AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i066_mjan_pyro_300.orf -o066_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ10210 108 M_jannaschii_chromosome #2 RMJ07147 170 M_jannaschii_chromosome #3 RMJ10711 205 M_jannaschii_chromosome #4 RMJ15659 136 M_jannaschii_chromosome #5 RMJ12354 24 M_jannaschii_chromosome #6 RMJ14401 113 M_jannaschii_chromosome Motif number 1 TATATGATAAAATAAAAATAACGCCCGGGA 1 80 0 AATAAAAATA 0.874925 -29 AGAAAACAAAATTAAAAATTATAAAAAT 2 9 0 ATTAAAAATT 0.978603 -162 TTTCCCTAACATTATAAAAAGAAAACAAAA 2 28 0 ATTATAAAAA 0.795329 -143 AATCATACTTAATAAAATTTCCCTAACATT 2 45 0 AATAAAATTT 0.800071 -126 TGCTATAATCATTAAAGATAATAATCAAAA 3 22 1 ATTAAAGATA 0.875371 -184 TACCTCAATTATTACAAAATGTTTTGATTA 3 43 0 ATTACAAAAT 0.934396 -163 TTTCAAAAGTATTAAAATTAATAAGGAACA 3 106 0 ATTAAAATTA 0.907823 -100 TTTGAAAGACATTAAAATTTTAAAACATTA 3 129 1 ATTAAAATTT 0.941491 -77 CATGATATTGATTTCAAAAATGATTAATGA 3 176 0 ATTTCAAAAA 0.585923 -30 AATAAGGTATATTTAAAAAT 4 1 0 ATTTAAAAAT 0.818509 -136 GTTAGCTAATATTAAAAAATAAGGTATATT 4 18 0 ATTAAAAAAT 0.968487 -119 AGATATTTAAATTAAAATTTTGCAAATATT 4 69 0 ATTAAAATTT 0.941491 -68 TAAATATCTTAATAAAGATTAAATCAATTT 4 90 1 AATAAAGATT 0.740513 -47 AAATCAATTTATTATAAATAACCTTAGAGG 4 110 1 ATTATAAATA 0.851658 -27 TGCAAATGTGATTAAAAACTAACTAAGGAA 6 27 1 ATTAAAAACT 0.905518 -87 GCCTTTCTTTATTACAAAATGTTTTACAAA 6 62 1 ATTACAAAAT 0.934396 -52 ********** Masking position 6 Map Score: 20.878 Number of sites scoring better than the average of aligned sites = 1911 Number in coding regions = 1338 Number in noncoding regions = 573 Number of orfs with sites within 600 bp upstream = 455 Fraction of orfs with sites within 600 bp upstream = 0.0730806 Motif number 2 ATCCTGGCTAGGCGACCCGGGCT 1 2 0 GGCCCCGGGC 0.997981 -107 CAGGCCAGCGCCCTATCCTGGCTAGGCGACCC 1 16 0 CCCTCCTGGC 0.979656 -93 TGAAAAAACTGGCTCCGCAGGCCAGCGCCCTA 1 33 0 GGCCGCAGGC 0.880965 -76 GGGTTCAAATCCCCTCCCGGGCGTTATTTTTA 1 66 1 CCCCCCGGGC 0.973924 -43 TATCTGGCTAGGCGACCCGGGCTTTATCATTT 2 131 0 GGCCCCGGGC 0.997981 -40 *** ******* Masking position 8 Map Score: 8.01096 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 0 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 TTATTTTTATTTTATCATATAAAGAATTGG 1 89 1 TTTATCATAT 0.786541 -20 ATTTTTATAATTTTTAATTTTGT 2 4 1 TTTATAATTT 0.587033 -167 CGACCCGGGCTTTATCATTTCTACGCCTAT 2 121 0 TTTATCATTT 0.947481 -50 TTAATCACCTTTGCTATAAT 3 1 1 TTAATCACCT 0.794659 -205 AGATAATAATCAAAACATTTTGTAATAATT 3 37 1 CAAAACATTT 0.829801 -169 CCTTATTAATTTTAATACTTTTGAAAGACA 3 110 1 TTTAATACTT 0.709864 -96 ATTAAAATTTTAAAACATTAAGTTTTTATA 3 139 1 TAAAACATTA 0.666805 -67 TATATTGTCATTAATCATTTTTGAAATCAA 3 169 1 TTAATCATTT 0.963792 -37 TACCTTATTTTTTAATATTAGCTAACACAA 4 22 1 TTTAATATTA 0.479901 -115 GCTAACACAACTTAACATTTTATGCTAAAT 4 42 1 CTTAACATTT 0.896601 -95 ACATTTTATGCTAAATATTTGCAAAATTTT 4 56 1 CTAAATATTT 0.768338 -81 AAATTTTAATTTAAATATCTTAATAAAGAT 4 79 1 TTAAATATCT 0.7125 -58 TAATAAAGATTAAATCAATTTATTATAAAT 4 99 1 TAAATCAATT 0.540209 -38 TAGTTAGTTTTTAATCACATTTGCAAAGAA 6 22 0 TTAATCACAT 0.714438 -92 TAGCTCTTTGTAAAACATTTTGTAATAAAG 6 68 0 TAAAACATTT 0.920199 -46 ********** Masking position 4 Map Score: 7.66889 Number of sites scoring better than the average of aligned sites = 1767 Number in coding regions = 1463 