AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -imalT_mjan_opreg_100.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ1022 80 alignment in /usr/local/projects/ARG/Intergenic/ARG_R428_orf1.nr #2 MJ1243 91 conserved hypothetical protein #3 MJ1245 148 M. jannaschii predicted coding region MJ1245 #4 MJ1368 122 sulfate transport system permease protein (cysT) #5 MJ1569 300 cobalamin biosynthesis protein (cbiM) #6 MJ1631 300 glycogen phosphorylase (glgP) Motif number 1 CCAACATTAATTTTATTAATGGTGATTATT 1 17 1 TTTTATTAAT 0.899926 -64 TATTAATGGTGATTATTAATATTCTTTTGA 1 30 1 GATTATTAAT 0.711688 -51 TTTTTGCGTTTTTTATTTGAGGAATTTTAG 2 46 0 TTTTATTTGA 0.777051 -46 CGCAAAAAACTTCTATTTAAAATGAGGAGA 2 68 1 TTCTATTTAA 0.844694 -24 TATCCTATTATTTAAAAATTTGAAA 3 6 1 TATTATTTAA 0.967953 -143 TTAAAATTTCTTTTTTTAATAACATATTAA 3 54 1 TTTTTTTAAT 0.746319 -95 ATGTCATCAATTTTGTTTAACACAAATTTT 4 47 1 TTTTGTTTAA 0.915215 -76 TTAACACAAATTTTATATAATTAGGTAATT 4 63 1 TTTTATATAA 0.659903 -60 TTATTTTTATTTTTGTTTAAGTATAAATCT 5 14 1 TTTTGTTTAA 0.915215 -287 TATTTTCAGATATTTTTCAATCCAGTGCAT 5 67 1 TATTTTTCAA 0.737375 -234 CTGAATCTTATATTTTTCAAATACTATATT 5 104 1 TATTTTTCAA 0.737375 -197 AGATACTAAATATTATTTTAATGGAATTTT 5 135 0 TATTATTTTA 0.877948 -166 TCAATTTTAATTTTATGTAACATTTTTTTA 5 173 1 TTTTATGTAA 0.747109 -128 TTATGTAACATTTTTTTATATTAGCTCAAG 5 185 1 TTTTTTTATA 0.554238 -116 TTTGTTTAAAGTTTATTAAAAATGTCTTGA 5 210 0 GTTTATTAAA 0.852996 -91 ATTTAAACTTTTTTGTTTAAAGTTTATTAA 5 221 0 TTTTGTTTAA 0.915215 -80 ATGTTGATAATACTATTTAAACTTTTTTGT 5 235 0 TACTATTTAA 0.804118 -66 ACCCTTTTGGTATTATTTAATTGTGTTATC 5 275 0 TATTATTTAA 0.967953 -26 TTATGTGGTTTATTTTTTAT 6 1 0 TATTTTTTAT 0.847602 -300 TTAATATCTATTTTATTTATGTGGTTTATT 6 17 0 TTTTATTTAT 0.957537 -284 TTAGTCGTAGTTTTATTTTTCGTAATATAT 6 93 1 TTTTATTTTT 0.842947 -208 TCCATAGTATGATTATTAAATATATTACGA 6 112 0 GATTATTAAA 0.814232 -189 TTGCCATACTGTTTATTTAATATAATCCAG 6 149 0 GTTTATTTAA 0.935684 -152 ATTAAGTTCATATTATTTTTAAGGCATTAC 6 192 1 TATTATTTTT 0.802019 -109 TGAAGTTCTTTATTTTTTAAGTAATGCCTT 6 212 0 TATTTTTTAA 0.908066 -89 CATAATAAATTTTTATTAATTGAAAGACGC 6 247 0 TTTTATTAAT 0.899926 -54 ATTTTTTTAGGATTATTCATAATAAATTTT 6 264 0 GATTATTCAT 0.63736 -37 TCTCCCCCAATTTTATTTTTTTAGGATTAT 6 278 0 TTTTATTTTT 0.842947 -23 ********** Masking position 6 Map Score: 35.9874 Number of sites scoring better than the average of aligned sites = 2124 Number in coding regions = 1542 Number in noncoding regions = 582 Number of orfs with sites within 600 bp upstream = 437 Fraction of orfs with sites within 600 bp upstream = 0.0701895 Motif number 2 TCACCATTAATAAAATTAATGTTGGGAGATT 1 10 0 TAAAATTAGT 0.911668 -71 TTTTGAGTTTTAAAATTAAAGTTGTTGATGTG 1 54 1 TAAAATTAGT 0.911668 -27 TCCTATTATTTAAAAATTTGAAAATTATAATA 3 13 1 TAAAAATTAA 0.700502 -136 CGATAATTGTTAAAATTTCTTTTTTTAATAAC 3 45 1 TAAAATTTTT 0.928042 -104 ATTTAACTGTTAAAAATATAGAATATAAAGTT 3 99 0 TAAAAATAGA 0.711863 -50 ATATTTTCATTAAAAATTTATTAAA 4 4 0 TAAAAATTTT 0.933835 -119 TTTGATAGTATAATATTTTCATTAAAAATTTA 4 16 0 TAATATTTAT 0.440318 -107 CCTAATTATATAAAATTTGTGTTAAACAAAAT 4 56 0 TAAAATTTGT 0.9293 -67 TTAATTACCTTAAAAATGATTAAGATTGATTA 4 92 1 TAAAAATGTA 0.630611 -31 TAAACAAAAATAAAAATAAGTT 5 1 0 TAAAAATATT 0.918139 -300 AATACTATATTAAAAATTCCATTAAAATAATA 5 123 1 TAAAAATTAT 0.915591 -178 ATTGAGATACTAAATATTATTTTAATGGAATT 5 137 0 TAAATATTTT 0.503886 -164 AAATGTTACATAAAATTAAAATTGACAAAATT 5 166 0 TAAAATTAAT 0.884937 -135 TAATTTTATGTAACATTTTTTTATATTAGCTC 5 180 1 TAACATTTTT 0.738046 -121 TAAAGTTTATTAAAAATGTCTTGAGCTAATAT 5 202 0 TAAAAATGTT 0.888706 -99 CTAAACTAATTAACATTACAATCCCTCAGAAA 6 65 0 TAACATTAAT 0.627546 -236 AGTAATGCCTTAAAAATAATATGAACTTAATG 6 191 0 TAAAAATAAT 0.89492 -110 TTTCAATTAATAAAAATTTATTATGAATAATC 6 252 1 TAAAAATTTT 0.933835 -49 CCTAAAAAAATAAAATTGGGGGAGATTA 6 283 1 TAAAATTGGG 0.482382 -18 ******** ** Masking position 7 Map Score: 21.2962 Number of sites scoring better than the average of aligned sites = 1304 Number in coding regions = 893 Number in noncoding regions = 411 Number of orfs with sites within 600 bp upstream = 360 Fraction of orfs with sites within 600 bp upstream = 0.057822 Motif number 3 CAACAACTTTAATTTTAAAACTCAAAAGAATATTA 1 46 0 AATTTTAACA 0.808435 -35 AAAATTCCTCAAATAAAAAACGCAAAAAACTTCTA 2 48 1 AAATAAAACA 0.980297 -44 AAAATTTGAAAATTATAATACGATAATTGTTAAAA 3 25 1 AATTATAACA 0.959239 -124 TAAGGAAACTAAATGAAAAACTTTATATTCTATAT 3 81 1 AAATGAAACA 0.972545 -68 TTTTTAAGGTAATTAAATTACCTAATTATATAAAA 4 73 0 AATTAAAACA 0.983367 -50 AAATTGACAAAATTGAGATACTAAATATTATTTTA 5 145 0 AATTGAGACA 0.887984 -156 ATGATAACACAATTAAATAATACCAAAAGGGTGAA 5 273 1 AATTAAAATA 0.823272 -28 ATAAAAAATAAACCACATAAATAAAATAGA 6 6 1 AAATAAAACA 0.980296 -295 TATGATTATTAAATATATTACGAAAAATAAAACTA 6 100 0 AAATATAACA 0.951962 -201 ATTACTTAAAAAATAAAGAACTTCATTTTGGCGTC 6 217 1 AAATAAAACA 0.980297 -84 AATTTTTATTAATTGAAAGACGCCAAAATGAAGTT 6 235 0 AATTGAAACA 0.976795 -66 ******* ** * Masking position 10 Map Score: 16.5154 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 75 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 AAAATTAATGTTGGGAGATT 1 1 0 TTGGGAGATT 0.965118 -80 CTATTTAAAATGAGGAGATTAT 2 80 1 TGAGGAGATT 0.984635 -12 TTCCACATAAGGGGGATATT 3 139 1 GGGGGATATT 0.977168 -10 TCCATACTGTAGAGGAGATTTATACTTAAA 5 29 0 AGAGGAGATT 0.97322 -272 AAATAAAATTGGGGGAGATTA 6 290 1 GGGGGAGATT 0.995543 -11 ********** Masking position 6 Map Score: 5.71695 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 96 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 CATCAACAACTTTAATTTTAAAACTCAAAAGA 1 52 0 TTATTTTAAA 0.59336 -29 TGAGGAATTTTAGCATATTAAAGAAACACCAC 2 27 0 TAATATTAAA 0.947805 -65 TATCCTATTATTTAAAAATTTGAAAAT 3 6 1 TAATTTAAAA 0.820382 -143 ATTATCGTATTATAATTTTCAAATTTTTAAAT 3 20 0 TAATTTTCAA 0.942993 -129 CTTTTTTTAATAACATATTAAGGAAACTAAAT 3 63 1 TAATATTAAG 0.924172 -86 GTTAAAAATATAGAATATAAAGTTTTTCATTT 3 91 0 TAATATAAAG 0.751513 -58 TTTGATAGTATAATATTTTCATTAAAAATTTA 4 16 0 TAATTTTCAT 