AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_mjan_reg_300.orf -o00561_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 MJ0818 162 M. jannaschii predicted coding region MJ0818 #2 MJ0820 263 M. jannaschii predicted coding region MJ0820 #3 MJ0821 70 M. jannaschii predicted coding region MJ0821 #4 MJ0822 300 S-layer structural protein #5 MJ1113 300 N-acetylglucosamine-1-phosphate transferase #6 MJ1214 49 type I restriction-modification enzyme 1, R subunit #7 MJ1217 41 conserved hypothetical protein #8 MJ1219 69 M. jannaschii predicted coding region MJ1219 #9 MJ1220 69 type I restriction-modification enzyme 1, M subunit #10 MJ1530 178 ribosomal protein S18 alanine acetyltransferase Motif number 1 GATGAAACTTTTTCTAAAAGTTTCTTTTAAAAC 1 31 1 TTTTAAATTT 0.928095 -132 CTAATAAATTATAGTAATCTTTTTATAGCGTTC 1 83 0 ATATAACTTT 0.681888 -80 TATATCACTTTAGAAATTCTTTAGTAACTTGC 1 141 0 TTAAAATTTT 0.894619 -22 TAGTTTATTTATTGAATATGTTTATAAGACTGG 2 210 1 ATTAATTTTT 0.809608 -54 AACTTTTTCTTTTTTATTTTTTTAGATGATTTA 3 18 1 TTTTATTTTT 0.95661 -53 TTATAATGAATTAGAAATTTTTTCTTTAAA 4 8 0 TTAAAATTTT 0.894619 -293 CCCCCACATATTTTTATAAGTTTCTACTAAATA 4 42 1 TTTTATATTT 0.936895 -259 TTATAAGTTTCTACTAAATATTTGGATATATCA 4 55 1 CTATAATTTT 0.755102 -246 TCAAAATTAATTTTTATCCATTTAAAAAAGTTG 4 85 1 TTTTATCTTT 0.882283 -216 GTTACAAATGTTTGCAACTTTTTTAAATGGATA 4 99 0 TTTCAATTTT 0.807655 -202 GTTGCAAACATTTGTAACTTTTTTTATTTTTTA 4 114 1 TTTTAATTTT 0.950413 -187 ATGAAAAATTTTATTATATCTTTGTTATACAAA 4 171 0 TTATATTTTT 0.950413 -130 TGAAACGGTTATAACAATAGTTTCTGAATGAAA 4 198 0 ATACAAATTT 0.48202 -103 AAGATATTAATTAGGATATTTTTATATTTCATA 5 14 0 TTAGATTTTT 0.807655 -287 AATATCCTAATTAATATCTTTTTACTGATTTTT 5 27 1 TTATATTTTT 0.950413 -274 TTACTGATTTTTTGGATATTTTTGGCTTATCTT 5 48 1 TTTGATTTTT 0.828472 -253 ATCTTTTACCATACTATCTATTTGTTTTTAAAT 5 76 1 ATATATTTTT 0.87887 -225 TATCTATTTGTTTTTAAATATTTTGAAAAGTAT 5 90 1 TTTTAATTTT 0.950413 -211 AAAGTCCATCATAAAATACTTTTCAAAATATTT 5 105 0 ATAAATCTTT 0.556886 -196 TGGTGCAATTTTTTTAATAGTTTTAGTTATCCT 5 146 1 TTTTAAATTT 0.928094 -155 TATAGAAATTCTTTTATTATTTTCCTTACTTCC 5 209 0 CTTTATATTT 0.733137 -92 AATAAAAGAATTTCTATAATTTTTTAGCAAAAA 5 224 1 TTTTATATTT 0.936895 -77 ATTTTTATTGTTAATAAAATTTTGCTGGTGAAA 7 17 1 TTATAAATTT 0.918174 -25 CTGGAAGTTAATTTAATTTGTTTGATTGATTAG 8 36 1 ATTAATTTTT 0.809605 -34 GTCCTTAGTATTTCAAAATGTTTTAAAAGACTC 10 48 1 TTTAAATTTT 0.907111 -131 AAAAGACTCTATAAAAAGAATTTAAAATAATAC 