AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00150_mjan_reg_300.orf -o00150_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 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #2 MJ1027 125 formate hydrogenlyase, subunit 5 #3 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #4 MJ1029 47 dimethyladenosine transferase (ksgA) #5 MJ1521 88 Na+/H+ antiporter #6 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #7 MJ1575 300 GMP synthase (guaA) #8 MJ1576 80 LemA protein #9 MJ1577 29 M. jannaschii predicted coding region MJ1577 #10 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) Motif number 1 TTATAAAATTACAATTAAAAACTTTTTTAGA 1 59 0 AAATTAAAAA 0.979532 -30 ATAATTTATCATAATTAATAATGATAATTAG 2 52 0 AAATTAATAA 0.966146 -74 CCAACAATTATAAACATGATAATA 2 112 0 AAATTATAAA 0.793556 -14 AAATATCAGTAAAATAAATAATGTAACAAAA 3 39 0 AAATAAATAA 0.906724 -22 AAGAGAAAAGAAAATAAAAAT 4 1 0 AAATAAAAAT 0.865202 -47 TCTCTTTTTTAGAATAAATAAAAAGTGAAAC 4 26 1 AAATAAATAA 0.906724 -22 TTACCACCAAAAAATTTATATGCTTTCTAAA 5 12 1 AAATTTATAT 0.903023 -77 ACTAAACTTTACATTTAGAAAGCATATAAAT 5 25 0 AATTTAGAAA 0.867212 -64 TTTTGAATTAAAAATTTAAAAATTGAAA 6 8 0 AAATTTAAAA 0.973115 -139 AATATAAGTTAAATTTTGAATTAAAAATTTA 6 21 0 AATTTTGAAT 0.670587 -126 ATATAAAATAAGAATATAAAAATATAAGTTA 6 41 0 AAATATAAAA 0.921777 -106 TATCAGAATAAGAATATAAAATAAGAATATA 6 54 0 AAATATAAAA 0.921777 -93 AAATATCAATAAAATTAAAAAGATAAGGTAA 6 88 0 AAATTAAAAA 0.979532 -59 AATTTTATTGATATTTAAAAACATAATAGTA 6 103 1 AATTTAAAAA 0.939431 -44 GAAAGACACTATATTTTAAAATTTCTTTTAT 7 44 0 AATTTTAAAA 0.921773 -257 CAAAGTTGTTAAAATTAATATTAATAATGGA 7 74 1 AAATTAATAT 0.923491 -227 TCTTTCAAAAACATTTTGAAAGAACCTTTTA 7 255 0 AATTTTGAAA 0.831628 -46 CTAATAATAAAATTTATATAAGTTGATAT 8 9 1 AAATTTATAT 0.903023 -72 ACCACAAAAAAGAATTTGAATTATTTGGATA 8 54 0 AAATTTGAAT 0.862122 -27 CCTAAAAATTAAAATTAATAA 9 1 0 AAATTAATAA 0.967595 -29 TAGGTCTTTCAAAATTAATAAAATTTACTTA 10 17 0 AAATTAATAA 0.967595 -50 * ********* Masking position 5 Map Score: 37.6677 Number of sites scoring better than the average of aligned sites = 1600 Number in coding regions = 1102 Number in noncoding regions = 498 Number of orfs with sites within 600 bp upstream = 360 Fraction of orfs with sites within 600 bp upstream = 0.057822 Motif number 2 TTTTATATAGTTTTGTTTTAATAAAGTTATC 2 14 0 TTTTTTTTAA 0.840265 -112 TTTAGTTAATTTCTATTTTGTTACATTATTT 3 24 1 TTCTTTTTGT 0.897094 -37 TTATTTTCTTTTCTCTTTTTTAGAATAAATA 4 15 1 TTCTTTTTTT 0.940111 -33 TGTTTCACTTTTTATTTATTCTAA 4 34 0 TTCATTTTTA 0.963919 -14 CCACCAATCTTTTAGTTTTTAATATCTGGAT 5 64 0 TTTATTTTTA 0.934938 -25 TTTCAATTTTTAAATTTTTAAT 6 2 1 TTCATTTTTA 0.963872 -145 AAAATATAAGTTAAATTTTGAATTAAAAATT 6 23 0 TTAATTTTGA 0.867879 -124 AAAATTTAACTTATATTTTTATATTCTTATT 6 35 1 TTATTTTTTA 0.958733 -112 TATTTTTATATTCTTATTTTATATTCTTATT 6 48 1 TTCTATTTTA 0.797746 -99 TATCTTTACCTTATCTTTTTAATTTTATTGA 6 83 1 TTATTTTTTA 0.959325 -64 TTTATTACTATTATGTTTTTAAATATCAATA 6 108 0 TTATTTTTTA 0.959325 -39 ATTTTAAAATTTCTTTTATTATGATTATCCT 7 32 0 TTCTTTATTA 0.918488 -269 TTTATCACCTTATATTTTATTAGTATCTTT 7 281 0 TTATTTTTAT 0.571075 -20 CTTATATAAATTTTATTATTAG 