AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_mjan_reg_100.orf -o00950_mjan_100.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 MJ0684 68 aspartate aminotransferase (aspB2) #4 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #5 MJ1027 125 formate hydrogenlyase, subunit 5 #6 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #7 MJ1029 47 dimethyladenosine transferase (ksgA) #8 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #9 MJ1575 300 GMP synthase (guaA) #10 MJ1576 80 LemA protein #11 MJ1577 29 M. jannaschii predicted coding region MJ1577 #12 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) #13 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 GGGATTGGTGAAAACCATTATCAACAAACCATGG 1 13 1 AAAAATTTAA 0.965266 -288 AGAGCATCAAAATACCAATTATAAAAAATTATAT 1 197 1 AATAAATAAA 0.846257 -104 CCAATTATAAAAAATTATATAAAAAATTACATAA 1 211 1 AAAAATAAAA 0.923182 -90 TAATATCTCCAAAATTATTAGAAATTCTAATTGG 1 264 0 AAAAATTGAA 0.75711 -37 CGCTTCGGTTAAATGAAAACTAAAAGAGTTTTCA 2 84 0 AAATAAATAA 0.83709 -217 AACAACCTAAAATAAAATAATAAAATGGTGCCGA 2 188 0 AATAATATAA 0.868704 -113 ATAAATCTAAAAAAATAAATATAACAACCTAAAA 2 210 0 AAAAAAAAAA 0.937291 -91 TTAAAAAATAAATACTATTTAAAAATAGTTAATC 2 245 0 AATAATTAAA 0.815694 -56 TGCCACCACGAAAAGTATTATTAATTAATAATAA 3 15 1 AAAAATTTAA 0.965265 -54 GTCACCAAAAATTTATTGTCAATTTAGCTAAA 4 9 1 AAATATTTAA 0.83709 -80 TAAGTTATCTAAAAAAGTTTTTAATTGTAATTTT 4 52 1 AAAAGTTTAA 0.856111 -37 TTATTAAAACAAAACTATATAAAAGGTTAAGCTA 5 21 1 AAAAATAAAA 0.923182 -105 ATAATGTAACAAAATAGAAATTAACTAAACTATT 6 19 0 AAAAGAATAA 0.856111 -42 TAAAAAAGAGAAAAGAAAATAAAAAT 7 3 0 AAAAAAAAAA 0.937291 -45 TTTTTAGAATAAATAAAAAGTGAAACA 7 31 1 AAATAAATAA 0.83709 -17 TTAAATTTTTAATTCAAAATTTAACTTATATTTT 8 20 1 AATTAAATAA 0.60341 -127 AAGAATATAAAATAAGAATATAAAAATATAAGTT 8 42 0 AATAAATTAA 0.910986 -105 TTTAAATATCAATAAAATTAAAAAGATAAGGTAA 8 88 0 AATAATTAAA 0.815694 -59 TAATCATAATAAAAGAAATTTTAAAATATAGTGT 9 36 1 AAAAAATTAA 0.971881 -265 CAAAGTTGTTAAAATTAATATTAATAATGGATAT 9 74 1 AAAAAATTAA 0.971881 -227 AGTATCTTTCAAAAACATTTTGAAAGAACCTTTT 9 256 0 AAAAATTTAA 0.965266 -45 TTTCACCACAAAAAAGAATTTGAATTATTTGGAT 10 55 0 AAAAAATTAA 0.971881 -26 AAATCCCCTAAAAATTAAAATTAATAA 11 4 0 AAAAAAATAA 0.965266 -26 GACCTACTATAAAAACAAAAACAAGAGGAGAAAT 12 42 1 AAAAAAAAAA 0.937291 -25 AAAAGTGTCTAAAATAATACACAAATAAAAGTCC 13 38 0 AAAAATAAAA 0.923182 -263 ATTCCTCCTCAAAATCAATATTAAGAGATAGTTC 13 108 0 AAAAAATTAA 0.971881 -193 GAGCTGTTAAAAAAGAGATTTTAAAGTTCCCAAA 13 147 1 AAAAGATTAA 0.88095 -154 **** *** * ** Masking position 2 Map Score: 43.5924 Number of sites scoring