AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_aful_reg_300.orf -o00450_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0288 300 adenylylsulfate 3-phosphotransferase (cysC) #2 AF0423 138 sulfite reductase, subunit alpha (dsrA) #3 AF0425 41 sulfite reductase, subunit gamma (dsrD) #4 AF1446 63 A. fulgidus predicted coding region AF1446 #5 AF1448 114 transcriptional regulatory protein, AsnC family #6 AF1449 33 pyruvate formate-lyase 2 (pflD) #7 AF1451 88 thermosome, subunit beta (thsB) #8 AF1452 117 signal-transducing histidine kinase #9 AF1453 37 methionyl-tRNA synthetase (metS) #10 AF1665 147 ornithine cyclodeaminase (arcB) #11 AF1667 158 sulfate adenylyltransferase (sat) #12 AF1669 48 adenylylsulfate reductase, subunit B (aprB) Motif number 1 GTGTTTGACTTCTAAAAACTTTTTATCTGTTAT 1 200 0 TTAAAACTTT 0.749993 -101 TCAAACACTATGGAGAATTATCTCATAACGTTA 1 225 1 TGAGAATATT 0.864881 -76 ATATCTGCAATCGAGAAGTTTTTTAACCTTCCC 2 24 0 TGAGAATTTT 0.952237 -115 AGCGCAAATTTCGAAATTCTTATATATTGCCTA 2 80 1 TGAAATCTTT 0.895022 -59 AAAAAATTGGTGGAAGTGTTTATAAAT 3 5 0 TGAAGTTTTT 0.789074 -37 TTTTTCCCTCTTAAAAACTTTCACCAGTACACA 4 15 0 TAAAAATTTA 0.600676 -49 AAATTCGTGATAGAAAAGCTTATATAGAAATAC 7 30 1 TGAAAACTTT 0.978515 -59 AAAAATTGAATAGAAAAATTTTTCTTACAGCAT 10 74 1 TGAAAATTTT 0.985646 -74 TCCTGTCTTCTTGAAAAGTATTAAAGTTAATGT 10 121 0 TGAAAATATA 0.902137 -27 GTAGAAAATTTTTTGAACTCCTTT 11 2 1 TGAAAATTTT 0.985486 -157 CCTTTTATTTTCGAAGAGTTTGAAAATTGCGCG 11 36 1 TGAAGATTTA 0.892702 -123 CTTTGAAAATTCGAAAACCTTTAATCATTAAAA 11 80 1 TGAAAACTTA 0.949485 -79 TATAAAGGTTTCGAAAAATATTTTAATGATTAA 11 100 0 TGAAAATATT 0.95662 -59 AATTTTTTTTTAGAAAAATGTATGAAAAGGTTG 12 14 1 TGAAAATGTT 0.92824 -35 * ***** *** * Masking position 4 Map Score: 15.8486 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 223 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 TGATAACAGATAAAAAGTTTTTAGAAGTCA 1 198 1 TAAAAAGTTT 0.628509 -103 GTGGGAAGGTTAAAAAACTTCTCGATTGCA 2 22 1 TAAAAAACTT 0.822734 -117 TAGGTCACCTTAAAAAAATTGGTGGAAGTG 3 20 0 TAAAAAAATT 0.901901 -22 AAACCTAATTAAAAAAGATTACGATTT 6 8 0 AAAAAAGATT 0.917636 -26 AATTCGTGATAGAAAAGCTTATATAGAAAT 7 31 1 AGAAAAGCTT 0.601576 -58 AGGTAACCAAAACAAAAATTAAAAA 8 6 0 AACAAAAATT 0.868948 -112 TGCTTTTATTTACAAAGATAGGCAATAGCC 8 97 1 TACAAAGATA 0.519281 -21 TATGGTAGATAAGAAAGATAAAACAATTTT 10 15 1 AAGAAAGATA 0.818341 -133 CATCTATTGAAGGAAAAATTGAATAGAAAA 10 61 1 AGGAAAAATT 0.834195 -87 GAGATGCTGTAAGAAAAATTTTTCTATTCA 10 80 0 AAGAAAAATT 0.949344 -68 ACAGCATCTCAAGAAAACTTGACATTAACT 10 100 1 AAGAAAACTT 0.904404 -48 