8 2 0 TTTTTTATTA 0.858359 -79 ATAATTCAAATTCTTTTTTGTGGTGAAATT 8 61 1 TTCTTTTTGT 0.897095 -20 TTATTAATTTTAATTTTTAGGGGATTTTT 9 9 1 TTTATTTTTA 0.934893 -21 ATTAATAAAATTTACTTATGAAAA 10 4 0 TTTATTATGA 0.633074 -63 CTCCTCTTGTTTTTGTTTTTATAGTAGGTCT 10 41 0 TTTTTTTTTA 0.965558 -26 **** ****** Masking position 7 Map Score: 29.4395 Number of sites scoring better than the average of aligned sites = 1416 Number in coding regions = 961 Number in noncoding regions = 455 Number of orfs with sites within 600 bp upstream = 346 Fraction of orfs with sites within 600 bp upstream = 0.0555734 Motif number 3 GTCACCAAAAATTTATTGTCAATTTAG 1 8 1 AAAATTTATT 0.966363 -81 AGTTATCTAAAAAAGTTTTTAATTGTAATT 1 54 1 AAAAGTTTTT 0.711722 -35 AACCTTTTATATAGTTTTGTTTTAATAAAG 2 19 0 ATAGTTTTGT 0.73271 -107 TAATGAATAGATAATTTATCATAATTAATA 2 63 0 ATAATTTATC 0.69397 -63 AGTTTAAAAATAGTTTAGTTAATTTCTAT 3 10 1 ATAGTTTAGT 0.916826 -51 ATTTTGTTACATTATTTATTTTACTGATAT 3 38 1 ATTATTTATT 0.590389 -23 TTACCACCAAAAAATTTATATGCTTTCTAA 5 12 1 AAAATTTATA 0.703009 -77 TTCTAAATGTAAAGTTTAGTGTCTGTATAT 5 36 1 AAAGTTTAGT 0.944612 -53 TCACATTCAAATAATTTATTACTATTATGT 6 123 0 ATAATTTATT 0.950104 -24 GATTATCCTCCAAATTTATTGAAGTCAGTT 7 11 0 CAAATTTATT 0.767744 -290 ACTATATTTTAAAATTTCTTTTATTATGAT 7 38 0 AAAATTTCTT 0.887615 -263 AAGAAATTTTAAAATATAGTGTCTTTCAAA 7 48 1 AAAATATAGT 0.585939 -253 CCTTTTACTAAAAGGTTCTTTCAAAATGTT 7 247 1 AAAGGTTCTT 0.70985 -54 GGTTCTTTCAAAATGTTTTTGAAAGATACT 7 260 1 AAATGTTTTT 0.535619 -41 TTATCACCTTATATTTTATTAGTATCTTTC 7 280 0 ATATTTTATT 0.898153 -21 CAACTTATATAAATTTTATTATTAG 8 6 0 AAATTTTATT 0.9317 -75 AATTATTTGGATAGTTTAGTATGTTTGATA 8 37 0 ATAGTTTAGT 0.916826 -44 TTTCATAAGTAAATTTTATTAATTTTGAAA 10 12 1 AAATTTTATT 0.9317 -55 ********** Masking position 7 Map Score: 16.7375 Number of sites scoring better than the average of aligned sites = 1100 Number in coding regions = 778 Number in noncoding regions = 322 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 4 ATAACTTACTATATAAATTTAGCTAAATTGA 1 29 0 ATATAAATTA 0.93427 -60 ACAAAACTATATAAAAGGTTAAGCTAATTAT 2 29 1 ATAAAAGGTA 0.876872 -97 ATGTAACAAAATAGAAATTAACTAAACTATT 3 19 0 ATAGAAATTA 0.709309 -42 TAAATATCAGTAAAATAAATAATG 3 47 0 ATATCAGTAA 0.89297 -14 TTTAGAATAAATAAAAAGTGAAACA 4 33 1 ATAAAAAGTA 0.770797 -15 TTTAGAAAGCATATAAATTTTTTGGTGGTAA 5 12 0 ATATAAATTT 0.583152 -77 TTAGTTTTTAATATCTGGATATACAGACACT 5 53 0 ATATCTGGAA 0.487515 -36 GAATATAAAAATATAAGTTAAATTTTGAATT 6 30 0 ATATAAGTTA 0.96784 -117 CAGAATAAGAATATAAAATAAGAATATAAAA 6 51 0 ATATAAAATA 0.817904 -96 TAAGGTAAAGATATCAGAATAAGAATATAAA 6 65 0 ATATCAGAAA 0.72502 -82 AAAATTAAAAAGATAAGGTAAAGATATCAGA 6 78 0 AGATAAGGTA 0.835698 -69 ATGTTTTTAAATATCAATAAAATTAAAAAGA 6 96 0 ATATCAATAA 0.79757 -51 TACTAATAAAATATAAGGTGATAAA 7 286 1 ATATAAGGTA 0.97212 -15 AATAAAATTTATATAAGTTGATATCAAACAT 8 16 1 ATATAAGTTA 0.967846 -65 ********* * Masking position 3 Map Score: 11.9108 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 321 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 TTTTTAAATTTTTAATTCAAAATTTAACTTA 6 17 1 TTTATTCAAA 0.852669 -130 AGTTTCACATTCAAATAATTTATTA 6 