better than the average of aligned sites = 1518 Number in coding regions = 1061 Number in noncoding regions = 457 Number of orfs with sites within 600 bp upstream = 342 Fraction of orfs with sites within 600 bp upstream = 0.0549309 Motif number 2 GATTGGTGAAAACCATTATCAACAAACCATGG 1 15 1 AAATTATCAA 0.685852 -286 CAATTATAAAAAATTATATAAAAAATTACATA 1 212 1 AATATATAAA 0.828722 -89 TTTATGGATTAACTATTTTTAAATAGTATTTA 2 239 1 AAATTTTTAA 0.923923 -62 ATCTTAACTTAACAGTTTTTAATGGTGAATTT 2 279 1 AAGTTTTTAA 0.785021 -22 CCACCACGAAAAGTATTATTAATTAATAATAA 3 17 1 AAATTATTAA 0.941489 -52 CACTAAAAGGAATTATTATTAATTAATAATAC 3 29 0 AAATTATTAA 0.941489 -40 AGTTATCTAAAAAAGTTTTTAATTGTAATTTT 4 54 1 AAGTTTTTAA 0.785021 -35 TTTTTAATTGTAATTTTATAAAATCGTAAG 4 69 1 TATTTATAAA 0.728505 -20 CTCGATAACTTTATTAAAACAAAACTA 5 6 1 TATTTATTAA 0.788331 -120 TATTAAAACAAAACTATATAAAAGGTTAAGCT 5 22 1 AATATATAAA 0.828722 -104 TTAAGCTAATTATCATTATTAATTATGATAAA 5 47 1 TAATTATTAA 0.885818 -79 CCAACAATTATAAACATGATAATA 5 112 0 AAATTATAAA 0.920591 -14 AAATTAACTAAACTATTTTTAAACT 6 4 0 AAATTTTTAA 0.923923 -57 AATTTTGAATTAAAAATTTAAAAATTGAAA 8 9 0 TAAATTTAAA 0.785275 -138 GAATATAAAATAAGAATATAAAAATATAAGTT 8 42 0 TAAATATAAA 0.829327 -105 GATATCAGAATAAGAATATAAAATAAGAATAT 8 55 0 TAAATATAAA 0.829327 -92 TTATTACTATTATGTTTTTAAATATCAATAAA 8 106 0 TATTTTTAAA 0.669447 -41 TAATAGTAATAAATTATTTGAATGTGAAACT 8 126 1 AATATTTGAA 0.648325 -21 ATCATAATAAAAGAAATTTTAAAATATAGTGT 9 38 1 AAAATTTTAA 0.91348 -263 AAGTTGTTAAAATTAATATTAATAATGGATAT 9 76 1 AAAATATTAA 0.933284 -225 TATCTTTCAAAAACATTTTGAAAGAACCTTTT 9 256 0 AAATTTTGAA 0.815402 -45 GTTTGATATCAACTTATATAAATTTTATTATT 10 13 0 AATATATAAA 0.828722 -68 TCACCACAAAAAAGAATTTGAATTATTTGGAT 10 55 0 AAAATTTGAA 0.793394 -26 TTATTAATTTTAATTTTTAGGGG 11 2 1 TAAATTTTAA 0.835804 -28 TTTCATAAGTAAATTTTATTAATTTTGAAAGA 12 12 1 AATTTATTAA 0.885384 -55 TCCTCCTCAAAATCAATATTAAGAGATAGTTC 13 108 0 AAAATATTAA 0.933284 -193 GCTGTTAAAAAAGAGATTTTAAAGTTCCCAAA 13 149 1 AAGATTTTAA 0.760456 -152 CATAGTCCTCTAAAATTATAAAACAATCTCTT 13 217 0 TAATTATAAA 0.848239 -84 ** ******** Masking position 7 Map Score: 34.4308 Number of sites scoring better than the average of aligned sites = 1603 Number in coding regions = 1141 Number in noncoding regions = 462 Number of orfs with sites within 600 bp upstream = 398 Fraction of orfs with sites within 600 bp upstream = 0.0639255 Motif number 3 TAGCGTTTAGTTAATTAAAGGTTTATTTGGATTGT 1 106 0 TTATAATTTA 0.793883 -195 ATGTAATTTTTTATATAATTTTTTATAATTGGTAT 1 208 0 TTATAATTTA 0.793897 -93 TCTGAAAGATTTTGTTTAACTTTTTCTAAAAGTTT 2 137 1 TTTTTATTTT 0.751255 -164 TTTTAGGTTGTTATATTTATTTTTTTAGATTTATG 2 210 1 TTATTTTTTT 0.841912 -91 TTAAAAACTGTTAAGTTAAGATTTAAAAAATAAAT 2 266 0 TTATTATTTA 0.939338 -35 ATAATGATAATTAGCTTAACCTTTTATATAGTTTT 5 31 0 TTATTATTTT 0.970581 -95 AAAATAGAAATTAACTAAACTATTTTTAAACT 6 8 0 TTATAAATTT 0.569783 -53 TTCTATTTTGTTACATTATTTATTTTACTGATATT 6 34 1 TTATTAATTT 0.841914 -27 AATTCAAAATTTAACTTATATTTTTATATTCTTAT 8 30 1 TTATTATTTT 0.970561 -117 TTTTATATTCTTATTTTATATTCTTATTCTGATAT 8 51 1 TTATTATCTT 0.807094 -96 TCTGATATCTTTACCTTATCTTTTTAATTTTATTG 8 78 1 TTATTATTTT 0.970581 -69 TTTATCACCTTATATTTTATTAGTATCTT 9 282 0 TCATTATTTA 0.662651 -19 TTATTAATTTTAATTTTTAGGGGATTTT 11 4 1 TTATTTTTTT 0.841485 -26 CCATTGTTATATAGATTAGGATTTTTCTC 13 5 0 ATATTATTTT 0.738419 -296 TAATGAATCATTAACTTATTATTTAAGAGATTGTT 13 193 1 TTATTATTTA 0.93935 -108 ATTTAAGAGATTGTTTTATAATTTTAGAGGACTAT 13 213 1 TTGTTATTTT 0.817394 -88 *** *** **** Masking position 6 Map Score: 16.8119 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 209 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 4 CTAATTGGACAACCACCCATTAATAGAGCATC 1 173 1 AACACCCATA 0.87028 -128 TGGAGATATTAAAAATCCAATAGC 1 287 1 AAAATCCATA 0.959235 -14 TCCAGCTATGAAAACTCTTTTAGTTTTCATTT 2 76 1 AAACTCTTTA 0.715174 -225 GAGAGCGTTCAAATATCCATTATTAATATTAA 9 88 0 AAAATCCATA 0.959235 -213 TGGATATTTGAACGCTCTCCTATAGGGAGGTG 9 101 1 AACCTCTCTA 0.930325 -200 AAGGTTCATCAAAAATCTAACACCTCCTCGCT 9 219 0 AAAATCTACA 0.716219 -82 AAAAATCCCCTAAAAATTAAAA 11 18 0 AAAATCCCTA 0.969304 -12 ATTAATTTTGAAAGACCTACTATAAAAACAAA 12 29 1 AAAACCTATA 0.835937 -38 GATATTGAAGAACTATCTCTTAATATTGATTT 13 99 1 AACATCTCTA 0.94196 -202 CTCTTTTTTAACAGCTCCATTAATTCCTCCTC 13 132 0 ACACTCCATA 0.768688 -169 AAAATTATAAAACAATCTCTTAAATAATAAGT 13 206 0 AACATCTCTA 0.941963 -95 AAATGCATCTAAAACTCCCCTACTGAATTCAT 13 273 0 AAACTCCCTA 0.962933 -28 *** ***** ** Masking position 1 Map Score: 8.67692 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 256 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 GTCCAATTAGAGAAACATTGAGAACTGATTAT 1 151 0 AGACATTGAG 0.858924 -150 CCAGCTATGAAAACTCTTTTAGTTTTCATTTA 2 77 1 AAACTTTTAG 0.98202 -224 AAAGTTAAACAAAATCTTTCAGATTTTGTAGC 2 128 0 AAACTTTCAG 0.919291 -173 GGGATACAAACGAAACTTTTAGAAAAAGTTAA 2 152 0 CGACTTTTAG 0.96565 -149 AATTAATAATAATTCCTTTTAGTGTTTATAAA 3 37 1 AATCTTTTAG 0.874049 -32 TTACAATTAAAAACTTTTTTAGATAACTTACT 4 50 0 AAATTTTTAG 0.811442 -39 ACATTTTGAAAGAACCTTTTAGTAAAAGGTTC 9 244 0 AGACTTTTAG 0.98654 -57 AGTATCTTTCAAAAACATTTTGAAAGAACCTT 9 258 0 AAACATTTTG 0.734239 -43 GTATTATTTTAGACACTTTTAGAGATGAGGCT 13 52 1 AGACTTTTAG 0.98654 -249 