAAGGAATTTAACAGACTTCATGGGAGTGAGGCCC 4 68 1 TTCTTCAGGG 0.976 -233 AGTGAGTTTTTTGTCTAGAGTTCAGGAGCATCTCTCCG 5 183 0 TTGTTCAGAG 0.779678 -118 ** ***** *** Masking position 12 Map Score: 10.3147 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 175 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TGAAAGCGCGAGCTATAGATTAGGAAAGCTTGAC 2 78 0 AGCTGATAGG 0.99619 -223 AGGGCCGTAGAGCTGAAGATGAGGTACTATAGGT 2 155 0 AGCTGATAGG 0.99619 -146 TATATCCTTAAGCTTTGGATAAGCTTCAAGGGCT 2 204 1 AGCTGATAGC 0.983594 -97 AAAGCGAGGAAGATTTTGAAAAGGGGAGGTACGT 4 256 1 AGATGAAAGG 0.908921 -45 AAAGCTGAGAAGCTCGCTATGAGGGATGATAATG 5 42 1 AGCTTATAGG 0.975875 -259 AGTATGAGCTAGCATTCGATAAGGAGAGGTTTAT 5 84 1 AGCAGATAGG 0.984734 -217 **** *** *** Masking position 9 Map Score: 5.34828 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 46 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 TGAACTTTCTAAAGAAAATTGGAAATCTTTGC 1 66 1 AAAGAATTGG 0.938725 -235 TAGTCATATTTAAAAGTATTGGGATAAATTTT 1 273 0 TAAAAGTTGG 0.879559 -28 AGGAAACGTTAAATATCTTTGGGGACTATATT 2 270 1 AAATATTTGG 0.88956 -31 ATTTACTTTATAAGAGTTTTGGAAATGGTTTT 3 41 0 TAAGAGTTGG 0.969631 -38 CTTTTTGACTAAAGAGGATTGACTCCCGAAAA 5 13 1 AAAGAGTTGA 0.856467 -288 TTTGCGCGATAAAGATAATCGGAGAGATGCTC 5 164 1 AAAGATTCGG 0.950267 -137 TAAGAGATATTAAAATGTTGGGGAGAAAATGA 5 253 0 TAAAATTGGG 0.808393 -48 AGTTCCTCTCAAAGATTCTTGGGGCAAAAGTC 6 51 0 AAAGATTTGG 0.984152 -250 GGTTCGTAGAAAAGATATTGGGTGAGGAAAGT 6 238 0 AAAGATTGGG 0.972348 -63 ****** **** Masking position 5 Map Score: 5.44434 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 179 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 CTTCCAGAGAGCACTCCAAGTGATCTACCT 1 199 0 GCACTCCAAG 0.915432 -102 AACTTTGCTATCTCCTCAAGGGGAACCCAC 2 127 1 TCTCCTCAAG 0.908575 -174 CAAGTTACTTGCACCCCCACAAGTTAAAAC 3 16 1 GCACCCCCAC 0.978063 -63 GAAATCCAAGGCATCCCAGGATATATCCTC 4 195 0 GCATCCCAGG 0.919938 -106 AATCTTCCTCGCTTTCCAAGATCTCAACTG 4 241 0 GCTTTCCAAG 0.871187 -60 CTCATAGCGAGCTTCTCAGCTTTTCGGGAG 5 35 0 GCTTCTCAGC 0.913392 -266 TCGGAGAGATGCTCCTGAACTCTAGACAAA 5 182 1 GCTCCTGAAC 0.881501 -119 GCCCTCATTTTCTCCCCAACATTTTAATAT 5 249 1 TCTCCCCAAC 0.940646 -52 GCATCTCCACCCAAGAGAGA 5 291 0 GCATCTCCAC 0.922667 -10 AAGCATAAAAGCTCCTCCAGTTAAAGGGGA 6 103 0 GCTCCTCCAG 0.976151 -198 ********** Masking position 2 Map Score: 7.66518 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 443 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 TTTCAATATCTCTCTGGGGGAATCGTGAGG 1 115 1 TCTCTGGGGG 0.963254 -186 ATTTAACGTTTCCTTGAGGGGTGAGAAAAG 2 254 0 TCCTTGAGGG 0.856995 -47 ACGTTAAATATCTTTGGGGACTATATTAAT 2 275 1 TCTTTGGGGA 0.973512 -26 CATTTGGAGATCTTTGCGCGATAAAGATAA 5 152 1 TCTTTGCGCG 0.901009 -149 GATATTAAAATGTTGGGGAGAAAATGAGGG 5 250 0 TGTTGGGGAG 0.867057 -51 ACCCTTTCTCTCTTGGGTGGAGATGC 5 285 1 TCTTGGGTGG 0.966038 -16 TCTCAAAGATTCTTGGGGCAAAAGTCGAGA 6 47 0 TCTTGGGGCA 