AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iglpR_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 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #2 MJ0084 261 CODH nickel-insertion accessory protein (cooC) #3 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #4 MJ0086 36 unspecified methyltransferase #5 MJ0087 23 hemin permease (hemU) #6 MJ0090 80 collagenase (prtC) #7 MJ0091 95 Na+/Ca+ exchanger protein, putative #8 MJ0955 48 histidinol-phosphate aminotransferase (hisC) #9 MJ0956 145 M. jannaschii predicted coding region MJ0956 Motif number 1 TTTTAGGCTTTCTTTATGATTCAAAAAAAT 1 74 1 TCTTTATGAT 0.650203 -227 TTCAAAATTTTTTTAAAGATTTTAAAGATT 1 143 1 TTTTAAAGAT 0.828093 -158 TTTAAAGATTTTTTTAATTTTATCATTTTA 1 163 1 TTTTTAATTT 0.977621 -138 TAATTTTATCATTTTAATATTATTATTTTA 1 177 1 ATTTTAATAT 0.773036 -124 ATTTTAACATTTTTTAGTAATTTTTAGGAT 1 201 1 TTTTTAGTAA 0.811231 -100 TTTTTAGTAATTTTTAGGATAAAATAGAAA 1 211 1 TTTTTAGGAT 0.795097 -90 ACCAACCTTTTTGTTAATATATTACTACAG 1 274 0 TTGTTAATAT 0.814346 -27 TCTTTATTATCTTATTTTAA 2 1 1 TCTTTATTAT 0.852406 -261 CTTATTTTAAGTTTTATTTTTTGGACTTTA 2 21 1 GTTTTATTTT 0.838801 -241 TTGGACTTTATTTTTAATTTTAAAATTTTA 2 41 1 TTTTTAATTT 0.977621 -221 AAGATATTAGGTTTTAATTAAATTTAAATC 2 226 1 GTTTTAATTA 0.801855 -36 CTTTTTTCTATTTTTTATATAATTTTTATG 3 11 1 TTTTTTATAT 0.915334 -124 TTTTATATAATTTTTATGAATATTGATGTA 3 23 1 TTTTTATGAA 0.782793 -112 TGAACAAAAATTTTTAATATCTAATATATA 3 88 0 TTTTTAATAT 0.985473 -47 TTTTTAATTTTTTATAATTT 4 1 1 TTTTTAATTT 0.977621 -36 TTTTTTATAATTTTTATTTTGGTGATAAA 4 18 1 TTTTTATTTT 0.95244 -19 CTATCACATTTTTTGAATTATT 5 3 0 TTTTGAATTA 0.695973 -21 TCTTTTTTATATAATGAGGTCA 6 3 1 TTTTTTATAT 0.915334 -78 TTAGAAATTTTTTTAAATTTTAAATTATAT 6 61 0 TTTTAAATTT 0.905146 -20 TTTTGCTTAAGTTTAAATATTATTGCAGAA 7 34 1 GTTTAAATAT 0.795478 -62 TAAAGTTTGTTTTTGAATATATTCTGCAAT 7 55 0 TTTTGAATAT 0.909686 -41 GATTTCTGGATTTTTTATTA 8 1 0 TTTTTTATTA 0.710804 -48 ACCAAAAATATTTTAAATAAGATTTCTGGA 8 21 0 TTTTAAATAA 0.84179 -28 ATCTTTTTAATTTTTGTTTTATT 9 4 1 TTTTTAATTT 0.977621 -142 TTTAATTTTTGTTTTATTATTTTATTTTTA 9 16 1 GTTTTATTAT 0.890859 -130 TATTATTTTATTTTTATTAATTTATCCATT 9 30 1 TTTTTATTAA 0.917999 -116 TTTTTATTATTCTTTAATTTAAATGGATAA 9 51 0 TCTTTAATTT 0.88928 -95 CATATAAAAGTTTTTATTATTCTTTAATTT 9 61 0 TTTTTATTAT 0.969147 -85 