AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_mjan_reg_300.orf -o012_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 RMJ06822 167 M_jannaschii_chromosome #2 RMJ10722 300 M_jannaschii_chromosome Motif number 1 AATATCATCATTTAGATTTTTAAATATAGT 1 11 1 TTTAGATTTT 0.948025 -157 CTTTCTAAGATTTATACTATATTTAAAAAT 1 26 0 TTTATACTAT 0.966559 -142 TTAGATAGTTTTTATACCTTTCTAAGATTT 1 43 0 TTTATACCTT 0.820179 -125 TCACAATGTTTTTATATTATCTAATTTAAA 1 80 0 TTTATATTAT 0.983549 -88 AACAATAAATATTATATTATGATGTACATA 1 112 0 ATTATATTAT 0.892241 -56 CAATTTCAATTTCAGATTTTAACAATAAAT 1 132 0 TTCAGATTTT 0.893548 -36 ATTTATGTGGTTTATTTTTTAT 2 3 0 TTTATTTTTT 0.979472 -298 TGAATTAATATCTATTTTATTTATGTGGTT 2 21 0 TCTATTTTAT 0.874379 -280 TAGTCGTAGTTTTATTTTTCGTAATATATT 2 94 1 TTTATTTTTC 0.87438 -207 ATATTTAATAATCATACTATGGATTGTTGG 2 119 1 ATCATACTAT 0.713935 -182 TGCCATACTGTTTATTTAATATAATCCAGC 2 148 0 TTTATTTAAT 0.834854 -153 TTTCATTAAGTTCATATTATTTTTAAGGCA 2 188 1 TTCATATTAT 0.966392 -113 AATGAAGTTCTTTATTTTTTAAGTAATGCC 2 214 0 TTTATTTTTT 0.979472 -87 CTCCCCCAATTTTATTTTTTTAGGATTATT 2 277 0 TTTATTTTTT 0.979472 -24 ********** Masking position 4 Map Score: 20.9164 Number of sites scoring better than the average of aligned sites = 1658 Number in coding regions = 1234 Number in noncoding regions = 424 Number of orfs with sites within 600 bp upstream = 330 Fraction of orfs with sites within 600 bp upstream = 0.0530035 Motif number 2 CATCATTTAGATTTTTAAATATAGTATAAAT 1 16 1 ATTTTAAATA 0.951995 -152 ATATAGTATAAATCTTAGAAAGGTATAAAAA 1 34 1 AATTTAGAAA 0.745078 -134 ATATAAAAACATTGTGATATATGTACATCAT 1 93 1 ATTTGATATA 0.694402 -75 TATAATATTTATTGTTAAAATCTGAAATTGA 1 126 1 ATTTTAAAAT 0.819571 -42 TGAAATTGAAATTGCTTTAAAGGGGTAATT 1 148 1 ATTCTTTAAA 0.82348 -20 GAGGGATTGTAATGTTAATTAGTTTAGTCGT 2 70 1 AATTTAATTA 0.675886 -231 TATTAAATATATTACGAAAAATAAAACTACG 2 98 0 ATTCGAAAAA 0.928092 -203 CCATAGTATGATTATTAAATATATTACGAAA 2 110 0 ATTTTAAATA 0.952578 -191 TTAAGTTCATATTATTTTTAAGGCATTACTT 2 193 1 ATTTTTTTAA 0.615601 -108 TTTTTAAGGCATTACTTAAAAAATAAAGAAC 2 207 1 ATTCTTAAAA 0.929177 -94 GCGTCTTTCAATTAATAAAAATTTATTATGA 2 247 1 ATTATAAAAA 0.932164 -54 TTTTAGGATTATTCATAATAAATTTTTATTA 2 259 0 ATTATAATAA 0.815962 -42 TATTATGAATAATCCTAAAAAAATAAAATTG 2 270 1 AATCTAAAAA 0.929178 -31 *** ******* Masking position 1 Map Score: 9.09124 Number of sites scoring better than the average of aligned sites = 2611 Number in coding regions = 1987 Number in noncoding regions = 624 Number of orfs with sites within 600 bp upstream = 434 Fraction of orfs with sites within 600 bp upstream = 0.0697077 Motif number 3 GATTTATACTATATTTAAAAATCTAAATGA 1 18 0 ATATTTAAAA 0.935847 -150 