AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_mjan_reg_300.orf -o00360_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ0002 300 M. jannaschii predicted coding region MJ0002 #2 MJ0102 300 Phenylacrylic acid decarboxylase #3 MJ0140 138 conserved hypothetical protein #4 MJ0684 68 aspartate aminotransferase (aspB2) #5 MJ0955 48 histidinol-phosphate aminotransferase (hisC) #6 MJ1054 300 UDP-glucose dehydrogenase, putative #7 MJ1159 36 replication factor A related protein #8 MJ1160 56 amidase #9 MJ1530 178 ribosomal protein S18 alanine acetyltransferase #10 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 CCATGGTTTGTTGATAATGGTTTTCACCAATCCC 1 13 0 TTTAATTTTT 0.94608 -288 GACGCATTGATTGGATATATTATATTTAGTGCTA 1 67 0 TTATATTATA 0.688608 -234 ATATAATTTTTTATAATTGGTATTTTGATGCTCT 1 197 0 TTAATTTATT 0.805386 -104 TTATGTAATTTTTTATATAATTTTTTATAATTGG 1 211 0 TTATATTTTT 0.945197 -90 CCAATTAGAATTTCTAATAATTTTGGAGATATTA 1 264 1 TTTAATTTTT 0.94608 -37 GAAAACTCTTTTAGTTTTCATTTAACCGAAGCGT 2 85 1 TTTTTTTTTA 0.634557 -216 CTGAAAGATTTTGTTTAACTTTTTCTAAAAGTTT 2 138 1 TTTTAATTTT 0.865981 -163 TCGGCACCATTTTATTATTTTATTTTAGGTTGTT 2 188 1 TTTTATTATT 0.93801 -113 TTTTAGGTTGTTATATTTATTTTTTTAGATTTAT 2 210 1 TTATTTTTTT 0.881268 -91 GATTAACTATTTTTAAATAGTATTTATTTTTTAA 2 245 1 TTAAATTATT 0.905806 -56 AGTTTATTATTTTTTATCAATATTTA 3 3 1 TTTTATTTTA 0.801203 -136 CAAGTTAAGTTTTTATTAAATATTGATAAAAAAT 3 19 0 TTATTATATT 0.603809 -120 AACAAGTGAATTTTAAAACTTATTATAGGGACTG 3 54 0 TTAAAATATT 0.740089 -85 TTATTATTAATTAATAATACTTTTCGTGGTGGCA 4 15 0 TTTAATTTTT 0.946079 -54 AGAAATCTTATTTAAAATATTTTTGGTTAAAAAT 5 24 1 TTAAATTTTT 0.932737 -25 AAATATAGCATTACTTATAATTTTCGTTATCAAT 6 147 0 TTTTATTTTT 0.956183 -154 AGTTTATTTATTAATAATTGTATAATATTATTAT 6 265 0 TTTAATTATA 0.692273 -36 AATTCTATTCAAAATAATTTTTTATGGTGAT 7 8 1 TTAAATTTTT 0.93274 -29 TTGACTTATATTTATTTATTTTTTG 8 2 0 TTTTTATTTT 0.735502 -55 GTAAATTTTTTTGGTTATAATATTGACTTATATT 8 24 0 TTTTATTATT 0.938013 -33 TTATAGAGTCTTTTAAAACATTTTGAAATACTAA 9 52 0 TTAAAATTTT 0.804163 -127 TTTAGTATTATTTTAAATTCTTTTTATAGAGTCT 9 75 0 TTAAATTTTT 0.93274 -104 AAATTCTATTTTAATTTTAGTATTATTTTAAATT 9 90 0 TTTTTTTATT 0.866883 -89 TCAATGAATGTTGTGTAATTTATTAAATTCTATT 9 114 0 TTGTAATATT 0.528042 -65 GGACTTTTATTTGTGTATTATTTTAGACACTTTT 10 38 1 TTGTATTTTT 0.844935 -263 GCTATAAGCTTTGGTTTTGATATTGAAGAACTAT 10 81 1 TTTTTTTATT 0.866883 -220 GAACTATCTCTTAATATTGATTTTGAGGAGGAAT 10 108 1 TTTATTTTTT 0.883053 -193 ** **** **** Masking position 11 Map Score: 35.3677 Number of