TTTAAGTAAATTTTAATTATCAAAAGACTT 9 92 0 TTTTAATTAT 0.8728 -54 TCTATATTATTTTTTAAGTAAATTTTAATT 9 104 0 TTTTTAAGTA 0.833657 -42 TAATATAGATTTTTTTATATAGTGGGTTTT 9 125 1 TTTTTTATAT 0.915334 -21 ********** Masking position 4 Map Score: 47.2964 Number of sites scoring better than the average of aligned sites = 3126 Number in coding regions = 2231 Number in noncoding regions = 895 Number of orfs with sites within 600 bp upstream = 581 Fraction of orfs with sites within 600 bp upstream = 0.0933183 Motif number 2 GAGGAATTCAAAATTTTTTTAAAGATTTTA 1 137 1 AAATTTTTTT 0.891767 -164 TAAAGATTTTAAAGATTTTTTTAATTTTAT 1 156 1 AAAGATTTTT 0.476205 -145 TTTATCATTTTAATATTATTATTTTAACAT 1 181 1 TAATATTATT 0.903785 -120 AGTAATAGGTATATAAAATTTTCTATTTTA 1 230 0 ATATAAAATT 0.1889 -71 CTTTTTGTTAATATATTACTACAGCTATAG 1 268 0 ATATATTACT 0.635924 -33 TCTTTATTATCTTATTTTAAGTTTTA 2 7 1 TTATCTTATT 0.74934 -255 ATCTTATTTTAAGTTTTATTTTTTGGACTT 2 19 1 AAGTTTTATT 0.782107 -243 TTTAATTTTAAAATTTTAATTGGAGGGCAT 2 53 1 AAATTTTAAT 0.662636 -209 AAATGTTTGAATCTATTATTATGCCCTCCA 2 73 0 ATCTATTATT 0.791229 -189 TCTCTTCCATTAATATTATTTTATCTAAAA 2 112 0 TAATATTATT 0.903785 -150 TATTTAGTATAAATCTTTTTCTAACAAGTG 2 197 0 AAATCTTTTT 0.851586 -65 TTAAAACCTAATATCTTATTTAGTATAAAT 2 213 0 ATATCTTATT 0.91355 -49 AGTCTGATTTAAATTTAATTAAAACCTAAT 2 231 0 AAATTTAATT 0.814898 -31 TTTCTATTTTTTATATAATTTTTATGAATA 3 15 1 TTATATAATT 0.593655 -120 ATGAATATTGATGTATTTTTAACGATTATT 3 38 1 ATGTATTTTT 0.596246 -97 AATATCTAATATATATTTTTCGGTAGTTTA 3 73 0 ATATATTTTT 0.891746 -62 ATTAGATATTAAAAATTTTTGTTCATATCA 3 93 1 AAAAATTTTT 0.310095 -42 AATTTTTTATAATTTTTATTTTGGTGATAA 4 16 1 AATTTTTATT 0.766986 -21 TTTATACTTCAAATATAATTTAAAATTTAA 6 49 1 AAATATAATT 0.684379 -32 TTAGAAATTTTTTTAAATTTTAAA 6 67 0 AAATTTTTTT 0.891767 -14 GCTTAAGTTTAAATATTATTGCAGAATATA 7 38 1 AAATATTATT 0.952015 -58 TTCAAAAACAAACTTTAATTAATTTAGTAG 7 68 1 AACTTTAATT 0.439192 -28 AGATTTCTGGATTTTTTATTA 8 2 0 ATTTTTTATT 0.702674 -47 AAAAATCCAGAAATCTTATTTAAAATATTT 8 16 1 AAATCTTATT 0.936753 -33 ATCTTATTTAAAATATTTTTGGTTAAAAAT 8 28 1 AAATATTTTT 0.830011 -21 TTTTGTTTTATTATTTTATTTTTATTAATT 9 22 1 TTATTTTATT 0.818461 -124 ATATAAAAGTTTTTATTATTCTTTAATTTA 9 60 0 TTTTATTATT 0.498292 -86 TTTTTTAAGTAAATTTTAATTATCAAAAGA 9 95 0 AAATTTTAAT 0.662636 -51 ATAAAAAAATCTATATTATTTTTTAAGTAA 9 113 