ATATCAAAACCAAAGCTTATAGCCTCATCTCT 13 72 0 CAACTTATAG 0.727028 -229 GGGGAGTTTTAGATGCATTTAGGGAG 13 285 1 AGACATTTAG 0.966881 -16 *** ******* Masking position 8 Map Score: 9.49656 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 101 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ATACCAATTATAAAAAATTATATAAAAAAT 1 208 1 TAAAAAATTA 0.842979 -93 AAAAATTATATAAAAAATTACATAAGTCCT 1 220 1 TAAAAAATTA 0.842979 -81 ATAAGTCCTATTATAAAATACTACCAATTA 1 241 1 TTATAAAATA 0.75096 -60 CAACCTAAAATAAAATAATAAAATGGTGCC 2 190 0 TAAAATAATA 0.793991 -111 TCCATAAATCTAAAAAAATAAATATAACAA 2 217 0 TAAAAAAATA 0.95376 -84 ATAAATACTATTTAAAAATAGTTAATCCAT 2 242 0 TTTAAAAATA 0.551026 -59 AAGTTAAGATTTAAAAAATAAATACTATTT 2 259 0 TTAAAAAATA 0.892151 -42 CTTACGATTTTATAAAATTACAATTAAAAA 4 69 0 TATAAAATTA 0.443221 -20 AGTTTAAAAATAGTTTAGTTAA 6 3 1 TTTAAAAATA 0.551026 -58 ATAAATAATGTAACAAAATAGAAATTAACT 6 27 0 TAACAAAATA 0.699116 -34 AATTTTGAATTAAAAATTTAAAAATTGAAA 8 11 0 TAAAAATTTA 0.608702 -136 AATAAGAATATAAAAATATAAGTTAAATTT 8 36 0 TAAAAATATA 0.856834 -111 GATATCAGAATAAGAATATAAAATAAGAAT 8 57 0 TAAGAATATA 0.402548 -90 TCAATAAAATTAAAAAGATAAGGTAAAGAT 8 84 0 TAAAAAGATA 0.687182 -63 TATTGATATTTAAAAACATAATAGTAATAA 8 108 1 TAAAAACATA 0.687182 -39 AACATAATAGTAATAAATTATTTGAATGTG 8 122 1 TAATAAATTA 0.660633 -25 AGGATAATCATAATAAAAGAAATTTTAAAA 9 32 1 TAATAAAAGA 0.536565 -269 AAAAGAAATTTTAAAATATAGTGTCTTTCA 9 46 1 TTAAAATATA 0.705794 -255 TGAAAGATACTAATAAAATATAAGGTGATA 9 279 1 TAATAAAATA 0.882446 -22 CTAATAATAAAATTTATATAAGTT 10 5 1 TAATAAAATT 0.428085 -76 CTTTCAAAATTAATAAAATTTACTTATGAA 12 13 0 TAATAAAATT 0.428085 -54 TAAAAGTGTCTAAAATAATACACAAATAAA 13 43 0 TAAAATAATA 0.793991 -258 AATGGAGCTGTTAAAAAAGAGATTTTAAAG 13 143 1 TTAAAAAAGA 0.559096 -158 AAACAATCTCTTAAATAATAAGTTAATGAT 13 199 0 TTAAATAATA 0.625762 -102 CATAGTCCTCTAAAATTATAAAACAATCTC 13 219 0 TAAAATTATA 0.52578 -82 ********** Masking position 1 Map Score: 24.4891 Number of sites scoring better than the average of aligned sites = 1986 Number in coding regions = 1472 Number in noncoding regions = 514 Number of orfs with sites within 600 bp upstream = 389 Fraction of orfs with sites within 600 bp upstream = 0.0624799 Motif number 7 AATTAAAGGTTTATTTGGATTGTTTGTTGA 1 99 0 TTATTTGGAT 0.952444 -202 TTTATAATTGGTATTTTGATGCTCTATTAA 1 192 0 GTATTTTGAT 0.835085 -109 GCAATGCATCCTATTTTGATGAAATGGAAA 2 37 1 CTATTTTGAT 0.931385 -264 TTATATTTATTTTTTTAGATTTATGGATTA 2 220 1 TTTTTTAGAT 0.772072 -81 AATTAAAAACTTTTTTAGATAACTTACTAT 4 48 0 TTTTTTAGAT 0.772072 -41 TAGTTAATTTCTATTTTGTTACATTATTTA 6 26 1 CTATTTTGTT 0.590923 -35 