AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -igalR_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 MJ0210 86 succinyl-CoA synthetase, beta subunit #2 MJ0210.1 43 M. jannaschii predicted coding region MJ0210.1 #3 MJ1054 300 UDP-glucose dehydrogenase, putative #4 MJ1081 130 conserved hypothetical protein #5 MJ1083 69 iron-sulfur flavoprotein (isf) #6 MJ1084 88 shikimate 5-dehydrogenase (aroE) #7 MJ1085 25 M. jannaschii predicted coding region MJ1085 #8 MJ1662 94 methyl coenzyme M reductase system, component A2-like #9 MJ1672 34 conserved hypothetical protein #10 MJ1674 113 M. jannaschii predicted coding region MJ1674 Motif number 1 TAAACCTATAAATTTATCACCAAATT 1 4 1 ATTAAATTTA 0.887291 -83 TAAAATTATCATATAAAAAATTTGGTGATAAAT 1 22 0 ATAAAAATTT 0.976487 -65 TTATATGATAATTTTAAAATTTTGCATTAAAAA 1 39 1 ATAAAATTTT 0.981844 -48 CTATCACCTTAAATGATAAATTTCTTTTTAATG 1 63 0 ATATAAATTT 0.935347 -24 AAATAATATAAAATAAAAATTATTTTG 2 5 0 ATAAAATTAT 0.951827 -39 TCCAACAATTAATTGTAAATATAGCATTACTTA 3 164 0 ATTAAATATA 0.587307 -137 TGTAAGAGAAATATAATAATATTATACAATTAT 3 253 1 ATATAATATT 0.80155 -48 TATAGTTATAATTTAATAATTTAGAAC 4 5 0 ATATAATTTA 0.935637 -126 ATTAAATTATAACTATAAATTATAACTATTCAA 4 21 1 ATTAAATTAT 0.81518 -110 TTCAAGTTTAATATTTAAAATTTAATTAAGGTC 4 49 1 ATTAAAATTT 0.582809 -82 AATCAAAAACATATCAAAAATTTAATTGGGTAT 4 93 1 ATAAAAATTT 0.976487 -38 AAAATACATTAGGTCAGAATTTATGTCCATAGG 5 38 1 ATAGAATTTA 0.817283 -32 TACAAAGAGAAGGTAAAAAATAAATATCAAATA 6 24 0 ATAAAAATAA 0.908753 -65 TTCTCTTTGTAATTTACAATTTTTAATTATAAA 6 46 1 ATACAATTTT 0.872986 -43 AAATATTTAATAAATTTAATAGAGG 7 5 1 ATATAAATTT 0.94527 -21 CTAAAACCTAAAACTTTTTGCTAAGTTT 8 6 1 ATAAACTTTT 0.825114 -89 ATATGTTAATAACTTATAAACTTAGCAAAAAGT 8 23 0 ATATAAACTT 0.769942 -72 TTATTAACATATTTAATAATTATTACTGCAAAT 8 44 1 ATATAATTAT 0.890649 -51 AAATTACCACCTTAAAATTAATTCATATTTG 10 9 1 ATAAAATTAA 0.927835 -105 TATTTTGTAAATTTGAAAATATACAAATATGAA 10 32 0 ATAAAATATA 0.864427 -82 CAAATTTACAAAATAAAAAACTATTTATATGAC 10 50 1 ATAAAAACTA 0.842055 -64 AATTTGTGGAACCTTAAAAATAATAAAAAAGTC 10 80 0 ATAAAAATAA 0.908753 -34 TTCACCTCAAAAATTTGTGGAACCTT 10 98 0 ATAAAAATTT 0.976741 -16 * * ******** Masking position 4 Map Score: 31.9011 Number of sites scoring better than the average of aligned sites = 1845 Number in coding regions = 1230 Number in noncoding regions = 615 Number of orfs with sites within 600 bp upstream = 432 Fraction of orfs with sites within 600 bp upstream = 0.0693864 Motif number 2 AATTATCATATAAAAAATTTGGTGATAAAT 1 22 0 TAAAAAATTT 0.690333 -65 TTTGCATTAAAAAGAAATTTATCATTTAAG 1 59 1 AAAGAAATTT 0.807226 -28 CAAAATAATTTTTATTTTATAT 2 3 1 AAATAATTTT 0.966221 -41 ATTAAAAAATTATGGGAAATAAT 2 31 