0 CTATATTATT 0.673192 -33 ********** Masking position 10 Map Score: 25.0068 Number of sites scoring better than the average of aligned sites = 2645 Number in coding regions = 1904 Number in noncoding regions = 741 Number of orfs with sites within 600 bp upstream = 522 Fraction of orfs with sites within 600 bp upstream = 0.083842 Motif number 3 CTCTGTGAGGAATTCAAAATTTTTTTAAAGATT 1 131 1 AATAAATTTT 0.917191 -170 TTTTTAAAGATTTTAAAGATTTTTTTAATTTTA 1 152 1 TTTAAATTTT 0.961299 -149 GATTTTTTTAATTTTATCATTTTAATATTATTA 1 169 1 ATTATATTTT 0.713489 -132 TAATATTATTATTTTAACATTTTTTAGTAATTT 1 191 1 ATTAAATTTT 0.958286 -110 AGGTATATAAAATTTTCTATTTTATCCTAAAAA 1 221 0 AATTCATTTT 0.481242 -80 ACCAACCTTTTTGTTAATATATTACTACAGCTA 1 271 0 TTTAAATATT 0.685621 -30 TTTATTTTTAATTTTAAAATTTTAATTGGAGGG 2 47 1 ATTAAATTTT 0.958283 -215 ATAATAATAGATTCAAACATTTTATCAAAAGTT 2 81 1 ATCAAATTTT 0.637984 -181 ATATTATTTTATCTAAAACTTTTGATAAAATGT 2 97 0 ATTAACTTTT 0.875614 -165 ATCTTATTTAGTATAAATCTTTTTCTAACAAGT 2 198 0 GTTAACTTTT 0.748512 -64 CTTTTTTCTATTTTTTATATAATT 3 2 1 TTTTCATTTT 0.675438 -133 TTTCTATTTTTTATATAATTTTTATGAATATTG 3 15 1 TTTTATTTTT 0.468717 -120 TTTTAATATCTAATATATATTTTTCGGTAGTTT 3 74 0 TATTAATTTT 0.804227 -61 ATATATTAGATATTAAAAATTTTTGTTCATATC 3 89 1 TATAAATTTT 0.922934 -46 ATTGTCACCATTTTAGGCTATATG 3 121 0 TTTACATTTT 0.858492 -14 TTTTTAATTTTTTATAATTTTTA 4 1 1 TTTAATTTTT 0.720035 -36 TTTATCACCAAAATAAAAATTATAAAAAATTAA 4 14 0 AATAAATTAT 0.492979 -23 TTAGAAATTTTTTTAAATTTTAAATTATATT 6 60 0 TTTTAATTTT 0.894965 -21 AATATGGATGAACTGAAAATTTTGCTTAAGTTT 7 15 1 AATAAATTTT 0.91719 -81 TTTTGCTTAAGTTTAAATATTATTGCAGAATAT 7 34 1 GTTAAATTAT 0.460278 -62 TAAAGTTTGTTTTTGAATATATTCTGCAATAAT 7 52 0 TTTAAATATT 0.685621 -44 TTTAAATAAGATTTCTGGATTTTTTATTA 8 7 0 ATTTGATTTT 0.569218 -42 AGAAATCTTATTTAAAATATTTTTGGTTAAAAA 8 24 1 TTAAAATTTT 0.693909 -25 TTTAATTTTTGTTTTATTATTTTATTTTTATTA 9 16 1 GTTATATTTT 0.512884 -130 ATTAAAGAATAATAAAAACTTTTATATGTAAGT 9 63 1 AAAAACTTTT 0.236422 -83 AAACTTTTATATGTAAGTCTTTTGATAATTAAA 9 78 1 ATTAGCTTTT 0.541358 -68 AGTCTTTTGATAATTAAAATTTACTTAAAAAAT 9 93 1 TATAAATTTA 0.364852 -53 ACTTAAAAAATAATATAGATTTTTTTATATAGT 9 115 1 TATTAATTTT 0.804232 -31 ** * ** ***** Masking position 10 Map Score: 28.5849 Number of sites scoring better than the average of aligned sites = 2718 