AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -intrC_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH130 171 cobalamin biosynthesis protein M #2 MTH132 86 cobalt transport protein Q #3 MTH133 167 cobalt transport ATP-binding protein O #4 MTH151 75 methyl coenzyme M reductase system, component A2 homolog #5 MTH478 49 sulfate transport system permease protein #6 MTH479 136 conserved protein #7 MTH480 91 unknown #8 MTH604 116 adhesion protein #9 MTH695 248 conserved protein #10 MTH1370 137 ABC transporter (ATP-binding protein) #11 MTH1570 74 glutamine synthetase #12 MTH1571 300 molybdopterin biosynthesis protein MoeB homolog #13 MTH1705 33 cobalt transport membrane protein #14 MTH1707 300 cobalamin biosynthesis protein M Motif number 1 TTGATTTCTGATACCTCCAGATGGTGGGCT 3 47 1 ATACCTCCAG 0.856698 -121 ATGACTCTCAGGTCCTTCATTAGAATCTAA 9 47 1 GGTCCTTCAT 0.905012 -202 CTCCTTTTCCAGTCCTTCAGCTTCCCTTTC 9 82 1 AGTCCTTCAG 0.905012 -167 GTTATAATAGGAACCTCCATCATATAATCA 9 226 1 GAACCTCCAT 0.856698 -23 TCTCTTATATGGACCTATATATAAAGGACC 10 33 1 GGACCTATAT 0.645688 -105 TATATATAAAGGACCCCCATATAATTAATT 10 48 1 GGACCCCCAT 0.976967 -90 CGCTACAGCGGGACCTCCAGTGGCTGACTG 10 109 1 GGACCTCCAG 0.995767 -29 TGAGTCCCCCAGTCAGCCACTG 10 126 0 AGTCCCCCAG 0.968565 -12 TGTCTGGGGCGGTCCTCTGGAGCCATTCTG 12 124 0 GGTCCTCTGG 0.891636 -177 CTTTCCCACAGGATCTCCAGTGATAGGCTC 12 179 1 GGATCTCCAG 0.944067 -122 ATAAGGCTGTGGTCCTACAGGATGACCCCC 12 224 1 GGTCCTACAG 0.967255 -77 ATACACCCTGAGACCCCCGGCAATGGTCAT 14 148 1 AGACCCCCGG 0.936307 -153 ********** Masking position 5 Map Score: 13.0039 Number of sites scoring better than the average of aligned sites = 1409 Number in coding regions = 1345 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 GAGGGAGTTATTCCCAGAAC 6 1 0 TTCCCAGAAC 0.986112 -136 TTCTCATTCCTTCACAGAACCGATATGTAT 6 68 1 TTCACAGAAC 0.985029 -69 AATGTATTTTTTCACTGAACATCAGATTCA 7 39 0 TTCACTGAAC 0.99192 -53 ATAAAACCCCTTCCCTGAACCGAACTGTTT 12 86 1 TTCCCTGAAC 0.992506 -215 ACATCTGCTTTTCACTGATCTGAAGAATCT 12 151 1 TTCACTGATC 0.968037 -150 TTTGTGCATTGTCGCTGAACACATAAAGAC 14 60 1 GTCGCTGAAC 0.963406 -241 ********** Masking position 8 Map Score: 7.9392 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 70 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 ATAAATTCTGATCTAAATTAAAGTTTCCTTGAT 1 88 0 ATAATTAAAG 0.916681 -84 CATTATATACCTCAATTTTAAAGTTTACTTTAG 1 127 1 CTATTTAAAG 0.856077 -45 AAGTCGGGGTCTTAAAAATAAAGTAGTATGTTA 5 18 0 CTAAATAAAG 0.805189 -32 TGGGATCGTCCTGAAAGATAAAGAAGGACTACT 6 33 0 CTAAATAAAG 0.951908 -104 TTCTGAGTTAATGGAGGTTAAAGACC 6 121 1 ATAGTTAAAG 0.935593 -16 TGAGAGTCATCTGGAGCTTAAAAATAATTTAAT 9 24 0 CTAGTTAAAA 0.736777 -225 CTTTAACGGAATGGAGCATAAAGAGCAGAGATT 9 143 0 ATAGATAAAG 0.921857 -106 GTTTTATTATCTCCAATTTAAAGAAACGTGATT 12 60 0 CTAATTAAAG 0.937511 -241 TCAAACATTCATATAATATAAAGGTTGAAGTGA 14 236 0 ATAAATAAAG 0.918228 -65 ** ** ****** Masking position 5 Map Score: 7.08771 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 9 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 ATTCATGATCTGTTTCATCGATCCGATAGGA 3 89 1 TTTTCATCGA 0.766521 -79 CTTCTAGTATATATTCATGGAGCCGGTGGCG 4 54 1 AATTCATGGA 0.866371 -22 ACTGAACATCAGATTCATGGACAAACTGATA 7 25 0 AATTCATGGA 0.866371 -67 