AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifnr_mjan_opreg_300.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0020 300 asparaginase (ansA) #2 MJ0076 80 conserved hypothetical protein) #3 MJ0292 186 conserved hypothetical protein #4 MJ0649 172 NADH oxidase (nox) #5 MJ0792 300 M. jannaschii predicted coding region MJ0792 #6 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #7 MJ0793 60 M. jannaschii predicted coding region MJ0793 #8 MJ0794 48 M. jannaschii predicted coding region MJ0794 #9 MJ0795 79 M. jannaschii predicted coding region MJ0795 #10 MJ0965 38 uroporphyrin-III C-methyltransferase (cobA) #11 MJ1225 80 conserved hypothetical protein Motif number 1 AAGTTCCTTAATATATTTAAATTGCATTCAA 1 11 1 ATATTTTAAA 0.862927 -290 CGCAGGAATAAAATCTTTAAAGGAAAGTTTA 1 47 0 AAATTTTAAA 0.929503 -254 TTTTATATTTAAATATATAAATTAATATTTG 1 199 0 AAATTATAAA 0.862927 -102 TTATATATTTAAATATAAAAATTTATATGAT 1 210 1 AAATTAAAAA 0.942103 -91 TAGGGTATAAAAATTATAAAAAGATAGCTAT 1 239 0 AAATATAAAA 0.971494 -62 AATCTAAAATAAATCATAAAATATATATACT 2 29 1 AAATATAAAA 0.971494 -52 ATTATCACCAAAAGTTATAAATAAGATTTAT 3 136 1 AAAGTATAAA 0.681545 -51 TAAGATTATTAAATAATAAAAGAGGGGATAG 4 12 0 AAATATAAAA 0.971494 -161 ATTACTAAAAATAACTTAAAAATAGAATAAG 4 39 0 ATAATTAAAA 0.820817 -134 TGATCATCAAAAAGGATAAAAAATAAT 4 156 1 AAAGATAAAA 0.920546 -17 TTATAATTTTATATCAAAAAATGAAATATAA 5 22 0 ATATAAAAAA 0.885968 -279 TTTTGATATAAAATTATAAAATAGTTAAAAA 5 34 1 AAATATAAAA 0.971494 -267 TAAAACAATTATAACTTTAAAAAAGTAAATT 5 66 0 ATAATTTAAA 0.639282 -235 TTAGAATTTTTAATAATAAAACAATTATAAC 5 82 0 TAATATAAAA 0.676881 -219 AAAAATTCTAATAAGTTAAAAATTTTAACAT 5 102 1 ATAATTAAAA 0.820817 -199 AGTAAATTATATATGTTAAAATTTTTAACTT 5 114 0 ATATTTAAAA 0.942104 -187 ATTATGATTTAAAGTTAAATAGTAAATTATA 5 134 0 AAAGTAAATA 0.486716 -167 ATTTAACTTTAAATCATAATATATATAGAGG 5 145 1 AAATATAATA 0.853841 -156 GGCACCATACAAAAAATTAAAGAATAGTTGG 5 218 1 AAAAATTAAA 0.787766 -83 AAAATTATTAAAATTAAAAAAGAAAAACATT 6 12 0 AAATAAAAAA 0.942103 -57 CACCTAAAAAATATCAAAAAATTATTAAAAT 6 29 0 ATATAAAAAA 0.885968 -40 ACGTTAAATGAAATATTAATATTATGTGTAA 11 16 1 AAATTTAATA 0.85384 -65 **** ****** Masking position 3 Map Score: 27.4059 Number of sites scoring better than the average of aligned sites = 2341 Number in coding regions = 1629 Number in noncoding regions = 712 Number of orfs with sites within 600 bp upstream = 470 Fraction of orfs with sites within 600 bp upstream = 0.0754899 Motif number 2 AAGTTCCTTAATATATTTAAATTGCATTC 1 8 1 TTAATATATA 0.803559 -293 CTTCGCAGGAATAAAATCTTTAAAGGAAAGTT 1 49 0 