0 AAAAAATTAT 0.759626 -13 TCACAAGATTAAAGAGGTTTTAAATAGATT 3 21 1 AAAGAGGTTT 0.714016 -280 AAGAGGTTTTAAATAGATTTCCAAGTAATA 3 32 1 AAATAGATTT 0.950094 -269 CTATATTTACAATTAATTGTTGGAGGAGTA 3 173 1 AATTAATTGT 0.756922 -128 GTTTATTTATTAATAATTGTATAATATTAT 3 268 0 TAATAATTGT 0.769133 -33 TATTAAACTTGAATAGTTATAATTTATAGT 4 32 0 GAATAGTTAT 0.649805 -99 ATAAGACCTTAATTAAATTTTAAATATTAA 4 56 0 AATTAAATTT 0.880945 -75 CGCAATACCCAATTAAATTTTTGATATGTT 4 100 0 AATTAAATTT 0.880945 -31 AAATAGGTTTTAATAGTTTTTC 5 3 0 TAATAGTTTT 0.942009 -67 ATTTTATCAGAAATAGGTTTTAATAGTTTT 5 13 0 AAATAGGTTT 0.914393 -57 AGAAGGTAAAAAATAAATATCAAATAACAC 6 20 0 AAATAAATAT 0.869493 -69 TATCACATTAAATTAGTTTTTATAATTAAA 6 67 0 AATTAGTTTT 0.938208 -22 AAATATTTAATAAATTTAATAGAGG 7 8 1 TAATAAATTT 0.887845 -18 TAAACTTAGCAAAAAGTTTTAGGTTTTAG 8 10 0 AAAAAGTTTT 0.909264 -85 TTGCTAAGTTTATAAGTTATTAACATATTT 8 28 1 TATAAGTTAT 0.411657 -67 ATATTTGCAGTAATAATTATTAAATATGTT 8 49 0 TAATAATTAT 0.831958 -46 TACAAATATGAATTAATTTTAAGGTGGTAA 10 14 0 AATTAATTTT 0.92574 -100 AAAGTCATATAAATAGTTTTTTATTTTGTA 10 56 0 AAATAGTTTT 0.971787 -58 ********** Masking position 8 Map Score: 25.2139 Number of sites scoring better than the average of aligned sites = 1563 Number in coding regions = 1132 Number in noncoding regions = 431 Number of orfs with sites within 600 bp upstream = 377 Fraction of orfs with sites within 600 bp upstream = 0.0605525 Motif number 3 AATTTTAAAATTATCATATAAAAAATTTGGTGA 1 27 0 TTATATAAAA 0.929304 -60 AAATTATGGGAAATAATATAAAATAAAAATTAT 2 15 0 AAATATAAAA 0.914123 -29 CTCTTTAATCTTGTGATAATAAATTC 3 4 0 TTGTATAAAA 0.754531 -297 ATAGATTTCCAAGTAATAGTAAATTCGATACGG 3 44 1 AAGTATAAAA 0.712998 -257 TTGATAACGAAAATTATAAGTAATGCTATATTT 3 148 1 AAATATATAA 0.834611 -153 AGTAATGCTATATTTACAATTAATTGTTGGAGG 3 166 1 TATTACATAA 0.650923 -135 CTCAGACATAAAATTACAGCTAAATAAACTCCA 3 211 0 AAATACATAA 0.880083 -90 AAGAGAAATATAATAATATTATACAATTATTAA 3 256 1 TAATATAATA 0.561879 -45 ATTATACAATTATTAATAAATAAACTCAGGGGA 3 273 1 TATTATATAA 0.561749 -28 AATTATTAAATTATAACTATAAATTATAACTAT 4 17 1 TTATACTAAA 0.85175 -114 AATTAAGGTCTTATCACATCAAATCAAAAACAT 4 72 1 TTATACAAAA 0.950381 -59 CATCAAATCAAAAACATATCAAAAATTTAATTG 4 88 1 AAAAATAAAA 0.432324 -43 AATAAATATCAAATAACACAAAAGTGTT 6 6 0 AAATACAAAA 0.939323 -83 AAATTAGTTTTTATAATTAAAAATTGTAAATTA 6 55 0 TTATATTAAA 0.791979 -34 ATTATCACATTAAATTAGTTTTTA 6 75 0 TTATACAAAA 0.950374 -14 TTAAATATGTTAATAACTTATAAACTTAGCAAA 8 27 0 TAATACTTAA 0.785083 -68 TATTTAATAATTATTACTGCAAATATTATCATC 8 53 1 TTATACTAAA 0.852147 -42 GGTTATCACCCATAACTGTGATGAT 8 80 0 TTATACCTAA 0.551487 -15 GGAACCTTAAAAATAATAAAAAAGTCATATAAA 10 73 0 AAATATAAAA 0.914123 -41 **** *** *** Masking position 6 