Number in coding regions = 1882 Number in noncoding regions = 836 Number of orfs with sites within 600 bp upstream = 533 Fraction of orfs with sites within 600 bp upstream = 0.0856087 Motif number 4 CCCACAATGGAACTTACGCAGAGGCTATAC 1 23 1 AACTTACGCA 0.993364 -278 TATTCAATAGAACTTACGCATTTTTTTGAA 1 93 0 AACTTACGCA 0.993364 -208 ATAATATTTAAACTTAAGCAAAATTTTCAG 7 27 0 AACTTAAGCA 0.980065 -69 ********** Masking position 6 Map Score: 2.94519 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 GCTATACTCTATTTGCTATTGATGATACTTTTA 1 46 1 ATTTTATGAT 0.963547 -255 CGTAAGTTCTATTGAATAGGGCTCACCTCTGTG 1 105 1 ATTGTAGGCT 0.954419 -196 CTTTAAAAAAATTTTGAATTCCTCACAGAGGTG 1 128 0 ATTTAATCCT 0.775519 -173 TTATTTTAACATTTTTTAGTAATTTTTAGGATA 1 199 1 ATTTTAGAAT 0.854058 -102 AAAATAGAAAATTTTATATACCTATTACTATCA 1 231 1 ATTTTATCCT 0.956359 -70 TATTACTATCATTTTCTATAGCTGTAGTAATAT 1 253 1 ATTTTATGCT 0.981107 -48 CTAATATCTTATTTAGTATAAATCTTTTTCTAA 2 203 0 ATTTTATAAT 0.847462 -59 ATGAGGTCATATTGGTTATTGCTATTTTATACT 6 24 1 ATTGTATGCT 0.962099 -57 ACTTTAATTAATTTAGTAGGGATAAGA 7 79 1 ATTTTAGGAT 0.956097 -17 **** *** *** Masking position 8 Map Score: 6.63733 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 189 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 AATAATATTAAAATGATAAAATTAAAAAAAT 1 170 0 AAATGATAAA 0.717063 -131 AAAAATGTTAAAATAATAATATTAAAATGAT 1 184 0 AAATAATATA 0.872764 -117 CAGCTATAGAAAATGATAGTAATAGGTATAT 1 246 0 AAATGATATA 0.941441 -55 AAAACTTAAAATAAGATAATAAAGA 2 5 0 ATAAGATATA 0.971798 -257 AAAGTTTTAGATAAAATAATATTAATGGAAG 2 108 1 ATAAAATATA 0.936328 -154 TTTATACTAAATAAGATATTAGGTTTTAATT 2 214 1 ATAAGATATA 0.971798 -48 AAAAATATATATTAGATATTAAAAATTTTTG 3 83 1 ATTAGATATA 0.829022 -52 ATTTTAGGCTATATGATATGAACAAAAATTT 3 105 0 ATATGATAGA 0.846137 -30 ATTAATAAAAATAAAATAATAAAACAAAAAT 9 20 0 ATAAAATATA 0.936328 -126 AAATTTACTTAAAAAATAATATAGATTTTTT 9 109 1 AAAAAATATA 0.909457 -37 ******** ** Masking position 6 Map Score: 11.824 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 189 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 ********** No masking Map Score: -1.3476e-12 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: -1.3476e-12 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: -1.3476e-12 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