ATAAAATCTA 0.728312 -252 TAGCTTTAAGTATATATACTTACCTCAATAGG 1 82 0 TATATATATA 0.411976 -219 TTAAAGCTACTTAATATATTTATGGCGGATGA 1 105 1 TTAATATATA 0.803559 -196 TATTTAAATATATAAATTAATATTTGCAAAAT 1 193 0 TATAAATTTA 0.780654 -108 TATTTAAATATAAAAATTTATATGATAGCTAT 1 215 1 TAAAAATTTA 0.521677 -86 AAAAATTATAAAAAGATAGCTATCATATAAAT 1 230 0 AAAAGATATA 0.635812 -71 AAAATAAATCATAAAATATATATACTATCTTG 2 34 1 ATAAAATATA 0.919644 -47 TATTAATCATTATAAATTCCTAATAAG 3 170 1 TATAAATTTA 0.789204 -17 TAAAAATAGAATAAGATTATTAAATAATAAAA 4 22 0 ATAAGATTTA 0.822091 -151 ATAATTGTGAAATAAATTTCTAATATATTACT 4 64 0 AATAAATTTA 0.821696 -109 GAACTTAACCAAAAAGTTTTTATAGAACTTCT 4 106 0 AAAAAGTTTA 0.681851 -67 ATATAAAATTATAAAATAGTTAAAAATAATTT 5 39 1 ATAAAATATA 0.919972 -262 TTTTAACTTATTAGAATTTTTAATAATAAAAC 5 91 0 TTAGAATTTA 0.734456 -210 ATTATATATGTTAAAATTTTTAACTTATTAGA 5 108 0 TTAAAATTTA 0.826678 -193 ACTTTAAATCATAATATATATAGAGGTTTTGT 5 150 1 ATAATATATA 0.82557 -151 ATATAGAGGTTTTGTATTATTACATTTGTGAA 5 167 1 TTTGTATTTA 0.452721 -134 AAAAAATATCAAAAAATTATTAAAATTAAAAA 6 23 0 AAAAAATTTA 0.925336 -46 AATAATGATGATAAAATAAATAATAACTTTAA 7 26 1 ATAAAATATA 0.919981 -35 ATACAGTGTATTAAAGTTACTATAAAATGAGG 9 51 1 TTAAAGTTTA 0.783242 -29 CCCATAAAAATTAGTATTAGAAGCTA 10 5 1 TAAAAATTTA 0.929875 -34 ATTCTTACACATAATATTAATATTTCATTTAA 11 19 0 ATAATATTTA 0.890827 -62 TAAATTTAAATTTGAATTCTTACACATAATAT 11 34 0 TTTGAATTTA 0.639598 -47 ******** ** Masking position 7 Map Score: 22.153 Number of sites scoring better than the average of aligned sites = 1498 Number in coding regions = 1021 Number in noncoding regions = 477 Number of orfs with sites within 600 bp upstream = 410 Fraction of orfs with sites within 600 bp upstream = 0.0658529 Motif number 3 ATCTAAAATAAATCATAAAATATATATACTAT 2 30 1 AATCATAATA 0.750423 -51 AAGATTATTAAATAATAAAAGAGGGGATAGT 4 10 0 AATAATAAGA 0.857604 -163 AAAATAACTTAAAAATAGAATAAGATTATTAA 4 31 0 AAAAATAATA 0.961695 -142 AGAACTTCTAACTAATACAATAATTGTGAAAT 4 83 0 ACTAATAATA 0.945473 -90 TTTTATATCAAAAAATGAAATATAACATAATC 5 15 0 AAAAATAATA 0.961695 -286 TTTGATATAAAATTATAAAATAGTTAAAAATA 5 35 1 AATTATAATA 0.669691 -266 TAGAATTTTTAATAATAAAACAATTATAACTT 5 80 0 AATAATAACA 0.765956 -221 TTTATTATTAAAAATTCTAATAAGTTAAAAAT 5 93 1 AAAATTAATA 0.824908 -208 CACATTTTTCACAAATGTAATAATACAAAACC 5 174 0 ACAAATAATA 0.958046 -127 GCACCATACAAAAAATTAAAGAATAGTTGGCG 5 219 1 AAAAATAAGA 0.888041 -82 TGTTACTTCAACTATTTAAATC 8 1 0 ACTATTAATC 0.485721 -48 AGTTGAAGTAACAAATACAATCATTGAAAAAT 8 20 1 ACAAATAATC 0.86891 -29 ACAATCATTGAAAAATCTAATAG 8 36 1 AAAAATAATA 0.961695 -13 