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 270 Fraction of orfs with sites within 600 bp upstream = 0.0433665 Motif number 4 TTATTTTATCATATAAAGAATTGG 1 95 1 ATATAAAGAA 0.527961 -14 ACATTATAAAAAGAAAACAAAATTAAAAAT 2 20 0 AAGAAAACAA 0.625354 -151 TGAGTATCAATAGAAAAGAAGTATAAAAGA 2 74 1 TAGAAAAGAA 0.906622 -97 AGAAAAGAAGTATAAAAGAACAAAAATTGC 2 85 1 TATAAAAGAA 0.811672 -86 CTACGCCTATTAATAAGCAATTTTTGTTCT 2 101 0 TAATAAGCAA 0.923722 -70 TTAATAGGCGTAGAAATGATAAAGCCCGGG 2 118 1 TAGAAATGAT 0.5545 -53 TCATTAAAGATAATAATCAAAACATTTTGT 3 30 1 TAATAATCAA 0.884189 -176 ATAATTGAGGTATTAATGAACGCCTTCTAT 3 61 1 TATTAATGAA 0.8377 -145 GTATTAAAATTAATAAGGAACACTTGAACG 3 98 0 TAATAAGGAA 0.967161 -108 TAATATTAAAAAATAAGGTATATTTAAAAA 4 12 0 AAATAAGGTA 0.697917 -125 TTAAATATCTTAATAAAGATTAAATCAATT 4 89 1 TAATAAAGAT 0.836096 -48 ATATAAAAATCTAATGGGGATAA 5 4 1 TAAAAATCTA 0.449681 -21 ATTAAAAACTAACTAAGGAAAGTATGCCTT 6 37 1 AACTAAGGAA 0.742041 -77 AAACATTTTGTAATAAAGAAAGGCATACTT 6 56 0 TAATAAAGAA 0.964518 -58 ********** Masking position 5 Map Score: 7.34991 Number of sites scoring better than the average of aligned sites = 2019 Number in coding regions = 1691 Number in noncoding regions = 328 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 5 AGCCCGGGTCGCCTAGCCAGGATAGGGC 1 9 1 TCGCCTAGCC 0.991767 -100 AAAGCCCGGGTCGCCTAGCCAGATAGCATG 2 138 1 TCGCCTAGCC 0.991767 -33 TCATCATCTCGCCCATGCTATCTGGCTA 2 153 0 TCGCCCATGC 0.986527 -18 TTAATCACCTTTGCTATAATCATT 3 5 1 TCACCTTTGC 0.980518 -201 TAGTTTTTAATCACATTTGCAAAGAACTAT 6 18 0 TCACATTTGC 0.905991 -96 ********** Masking position 1 Map Score: 4.01331 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 CGCCCTATCCTGGCTAGGCGACCCGGGCT 1 10 0 TGGCTAGGCG 0.973912 -99 AAATTGCTTATTAATAGGCGTAGAAATGAT 2 108 1 TTAATAGGCG 0.868879 -63 CCATGCTATCTGGCTAGGCGACCCGGGCTT 2 139 0 TGGCTAGGCG 0.973912 -32 CTAGCCAGATAGCATGGGCGAGATGATGA 2 152 1 AGCATGGGCG 0.983761 -19 TAATGATTATAGCAAAGGTGATTAA 3 6 0 AGCAAAGGTG 0.953466 -200 TGAAATCAATATCATGGGTGTAATGT 3 190 1 ATCATGGGTG 0.896418 -16 AATAGTTCTTTGCAAATGTGATTAAAAACT 6 17 1 TGCAAATGTG 0.775935 -97 ********** Masking position 8 Map Score: 2.33098 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 61 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 TGTTCTTTTATACTTCTTTTCTATTGATAC 2 77 0 TACTTCTTTT 0.93572 -94 TAAGCAATTTTTGTTCTTTTATACTTCTTT 2 88 0 TTGTTCTTTT 0.939682 -83 AAAACCAATAGTTCTTTGCAAATGTGAT 6 9 1 TAGTTCTTTG 0.991415 -105 TAGTTATTTGTAGCTCTTTGTAAAACATTT 6 78 0 TAGCTCTTTG 0.98114 -36 ACACCAAAAATAGTTATTTGTAGCTCTTTG 6 88 0 TAGTTATTTG 0.956765 -26 ********** Masking position 5 Map Score: 3.86104 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 36 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 GGAGGGGATTTGAACCCCTGAAAAAACTGG 1 53 0 TGAACCCCTG 0.986977 -56 GAGGTATTAATGAACGCCTTCTATAAGAAG 3 67 1 TGAACGCCTT 0.994007 -139 AAGGAACACTTGAACGTCTTCTTATAGAAG 3 84 0 TGAACGTCTT 0.983805 -122 ********** Masking position 4 Map Score: 0.51562 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 3 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 ********** No masking Map Score: 9.40348e-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: 9.40348e-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: 9.40348e-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