0.952327 -254 GCCCCAAGAATCTTTGAGAGGAACTTTATA 6 58 1 TCTTTGAGAG 0.875013 -243 GTAGAAAAGATATTGGGTGAGGAAAGTGCT 6 235 0 TATTGGGTGA 0.510052 -66 ********** Masking position 1 Map Score: 2.01661 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 349 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 CTTTGGCATGTGTGAACTTTCTAAAGAAAA 1 54 1 TGTGAACTTT 0.954838 -247 AAAATACTAGTGTTAGCTTTCAATTGCTCC 1 232 0 TGTTAGCTTT 0.841614 -69 AACACTAGTATTTTGCCTTTTCTTCAAAAT 1 248 1 TTTTGCCTTT 0.568359 -53 TAGGAAAGCTTGACGACTTTGGATTGGTCG 2 62 0 TGACGACTTT 0.854543 -239 TATCCATCCTTGCGAACTTTGCTATCTCCT 2 113 1 TGCGAACTTT 0.831645 -188 CTGCAAAACCTGTGGCCTTTACGATTACTT 4 164 1 TGTGGCCTTT 0.928423 -137 CTTTCAACTTTATATTTTACA 4 290 0 TTTCAACTTT 0.887231 -11 ATAGCGAGCTTCTCAGCTTTTCGGGAGTCA 5 32 0 TCTCAGCTTT 0.873281 -269 GCCAACAAAATGTCAACATTTGGAGATCTT 5 136 1 TGTCAACATT 0.828771 -165 CCCCTAATTATCTCGACTTTTGCCCCAAGA 6 37 1 TCTCGACTTT 0.929503 -264 ********** Masking position 9 Map Score: 2.55009 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 177 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 GCTTTCAATATCCATCCTTGCGAACTTTGC 2 105 1 TCCATCCTTG 0.982432 -196 CTCAAGCTTTTCCATTTTTAATCTCCTCCT 4 33 0 TCCATTTTTA 0.852658 -268 TGTTGGCCTTTCCTTCCTTATTTCGATAAA 5 113 0 TCCTTCCTTA 0.94542 -188 CTTTATAAGTTCCTTATTTGCCTCCCCTTT 6 81 1 TCCTTATTTG 0.900986 -220 GAATTATTGTTCCATCTTTGGTTTCCTTAA 6 206 1 TCCATCTTTG 0.981062 -95 ********** Masking position 5 Map Score: 0.507824 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 140 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 AGATTTCCAATTTTCTTTAGAAAGTTCACAC 1 63 0 TTTTCTTAGA 0.720394 -238 GATGGTATGTTTTTCAATATCTCTCTGGGGG 1 104 1 TTTTCAAATC 0.624244 -197 CGTTAGTTGATATCCTATATAACCCATGTCA 2 21 1 TATCCTAATA 0.77295 -280 CTGAAGTCTATATCCTTAAGCTTTGGATAAG 2 196 1 TATCCTTAGC 0.922701 -105 ATATTTAACGTTTCCTTGAGGGGTGAGAAAA 2 255 0 TTTCCTTAGG 0.810159 -46 GTAATTCAAATTTACTTTATAAGAGTTTTGG 3 51 0 TTTACTTATA 0.581352 -28 AGTCTGTTAAATTCCTTGATAACTCTCTCAA 4 58 0 ATTCCTTATA 0.628452 -243 TCTTCCTCGCTTTCCAAGATCTCAACTGGTT 4 238 0 TTTCCAAATC 0.882705 -63 GTACCTCCCCTTTTCAAAATCTTCCTCGCTT 4 257 0 TTTTCAAATC 0.624244 -44 CATACTGCTTTATCCATTATCATCCCTCATA 5 59 0 TATCCATATC 0.8827 -242 CGTTCAAATTTTTCCTTCATATTTCAGTGAG 5 215 0 TTTCCTTATA 0.940808 -86 CTTTTATGCTTATCCTTATTCTATTTTTCCA 6 122 1 TATCCTTTTC 0.633691 -179 CCATCTTTGGTTTCCTTAAGCACTTTCCTCA 6 217 1 TTTCCTTAGC 0.962665 -84 ******* *** Masking position 3 Map Score: 4.70367 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 912 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 12 ********** No masking Map Score: 3.00803e-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: 3.00803e-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 14 ********** No masking Map Score: 3.00803e-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