AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_mjan_reg_300.orf -o150_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 RMJ14255 46 M_jannaschii_chromosome #2 RMJ07874 39 M_jannaschii_chromosome #3 RMJ02086 103 M_jannaschii_chromosome #4 RMJ01059 65 M_jannaschii_chromosome #5 RMJ11240 103 M_jannaschii_chromosome #6 RMJ01575 88 M_jannaschii_chromosome #7 RMJ04104 300 M_jannaschii_chromosome #8 RMJ09479 80 M_jannaschii_chromosome #9 RMJ15216 108 M_jannaschii_chromosome Motif number 1 AAGAGTTTGTAAAGTTTTAAGGAAAGGAAT 1 11 0 AAAGTTTTAA 0.950648 -36 ATTTTTATAAAAATTTTTAAATTCAAAGAA 4 24 0 AAATTTTTAA 0.974026 -42 TGTTAAAATTAAATTTTTATAAAAATTTTT 4 36 0 AAATTTTTAT 0.95825 -30 TGAGTATTGGAAAGATTTAAATAATCTTGA 5 17 0 AAAGATTTAA 0.900228 -87 TTTTTTGTTTTTATATTTTATTGTTATATT 5 46 0 TTATATTTTA 0.480771 -58 CATTTTTGTCTAAGTTTTAAGTTGTATTTT 5 72 0 TAAGTTTTAA 0.931775 -32 ACTCTATCAAATATTTTTAATA 6 3 0 ATATTTTTAA 0.92391 -86 TATGTATATAAAATTTTTTATCTCTGACTC 6 29 0 AAATTTTTTA 0.896635 -60 CAGTTATTGGTAATATTTTAAAATAGGGTT 6 58 0 TAATATTTTA 0.741902 -31 TTTAAAAACGAAATTTTTAA 7 1 0 AAATTTTTAA 0.974026 -300 TTTAAAATTGTAATCTTTATTAATTTAAAT 7 25 1 TAATCTTTAT 0.736421 -276 TTTTAGGTAATAATATTTATTAATTTAAAT 7 47 0 TAATATTTAT 0.883792 -254 ACTTATTAATATATATTTATCTTTTGCACG 7 222 0 ATATATTTAT 0.77615 -79 TATAACCATTAAATTTTTATGTTATAACGT 8 12 1 AAATTTTTAT 0.95825 -69 ACGTTGCTAATAATTTTTACTTATAAAAGT 8 38 1 TAATTTTTAC 0.833555 -43 TTATTTATAATTAGTTTTAAAATCTCTTAC 9 60 1 TTAGTTTTAA 0.815574 -49 AAAAAGGTCTAAATTTTTATGTAAGAGATT 9 80 0 AAATTTTTAT 0.95825 -29 ********** Masking position 6 Map Score: 25.3444 Number of sites scoring better than the average of aligned sites = 1633 Number in coding regions = 1057 Number in noncoding regions = 576 Number of orfs with sites within 600 bp upstream = 450 Fraction of orfs with sites within 600 bp upstream = 0.0722775 Motif number 2 AAGATTACGATAAAACCAATAAAAACGTTAA 2 19 1 TAAAACAATA 0.893823 -21 TAAAAATTTTTAAATTCAAAGAAGGAGCTGA 4 16 0 TAAATCAAAG 0.705311 -50 CAATACTCAATATAACAATAAAATATAAAAA 5 38 1 TATAAAATAA 0.899204 -66 CAATAAAATATAAAAACAAAAAATACAACTT 5 53 1 TAAAACAAAA 0.966406 -51 TAAAAAATTTTATATACATAACCCTATTTTA 6 39 1 TATATCATAA 0.904397 -50 ATTACAATTTTAAAAACGAAATTTTTAA 7 8 0 TAAAACGAAA 0.807556 -293 TTTATTAATTTAAATTAATAAATATTATTAC 7 40 1 TAAATAATAA 0.870132 -261 TATTATTACCTAAAATAAAAATGGTGCAGGG 7 62 1 TAAAAAAAAA 0.939293 -239 AAGATAAATATATATTAATAAGTTTTCCCAT 7 229 1 TATATAATAA 0.83573 -72 CTATAACCATTAAATTTTTATG 8 2 1 TATAACATTA 0.829168 -79 AGCAACGTTATAACATAAAAATTTAATGGTT 8 15 0 TAACAAAAAA 0.692969 -66 TCTCCACTTTTATAAGTAAAAATTATTAGCA 8 42 0 TATAATAAAA 0.709234 -39 TAGCTTACTCTATAATCAAAACCATAATTTA 9 32 1 TATAACAAAA 0.956224 -77 AAACTAATTATAAATAAATTATGGTTTTGAT 9 46 0 TAAATAATTA 0.661598 -63 ***** ***** Masking position 2 Map Score: 11.2233 Number of sites scoring better than the average of aligned sites = 1384 Number in coding regions = 1064 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 3 ACTTCCACCTGCAGTTATTGGTAAT 6 74 0 CACCTGCAGT 0.9478 -15 CAAATCCCCTCCCCTGCACCATTTTTATTT 7 74 0 CCCCTGCACC 0.998671 -227 GGGATTTGAACCCCCGAACCCCTACGGGAC 7 96 1 CCCCCGAACC 0.984823 -205 GGCTTGGCGACCCCTGCACCGCAAGCGAAT 