sites scoring better than the average of aligned sites = 1931 Number in coding regions = 1387 Number in noncoding regions = 544 Number of orfs with sites within 600 bp upstream = 389 Fraction of orfs with sites within 600 bp upstream = 0.0624799 Motif number 2 AAAATACCAATTATAAAAAATTATATAAAAAA 1 205 1 TTATAAAAAT 0.937404 -96 ATAAGTCCTATTATAAAATACTACCAATTAGA 1 241 1 TTATAAAAAT 0.937404 -60 GTTATATTTATTTTTTTAGATTTATGGATTAA 2 219 1 TTTTTTTAAT 0.445866 -82 ATAAATACTATTTAAAAATAGTTAATCCATAA 2 240 0 TTTAAAAAAT 0.922337 -61 AAGTTAAGATTTAAAAAATAAATACTATTTAA 2 257 0 TTAAAAAAAA 0.766404 -44 TTAAATATTGATAAAAAATAATAAACT 3 6 0 ATAAAAAAAT 0.636807 -133 TTATCAATATTTAATAAAAACTTAACTTGACA 3 24 1 TTAATAAAAT 0.922339 -115 ATAGTGAATATTATATTAGAGTTAGAACAAGT 3 81 0 TTATATTAAT 0.753844 -58 GGAATTATTATTAATTAATAATACTTTTCGTG 4 21 0 TTAATTAAAT 0.85843 -48 GACATCACCATTTATAAACACTAAAAGGAATT 4 47 0 TTTATAAAAT 0.85891 -22 CAAAAATATTTTAAATAAGATTTCTGGATTTT 5 17 0 TTAAATAAAT 0.922341 -32 TTAAAGAGGTTTTAAATAGATTTCCAAGTAAT 6 29 1 TTTAAATAAT 0.82573 -272 CCTGAGTTTATTTATTAATAATTGTATAATAT 6 271 0 TTTATTAAAT 0.733812 -30 TTTCAAAATGTTTTAAAAGACTCTATAAAAAG 9 58 1 TTTTAAAAAT 0.884744 -121 AATTTTAGTATTATTTTAAATTCTTTTTATAG 9 80 0 TTATTTTAAT 0.610856 -99 AATACTAAAATTAAAATAGAATTTAATAAATT 9 100 1 TTAAAATAAT 0.902379 -79 AATGGAGCTGTTAAAAAAGAGATTTTAAAGTT 10 143 1 TTAAAAAAAA 0.766443 -158 TCCTCTAAAATTATAAAACAATCTCTTAAATA 10 212 0 TTATAAAAAT 0.937404 -89 ******** * * Masking position 2 Map Score: 14.689 Number of sites scoring better than the average of aligned sites = 1711 Number in coding regions = 1272 Number in noncoding regions = 439 Number of orfs with sites within 600 bp upstream = 353 Fraction of orfs with sites within 600 bp upstream = 0.0566977 Motif number 3 AAACGCTAAATATTCTCCATAATCAGTTCTC 1 133 1 TATTCTCATA 0.759334 -168 CATTAATAGAGCATCAAAATACCAATTATAA 1 190 1 GCATCAAATA 0.851551 -111 GCTTTCCATTTCATCAAAATAGGATGCATTG 2 38 0 TCATCAAATA 0.973239 -263 TCTAATATAATATTCACTATATCTAATAAAT 3 93 1 TATTCACATA 0.872052 -46 AATTCTATTCAAAATAATTTTTTATG 7 6 1 TATTCAAATA 0.868529 -31 AAATCATCACCATAAAAAATTATT 7 23 0 TCATCACATA 0.973726 -14 CTCATCACCGTAAATTTTTTTG 8 45 0 TCATCACGTA 0.921313 -12 TGAATAATTTTAATCAATGAATGTTGTGTAA 9 130 0 TAATCAAGAA 0.482553 -49 AGAAAAATCCTAATCTATATAACAATGGACT 10 12 1 TAATCTAATA 0.86997 -289 GCTTATAGCCTCATCTCTAAAAGTGTCTAAA 10 59 0 TCATCTCAAA 0.777985 -242 AAGAGATAGTTCTTCAATATCAAAACCAAAG 10 89 0 TCTTCAAATC 0.726447 -212 ATCTAAATAATCATCAACATAGTCCTCTAAA 10 235 0 TCATCAAATA 