TTGGGGAGAGAGATATATGGAATGGTGATAA 7 70 1 AATATATGGA 0.857447 -22 AAATTTATTAAATTTTATCGTTTATATTAAC 8 52 1 ATTTTATCGT 0.737491 -65 TATTAACAATTATTATATGGTTGCGTTGACA 8 76 1 TTTATATGGT 0.685254 -41 GTAGCGGTTGACTTTTATGGATCTTTAACGG 9 167 0 ATTTTATGGA 0.970255 -82 TTAACTACTCTCTTATATGGACCTATATATA 10 25 1 TTTATATGGA 0.897694 -113 TTCCTGAATTAATTATATGGGGGTCCTTTAT 10 53 0 ATTATATGGG 0.779163 -85 TAGCGATAACATTTTTATCGAGTGCATCAAT 10 83 0 ATTTTATCGA 0.918849 -55 TCATCTTTTCTGTTTTAAGGATAAAAAAGT 12 10 0 TTTTTAAGGA 0.662113 -291 TGATGTTTTTAATTTTATGGAATCTATATAT 14 25 1 ATTTTATGGA 0.970255 -276 * ********* Masking position 7 Map Score: 7.37189 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 137 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 CCTCTGAAAGGATAATATATGTAAGATATG 1 47 0 GATAATATAT 0.883663 -125 AAGATCCTATCTTAATAAATGTTTATATAT 8 13 1 CTTAATAAAT 0.845568 -104 CTTAATAAATGTTTATATATTTTATGTTAA 8 23 1 GTTTATATAT 0.913895 -94 AACGATAAAATTTAATAAATTTTAACATAA 8 44 0 TTTAATAAAT 0.775471 -73 TATAATAATTGTTAATATAAACGATAAAAT 8 63 0 GTTAATATAA 0.838842 -54 TATGGGGGTCCTTTATATATAGGTCCATAT 10 39 0 CTTTATATAT 0.845568 -99 CCTTCTACTGGTTTATATATTTTTTGT 11 8 0 GTTTATATAT 0.913895 -67 TTAAATTGGAGATAATAAAACCCCTTCCCT 12 72 1 GATAATAAAA 0.662317 -229 TTAAAAACATCATTATAAATCATTAA 14 7 0 CATTATAAAT 0.673655 -294 AATGCACAAAGTTTATATATAGATTCCATA 14 40 0 GTTTATATAT 0.913895 -261 CATGGACCTTTTTAATAAATGGTGGGGATG 14 89 1 TTTAATAAAT 0.775471 -212 CAAACATTCATATAATATAAAGGTTGAAGT 14 238 0 TATAATATAA 0.469509 -63 ********** Masking position 5 Map Score: 6.83711 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 27 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 ATGCCTCCATGGCATGAGCTTAACTTCACC 11 50 0 GGCATGAGCT 0.95312 -25 ATGCCATGGAGGCATAACCC 11 65 1 GGCATAACCC 0.805448 -10 ATCTGCTTGCAGCATGAGCCTATCACTGGA 12 194 0 AGCATGAGCC 0.972898 -107 GTGGTCCTACAGGATGACCCCCTCATGATT 12 232 1 AGGATGACCC 0.972898 -69 ATAAATGGTGGGGATGTGCCAGATAGGCGG 14 103 1 GGGATGTGCC 0.821334 -198 CCTGAGCGGAGGGATGACCATTGCCGGGGG 14 161 0 GGGATGACCA 0.956054 -140 ********** Masking position 5 Map Score: 2.89618 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 186 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 TGATGGTTGCGGGGGCCTCTGAAAGGATAATA 1 60 0 GGGGCTCTGA 0.874682 -112 TCACCTTCTTGAATCCTTCTAAAGTAAACTTT 1 146 0 GAACTTCTAA 0.702165 -26 GTACCTCAAAGGATTATTCTGATGATTCACCC 2 54 0 GGATTTCTGA 0.973727 -33 TCCTCTGAGATCTGCTGATATCCTCACA 3 7 1 GAGTTGCTGA 0.911426 -161 TTAAGACCCCGACTTTTTCTGAAG 5 36 1 GACTTTCTGA 0.909895 -14 AGATAAAGAAGGACTACTCTGAGGGAGTTATT 6 19 0 GGATCTCTGA 0.934316 -118 TGAGAACATGGGATCGTCCTGAAAGATAAAGA 6 42 0 GGACTCCTGA 0.945251 -95 CATGTCGATATAGGTGTTCTGAGTTAATGGAG 6 105 1 TAGTTTCTGA 0.776295 -32 CAGAAAAGATGAATTCTTCTGAAAAAACAAAA 12 29 1 GAATTTCTGA 0.965056 -272 CGGTCCTCTGGAGCCATTCTGAAATCGAAAAA 12 113 0 GAGCTTCTGA 0.979472 -188 AATCATGAGGGGGTCATCCTGTAGGACCACAG 12 230 0 GGGCTCCTGT 0.777697 -71 *** * ****** Masking position 10 Map Score: 3.72502 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 484 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 AAAAACCGATGTGAGGATATCAGCAGATCTC 3 17 0 GTGAGATATC 0.938999 -151 GTTCTGGGAATAACTCCCTCAGAG 6 4 1 CTGGAATAAC 0.812523 -133 GGACAAACTGATAAAGATATCCGGAAG 