AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_mjan_reg_300.orf -o00860_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 MJ0140 138 conserved hypothetical protein #2 MJ0570 300 conserved hypothetical protein #3 MJ0605 74 M. jannaschii predicted coding region MJ0605 #4 MJ0607 172 M. jannaschii predicted coding region MJ0607 #5 MJ0608 239 exopolyphosphatase (ppx1) #6 MJ0610 300 conserved hypothetical protein #7 MJ0642 166 M. jannaschii predicted coding region MJ0642 #8 MJ0965 38 uroporphyrin-III C-methyltransferase (cobA) #9 MJ0995 57 VAR1 protein isolog #10 MJ1377 184 glutamyl-tRNA synthetase (gltX) Motif number 1 TAAATATTGATAAAAAATAATAAACT 1 3 0 TAAAATTAAA 0.963829 -136 TATCAATATTTAATAAAAACTTAACTTGACAGTC 1 25 1 TAAAAATTAA 0.93029 -114 ACAGTCCCTATAATAAGTTTTAAAATTCACTTGT 1 53 1 TAAAATTAAA 0.96335 -86 TTTTTGAAAATAAAAATTAAATAATTATCTAAAT 2 20 0 TAAAATATAA 0.877326 -281 TTCAATAAACTTAAATATTCTAAATAATCAAACC 2 63 1 TTAATTTAAA 0.700278 -238 CAGCAAACCCTTAGAAATTAAATAAAAATCCTTT 2 96 1 TTAAATAATA 0.80482 -205 TTGAACTAATTAATAACTTCTAAATGCTCTTATT 2 128 1 TAAAATTAAA 0.963929 -173 TTGGATAAGTTTAGAATTTGAAAATAAGAGCATT 2 150 0 TTAAATAAAA 0.867085 -151 AAAATTATGGTAACAAAAAATATATACTTTACTC 2 241 1 TAAAAATATA 0.944117 -60 CTTAACAATAAATATATAGCTCCATA 3 59 0 TAAAAATATA 0.944117 -16 CCAAGTTCTTTAAGAAGTTCTTTAGAAGTTAATA 4 48 0 TAAAATTTTA 0.900824 -125 AGATTAGTTATAAAAAGATGAAAAATAAAGAATG 4 129 1 TAAAAAAAAA 0.93495 -44 CTCTATGCGGTTATATAAAATTTAGCACAAACAA 5 199 1 TTAATATTTA 0.436058 -41 AGCTGTGGCATAAAAACACTAATAATAAACATAG 6 119 1 TAAAAAAATA 0.900833 -182 ACACATTTATTTATAATTCGTTTATATTATTGTT 6 202 1 TTAAATTTTA 0.803833 -99 GTGATATTTGTTATAAAACAATAATATAAACGAA 6 218 0 TTAAAAATAA 0.777778 -83 AATAACTTATTAAAATAATCTAAAAATGTCACAT 6 256 0 TAAATATAAA 0.837278 -45 TTAAAACTTCTAAAAACATAAAAATCTTAGAGGG 7 11 0 TAAAAAAAAA 0.93495 -156 GCAAAAACCTTAAAAACTTTAAAATGATAATTAG 7 85 0 TAAAATAAAA 0.933906 -82 AAAATTAACTTAATAATTATTTAAGATTTCTTTA 7 133 0 TAAAATTTAA 0.722623 -34 TAAAATAAGTTATAGCTTCTAATA 8 25 0 TAAATATATA 0.764346 -14 AAATATTTTATAAAAAGTATTTTAATGTCTTTGG 9 18 0 TAAAATTTTA 0.866956 -40 CTTATAATAATAGTTAAAATATTTTATA 9 40 0 TAAAAATAAA 0.963586 -18 CAATAATATTTTACAATATTTATATATTTAACTA 10 23 1 TTAAAATATA 0.881969 -162 ATAATCTGAATAATAATAGTTAAATATATAAATA 10 39 0 TAAAAATAAA 0.963586 -146 GGATGAGCTTTTAAAATTGCATAACTATATTTAT 10 84 1 