0.97324 -66 TTCATCACCCTCATCTAAATAATCATCAACA 10 247 0 TCATCTAATA 0.943934 -54 ******* *** Masking position 4 Map Score: 11.4521 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 387 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 ATAATCAGTTCTCAATGTTTCTCTAATTGGAC 1 151 1 CTCAATGTCT 0.802129 -150 TAAATGAAAACTAAAAGAGTTTTCATAGCTGG 2 77 0 CTAAAAGTTT 0.976444 -224 GCTACAAAATCTGAAAGATTTTGTTTAACTTT 2 128 1 CTGAAAGTTT 0.886442 -173 TTAACTTTTTCTAAAAGTTTCGTTTGTATCCC 2 152 1 CTAAAAGTCG 0.900314 -149 AAATCTTAACTTAACAGTTTTTAATGGTGAAT 2 277 1 TTAACAGTTT 0.875684 -24 TTTATAAACACTAAAAGGAATTATTATTAATT 4 37 0 CTAAAAGATT 0.815196 -32 GAAATCTTATTTAAAATATTTTTGGTTAAAAA 5 25 1 TTAAAATTTT 0.594905 -24 AGTCGTTAACTTAACAGCCTCTGGTATTGATA 6 122 1 TTAACAGTCT 0.906821 -179 TCAAAATGTTTTAAAAGACTCTATAAAAAGAA 9 60 1 TTAAAAGTCT 0.968558 -119 AAAGACTCTATAAAAAGAATTTAAAATAATAC 9 73 1 TAAAAAGTTT 0.703502 -106 ATTAAAATTATTCAAAGGCTTTACTAAAGGTT 9 147 1 TTCAAAGTTT 0.885416 -32 AGCCTCATCTCTAAAAGTGTCTAAAATAATAC 10 52 0 CTAAAAGTCT 0.982838 -249 CTCCCTAAATGCATCTAAAACTCCCC 10 285 0 CTAAATGTCT 0.92124 -16 ******* *** Masking position 4 Map Score: 9.22131 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 273 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 AATTATATAAAAAATTACATAAGTCCTATTAT 1 223 1 AAAATACAAA 0.894754 -78 TGGAGATATTAAAAATCCAATAGC 1 287 1 AAAATCCATA 0.971091 -14 TAATAAAAAATCCAGAAATCTTATTTA 5 6 1 AAAATCCAAA 0.980071 -43 AGTTGAGTAAAAAGCTCCATAATGTTCTACAA 6 82 1 AAAGTCCAAA 0.972234 -219 TACAGCTAAATAAACTCCAAAATAAACTACTC 6 198 0 TAAATCCAAA 0.931837 -103 TAGAATTTAATAAATTACACAACATTCATTGA 9 116 1 TAAATACAAA 0.702669 -63 ATACACAAATAAAAGTCCATTGTTATATAGAT 10 24 0 AAAATCCATG 0.875084 -277 CTCTTTTTTAACAGCTCCATTAATTCCTCCTC 10 132 0 ACAGTCCATA 0.832995 -169 AAGAGATTTTAAAGTTCCCAAAAACAGAGGTT 10 159 1 AAAGTCCCAA 0.937718 -142 AAATGCATCTAAAACTCCCCTACTGAATTCAT 10 273 0 AAAATCCCTA 0.935249 -28 **** **** ** Masking position 6 Map Score: 7.21369 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 345 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 CTGGGATTGGTGAAAACCATT 1 2 1 TGGGATTGGT 0.753436 -299 CAGCGTTCCCATGGTTTGTTGATAATGGTT 1 25 0 ATGGTTTGTT 0.549838 -276 AAAGGTTTATTTGGATTGTTTGTTGACGCA 1 95 0 TTGGATTGTT 0.789889 -206 TGCTCTATTAATGGGTGGTTGTCCAATTAG 1 173 0 ATGGGTGGTT 0.840366 -128 AATGGTGCCGAGGGAGGGATACAAACGAAA 2 169 0 AGGGAGGGAT 0.829996 -132 TTATTTTATTTTAGGTTGTTATATTTATTT 2 202 1 TTAGGTTGTT 0.763957 -99 TTTCTAACTATGGGAGGGATAAT 3 126 1 TGGGAGGGAT 0.757262 -13 