0.789293 -107 ATGGACATTGTAATATTTTCAGATATTTTTCA 5 54 1 TAATTTTCAG 0.917258 -247 ATTTGAAAAATATAAGATTCAGTGATATCATG 5 94 0 TAAGATTCAG 0.58434 -207 ATTTTTCAAATACTATATTAAAAATTCCATTA 5 115 1 TAATATTAAA 0.94817 -186 AGATACTAAATATTATTTTAATGGAATTTTTA 5 133 0 TAATTTTAAT 0.804626 -168 TGTCTTGAGCTAATATAAAAAAATGTTACATA 5 186 0 TAATAAAAAA 0.424581 -115 AAAGTTTAAATAGTATTATCAACATTAGATAT 5 240 1 TAATTATCAA 0.729644 -61 TTATTTTTCGTAATATATTTAATAATCATACT 6 105 1 TAATATTTAA 0.818664 -196 TTGTTGGCTGGATTATATTAAATAAACAGTAT 6 142 1 GAATATTAAA 0.699643 -159 ATTAAGTTCATATTATTTTTAAGGCATTACTT 6 192 1 TAATTTTTAA 0.820047 -109 ** ******** Masking position 5 Map Score: 14.4494 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 593 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 6 AATTTTAGCATATTAAAGAAACACCACATG 2 24 0 TATTAAAGAA 0.910091 -68 ATTTTCAAATTTTTAAATAATAGGATA 3 8 0 TTTTAAATAA 0.871105 -141 CTTAATATGTTATTAAAAAAAGAAATTTTA 3 55 0 TATTAAAAAA 0.767821 -94 TTTAATAACATATTAAGGAAACTAAATGAA 3 68 1 TATTAAGGAA 0.941379 -81 TTTAATAAATTTTTAATGAAAATATTATAC 4 11 1 TTTTAATGAA 0.951267 -112 TCTTAATCATTTTTAAGGTAATTAAATTAC 4 87 0 TTTTAAGGTA 0.874781 -36 TTAATGGAATTTTTAATATAGTATTTGAAA 5 118 0 TTTTAATATA 0.640057 -183 CTAAATATTATTTTAATGGAATTTTTAATA 5 130 0 TTTTAATGGA 0.820172 -171 CTCAAGACATTTTTAATAAACTTTAAACAA 5 209 1 TTTTAATAAA 0.864766 -92 ATAAAATAGATATTAATTCATGCAACAGTG 6 31 1 TATTAATTCA 0.695943 -270 GGCTGGATTATATTAAATAAACAGTATGGC 6 147 1 TATTAAATAA 0.812038 -154 TTCATATTATTTTTAAGGCATTACTTAAAA 6 198 1 TTTTAAGGCA 0.915299 -103 GTTCTTTATTTTTTAAGTAATGCCTTAAAA 6 208 0 TTTTAAGTAA 0.914711 -93 ********** Masking position 5 Map Score: 14.1977 Number of sites scoring better than the average of aligned sites = 770 Number in coding regions = 612 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 7 AGAATATTAATAATCACCATTAATAAAATTA 1 24 0 TAATCACCTT 0.944817 -57 TTTATCACATCAACAACTTTAATTTTAAAA 1 61 0 TCAACAACTT 0.734795 -20 TTTAATAAATTTTTAATGAAAAT 4 3 1 TAATAAATTT 0.903656 -120 CTATCAAATGTCATCAATTTTGTTTAACACA 4 40 1 TCATCAATTT 0.942025 -83 GCCTATCCCTAATCAATCTTAATCATTTTT 4 103 0 TAATCAATTT 0.970796 -20 TATCTCAATTTTGTCAATTTTAATTTTATGT 5 160 1 TTGTCAATTT 0.686593 -141 AAGACATTTTTAATAAACTTTAAACAAAAAA 5 212 1 TAATAAACTT 0.926401 -89 TTAAATAGTATTATCAACATTAGATATGATG 5 245 1 TTATCAACTT 0.933762 -56 CCCTCAGAAATATTCACTGTTGCATGAATTA 6 44 0 TATTCACTTT 0.642244 -257 ACGACTAAACTAATTAACATTACAATCCCTC 6 70 0 TAATTAACTT 0.832821 -231 GGATTATTCATAATAAATTTTTATTAATTGA 6 254 0 TAATAAATTT 0.903656 -47 ******** ** Masking position 6 Map Score: 8.88418 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 365 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 8 ********** No masking Map Score: -8.99385e-14 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 9 ********** No masking Map Score: -8.99385e-14 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: -8.99385e-14 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