TTAAATATAA 0.777395 -101 *** ** * **** Masking position 1 Map Score: 36.5145 Number of sites scoring better than the average of aligned sites = 1498 Number in coding regions = 979 Number in noncoding regions = 519 Number of orfs with sites within 600 bp upstream = 403 Fraction of orfs with sites within 600 bp upstream = 0.0647286 Motif number 2 AGTTTATTATTTTTTATCAATATTT 1 3 1 TTTATTTTTT 0.712228 -136 ACAAGTGAATTTTAAAACTTATTATAGGGACTG 1 54 0 TTTAATTATT 0.946177 -85 TAGATAATTATTTAATTTTTATTTTCAAAAATC 2 23 1 TTTATTTATT 0.677646 -278 TTTATTGAATTATTCAGATTTTTGAAAATAAAA 2 39 0 TATTATTTTT 0.765591 -262 TTATTTAGAATATTTAAGTTTATTGAATTATTC 2 57 0 TATTATTTAT 0.5797 -244 GTTCAAAGGATTTTTATTTAATTTCTAAGGGTT 2 101 0 TTTTATAATT 0.744833 -200 AATAAGAGCATTTAGAAGTTATTAATTAGTTCA 2 129 0 TTTAATTATT 0.946179 -172 TATACTTTACTCTATATTTTTATAACCAACCAA 2 263 1 TCTAATTTAT 0.605849 -38 ATCTTTTTAATTTTTTGTGATACTAT 4 4 1 TTTTATTTTT 0.966348 -169 TAAGAAGTTCTTTAGAAGTTAATATATCAGCTC 4 39 0 TTTAATTAAT 0.88129 -134 TCAATATCTCTTTTAAAATCTTTTCCAAGTTCT 4 73 0 TTTTATCTTT 0.885583 -100 AAGATATAGATTTAGAATTTTATGAGATTAGTT 4 105 1 TTTAATTTAT 0.897298 -68 CATTCTTTATTTTTCATCTTTTTATAACTAATC 4 130 0 TTTTATTTTT 0.966348 -43 ATTTTAACATTATTAACATTAAAG 5 2 1 TTTTATTATT 0.960629 -238 TTATGTGACATTTTTAGATTATTTTAATAAGTT 6 254 1 TTTTATTATT 0.960631 -47 CAATCACCTTTTTATAGGTCAATAACTTATTAA 6 277 0 TTTAATCAAT 0.666785 -24 CCCTCTAAGATTTTTATGTTTTTAGAAGTTTTA 7 11 1 TTTTATTTTT 0.966348 -156 CTAATTATCATTTTAAAGTTTTTAAGGTTTTTG 7 85 1 TTTTATTTTT 0.966348 -82 ATTTAAGATTTCTTTATATTTATTCTTTCTGCA 7 116 0 TCTTATTTAT 0.680864 -51 ATAAAAAGTATTTTAATGTCTTTGGTGATAAC 9 10 0 TTTTATCTTT 0.885583 -48 TATAAAATATTTTAACTATTATTATAAG 9 40 1 TTTACTTATT 0.825725 -18 CACAATAATATTTTACAATATTTATATATTTAA 10 21 1 TTTTCTATTT 0.480764 -164 TATTTATATATTTAACTATTATTATTCAGATTA 10 39 1 TTTACTTATT 0.825725 -146 CAGTTAAGGTTTTTAAAGTTAATGGTAGGTAAA 10 152 1 TTTTATTAAT 0.911504 -33 **** * ***** Masking position 9 Map Score: 29.7028 Number of sites scoring better than the average of aligned sites = 2143 Number in coding regions = 1522 Number in noncoding regions = 621 Number of orfs with sites within 600 bp upstream = 445 Fraction of orfs with sites within 600 bp upstream = 0.0714745 Motif number 3 AATATTTAATAAAAACTTAACTTGACAGTCCC 1 29 1 AAAACTTACT 0.923576 -110 AATAAAAATTAAATAATTATCTAAATAAGATT 