TATCAATACCAGAGGCTGTTAAGTTAACGA 6 124 0 AGAGGCTGTT 0.804575 -177 GCTTTCATAAAGGGGGTGTTTATTGGTCCT 9 23 1 AGGGGGTGTT 0.964222 -156 ATCAATATTAAGAGATAGTTCTTCAATATC 10 99 0 AGAGATAGTT 0.607707 -202 TCCCAAAAACAGAGGTTGATAATGAATCAT 10 174 1 AGAGGTTGAT 0.901373 -127 TTATTATTTAAGAGATTGTTTTATAATTTT 10 208 1 AGAGATTGTT 0.916732 -93 ATTATTTAGATGAGGGTGATGAATTCAGTA 10 255 1 TGAGGGTGAT 0.827711 -46 ********** Masking position 10 Map Score: 5.13293 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 806 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 ACCTAAAATAAAATAATAAAATGGTGCCGA 2 188 0 AAATAATAAA 0.966745 -113 CATAAATCTAAAAAAATAAATATAACAACC 2 215 0 AAAAAATAAA 0.923969 -86 GTTAAGATTTAAAAAATAAATACTATTTAA 2 257 0 AAAAAATAAA 0.923969 -44 TATTGATAAAAAATAATAAACT 3 3 0 AAATAATAAA 0.966745 -136 TTTTATCAATATTTAATAAAAACTTAACTT 3 22 1 ATTTAATAAA 0.695165 -117 AATTATTATTAATTAATAATACTTTTCGTG 4 21 0 AATTAATAAT 0.606937 -48 TTGATAACGAAAATTATAAGTAATGCTATA 6 148 1 AAATTATAAG 0.733609 -153 TACAATTATTAATAAATAAACTCAGGGGAT 6 277 1 AATAAATAAA 0.835534 -24 CAAAAAATAAATAAATATAAG 8 2 1 AAAAAATAAA 0.923969 -55 AAACATTTTGAAATACTAAGGACCAATAAA 9 41 0 AAATACTAAG 0.681606 -138 TTAAAATAGAATTTAATAAATTACACAACA 9 110 1 ATTTAATAAA 0.695165 -69 AAAGTGTCTAAAATAATACACAAATAAAAG 10 41 0 AAATAATACA 0.809182 -260 ACAATCTCTTAAATAATAAGTTAATGATTC 10 197 0 AAATAATAAG 0.936206 -104 TAGTCCTCTAAAATTATAAAACAATCTCTT 10 217 0 AAATTATAAA 0.845084 -84 ********** Masking position 8 Map Score: 15.4994 Number of sites scoring better than the average of aligned sites = 693 Number in coding regions = 429 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 8 ATGAAATGGAAAGCTACGCTTTCCAGCTATG 2 55 1 AAGCTACGTT 0.661453 -246 CCCGAAGCTAACGCTTCGGTTAAATGAAAAC 2 98 0 ACGCTTCGTT 0.93861 -203 CTTTTTCTAAAAGTTTCGTTTGTATCCCTCC 2 156 1 AAGTTTCGTT 0.96371 -145 AAAAACTGTTAAGTTAAGATTTAAAAAATAA 2 268 0 AAGTTAAGTT 0.907606 -33 AGGGACTGTCAAGTTAAGTTTTTATTAAATA 3 31 0 AAGTTAAGTT 0.907606 -108 ATGAGGCTATAAGCTTTGGTTTTGATATTGA 10 76 1 AAGCTTTGTT 0.890317 -225 ******** ** Masking position 5 Map Score: 1.48542 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 41 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 TTAATTAAAGGTTTATTTGGATTGTTTGTT 1 101 0 GTTTATTTGG 0.889689 -200 ATTGAGAACTGATTATGGAGAATATTTAGC 1 137 0 GATTATGGAG 0.839671 -164 AAATCTTTCAGATTTTGTAGCCCGAAGCTA 2 119 0 GATTTTGTAG 0.779424 -182 TGGAGGAGTAGTTTATTTTGGAGTTTATTT 6 193 1 GTTTATTTTG 0.932202 -108 TTATTTTGGAGTTTATTTAGCTGTAATTTT 6 205 1 GTTTATTTAG 