AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i277_hypothetical21_mjan_reg_300.orf -o277_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 RMJ05553 32 M_jannaschii_chromosome #2 RMJ08933 20 M_jannaschii_chromosome #3 RMJ14466 42 M_jannaschii_chromosome #4 RMJ13617 163 M_jannaschii_chromosome #5 RMJ06576 178 M_jannaschii_chromosome #6 RMJ11498 66 M_jannaschii_chromosome Motif number 1 TTTAATTTTTATAAATTTTTG 1 2 1 TTAATTTTTA 0.983653 -31 TTAATTTTTATAAATTTTTGGAATATCTGA 1 12 1 TAAATTTTTG 0.91379 -21 ATTATTTTTAATTTTTAATTTTTCTTT 3 8 1 TTAATTTTTA 0.983653 -35 TTCGCAGGAATAAATTTTTATTGAACAATG 4 20 1 TAAATTTTTA 0.914351 -144 CTATTAAAAGATAATCTTTAAATATAATGA 4 101 1 ATAATCTTTA 0.961497 -63 ATTAGAATATTAAATTTATAACTTTACAAA 5 66 0 TAAATTTATA 0.889889 -113 ATGCAAACACAAAAGTTCTATTAGATACTA 5 101 1 AAAAGTTCTA 0.817739 -78 GTAGCAAAAAATAGTTTTTAGTATCTAATA 5 119 0 ATAGTTTTTA 0.885512 -60 TGCTACTTTTATAATTTTTAAAGAACAATT 5 143 1 ATAATTTTTA 0.976166 -36 AAAAAACATCTAAAGCTTTATATACAAATA 6 21 1 TAAAGCTTTA 0.499132 -46 AAATATAAGCTTAAGCTTTATATATAGATT 6 46 1 TTAAGCTTTA 0.698438 -21 ********** Masking position 3 Map Score: 17.6121 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 607 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 2 CAGATATTCCAAAAATTTATAAAAATTAAA 1 5 0 AAATAAAAAT 0.967306 -28 TAATAAGAGGGTGAAAATAA 2 3 1 ATAAGAAAAT 0.973789 -18 AAAAAGAAAAATTAAAAATTAAAAATAAT 3 4 0 ATAAAAAAAT 0.98683 -39 TTTAGGTATCATTGTTCAATAAAAATTTATTCCTGC 4 23 0 ATGTAAAAAT 0.876516 -141 AGTCTATATTATTAAATTTGGAAAATAGATGCCTTT 4 56 0 ATAAGAAAAT 0.973779 -108 TATTAAATTTATAACTTTACAAAAATATGGATATCG 5 53 0 ATATAAAAAT 0.989289 -126 CAAAAGTTCTATTAGATACTAAAAACTATTTTTTGC 5 110 1 ATAAAAAAAC 0.946685 -69 TAAAAATTATAAAAGTAGCAAAAAATAGTTTTTAGT 5 127 0 AAATAAAAAT 0.967306 -52 CTACTCTTCAATTGTTCTTTAAAAATTATAAAAGTA 5 146 0 ATGTAAAAAT 0.876516 -33 ** * * ****** Masking position 12 Map Score: 13.0834 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 263 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 3 AATAGGACTTTCGCAGGAATAAATT 4 2 1 ATAGGACTGA 0.9978 -162 ATAAATTTTTATTGAACAATGATACCTAAAGGCA 4 29 1 ATTGAACTAA 0.910013 -135 TTATCTTTTAATAGGACTTTCGCAGTCTATATTA 4 81 0 ATAGGACTGA 0.9978 -83 ATAGAACTCTCGTAATGAATAAAT 5 1 1 ATAGAACTGA 0.997344 -178 TTGTGTTTGCATATGACATTAGAATATTAAATTT 5 79 0 ATATGACTGA 0.983284 -100 TTAGTATCTAATAGAACTTTTGTGTTTGCATATG 5 98 0 ATAGAACTGG 0.99142 -81 TATAATTTTTAAAGAACAATTGAAGAGTAGGATA 5 152 1 AAAGAACTGA 0.987336 -27 ******* * * * Masking position 6 Map Score: 12.2818 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 21 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 ATTATTTTTAATTTTTAATTTTTCTTTTTA 3 11 1 ATTTTTAATT 0.912986 -32 CGCAGTCTATATTATTAAATTTGGAAAATA 4 65 0 ATTATTAAAT 0.854624 -99 TTTAAAGATTATCTTTTAATAGGACTTTCG 4 93 0 ATCTTTTAAT 0.945331 -71 TTAAAAGATAATCTTTAAATATAATGATAT 4 104 1 ATCTTTAAAT 0.969682 -60 TTGCCAATAAATTATTTATTCATTACGAGA 5 18 0 ATTATTTATT 0.590268 -161 ATTTTTGTAAAGTTATAAATTTAATATTCT 5 63 1 AGTTATAAAT 0.722351 -116 AGCAAAAAATAGTTTTTAGTATCTAATAGA 5 117 0 AGTTTTTAGT 0.825413 -62 TACTTTTATAATTTTTAAAGAACAATTGAA 5 146 1 ATTTTTAAAG 0.879286 -33 AAACATCTAAAGCTTTATATACAAATATAA 6 24 1 AGCTTTATAT 0.922138 -43 TATAAGCTTAAGCTTTATATATAGATTT 6 49 1 AGCTTTATAT 0.922138 -18 ********** Masking position 6 Map Score: 7.88389 Number of sites scoring better than the average of aligned sites = 2066 Number in coding regions = 1547 Number in noncoding regions = 519 Number of orfs with sites within 600 bp upstream = 450 Fraction of orfs with sites within 600 bp upstream = 0.0722775 Motif number 5 TTCGCAGTCTATATTATTAAATTTGGAAAATA 4 65 0 ATATTTAAAT 0.902339 -99 TTAACTAATTATATCATTATATTTAAAGATTA 4 112 0 ATATCTATAT 0.77797 -52 AAAAATATGGATATCGACATATTGCCAATAAA 5 37 0 ATATCCATAT 0.767959 -142 GCTTAAGCTTATATTTGTATATAAAGCTTTAG 6 30 0 ATATTTATAT 0.767689 -37 AAATCTATATATAAAGCTTAAG 6 55 0 AAATCTATAT 0.943495 -12 ***** ***** Masking position 4 Map Score: 2.55305 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 35 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 AATAGGACTTTCGCAGGAATAAATTTT 4 8 1 CTTTCGCAGG 0.975121 -156 TTTAATAGGACTTTCGCAGTCTATATTATT 4 79 0 CTTTCGCAGT 0.991115 -85 ATGGTTGTGGCATTGGCATTAACTAATTAT 4 132 0 CATTGGCATT 0.977684 -32 ATAAATAATTTATTGGCAATATGTCGATAT 5 29 1 TATTGGCAAT 0.917602 -150 ********** Masking position 4 Map Score: 0.118478 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 69 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 ********** No masking Map Score: 6.56131e-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: 6.56131e-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 9 ********** No masking Map Score: 6.56131e-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