2 14 0 AAAAATTACT 0.742326 -287 CAGAAATTCCAAACCTATATCTATAATAAAAT 2 214 1 AAACTATACT 0.977215 -87 TGGTAACAAAAAATATATACTTTACTCTATAT 2 248 1 AAAATATATT 0.753055 -53 CTTAACAATAAATATATAGCTCCATAGCCTT 3 54 0 AAAATATACT 0.96964 -21 ATAAAATTCTAAATCTATATCTTCAATATCTC 4 96 0 AAACTATACT 0.973123 -77 CGTTGGGGATAAATATATATCTCTATGCGGTT 5 179 1 AAAATATACT 0.849564 -61 AACACTAATAATAAACATAGCTATGCAAATCC 6 133 1 ATAACATACT 0.892289 -168 ATTAGTATTAGAAGCTATAACTTATTTTA 8 20 1 GAACTATACT 0.880926 -19 TACAATATTTATATATTTAACTATTATTATTC 10 34 1 ATAATTTACT 0.872695 -151 TTAAAATTGCATAACTATATTTATGTTACTTA 10 94 1 ATACTATATT 0.680092 -91 ATTAACTTTAAAAACCTTAACTGATTATTAGG 10 143 0 AAACCTTACT 0.93333 -42 *** ***** ** Masking position 9 Map Score: 10.7572 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 373 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 TTCCAAACTTTCTTCATCATATTCTAATAAC 3 15 0 TCTTCTCATA 0.784945 -60 TTCTAAATCTATATCTTCAATATCTCTTTTA 4 91 0 ATATCTCAAT 0.725328 -82 CATTCTTTATTTTTCATCTTTTTATAACTAA 4 132 0 TTTTCTCTTT 0.640801 -41 TCATCCCTAATTTTCCTCATTCTTTATTTTT 4 149 0 TTTTCTCATT 0.933512 -24 TGTATCGTGGTCATCTTCATTGAGCAAAAGC 5 51 1 TCATCTCATT 0.970558 -189 AGATATATATTTATCCCCAACGAACCGACCC 5 170 0 TTATCCCAAC 0.752555 -70 TCTCTCACCTTCATTATTTGTTTGT 5 225 0 TCACCTCATT 0.861264 -15 TTTTAATAGATTATCGTCATTTGTAGAAACT 7 39 1 TTATCTCATT 0.972413 -128 GTTATCACCAAAGACATTAAAA 9 2 1 TTATCCCAAA 0.783475 -56 TTTTAAAAGCTCATCCTCAATATTAAGATAA 10 69 0 TCATCTCAAT 0.951067 -116 ATTATCACCATTTACCTACCAT 10 173 0 TTATCCCATT 0.956667 -12 ***** ***** Masking position 5 Map Score: 6.09407 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 425 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AGTTTATTATTTTTTATCAATATTT 1 6 1 ATTATTTTTT 0.508592 -133 TTAGATAATTATTTAATTTTTATTTTCAAA 2 22 1 ATTTAATTTT 0.669418 -279 TAAAGTATATATTTTTTGTTACCATAATTT 2 242 0 ATTTTTTGTT 0.958255 -59 TAACCAACCAATTTTATGGTGATTGT 2 285 1 ATTTTATGGT 0.7705 -16 GGAGCTATATATTTATTGTTAAG 3 62 1 ATTTATTGTT 0.951957 -13 ATCTTTTTAATTTTTTGTGATACTATGGG 4 10 1 ATTTTTTGTG 0.783574 -163 TTTCCTCATTCTTTATTTTTCATCTTTTTA 4 139 0 CTTTATTTTT 0.709753 -34 CCTCCTACAGCTTTAATGTTAATAATGTTA 5 15 0 CTTTAATGTT 0.836819 -225 CCCAGACCTCCTTTTTTGTTCCCCCAACTT 5 99 1 CTTTTTTGTT 0.927708 -141 TCTCACCTTCATTATTTGTTTGTGCTAAAT 5 218 0 ATTATTTGTT 0.824203 -22 GGCATAACTCATTTATTGGTGAATATGTT 