GTAGAAAATTTTTTGAACTCC 11 2 1 TAGAAAATTT 0.739986 -157 TAAGGCTGTGAAAAAAAATACATCATAGGT 11 133 1 AAAAAAAATA 0.798789 -26 CATTTTTCTAAAAAAAAATTAAA 12 4 0 AAAAAAAATT 0.931341 -45 AATTTTTTTTTAGAAAAATGTATGAAAAGG 12 14 1 TAGAAAAATG 0.68559 -35 ********** Masking position 5 Map Score: 12.5387 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 198 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 3 GAGGTTTAAATGGGTGAGATGACAAAAC 1 8 0 TGGGTGAGTG 0.957403 -293 CTAAGAAACCGAGGTGTCATGATAACAGATA 1 179 1 GAGGTGTCTG 0.942281 -122 TAATCGAAAGAAGGTGATGTAG 1 289 1 AAGGTGATTA 0.8845 -12 AAGGGGGAGTTGTGGGAAGGTT 2 2 1 AGGGGGAGTG 0.976676 -137 GCCTAAAAAGAGGGGGACTTGCAATTACAGG 2 108 1 AGGGGGACTG 0.976676 -31 CAATTTTTTTAAGGTGACCTAAA 3 29 1 AAGGTGACTA 0.930291 -13 TCTGCAATAGGAGGTGATGTGAA 7 76 1 GAGGTGATTG 0.975864 -13 GAAAAGGTTGGAGGTGAGTTGA 12 37 1 GAGGTGAGTG 0.989141 -12 ******** ** Masking position 10 Map Score: 7.1529 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 188 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 4 ATTTGGCGTTCGCCCACTCTGTCGCAAGCTGAGAGCTTGC 1 75 1 CCCATGCGAT 0.946343 -226 GCTATCAACACTCCGCGTGTTACGTAGTCAGCAAGCTCTC 1 105 0 CCCCTTCGAA 0.98869 -196 AGGAATGCATCCCCTATATTTTGGGAACTTCTAGTAGCTA 1 141 0 CCCATTGGAT 0.982007 -160 TTCGATTACGCTCTTCTGGTTCCATAGAGTATTAAAAAAT 1 257 0 CCTCTTCAAT 0.875688 -44 TTCTCGATTGCAGATATTTTTAGGTAAGCTTAAACCAGAA 2 40 1 CGAATTGGAT 0.735361 -99 ATTGCAAGTCCCCCTCTTTTTAGGCAATATATAAGAATTT 2 93 0 CCCCTTGGAT 0.992241 -46 TCTGCTCCACCTTCGAAGTAATTGGATTTTT 4 43 0 CGCCCTCGAA 0.905599 -21 TTCACATCACCTCCTATTGCAGAAATTGGTGGATTGG 7 62 0 CCCCTTCAAT 0.987749 -27 TATTTGCTGGCGGCAGTTTTTTGGAATGGATTGCATCTGA 8 44 1 CGCGTTGGAA 0.850901 -74 ACATTCAAAACCGCGCAATTTTCAAACTCTTCGAAAATAA 11 40 0 CGCCTTCAAT 0.979161 -119 TCAACTCACCTCCAACCTTTTCATACATTTTTCTAAAAA 12 20 0 CCCATTCAAT 0.971758 -29 * ** * ** ** * * Masking position 16 Map Score: 5.74352 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 336 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GAGAGGTTTAAATGGGTGAGATGACAAAAC 1 10 0 AATGGGTGGA 0.884107 -291 TCAGCTTGCGACAGAGTGGGCGAACGCCAAA 1 76 0 ACAGAGTGGC 0.725973 -225 TTCCCAAAATATAGGGGATGCATTCCTAAGA 1 154 1 ATAGGGGAGC 0.820228 -147 AGCGTAATCGAAAGAAGGTGATGTAG 1 285 1 AAAGAAGGGA 0.926384 -16 TATTGCCTAAAAAGAGGGGGACTTGCAATTA 2 104 1 AAAGAGGGGA 0.95229 -35 ACTTGCAATTACAGGAGGTGAACGA 2 124 1 ACAGGAGGGA 0.955356 -15 CAATTACTTCGAAGGTGGAGCAGA 4 50 1 GAAGGTGGGC 0.895857 -14 CCTAATTAAAAAAGATTACGATTT 6 4 0 AAAGATTAGA 0.647999 -30 AATTTCTGCAATAGGAGGTGATGTGAA 7 72 1 ATAGGAGGGA 0.962703 -17 