132 0 TCACTTCAAA 0.816283 -15 TTATTATGATTATCCTCCAAATTTATTGAAG 7 17 0 TATCTCCAAA 0.927845 -284 TAAAATATAGTGTCTTTCAAAGTTGTTAAAA 7 57 1 TGTCTTCAAA 0.978553 -244 CCCTATAGGAGAGCGTTCAAATATCCATTAT 7 97 0 GAGCTTCAAA 0.934762 -204 TTACTAAAAGGTTCTTTCAAAATGTTTTTGA 7 251 1 GTTCTTCAAA 0.966569 -50 ATTTTATTAGTATCTTTCAAAAACATTTTGA 7 267 0 TATCTTCAAA 0.982154 -34 AAACTATCCAAATAATTCAAATTCTTTTTTG 8 50 1 AATATTCAAA 0.727794 -31 TTTTATAGTAGGTCTTTCAAAATTAATAAAA 10 25 0 GGTCTTCAAA 0.97813 -42 **** ****** Masking position 6 Map Score: 7.3334 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 122 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 TATTGTCAATTTAGCTAAATTTATATAGTA 1 24 1 TTAGCTAAAT 0.739407 -65 TATAAAAGGTTAAGCTAATTATCATTATTA 2 38 1 TAAGCTAATT 0.944803 -88 TATGACTCACTAAGGTAATGAATAGATAAT 2 78 0 TAAGGTAATG 0.94375 -48 TAAAAATAGTTTAGTTAATTTCTATTTTGT 3 15 1 TTAGTTAATT 0.867101 -46 TATAAAAATATAAGTTAAATTTTGAATTAA 6 28 0 TAAGTTAAAT 0.915473 -119 ATTAAAAAGATAAGGTAAAGATATCAGAAT 6 76 0 TAAGGTAAAG 0.897969 -71 TAATAAAATATAAGGTGATAAA 7 289 1 TAAGGTGATA 0.841316 -12 AAAATTTATATAAGTTGATATCAAACATAC 8 19 1 TAAGTTGATA 0.814485 -62 TTTTCATAAGTAAATTTTATTAATTT 10 7 1 TAAGTAAATT 0.764971 -60 ********** Masking position 3 Map Score: 4.4093 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 222 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 ATTTTATAAAATTACAATTAAAAACTTTTTT 1 62 0 ATTACATTAA 0.904694 -27 GGTTAAGCTAATTATCATTATTAATTATGAT 2 45 1 ATTATATTAT 0.774624 -81 ATCATTATTAATTATGATAAATTATCTATTC 2 58 1 ATTATATAAA 0.628719 -68 CCAACAATTATAAACATGATAATAGGT 2 109 0 ATTATAACAT 0.826719 -17 CAAATAATTTATTACTATTATGTTTTTAAAT 6 115 0 ATTACATTAT 0.942998 -32 AATTTCTTTTATTATGATTATCCTCCAAATT 7 25 0 ATTATATTAT 0.774624 -276 TCAAATATCCATTATTAATATTAATTTTAAC 7 81 0 ATTATAATAT 0.921068 -220 ***** ***** Masking position 7 Map Score: 4.17437 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 139 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 AGGCATTAATGAACACCTCCCTATAGGAGA 7 116 0 GAACACCTCC 0.991611 -185 TCCTTCTGAGTTGCACCTCCGAGCGTAAGC 7 192 1 TTGCACCTCC 0.985333 -109 ATCAAAAATCTAACACCTCCTCGCTTACGC 7 214 0 TAACACCTCC 0.992954 -87 ********** Masking position 5 Map Score: 0.506222 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 2 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TGACAATAAATTTTTGGTGAC 1 2 0 TTTTTGGTGA 0.989448 -87 TTAAAAACTTTTTTAGATAACTTACTATAT 1 46 0 TTTTAGATAA 0.72427 -43 GCATATAAATTTTTTGGTGGTAAT 5 5 0 TTTTTGGTGG 0.971659 -84 AGGTGTTAGATTTTTGATGAACCTTTTACT 7 226 1 TTTTTGATGA 0.969402 -75 CAAATTCTTTTTTGTGGTGAAATT 8 67 1 TTTGTGGTGA 0.971659 -14 TAATTTTAATTTTTAGGGGATTTTT 9 15 1 TTTTAGGGGA 0.948388 -15 ********** Masking position 3 Map Score: 4.7464 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 177 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 10 ********** No masking Map Score: -1.04149e-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: -1.04149e-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 12 ********** No masking Map Score: -1.04149e-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