Map Score: 18.1254 Number of sites scoring better than the average of aligned sites = 1129 Number in coding regions = 839 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 4 TTATTTCCCATAATTTTTTAAT 2 32 1 TAATTTTTTA 0.796799 -12 GAATTTATTATCACAAGATT 3 1 1 GAATTTATTA 0.96656 -300 CAACCGTATCGAATTTACTATTACTTGGAA 3 50 0 GAATTTACTA 0.840147 -251 GTTGGAGGAGTAGTTTATTTTGGAGTTTAT 3 191 1 TAGTTTATTT 0.922814 -110 GTTTATTTTGGAGTTTATTTAGCTGTAATT 3 203 1 GAGTTTATTT 0.951388 -98 TAAATCCCCTGAGTTTATTTATTAATAATT 3 280 0 GAGTTTATTT 0.951388 -21 TTTATAGTTATAATTTAATAATTTAGAAC 4 10 0 TAATTTAATA 0.689985 -121 AATTCTGACCTAATGTATTTTATCAGAAAT 5 29 0 TAATGTATTT 0.722738 -41 CATTAGGTCAGAATTTATGTCCATAGGTGA 5 44 1 GAATTTATGT 0.808073 -26 CCTCTATTAAATTTATTAAATATTT 7 8 0 AAATTTATTA 0.767947 -18 GCTAAGTTTATAAGTTATTAACATATTTAA 8 30 1 TAAGTTATTA 0.751875 -65 ATACAAATATGAATTAATTTTAAGGTGGTA 10 15 0 GAATTAATTT 0.726801 -99 GTCATATAAATAGTTTTTTATTTTGTAAAT 10 53 0 TAGTTTTTTA 0.743285 -61 ********** Masking position 2 Map Score: 10.0714 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 493 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 5 AAAAATTTGGTGATAAATTTATAGGTTTA 1 10 0 TGATAAATTT 0.965838 -77 ATTTTTTATATGATAATTTTAAAATTTTGC 1 34 1 TGATAATTTT 0.892177 -53 TTCTTTTTAATGCAAAATTTTAAAATTATC 1 45 0 TGCAAAATTT 0.77824 -42 TCACCTTAAATGATAAATTTCTTTTTAATG 1 63 0 TGATAAATTT 0.965838 -24 ATAATTTTTATTTTATATTATTTCCCATAA 2 15 1 TTTTATATTA 0.298782 -29 TACCAGAGGCTGTTAAGTTAACGACTTCAC 3 118 0 TGTTAAGTTA 0.690928 -183 ATAGCATTACTTATAATTTTCGTTATCAAT 3 147 0 TTATAATTTT 0.758478 -154 TTATAAGTAATGCTATATTTACAATTAATT 3 161 1 TGCTATATTT 0.843259 -140 GTTCTAAATTATTAAATTATA 4 2 1 TTCTAAATTA 0.792005 -129 AAGTTTAATATTTAAAATTTAATTAAGGTC 4 52 1 TTTAAAATTT 0.392056 -79 ATTAAATTTTTGATATGTTTTTGATTTGAT 4 89 0 TGATATGTTT 0.750593 -42 AACCTATTTCTGATAAAATACATTAGGTCA 5 24 1 TGATAAAATA 0.647884 -46 TAATTAAAAATTGTAAATTACAAAGAGAAG 6 45 0 TTGTAAATTA 0.665579 -44 AAATATTTAATAAATTTAATAGAGG 7 8 1 TAATAAATTT 0.690136 -18 TAAAACTTTTTGCTAAGTTTATAAGTTATT 8 19 1 TGCTAAGTTT 0.914556 -76 ATAACTGTGATGATAATATTTGCAGTAATA 8 64 0 TGATAATATT 0.555252 -31 GTTTTTTATTTTGTAAATTTGAAAATATAC 10 41 0 TTGTAAATTT 0.821872 -73 ********** Masking position 5 Map Score: 13.7712 Number of sites scoring better than the average of aligned sites = 1337 Number in coding regions = 1071 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 6 ********** No masking Map Score: 3.03645e-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 7 ********** No masking Map Score: 3.03645e-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: 3.03645e-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