10 72 1 ATAAAAATTT 0.683967 -107 TATTTTAATTTTAGTATTATTTTAAATTCTTTT 10 85 0 TTATATATTT 0.928089 -94 TAGTAAAGCCTTTGAATAATTTTAATCAATGAA 10 140 0 TTTAATATTT 0.883238 -39 *** *** * *** Masking position 6 Map Score: 34.4922 Number of sites scoring better than the average of aligned sites = 2513 Number in coding regions = 1764 Number in noncoding regions = 749 Number of orfs with sites within 600 bp upstream = 493 Fraction of orfs with sites within 600 bp upstream = 0.0791841 Motif number 2 TAAGATATATATTCAATTTTGATGAAAC 1 9 1 ATATTCAATT 0.364066 -154 GTAACTTGCTATTTTTTAATAAGGCAGGAT 1 120 0 ATTTTTTAAT 0.783173 -43 GAGTAGAAGGTAATTCTATTTAAATCCAAC 2 35 1 TAATTCTATT 0.814716 -229 AGAAGTTATTAAATTTAATTGAGGAGTTGG 2 60 0 AAATTTAATT 0.804558 -204 TTTCACCAATTAATTTAAATTTATGAATTA 3 49 0 TAATTTAAAT 0.804567 -22 TTAAAGAAAAAATTTCTAATTCATTATAAA 4 12 1 AATTTCTAAT 0.70917 -289 AACCCCCACATATTTTTATAAGTTTCTACT 4 40 1 TATTTTTATA 0.654287 -261 TGTTTGCAACTTTTTTAAATGGATAAAAAT 4 94 0 TTTTTTAAAT 0.721687 -207 CATTTGTAACTTTTTTTATTTTTTAATAGA 4 122 1 TTTTTTTATT 0.900392 -179 TTGTTATACAAAATTTAATTTATAATATCG 4 153 0 AAATTTAATT 0.804558 -148 TCTGAATGAAAAATTTTATTATATCTTTGT 4 179 0 AAATTTTATT 0.900704 -122 TAAGTTTTTGTATTGTTATTTGATTGACGG 4 270 0 TATTGTTATT 0.604398 -31 TTAATTAGGATATTTTTATATTTCATAATT 5 11 0 TATTTTTATA 0.654287 -290 ATTGGTGCAATTTTTTTAATAGTTTTAGTT 5 144 1 TTTTTTTAAT 0.851059 -157 ATTATTAATCTACTTTTATTGCTTAGGGAA 5 183 1 TACTTTTATT 0.832587 -118 ATTATAGAAATTCTTTTATTATTTTCCTTA 5 214 0 TTCTTTTATT 0.692979 -87 TCCTCAATGGATTTTTTAATGTATGGATT 6 10 0 ATTTTTTAAT 0.783173 -40 AGGAAGATTTAATTTTTATTTCAG 6 36 1 AATTTTTATT 0.926407 -14 AATAAAATTTTTATTGTTAATAAAA 7 6 1 AATTTTTATT 0.926407 -36 TTCACCAGCAAAATTTTATTAACAATAAAA 7 19 0 AAATTTTATT 0.900704 -23 AGCTGGAAGTTAATTTAATTTGTTTGATTG 8 34 1 TAATTTAATT 0.866891 -36 CTTACTTATTTCTAATCAATCAAACA 8 54 0 TATTTCTAAT 0.794149 -16 ACTTAGATAGTTATTTTAATGTTTTCACTA 9 40 0 TTATTTTAAT 0.804567 -30 ATTTTAGTATTATTTTAAATTCTTTTTATA 10 81 0 TATTTTAAAT 0.851023 -98 TATTAAATTCTATTTTAATTTTAGTATTAT 10 98 0 TATTTTAATT 0.900309 -81 AGCCTTTGAATAATTTTAATCAATGAATGT 10 137 0 TAATTTTAAT 0.900704 -42 ********** Masking position 4 Map Score: 29.5177 Number of sites scoring better than the average of aligned sites = 2781 Number in coding regions = 1859 Number in noncoding regions = 922 Number of orfs with sites within 600 bp upstream = 564 Fraction of orfs with sites within 600 bp