TATAGTTGATACAAACCAAATATAACTGTTGG 9 22 0 ACAAACAATA 0.769112 -58 ****** **** Masking position 9 Map Score: 12.5511 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 307 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 AAGAATCAGTTTTTAAGGTGGAACG 1 286 1 TTTTAAGGTG 0.979708 -15 TTAGATTTAGTATTATGGTGAAAGA 2 6 0 TATTATGGTG 0.962014 -75 CTCAAATCTTTATTAAAGTGAGGTTGTCTT 3 52 1 TATTAAAGTG 0.960895 -135 TAATTTACTTTTTTAAAGTTATAATTGTTT 5 65 1 TTTTAAAGTT 0.828732 -236 CTTTAATTTTTTGTATGGTGCCCCTATTAT 5 210 0 TTGTATGGTG 0.925258 -91 ATTGCCACCTCTTAAGGTGGTTGTGTAGG 5 282 0 TCTTAAGGTG 0.956042 -19 TTTTTGATATTTTTTAGGTGATATAATGGG 6 40 1 TTTTTAGGTG 0.883867 -29 CATTATTGTATAGTATAGTGTT 7 3 0 TAGTATAGTG 0.863021 -58 CTATACAGTGTATTAAAGTTACTATAAAAT 9 49 1 TATTAAAGTT 0.828731 -31 ********** Masking position 4 Map Score: 8.04404 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 63 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 TATACCCTAATCTATAACAATCTCTAAGAAT 1 261 1 TTATAACAAT 0.800354 -40 TCTTTCACCATAATACTAAAT 2 1 1 TTTTCACCAT 0.959631 -80 ACCTCGCTCGGGTATCCCAATAGGGGTTTTC 3 86 1 GTATCCCAAT 0.780535 -101 CCCAATAGGGGTTTTCCCCATGGCAATATAA 3 101 1 GTTTCCCCAT 0.807636 -86 ATATAAGCCTATTATCACCAAAAGTTATAAA 3 126 1 ATATCACCAA 0.57198 -61 CCTCTTTTATTATTTAATAATCTTATTCTAT 4 18 1 TTTTAATAAT 0.506117 -155 ATTAGAAATTTATTTCACAATTATTGTATTA 4 72 1 TTTTCACAAT 0.958884 -101 TTTATAATTTTATATCAAAAAATGAAATATA 5 23 0 TTATCAAAAA 0.446778 -278 CTTATTAGAATTTTTAATAATAAAACAATTA 5 86 0 TTTTAATAAT 0.505158 -215 ATTTTCCACATTTTTCACAAATGTAATAATA 5 181 0 TTTTCACAAA 0.914569 -120 TATCACCCATTATATCACCTAAAAAATATCA 6 44 0 TTATCACCTA 0.502706 -25 TATTATTTATTTTATCATCATTATTGTATAG 7 20 0 TTATCATCAT 0.819055 -41 GGTTTCACAATTGTTAAAGTT 7 50 0 GTTTCACAAT 0.928782 -11 * ********* Masking position 5 Map Score: 2.98452 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 625 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 6 CAGGAATAAAATCTTTAAAGGAAAGTTTAA 1 46 0 ATCTTTAAAG 0.673379 -255 TCGCCCATCAATCATCATAGCTCAGCAGCT 1 147 0 ATCATCATAG 0.86736 -154 ATGCTCTCAAATCTTTATTAAAGTGAGGTT 3 47 1 ATCTTTATTA 0.642927 -140 TAAGCCTATTATCACCAAAAGTTATAAATA 3 129 1 ATCACCAAAA 0.792224 -58 AATAAGATTTATCATTATTAATCATTATAA 3 155 1 ATCATTATTA 0.878887 -32 ATCATTATTAATCATTATAAATTCCTAATA 3 165 1 ATCATTATAA 0.947967 -22 CAAAATCATGATCATCAAAAAGGATAAAAA 4 148 1 ATCATCAAAA 0.952934 -25 TAATTGTTTTATTATTAAAAATTCTAATAA 5 86 1 ATTATTAAAA 0.769337 -215 ATATCAAAAAATTATTAAAATTAAAAAAGA 6 20 0 ATTATTAAAA 0.769337 -49 TATTTATTTTATCATCATTATTGTATAGTA 7 18 0 ATCATCATTA 