AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i156_HYP_operon_mjan_reg_100.orf -o156_mjan_100.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 RMJ06415 136 M_jannaschii_chromosome #2 RMJ01449 116 M_jannaschii_chromosome #3 RMJ03306 46 M_jannaschii_chromosome #4 RMJ02791 283 M_jannaschii_chromosome #5 RMJ03929 123 M_jannaschii_chromosome #6 RMJ08818 185 M_jannaschii_chromosome #7 RMJ07253 72 M_jannaschii_chromosome Motif number 1 GTATTTAACTAAATCTAATTAATATAAACTGCAC 1 14 0 AAATAATTAA 0.941036 -123 TTAAATACTTAAAAAGCAATAAAAAACATTTTTA 1 40 1 AAAACAATAA 0.879714 -97 TAATTTCATAAACAGAATTTTATATTAAAAGACT 1 91 1 AACAATTTAA 0.864985 -46 TTTATCACCAAAAATAAATTACAGTCTTTTAAT 1 114 0 AAAAAAATAA 0.966985 -23 TAGTTTTGATTAAACCTTTTTAAAAAGTTGGATT 2 28 1 TAAATTTTAA 0.719869 -89 TGGATTAAGGAAATTGTTATTAAAGGGCTAAAAT 2 56 1 AAATTTATAA 0.899432 -61 ATAAAATAAAAATTAGAAATAAGAATTCTAAT 3 9 0 AATTAAATAA 0.706234 -38 CATATAAAAACCATATAAAATAAAAATTAG 3 27 0 AAAAATATAA 0.964171 -20 TCGGGCTATGAAAACTCTTTAAGAGTTTTCATGT 4 26 0 AAAACTTTAA 0.849119 -258 ATATACCCCCAAATTTAATTTACACCTCCGAGCG 4 101 0 AAATAATTAA 0.941037 -183 CAAAGTTCCAAACTGAATATTATAAAGCTGTGAA 4 145 0 AACTATATAA 0.832682 -139 CAAAATTAAAAAAATGAAGTAAAATTCAAAT 5 8 0 AAAAAAGTAA 0.822054 -116 ATAAAATTTTAAAACAAAATTAAAAAAATGAAGT 5 22 0 AAAAAAATAA 0.966985 -102 TTTTGTTTTAAAATTTTATTGAAAGATTGTAAAA 5 37 1 AAATTATTAA 0.890743 -87 AAAGATTGTAAAAAATATATCAAAATATTTAAGT 5 58 1 AAAAATATAA 0.964171 -66 AAGTTTATATAAAACAAATTCAAACATAATTAAA 6 34 0 AAAAAATTAA 0.960832 -152 TTGTTTTATATAAACTTTATCATAAAATTTAATA 6 51 1 TAAATTATAA 0.754192 -135 TTGATATTATTAAAATTTTTAATATACATATTAA 6 79 0 TAAATTTTAA 0.714818 -107 GTAGTTTTGAAAATCTAATTGATATTATTAAAAT 6 97 0 AAATAATTAA 0.941037 -89 TACATATTAAAAAATTAAATAATAATCAAATTTA 6 128 1 AAAAAAATAA 0.966985 -58 ATAATAATCAAATTTAAAATTAAATGGAGATATT 6 146 1 AATTAAATAA 0.706234 -40 AAAGACATTAAAATACTTTTTATAAAATATTTTA 7 20 1 AAATTTTTAA 0.8822 -53 ATAATCACCATACATCTTATAATAATAGTTAAAA 7 49 0 TACATTATAA 0.465854 -24 **** **** * * Masking position 10 Map Score: 29.867 Number of sites scoring better than the average of aligned sites = 2173 Number in coding regions = 1559 Number in noncoding regions = 614 Number of orfs with sites within 600 bp upstream = 449 Fraction of orfs with sites within 600 bp upstream = 0.0721169 Motif number 2 TTAGATTTAGTTAAATACTTAAAAAGCAATA 1 30 1 TTAAATATTA 0.86573 -107 TTAGTATTAATAAAAATGTTTTTTATTGCTT 1 53 0 TAAAAATTTT 0.929097 -84 TCTTTTAATATAAAATTCTGTTTATGAAATT 1 92 0 TAAAATTTGT 0.788586 -45 AATTTTATATTAAAAGACTGTAATTTATTTT 1 106 1 TAAAAGATGT 0.877339 -31 ATCAAAACTATAAAAATCTTAATAATT 2 7 0 TAAAAATTTA 0.662666 -110 TCCAACTTTTTAAAAAGGTTTAATCAAAACT 2 29 0 TAAAAAGTTT 0.805527 -88 CCATATAAAATAAAAATTAGAAATAAGAATT 3 16 0 TAAAAATAGA 0.539331 -31 AACTTTAAGAAAGTTACATGAAAACT 4 6 1 TAAGAAATTA 0.753734 -278 ATGAAAACTCTTAAAGAGTTTTCATAGCCCG 4 28 1 TTAAAGATTT 0.851419 -256 AAAACAAAATTAAAAAAATGAAGTAAAATTC 5 15 0 TAAAAAATGA 0.94505 -109 TAATTTTGTTTTAAAATTTTATTGAAAGATT 5 34 1 TTAAAATTTA 0.775777 -90 TGAAAGATTGTAAAAAATATATCAAAATATT 5 56 1 TAAAAAAATA 0.793722 -68 TATTGAATACTTAAATATTTTGATATATTTT 5 69 0 TTAAATATTT 0.853863 -55 TCAATAAAAGTTAAAGAGTGAGATTATGAAA 5 94 1 TTAAAGATGA 0.7897 -30 TAATTAAACGTAAAAAATTTTGGTGGAGAGT 6 11 0 TAAAAAATTT 0.961592 -175 ATATGTATATTAAAAATTTTAATAATATCAA 6 82 1 TAAAAATTTA 0.513084 -104 AAACTACATATTAAAAAATTAAATAATAATC 6 124 1 TTAAAAATTA 0.932346 -62 CCAAAGACATTAAAATACTTTTTATAAAATA 7 18 1 TAAAATATTT 0.924614 -55 ATACTTTTTATAAAATATTTTAACTATTATT 7 32 1 TAAAATATTT 0.921465 -41 ******* *** Masking position 1 Map Score: 23.5034 Number of sites scoring better than the average of aligned sites = 1833 Number in coding regions = 1317 Number in noncoding regions = 516 Number of orfs with sites within 600 bp upstream = 395 Fraction of orfs with sites within 600 bp upstream = 0.0634436 Motif number 3 TATTAATAAAAATGTTTTTTATTGCTTTTT 1 50 0 AATGTTTTTT 0.690178 -87 AAAAGACTGTAATTTATTTTTGGTGATAAA 1 117 1 AATTTATTTT 0.729353 -20 AATTATTAAGATTTTTATAGTTTTG 2 6 1 TTAAGATTTT 0.806989 -111 TTATTTCTAATTTTTATTTTATATGGTTTT 3 21 1 TTTTTATTTT 0.730912 -26 TTTTATTTTATATGGTTTTTATATG 3 32 1 TATGGTTTTT 0.502115 -15 ATTTGAATTTTACTTCATTTT 5 2 1 TTTGAATTTT 0.791766 -122 CAATCTTTCAATAAAATTTTAAAACAAAAT 5 36 0 ATAAAATTTT 0.823526 -88 AATATTTTGATATATTTTTTACAATCTTTC 5 57 0 TATATTTTTT 0.74794 -67 ATTGAATACTTAAATATTTTGATATATTTT 5 69 0 TAAATATTTT 0.772493 -55 AATTAAACGTAAAAAATTTTGGTGGAGAGT 6 11 0 AAAAAATTTT 0.505419 -175 TAATATACATATTAAATTTTATGATAAAGT 6 64 0 ATTAAATTTT 0.885665 -122 ATTGATATTATTAAAATTTTTAATATACAT 6 84 0 TTAAAATTTT 0.834549 -102 AATAATATCAATTAGATTTTCAAAACTACA 6 102 1 ATTAGATTTT 0.865502 -84 TGATTATTATTTAATTTTTTAATATGTAGT 6 126 0 TTAATTTTTT 0.74794 -60 TAATATCTCCATTTAATTTTAAATTTGATT 6 151 0 ATTTAATTTT 0.69549 -35 AAATGGAGATATTATTTTTTGGTGTTAAA 6 167 1 ATTATTTTTT 0.820044 -19 TATTTTATAAAAAGTATTTTAATGTCTTTG 7 19 