AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_mjan_reg_300.orf -o111_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 RMJ07139 300 M_jannaschii_chromosome #2 RMJ17018 68 M_jannaschii_chromosome #3 RMJ13056 60 M_jannaschii_chromosome #4 RMJ03208 57 M_jannaschii_chromosome #5 RMJ10366 79 M_jannaschii_chromosome #6 RMJ14894 19 M_jannaschii_chromosome #7 RMJ03938 66 M_jannaschii_chromosome Motif number 1 ATTGATTATGTTATATTTCATTTTTTGATATAA 1 12 1 TTAATTTATT 0.797756 -289 TTTAACTATTTTATAATTTTATATCAAAAAATG 1 30 0 TTAAATTTTA 0.980422 -271 AAAAAGTAAATTATTTTTAACTATTTTATAATT 1 45 0 TTATTTTATA 0.904885 -256 TAAAAATAATTTACTTTTTTAAAGTTATAATTG 1 59 1 TTATTTTTAA 0.939893 -242 TTTTTTAAAGTTATAATTGTTTTATTATTAAAA 1 73 1 TTAAATTTTT 0.920923 -228 TTTTAACTTATTAGAATTTTTAATAATAAAACA 1 90 0 TTAAATTTAA 0.957585 -211 ATTATATATGTTAAAATTTTTAACTTATTAGAA 1 107 0 TTAAATTTAA 0.701952 -194 ATATTATGATTTAAAGTTAAATAGTAAATTATA 1 134 0 TTAAGTTATA 0.819148 -167 TTTTGTATTATTACATTTGTGAAAAATGTGGAA 1 176 1 TTAATTTTAA 0.965553 -125 CAACTATTCTTTAATTTTTTGTATGGTGCCCCT 1 215 0 TTATTTTTTA 0.956624 -86 CAAAAAATTATTAAAATTAAAAAAGAAAAACAT 2 13 0 TTAAATTAAA 0.932743 -56 TAATAATTTTTTGATATTTTTTAGGTGATATAA 2 33 1 TTGTATTTTA 0.760122 -36 TATTTTATCATCATTATTGTATAGTATAGTGTT 3 11 0 TCATATTTTA 0.867657 -50 ATTGTTAAAGTTATTATTTATTTTATCATCATT 3 29 0 TTATATTATT 0.736963 -32 GGTTTCACAATTGTTAAAGTTATTATT 3 44 0 TCAAATTTAA 0.892823 -17 GTATCACCTATTAGATTTTTCAATGATTGTATT 4 33 0 TTAATTTTAA 0.96552 -25 AAGCTTAAGCTTATATTTGTATATAAAGCTTTA 7 24 1 TTAATTTTTA 0.975329 -43 *** **** * ** Masking position 7 Map Score: 27.0678 Number of sites scoring better than the average of aligned sites = 1240 Number in coding regions = 783 Number in noncoding regions = 457 Number of orfs with sites within 600 bp upstream = 381 Fraction of orfs with sites within 600 bp upstream = 0.061195 Motif number 2 TATTGATTATGTTATATTTCATTTTT 1 2 1 ATTTGTTATA 0.748183 -299 ATATAAAATTATAAAATAGTTAAAAATAATTTACT 1 39 1 ATATTTAAAA 0.768696 -262 GTTAAAAATAATTTACTTTTTTAAAGTTATAATTG 1 57 1 ATCTTTTAAA 0.742251 -244 TTATTAAAAATTCTAATAAGTTAAAAATTTTAACA 1 97 1 TTATGTTAAA 0.897025 -204 TAAATAGTAAATTATATATGTTAAAATTTTTAACT 1 115 0 ATATGTTAAA 0.984122 -186 ACCTCTATATATATTATGATTTAAAGTTAAATAGT 1 142 0 ATATTTTAAA 0.959382 -159 GTTTTGTATTATTACATTTGTGAAAAATGTGGAAA 1 175 1 ATATGTGAAA 0.986999 -126 TAGGGGCACCATACAAAAAATTAAAGAATAGTTGG 1 214 1 ATAAATTAAA 0.678922 -87 TTTTTAGGTGATATAATGGGTGATAATAC 2 50 1 ATATGTGATA 0.977655 -19 AATAATAACTTTAACAATTGTGAAACC 3 44 1 TTAAGTGAAA 0.835808 -17 GATTTAAATAGTTGAAGTAACAAATA 4 2 1 ATAAGTTGAA 0.760809 -56 GAAGTAACAAATACAATCATTGAAAAATCTAATAG 4 24 1 ATATTTGAAA 0.96602 -34 TCATTGAAAAATCTAATAGGTGATACTA 4 40 1 ATATGTGATA 0.977655 -18 CTGCACTAATTCCAACAGTTATATTTGGTTTGT 5 9 1 ATAAGTTATA 0.937394 -71 ACTTTAATACACTGTATAGTTGATACAAACCAAAT 5 33 0 ACATTTGATA 0.664069 -47 TAAAGTTACTATAAAATGAGGGAAAAAG 5 62 1 ATATGGGAAA 0.903109 -18 CCCAAAAAACATCTAAAGCTTTATATACAAATATA 7 35 0 ATAATTTATA 0.850405 -32 ** ** ****** Masking position 15 Map Score: 21.2835 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 596 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 3 TATTGATTATGTTATATTTCATTTTTTGA 1 9 1 ATTTATATTT 0.691383 -292 ATATAAAATTATAAAATAGTTAAAAATAATT 1 39 1 ATAAATAGTT 0.915839 -262 TTTTTTAAAGTTATAATTGTTTTATTATTAA 1 73 1 TTTAATTGTT 