upstream = 0.0905879 Motif number 3 AAGATTACTATAATTTATTAGGATAATCCTG 1 95 1 TATTTATTAG 0.940822 -68 TAGTAACTTGCTATTTTTTAATAAGGCAGGA 1 121 0 CATTTTTTAA 0.705033 -42 GTCGGATAGTTTATTTATTGAATATGTTTAT 2 204 1 TATTTATTGA 0.896465 -60 TTTTCTTTTTTATTTTTTTAGATGATTTAAT 3 22 1 TTTTTTTTAG 0.843512 -49 GTAACTTTTTTTATTTTTTAATAGAGCGATA 4 127 1 TATTTTTTAA 0.938095 -174 TTTGTATTGTTATTTGATTGACGGTATATAC 4 263 0 TTTTGATTGA 0.627318 -38 ATCTTTTTACTGATTTTTTGGATATTTTTGG 5 42 1 TATTTTTTGG 0.924314 -259 TAATCTACTTTTATTGCTTAGGGAAGTAAGG 5 188 1 TATTGCTTAG 0.764358 -113 AGAATTTCTATAATTTTTTAGCAAAAAACAT 5 230 1 TATTTTTTAG 0.948501 -71 CTTCCTCAATGGATTTTTTAATGTATGGATT 6 11 0 GATTTTTTAA 0.705036 -39 ATATTTTTTTGAGGGATTTTAA 8 2 1 TTTTTTTTGA 0.746248 -68 TTAATTTGTTTGATTGATTAGAAATAAGTAA 8 48 1 TATTGATTAG 0.913358 -22 GAATGTTGTGTAATTTATTAAATTCTATTTT 10 112 0 TATTTATTAA 0.92898 -67 TACACAACATTCATTGATTAAAATTATTCAA 10 131 1 TATTGATTAA 0.896521 -48 * ********* Masking position 5 Map Score: 11.9516 Number of sites scoring better than the average of aligned sites = 664 Number in coding regions = 484 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 4 AAAAGCTTTGAGGTTTTAAAAGAAACTTTTAG 1 44 0 AGGTTTTAAG 0.911179 -119 TCCTTTTTGTGGATTTAGAGAGTAGAAGGTAA 2 16 1 GGATTTAAAG 0.981975 -248 TTGAGGAGTTGGATTTAAATAGAATTACCTTC 2 40 0 GGATTTAAAG 0.98185 -224 ACTAAGAATTGGGTTTAAAGACAGGGATAACA 2 127 0 GGGTTTAAAC 0.9263 -137 AAATATGTGGGGGTTTATAATGAATTAGAAAT 4 23 0 GGGTTTAATG 0.96024 -278 TCATATCGTAAGATTTATATAGTAGTTTGTCG 4 228 1 AGATTTAAAG 0.904012 -73 ATTTTATGATGGACTTTAAAAGCATTGGTGCA 5 121 1 GGACTTTAAG 0.885852 -180 TTTTTTTGAGGGATTTTAAGAGCTGGAAGTTA 8 14 1 GGATTTTAAG 0.97383 -56 ATTGGATGTAGGGTGTATATAAAGG 9 4 0 GGGTGTAAAA 0.785508 -66 TTCATAAAGGGGGTGTTTATTGGTCCTTAGTA 10 26 1 GGGTGTTATG 0.876436 -153 ******* * ** Masking position 6 Map Score: 8.6348 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 170 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 ATATATATTCAATTTTGATGAAACTTTTTC 1 15 1 AATTTTGATG 0.809881 -148 AAAGCTTTTTAATTTGGAACGCTATAAAAA 1 67 1 AATTTGGAAC 0.886119 -96 TACTATAATTTATTAGGATAATCCTGCCTT 1 100 1 TATTAGGATA 0.776075 -63 AACCCCCACATATTTTTATAAGTTTCTACT 4 40 1 TATTTTTATA 0.622724 -261 TTCTACTAAATATTTGGATATATCAAAATT 4 63 1 TATTTGGATA 0.922293 -238 GATAAAAATTAATTTTGATATATCCAAATA 4 73 0 AATTTTGATA 0.953323 -228 TATCAAAATTAATTTTTATCCATTTAAAAA 4 83 1 AATTTTTATC 0.654906 -218 AATTATGAAATATAAAAATA 5 