7 7 0 ATAAGATATC 0.587454 -85 GATATATGGAATGGTGATAAC 7 81 1 ATGGGATAAC 0.921757 -11 GCTGGTTAAAATGACAATCTCTGCTCTTTAT 9 128 1 ATGAAATCTC 0.774185 -121 CTTAAGCCCTGTGGAAATCACATCTGATGGT 9 196 0 GTGGAATCAC 0.959893 -53 TAGTTAAGCGGTGATGATCAC 10 1 0 GTGAGATCAC 0.656593 -137 AGGTCCCGCTGTAGCGATAACATTTTTATCG 10 94 0 GTAGGATAAC 0.910264 -44 CCCTTATATTGTGGTAATATCGCACCCTGAG 14 185 0 GTGGAATATC 0.938999 -116 CCGAAGATTAGTAATAATCACTTCAACCTTT 14 219 1 GTAAAATCAC 0.781888 -82 **** ****** Masking position 7 Map Score: 4.35363 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 192 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 TTTATCACCTTCTTGAATCCTTCT 1 158 0 ATCCCTTCTT 0.732852 -14 ATATCCTCACATCGGTTTTTTGATTTCTGAT 3 28 1 ATCGTTTTTT 0.647356 -140 GGATATCTTTATCAGTTTGTCCATGAATCTG 7 16 1 ATCGTTTGTC 0.772204 -76 GTTATCACCATTCCATATATCTCT 7 78 0 ATCCCATTCC 0.673145 -14 AACTCCCTTTTTCATTAAATTAT 9 3 1 CTCCTTTTTC 0.709889 -246 AATCTAAGTGTTCTCCTTTTCCAGTCCTTCA 9 70 1 TTCCCTTTTC 0.93183 -179 TTTCCAGTCCTTCAGCTTCCCTTTCTAAGTG 9 87 1 TTCGCTTCCC 0.91961 -162 TGTCATTTTAACCAGCTTTTCATAGCCACTT 9 113 0 ACCGCTTTTC 0.87303 -136 TTCAGAAGAATTCATCTTTTCTGTTTTAAGG 12 21 0 TTCTCTTTTC 0.678938 -280 GAGATAATAAAACCCCTTCCCTGAACCGAAC 12 80 1 AACCCTTCCC 0.781043 -221 CCCTGAACCGAACTGTTTTTCGATTTCAGAA 12 98 1 AACGTTTTTC 0.764748 -203 CGCCCCAGACATCTGCTTTTCACTGATCTGA 12 143 1 ATCGCTTTTC 0.973342 -158 ATTACTAATCTTCGGTTTCCCTTATATTGTG 14 203 0 TTCGTTTCCC 0.819681 -98 *** ******* Masking position 8 Map Score: 1.30572 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 455 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 AAGTTTCCTTGATGGTTGCGGGGGCCTCTG 1 71 0 GATGGTTGCG 0.98898 -101 GATACCTCCAGATGGTGGGCTATGAATTTA 3 56 1 GATGGTGGGC 0.960369 -112 TATTCATGGAGCCGGTGGCGA 4 65 1 GCCGGTGGCG 0.964329 -11 ACAATTATTATATGGTTGCGTTGACATAAC 8 81 1 TATGGTTGCG 0.945046 -36 AATCACATCTGATGGTAGCGGTTGACTTTT 9 182 0 GATGGTAGCG 0.98073 -67 CTTTTTAATAAATGGTGGGGATGTGCCAGA 14 96 1 AATGGTGGGG 0.952946 -205 ********** Masking position 6 Map Score: 2.55311 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 144 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 ********** No masking Map Score: 1.98485e-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: 1.98485e-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 ATATATCTCTCTCCCCAATAATGTATTTTTTCACTGAA 7 50 0 CCCCTATATT 0.99241 -42 CCAACCACCCTGTTAAGTTATGTCAACGCAACC 8 94 0 CCCCTATATT 0.99241 -23 AACTCCCTTTTTCATTAAATTATTTTTAAG 9 3 1 CCCCTCTAAT 0.861557 -246 AGTGCATCAATTCCTGAATTAATTATATGGGGGTCCTT 10 56 0 TCCTTATATT 0.850902 -82 AACTTTCCTTCTACTGGTTTATATATTTTTTGT 11 6 0 CACTTATATT 0.850902 -69 TACAGGATGACCCCCTCATGATTTATATCAACACACAC 12 239 1 CCCCTATATT 0.99241 -62 TCCTCCCAATTAATTTTTTTCTGGTGAAGT 13 3 1 CCCCTATTTT 0.979535 -31 GCTATTCGCCTCCTTAATCTTTTTTTAATTCCAA 14 277 0 CCCTTATTTT 0.949262 -24 * *** * * *** * Masking position 9 Map Score: 4.07515 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 32 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 ********** No masking Map Score: 1.98485e-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 15 ********** No masking Map Score: 1.98485e-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