0.832356 -228 TTATTAGAATTTTTAATAATAAAACAATTAT 1 85 0 TTTAATAATA 0.868236 -216 TTATTAAAAATTCTAATAAGTTAAAAATTTT 1 97 1 TTTAATAAGT 0.911734 -204 ACCTCTATATATATTATGATTTAAAGTTAAA 1 146 0 ATTTATGATT 0.777044 -155 TTTTTCACAAATGTAATAATACAAAACCTCT 1 171 0 ATTAATAATA 0.900781 -130 TCTTTTTTAATTTTAATAATTTTTTGATATT 2 20 1 TTTAATAATT 0.948676 -49 TTTTTAGGTGATATAATGGGTGATAATAC 2 50 1 ATTAATGGGT 0.912455 -19 GATTTAAATAGTTGAAGTAACAA 4 3 1 TTAAATAGTT 0.887698 -55 TCATTGAAAAATCTAATAGGTGATACTA 4 40 1 ATTAATAGGT 0.963499 -18 TTTTTCCCTCATTTTATAGTAACTTTAATAC 5 58 0 ATTTATAGTA 0.859946 -22 ** ******** Masking position 6 Map Score: 8.35016 Number of sites scoring better than the average of aligned sites = 864 Number in coding regions = 681 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 4 TTATATTTCATTTTTTGATATAAAATTATA 1 22 1 TTTTTTGATA 0.87971 -279 CTTTAATTTTTTGTATGGTGCCCCTATTAT 1 210 0 TTGTATGGTG 0.940093 -91 ATTGCCACCTCTTAAGGTGGTTGTGTAGG 1 282 0 TCTTAAGGTG 0.894103 -19 ATTTTAATAATTTTTTGATATTTTTTAGGT 2 29 1 TTTTTTGATA 0.87971 -40 TTTTTGATATTTTTTAGGTGATATAATGGG 2 40 1 TTTTTAGGTG 0.980769 -29 TTTTCCCTCATTTTATAGTAACTTTAATAC 5 58 0 TTTTATAGTA 0.689807 -22 AAATTCTTAGGGGGAATTT 6 4 1 TTCTTAGGGG 0.898837 -16 GCTTTAGATGTTTTTTGGGGAAGTCT 7 51 1 TTTTTTGGGG 0.97887 -16 ********** Masking position 4 Map Score: 3.40316 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 476 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 5 TCATTTTTTGATATAAAATTATAAAATAGT 1 29 1 ATATAAAATT 0.873253 -272 ATATATTATGATTTAAAGTTAAATAGTAAA 1 139 0 ATTTAAAGTT 0.916573 -162 ATCATAATATATATAGAGGTTTTGTATTAT 1 157 1 ATATAGAGGT 0.968782 -144 GACGCTCCCTATATGGAGCTGAGCCAGTGC 1 253 1 ATATGGAGCT 0.968171 -48 AAATCTATATATAAAGCTTAAGCTTATA 7 9 1 ATATAAAGCT 0.990131 -58 TTATATTTGTATATAAAGCTTTAGATGTTT 7 34 1 ATATAAAGCT 0.990131 -33 ********** Masking position 4 Map Score: 5.81247 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 189 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CCCCTATTATTTTCCACATTTTTCACAAAT 1 190 0 TTTCCACATT 0.947764 -111 TTATTTATTTTATCATCATTATTGTATAGT 3 19 0 TATCATCATT 0.943755 -42 AAGTAACAAATACAATCATTGAAAAATCTA 4 25 1 TACAATCATT 0.878882 -33 CTGCACTAATTCCAACAGTTATATTTGGT 5 10 1 TTCCAACAGT 0.944628 -70 CTTTTTCCCTCATTTTATAGTAAC 5 66 0 TTCCCTCATT 0.983215 -14 ********** Masking position 8 Map Score: 0.218303 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 182 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AACTTTAAAAAAGTAAATTATTTTTAACTA 1 55 0 AAGTAAATTA 0.726896 -246 AATAAAACAATTATAACTTTAAAAAAGTAA 1 69 0 TTATAACTTT 0.866508 -232 TTAAAAATTCTAATAAGTTAAAAATTTTAA 1 100 1 TAATAAGTTA 0.898847 -201 TAAAGTTAAATAGTAAATTATATATGTTAA 1 126 0 TAGTAAATTA 0.92715 -175 TTTTTAATTTTAATAATTTTTTGATATTTT 2 23 1 TAATAATTTT 0.88711 -46 ATAAAATAAATAATAACTTTAACAATTGTG 3 36 1 TAATAACTTT 0.968846 -25 CCTCATTTTATAGTAACTTTAATACACTGT 5 53 0 TAGTAACTTT 0.974193 -27 ********** Masking position 5 Map Score: 4.48211 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 162 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 8 ********** No masking Map Score: 1.58694e-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: 1.58694e-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 10 ********** No masking Map Score: 1.58694e-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