GGAGGGAAAAGGTTGCGAGGGGTAAATA 9 20 0 AAAGGTTGGA 0.96668 -18 AGCCTTATATAAAGGTTTCGAAAAATATTTT 11 109 0 AAAGGTTTGA 0.717087 -50 AAAATACATCATAGGTTAGGAG 11 147 1 ATAGGTTAGA 0.790621 -12 GTATGAAAAGGTTGGAGGTGAGTTGA 12 33 1 GTTGGAGGGA 0.624845 -16 ******** ** Masking position 4 Map Score: 7.03755 Number of sites scoring better than the average of aligned sites = 1741 Number in coding regions = 1647 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 GTCGCAAGCTGAGAGCTTGCTGACTACGTA 1 95 1 GAGAGCTTGC 0.942405 -206 GCGGAGTGTTGATAGCTACTAGAAGTTCCC 1 129 1 GATAGCTACT 0.885583 -172 GGTTTCTTAGGAATGCATCCCCTATATTTT 1 159 0 GAATGCATCC 0.866867 -142 TATGGATAAAGACAGCTACTTCAATTACAA 5 28 0 GACAGCTACT 0.923027 -87 ACTGACGTTGGAGAGCATGCAGTATGGATA 5 50 0 GAGAGCATGC 0.963475 -65 TTTTGGAATGGATTGCATCTGAATAATCGG 8 62 1 GATTGCATCT 0.925533 -56 CCTGCCCTTCGAGAGCATCTATTGAAGGAA 10 46 1 GAGAGCATCT 0.987103 -102 AAATTTTTCTTACAGCATCTCAAGAAAACT 10 89 1 TACAGCATCT 0.854448 -59 ********** Masking position 2 Map Score: 3.41973 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 469 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ATTATCTCATAACGTTATTTTTTAATACTC 1 241 1 AACGTTATTT 0.982581 -60 CATGCTCTCCAACGTCAGTTTATAAGGTAA 5 61 1 AACGTCAGTT 0.947648 -54 TTATAAGGTAAACTTTATTTACAATGAAAG 5 80 1 AACTTTATTT 0.932463 -35 GTAAAACGTTATTTACCCCTCGCA 9 5 1 AACGTTATTT 0.982581 -33 ********** Masking position 5 Map Score: 1.61785 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 7 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TGAAATAAAGAGAGGTTTAAATGGGTGAGA 1 20 0 AGAGGTTTAA 0.562447 -281 AAAAGTTTTTAGAAGTCAAACACTATGGAG 1 210 1 AGAAGTCAAA 0.885774 -91 GGGAGTTGTGGGAAGGTTAAAAAACTTCTC 2 15 1 GGAAGGTTAA 0.88581 -124 AAAGTTTTTAAGAGGGAAAAATCCAATTAC 4 27 1 AGAGGGAAAA 0.953827 -37 ACGTCAGTTTATAAGGTAAACTTTATTTAC 5 72 1 ATAAGGTAAA 0.736614 -43 GGAGGGAAAAGGTTGCGAGG 9 28 0 GGAGGGAAAA 0.952937 -10 GCTCTCGAAGGGCAGGCAAAATTGTTTTAT 10 32 0 GGCAGGCAAA 0.900186 -116 GAGCATCTATTGAAGGAAAAATTGAATAGA 10 58 1 TGAAGGAAAA 0.860697 -90 CTTCGAAAATAAAAGGCAAAGGAGTTCAAA 11 22 0 AAAAGGCAAA 0.814733 -137 ********** Masking position 9 Map Score: 1.96491 Number of sites scoring better than the average of aligned sites = 1022 Number in coding regions = 945 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 9 ********** No masking Map Score: 3.1004e-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 10 ********** No masking Map Score: 3.1004e-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: 3.1004e-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