1 1 AATTATGAAA 0.773208 -300 AAAAGATATTAATTAGGATATTTTTATATT 5 19 0 AATTAGGATA 0.844641 -282 TTTTACTGATTTTTTGGATATTTTTGGCTT 5 46 1 TTTTTGGATA 0.538834 -255 TGTTTTTAAATATTTTGAAAAGTATTTTAT 5 98 1 TATTTTGAAA 0.881562 -203 TGAATTTTGAACGCTTTCATAA 10 3 1 AATTTTGAAC 0.895341 -176 TCTTTTAAAACATTTTGAAATACTAAGGAC 10 48 0 CATTTTGAAA 0.731327 -131 GCCTTTGAATAATTTTAATCAATGAATGTT 10 136 0 AATTTTAATC 0.518346 -43 ********** Masking position 8 Map Score: 7.5624 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 596 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 6 GGAACGCTATAAAAAGATTACTATAATTTA 1 82 1 AAAAAGATTA 0.354524 -81 ATTTAGAGAGTAGAAGGTAATTCTATTTAA 2 28 1 TAGAAGGTAA 0.614555 -236 AACTCCTCAATTAAATTTAATAACTTCTCA 2 62 1 TTAAATTTAA 0.410785 -202 TAAAATATAATCAGCTCTTC 2 254 0 TAAAATATAA 0.818718 -10 AATAAAAAAGAAAAAGTTAAGGAAT 3 6 0 AAAAAGTTAA 0.926464 -65 TAAATCATCTAAAAAAATAAAAAAGAAAAA 3 21 0 AAAAAAATAA 0.688231 -50 GATTTAATTCATAAATTTAAATTAATTGGT 3 45 1 ATAAATTTAA 0.490798 -26 TTTAAATGGATAAAAATTAATTTTGATATA 4 81 0 TAAAAATTAA 0.797825 -220 TAAAAAATAAAAAAAGTTACAAATGTTTGC 4 117 0 AAAAAGTTAC 0.559149 -184 ATCGCTCTATTAAAAAATAAAAAAAGTTAC 4 127 0 TAAAAAATAA 0.728375 -174 CTTTGTTATACAAAATTTAATTTATAATAT 4 155 0 CAAAATTTAA 0.535564 -146 AATTATGAAATATAAAAATATCCTA 5 6 1 TGAAATATAA 0.498959 -295 AAAAATCAGTAAAAAGATATTAATTAGGAT 5 30 0 AAAAAGATAT 0.366163 -271 GATAGTATGGTAAAAGATAAGCCAAAAATA 5 64 0 TAAAAGATAA 0.911836 -237 ATGAAGATAAAAGAAGTTAAAGTTTAGGAT 5 265 0 AAGAAGTTAA 0.892717 -36 CCCCTTTATAATGAAGATAAAAGAAGTTAA 5 275 0 ATGAAGATAA 0.532711 -26 CTGAAATAAAAATTAAATCTTCCTCA 6 34 0 TAAAAATTAA 0.797825 -16 TTTTAAGAGCTGGAAGTTAATTTAATTTGT 8 27 1 TGGAAGTTAA 0.688919 -43 ACTCTATAAAAAGAATTTAAAATAATACTA 10 77 1 AAGAATTTAA 0.785279 -102 AAAATTAAAATAGAATTTAATAAATTACAC 10 106 1 TAGAATTTAA 0.815289 -73 AAGGCTTTACTAAAGGTTAAGTGAGAAC 10 161 1 TAAAGGTTAA 0.594279 -18 ********** Masking position 8 Map Score: 12.877 Number of sites scoring better than the average of aligned sites = 2086 Number in coding regions = 1541 Number in noncoding regions = 545 Number of orfs with sites within 600 bp upstream = 419 Fraction of orfs with sites within 600 bp upstream = 0.0672984 Motif number 7 TTAAATTAATTGGTGAAATT 3 61 1 TGGTGAAATT 0.985969 -10 TTAAAAGCATTGGTGCAATTTTTTTAATAG 5 136 1 TGGTGCAATT 0.983347 -165 AAAATTTTGCTGGTGAAATT 7 32 1 TGGTGAAATT 0.985969 -10 TCAATGAATGTTGTGTAATTTATTAAATTC 10 118 0 