0.95663 -96 AATCCCCTGAGTTTATTTATTAATAATTGT 6 278 0 GTTTATTTAT 0.683785 -23 CACCATAAAAAATTATTTTGAATAGAATT 7 10 0 AATTATTTTG 0.624157 -27 AATTTTAGAGGACTATGTTGATGATTATTT 10 232 1 GACTATGTTG 0.765512 -69 CTATGTTGATGATTATTTAGATGAGGGTGA 10 244 1 GATTATTTAG 0.964508 -57 ********** Masking position 6 Map Score: 1.87222 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 274 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 CTGGGATTGGTGAAAACCATTATCA 1 6 1 ATTGGTGAAA 0.622597 -295 TGACGCATTGATTGGATATATTATATTTAG 1 72 0 ATTGGATATA 0.890759 -229 TGGTTGTCCAATTAGAGAAACATTGAGAAC 1 158 0 ATTAGAGAAA 0.800222 -143 TTCTAATAATTTTGGAGATATTAAAAATCC 1 275 1 TTTGGAGATA 0.947276 -26 TATTTATTTTTTTAGATTTATGGATTAACT 2 223 1 TTTAGATTTA 0.775033 -78 AACTGTTAAGTTAAGATTTAAAAAATAAAT 2 266 0 TTAAGATTTA 0.435639 -35 TGAATATTATATTAGAGTTAGAACAAGTGA 3 79 0 ATTAGAGTTA 0.800223 -60 GAAAGTATTTATTAGATATAGTGAATATTA 3 100 0 ATTAGATATA 0.875607 -39 TTAAAATATTTTTGGTTAAAAATT 5 35 1 TTTGGTTAAA 0.58654 -14 CGTAAATTTTTTTGGTTATAATATTGACTT 8 29 0 TTTGGTTATA 0.799636 -28 TTTAGACACTTTTAGAGATGAGGCTATAAG 10 59 1 TTTAGAGATG 0.726969 -242 AAAATCAATATTAAGAGATAGTTCTTCAAT 10 102 0 TTAAGAGATA 0.776539 -199 ********** Masking position 2 Map Score: 3.35767 Number of sites scoring better than the average of aligned sites = 1305 Number in coding regions = 1165 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 11 GAGGCAATGCATCCTATTTTGATGAAATGG 2 34 1 ATCCTATTTT 0.802586 -267 CCAGCTATGAAAACTCTTTTAGTTTTCATT 2 77 1 AAACTCTTTT 0.829935 -224 TAAAAAATAAATACTATTTAAAAATAGTTA 2 248 0 ATACTATTTA 0.68199 -53 ATCTATTTAAAACCTCTTTAATCTTGTGAT 6 20 0 AACCTCTTTA 0.928923 -281 ATTACTTGGAAATCTATTTAAAACCTCTTT 6 31 0 AATCTATTTA 0.908552 -270 ATTATTTTAAATTCTTTTTATAGAGTCTTT 9 73 0 ATTCTTTTTA 0.591041 -106 AATTTATTAAATTCTATTTTAATTTTAGTA 9 102 0 ATTCTATTTT 0.831338 -77 GAAAAATCCTAATCTATATAACAATGGACT 10 13 1 AATCTATATA 0.582986 -288 GGAACTTTAAAATCTCTTTTTTAACAGCTC 10 147 0 AATCTCTTTT 0.930229 -154 ATTCATTATCAACCTCTGTTTTTGGGAACT 10 171 0 AACCTCTGTT 0.69637 -130 ATTATAAAACAATCTCTTAAATAATAAGTT 10 205 0 AATCTCTTAA 0.668131 -96 ********** Masking position 1 Map Score: 3.44142 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 662 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 12 ********** No masking Map Score: -8.85746e-13 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: -8.85746e-13 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: -8.85746e-13 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