0 AAAGTATTTT 0.737953 -54 TACTTTTTATAAAATATTTTAACTATTATT 7 33 1 AAAATATTTT 0.493048 -40 ********** Masking position 7 Map Score: 15.076 Number of sites scoring better than the average of aligned sites = 2797 Number in coding regions = 1954 Number in noncoding regions = 843 Number of orfs with sites within 600 bp upstream = 584 Fraction of orfs with sites within 600 bp upstream = 0.0938002 Motif number 4 AAAAGGTTTAATCAAAACTATAAAAATCTT 2 18 0 ATCAAAACTA 0.937385 -99 ACCATATAAAATAAAAATTAGAAATAAGAA 3 18 0 ATAAAAATTA 0.790121 -29 AACTTTAAGAAAGTTACATGAAAACT 4 7 1 AAGAAAGTTA 0.810147 -277 AGAAAGTTACATGAAAACTCTTAAAGAGTT 4 18 1 ATGAAAACTC 0.931584 -266 GCTTCGGGCTATGAAAACTCTTTAAGAGTT 4 33 0 ATGAAAACTC 0.931584 -251 CTTCGGTTTCATCAAAGCTAACACCTCCTT 4 67 1 ATCAAAGCTA 0.953881 -217 TTATAAAGCTGTGAAAGTTCTGTGGATATA 4 130 0 GTGAAAGTTC 0.912598 -154 CCTAAAAGGCGTCAAAGTTCCAAACTGAAT 4 161 0 GTCAAAGTTC 0.912598 -123 ATACTTTCCTGTGAAAGTTCTGTGCCAATA 4 208 1 GTGAAAGTTC 0.912598 -76 AAAATTTTAAAACAAAATTAAAAAAATGAA 5 24 0 AACAAAATTA 0.755419 -100 TAAGTATTCAATAAAAGTTAAAGAGTGAGA 5 87 1 ATAAAAGTTA 0.838742 -37 GAGTGAGATTATGAAAATCACACGA 5 109 1 ATGAAAATCA 0.705967 -15 CAATTAGATTTTCAAAACTACATATTAAAA 6 110 1 TTCAAAACTA 0.65543 -76 TTAAATAATAATCAAATTTAAAATTAAATG 6 142 1 ATCAAATTTA 0.746811 -44 ********** Masking position 5 Map Score: 14.5066 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 225 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 AACATTTTTATTAATACTAAAAACAGATAAT 1 64 1 TTATACTAAA 0.648597 -73 TTTATCACCAAAAATAAATTAC 1 125 0 TTACACCAAA 0.993287 -12 CATATAAAAACCATATAAAATAAAA 3 32 0 TAAAACCATA 0.719121 -15 TTCTGTGGATATACCCCCAAATTTAATTTAC 4 112 0 ATACCCCAAA 0.812853 -172 CAATAAAATTTTAAAACAAAATTAAAAAAAT 5 27 0 TTAAACAAAA 0.85161 -97 ACTCTCCACCAAAATTTTTTACG 6 3 1 TCTCACCAAA 0.846901 -183 TATATAAACTTTATCATAAAATTTAATATGT 6 57 1 TTACATAAAA 0.718012 -129 TTTAACACCAAAAAATAATATC 6 174 0 TTACACCAAA 0.993288 -12 GTTATCACCAAAGACATTAAAA 7 2 1 TTACACCAAA 0.993287 -71 ATAATCACCATACATCTTATAA 7 61 0 TAACACCATA 0.928581 -12 *** ******* Masking position 9 Map Score: 7.23149 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 326 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 6 ********** No masking Map Score: 2.8375e-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: 2.8375e-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: 2.8375e-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