TTGTGTAATT 0.909339 -61 ********** Masking position 4 Map Score: 2.52628 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 25 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 CTTGCTATTTTTTAATAAGGCAGGATTATC 1 116 0 TTTAATAAGG 0.893825 -47 AAAATAGCAAGTTACTAAAGAATTTCTAAA 1 135 1 GTTACTAAAG 0.857023 -28 AGTTATTAAATTTAATTGAGGAGTTGGATT 2 57 0 TTTAATTGAG 0.801674 -207 CTTAGTTGCTTTAACTAAAGTCCAACATTT 2 153 1 TTAACTAAAG 0.801778 -111 TTTTTATCCATTTAAAAAAGTTGCAAACAT 4 95 1 TTTAAAAAAG 0.850299 -206 TTTTTTATTTTTTAATAGAGCGATATTATA 4 133 1 TTTAATAGAG 0.966363 -168 TTTTGAACGCTTTCATAAAGGGGGTGTTTA 10 15 1 TTTCATAAAG 0.904019 -164 TTTAAATTCTTTTTATAGAGTCTTTTAAAA 10 68 0 TTTTATAGAG 0.819101 -111 TAAAATAGAATTTAATAAATTACACAACAT 10 111 1 TTTAATAAAT 0.77864 -68 ATTCAAAGGCTTTACTAAAGGTTAAGTGAG 10 156 1 TTTACTAAAG 0.966363 -23 ********** Masking position 2 Map Score: 5.27296 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 284 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 9 AATCCTAATATTATTGTTATCCCTGTCTTT 2 113 1 TTATTGTTAT 0.866252 -151 TATGCCATGTTTTTTGTTTATCGTCGGATA 2 182 1 TTTTTGTTTA 0.888266 -82 ATTCCTTAACTTTTTCTTTTTTATTTTTTT 3 11 1 TTTTTCTTTT 0.86619 -60 TTTTTCTTTTTTATTTTTTTAGATGATTTA 3 21 1 TTATTTTTTT 0.575117 -50 AATTAGAAATTTTTTCTTTAAA 4 3 0 TTTTTCTTTA 0.654514 -298 TTTGTAACTTTTTTTATTTTTTAATAGAGC 4 124 1 TTTTTATTTT 0.807131 -177 TTTTATTATATCTTTGTTATACAAAATTTA 4 166 0 TCTTTGTTAT 0.66095 -135 ATCACCTAAGTTTTTGTATTGTTATTTGAT 4 276 0 TTTTTGTATT 0.727783 -25 CCATACTATCTATTTGTTTTTAAATATTTT 5 84 1 TATTTGTTTT 0.847284 -217 TTTTTAATAGTTTTAGTTATCCTTGCCATT 5 156 1 TTTTAGTTAT 0.527779 -145 AGAAATTCTTTTATTATTTTCCTTACTTCC 5 209 0 TTATTATTTT 0.704738 -92 GTTTAGGATATATATGTTTTTTGCTAAAAA 5 244 0 TATATGTTTT 0.51007 -57 AATAAAATTTTTATTGTTAATAAAATTTTG 7 11 1 TTATTGTTAA 0.654618 -31 GATAGTTATTTTAATGTTTTCACTATGTAA 9 35 0 TTAATGTTTT 0.744066 -35 ********** Masking position 7 Map Score: 4.83405 Number of sites scoring better than the average of aligned sites = 1979 Number in coding regions = 1507 Number in noncoding regions = 472 Number of orfs with sites within 600 bp upstream = 346 Fraction of orfs with sites within 600 bp upstream = 0.0555734 Motif number 10 ********** No masking Map Score: 3.20698e-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: 3.20698e-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: 3.20698e-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