0.871573 -43 AACAAATACAATCATTGAAAAATCTAATAG 8 29 1 ATCATTGAAA 0.803036 -20 ********** Masking position 1 Map Score: 6.51762 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 515 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 7 ATACTTACCTCAATAGGACTTCGCAGGAAT 1 69 0 CAATAGGACT 0.952943 -232 GAGAGCATATCAATAGGAGCAAAACCCTTG 3 25 0 CAATAGGAGC 0.988231 -162 TCGGGTATCCCAATAGGGGTTTTCCCCATG 3 93 1 CAATAGGGGT 0.988231 -94 ATGTGGAAAATAATAGGGGCACCATACAAA 5 201 1 TAATAGGGGC 0.970319 -100 ********** Masking position 5 Map Score: 0.573448 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 17 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 GACGCCACTTTTTATTTTGCAAATATTAATT 1 180 1 TTTATTTTCA 0.625926 -121 TTTTGCAAATATTAATTTATATATTTAAATA 1 194 1 ATTAATTTTA 0.799234 -107 TAGCTATCATATAAATTTTTATATTTAAATA 1 215 0 ATAAATTTTA 0.713095 -86 TAGATTTAGTATTATGGTGAAAGA 2 4 0 ATTATGGTAA 0.289229 -77 TATTTTATGATTTATTTTAGATTTAGTATTA 2 21 0 TTTATTTTGA 0.476223 -60 TCACCGTGTAATACTTTTATACAAGATAGTA 2 56 0 ATACTTTTTA 0.796261 -25 CCCCTCTTTTATTATTTAATAATCTTATTCT 4 16 1 ATTATTTATA 0.724849 -157 TAATTGTGAAATAAATTTCTAATATATTACT 4 64 0 ATAAATTTTA 0.713096 -109 AACTAATACAATAATTGTGAAATAAATTTCT 4 75 0 ATAATTGTAA 0.471952 -98 ATTATTTTTTATCCTTTTTGA 4 162 0 ATTATTTTTA 0.956562 -11 TATTGATTATGTTATATTTCATTTTT 5 6 1 ATTATGTTTA 0.862254 -295 TAACTATTTTATAATTTTATATCAAAAAATG 5 30 0 ATAATTTTTA 0.932199 -271 AAAAAAGTAAATTATTTTTAACTATTTTATA 5 48 0 ATTATTTTAA 0.826417 -253 TAAAAATAATTTACTTTTTTAAAGTTATAAT 5 59 1 TTACTTTTTA 0.559936 -242 TTTAACATATATAATTTACTATTTAACTTTA 5 125 1 ATAATTTATA 0.621893 -176 CTCTATATATATTATGATTTAAAGTTAAATA 5 144 0 ATTATGATTA 0.32145 -157 TGGTGCCCCTATTATTTTCCACATTTTTCAC 5 194 0 ATTATTTTCA 0.837122 -107 AAATGTTTTTCTTTTTTAATTTTAATAA 6 8 1 TTTCTTTTTA 0.670833 -61 TTTAATTTTAATAATTTTTTGATATTTTTTA 6 25 1 ATAATTTTTG 0.580261 -44 TTTTATCATCATTATTGTATAGTATAGTGTT 7 11 0 ATTATTGTTA 0.86879 -50 AAAGTTATTATTTATTTTATCATCATTATTG 7 25 0 TTTATTTTTC 0.418901 -36 ******** ** Masking position 2 Map Score: 12.0342 Number of sites scoring better than the average of aligned sites = 1853 Number in coding regions = 1323 Number in noncoding regions = 530 Number of orfs with sites within 600 bp upstream = 403 Fraction of orfs with sites within 600 bp upstream = 0.0647286 Motif number 9 ********** No masking Map Score: -4.73059e-14 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: -4.73059e-14 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: -4.73059e-14 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