7 154 1 CCCCTGCACC 0.998671 -147 CATGTAAATCCCTCTCCACTTTTATAAGTA 8 55 0 CCTCTCCACT 0.9478 -26 ********** Masking position 8 Map Score: 4.95767 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 11 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TCCATAGGAAAACCCTATTGAAATACCGAA 3 43 0 AACCCTATTG 0.947982 -61 TATTAAAAATATTTGATAGAGTCA 6 5 1 AAAAATATTT 0.836694 -84 TTATATACATAACCCTATTTTAAAATATTA 6 48 1 AACCCTATTT 0.983308 -41 ATAATTATAAAAACCTATTTAAATAGGAAA 7 258 1 AAACCTATTT 0.978492 -43 TTTAAATAGGAAACATATTTCCTCCTGAGG 7 275 1 AAACATATTT 0.926691 -26 CTATAATCAAAACCATAATTTATTTATAAT 9 41 1 AACCATAATT 0.925651 -68 AAGAGATTTTAAAACTAATTATAAATAAAT 9 58 0 AAAACTAATT 0.853295 -51 ********** Masking position 7 Map Score: 7.63423 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 124 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AACAAGATACTAATTGCCTCTCTAATGAATTC 3 14 1 TAATGCCTCC 0.973881 -90 AACTTCTCTGTAATTCTCGCCCTCCATAGGAA 3 63 0 TAATCTCGCC 0.977827 -41 TCGGGGGTTCAAATCCCCTCCCCTGCACCATT 7 81 0 AAACCCCTCC 0.96291 -220 GACCGGATCTTAAGTCCGGCGCCTTTGGCCAG 7 123 1 TAATCCGGCC 0.961671 -178 ATCTATTCTATAATTCGCTTGCGGTGCAGGGG 7 164 0 TAATCGCTTC 0.937603 -137 TCTCTGCATGTAAATCCCTCTCCACTTTTATA 8 59 0 TAATCCCTCC 0.99487 -22 AATTAGTTTTAAAATCTCTTACATAAAAATTT 9 68 1 AAATCTCTTC 0.88607 -41 *** ****** * Masking position 3 Map Score: 3.23246 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 173 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TTAACGTTTTTATTGGTTTTATCGTAATC 2 21 0 TTATTGGTTT 0.897144 -19 GTTTTTATATTTTATTGTTATATTGAGTAT 5 40 0 TTTATTGTTA 0.844604 -64 TTAAGTTGTATTTTTTGTTTTTATATTTTA 5 56 0 TTTTTTGTTT 0.889446 -48 CCACCTGCAGTTATTGGTAATATTTTAAAA 6 65 0 TTATTGGTAA 0.87008 -24 ACCATTTTTATTTTAGGTAATAATATTTAT 7 57 0 TTTTAGGTAA 0.883913 -244 ATATATATACTTTTCGGTTTCGTGCAAAAG 7 202 1 TTTTCGGTTT 0.853292 -99 ACATAAAAATTTAATGGTTATAG 8 4 0 TTAATGGTTA 0.854914 -77 ACCATTAAATTTTTATGTTATAACGTTGCT 8 16 1 TTTTATGTTA 0.860699 -65 TTATAAATAAATTATGGTTTTGATTATAGA 9 40 0 ATTATGGTTT 0.525678 -69 AGGTCTAAATTTTTATGTAAGAGATTTTAA 9 76 0 TTTTATGTAA 0.736672 -33 AATTTAGACCTTTTTGGTGAAAAG 9 95 1 TTTTTGGTGA 0.907959 -14 ********** Masking position 8 Map Score: 7.00493 Number of sites scoring better than the average of aligned sites = 827 Number in coding regions = 658 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 7 ATCATCACCTCAAATAAAGAGT 1 35 0 CATCACCTCA 0.887853 -12 CAATTTCACCTGTTAAAATTAAA 4 53 0 TTTCACCTGT 0.923914 -13 ATAATATCACCTCATTTTTGTCTA 5 90 0 TATCACCTCA 0.921661 -14 ACTTCCACCTGCAGTTATTGGT 6 77 0 TTCCACCTGC 0.975608 -12 GTTCAAATCCCCTCCCCTGCACCATTTTTA 7 77 0 CCTCCCCTGC 0.91553 -224 GGAAACATATTTCCTCCTGAGGTAAAGT 7 283 1 TTCCTCCTGA 0.962767 -18 AATATCCCTCCTGATATTTTATAG 9 5 1 TCCCTCCTGA 0.965414 -104 ********** Masking position 8 Map Score: 1.95572 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 61 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 ********** No masking Map Score: 6.77448e-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: 6.77448e-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 10 ********** No masking Map Score: 6.77448e-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