6 10 0 ATTTATTGGT 0.862259 -291 CCCTCTAAGATTTTTATGTTTTTAGAAGTT 7 11 1 TTTTTATGTT 0.599244 -156 ATTTCTTTATATTTATTCTTTCTGCAAAAA 7 112 0 ATTTATTCTT 0.719555 -55 ********** Masking position 7 Map Score: 7.32664 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 634 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 TTATCAATATTTAATAAAAACTTAACTTGACA 1 24 1 TTAATAAAAT 0.604288 -115 TTGACAGTCCCTATAATAAGTTTTAAAATTCA 1 50 1 CTATAATAAT 0.903761 -89 TGTTCTAACTCTAATATAATATTCACTATATC 1 84 1 CTAATATAAT 0.724327 -55 TTCACTATATCTAATAAATACTTTCTAACTAT 1 105 1 CTAATAAATT 0.711871 -34 ATTCAATAAACTTAAATATTCTAAATAATCAA 2 62 1 CTTAAATATT 0.366446 -239 AAACCTATATCTATAATAAAATTATGGTAACA 2 224 1 CTATAATAAT 0.903682 -77 AATTGGTTGGTTATAAAAATATAGAGTAAAGT 2 266 0 TTATAAAAAT 0.843718 -35 TTTCCAAGTTCTTTAAGAAGTTCTTTAGAAGT 4 53 0 CTTTAAGAAT 0.684389 -120 TTCAATATCTCTTTTAAAATCTTTTCCAAGTT 4 75 0 CTTTTAAAAT 0.913341 -98 ATGAGATTAGTTATAAAAAGATGAAAAATAAA 4 126 1 TTATAAAAAT 0.843718 -47 CAAATCCCCACTATTAAAATGTTAATCATTTT 6 158 1 CTATTAAAAT 0.953619 -143 AGTTATTGACCTATAAAAAGGTGATTGA 6 283 1 CTATAAAAAT 0.966667 -18 TGACGATAATCTATTAAAACTTCTAAAAACAT 7 26 0 CTATTAAAAT 0.953622 -141 TAGGAAATATCTAAGAAAAGTTTCTACAAATG 7 56 0 CTAAGAAAAT 0.685415 -111 ACCTTAAAAACTTTAAAATGATAATTAGGAAA 7 81 0 CTTTAAAATT 0.817426 -86 AAAATACTTTTTATAAAATATTTTAACTATTA 9 29 1 TTATAAAATT 0.619196 -29 TGAGGATGAGCTTTTAAAATTGCATAACTATA 10 81 1 CTTTTAAAAG 0.54163 -104 CTACCATTAACTTTAAAAACCTTAACTGATTA 10 148 0 CTTTAAAAAT 0.936969 -37 ********* * Masking position 2 Map Score: 14.6683 Number of sites scoring better than the average of aligned sites = 987 Number in coding regions = 800 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 7 TTTGATTATTTAGAATATTTAAGTTTATTGA 2 64 0 TAGATATTTA 0.745729 -237 AATTAGTTCAAAGGATTTTTATTTAATTTCT 2 108 0 AAGATTTTTA 0.922353 -193 TGGATAAGTTTAGAATTTGAAAATAAGAGCA 2 152 0 TAGATTTGAA 0.750343 -149 AGAACTTGGAAAAGATTTTAAAAGAGATATT 4 73 1 AAAATTTTAA 0.81808 -100 GATATAGATTTAGAATTTTATGAGATTAGTT 4 107 1 TAGATTTTAT 0.669708 -66 AAGTAATTACAAGCATATTTATGCATGCAGG 6 38 0 AAGATATTTA 0.690329 -263 TGTTTATTATTAGTGTTTTTATGCCACAGCT 6 119 0 TAGGTTTTTA 0.711614 -182 AGAAAATGATTAACATTTTAATAGTGGGGAT 6 161 0 TAAATTTTAA 0.8555 -140 CCCTCTAAGATTTTTATGTTTTTAGA 7 6 1 TAAATTTTTA 0.816237 -161 TTTATGTTTTTAGAAGTTTTAATAGATTATC 7 23 1 TAGAGTTTTA 