TTTTATATTCTTATTCTGATATCTTTACCT 8 64 1 TTATTCTGAT 0.806512 -83 TAGTAATAAATTATTTGAATGTGAAACT 8 129 1 TTATTTGAAT 0.568807 -18 AAAATTTCTTTTATTATGATTATCCTCCAA 9 28 0 TTATTATGAT 0.737696 -273 AGAATTTGAATTATTTGGATAGTTTAGTAT 10 45 0 TTATTTGGAT 0.952444 -36 AAGTCCATTGTTATATAGATTAGGATTTTT 13 14 0 TTATATAGAT 0.657648 -287 TTTTAGAGGACTATGTTGATGATTATTTAG 13 234 1 CTATGTTGAT 0.699724 -67 ATGTTGATGATTATTTAGATGAGGGTGATG 13 246 1 TTATTTAGAT 0.943133 -55 ********** Masking position 4 Map Score: 9.19839 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 221 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 TAAGAGGCATTGCCGAGCGTAGCG 2 5 1 AGGCATTGCC 0.940699 -296 TCAAAATAGGATGCATTGCCTCGCTACGCT 2 26 0 ATGCATTGCC 0.977469 -275 GTCACCAAAAATTTATTGTCAATTTAGCTA 4 11 1 ATTTATTGTC 0.7323 -78 TAAATTATCTATTCATTACCTTAGTGAGTC 5 75 1 ATTCATTACC 0.970827 -51 TAAGTTAATGATTCATTATCAACCTCTGTT 13 181 0 ATTCATTATC 0.918336 -120 CCCCTACTGAATTCATCACCCTCATCTAAA 13 259 0 ATTCATCACC 0.924061 -42 ********** Masking position 5 Map Score: 0.514658 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 59 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 CAACCACCCATTAATAGAGCATCAAAATAC 1 182 1 TTAATAGAGC 0.537213 -119 ATAAAATAATAAAATGGTGCCGAGGGAGGG 2 181 0 AAAATGGTGC 0.846165 -120 ATACTATTTAAAAATAGTTAATCCATAAAT 2 238 0 AAAATAGTTA 0.54254 -63 TTAACAGTTTTTAATGGTGAATTT 2 287 1 TTAATGGTGA 0.83208 -14 TTAGTGTTTATAAATGGTGATGTC 3 55 1 TAAATGGTGA 0.928587 -14 CAAAACTATATAAAAGGTTAAGCTAATTAT 5 30 1 TAAAAGGTTA 0.861508 -96 TATTTATTCTAAAAAAGAGAAAAGAAAATA 7 16 0 AAAAAAGAGA 0.684689 -32 TTAGAATAAATAAAAAGTGAAACA 7 34 1 TAAAAAGTGA 0.861508 -14 TCAATAAAATTAAAAAGATAAGGTAAAGAT 8 84 0 TAAAAAGATA 0.639545 -63 ATTAATATTAATAATGGATATTTGAACGCT 9 87 1 ATAATGGATA 0.42127 -214 AACCTTTTAGTAAAAGGTTCATCAAAAATC 9 234 0 TAAAAGGTTC 0.836313 -67 AACCTTTTACTAAAAGGTTCTTTCAAAATG 9 245 1 TAAAAGGTTC 0.836313 -56 ACTAATAAAATATAAGGTGATAAA 9 287 1 TATAAGGTGA 0.575048 -14 TGAGGAGGAATTAATGGAGCTGTTAAAAAA 13 131 1 TTAATGGAGC 0.73393 -170 TGGAGCTGTTAAAAAAGAGATTTTAAAGTT 13 145 1 AAAAAAGAGA 0.684689 -156 ********** Masking position 4 Map Score: 8.11759 Number of sites scoring better than the average of aligned sites = 879 Number in coding regions = 741 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 10 ********** No masking Map Score: 7.34291e-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 11 ********** No masking Map Score: 7.34291e-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 12 ********** No masking Map Score: 7.34291e-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