TATCTAATAGATACTTTAAATTAGATAATA 1 66 1 ATACTTTAAA 0.946313 -102 GAAATTGAAATTGCTTTAAAGGGGTAATT 1 149 1 TTGCTTTAAA 0.843291 -19 TTTATGTGGTTTATTTTTTAT 2 2 0 TTATTTTTTA 0.670052 -299 AATAAACCACATAAATAAAATAGATATTAA 2 17 1 ATAAATAAAA 0.637101 -284 TTTTCGTAATATATTTAATAATCATACTAT 2 109 1 ATATTTAATA 0.802301 -192 GTTGGCTGGATTATATTAAATAAACAGTAT 2 144 1 TTATATTAAA 0.859782 -157 TAAGTTCATATTATTTTTAAGGCATTACTT 2 194 1 TTATTTTTAA 0.861638 -107 TTTTAAGGCATTACTTAAAAAATAAAGAAC 2 208 1 TTACTTAAAA 0.953732 -93 TAAATTTTTATTAATTGAAAGACGCCAAAA 2 242 0 TTAATTGAAA 0.805667 -59 ********** Masking position 6 Map Score: 5.41244 Number of sites scoring better than the average of aligned sites = 1840 Number in coding regions = 1353 Number in noncoding regions = 487 Number of orfs with sites within 600 bp upstream = 347 Fraction of orfs with sites within 600 bp upstream = 0.055734 Motif number 4 CATCATAATATAATATTTATTGTTAAAATCT 1 118 1 TAATATTATT 0.891376 -50 TAAATAAAATAGATATTAATTCATGCAACAG 2 28 1 AGATATTATT 0.97985 -273 AATCCCTCAGAAATATTCACTGTTGCATGAA 2 47 0 AAATATTACT 0.920772 -254 AGTATGGCAAAGAGATTGATTTCATTAAGTT 2 169 1 AGAGATTATT 0.968341 -132 TAAAAAATAAAGAACTTCATTTTGGCGTCTT 2 223 1 AGAACTTATT 0.930339 -78 TTCAATTAATAAAAATTTATTATGAATAATC 2 253 1 AAAAATTATT 0.956123 -48 ******* *** Masking position 6 Map Score: 2.77121 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 281 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 TATATTTAAAAATCTAAATGATGATATT 1 8 0 AATCTAATGA 0.82137 -160 AAAGGTATAAAAACTATCTAATAGATACTTT 1 52 1 AAACTACTAA 0.965003 -116 TAGATACTTTAAATTAGATAATATAAAAACA 1 73 1 AAATTAATAA 0.929985 -95 ATAAAAAATAAACCACATAAATAAAATAGA 2 10 1 AAACCAATAA 0.954416 -291 CCACATAAATAAAATAGATATTAATTCATGC 2 23 1 AAAATAATAT 0.728098 -278 AACTACGACTAAACTAATTAACATTACAATC 2 74 0 AAACTATTAA 0.946881 -227 TATTTTTCGTAATATATTTAATAATCATACT 2 106 1 AATATATTAA 0.759333 -195 TATTTAATATAATCCAGCCAACAATCCATAG 2 135 0 AATCCACCAA 0.556407 -166 TGGCTGGATTATATTAAATAAACAGTATGGC 2 146 1 ATATTAATAA 0.651301 -155 CATTACTTAAAAAATAAAGAACTTCATTTTG 2 216 1 AAAATAAGAA 0.816416 -85 ****** **** Masking position 6 Map Score: 2.51623 Number of sites scoring better than the average of aligned sites = 1215 Number in coding regions = 870 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 288 Fraction of orfs with sites within 600 bp upstream = 0.0462576 Motif number 6 ********** No masking Map Score: 5.06917e-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 7 ********** No masking Map Score: 5.06917e-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 8 ********** No masking Map Score: 5.06917e-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