0.693639 -144 ATTTCCTAATTATCATTTTAAAGTTTTTAAG 7 80 1 TATATTTTAA 0.642868 -87 ATTTTATAAAAAGTATTTTAATGTCTTTGGT 9 17 0 AAGATTTTAA 0.939922 -41 ACTTTTTATAAAATATTTTAACTATTATTAT 9 34 1 AAAATTTTAA 0.81808 -24 ATAATCAGTTAAGGTTTTTAAAGTTAATGGT 10 147 1 AAGTTTTTAA 0.624751 -38 *** ******* Masking position 2 Map Score: 8.01077 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 487 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 8 TATGGTAACAAAAAATATATACTTTACTCT 2 246 1 AAAAATATAT 0.707169 -55 TTGGTTGGTTATAAAAATATAGAGTAAAGT 2 266 0 ATAAAAATAT 0.707376 -35 CTTAACAATAAATATATAGCTCCATAG 3 58 0 ATAAATATAT 0.932344 -17 TTCGTTGGGGATAAATATATATCTCTATGC 5 177 1 ATAAATATAT 0.932344 -63 ATATTCACCAATAAATGAGTTATGCCTGCA 6 14 1 ATAAATGAGT 0.586514 -287 GCCTGCATGCATAAATATGCTTGTAATTAC 6 37 1 ATAAATATGC 0.825598 -264 CGAATTATAAATAAATGTGTGGGGGAGGGT 6 192 0 ATAAATGTGT 0.917253 -109 AAAATGTCACATAAATGTGATATTTGTTAT 6 238 0 ATAAATGTGA 0.779089 -63 TGCAGAAAGAATAAATATAAAGAAATCTTA 7 116 1 ATAAATATAA 0.855499 -51 ATAATAATAGTTAAATATATAAATATTGTA 10 34 0 TTAAATATAT 0.703458 -151 GTTAAGTAACATAAATATAGTTATGCAATT 10 98 0 ATAAATATAG 0.83456 -87 ********** Masking position 5 Map Score: 6.67355 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 295 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 9 ATAATAAGTTTTAAAATTCACTTGTTCTAAC 1 62 1 TTAAAATTAC 0.916975 -77 TAACTCTAATATAATATTCACTATATCTAAT 1 89 1 ATAATATTAC 0.824715 -50 TATATCTATAATAAAATTATGGTAACAAAAA 2 229 1 ATAAAATTTG 0.732889 -72 ATGCGGTTATATAAAATTTAGCACAAACAAA 5 203 1 ATAAAATTAG 0.944316 -37 ATCAGTTATTAAAATTAACTTAATAATTA 7 148 0 TTAAAATTAC 0.916975 -19 CCCATAAAAATTAGTATTAGAAGC 8 4 1 ATAAAAATAG 0.73234 -35 TATTTAACTATTATTATTCAGATTATCTTAA 10 47 1 TTATTATTAG 0.63941 -138 TCAGATTATCTTAATATTGAGGATGAGCTTT 10 64 1 TTAATATTAG 0.918351 -121 AAAAGGATACTTAAAGTTAAGTAACATAAAT 10 112 0 TTAAAGTTAG 0.833575 -73 ******** ** Masking position 8 Map Score: 2.0806 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 203 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 10 ********** No masking Map Score: -3.47212e-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 11 ********** No masking Map Score: -3.47212e-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 12 ********** No masking Map Score: -3.47212e-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